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Articles 1 - 30 of 38
Full-Text Articles in Genetics and Genomics
Surveys Of Aphonopelma Hentzi In Missouri: Conservation Efforts Through Population, Genetics, And Habitat Studies, Anderson B. Spencer Mr., Becky Hansis-O'Niell
Surveys Of Aphonopelma Hentzi In Missouri: Conservation Efforts Through Population, Genetics, And Habitat Studies, Anderson B. Spencer Mr., Becky Hansis-O'Niell
Undergraduate Research Symposium
Aphonopelma hentzi and other tarantula species are greatly understudied organisms. In the Missouri regions there is little knowledge on their mating patterns, gene diversity, or population sizes. The focal glades in this experiment display regional fragmentation, which could prevent tarantulas from traveling and mating between regions of their glades. Due to the lack of knowledge surrounding them, methods for determining gene diversity are harmful to the organism. Our recent work has shown that it is possible to extract genetic information from the molts of burrowing tarantulas. This will allow us to safely determine the lineages and interbreeding patterns of the …
Recovering Ancient Dna Using The Polymerase Chain Reaction, Rose Jennings
Recovering Ancient Dna Using The Polymerase Chain Reaction, Rose Jennings
Undergraduate Research Symposium
Investigations into aDNA offer a window into the past that modern DNA and paleontological studies alone cannot provide and help address the evolution and connections between hominids, domestication timelines, the analysis of populations over time, and general diversity. Progress in aDNA research has been inherently technology-driven, with modern molecular biology methods, such as the inventions of Polymerase Chain Reaction (PCR) and Next Generation Sequencing (NGS), substantially increasing the analysis possibilities of aDNA. My research this semester has taken me along two parallel paths of investigation: literary research into aDNA and practical exposure to the laboratory techniques used in its analysis. …
Resolving The Repression Pathway Of Virulence Gene Hila In Salmonella, Alexandra King, Lon Chubiz Phd, Brenda Pratte, Lauren Daugherty
Resolving The Repression Pathway Of Virulence Gene Hila In Salmonella, Alexandra King, Lon Chubiz Phd, Brenda Pratte, Lauren Daugherty
Undergraduate Research Symposium
Salmonella is a relatively abundant, virulent species of bacteria that is most known for spreading gastrointestinal diseases through food. These illnesses result in approximately 1.35 million infections, including over 25,000 hospitalizations each year, in the U.S. alone (CDC.gov). As antibiotic resistance becomes an increasingly urgent public health problem, the importance of developing alternative treatment methods is only becoming more crucial. One of the genes responsible for this virulence is known as hilA. HilA is the main transcriptional regulator of Salmonella Pathogenicity Island-1 gene (UniProt). SPI-1 plays an important role in the invasion of Salmonella into epithelial cells. The proteins encoded …
Mutations In Several Auxin Biosynthesis Genes And Their Effects On Plant Phenotypes In Arabidopsis, Gabriela Hernandez, Lauren Huebner, Bethany Karlin Zolman
Mutations In Several Auxin Biosynthesis Genes And Their Effects On Plant Phenotypes In Arabidopsis, Gabriela Hernandez, Lauren Huebner, Bethany Karlin Zolman
Undergraduate Research Symposium
Auxins are important hormones in plants that regulate growth and development. Disruptions in the auxin biosynthesis pathway result in morphological changes in phenotypes in the model plant Arabidopsis thaliana, including differences in root and leaf formation. Mutations in the Tryptophan Aminotransferase of Arabidopsis (TAA1) and YUCCA (YUC4) genes interfere with the plant's ability to synthesize Indole-3-acetic acid (IAA), the primary auxin involved in plant development. IBR1 and IBR3 act in the multistep conversion of indole-3-butyric acid (IBA) to IAA. ILL2, IAR3, and ILR1 hydrolyze IAA-amino acid conjugates into free IAA. The goal of …
Covid-19 And The Differential Dilemma, Sharlee Climer
Covid-19 And The Differential Dilemma, Sharlee Climer
Computer Science Faculty Works
The conundrums of choosing candidate genes, via differential expression between treated and mock specimens, are tackled by Ghandikota et al. in this issue of Patterns in their efforts to tease out genetic patterns that are characteristic of coronavirus disease 2019 (COVID-19) outcomes.
