TY - JOUR TI - Abnormal Dosage Compensation of Reporter Genes Driven by the Drosophila Glass Multiple Reporter (GMR) Enhancer-Promoter AU - Laverty, Corey AU - Li, Fang AU - Belikoff, Esther J. AU - Scott, Maxwell J. T2 - PLoS ONE AB - In Drosophila melanogaster the male specific lethal (MSL) complex is required for upregulation of expression of most X-linked genes in males, thereby achieving X chromosome dosage compensation. The MSL complex is highly enriched across most active X-linked genes with a bias towards the 3′ end. Previous studies have shown that gene transcription facilitates MSL complex binding but the type of promoter did not appear to be important. We have made the surprising observation that genes driven by the glass multiple reporter (GMR) enhancer-promoter are not dosage compensated at X-linked sites. The GMR promoter is active in all cells in, and posterior to, the morphogenetic furrow of the developing eye disc. Using phiC31 integrase-mediated targeted integration, we measured expression of lacZ reporter genes driven by either the GMR or armadillo (arm) promoters at each of three X-linked sites. At all sites, the arm-lacZ reporter gene was dosage compensated but GMR-lacZ was not. We have investigated why GMR-driven genes are not dosage compensated. Earlier or constitutive expression of GMR-lacZ did not affect the level of compensation. Neither did proximity to a strong MSL binding site. However, replacement of the hsp70 minimal promoter with a minimal promoter from the X-linked 6-Phosphogluconate dehydrogenase gene did restore partial dosage compensation. Similarly, insertion of binding sites for the GAGA and DREF factors upstream of the GMR promoter led to significantly higher lacZ expression in males than females. GAGA and DREF have been implicated to play a role in dosage compensation. We conclude that the gene promoter can affect MSL complex-mediated upregulation and dosage compensation. Further, it appears that the nature of the basal promoter and the presence of binding sites for specific factors influence the ability of a gene promoter to respond to the MSL complex. DA - 2011/5/31/ PY - 2011/5/31/ DO - 10.1371/journal.pone.0020455 VL - 6 IS - 5 SP - e20455 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0020455 DB - Crossref ER - TY - JOUR TI - Gene Expression profile and response to maize kernels by Aspergillus flavus AU - Reese, B.N. AU - Payne, G.A. AU - Nielsen, D.M. AU - Woloshuk, C.P. T2 - Phytopathology AB - Aspergillus flavus causes an ear rot of maize, often resulting in the production of aflatoxin, a potent liver toxin and carcinogen that impacts the health of humans and animals. Many aspects of kernel infection and aflatoxin biosynthesis have been studied but the precise effects of the kernel environment on A. flavus are poorly understood. The goal of this research was to study the fungal response to the kernel environment during colonization. Gene transcription in A. flavus was analyzed by microarrays after growth on kernels of the four developmental stages: blister (R2), milk (R3), dough (R4), and dent (R5). Five days after inoculation, total RNA was isolated from kernels and hybridized to Affymetrix Gene Chip arrays containing probes representing 12,834 A. flavus genes. Statistical comparisons of the expression profile data revealed significant differences that included unique sets of upregulated genes in each kernel stage and six patterns of expression over the four stages. Among the genes expressed in colonized dent kernels were a phytase gene and six putative genes involved in zinc acquisition. Disruption of the phytase gene phy1 resulted in reduced growth on medium containing phytate as the sole source of phosphate. Furthermore, growth of the mutant (Δphy1) was 20% of the wild-type strain when wound inoculated into maize ears. In contrast, no difference was detected in the amount of aflatoxin produced relative to fungal growth, indicating that phy1 does not affect aflatoxin production. The study revealed the genome-wide effects of immature maize kernels on A. flavus and suggest that phytase has a role in pathogenesis. DA - 2011/// PY - 2011/// DO - 10.1094/PHYTO-09-10-0261 VL - 101 IS - 7 SP - 797–804 ER - TY - JOUR TI - Genome-wide linkage study of atopic dermatitis in West Highland White Terriers AU - Salzmann, Cary A AU - Olivry, Thierry JM AU - Nielsen, Dahlia M AU - Paps, Judith S AU - Harris, Tonya L AU - Olby, Natasha J T2 - BMC Genetics AB - Abstract Background Canine atopic dermatitis (AD) is a common, heritable, chronic allergic skin condition prevalent in the West Highland White Terrier (WHWT). In canine AD, environmental allergens trigger an inflammatory response causing visible skin lesions and chronic pruritus that can lead to secondary bacterial and yeast infections. The disorder shares many of the clinical and histopathological characteristics of human AD and represents an animal model of this disorder that could be used to further elucidate genetic causes of human AD. Microsatellite markers genotyped in families of WHWTs affected with AD were used to perform a genome-wide linkage study in order to isolate chromosomal regions associated with the disorder. Results Blood samples and health questionnaires were collected from 108 WHWTs spanning three families. A linkage simulation using these 108 dogs showed high power to detect a highly penetrant mutation. Ninety WHWTs were genotyped using markers from the Minimal Screening Set 2 (MSS-2). Two hundred and fifty six markers were informative and were used for linkage analysis. Using a LOD score of 2.7 as a significance threshold, no chromosomal regions were identified with significant linkage to AD. LOD scores greater than 1.0 were located in a 56 cM region of chromosome 7. Conclusions The study was unable to detect any chromosomal regions significantly linked to canine AD. This could be a result of factors such as environmental modification of phenotype, incorrect assignment of phenotype, a mutation of low penetrance, or incomplete genome coverage. A genome-wide SNP association study in a larger cohort of WHWTs may prove more successful by providing higher density coverage and higher statistical power. DA - 2011/// PY - 2011/// DO - 10.1186/1471-2156-12-37 VL - 12 IS - 1 SP - 37 J2 - BMC Genet LA - en OP - SN - 1471-2156 UR - http://dx.doi.org/10.1186/1471-2156-12-37 DB - Crossref 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 - 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 - 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 - The Arabidopsis YUCCA1 Flavin Monooxygenase Functions in the Indole-3-Pyruvic Acid Branch of Auxin Biosynthesis AU - Stepanova, Anna N. AU - Yun, Jeonga AU - Robles, Linda M. AU - Novak, Ondrej AU - He, Wenrong AU - Guo, Hongwei AU - Ljung, Karin AU - Alonso, Jose M. T2 - PLANT CELL AB - Abstract The effects of auxins on plant growth and development have been known for more than 100 years, yet our understanding of how plants synthesize this essential plant hormone is still fragmentary at best. Gene loss- and gain-of-function studies have conclusively implicated three gene families, CYTOCHROME P450 79B2/B3 (CYP79B2/B3), YUCCA (YUC), and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE-RELATED (TAA1/TAR), in the production of this hormone in the reference plant Arabidopsis thaliana. Each of these three gene families is believed to represent independent routes of auxin biosynthesis. Using a combination of pharmacological, genetic, and biochemical approaches, we examined the possible relationships between the auxin biosynthetic pathways defined by these three gene families. Our findings clearly indicate that TAA1/TARs and YUCs function in a common linear biosynthetic pathway that is genetically distinct from the CYP79B2/B3 route. In the redefined TAA1-YUC auxin biosynthetic pathway, TAA1/TARs are required for the production of indole-3-pyruvic acid (IPyA) from Trp, whereas YUCs are likely to function downstream. These results, together with the extensive genetic analysis of four pyruvate decarboxylases, the putative downstream components of the TAA1 pathway, strongly suggest that the enzymatic reactions involved in indole-3-acetic acid (IAA) production via IPyA are different than those previously postulated, and a new and testable model for how IAA is produced in plants is needed. DA - 2011/11// PY - 2011/11// DO - 10.1105/tpc.111.088047 VL - 23 IS - 11 SP - 3961-3973 SN - 1532-298X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84855168181&partnerID=MN8TOARS ER - TY - PCOMM TI - Probiotic and prebiotic claims in Europe: seeking a clear roadmap AU - Guarner, Francisco AU - Sanders, Mary Ellen AU - Gibson, Glenn AU - Klaenhammer, Todd AU - Cabana, Michael AU - Scott, Karen AU - Reid, Gregor AU - Delzenne, Nathalie M. AU - Fahey, George C., Jr. AU - Hill, Colin AB - An abstract is not available for this content. As you have access to this content, full HTML content is provided on this page. A PDF of this content is also available in through the ‘Save PDF’ action button. DA - 2011/12// PY - 2011/12// DO - 10.1017/s0007114511002248 SP - 1765-1767 ER - TY - JOUR TI - A Small-Molecule Screen Identifies L-Kynurenine as a Competitive Inhibitor of TAA1/TAR Activity in Ethylene-Directed Auxin Biosynthesis and Root Growth in Arabidopsis AU - He, Wenrong AU - Brumos, Javier AU - Li, Hongjiang AU - Ji, Yusi AU - Ke, Meng AU - Gong, Xinqi AU - Zeng, Qinglong AU - Li, Wenyang AU - Zhang, Xinyan AU - An, Fengying AU - Wen, Xing AU - Li, Pengpeng AU - Chu, Jinfang AU - Sun, Xiaohong AU - Yan, Cunyu AU - Yan, Nieng AU - Xie, De-Yu AU - Raikhel, Natasha AU - Yang, Zhenbiao AU - Stepanova, Anna N. AU - Alonso, Jose M. AU - Guo, Hongwei T2 - PLANT CELL AB - Abstract The interactions between phytohormones are crucial for plants to adapt to complex environmental changes. One example is the ethylene-regulated local auxin biosynthesis in roots, which partly contributes to ethylene-directed root development and gravitropism. Using a chemical biology approach, we identified a small molecule, l-kynurenine (Kyn), which effectively inhibited ethylene responses in Arabidopsis thaliana root tissues. Kyn application repressed nuclear accumulation of the ETHYLENE INSENSITIVE3 (EIN3) transcription factor. Moreover, Kyn application decreased ethylene-induced auxin biosynthesis in roots, and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE RELATEDs (TAA1/TARs), the key enzymes in the indole-3-pyruvic acid pathway of auxin biosynthesis, were identified as the molecular targets of Kyn. Further biochemical and phenotypic analyses revealed that Kyn, being an alternate substrate, competitively inhibits TAA1/TAR activity, and Kyn treatment mimicked the loss of TAA1/TAR functions. Molecular modeling and sequence alignments suggested that Kyn effectively and selectively binds to the substrate pocket of TAA1/TAR proteins but not those of other families of aminotransferases. To elucidate the destabilizing effect of Kyn on EIN3, we further found that auxin enhanced EIN3 nuclear accumulation in an EIN3 BINDING F-BOX PROTEIN1 (EBF1)/EBF2-dependent manner, suggesting the existence of a positive feedback loop between auxin biosynthesis and ethylene signaling. Thus, our study not only reveals a new level of interactions between ethylene and auxin pathways but also offers an efficient method to explore and exploit TAA1/TAR-dependent auxin biosynthesis. DA - 2011/11// PY - 2011/11// DO - 10.1105/tpc.111.089029 VL - 23 IS - 11 SP - 3944-3960 SN - 1040-4651 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84855168209&partnerID=MN8TOARS 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 - Wing patterning gene redefines the mimetic history of Heliconius butterflies AU - Hines, Heather M. AU - Counterman, Brian A. AU - Papa, Riccardo AU - Moura, Priscila Albuquerque AU - Cardoso, Marcio Z. AU - Linares, Mauricio AU - Mallet, James AU - Reed, Robert D. AU - Jiggins, Chris D. AU - Kronforst, Marcus R. AU - McMillan, W. Owen T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - The mimetic butterflies Heliconius erato and Heliconius melpomene have undergone parallel radiations to form a near-identical patchwork of over 20 different wing-pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries, and therefore might not represent the history of the adaptive traits as accurately as markers linked to color pattern genes. To assess the evolutionary histories across different loci, we compared relationships among races within H. erato and within H. melpomene using a series of unlinked genes, genes linked to color pattern loci, and optix, a gene recently shown to control red color-pattern variation. We found that although unlinked genes partition populations by geographic region, optix had a different history, structuring lineages by red color patterns and supporting a single origin of red-rayed patterns within each species. Genes closely linked (80-250 kb) to optix exhibited only weak associations with color pattern. This study empirically demonstrates the necessity of examining phenotype-determining genomic regions to understand the history of adaptive change in rapidly radiating lineages. With these refined relationships, we resolve a long-standing debate about the origins of the races within each species, supporting the hypothesis that the red-rayed Amazonian pattern evolved recently and expanded, causing disjunctions of more ancestral patterns. DA - 2011/12/6/ PY - 2011/12/6/ DO - 10.1073/pnas.1110096108 VL - 108 IS - 49 SP - 19666-19671 SN - 0027-8424 KW - Mullerian mimicry KW - population genetics KW - phylogeography 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 - The Fur regulon in anaerobically grown Salmonella enterica sv. Typhimurium: identification of new Fur targets AU - Troxell, Bryan AU - Fink, Ryan C. AU - Porwollik, Steffen AU - McClelland, Michael AU - Hassan, Hosni M. T2 - BMC MICROBIOLOGY AB - Abstract Background The Ferric uptake regulator (Fur) is a transcriptional regulator that controls iron homeostasis in bacteria. Although the regulatory role of Fur in Escherichia coli is well characterized, most of the studies were conducted under routine culture conditions, i.e., in ambient oxygen concentration. To reveal potentially novel aspects of the Fur regulon in Salmonella enterica serovar Typhimurium under oxygen conditions similar to that encountered in the host, we compared the transcriptional profiles of the virulent wild-type strain (ATCC 14028s) and its isogenic Δ fur strain under anaerobic conditions. Results Microarray analysis of anaerobically grown Δ fur S . Typhimurium identified 298 differentially expressed genes. Expression of several genes controlled by Fnr and NsrR appeared to be also dependent on Fur. Furthermore, Fur was required for the activity of the cytoplasmic superoxide disumutases (MnSOD and FeSOD). The regulation of FeSOD gene, sodB , occurred via small RNAs (i.e., the ryhB homologs, rfrA and rfrB ) with the aid of the RNA chaperone Hfq. The transcription of sodA was increased in Δ fur; however, the enzyme was inactive due to the incorporation of iron instead of manganese in SodA. Additionally, in Δ fur , the expression of the gene coding for the ferritin-like protein ( ftnB ) was down-regulated, while the transcription of the gene coding for the nitric oxide (NO · ) detoxifying flavohemoglobin ( hmpA ) was up-regulated. The promoters of ftnB and hmpA do not contain recognized Fur binding motifs, which indicated their probable indirect regulation by Fur. However, Fur activation of ftnB was independent of Fnr. In addition, the expression of the gene coding for the histone-like protein, H-NS ( hns ) was increased in Δ fur . This may explain the observed down-regulation of the tdc operon, responsible for the anaerobic degradation of threonine, and ftnB in Δ fur . Conclusions This study determined that Fur is a positive factor in ftnB regulation, while serving to repress the expression of hmpA . Furthermore, Fur is required for the proper expression and activation of the antioxidant enzymes, FeSOD and MnSOD. Finally, this work identified twenty-six new targets of Fur regulation, and demonstrates that H-NS repressed genes are down-regulated in Δ fur . DA - 2011/10/21/ PY - 2011/10/21/ DO - 10.1186/1471-2180-11-236 VL - 11 SP - SN - 1471-2180 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 - Production of ELOVL4 transgenic pigs: a large animal model for Stargardt-like macular degeneration AU - Sommer, Jeffrey R. AU - Estrada, Jose L. AU - Collins, Edwin B. AU - Bedell, Matthew AU - Alexander, Curtis A. AU - Yang, Zhenglin AU - Hughes, Guy AU - Mir, Bashir AU - Gilger, Brian C. AU - Grob, Seanna AU - Wei, Xinran AU - Piedrahita, Jorge A. AU - Shaw, Peter X. AU - Petters, Robert M. AU - Zhang, Kang T2 - BRITISH JOURNAL OF OPHTHALMOLOGY AB - Truncation mutations in the elongation of very long chain fatty acids-4 (AF277094, MIM #605512) (ELOVL4) gene cause Stargardt-like macular dystrophy type 3 (STGD3). Mice expressing truncated ELOVL4 develop rapid retinal degeneration, but are poor STGD3 models since mice lack a macula. Photoreceptor topography in the pig retina is more similar to that in humans as it includes the cone rich, macula-like area centralis. The authors generated transgenic pigs expressing human disease-causing ELOVL4 mutations to better model the pathobiology of this macular disease.Pronuclear DNA microinjection and somatic cell nuclear transfer were used to produce transgenic pigs for two different ELOVL4 mutations: the 5 base pair deletion (5 bpdel) and the 270 stop mutation (Y270terEYFP). Retinal transgene expression, morphology and electrophysiology were examined.The authors obtained four lines of Y270terEYFP and one line of 5 bpdel transgenic animals. Direct fluorescence microscopy indicated that the Y270terEYFP protein is expressed in photoreceptors and mislocalised within the cell. Immunohistochemical examination of transgenic pigs showed photoreceptor loss and disorganised inner and outer segments. Electroretinography demonstrated diminished responses in both transgenic models.These transgenic pigs provide unique animal models for examining macular degeneration and STGD3 pathogenesis. DA - 2011/12// PY - 2011/12// DO - 10.1136/bjophthalmol-2011-300417 VL - 95 IS - 12 SP - 1749-1754 SN - 1468-2079 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 - Genetic Modulation of Rpd3 Expression Impairs Long-Term Courtship Memory in Drosophila AU - Fitzsimons, Helen L. AU - Scott, Maxwell J. T2 - PLoS ONE AB - There is increasing evidence that regulation of local chromatin structure is a critical mechanism underlying the consolidation of long-term memory (LTM), however considerably less is understood about the specific mechanisms by which these epigenetic effects are mediated. Furthermore, the importance of histone acetylation in Drosophila memory has not been reported. The histone deacetylase (HDAC) Rpd3 is abundant in the adult fly brain, suggesting a post-mitotic function. Here, we investigated the role of Rpd3 in long-term courtship memory in Drosophila. We found that while modulation of Rpd3 levels predominantly in the adult mushroom body had no observed impact on immediate recall or one-hour memory, 24-hour LTM was severely impaired. Surprisingly, both overexpression as well as RNAi-mediated knockdown of Rpd3 resulted in impairment of long-term courtship memory, suggesting that the dose of Rpd3 is critical for normal LTM. DA - 2011/12/15/ PY - 2011/12/15/ DO - 10.1371/journal.pone.0029171 VL - 6 IS - 12 SP - e29171 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0029171 DB - Crossref ER - TY - JOUR TI - Epidermal growth factor receptor promotes glomerular injury and renal failure in rapidly progressive crescentic glomerulonephritis AU - Bollee, G. AU - Flamant, M. AU - Schordan, S. AU - Fligny, C. AU - Rumpel, E. AU - Milon, M. AU - Schordan, E. AU - Sabaa, N. AU - Vandermeersch, S. AU - Galaup, A. AU - Rodenas, A. AU - Casal, I. AU - Sunnarborg, S. W. AU - Salant, D. J. AU - Kopp, J. B. AU - Threadgill, D. W. AU - Quaggin, S. E. AU - Dussaule, J. C. T2 - Nature Medicine DA - 2011/// PY - 2011/// VL - 17 IS - 10 SP - 1242-272 ER - TY - JOUR TI - Comparing the genetic architecture and potential response to selection of invasive and native populations of reed canary grass AU - Calsbeek, Brittny AU - Lavergne, Sebastien AU - Patel, Manisha AU - Molofsky, Jane T2 - EVOLUTIONARY APPLICATIONS AB - Evolutionary processes such as migration, genetic drift, and natural selection are thought to play a prominent role in species invasions into novel environments. However, few empirical studies have explored the mechanistic basis of invasion in an evolutionary framework. One promising tool for inferring evolutionarily important changes in introduced populations is the genetic variance-covariance matrix (G matrix). G matrix comparisons allow for the inference of changes in the genetic architecture of introduced populations relative to their native counterparts that may facilitate invasion. Here, we compare the G matrices of reed canary grass (Phalaris arundinacea L.) populations across native and invasive ranges, and between populations along a latitudinal gradient within each range. We find that the major differences in genetic architecture occur between populations at the Northern and Southern margins within each range, not between native and invasive populations. Previous studies have found that multiple introductions in introduced populations caused an increase in genetic variance on which selection could act. In addition, we find that differences in the evolutionary potential of Phalaris populations are driven by differences in latitude, suggesting that selection also shapes the evolutionary trajectory of invasive populations. DA - 2011/11// PY - 2011/11// DO - 10.1111/j.1752-4571.2011.00195.x VL - 4 IS - 6 SP - 726-735 SN - 1752-4571 KW - G matrix KW - invasive species KW - quantitative genetics KW - reed canary grass KW - selection skewers ER - TY - JOUR TI - Transcriptomic Characterization of a Synergistic Genetic Interaction during Carpel Margin Meristem Development in Arabidopsis thaliana AU - Wynn, April N. AU - Rueschhoff, Elizabeth E. AU - Franks, Robert G. T2 - PLOS ONE AB - In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thaliana ovules initiate within the developing gynoecium from meristematic tissue located along the margins of the floral carpels. When fertilized the ovules will develop into seeds. SEUSS (SEU) and AINTEGUMENTA (ANT) encode transcriptional regulators that are critical for the proper formation of ovules from the carpel margin meristem (CMM). The synergistic loss of ovule initiation observed in the seu ant double mutant suggests that SEU and ANT share overlapping functions during CMM development. However the molecular mechanism underlying this synergistic