TY - CHAP TI - Factorization of multivariate polynomials AU - Kaltofen, Erich AU - Lecerf, Grégoire T2 - Handbook of Finite Fields A2 - Mullen, Gary L. A2 - Panario, Daniel PY - 2013/// SP - 382–392 PB - CRC Press, Taylor & Francis Group ER - TY - JOUR TI - Evaluation of the role of tick-borne disease in 25 cases of high grade second degree or complete atrioventricular block in dogs AU - Hodge, T.E. AU - DeFrancesco, T.C. AU - Ames, M.K. AU - Stern, JA AU - Tou, SP AU - Atkins, C AU - Keene, BW AU - Trafny, DJ AU - Oyama, M AU - Breitschwerdt, EB T2 - Journal of Veterinary Internal Medicine DA - 2013/// PY - 2013/// VL - 27 IS - 3 SP - 642 ER - TY - JOUR TI - ID-13 Trends in Tick-Borne Disease Exposure in Dogs from the USA and Canada Determined by Species-Specific Peptide Assay AU - Qurollo, B.A. AU - Chandrashekar, R. AU - Hegarty, B.C. AU - Beall, M.J. AU - Stillman, B. AU - Liu, J. AU - Thatcher, B. AU - Cerrito, B. AU - Walsh, M. AU - Breitschwerdt, E.B. T2 - Journal of Veterinary Internal Medicine DA - 2013/// PY - 2013/// VL - 27 IS - 3 SP - 724 ER - TY - JOUR TI - Introducing primary scientific literature to first-year undergraduate researchers AU - Carson, S AU - Miller, Es T2 - Council on Undergraduate Research on the Web DA - 2013/// PY - 2013/// VL - 34 IS - 4 SP - 17-22 ER - TY - JOUR TI - Analysis of Seroreactivity against Cell Culture-DerivedBartonellaspp. Antigens in Dogs AU - Hegarty, B.C. AU - Bradley, J.M. AU - Lappin, M.R. AU - Balakrishnan, N. AU - Mascarelli, P.E. AU - Breitschwerdt, E.B. T2 - Journal of Veterinary Internal Medicine AB - Background Little is known about the specificity of Bartonella spp. immunofluorescent antibody ( IFA ) assays in dogs. Bacteremia in sick dogs most often has been associated with Bartonella henselae ( Bh ) , Bartonella vinsonii subspecies berkhoffii ( Bvb ), and Bartonella koehlerae ( Bk ). Clarification of the diagnostic utility of IFA serology when testing against these organisms is needed. Objective To evaluate the specificity of Bartonella IFA assays utilizing 6 cell culture–grown antigen preparations. Animals Archived sera from SPF dogs (n = 29) and from dogs experimentally infected with Bvb (n = 10) and Bh (n = 3). Methods Antibodies (Abs) to Bvb genotypes I, II, and III, Bh serotype I, strains H‐1 and SA 2, and to Bk were determined by IFA testing. Results Serum from naïve SPF dogs shown to be negative for Bartonella bacteremia did not react with any of the 6 Bartonella antigens by IFA testing. Dogs experimentally infected with Bvb genotype I developed Abs against homologous antigens, with no cross‐reactivity to heterologous Bvb genotypes, Bh H‐1, SA 2 strains, or to Bk . Dogs experimentally infected with Bh serotype I developed Abs against Bh H‐1, but not to Bh SA 2 strain with no cross‐reactive Abs to Bvb genotypes I– III or to Bk . Conclusions and Clinical Importance Bartonella spp. Ab responses during acute experimental infections are species and type specific. DA - 2013/12/16/ PY - 2013/12/16/ DO - 10.1111/jvim.12263 VL - 28 IS - 1 SP - 38-41 J2 - J Vet Intern Med LA - en OP - SN - 0891-6640 UR - http://dx.doi.org/10.1111/jvim.12263 DB - Crossref KW - Bartonella henselae KW - Bartonella koehlerae KW - Bartonella vinsonii KW - Serodiagnostic limitations KW - Specificity ER - TY - JOUR TI - Infection with Panola MountainEhrlichiasp. in a Dog with Atypical Lymphocytes and Clonal T-Cell Expansion AU - Qurollo, B.A. AU - Davenport, A.C. AU - Sherbert, B.M. AU - Grindem, C.B. AU - Birkenheuer, A.J. AU - Breitschwerdt, E.B. T2 - Journal of Veterinary Internal Medicine AB - An 11-year-old, castrated male Scottish Terrier from Raleigh, NC that lived predominantly indoors and had no travel history was referred to the North Carolina State University Veterinary Health Complex (NCSU-VHC) in October 2012 for routine reevaluation of hepatobiliary disease. The dog's previous 3-year medical history included biliary mucocele (2010); neutrophilic hepatitis (2011); recurrent Escherichia coli urinary tract infections, esophageal dysmotility, aspiration pneumonia, and transient thrombocytopenia (2012); and food responsive enteropathy (2009–2012). All of these medical problems were well controlled at the time of examination and no clinical abnormalities were reported by the dog's owners. In the months before the present examination, ticks occasionally were noted and fleas were commonly found on the dog despite reported use of preventive therapies. On physical examination, the dog was obese (body condition score, 7 out of 9) and had mild hepatomegaly, both of which had been present for more than a year. Notable CBC findings included mild thrombocytopenia (platelet count, 143,000/μL; reference interval [RI], 190,000–468,000/μL) and an increased number of atypical lymphocytes (1,773/μL), with normal appearing lymphocytes within the laboratory reference range (1,854/μL; RI, 594–3,305/μL) and an otherwise normal differential cell count. A review of the blood smear by a pathologist identified a population of immature lymphocytes with angular nuclei and cell shape, multiple nucleoli, and deeply basophilic, vacuolated cytoplasm that had a tendency to mold into surrounding cells (Fig 1). These morphologic abnormalities raised the suspicion of possible lymphoid neoplasia, although these changes can be seen secondary to reactive processes such as chronic inflammatory or infectious diseases. Serum biochemical abnormalities included an increase in alkaline phosphatase activity (ALP; 817 IU/L; RI, 16–140 IU/L) and alanine aminotransferase activity (ALT; 60 IU/L; RI, 12–54). During the previous 12-month period, ALT activity varied between normal and 80 IU/L and ALP activity varied between 359 and 534 IU/L. Because these hematological and serum biochemical abnormalities were present 2 weeks later, abdominal ultrasound examination was repeated and identified mottled splenic parenchyma and several previously identified changes including hyperechoic nodular hepatomegaly; mild dystrophic mineralization of the spleen, liver, kidneys, and prostate; and, a thickened urinary bladder apex. Splenic cytology identified a mixed lymphoid population and mild extramedullary hematopoiesis. Liver cytology identified normal hepatocytes and an expansion of intermediate lymphocytes, raising concern for lymphoma. Cytology of a palpably normal popliteal lymph node identified expansion of intermediate to large lymphocytes, most consistent with lymphoma (Fig 2). T-cell clonality was documented in a liver aspirate after submission to NCSU-CVM Clinical Immunology Laboratory for polymerase chain reaction (PCR) to identify antigen receptor rearrangements (PARR). Aseptically collected ethylenediamine tetraacetic acid (EDTA)-anticoagulated whole blood and serum were submitted to the NCSU-CVM Vector Borne Diseases Diagnostic Laboratory (VBDDL) for a vector-borne pathogen serology panel and Bartonella alpha-Proteobacteria Growth Medium (BAPGM) enrichment blood culture PCR platform. The dog was seronegative for antibodies to Anaplasma phagocytophilum, Anaplasma platys, and Borrelia burgdorferi and for Dirofilaria immitis antigen using a commercial enzyme-linked immunosorbent assay based kit (SNAP® 4Dx® Plusa); the dog was seronegative for antibodies to Babesia canis, Babesia gibsoni, Bartonella henselae, and Bartonella vinsonii subsp. berkhoffii, using indirect immunofluorescent antibody (IFA) testing. By IFA, the dog was seroreactive to Rickettsia rickettsii (1:64; laboratory cut-off value, 1:64) and Ehrlichia canis (1:1028; laboratory cut-off value, 1:64) antigens, but seronegative to Ehrlichia spp. peptides in the SNAP 4Dx Plusa kit, which is known to detect antibodies against E. canis, E. chaffeensis, and E. ewingii. Bartonella enrichment blood culture and PCR were negative. Nine months before this presentation, the dog was seronegative in the NCSU-CVM-VBDDL to the vector-borne pathogens tested above. Because of the discrepancy between the E. canis IFA and SNAP 4Dx Plusa test results, Ehrlichia spp. PCR was performed on DNA extracted from the dog's EDTA-anticoagulated whole blood using a previously described 16S ribosomal RNA PCR assay.1 A 351 base pair portion of the 16S rRNA gene was amplified, sequenced, and investigated in the NCBI GenBank nucleotide database. The partial 16S rRNA gene identified infection with the Panola Mountain Ehrlichia sp. (PME) with 100% coverage (331 bp) and 100% identity to PME 16S ribosomal RNA gene (DQ324367.1). To confirm these results, alternative PME genes, including gltA and map1 were targeted. Furthermore, sodb, a gene not previously sequenced for PME, was amplified using newly developed primers designed to amplify Ehrlichia spp. sodb genes. Primers designed to amplify a 311 bp portion of PME gltA (EPM-gltA-Forward, 5′-CGTGTTTTTCTGCCTTAGCTGCAC and EPM-gltA-Reverse, 5′-CGGCCCAGAAGAACC TGTCA) based on a published PME gltA sequence (DQ363995.1) and a second set of primers designed to target a 480 bp portion of PME map1 (EPM-map1-Forward-3, 5′-CGAGAGCCAACGTTTACAT and EPM-map1-Reverse-2, 5′-GTACCAATACCTGCACATAC) based on published PME map1 sequences (DQ324368.1, EU272373.1 and EU272355.1) were used. Primers designed to amplify a 300 bp portion of sodb (sodb-Forward, 5′-TTTAATAATGCTGGTCAAGTATGGAATCAT and sodb-Reverse, 5′-AAGCGTGTTCCCATACATCCATAG) based on published Ehrlichia spp. sodb sequences (AF392615.1, CP000107.1) were used. Reactions contained 5 μL of DNA extract, 12.5 μL of MyTaqHS-2Xb, 0.125 μM (or 0.25 μM for sodb primers) of each primerc and RNAse-free, molecular-grade water to a final volume of 25 μL. All reactions were performed in a thermocyclerd with an aluminum block under the following conditions, with respective primer annealing temperatures specified: initial temperature at 94°C for 3 minutes, 55 cycles consisting of denaturation at 94°C for 10 seconds, annealing at 68°C (gltA), 62°C (map1), 58°C (sodb) for 10 seconds, extension at 72°C for 15 seconds, and a final extension at 72°C for 30 seconds. Negative controls (RNAse-free, molecular-grade water and uninfected canine genomic DNA) were included in all assays. Amplified PCR products were sequenced directlye and alignments were made with GenBank sequences using AlignX software.f Sequence identities for the partial gltA and map1 genes are as follows, all with 100% coverage: gltA, 100% similar (269 bp) to PME partial gltA gene from an infected goat (DQ363995.1) and Amblyomma americanum tick (EU272374.1); map1, 100% similar (460 bp) to PME partial map1 gene from an infected goat (DQ324368.1) and A. americanum tick (EU272373.1). Before this study, there was no sequence for PME sodb deposited in GenBank. The highest sequence identities assigned by BLASTg for the partial gene amplified using Ehrlichia spp. sodb primers are as follows, all with 100% coverage: sodb, 89% (264/295 bp) similar to multiple strains of E. ruminantium sodb gene, with the highest Max scores reported for Senegal (DQ647026.1), Pokoase (DQ647024.1), and Kumm1 (DQ647023.1) strains, 83% (245/295 bp) similar to E. canis strain Jake sodb (CP000107.1) and 80% (236/295 bp) similar to E. chaffeensis strain Arkansas sodb (AF392615.1). The PME partial sodb gene sequence was submitted to Genbank (Accession number KC702804). Primer sets specific for Rickettsia ompA, E. canis p30, E. ewingii p28, and E. chaffeensis p28 did not amplify DNA from the PME-infected blood sample, suggesting this dog was not likely coinfected with Rickettsia or other Ehrlichia species. Retrospective PCRs using DNA extracted from predoxycycline splenic cytologic smears were negative (16S rRNA, gltA, map1, sodb, E. canis p30, E. ewingii p28, and E. chaffeensis p28) for pathogen DNA. Treatment for suspected lymphoma was not initiated because of the possibility that lymphocytosis and other lymphocytic abnormalities were due to a reactive process secondary to ehrlichiosis.2-4 Treatment with doxycycline (approximately 5 mg/kg PO q12h) was commenced for 30 days. After starting doxycycline treatment, occasional vomiting was noted. Resolution of the thrombocytopenia and lymphocytosis occurred 1 week after starting the treatment. ALP and ALT activities remained increased at 1,989 IU/L and 119 IU/L, respectively. One week after completion of doxycycline, repeat aspiration cytology identified a mixed lymphoid population with expansion of intermediate lymphocytes and mild extramedullary hematopoiesis within the spleen, a mixed lymphoid population within the popliteal lymph node, and an expansion of intermediate lymphocytes and mild vacuolar change within the liver. Flow cytometry of the liver showed a population of large, granular cells with positive intracellular staining for CD3, consistent with T-cell lymphoma. When cytology was repeated again 4 weeks after completion of doxycycline, there was resolution of the abnormal lymphoid population in liver and lymph nodes, but there were increased numbers of lymphoblasts and mild persistent extramedullary hematopoiesis within the spleen (Fig 3). ALP and ALT activities had decreased to 1,352 IU/L and 66 IU/L, respectively. Throughout the 3-month time period described in this case report, the owners reported no clinical abnormalities other than occasional gastrointestinal signs, but felt in retrospect that the dog may have been slightly lethargic as they reported it was more energetic after completion of the doxycycline treatment regimen. Furthermore, 5 subsequent CBCs performed over the next 6 months remained normal. EDTA-anticoagulated whole blood and convalescent serum samples collected from the dog approximately 2 weeks after starting doxycycline treatment were PCR negative for PME (16S rRNA, gltA, map1 and sodb) and the SNAP 4Dx Plus was positive for anti-Ehrlichia spp. antibodies, respectively. Convalescent serum, collected approximately 5 weeks after completion of antibiotic treatment, was minimally reactive (1:32) to R. rickettsii antigens, whereas the dog remained E. canis seroreactive by both IFA (1:512) and SNAP 4Dx Plusa (weak Ehrlichia spp. positive). EDTA whole blood collected at this time remained PCR negative (16S rRNA, gltA, map1 and sodb) for PME. In this report, we provide molecular evidence of PME in a thrombocytopenic dog with abnormal lymphocytosis and clonal T-cell expansion. Treatment with doxycycline resulted in resolution of thrombocytopenia, abnormal lymphocytosis, and abnormal lymphoid cells in liver and lymph nodes, supporting a potential role for PME as a cause of host immune dysregulation. These findings also support a potential pathogenic role for PME as a cause of thrombocytopenia in dogs from the United States. Cytopathology and flow cytometry in this case identified a large number of atypical lymphocytes in the peripheral blood and in hepatic and splenic tissue aspirates with a high number of intermediate lymphocytes, granular CD3+ cells, and clonal T-cell expansion. Intracellular infections that induce cell-mediated immunity can cause cytological changes similar to malignancy.5, 6 A study characterizing peripheral blood smears in human ehrlichiosis patients infected with either E. chaffeensis or E. ewingii documented prominent large granular lymphocytes with atypical, folded, hyperchromatic nuclei that might be confused with neoplastic NK or NK-like T-cells.6 Immunophenotypes compared between dogs with naturally acquired canine monocytic ehrlichiosis (CME) and healthy dogs found that dogs with CME had higher relative numbers of CD3+ T-cells in peripheral blood than did healthy dogs.7 Additional studies found that dogs experimentally infected with E. canis had transitory CD8+ lymphocytosis in both peripheral blood and lymph nodes.8, 9 Additional studies describe clinically ill, E. canis-seropositive dogs with an increasing percentage of peripheral blood CD8+ lymphocytes.3, 10 PARR results from the dog in this case demonstrated clonal T-cell expansion, typically associated with malignancy. At least 2 reports, however, describe this phenomenon in dogs with E. canis infections.2, 4 In a previous report, an E. canis-seropositive dog with pancytopenia and clonal T-cell expansion was treated with doxycycline, which resolved the pancytopenia and the dog remained healthy 2 years later.2 Further investigation is needed to determine if expanded T-cells in E. canis infections are transitory or potentially could develop into lymphoid malignancy, particularly in association with chronic undiagnosed infections. As current evidence suggests, a role for Ehrlichia spp. in immune dysregulation is likely, but the extent may be subject to host factors, species and strain virulence, as well as phase of the disease. CME has acute, subclinical, and chronic phases representing different infection durations and variations in clinical disease manifestations. One recent study, however, found no statistically significant differences among CD3+, CD8+, and, CD4+ cells in peripheral blood samples from dogs with clinical or subclinical CME.11 Signs of lymphoid malignancy continue to be monitored in the dog of this report. Resolution of the immunologic abnormalities noted in liver, lymph node, and blood after doxycycline treatment, however, strongly supports an infectious etiology. To the authors’ knowledge, this is the first report of PME infection in a dog. Genetically and antigenically similar to E. ruminantium, PME was first identified by PCR in a goat experimentally infested with A. americanum ticks collected from Panola Mountain State Park, Georgia.12 Goats infected with PME developed serous nasal discharge and febrile illness with hematologic changes consisting of decreased ALP activities and neutropenia; rare morulae in mononuclear cells were identified in 1 goat.12, 13 PME also was detected by PCR in whole blood from a man in Atlanta, GA who developed myalgia after being bitten by a nymphal A. americanum tick.14 No hematologic abnormalities were reported, and clinical signs resolved after doxycycline treatment. The role, if any, of PME in the overall pathogenesis of the various disease manifestations described in the dog of this report over its 3 year history of illness is impossible to assess. At the time PME was identified, the dog was asymptomatic and hematological abnormalities were limited to thrombocytopenia, increased numbers of atypical lymphocytes, and progressively increasing ALP activity (after initiation of doxycycline). The most notable characteristics of illness that potentially were related to PME infection in this dog included thrombocytopenia, cytological changes in the liver, lymph node and spleen, and clonal T-cell expansion. After treatment with doxycycline, sequential resolution of most of these abnormalities occurred. It is not clear when the dog became infected with PME, but serum screened for exposure to vector-borne pathogens 8 months earlier was negative, and the dog's owners reported flea and tick exposure over the previous 6-month time period. PME exposure presumably occurred in central NC because the dog had no travel history outside of the state. This is not a surprising finding, given documentation of PME in A. americanum from the eastern United States, with PME-positive ticks detected in FL, GA, KY, NJ, and NY.15 In addition, deer from AR, NC, and VA were PCR positive for PME and were shown to be competent reservoirs for the pathogen.16 Documentation of PME in this dog supports the possibility that this tick-borne organism may represent an unrecognized human or ruminant pathogen in NC and surrounding states. Currently, serological diagnostics specific for PME are not available. Serum from goats infected with PME was weakly IFA seropositive to E. chaffeensis and seropositive by ELISA to the MAP1 protein from E. ruminantium.12, 13 Serum from the dog of this report reacted strongly with E. canis antigen by IFA, but less strongly with the synthetic antigens used in a commercial ELISA (SNAP 4Dx Plus). Antibodies to other Ehrlichia spp. such as E. chaffeensis have been shown to cross-react with E. canis antigens, and it is likely that the reactivity from this PME-infected dog also represented a cross-reaction.17 Whereas E. canis, E. ewingii, and E. chaffeensis were not detected by PCR, we cannot rule out the possibility that seroreactivity was because of previous exposure with one of these pathogens. In addition to highlighting the emergence of vector-borne pathogens in a novel host species, the findings in this case report underscore the challenges faced in diagnosing canine lymphocytic malignancies and reinforce the need to better understand the immunopathology of canine ehrlichiosis, which can be caused by E. canis, E. chaffeensis, E. ewingii, E. muris, and PME in dogs in North America. Documentation of abnormal or expanded lymphocyte populations in the blood or tissues of dogs should prompt diagnostic consideration of infection with an intracellular pathogen, including Ehrlichia spp. Conflict of Interest: Authors disclose no conflict of interest. DA - 2013/7/22/ PY - 2013/7/22/ DO - 10.1111/jvim.12148 VL - 27 IS - 5 SP - 1251-1255 J2 - J Vet Intern Med LA - en OP - SN - 0891-6640 UR - http://dx.doi.org/10.1111/jvim.12148 DB - Crossref KW - Lymphocytosis KW - Panola Mountain Ehrlichia sp. KW - Clonal T-cell expansion KW - Bacteria KW - Tick vector ER - TY - JOUR TI - Spontaneous onset of complex regional pain syndrome Type I in a woman infected with Bartonella koehlerae AU - Vera, Cristina Pérez AU - Maggi, Ricardo G. AU - Woods, Christopher W. AU - Mascarelli, Patricia E. AU - Breitschwerdt, Edward B. T2 - Medical Microbiology and Immunology AB - After a short-term fever, complex regional pain syndrome, characterized by hyperalgesia, intermittent swelling, erythema and cyanosis of both feet, was diagnosed in a female veterinarian. The woman was infected with Bartonella koehlerae and she was also Bartonella vinsonii subsp. berkhoffii seroreactive. Having failed other treatments, symptoms resolved following initiation of antibiotics. DA - 2013/12/10/ PY - 2013/12/10/ DO - 10.1007/s00430-013-0320-3 VL - 203 IS - 2 SP - 101-107 J2 - Med Microbiol Immunol LA - en OP - SN - 0300-8584 1432-1831 UR - http://dx.doi.org/10.1007/s00430-013-0320-3 DB - Crossref KW - Pain KW - Bacteria KW - Spider KW - Veterinarian KW - Neuropathogenesis ER - TY - JOUR TI - Comparative microbiological features of Bartonella henselae infection in a dog with fever of unknown origin and granulomatous lymphadenitis AU - Drut, Amandine AU - Bublot, Isabelle AU - Breitschwerdt, Edward B. AU - Chabanne, Luc AU - Vayssier-Taussat, Muriel AU - Cadoré, Jean-Luc T2 - Medical Microbiology and Immunology AB - We report the first documented case of Bartonella henselae infection in a dog from France and the first isolation of B. henselae from a dog with fever of unknown origin. This observation contributes to the “One Health” concept focusing on zoonotic pathogens emerging from companion animals. A 1-year-old female German shepherd dog was referred for evaluation of fever of unknown origin of 1 month duration. Diagnostic investigations confirmed diffuse pyogranulomatous lymphadenitis. The dog became afebrile, and lymph node size normalized in response to a 6-week course of doxycycline. Retrospectively, Bartonella DNA was amplified from an EDTA-anticoagulated blood sample obtained before antimicrobial therapy, with the gtlA fragment sharing 99 % identity with the 350-bp gtlA fragment of the B. henselae Houston-1 strain. The same strain was isolated in the blood of three healthy cats from the household. Two months after discontinuation of doxycycline, the dog experienced a febrile relapse. Bartonella DNA was again amplified from blood prior to and immediately after administration of a 6-week course azithromycin therapy. However, without administration of additional medications, PCR was negative 9 months after azithromycin therapy and the dog remains clinically healthy 12 months following the second course of antibiotics. The medical management of this case raises several clinically relevant comparative infectious disease issues, including the extent to which Bartonella spp. contribute to fever of unknown origin and pyogranulomatous inflammatory diseases in dogs and humans, and the potential of doxycycline and azithromycin treatment failures. The possibility that dogs could constitute an underestimated reservoir for B. henselae transmission to people is also discussed. DA - 2013/12/6/ PY - 2013/12/6/ DO - 10.1007/s00430-013-0318-x VL - 203 IS - 2 SP - 85-91 J2 - Med Microbiol Immunol LA - en OP - SN - 0300-8584 1432-1831 UR - http://dx.doi.org/10.1007/s00430-013-0318-x DB - Crossref KW - Bartonella henselae KW - Cat-scratch disease KW - Dog KW - Fever of unknown origin KW - Granulomatous lymphadenitis ER - TY - JOUR TI - Amphiphilic chlorins and bacteriochlorins in micellar environments. Molecular design, de novo synthesis, and photophysical properties AU - Aravindu, Kunche AU - Mass, Olga AU - Vairaprakash, Pothiappan AU - Springer, Joseph W. AU - Yang, Eunkyung AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - Chemical Science AB - The incorporation of amphiphilic tetrapyrrole macrocycles in organized media is of great value for a variety of fundamental photochemical studies, yet work to date has chiefly employed porphyrins rather than chlorins or bacteriochlorins. The latter absorb strongly in the red or near-infrared spectral region, respectively. Here, eight amphiphilic macrocycles (six chlorins and two bacteriochlorins) have been designed, synthesized and characterized; the compounds differ in long wavelength absorption (610–745 nm) and peripheral substituents (type of auxochrome, hydrophobic/hydrophilic groups). A methyl pyridinium or benzoic acid substituent at the 15-position provides a polar “tail” whereas a hydrophobic group distal thereto (in the chlorins) provides a lipophilic “head” for the spontaneous incorporation in organized media. The eight (bacterio)chlorins are characterized by static and time-resolved absorption and fluorescence spectroscopy in N,N-dimethylformamide (DMF) and three micellar environments (TX-100, CTAB, and SDS) as well as ultrafast transient absorption studies in DMF. In most cases, a long-lived excited singlet state was observed [free base chlorins (Φf = 0.14–0.20; τS = 7.9–12.1 ns; Φisc = 0.5), zinc chlorins (Φf = 0.08–0.19; τS = 2.0–3.4 ns; Φisc = 0.6–0.8) and free base bacteriochlorins (Φf = 0.06–0.16; τS = 1.8–4.6 ns; Φisc = 0.4)]. In the case of bacteriochlorins, minimal medium dependence was observed whereas changing the hydrophilic group from methyl pyridinium to benzoic acid increases the fluorescence yield and excited-state lifetime by 50%. In the case of chlorins, the zinc chelate with methyl pyridinium substitution exhibits substantial environmental dependence due to interaction of the solvent with the methyl pyridinium group and the central zinc metal. Collectively, the studies provide valuable information for the design of red or near-infrared absorbing chromophores for incorporation into amphiphilic environments such as micelles, membranes, or proteins. DA - 2013/// PY - 2013/// DO - 10.1039/C3SC51335A VL - 4 IS - 9 SP - 3459 J2 - Chem. Sci. LA - en OP - SN - 2041-6520 2041-6539 UR - http://dx.doi.org/10.1039/C3SC51335A DB - Crossref ER - TY - JOUR TI - Synthetic bacteriochlorins with integral spiro-piperidine motifs AU - Reddy, Kanumuri Ramesh AU - Lubian, Elisa AU - Pavan, M. Phani AU - Kim, Han-Je AU - Yang, Eunkyung AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - A new molecular design incorporates a spiro-piperidine unit in each pyrroline ring of synthetic bacteriochlorins, thereby (1) replacing the previous geminal dimethyl group with a functionally equivalent motif to suppress adventitious dehydrogenation, (2) enabling tailoring of the bacteriochlorin by nitrogen derivatization, and (3) leaving the β-pyrrolic positions available for introduction of auxochromes to tune the spectral properties. Conversion of an N-protected 4-piperidone to the N-protected α,β-unsaturated ketone, Michael reaction with 4-(ethoxycarbonyl)-3-ethyl-2-(2-nitroethyl)pyrrole, and subsequent reductive cyclization provided the spiro-piperidine-1-methyldihydrodipyrrin. Treatment with SeO2 followed by trimethyl orthoformate under acid catalysis converted the 1-methyl group to a 1-(1,1-dimethoxymethyl) motif. Self-condensation of the resulting spiro-piperidine-dihydrodipyrrin-acetal afforded the 5-methoxy- or 5-unsubstituted bacteriochlorin, each bearing two spiro-piperidine units. The spiro-piperidine units were derivatized at the nitrogens by methylation, sulfonylation, acylation, or quaternization; the latter with methyl iodide afforded two dicationic, hydrophilic bacteriochlorins. Altogether, eight spiro-piperidine-bacteriochlorins were prepared. Spectroscopic characterization was carried out in DMF (and in water for the quaternized, 5-methoxybacteriochlorin). Compared to the 5-unsubstituted analogue, the quaternized, 5-methoxybacteriochlorin has in DMF a shorter wavelength of the intense near-infrared absorption band (733 vs. 752 nm) and fluorescence band (739 vs. 760 nm), modestly greater fluorescence yield (0.15 vs. 0.08) and modestly longer lifetime of the lowest singlet excited state (4.7 vs. 3.3 ns). In general, the spiro-piperidinyl moiety does not significantly alter the rate constants or yields of the decay pathways (fluorescence, intersystem crossing, internal conversion) of the lowest singlet excited state of the bacteriochlorin. Taken together, the results describe a new molecular design for tailoring the polarity of near-infrared absorbers. DA - 2013/// PY - 2013/// DO - 10.1039/C3NJ41161C VL - 37 IS - 4 SP - 1157 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/C3NJ41161C DB - Crossref ER - TY - JOUR TI - Expanded combinatorial formation of porphyrin macrocycles in aqueous solution containing vesicles. A prebiotic model AU - Soares, Ana R. M. AU - Taniguchi, Masahiko AU - Chandrashaker, Vanampally AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - The role of combinatorial processes in the origin of life remains relatively unexplored. In a chemical model for the possible prebiogenesis of tetrapyrrole macrocycles reported previously, a tandem combinatorial reaction of two diones (substituents = methyl, acetic acid) and two aminoketones (substituents = ethyl, propanoic acid) afforded up to 538 porphyrins (upon oxidation of the corresponding porphyrinogens). The reaction was performed at a 1 : 1 ratio of hydrophobic and hydrophilic substituents in each pool of reactants, and the resulting porphyrins partitioned in ∼1 : 1 ratio between aqueous solution and phosphatidylcholine vesicle membranes. Here, a change in the ratio of hydrophobic and hydrophilic substituents of the [2 × 2] reaction gave corresponding changes in the polarity profile of the resulting porphyrins (3.5–9.0% yield). Reaction of four diones and four aminoketones (bearing hydrophilic or hydrophobic substituents) in the presence of lipid vesicles followed by photooxidation afforded porphyrins in 8.7% yield. The resulting porphyrins partitioned in ∼1 : 1 ratio between phosphatidylcholine vesicles and aqueous solution, as observed previously for the [2 × 2] reaction. Both the aqueous fraction and the vesicles fraction were photochemically active as evidenced by the fluorescence quantum yield (Φf ∼ 0.1). Software (PorphyrinViLiGe) for virtual library generation indicates that the [4 × 4] reaction affords up to 131 464 porphyrins. The relative insensitivity of physicochemical properties (partitioning, photoactivity) toward combinatorial expansion may be a valuable yet unappreciated attribute for prebiotic functionality. DA - 2013/// PY - 2013/// DO - 10.1039/c3nj41041b VL - 37 IS - 4 SP - 1073 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/c3nj41041b DB - Crossref ER - TY - JOUR TI - Serendipitous synthetic entrée to tetradehydro analogues of cobalamins AU - Deans, Richard M. AU - Mass, Olga AU - Diers, James R. AU - Bocian, David F. AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - Tetradehydrocorrin macrocycles occupy a saturation level halfway between that of octadehydrocorrins and corrins (e.g., cyanocobalamin). While octadehydrocorrin chemistry is relatively well understood, few studies have been done on more reduced macrocycles owing to synthetic limitations. The reaction of a 2,3-dihydro-1,3,3-trimethyldipyrrin (Western half) bearing a 7-(4-iodophenyl) group and a 1-(dimethoxymethyl)-9-bromo-2,3-dihydro-3,3-dimethyldipyrrin (Eastern half) bearing a 7-p-tolyl group in the presence of Ga(OTf)3 afforded the corresponding B,D-tetradehydrocorrin (1) in 24% yield. Use of a Western half bearing a 7-(4-ethylphenyl) group afforded the B,D-tetradehydrocorrin (2) in 29% yield. Each tetradehydrocorrin bears a 1-methyl group at the A–D ring junction (and hence is enantiomeric), a geminal dimethyl group in each pyrroline ring, and distinct substituents at the 7- and 17-positions; characterization included 1H and 13C NMR spectroscopies, absorption spectroscopy, mass spectrometry, and X-ray crystallography (2 only). Treatment of 1 or 2 with CoCl2 afforded the cobalt chelate as a mixture of stereoisomers containing an apical methoxide or hydroxide ligand. The cobalt-tetradehydrocorrin was characterized by absorption spectroscopy, mass spectrometry, infrared spectroscopy and electrochemistry. The cobalt chelate was smoothly titrated with THF, pyridine, and KCN or Bu4NCN. While the assignment of the oxidation state of the cobalt remains provisional, the use of natural abundance versus isotopically substituted solvents or titrants (CD3OD, K13CN) enabled clear identification of the apical ligands. The facile access to stable, synthetically tailored B,D-tetradehydrocorrins should open the door to fundamental studies of simple surrogates of cyanocobalamin. DA - 2013/// PY - 2013/// DO - 10.1039/C3NJ00574G VL - 37 IS - 12 SP - 3964 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/C3NJ00574G DB - Crossref ER - TY - JOUR TI - Are vector-borne pathogen co-infections complicating the clinical presentation in dogs? AU - De Tommasi, Anna Sara AU - Otranto, Domenico AU - Dantas-Torres, Filipe AU - Capelli, Gioia AU - Breitschwerdt, Edward B AU - de Caprariis, Donato T2 - Parasites & Vectors AB - Infection by two or more canine vector-borne disease (CVBD)-causing pathogens is common in subtropical and tropical regions where vectors are plentiful. Co-infections may potentiate disease pathogenesis, thereby altering clinical manifestations typically associated with singular infections. These factors complicate diagnosis, treatment and can adversely influence prognosis if the practitioner fails to suspect, document, and treat each concurrent infection. The spectrum of pathogens co-infecting dogs may change over time in a given practice location due to the rapid expansion of arthropods and their associated vectored agents, and international transit among pets and wild animals. This applies, for example, to Dirofilaria immitis and Leishmania infantum, the distributions of which have expanded from northern to southern Italy, and vice versa, respectively. Indeed, mixed infections by D. immitis and L. infantum have only been reported once in Italy, probably due to the fact that competent vectors for these infections do not usually occur in the same geographical areas. Thus, information that would help practitioners to identify clinical presentations in dogs co-infected by D. immitis and L. infantum and other CVBD-causing pathogens is scant.This manuscript describes the clinical history and physical examination of findings for 7 CVBD co-infected dogs that were examined because of a spectrum of clinical signs. Five dogs were co-infected with L. infantum and Ehrlichia canis, one dog with L. infantum, E. canis and D. immitis and the remaining dog with L. infantum and D. immitis.The clinical signs and haematological abnormalities associated with the diagnostic evaluation and treatment of these dogs is discussed. Also, the usefulness of bone marrow specimens for the molecular diagnosis of CVBDs and for the enhanced monitoring of treatment response is emphasized. DA - 2013/// PY - 2013/// DO - 10.1186/1756-3305-6-97 VL - 6 IS - 1 SP - 97 J2 - Parasites & Vectors LA - en OP - SN - 1756-3305 UR - http://dx.doi.org/10.1186/1756-3305-6-97 DB - Crossref KW - Co-infection KW - Dirofilaria immitis KW - Ehrlichia canis KW - Leishmania infantum KW - Bone marrow ER - TY - JOUR TI - Survey of Bartonella spp. in U.S. Bed Bugs Detects Burkholderia multivorans but Not Bartonella AU - Saenz, Virna L. AU - Maggi, Ricardo G. AU - Breitschwerdt, Edward B. AU - Kim, Jung AU - Vargo, Edward L. AU - Schal, Coby T2 - PLoS ONE AB - Bed bugs (Cimex lectularius L.) have resurged in the United States and globally. Bed bugs are hematophagous ectoparasites of humans and other animals, including domestic pets, chickens, and bats, and their blood feeding habits contribute to their potential as disease vectors. Several species of Bartonella are re-emergent bacterial pathogens that also affect humans, domestic pets, bats and a number of other wildlife species. Because reports of both bed bugs and Bartonella have been increasing in the U.S., and because their host ranges can overlap, we investigated whether the resurgences of these medically important pathogens and their potential vector might be linked, by screening for Bartonella spp. in bed bugs collected from geographic areas where these pathogens are prevalent and from bed bugs that have been in culture in the laboratory for several years. We screened a total of 331 bed bugs: 316 bed bugs from 36 unique collections in 29 geographic locations in 13 states, 10 bed bugs from two colonies maintained in the laboratory for 3 yr, and 5 bed bugs from a colony that has been in culture since before the recent resurgence of bed bugs. Bartonella spp. DNA was screened using a polymerase chain reaction assay targeting the 16S–23S rRNA intergenic transcribed spacer region. Bartonella DNA was not amplified from any bed bug, but five bed bugs from four different apartments of an elderly housing building in North Carolina contained DNA sequences that corresponded to Burkholderia multivorans, an important pathogen in nosocomial infections that was not previously linked to an arthropod vector. DA - 2013/9/9/ PY - 2013/9/9/ DO - 10.1371/journal.pone.0073661 VL - 8 IS - 9 SP - e73661 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0073661 DB - Crossref ER - TY - CHAP TI - Constructing Conditional Reference Charts for Grip Strength Measured with Error AU - Torres, Pedro A. AU - Zhang, Daowen AU - Wang, Huixia Judy T2 - Springer Proceedings in Mathematics & Statistics AB - Muscular strength, usually quantified through the grip strength, can be used in humans and animals as an indicator of neuromuscular function or to assess hand function in patients with trauma or congenital problems. Because grip strength cannot be accurately measured, several contaminated measurements are often taken on the same subject. A research interest in grip strength studies is estimating the conditional quantiles of the latent grip strength, which can be used to construct conditional grip strength charts. Current work in the literature often applies conventional quantile regression method using the subject-specific average of the repeated measurements as the response variable. We show that this approach suffers from model misspecification and often leads to biased estimates of the conditional quantiles of the latent grip strength. We propose a new semi-nonparametric estimation approach, which is able to account for measurement errors and allows the subject-specific random effects to follow a flexible distribution. We demonstrate through simulation studies that the proposed method leads to consistent and efficient estimates of the conditional quantiles of the latent response variable. The value of the proposed method is assessed by analyzing a grip strength data set on laboratory mice. PY - 2013/// DO - 10.1007/978-1-4614-7846-1_24 SP - 299-310 OP - PB - Springer New York SN - 9781461478454 9781461478461 UR - http://dx.doi.org/10.1007/978-1-4614-7846-1_24 DB - Crossref ER - TY - JOUR TI - Solution NMR studies of the plant peptide hormone CEP inform function AU - Bobay, B.G. AU - Digennaro, P. AU - Scholl, E. AU - Imin, N. AU - Djordjevic, M.A. AU - McK Bird, D. T2 - FEBS Letters AB - The C-terminally Encoded Peptide (CEP) family of regulatory peptides controls root development in vascular plants. Here, we present the first NMR structures of CEP. We show that root-knot nematode (RKN: Meloidogyne spp.) also encodes CEP, presumably to mimic plant CEP as part of their stereotypic, parasitic interaction with vascular plants. Molecular dynamics simulations of plant- and nematode-encoded CEP displaying known posttranslational modifications (PTM) provided insight into the structural effects of PTM and the conformational plasticity and rigidity of CEP. Potential mechanisms of action are discussed with respect to the structure and sampling of conformational space. DA - 2013/// PY - 2013/// DO - 10.1016/j.febslet.2013.10.033 VL - 587 IS - 24 SP - 3979-3985 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84888642079&partnerID=MN8TOARS KW - NMR KW - Molecular dynamic KW - CEP KW - Root-knot nematode KW - Peptide KW - CLE KW - Meloidogyne ER - TY - CONF TI - Teaching tropical plant pathology to a global audience AU - Ristaino, JB AU - Daub, M T2 - AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA C2 - 2013/// C3 - PHYTOPATHOLOGY DA - 2013/// VL - 103 SP - 189-189 M1 - 6 ER - TY - JOUR TI - The Pandemic in 2009 AU - Fry, WE AU - McGrath, MT AU - Seaman, A AU - Zitter, TA AU - McLeod, A AU - Danies, G AU - Small, IM AU - Myers, K AU - Everts, K AU - Gevens, AJ AU - others T2 - Plant Disease DA - 2013/// PY - 2013/// VL - 97 IS - 3 SP - 297 ER - TY - JOUR TI - The 2009 late blight pandemic in the eastern United States--causes and results AU - Fry, WE AU - McGrath, MT AU - Seaman, A AU - Zitter, TA AU - McLeod, A AU - Danies, G AU - Small, IM AU - Myers, K AU - Everts, K AU - Gevens, AJ AU - others T2 - Plant Disease DA - 2013/// PY - 2013/// VL - 97 IS - 3 SP - 296-306 ER - TY - JOUR TI - Reconstructing genome evolution in historic samples of the Irish potato famine pathogen AU - Martin, Michael D AU - Cappellini, Enrico AU - Samaniego, Jose A AU - Zepeda, M Lisandra AU - Campos, Paula F AU - Seguin-Orlando, Andaine AU - Wales, Nathan AU - Orlando, Ludovic AU - Ho, Simon YW AU - Dietrich, Fred S AU - others T2 - Nature communications DA - 2013/// PY - 2013/// VL - 4 SP - 2172 ER - TY - BOOK TI - Worldwide Migrations, Host Shifts, and Reemergence of Phytophthora Infestans, the Plant Destroyer AU - Ristaino, J.B. AB - This chapter contains sections titled: Introduction Emergence of Late Blight in the United States and Europe Evolutionary Position and Phylogenetic Relationships of Phytophthora spp. Life History of the Pathogen Population Biology: Migration Theories of P. Infestans in the 19th Century What mtDNA Haplotype Caused the Famine and Where did It Come From? When did the mtDNA Haplotype lb Migrate from South America? Historic Migrations: “Out-of-South America” Migration Hypothesis Host Shifts and Jumps Why is Late Blight a Reemerging Disease? Conclusions DA - 2013/// PY - 2013/// DO - 10.1002/9781118308165.ch10 SE - 192-207 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84876792801&partnerID=MN8TOARS ER - TY - CONF TI - Sparse multivariate function recovery from values with noise and outlier errors AU - Kaltofen, Erich L. AU - Yang, Zhengfeng T2 - the 38th international symposium AB - Error-correcting decoding is generalized to multivariate sparse rational function recovery from evaluations that can be numerically inaccurate and where several evaluations can have severe errors ("outliers"). The generalization of the Berlekamp-Welch decoder to exact Cauchy interpolation of univariate rational functions from values with faults is by Kaltofen and Pernet in 2012. We give a different univariate solution based on structured linear algebra that yields a stable decoder with floating point arithmetic. Our multivariate polynomial and rational function interpolation algorithm combines Zippel's symbolic sparse polynomial interpolation technique [Ph.D. Thesis MIT 1979] with the numeric algorithm by Kaltofen, Yang, and Zhi [Proc. SNC 2007], and removes outliers ("cleans up data") through techniques from error correcting codes. Our multivariate algorithm can build a sparse model from a number of evaluations that is linear in the sparsity of the model. C2 - 2013/// C3 - Proceedings of the 38th international symposium on International symposium on symbolic and algebraic computation - ISSAC '13 DA - 2013/// DO - 10.1145/2465506.2465524 PB - ACM Press SN - 9781450320597 UR - http://dx.doi.org/10.1145/2465506.2465524 DB - Crossref ER - TY - JOUR TI - Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification AU - Huang, Lingkang AU - Zhang, Hao Helen AU - Zeng, Zhao-Bang AU - Bushel, Pierre R. T2 - Cancer Informatics AB - Microarray techniques provide promising tools for cancer diagnosis using gene expression profiles. However, molecular diagnosis based on high-throughput platforms presents great challenges due to the overwhelming number of variables versus the small sample size and the complex nature of multi-type tumors. Support vector machines (SVMs) have shown superior performance in cancer classification due to their ability to handle high dimensional low sample size data. The multi-class SVM algorithm of Crammer and Singer provides a natural framework for multi-class learning. Despite its effective performance, the procedure utilizes all variables without selection. In this paper, we propose to improve the procedure by imposing shrinkage penalties in learning to enforce solution sparsity.The original multi-class SVM of Crammer and Singer is effective for multi-class classification but does not conduct variable selection. We improved the method by introducing soft-thresholding type penalties to incorporate variable selection into multi-class classification for high dimensional data. The new methods were applied to simulated data and two cancer gene expression data sets. The results demonstrate that the new methods can select a small number of genes for building accurate multi-class classification rules. Furthermore, the important genes selected by the methods overlap significantly, suggesting general agreement among different variable selection schemes.High accuracy and sparsity make the new methods attractive for cancer diagnostics with gene expression data and defining targets of therapeutic intervention.The source MATLAB code are available from http://math.arizona.edu/~hzhang/software.html. DA - 2013/1// PY - 2013/1// DO - 10.4137/cin.s10212 VL - 12 SP - CIN.S10212 J2 - Cancer Inform LA - en OP - SN - 1176-9351 1176-9351 UR - http://dx.doi.org/10.4137/cin.s10212 DB - Crossref KW - support vector machine (SVM) KW - multi-class SVM KW - variable selection KW - shrinkage methods KW - classification KW - microarray KW - cancer classification ER - TY - JOUR TI - Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments AU - Loziuk, Philip L. AU - Wang, Jack AU - Li, Quanzi AU - Sederoff, Ronald R. AU - Chiang, Vincent L. AU - Muddiman, David C. T2 - JOURNAL OF PROTEOME RESEARCH AB - Workflows in bottom-up proteomics have traditionally implemented the use of proteolysis during sample preparation; enzymatic digestion is most commonly performed using trypsin. This results in the hydrolysis of peptide bonds forming tryptic peptides, which can then be subjected to LC–MS/MS analysis. While the structure, specificity, and kinetics of trypsin are well characterized, a lack of consensus and understanding has remained regarding fundamental parameters critical to obtaining optimal data from a proteomics experiment. These include the type of trypsin used, pH during digestion, incubation temperature as well as enzyme-to-substrate ratio. Through the use of design of experiments (DOE), we optimized these parameters, resulting in deeper proteome coverage and a greater dynamic range of measurement. The knowledge gained from optimization of a discovery-based proteomics experiment was applied to targeted LC–MS/MS experiments using protein cleavage-isotope dilution mass spectrometry for absolute quantification. We demonstrated the importance of these digest parameters with respect to our limit of detection as well as our ability to acquire more accurate quantitative measurements. Additionally, we were able to quantitatively account for peptide decay observed in previous studies, caused by nonspecific activity of trypsin. The tryptic digest optimization described here has eliminated this previously