TY - CONF TI - Symmetric determinantal representation of weakly skew circuits AU - Grenet, Bruno AU - Kaltofen, Erich L. AU - Koiran, Pascal AU - Portier, Natacha T2 - Symposium on Theoretical Aspects of Computer Science (STACS 2011) A2 - Dürr, Christoph A2 - Schwentick, Thomas C2 - 2011/// C3 - Proceedings of the Symposium on Theoretical Aspects of Computer Science (STACS 2011) CY - Dortmund, Germany DA - 2011/// PY - 2011/3// SP - 543–554 ER - TY - JOUR TI - The genome of the green anole lizard and a comparative analysis with birds and mammals AU - Alföldi, Jessica AU - Di Palma, Federica AU - Grabherr, Manfred AU - Williams, Christina AU - Kong, Lesheng AU - Mauceli, Evan AU - Russell, Pamela AU - Lowe, Craig B. AU - Glor, Richard E. AU - Jaffe, Jacob D. AU - Ray, David A. AU - Boissinot, Stephane AU - Shedlock, Andrew M. AU - Botka, Christopher AU - Castoe, Todd A. AU - Colbourne, John K. AU - Fujita, Matthew K. AU - Moreno, Ricardo Godinez AU - ten Hallers, Boudewijn F. AU - Haussler, David AU - Heger, Andreas AU - Heiman, David AU - Janes, Daniel E. AU - Johnson, Jeremy AU - de Jong, Pieter J. AU - Koriabine, Maxim Y. AU - Lara, Marcia AU - Novick, Peter A. AU - Organ, Chris L. AU - Peach, Sally E. AU - Poe, Steven AU - Pollock, David D. AU - de Queiroz, Kevin AU - Sanger, Thomas AU - Searle, Steve AU - Smith, Jeremy D. AU - Smith, Zachary AU - Swofford, Ross AU - Turner-Maier, Jason AU - Wade, Juli AU - Young, Sarah AU - Zadissa, Amonida AU - Edwards, Scott V. AU - Glenn, Travis C. AU - Schneider, Christopher J. AU - Losos, Jonathan B. AU - Lander, Eric S. AU - Breen, Matthew AU - Ponting, Chris P. AU - Lindblad-Toh, Kerstin T2 - Nature AB - The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations. DA - 2011/8/31/ PY - 2011/8/31/ DO - 10.1038/nature10390 VL - 477 IS - 7366 SP - 587-591 J2 - Nature LA - en OP - SN - 0028-0836 1476-4687 UR - http://dx.doi.org/10.1038/nature10390 DB - Crossref ER - TY - JOUR TI - A case of granulomatous hepatitis due to bartonella henselae infection AU - VanderHeyden, T., Jr. AU - Fimmel, C. AU - Breitschwerdt, E. AU - Parada, J. AU - Yong, S. AU - Mihalik, A. T2 - American Journal of Gastroenterology DA - 2011/10// PY - 2011/10// VL - 106 SP - S280 ER - TY - CONF TI - The role of infectious agents in granulomatous hepatitis in dogs AU - Hutchins, R.G. AU - Breitschwerdt, E.B. AU - Cullen, J.M. AU - Bissett, S.A. AU - Gookin, J.L. T2 - American College Of Veterinary Internal Medicine C2 - 2011/// C3 - Journal of Veterinary Internal Medicine CY - Denver, Colorado DA - 2011/// PY - 2011/6/15/ VL - 25 SP - 704 M1 - 3 ER - TY - CONF TI - Canine bartonellosis mimics other tick-borne diseases AU - Perez, C. AU - Diniz, P.P.V.P. AU - Maggi, R.G. AU - Breitschwerdt, E.B. T2 - American College Of Veterinary Internal Medicine Forum C2 - 2011/// C3 - Journal of Veterinary Internal Medicine CY - Denver, Colorado DA - 2011/// PY - 2011/6/15/ VL - 25 SP - 706–707 M1 - 3 ER - TY - CONF TI - Canine granulocytic anaplasmosis and granulocytic ehrlichiosis - a field-based comparison AU - Beall, M.J. AU - Andrews, B. AU - Eberts, M. AU - Breitschwerdt, EB T2 - American College of Veterinary Internal Medicine Forum C2 - 2011/// C3 - Journal of Veterinary Internal Medicine CY - Denver, Colorado DA - 2011/// PY - 2011/6/15/ VL - 25 SP - 712 M1 - 3 ER - TY - JOUR TI - Seroprevalence of three ehrlichia species in dogs - a multi-institutional study AU - Beall, M.J. AU - Breitschwerdt, E.B. AU - Cohn, L.A. AU - Couto, G AU - Dryden, M AU - Eddlestone, S. AU - Guptill, LC AU - Hoffman, W.E. AU - Kennedy, M.A. AU - Lathan, P AU - Little, SE AU - Roy, AF AU - Sayler, K AU - Sinsabaugh, J. AU - Snowden, K. AU - Stillman, BA AU - Welles, EG AU - Yabsley, M T2 - Journal of Veterinary Internal Medicine DA - 2011/// PY - 2011/// VL - 25 IS - 3 SP - 748 ER - TY - JOUR TI - Antimicrobial Use Guidelines for Treatment of Urinary Tract Disease in Dogs and Cats: Antimicrobial Guidelines Working Group of the International Society for Companion Animal Infectious Diseases AU - Weese, J. Scott AU - Blondeau, Joseph M. AU - Boothe, Dawn AU - Breitschwerdt, Edward B. AU - Guardabassi, Luca AU - Hillier, Andrew AU - Lloyd, David H. AU - Papich, Mark G. AU - Rankin, Shelley C. AU - Turnidge, John D. AU - Sykes, Jane E. T2 - Veterinary Medicine International AB - Urinary tract disease is a common reason for use (and likely misuse, improper use, and overuse) of antimicrobials in dogs and cats. There is a lack of comprehensive treatment guidelines such as those that are available for human medicine. Accordingly, guidelines for diagnosis and management of urinary tract infections were created by a Working Group of the International Society for Companion Animal Infectious Diseases. While objective data are currently limited, these guidelines provide information to assist in the diagnosis and management of upper and lower urinary tract infections in dogs and cats. DA - 2011/// PY - 2011/// DO - 10.4061/2011/263768 VL - 2011 SP - 1-9 J2 - Veterinary Medicine International LA - en OP - SN - 2042-0048 UR - http://dx.doi.org/10.4061/2011/263768 DB - Crossref ER - TY - JOUR TI - Molecular and Serological Diagnosis of Bartonella Infection in 61 Dogs from the United States AU - Pérez, C. AU - Maggi, R.G. AU - Diniz, P.P.V.P. AU - Breitschwerdt, E.B. T2 - Journal of Veterinary Internal Medicine AB - Molecular diagnosis of canine bartonellosis can be extremely challenging and often requires the use of an enrichment culture approach followed by PCR amplification of bacterial DNA.(1) The use of enrichment culture with PCR will increase molecular detection of bacteremia and will expand the diversity of Bartonella species detected. (2) Serological testing for Bartonella henselae and Bartonella vinsonii subsp. berkhoffii does not correlate with documentation of bacteremia.Between 2003 and 2009, 924 samples from 663 dogs were submitted to the North Carolina State University, College of Veterinary Medicine, Vector Borne Diseases Diagnostic Laboratory for diagnostic testing with the Bartonella α-Proteobacteria growth medium (BAPGM) platform. Test results and medical records of those dogs were retrospectively reviewed.PCR amplification of Bartonella sp. DNA after extraction from patient samples was compared with PCR after BAPGM enrichment culture. Indirect immunofluorescent antibody assays, used to detect B. henselae and B. vinsonii subsp. berkhoffii antibodies, were compared with PCR.Sixty-one of 663 dogs were culture positive or had Bartonella DNA detected by PCR, including B. henselae (30/61), B. vinsonii subsp. berkhoffii (17/61), Bartonella koehlerae (7/61), Bartonella volans-like (2/61), and Bartonella bovis (2/61). Coinfection with more than 1 Bartonella sp. was documented in 9/61 dogs. BAPGM culture was required for PCR detection in 32/61 cases. Only 7/19 and 4/10 infected dogs tested by IFA were B. henselae and B. vinsonii subsp. berkhoffii seroreactive, respectively.Dogs were most often infected with B. henselae or B. vinsonii subsp. berkhoffii based on PCR and enrichment culture, coinfection was documented, and various Bartonella species were identified. Most infected dogs did not have detectable Bartonella antibodies. DA - 2011/5/25/ PY - 2011/5/25/ DO - 10.1111/j.1939-1676.2011.0736.x VL - 25 IS - 4 SP - 805-810 LA - en OP - SN - 0891-6640 UR - http://dx.doi.org/10.1111/j.1939-1676.2011.0736.x DB - Crossref KW - Bacteria KW - BAPGM KW - Bartonella KW - Blood culture ER - TY - JOUR TI - Rickettsia rickettsiiTransmission by a Lone Star Tick, North Carolina AU - Breitschwerdt, Edward B. AU - Hegarty, Barbara C. AU - Maggi, Ricardo G. AU - Lantos, Paul M. AU - Aslett, Denise M. AU - Bradley, Julie M. T2 - Emerging Infectious Diseases AB - Abstract Only indirect or circumstantial evidence has been published to support transmission of Rickettsia rickettsii by Amblyomma americanum (lone star) ticks in North America. This study provides molecular evidence that A. americanum ticks can function, although most likely infrequently, as vectors of Rocky Mountain spotted fever for humans. DA - 2011/5// PY - 2011/5// DO - 10.3201/eid1705.101530 VL - 17 IS - 5 SP - 873-875 J2 - Emerg. Infect. Dis. OP - SN - 1080-6040 1080-6059 UR - http://dx.doi.org/10.3201/eid1705.101530 DB - Crossref ER - TY - JOUR TI - Identification of Bartonella henselae in 2 Cats With Pyogranulomatous Myocarditis and Diaphragmatic Myositis AU - Varanat, M. AU - Broadhurst, J. AU - Linder, K. E. AU - Maggi, R. G. AU - Breitschwerdt, E. B. T2 - Veterinary Pathology AB - Most cats infected with Bartonella henselae remain outwardly healthy carriers for years; however, self-limiting fever, transient anemia, neurologic dysfunction, lymphadenopathy, reproductive disorders, aortic valvular endocarditis, and neutrophilic myocarditis have been described in experimentally or naturally infected cats. Two cats in a North Carolina shelter died with pyogranulomatous myocarditis and diaphragmatic myositis. Bacteria were visualized in the lesions by Warthin-Starry silver impregnation and by B. henselae immunohistochemistry. B. henselae DNA was amplified and sequenced from the heart of 1 cat and from multiple tissue samples, including heart and diaphragm, from the second cat. This study supports a potential association between B. henselae and what has been historically described as "transmissible myocarditis and diaphragmitis" of undetermined cause in cats. DA - 2011/4/13/ PY - 2011/4/13/ DO - 10.1177/0300985811404709 VL - 49 IS - 4 SP - 608-611 J2 - Vet Pathol LA - en OP - SN - 0300-9858 1544-2217 UR - http://dx.doi.org/10.1177/0300985811404709 DB - Crossref KW - Bartonella KW - cats KW - diaphragmatic myositis KW - myocarditis ER - TY - JOUR TI - New approach for the study of mite reproduction: The first transcriptome analysis of a mite, Phytoseiulus persimilis (Acari: Phytoseiidae) AU - Cabrera, Ana R. AU - Donohue, Kevin V. AU - Khalil, Sayed M.S. AU - Scholl, Elizabeth AU - Opperman, Charles AU - Sonenshine, Daniel E. AU - Roe, R. Michael T2 - Journal of Insect Physiology AB - Many species of mites and ticks are of agricultural and medical importance. Much can be learned from the study of transcriptomes of acarines which can generate DNA-sequence information of potential target genes for the control of acarine pests. High throughput transcriptome sequencing can also yield sequences of genes critical during physiological processes poorly understood in acarines, i.e., the regulation of female reproduction in mites. The predatory mite, Phytoseiulus persimilis, was selected to conduct a transcriptome analysis using 454 pyrosequencing. The objective of this project was to obtain DNA-sequence information of expressed genes from P. persimilis with special interest in sequences corresponding to vitellogenin (Vg) and the vitellogenin receptor (VgR). These genes are critical to the understanding of vitellogenesis, and they will facilitate the study of the regulation of mite female reproduction. A total of 12,556 contiguous sequences (contigs) were assembled with an average size of 935bp. From these sequences, the putative translated peptides of 11 contigs were similar in amino acid sequences to other arthropod Vgs, while 6 were similar to VgRs. We selected some of these sequences to conduct stage-specific expression studies to further determine their function. DA - 2011/1// PY - 2011/1// DO - 10.1016/j.jinsphys.2010.09.006 VL - 57 IS - 1 SP - 52-61 J2 - Journal of Insect Physiology LA - en OP - SN - 0022-1910 UR - http://dx.doi.org/10.1016/j.jinsphys.2010.09.006 DB - Crossref KW - Mite KW - Acari KW - Phytoseiidae KW - Transcriptome KW - 454 KW - Vitellogenin KW - Vitellin KW - Yolk protein KW - Vitellogenin receptor KW - Yolk protein receptor KW - Tick KW - Female reproduction ER - TY - JOUR TI - Complex genetic architecture of Drosophila aggressive behavior AU - Zwarts, L. AU - Magwire, M. M. AU - Carbone, M. A. AU - Versteven, M. AU - Herteleer, L. AU - Anholt, R. R. H. AU - Callaerts, P. AU - Mackay, T. F. C. T2 - Proceedings of the National Academy of Sciences AB - Epistasis and pleiotropy feature prominently in the genetic architecture of quantitative traits but are difficult to assess in outbred populations. We performed a diallel cross among coisogenic Drosophila P-element mutations associated with hyperaggressive behavior and showed extensive epistatic and pleiotropic effects on aggression, brain morphology, and genome-wide transcript abundance in head tissues. Epistatic interactions were often of greater magnitude than homozygous effects, and the topology of epistatic networks varied among these phenotypes. The transcriptional signatures of homozygous and double heterozygous genotypes derived from the six mutations imply a large mutational target for aggressive behavior and point to evolutionarily conserved genetic mechanisms and neural signaling pathways affecting this universal fitness trait. DA - 2011/9/26/ PY - 2011/9/26/ DO - 10.1073/pnas.1113877108 VL - 108 IS - 41 SP - 17070-17075 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.1113877108 DB - Crossref ER - TY - JOUR TI - Control of skin cancer by the circadian rhythm AU - Gaddameedhi, S. AU - Selby, C. P. AU - Kaufmann, W. K. AU - Smart, R. C. AU - Sancar, A. T2 - Proceedings of the National Academy of Sciences AB - Skin cancer is the most common form of cancer in the United States. The main cause of this cancer is DNA damage induced by the UV component of sunlight. In humans and mice, UV damage is removed by the nucleotide excision repair system. Here, we report that a rate-limiting subunit of excision repair, the xeroderma pigmentosum group A (XPA) protein, and the excision repair rate exhibit daily rhythmicity in mouse skin, with a minimum in the morning and a maximum in the afternoon/evening. In parallel with the rhythmicity of repair rate, we find that mice exposed to UV radiation (UVR) at 4:00 AM display a decreased latency and about a fivefold increased multiplicity of skin cancer (invasive squamous cell carcinoma) than mice exposed to UVR at 4:00 PM. We conclude that time of day of exposure to UVR is a contributing factor to its carcinogenicity in mice, and possibly in humans. DA - 2011/10/24/ PY - 2011/10/24/ DO - 10.1073/pnas.1115249108 VL - 108 IS - 46 SP - 18790-18795 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.1115249108 DB - Crossref KW - circadian clock KW - cryptochrome KW - sunbathing KW - tanning salons ER - TY - JOUR TI - Abstracts of NEMASYM: The Third Nematode-Bacteria Symbioses Research Coordination Network Meeting AU - Stock, S. Patricia AU - Bird, David McK AU - Ghedin, Elodie AU - Goodrich-Blair, Heidi T2 - Symbiosis DA - 2011/11// PY - 2011/11// DO - 10.1007/s13199-011-0135-1 VL - 55 IS - 3 SP - 97-109 J2 - Symbiosis LA - en OP - SN - 0334-5114 1878-7665 UR - http://dx.doi.org/10.1007/s13199-011-0135-1 DB - Crossref ER - TY - JOUR TI - The Potato Late Blight pathogen in Ireland, 1846: reconnecting Irish specimens with the Moore--Berkeley correspondence AU - Nelson, E Charles AU - Ristaino, Jean Beagle T2 - Archives of natural history DA - 2011/// PY - 2011/// VL - 38 IS - 2 SP - 356-359 ER - TY - CONF TI - A LUCID Key to the common Phytophthora species AU - Ristaino, JB T2 - AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA C2 - 2011/// C3 - PHYTOPATHOLOGY DA - 2011/// VL - 101 SP - S153-S153 M1 - 6 ER - TY - JOUR TI - Key for identification of common Phytophthora species AU - Ristaino, JB T2 - CD-Rom format. American Phytopathological Society DA - 2011/// PY - 2011/// ER - TY - CONF TI - Deployment of rapid diagnostic tools for Phytophthora on horticultural crops in Central America AU - Ristaino, Jean Beagle AU - Ivors, Kelly AU - Meneses, Monica Blanco AU - Rueda, Dinie Espinal AU - Bonants, Peter C2 - 2011/// C3 - APS-IPPC Joint Meeting" Emerging Pests/Invasive Species. Digital Identification Tools: Their role in Biosecurity and Pest-Management", Honolulu, Hawaii, USA DA - 2011/// ER - TY - JOUR TI - DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer AU - Robideau, Gregg P AU - Cock, Arthur WAM AU - Coffey, Michael D AU - Voglmayr, Hermann AU - Brouwer, Henk AU - Bala, Kanak AU - Chitty, David W AU - Désaulniers, Nicole AU - Eggertson, Quinn A AU - Gachon, Claire MM AU - others T2 - Molecular ecology resources DA - 2011/// PY - 2011/// VL - 11 IS - 6 SP - 1002-1011 ER - TY - JOUR TI - DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer T2 - Molecular Ecology Resources AB - Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes. DA - 2011/// PY - 2011/// DO - 10.1111/j.1755-0998.2011.03041.x VL - 11 IS - 6 SP - 1002-1011 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-80054066292&partnerID=MN8TOARS KW - cytochrome c oxidase subunit I KW - DNA barcoding KW - internal transcribed spacer KW - oomycete KW - species identification ER - TY - CONF TI - Quadratic-time certificates in linear algebra AU - Kaltofen, Erich L. AU - Nehring, Michael AU - Saunders, B. David T2 - the 36th international symposium AB - We present certificates for the positive semidefiniteness of an n by n matrix A, whose entries are integers of binary length log ||A||, that can be verified in O(n(2+µ) (log ||A||)(1+µ) binary operations for any µ > 0. The question arises in Hilbert/Artin-based rational sum-of-squares certificates (proofs) for polynomial inequalities with rational coefficients. We allow certificates that are validated by Monte Carlo randomized algorithms, as in Rusins Freivalds's famous 1979 quadratic time certification for the matrix product. Our certificates occupy O(n(3+µ) (log ||A||)(1+µ) bits, from which the verfication algorithm randomly samples a quadratic amount. C2 - 2011/// C3 - Proceedings of the 36th international symposium on Symbolic and algebraic computation - ISSAC '11 DA - 2011/// DO - 10.1145/1993886.1993915 PB - ACM Press SN - 9781450306751 UR - http://dx.doi.org/10.1145/1993886.1993915 DB - Crossref ER - TY - CONF TI - Supersparse black box rational function interpolation AU - Kaltofen, Erich L. AU - Nehring, Michael T2 - the 36th international symposium AB - We present a method for interpolating a supersparse blackbox rational function with rational coefficients, for example, a ratio of binomials or trinomials with very high degree. We input a blackbox rational function, as well as an upper bound on the number of non-zero terms and an upper bound on the degree. The result is found by interpolating the rational function modulo a small prime p, and then applying an effective version of Dirichlet's Theorem on primes in an arithmetic progression progressively lift the result to larger primes. Eventually we reach a prime number that is larger than the inputted degree bound and we can recover the original function exactly. In a variant, the initial prime p is large, but the exponents of the terms are known modulo larger and larger factors of p-1. C2 - 2011/// C3 - Proceedings of the 36th international symposium on Symbolic and algebraic computation - ISSAC '11 DA - 2011/// DO - 10.1145/1993886.1993916 PB - ACM Press SN - 9781450306751 UR - http://dx.doi.org/10.1145/1993886.1993916 DB - Crossref ER - TY - CONF TI - Fast estimates of Hankel matrix condition numbers and numeric sparse interpolation AU - Kaltofen, Erich L. AU - Lee, Wen-shin AU - Yang, Zhengfeng T2 - the 2011 International Workshop AB - We investigate our early termination criterion for sparse polynomial interpolation when substantial noise is present in the values of the polynomial. Our criterion in the exact case uses Monte Carlo randomization which introduces a second source of error. We harness the Gohberg-Semencul formula for the inverse of a Hankel matrix to compute estimates for the structured condition numbers of all arising Hankel matrices in quadratic arithmetic time overall, and explain how false ill-conditionedness can arise from our randomizations. Finally, we demonstrate by experiments that our condition number estimates lead to a viable termination criterion for polynomials with about 20 non-zero terms and of degree about 100, even in the presence of noise of relative magnitude 10-5. C2 - 2011/// C3 - Proceedings of the 2011 International Workshop on Symbolic-Numeric Computation - SNC '11 DA - 2011/// DO - 10.1145/2331684.2331704 PB - ACM Press SN - 9781450305150 UR - http://dx.doi.org/10.1145/2331684.2331704 DB - Crossref ER - TY - ER - TY - CHAP TI - The “Seven Dwarfs” of Symbolic Computation AU - Kaltofen, Erich L. T2 - Texts & Monographs in Symbolic Computation AB - We present the Seven Dwarfs of Symbolic Computation, which are sequential and parallel algorithmic methods that today carry a great majority of all exact and hybrid symbolic compute cycles. We will elaborate on each dwarf and compare with Colella’s seven and the Berkeley team’s thirteen dwarfs of scientific computing. PY - 2011/10/12/ DO - 10.1007/978-3-7091-0794-2_5 SP - 95-104 OP - PB - Springer Vienna SN - 9783709107935 9783709107942 UR - http://dx.doi.org/10.1007/978-3-7091-0794-2_5 DB - Crossref ER - TY - JOUR TI - QTL Mapping for Days to Flowering under Drought Condition in Rice (Oryza sativa L.) Genome AU - Chakraborty, Supriyo AU - Zeng, Zhao Bang T2 - Notulae Botanicae Horti Agrobotanici Cluj-Napoca AB - QTL for days to flowering in rice under drought condition were mapped using a DH population derived from a cross between a deep-rooted upland adapted japonica genotype CT9993-5-10-1-M and a lowland adapted shallow-rooted moderately drought tolerant indica genotype IR62266-42-6-2. QTL mapping was performed following three different mapping models viz. simple (SIM), composite (CIM) and multiple mapping model (MIM) using WinQTL Cartographer version 2.5.006. SIM located 12 QTL for days to flowering spread over nine chromosomes whereas CIM and MIM each located 5 QTL with a threshold LOD score of 2.5. A comparison of the QTL detected by three different models identified five QTL that were common across at least two models for days to flowering. In MIM analysis, the detected QTL (qHD-1-b) between