interaction is unknown. Using the ATH1 transcriptomics platform we identified transcripts that were differentially expressed in seu ant double mutant relative to wild type and single mutant gynoecia. In particular we sought to identify transcripts whose expression was dependent on the coordinated activities of the SEU and ANT gene products. Our analysis identifies a diverse set of transcripts that display altered expression in the seu ant double mutant tissues. The analysis of overrepresented Gene Ontology classifications suggests a preponderance of transcriptional regulators including multiple members of the REPRODUCTIVE MERISTEMS (REM) and GROWTH-REGULATING FACTOR (GRF) families are mis-regulated in the seu ant gynoecia. Our in situ hybridization analyses indicate that many of these genes are preferentially expressed within the developing CMM. This study is the first step toward a detailed description of the transcriptional regulatory hierarchies that control the development of the CMM and ovule initiation. Understanding the regulatory hierarchy controlled by SEU and ANT will clarify the molecular mechanism of the functional redundancy of these two genes and illuminate the developmental and molecular events required for CMM development and ovule initiation. DA - 2011/10/21/ PY - 2011/10/21/ DO - 10.1371/journal.pone.0026231 VL - 6 IS - 10 SP - SN - 1932-6203 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-80054838468&partnerID=MN8TOARS ER - TY - JOUR TI - The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate AU - McFerrin, Lisa G. AU - Stone, Eric A. T2 - BMC GENOMICS AB - Protein sequences are subject to a mosaic of constraint. Changes to functional domains and buried residues, for example, are more apt to disrupt protein structure and function than are changes to residues participating in loops or exposed to solvent. Regions of constraint on the tertiary structure of a protein often result in loose segmentation of its primary structure into stretches of slowly- and rapidly-evolving amino acids. This clustering can be exploited, and existing methods have done so by relying on local sequence conservation as a signature of selection to help identify functionally important regions within proteins. We invert this paradigm by leveraging the regional nature of protein structure and function to both illuminate and make use of genome-wide patterns of local sequence conservation.Our hypothesis is that the regional nature of structural and functional constraints will assert a positive autocorrelation on the evolutionary rates of neighboring sites, which, in a pairwise comparison of orthologous proteins, will manifest itself as the clustering of non-synonymous changes across the amino acid sequence. We introduce a dispersion ratio statistic to test this and related hypotheses. Using genome-wide interspecific comparisons of orthologous protein pairs, we reveal a strong log-linear relationship between the degree of clustering and the intensity of constraint. We further demonstrate how this relationship varies with the evolutionary distance between the species being compared. We provide some evidence that proteins with a history of positive selection deviate from genome-wide trends.We find a significant association between the evolutionary rate of a protein and the degree to which non-synonymous changes cluster along its primary sequence. We show that clustering is a non-redundant predictor of evolutionary rate, and we speculate that conflicting signals of clustering and constraint may be indicative of a historical period of relaxed selection. DA - 2011/8/16/ PY - 2011/8/16/ DO - 10.1186/1471-2164-12-415 VL - 12 SP - SN - 1471-2164 ER - TY - JOUR TI - Phenotypic stability of Pro347Leu rhodopsin transgenic pigs as indicated by photoreceptor cell degeneration AU - Sommer, Jeffrey R. AU - Wong, Fulton AU - Petters, Robert M. T2 - TRANSGENIC RESEARCH DA - 2011/12// PY - 2011/12// DO - 10.1007/s11248-011-9491-0 VL - 20 IS - 6 SP - 1391-1395 SN - 0962-8819 KW - Transgenic KW - Pig KW - Rhodopsin KW - Phenotype 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 - Identification of RNA binding motif proteins essential for cardiovascular development AU - Maragh, Samantha AU - Miller, Ronald A. AU - Bessling, Seneca L. AU - McGaughey, David M. AU - Wessels, Marja W. AU - Graaf, Bianca AU - Stone, Eric A. AU - Bertoli-Avella, Aida M. AU - Gearhart, John D. AU - Fisher, Shannon AU - McCallion, Andrew S. T2 - BMC DEVELOPMENTAL BIOLOGY AB - Abstract Background We recently identified Rbm24 as a novel gene expressed during mouse cardiac development. Due to its tightly restricted and persistent expression from formation of the cardiac crescent onwards and later in forming vasculature we posited it to be a key player in cardiogenesis with additional roles in vasculogenesis and angiogenesis. Results To determine the role of this gene in cardiac development, we have identified its zebrafish orthologs ( rbm24 a and rbm24b ), and functionally evaluated them during zebrafish embryogenesis. Consistent with our underlying hypothesis, reduction in expression of either ortholog through injection of morpholino antisense oligonucleotides results in cardiogenic defects including cardiac looping and reduced circulation, leading to increasing pericardial edema over time. Additionally, morphant embryos for either ortholog display incompletely overlapping defects in the forming vasculature of the dorsal aorta (DA), posterior caudal vein (PCV) and caudal vein (CV) which are the first blood vessels to form in the embryo. Vasculogenesis and early angiogenesis in the trunk were similarly compromised in rbm24 morphant embryos at 48 hours post fertilization (hpf). Subsequent vascular maintenance was impaired in both rbm24 morphants with substantial vessel degradation noted at 72 hpf. Conclusion Taken collectively, our functional data support the hypothesis that rbm24a and rbm24b are key developmental cardiac genes with unequal roles in cardiovascular formation. DA - 2011/10/19/ PY - 2011/10/19/ DO - 10.1186/1471-213x-11-62 VL - 11 SP - SN - 1471-213X ER - TY - JOUR TI - Characterization of Canine Osteosarcoma by Array Comparative Genomic Hybridization and RT-qPCR: Signatures of Genomic Imbalance in Canine Osteosarcoma Parallel the Human Counterpart AU - Angstadt, Andrea Y. AU - Motsinger-Reif, Alison AU - Thomas, Rachael AU - Kisseberth, William C. AU - Couto, C. Guillermo AU - Duval, Dawn L. AU - Nielsen, Dahlia M. AU - Modiano, Jaime F. AU - Breen, Matthew T2 - GENES CHROMOSOMES & CANCER AB - Abstract Osteosarcoma (OS) is the most commonly diagnosed malignant bone tumor in humans and dogs, characterized in both species by extremely complex karyotypes exhibiting high frequencies of genomic imbalance. Evaluation of genomic signatures in human OS using array comparative genomic hybridization (aCGH) has assisted in uncovering genetic mechanisms that result in disease phenotype. Previous low‐resolution (10–20 Mb) aCGH analysis of canine OS identified a wide range of recurrent DNA copy number aberrations, indicating extensive genomic instability. In this study, we profiled 123 canine OS tumors by 1 Mb‐resolution aCGH to generate a dataset for direct comparison with current data for human OS, concluding that several high frequency aberrations in canine and human OS are orthologous. To ensure complete coverage of gene annotation, we identified the human refseq genes that map to these orthologous aberrant dog regions and found several candidate genes warranting evaluation for OS involvement. Specifically, subsequenct FISH and qRT‐PCR analysis of RUNX2 , TUSC3 , and PTEN indicated that expression levels correlated with genomic copy number status, showcasing RUNX2 as an OS associated gene and TUSC3 as a possible tumor suppressor candidate. Together these data demonstrate the ability of genomic comparative oncology to identify genetic abberations which may be important for OS progression. Large scale screening of genomic imbalance in canine OS further validates the use of the dog as a suitable model for human cancers, supporting the idea that dysregulation discovered in canine cancers will provide an avenue for complementary study in human counterparts. © 2011 Wiley‐Liss, Inc. DA - 2011/11// PY - 2011/11// DO - 10.1002/gcc.20908 VL - 50 IS - 11 SP - 859-874 SN - 1098-2264 ER - TY - JOUR TI - Bypassing Transcription: A Shortcut in Cytokinin-Auxin Interactions AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - DEVELOPMENTAL CELL AB - In this issue of Developmental Cell, Marhavý et al. (2011) uncover a transcription-independent molecular mechanism of interaction between auxin and cytokinin in the regulation of plant meristem function. By modulating endocytic trafficking of PIN1, cytokinin controls auxin flux and, therefore, auxin gradients. DA - 2011/10/18/ PY - 2011/10/18/ DO - 10.1016/j.devcel.2011.09.016 VL - 21 IS - 4 SP - 608-610 SN - 1534-5807 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-80054765937&partnerID=MN8TOARS ER - TY - JOUR TI - Assessment of Lactobacillus gasseri as a Candidate Oral Vaccine Vector AU - Stoeker, Laura AU - Nordone, Shila AU - Gunderson, Sara AU - Zhang, Lin AU - Kajikawa, Akinobu AU - LaVoy, Alora AU - Miller, Michael AU - Klaenhammer, Todd R. AU - Dean, Gregg A. T2 - CLINICAL AND VACCINE IMMUNOLOGY AB - Lactobacillus species are commensal bacteria that have long been recognized as probiotic microbes and are generally regarded as safe (GRAS) for human consumption. We have investigated the use of L. gasseri as a vaccine vector for oral immunization against mucosal pathogens. Recent research has shown that the immune response to different lactobacilli can vary widely depending on the species or subspecies of Lactobacillus being studied. While some lactobacilli seem to induce oral tolerance, others induce an adaptive immune response. This study characterized the systemic and mucosal immune response to wild-type and genetically modified L. gasseri. L. gasseri primarily activates TLR2/6, with additional activation through the TLR2 homodimer. To expand the Toll-like receptor (TLR) activation profile of L. gasseri and the immunogenicity of the vector, a plasmid containing fliC, the gene encoding bacterial flagellin, was introduced which resulted in the strong activation of TLR5. The treatment of human myeloid dendritic cells with recombinant lactobacilli expressing flagellin triggered phenotypic maturation and the release of proinflammatory cytokines. In contrast, bacterial treatment also resulted in a statistically significant increase in IL-10 production. In vivo studies established that treatment with L. gasseri led to a diversification of B-cell populations in the lamina propria of the murine colon. Furthermore, treatment with genetically modified L. gasseri led to a significant decrease in the percentage of FoxP3(+) colonic lymphocytes. Taken together, these data clarify the interaction of L. gasseri with the host immune system and support further investigation of the in vivo immunogenicity of L. gasseri expressing both flagellin and candidate vaccine antigens. DA - 2011/11// PY - 2011/11// DO - 10.1128/cvi.05277-11 VL - 18 IS - 11 SP - 1834-1844 SN - 1556-6811 ER - TY - JOUR TI - Transcriptional and functional analysis of galactooligosaccharide uptake by lacS in Lactobacillus acidophilus AU - Andersen, Joakim M. AU - Barrangou, Rodolphe AU - Abou Hachem, Maher AU - Lahtinen, Sampo AU - Goh, Yong Jun AU - Svensson, Birte AU - Klaenhammer, Todd R. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Probiotic microbes rely on their ability to survive in the gastrointestinal tract, adhere to mucosal surfaces, and metabolize available energy sources from dietary compounds, including prebiotics. Genome sequencing projects have proposed models for understanding prebiotic catabolism, but mechanisms remain to be elucidated for many prebiotic substrates. Although β-galactooligosaccharides (GOS) are documented prebiotic compounds, little is known about their utilization by lactobacilli. This study aimed to identify genetic loci in Lactobacillus acidophilus NCFM responsible for the transport and catabolism of GOS. Whole-genome oligonucleotide microarrays were used to survey the differential global transcriptome during logarithmic growth of L. acidophilus NCFM using GOS or glucose as a sole source of carbohydrate. Within the 16.6-kbp gal-lac gene cluster, lacS, a galactoside-pentose-hexuronide permease-encoding gene, was up-regulated 5.1-fold in the presence of GOS. In addition, two β-galactosidases, LacA and LacLM, and enzymes in the Leloir pathway were also encoded by genes within this locus and up-regulated by GOS stimulation. Generation of a lacS-deficient mutant enabled phenotypic confirmation of the functional LacS permease not only for the utilization of lactose and GOS but also lactitol, suggesting a prominent role of LacS in the metabolism of a broad range of prebiotic β-galactosides, known to selectively modulate the beneficial gut microbiota. DA - 2011/10/25/ PY - 2011/10/25/ DO - 10.1073/pnas.1114152108 VL - 108 IS - 43 SP - 17785-17790 SN - 0027-8424 KW - lactose permease KW - catabolite repression element ER - TY - JOUR TI - Invited review: Application of omics tools to understanding probiotic functionality AU - Baugher, J. L. AU - Klaenhammer, T. R. T2 - JOURNAL OF DAIRY SCIENCE AB - The human gut microbiota comprises autochthonous species that colonize and reside at high levels permanently and allochthonous species that originate from another source and are transient residents of the human gut. The interactions between bacteria and the human host can be classified as a continuum from symbiosis and commensalism (mutualism) to pathogenesis. Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Recent advances in omics tools and sequencing techniques have furthered our understanding of probiotic functionality and the specific interactions between probiotics and their human hosts. Although it is known that not all probiotics use the same mechanisms to confer benefits on hosts, some specific mechanisms of action have been revealed through omic investigations. These include competitive exclusion, bacteriocin-mediated protection against intestinal pathogens, intimate interactions with mucin and the intestinal epithelium, and modulation of the immune system. The ability to examine fully sequenced and annotated genomes has greatly accelerated the application of genetic approaches to elucidate many important functional roles of probiotic microbes. DA - 2011/10// PY - 2011/10// DO - 10.3168/jds.2011-4384 VL - 94 IS - 10 SP - 4753-4765 SN - 1525-3198 KW - probiotics KW - omics KW - function KW - mechanism ER - TY - JOUR TI - MicroRNA expression in the livers of inbred mice AU - Gatti, Daniel M. AU - Lu, Lu AU - Williams, Robert W. AU - Sun, Wei AU - Wright, Fred A. AU - Threadgill, David W. AU - Rusyn, Ivan T2 - MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS AB - MicroRNAs are short, non-coding RNA sequences that regulate genes at the post-transcriptional level and have been shown to be important in development, tissue differentiation, and disease. Limited attention has been given to the natural variation in miRNA expression across genetically diverse populations even though it is well established that genetic polymorphisms can have a profound effect on mRNA levels. Expression level of 577 miRNAs in the livers of 70 strains of inbred mice was assessed, and we found that miRNA expression is highly stable across different strains. Globally, the expression of miRNA target transcripts does not correlate with miRNA expression, primarily due to the low variance of miRNA but high variance of mRNA expression across strains. Our results show that there is little genetic effect on the baseline miRNA levels in murine liver. The stability of mouse liver miRNA expression in a genetically diverse population suggests that treatment-induced disruptions in liver miRNA expression, a phenomenon established for a large number of toxicants, may indicate an important mechanism for the disturbance of normal liver function, and may prove to be a useful genetic background-independent biomarker of toxicant effect. DA - 2011/9/1/ PY - 2011/9/1/ DO - 10.1016/j.mrfmmm.2011.05.007 VL - 714 IS - 1-2 SP - 126-133 SN - 1873-135X KW - MicroRNA KW - Liver KW - Mouse KW - Gene expression ER - TY - JOUR TI - Evolution of the Max and Mlx Networks in Animals AU - McFerrin, Lisa G. AU - Atchley, William R. T2 - GENOME BIOLOGY AND EVOLUTION AB - Transcription factors (TFs) are essential for the regulation of gene expression and often form emergent complexes to perform vital roles in cellular processes. In this paper, we focus on the parallel Max and Mlx networks of TFs because of their critical involvement in cell cycle regulation, proliferation, growth, metabolism, and apoptosis. A basic-helix-loop-helix-zipper (bHLHZ) domain mediates the competitive protein dimerization and DNA binding among Max and Mlx network members to form a complex system of cell regulation. To understand the importance of these network interactions, we identified the bHLHZ domain of Max and Mlx network proteins across the animal kingdom and carried out several multivariate statistical analyses. The presence and conservation of Max and Mlx network proteins in animal lineages stemming from the divergence of Metazoa indicate that these networks have ancient and essential functions. Phylogenetic analysis of the bHLHZ domain identified clear relationships among protein families with distinct points of radiation and divergence. Multivariate discriminant analysis further isolated specific amino acid changes within the bHLHZ domain that classify proteins, families, and network configurations. These analyses on Max and Mlx network members provide a model for characterizing the evolution of TFs involved in essential networks. DA - 2011/// PY - 2011/// DO - 10.1093/gbe/evr082 VL - 3 SP - 915-937 SN - 1759-6653 KW - protein evolution KW - basic-helix-loop-helix-leucine zipper (bHLHZ) domain KW - Myc/Max/Mad network KW - Mlx and Mondo Network KW - phylogenetic tree KW - discriminant analysis ER - TY - JOUR TI - Directed Chromosomal Integration and Expression of the Reporter Gene gusA3 in Lactobacillus acidophilus NCFM AU - Douglas, Grace L. AU - Klaenhammer, Todd R. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Lactobacillus acidophilus NCFM is a probiotic microbe that survives passage through the human gastrointestinal tract and interacts with the host epithelium and mucosal immune cells. The potential for L. acidophilus to express antigens at mucosal surfaces has been investigated with various antigens and plasmid expression vectors. Plasmid instability and antibiotic selection complicate the possibility of testing these constructs in human clinical trials. Integrating antigen encoding genes into the chromosome for expression is expected to eliminate selection requirements and provide genetic stability. In this work, a reporter gene encoding a β-glucuronidase (GusA3) was integrated into four intergenic chromosomal locations. The integrants were tested for genetic stability and GusA3 activity. Two locations were selected for insertion downstream of constitutively highly expressed genes, one downstream of slpA (LBA0169), encoding a highly expressed surface-layer protein, and one downstream of phosphopyruvate hydratase (LBA0889), a highly expressed gene with homologs in other lactic acid bacteria. An inducible location was selected downstream of lacZ (LBA1462), encoding a β-galactosidase. A fourth location was selected in a low-expression region. The expression of gusA3 was evaluated from each location by measuring GusA3 activity on 4-methyl-umbelliferyl-β-d-glucuronide (MUG). GusA3 activity from both highly expressed loci was more than three logs higher than the gusA3-negative parent, L. acidophilus NCK1909. GusA3 activity from the lacZ locus was one log higher in cells grown in lactose than in glucose. The differences in expression levels between integration locations highlights the importance of rational targeting with gene cassettes intended for chromosomal expression. DA - 2011/10// PY - 2011/10// DO - 10.1128/aem.06028-11 VL - 77 IS - 20 SP - 7365-7371 SN - 0099-2240 ER - TY - JOUR TI - optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry AU - Reed, Robert D. AU - Papa, Riccardo AU - Martin, Arnaud AU - Hines, Heather M. AU - Counterman, Brian A. AU - Pardo-Diaz, Carolina AU - Jiggins, Chris D. AU - Chamberlain, Nicola L. AU - Kronforst, Marcus R. AU - Chen, Rui AU - Halder, Georg AU - Nijhout, H. Frederik AU - McMillan, W. Owen T2 - SCIENCE AB - Mimicry--whereby warning signals in different species evolve to look similar--has long served as a paradigm of convergent evolution. Little is known, however, about the genes that underlie the evolution of mimetic phenotypes or to what extent the same or different genes drive such convergence. Here, we characterize one of the major genes responsible for mimetic wing pattern evolution in Heliconius butterflies. Mapping, gene expression, and population genetic work all identify a single gene, optix, that controls extreme red wing pattern variation across multiple species of Heliconius. Our results show that the cis-regulatory evolution of a single transcription factor can repeatedly drive the convergent evolution of complex color patterns in distantly related species, thus blurring the distinction between convergence and homology. DA - 2011/8/26/ PY - 2011/8/26/ DO - 10.1126/science.1208227 VL - 333 IS - 6046 SP - 1137-1141 SN - 1095-9203 ER - TY - JOUR TI - Dissimilar Properties of Two Recombinant Lactobacillus acidophilus Strains Displaying Salmonella FliC with Different Anchoring Motifs AU - Kajikawa, Akinobu AU - Nordone, Shila K. AU - Zhang, Lin AU - Stoeker, Laura L. AU - LaVoy, Alora S. AU - Klaenhammer, Todd R. AU - Dean, Gregg A. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Display of heterologous antigens on the cell surface is considered a useful technique for vaccine delivery by recombinant lactobacilli. In this study, two recombinant Lactobacillus acidophilus derivatives displaying Salmonella flagellin (FliC) were constructed using different anchor motifs. In one instance, the FliC protein was fused to the C-terminal region of a cell envelope proteinase (PrtP) and was bound to the cell wall by electrostatic bonds. In the other case, the same antigen was conjugated to the anchor region of mucus binding protein (Mub) and was covalently associated with the cell wall by an LPXTG motif. These two recombinant L. acidophilus cell surface displays resulted in dissimilar maturation and cytokine production by human myeloid dendritic cells. The surface-associated antigen was highly sensitive to simulated gastric and small intestinal juices. By supplementation with bicarbonate buffer and soybean trypsin inhibitor, the cell surface antigen was protected from proteolytic enzymes during gastric challenge in vitro . The protective reagents also increased the viability of the L. acidophilus cells upon challenge with simulated digestive juices. These results demonstrate the importance of protecting cells and their surface-associated antigens during oral immunization. DA - 2011/9// PY - 2011/9// DO - 10.1128/aem.05153-11 VL - 77 IS - 18 SP - 6587-6596 SN - 0099-2240 ER - TY - JOUR TI - Coordinated Genome-Wide Modifications within Proximal Promoter Cis-regulatory Elements during Vertebrate Evolution AU - Yokoyama, Ken Daigoro AU - Thorne, Jeffrey L. AU - Wray, Gregory A. T2 - GENOME BIOLOGY AND EVOLUTION AB - There often exists a "one-to-many" relationship between a transcription factor and a multitude of binding sites throughout the genome. It is commonly assumed that transcription factor binding motifs remain largely static over the course of evolution because changes in binding specificity can alter the interactions with potentially hundreds of sites across the genome. Focusing on regulatory motifs overrepresented at specific locations within or near the promoter, we find that a surprisingly large number of cis-regulatory elements have been subject to coordinated genome-wide modifications during vertebrate evolution, such that the motif frequency changes on a single branch of vertebrate phylogeny. This was found to be the case even between closely related mammal species, with nearly a third of all location-specific consensus motifs exhibiting significant modifications within the human or mouse lineage since their divergence. Many of these modifications are likely to be compensatory changes throughout the genome following changes in protein factor binding affinities, whereas others may be due to changes in mutation rates or effective population size. The likelihood that this happened many times during vertebrate evolution highlights the need to examine additional taxa and to understand the evolutionary and molecular mechanisms underlying the evolution of protein-DNA interactions. DA - 2011/// PY - 2011/// DO - 10.1093/gbe/evq078 VL - 3 SP - 66-74 SN - 1759-6653 KW - gene expression KW - transcriptional regulation KW - protein-DNA coevolution KW - cis-regulatory evolution ER - TY - JOUR TI - Construction of vectors for inducible and constitutive gene expression in Lactobacillus AU - Duong, T. AU - Miller, M. J. AU - Barrangou, R. AU - Azcarate-Peril, M. A. AU - Klaenhammer, T. R. T2 - Microbial Biotechnology AB - Microarray analysis of the genome of Lactobacillus acidophilus identified a number of operons that were differentially expressed in response to carbohydrate source or constitutively expressed regardless of carbohydrate source. These included operons implicated in the transport and catabolism of fructooligosaccharides (FOS), lactose (lac), trehalose (tre) and genes directing glycolysis. Analysis of these operons identified a number of putative promoter and repressor elements, which were used to construct a series of expression vectors for use in lactobacilli, based on the broad host range pWV01 replicon. A β-glucuronidase (GusA3) reporter gene was cloned into each vector to characterize expression from each promoter. GUS reporter assays showed FOS, lac and tre based vectors to be highly inducible by their specific carbohydrate and repressed by glucose. Additionally, a construct based on the phosphoglycerate mutase (pgm) promoter was constitutively highly expressed. To demonstrate the potential utility of these vectors, we constructed a plasmid for the overexpression of the oxalate degradation pathway (Frc and Oxc) of L. acidophilus NCFM. This construct was able to improve oxalate degradation by L. gasseri ATCC 33323 and compliment a L. acidophilus oxalate-deficient mutant. Development of these expression vectors could support several novel applications, including the expression of enzymes, proteins, vaccines and biotherapeutics by intestinal lactobacilli. DA - 2011/// PY - 2011/// DO - 10.1111/j.1751-7915.2010.00200.x VL - 4 IS - 3 SP - 357-367 ER - TY - JOUR TI - Why the Phylogenetic Regression Appears Robust to Tree Misspecification AU - Stone, Eric A. T2 - SYSTEMATIC BIOLOGY AB - The phylogenetic comparative method uses estimates of evolutionary relationships to explicitly model the covariance structure of interspecific data. By accounting for common ancestry, the coevolution between 2 or more traits, as a response to one another or to environmental variables, can be studied without confounding similarities due to identity by descent. Because the true phylogeny is unknowable, an estimate must be used, introducing a source of error into phylogenetic comparative analysis that can be difficult to quantify. This manuscript aims to elucidate how tree misspecification is propagated through a comparative analysis. I focus on the phylogenetic regression under a Brownian motion model of evolution and consider the effect of local phylogenetic perturbations on the regression fit. Motivated by Felsenstein's method of independent contrasts, I derive a matrix square root of the phylogenetic covariance matrix that has an obvious phylogenetic interpretation. I use this result to transform the perturbed phylogenetic regression model into an ordinary linear regression in which one interpretable point has been affected. The simplicity of this formulation allows the contributions of data and phylogeny to be disentangled when studying the effect of tree misspecification. Consequentially, I find that branch length misspecification can be easily explained in terms of the reweighting of contrast scores between subtrees. An analytical consideration of this and other perturbations helps to explain why the phylogenetic regression appears generally to be robust to tree misspecification, and I am able to identify conditions under which the regression may not yield robust results. I discuss why soft polytomies do not meet these problematic conditions, leading to the conclusion that unresolved bifurcations should have only modest effects on the regression fit. DA - 2011/5// PY - 2011/5// DO - 10.1093/sysbio/syq098 VL - 60 IS - 3 SP - 245-260 SN - 1063-5157 KW - Comparative method KW - independent contrasts KW - phylogenetic regression KW - robustness ER - TY - JOUR TI - Osteoblast adhesion to functionally graded hydroxyapatite coatings doped with silver AU - Sandukas, Stefan AU - Yamamoto, Akiko AU - Rabiei, Afsaneh T2 - JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A AB - Abstract Silver‐doped functionally graded hydroxyapatite (Ag‐FGHA) coatings have been prepared on glass and titanium substrates by ion beam assisted deposition (IBAD) method with in situ heat treatment, and the biological response and dissolution properties of the coatings have been examined. Three Ag‐FGHA coatings with different percentages of silver (1, 3, and 6.6 wt % Ag) were compared with pure FGHA (without Ag) as a control. MC 3T3‐E1 murine osteoblast cells were cultured on FGHA and Ag‐FGHA coating surfaces, and the number of adhered cells after 1, 4, and 7 days was counted. Micromanipulation of live single cells was performed to quantitatively compare cell affinity among the four coating compositions. Results showed that FGHA‐Ag1 coating (with 1 wt % Ag) had the highest number of adhered cells after each incubation period, as well as the highest cell affinity after 24‐h incubation. Surface profilometry was performed to determine surface roughness average ( R a ) of coating surfaces before and after immersion in high‐purity water, showing that all surfaces initially had roughness averages below 200 nm, while after immersion, roughness average of FGHA‐Ag1 surface was significantly increased ( R a = 404 +/− 100.8 nm), attributed to the highest rate of dissolution. Release rate of Ag + ions in solution was measured, showing release rates of silver ions for all Ag‐doped coatings were initially high and then gradually decreased to a minimum over time, which is the expected dissolution of functionally graded coatings. It is concluded that FGHA‐Ag1 coating promoted the highest degree of osteoblast adhesion because of optimal dissolution rate and nontoxic Ag percentage. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2011. DA - 2011/6// PY - 2011/6// DO - 10.1002/jbm.a.33081 VL - 97A IS - 4 SP - 490-497 SN - 1552-4965 KW - hydroxyapatite coating KW - osteoblast KW - biological response KW - functionally graded KW - silver ER - TY - JOUR TI - MATE PREFERENCE ACROSS THE SPECIATION CONTINUUM IN A CLADE OF MIMETIC BUTTERFLIES AU - Merrill, Richard M. AU - Gompert, Zachariah AU - Dembeck, Lauren M. AU - Kronforst, Marcus R. AU - McMillan, W. Owen AU - Jiggins, Chris D. T2 - EVOLUTION AB - Premating behavioral isolation is increasingly recognized as an important part of ecological speciation, where divergent natural selection causes the evolution of reproductive barriers. A number of studies have now demonstrated that traits under divergent natural selection also affect mate preferences. However, studies of single species pairs only capture a snapshot of the speciation process, making it difficult to assess the role of mate preferences throughout the entire process. Heliconius butterflies are well known for their brightly colored mimetic warning patterns, and previous studies have shown that these patterns are also used as mate recognition cues. Here, we present mate preference data for four pairs of sister taxa, representing different stages of divergence, which together allow us to compare diverging mate preferences across the continuum of Heliconius speciation. Using a novel Bayesian approach, our results support a model of ecological speciation in which strong premating isolation arises early, but continues to increase throughout the continuum from polymorphic populations through to "good," sympatric ecologically divergent species. DA - 2011/5// PY - 2011/5// DO - 10.1111/j.1558-5646.2010.01216.x VL - 65 IS - 5 SP - 1489-1500 SN - 1558-5646 KW - Assortative mating KW - Heliconius KW - mate choice KW - reproductive isolation KW - speciation ER - TY - JOUR TI - MADS-box genes of maize: frequent targets of selection during domestication AU - Zhao, Q. AU - Weber, A. L. AU - McMullen, M. D. AU - Guill, K. AU - Doebley, J. T2 - Genetical Research DA - 2011/// PY - 2011/// VL - 93 IS - 1 SP - 65-75 ER - TY - JOUR TI - Inference on treatment effects from a randomized clinical trial in the presence of premature treatment discontinuation: the SYNERGY trial AU - Zhang, Min AU - Tsiatis, Anastasios A. AU - Davidian, Marie AU - Pieper, Karen S. AU - Mahaffey, Kenneth W. T2 - BIOSTATISTICS AB - The Superior Yield of the New Strategy of Enoxaparin, Revascularization, and GlYcoprotein IIb/IIIa inhibitors (SYNERGY) was a randomized, open-label, multicenter clinical trial comparing 2 anticoagulant drugs on the basis of time-to-event endpoints. In contrast to other studies of these agents, the primary, intent-to-treat analysis did not find evidence of a difference, leading to speculation that premature discontinuation of the study agents by some subjects may have attenuated the apparent treatment effect and thus to interest in inference on the difference in survival distributions were all subjects in the population to follow the assigned regimens, with no discontinuation. Such inference is often attempted