observed peptide decay as well as provided a greater understanding and standardization for a common but critical sample treatment used across the field of proteomics. DA - 2013/12// PY - 2013/12// DO - 10.1021/pr4008442 VL - 12 IS - 12 SP - 5820-5829 SN - 1535-3907 KW - design of experiments KW - proteolytic digestion KW - LC-MS/MS KW - Populus trichocarpa ER - TY - JOUR TI - The BRASSINOSTEROID INSENSITIVE1-LIKE3 Signalosome Complex Regulates Arabidopsis Root Development AU - Fabregas, Norma AU - Li, Na AU - Boeren, Sjef AU - Nash, Tara E. AU - Goshe, Michael B. AU - Clouse, Steven D. AU - Vries, Sacco AU - Cano-Delgado, Ana I. T2 - PLANT CELL AB - Brassinosteroid (BR) hormones are primarily perceived at the cell surface by the leucine-rich repeat receptor-like kinase brassinosteroid insensitive1 (BRI1). In Arabidopsis thaliana, BRI1 has two close homologs, BRI1-LIKE1 (BRL1) and BRL3, respectively, which are expressed in the vascular tissues and regulate shoot vascular development. Here, we identify novel components of the BRL3 receptor complex in planta by immunoprecipitation and mass spectrometry analysis. Whereas BRI1 associated kinase1 (BAK1) and several other known BRI1 interactors coimmunoprecipitated with BRL3, no evidence was found of a direct interaction between BRI1 and BRL3. In addition, we confirmed that BAK1 interacts with the BRL1 receptor by coimmunoprecipitation and fluorescence microscopy analysis. Importantly, genetic analysis of brl1 brl3 bak1-3 triple mutants revealed that BAK1, BRL1, and BRL3 signaling modulate root growth and development by contributing to the cellular activities of provascular and quiescent center cells. This provides functional relevance to the observed protein-protein interactions of the BRL3 signalosome. Overall, our study demonstrates that cell-specific BR receptor complexes can be assembled to perform different cellular activities during plant root growth, while highlighting that immunoprecipitation of leucine-rich repeat receptor kinases in plants is a powerful approach for unveiling signaling mechanisms with cellular resolution in plant development. DA - 2013/9// PY - 2013/9// DO - 10.1105/tpc.113.114462 VL - 25 IS - 9 SP - 3377-3388 SN - 1532-298X ER - TY - JOUR TI - The Amborella Genome and the Evolution of Flowering Plants AU - Albert, Victor A. AU - Barbazuk, W. Bradley AU - dePamphilis, Claude W. AU - Der, Joshua P. AU - Leebens-Mack, James AU - Ma, Hong AU - Palmer, Jeffrey D. AU - Rounsley, Steve AU - Sankoff, David AU - Schuster, Stephan C. AU - Soltis, Douglas E. AU - Soltis, Pamela S. AU - Wessler, Susan R. AU - Wing, Rod A. AU - Albert, Victor A. AU - Ammiraju, Jetty S. S. AU - Barbazuk, W. Bradley AU - Chamala, Srikar AU - Chanderbali, Andre S. AU - dePamphilis, Claude W. AU - Der, Joshua P. AU - Determann, Ronald AU - Leebens-Mack, James AU - Ma, Hong AU - Ralph, Paula AU - Rounsley, Steve AU - Schuster, Stephan C. AU - Soltis, Douglas E. AU - Soltis, Pamela S. AU - Talag, Jason AU - Tomsho, Lynn AU - Walts, Brandon AU - Wanke, Stefan AU - Wing, Rod A. AU - Albert, Victor A. AU - Barbazuk, W. Bradley AU - Chamala, Srikar AU - Chanderbali, Andre S. AU - Chang, Tien-Hao AU - Determann, Ronald AU - Lan, Tianying AU - Soltis, Douglas E. AU - Soltis, Pamela S. AU - Arikit, Siwaret AU - Axtell, Michael J. AU - Ayyampalayam, Saravanaraj AU - Barbazuk, W. Bradley AU - Burnette, James M., III AU - Chamala, Srikar AU - De Paoli, Emanuele AU - dePamphilis, Claude W. AU - Der, Joshua P. AU - Estill, James C. AU - Farrell, Nina P. AU - Harkess, Alex AU - Jiao, Yuannian AU - Leebens-Mack, James AU - Liu, Kun AU - Mei, Wenbin AU - Meyers, Blake C. AU - Shahid, Saima AU - Wafula, Eric AU - Walts, Brandon AU - Wessler, Susan R. AU - Zhai, Jixian AU - Zhang, Xiaoyu AU - Albert, Victor A. AU - Carretero-Paulet, Lorenzo AU - dePamphilis, Claude W. AU - Der, Joshua P. AU - Jiao, Yuannian AU - Leebens-Mack, James AU - Lyons, Eric AU - Sankoff, David AU - Tang, Haibao AU - Wafula, Eric AU - Zheng, Chunfang AU - Albert, Victor A. AU - Altman, Naomi S. AU - Barbazuk, W. Bradley AU - Carretero-Paulet, Lorenzo AU - dePamphilis, Claude W. AU - Der, Joshua P. AU - Estill, James C. AU - Jiao, Yuannian AU - Leebens-Mack, James AU - Liu, Kun AU - Mei, Wenbin AU - Wafula, Eric AU - Altman, Naomi S. AU - Arikit, Siwaret AU - Axtell, Michael J. AU - Chamala, Srikar AU - Chanderbali, Andre S. AU - Chen, Feng AU - Chen, Jian-Qun AU - Chiang, Vincent AU - De Paoli, Emanuele AU - dePamphilis, Claude W. AU - Der, Joshua P. AU - Determann, Ronald AU - Fogliani, Bruno AU - Guo, Chunce AU - Harholt, Jesper AU - Harkess, Alex AU - Job, Claudette AU - Job, Dominique AU - Kim, Sangtae AU - Kong, Hongzhi AU - Leebens-Mack, James AU - Li, Guanglin AU - Li, Lin AU - Liu, Jie AU - Ma, Hong AU - Meyers, Blake C. AU - Park, Jongsun AU - Qi, Xinshuai AU - Rajjou, Loic AU - Burtet-Sarramegna, Valerie AU - Sederoff, Ron AU - Shahid, Saima AU - Soltis, Douglas E. AU - Soltis, Pamela S. AU - Sun, Ying-Hsuan AU - Ulvskov, Peter AU - Villegente, Matthieu AU - Xue, Jia-Yu AU - Yeh, Ting-Feng AU - Yu, Xianxian AU - Zhai, Jixian AU - Acosta, Juan J. AU - Albert, Victor A. AU - Barbazuk, W. Bradley AU - Bruenn, Riva A. AU - Chamala, Srikar AU - Kochko, Alexandre AU - dePamphilis, Claude W. AU - Der, Joshua P. AU - Herrera-Estrella, Luis R. AU - Ibarra-Laclette, Enrique AU - Kirst, Matias AU - Leebens-Mack, James AU - Pissis, Solon P. AU - Poncet, Valerie AU - Schuster, Stephan C. AU - Soltis, Douglas E. AU - Soltis, Pamela S. AU - Tomsho, Lynn T2 - SCIENCE AB - Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams ). To validate and assemble the sequence, Chamala et al. (p. 1516 ) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089 ) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468 ) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae. DA - 2013/12/20/ PY - 2013/12/20/ DO - 10.1126/science.1241089 VL - 342 IS - 6165 SP - 1467-+ SN - 1095-9203 ER - TY - JOUR TI - Specificity of the receptor for the major sex pheromone component in Heliothis virescens AU - Vasquez, G. M. AU - Syed, Z. AU - Estes, P. A. AU - Leal, W. S. AU - Gould, F. T2 - Journal of Insect Science (Tucson, AZ) AB - In a previous study, the Drosophila melanogaster OR67d(GAL4);UAS system was used to functionally characterize the receptor for the major component of the sex pheromone in the tobacco budworm, Heliothis virescens Fabricius (Lepidoptera: Noctuidae), HvOR13. Electrophysiological and behavioral assays showed that transgenic flies expressing HvOR13 responded to (Z)-11-hexadecenal (Z11-16:Ald). However, tests were not performed to determine whether these flies would also respond to secondary components of the H. virescens sex pheromone. Thus, in this study the response spectrum of HvOR13 expressed in this system was examined by performing single cell recordings from odor receptor neuron in trichoid T1 sensilla on antennae of two Or67d(GAL4 [1]); UAS-HvOR13 lines stimulated with Z11-16:Ald and six H. virescens secondary pheromone components. Fly courtship assays were also performed to examine the behavioral response of the Or67d(GAL4[1]); UAS-HvOR13 flies to Z11-16:Ald and the secondary component Z9-14:Ald. Our combined electrophysiological and behavioral studies indicated high specificity and sensitivity of HvOR13 to Z11-16:Ald. Interestingly, a mutation leading to truncation in the HvOR13 C-terminal region affected but did not abolish pheromone receptor response to Z11-16:Ald. The findings are assessed in relationship to other HvOR13 heterologous expression studies, and the role of the C-terminal domain in receptor function is discussed. A third line expressing HvOR15 was also tested but did not respond to any of the seven pheromone components. DA - 2013/// PY - 2013/// DO - 10.1673/031.013.16001 VL - 13 ER - TY - JOUR TI - SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa AU - Lin, Ying-Chung AU - Li, Wei AU - Sun, Ying-Hsuan AU - Kumari, Sapna AU - Wei, Hairong AU - Li, Quanzi AU - Tunlaya-Anukit, Sermsawat AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PLANT CELL AB - Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)-directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1-DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling-based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1-directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable. DA - 2013/11// PY - 2013/11// DO - 10.1105/tpc.113.117697 VL - 25 IS - 11 SP - 4324-4341 SN - 1532-298X ER - TY - JOUR TI - Polymeric Systems Incorporating Plant Viral Nanoparticles for Tailored Release of Therapeutics AU - Honarbakhsh, Sara AU - Guenther, Richard H. AU - Willoughby, Julie A. AU - Lommel, Steven A. AU - Pourdeyhimi, Behnam T2 - ADVANCED HEALTHCARE MATERIALS AB - Therapeutic polylactide (PLA) nanofibrous matrices are fabricated by incorporating plant viral nanoparticles (PVNs) infused with fluorescent agents ethidium bromide (EtBr) and rhodamine (Rho), and cancer therapeutic doxorubicin (Dox). The native virus, Red clover necrotic mosaic virus (RCNMV), reversibly opens and closes upon exposure to the appropriate environmental stimuli. Infusing RCNMV with small molecules allows the incorporation of PVN(Active) into fibrous matrices via two methods: direct processing by in situ electrospinning of a polymer and PVNs solution or immersion of the matrix into a viral nanoparticle solution. Five organic solvents commonly in-use for electrospinning are evaluated for potential negative impact on RCNMV stability. In addition, leakage of rhodamine from the corresponding PVN(Rho) upon solvent exposure is determined. Incorporation of the PVN into the matrices are evaluated via transmission electron, scanning electron and fluorescent microscopies. Finally, the percent cumulative release of doxorubicin from both PLA nanofibers and PLA and polyethylene oxide (PEO) hybrid nanofibers demonstrate tailored release due to the incorporation of PVN(Dox) as compared to the control nanofibers with free Dox. Preliminary kinetic analysis results suggest a two-phase release profile with the first phase following a hindered Fickian transport mechanism for the release of Dox for the polymer-embedded PVNs. In contrast, the nanofiber matrices that incorporate PVNs through the immersion processing method followed a pseudo-first order kinetic transport mechanism. DA - 2013/7// PY - 2013/7// DO - 10.1002/adhm.201200434 VL - 2 IS - 7 SP - 1001-1007 SN - 2192-2659 KW - controlled release KW - drug delivery KW - nanofibers KW - plant viral nanoparticles KW - virus ER - TY - JOUR TI - Lengthening the Intersubunit Linker of Procaspase 3 Leads to Constitutive Activation AU - MacKenzie, Sarah H. AU - Schipper, Joshua L. AU - England, Erika J. AU - Thomas, Melvin E., III AU - Blackburn, Kevin AU - Swartz, Paul AU - Clark, A. Clay T2 - BIOCHEMISTRY AB - The conformational ensemble of procaspase 3, the primary executioner in apoptosis, contains two major forms, inactive and active, with the inactive state favored in the native ensemble. A region of the protein known as the intersubunit linker (IL) is cleaved during maturation, resulting in movement of the IL out of the dimer interface and subsequent active site formation (activation-by-cleavage mechanism). We examined two models for the role of the IL in maintaining the inactive conformer, an IL-extension model versus a hydrophobic cluster model, and we show that increasing the length of the IL by introducing 3-5 alanines results in constitutively active procaspases. Active site labeling and subsequent analyses by mass spectrometry show that the full-length zymogen is enzymatically active. We also show that minor populations of alternately cleaved procaspase result from processing at D169 when the normal cleavage site, D175, is unavailable. Importantly, the alternately cleaved proteins have little to no activity, but increased flexibility of the linker increases the exposure of D169. The data show that releasing the strain of the short IL, in and of itself, is not sufficient to populate the active conformer of the native ensemble. The IL must also allow for interactions that stabilize the active site, possibly from a combination of optimal length, flexibility in the IL, and specific contacts between the IL and interface. The results provide further evidence that substantial energy is required to shift the protein to the active conformer. As a result, the activation-by-cleavage mechanism dominates in the cell. DA - 2013/9/10/ PY - 2013/9/10/ DO - 10.1021/bi400793s VL - 52 IS - 36 SP - 6219-6231 SN - 0006-2960 ER - TY - JOUR TI - Phosphatidylinositol 4,5-Bisphosphate Influences PIN Polarization by Controlling Clathrin-Mediated Membrane Trafficking in Arabidopsis AU - Ischebeck, Till AU - Werner, Stephanie AU - Krishnamoorthy, Praveen AU - Lerche, Jennifer AU - Meijon, Monica AU - Stenzel, Irene AU - Loefke, Christian AU - Wiessner, Theresa AU - Im, Yang Ju AU - Perera, Imara Y. AU - Iven, Tim AU - Feussner, Ivo AU - Busch, Wolfgang AU - Boss, Wendy F. AU - Teichmann, Thomas AU - Hause, Bettina AU - Persson, Staffan AU - Heilmann, Ingo T2 - PLANT CELL AB - Abstract The functions of the minor phospholipid phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P2] during vegetative plant growth remain obscure. Here, we targeted two related phosphatidylinositol 4-phosphate 5-kinases (PI4P 5-kinases) PIP5K1 and PIP5K2, which are expressed ubiquitously in Arabidopsis thaliana. A pip5k1 pip5k2 double mutant with reduced PtdIns(4,5)P2 levels showed dwarf stature and phenotypes suggesting defects in auxin distribution. The roots of the pip5k1 pip5k2 double mutant had normal auxin levels but reduced auxin transport and altered distribution. Fluorescence-tagged auxin efflux carriers PIN-FORMED (PIN1)–green fluorescent protein (GFP) and PIN2-GFP displayed abnormal, partially apolar distribution. Furthermore, fewer brefeldin A–induced endosomal bodies decorated by PIN1-GFP or PIN2-GFP formed in pip5k1 pip5k2 mutants. Inducible overexpressor lines for PIP5K1 or PIP5K2 also exhibited phenotypes indicating misregulation of auxin-dependent processes, and immunolocalization showed reduced membrane association of PIN1 and PIN2. PIN cycling and polarization require clathrin-mediated endocytosis and labeled clathrin light chain also displayed altered localization patterns in the pip5k1 pip5k2 double mutant, consistent with a role for PtdIns(4,5)P2 in the regulation of clathrin-mediated endocytosis. Further biochemical tests on subcellular fractions enriched for clathrin-coated vesicles (CCVs) indicated that pip5k1 and pip5k2 mutants have reduced CCV-associated PI4P 5-kinase activity. Together, the data indicate an important role for PtdIns(4,5)P2 in the control of clathrin dynamics and in auxin distribution in Arabidopsis. DA - 2013/12// PY - 2013/12// DO - 10.1105/tpc.113.116582 VL - 25 IS - 12 SP - 4894-4911 SN - 1532-298X ER - TY - JOUR TI - On the Matrix Berlekamp-Massey Algorithm AU - Kaltofen, Erich AU - Yuhasz, George T2 - ACM TRANSACTIONS ON ALGORITHMS AB - We analyze the Matrix Berlekamp/Massey algorithm, which generalizes the Berlekamp/Massey algorithm [Massey 1969] for computing linear generators of scalar sequences. The Matrix Berlekamp/Massey algorithm computes a minimal matrix generator of a linearly generated matrix sequence and has been first introduced by Rissanen [1972a], Dickinson et al. [1974], and Coppersmith [1994]. Our version of the algorithm makes no restrictions on the rank and dimensions of the matrix sequence. We also give new proofs of correctness and complexity for the algorithm, which is based on self-contained loop invariants and includes an explicit termination criterion for a given determinantal degree bound of the minimal matrix generator. DA - 2013/9// PY - 2013/9// DO - 10.1145/2500122 VL - 9 IS - 4 SP - SN - 1549-6333 KW - Linear generated sequences KW - matrix polynomials KW - minimal generators KW - vector Berlekamp/Massey algorithm KW - multivariable linear control ER - TY - JOUR TI - Experimental infection of dogs with Bartonella henselae and Bartonella vinsonii subsp. berkhoffii AU - Balakrishnan, Nandhakumar AU - Cherry, Natalie A. AU - Linder, Keith E. AU - Pierce, Eric AU - Sontakke, Neal AU - Hegarty, Barbara C. AU - Bradley, Julie M. AU - Maggi, Ricardo G. AU - Breitschwerdt, Edward B. T2 - Veterinary Immunology and Immunopathology AB - The lack of a suitable infection model remains an important obstacle for the pathophysiological understanding of Bartonella spp. The following pilot study was designed to determine whether cell culture-grown Bartonella henselae SA2 and Bartonella vinsonii subsp. berkhoffii genotype III would cause persistent bacteremia in dogs. Pre-inoculation screening established that two laboratory-raised Golden retrievers were naturally-infected with Bartonella koehlerae. Despite prior infection, one dog each was inoculated subcutaneously with 5 × 10(4)B. henselae (SA2 strain) or 3 × 10(4)B. vinsonii subsp. berkhoffii genotype III. Dogs were bled weekly for serological testing and culture using Bartonella alpha proteobacteria growth medium (BAPGM) diagnostic platform. Dog 1 seroconverted to B. henselae and Dog 2 seroconverted to B. vinsonii subsp. berkhoffii genotype III. Throughout the study period, Bartonella spp. DNA was neither amplified nor isolated in ante-mortem BAPGM enrichment blood cultures. B. henselae SA2 was isolated from a postmortem bone marrow from Dog 1 and B. koehlerae DNA was amplified from postmortem lung from Dog 2 following BAPGM enrichment culture. Limitations include lack of uninfected controls, a potentially suboptimal B. vinsonii subsp. berkhoffii inoculum and a relatively short duration of study. We conclude that following intradermal infection, sequestration of Bartonella spp. in tissues may limit diagnostic detection of these bacteria in dog blood samples. DA - 2013/11// PY - 2013/11// DO - 10.1016/j.vetimm.2013.09.007 VL - 156 IS - 1-2 SP - 153-158 J2 - Veterinary Immunology and Immunopathology LA - en OP - SN - 0165-2427 UR - http://dx.doi.org/10.1016/j.vetimm.2013.09.007 DB - Crossref KW - PCR KW - Bacteria KW - Bartonella henselae SA2 KW - Bartonella vinsonii subsp berkhoffii genotype III KW - Isolation KW - Dog model ER - TY - JOUR TI - The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae) AU - Eckert, Andrew J. AU - Wegrzyn, Jill L. AU - Liechty, John D. AU - Lee, Jennifer M. AU - Cumbie, W. Patrick AU - Davis, John M. AU - Goldfarb, Barry AU - Loopstra, Carol A. AU - Palle, Sreenath R. AU - Quesada, Tania AU - Langley, Charles H. AU - Neale, David B. T2 - GENETICS AB - Abstract A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for &gt;7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the &gt;1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits. DA - 2013/12// PY - 2013/12// DO - 10.1534/genetics.113.157198 VL - 195 IS - 4 SP - 1353-+ SN - 1943-2631 KW - association mapping KW - complex traits KW - Pinus taeda KW - natural selection KW - population genomics ER - TY - JOUR TI - Synthesis and photophysical properties of chlorins bearing 0–4 distinct meso-substituents AU - Aravindu, Kunche AU - Kim, Han-Je AU - Taniguchi, Masahiko AU - Dilbeck, Preston L. AU - Diers, James R. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - Photochemical & Photobiological Sciences AB - The presence of substituents at designated sites about the chlorin macrocycle can alter the spectral properties, a phenomenon that can be probed through synthesis. Prior syntheses have provided access to chlorins bearing distinct aryl substituents (individually or collectively) at the 5, 10, and 15-positions, but not the 20-position. A new Western half (5-phenyl-2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin) has been employed in condensation with an Eastern half (9-bromodipyrromethane-1-carboxaldehyde) followed by oxidative cyclization to give (5% yield) the zinc(II) 20-phenylchlorin. Condensation of the same Western half and a diaryl-substituted Eastern half provided (11% yield) the zinc(II) 5,10,20-triarylchlorin; demetalation with TFA followed by 15-bromination and Suzuki coupling gave the free base 5,10,15,20-tetraarylchlorin. Altogether, 10 new synthetic chlorins have been prepared. The near-UV (B) absorption band of the free base chlorins shifts bathochromically from 389 to 429 nm and that for the zinc chlorins from 398 to 420 nm as the number of meso-aryl rings is increased stepwise from 0-4. The long-wavelength (Q(y)) absorption band undergoes a bathochromic and hypochromic shift upon increase in number of meso-aryl groups. Regardless of the number and positions of the meso-aryl substituents (including "walking a phenyl group around the ring"), the respective fluorescence quantum yields (0.17 to 0.27) and singlet excited-state lifetimes (9.4 to 13.1 ns) are comparable among the free base chlorins and the same is true for the zinc chelates (0.057 to 0.080; 1.2 to 1.6 ns). Density functional theory calculations show that of the frontier molecular orbitals of the chlorin, the energy of the HOMO-1 is the most affected by meso-aryl substituents, undergoing progressive destabilization as the number of meso-aryl groups is increased. The availability of chlorins with 0-4 distinct meso-aryl substituents provides the individual stepping-stones to bridge the known unsubstituted chlorin and the meso-tetraarylchlorins. DA - 2013/// PY - 2013/// DO - 10.1039/C3PP50240F VL - 12 IS - 12 SP - 2089 J2 - Photochem. Photobiol. Sci. LA - en OP - SN - 1474-905X 1474-9092 UR - http://dx.doi.org/10.1039/C3PP50240F DB - Crossref ER - TY - JOUR TI - Naturally occuring canine cancers: powerful models for stimulating pharmacogenomic advancement in human medicine AU - Rotroff, Daniel M. AU - Thomas, Rachael AU - Breen, Matthew AU - Motsinger-Reif, Alison A. T2 - PHARMACOGENOMICS AB - PharmacogenomicsVol. 