Multidrug Resistance Regulators Mara, Soxs, Rob, And Rama Repress Flagellar Gene Expression And Motility In Salmonella Enterica Serovar Typhimurium, Srinivas Thota, Lon Chubiz
Multidrug Resistance Regulators Mara, Soxs, Rob, And Rama Repress Flagellar Gene Expression And Motility In Salmonella Enterica Serovar Typhimurium, Srinivas Thota, Lon Chubiz
Biology Department Faculty Works
Production of flagella is costly and subject to global multilayered regulation, which is reflected in the hierarchical control of flagellar production in many bacterial species. For Salmonella enterica serovar Typhimurium and its relatives, global regulation of flagellar production primarily occurs through the control of flhDC transcription and mRNA translation. In this study, the roles of the homologous multidrug resistance regulators MarA, SoxS, Rob, and RamA (constituting the mar-sox-rob regulon in S. Typhimurium) in regulating flagellar gene expression were explored. Each of these regulators was found to inhibit flagellar gene expression, production of flagella, and motility. To different degrees, repression via …
Immunogenetic Response Of The Bananaquit In The Face Of Malarial Parasites, Jennifer Antonides, Samarth Mathur, Mekala Sundaram, Robert Ricklefs, J. Dewoody
Immunogenetic Response Of The Bananaquit In The Face Of Malarial Parasites, Jennifer Antonides, Samarth Mathur, Mekala Sundaram, Robert Ricklefs, J. Dewoody
Biology Department Faculty Works
Background: In the arms race between hosts and parasites, genes involved in the immune response are targets for natural selection. Toll-Like Receptor (TLR) genes play a role in parasite detection as part of the innate immune system whereas Major Histocompatibility Complex (MHC) genes encode proteins that display antigens as part of the vertebrate adaptive immune system. Thus, both gene families are under selection pressure from pathogens. The bananaquit (Coereba flaveola) is a passerine bird that is a common host of avian malarial parasites (Plasmodium sp. and Haemoproteus sp.). We assessed molecular variation of TLR and MHC genes in a wild …
High-Coverage Genomes To Elucidate The Evolution Of Penguins., Hailin Pan, Hailin Pan, Theresa Cole, Theresa Cole, Xupeng Bi, Miaoquan Fang, Chengran Zhou, Zhengtao Yang, Daniel Ksepka, Tom Hart, Juan Bouzat, Lisa Argilla, Mads Bertelsen, Mads Bertelsen, P. Boersma, Charles Bost, Yves Cherel, Peter Dann, Steven Fiddaman, Pauline Howard, Kim Labuschagne, Thomas Mattern, Gary Miller, Gary Miller, Patricia Parker, Richard Phillips, Petra Quillfeldt, Peter Ryan, Helen Taylor, David Thompson, Melanie Young, Martin Ellegaard, M. Gilbert, M. Gilbert, Mikkel Sinding, George Pacheco, Lara Shepherd, Alan Tennyson, Stefanie Grosser, Stefanie Grosser, Emily Kay, Emily Kay, Lisa Nupen, Ursula Ellenberg, Ursula Ellenberg, David Houston, Andrew Reeve, Andrew Reeve, Kathryn Johnson
High-Coverage Genomes To Elucidate The Evolution Of Penguins., Hailin Pan, Hailin Pan, Theresa Cole, Theresa Cole, Xupeng Bi, Miaoquan Fang, Chengran Zhou, Zhengtao Yang, Daniel Ksepka, Tom Hart, Juan Bouzat, Lisa Argilla, Mads Bertelsen, Mads Bertelsen, P. Boersma, Charles Bost, Yves Cherel, Peter Dann, Steven Fiddaman, Pauline Howard, Kim Labuschagne, Thomas Mattern, Gary Miller, Gary Miller, Patricia Parker, Richard Phillips, Petra Quillfeldt, Peter Ryan, Helen Taylor, David Thompson, Melanie Young, Martin Ellegaard, M. Gilbert, M. Gilbert, Mikkel Sinding, George Pacheco, Lara Shepherd, Alan Tennyson, Stefanie Grosser, Stefanie Grosser, Emily Kay, Emily Kay, Lisa Nupen, Ursula Ellenberg, Ursula Ellenberg, David Houston, Andrew Reeve, Andrew Reeve, Kathryn Johnson
Biology Department Faculty Works
BackgroundPenguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive …
Landscape Genomics: Natural Selection Drives The Evolution Of Mitogenome In Penguins, Barbara Ramos, Daniel González-Acuña, David Loyola, Warren Johnson, Patricia Parker, Melanie Massaro, Gisele Dantas, Marcelo Miranda, Juliana Vianna
Landscape Genomics: Natural Selection Drives The Evolution Of Mitogenome In Penguins, Barbara Ramos, Daniel González-Acuña, David Loyola, Warren Johnson, Patricia Parker, Melanie Massaro, Gisele Dantas, Marcelo Miranda, Juliana Vianna
Biology Department Faculty Works
BackgroundMitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes and …