via ad hoc analyses that are not based on a formal definition of this treatment effect. We use SYNERGY as a context in which to describe how this effect may be conceptualized and to present a statistical framework in which it may be precisely identified, which leads naturally to inferential methods based on inverse probability weighting. DA - 2011/4// PY - 2011/4// DO - 10.1093/biostatistics/kxq054 VL - 12 IS - 2 SP - 258-269 SN - 1465-4644 KW - Dynamic treatment regime KW - Inverse probability weighting KW - Potential outcomes KW - Proportional hazards model ER - TY - JOUR TI - History Can Matter: Non-Markovian Behavior of Ancestral Lineages AU - Cartwright, Reed A. AU - Lartillot, Nicolas AU - Thorne, Jeffrey L. T2 - SYSTEMATIC BIOLOGY AB - Although most of the important evolutionary events in the history of biology can only be studied via interspecific comparisons, it is challenging to apply the rich body of population genetic theory to the study of interspecific genetic variation. Probabilistic modeling of the substitution process would ideally be derived from first principles of population genetics, allowing a quantitative connection to be made between the parameters describing mutation, selection, drift, and the patterns of interspecific variation. There has been progress in reconciling population genetics and interspecific evolution for the case where mutation rates are sufficiently low, but when mutation rates are higher, reconciliation has been hampered due to complications from how the loss or fixation of new mutations can be influenced by linked nonneutral polymorphisms (i.e., the Hill–Robertson effect). To investigate the generation of interspecific genetic variation when concurrent fitness-affecting polymorphisms are common and the Hill–Robertson effect is thereby potentially strong, we used the Wright–Fisher model of population genetics to simulate very many generations of mutation, natural selection, and genetic drift. This was done so that the chronological history of advantageous, deleterious, and neutral substitutions could be traced over time along the ancestral lineage. Our simulations show that the process by which a nonrecombining sequence changes over time can markedly deviate from the Markov assumption that is ubiquitous in molecular phylogenetics. In particular, we find tendencies for advantageous substitutions to be followed by deleterious ones and for deleterious substitutions to be followed by advantageous ones. Such non-Markovian patterns reflect the fact that the fate of the ancestral lineage depends not only on its current allelic state but also on gene copies not belonging to the ancestral lineage. Although our simulations describe nonrecombining sequences, we conclude by discussing how non-Markovian behavior of the ancestral lineage is plausible even when recombination rates are not low. As a result, we believe that increased attention needs to be devoted to the robustness of evolutionary inference procedures that rely upon the Markov assumption. DA - 2011/5// PY - 2011/5// DO - 10.1093/sysbio/syr012 VL - 60 IS - 3 SP - 276-290 SN - 1076-836X KW - Ancestral lineage KW - ancestral process KW - Hill-Robertson effect KW - population genetics ER - TY - JOUR TI - Group-specific comparison of four lactobacilli isolated from human sources using differential blast analysis AU - Altermann, Eric AU - Klaenhammer, Todd R. T2 - GENES AND NUTRITION AB - Lactic acid bacteria (LAB) have been used in fermentation processes for centuries. More recent applications including the use of LAB as probiotics have significantly increased industrial interest. Here we present a comparative genomic analysis of four completely sequenced Lactobacillus strains, isolated from the human gastrointestinal tract, versus 25 lactic acid bacterial genomes present in the public database at the time of analysis. Lactobacillus acidophilus NCFM, Lactobacillus johnsonii NCC533, Lactobacillus gasseri ATCC33323, and Lactobacillus plantarum WCFS1are all considered probiotic and widely used in industrial applications. Using Differential Blast Analysis (DBA), each genome was compared to the respective remaining three other Lactobacillus and 25 other LAB genomes. DBA highlighted strain-specific genes that were not represented in any other LAB used in this analysis and also identified group-specific genes shared within lactobacilli. Initial comparative analyses highlighted a significant number of genes involved in cell adhesion, stress responses, DNA repair and modification, and metabolic capabilities. Furthermore, the range of the recently identified potential autonomous units (PAUs) was broadened significantly, indicating the possibility of distinct families within this genetic element. Based on in silico results obtained for the model organism L. acidophilus NCFM, DBA proved to be a valuable tool to identify new key genetic regions for functional genomics and also suggested re-classification of previously annotated genes. DA - 2011/8// PY - 2011/8// DO - 10.1007/s12263-010-0191-9 VL - 6 IS - 3 SP - 319-340 SN - 1555-8932 KW - In silico analysis KW - PAU KW - Adhesion KW - Stress response KW - Bacteriophage ER - TY - JOUR TI - Architecture of energy balance traits in emerging lines of the Collaborative Cross AU - Mathes, Wendy Foulds AU - Aylor, David L. AU - Miller, Darla R. AU - Churchill, Gary A. AU - Chesler, Elissa J. AU - Villena, Fernando Pardo-Manuel AU - Threadgill, David W. AU - Pomp, Daniel T2 - AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM AB - The potential utility of the Collaborative Cross (CC) mouse resource was evaluated to better understand complex traits related to energy balance. A primary focus was to examine if genetic diversity in emerging CC lines (pre-CC) would translate into equivalent phenotypic diversity. Second, we mapped quantitative trait loci (QTL) for 15 metabolism- and exercise-related phenotypes in this population. We evaluated metabolic and voluntary exercise traits in 176 pre-CC lines, revealing phenotypic variation often exceeding that seen across the eight founder strains from which the pre-CC was derived. Many phenotypic correlations existing within the founder strains were no longer significant in the pre-CC population, potentially representing reduced linkage disequilibrium (LD) of regions harboring multiple genes with effects on energy balance or disruption of genetic structure of extant inbred strains with substantial shared ancestry. QTL mapping revealed five significant and eight suggestive QTL for body weight (Chr 4, 7.54 Mb; CI 3.32-10.34 Mb; Bwq14), body composition, wheel running (Chr 16, 33.2 Mb; CI 32.5-38.3 Mb), body weight change in response to exercise (1: Chr 6, 77.7Mb; CI 72.2-83.4 Mb and 2: Chr 6, 42.8 Mb; CI 39.4-48.1 Mb), and food intake during exercise (Chr 12, 85.1 Mb; CI 82.9-89.0 Mb). Some QTL overlapped with previously mapped QTL for similar traits, whereas other QTL appear to represent novel loci. These results suggest that the CC will be a powerful, high-precision tool for examining the genetic architecture of complex traits such as those involved in regulation of energy balance. DA - 2011/6// PY - 2011/6// DO - 10.1152/ajpendo.00707.2010 VL - 300 IS - 6 SP - E1124-E1134 SN - 1522-1555 KW - genetics KW - wheel running KW - adiposity KW - body weight KW - quantitative trait loci ER - TY - JOUR TI - Variation in genome-wide mutation rates within and between human families AU - Conrad, D. F. AU - Keebler, J. E. M. AU - DePristo, M. A. AU - Lindsay, S. J. AU - Zhang, Y. J. AU - Casals, F. AU - Idaghdour, Y. AU - Hartl, C. L. AU - Torroja, C. AU - Garimella, K. V. AU - Zilversmit, M. AU - Cartwright, R. AU - Rouleau, G. A. AU - Daly, M. AU - Stone, E. A. AU - Hurles, M. E. T2 - Nature Genetics DA - 2011/// PY - 2011/// VL - 43 IS - 7 SP - 712-137 ER - TY - JOUR TI - Genetic analysis of complex traits in the emerging Collaborative Cross AU - Aylor, David L. AU - Valdar, William AU - Foulds-Mathes, Wendy AU - Buus, Ryan J. AU - Verdugo, Ricardo A. AU - Baric, Ralph S. AU - Ferris, Martin T. AU - Frelinger, Jeff A. AU - Heise, Mark AU - Frieman, Matt B. AU - Gralinski, Lisa E. AU - Bell, Timothy A. AU - Didion, John D. AU - Hua, Kunjie AU - Nehrenberg, Derrick L. AU - Powell, Christine L. AU - Steigerwalt, Jill AU - Xie, Yuying AU - Kelada, Samir N. P. AU - Collins, Francis S. AU - Yang, Ivana V. AU - Schwartz, David A. AU - Branstetter, Lisa A. AU - Chesler, Elissa J. AU - Miller, Darla R. AU - Spence, Jason AU - Liu, Eric Yi AU - McMillan, Leonard AU - Sarkar, Abhishek AU - Wang, Jeremy AU - Wang, Wei AU - Zhang, Qi AU - Broman, Karl W. AU - Korstanje, Ron AU - Durrant, Caroline AU - Mott, Richard AU - Iraqi, Fuad A. AU - Pomp, Daniel AU - Threadgill, David AU - Villena, Fernando Pardo-Manuel AU - Churchill, Gary A. T2 - GENOME RESEARCH AB - The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites-all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping approaches. Analysis based on inferred haplotypes improves power, reduces false discovery, and provides information to identify and prioritize candidate genes that is unique to multifounder crosses like the CC. The number of expression QTLs discovered here exceeds all previous efforts at eQTL mapping in mice, and we map local eQTL at 1-Mb resolution. We demonstrate that the genetic diversity of the CC, which derives from random mixing of eight founder strains, results in high phenotypic diversity and enhances our ability to map causative loci underlying complex disease-related traits. DA - 2011/8// PY - 2011/8// DO - 10.1101/gr.111310.110 VL - 21 IS - 8 SP - 1213-1222 SN - 1088-9051 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 - 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 - The Impact of Omic Technologies on the Study of Food Microbes AU - O'Flaherty, Sarah AU - Klaenhammer, Todd R. T2 - ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 2 AB - The advent of the molecular biology era in the 1950s and the subsequent emergence of new technologies positively impacted on all areas of biology. New discoveries in molecular biology and experimental tools were developed over the next 60 years that have revolutionized the study of food microbiology. Previously, food microbiology relied on classic microbiology techniques, which had remained relatively unchanged since the discoveries of Louis Pasteur in the 1800s. More recently, new advances resulting in "omic" technologies have exploded the areas of genomics, transcriptomics, and proteomics and revealed many fundamental processes driven by both pathogens and commensals. This review outlines advances in omic technologies and how these have impacted food microbiology through providing examples of recently published landmark work. DA - 2011/// PY - 2011/// DO - 10.1146/annurev-food-030810-110338 VL - 2 SP - 353-371 SN - 1941-1421 KW - sequencing KW - genome KW - probiotic KW - pathogen KW - microbiome KW - transcriptome ER - TY - JOUR TI - The Effects of Weak Genetic Perturbations on the Transcriptome of the Wing Imaginal Disc and Its Association With Wing Shape in Drosophila melanogaster AU - Dworkin, Ian AU - Anderson, Julie A. AU - Idaghdour, Youssef AU - Parker, Erin Kennerly AU - Stone, Eric A. AU - Gibson, Greg T2 - GENETICS AB - Abstract A major objective of genomics is to elucidate the mapping between genotypic and phenotypic space as a step toward understanding how small changes in gene function