14, No. 16 EditorialFree AccessNaturally occuring canine cancers: powerful models for stimulating pharmacogenomic advancement in human medicineDaniel M Rotroff, Rachael Thomas, Matthew Breen & Alison A Motsinger-ReifDaniel M RotroffBioinformatics Research Center, Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA.Search for more papers by this author, Rachael ThomasDepartment of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA and Center for Comparative Medicine & Translational Research, North Carolina State University, Raleigh, NC, USA.Search for more papers by this author, Matthew BreenDepartment of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA and Center for Comparative Medicine & Translational Research, North Carolina State University, Raleigh, NC, USA and Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA.Search for more papers by this author & Alison A Motsinger-Reif* Author for correspondenceBioinformatics Research Center, Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA. Search for more papers by this authorEmail the corresponding author at motsinger@stat.ncsu.eduPublished Online:26 Nov 2013https://doi.org/10.2217/pgs.13.178AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareShare onFacebookTwitterLinkedInRedditEmail Keywords: cancercanine modelchemotherapyclinical trialsAn estimated 1.6 million new cases of cancer were diagnosed in the USA in 2012 [101]. The pharmaceutical industry is working furiously to develop new efficacious chemotherapeutics; however, the vast majority of compounds that show anticancer activity in preclinical studies fail during subsequent human clinical trials, hindering progress in patient care and further increasing costs for drug development [1–3]. Modern cancer research places a heavy emphasis on murine models for investigating cancer etiology and for driving the development of new therapies. Mice represent excellent models for studying cancer due to their short lifespans, ease of maintenance and opportunities for genetic manipulation [4]. While their attributes have led to numerous fundamental advances in identifying novel therapies, several important limitations exist. Murine models of cancer are generally induced by genetic engineering, or by subcutaneous xenografts. The limitations and advantages of various methods of inducing neoplasms in mice are well reviewed elsewhere [4,5]. Induced murine neoplasms are developed in a short period of time and they lack heterogeneity in the tumor cell population, the microenvironment and the stroma, all of which are inconsistent with most human cancers. Furthermore, human cancers typically display increased genomic instability compared with their induced murine counterparts, which limits their utility as tools for pharmacogenomics [6]. Many of these limitations may be addressed by using the domestic dog as a complementary model system. Canines share our environment and develop many age-related diseases with similar pathologies to humans. Perhaps most importantly, dogs exhibit a wide variety of spontaneous cancers that share extensive clinicopathologic features with those of human patients, offering a unique opportunity for comparative analysis of naturally occurring cancers towards advancing treatment strategies in both species.Why canines make promising models of human cancerA survey conducted from 2011–2012 indicates that approximately 78 million domestic dogs currently reside in the USA [102]. The domestic dog suffers from more than 450 spontaneous diseases, approximately 360 of which have a human analog [7]. Cancer is the leading cause of death in several of the most popular dog breeds, such as golden retrievers, Labrador retrievers and boxers, which succumb to cancer with frequencies of 50, 34 and 44%, respectively [8]. When evaluated by breed, there are clear differences in predispositions for a variety of cancers. In turn, several canine cancers exhibit breed-associated profiles of tumor-associated genomic aberrations, including lymphoma, osteosarcoma (OS) and intracranial malignancies. Moreover, comparative studies have revealed conserved genomic signatures in canine and human counterparts of the same cancer [9–12]. Based on the large population of dogs that develop cancer and the clinical and pathological similarity between many dog and human cancers, research into canine cancer may offer a wealth of insight into driver mechanisms of human carcinogenesis and provide a more representative model for testing new therapies.Canine pharmacogenomicsThe availability of a high-quality canine genome sequence assembly [13] has opened the door for identifying key drivers of disease that may also impact human patients. In an effort to identify putative drivers of OS, Angstadt et al. combined bioinformatics and experimental methods to conduct a genome-wide assessment of tumor-associated DNA copy number aberrations in spontaneous canine and human OS [10]. OS in both species exhibits extensive genomic instability and a similar pathophysiological profile. Critically, however, human OS represents <1000 new diagnoses per year in the USA compared with >10,000/year in canines, thus providing tremendous sources of clinical materials [10]. Comparative analysis of recurrent copy number aberrations in human and canine OS revealed discrete gene sets that were common to both species, disrupting fundamental cellular functions such as osteoblast fate commitment, regulation of organ growth, telomerase activity and homophilic cell adhesion, among others [10]. These results shed new light on gene candidates that may play a role in OS development and progression in both species [10], reinforcing the enormous potential for advancement through cross-species approaches.Clinical potential of caninesIn addition to using tumor-bearing canines as preclinical models, methods for incorporating dogs into the existing clinical testing framework have been proposed, and a logical integrated approach has been well described by Paoloni and Khanna [6]. Since canine clinical management strategies utilize similar diagnostic and therapeutic modalities to those in human medicine, the diagnostic nomenclature of canine cancers broadly follows that of their human counterparts. Canine chemotherapy protocols focus on more palliative approaches and are therefore prescribed at lower doses than the equivalent human protocols [6]. For example, the standard protocol for canine B-cell non-Hodgkin’s lymphoma (NHL) is cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP), which, until recently, was also the first-line treatment for humans with B-cell NHL. In human patients, the recent addition of the monoclonal antibody rituximab to the CHOP regimen (i.e., R-CHOP) has become the first-line treatment for humans with B-cell NHL.In the search for targeted lymphoma and autoimmune-related therapies, activation of the B-cell antigen receptor signaling pathway has become a high priority since being identified as critical for the survival of B-cell NHL cells [14]. Btk represents a key component for B-cell antigen receptor activation, making the recent discovery of ibrutinib, the small-molecule irreversible inhibitor of Btk, a promising advance in the search for new and effective therapies for NHL [14,15]. In a recent study by Honigberg et al., murine models were used to demonstrate ibrutinib’s efficacy for treating lupus and arthritis, and dogs with spontaneous B-cell NHL were enrolled in a trial to test whether ibrutinib would affect disease progression [15]. At the time the study was published, eight dogs had been treated, with three partial responses (one dog with a 77% reduction in tumor burden) and three incidences of stable disease [15]. Upon these findings, a human clinical trial was promptly conducted on patients with refractory and relapsed B-cell NHL. Promising results were achieved, with a complete response in 16% of patients, while 60% of patients reached the objective response rate, and the median progression-free survival at the end of the trial for all patients was 13.6 months [16]. The US FDA has granted ibrutinib three ‘breakthrough’ designations and it is currently pending FDA approval. Hopes are high that it will see approval by the end of the year.Ethics of the canine modelWhile the use of companion animals has enormous potential for comparative medicine, it is important to recognize that these canine patients are presenting with naturally occurring disorders and are receiving medical care for their own well-being with informed owner consent. Any time that research is performed in a clinical setting (rather than a laboratory setting), there are a number of additional factors that must be considered. These include the patient environment, owners of animals and the perspective of the general public.Many of the ethical concerns regarding involving companion animals in clinical research studies are shared with basic principles of human subjects, including autonomy (informed consent, in this case of the owners) and non-malfeasance (an absence of any sort of fraud or harmful deceit, as well as avoiding harm to the animal). Research conducted in this setting requires rigorous protection of confidential patient/owner data and must be performed to a high ethical standard. As such, companion animal studies are subject to strict regulatory oversight that is highly comparable to that enforced for human patients. These principles will inevitably impact the design of canine studies, but are also critical for assuaging concerns.ConclusionThe murine model will continue to be an indispensable resource for cancer research and is deserving of enormous credit for the advancements in cancer therapy over previous decades. We believe that the large numbers of available canine patients with spontaneous cancers can offer an unequalled opportunity for stimulating advancement in the clinical management of human and companion animal cancers. We propose that, for applicable diseases, the canine model should be integrated into existing preclinical and clinical frameworks (including pharmacogenomics studies) in a way that not only benefits human drug development and disease understanding, but also improves the quality of treatment for our four-legged friends. Although we have focused primarily on cancer, it should also be noted that dogs are successfully used to study and develop treatments for many other diseases and disorders, such as wound healing, blindness and other vision disorders, heart disease, epilepsy, autoimmune diseases and narcolepsy [17,18]. It is our hope that with continued integration in these areas, we can expedite both the identification of druggable targets and improve the efficiency of the drug development system, for the benefit of both humans and canines.Financial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.No writing assistance was utilized in the production of this manuscript.References1 DiMasi JA, Grabowski HG. Economics of new oncology drug development. J. Clin. Oncol.25(2),209–216 (2007).Crossref, Medline, Google Scholar2 Arrowsmith J. Trial watch: Phase II failures: 2008–2010. Nat. Rev. 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Cancer treatment and survivorship facts and figures 2012–2013 (2012). www.cancer.org/acs/groups/content/@epidemiologysurveilance/documents/document/acspc-033876.pdfGoogle Scholar102 2011–2012 APPA National Pet Owners Survey. www.humaneresearch.org/content/2011-2012-appa-national-pet-owners-surveyGoogle ScholarFiguresReferencesRelatedDetailsCited ByComparative neurogenetics of dog behavior complements efforts towards human neuropsychiatric genetics14 August 2023 | Human Genetics, Vol. 142, No. 8DNA methylation and targeted sequencing of methyltransferases family genes in canine acute myeloid leukaemia, modelling human myeloid leukaemia21 April 2016 | Veterinary and Comparative Oncology, Vol. 15, No. 3Embracing Integrative Multiomics ApproachesInternational Journal of Genomics, Vol. 2016Canine Spontaneous Head and Neck Squamous Cell Carcinomas Represent Their Human Counterparts at the Molecular Level1 June 2015 | PLOS Genetics, Vol. 11, No. 6 Vol. 14, No. 16 STAY CONNECTED Metrics History Published online 26 November 2013 Published in print December 2013 Information© Future Medicine LtdKeywordscancercanine modelchemotherapyclinical trialsFinancial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.No writing assistance was utilized in the production of this manuscript.PDF download DA - 2013/12// PY - 2013/12// DO - 10.2217/pgs.13.178 VL - 14 IS - 16 SP - 1929-1931 SN - 1744-8042 KW - cancer KW - canine model KW - chemotherapy KW - clinical trials ER - TY - JOUR TI - Enumeration of Virtual Libraries of Combinatorial Modular Macrocyclic (Bracelet, Necklace) Architectures and Their Linear Counterparts AU - Taniguchi, Masahiko AU - Du, Hai AU - Lindsey, Jonathan S. T2 - JOURNAL OF CHEMICAL INFORMATION AND MODELING AB - A wide variety of cyclic molecular architectures are built of modular subunits and can be formed combinatorially. The mathematics for enumeration of such objects is well-developed yet lacks key features of importance in chemistry, such as specifying (i) the structures of individual members among a set of isomers, (ii) the distribution (i.e., relative amounts) of products, and (iii) the effect of nonequal ratios of reacting monomers on the product distribution. Here, a software program (Cyclaplex) has been developed to determine the number, identity (including isomers), and relative amounts of linear and cyclic architectures from a given number and ratio of reacting monomers. The program includes both mathematical formulas and generative algorithms for enumeration; the latter go beyond the former to provide desired molecular-relevant information and data-mining features. The program is equipped to enumerate four types of architectures: (i) linear architectures with directionality (macroscopic equivalent = electrical extension cords), (ii) linear architectures without directionality (batons), (iii) cyclic architectures with directionality (necklaces), and (iv) cyclic architectures without directionality (bracelets). The program can be applied to cyclic peptides, cycloveratrylenes, cyclens, calixarenes, cyclodextrins, crown ethers, cucurbiturils, annulenes, expanded meso-substituted porphyrin(ogen)s, and diverse supramolecular (e.g., protein) assemblies. The size of accessible architectures encompasses up to 12 modular subunits derived from 12 reacting monomers or larger architectures (e.g. 13-17 subunits) from fewer types of monomers (e.g. 2-4). A particular application concerns understanding the possible heterogeneity of (natural or biohybrid) photosynthetic light-harvesting oligomers (cyclic, linear) formed from distinct peptide subunits. DA - 2013/9// PY - 2013/9// DO - 10.1021/ci400175f VL - 53 IS - 9 SP - 2203-2216 SN - 1549-960X ER - TY - JOUR TI - (R)-nicotine biosynthesis, metabolism and translocation in tobacco as determined by nicotine demethylase mutants AU - Cai, Bin AU - Jack, Anne M. AU - Lewis, Ramsey S. AU - Dewey, Ralph E. AU - Bush, Lowell P. T2 - PHYTOCHEMISTRY AB - Nicotine is a chiral compound and consequently exists as two enantiomers. Since (R)-nicotine consists of less than 0.5% of total nicotine pool in tobacco, few investigations relating to (R)-nicotine have been reported. However, previous studies of nicotine demethylases suggested there was substantial amount of (R)-nicotine at synthesis in the tobacco plant. In this study, the accumulation and translocation of (R)-nicotine in tobacco was analyzed. The accumulation of nicotine and its demethylation product the nornicotine enantiomers, were investigated in different tobacco plant parts and at different growth and post-harvest stages. Scion/rootstock grafts were used to separate the contributions of roots (source) from leaves (sink) to the final accumulation of nicotine and nornicotine in leaf tissue. The results indicate that 4% of nicotine is in the (R) form at synthesis in the root. After the majority of (R)-nicotine is selectively demethylated by CYP82E4, CYP82E5v2 and CYP82E10 in the root, nicotine and nornicotine are translocated to leaf, where more nicotine becomes demethylated. Depending on the CYP82E4 activity in senescing leaf, constant low (R)-nicotine remains in the tobacco leaf and variable nornicotine composition is produced. These results confirmed the enantioselectivity of three nicotine demethylases in planta, could be used to predict the changes of nicotine and nornicotine composition, and may facilitate demethylase discovery in the future. DA - 2013/11// PY - 2013/11// DO - 10.1016/j.phytochem.2013.06.012 VL - 95 SP - 188-196 SN - 0031-9422 KW - Nicotiana tabacum L. KW - Tobacco KW - Solanaceae KW - (R)-nicotine KW - Nornicotine KW - Enantioselectivity KW - Nicotine demethylase ER - TY - JOUR TI - The evolving role of the orphan nuclear receptor ftz-f1, a pair-rule segmentation gene AU - Heffer, Alison AU - Grubbs, Nathaniel AU - Mahaffey, James AU - Pick, Leslie T2 - EVOLUTION & DEVELOPMENT AB - SUMMARY Segmentation is a critical developmental process that occurs by different mechanisms in diverse taxa. In insects, there are three common modes of embryogenesis—short‐, intermediate‐, and long‐germ development—which differ in the number of segments specified at the blastoderm stage. While genes involved in segmentation have been extensively studied in the long‐germ insect Drosophila melanogaster ( Dm ), it has been found that their expression and function in segmentation in short‐ and intermediate‐germ insects often differ. Drosophila ftz‐f1 encodes an orphan nuclear receptor that functions as a maternally expressed pair‐rule segmentation gene, responsible for the formation of alternate body segments during Drosophila embryogenesis. Here we investigated the expression and function of ftz‐f1 in the short‐germ beetle, Tribolium castaneum ( Tc ). We found that Tc‐ftz‐f1 is expressed in stripes in Tribolium embryos. These stripes overlap alternate Tc ‐Engrailed ( Tc ‐En) stripes, indicative of a pair‐rule expression pattern. To test whether Tc‐ftz‐f1 has pair‐rule function, we utilized embryonic RNAi, injecting double‐stranded RNA corresponding to Tc‐ftz‐f1 coding or non‐coding regions into early Tribolium embryos. Knockdown of Tc‐ftz‐f1 produced pair‐rule segmentation defects, evidenced by loss of expression of alternate En stripes. In addition, a later role for Tc‐ftz‐f1 in cuticle formation was revealed. These results identify a new pair‐rule gene in Tribolium and suggest that its role in segmentation may be shared among holometabolous insects. Interestingly, while Tc‐ftz‐f1 is expressed in pair‐rule stripes, the gene is ubiquitously expressed in Drosophila embryos. Thus, the pair‐rule function of ftz‐f1 is conserved despite differences in expression patterns of ftz‐f1 genes in different lineages. This suggests that ftz‐f1 expression changed after the divergence of lineages leading to extant beetles and flies, likely due to differences in cis ‐regulatory sequences. We propose that the dependence of Dm ‐Ftz‐F1 on interaction with the homeodomain protein Ftz which is expressed in stripes in Drosophila , loosened constraints on Dm ‐ ftz‐f1 expression, allowing for ubiquitous expression of this pair‐rule gene in Drosophila . DA - 2013/11// PY - 2013/11// DO - 10.1111/ede.12050 VL - 15 IS - 6 SP - 406-417 SN - 1525-142X ER - TY - JOUR TI - Serendipitous synthetic entree to tetradehydro analogues of cobalamins AU - Deans, R. M. AU - Mass, O. AU - Diers, J. R. AU - Bocian, D. F. AU - Lindsey, J. S. T2 - New Journal of Chemistry DA - 2013/// PY - 2013/// VL - 37 IS - 12 SP - 3964-3975 ER - TY - JOUR TI - Productivity differences among loblolly pine genotypes are independent of individual-tree biomass partitioning and growth efficiency AU - Aspinwall, Michael J. AU - King, John S. AU - McKeand, Steven E. T2 - TREES-STRUCTURE AND FUNCTION DA - 2013/6// PY - 2013/6// DO - 10.1007/s00468-012-0806-4 VL - 27 IS - 3 SP - 533-545 SN - 1432-2285 KW - Allometry KW - Clone KW - Growth efficiency KW - Loblolly pine KW - Productivity ER - TY - JOUR TI - Phylogenetic Diversity of Bacteria Isolated from Sick Dogs Using the BAPGM Enrichment Culture Platform AU - Davenport, A.C. AU - Mascarelli, P.E. AU - Maggi, R.G. AU - Breitschwerdt, E.B. T2 - Journal of Veterinary Internal Medicine AB - Background Bartonella alpha‐ Proteobacteria growth medium ( BAPGM ) enrichment culture has proven useful for documenting Bartonella species infection and has facilitated growth of other fastidious bacteria from human samples. Purpose To report non‐ Bartonella bacterial isolates obtained from canine samples cultured using BAPGM enrichment culture. Animals Between 2004 and 2008, 695 specimens from 513 dogs were tested by the NCSU‐IPRL using the BAPGM enrichment culture. Over the same period of time, blood samples from 270 dogs were cultured by the NCSU‐CML using Bactec‐Plus Aerobic/F media. Methods BAPGM isolates were characterized using Bartonella genus primers and 16S r DNA primers followed by DNA sequencing. NCSU medical records were retrospectively reviewed. Blood culture results from the NCSU‐CML were compared with BAPGM blood culture results. Results Seventy‐nine non‐ Bartonella isolates were obtained from 69/513 dogs. The most commonly isolated phylum was Proteobacteria (48.1%) with alpha‐Proteobacteria being the most commonly isolated class. Staphylococcus and Sphingomonas were the most commonly isolated genera. The majority of the remaining isolates were bacteria that are rarely isolated from canine samples. Comparison of NCSU‐CML and IPRL ( BAPGM ) blood culture isolates showed alpha‐Proteobacteria were isolated more often from BAPGM . Conclusions and Clinical Importance Use of insect cell culture enrichment medium, such as BAPGM , appears to enhance the growth of alpha‐Proteobacteria, but also results in isolation of non‐alpha‐Proteobacteria from sick dogs. Future studies are needed to elucidate the utility of BAPGM and other “nonconventional” growth media and methods for isolation of fastidious organisms and to determine if these organisms play a causal role in disease development. DA - 2013/5/6/ PY - 2013/5/6/ DO - 10.1111/jvim.12094 VL - 27 IS - 4 SP - 854-861 J2 - J Vet Intern Med LA - en OP - SN - 0891-6640 UR - http://dx.doi.org/10.1111/jvim.12094 DB - Crossref KW - Fastidious KW - Infection KW - Isolation KW - Sphingomonas ER - TY - JOUR TI - Localization, morphology and transcriptional profile of Aspergillus flavus during seed colonization AU - Dolezal, Andrea L. AU - Obrian, Gregory R. AU - Nielsen, Dahlia M. AU - Woloshuk, Charles P. AU - Boston, Rebecca S. AU - Payne, Gary A. T2 - MOLECULAR PLANT PATHOLOGY AB - Summary A spergillus flavus is an opportunistic fungal pathogen that infects maize kernels pre‐harvest, creating major human health concerns and causing substantial agricultural losses. Improved control strategies are needed, yet progress is hampered by the limited understanding of the mechanisms of infection. A series of studies were designed to investigate the localization, morphology and transcriptional profile of A . flavus during internal seed colonization. Results from these studies indicate that A . flavus is capable of infecting all tissues of the immature kernel by 96 h after infection. Mycelia were observed in and around the point of inoculation in the endosperm and were found growing down to the germ. At the endosperm–germ interface, hyphae appeared to differentiate and form a biofilm‐like structure that surrounded the germ. The exact nature of this structure remains unclear, but is discussed. A custom‐designed A . flavus A ffymetrix GeneChip ® microarray was used to monitor genome‐wide transcription during pathogenicity. A total of 5061 genes were designated as being differentially expressed. Genes encoding secreted enzymes, transcription factors and secondary metabolite gene clusters were up‐regulated and considered to be potential effector molecules responsible for disease in the kernel. Information gained from this study will aid in the development of strategies aimed at preventing or slowing down A . flavus colonization of the maize kernel. DA - 2013/12// PY - 2013/12// DO - 10.1111/mpp.12056 VL - 14 IS - 9 SP - 898-909 SN - 1364-3703 ER - TY - JOUR TI - Genomic Estimated Breeding Values Using Genomic Relationship Matrices in a Cloned Population of Loblolly Pine AU - Zapata-Valenzuela, Jaime AU - Whetten, Ross W. AU - Neale, David AU - McKeand, Steve AU - Isik, Fikret T2 - G3-GENES GENOMES GENETICS AB - Abstract Replacement of the average numerator relationship matrix derived from the pedigree with the realized genomic relationship matrix based on DNA markers might be an attractive strategy in forest tree breeding for predictions of genetic merit. We used genotypes from 3461 single-nucleotide polymorphism loci to estimate genomic relationships for a population of 165 loblolly pine (Pinus taeda L.) individuals. Phenotypes of the 165 individuals were obtained from clonally replicated field trials and were used to estimate breeding values for growth (stem volume). Two alternative methods, based on allele frequencies or regression, were used to generate the genomic relationship matrices. The accuracies of genomic estimated breeding values based on the genomic relationship matrices and breeding values estimated based on the average numerator relationship matrix were compared. On average, the accuracy of predictions based on genomic relationships ranged between 0.37 and 0.74 depending on the validation method. We did not detect differences in the accuracy of predictions based on genomic relationship matrices estimated by two different methods. Using genomic relationship matrices allowed modeling of Mendelian segregation within full-sib families, an important advantage over a traditional genetic evaluation system based on pedigree. We conclude that estimation of genomic relationships could be a powerful tool in forest tree breeding because it accurately accounts both for genetic relationships among individuals and for nuisance effects such as location and replicate effects, and makes more accurate selection possible within full-sib crosses. DA - 2013/5/1/ PY - 2013/5/1/ DO - 10.1534/g3.113.005975 VL - 3 IS - 5 SP - 909-916 SN - 2160-1836 KW - GenPred KW - Shared data resource KW - Pinus taeda quantitative genetics best linear unbiased prediction ER - TY - JOUR TI - Enhancing Agrobacterium tumefaciens-mediated transformation efficiency of perennial ryegrass and rice using heat and high maltose treatments during bacterial infection AU - Patel, Minesh AU - Dewey, Ralph E. AU - Qu, Rongda T2 - PLANT CELL TISSUE AND ORGAN CULTURE DA - 2013/7// PY - 2013/7// DO - 10.1007/s11240-013-0301-7 VL - 114 IS - 1 SP - 19-29 SN - 1573-5044 KW - Heat shock KW - Maltose KW - Rice KW - Perennial ryegrass KW - Transformation ER - TY - JOUR TI - Slow folding and assembly of a procaspase-3 