Identification Of The Potentiating Mutations And Synergistic Epistasis That Enabled The Evolution Of Inter-Species Cooperation, Sarah Douglas, Lon Chubiz, William Harcombe, Christopher Marx
Identification Of The Potentiating Mutations And Synergistic Epistasis That Enabled The Evolution Of Inter-Species Cooperation, Sarah Douglas, Lon Chubiz, William Harcombe, Christopher Marx
Biology Department Faculty Works
Microbes often engage in cooperation through releasing biosynthetic compounds required by other species to grow. Given that production of costly biosynthetic metabolites is generally subjected to multiple layers of negative feedback, single mutations may frequently be insufficient to generate cooperative phenotypes. Synergistic epistatic interactions between multiple coordinated changes may thus often underlie the evolution of cooperation through overproduction of metabolites. To test the importance of synergistic mutations in cooperation we used an engineered bacterial consortium of an Escherichia coli methionine auxotroph and Salmonella enterica. S. enterica relies on carbon by-products from E. coli if lactose is the only carbon source. …
Parallel Mutations Result In A Wide Range Of Cooperation And Community Consequences In A Two-Species Bacterial Consortium, Sarah Douglas, Lon Chubiz, William Harcombe, F. Ytreberg, Christopher Marx
Parallel Mutations Result In A Wide Range Of Cooperation And Community Consequences In A Two-Species Bacterial Consortium, Sarah Douglas, Lon Chubiz, William Harcombe, F. Ytreberg, Christopher Marx
Biology Department Faculty Works
Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium, we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determine community dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymous mutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica …
A Novel Variant In Cmah Is Associated With Blood Type Ab In Ragdoll Cats, Barbara Gandolfi, Robert Grahn, Nicholas Gustafson, Daniela Proverbio, Eva Spada, Badri Adhikari, Janling Cheng, Gordon Andrews, Leslie Lyons, Chris Helps
A Novel Variant In Cmah Is Associated With Blood Type Ab In Ragdoll Cats, Barbara Gandolfi, Robert Grahn, Nicholas Gustafson, Daniela Proverbio, Eva Spada, Badri Adhikari, Janling Cheng, Gordon Andrews, Leslie Lyons, Chris Helps
Computer Science Faculty Works
The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase is associated with the production of sialic acids on cat red blood cells. The cat has one major blood group with three serotypes; the most common blood type A being dominant to type B. A third rare blood type is known as AB and has an unclear mode of inheritance. Cat blood type antigens are defined, with N-glycolylneuraminic acid being associated with type A and N-acetylneuraminic acid with type B. Blood type AB is serologically characterized by agglutination using typing reagents directed against both A and B epitopes. While a genetic characterization of blood …
Evolution Of Kaic-Dependent Timekeepers: A Proto-Circadian Timing Mechanism Confers Adaptive Fitness In The Purple Bacterium Rhodopseudomonas Palustris, Peijun Ma, Tetsuya Mori, Chi Zhao, Teresa Thiel, Carl Johnson
Evolution Of Kaic-Dependent Timekeepers: A Proto-Circadian Timing Mechanism Confers Adaptive Fitness In The Purple Bacterium Rhodopseudomonas Palustris, Peijun Ma, Tetsuya Mori, Chi Zhao, Teresa Thiel, Carl Johnson
Biology Department Faculty Works
Circadian (daily) rhythms are a fundamental and ubiquitous property of eukaryotic organisms. However, cyanobacteria are the only prokaryotic group for which bona fide circadian properties have been persuasively documented, even though homologs of the cyanobacterial kaiABC central clock genes are distributed widely among Eubacteria and Archaea. We report the purple non-sulfur bacterium Rhodopseudomonas palustris (that harbors homologs of kaiB and kaiC) only poorly sustains rhythmicity in constant conditions–a defining characteristic of circadian rhythms. Moreover, the biochemical characteristics of the Rhodopseudomonas homolog of the KaiC protein in vivo and in vitro are different from those of cyanobacterial KaiC. Nevertheless, R. palustris …
Progress In Pathogen Detection By Whole-Genome Sequencing, Chung Wong
Progress In Pathogen Detection By Whole-Genome Sequencing, Chung Wong
Chemistry & Biochemistry Faculty Works
No abstract provided.