flanking markers (RG109 – ME1014) located on chromosome 1 recorded positive effect (1.4090) but the remaining four QTL had negative effect. The QTL (qHD-3-a) detected between flanking markers (RG104 – RG409) by both MIM and SIM in the present study was also reported earlier as linked with the marker RG104. The five common QTL detected by at least two models could be considered as stable QTL for days to flowering under drought and might be of practical use in marker assisted selection. DA - 2011/5/30/ PY - 2011/5/30/ DO - 10.15835/nbha3915610 VL - 39 IS - 1 SP - 58 J2 - Not Bot Hort Agrobot Cluj OP - SN - 1842-4309 0255-965X UR - http://dx.doi.org/10.15835/nbha3915610 DB - Crossref ER - TY - JOUR TI - Bartonella spp. bacteremia in high-risk immunocompetent patients AU - Maggi, Ricardo G. AU - Mascarelli, Patricia E. AU - Pultorak, Elizabeth L. AU - Hegarty, Barbara C. AU - Bradley, Julie M. AU - Mozayeni, B. Robert AU - Breitschwerdt, Edward B. T2 - Diagnostic Microbiology and Infectious Disease AB - Serum and blood samples from 192 patients, who reported animal exposure (100.0%) and recent animal bites or scratches (88.0%), were screened for antibodies by indirect immunofluorescence assays and for bacteremia using the BAPGM (Bartonella alpha Proteobacteria growth medium) platform. Predominant symptoms included fatigue (79.2%), sleeplessness (64.1%), joint pain (64.1%), and muscle pain (63.0%). Bartonella spp. seroreactivity or bacteremia was documented in 49.5% (n = 95) and 23.9% (n = 46) of the patients, respectively; however, indirect immunofluorescence antibodies were not detected in 30.4% (n = 14) of bacteremic patients. Regarding components of the BAPGM platform, Bartonella DNA was amplified from 7.5% of blood (n = 21), 8.7% of serum (n = 25), and 10.3% of enrichment culture samples (n = 29). Polymerase chain reaction (PCR) on only extracted blood would not have detected Bartonella infection in 34.7% (16/46) of bacteremic patients. Serology, in conjunction with blood, serum, and BAPGM enrichment culture PCR, facilitates the diagnosis of Bartonella spp. bacteremia in immunocompetent patients. DA - 2011/12// PY - 2011/12// DO - 10.1016/j.diagmicrobio.2011.09.001 VL - 71 IS - 4 SP - 430-437 J2 - Diagnostic Microbiology and Infectious Disease LA - en OP - SN - 0732-8893 UR - http://dx.doi.org/10.1016/j.diagmicrobio.2011.09.001 DB - Crossref KW - Bartonella KW - BAPGM KW - Whole blood culture KW - Human KW - Isolation KW - PCR detection KW - IFA ER - TY - JOUR TI - Total and merchantable stem volume equations for midrotation loblolly pine (Pinus taeda L.) AU - Sherrill, J. R. AU - Bullock, B. P. AU - Mullin, T. J. AU - McKeand, S. E. AU - Purnell, R. C. T2 - Southern Journal of Applied Forestry DA - 2011/// PY - 2011/// VL - 35 IS - 3 SP - 105-108 ER - TY - JOUR TI - Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata AU - Katz, Laura A. AU - DeBerardinis, Jennifer AU - Hall, Meaghan S. AU - Kovner, Alexandra M. AU - Dunthorn, Micah AU - Muse, Spencer V. T2 - JOURNAL OF MOLECULAR EVOLUTION AB - While molecular analyses have provided insight into the phylogeny of ciliates, the few studies assessing intraspecific variation have largely relied on just a single locus [e.g., nuclear small subunit rDNA (nSSU-rDNA) or mitochondrial cytochrome oxidase I]. In this study, we characterize the diversity of several nuclear protein-coding genes plus both nSSU-rDNA and mitochondrial small subunit rDNA (mtSSU-rDNA) of five isolates of the ciliate morphospecies Chilodonella uncinata. Although these isolates have nearly identical nSSU-rDNA sequences, they differ by up to 8.0% in mtSSU-rDNA. Comparative analyses of all loci, including β-tubulin paralogs, indicate a lack of recombination between strains, demonstrating that the morphospecies C. uncinata consists of multiple cryptic species. Further, there is considerable variation in substitution rates among loci as some protein-coding domains are nearly identical between isolates, while others differ by up to 13.2% at the amino acid level. Combining insights on macronuclear variation among isolates, the focus of this study, with published data from the micronucleus of two of these isolates, indicates that C. uncinata lineages are able to maintain both highly divergent and highly conserved genes within a rapidly evolving germline genome. DA - 2011/12// PY - 2011/12// DO - 10.1007/s00239-011-9468-x VL - 73 IS - 5-6 SP - 266-272 SN - 1432-1432 KW - Cryptic species KW - Molecular evolution KW - Genome architecture KW - Ciliate ER - TY - JOUR TI - Encoding isotopic watermarks in molecular electronic materials as an anti-counterfeiting strategy. Application to porphyrins for information storage AU - Lindsey, Jonathan S. AU - Thamyongkit, Patchanita AU - Taniguchi, Masahiko AU - Bocian, David F. T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - An approach for information storage employs tetrapyrrole macrocycles as charge-storage elements attached to a (semi)conductor in hybrid chips. Anti-counterfeiting measures must cohere with the tiny amounts of such electroactive material and strict constraints on composition in chips; accordingly, the incorporation of typical anti-counterfeiting taggants or microcarriers is precluded. The provenance of the tetrapyrroles can be established through the use of isotopic substitution integral to the macrocycle. The isotopic substitution can be achieved by rational site-specific incorporation or by combinatorial procedures. The formation of a mixture of such macrocycles with various isotopic composition (isotopically unmodified, isotopologues, isotopomers) provides the molecular equivalent of an indelible printed watermark. Resonance Raman spectroscopic examination can reveal the watermark, but not the underlying molecular and isotopic composition; imaging mass spectrometry can reveal the presence of isotopologues but cannot discriminate among isotopomers. Hence, deciphering the code that encrypts the watermark in an attempt at forgery is expected to be prohibitive. A brief overview is provided of strategies for incorporating isotopes in meso-substituted tetrapyrrole macrocycles. DA - 2011/// PY - 2011/// DO - 10.1142/s1088424611003458 VL - 15 IS - 7-8 SP - 505-516 SN - 1099-1409 KW - watermark KW - mass encoding KW - isotope KW - porphyrin KW - capacitor KW - chip KW - resonance Raman KW - mass spectrometry ER - TY - JOUR TI - Effects of propagule type on genetic parameters of wood density and growth in a loblolly pine progeny test at ages 10 and 11 years AU - Cumbie, W. Patrick AU - Isik, Fikret AU - Li, Bailian AU - Goldfarb, Barry T2 - TREE GENETICS & GENOMES DA - 2011/12// PY - 2011/12// DO - 10.1007/s11295-011-0402-6 VL - 7 IS - 6 SP - 1147-1158 SN - 1614-2942 KW - Pinus taeda KW - Wood density KW - Heritability KW - Clones KW - Vegetative propagation ER - TY - JOUR TI - A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken AU - Dorshorst, Ben AU - Molin, Anna-Maja AU - Rubin, Carl-Johan AU - Johansson, Anna M. AU - Stromstedt, Lina AU - Pham, Manh-Hung AU - Chen, Chih-Feng AU - Hallbook, Finn AU - Ashwell, Chris AU - Andersson, Leif T2 - PLOS GENETICS AB - Dermal hyperpigmentation or Fibromelanosis (FM) is one of the few examples of skin pigmentation phenotypes in the chicken, where most other pigmentation variants influence feather color and patterning. The Silkie chicken is the most widespread and well-studied breed displaying this phenotype. The presence of the dominant FM allele results in extensive pigmentation of the dermal layer of skin and the majority of internal connective tissue. Here we identify the causal mutation of FM as an inverted duplication and junction of two genomic regions separated by more than 400 kb in wild-type individuals. One of these duplicated regions contains endothelin 3 (EDN3), a gene with a known role in promoting melanoblast proliferation. We show that EDN3 expression is increased in the developing Silkie embryo during the time in which melanoblasts are migrating, and elevated levels of expression are maintained in the adult skin tissue. We have examined four different chicken breeds from both Asia and Europe displaying dermal hyperpigmentation and conclude that the same structural variant underlies this phenotype in all chicken breeds. This complex genomic rearrangement causing a specific monogenic trait in the chicken illustrates how novel mutations with major phenotypic effects have been reused during breed formation in domestic animals. DA - 2011/12// PY - 2011/12// DO - 10.1371/journal.pgen.1002412 VL - 7 IS - 12 SP - SN - 1553-7404 ER - TY - JOUR TI - Enteric Microbiome Metabolites Correlate with Response to Simvastatin Treatment AU - Kaddurah-Daouk, Rima AU - Baillie, Rebecca A. AU - Zhu, Hongjie AU - Zeng, Zhao-Bang AU - Wiest, Michelle M. AU - Nguyen, Uyen Thao AU - Wojnoonski, Katie AU - Watkins, Steven M. AU - Trupp, Miles AU - Krauss, Ronald M. T2 - PLOS ONE AB - Although statins are widely prescribed medications, there remains considerable variability in therapeutic response. Genetics can explain only part of this variability. Metabolomics is a global biochemical approach that provides powerful tools for mapping pathways implicated in disease and in response to treatment. Metabolomics captures net interactions between genome, microbiome and the environment. In this study, we used a targeted GC-MS metabolomics platform to measure a panel of metabolites within cholesterol synthesis, dietary sterol absorption, and bile acid formation to determine metabolite signatures that may predict variation in statin LDL-C lowering efficacy. Measurements were performed in two subsets of the total study population in the Cholesterol and Pharmacogenetics (CAP) study: Full Range of Response (FR), and Good and Poor Responders (GPR) were 100 individuals randomly selected from across the entire range of LDL-C responses in CAP. GPR were 48 individuals, 24 each from the top and bottom 10% of the LDL-C response distribution matched for body mass index, race, and gender. We identified three secondary, bacterial-derived bile acids that contribute to predicting the magnitude of statin-induced LDL-C lowering in good responders. Bile acids and statins share transporters in the liver and intestine; we observed that increased plasma concentration of simvastatin positively correlates with higher levels of several secondary bile acids. Genetic analysis of these subjects identified associations between levels of seven bile acids and a single nucleotide polymorphism (SNP), rs4149056, in the gene encoding the organic anion transporter SLCO1B1. These findings, along with recently published results that the gut microbiome plays an important role in cardiovascular disease, indicate that interactions between genome, gut microbiome and environmental influences should be considered in the study and management of cardiovascular disease. Metabolic profiles could provide valuable information about treatment outcomes and could contribute to a more personalized approach to therapy. DA - 2011/10/13/ PY - 2011/10/13/ DO - 10.1371/journal.pone.0025482 VL - 6 IS - 10 SP - SN - 1932-6203 ER - TY - JOUR TI - Tomato SlSnRK1 Protein Interacts with and Phosphorylates beta C1, a Pathogenesis Protein Encoded by a Geminivirus beta-Satellite AU - Shen, Qingtang AU - Liu, Zhou AU - Song, Fengming AU - Xie, Qi AU - Hanley-Bowdoin, Linda AU - Zhou, Xueping T2 - PLANT PHYSIOLOGY AB - The βC1 protein of tomato yellow leaf curl China β-satellite functions as a pathogenicity determinant. To better understand the molecular basis of βC1 in pathogenicity, a yeast two-hybrid screen of a tomato (Solanum lycopersicum) cDNA library was carried out using βC1 as bait. βC1 interacted with a tomato SUCROSE-NONFERMENTING1-related kinase designated as SlSnRK1. Their interaction was confirmed using a bimolecular fluorescence complementation assay in Nicotiana benthamiana cells. Plants overexpressing SnRK1 were delayed for symptom appearance and contained lower levels of viral and satellite DNA, while plants silenced for SnRK1 expression developed symptoms earlier and accumulated higher levels of viral DNA. In vitro kinase assays showed that βC1 is phosphorylated by SlSnRK1 mainly on serine at position 33 and threonine at position 78. Plants infected with βC1 mutants containing phosphorylation-mimic aspartate residues in place of serine-33 and/or threonine-78 displayed delayed and attenuated symptoms and accumulated lower levels of viral DNA, while plants infected with phosphorylation-negative alanine mutants contained higher levels of viral DNA. These results suggested that the SlSnRK1 protein attenuates geminivirus infection by interacting with and phosphorylating the βC1 protein. DA - 2011/11// PY - 2011/11// DO - 10.1104/pp.111.184648 VL - 157 IS - 3 SP - 1394-1406 SN - 0032-0889 ER - TY - JOUR TI - Re-evaluation of the life-cycle of the nematode-parasitic bacterium Pasteuria penetrans in root-knot nematodes, Meloidogyne spp. AU - Davies, Keith G. AU - Rowe, Janet AU - Manzanilla-Lopez, Rosa AU - Opperman, Charles H. T2 - NEMATOLOGY AB - Abstract Comparisons of the growth of Pasteuria penetrans in adult root-knot nematode females infected with P. penetrans dissected from the roots of tomato plants were undertaken using bright-field and scanning electron microscopy. Samples of infected females were nutritionally compromised by maintaining them in sterile saline at 30°C for different periods of time following their removal from the root system. Observations of these females maintained in saline revealed a series of growth stages of Pasteuria hitherto not documented, consisting of rhizoids, rod-like bacilli and granular masses. A new life-cycle for Pasteuria is described consisting of three phases: Phase I: attachment and germination; Phase II: rhizoid production and exponential growth; and Phase III: sporogenesis. These newly observed stages of the life cycle show a high degree of similarity to the developmental stages seen in other Bacillus spp. DA - 2011/// PY - 2011/// DO - 10.1163/138855410x552670 VL - 13 SP - 825-835 SN - 1388-5545 KW - bacteria KW - biological control KW - rod-shaped bacilli KW - scanning electron microscopy ER - TY - JOUR TI - Molecular Analysis of Mutant Alleles for Elevated Palmitate Concentration in Soybean AU - De Vries, Brian D. AU - Fehr, Walter R. AU - Welke, Grace A. AU - Dewey, Ralph E. T2 - CROP SCIENCE AB - ABSTRACT S oybean [ Glycine max (L.) Merr.] oil with increased palmitate concentration may be useful for some food and industrial applications. Chemical mutagenesis was used to develop mutant alleles for elevated palmitate concentration that were designated as fap2 (A21), fap4 (A24), fap5 (A27), fap6 (A25), and fap7 (A30) based on classical genetic analysis. The objective of our study was to determine whether the elevated palmitate phenotypes in any of these lines were associated with mutations in either of the two known 3‐ketoacyl‐ACP synthase II (KAS II) genes of soybean, GmKAS IIA and GmKAS IIB . Deoxyribonucleic acid sequence analysis revealed single nucleotide polymorphisms (SNPs) that differentiated mutant and wild‐type alleles in one of the GmKAS genes in lines A21, A25, A27, and A30 but not in A24. The identified SNPs resulted in nonconservative amino acid substitutions that were predicted to impair enzyme function. The fap2 (A21) allele was associated with two consecutive SNPs within the GmKAS IIA gene, confirming its allelic relationship to fap2 (C1727) that was known to have a mutant SNP within the same gene. The allele designated fap5 (A27) also had a SNP within the GmKAS IIA gene, indicating that its designation should be changed to fap2 (A27). The fap6 (A25) and fap7 (A30) alleles each contained a single SNP at different locations within the GmKAS IIB gene. We propose that the designation of the mutant allele in A25 remain fap6 (A25) and that the allele in A30 be changed from fap7 (A30) to fap6 (A30). DA - 2011/11// PY - 2011/11// DO - 10.2135/cropsci2011.03.0156 VL - 51 IS - 6 SP - 2554-2560 SN - 1435-0653 ER - TY - JOUR TI - Membrane protein complexes catalyze both 4-and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis AU - Chen, Hsi-Chuan AU - Li, Quanzi AU - Shuford, Christopher M. AU - Liu, Jie AU - Muddiman, David C. AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - The hydroxylation of 4- and 3-ring carbons of cinnamic acid derivatives during monolignol biosynthesis are key steps that determine the structure and properties of lignin. Individual enzymes have been thought to catalyze these reactions. In stem differentiating xylem (SDX) of Populus trichocarpa, two cinnamic acid 4-hydroxylases (PtrC4H1 and PtrC4H2) and a p-coumaroyl ester 3-hydroxylase (PtrC3H3) are the enzymes involved in these reactions. Here we present evidence that these hydroxylases interact, forming heterodimeric (PtrC4H1/C4H2, PtrC4H1/C3H3, and PtrC4H2/C3H3) and heterotrimeric (PtrC4H1/C4H2/C3H3) membrane protein complexes. Enzyme kinetics using yeast recombinant proteins demonstrated that the enzymatic efficiency (V(max)/k(m)) for any of the complexes is 70-6,500 times greater than that of the individual proteins. The highest increase in efficiency was found for the PtrC4H1/C4H2/C3H3-mediated p-coumaroyl ester 3-hydroxylation. Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for these multiprotein complexes. The activities of the recombinant and SDX plant proteins demonstrate two protein-complex-mediated 3-hydroxylation paths in monolignol biosynthesis in P. trichocarpa SDX; one converts p-coumaric acid to caffeic acid and the other converts p-coumaroyl shikimic acid to caffeoyl shikimic acid. Cinnamic acid 4-hydroxylation is also mediated by the same protein complexes. These results provide direct evidence for functional involvement of membrane protein complexes in monolignol biosynthesis. DA - 2011/12/27/ PY - 2011/12/27/ DO - 10.1073/pnas.1116416109 VL - 108 IS - 52 SP - 21253-21258 SN - 0027-8424 ER - TY - JOUR TI - Interaction between Geminivirus Replication Protein and the SUMO-Conjugating Enzyme Is Required for Viral Infection AU - Sanchez-Duran, Miguel A. AU - Dallas, Mary B. AU - Ascencio-Ibanez, Jose T. AU - Reyes, Maria Ines AU - Arroyo-Mateos, Manuel AU - Ruiz-Albert, Javier AU - Hanley-Bowdoin, Linda AU - Bejarano, Eduardo R. T2 - JOURNAL OF VIROLOGY AB - Geminiviruses are small DNA viruses that replicate in nuclei of infected plant cells by using plant DNA polymerases. These viruses encode a protein designated AL1, Rep, or AC1 that is essential for viral replication. AL1 is an oligomeric protein that binds to double-stranded DNA, catalyzes the cleavage and ligation of single-stranded DNA, and induces the accumulation of host replication machinery. It also interacts with several host proteins, including the cell cycle regulator retinoblastoma-related protein (RBR), the DNA replication protein PCNA (proliferating cellular nuclear antigen), and the sumoylation enzyme that conjugates SUMO to target proteins (SUMO-conjugating enzyme [SCE1]). The SCE1-binding motif was mapped by deletion to a region encompassing AL1 amino acids 85 to 114. Alanine mutagenesis of lysine residues in the binding region either reduced or eliminated the interaction with SCE1, but no defects were observed for other AL1 functions, such as oligomerization, DNA binding, DNA cleavage, and interaction with AL3 or RBR. The lysine mutations reduced or abolished virus infectivity in plants and viral DNA accumulation in transient-replication assays, suggesting that the AL1-SCE1 interaction is required for viral DNA replication. Ectopic AL1 expression did not result in broad changes in the sumoylation pattern of plant cells, but specific changes were detected, indicating that AL1 modifies the sumoylation state of selected host proteins. These results established the importance of AL1-SCE1 interactions during geminivirus infection of plants and suggested that AL1 alters the sumoylation of selected host factors to create an environment suitable for viral infection. DA - 2011/10// PY - 2011/10// DO - 10.1128/jvi.02566-10 VL - 85 IS - 19 SP - 9789-9800 SN - 1098-5514 ER - TY - JOUR TI - DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer AU - Robideau, G. P. AU - Cock, A. W. A. M. AU - Coffey, M. D. AU - Voglmayr, H. AU - Brouwer, H. AU - Bala, K. AU - Chitty, D. W. AU - Desaulniers, N. AU - Eggertson, Q. A. AU - Gachon, C. M. M. AU - Hu, C. H. AU - Kupper, F. C. AU - Rintoul, T. L. AU - Sarhan, E. AU - Verstappen, E. C. P. AU - Zhang, Y. H. T2 - Molecular Ecology Resources DA - 2011/// PY - 2011/// VL - 11 IS - 6 SP - 1002-1011 ER - TY - JOUR TI - Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes AU - Becker, Shannon E. Duke AU - Thomas, Rachael AU - Trifonov, Vladimir A. AU - Wayne, Robert K. AU - Graphodatsky, Alexander S. AU - Breen, Matthew T2 - CHROMOSOME RESEARCH DA - 2011/8// PY - 2011/8// DO - 10.1007/s10577-011-9233-4 VL - 19 IS - 6 SP - 685-708 SN - 1573-6849 KW - B chromosomes KW - fragile breakage model KW - breakpoint reuse theory KW - fluorescence in situ hybridization KW - phylogenetic KW - Canidae ER - TY - JOUR TI - Virtual Libraries of Tetrapyrrole Macrocycles. Combinatorics, Isomers, Product Distributions, and Data Mining AU - Taniguchi, Masahiko AU - Du, Hai AU - Lindsey, Jonathan S. T2 - JOURNAL OF CHEMICAL INFORMATION AND MODELING AB - A software program (PorphyrinViLiGe) has been developed to enumerate the type and relative amounts of substituted tetrapyrrole macrocycles in a virtual library formed by one of four different classes of reactions. The classes include (1) 4-fold reaction of n disubstituted heterocycles (e.g., pyrroles or diiminoisoindolines) to form β-substituted porphyrins, β-substituted tetraazaporphyrins, or α- or β-substituted phthalocyanines; (2) combination of m aminoketones and n diones to form m × n pyrroles, which upon 4-fold reaction give β-substituted porphyrins; (3) derivatization of an 8-point tetrapyrrole scaffold with n reagents, and (4) 4-fold reaction of