interface variant AU - MacKenzie, S. H. AU - Clark, A. C. T2 - Biochemistry DA - 2013/// PY - 2013/// VL - 52 IS - 20 SP - 3415-3427 ER - TY - JOUR TI - Reconstructing genome evolution in historic samples of the Irish potato famine pathogen AU - Martin, Michael D. AU - Cappellini, Enrico AU - Samaniego, Jose A. AU - Zepeda, M. Lisandra AU - Campos, Paula F. AU - Seguin-Orlando, Andaine AU - Wales, Nathan AU - Orlando, Ludovic AU - Ho, Simon Y. W. AU - Dietrich, Fred S. AU - Mieczkowski, Piotr A. AU - Heitman, Joseph AU - Willerslev, Eske AU - Krogh, Anders AU - Ristaino, Jean B. AU - Gilbert, M. Thomas P. T2 - NATURE COMMUNICATIONS AB - Responsible for the Irish potato famine of 1845-49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era strain remains entirely unknown. Here we characterize temporal genomic changes in introduced P. infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples--including the oldest known European specimen, collected in 1845 from the first reported source of introduction. We then compare their genomes to those of extant isolates. We report multiple distinct genotypes in historical Europe and a suite of infection-related genes different from modern strains. At virulence-related loci, several now-ubiquitous genotypes were absent from the historical gene pool. At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century's episodic replacements of European P. infestans lineages. DA - 2013/7// PY - 2013/7// DO - 10.1038/ncomms3172 VL - 4 SP - SN - 2041-1723 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84892942971&partnerID=MN8TOARS ER - TY - JOUR TI - Peptide Aptamers That Bind to Geminivirus Replication Proteins Confer a Resistance Phenotype to Tomato Yellow Leaf Curl Virus and Tomato Mottle Virus Infection in Tomato AU - Reyes, Maria Ines AU - Nash, Tara E. AU - Dallas, Mary M. AU - Ascencio-Ibanez, J. Trinidad AU - Hanley-Bowdoin, Linda T2 - JOURNAL OF VIROLOGY AB - ABSTRACT Geminiviruses constitute a large family of single-stranded DNA viruses that cause serious losses in important crops worldwide. They often exist in disease complexes and have high recombination and mutation rates, allowing them to adapt rapidly to new hosts and environments. Thus, an effective resistance strategy must be general in character and able to target multiple viruses. The geminivirus replication protein (Rep) is a good target for broad-based disease control because it is highly conserved and required for viral replication. In an earlier study, we identified a set of peptide aptamers that bind to Rep and reduce viral replication in cultured plant cells. In this study, we selected 16 of the peptide aptamers for further analysis in yeast two-hybrid assays. The results of these experiments showed that all 16 peptide aptamers interact with all or most of the Rep proteins from nine viruses representing the three major Geminiviridae genera and identified two peptide aptamers (A22 and A64) that interact strongly with different regions in the Rep N terminus. Transgenic tomato lines expressing A22 or A64 and inoculated with Tomato yellow leaf curl virus or Tomato mottle virus exhibited delayed viral DNA accumulation and often contained lower levels of viral DNA. Strikingly, the effect on symptoms was stronger, with many of the plants showing no symptoms or strongly attenuated symptoms. Together, these results established the efficacy of using Rep-binding peptide aptamers to develop crops that are resistant to diverse geminiviruses. DA - 2013/9// PY - 2013/9// DO - 10.1128/jvi.01095-13 VL - 87 IS - 17 SP - 9691-9706 SN - 1098-5514 ER - TY - JOUR TI - New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering AU - Martin, Stanton L. AU - He, Lilin AU - Meilleur, Flora AU - Guenther, Richard H. AU - Sit, Tim L. AU - Lommel, Steven A. AU - Heller, William T. T2 - ARCHIVES OF VIROLOGY DA - 2013/8// PY - 2013/8// DO - 10.1007/s00705-013-1650-6 VL - 158 IS - 8 SP - 1661-1669 SN - 0304-8608 ER - TY - JOUR TI - Molecular genetics of alkaloid biosynthesis in Nicotiana tabacum AU - Dewey, Ralph E. AU - Xie, Jiahua T2 - PHYTOCHEMISTRY AB - Alkaloids represent an extensive group of nitrogen-containing secondary metabolites that are widely distributed throughout the plant kingdom. The pyridine alkaloids of tobacco (Nicotiana tabacum L.) have been the subject of particularly intensive investigation, driven largely due to the widespread use of tobacco products by society and the role that nicotine (16) (see Fig. 1) plays as the primary compound responsible for making the consumption of these products both pleasurable and addictive. In a typical commercial tobacco plant, nicotine (16) comprises about 90% of the total alkaloid pool, with the alkaloids nornicotine (17) (a demethylated derivative of nicotine), anatabine (15) and anabasine (5) making up most of the remainder. Advances in molecular biology have led to the characterization of the majority of the genes encoding the enzymes directly responsible the biosynthesis of nicotine (16) and nornicotine (17), while notable gaps remain within the anatabine (15) and anabasine (5) biosynthetic pathways. Several of the genes involved in the transcriptional regulation and transport of nicotine (16) have also been elucidated. Investigations of the molecular genetics of tobacco alkaloids have not only provided plant biologists with insights into the mechanisms underlying the synthesis and accumulation of this important class of plant alkaloids, they have also yielded tools and strategies for modifying the tobacco alkaloid composition in a manner that can result in changing the levels of nicotine (16) within the leaf, or reducing the levels of a potent carcinogenic tobacco-specific nitrosamine (TSNA). This review summarizes recent advances in our understanding of the molecular genetics of alkaloid biosynthesis in tobacco, and discusses the potential for applying information accrued from these studies toward efforts designed to help mitigate some of the negative health consequences associated with the use of tobacco products. DA - 2013/10// PY - 2013/10// DO - 10.1016/j.phytochem.2013.06.002 VL - 94 SP - 10-27 SN - 1873-3700 KW - Nicotiana tabacum KW - Solanaceae KW - Nicotine KW - Nornicotine KW - Tobacco-specific nitrosamines KW - Alkaloid biosynthetic genes ER - TY - JOUR TI - Integration of multiple chromophores with native photosynthetic antennas to enhance solar energy capture and delivery AU - Harris, Michelle A. AU - Parkes-Loach, Pamela S. AU - Springer, Joseph W. AU - Jiang, Jianbing AU - Martin, Elizabeth C. AU - Qian, Pu AU - Jiao, Jieying AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Olsen, John D. AU - Bocian, David F. AU - Holten, Dewey AU - Hunter, C. Neil AU - Lindsey, Jonathan S. AU - Loach, Paul A. T2 - Chemical Science AB - Native length bacterial light-harvesting peptides carrying covalently attached designer chromophores have been created that self-assemble with native bacteriochlorophyll a (BChl a) to afford stable antennas with enhanced spectral coverage. Native (or native-like) α- and β-peptides interact with each other and BChl a to form a heterodimeric (αβ-dyad) unit that can then oligomerize to form biohybrid analogs of the bacterial core light-harvesting complex (LH1). Pairs of distinct synthetic chromophores were incorporated in αβ-dyads at selected distances from the BChl a target site (position 0). Two designs were explored. One design used green-yellow absorbing/emitting Oregon Green at the −34 position (toward the N-terminus relative to the BChl a coordination site) of β and orange-red absorbing/emitting Rhodamine Red at the −20 position of α, which combine with BChl a to give homogeneous oligomers. A second design used two different β-peptide conjugates, one with Oregon Green at the −34 position and the second with a near-infrared absorbing/emitting synthetic bacteriochlorin at the −14 position, which combine with α and BChl a to give a heterogeneous mixture of oligomers. The designs afford antennas with ∼45 to ∼60 pigments, provide enhanced spectral coverage across the visible and near-infrared regions relative to native antennas, and accommodate pigments at remote sites that contribute to solar light harvesting via an energy-transfer cascade. The efficiencies of energy-transfer to the BChl a target in the biohybrid antennas are comparable to native antennas, as revealed by static and time-resolved absorption and emission studies. The results show that the biohybrid approach, where designer chromophores are integrated via semisynthesis with native-like scaffolding, constitutes a versatile platform technology for rapid prototyping of antennas for solar energy capture without the laborious synthesis typically required for creating artificial photosynthetic light-harvesting architectures. DA - 2013/// PY - 2013/// DO - 10.1039/C3SC51518D VL - 4 IS - 10 SP - 3924 J2 - Chem. Sci. LA - en OP - SN - 2041-6520 2041-6539 UR - http://dx.doi.org/10.1039/C3SC51518D DB - Crossref ER - TY - JOUR TI - Infection with Hemotropic Mycoplasma Species in Patients with or without Extensive Arthropod or Animal Contact AU - Maggi, R. G. AU - Compton, S. M. AU - Trull, C. L. AU - Mascarelli, P. E. AU - Mozayeni, B. R. AU - Breitschwerdt, E. B. T2 - Journal of Clinical Microbiology AB - PCR amplification targeting the 16S rRNA gene was used to test individuals with and without extensive arthropod and animal contact for the possibility of hemotropic mycoplasma infection. The prevalence of hemotropic mycoplasma infection (4.7%) was significantly greater in previously reported cohorts of veterinarians, veterinary technicians, spouses of veterinary professionals, and others with extensive arthropod exposure and/or frequent animal contact than in a previously reported cohort of patients examined by a rheumatologist because of chronic joint pain or evidence of small-vessel disease (0.7%). Based upon DNA sequence analysis, a Mycoplasma ovis-like species was the most prevalent organism detected; however, infection with "Candidatus Mycoplasma haematoparvum" and a potentially novel, but incompletely characterized, hemotropic Mycoplasma species was also documented. Historical exposure to animals and arthropod vectors that can harbor hemotropic Mycoplasma spp. should be considered during epidemiological investigations and in the evaluation of individual patients. DA - 2013/7/17/ PY - 2013/7/17/ DO - 10.1128/jcm.01125-13 VL - 51 IS - 10 SP - 3237-3241 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/JCM.01125-13 DB - Crossref ER - TY - JOUR TI - High-level gene expression in differentiating xylem of tobacco driven by a 2.0 kb Poplar COMT2 promoter and a 4 x 35S enhancer AU - Liu, Enying AU - Peng, Shaobing AU - Li, Quanzi AU - Sun, Ying-Hsuan AU - Chiang, Vincent L. AU - Sederoff, Ronald R. T2 - PLANT BIOTECHNOLOGY AB - Promoter constructs with high levels of xylem specific expression are needed to obtain efficient expression of candidate genes, microRNAs (miRNAs) and artificial microRNAs (amiRNAs) for the genetic modification of wood properties. The gene for caffeic acid O-methytransferase (PtrCOMT2) has the second most abundant transcript level of all the genes in monolignol biosynthesis in Populus trichocarpa and a high level of specificity in differentiating xylem. To characterize the PtrCOMT2 promoter, we cloned a short (2.0 kb) and a long (3.3 kb) promoter segment and compared their expression using GUS as a reporter gene in the differentiating xylem of Nicotiana tabacum. Both the 2.0 kb and the 3.3 kb promoter segments showed high specificity for differentiating xylem in this heterologous system. GUS activity increased as much as 5 times when the 4×35S enhancer was inserted in front of the 2.0 kb promoter, but GUS activity was only increased 2 times when the enhancer was inserted behind the promoter. The enhancer inserted upstream reduced the expression of the 3.3 kb promoter. While expression of some of the enhancer-plus-promoter constructs increased expression, there was a loss of specificity. DA - 2013/// PY - 2013/// DO - 10.5511/plantbiotechnology.13.0213a VL - 30 IS - 2 SP - 191-198 SN - 1342-4580 KW - PtrCOMT2 promoter KW - xylem-specific KW - 4 x 35S enhancer KW - woody plants KW - genetic engineering ER - TY - JOUR TI - Hemlock woolly adelgid (Adelges tsugae) infestation affects water and carbon relations of eastern hemlock (Tsuga canadensis) and Carolina hemlock (Tsuga caroliniana) AU - Domec, Jean-Christophe AU - Rivera, Laura N. AU - King, John S. AU - Peszlen, Ilona AU - Hain, Fred AU - Smith, Benjamin AU - Frampton, John T2 - NEW PHYTOLOGIST AB - Summary Hemlock woolly adelgid ( HWA ) is an exotic insect pest causing severe decimation of native hemlock trees. Extensive research has been conducted on the ecological impacts of HWA , but the exact physiological mechanisms that cause mortality are not known. Water relations, anatomy and gas exchange measurements were assessed on healthy and infested eastern ( T suga canadensis ) and C arolina ( T suga caroliniana ) hemlock trees. These data were then used in a mechanistic model to test whether the physiological responses to HWA infestation were sufficiently significant to induce changes in whole‐plant water use and carbon uptake. The results indicated coordinated responses of functional traits governing water relations in infested relative to healthy trees. In response to HWA , leaf water potential, carbon isotope ratios, plant hydraulic properties and stomatal conductance were affected, inducing a reduction in tree water use by > 40% and gross primary productivity by 25%. Anatomical changes also appeared, including the activation of traumatic cells. HWA infestation had a direct effect on plant water relations. Despite some leaf compensatory mechanisms, such as an increase in leaf hydraulic conductance and nitrogen content, tree water use and carbon assimilation were diminished significantly in infested trees, which could contribute to tree mortality. DA - 2013/7// PY - 2013/7// DO - 10.1111/nph.12263 VL - 199 IS - 2 SP - 452-463 SN - 1469-8137 KW - carbon isotope KW - hydraulic conductivity KW - mortality KW - soil-plant-atmosphere model KW - stomatal conductance KW - traumatic resin canals KW - water potential KW - wood anatomy ER - TY - JOUR TI - A fraction free Matrix Berlekamp/Massey algorithm AU - Kaltofen, Erich AU - Yuhasz, George T2 - LINEAR ALGEBRA AND ITS APPLICATIONS AB - We describe a fraction free version of the Matrix Berlekamp/Massey algorithm. The algorithm computes a minimal matrix generator of linearly generated square matrix sequences in an integral domain. The algorithm performs all operations in the integral domain, so all divisions performed are exact. For scalar sequences, the matrix algorithm specializes to a different algorithm than the algorithm currently in the literature. This new scalar algorithm has smaller intermediate values than the known fraction free Berlekamp/Massey algorithm. DA - 2013/11/1/ PY - 2013/11/1/ DO - 10.1016/j.laa.2013.06.016 VL - 439 IS - 9 SP - 2515-2526 SN - 1873-1856 KW - Exact division KW - Linear recurrences KW - Matrix recurrences KW - Block Hankel systems KW - Block Toeplitz systems KW - Integer sequences ER - TY - JOUR TI - A flexible model for the mean and variance functions, with application to medical cost data AU - Chen, Jinsong AU - Liu, Lei AU - Zhang, Daowen AU - Shih, Ya-Chen T. T2 - STATISTICS IN MEDICINE AB - Medical cost data are often skewed to the right and heteroscedastic, having a nonlinear relation with covariates. To tackle these issues, we consider an extension to generalized linear models by assuming nonlinear associations of covariates in the mean function and allowing the variance to be an unknown but smooth function of the mean. We make no further assumption on the distributional form. The unknown functions are described by penalized splines, and the estimation is carried out using nonparametric quasi‐likelihood. Simulation studies show the flexibility and advantages of our approach. We apply the model to the annual medical costs of heart failure patients in the clinical data repository at the University of Virginia Hospital System. Copyright © 2013 John Wiley & Sons, Ltd. DA - 2013/10/30/ PY - 2013/10/30/ DO - 10.1002/sim.5838 VL - 32 IS - 24 SP - 4306-4318 SN - 1097-0258 KW - generalized linear model KW - semiparametric regression KW - health econometrics KW - smoothing parameter KW - generalized cross-validation ER - TY - JOUR TI - A Novel Candidate Vaccine for Cytauxzoonosis Inferred from Comparative Apicomplexan Genomics AU - Tarigo, Jaime L. AU - Scholl, Elizabeth H. AU - Bird, David McK AU - Brown, Corrie C. AU - Cohn, Leah A. AU - Dean, Gregg A. AU - Levy, Michael G. AU - Doolan, Denise L. AU - Trieu, Angela AU - Nordone, Shila K. AU - Felgner, Philip L. AU - Vigil, Adam AU - Birkenheuer, Adam J. T2 - PLOS ONE AB - Cytauxzoonosis is an emerging infectious disease of domestic cats (Felis catus) caused by the apicomplexan protozoan parasite Cytauxzoon felis. The growing epidemic, with its high morbidity and mortality points to the need for a protective vaccine against cytauxzoonosis. Unfortunately, the causative agent has yet to be cultured continuously in vitro, rendering traditional vaccine development approaches beyond reach. Here we report the use of comparative genomics to computationally and experimentally interpret the C. felis genome to identify a novel candidate vaccine antigen for cytauxzoonosis. As a starting point we sequenced, assembled, and annotated the C. felis genome and the proteins it encodes. Whole genome alignment revealed considerable conserved synteny with other apicomplexans. In particular, alignments with the bovine parasite Theileria parva revealed that a C. felis gene, cf76, is syntenic to p67 (the leading vaccine candidate for bovine theileriosis), despite a lack of significant sequence similarity. Recombinant subdomains of cf76 were challenged with survivor-cat antiserum and found to be highly seroreactive. Comparison of eleven geographically diverse samples from the south-central and southeastern USA demonstrated 91-100% amino acid sequence identity across cf76, including a high level of conservation in an immunogenic 226 amino acid (24 kDa) carboxyl terminal domain. Using in situ hybridization, transcription of cf76 was documented in the schizogenous stage of parasite replication, the life stage that is believed to be the most important for development of a protective immune response. Collectively, these data point to identification of the first potential vaccine candidate antigen for cytauxzoonosis. Further, our bioinformatic approach emphasizes the use of comparative genomics as an accelerated path to developing vaccines against experimentally intractable pathogens. DA - 2013/8/20/ PY - 2013/8/20/ DO - 10.1371/journal.pone.0071233 VL - 8 IS - 8 SP - SN - 1932-6203 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84882652524&partnerID=MN8TOARS ER - TY - JOUR TI - The red clover necrotic mosaic virus capsid protein N-terminal amino acids possess specific RNA binding activity and are required for stable virion assembly AU - Park, Sang-Ho AU - Sit, Tim L. AU - Kim, Kook-Hyung AU - Lommel, Steven A. T2 - VIRUS RESEARCH AB - The red clover necrotic mosaic virus (RCNMV) bipartite RNA genome is packaged into two virion populations containing either RNA-1 and RNA-2 or multiple copies of RNA-2 only. To understand this distinctive packaging scheme, we investigated the RNA-binding properties of the RCNMV capsid protein (CP). Maltose binding protein-CP fusions exhibited the highest binding affinities for RNA probes containing the RNA-2 trans-activator or the 3′ non-coding region from RNA-1. Other viral and non-viral RNA probes displayed CP binding but to a much lower degree. Deletion of the highly basic N-terminal 50 residues abolished CP binding to viral RNA transcripts. In planta studies of select CP deletion mutants within this N-terminal region revealed that it was indispensable for stable virion formation and the region spanning CP residues 5–15 is required for systemic movement. Thus, the N-terminal region of the CP is involved in both producing two virion populations due to its RNA binding properties and virion stability. DA - 2013/9// PY - 2013/9// DO - 10.1016/j.virusres.2013.05.014 VL - 176 IS - 1-2 SP - 107-118 SN - 0168-1702 KW - RCNMV KW - Virus assembly KW - RNA-CP interactions KW - TABS KW - TA KW - Co-packaging ER - TY - JOUR TI - Reactive Oxygen Species in Plant Pathogenesis: The Role of Perylenequinone Photosensitizers AU - Daub, Margaret E. AU - Herrero, Sonia AU - Chung, Kuang-Ren T2 - ANTIOXIDANTS & REDOX SIGNALING AB - Reactive oxygen species (ROS) play multiple roles in interactions between plants and microbes, both as host defense mechanisms and as mediators of pathogenic and symbiotic associations. One source of ROS in these interactions are photoactivated, ROS-generating perylenequinone pigments produced via polyketide metabolic pathways in plant-associated fungi. These natural products, including cercosporin, elsinochromes, hypocrellins, and calphostin C, are being utilized as medicinal agents, enzyme inhibitors, and in tumor therapy, but in nature, they play a role in the establishment of pathogenic associations between fungi and their plant hosts.Photoactivated perylenequinones are photosensitizers that use light energy to form singlet oxygen (¹O₂) and free radical oxygen species which damage cellular components based on localization of the perylenequinone molecule. Production of perylenequinones during infection commonly results in lipid peroxidation and membrane damage, leading to leakage of nutrients from cells into the intercellular spaces colonized by the pathogen. Perylenequinones show almost universal toxicity against organisms, including plants, mice, bacteria, and most fungi. The producing fungi are resistant, however, and serve as models for understanding resistance mechanisms.Studies of resistance mechanisms by perylenequinone-producing fungi such as Cercospora species are leading to an understanding of cellular resistance to ¹O₂ and oxidative stress. Recent studies show commonalities between resistance mechanisms in these fungi with extensive studies of ¹O₂ and oxidative stress responses in photosynthetic organisms.Such studies hold promise both for improved medical use and for engineering crop plants for disease resistance. DA - 2013/9/20/ PY - 2013/9/20/ DO - 10.1089/ars.2012.5080 VL - 19 IS - 9 SP - 970-989 SN - 1557-7716 ER - TY - JOUR TI - Partial cytogenetic response with toceranib and prednisone treatment in a young dog with chronic monocytic leukemia AU - Perez, Mayrim L. AU - Culver, Sarah AU - Owen, Jennifer L. AU - Dunbar, Mark AU - Kow, Kelvin AU - Breen, Matthew AU - Milner, Rowan J. T2 - ANTI-CANCER DRUGS AB - Treatment of chronic monocytic leukemia (CMoL) in dogs has traditionally consisted of hydroxyurea. The use of tyrosine kinase inhibitors has been proposed as a treatment option for dogs with CMoL but has never been reported. We report a case of CMoL in a young dog that achieved clinical remission with treatment with the tyrosine kinase inhibitor toceranib and prednisone. DA - 2013/11// PY - 2013/11// DO - 10.1097/cad.0000000000000018 VL - 24 IS - 10 SP - 1098-1103 SN - 1473-5741 KW - cytogenetic analysis KW - fluorescence in-situ hybridization KW - monocytosis KW - toceranib KW - tyrosine kinase inhibitor ER - TY - JOUR TI - Molecular characterization of canine BCR-ABL-positive chronic myelomonocytic leukemia before and after chemotherapy AU - Culver, Sarah AU - Ito, Daisuke AU - Borst, Luke AU - Bell, Jerold S. AU - Modiano, Jaime F. AU - Breen, Matthew T2 - VETERINARY CLINICAL PATHOLOGY AB - Abstract Genetic aberrations linked to tumorigenesis have been identified in both canine and human hematopoietic malignancies. While the response of human patients to cancer treatments is often evaluated using cytogenetic techniques, this approach has not been used for dogs with comparable neoplasias. The aim of this study was to demonstrate the applicability of cytogenetic techniques to evaluate the cytogenetic response of canine leukemia to chemotherapy. Cytology and flow cytometric techniques were used to diagnose chronic myelomonocytic leukemia in a dog. High‐resolution oligonucleotide array comparative genomic hybridization (oaCGH) and multicolor fluorescence in situ hybridization (FISH) were performed to identify and characterize DNA copy number aberrations (CNAs) and targeted structural chromosome aberrations in peripheral blood WBC at the time of diagnosis and following one week of chemotherapy. At the time of diagnosis, oaCGH indicated the presence of 22 distinct CNAs, of which trisomy of dog chromosome 7 (CFA 7) was the most evident. FISH analysis revealed that this CNA was present in 42% of leukemic cells; in addition, a breakpoint cluster region‐Abelson murine leukemia viral oncogene homolog (BCR‐ABL) translocation was evident in 17.3% of cells. After one week of treatment, the percentage of cells affected by trisomy of CFA7 and BCR‐ABL translocation was reduced to 2% and 3.3%, respectively. Chromosome aberrations in canine leukemic cells may be monitored by molecular cytogenetic techniques to demonstrate cytogenetic remission following treatment. Further understanding of the genetic aberrations involved in canine leukemia may be crucial to improve treatment protocols. DA - 2013/9// PY - 2013/9// DO - 10.1111/vcp.12055 VL - 42 IS - 3 SP - 314-322 SN - 1939-165X KW - Chromosome KW - cytogenetics KW - hematopoietic cells KW - remission KW - vincristine ER - TY - JOUR TI - Geminiviruses: masters at redirecting and reprogramming plant processes AU - Hanley-Bowdoin, Linda AU - Bejarano, Eduardo R. AU - Robertson, Dominique AU - Mansoor, Shahid T2 - NATURE REVIEWS MICROBIOLOGY AB - Geminiviruses are important plant pathogens that cause devastating crop losses worldwide. Here, Hanley-Bowdoin and colleagues review how viral proteins interact with cellular machineries and reprogramme cellular control pathways in their plant host to support viral DNA replication, gene expression and trafficking, and to interfere with host defences. The family Geminiviridae is one of the largest and most important families of plant viruses. The small, single-stranded DNA genomes of geminiviruses encode 5–7 proteins that redirect host machineries and processes to establish a productive infection. These interactions reprogramme plant cell cycle and transcriptional controls, inhibit cell death pathways, interfere with cell signalling and protein turnover, and suppress defence pathways. This Review describes our current knowledge of how geminiviruses interact with their plant hosts and the functional consequences of these interactions. DA - 2013/11// PY - 2013/11// DO - 10.1038/nrmicro3117 VL - 11 IS - 11 SP - 777-788 SN - 1740-1534 ER - TY - JOUR TI - Distinct Photophysical and Electronic Characteristics of Strongly Coupled Dyads Containing a Perylene Accessory Pigment and a Porphyrin, Chlorin, or Bacteriochlorin AU - Wang, Jieqi AU - Yang, Eunkrung AU - Diers, James R. AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Bocian, David F. AU - Lindsey, Jonathan S. AU - Holten, Dewey T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - The synthesis, photophysical, redox, and molecular-orbital characteristics of three perylene-tetrapyrrole dyads were investigated to elucidate characteristics favorable for use in next-generation light-harvesting assemblies. Each dyad contains a common perylene-monoimide that is linked at the 9-position via an ethynyl group to the meso-position of the tetrapyrrole. The tetrapyrroles include a porphyrin, chlorin, and bacteriochlorin, which have zero, one, and two reduced pyrrole rings, respectively. The increased pyrrole-ring reduction results in a progressive red shift and intensification of the lowest-energy absorption band, as exemplified by benchmark monomers. The direct ethyne linkage and accompanying strong perylene-tetrapyrrole electronic coupling in the dyads is evident by significant differences in optical absorption versus the sum of the features of the constituents. The perturbations decrease for the tetrapyrrole constituent along the series porphyrin > chlorin > bacteriochlorin. This trend is explained by the relative configurational mixing in the tetrapyrrole excited states and how the configuration-interaction energy (and not simply the energies of the configurations) is affected by coupling to the perylene. The perylene-tetrapyrrole electronic coupling is further evidenced in the redox and MO characteristics of the three dyads. All three dyads in nonpolar solvents exhibit relatively long singlet excited-state lifetimes (3.3-6.5 ns) and relatively large fluorescence quantum yields (0.14-0.40). Collectively, the physicochemical characteristics of the strongly coupled perylene-tetrapyrrole dyads render these architectures excellent candidates for light-harvesting materials with significant, even panchromatic, near-ultraviolet to near-infrared absorption. DA - 2013/8/8/ PY - 2013/8/8/ DO - 10.1021/jp405004d VL - 117 IS - 31 SP - 9288-9304 SN - 1520-5207 ER - TY - JOUR TI - An unmatched case controlled study of clinicopathologic abnormalities in dogs with Bartonella infection AU - Pérez Vera, Cristina AU - Diniz, Pedro Paulo V.P. AU - Pultorak, Elizabeth L. AU - Maggi, Ricardo G. AU - Breitschwerdt, Edward B. T2 - Comparative Immunology, Microbiology and Infectious Diseases AB - We compared clinicopathologic findings in dogs with Bartonella infection to Bartonella spp. negative dogs suspected of a vector-borne disease. Cases (n = 47) and controls (n = 93) were selected on the basis of positive or negative enrichment culture PCR results, respectively. Signalment, clinicopathologic findings and treatments were extracted from medical records. DNA sequencing identified Bartonella henselae (n = 28, 59.6%), Bartonella vinsonii subsp. berkhoffii (n = 20, 42.6%), Bartonella koehlerae (n = 3, 6.4%), Bartonella volans-like (n = 3, 6.4%) and Bartonella bovis (n = 1, 2.1%). There were no significant differences in age, breed, size, sex or neuter status between cases and controls. Dogs infected with Bartonella sp. often had a history of weight loss [OR = 2.82; 95% CI: 1.08–7.56] and were hypoglobulinemic [OR = 4.26; 95% CI: 1.31–14.41]. With the exception of weight loss and hypoglobulinemia, clinicopathologic abnormalities in Bartonella-infected dogs in this study were similar to dogs suspected of other vector-borne infections. DA - 2013/9// PY - 2013/9// DO - 10.1016/j.cimid.2013.04.001 VL - 36 IS - 5 SP - 481-487 J2 - Comparative Immunology, Microbiology and Infectious Diseases LA - en OP - SN - 0147-9571 UR - http://dx.doi.org/10.1016/j.cimid.2013.04.001 DB - Crossref KW - Bartonella KW - Dogs KW - BAPGM KW - Enrichment PCR KW - Hypoglobulinemia ER - TY - JOUR TI - Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa AU - Shi, R. AU - Shuford, C. M. AU - Wang, J. P. AU - Sun, Y. H. AU - Yang, Z. C. AU - Chen, H. C. AU - Tunlaya-Anukit, S. AU - Li, Q. Z. AU - Liu, J. AU - Muddiman, D. C. AU - Sederoff, R. R. AU - Chiang, V. L. T2 - Planta DA - 2013/// PY - 2013/// DO - 10.1007/s00425-013-1905-1 VL - 238 IS - 3 SP - 487-497 ER - TY - JOUR TI - Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa AU - Lu, Shanfa AU - Li, Quanzi AU - Wei, Hairong AU - Chang, Mao-Ju AU - Tunlaya-Anukit, Sermsawat AU - Kim, Hoon AU - Liu, Jie AU - Song, Jingyuan AU - Sun, Ying-Hsuan AU - Yuan, Lichai AU - Yeh, Ting-Feng AU - Peszlen, Ilona AU - Ralph, John AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Laccases, as early as 1959, were proposed to catalyze the oxidative polymerization of monolignols. Genetic evidence in support of this hypothesis has been elusive due to functional redundancy of laccase genes. An Arabidopsis double mutant demonstrated the involvement of laccases in lignin biosynthesis. We previously identified a subset of laccase genes to be targets of a microRNA (miRNA) ptr-miR397a in Populus trichocarpa . To elucidate the roles of ptr-miR397a and its targets, we characterized the laccase gene family and identified 49 laccase gene models, of which 29 were predicted to be targets of ptr-miR397a. We overexpressed Ptr-MIR397a in transgenic P. trichocarpa . In each of all nine transgenic lines tested, 17 PtrLAC s were down-regulated as analyzed by RNA-seq. Transgenic lines with severe reduction in the expression of these laccase genes resulted in an ∼40% decrease in the total laccase activity. Overexpression of Ptr-MIR397a in these transgenic lines also reduced lignin content, whereas levels of all monolignol biosynthetic gene transcripts remained unchanged. A hierarchical genetic regulatory network (GRN) built by a bottom-up graphic Gaussian model algorithm provides additional support for a role of ptr-miR397a as a negative regulator of laccases for lignin biosynthesis. Full transcriptome–based differential gene expression in the overexpressed transgenics and protein domain analyses implicate previously unidentified transcription factors and their targets in an extended hierarchical GRN including ptr-miR397a and laccases that coregulate lignin biosynthesis in wood formation. Ptr-miR397a, laccases, and other regulatory components of this network may provide additional strategies for genetic manipulation of lignin content. DA - 2013/6/25/ PY - 2013/6/25/ DO - 10.1073/pnas.1308936110 VL - 110 IS - 26 SP - 10848-10853 SN - 0027-8424 ER - TY - JOUR TI - Identification and Functional Analysis of Tomato BRI1 and BAK1 Receptor Kinase Phosphorylation Sites AU - Bajwa, Vikramjit S. AU - Wang, Xiaofeng AU - Blackburn, R. Kevin AU - Goshe, Michael B. AU - Mitra, Srijeet K. AU - Williams, Elisabeth L. AU - Bishop, Gerard J. AU - Krasnyanski, Sergei AU - Allen, George AU - Huber, Steven C. AU - Clouse, Steven D. T2 - PLANT PHYSIOLOGY AB - Brassinosteroids (BRs) are plant hormones that are perceived at the cell surface by a membrane-bound receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1). BRI1 interacts with BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) to initiate a signal transduction pathway in which autophosphorylation and transphosphorylation of BRI1 and BAK1, as well as phosphorylation of multiple downstream substrates, play critical roles. Detailed mechanisms of BR signaling have been examined in Arabidopsis (Arabidopsis thaliana), but the role of BRI1 and BAK1 phosphorylation in crop plants is unknown. As a foundation for understanding the mechanism of BR signaling in tomato (Solanum lycopersicum), we used liquid chromatography-tandem mass spectrometry to identify multiple in vitro phosphorylation sites of the tomato BRI1 and BAK1 cytoplasmic domains. Kinase assays showed that both tomato BRI1 and BAK1 are active in autophosphorylation as well as transphosphorylation of each other and specific peptide substrates with a defined sequence motif. Site-directed mutagenesis revealed that the highly conserved kinase domain activation loop residue threonine-1054 was essential for tomato BRI1 autophosphorylation and peptide substrate phosphorylation in vitro. Furthermore, analysis of transgenic lines expressing full-length tomato BRI1-Flag constructs in the weak tomato bri1 allele, curl3(-abs1), demonstrated that threonine-1054 is also essential for normal BRI1 signaling and tomato growth in planta. Finally, we cloned the tomato ortholog of TGF-β Receptor Interacting Protein (TRIP1), which was previously shown to be a BRI1-interacting protein and kinase domain substrate in Arabidopsis, and found that tomato TRIP1 is a substrate of both tomato BRI1 and BAK1 kinases in vitro. DA - 2013/9// PY - 2013/9// DO - 10.1104/pp.113.221465 VL - 163 IS - 1 SP - 30-42 SN - 1532-2548 ER - TY - JOUR TI - High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants AU - Howard, Brian E. AU - Hu, Qiwen AU - Babaoglu, Ahmet Can AU - Chandra, Manan AU - Borghi, Monica AU - Tan, Xiaoping AU - He, Luyan AU - Winter-Sederoff, Heike AU - Gassmann, Walter AU - Veronese, Paola AU - Heber, Steffen T2 - PLOS ONE AB - We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time course RNA-Seq experiment uses over 500 million read pairs to provide a detailed characterization of the response to infection in both susceptible and resistant hosts. The set of observed differentially expressed genes is consistent with previous studies, confirming and extending existing findings about genes likely to play an important role in the defense response to Pseudomonas syringae. The high coverage of the Arabidopsis transcriptome resulted in the discovery of a surprisingly large number of alternative splicing (AS) events--more than 44% of multi-exon genes showed evidence for novel AS in at least one of the probed conditions. This demonstrates that the Arabidopsis transcriptome annotation is still highly incomplete, and that AS events are more abundant than expected. To further refine our predictions, we identified genes with statistically significant changes in the ratios of alternative isoforms between treatments. This set includes several genes previously known to be alternatively spliced or expressed during the defense response, and it may serve as a pool of candidate genes for regulated alternative splicing with possible biological relevance for the defense response against invasive pathogens. DA - 2013/10/1/ PY - 2013/10/1/ DO - 10.1371/journal.pone.0074183 VL - 8 IS - 10 SP - SN - 1932-6203 ER - TY - JOUR TI - Extrauterine Listeriosis in the Gravid Mouse Influences Embryonic Growth and Development AU - Suyemoto, M. Mitsu AU - Hamrick, Terri S. AU - Spears, Patricia A. AU - Horton, John R. AU - Washington, Ida M. AU - Havell, Edward A. AU - Borst, Luke B. AU - Orndorff, Paul E. T2 - PLoS ONE AB - Gravid mice and other rodents inoculated with Listeria monocytogenes typically fail to clear an intrauterine infection and either succumb or expel their intrauterine contents. We took advantage of this property to investigate the effects of an extrauterine infection on parameters of pregnancy success. Pregnant mice were selected for our study if they showed no clinical signs of listeriosis following oral inoculation at 7.5 gestational days (gd), and had no detectable intrauterine colony forming units (cfu) at near term (18.5 gd). The range of oral doses employed was 10⁶-10⁸ cfu per mouse for two listerial serotype strains (4nonb and 1/2a). At all doses, inoculation resulted in a decrease in average near-term (18.5 gd) fetal weight per litter compared to sham inoculated controls. Additionally, embryonic death (indicated by intrauterine resorptions) was exhibited by some inoculated mice but was absent in all sham inoculated animals. In parallel experiments designed to detect possible loss of placental function, gravid uteruses were examined histopathologically and microbiologically 96 h after oral inoculation. Placental lesions were associated with high (> 10⁶), but not low (< 10²) or absent intrauterine cfu. In vitro, mouse embryonic trophoblasts were indistinguishable from mouse enterocytes in terms of their sensitivity to listerial exposure. A model consistent with our observations is one in which products (host or bacterial) generated during an acute infection enter embryos transplacentally and influences embryonic survival and slows normal growth in utero. DA - 2013/8/14/ PY - 2013/8/14/ DO - 10.1371/journal.pone.0072601 VL - 8 IS - 8 SP - e72601 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0072601 DB - Crossref ER - TY - JOUR TI - Efficacy of an imidacloprid/flumethrin collar against fleas, ticks and tick-borne pathogens in dogs AU - Dantas-Torres, Filipe AU - Capelli, Gioia AU - Giannelli, Alessio AU - Ramos, Rafael Antonio AU - Lia, Riccardo AU - Cantacessi, Cinzia AU - de Caprariis, Donato AU - De Tommasi, Anna AU - Latrofa, Maria AU - Lacasella, Vita AU - Tarallo, Viviana AU - Di Paola, Giancarlo AU - Qurollo, Barbara AU - Breitschwerdt, Edward AU - Stanneck, Dorothee AU - Otranto, Domenico T2 - Parasites & Vectors AB - Tick-borne diseases comprise a group of maladies that are of substantial medical and veterinary significance. A range of tick-borne pathogens, including diverse species of bacteria and protozoa, can infect both dogs and humans. Hence, the control of tick infestations is pivotal to decrease or prevent tick-borne pathogen transmission. Therefore, different commercial products with insecticidal, repellent or both properties have been developed for use on dogs. Recently, a collar containing a combination of imidacloprid 10% and flumethrin 4.5% has proven effective to prevent tick and flea infestations in dogs under field conditions and the infection by some vector-borne pathogens they transmit under laboratory-controlled conditions.From March 2011 to April 2012, a field study was conducted in a private shelter in southern Italy to assess the efficacy of the imidacloprid/flumethrin collar against tick and flea infestations and to determine if this strategy would decrease tick-borne pathogen transmission in young dogs. A total of 122 animals were enrolled in the study and randomly assigned to group A (n = 64; collared) or group B (n = 58; untreated controls). Dogs were examined monthly for ticks and fleas and systematically tested for selected tick-borne pathogens.Compared to controls, the collar provided overall efficacies of 99.7% and 100% against tick and flea infestation, respectively. The overall efficacy for the prevention of tick-borne pathogens (i.e., Anaplasma platys and Babesia vogeli) was 91.6%.This study demonstrates that the imidacloprid/flumethrin collar is efficacious against flea and tick infestation as well as tick-borne pathogen transmission to dogs under field conditions. DA - 2013/// PY - 2013/// DO - 10.1186/1756-3305-6-245 VL - 6 IS - 1 SP - 245 J2 - Parasites & Vectors LA - en OP - SN - 1756-3305 UR - http://dx.doi.org/10.1186/1756-3305-6-245 DB - Crossref KW - Canine vector-borne diseases KW - Anaplasma platys KW - Babesia vogeli KW - Hepatozoon canis KW - Prevention KW - Dog KW - Imidacloprid KW - Flumethrin KW - Tick ER - TY - JOUR TI - Catalytic diversification upon metal scavenging in a prebiotic model for formation of tetrapyrrole macrocycles AU - Soares, Ana R. M. AU - Anderson, Dana R. AU - Chandrashaker, Vanampally AU - Lindsey, Jonathan S. T2 - NEW JOURNAL OF CHEMISTRY AB - A prebiotic model for the formation of tetrapyrrole macrocycles was examined in aqueous solution containing representative Earth-available metals [Mg(II), Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II) and Pd(II)]. First, a hydrophilic porphyrin (uroporphyrin I) was found to undergo metalation with all metals examined except Mg(II). Second, a competition experiment among the eight metals with uroporphyrin in limiting quantity afforded preferential metalation with Mn(II), Co(II), Cu(II) and Ni(II). A multicomponent analysis method enabled absorption spectrophotometric detection of 8 distinct uroporphyrins (7 metallo-, 1 free base) in a single mixture. Third, a dione–aminoketone reaction was performed in aqueous solution containing the metals followed by photooxidation in the presence of a quinone. The reaction proceeds through multiple stages: (1) dione–aminoketone condensation to give a pyrrole equipped for self-condensation, (2) tetramerization of the pyrrole and cyclization to give uroporphyrinogens, (3) 6e−/6H+ dehydrogenation (e.g., photooxidation) to give the uroporphyrins, and (4) metalation of the uroporphyrins. The presence versus absence of metals resulted in lower yields, yet Mn(II), Fe(II), Co(II), Cu(II) and Zn(II) each individually gave the corresponding metallouroporphyrin [with trivalent metals observed in three cases: Mn(III), Fe(III), and Co(III)]. Analogous reaction in the presence of all eight metals together gave the free base, Mn(III), and Zn(II) chelates whereas other metal chelates could not be reliably detected by absorption spectroscopy or mass spectrometry. Such metalloporphyrins greatly broaden the accessible redox levels, catalytic avenues, and photochemical features versus those of the free base porphyrins. Taken together, scavenging of metals is expected to increase the functional diversity of tetrapyrroles on early Earth. DA - 2013/// PY - 2013/// DO - 10.1039/c3nj00498h VL - 37 IS - 9 SP - 2716-2732 SN - 1369-9261 ER - TY - JOUR TI - A molecular mechanism for glaucoma: endoplasmic reticulum stress and the unfolded protein response AU - Anholt, Robert R. H. AU - Carbone, Mary Anna T2 - TRENDS IN MOLECULAR MEDICINE AB - Primary open angle glaucoma (POAG) is a common late-onset neurodegenerative disease. Ocular hypertension represents a major risk factor, but POAG etiology remains poorly understood. Some cases of early-onset congenital glaucoma and adult POAG are linked to mutations in myocilin, a secreted protein of poorly defined function. Transgenic overexpression of myocilin in Drosophila and experiments in mice and human populations implicate the unfolded protein response (UPR) in the pathogenesis of glaucoma. We postulate that compromised ability of the UPR to eliminate misfolded mutant or damaged proteins, including myocilin, causes endoplasmic reticulum stress, resulting in functional impairment of trabecular meshwork cells that regulate intraocular pressure. This mechanism of POAG is reminiscent of other age-dependent neurodegenerative diseases that involve accumulation of protein aggregates. DA - 2013/10// PY - 2013/10// DO - 10.1016/j.molmed.2013.06.005 VL - 19 IS - 10 SP - 586-593 SN - 1471-499X KW - primary open angle glaucoma KW - ocular hypertension KW - myocilin KW - neurodegenerative disease ER - TY - JOUR TI - The SOS4 pyridoxal kinase is required for maintenance of vitamin B-6-mediated processes in chloroplasts AU - Rueschhoff, Elizabeth E. AU - Gillikin, Jeffrey W. AU - Sederoff, Heike W. AU - Daub, Margaret E. T2 - PLANT PHYSIOLOGY AND BIOCHEMISTRY AB - Vitamin B(6) (pyridoxal 5'-phosphate and its vitamers) is an important cofactor in numerous enzymatic reactions. In spite of its importance, the consequences of altering vitamin B(6) content on plant growth and development are not well understood. This study compares two mutants for vitamin B(6)-metabolizing enzymes in Arabidopsis thaliana: a pdx1.3 mutant in the de novo synthesis pathway and a salvage pathway sos4 mutant that accumulates more vitamin B(6). We show that despite a difference in total B(6) content in leaf tissue, both mutants share similar phenotypes, including chlorosis, decreased size, altered chloroplast ultrastructure, and root sensitivity to sucrose. Assay of B(6) vitamer content from isolated chloroplasts showed that, despite differing B(6) vitamer content in whole leaf tissue, both mutants share a common deficiency in total and phosphorylated vitamers in chloroplasts. One of the splice variants of the SOS4 proteins was shown to be located in the chloroplast. Our data indicate that some of the phenotypic consequences shared between the pdx1.3 and sos4 mutants are due to B(6) deficiency in chloroplasts, and show that SOS4 is required for maintenance of phosphorylated B(6) vitamer concentrations in chloroplasts. Further, our data are consistent with a diffusion model for transport of vitamin B(6) into chloroplasts. DA - 2013/2// PY - 2013/2// DO - 10.1016/j.plaphy.2012.12.003 VL - 63 SP - 281-291 SN - 0981-9428 KW - Pyridoxine KW - Pyridoxamine KW - Pyridoxal kinase KW - Pyridoxal phosphate synthase ER - TY - JOUR TI - Palette of lipophilic bioconjugatable bacteriochlorins for construction of biohybrid light-harvesting architectures AU - Reddy, Kanumuri Ramesh AU - Jiang, Jianbing AU - Krayer, Michael AU - Harris, Michelle A. AU - Springer, Joseph W. AU - Yang, Eunkyung AU - Jiao, Jieying AU - Niedzwiedzki, Dariusz M. AU - Pandithavidana, Dinesh AU - Parkes-Loach, Pamela S. AU - Kirmaier, Christine AU - Loach, Paul A. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - Chemical Science AB - The challenge of creating both pigment building blocks and scaffolding to organize a large number of such pigments has long constituted a central impediment to the construction of artificial light-harvesting architectures. Light-harvesting (LH) antennas in photosynthetic bacteria are formed in a two-tiered self-assembly process wherein (1) a peptide dyad containing two bacteriochlorophyll a molecules forms, and (2) the dyads associate to form cyclic oligomers composed of 8 or 9 dyads in LH2 and 15 or 16 in LH1 of purple photosynthetic bacteria. While such antenna systems generally have near-quantitative transfer of excitation energy among pigments, only a fraction of the solar spectrum is typically absorbed. A platform architecture for study of light-harvesting phenomena has been developed that employs native photosynthetic peptide analogs, native bacteriochlorophyll a, and synthetic near-infrared-absorbing bacteriochlorins. Herein, the syntheses of 10 lipophilic bacteriochlorins are reported, of which 7 contain bioconjugatable handles (maleimide, iodoacetamide, formyl, carboxylic acid) for attachment to the peptide chassis. The bioconjugatable bacteriochlorins typically exhibit a long-wavelength absorption band in the range 710 to 820 nm, fluorescence yield of 0.1–0.2, and lifetime of the lowest singlet excited state of 2–5 ns. The α-helical structure of the native-like peptide is retained upon conjugation with a synthetic bacteriochlorin, as judged by single-reflection infrared studies. Static and time-resolved optical studies of the oligomeric biohybrid architectures in aqueous detergent solution reveal efficient (∼90%) excitation energy transfer from the attached bacteriochlorin to the native-like bacteriochlorophyll a sites. The biohybrid light-harvesting architectures thus exploit the self-constituting features of the natural systems yet enable versatile incorporation of members from a palette of synthetic chromophores, thereby opening the door to a wide variety of studies in artificial photosynthesis. DA - 2013/// PY - 2013/// DO - 10.1039/C3SC22317E VL - 4 IS - 5 SP - 2036 J2 - Chem. Sci. LA - en OP - SN - 2041-6520 2041-6539 UR - http://dx.doi.org/10.1039/C3SC22317E DB - Crossref ER - TY - JOUR TI - New Components of Drosophila Leg Development Identified through Genome Wide Association Studies AU - Grubbs, Nathaniel AU - Leach, Megan AU - Su, Xin AU - Petrisko, Tiffany AU - Rosario, Juan B. AU - Mahaffey, James W. T2 - PLOS ONE AB - The adult Drosophila melanogaster body develops from imaginal discs, groups of cells set-aside during embryogenesis and expanded in number during larval stages. Specification and development of Drosophila imaginal discs have been studied for many years as models of morphogenesis. These studies are often based on mutations with large developmental effects, mutations that are often lethal in embryos when homozygous. Such forward genetic screens can be limited by factors such as early lethality and genetic redundancy. To identify additional genes and genetic pathways involved in leg imaginal disc development, we employed a Genome Wide Association Study utilizing the natural genetic variation in leg proportionality found in the Drosophila Genetic Reference Panel fly lines. In addition to identifying genes already known to be involved in leg development, we identified several genes involved in pathways that had not previously been linked with leg development. Several of the genes appear to be involved in signaling activities, while others have no known roles at this time. Many of these uncharacterized genes are conserved in mammals, so we can now begin to place these genes into developmental contexts. Interestingly, we identified five genes which, when their function is reduced by RNAi, cause an antenna-to-leg transformation. Our results demonstrate the utility of this approach, integrating the tools of quantitative and molecular genetics to study developmental processes, and provide new insights into the pathways and networks involved in Drosophila leg development. DA - 2013/4/1/ PY - 2013/4/1/ DO - 10.1371/journal.pone.0060261 VL - 8 IS - 4 SP - SN - 1932-6203 ER - TY - JOUR TI - Koch's Postulates and the Pathogenesis of Comparative Infectious Disease Causation Associated with Bartonella species AU - Breitschwerdt, E. B. AU - Linder, K. L. AU - Day, M. J. AU - Maggi, R. G. AU - Chomel, B. B. AU - Kempf, V. A. J. T2 - JOURNAL OF COMPARATIVE PATHOLOGY AB - In his homage to Lucretius (‘Georgica’), Vergil is credited with stating: ‘Felix qui potuit rerum cognoscere causas’ (‘Fortunate is he who knows the causes of things’). Based on numerous commentaries and publications it is obvious that clinicians, diagnosticians and biomedical research scientists continue to struggle with disease causation, particularly in the assessment of the pathogenic role of ‘stealth pathogens’ that produce persistent infections in the host. Bartonella species, because of their evolutionary ability to induce persistent intravascular infections, present substantial challenges for researchers attempting to clarify the ability of these stealth bacteria to cause disease. By studying the comparative biological and pathological behaviour of microbes across mammalian genera, researchers might be able more rapidly to advance medical science and, subsequently, patient care by undertaking focused research efforts involving a single mammalian species or by attempting to recapitulate a complex disease in an rodent model. Therefore, in an effort to further assist in the establishment of disease causation by stealth pathogens, we use recent research observations involving the genus Bartonella to propose an additional postulate of comparative infectious disease causation to Koch's postulates. DA - 2013/// PY - 2013/// DO - 10.1016/j.jcpa.2012.12.003 VL - 148 IS - 2-3 SP - 115-125 SN - 1532-3129 KW - disease KW - infection KW - pathology KW - Koch's postulates ER - TY - JOUR TI - Infection of human brain vascular pericytes (HBVPs) by Bartonella henselae AU - Varanat, Mrudula AU - Maggi, Ricardo G. AU - Linder, Keith E. AU - Breitschwerdt, Edward B. T2 - MEDICAL MICROBIOLOGY AND IMMUNOLOGY DA - 2013/4// PY - 2013/4// DO - 10.1007/s00430-012-0279-5 VL - 202 IS - 2 SP - 143-151 SN - 1432-1831 KW - Blood vessels KW - Bacteria KW - Cytokines KW - Vascular endothelial growth factor KW - Pericyte coverage ER - TY - JOUR TI - Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data AU - Su, Y. H. AU - Nielsen, D. AU - Zhu, L. AU - Richards, K. AU - Suter, S. AU - Breen, M. AU - Motsinger-Reif, A. AU - Osborne, J. T2 - Human Genomics DA - 2013/// PY - 2013/// VL - 7 ER - TY - JOUR TI - Chikungunya Virus Host Range E2 Transmembrane Deletion Mutants Induce Protective Immunity against Challenge in C57BL/6J Mice AU - Piper, Amanda AU - Ribeiro, Mariana AU - Smith, Katherine M. AU - Briggs, Caitlin M. AU - Huitt, Emerson AU - Nanda, Kavita AU - Spears, Carla J. AU - Quiles, Michelle AU - Cullen, John AU - Thomas, Malcolm E. AU - Brown, Dennis T. AU - Hernandez, Raquel T2 - JOURNAL OF VIROLOGY AB - A vaccine against Chikungunya virus (ChikV), a reemerging pathogenic arbovirus, has been made by attenuating wild-type (WT) virus via truncation of the transmembrane domain (TMD) of E2 and selecting for host range (HR) mutants. Mice are a standard model system for ChikV disease and display the same symptoms of the disease seen in humans. Groups of mice were inoculated with one of three ChikV HR mutants to determine the ability of each mutant strain to elicit neutralizing antibody and protective immunity upon virus challenge. One mutant, ChikV TM17-2, fulfilled the criteria for a good vaccine candidate. It displayed no reactogenicity at the site of injection, no tissue disease in the foot/ankle and quadriceps, and no evidence of viral persistence in foot/ankle tissues 21 days after infection. Upon challenge with a highly pathogenic strain of ChikV, the mutant blocked viral replication in all tissues tested. This study identified a ChikV HR mutant that grows to high levels in insect cells but was restricted in the ability to assemble virus in mammalian cells in vitro. The study demonstrates that these HR strains are attenuated in the mammalian host and warrant further development as live-attenuated vaccine strains. DA - 2013/6// PY - 2013/6// DO - 10.1128/jvi.03357-12 VL - 87 IS - 12 SP - 6748-6757 SN - 1098-5514 ER - TY - JOUR TI - Biocompatibility analysis of an electrically-activated silver-based antibacterial surface system for medical device applications AU - Samberg, Meghan E. AU - Tan, Zhuo AU - Monteiro-Riviere, Nancy A. AU - Orndorff, Paul E. AU - Shirwaiker, Rohan A. T2 - JOURNAL OF MATERIALS SCIENCE-MATERIALS IN MEDICINE DA - 2013/3// PY - 2013/3// DO - 10.1007/s10856-012-4838-5 VL - 24 IS - 3 SP - 755-760 SN - 1573-4838 ER - TY - JOUR TI - Synthesis and evaluation of cationic bacteriochlorin amphiphiles with effective in vitro photodynamic activity against cancer cells at low nanomolar concentration AU - Sharma, Sulbha K. AU - Krayer, Michael AU - Sperandio, Felipe F. AU - Huang, Liyi AU - Huang, Ying-Ying AU - Holten, Dewey AU - Lindsey, Jonathan S. AU - Hamblin, Michael R. T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - Bacteriochlorins are attractive candidates as photosensitizers for photodynamic therapy (PDT) due to their intense absorption in the near-infrared (NIR) region of the spectrum where light transmission through tissue is maximal. Many naturally occurring bacteriochlorins are inherently unstable due to adventitious atmospheric oxidation. A de novo synthesis affords bacteriochlorins that contain a geminal dimethyl group in each reduced pyrrole ring to increase stability against oxidation. Here, three new synthetic bacteriochlorins, each bearing a single side-chain containing one or two positive charges, were investigated for their in vitro PDT activity against HeLa human cancer cells. All bacteriochlorins were active at low nanomolar concentration when activated with NIR light; those bearing a single positive charge exhibited faster uptake and higher activity. The bacteriochlorins were localized in mitochondria, lysosomes and endoplasmic reticulum as shown by organelle specific fluorescent probes. Cell death was via apoptosis as shown by cell morphology and nuclear condensation. Taken together, the results show the importance of appropriate peripheral groups about a photosensitizer for effective PDT applications. DA - 2013/// PY - 2013/// DO - 10.1142/s108842461250126x VL - 17 IS - 1-2 SP - 73-85 SN - 1099-1409 KW - photodynamic therapy KW - HeLa cancer cells KW - bacteriochlorins KW - confocal microscopy KW - subcellular localization KW - apoptosis ER - TY - JOUR TI - Neural development is dependent on the function of specificity protein 2 in cell cycle progression AU - Liang, Huixuan AU - Xiao, Guanxi AU - Yin, Haifeng AU - Hippenmeyer, Simon AU - Horowitz, Jonathan M. AU - Ghashghaei, H. Troy T2 - DEVELOPMENT AB - Faithful progression through the cell cycle is crucial to the maintenance and developmental potential of stem cells. Here, we demonstrate that neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs) employ a zinc-finger transcription factor specificity protein 2 (Sp2) as a cell cycle regulator in two temporally and spatially distinct progenitor domains. Differential conditional deletion of Sp2 in early embryonic cerebral cortical progenitors, and perinatal olfactory bulb progenitors disrupted transitions through G1, G2 and M phases, whereas DNA synthesis appeared intact. Cell-autonomous function of Sp2 was identified by deletion of Sp2 using mosaic analysis with double markers, which clearly established that conditional Sp2-null NSCs and NPCs are M phase arrested in vivo. Importantly, conditional deletion of Sp2 led to a decline in the generation of NPCs and neurons in the developing and postnatal brains. Our findings implicate Sp2-dependent mechanisms as novel regulators of cell cycle progression, the absence of which disrupts neurogenesis in the embryonic and postnatal brain. DA - 2013/2/1/ PY - 2013/2/1/ DO - 10.1242/dev.085621 VL - 140 IS - 3 SP - 552-561 SN - 0950-1991 KW - Neurogenesis KW - Neural stem cells KW - Neural progenitors KW - Sp2 KW - Cell cycle KW - M phase KW - Mouse ER - TY - JOUR TI - Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes AU - Chen, Hsi-Chuan AU - Song, Jina AU - Williams, Cranos M. AU - Shuford, Christopher M. AU - Liu, Jie AU - Wang, Jack P. AU - Li, Quanzi AU - Shi, Rui AU - Gokce, Emine AU - Ducoste, Joel AU - Muddiman, David C. AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PLANT PHYSIOLOGY AB - 4-Coumaric acid:coenzyme A ligase (4CL) is involved in monolignol biosynthesis for lignification in plant cell walls. It ligates coenzyme A (CoA) with hydroxycinnamic acids, such as 4-coumaric and caffeic acids, into hydroxycinnamoyl-CoA thioesters. The ligation ensures the activated state of the acid for reduction into monolignols. In Populus spp., it has long been thought that one monolignol-specific 4CL is involved. Here, we present evidence of two monolignol 4CLs, Ptr4CL3 and Ptr4CL5, in Populus trichocarpa. Ptr4CL3 is the ortholog of the monolignol 4CL reported for many other species. Ptr4CL5 is novel. The two Ptr4CLs exhibited distinct Michaelis-Menten kinetic properties. Inhibition kinetics demonstrated that hydroxycinnamic acid substrates are also inhibitors of 4CL and suggested that Ptr4CL5 is an allosteric enzyme. Experimentally validated flux simulation, incorporating reaction/inhibition kinetics, suggested two CoA ligation paths in vivo: one through 4-coumaric acid and the other through caffeic acid. We previously showed that a membrane protein complex mediated the 3-hydroxylation of 4-coumaric acid to caffeic acid. The demonstration here of two ligation paths requiring these acids supports this 3-hydroxylation function. Ptr4CL3 regulates both CoA ligation paths with similar efficiencies, whereas Ptr4CL5 regulates primarily the caffeic acid path. Both paths can be inhibited by caffeic acid. The Ptr4CL5-catalyzed caffeic acid metabolism, therefore, may also act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux. A high level of caffeic acid was detected in stem-differentiating xylem of P. trichocarpa. Our results suggest that Ptr4CL5 and caffeic acid coordinately modulate the CoA ligation flux for monolignol biosynthesis. DA - 2013/3// PY - 2013/3// DO - 10.1104/pp.112.210971 VL - 161 IS - 3 SP - 1501-1516 SN - 0032-0889 ER - TY - JOUR TI - Growth Requirements and Chromosomal Instability of Induced Pluripotent Stem Cells Generated from Adult Canine Fibroblasts AU - Koh, Sehwon AU - Thomas, Rachael AU - Tsai, Shengdar AU - Bischoff, Steve AU - Lim, Ji-Hey AU - Breen, Matthew AU - Olby, Natasha J. AU - Piedrahita, Jorge A. T2 - STEM CELLS AND DEVELOPMENT AB - In mice and humans, it has been shown that embryonic and adult fibroblasts can be reprogrammed into pluripotency by introducing 4 transcription factors, Oct3/4, Klf4, Sox2, and c-Myc (OKSM). Here, we report the derivation of induced pluripotent stem cells (iPSCs) from adult canine fibroblasts by retroviral OKSM transduction. The isolated canine iPSCs (ciPSCs) were expanded in 3 different culture media [fibroblast growth factor 2 (FGF2), leukemia inhibitory factor (LIF), or FGF2 plus LIF]. Cells cultured in both FGF2 and LIF expressed pluripotency markers [POU5F1 (OCT4), SOX2, NANOG, and LIN28] and embryonic stem cell (ESC)-specific genes (PODXL, DPPA5, FGF5, REX1, and LAMP1) and showed strong levels of alkaline phosphatase expression. In vitro differentiation by formation of embryoid bodies and by directed differentiation generated cell derivatives of all 3 germ layers as confirmed by mRNA and protein expression. In vivo, the ciPSCs created solid tumors, which failed to reach epithelial structure formation, but expressed markers for all 3 germ layers. Array comparative genomic hybridization and chromosomal fluorescence in situ hybridization analyses revealed that while retroviral transduction per se did not result in significant DNA copy number imbalance, there was evidence for the emergence of low-level aneuploidy during prolonged culture or tumor formation. In summary, we were able to derive ciPSCs from adult fibroblasts by using 4 transcription factors. The isolated iPSCs have similar characteristics to ESCs from other species, but the exact cellular mechanisms behind their unique co-dependency on both FGF2 and LIF are still unknown. DA - 2013/3// PY - 2013/3// DO - 10.1089/scd.2012.0393 VL - 22 IS - 6 SP - 951-963 SN - 1557-8534 ER - TY - JOUR TI - Genetic variation in resistance to Phytophthora cinnamomi in seedlings of two Turkish Abies species AU - Frampton, John AU - Isik, Fikret AU - Benson, D. Michael T2 - TREE GENETICS & GENOMES DA - 2013/2// PY - 2013/2// DO - 10.1007/s11295-012-0529-0 VL - 9 IS - 1 SP - 53-63 SN - 1614-2942 KW - Abies bornmuelleriana KW - Abies equi-trojani KW - Christmas trees KW - Root rot KW - Trojan fir KW - Turkish fir ER - TY - JOUR TI - Alphavirus Genome Delivery Occurs Directly at the Plasma Membrane in a Time- and Temperature-Dependent Process AU - Vancini, Ricardo AU - Wang, Gongbo AU - Ferreira, Davis AU - Hernandez, Raquel AU - Brown, Dennis T. T2 - JOURNAL OF VIROLOGY AB - It is widely held that arboviruses such as the alphavirus Sindbis virus gain entry into cells by a process of receptor-mediated endocytosis followed by membrane fusion in the acid environment of the endosome. We have used an approach of direct observation of Sindbis virus entry into cells by electron microscopy and immunolabeling of virus proteins with antibodies conjugated to gold beads. We found that upon attaching to the cell surface, intact RNA-containing viruses became empty shells that could be identified only by antibody labeling. We found that the rate at which full particles were converted to empty particles increased with time and temperature. We found that this entry event takes place at temperatures that inhibit both endosome formation and membrane fusion. We conclude that entry of alphaviruses is by direct penetration of cell plasma membranes through a pore structure formed by virus and, possibly, host proteins. DA - 2013/4// PY - 2013/4// DO - 10.1128/jvi.03412-12 VL - 87 IS - 8 SP - 4352-4359 SN - 0022-538X ER - TY - JOUR TI - "Candidatus Mycoplasma haemomacaque" and Bartonella quintana Bacteremia in Cynomolgus Monkeys AU - Maggi, R. G. AU - Mascarelli, P. E. AU - Balakrishnan, N. AU - Rohde, C. M. AU - Kelly, C. M. AU - Ramaiah, L. AU - Leach, M. W. AU - Breitschwerdt, E. B. T2 - Journal of Clinical Microbiology AB - Here, we report latent infections with Bartonella quintana and a hemotropic Mycoplasma sp. in a research colony of cynomolgus monkeys (Macaca fascicularis). Sequence alignments, evolutionary analysis, and signature nucleotide sequence motifs of the hemotropic Mycoplasma 16S rRNA and RNase P genes indicate the presence of a novel organism. DA - 2013/2/13/ PY - 2013/2/13/ DO - 10.1128/jcm.03019-12 VL - 51 IS - 5 SP - 1408-1411 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/JCM.03019-12 DB - Crossref ER - TY - JOUR TI - The 2009 Late Blight Pandemic in the Eastern United States - Causes and Results AU - Fry, W. E. AU - McGrath, M. T. AU - Seaman, A. AU - Zitter, T. A. AU - McLeod, A. AU - Danies, G. AU - Small, I. M. AU - Myers, K. AU - Everts, K. AU - Gevens, A. J. AU - Gugino, B. K. AU - Johnson, S. B. AU - Judelson, H. AU - Ristaino, J. AU - Roberts, R. AU - Secor, G. AU - Seebold, K., Jr. AU - Snover-Clift, K. AU - Wyenandt, A. AU - Gruenwald, N. J. AU - Smart, C. D. T2 - PLANT DISEASE AB - The tomato late blight pandemic of 2009 made late blight into a household term in much of the eastern United States. Many home gardeners and many organic producers lost most if not all of their tomato crop, and their experiences were reported in the mainstream press. Some CSAs (Community Supported Agriculture) could not provide tomatoes to their members. In response, many questions emerged: How did it happen? What was unusual about this event compared to previous late blight epidemics? What is the current situation in 2012 and what can be done? It's easiest to answer these questions, and to understand the recent epidemics of late blight, if one knows a bit of the history of the disease and the biology of the causal agent, Phytophthora infestans. DA - 2013/3// PY - 2013/3// DO - 10.1094/pdis-08-12-0791-fe VL - 97 IS - 3 SP - 296-306 SN - 0191-2917 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84873925561&partnerID=MN8TOARS ER - TY - JOUR TI - Serial Testing from a 3-Day Collection Period by Use of the Bartonella Alphaproteobacteria Growth Medium Platform May Enhance the Sensitivity of Bartonella Species Detection in Bacteremic Human Patients AU - Pultorak, E. L. AU - Maggi, R. G. AU - Mascarelli, P. E. AU - Breitschwerdt, E. B. T2 - Journal of Clinical Microbiology AB - ABSTRACT Patients with infection from bacteremic Bartonella spp., tested using Bartonella Alphaproteobacteria growth medium (BAPGM), were retrospectively categorized into one of two groups that included those whose blood was collected once (group 1; n = 55) or three times (group 2; n = 36) within a 1-week period. Overall, 19 patients (20.8%) were PCR positive for one or more Bartonella spp. using the BAPGM platform. Seven patients (12.7%) in group 1 tested positive, and 12 patients (33.3%) in group 2 tested positive. Detection was improved when the patients were tested three times within a 1-week period (odds ratio, 3.4 [95% confidence interval, 1.2 to 9.8]; P = 0.02). Obtaining three sequential blood samples during a 1-week period should be considered a diagnostic approach when bartonellosis is suspected. DA - 2013/3/13/ PY - 2013/3/13/ DO - 10.1128/jcm.00123-13 VL - 51 IS - 6 SP - 1673-1677 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/JCM.00123-13 DB - Crossref ER - TY - JOUR TI - Photophysical Properties and Electronic Structure of Bacteriochlorin-Chalcones with Extended Near-Infrared Absorption AU - Yang, Eunkyung AU - Ruzie, Christian AU - Krayer, Michael AU - Diers, James R. AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Lindsey, Jonathan S. AU - Bocian, David F. AU - Holten, Dewey T2 - PHOTOCHEMISTRY AND PHOTOBIOLOGY AB - Abstract Synthetic bacteriochlorins enable systematic tailoring of substituents about the bacteriochlorin chromophore and thereby provide insights concerning the native bacteriochlorophylls of bacterial photosynthesis. Nine free‐base bacteriochlorins (eight prepared previously and one prepared here) have been examined that bear diverse substituents at the 13‐ or 3,13‐positions. The substituents include chalcone (3‐phenylprop‐2‐en‐1‐onyl) derivatives with groups attached to the phenyl moiety, a “reverse chalcone” (3‐phenyl‐3‐oxo‐1‐enyl), and extended chalcones (5‐phenylpenta‐2,4‐dien‐1‐onyl, retinylidenonyl). The spectral and photophysical properties ( τ s , Φ f , Φ ic , Φ isc , τ T , k f , k ic , k isc ) of the bacteriochlorins have been characterized. The bacteriochlorins absorb strongly in the 780–800 nm region and have fluorescence quantum yields ( Φ f ) in the range 0.05–0.11 in toluene and dimethylsulfoxide. Light‐induced electron promotions between orbitals with predominantly substituent or macrocycle character or both may give rise to some net macrocycle ↔ substituent charge‐transfer character in the lowest and higher singlet excited states as indicated by density functional theory ( DFT ) and time‐dependent DFT calculations. Such calculations indicated significant participation of molecular orbitals beyond those ( HOMO − 1 to LUMO + 1) in the Gouterman four‐orbital model. Taken together, the studies provide insight into the fundamental properties of bacteriochlorins and illustrate designs for tuning the spectral and photophysical features of these near‐infrared‐absorbing tetrapyrrole chromophores. DA - 2013/// PY - 2013/// DO - 10.1111/php.12053 VL - 89 IS - 3 SP - 586-604 SN - 1751-1097 ER - TY - JOUR TI - Molecular Electronic Tuning of Photosensitizers to Enhance Photodynamic Therapy: Synthetic Dicyanobacteriochlorins as a Case Study AU - Yang, Eunkyung AU - Diers, James R. AU - Huang, Ying-Ying AU - Hamblin, Michael R. AU - Lindsey, Jonathan S. AU - Bocian, David F. AU - Holten, Dewey T2 - PHOTOCHEMISTRY AND PHOTOBIOLOGY AB - Abstract Photophysical, photostability, electrochemical and molecular‐orbital characteristics are analyzed for a set of stable dicyanobacteriochlorins that are promising photosensitizers for photodynamic therapy (PDT). The bacteriochlorins are the parent compound (BC), dicyano derivative (NC) 2 BC and corresponding zinc (NC) 2 BC‐Zn and palladium chelate (NC) 2 BC‐Pd. The order of PDT activity against HeLa human cancer cells in vitro is (NC) 2 BC‐Pd > (NC) 2 BC > (NC) 2 BC‐Zn ≈ BC. The near‐infrared absorption feature of each dicyanobacteriochlorin is bathochromically shifted 35–50 nm (748–763 nm) from that for BC (713 nm). Intersystem crossing to the PDT‐active triplet excited state is essentially quantitative for (NC) 2 BC‐Pd. Phosphorescence from (NC) 2 BC‐Pd occurs at 1122 nm (1.1 eV). This value and the measured ground‐state redox potentials fix the triplet