Interactions Of Two Large Antiviral Polyamides With The Long Control Region Of Hpv16., Elena Vasilieva, Jacquelyn Niederschulte, Yang Song, George Harris, Kevin Koeller, Puhong Liao, James Bashkin, Cynthia Dupureur
Interactions Of Two Large Antiviral Polyamides With The Long Control Region Of Hpv16., Elena Vasilieva, Jacquelyn Niederschulte, Yang Song, George Harris, Kevin Koeller, Puhong Liao, James Bashkin, Cynthia Dupureur
Chemistry & Biochemistry Faculty Works
No abstract provided.
Heterogeneous Dynamics In Dna Site Discrimination By The Structurally Homologous Dna-Binding Domains Of Ets-Family Transcription Factors, Gaofei He, Ana Tolic, James Bashkin, Gregory Poon
Heterogeneous Dynamics In Dna Site Discrimination By The Structurally Homologous Dna-Binding Domains Of Ets-Family Transcription Factors, Gaofei He, Ana Tolic, James Bashkin, Gregory Poon
Chemistry & Biochemistry Faculty Works
The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only …
Phenotypic Heterogeneity In Metabolic Traits Among Single Cells Of A Rare Bacterial Species In Its Natural Environment Quantified With A Combination Of Flow Cell Sorting And Nanosims, Matthias Zimmermann, Matthias Zimmermann, Stéphanie Escrig, Thomas Hübschmann, Mathias Kirf, Mathias Kirf, Andreas Brand, Andreas Brand, R. Inglis, R. Inglis, Niculina Musat, Susann Müller, Andres Meibom, Andres Meibom, Martin Ackermann, Martin Ackermann, Frank Schreiber, Frank Schreiber
Phenotypic Heterogeneity In Metabolic Traits Among Single Cells Of A Rare Bacterial Species In Its Natural Environment Quantified With A Combination Of Flow Cell Sorting And Nanosims, Matthias Zimmermann, Matthias Zimmermann, Stéphanie Escrig, Thomas Hübschmann, Mathias Kirf, Mathias Kirf, Andreas Brand, Andreas Brand, R. Inglis, R. Inglis, Niculina Musat, Susann Müller, Andres Meibom, Andres Meibom, Martin Ackermann, Martin Ackermann, Frank Schreiber, Frank Schreiber
Biology Department Faculty Works
Populations of genetically identical microorganisms residing in the same environment can display marked variability in their phenotypic traits; this phenomenon is termed phenotypic heterogeneity. The relevance of such heterogeneity in natural habitats is unknown, because phenotypic characterization of a sufficient number of single cells of the same species in complex microbial communities is technically difficult. We report a procedure that allows to measure phenotypic heterogeneity in bacterial populations from natural environments, and use it to analyze N2 and CO2 fixation of single cells of the green sulfur bacterium Chlorobium phaeobacteroides from the meromictic lake Lago di Cadagno. We incubated lake …
Species Interactions Differ In Their Genetic Robustness, Lon Chubiz, Brian Granger, Daniel Segrè, William Harcombe
Species Interactions Differ In Their Genetic Robustness, Lon Chubiz, Brian Granger, Daniel Segrè, William Harcombe
Biology Department Faculty Works
Conflict and cooperation between bacterial species drive the composition and function of microbial communities. Stability of these emergent properties will be influenced by the degree to which species’ interactions are robust to genetic perturbations. We use genome-scale metabolic modeling to computationally analyze the impact of genetic changes when Escherichia coli and Salmonella enterica compete, or cooperate. We systematically knocked out in silico each reaction in the metabolic network of E. coli to construct all 2583 mutant stoichiometric models. Then, using a recently developed multi-scale computational framework, we simulated the growth of each mutant E. coli in the presence of S. …
Parallel And Divergent Evolutionary Solutions For The Optimization Of An Engineered Central Metabolism In Methylobacterium Extorquens Am1, Sean Carroll, Lon Chubiz, Deepa Agashe, Christopher Marx