n aldehydes and pyrrole to form meso-substituted porphyrins. The program accommodates variable ratios of reactants, reversible or irreversible reaction (reaction classes 1 and 2), and degenerate modes of formation. Pólya's theorem (for enumeration of cyclic entities) has also been implemented and provides validation for reaction classes 3 and 4. The output includes the number and identity of distinct reaction-accessible substituent combinations, the number and identity of isomers thereof, and the theoretical mass spectrum. Provisions for data mining enable assessment of the number of products having a chosen pattern of substituents. Examples include derivatization of an octa-substituted phthalocyanine with eight reagents to afford a library of 2,099,728 members (yet only 6435 distinct substituent combinations) and reversible reaction of six distinct disubstituted pyrroles to afford 2649 members (yet only 126 distinct substituent combinations). In general, libraries of substituted tetrapyrrole macrocycles occupy a synthetically accessible region of chemical space that is rich in isomers (>99% or 95% for the two examples, respectively). DA - 2011/9// PY - 2011/9// DO - 10.1021/ci200240e VL - 51 IS - 9 SP - 2233-2247 SN - 1549-960X ER - TY - JOUR TI - Typical and Atypical Manifestations of Anaplasma phagocytophilum Infection in Dogs AU - Eberts, Matthew D. AU - Diniz, Pedro Paulo Vissotto de Paiva AU - Beall, Melissa J. AU - Stillman, Brett A. AU - Chandrashekar, Ramaswamy AU - Breitschwerdt, Edward B. T2 - JOURNAL OF THE AMERICAN ANIMAL HOSPITAL ASSOCIATION AB - Eighteen clinically ill dogs, naturally infected with Anaplasma phagocytophilum, were examined at a veterinary practice in Baxter, Minnesota. A clinical examination, complete blood cell count, enzyme- linked immunosorbent assay (ELISA) for A phagocytophilum, Borrelia burgdorferi, and Ehrlichia canis antibodies and Dirofilaria immitis antigen, and a polymerase chain reaction test for A phagocytophilum DNA were obtained for all dogs. Physical examination findings included fever, arthropathy, lymphadenopathy, epistaxis, acute gastritis, cervical hyperpathia, and central nervous system dysfunction. Complete blood cell count abnormalities included thrombocytopenia, morulae in neutrophils, anemia, leukopenia, eosinopenia, lymphopenia, and monocytosis. Seroreactivity to A phagocytophilum was found in 61%, B burgdorferi antibodies in 17%, and D immitis antigen in 5% of the dogs. Fever, arthropathy, neurologic dysfunction, and epistaxis are clinical syndromes that can be associated with A phagocytophilum infection. Treatment with doxycycline resulted in rapid resolution of clinical signs in all dogs. DA - 2011/// PY - 2011/// DO - 10.5326/jaaha-ms-5578 VL - 47 IS - 6 SP - E86-E94 SN - 1547-3317 ER - TY - JOUR TI - Two novel techniques to screen Abies seedlings for resistance to the balsam woolly adelgid, Adelges piceae AU - Newton, L. AU - Frampton, J. AU - Monahan, J. AU - Goldfarb, B. AU - Hain, F. T2 - Journal of Insect Science (Tucson, AZ) DA - 2011/// PY - 2011/// VL - 11 ER - TY - JOUR TI - The Potato Late Blight pathogen in Ireland, 1846: reconnecting Irish specimens with the Moore-Berkeley correspondence AU - Nelson, E. Charles AU - Ristaino, Jean Beagle T2 - ARCHIVES OF NATURAL HISTORY DA - 2011/10// PY - 2011/10// DO - 10.3366/anh.2011.0042 VL - 38 IS - 2 SP - 356-359 SN - 1755-6260 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84864343649&partnerID=MN8TOARS ER - TY - JOUR TI - Mastermind mutations generate a unique constellation of midline cells within the drosophila CNS AU - Zhang, Y. AU - Wheatley, R. AU - Fulkerson, E. AU - Tapp, A. AU - Estes, P. A. T2 - PLoS One DA - 2011/// PY - 2011/// VL - 6 IS - 10 ER - TY - JOUR TI - In Vitro Properties of a Listeria monocytogenes Bacteriophage-Resistant Mutant Predict Its Efficacy as a Live Oral Vaccine Strain AU - Spears, Patricia A. AU - Suyemoto, M. Mitsu AU - Hamrick, Terri S. AU - Wolf, Rebecca L. AU - Havell, Edward A. AU - Orndorff, Paul E. T2 - INFECTION AND IMMUNITY AB - ABSTRACT A Listeria monocytogenes glcV mutation precludes the binding of certain listerial phages and produces a profound attenuation characterized by the absence of detectable mutants in the livers and spleens of orally inoculated mice. In vitro , we found that the mutant formed plaques on mouse enterocyte monolayers as efficiently as the parent but the plaques formed were smaller. Intracellular growth rate determinations and examination of infected enterocytes by light and fluorescence microscopy established that the mutant was impaired not in intracellular growth rate but in cell-to-cell spreading. Because this property is shared by other immunogenic mutants (e.g., actA mutants), our glcV mutant was tested for vaccine efficacy. Oral immunization with the mutant and subsequent oral challenge (22 days postvaccination) with the parent revealed a ca. 10,000-fold increase in protection afforded by the mutant compared to sham-vaccinated controls. The glcV mutant did not stimulate innate immunity under the dose and route employed for vaccination, and an infectivity index time course experiment revealed pronounced mutant persistence in Peyer's patches. The immunogenicity of the glcV mutant compared to an isogenic actA mutant reference strain was next tested in an experiment with a challenge given 52 days postvaccination. Both mutant strains showed scant vital organ infectivity and high levels of protection similar to those seen using the glcV mutant in the 22-day postvaccination challenge. Our results indicate that oral administration of a profoundly attenuated listerial mutant can safely elicit solid protective immunity. DA - 2011/12// PY - 2011/12// DO - 10.1128/iai.05700-11 VL - 79 IS - 12 SP - 5001-5009 SN - 1098-5522 ER - TY - JOUR TI - Host immune responses that promote initial HIV spread AU - Wendelsdorf, K. AU - Dean, G. AU - Hu, Shuhua AU - Nordone, S. AU - Banks, H. T. T2 - JOURNAL OF THEORETICAL BIOLOGY AB - The host inflammatory response to HIV invasion is a necessary component of the innate antiviral activity that vaccines and early interventions seek to exploit/enhance. However, the response is dependent on CD4+ T-helper cell 1 (Th1) recruitment and activation. It is this very recruitment of HIV-susceptible target cells that is associated with the initial viral proliferation. Hence, global enhancement of the inflammatory response by T-cells and dendritic cells will likely feed viral propagation. Mucosal entry sites contain inherent pathways, in the form of natural regulatory T-cells (nTreg), that globally dampen the inflammatory response. We created a model of this inflammatory response to virus as well as inherent nTreg-mediated regulation of Th1 recruitment and activation. With simulations using this model we sought to address the net effect of nTreg activation and its specific functions as well as identify mechanisms of the natural inflammatory response that are best targeted to inhibit viral spread without compromising initial antiviral activity. Simulation results provide multiple insights that are relevant to developing intervention strategies that seek to exploit natural immune processes: (i) induction of the regulatory response through nTreg activation expedites viral proliferation due to viral production by nTreg itself and not to reduced Natural Killer (NK) cell activity; (ii) at the same time, induction of the inflammation response through either DC activation or Th1 activation expedites viral proliferation; (iii) within the inflammatory pathway, the NK response is an effective controller of viral proliferation while DC-mediated stimulation of T-cells is a significant driver of viral proliferation; and (iv) nTreg-mediated DC deactivation plays a significant role in slowing viral proliferation by inhibiting T-cell stimulation, making this function an aide to the antiviral immune response. DA - 2011/11/21/ PY - 2011/11/21/ DO - 10.1016/j.jtbi.2011.08.012 VL - 289 SP - 17-35 SN - 1095-8541 KW - HIV KW - Innate inflammatory response pathway KW - Regulatory response pathway KW - Mathematical model ER - TY - JOUR TI - Ecological Diversity ofBartonellaSpecies Infection Among Dogs and Their Owner in Virginia AU - Cherry, Natalie A. AU - Maggi, Ricardo G. AU - Rossmeisl, John H. AU - Hegarty, Barbara C. AU - Breitschwerdt, Edward B. T2 - Vector-Borne and Zoonotic Diseases AB - Bartonella species comprise a genus of gram-negative, fastidious, intracellular bacteria that have been implicated in association with an increasing spectrum of disease manifestations in dogs and human patients. In this study, chronic canine and human disease, for which causation was not diagnostically defined, were reported by the breeder of a kennel of Doberman pinschers. In addition to other diagnostic tests, serology, polymerase chain reaction, and enrichment blood culture were used to assess the prevalence of Bartonella sp. infection in the dogs and their owner. From five dogs, Bartonella vinsonii subsp. berkhoffii genotype I, multiple Bartonella henselae strains, and a species most similar to Candidatus B. volans, a rodent-associated Bartonella sp., were amplified and sequenced from biopsy tissues, cerebrospinal fluid, or blood enrichment cultures. The owner was bacteremic with B. vinsonii subsp. berkhoffii genotype I, the same subsp. and genotype detected in one of her dogs. These results further emphasize the ecological complexity of Bartonella sp. transmission in nature. DA - 2011/11// PY - 2011/11// DO - 10.1089/vbz.2010.0201 VL - 11 IS - 11 SP - 1425-1432 J2 - Vector-Borne and Zoonotic Diseases LA - en OP - SN - 1530-3667 1557-7759 UR - http://dx.doi.org/10.1089/vbz.2010.0201 DB - Crossref KW - Bacteria KW - Disease KW - Ecology KW - Vector ER - TY - JOUR TI - De novo synthesis and properties of analogues of the self-assembling chlorosomal bacteriochlorophylls AU - Mass, Olga AU - Pandithavidana, Dinesh R. AU - Ptaszek, Marcin AU - Santiago, Koraliz AU - Springer, Joseph W. AU - Jiao, Jieying AU - Tang, Qun AU - Kirmaier, Christine AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - Natural photosynthetic pigments bacteriochlorophyllsc, d and e in green bacteria undergo self-assembly to create an organized antenna system known as the chlorosome, which collects photons and funnels the resulting excitation energy toward the reaction centers. Mimicry of chlorosome function is a central problem in supramolecular chemistry and artificial photosynthesis, and may have relevance for the design of photosynthesis-inspired solar cells. The main challenge in preparing artificial chlorosomes remains the synthesis of the appropriate pigment (chlorin) equipped with a set of functional groups suitable to direct the assembly and assure efficient energy transfer. Prior approaches have entailed derivatization of porphyrins or semisynthesis beginning with chlorophylls. This paper reports a third approach, the de novo synthesis of macrocycles that contain the same hydrocarbon skeleton as chlorosomal bacteriochlorophylls. The synthesis here of Zn(II) 3-(1-hydroxyethyl)-10-aryl-131-oxophorbines (the aryl group consists of phenyl, mesityl, or pentafluorophenyl) entails selective bromination of a 3,13-diacetyl-10-arylchlorin, palladium-catalyzed 131-oxophorbine formation, and selective reduction of the 3-acetyl group using BH3·tBuNH2. Each macrocycle contains a geminal dimethyl group in the pyrroline ring to provide stability toward adventitious dehydrogenation. A Zn(II) 7-(1-hydroxyethyl)-10-phenyl-17-oxochlorin also has been prepared. Altogether, 30 new hydroporphyrins were synthesized. The UV-Vis absorption spectra of the new chlorosomal bacteriochlorophyll mimics reveal a bathochromic shift of ∼1800 cm−1 of the Qy band in nonpolar solvent, indicating extensive assembly in solution. The Zn(II) 3-(1-hydroxyethyl)-10-aryl-131-oxophorbines differ in the propensity to form assemblies based on the 10-substituent in the following order: mesityl full-sib > clone). To examine genetic effects on stand uniformity and productivity, we grew ten different genotypes (three open-pollinated families, three full-sib families, three clones, and one seed orchard mix variety) in a plantation setting for 4 years, at two different planting densities (∼539 and 1077 trees ha−1), and used allometric relationships to estimate standing dry mass and annual dry mass production. In the low planting density treatment, age 3 total standing dry mass of the most productive genotype (5824 kg ha−1) was 82% higher than that of the least productive genotype (3207 kg ha−1). In the high planting density treatment, age 3 total standing dry mass of the most productive genotype (11,393 kg ha−1) was 110% higher than that of the least productive genotype (5427 kg ha−1). Genetic differences in annual dry mass production were of a similar magnitude with peak rates during the third year as high as 4221 and 8198 kg ha−1 yr−1 in the low and high planting density treatments, respectively. More genetically homogeneous genotypes did not show greater stand-level uniformity under operational management conditions. Over time, genotypes showed no consistent differences in the coefficient of variation (CV) for ground-level diameter; however, two full-sib and two half-sib families showed significantly lower CV’s for total tree height than all three clones. Moreover, genotypes with lower CV’s for height growth displayed greater stand-level dry mass production which supports the premise that greater stand uniformity will lead to enhanced productivity. Since uniformity and stand-level productivity of loblolly pine clones will be principally governed by environmental heterogeneity, our results highlight the need for silvicultural prescriptions that maximize site uniformity. In addition, our results demonstrate how the deployment of highly productive loblolly pine genotypes may provide a means of enhancing southern pine ecosystem sustainability by sequestering C in both harvestable aboveground biomass and woody belowground biomass. DA - 2011/8/15/ PY - 2011/8/15/ DO - 10.1016/j.foreco.2011.04.029 VL - 262 IS - 4 SP - 609-619 SN - 1872-7042 KW - Pinus taeda L. clone KW - Genetic variation KW - Dry mass production KW - Stand uniformity ER - TY - JOUR TI - Evolution of clinical, haematological and biochemical findings in young dogs naturally infected by vector-borne pathogens AU - de Caprariis, Donato AU - Dantas-Torres, Filipe AU - Capelli, Gioia AU - Mencke, Norbert AU - Stanneck, Dorothee AU - Breitschwerdt, Edward B. AU - Otranto, Domenico T2 - Veterinary Microbiology AB - Longitudinal studies evaluating the evolution of clinical, haematological, biochemical findings in young dogs exposed for the first time to multiple vector-borne pathogens have not been reported. With the objective of assessing the evolution of clinical, haematological and biochemical findings, these parameters were serially monitored in naturally infected dogs throughout a 1-year follow-up period. Young dogs, infected by vector-borne pathogens based on cytology or polymerase chain reaction, were examined clinically and blood samples were obtained at seven different follow-up time points. Dogs were randomized to group A (17 dogs treated with a spot-on formulation of imidacloprid 10% and permethrin 50%) or to group B (17 dogs untreated). In addition, 10 4-month-old beagles were enrolled in each group and used as sentinel dogs. At baseline, Anaplasma platys was the most frequently detected pathogen, followed by Babesia vogeli, Bartonella spp., Ehrlichia canis and Hepatozoon canis. Co-infections with A. platys and B. vogeli, followed by E. canis and B. vogeli, A. platys and H. canis and A. platys and Bartonella spp. were also diagnosed. In dogs from group B, abnormal clinical signs were recorded at different time points throughout the study. No abnormal clinical signs were recorded in group A dogs. Thrombocytopenia was the most frequent haematological alteration recorded in A. platys-infected dogs, B. vogeli-infected dogs and in dogs co-infected with A. platys and B. vogeli or A. platys and Bartonella spp. Lymphocytosis was frequently detected among dogs infected with B. vogeli or co-infected with A. platys and B. vogeli. Beagles were often infected with a single pathogen rather than with multiple canine vector-borne pathogens. There was a significant association (p < 0.01) between tick infestation and A. platys or B. vogeli, as single infections, and A. platys and B. vogeli or A. platys and Bartonella spp. co-infections. This study emphasizes the clinical difficulties associated with assigning a specific clinical sign or haematological abnormality to a particular canine vector-borne disease. DA - 2011/4// PY - 2011/4// DO - 10.1016/j.vetmic.2010.10.006 VL - 149 IS - 1-2 SP - 206-212 J2 - Veterinary Microbiology LA - en OP - SN - 0378-1135 UR - http://dx.doi.org/10.1016/j.vetmic.2010.10.006 DB - Crossref KW - Vector-borne diseases KW - Clinical signs KW - Haematological alterations KW - Diagnosis ER - TY - JOUR TI - Antibacterial efficacy of silver nanoparticles of different sizes, surface conditions and synthesis methods AU - Samberg, Meghan E. AU - Orndorff, Paul E. AU - Monteiro-Riviere, Nancy A. T2 - NANOTOXICOLOGY AB - Silver nanoparticles (Ag-nps) are used as a natural biocide to prevent undesired bacterial growth in clothing and cosmetics. The objective of this study was to assess the antibacterial efficacy of Ag-nps of different sizes, surface conditions, and synthesis methods against Escherichia coli, Ag-resistant E. coli, Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), and Salmonella sp. Ag-nps samples were synthesized by: Base reduction with unmodified surfaces and used as synthesized ('unwashed'; 20, 50 and 80 nm) or after 20 phosphate buffer washes ('washed'; 20, 50 and 80 nm), or synthesized by laser ablation with carbon-stabilized surfaces ('carbon-coated'; 25 and 35 nm). Unwashed Ag-nps were toxic to all bacterial strains at concentrations between 3.0-8.0 μg/ml. The washed Ag-nps and carbon-coated Ag-nps were toxic to all bacterial strains except Ag-resistant E. coli at concentrations between 64.0-1024.0 μg/ml. Ag-resistant E. coli died only when treated with unwashed Ag-nps or its supernatant, both of which contained formaldehyde. DA - 2011/6// PY - 2011/6// DO - 10.3109/17435390.2010.525669 VL - 5 IS - 2 SP - 244-253 SN - 1743-5404 KW - Silver KW - nanoparticles KW - nanotechnology KW - nanotoxicity KW - microbiology ER - TY - JOUR TI - "Candidatus Neoehrlichia mikurensis" Infection in a Dog from Germany AU - Diniz, P. P. V. P. AU - Schulz, B. S. AU - Hartmann, K. AU - Breitschwerdt, E. B. T2 - Journal of Clinical Microbiology AB - "Candidatus Neoehrlichia mikurensis" is a new intracellular pathogen associated with human infection and death. "Candidatus Neoehrlichia mikurensis" infection in a chronically neutropenic dog from Germany was confirmed by DNA sequencing. The same organism was previously described from ticks and two sick human beings from Germany. DA - 2011/3/2/ PY - 2011/3/2/ DO - 10.1128/jcm.02327-10 VL - 49 IS - 5 SP - 2059-2062 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/JCM.02327-10 DB - Crossref ER - TY - JOUR TI - Structural mutants of dengue virus 2 transmembrane domains exhibit host-range phenotype AU - Smith, Katherine M. AU - Nanda, Kavita AU - Spears, Carla J. AU - Ribeiro, Mariana AU - Vancini, Ricardo AU - Piper, Amanda AU - Thomas, Gwynneth S. AU - Thomas, Malcolm E. AU - Brown, Dennis T. AU - Hernandez, Raquel T2 - VIROLOGY JOURNAL AB - There are over 700 known arboviruses and at least 80 immunologically distinct types that cause disease in humans. Arboviruses are transmitted among vertebrates by biting insects, chiefly mosquitoes and ticks. These viruses are widely distributed throughout the world, depending on the presence of appropriate hosts (birds, horses, domestic animals, humans) and vectors. Mosquito-borne arboviruses present some of the most important examples of emerging and resurgent diseases of global significance. A strategy has been developed by which host-range mutants of Dengue virus can be constructed by generating deletions in the transmembrane domain (TMD) of the E glycoprotein. The host-range mutants produced and selected favored growth in the insect hosts. Mouse trials were conducted to determine if these mutants could initiate an immune response in an in vivo system. The DV2 E protein TMD defined as amino acids 452SWTMKILIGVIITWIG467 was found to contain specific residues which were required for the production of this host-range phenotype. Deletion mutants were found to be stable in vitro for 4 sequential passages in both host cell lines. The host-range mutants elicited neutralizing antibody above that seen for wild-type virus in mice and warrant further testing in primates as potential vaccine candidates. Novel host-range mutants of DV2 were created that have preferential growth in insect cells and impaired infectivity in mammalian cells. This method for creating live, attenuated viral mutants that generate safe and effective immunity may be applied to many other insect-borne viral diseases for which no current effective therapies exist. DA - 2011/6/9/ PY - 2011/6/9/ DO - 10.1186/1743-422x-8-289 VL - 8 SP - SN - 1743-422X ER - TY - JOUR TI - Rickettsia rickettsii transmission by a lone star tick, North Carolina AU - Breitschwerdt, E. B. AU - Hegarty, B. C. AU - Maggi, R. G. AU - Lantos, P. M. AU - Aslett, D. M. AU - Bradley, J. M. T2 - Emerging Infectious Diseases DA - 2011/// PY - 2011/// VL - 17 IS - 5 SP - 873-875 ER - TY - JOUR TI - RNAi Effector Diversity in Nematodes AU - Dalzell, Johnathan J. AU - McVeigh, Paul AU - Warnock, Neil D. AU - Mitreva, Makedonka AU - Bird, David McK AU - Abad, Pierre AU - Fleming, Colin C. AU - Day, Tim A. AU - Mousley, Angela AU - Marks, Nikki J. AU - Maule, Aaron G. T2 - PLOS NEGLECTED TROPICAL DISEASES AB - While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes. DA - 2011/6// PY - 2011/6// DO - 10.1371/journal.pntd.0001176 VL - 5 IS - 6 SP - SN - 1935-2735 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-79959846596&partnerID=MN8TOARS ER - TY - JOUR TI - PTEN Positively Regulates UVB-Induced DNA Damage Repair AU - Ming, Mei AU - Feng, Li AU - Shea, Christopher R. AU - Soltani, Keyoumars AU - Zhao, Baozhong AU - Han, Weinong AU - Smart, Robert C. AU - Trempus, Carol S. AU - He, Yu-Ying T2 - CANCER RESEARCH AB - Nonmelanoma skin cancer is the most common cancer in the United States, where DNA-damaging ultraviolet B (UVB) radiation from the sun remains the major environmental risk factor. However, the critical genetic targets of UVB radiation are undefined. Here we show that attenuating PTEN in epidermal keratinocytes is a predisposing factor for UVB-induced skin carcinogenesis in mice. In skin papilloma and squamous cell carcinoma (SCC), levels of PTEN were reduced compared with skin lacking these lesions. Likewise, there was a reduction in PTEN levels in human premalignant actinic keratosis and malignant SCCs, supporting a key role for PTEN in human skin cancer formation and progression. PTEN downregulation impaired the capacity of global genomic nucleotide excision repair (GG-NER), a critical mechanism for removing UVB-induced mutagenic DNA lesions. In contrast to the response to ionizing radiation, PTEN downregulation prolonged UVB-induced growth arrest and increased the activation of the Chk1 DNA damage pathway in an AKT-independent manner, likely due to reduced DNA repair. PTEN loss also suppressed expression of the key GG-NER protein xeroderma pigmentosum C (XPC) through the AKT/p38 signaling axis. Reconstitution of XPC levels in PTEN-inhibited cells restored GG-NER capacity. Taken together, our findings define PTEN as an essential genomic gatekeeper in the skin through its ability to positively regulate XPC-dependent GG-NER following DNA damage. DA - 2011/8/1/ PY - 2011/8/1/ DO - 10.1158/0008-5472.can-10-4614 VL - 71 IS - 15 SP - 5287-5295 SN - 0008-5472 ER - TY - JOUR TI - Molecular Characterization of the Mutant fap3(A22) Allele for Reduced Palmitate Concentration in Soybean AU - De Vries, Brian D. AU - Fehr, Walter R. AU - Welke, Grace A. AU - Dewey, Ralph E. T2 - CROP SCIENCE AB - ABSTRACT Reduction of the palmitate concentration in soybean [ Glycine max (L.) Merr.] oil is desirable for reducing the amount of saturated fat in the human diet. Chemical mutagenesis was used to develop the line A22 with the mutant allele designated fap3 (A22) that reduces palmitate concentration in the seed oil. The objective of our study was to determine the molecular basis of the fap3 (A22) mutation and develop a corresponding molecular marker to assist in future efforts for developing soybean cultivars with low saturated fat. DNA sequence analysis of the GmFATB1a gene of soybean revealed a single nucleotide polymorphism (SNP) resulting in a nonconservative amino acid substitution that was likely to be detrimental to the function of the 16:0–acyl carrier protein (ACP) thioesterase (TE) enzyme. An association analysis was conducted using F 2 –derived lines from a cross between the cultivar Archer ( Fap3Fap3 ) and A22 ( fap3fap3 ) that had been analyzed for their palmitate concentration by gas chromatography. Molecular genotyping of these lines established a perfect correlation between lines phenotypically classified as homozygous for the Fap3 allele or homozygous for the fap3 (A22) allele based on their palmitate concentration. The polymorphism in the GmFATB1a gene was used to develop a functional, codominant marker that could be used to distinguish the Fap3 and fap3 (A22) alleles in segregating populations. This marker will be useful for breeders who are developing low‐saturate cultivars with the fap3 (A22) allele. DA - 2011/7// PY - 2011/7// DO - 10.2135/cropsci2010.10.0619 VL - 51 IS - 4 SP - 1611-1616 SN - 0011-183X ER - TY - JOUR TI - Molecular Analysis of GmFAD3A in Two Soybean Populations Segregating for the fan, fap1, and fap(nc) Loci AU - Cardinal, Andrea J. AU - Burton, Joseph W. AU - Camacho-Roger, Ana Maria AU - Whetten, Rebecca AU - Chappell, Andrew S. AU - Bilyeu, Kristin D. AU - Auclair, Jerome AU - Dewey, Ralph E. T2 - CROP SCIENCE AB - Soybeans [ Glycine max (L.) Merr.] have undesirable levels of polyunsaturated fatty acids in their oil that result in oxidative instability and poor flavor. The process of hydrogenation improves the stability but creates undesirable trans fats. Lines carrying fan genes have decreased linolenic acid (18:3) content. Changes in transcription or activity of the desaturase encoded by the GmFAD3 gene cause a reduction in 18:3 content in certain lines. The objectives of this study were to determine the molecular basis of the fan allele in PI 123440, develop molecular markers to assay for the GmFAD3 gene in lines carrying fan (PI 123440), and estimate the variation in the 18:3 explained by the GmFAD3A locus. Sequence analysis of the GmFAD3A from ‘Soyola’, the fan (PI 123440) allele, and ‘Dare’ showed no sequence polymorphisms that would alter the amino acid sequence of the enzyme. RNA blot analysis of a low‐18:3 line carrying a fan (PI 123440) allele, a line with normal 18:3 content, and three of their progenies showed a decrease in steady‐state FAD3A RNA levels in low‐18:3 lines. A marker for GmFAD3A was tested in two populations segregating for fan (PI 123440). Lines homozygous the GmFAD3A allele inherited from PI 123440 had a significant reduction in 18:3 when compared to lines homozygous for the GmFAD3A allele from the normal 18:3 parent. The differences between the two groups explained more than 77.5% of the genetic variation in 18:3 seed‐oil content in the populations. In summary, a reduction in the steady‐state mRNA levels of the GmFAD3A leads to a reduction in 18:3 synthesis within the developing seed in plants containing the fan (PI 123440) allele. DA - 2011/9// PY - 2011/9// DO - 10.2135/cropsci2010.08.0500 VL - 51 IS - 5 SP - 2104-2112 SN - 1435-0653 ER - TY - JOUR TI - Genetic effects on transpiration, canopy conductance, stomatal sensitivity to vapour pressure deficit, and cavitation resistance in loblolly pine AU - Aspinwall, Michael J. AU - King, John S. AU - Domec, Jean-Christophe AU - McKeand, Steven E. AU - Isik, Fikret T2 - ECOHYDROLOGY AB - Physiological uniformity and genetic effects on canopy-level gas-exchange and hydraulic function could impact loblolly pine (Pinus taeda L.) plantation sustainability and ecosystem dynamics under projected changes in climate. Over a 1-year period, we examined genetic effects on mean and maximum mid-day canopy conductance (Gs, Gsmax) and transpiration (E, max-E) within a juvenile loblolly pine plantation composed of ‘genotypes’ (e.g. different genetic entries) from each of the three different genetic groups (clones, full-sibs, open-pollinated). We also compared reference canopy conductance (Gs−ref or Gs at a vapour pressure deficit (D) = 1 kPa), maximum E (Emax) in response to D, stomatal sensitivity to D, specific hydraulic conductivity (ks), and cavitation resistance among genotypes. Based on genetic and physiological principles, we hypothesized that (1) within genotypes, physiological uniformity will increase as inherent genetic diversity decreases and (2) genotypes with greater ks and higher canopy-level gas-exchange rates will be more sensitive to increases in D, and more susceptible to loss of ks. In our results, high- and low-genetic diversity genotypes showed no differences in E and Gs uniformity over time. However, E and max-E were significantly different among genotypes, and genotypes showed significant seasonal variability in Gs and Gsmax. Additionally, there were significant differences in Emax, Gs−ref, Gs sensitivity to D, and the pressure at which 50% loss of ks occurs (P50) among individual genotypes. We found no relationship between mean hydraulic conductivity parameters and overall Gs−ref or Gs sensitivity. However, the genotype full embolism point (P88) and loss of ks rate (LCrate) both showed a significant positive relationship with genotype Gs−ref during the spring, indicating that genotypes with higher Gs were less resistant to cavitation. Overall, genetic effects on canopy-level gas-exchange and cavitation resistance were significant, implying that physiological differences among genotypes might affect stand water use, carbon gain, drought tolerance, and hydrologic processes. Contrary to our expectations, uniformity in physiological process rates did not increase as inherent genetic diversity decreased, suggesting that clonal genotypes exhibit high physiological plasticity under plantation conditions. Lastly, our results imply that genotypes with higher spring-time gas-exchange rates may be more susceptible to catastrophic loss of ks. With changes in climate expected to continue, physiological differences among genotypes may affect loblolly pine plantation carbon and water cycling. Copyright © 2011 John Wiley & Sons, Ltd. DA - 2011/3// PY - 2011/3// DO - 10.1002/eco.197 VL - 4 IS - 2 SP - 168-182 SN - 1936-0592 KW - climate change KW - clone KW - drought resistance KW - hydraulic conductivity KW - water use ER - TY - JOUR TI - Functional dissection of Odorant binding protein genes in Drosophila melanogaster AU - Swarup, S. AU - Williams, T. I. AU - Anholt, R. R. H. T2 - GENES BRAIN AND BEHAVIOR AB - Most organisms rely on olfaction for survival and reproduction. The olfactory system of Drosophila melanogaster is one of the best characterized chemosensory systems and serves as a prototype for understanding insect olfaction. Olfaction in Drosophila is mediated by multigene families of odorant receptors and odorant binding proteins (OBPs). Although molecular response profiles of odorant receptors have been well documented, the contributions of OBPs to olfactory behavior remain largely unknown. Here, we used RNAi-mediated suppression of Obp gene expression and measurements of behavioral responses to 16 ecologically relevant odorants to systematically dissect the functions of 17 OBPs. We quantified the effectiveness of RNAi-mediated suppression by quantitative real-time polymerase chain reaction and used a proteomic liquid chromatography and tandem mass spectrometry procedure to show target-specific suppression of OBPs expressed in the antennae. Flies in which expression of a specific OBP is suppressed often show altered behavioral responses to more than one, but not all, odorants, in a sex-dependent manner. Similarly, responses to a specific odorant are frequently affected by suppression of expression of multiple, but not all, OBPs. These results show that OBPs are essential for mediating olfactory behavioral responses and suggest that OBP-dependent odorant recognition is combinatorial. DA - 2011/8// PY - 2011/8// DO - 10.1111/j.1601-183x.2011.00704.x VL - 10 IS - 6 SP - 648-657 SN - 1601-183X KW - Behavioral genetics KW - chemoreception KW - olfaction KW - proteomics KW - RNAi ER - TY - JOUR TI - Detection and Quantification of Peronospora tabacina Using a Real-Time Polymerase Chain Reaction Assay AU - Blanco-Meneses, Monica AU - Ristaino, Jean Beagle T2 - PLANT DISEASE AB - Peronospora tabacina is an obligate plant pathogen that causes blue mold of tobacco. The disease is difficult to diagnose before the appearance of symptoms and can be easily spread in nonsymptomatic tobacco seedlings. We developed a real-time polymerase chain reaction (PCR) assay for P. tabacina that uses 5′ fluorogenic exonuclease (TaqMan) chemistry to detect and quantify pathogen DNA from diseased tissue. The primers and probe were designed using 5.8S ribosomal DNA sequences from 12 fungal and oomycete tobacco pathogens and 24 Peronospora spp. The PtabBM TaqMan assay was optimized and performed with a final concentration of 450 nM primers and 125 nM probe. The real-time TaqMan assay was assessed for sensitivity and the lower detection limit was 1 fg of DNA. The assay was specific for P. tabacina. None of the DNA from other tobacco pathogens, nonpathogens, or the host were amplified. The PtabBM TaqMan assay was useful for detection of P. tabacina in field samples, artificially inoculated leaves, roots, and systemically infected tobacco seedlings. The assay was used to quantify host resistance and it was possible to detect the pathogen 4 days postinoculation in both medium-resistant and susceptible tobacco cultivars. The real-time PCR assay for P. tabacina will be a valuable tool for the detection of the pathogen and of use to regulatory agencies interested in preventing the spread of blue mold. DA - 2011/6// PY - 2011/6// DO - 10.1094/pdis-05-10-0333 VL - 95 IS - 6 SP - 673-682 SN - 0191-2917 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-79959308900&partnerID=MN8TOARS ER - TY - JOUR TI - Brassinosteroid signal transduction: from receptor kinase activation to transcriptional networks regulating plant development AU - Clouse, S. D. T2 - Plant Cell AB - Brassinosteroid (BR) signal transduction research has progressed rapidly from the initial discovery of the BR receptor to a complete definition of the basic molecular components required to relay the BR signal from perception by receptor kinases at the cell surface to activation of a small family of transcription factors that regulate the expression of more than a thousand genes in a BR-dependent manner. These mechanistic advances have helped answer the intriguing question of how a single molecule, such as a hormone, can have dramatic pleiotropic effects on a broad range of diverse developmental pathways and have shed light on how BRs interact with other plant hormones and environmental cues to shape the growth of the whole plant. This review summarizes the current state of BR signal transduction research and then examines recent articles uncovering gene regulatory networks through which BR influences both vegetative and reproductive development. DA - 2011/// PY - 2011/// DO - 10.1105/tpc.111.084475 VL - 23 IS - 4 SP - 1219-1230 ER - TY - JOUR TI - Bartonella spp. in Feral Pigs, Southeastern United States AU - Beard, Adam W. AU - Maggi, Ricardo G. AU - Kennedy-Stoskopf, Suzanne AU - Cherry, Natalie A. AU - Sandfoss, Mark R. AU - DePerno, Christopher S. AU - Breitschwerdt, Edward B. T2 - Emerging Infectious Diseases AB - Abstract In conjunction with efforts to assess pathogen exposure in feral pigs from the southeastern United States, we amplified Bartonella henselae, B. koehlerae, and B. vinsonii subsp. berkhoffii from blood samples. Feral pigs may represent a zoonotic risk for hunters or butchers and pose a potential threat to domesticated livestock. DA - 2011/5// PY - 2011/5// DO - 10.3201/eid1705.100141 VL - 17 IS - 5 SP - 893–895 SN - 1080-6040 1080-6059 UR - http://dx.doi.org/10.3201/eid1705.100141 ER - TY - JOUR TI - Assessment of urine solute and matrix effects on the performance of an enzyme-linked immunosorbent assay for measurement of interleukin-6 in dog urine AU - Wood, Michael W. AU - Nordone, Sushila K. AU - Vaden, Shelly L. AU - Breitschwerdt, Edward B. T2 - JOURNAL OF VETERINARY DIAGNOSTIC INVESTIGATION AB - Measurement of cytokine concentrations within body fluids is a means of recognizing subclinical and/or unresolved, infectious and inflammatory states in patients. In the urinary tract, such information may be useful for identifying patients with pyelonephritis, asymptomatic bacteriuria, recurrent infections, and cystitis. One such cytokine, interleukin-6 (IL-6), is recognized as a primary cytokine that is produced following exposure of the urothelium to bacterial virulence factors. Complicating reliable testing for this and other cytokines is the nature of urine itself. Urine varies widely in its composition as indicated by the range of pH and urine specific gravity (USG) observed in healthy patients. An additional variable is the protein and carbohydrate matrix capable of hindering immunologic testing modalities, such as enzyme-linked immunosorbent assays (ELISAs). The purpose of the current study was to examine the role of urine pH, USG, and matrix while optimizing a canine-specific chemiluminescent ELISA for the measurement of IL-6 in the urine of dogs. Urine spiked with IL-6 obtained maximal IL-6 quantitative recoveries of only 55 ± 10% (mean ± 1 standard deviation) when an ELISA optimized for cell culture supernatants was used. The urine matrix and variations in USG were determined to by contributing to this poor IL-6 recovery. Using specific matrix inhibitors and optimal dilutions improved the IL-6 quantitative recovery to 91 ± 5%. Urine pH (5.5-9.5) had no effect. The current work underscores the importance of critically optimizing testing modalities for biomarkers, particularly if they are immunologic in origin. DA - 2011/3// PY - 2011/3// DO - 10.1177/104063871102300219 VL - 23 IS - 2 SP - 316-320 SN - 1040-6387 KW - Cytokine KW - enzyme-linked immunosorbent assay KW - interleukin-6 KW - matrix KW - urine ER - TY - JOUR TI - Alphavirus adsorption to mosquito cells as viewed by freeze fracture immunolabeling AU - Kononchik, Joseph P. AU - Vancini, Ricardo AU - Brown, Dennis T. T2 - VIROLOGY AB - Sindbis Virus (SV), the prototype alphavirus in the family togaviridae, infects both mammalian and insect cells. The ability of SV to infect cells possessing significantly different biochemical environments suggests that there may be a common mode of entry into each cell type. Previous studies show that up to 4h post infection cells are permeable to small ions and alpha sarcin suggesting that the plasma membrane is compromised as infection takes place. Thin-section electron microscopy has also shown SV to bind to the plasma membrane and lose its electron dense core through a pore like structure developed upon interaction of the virus with the cell surface. Using freeze-fracture replicas, thin-sections and antibody labeling the data presented herein show virus associated with intramembrane particles on mosquito cells. These data suggest that the intramembrane particles associated with SV may be part of the pore structure consisting of virus proteins and cell receptor. DA - 2011/7/5/ PY - 2011/7/5/ DO - 10.1016/j.virol.2011.04.011 VL - 415 IS - 2 SP - 132-140 SN - 0042-6822 KW - Alphavirus KW - Cell penetration KW - Insect cells KW - Freeze-fracture KW - Electron microscopy ER - TY - JOUR TI - Walter M. Fitch (1929-2011) AU - Atchley, William R. T2 - SCIENCE AB - A meticulous biologist developed fundamental tools for the field of molecular evolution. DA - 2011/5/13/ PY - 2011/5/13/ DO - 10.1126/science.1207426 VL - 332 IS - 6031 SP - 804-804 SN - 0036-8075 ER - TY - JOUR TI - Synthesis and Photophysical Characterization of Stable Indium Bacteriochlorins AU - Krayer, Michael AU - Yang, Eunkyung AU - Kim, Han-Je AU - Kee, Hooi Ling AU - Deans, Richard M. AU - Sluder, Camille E. AU - Diers, James R. AU - Kirmaier, Christine AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - INORGANIC CHEMISTRY AB - Bacteriochlorins have wide potential in photochemistry because of their strong absorption of near-infrared light, yet metallobacteriochlorins traditionally have been accessed with difficulty. Established acid-catalysis conditions [BF(3)·OEt(2) in CH(3)CN or TMSOTf/2,6-di-tert-butylpyridine in CH(2)Cl(2)] for the self-condensation of dihydrodipyrrin-acetals (bearing a geminal dimethyl group in the pyrroline ring) afford stable free base bacteriochlorins. Here, InBr(3) in CH(3)CN at room temperature was found to give directly the corresponding indium bacteriochlorin. Application of the new acid catalysis conditions has afforded four indium bacteriochlorins bearing aryl, alkyl/ester, or no substituents at the β-pyrrolic positions. The indium bacteriochlorins exhibit (i) a long-wavelength absorption band in the 741-782 nm range, which is shifted bathochromically by 22-32 nm versus the analogous free base species, (ii) fluorescence quantum yields (0.011-0.026) and average singlet lifetime (270 ps) diminished by an order of magnitude versus that (0.13-0.25; 4.0 ns) for the free base analogues, and (iii) higher average yield (0.9 versus 0.5) yet shorter average lifetime (30 vs 105 μs) of the lowest triplet excited state compared to the free base compounds. The differences in the excited-state properties of the indium chelates versus free base bacteriochlorins derive primarily from a 30-fold greater rate constant for S(1) → T(1) intersystem crossing, which stems from the heavy-atom effect on spin-orbit coupling. The trends in optical properties of the indium bacteriochlorins versus free base analogues, and the effects of 5-OMe versus 5-H substituents, correlate well with frontier molecular-orbital energies and energy gaps derived from density functional theory calculations. Collectively the synthesis, photophysical properties, and electronic characteristics of the indium bacteriochlorins and free base analogues reported herein should aid in the further design of such chromophores for diverse applications. DA - 2011/5/16/ PY - 2011/5/16/ DO - 10.1021/ic200325d VL - 50 IS - 10 SP - 4607-4618 SN - 1520-510X ER - TY - JOUR TI - Starch Self-Processing in Transgenic Sweet Potato Roots Expressing a Hyperthermophilic alpha-Amylase AU - Santa-Maria, Monica C. AU - Yencho, Craig G. AU - Haigler, Candace H. AU - Thompson, William F. AU - Kelly, Robert M. AU - Sosinski, Bryon T2 - BIOTECHNOLOGY PROGRESS AB - Abstract Sweet potato is a major crop in the southeastern United States, which requires few inputs and grows well on marginal land. It accumulates large quantities of starch in the storage roots and has been shown to give comparable or superior ethanol yields to corn per cultivated acre in the southeast. Starch conversion to fermentable sugars (i.e., for ethanol production) is carried out at high temperatures and requires the action of thermostable and thermoactive amylolytic enzymes. These enzymes are added to the starch mixture impacting overall process economics. To address this shortcoming, the gene encoding a hyperthermophilic α‐amylase from Thermotoga maritima was cloned and expressed in transgenic sweet potato, generated by Agrobacterium tumefaciens‐mediated transformation, to create a plant with the ability to self‐process starch. No significant enzyme activity could be detected below 40°C, but starch in the transgenic sweet potato storage roots was readily hydrolyzed at 80°C. The transgene did not affect normal storage root formation. The results presented here demonstrate that engineering plants with hyperthermophilic glycoside hydrolases can facilitate cost effective starch conversion to fermentable sugars. Furthermore, the use of sweet potato as an alternative near‐term energy crop should be considered. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011 DA - 2011/// PY - 2011/// DO - 10.1002/btpr.573 VL - 27 IS - 2 SP - 351-359 SN - 1520-6033 UR - http://europepmc.org/abstract/med/21365786 KW - hyperthermophilic enzymes KW - starch conversion KW - transgenic plants KW - sweet potato KW - biofuels ER - TY - JOUR TI - Performance of the loblolly pine fusiform rust disease resistance gene (Fr1) in a slashXloblolly pine hybrid family AU - Huber, Dudley AU - Amerson, Henry T2 - TREE GENETICS & GENOMES AB - Unexpectedly high levels of field susceptibility to the fusiform rust fungus observed for slashXloblolly hybrid families in the Cooperative Forest Genetics Research Program Pine Hybrid Trials led to several hypotheses concerning causation of the observed susceptibility. One of these hypotheses involved the failure of major resistance genes to appropriately function in this particular hybrid combination. This current work, involving the loblolly pine resistance gene Fr1 and a fusiform rust inoculum avirulent against Fr1 resistance in a greenhouse trial, delineates the investigation of major gene resistance for a particular slashXloblolly hybrid family. In this trial, the Fr1 resistance allele, derived from the heterozygous (Fr1/fr1) loblolly male parent and transferred to hybrid offspring that should have been segregating 1:1 for resistance, was fully penetrant. Likewise, in the pure-species loblolly control, the Fr1 resistance allele was again fully penetrant, and the performances of our hybrid family and the loblolly control family (both of which segregated for Fr1 resistance) were comparable. These results by inductive reasoning refute the hypothesis that major resistance genes are not appropriately functional in a slashXloblolly hybrid background. DA - 2011/6// PY - 2011/6// DO - 10.1007/s11295-010-0353-3 VL - 7 IS - 3 SP - 535-540 SN - 1614-2950 KW - Forest pathology KW - Marker-trait association KW - RAPD markers ER - TY - JOUR TI - Pectobacterium carotovorum Elicits Plant Cell Death with DspE/F but the P. carotovorum DspE Does Not Suppress Callose or Induce Expression of Plant Genes Early in Plant-Microbe Interactions AU - Kim, Hye-Sook AU - Thammarat, Phanit AU - Lommel, Steven A. AU - Hogan, Clifford S. AU - Charkowski, Amy O. T2 - MOLECULAR PLANT-MICROBE INTERACTIONS AB - The broad-host-range bacterial soft rot pathogen Pectobacterium carotovorum causes a DspE/F-dependent plant cell death on Nicotiana benthamiana within 24 h postinoculation (hpi) followed by leaf maceration within 48 hpi. P. carotovorum strains with mutations in type III secretion system (T3SS) regulatory and structural genes, including the dspE/F operon, did not cause hypersensitive response (HR)-like cell death and or leaf maceration. A strain with a mutation in the type II secretion system caused HR-like plant cell death but no maceration. P. carotovorum was unable to impede callose deposition in N. benthamiana leaves, suggesting that P. carotovorum does not suppress this basal immunity function. Within 24 hpi, there was callose deposition along leaf veins and examination showed that the pathogen cells were localized along the veins. To further examine HR-like plant cell death induced by P. carotovorum, gene expression profiles in N. benthamiana leaves inoculated with wild-type and mutant P. carotovorum and Pseudomonas syringae strains were compared. The N. benthamiana gene expression profile of leaves infiltrated with Pectobacterium carotovorum was similar to leaves infiltrated with a Pseudomonas syringae T3SS mutant. These data support a model where Pectobacterium carotovorum uses the T3SS to induce plant cell death in order to promote leaf maceration rather than to suppress plant immunity. DA - 2011/7// PY - 2011/7// DO - 10.1094/mpmi-06-10-0143 VL - 24 IS - 7 SP - 773-786 SN - 1943-7706 ER - TY - JOUR TI - Joint analysis of transcriptional and post-transcriptional brain tumor data: searching for emergent properties of cellular systems AU - Fronza, R. AU - Tramonti, M. AU - Atchley, W. R. AU - Nardini, C. T2 - BMC Bioinformatics DA - 2011/// PY - 2011/// VL - 12 ER - TY - JOUR TI - Identification and characterization of a pyridoxal reductase involved in the vitamin B6 salvage pathway in Arabidopsis AU - Herrero, Sonia AU - Gonzalez, Eugenia AU - Gillikin, Jeffrey W. AU - Velez, Heriberto AU - Daub, Margaret E. T2 - PLANT MOLECULAR BIOLOGY DA - 2011/5// PY - 2011/5// DO - 10.1007/s11103-011-9777-x VL - 76 IS - 1-2 SP - 157-169 SN - 1573-5028 KW - Vitamin B6 KW - Pyridoxal phosphate KW - Pyridoxine KW - Pyridoxal reductase KW - B6 salvage pathway KW - Arabidopsis KW - Abiotic stress ER - TY - JOUR TI - Genomic regions associated with antibody response to sheep red blood cells in the chicken AU - Dorshorst, B. J. AU - Siegel, P. B. AU - Ashwell, C. M. T2 - ANIMAL GENETICS AB - Summary F 1 and F 2 populations were generated by crossing two lines of chickens divergently selected from a common founder population for 32 generations for either high or low antibody response 5 days post‐injection of a non‐pathogenic antigen, sheep red blood cells (SRBCs). The number of loci with major effects on day 5 SRBC titers was estimated to be more than 7 in this population. There was a significant association between MHC haplotype and day 5 antibody titers as well as body weight at sexual maturity. A significant difference between reciprocal F 2 crosses for both 5‐ and 12‐day antibody titers suggests that sex chromosome and/or parent of origin effects on autosomal loci have an important role in immune response. A single marker‐trait association analysis on 1024 genetic markers and 128 F 2 individuals detected 11 genomic regions associated with antibody response traits and 17 regions associated with body weight gain. Several of the genomic regions identified as being associated with antibody response have been described previously, while novel regions associated with antibody response were identified on chromosomes 11 and 24. Based on the lack of overlap of the regions associated with body weight and antibody response, we conclude that while these phenotypes are inversely correlated in the selected lines, they are controlled by distinct genetic loci and may be reflective of intense selection pressure on loci affecting the partitioning of nutrients between the immune system and growth pathways. DA - 2011/6// PY - 2011/6// DO - 10.1111/j.1365-2052.2010.02146.x VL - 42 IS - 3 SP - 300-308 SN - 0268-9146 KW - association analysis KW - chicken KW - immune response KW - major histocompatibility complex KW - quantitative trait loci estimation KW - sheep red blood cells ER - TY - JOUR TI - C/EBP alpha Expression Is Downregulated in Human Nonmelanoma Skin Cancers and Inactivation of C/EBP alpha Confers Susceptibility to UVB-Induced Skin Squamous Cell Carcinomas AU - Thompson, Elizabeth A. AU - Zhu, Songyun AU - Hall, Jonathan R. AU - House, John S. AU - Ranjan, Rakesh AU - Burr, Jeanne A. AU - He, Yu-Ying AU - Owens, David M. AU - Smart, Robert C. T2 - JOURNAL OF INVESTIGATIVE DERMATOLOGY AB - Human epidermis is routinely subjected to DNA damage induced by UVB solar radiation. Cell culture studies have revealed an unexpected role for C/EBPα (CCAAT/enhancer-binding protein-α) in the DNA damage response network, where C/EBPα is induced following UVB DNA damage, regulates the G1 checkpoint, and diminished or ablated expression of C/EBPα results in G1 checkpoint failure. In the current study we observed that C/EBPα is induced in normal human epidermal keratinocytes and in the epidermis of human subjects exposed to UVB radiation. The analysis of human skin precancerous and cancerous lesions (47 cases) for C/EBPα expression was conducted. Actinic keratoses, a precancerous benign skin growth and precursor to squamous cell carcinoma (SCC), expressed levels of C/EBPα similar to normal epidermis. Strikingly, all invasive SCCs no longer expressed detectable levels of C/EBPα. To determine the significance of C/EBPα in UVB-induced skin cancer, SKH-1 mice lacking epidermal C/EBPα (CKOα) were exposed to UVB. CKOα mice were highly susceptible to UVB-induced SCCs and exhibited accelerated tumor progression. CKOα mice displayed keratinocyte cell cycle checkpoint failure in vivo in response to UVB that was characterized by abnormal entry of keratinocytes into S phase. Our results demonstrate that C/EBPα is silenced in human SCC and loss of C/EBPα confers susceptibility to UVB-induced skin SCCs involving defective cell cycle arrest in response to UVB. Human epidermis is routinely subjected to DNA damage induced by UVB solar radiation. Cell culture studies have revealed an unexpected role for C/EBPα (CCAAT/enhancer-binding protein-α) in the DNA damage response network, where C/EBPα is induced following UVB DNA damage, regulates the G1 checkpoint, and diminished or ablated expression of C/EBPα results in G1 checkpoint failure. In the current study we observed that C/EBPα is induced in normal human epidermal keratinocytes and in the epidermis of human subjects exposed to UVB radiation. The analysis of human skin precancerous and cancerous lesions (47 cases) for C/EBPα expression was conducted. Actinic keratoses, a precancerous benign skin growth and precursor to squamous cell carcinoma (SCC), expressed levels of C/EBPα similar to normal epidermis. Strikingly, all invasive SCCs no longer expressed detectable levels of C/EBPα. To determine the significance of C/EBPα in UVB-induced skin cancer, SKH-1 mice lacking epidermal C/EBPα (CKOα) were exposed to UVB. CKOα mice were highly susceptible to UVB-induced SCCs and exhibited accelerated tumor progression. CKOα mice displayed keratinocyte cell cycle checkpoint failure in vivo in response to UVB that was characterized by abnormal entry of keratinocytes into S phase. Our results demonstrate that C/EBPα is silenced in human SCC and loss of C/EBPα confers susceptibility to UVB-induced skin SCCs involving defective cell cycle arrest in response to UVB. CCAAT/enhancer-binding protein-α DNA damage response immunohistochemical keratin 5 minimum erythemic dose phosphate-buffered saline squamous cell carcinoma 12-O-tetradecanoylphorbol-13-acetate The epidermis is routinely subject to DNA damage by UVB, which is considered to be the principal carcinogenic component of sunlight. Exposure to UVB results in DNA damage in the form of cyclobutane pyrimidine dimers, 6–4 photoproducts, DNA strand breaks, and DNA crosslinks (Brash, 1997Brash D.E. Sunlight and the onset of skin cancer.Trends Genet. 1997; 13: 410-414Abstract Full Text PDF PubMed Scopus (259) Google Scholar; de Gruijl et al., 2001de Gruijl F.R. van Kranen H.J. Mullenders L.H. UV-induced DNA damage, repair, mutations and oncogenic pathways in skin cancer.J Photochem Photobiol B. 2001; 63: 19-27Crossref PubMed Scopus (385) Google Scholar). If not repaired or if misrepaired, this DNA damage can result in mutations in the genome, and can ultimately contribute to the development of skin cancers (Brash et al., 1991Brash D.E. Rudolph J.A. Simon J.A. et al.A role for sunlight in skin cancer: UV-induced p53 mutations in squamous cell carcinoma.Proc Natl Acad Sci USA. 1991; 88: 10124-10128Crossref PubMed Scopus (1643) Google Scholar). Solar radiation is responsible for >1,000,000 nonmelanoma skin cancer cases per year in the United States, and these cases account for 40% of all new cancer cases diagnosed each year in the United States (American Cancer Society, 2008American Cancer SocietyCancer Facts & Figures 2008.in: 2008http://www.cancer.org/Research/CancerFactsFigures/cancer-facts-figures-2008Google Scholar). To maintain genome integrity and to prevent heritable mutations that lead to cancer, cells respond to DNA damage produced by intrinsic or environmental factors by engaging the DNA damage response (DDR) network. This network entails signaling pathways involving cell cycle checkpoints, DNA repair, transcription programs, and apoptosis. Cell cycle checkpoints can occur in any phase of the cell cycle and are characterized as a pause in the cell cycle that allows time for the repair of damaged DNA. Defective checkpoints can contribute to genome instability and cancer pathogenesis (Kastan and Bartek, 2004Kastan M.B. Bartek J. Cell-cycle checkpoints and cancer.Nature. 2004; 432: 316-323Crossref PubMed Scopus (2028) Google Scholar). C/EBPα (CCAAT/enhancer-binding protein-α) is one of the six members of the C/EBP family of basic leucine zipper transcription factors (Ramji and Foka, 2002Ramji D.P. Foka P. CCAAT/enhancer-binding proteins: structure, function and regulation.Biochem J. 2002; 365: 561-575Crossref PubMed Google Scholar; Johnson, 2005Johnson P.F. Molecular stop signs: regulation of cell-cycle arrest by C/EBP transcription factors.J Cell Sci. 2005; 118: 2545-2555Crossref PubMed Scopus (221) Google Scholar). C/EBPα has been established as a tumor-suppressor gene in human acute myeloid leukemia (Pabst et al., 2001Pabst T. Mueller B.U. Zhang P. et al.Dominant-negative mutations of CEBPA, encoding CCAAT/enhancer binding protein-alpha (C/EBPalpha), in acute myeloid leukemia.Nat Genet. 2001; 27: 263-270Crossref PubMed Scopus (705) Google Scholar). Additionally, there is circumstantial evidence for its function as a tumor suppressor based on diminished C/EBPα expression in a multitude of human tumor types including liver (Xu et al., 2001Xu L. Hui L. Wang S. et al.Expression profiling suggested a regulatory role of liver-enriched transcription factors in human hepatocellular carcinoma.Cancer Res. 2001; 61: 3176-3181PubMed Google Scholar), lung (Halmos et al., 2002Halmos B. Huettner C.S. Kocher O. et al.Down-regulation and antiproliferative.Cancer Res. 2002; 62: 528-534PubMed Google Scholar), breast (Gery et al., 2005Gery S. Tanosaki S. Bose S. et al.Down-regulation and growth inhibitory role of C/EBPalpha in breast cancer.Clin Cancer Res. 2005; 11: 3184-3190Crossref PubMed Scopus (76) Google Scholar), endometrial (Takai et al., 2005Takai N. Kawamata N. Walsh C.S. et al.Discovery of epigenetically masked tumor suppressor genes in endometrial cancer.Mol Cancer Res. 2005; 3: 261-269Crossref PubMed Scopus (63) Google Scholar), and head and neck squamous cell carcinomas (SCCs; Bennett et al., 2007Bennett K.L. Hackanson B. Smith L.T. et al.Tumor suppressor activity of CCAAT/e.Cancer Res. 2007; 67: 4657-4664Crossref PubMed Scopus (70) Google Scholar). The traditional view of C/EBPα in cell biology involves its role in cellular differentiation and metabolism (Roesler, 2001Roesler W.J. The role of C/EBP in nutrient and hormonal regulation of gene expression.Annu Rev Nutr. 2001; 21: 141-165Crossref PubMed Scopus (81) Google Scholar); in cancer, the traditional view holds that it has a tumor-suppressor role, where the loss of expression/function results in an impaired differentiation commitment accompanied by deregulated proliferation (Schuster and Porse, 2006Schuster M.B. Porse B.T. C/EBPalpha: a tumour suppressor in multiple tissues?.Biochim Biophys Acta. 2006; 1766: 88-103PubMed Google Scholar; Koschmieder et al., 2009Koschmieder S. Halmos B. Levantini E. et al.Dysregulation of the C/EBPalpha differentiation pathway in human cancer.J Clin Oncol. 2009; 27: 619-628Crossref PubMed Scopus (155) Google Scholar). However, recent studies indicate that the role of C/EBPα in cells/cancer is more complex and multifaceted than originally thought (Yoon and Smart, 2004Yoon K. Smart R.C. C/EBPalpha is a DNA damage-inducible p53-regulated mediator of the G1 checkpoint in keratinocytes.Mol Cell Biol. 2004; 24: 10650-10660Crossref PubMed Scopus (53) Google Scholar; Loomis et al., 2007Loomis K.D. Zhu S. Yoon K. et al.Genetic ablation of CCAAT/enhancer binding protein {alpha.Cancer Res. 2007; 67: 6768-6776Crossref PubMed Scopus (34) Google Scholar; Ranjan et al., 2009Ranjan R. Thompson E.A. Yoon K. et al.C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint.Oncogene. 2009; 28: 3235-3245Crossref PubMed Scopus (8) Google Scholar). Cell culture studies have revealed an unexpected role for C/EBPα in the DDR in keratinocytes where C/EBPα is induced following UVB-induced DNA damage, and it regulates the G1 checkpoint. Diminished or ablated expression of C/EBPα results in G1 checkpoint failure following UVB-induced DNA damage (Yoon and Smart, 2004Yoon K. Smart R.C. C/EBPalpha is a DNA damage-inducible p53-regulated mediator of the G1 checkpoint in keratinocytes.Mol Cell Biol. 2004; 24: 10650-10660Crossref PubMed Scopus (53) Google Scholar; Ranjan et al., 2009Ranjan R. Thompson E.A. Yoon K. et al.C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint.Oncogene. 2009; 28: 3235-3245Crossref PubMed Scopus (8) Google Scholar). In further support of a nonparadigmatic C/EBPα tumor-suppressor function, mice lacking C/EBPα in their epidermis do not display alterations in differentiation or proliferation and are susceptible to chemical carcinogen-induced skin tumorigenesis (Loomis et al., 2007Loomis K.D. Zhu S. Yoon K. et al.Genetic ablation of CCAAT/enhancer binding protein {alpha.Cancer Res. 2007; 67: 6768-6776Crossref PubMed Scopus (34) Google Scholar). Given the function of C/EBPα as a mediator of the G1 checkpoint in keratinocytes in response to UVB, it is possible that C/EBPα functions as a suppressor of UVB-induced tumorigenesis. Whereas C/EBPα expression is diminished in mouse skin SCCs (Oh and Smart, 1998Oh H.S. Smart R.C. Expression of CCAAT/enhancer binding proteins (C/EBP) is associated with squamous differentiation in epidermis and isolated primary keratinocytes and is altered in skin neoplasms.J Invest Dermatol. 1998; 110: 939-945Crossref PubMed Scopus (79) Google Scholar; Shim et al., 2005Shim M. Powers K.L. Ewing S.J. et al.Diminished expression of C/EBPalpha in skin carcinomas is linked to oncogenic Ras and reexpression of C/EBPalpha in carcinoma cells inhibits proliferation.Cancer Res. 2005; 65: 861-867PubMed Google Scholar), C/EBPα levels have not been examined in human skin precancerous and cancerous lesions. Therefore, the objectives of this study were: to examine the expression of C/EBPα in human skin precancerous and cancerous lesions, to characterize the response of C/EBPα to UVB in human keratinocytes and human skin; and to develop an in vivo SKH-1 mouse model to determine the in vivo physiological significance of C/EBPα in UVB-induced skin tumorigenesis. We examined the expression of C/EBPα in normal human epidermis, precancerous actinic keratoses, keratoacanthomas, SCCs in situ, and invasive SCCs as well as basal cell carcinomas. Immunohistochemical (IHC) staining for C/EBPα in human skin showed that C/EBPα was extensively expressed in the nuclei of nondividing keratinocytes of the suprabasal layers of the epidermis (Figure 1a). C/EBPα expression was also detected, although less frequently, in keratinocytes in the proliferative basal layer of epidermis. Actinic keratoses, a precancerous benign skin growth of which a small percentage progress to SCC, expressed levels of C/EBPα similar to normal epidermis (Figure 1a and b). Keratoacanthomas, once considered as terminally benign but now regarded and treated by many dermatologists as a malignant growth that can progress to SCC, expressed reduced levels of C/EBPα with 20% of keratoacanthomas no longer expressing detectable levels of C/EBPα (Figure 1a and b). Most striking, however, were the SCCs where the majority of both SCCs in situ (80%) and invasive SCCs (100%) no longer expressed detectable levels of C/EBPα (Figure 1a and b). Similarly, the IHC staining for C/EBPα was absent in 14/16 basal cell carcinoma cases (data not shown). Most human nonmelanoma skin cancers are caused by solar radiation, and UVB radiation is considered the most carcinogenic component of sunlight. To characterize the effects of UVB exposure on the expression of C/EBPα in human keratinocytes, we exposed subconfluent proliferating normal human epidermal keratinocytes to 5, 10, or 15mJcm2 UVB. Immunoblot analysis for C/EBPα revealed that the expression of C/EBPα protein was induced at all doses (Figure 2a). To characterize the effects of UVB exposure on the expression of C/EBPα in human skin in vivo, biopsies from UVB-treated human skin (1 minimum erythemic dose (MED) UVB) (N=5) were compared with biopsies from non-sun-exposed human skin (N=5) for C/EBPα expression. C/EBPα levels were increased throughout the epidermis of UVB-treated human skin as determined by the increased C/EBPα IHC nuclear staining intensity as well as by the overall statistically significant increase in the number of keratinocytes staining positively for C/EBPα (Figure 2b–d and Supplementary Figure S1 online). Although UVB treatment increased the percentage of C/EBPα-expressing keratinocytes in the spinous and granular nondividing suprabasal layers by 2.3-fold, we observed a 4.3-fold increase in the number of basal keratinocytes expressing C/EBPα (Figure 2b–d). Download .pdf (.66 MB) Help with pdf files Supplementary Figures S1 and S2 We treated SKH-1 hairless mice, a well-characterized mouse model frequently utilized to study the effects of UVB in skin in vivo (Benavides et al., 2009Benavides F. Oberyszyn T.M. VanBuskirk A.M. et al.The hairless mouse in skin research.J Dermatol Sci. 2009; 53: 10-18Abstract Full Text Full Text PDF PubMed Scopus (153) Google Scholar), with UVB (50mJcm2) and, similar to human skin, we