excited‐state redox properties, which underpin PDT activity via Type‐1 (electron transfer) pathways. A perhaps counterintuitive (but readily explicable) result is that of the three dicyanobacteriochlorins, the photosensitizer with the shortest triplet lifetime (7 μs), (NC) 2 BC‐Pd has the highest activity. Photostabilities of the dicyanobacteriochlorins and other bacteriochlorins studied recently are investigated and discussed in terms of four phenomena: aggregation, reduction, oxidation and chemical reaction. Collectively, the results and analysis provide fundamental insights concerning the molecular design of PDT agents. DA - 2013/// PY - 2013/// DO - 10.1111/php.12021 VL - 89 IS - 3 SP - 605-618 SN - 1751-1097 ER - TY - JOUR TI - Isolation of a Novel Strain of Mycobacterium iranicum from a Woman in the United States AU - Balakrishnan, Nandhakumar AU - Tortoli, Enrico AU - Engel, Susan L. AU - Breitschwerdt, Edward B. T2 - JOURNAL OF CLINICAL MICROBIOLOGY AB - A novel strain of Mycobacterium iranicum, a recently described nontuberculous Mycobacterium species, was isolated from the sputum of a woman. The source of infection was not determined; however, fomite transmission of inhaled aerosolized secretions from her husband's sleep apnea equipment was historically possible. DA - 2013/2// PY - 2013/2// DO - 10.1128/jcm.02560-12 VL - 51 IS - 2 SP - 705-707 SN - 0095-1137 ER - TY - JOUR TI - GENOMICS A spruce sequence AU - Sederoff, Ronald T2 - NATURE DA - 2013/5/30/ PY - 2013/5/30/ DO - 10.1038/nature12250 VL - 497 IS - 7451 SP - 569-570 SN - 0028-0836 ER - TY - JOUR TI - Flavivirus infection from mosquitoes in vitro reveals cell entry at the plasma membrane AU - Vancini, Ricardo AU - Kramer, Laura D. AU - Ribeiro, Mariana AU - Hernandez, Raquel AU - Brown, Dennis T2 - VIROLOGY AB - Dengue and West Nile viruses are enveloped RNA viruses that belong to genus Flavivirus (family Flaviviridae) and are considered important mosquito-borne viral pathogenic agents worldwide. A potential target for intervention strategies is the virus cell entry mechanism. Previous studies of flavivirus entry have focused on the effects of biochemical and molecular inhibitors on viral entry leading to controversial conclusions suggesting that the process is dependent upon endocytosis and low pH mediated membrane fusion. In this study we analyzed the early events in the infection process by means of electron microscopy and immuno-gold labeling of viral particles during cell entry, and used as a new approach for infecting cells with viruses obtained directly from mosquitoes. The results show that Dengue and West Nile viruses may infect cells by a mechanism that involves direct penetration of the host cell plasma membrane as proposed for alphaviruses. DA - 2013/1/20/ PY - 2013/1/20/ DO - 10.1016/j.virol.2012.10.013 VL - 435 IS - 2 SP - 406-414 SN - 0042-6822 KW - Flavivirus KW - Virus entry KW - Mosquitoes KW - Electron microscopy ER - TY - JOUR TI - Evidence for presence of the founder Ia mtDNA haplotype of Phytophthora infestans in 19th century potato tubers from the Rothamsted archives AU - Ristaino, J. B. AU - Hu, C. H. AU - Fitt, B. D. L. T2 - PLANT PATHOLOGY AB - Late blight remained a significant disease for potato growers in Europe long after the famine of the 1840s. Of the four mitochondrial haplotypes of Phytophthora infestans , only the Ia mitochondrial DNA (mtDNA) haplotype has been identified previously in infected potato leaves from famine‐era herbarium specimens collected in England, Ireland and Europe in the 19th century. Long‐term soil fertility experiments were conducted on potato between 1876 and 1901 in Rothamsted to investigate effects of combinations of organic manures and mineral fertilizers on disease and yield. This report identifies for the first time the same Ia mtDNA haplotype of P. infestans in three diseased tubers from 1877 from the long‐term Rothamsted trials, thus providing the earliest evidence of the presence of the founder Ia mtDNA haplotype of P. infestans in potato tubers in England. Soil amendments had a significant impact on disease and yield. A real‐time PCR assay was used to detect and quantify P. infestans in tubers. The level of pathogen DNA was greatest in tubers from highest yielding plots that received combinations of inorganic nitrogenous and mineral fertilizers and least in tubers from plots with organic farmyard manures or non‐nitrogenous mineral fertilizers. The Ia mtDNA haplotype was also confirmed from diseased potato leaves during the same time period. Thus, the founder Ia mtDNA haplotype survived in potato tubers after 1846 and was present over 30 years later in the UK. DA - 2013/6// PY - 2013/6// DO - 10.1111/j.1365-3059.2012.02680.x VL - 62 IS - 3 SP - 492-500 SN - 0032-0862 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84876811780&partnerID=MN8TOARS KW - late blight KW - oomycetes KW - Phytophthora infestans KW - potato famine ER - TY - JOUR TI - Aqueous–membrane partitioning of β-substituted porphyrins encompassing diverse polarity AU - Soares, Ana R. M. AU - Thanaiah, Yugaananthy AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - Understanding the partitioning of organic molecules between aqueous solution and lipid membranes is critical to problems in fields ranging from drug design to environmental science to studies of the origin of life. Here, six β-substituted porphyrins of diverse polarity were examined for partitioning between the membranes of phosphatidylcholine vesicles and aqueous solution. The porphyrins include uroporphyrin I (number of carboxylic acid substituents = 8), heptacarboxylic acid porphyrin I (7), hexacarboxylic acid porphyrin I (6), coproporphyrin I (4), mesoporphyrin IX (2) and etioporphyrin I (0). The porphyrins were examined individually and collectively. In each case, size-exclusion chromatography was used to separate a porphyrins/vesicles fraction and a porphyrins/aqueous fraction. Each fraction was analyzed quantitatively by reversed-phase HPLC with fluorescence detection or by UV-Visible absorption spectroscopy to give partition coefficients. The partition coefficients for the six porphyrins also were calculated (clog P) using seven software programs: ACD/Labs, ALOGPS 2.1, Chemdraw, Molinspiration, KowWin, MarvinSketch, and XLOGP3. For perspective, clog P values for seven other porphyrins and 18 non-porphyrins also were calculated. Wide variation among programs was observed for almost all of the porphyrins and non-porphyrins of similar molecular weight. The dearth of porphyrins with requisite substituent patterns for experimental examination and the unreliability of calculation preclude definitive predictions concerning partitioning of unknown porphyrins; however, the results afford heuristics to predict aqueous–membrane partitioning of diverse β-substituted porphyrins. DA - 2013/// PY - 2013/// DO - 10.1039/c3nj41042k VL - 37 IS - 4 SP - 1087 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/c3nj41042k DB - Crossref ER - TY - JOUR TI - A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica) AU - Kubisiak, T. L. AU - Nelson, C. D. AU - Staton, M. E. AU - Zhebentyayeva, T. AU - Smith, C. AU - Olukolu, B. A. AU - Fang, G. -C. AU - Hebard, F. V. AU - Anagnostakis, S. AU - Wheeler, N. AU - Sisco, P. H. AU - Abbott, A. G. AU - Sederoff, R. R. T2 - TREE GENETICS & GENOMES AB - The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. Two mapping populations were established with three Chinese chestnut parents, ‘Mahogany’, ‘Nanking’, and ‘Vanuxem’, totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM, providing the the most comprehensive genetic map for a Fagaceae species to date. Over 75 % of the mapped markers from the Chinese chestnut consensus genetic map were placed on the physical map using overgo hybridization, providing a fully integrated genetic and physical map resource for Castanea spp. About half (57 %) of the Chinese chestnut genetic map could be assigned to regions of segmental homology with 58 % of the peach (Prunus persica) genome assembly. A three quantitative trait loci (QTL) model for blight resistance was verified using the new genetic markers and an existing interspecies (C. mollissima × C. dentata) F2 mapping population. Two of the blight resistance QTLs in chestnut shared synteny with two QTLs for powdery mildew resistance in peach, indicating the potential conservation of disease resistance genes at these loci. DA - 2013/4// PY - 2013/4// DO - 10.1007/s11295-012-0579-3 VL - 9 IS - 2 SP - 557-571 SN - 1614-2950 KW - Fagaceae KW - Castanea spp. KW - Chestnut KW - Genetic map KW - Comparative genomics KW - Disease resistance ER - TY - JOUR TI - Synthesis and characterization of lipophilic, near-IR absorbing metallobacteriochlorins AU - Sun, E. J. AU - Chen, C. Y. AU - Lindsey, J. S. T2 - Chemical Journal of Chinese Universities DA - 2013/// PY - 2013/// VL - 34 IS - 4 SP - 776-781 ER - TY - JOUR TI - Reading between the lines: molecular characterization of five widely used canine lymphoid tumour cell lines AU - Seiser, E. L. AU - Thomas, R. AU - Richards, K. L. AU - Kelley, M. Kathryn AU - Moore, P. AU - Suter, S. E. AU - Breen, M. T2 - VETERINARY AND COMPARATIVE ONCOLOGY AB - Molecular characterization of tumour cell lines is increasingly regarded as a prerequisite for defining their validity as models of in vivo neoplasia. We present the first comprehensive catalogue of genomic and transcriptional characteristics of five widely used canine lymphoid tumour cell lines. High‐resolution microarray‐based comparative genomic hybridization defined their unique profiles of genomic DNA copy number imbalance. Multicolour fluorescence in situ hybridization identified aberrant gains of MYC , KIT and FLT3 and deletions of PTEN and CDKN2 in individual cell lines, and also revealed examples of extensive structural chromosome reorganization. Gene expression profiling and RT‐PCR analyses defined the relationship between genomic imbalance and transcriptional dysregulation in each cell line, clarifying their relevance as models of discrete functional pathways with biological and therapeutic significance. In combination, these data provide an extensive resource of molecular data for directing the appropriate use of these cell lines as tools for studying canine lymphoid neoplasia. DA - 2013/3// PY - 2013/3// DO - 10.1111/j.1476-5829.2011.00299.x VL - 11 IS - 1 SP - 30-50 SN - 1476-5829 KW - canine KW - cell line KW - comparative KW - lymphoid neoplasia KW - microarray KW - model ER - TY - JOUR TI - Prevention of Canine Leishmaniosis in a Hyper-Endemic Area Using a Combination of 10% Imidacloprid/4.5% Flumethrin AU - Otranto, Domenico AU - Dantas-Torres, Filipe AU - Caprariis, Donato AU - Di Paola, Giancarlo AU - Tarallo, Viviana D. AU - Latrofa, Maria S. AU - Lia, Riccardo P. AU - Annoscia, Giada AU - Breitshwerdt, Edward B. AU - Cantacessi, Cinzia AU - Capelli, Gioia AU - Stanneck, Dorothee T2 - PLOS ONE AB - Dogs are the main reservoir hosts of Leishmania infantum, the agent of human zoonotic visceral leishmaniosis. This study investigated the efficacy of a polymer matrix collar containing a combination of 10% imidacloprid and 4.5% flumethrin as a novel prophylactic measure to prevent L. infantum infections in young dogs from a hyper-endemic area of southern Italy, with a view towards enhancing current control strategies against both human and canine leishmaniosis.The study was carried out on 124 young dogs, of which 63 were collared (Group A) while 61 were left untreated (Group B), from March-April 2011 until March 2012. Blood and skin samples were collected at baseline (April 2011) and at the first, second, third and fourth follow-up time points (July, September 2011 and November 2011, and March 2012, respectively). Bone marrow and conjunctiva were sampled at baseline and at the fourth follow-up. Serological, cytological and molecular tests were performed to detect the presence of L. infantum in the different tissues collected. At the end of the trial, no dog from Group A proved positive for L. infantum at any follow-up, whereas 22 dogs from Group B were infected (incidence density rate = 45.1%); therefore, the combination of 10% imidacloprid and 4.5% flumethrin was 100% efficacious for the prevention of L. infantum infection in young dogs prior to their first exposure to the parasite in a hyper-endemic area for CanL.The use of collars containing 10% imidacloprid and 4.5% flumethrin conferred long-term protection against infection by L. infantum to dogs located in a hyper-endemic area, thus representing a reliable and sustainable strategy to decrease the frequency and spread of this disease among the canine population which will ultimately result in the reduction of associated risks to human health. DA - 2013/2/25/ PY - 2013/2/25/ DO - 10.1371/journal.pone.0056374 VL - 8 IS - 2 SP - SN - 1932-6203 ER - TY - JOUR TI - Enhanced Agrobacterium-mediated transformation efficiencies in monocot cells is associated with attenuated defense responses AU - Zhang, Wan-Jun AU - Dewey, Ralph E. AU - Boss, Wendy AU - Phillippy, Brian Q. AU - Qu, Rongda T2 - PLANT MOLECULAR BIOLOGY DA - 2013/2// PY - 2013/2// DO - 10.1007/s11103-012-9997-8 VL - 81 IS - 3 SP - 273-286 SN - 1573-5028 KW - Cold shock KW - Glutamine KW - myo-inositol KW - Plant defense response KW - Transformation ER - TY - JOUR TI - Co-infection with Anaplasma platys, Bartonella henselae and Candidatus Mycoplasma haematoparvum in a veterinarian AU - Maggi, Ricardo G AU - Mascarelli, Patricia E AU - Havenga, Lauren N AU - Naidoo, Vinny AU - Breitschwerdt, Edward B T2 - Parasites & Vectors AB - Abstract Background During a two year period, a 27-year-old female veterinarian experienced migraine headaches, seizures, including status epilepticus, and other neurological and neurocognitive abnormalities. Prior to and during her illness, she had been actively involved in hospital-based work treating domestic animals, primarily cats and dogs, in Grenada and Ireland and anatomical research requiring the dissection of wild animals (including lions, giraffe, rabbits, mongoose, and other animals), mostly in South Africa. The woman reported contact with fleas, ticks, lice, biting flies, mosquitoes, spiders and mites and had also been scratched or bitten by dogs, cats, birds, horses, reptiles, rabbits and rodents. Prior diagnostic testing resulted in findings that were inconclusive or within normal reference ranges and no etiological diagnosis had been obtained to explain the patient’s symptoms. Methods PCR assays targeting Anaplasma spp. Bartonella spp. and hemotopic Mycoplasma spp. were used to test patient blood samples. PCR positive amplicons were sequenced directly and compared to GenBank sequences. In addition, Bartonella alpha Proteobacteria growth medium (BAPGM) enrichment blood culture was used to facilitate bacterial growth and Bartonella spp. serology was performed by indirect fluorescent antibody testing. Results Anaplasma platys, Bartonella henselae and Candidatus Mycoplasma haematoparvum DNA was amplified and sequenced from the woman’s blood, serum or blood culture samples. Her serum was variably seroreactive to several Bartonella sp. antigens. Despite symptomatic improvement, six months of doxycycline most likely failed to eliminate the B. henselae infection, whereas A. platys and Candidatus M. haematoparvum DNA was no longer amplified from post-treatment samples. Conclusions As is typical of many veterinary professionals, this individual had frequent exposure to arthropod vectors and near daily contact with persistently bacteremic reservoir hosts, including cats, the primary reservoir host for B. henselae, and dogs, the presumed primary reservoir host for A. platys and Candidatus Mycoplasma haematoparvum. Physicians caring for veterinarians should be aware of the occupational zoonotic risks associated with the daily activities of these animal health professionals. DA - 2013/// PY - 2013/// DO - 10.1186/1756-3305-6-103 VL - 6 IS - 1 SP - 103 J2 - Parasites & Vectors LA - en OP - SN - 1756-3305 UR - http://dx.doi.org/10.1186/1756-3305-6-103 DB - Crossref KW - Bartonella KW - Mycoplasma KW - Anaplasma KW - Headache KW - Migraines KW - Seizures KW - Serology KW - PCR ER - TY - JOUR TI - Bartonella henselae infection in a man with hypergammaglobulinaemia, splenomegaly and polyclonal plasmacytosis AU - Balakrishnan, Nandhakumar AU - Jawanda, Jaspaul S. AU - Miller, Melissa B. AU - Breitschwerdt, Edward B. T2 - JOURNAL OF MEDICAL MICROBIOLOGY AB - Bartonella henselae is an infrequently reported cause of polyclonal plasmacytosis and hypergammaglobulinaemia. We herein document B. henselae infection in a 66-year-old patient who presented with hypergammaglobulinaemia, splenomegaly with polyclonal plasmacytosis, stroke, and suspected prosthetic aortic arch infection. Clinicians should remain cognizant of the heterogeneous clinical presentations associated with bartonellosis. DA - 2013/2// PY - 2013/2// DO - 10.1099/jmm.0.052134-0 VL - 62 IS - 2 SP - 338-341 SN - 0022-2615 ER - TY - JOUR TI - Bartonella henselae infection in a family experiencing neurological and neurocognitive abnormalities after woodlouse hunter spider bites AU - Mascarelli, Patricia E AU - Maggi, Ricardo G AU - Hopkins, Sarah AU - Mozayeni, B Robert AU - Trull, Chelsea L AU - Bradley, Julie M AU - Hegarty, Barbara C AU - Breitschwerdt, Edward B T2 - Parasites & Vectors AB - Abstract Background Bartonella species comprise a group of zoonotic pathogens that are usually acquired by vector transmission or by animal bites or scratches. Methods PCR targeting the Bartonella 16S-23S intergenic spacer (ITS) region was used in conjunction with BAPGM (Bartonella alpha Proteobacteria growth medium) enrichment blood culture to determine the infection status of the family members and to amplify DNA from spiders and woodlice. Antibody titers to B. vinsonii subsp. berkhoffii ( Bvb ) genotypes I-III, B. henselae ( Bh ) and B. koehlerae ( Bk ) were determined using an IFA test. Management of the medical problems reported by these patients was provided by their respective physicians. Results In this investigation, immediately prior to the onset of symptoms two children in a family experienced puncture-like skin lesions after exposure to and presumptive bites from woodlouse hunter spiders. Shortly thereafter, the mother and both children developed hive-like lesions. Over the ensuing months, the youngest son was diagnosed with Guillain-Barre (GBS) syndrome followed by Chronic Inflammatory Demyelinating Polyradiculoneuropathy (CIDP). The older son developed intermittent disorientation and irritability, and the mother experienced fatigue, headaches, joint pain and memory loss. When tested approximately three years after the woodlouse hunter spider infestation, all three family members were Bartonella henselae seroreactive and B. henselae DNA was amplified and sequenced from blood, serum or Bartonella alpha-proteobacteria (BAPGM) enrichment blood cultures from the mother and oldest son. Also, B. henselae DNA was PCR amplified and sequenced from a woodlouse and from woodlouse hunter spiders collected adjacent to the family’s home. Conclusions Although it was not possible to determine whether the family’s B. henselae infections were acquired by spider bites or whether the spiders and woodlice were merely accidental hosts, physicians should consider the possibility that B. henselae represents an antecedent infection for GBS, CIDP, and non-specific neurocognitive abnormalities. DA - 2013/// PY - 2013/// DO - 10.1186/1756-3305-6-98 VL - 6 IS - 1 SP - 98 J2 - Parasites & Vectors LA - en OP - SN - 1756-3305 UR - http://dx.doi.org/10.1186/1756-3305-6-98 DB - Crossref KW - Bartonella KW - Spiders KW - Neurological disease KW - Guillain-Barre Syndrome KW - Serology KW - PCR ER - TY - JOUR TI - Bartonella henselae bacteremia in a mother and son potentially associated with tick exposure AU - Maggi, Ricardo G AU - Ericson, Marna AU - Mascarelli, Patricia E AU - Bradley, Julie M AU - Breitschwerdt, Edward B T2 - Parasites & Vectors AB - Bartonella henselae is a zoonotic, alpha Proteobacterium, historically associated with cat scratch disease (CSD), but more recently associated with persistent bacteremia, fever of unknown origin, arthritic and neurological disorders, and bacillary angiomatosis, and peliosis hepatis in immunocompromised patients. A family from the Netherlands contacted our laboratory requesting to be included in a research study (NCSU-IRB#1960), designed to characterize Bartonella spp. bacteremia in people with extensive arthropod or animal exposure. All four family members had been exposed to tick bites in Zeeland, southwestern Netherlands. The mother and son were exhibiting symptoms including fatigue, headaches, memory loss, disorientation, peripheral neuropathic pain, striae (son only), and loss of coordination, whereas the father and daughter were healthy.Each family member was tested for serological evidence of Bartonella exposure using B. vinsonii subsp. berkhoffii genotypes I-III, B. henselae and B. koehlerae indirect fluorescent antibody assays and for bacteremia using the BAPGM enrichment blood culture platform.The mother was seroreactive to multiple Bartonella spp. antigens and bacteremia was confirmed by PCR amplification of B. henselae DNA from blood, and from a BAPGM blood agar plate subculture isolate. The son was not seroreactive to any Bartonella sp. antigen, but B. henselae DNA was amplified from several blood and serum samples, from BAPGM enrichment blood culture, and from a cutaneous striae biopsy. The father and daughter were seronegative to all Bartonella spp. antigens, and negative for Bartonella DNA amplification.Historically, persistent B. henselae bacteremia was not thought to occur in immunocompetent humans. To our knowledge, this study provides preliminary evidence supporting the possibility of persistent B. henselae bacteremia in immunocompetent persons from Europe. Cat or flea contact was considered an unlikely source of transmission and the mother, a physician, reported that clinical symptoms developed following tick exposure. To our knowledge, this is the first time that a B. henselae organism has been visualized in and amplified from a striae lesion. As the tick bites occurred three years prior to documentation of B. henselae bacteremia, the mode of transmission could not be determined. DA - 2013/4/15/ PY - 2013/4/15/ DO - 10.1186/1756-3305-6-101 VL - 6 IS - 1 SP - J2 - Parasites Vectors LA - en OP - SN - 1756-3305 UR - http://dx.doi.org/10.1186/1756-3305-6-101 DB - Crossref KW - Bartonella KW - BAPGM KW - Bacteremia KW - Striae KW - Neuropathy KW - Neurological disorder ER - TY - JOUR TI - Are vector-borne pathogen co-infections complicating the clinical presentation in dogs? T2 - Parasites & Vectors DA - 2013/// PY - 2013/// VL - 6 ER - TY - JOUR TI - Methodology for Inoculating Sweetpotato Virus Disease: Discovery of Tip Dieback, and Plant Recovery and Reversion in Different Clones AU - Mwanga, R. O. M. AU - Yencho, G. C. AU - Gibson, R. W. AU - Moyer, J. W. T2 - PLANT DISEASE AB - Evaluating sweetpotato (Ipomoea batatas) genotypes for resistance to sweetpotato virus disease (SPVD) has been slow and inefficient. Ipomoea setosa plants, normally used as the source of scions for graft-infecting sweetpotatoes with viral diseases, are often severely stunted and their mortality is 10 to 30% when infected with SPVD, making them unsuitable as scions. Tanzania, a landrace of I. batatas widely grown in East Africa, was found to be a superior host for maintaining and increasing SPVD inoculum (scions) for mass grafting. Modifications to a cleft-grafting technique also increased survival of grafted SPVD-affected scions from 5 to 100%. These modifications, coupled with an efficient SPVD scoring technique, allowed rapid screening of large sweetpotato populations for SPVD resistance. Plant recovery from SPVD is reported here as a component of SPVD resistance. Differences in recovery from SPVD were detected among progenies, indicating its genetic basis. Plant tip dieback, a hypersensitivity response, was observed only in families with cv. Wagabolige as a parent. These findings may open up new opportunities for improved understanding and control of this devastating disease. DA - 2013/1// PY - 2013/1// DO - 10.1094/pdis-12-11-1072-re VL - 97 IS - 1 SP - 30-36 SN - 1943-7692 ER -