can lead to elaborate phenotypic changes. One approach that has been utilized is to examine overall patterns of covariation between phenotypic variables of interest, such as morphology, physiology, and behavior, and underlying aspects of gene activity, in particular transcript abundance on a genome-wide scale. Numerous studies have demonstrated that such patterns of covariation occur, although these are often between samples with large numbers of unknown genetic differences (different strains or even species) or perturbations of large effect (sexual dimorphism or strong loss-of-function mutations) that may represent physiological changes outside of the normal experiences of the organism. We used weak mutational perturbations in genes affecting wing development in Drosophila melanogaster that influence wing shape relative to a co-isogenic wild type. We profiled transcription of 1150 genes expressed during wing development in 27 heterozygous mutants, as well as their co-isogenic wild type and one additional wild-type strain. Despite finding clear evidence of expression differences between mutants and wild type, transcriptional profiles did not covary strongly with shape, suggesting that information from transcriptional profiling may not generally be predictive of final phenotype. We discuss these results in the light of possible attractor states of gene expression and how this would affect interpretation of covariation between transcriptional profiles and other phenotypes. DA - 2011/4// PY - 2011/4// DO - 10.1534/genetics.110.125922 VL - 187 IS - 4 SP - 1171-U314 SN - 1943-2631 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 - 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 - Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium AU - Evans, Matthew R. AU - Fink, Ryan C. AU - Vazquez-Torres, Andres AU - Porwollik, Steffen AU - Jones-Carson, Jessica AU - McClelland, Michael AU - Hassan, Hosni M. T2 - BMC MICROBIOLOGY AB - Salmonella enterica serovar Typhimurium (S. Typhimurium) is a Gram-negative pathogen that must successfully adapt to the broad fluctuations in the concentration of dissolved dioxygen encountered in the host. In Escherichia coli, ArcA (Aerobic Respiratory Control) helps the cells to sense and respond to the presence of dioxygen. The global role of ArcA in E. coli is well characterized; however, little is known about its role in anaerobically grown S. Typhimurium.We compared the transcriptional profiles of the virulent wild-type (WT) strain (ATCC 14028s) and its isogenic arcA mutant grown under anaerobic conditions. We found that ArcA directly or indirectly regulates 392 genes (8.5% of the genome); of these, 138 genes are poorly characterized. Regulation by ArcA in S. Typhimurium is similar, but distinct from that in E. coli. Thus, genes/operons involved in core metabolic pathways (e.g., succinyl-CoA, fatty acid degradation, cytochrome oxidase complexes, flagellar biosynthesis, motility, and chemotaxis) were regulated similarly in the two organisms. However, genes/operons present in both organisms, but regulated differently by ArcA in S. Typhimurium included those coding for ethanolamine utilization, lactate transport and metabolism, and succinate dehydrogenases. Salmonella-specific genes/operons regulated by ArcA included those required for propanediol utilization, flagellar genes (mcpAC, cheV), Gifsy-1 prophage genes, and three SPI-3 genes (mgtBC, slsA, STM3784). In agreement with our microarray data, the arcA mutant was non-motile, lacked flagella, and was as virulent in mice as the WT. Additionally, we identified a set of 120 genes whose regulation was shared with the anaerobic redox regulator, Fnr.We have identified the ArcA regulon in anaerobically grown S. Typhimurium. Our results demonstrated that in S. Typhimurium, ArcA serves as a transcriptional regulator coordinating cellular metabolism, flagella biosynthesis, and motility. Furthermore, ArcA and Fnr share in the regulation of 120 S. Typhimurium genes. DA - 2011/3/21/ PY - 2011/3/21/ DO - 10.1186/1471-2180-11-58 VL - 11 SP - SN - 1471-2180 ER - TY - JOUR TI - A recombineering-based gene tagging system for Arabidopsis AU - Zhou, Rongrong AU - Benavente, Larissa M. AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - PLANT JOURNAL AB - One of the most information-rich aspects of gene functional studies is characterization of gene expression profiles at cellular resolution, and subcellular localization of the corresponding proteins. These studies require visualization of the endogenous gene products using specific antibodies, or, more commonly, generation of whole-gene translational fusions with a reporter gene such as a fluorescent protein. To facilitate the generation of such translational fusions and to ensure that all cis-regulatory sequences are included, we have used a bacterial homologous recombination system (recombineering) to insert fluorescent protein tags into genes of interest harbored by transformation-competent bacterial artificial chromosomes (TACs). This approach has several advantages compared to other classical strategies. First, the researcher does not have to guess what the regulatory sequences of a gene are, as tens of thousands of base pairs flanking the gene of interest can be included in the construct. Second, because the genes of interest are not amplified by PCR, there are practically no limits to the size of a gene that can be tagged. Third, there are no restrictions on the location in which the fluorescent protein can be inserted, as the position is determined by sequence homology with the recombination primers. Finally, all of the required strains and TAC clones are publically available, and the experimental procedures described here are simple and robust. Thus, we suggest that recombineering-based gene tagging should be the gold standard for gene expression studies in Arabidopsis. DA - 2011/5// PY - 2011/5// DO - 10.1111/j.1365-313X.2011.04524.x VL - 66 IS - 4 SP - 712-723 SN - 0960-7412 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-79955809131&partnerID=MN8TOARS KW - Arabidopsis KW - recombineering KW - Aux KW - IAA KW - gene tagging KW - fluorescent KW - proteins ER - TY - JOUR TI - grassy tillers1 promotes apical dominance in maize and responds to shade signals in the grasses AU - Whipple, C. J. AU - Kebrom, T. H. AU - Weber, A. L. AU - Yang, F. AU - Hall, D. AU - Meeley, R. AU - Schmidt, R. AU - Doebley, J. AU - Brutnell, T. P. AU - Jackson, D. P. T2 - Proceedings of the National Academy of Sciences of the United States of America DA - 2011/// PY - 2011/// VL - 108 IS - 33 SP - E506-512 ER - TY - JOUR TI - Phylogeny-based developmental analyses illuminate evolution of inflorescence architectures in dogwoods (Cornus s. l., Cornaceae) AU - Feng, Chun-Miao AU - Xiang, Qiu-Yun AU - Franks, Robert G. T2 - NEW PHYTOLOGIST AB - • Inflorescence architecture is important to angiosperm reproduction, but our knowledge of the developmental basis underlying the evolution of inflorescence architectures is limited. Using a phylogeny-based comparative analysis of developmental pathways, we tested the long-standing hypothesis that umbel evolved from elongated inflorescences by suppression of inflorescence branches, while head evolved from umbels by suppression of pedicels. • The developmental pathways of six species of Cornus producing different inflorescence types were characterized by scanning electron microscopy (SEM) and histological analysis. Critical developmental events were traced over the molecular phylogeny to identify evolutionary changes leading to the formation of umbels and heads using methods accounting for evolutionary time and phylogenetic uncertainty. • We defined 24 developmental events describing the developmental progression of the different inflorescence types. The evolutionary transition from paniculate cymes to umbels and heads required alterations of seven developmental events occurring at different evolutionary times. • Our results indicate that heads and umbels evolved independently in Cornus from elongated forms via an umbellate dichasium ancestor and this process involved several independent changes. Our findings shed novel insights into head and umbel evolution concealed by outer morphology. Our work illustrates the importance of combining developmental and phylogenetic data to better define morphological evolutionary processes. DA - 2011/// PY - 2011/// DO - 10.1111/j.1469-8137.2011.03716.x VL - 191 IS - 3 SP - 850-869 SN - 1469-8137 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-79960555236&partnerID=MN8TOARS KW - ancestral character state reconstruction KW - Cornus KW - evolutionary development KW - inflorescence evolution KW - umbels and heads 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 - The Collaborative Cross: A Recombinant Inbred Mouse Population for the Systems Genetic Era AU - Threadgill, David W. AU - Miller, Darla R. AU - Churchill, Gary A. AU - Villena, Fernando Pardo-Manuel T2 - ILAR JOURNAL AB - The mouse is the most extensively used mammalian model for biomedical and aging research, and an extensive catalogue of laboratory resources is available to support research using mice: classical inbred lines, genetically modified mice (knockouts, transgenics, and humanized mice), selectively bred lines, consomics, congenics, recombinant inbred panels, outbred and heterogeneous stocks, and an expanding set of wild-derived strains. However, these resources were not designed or intended to model the heterogeneous human population or for a systematic analysis of phenotypic effects due to random combinations of uniformly distributed natural variants. The Collaborative Cross (CC) is a large panel of recently established multiparental recombinant inbred mouse lines specifically designed to overcome the limitations of existing mouse genetic resources for analysis of phenotypes caused by combinatorial allele effects. The CC models the complexity of the human genome and supports analyses of common human diseases with complex etiologies originating through interactions between allele combinations and the environment. The CC is the only mammalian resource that has high and uniform genomewide genetic variation effectively randomized across a large, heterogeneous, and infinitely reproducible population. The CC supports data integration across environmental and biological perturbations and across space (different labs) and time. DA - 2011/// PY - 2011/// DO - 10.1093/ilar.52.1.24 VL - 52 IS - 1 SP - 24-31 SN - 1930-6180 KW - aging KW - Collaborative Cross (CC) KW - mouse model KW - recombinant inbred mice KW - systems genetics KW - genetic reference population ER - TY - JOUR TI - Efficient germ-line transformation of the economically important pest species Lucilia cuprina and Lucilia sericata (Diptera, Calliphoridae) AU - Concha, Carolina AU - Belikoff, Esther J. AU - Carey, Brandi-lee AU - Li, Fang AU - Schiemann, Anja H. AU - Scott, Maxwell J. T2 - Insect Biochemistry and Molecular Biology AB - The green blowfly species Lucilia cuprina and Lucilia sericata are economically important pests for the sheep industries of Australia and New Zealand. L. cuprina has long been considered a good target for a genetic pest management program. In addition, L. sericata maggots are used in the cleaning of wounds and necrotic tissue of patients suffering from ulcers that are difficult to treat by other methods. Development of efficient transgenesis methods would greatly facilitate the development of strains ideal for genetic control programs or could potentially improve “maggot therapy”. We have previously reported the germ-line transformation of L. cuprina and the design of a “female killing system” that could potentially be applied to this species. However, the efficiency of transformation obtained was low and transformed lines were difficult to detect due to the low expression of the EGFP marker used. Here we describe an efficient and reliable method for germ-line transformation of L. cuprina using new piggyBac vector and helper plasmids containing the strong promoter from the L. cuprina hsp83 gene to drive expression of the transposase and fluorescent protein marker gene. We also report, for the first time, the germ-line transformation of L. sericata using the new piggyBac vector/helper combination. DA - 2011/1// PY - 2011/1// DO - 10.1016/j.ibmb.2010.09.006 VL - 41 IS - 1 SP - 70-75 J2 - Insect Biochemistry and Molecular Biology LA - en OP - SN - 0965-1748 UR - http://dx.doi.org/10.1016/j.ibmb.2010.09.006 DB - Crossref KW - Lucilia cuprina KW - Lucilia sericata KW - PiggyBac KW - Transformation KW - Transgenesis KW - Maggot therapy KW - Flystrike 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 - 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 - A rendezvous with our microbes AU - Gordon, Jeffrey I. AU - Klaenhammer, Todd R. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - On November 2–3, 2009 an international group of scientists representing multiple disciplines gathered to consider the current state of our understanding of the symbiotic and beneficial relationships between microbes and humans and to define the challenges, gaps in knowledge, and opportunities that this exciting field of study now offers. A number of adjectives come to mind when describing the subject of microbes and health, ranging from ancient and historic , to integrative and interdisciplinary , to timely and pressing . Coexistence and coevolution with microbes has been a theme of life on Earth for all metazoans past and present. Historically, the discovery that microbes are an integral part of us was made as soon as Antonie van Leeuwenhoek peered through his microscope and examined dental plaque sampled from himself and others (without institutional review board approval!). His sense of awe and his early appreciation of the diversity our microbial partners were evident in the words he chose for a letter written to the Royal Society of London in September 1683: > “Though my teeth are kept usually very clean, nevertheless, when I view them in a magnifying glass, I find growing between them a little white matter as thick as wetted flower: in this substance though I could not perceive any motion, I judged there might probably be living creatures. I therefore took some of this flower and mixed it either with pure rain water wherein were no animals, or else with some of my spittle (having no air bubbles to cause a motion in it) and then to my great surprise perceived that the aforesaid matter maintained very many small living animals, which moved themselves very extravagantly. ….The spittle of an old man that had lived soberly, had no animals in it; but the substance upon and between his teeth … [↵][1]1To whom correspondence should be addressed. E-mail: jgordon{at}wustl.edu. [1]: #xref-corresp-1-1 DA - 2011/3/15/ PY - 2011/3/15/ DO - 10.1073/pnas.1101958108 VL - 108 SP - 4513-4515 SN - 0027-8424 ER - TY - JOUR TI - Interstrain Differences in the Liver Effects of Trichloroethylene in a Multistrain Panel of Inbred Mice AU - Bradford, Blair U. AU - Lock, Eric F. AU - Kosyk, Oksana AU - Kim, Sungkyoon AU - Uehara, Takeki AU - Harbourt, David AU - DeSimone, Michelle AU - Threadgill, David W. AU - Tryndyak, Volodymyr AU - Pogribny, Igor P. AU - Bleyle, Lisa AU - Koop, Dennis R. AU - Rusyn, Ivan T2 - TOXICOLOGICAL SCIENCES AB - Trichloroethylene (TCE) is a widely used industrial chemical and a common environmental contaminant. It is a well-known carcinogen in rodents and a probable carcinogen in humans. Studies utilizing panels of mouse inbred strains afford a unique opportunity to understand both metabolic and genetic basis for differences in responses to TCE. We tested the hypothesis that strain- and liver-specific toxic effects of TCE are genetically controlled and that the mechanisms of toxicity and susceptibility can be uncovered by exploring responses to TCE using a diverse panel of inbred mouse strains. TCE (2100 mg/kg) or corn oil vehicle was administered by gavage to 6- to 8-week-old male mice of 15 mouse strains. Serum and liver were collected at 2, 8, and 24 h postdosing and were analyzed for TCE metabolites, hepatocellular injury, and gene expression of liver. TCE metabolism, as evident from the levels of individual oxidative and conjugative metabolites, varied considerably between strains. TCE treatment-specific effect on the liver transcriptome was strongly dependent on genetic background. Peroxisome proliferator–activated receptor–mediated molecular networks, consisting of the metabolism genes known to be induced by TCE, represent some of the most pronounced molecular effects of TCE treatment in mouse liver that are dependent on genetic background. Conversely, cell death, liver necrosis, and immune-mediated response pathways, which are altered by TCE treatment in liver, are largely genetic background independent. These studies provide better understanding of the mechanisms of TCE-induced toxicity anchored on metabolism and genotype-phenotype correlations that may define susceptibility or resistance. DA - 2011/3// PY - 2011/3// DO - 10.1093/toxsci/kfq362 VL - 120 IS - 1 SP - 206-217 SN - 1096-0929 KW - trichloroethylene KW - metabolism KW - genetics KW - peroxisome proliferator-activated receptor alpha KW - acute exposure KW - gene expression ER - TY - JOUR TI - Epiregulin-dependent amphiregulin expression and ERBB2 signaling are involved in luteinizing hormone-induced paracrine signaling pathways in mouse ovary AU - Kim, Kyoungmi AU - Lee, Hyunji AU - Threadgill, David W. AU - Lee, Daekee T2 - BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS AB - Sustained EGF receptor (EGFR) phosphorylation by de novo synthesis of EGFR ligands plays an essential role in mediating luteinizing hormone (LH)-induced ovulation process in the preovulatory follicles (POFs). In the present study, the effect of epiregulin (EREG) on oocyte maturation and ovulation was investigated using Ereg knockout (Ereg−/−) mice congenic on a C57BL/6 background. Rate of spontaneous oocyte meiotic resumption of denuded oocytes (DOs) or cumulus cell-oocyte complexes (COCs) in vitro is similar between wild-type and Ereg−/− mice. However, gonadotropin-induced meiotic resumption in vivo is attenuated, and the number of COCs with expanded cumulus matrix and superovulated eggs dramatically decrease in Ereg−/− mice. Nonetheless, the number of eggs ovulated during normal estrus cycles and litter sizes in Ereg−/− mice are comparable to those of wild-type littermates. In contrast to other EGFR ligands, induction of amphiregulin (Areg) mRNA is severely reduced in ovaries collected from Ereg−/− mice either after human chorionic gonadotropin (hCG) treatment in immature mice or LH surge in adults. Gonadotropin-induced EGFR and ERBB2 phosphorylation in ovaries is attenuated in immature Ereg−/− mice, and MAPK3/1 phosphorylation and prostaglandin synthase 2 (PTGS2) protein levels are reduced. This attenuation, however, is no longer detectable in adult Ereg−/− mice after LH surge. This study implicates that EREG mediates signals downstream of Areg mRNA expression and that EGFR-ERBB2 signals contributes to regulation of ovulation process. DA - 2011/2/11/ PY - 2011/2/11/ DO - 10.1016/j.bbrc.2011.01.039 VL - 405 IS - 2 SP - 319-324 SN - 1090-2104 KW - Amphiregulin KW - Epiregulin KW - EGFR and ERBB2 phosphorylation KW - Oocyte maturation KW - Ovulation ER - TY - JOUR TI - A population genetic approach to mapping neurological disorder genes using deep resequencing AU - Myers, R. A. AU - Casals, F. AU - Gauthier, J. AU - Hamdan, F. F. AU - Keebler, J. AU - Boyko, A. R. AU - Bustamante, C. D. AU - Piton, A. M. AU - Spiegelman, D. AU - Henrion, E. AU - Zilversmit, M. AU - Hussin, J. AU - Quinlan, J. AU - Yang, Y. AU - Lafreniere, R. G. AU - Griffing, A. R. AU - Stone, E. A. T2 - PLoS Genetics DA - 2011/// PY - 2011/// VL - 7 IS - 2 ER - TY - JOUR TI - Organisation and expression of a cluster of yolk protein genes in the Australian sheep blowfly, Lucilia cuprina AU - Scott, Maxwell J. AU - Atapattu, Asela AU - Schiemann, Anja H. AU - Concha, Carolina AU - Henry, Rebecca AU - Carey, Brandi-lee AU - Belikoff, Esther J. AU - Heinrich, Joerg C. AU - Sarkar, Abhimanyu T2 - GENETICA DA - 2011/1// PY - 2011/1// DO - 10.1007/s10709-010-9492-6 VL - 139 IS - 1 SP - 63-70 SN - 0016-6707 KW - Yolk protein KW - Sterile insect technique KW - Lucilia cuprina 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 - Genome-wide association study of leaf architecture in the maize nested association mapping population AU - Tian, Feng AU - Bradbury, Peter J. AU - Brown, Patrick J. AU - Hung, Hsiaoyi AU - Sun, Qi AU - Flint-Garcia, Sherry AU - Rocheford, Torbert R. AU - McMullen, Michael D. AU - Holland, James B. AU - Buckler, Edward S. T2 - NATURE GENETICS DA - 2011/2// PY - 2011/2// DO - 10.1038/ng.746 VL - 43 IS - 2 SP - 159-U113 SN - 1546-1718 ER - TY - JOUR TI - Fur Negatively Regulates hns and Is Required for the Expression of HilA and Virulence in Salmonella enterica Serovar Typhimurium AU - Troxell, Bryan AU - Sikes, Michael L. AU - Fink, Ryan C. AU - Vazquez-Torres, Andres AU - Jones-Carson, Jessica AU - Hassan, Hosni M. T2 - JOURNAL OF BACTERIOLOGY AB - Iron is an essential element for the survival of living cells. However, excess iron is toxic, and its uptake is exquisitely regulated by the ferric uptake regulator, Fur. In Salmonella, the Salmonella pathogenicity island 1 (SPI-1) encodes a type three secretion system, which is required for invasion of host epithelial cells in the small intestine. A major activator of SPI-1 is HilA, which is encoded within SPI-1. One known regulator of hilA is Fur. The mechanism of hilA regulation by Fur is unknown. We report here that Fur is required for virulence in Salmonella enterica serovar Typhimurium and that Fur is required for the activation of hilA, as well as of other HilA-dependent genes, invF and sipC. The Fur-dependent regulation of hilA was independent of PhoP, a known repressor of hilA. Instead, the expression of the gene coding for the histone-like protein, hns, was significantly derepressed in the fur mutant. Indeed, the activation of hilA by Fur was dependent on 28 nucleotides located upstream of hns. Moreover, we used chromatin immunoprecipitation to show that Fur bound, in vivo, to the upstream region of hns in a metal-dependent fashion. Finally, deletion of fur in an hns mutant resulted in Fur-independent activation of hilA. In conclusion, Fur activates hilA by repressing the expression of hns. DA - 2011/1// PY - 2011/1// DO - 10.1128/jb.00942-10 VL - 193 IS - 2 SP - 497-505 SN - 1098-5530 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 - A new technique using metal tags to track small seeds over short distances AU - Canner, J. E. AU - Spence, M. T2 - Ecological Research DA - 2011/// PY - 2011/// VL - 26 IS - 1 SP - 233-236 ER -