observed a significant increase in C/EBPα-expressing keratinocytes in the suprabasal and basal proliferative compartments of epidermis (Figure 3a). There was an ∼2-fold increase in the number of C/EBPα positively stained suprabasal cells, and a 3-fold increase in the number of C/EBPα positively stained basal keratinocytes (Figure 3b). To begin to determine the physiological significance of UVB-induced epidermal C/EBPα in vivo, we generated an epidermal-specific C/EBPα knockout SKH-1 mouse, hereafter referred to as conditional knockout (CKOα). CKOα mice were generated from C/EBPαfl/fl SKH-1 mice and keratin 5 (K5) Cre (K5Cre) SKH-1 mice where the K5 promoter directs Cre recombinase expression to the epidermis and other stratified squamous epithelia. As shown in Figure 3c, C/EBPα protein was not detectable in epidermal protein extracts prepared from CKOα mice. CKOα mice did not display any abnormal gross or morphological skin phenotype (data not shown). The most susceptible human population to UVB-induced damage is classified as type 1 according to the Fitzpatrick Classification Scale. These individuals have very fair and often freckled skin, have blond or red hair, always sun burn, and are highly susceptible to solar radiation-induced nonmelanoma skin cancer. The MED of UVB for this susceptible population is ∼20–25mJcm2. Therefore, we exposed CKOα and K5Cre control mice to 20mJcm2 UVB three times weekly to test whether the loss of C/EBPα in skin keratinocytes confers susceptibility to UVB-induced tumorigenesis. As shown in Figure 4a and b, CKOα mice were highly susceptibility to UVB-induced skin tumorigenesis as evidenced by decreased latency (18 weeks), increased tumor incidence (85 vs. 25%), and a 6-fold increase in tumor multiplicity. Histological analysis of all skin tumors at the termination of experiment revealed that the majority of tumors (∼90%) in both genotypes were SCCs (in situ or invasive). Most importantly, we observed that 48% of SCCs in CKOα mice were invasive SCCs compared with 15% in the UVB-treated K5Cre control mice (Figure 4c). Invasive carcinomas were identified by severe dysplasia to anaplastic growth, marked atypia in all cell layers, and most importantly, invasion through the panniculus carnosus and/or basement membrane (Supplementary Figure S2 online). To demonstrate that these tumors were the result of UVB treatment and not advanced age, 8 CKOα mice were held for 52 weeks and no skin tumors of any kind were detected. Collectively, these results indicate that loss of C/EBPα confers susceptibility to UVB-induced skin cancer at a biologically relevant dose and loss of C/EBPα accelerates skin tumor progression. To determine whether the ablation of epidermal C/EBPα alters the ability of keratinocytes to undergo a cell cycle arrest in response to UVB treatment in vivo in mouse skin, we treated K5Cre control mice and CKOα mice with UVB, and then examined the number of actively replicating keratinocytes post-UVB by measuring the incorporation of the nucleotide analog BrdU (1hour BrdU pulse before skin collection). As shown in Figure 5a, UVB-treated control mice (K5Cre) displayed a significant cell cycle arrest; at 4hours post-UVB treatment, there was ∼60% decrease in the number of BrdU-positive S-phase basal keratinocytes in the epidermis and this decrease was sustained at 6 and 10hours post-UVB (Figure 5a). At 12hours post-UVB, the number of BrdU-positive S-phase basal keratinocytes returned to untreated control levels (data not shown). Although UVB-treated CKOα mice displayed a similar cell cycle arrest as UVB-treated control mice at 4hours post-UVB treatment, this inhibition was not sustained and cells resumed their progression in the cell cycle prematurely. At 6hours post-UVB, the number of BrdU-positive S-phase cells was significantly increased and by 10hours post-UVB treatment, there was a 3-fold increase in BrdU-positive S-phase basal keratinocytes in CKOα epidermis compared with UVB-treated control mice. Representative examples of BrdU-positive S-phase staining at 10hours post-UVB in K5Cre and CKOα mouse epidermis are shown in Figure 5a (right panel). These results indicate that the loss of C/EBPα in epidermis results in an impaired cell cycle arrest in response to UVB in vivo. To further investigate the role of C/EBPα in UVB-induced cell cycle checkpoints in epidermis in vivo, we utilized an in vivo model of cell cycle regulation involving the induction of synchronous cell proliferation induced by the potent mitogen, 12-O-tetradecanoylphorbol-13-acetate (TPA) (Foley et al., 1993Foley J. Ton T. Maronpot R. et al.Comparison of proliferating cell nuclear antigen to tritiated thymidine as a marker of proliferating hepatocytes in rats.Environ Health Perspect. 1993; 101: 199-205Crossref PubMed Scopus (96) Google Scholar; Kim et al., 1997Kim T.W. Porter K.L. Foley J.F. et al.Evidence that mirex promotes a unique population of epidermal cells that cannot be distinguished by their mutant Ha-ras genotype.Mol Carcinog. 1997; 20: 115-124Crossref PubMed Scopus (9) Google Scholar; Rodriguez-Puebla et al., 1998Rodriguez-Puebla M.L. Robles A.I. Johnson D.G. et al.Synchronized proliferation induced by 12-O-tetradecanoylphorbol-13-acetate treatment of mouse skin: an in vivo model for cell cycle regulation.Cell Growth Differ. 1998; 9: 31-39PubMed Google Scholar). A single topical treatment of TPA resulted in synchronous entry of G1 keratinocytes into S phase as determined by BrdU-positive basal cells at 12hours post-TPA treatment and S-phase cells further increased at 14 and 16hours in control mice (1hour BrdU pulse before skin collection; Figure 5b). TPA-treated CKOα mice responded similarly and the numbers of S-phase cells were not significantly different from TPA-treated control mice at all time points (P>0.3, data not shown). To determine the effect of UVB on this entry into S phase, K5Cre and CKOα mice were treated with TPA, and 4hours later, a time when keratinocytes are still in G1, were either treated with UVB (50mJcm2) or left untreated. The number of BrdU-positive S-phase cells were then determined at 14hours post-TPA treatment and 10hours post-UVB. As shown in Figure 5c, TPA-treated K5Cre and CKOα mice not exposed to UVB displayed a 3-fold increase in the number of BrdU-positive S-phase keratinocytes. UVB treatment of TPA-treated mice resulted in dramatic decreases in the number of BrdU-positive S-phase cells in the epidermis of both genotypes compared with TPA treatment alone (Figure 5c). However, CKOα mice displayed ∼3 times more BrdU-positive S-phase cells than similarly treated K5Cre mice. Collectively, our findings suggest that the loss of epidermal C/EBPα results in an impaired cell cycle arrest involving the G1- to S-phase transition in response to UVB in vivo in mouse epidermis. Because p53 is an important player in the DDR and a key mediator of checkpoints following DNA damage, we wanted to determine whether the impaired cell cycle arrest at the G1- to S-phase transition observed in the CKOα mice following UVB treatment could be related to deficiencies in p53. We performed immunoblot analysis for p53 on epidermal lysates from both UVB-treated (50mJcm2) and untreated K5Cre and CKOα mice, and observed an induction in p53 protein in both genotypes following UVB treatment (Figure 5d). To further determine whether p53 was induced to a similar extent in both genotypes, IHC staining and quantitation of p53-positive basal cells were performed, and no statistically significant differences were found (Figure 5d). C/EBPα is abundantly expressed in the mouse and human epidermis (Swart et al., 1997Swart G.W. van Groningen J.J. van Ruissen F. et al.Transcription factor C/EBPalpha: novel sites of expression and cloning of the human gene.Biol Chem. 1997; 378: 373-379Crossref PubMed Scopus (29) Google Scholar; Maytin and Habener, 1998Maytin E.V. Habener J.F. Transcription factors C/EBP alpha, C/EBP beta, and CHOP (Gadd153) expressed during the differentiation program of keratinocytes in vitro and in vivo.J Invest Dermatol. 1998; 110: 238-246Crossref PubMed Scopus (119) Google Scholar; Oh and Smart, 1998Oh H.S. Smart R.C. Expression of CCAAT/enhancer binding proteins (C/EBP) is associated with squamous differentiation in epidermis and isolated primary keratinocytes and is altered in skin neoplasms.J Invest Dermatol. 1998; 110: 939-945Crossref PubMed Scopus (79) Google Scholar) and in this study we report that C/EBPα is induced by UVB in human epidermal keratinocytes and human epidermis. Analysis of C/EBPα expression in human skin and human skin precancerous and cancerous lesions revealed that C/EBPα expression is downregulated in SCCs in situ and in invasive SCCs and that expression of C/EBPα is normal in actinic keratoses. These results indicate that loss of C/EBPα expression is not an early event in SCC development but occurs during progression from actinic keratoses to invasive SCCs. The mechanism through which C/EBPα is downregulated in human and mouse SCCs is unknown; however, promoter hypermethylation is a candidate as C/EBPα promoter hypermethylation has been shown to be important in the decreased expression of C/EBPα in breast cancer as well as head and neck cancers (Gery et al., 2005Gery S. Tanosaki S. Bose S. et al.Down-regulation and growth inhibitory role of C/EBPalpha in breast cancer.Clin Cancer Res. 2005; 11: 3184-3190Crossref PubMed Scopus (76) Google Scholar; Bennett et al., 2007Bennett K.L. Hackanson B. Smith L.T. et al.Tumor suppressor activity of CCAAT/e.Cancer Res. 2007; 67: 4657-4664Crossref PubMed Scopus (70) Google Scholar). p53 is frequently mutated in human skin cancer and this is an early essential event (Brash, 1997Brash D.E. Sunlight and the onset of skin cancer.Trends Genet. 1997; 13: 410-414Abstract Full Text PDF PubMed Scopus (259) Google Scholar). Although actinic keratoses are the precursor lesion to SCCs, only a small percentage of actinic keratoses (1–10%) actually progress to SCCs, even though both actinic keratoses and SCCs share a high frequency (70%) of mutant p53 and similar p53 mutation spectra (Callen et al., 1997Callen J.P. Bickers D.R. Moy R.L. Actinic keratoses.J Am Acad Dermatol. 1997; 36: 650-653Abstract Full Text Full Text PDF PubMed Scopus (147) Google Scholar; Ortonne, 2002Ortonne J.P. From actinic keratosis to squamous cell carcinoma.Br J Dermatol. 2002; 146: 20-23Crossref PubMed Scopus (101) Google Scholar; Giglia-Mari and Sarasin, 2003Giglia-Mari G. Sarasin A. TP53 mutations in human skin cancers.Hum Mutat. 2003; 21: 217-228Crossref PubMed Scopus (197) Google Scholar; Stockfleth and Kerl, 2006Stockfleth E. Kerl H. Guidelines for the management of actinic keratoses.Eur J Dermatol. 2006; 16: 599-606PubMed Google Scholar). These results indicate that mutant p53 is not sufficient for the progression of actinic keratoses to SCCs and that additional events are required for actinic keratosis progression. One such event may be the loss of C/EBPα, as C/EBPα expression is retained in actinic keratoses, but C/EBPα expression is silenced in SCCs. These results suggest that loss of C/EBPα expression may be a critical event in the progression of precancerous actinic keratoses to invasive SCCs. Our current results in CKOα mice demonstrate that the ablation of C/EBPα in mouse epidermis confers susceptibility to UVB-induced SCCs at a biologically relevant dose and results in the acceleration of skin cancer progression to invasive SCCs. Additionally, earlier studies showed that mice lacking C/EBPα in their epidermis are also more susceptible to chemical carcinogen-induced skin tumorigenesis, and tumors that develop in these mice exhibited an accelerated rate of malignant progression to invasive SCCs (Loomis et al., 2007Loomis K.D. Zhu S. Yoon K. et al.Genetic ablation of CCAAT/enhancer binding protein {alpha.Cancer Res. 2007; 67: 6768-6776Crossref PubMed Scopus (34) Google Scholar). Collectively, these results indicate an important role for the loss of C/EBPα in skin cancer progression induced by UVB radiation or chemical carcinogens. The recent comprehensive genomic characterization of human cancers has revealed that genomic instability is a common characteristic of cancer, that human cancer cells contain hundreds if not thousands of mutations, and that the mutation rate in cancer cells greatly exceeds that in normal cells (Lengauer et al., 1998Lengauer C. Kinzler K.W. Vogelstein B. Genetic instabilities in human cancers.Nature. 1998; 396: 643-649Crossref PubMed Scopus (3268) Google Scholar; Bielas et al., 2006Bielas J.H. Loeb K.R. Rubin B.P. et al.Human cancers express a mutator phenotype.Proc Natl Acad Sci USA. 2006; 103: 18238-18242Crossref PubMed Scopus (276) Google Scholar; The Cancer Genome Atlas Research Network, 2008The Cancer Genome Atlas Research NetworkComprehensive genomic characterization defines human glioblastoma genes and core pathways.Nature. 2008; 455: 1061-1068Crossref PubMed Scopus (5212) Google Scholar; Ding et al., 2008Ding L. Getz G. 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Yoon K. et al.C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint.Oncogene. 2009; 28: 3235-3245Crossref PubMed Scopus (8) Google Scholar). The genetic ablation or knockdown of C/EBPα in keratinocytes results in G1 checkpoint failure in which cells inappropriately enter S phase following U DA - 2011/6// PY - 2011/6// DO - 10.1038/jid.2011.31 VL - 131 IS - 6 SP - 1339-1346 SN - 0022-202X ER - TY - JOUR TI - Bartonella spp. DNA in Cardiac Tissues from Dogs in Colorado and Wyoming AU - Fenimore, A. AU - Varanat, M. AU - Maggi, R. AU - Schultheiss, P. AU - Breitschwerdt, E. AU - Lappin, M. R. T2 - Journal of Veterinary Internal Medicine AB - Several Bartonella species (spp.) have been identified in dogs diagnosed with infectious endocarditis (IE) or myocarditis.To interrogate cardiac tissues of dogs with suspected IE for the presence of Bartonella spp. DNA of dogs in the Rocky Mountain states.Nine dogs with a clinical diagnosis of endocarditis from January 1990 to June 2008 were included.In this retrospective study, medical records at the Veterinary Teaching Hospital were searched. Animals were excluded if there was no diagnosis of IE in the original necropsy report. Paraffin embedded tissue blocks and medical records were available from 9 dogs. Total DNA was extracted from the cardiac tissues and assessed for Bartonella spp. DNA by 3 polymerase chain reaction (PCR) methods. For positive samples, the Bartonella spp. were determined by genetic sequencing or fluorogenic real-time PCR.Bartonella henselae DNA was amplified from the tissues of 7 dogs; Bartonella vinsonii subsp berkhoffii DNA was amplified concurrently from 3 dogs. Six dogs were from Colorado and 1 was from Wyoming. Flea or tick infestations were reported in 2 dogs.Bartonella spp. should be on the differential list for dogs in the Rocky Mountain states. The results emphasize the need for routine use of external parasite control products even in regions perceived to have low risk for flea and tick infestations. DA - 2011/5// PY - 2011/5// DO - 10.1111/j.1939-1676.2011.0722.x VL - 25 IS - 3 SP - 613-616 LA - en OP - SN - 0891-6640 UR - http://dx.doi.org/10.1111/j.1939-1676.2011.0722.x DB - Crossref KW - Bartonella species KW - Blood cultures KW - Polymerase chain reaction assays ER - TY - JOUR TI - Refining tumor-associated aneuploidy through 'genomic recoding' of recurrent DNA copy number aberrations in 150 canine non-Hodgkin lymphomas AU - Thomas, Rachael AU - Seiser, Eric L. AU - Motsinger-Reif, Alison AU - Borst, Luke AU - Valli, Victor E. AU - Kelley, Kathryn AU - Suter, Steven E. AU - Argyle, David AU - Burgess, Kristine AU - Bell, Jerold AU - Lindblad-Toh, Kerstin AU - Modiano, Jaime F. AU - Breen, Matthew T2 - LEUKEMIA & LYMPHOMA AB - Identification of the genomic regions most intimately associated with non-Hodgkin lymphoma (NHL) pathogenesis is confounded by the genetic heterogeneity of human populations. We hypothesize that the restricted genetic variation of purebred dogs, combined with the contrasting architecture of the human and canine karyotypes, will increase the penetrance of fundamental NHL-associated chromosomal aberrations in both species. We surveyed non-random aneuploidy in 150 canine NHL cases, revealing limited genomic instability compared to their human counterparts and no evidence for CDKN2A/B deletion in canine B-cell NHL. 'Genomic recoding' of canine NHL data into a 'virtual human' chromosome format showed remarkably few regions of copy number aberration (CNA) shared between both species, restricted to regions of dog chromosomes 13 and 31, and human chromosomes 8 and 21. Our data suggest that gene discovery in NHL may be enhanced through comparative studies exploiting the less complex association between CNAs and tumor pathogenesis in canine patients. DA - 2011/7// PY - 2011/7// DO - 10.3109/10428194.2011.559802 VL - 52 IS - 7 SP - 1321-1335 SN - 1029-2403 KW - Comparative genomic hybridization (CGH) KW - canine KW - lymphoma KW - chromosome KW - microarray ER - TY - JOUR TI - Passive Immunization with a Polyclonal Antiserum to the Hemoglobin Receptor of Haemophilus ducreyi Confers Protection against a Homologous Challenge in the Experimental Swine Model of Chancroid AU - Leduc, Isabelle AU - Fusco, William G. AU - Choudhary, Neelima AU - Routh, Patty A. AU - Cholon, Deborah M. AU - Hobbs, Marcia M. AU - Almond, Glen W. AU - Orndorff, Paul E. AU - Elkins, Christopher T2 - INFECTION AND IMMUNITY AB - Haemophilus ducreyi, the etiologic agent of chancroid, has an obligate requirement for heme. Heme is acquired by H. ducreyi from its human host via TonB-dependent transporters expressed at its bacterial surface. Of 3 TonB-dependent transporters encoded in the genome of H. ducreyi, only the hemoglobin receptor, HgbA, is required to establish infection during the early stages of the experimental human model of chancroid. Active immunization with a native preparation of HgbA (nHgbA) confers complete protection in the experimental swine model of chancroid, using either Freund's or monophosphoryl lipid A as adjuvants. To determine if transfer of anti-nHgbA serum is sufficient to confer protection, a passive immunization experiment using pooled nHgbA antiserum was conducted in the experimental swine model of chancroid. Pigs receiving this pooled nHgbA antiserum were protected from a homologous, but not a heterologous, challenge. Passively transferred polyclonal antibodies elicited to nHgbA bound the surface of H. ducreyi and partially blocked hemoglobin binding by nHgbA, but were not bactericidal. Taken together, these data suggest that the humoral immune response to the HgbA vaccine is protective against an H. ducreyi infection, possibly by preventing acquisition of the essential nutrient heme. DA - 2011/8// PY - 2011/8// DO - 10.1128/iai.00017-11 VL - 79 IS - 8 SP - 3168-3177 SN - 1098-5522 ER - TY - JOUR TI - Genes of the Unfolded Protein Response Pathway Harbor Risk Alleles for Primary Open Angle Glaucoma AU - Carbone, Mary Anna AU - Chen, Yuhong AU - Hughes, Guy A. AU - Weinreb, Robert N. AU - Zabriskie, Norman A. AU - Zhang, Kang AU - Anholt, Robert R. H. T2 - PLOS ONE AB - The statistical power of genome-wide association (GWA) studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG). Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG) remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR) upon overexpression of transgenic human glaucoma-associated myocilin (MYOC). We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention. DA - 2011/5/31/ PY - 2011/5/31/ DO - 10.1371/journal.pone.0020649 VL - 6 IS - 5 SP - SN - 1932-6203 ER - TY - JOUR TI - Facile synthesis of a B,D-tetradehydrocorrin and rearrangement to bacteriochlorins AU - Aravindu, Kunche AU - Krayer, Michael AU - Kim, Han-Je AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - Tetradehydrocorrins contain an A–D ring junction and a level of saturation intermediate between that of a corrin (characteristic of vitamin B12) and that of a corrole. Self-condensation of a p-tolyl-substituted dihydrodipyrrin-acetal (DHDPA-T) in CH2Cl2 containing Yb(OTf)3 at room temperature afforded the corresponding free base B,D-tetradehydrocorrin (TDC-T) as the sole macrocycle in 77% yield. The presence of a geminal dimethyl group in each of the reduced rings in TDC-T affords stability toward adventitious dehydrogenation. Treatment of TDC-T to acidic conditions results in rearrangement and loss of methanol to give a bacteriochlorin with or without a 5-methoxy substituent; the yield was 56% (5-methoxybacteriochlorin MeOBC-T), 35% (MeOBC-T) or 20% (5-unsubstituted bacteriochlorin HBC-T) with TMSOTf/CH2Cl2, BF3·OEt2/CH3CN or BF3·OEt2/CH2Cl2, respectively. TDC-T undergoes regioselective bromination with NBS to give the 10-bromotetradehydrocorrin in 22% yield. The conversion of the (non-aromatic) tetradehydrocorrin to the (aromatic) bacteriochlorin reflects the relative stability of the two macrocycles and indicates the former may be an intermediate—kinetically trapped or transient depending on catalysis conditions—upon dihydrodipyrrin-acetal self-condensation. DA - 2011/// PY - 2011/// DO - 10.1039/c1nj20027e VL - 35 IS - 7 SP - 1376 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/c1nj20027e DB - Crossref ER - TY - JOUR TI - Association genetics of carbon isotope discrimination, height and foliar nitrogen in a natural population of Pinus taeda L AU - Cumbie, W. P. AU - Eckert, A. AU - Wegrzyn, J. AU - Whetten, R. AU - Neale, D. AU - Goldfarb, B. T2 - HEREDITY AB - Loblolly pine, Pinus taeda L., is one of the most widely planted, commercially and ecologically important tree species in North America. We took an association genetics approach, using an unimproved population of 380 clonally replicated unrelated trees, to test 3,938 single nucleotide polymorphisms (SNPs) in as many genes for association with phenotypic variation in carbon isotope discrimination, foliar nitrogen concentration and total tree height after two growing seasons. Best linear unbiased prediction (BLUP) was used with a spatial adjustment to remove environmental variation from phenotypic data derived from a common garden experiment. After correction for multiple testing, a total of 14 SNPs were associated with the traits of carbon isotope discrimination (n = 7), height (n = 1) and foliar nitrogen concentration (n = 6) using 380 clones. Tails of the population phenotypic distribution were compared for allele frequency differences, revealing 10 SNPs with allele frequency in at least one tail significantly different from the overall population. Eight associated SNPs were in sequences similar to known genes, such as an AP2 transcription factor related to carbon isotope discrimination and glutamate decarboxylase associated with foliar nitrogen concentration, and others were from unknown genes without homologs in Arabidopsis. DA - 2011/8// PY - 2011/8// DO - 10.1038/hdy.2010.168 VL - 107 IS - 2 SP - 105-114 SN - 0018-067X KW - water use efficiency KW - forest tree KW - population genetics KW - loblolly pine ER - TY - JOUR TI - Identification of Bartonella henselae in a horse from Germany AU - Cherry, N.A. AU - Liebisch, G. AU - Liebisch, A. AU - Breitschwerdt, E.B. AU - Jones, S.L. AU - Ulrich, R. AU - Allmers, E. AU - Wolf, P. AU - Hewicker-Trautwein, M. T2 - Veterinary Microbiology AB - To investigate the occurrence of Bartonella sp. infection in asymptomatic horses and donkeys living in Tuscany, Central Italy.Blood samples were collected from 77 horses and 15 donkeys and tested by indirect immunofluorescent test to detect antibodies against Bartonella sp. and by PCR to detect the pathogen.Fifty-four (58.69%; 95% CI: 47.95%–68.87%) animals, 9 donkeys and 45 horses, were seropositive with antibody titers ranging from 1:64 to 1:512. PCR assays detected 9 horses positive for Bartonella sp. and 3 donkeys for Bartonella henselae genotype I.The detected sero-prevalence suggests a common and frequent exposure of equids living in Central Italy to bartonellae and PCR results show that Bartonella sp. infection is possible both in horses and donkeys. At the best of our knowledge, this is the first report of Bartonella henselae infection in donkeys. DA - 2011/6// PY - 2011/6// DO - 10.1016/j.vetmic.2011.02.010 VL - 150 IS - 3-4 SP - 414-415 J2 - Veterinary Microbiology LA - en OP - SN - 0378-1135 UR - http://dx.doi.org/10.1016/j.vetmic.2011.02.010 DB - Crossref ER - TY - JOUR TI - Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3 AU - Walters, Jad AU - Swartz, Paul AU - Mattos, Carla AU - Clark, A. Clay T2 - ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS AB - Interactions between loops 2, 2' and 4, known as the loop bundle, stabilize the active site of caspase-3. Loop 4 (L4) is of particular interest due to its location between the active site and the dimer interface. We have disrupted a salt bridge between K242 and E246 at the base of L4 to determine its role in overall conformational stability and in maintaining the active site environment. Stability measurements show that only the K242A single mutant decreases stability of the dimer, whereas both single mutants and the double mutant demonstrate much lower activity compared to wild-type caspase-3. Structural studies of the caspase-3 variants show the involvement of K242 in hydrophobic interactions that stabilize helix 5, near the dimer interface, and the role of E246 appears to be to neutralize the positive charge of K242 within the hydrophobic cluster. Overall, the results suggest E246 and K242 are important in procaspase-3 for their interaction with neighboring residues, not with one another. Conversely, formation of the K242-E246 salt bridge in caspase-3 is needed for an accurate, stable conformation of loop L4 and proper active site formation in the mature enzyme. DA - 2011/4/1/ PY - 2011/4/1/ DO - 10.1016/j.abb.2011.01.011 VL - 508 IS - 1 SP - 31-38 SN - 1096-0384 KW - Apoptosis KW - Caspase activation KW - Enzyme activity KW - Protein folding and assembly ER - TY - JOUR TI - Regulation of induced colonic inflammation by Lactobacillus acidophilus deficient in lipoteichoic acid AU - Mohamadzadeh, Mansour AU - Pfeiler, Erika A. AU - Brown, Jeffrey B. AU - Zadeh, Mojgan AU - Gramarossa, Matthew AU - Managlia, Elizabeth AU - Bere, Praveen AU - Sarraj, Bara AU - Khan, Mohammad W. AU - Pakanati, Krishna Chaitanya AU - Ansari, M. Javeed AU - O'Flaherty, Sarah AU - Barrett, Terrence AU - Klaenhammer, Todd R. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Imbalance in the regulatory immune mechanisms that control intestinal cellular and bacterial homeostasis may lead to induction of the detrimental inflammatory signals characterized in humans as inflammatory bowel disease. Induction of proinflammatory cytokines (i.e., IL-12) induced by dendritic cells (DCs) expressing pattern recognition receptors may skew naive T cells to T helper 1 polarization, which is strongly implicated in mucosal autoimmunity. Recent studies show the ability of probiotic microbes to treat and prevent numerous intestinal disorders, including Clostridium difficile -induced colitis. To study the molecular mechanisms involved in the induction and repression of intestinal inflammation, the phosphoglycerol transferase gene that plays a key role in lipoteichoic acid (LTA) biosynthesis in Lactobacillus acidophilus NCFM (NCK56) was deleted. The data show that the L. acidophilus LTA-negative in LTA (NCK2025) not only down-regulated IL-12 and TNFα but also significantly enhanced IL-10 in DCs and controlled the regulation of costimulatory DC functions, resulting in their inability to induce CD4 + T-cell activation. Moreover, treatment of mice with NCK2025 compared with NCK56 significantly mitigated dextran sulfate sodium and CD4 + CD45RB high T cell-induced colitis and effectively ameliorated dextran sulfate sodium-established colitis through a mechanism that involves IL-10 and CD4 + FoxP3 + T regulatory cells to dampen exaggerated mucosal inflammation. Directed alteration of cell surface components of L. acidophilus NCFM establishes a potential strategy for the treatment of inflammatory intestinal disorders. DA - 2011/3/15/ PY - 2011/3/15/ DO - 10.1073/pnas.1005066107 VL - 108 SP - 4623-4630 SN - 0027-8424 KW - antiinflammatory KW - lactobacilli KW - Toll-like receptor 2 KW - innate immunity ER - TY - JOUR TI - Leaf-level gas-exchange uniformity and photosynthetic capacity among loblolly pine (Pinus taeda L.) genotypes of contrasting inherent genetic variation AU - Aspinwall, Michael J. AU - King, John S. AU - McKeand, Steven E. AU - Domec, Jean-Christophe T2 - TREE PHYSIOLOGY AB - Variation in leaf-level gas exchange among widely planted genetically improved loblolly pine (Pinus taeda L.) genotypes could impact stand-level water use, carbon assimilation, biomass production, C allocation, ecosystem sustainability and biogeochemical cycling under changing environmental conditions. We examined uniformity in leaf-level light-saturated photosynthesis (Asat), stomatal conductance (gs), and intrinsic water-use efficiency (Asat/gs or δ) among nine loblolly pine genotypes (selected individuals): three clones, three full-sib families and three half-sib families, during the early years of stand development (first 3 years), with each genetic group possessing varying amounts of inherent genetic variation. We also compared light- and CO2-response parameters between genotypes and examined the relationship between genotype productivity, gas exchange and photosynthetic capacity. Within full-sib, half-sib and clonal genotypes, the coefficient of variation (CV) for gas exchange showed no consistent pattern; the CV for gs and δ was similar within clonal (44.3–46.9 and 35.5–38.6%) and half-sib (41.0–49.3 and 36.8–40.9%) genotypes, while full-sibs showed somewhat higher CVs (46.9–56.0 and 40.1–45.4%). In contrast, the CVs for Asat were generally higher within clones. With the exception of δ, differences in gas exchange among genotypes were generally insignificant. Tree volume showed a significant positive correlation with Asat and δ, but the relationship varied by season. Individual-tree volume and genotype volume were positively correlated with needle dark respiration (Rd). Our results suggest that uniformity in leaf-level physiological rates is not consistently related to the amount of genetic variation within a given genotype, and δ, Asat and Rd were the leaf-level physiological parameters that were most consistently related to individual-tree and genotype productivity. An enhanced understanding of molecular and environmental factors that influence physiological variation within and between loblolly pine genotypes may improve assessments of genotype growth potential and sensitivity to global climate change. DA - 2011/1// PY - 2011/1// DO - 10.1093/treephys/tpq107 VL - 31 IS - 1 SP - 78-91 SN - 1758-4469 KW - gas exchange KW - genetic variation KW - photosynthesis KW - productivity KW - water use ER - TY - JOUR TI - Incorporation of secretory immunoglobulin A into biofilms can decrease their resistance to ciprofloxacin AU - Lee, Yu-Huei AU - Su, Kuei-Ying AU - Wyse, Aaron AU - Barbas, Andrew AU - Palestrandt, Daniel AU - Shieh, Karl AU - Everett, Mary Lou AU - Devalapalli, Aditya AU - Orndorff, Paul E. AU - Bollinger, R. Randal AU - Parker, William T2 - MICROBIOLOGY AND IMMUNOLOGY AB - Extracellular matrices utilized by biofilms growing on inert surfaces are generally produced entirely by the bacteria growing within those biofilms, whereas symbiotic (mutualistic) biofilms growing in or on a wide range of plants and animals utilize host-derived macromolecules, such as mucoid substances, as components of their extracellular matrix. Incorporation of host-derived molecules may have a profound effect on the resistance to antibiotics of symbiotic biofilms, which may have important implications for medicine and biology. As an initial probe of the potential effects of host-derived molecules in the extracellular matrix on the sensitivity of biofilms to antibiotics, an in vitro model was used to evaluate the effects of ciprofloxacin on biofilms grown in the presence and absence of SIgA, a host-derived glycoprotein associated with biofilms in the mammalian gut. In five out of six strains of Escherichia coli tested, the incorporation of SIgA into the biofilms apparently reduced the resistance of the bacteria to ciprofloxacin. On the other hand, SIgA generally increased the resistance of planktonic bacteria to ciprofloxacin, perhaps due in part to the SIgA-mediated aggregation of the bacteria. These findings suggest that incorporation of host-derived molecules into the extracellular matrix of symbiotic biofilms might profoundly alter the properties of those biofilms, including the resistance of those biofilms to antibiotics. DA - 2011/3// PY - 2011/3// DO - 10.1111/j.1348-0421.2010.00297.x VL - 55 IS - 3 SP - 174-183 SN - 1348-0421 KW - antibiotic KW - ciprofloxacin KW - Escherichia coli KW - host-supported biofilms ER - TY - JOUR TI - High-Confidence Discovery of Genetic Network Regulators in Expression Quantitative Trait Loci Data AU - Duarte, Christine W. AU - Zeng, Zhao-Bang T2 - GENETICS AB - Abstract Expression QTL (eQTL) studies involve the collection of microarray gene expression data and genetic marker data from segregating individuals in a population to search for genetic determinants of differential gene expression. Previous studies have found large numbers of trans-regulated genes (regulated by unlinked genetic loci) that link to a single locus or eQTL “hotspot,” and it would be desirable to find the mechanism of coregulation for these gene groups. However, many difficulties exist with current network reconstruction algorithms such as low power and high computational cost. A common observation for biological networks is that they have a scale-free or power-law architecture. In such an architecture, highly influential nodes exist that have many connections to other nodes. If we assume that this type of architecture applies to genetic networks, then we can simplify the problem of genetic network reconstruction by focusing on discovery of the key regulatory genes at the top of the network. We introduce the concept of “shielding” in which a specific gene expression variable (the shielder) renders a set of other gene expression variables (the shielded genes) independent of the eQTL. We iteratively build networks from the eQTL to the shielder down using tests of conditional independence. We have proposed a novel test for controlling the shielder false-positive rate at a predetermined level by requiring a threshold number of shielded genes per shielder. Using simulation, we have demonstrated that we can control the shielder false-positive rate as well as obtain high shielder and edge specificity. In addition, we have shown our method to be robust to violation of the latent variable assumption, an important feature in the practical application of our method. We have applied our method to a yeast expression QTL data set in which microarray and marker data were collected from the progeny of a backcross of two species of Saccharomyces cerevisiae (Bremet al. 2002). Seven genetic networks have been discovered, and bioinformatic analysis of the discovered regulators and corresponding regulated genes has generated plausible hypotheses for mechanisms of regulation that can be tested in future experiments. DA - 2011/3// PY - 2011/3// DO - 10.1534/genetics.110.124685 VL - 187 IS - 3 SP - 955-964 SN - 0016-6731 ER - TY - JOUR TI - BCR-ABL translocation in a dog with chronic monocytic leukemia AU - Cardona, Janice A. Cruz AU - Milner, Rowan AU - Alleman, A. Rick AU - Williams, Christina AU - Vernau, William AU - Breen, Matthew AU - Tompkins, Mary T2 - VETERINARY CLINICAL PATHOLOGY AB - A 9-year-old female spayed mixed breed dog was evaluated at the University of Florida Small Animal Hospital for marked leukocytosis with no associated clinical signs. CBC abnormalities included marked leukocytosis (106,000/μL), marked monocytosis (78,000/μL), and the presence of 13% blast cells (13,832/μL), supporting a diagnosis of leukemia. Cytopenias and dysplastic changes in other cell lines were not present. Microscopic examination of bone marrow showed hypercellular uniparticles with a marginal increase in frequency of unclassified blast cells (2%), but was otherwise unremarkable. Flow cytometric immunophenotyping of blood cells determined that leukemic cells were CD45(+) , CD14(+) , and CD34(-) , and based on side scatter and CD45 reactivity the marrow contained 19% monoblasts. By immunocytochemical staining, the leukemic cells in the bone marrow were CD11b(+) , CD11c(+) , CD11d(+) , MHC-II(+) , MPO(+) , and CD34(-) . Fluorescence in situ hybridization (FISH) analysis of peripheral blood leukocytes documented a chromosomal translocation producing a BCR-ABL gene hybrid, similar to the "Philadelphia" chromosome abnormality recognized in human chronic myelogenous leukemia, as well as a phosphatase and tensin homolog (PTEN) gene deletion. Hydroxyurea therapy was attempted, but was ineffective; the dog died 7 months after initial presentation. Clinical and laboratory findings and the protracted course supported a diagnosis of chronic monocytic leukemia (CMoL) and, to our knowledge, this is the first case of CMoL with a BCR-ABL chromosomal abnormalitiy described in dogs. This may have clinical implications for treatment of dogs with chronic leukemias associated with particular genetic mutations. However, more case studies are needed to further characterize this disease. DA - 2011/3// PY - 2011/3// DO - 10.1111/j.1939-165x.2010.00277.x VL - 40 IS - 1 SP - 40-47 SN - 0275-6382 KW - FISH KW - flow cytometry KW - monocytosis KW - myeloproliferative disorder ER - TY - JOUR TI - The Red clover necrotic mosaic virus Capsid as a Multifunctional Cell Targeting Plant Viral Nanoparticle AU - Lockney, Dustin M. AU - Guenther, Richard N. AU - Loo, Lina AU - Overton, Wesley AU - Antonelli, Ray AU - Clark, Jennifer AU - Hu, Mei AU - Luft, Chris AU - Lommel, Steven A. AU - Franzen, Stefan T2 - BIOCONJUGATE CHEMISTRY AB - Multifunctional nanoparticles hold promise as the next generation of therapeutic delivery and imaging agents. Nanoparticles comprising many types of materials are being tested for this purpose, including plant viral capsids. It has been found that Red clover necrotic mosaic virus (RCNMV) can be loaded with significant amounts of therapeutic molecules with molecular weights of 600 or even greater. Formulation of RCNMV into a plant viral nanoparticle (PVN) involves the loading of cargo and attachment of peptides. In this study, we show that targeting peptides (less than 16 amino acids) can be conjugated to the capsid using the heterobifunctional chemical linker sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (Sulfo-SMCC). The uptake of both native RCNMV capsids and peptide-conjugated RCNMV was tested in the HeLa cell line for peptides with and without fluorescent labels. Uptake of RCNMV conjugate with a CD46 targeting peptide was monitored by flow cytometry. When formulated PVNs loaded with doxorubicin and armed with a targeting peptide were delivered to HeLa cells, a cytotoxic effect was observed. The ability to modify RCNMV for specific cell targeting and cargo delivery offers a method for the intracellular delivery of reagents for research assays as well as diagnostic and therapeutic applications. DA - 2011/1// PY - 2011/1// DO - 10.1021/bc100361z VL - 22 IS - 1 SP - 67-73 SN - 1520-4812 ER - TY - JOUR TI - Structural characteristics that make chlorophylls green: interplay of hydrocarbon skeleton and substituents AU - Mass, Olga AU - Taniguchi, Masahiko AU - Ptaszek, Marcin AU - Springer, Joseph W. AU - Faries, Kaitlyn M. AU - Diers, James R. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - NEW JOURNAL OF CHEMISTRY AB - Understanding the effects of substituents on natural photosynthetic pigments is essential for gaining a deep understanding of why such pigments were selected over the course of evolution for use in photosynthetic systems. This knowledge should provide for a more thoughtful design of artificial light-harvesting systems. The hydrocarbon skeleton of all chlorophylls is phorbine, which contains an annulated five-membered (isocyclic) ring in addition to the reduced pyrrole ring characteristic of chlorins. A phorbine and a 131-oxophorbine (which bears an oxo group in the isocyclic ring) were synthesized as benchmark molecules for fundamental spectral and photophysical studies. The phorbine and 131-oxophorbine macrocycles lack peripheral substituents other than a geminal dimethyl group in the reduced ring to stabilize the chlorin chromophore. The spectral properties and electronic structure of the zinc or free base 131-oxophorbine closely resemble those of the corresponding analogues of chlorophyll a. Accordingly, the fundamental electronic properties of chlorophylls are primarily a consequence of the 131-oxophorbine base macrocycle. DA - 2011/// PY - 2011/// DO - 10.1039/c0nj00652a VL - 35 IS - 1 SP - 76-88 SN - 1369-9261 ER - TY - JOUR TI - Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.) AU - Palle, Sreenath Reddy AU - Seeve, Candace M. AU - Eckert, Andrew J. AU - Cumbie, W. Patrick AU - Goldfarb, Barry AU - Loopstra, Carol A. T2 - TREE GENETICS & GENOMES AB - Gene expression analyses using native populations can contribute to the understanding of plant development and adaptation in multiple ways. These include the identification of candidate genes and genetic polymorphisms affecting expression and phenotypic traits and characterization of transcriptional networks. We analyzed the expression of 111 genes with probable roles in xylem/wood development in a population of loblolly pine (Pinus taeda L.) covering much of the natural range. Loblolly pine is one of the most commercially important forest tree species in the United States, and the discovery of genes and alleles contributing to desirable wood properties would be valuable. Of the 111 genes analyzed using quantitative reverse transcription–polymerase chain reaction, there were significant differences in gene expression between clones for 106 genes. Genes encoding lignin biosynthetic enzymes and arabinogalactan proteins were more variable than those encoding cellulose synthases or those involved in signal transduction. Several groups of genes with related functions form clusters. A network analysis identified transcription factors that may be key regulators of xylem development in pine. Secondary wall-associated NAC domain protein 1 (SND1) in particular appears to be involved in the regulation of many other genes. The cluster analysis using clones did not result in discrete populations but did identify some expression differences between regions. In the future, the gene expression data will be used for association analyses and promoter studies to understand how these gene expression differences are associated with specific genetic polymorphisms in other genes and promoters. DA - 2011/2// PY - 2011/2// DO - 10.1007/s11295-010-0325-7 VL - 7 IS - 1 SP - 193-206 SN - 1614-2950 KW - Gene expression KW - Natural variation KW - Pinus taeda L KW - Xylem ER - TY - JOUR TI - FLT3 mutations in canine acute lymphocytic leukemia AU - Suter, Steven E. AU - Small, George W. AU - Seiser, Eric L. AU - Thomas, Rachael AU - Breen, Matthew AU - Richards, Kristy L. T2 - BMC CANCER AB - Abstract Background FMS-like tyrosine kinase 3 (FLT3) is a commonly mutated protein in a variety of human acute leukemias. Mutations leading to constitutively active FLT3, including internal tandem duplications of the juxtamembrane domain (ITD), result in continuous cellular proliferation, resistance to apoptotic cell death, and a poorer prognosis. A better understanding of the molecular consequences of FLT3 activation would allow improved therapeutic strategies in these patients. Canine lymphoproliferative diseases, including lymphoma and acute leukemias, share evolutionarily conserved chromosomal aberrations and exhibit conserved mutations within key oncogenes when compared to their human counterparts. A small percentage of canine acute lymphocytic leukemias (ALL) also exhibit FLT3 ITD mutations. Methods We molecularly characterized FLT3 mutations in two dogs and one cell line, by DNA sequencing, gene expression analysis via quantitative real-time PCR, and sensitivity to the FLT3 inhibitor lestaurtinib via in vitro proliferation assays. FLT 3 and downstream mediators of FLT3 activation were assessed by Western blotting. Results The canine B-cell leukemia cell line, GL-1, and neoplastic cells from 2/7 dogs diagnosed cytologically with ALL were found to have FLT3 ITD mutations and FLT3 mRNA up-regulation. Lestaurtinib, a small molecule FLT3 inhibitor, significantly inhibited the growth of GL-1 cells, while not affecting the growth of two other canine lymphoid cell lines without the FLT3 mutation. Finally, western blots were used to confirm the conserved downstream mediators of FLT3 activating mutations. Conclusions These results show that ALL and FLT3 biology is conserved between canine and human patients, supporting the notion that canine ALL, in conjunction with the GL-1 cell line, will be useful in the development of a relevant large animal model to aid in the study of human FLT3 mutant leukemias. DA - 2011/1/27/ PY - 2011/1/27/ DO - 10.1186/1471-2407-11-38 VL - 11 SP - SN - 1471-2407 ER - TY - JOUR TI - Computational and phylogenetic validation of nematode horizontal gene transfer AU - Scholl, Elizabeth H. AU - Bird, David McK T2 - BMC BIOLOGY AB - Sequencing of expressed genes has shown that nematodes, particularly the plant-parasitic nematodes, have genes purportedly acquired from other kingdoms by horizontal gene transfer. The prevailing orthodoxy is that such transfer has been a driving force in the evolution of niche specificity, and a recent paper in BMC Evolutionary Biology that presents a detailed phylogenetic analysis of cellulase genes in the free-living nematode Pristionchus pacificus at the species, genus and family levels substantiates this hypothesis. DA - 2011/2/22/ PY - 2011/2/22/ DO - 10.1186/1741-7007-9-9 VL - 9 SP - SN - 1741-7007 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-79951811845&partnerID=MN8TOARS ER - TY - JOUR TI - Abiotic formation of uroporphyrinogen and coproporphyrinogen from acyclic reactants AU - Lindsey, Jonathan S. AU - Chandrashaker, Vanampally AU - Taniguchi, Masahiko AU - Ptaszek, Marcin T2 - NEW JOURNAL OF CHEMISTRY AB - Tetrapyrrole macrocycles (e.g., porphyrins) have long been proposed as key ingredients in the emergence of life, yet plausible routes for forming their essential pyrrole precursor have previously not been identified. Here, the anaerobic reaction of δ-aminolevulinic acid (ALA, 5–240 mM) with 5-methoxy-3-(methoxyacetyl)levulinic acid (1-AcOH, 5–240 mM) in water (pH 5–7) at 25–85 °C for a few hours to a few days affords uroporphyrinogen, which upon chemical oxidation gives uroporphyrin in overall yield of up to 10%. The key intermediate is the α-methoxymethyl-substituted analogue of the pyrrole porphobilinogen (PBG). Reaction of ALA and the decarboxy analogue of 1-AcOH (1-Me) gave coproporphyrinogen (without its biosynthetic precursor uroporphyrinogen as an intermediate); oxidation gave the corresponding coproporphyrin in yields comparable to those for uroporphyrin. In each case a mixture of porphyrin isomers was obtained, consistent with reversible oligopyrromethane formation. The route investigated here differs from the universal extant biosynthetic pathway to tetrapyrrole macrocycles, where uroporphyrinogen (isomer III) – nature's last common precursor to corrins, heme, and chlorophylls – is derived from eight molecules of ALA (via four molecules of PBG). The demonstration of the spontaneous self-organization of eight acyclic molecules to form the porphyrinogen under simple conditions may open the door to the development of a chemical model for the prebiogenesis of tetrapyrrole macrocycles. DA - 2011/// PY - 2011/// DO - 10.1039/c0nj00716a VL - 35 IS - 1 SP - 65-75 SN - 1369-9261 ER - TY - JOUR TI - A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme AU - Kubisiak, Thomas L. AU - Anderson, Claire L. AU - Amerson, Henry V. AU - Smith, Jason A. AU - Davis, John M. AU - Nelson, C. Dana T2 - FUNGAL GENETICS AND BIOLOGY AB - A novel approach is presented to map avirulence gene Avr1 in the basidiomycete Cronartium quercuum f.sp. fusiforme, the causal agent of fusiform rust disease in pines. DNA markers tightly linked to resistance gene Fr1 in loblolly pine tree 10-5 were used to classify 10-5 seedling progeny as either resistant or susceptible. A single dikaryotic isolate (P2) heterozygous at the corresponding Avr1 gene was developed by crossing Fr1 avirulent isolate SC20-21 with Fr1 virulent isolate NC2-40. Bulk basidiospore inoculum derived from isolate P2 was used to challenge the pine progeny. The ability to unambiguously marker classify 10-5 progeny as resistant (selecting for virulence) or susceptible (non-selecting) permitted the genetic mapping of the corresponding Avr1 gene by bulked segregant analysis. Using this approach, 14 genetic markers significantly linked to Avr1 were identified and placed within the context of a genome-wide linkage map produced for isolate P2 using samples from susceptible seedlings. DA - 2011/3// PY - 2011/3// DO - 10.1016/j.fgb.2010.09.008 VL - 48 IS - 3 SP - 266-274 SN - 1096-0937 KW - AFLP KW - Avirulence gene KW - Cronartium quercuum f.sp fusiforme KW - Fusiform rust KW - Linkage map KW - RAPD KW - Gene-for-gene interaction ER - TY - JOUR TI - Role of the Vacuolar-ATPase in Sindbis Virus Infection AU - Hunt, Sabrina R. AU - Hernandez, Raquel AU - Brown, Dennis T. T2 - JOURNAL OF VIROLOGY AB - Bafilomycin A(1) is a specific inhibitor of the vacuolar-ATPase (V-ATPase), which is responsible for pH homeostasis of the cell and for the acidification of endosomes. Bafilomycin A(1) has been commonly used as a method of inhibition of infection by viruses known or suspected to follow the path of receptor-mediated endocytosis and low-pH-mediated membrane fusion. The exact method of entry for Sindbis virus, the prototype alphavirus, remains undetermined. To further investigate the role of the V-ATPase in Sindbis virus infection, the effects of bafilomycin A(1) on the infection of BHK and insect cells by Sindbis virus were studied. Bafilomycin A(1) was found to block the expression of a virus-encoded reporter gene in both infection and transfection of BHK cells. The inhibitory effects of bafilomycin A(1) were found to be reversible. The results suggest that in BHK cells in the presence of bafilomycin A(1), virus RNA enters the cell and is translated, but replication and proper folding of the product proteins requires the function of the V-ATPase. Bafilomycin A(1) had no significant effect on the outcome of infection in insect cells. DA - 2011/2// PY - 2011/2// DO - 10.1128/jvi.01864-10 VL - 85 IS - 3 SP - 1257-1266 SN - 1098-5514 ER - TY - JOUR TI - Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia AU - Kaye, A. C. AU - Moyer, J. W. AU - Parks, E. J. AU - Carbone, I. AU - Cubeta, M. A. T2 - PHYTOPATHOLOGY AB - Exploring the genetic diversity and evolutionary history of plant viruses is critical to understanding their ecology and epidemiology. In this study, maximum-likelihood and population genetics-based methods were used to investigate the population structure, genetic diversity, and sources of genetic variation in field isolates of Tomato spotted wilt virus (TSWV) from peanut in North Carolina and Virginia. Selected regions of the nucleocapsid, movement, and RNA-dependent RNA polymerase genes were amplified and sequenced to identify haplotypes and infer genetic relationships between isolates of TSWV with heuristic methods. The haplotype structure of each locus consisted of 1 or 2 predominant haplotypes and >100 haplotypes represented by a single isolate. No specific haplotypes were associated with geographic area, peanut cultivar, or year of isolation. The population was panmictic at the regional level and high levels of genetic diversity were observed among isolates. There was evidence for positive selection on single amino acids in each gene on a background of predominant purifying selection acting upon each locus. The results of compatibility analyses and the persistence of specific gene sequences in isolates collected over three field seasons suggest that recombination was occurring in the population. Estimates of the population mutation rate suggest that mutation has had a significant effect on the shaping of this population and, together with purifying selection, these forces have been the predominant evolutionary forces influencing the TSWV population in peanut in North Carolina and Virginia. DA - 2011/1// PY - 2011/1// DO - 10.1094/phyto-01-10-0035 VL - 101 IS - 1 SP - 147-153 SN - 1943-7684 KW - population diversity ER - TY - JOUR TI - Glycine and a Glycine Dehydrogenase (GLDC) SNP as Citalopram/Escitalopram Response Biomarkers in Depression: Pharmacometabolomics-Informed Pharmacogenomics AU - Ji, Y. AU - Hebbring, S. AU - Zhu, H. AU - Jenkins, G. D. AU - Biernacka, J. AU - Snyder, K. AU - Drews, M. AU - Fiehn, O. AU - Zeng, Z. AU - Schaid, D. AU - Mrazek, D. A. AU - Kaddurah-Daouk, R. AU - Weinshilboum, R. M. T2 - CLINICAL PHARMACOLOGY & THERAPEUTICS AB - Major depressive disorder (MDD) is a common psychiatric disease. Selective serotonin reuptake inhibitors (SSRIs) are an important class of drugs used in the treatment of MDD. However, many patients do not respond adequately to SSRI therapy. We used a pharmacometabolomics-informed pharmacogenomic research strategy to identify citalopram/escitalopram treatment outcome biomarkers. Metabolomic assay of plasma samples from 20 escitalopram remitters and 20 nonremitters showed that glycine was negatively associated with treatment outcome (P = 0.0054). This observation was pursued by genotyping tag single-nucleotide polymorphisms (SNPs) for genes encoding glycine synthesis and degradation enzymes, using 529 DNA samples from SSRI-treated MDD patients. The rs10975641 SNP in the glycine dehydrogenase (GLDC) gene was associated with treatment outcome phenotypes. Genotyping for rs10975641 was carried out in 1,245 MDD patients in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, and its presence was significant (P = 0.02) in DNA taken from these patients. These results highlight a possible role for glycine in SSRI response and illustrate the use of pharmacometabolomics to “inform” pharmacogenomics. Clinical Pharmacology & Therapeutics (2011) 89 1, 97–104. doi: 10.1038/clpt.2010.250 DA - 2011/1// PY - 2011/1// DO - 10.1038/clpt.2010.250 VL - 89 IS - 1 SP - 97-104 SN - 1532-6535 ER - TY - JOUR TI - Functional Analysis of a Novel Motif Conserved across Geminivirus Rep Proteins AU - Nash, Tara E. AU - Dallas, Mary B. AU - Reyes, Maria Ines AU - Buhrman, Gregory K. AU - Ascencio-Ibanez, J. Trinidad AU - Hanley-Bowdoin, Linda T2 - JOURNAL OF VIROLOGY AB - ABSTRACT Members of the Geminiviridae have single-stranded DNA genomes that replicate in nuclei of infected plant cells. All geminiviruses encode a conserved protein (Rep) that catalyzes initiation of rolling-circle replication. Earlier studies showed that three conserved motifs—motifs I, II, and III—in the N termini of geminivirus Rep proteins are essential for function. In this study, we identified a fourth sequence, designated GRS ( g eminivirus R ep s equence), in the Rep N terminus that displays high amino acid sequence conservation across all geminivirus genera. Using the Rep protein of Tomato golden mosaic virus (TGMV AL1), we show that GRS mutants are not infectious in plants and do not support viral genome replication in tobacco protoplasts. GRS mutants are competent for protein-protein interactions and for both double- and single-stranded DNA binding, indicating that the mutations did not impair its global conformation. In contrast, GRS mutants are unable to specifically cleave single-stranded DNA, which is required to initiate rolling-circle replication. Interestingly, the Rep proteins of phytoplasmal and algal plasmids also contain GRS-related sequences. Modeling of the TGMV AL1 N terminus suggested that GRS mutations alter the relative positioning of motif II, which coordinates metal ions, and motif III, which contains the tyrosine involved in DNA cleavage. Together, these results established that the GRS is a conserved, essential motif characteristic of an ancient lineage of rolling-circle initiators and support the idea that geminiviruses may have evolved from plasmids associated with phytoplasma or algae. DA - 2011/2// PY - 2011/2// DO - 10.1128/jvi.02143-10 VL - 85 IS - 3 SP - 1182-1192 SN - 1098-5514 ER - TY - JOUR TI - Fatal Aortic Endocarditis Associated with Community-Acquired Serratia marcescens Infection in a Dog AU - Perez, Cristina AU - Fujii, Yoko AU - Fauls, Megan AU - Hummel, James AU - Breitschwerdt, Edward T2 - JOURNAL OF THE AMERICAN ANIMAL HOSPITAL ASSOCIATION AB - A 12 yr old Dalmatian was referred for evaluation of acute lethargy, fever, neurologic signs, and a recently ausculted heart murmur. Echocardiography in combination with blood cultures resulted in a diagnosis of nonhospital-acquired Serratia marcescens bacteremia and aortic valve endocarditis. Despite early diagnosis and aggressive therapy, the dog failed to respond to antimicrobials and died within 6 hr after admission. Necropsy findings included aortic valve endocarditis, septicemia, and diffuse thromboembolic disease. There was no history of pre-existing underlying disease or immunosuppressive therapy, and the dog had not been hospitalized before referral. DA - 2011/// PY - 2011/// DO - 10.5326/jaaha-ms-5616 VL - 47 IS - 2 SP - 133-137 SN - 1547-3317 ER - TY - JOUR TI - Autocrine Effects of Interleukin-6 Mediate Acute-Phase Proinflammatory and Tissue-Reparative Transcriptional Responses of Canine Bladder Mucosa AU - Wood, Michael W. AU - Breitschwerdt, Edward B. AU - Gookin, Jody L. T2 - INFECTION AND IMMUNITY AB - During early urinary tract infection (UTI) the interplay between invading bacteria and the urothelium elicits a mucosal response aimed at clearing infection. Unfortunately, the resultant inflammation and associated local tissue injury are responsible for patient symptoms. Interleukin-6 (IL-6), a cytokine released during acute UTI, has both pro- and anti-inflammatory effects on other body systems. Within the urothelium, the IL-6 native-tissue origin, the target cell type(s), and ultimate effect of the cytokine on target cells are largely unknown. In the present study we modeled the UTI IL-6 response ex vivo using canine bladder mucosa mounted in Ussing chambers to determine the inflammatory and reparative role of IL-6. We demonstrated that uropathogenic Escherichia coli infection stimulates the synthesis of IL-6 by all urothelial cell layers, with the urothelial cells alone representing the only site of unequivocal IL-6 receptor expression. Autocrine effects of IL-6 were supported by the activation of urothelial STAT3 signaling and SOCS3 expression. Using exogenous IL-6, a microarray approach, and quantitative reverse transcriptase PCR (q-RT-PCR), 5 target genes (tumor necrosis factor alpha, interleukin-1β, matrix metallopeptidase 2, heparan sulfate d-glucosaminyl 3-O-sulfotransferase 3A1, and hyaluronan synthase 2) that have direct or indirect roles in promoting a proinflammatory state were identified. Two of these genes, heparan sulfate d-glucosaminyl 3-O-sulfotransferase 3A1 and hyaluronan synthase 2, are also potentially important mediators of wound repair via the production of glycosaminoglycan components. These findings suggest that IL-6 secretion during acute UTI may serve a dual biological role by initiating the inflammatory response while also repairing urothelial defenses. DA - 2011/2// PY - 2011/2// DO - 10.1128/iai.01102-10 VL - 79 IS - 2 SP - 708-715 SN - 0019-9567 ER - TY - JOUR TI - Tapping the near-infrared spectral region with bacteriochlorin arrays AU - Lindsey, Jonathan S. AU - Mass, Olga AU - Chen, Chih-Yuan T2 - NEW JOURNAL OF CHEMISTRY AB - Bacteriochlorophylls—natural pigments for absorption of near-infrared (NIR) light—underlie light-absorption and energy transduction in photosynthetic bacteria. Capturing and utilizing NIR light is valuable in fields ranging from artificial photosynthesis to photomedicine (photodynamic therapy, imaging, and diagnostics). The desired photochemical features may be best elicited with multicomponent architectures that support efficient excited-state energy and/or electron transfer, yet few such arrays containing bacteriochlorins (the core chromophore of bacteriochlorophylls) are known. This review outlines three synthetic approaches toward bacteriochlorins, surveys all known bacteriochlorin arrays, and compares molecular design strategies for light-harvesting arrays containing bacteriochlorinsversus (the better known) porphyrins. DA - 2011/// PY - 2011/// DO - 10.1039/c0nj00977f VL - 35 IS - 3 SP - 511-516 SN - 1144-0546 ER - TY - JOUR TI - Partial Regulatory T Cell Depletion Prior to Acute Feline Immunodeficiency Virus Infection Does Not Alter Disease Pathogenesis AU - Mikkelsen, S. Rochelle AU - Long, Julie M. AU - Zhang, Lin AU - Galemore, Erin R. AU - VandeWoude, Sue AU - Dean, Gregg A. T2 - PLOS ONE AB - Feline immunodeficiency virus (FIV) infection in cats follows a disease course similar to HIV-1, including a short acute phase characterized by high viremia, and a prolonged asymptomatic phase characterized by low viremia and generalized immune dysfunction. CD4(+)CD25(hi)FoxP3(+) immunosuppressive regulatory T (Treg) cells have been implicated as a possible cause of immune dysfunction during FIV and HIV-1 infection, as they are capable of modulating virus-specific and inflammatory immune responses. Additionally, the immunosuppressive capacity of feline Treg cells has been shown to be increased during FIV infection. We have previously shown that transient in vivo Treg cell depletion during asymptomatic FIV infection reveals FIV-specific immune responses suppressed by Treg cells. In this study, we sought to determine the immunological influence of Treg cells during acute FIV infection. We asked whether Treg cell depletion prior to infection with the highly pathogenic molecular clone FIV-C36 in cats could alter FIV pathogenesis. We report here that partial Treg cell depletion prior to FIV infection does not significantly change provirus, viremia, or CD4(+) T cell levels in blood and lymphoid tissues during the acute phase of disease. The effects of anti-CD25 mAb treatment are truncated in cats acutely infected with FIV-C36 as compared to chronically infected cats or FIV-naïve cats, as Treg cell levels were heightened in all treatment groups included in the study within two weeks post-FIV infection. Our findings suggest that the influence of Treg cell suppression during FIV pathogenesis is most prominent after Treg cells are activated in the environment of established FIV infection. DA - 2011/2/25/ PY - 2011/2/25/ DO - 10.1371/journal.pone.0017183 VL - 6 IS - 2 SP - SN - 1932-6203 ER - TY - JOUR TI - Grafting fraser fir (Abies fraseri): Effect of scion origin (crown position and branch order) AU - Hibbert-Frey, H. AU - Frampton, J. AU - Blazich, F. A. AU - Hundley, D. AU - Hinesley, L. E. T2 - HortScience DA - 2011/// PY - 2011/// VL - 46 IS - 1 SP - 91-94 ER - TY - JOUR TI - De novo synthesis and photophysical characterization of annulated bacteriochlorins. Mimicking and extending the properties of bacteriochlorophylls AU - Krayer, Michael AU - Yang, Eunkyung AU - Diers, James R. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - Bacteriochlorophylls contain the bacteriochlorin chromophore and a fifth, five-membered oxopentano ring that encompasses positions 13–15 known as the “isocyclic” ring E. Such bacterio-131-oxophorbines have heretofore only been available in the naturally occurring compounds, and analogues bearing six-membered rings have only been available by derivatization of bacteriochlorophylls. A de novo route to synthetic bacteriochlorins, which bear a geminal dimethyl group in each pyrroline ring, has been extended to gain access to a bacterio-131-oxophorbine and bacteriochlorin-13,15-dicarboximides. The route relies on acid-catalyzed condensation of a dihydrodipyrrin-acetal to form the bacteriochlorin, which then is subjected to regioselective 15-bromination. Pd-mediated cyclization of the 15-bromobacteriochlorin bearing a 13-acetyl group (intramolecular α-arylation) or 13-ethoxycarbonyl group (carbamoylation and intramolecular imidation) gives the bacterio-131-oxophorbine or bacteriochlorin-13,15-dicarboximide, respectively. The resulting macrocycles exhibit absorption in the near-infrared spectral region (733–818 nm), which extends the spectral coverage beyond that obtained previously with synthetic bacteriochlorins that lack a fifth ring. The macrocycles also exhibit excited singlet-state lifetimes (1.9–4.6 ns) comparable to or longer than those of natural photosynthetic pigments. Density functional theory calculations predict that the bathochromically shifted absorption is primarily due to lowering of the energy of the lowest unoccupied molecular orbital. The new route complements existing semisynthetic routes and should enable fundamental spectroscopic studies and diverse photochemical applications. DA - 2011/// PY - 2011/// DO - 10.1039/c0nj00771d VL - 35 IS - 3 SP - 587 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/c0nj00771d DB - Crossref ER - TY - JOUR TI - Common motifs shared by conserved enhancers of Drosophila midline glial genes AU - Fulkerson, E. AU - Estes, P. A. T2 - Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution DA - 2011/// PY - 2011/// VL - 316B IS - 1 SP - 61-75 ER -