Parallel And Divergent Evolutionary Solutions For The Optimization Of An Engineered Central Metabolism In Methylobacterium Extorquens Am1, Sean Carroll, Lon Chubiz, Deepa Agashe, Christopher Marx
Biology Department Faculty Works
Bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. Here, we highlight experimental evolution as an effective means for optimizing an engineered Methylobacterium extorquens AM1. Replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered Methylobacterium, but growth rapidly recovered after six hundred generations of evolution on methanol. We used whole-genome sequencing to identify the basis of adaptation in eight replicate evolved strains, and examined genomic changes in light of other growth and physiological data. We observed great variety …
Human Gephyrin Is Encompassed Within Giant Functional Noncoding Yin–Yang Sequences, Sharlee Climer, Alan Templeton, Weixiong Zhang
Human Gephyrin Is Encompassed Within Giant Functional Noncoding Yin–Yang Sequences, Sharlee Climer, Alan Templeton, Weixiong Zhang
Computer Science Faculty Works
Gephyrin is a highly conserved gene that is vital for the organization of proteins at inhibitory receptors, molybdenum cofactor biosynthesis and other diverse functions. Its specific function is intricately regulated and its aberrant activities have been observed for a number of human diseases. Here we report a remarkable yin–yang haplotype pattern encompassing gephyrin. Yin–yang haplotypes arise when a stretch of DNA evolves to present two disparate forms that bear differing states for nucleotide variations along their lengths. The gephyrin yin–yang pair consists of 284 divergent nucleotide states and both variants vary drastically from their mutual ancestral haplotype, suggesting rapid evolution. …
Fighting Microbial Drug Resistance: A Primer On The Role Of Evolutionary Biology In Public Health, Gabriel Perron, R. Inglis, Pleuni Pennings, Sarah Cobey
Fighting Microbial Drug Resistance: A Primer On The Role Of Evolutionary Biology In Public Health, Gabriel Perron, R. Inglis, Pleuni Pennings, Sarah Cobey
Biology Department Faculty Works
Although microbes have been evolving resistance to antimicrobials for millennia, the spread of resistance in pathogen populations calls for the development of new drugs and treatment strategies. We propose that successful, long-term resistance management requires a better understanding of how resistance evolves in the first place. This is an opportunity for evolutionary biologists to engage in public health, a collaboration that has substantial precedent. Resistance evolution has been an important tool for developing and testing evolutionary theory, especially theory related to the genetic basis of new traits and constraints on adaptation. The present era is no exception. The articles in …
Regulation Of Three Nitrogenase Gene Clusters In The Cyanobacterium Anabaena Variabilis Atcc 29413, Teresa Thiel, Brenda Pratte
Regulation Of Three Nitrogenase Gene Clusters In The Cyanobacterium Anabaena Variabilis Atcc 29413, Teresa Thiel, Brenda Pratte
Biology Department Faculty Works
The filamentous cyanobacterium Anabaena variabilis ATCC 29413 fixes nitrogen under aerobic conditions in specialized cells called heterocysts that form in response to an environmental deficiency in combined nitrogen. Nitrogen fixation is mediated by the enzyme nitrogenase, which is very sensitive to oxygen. Heterocysts are microxic cells that allow nitrogenase to function in a filament comprised primarily of vegetative cells that produce oxygen by photosynthesis. A. variabilis is unique among well-characterized cyanobacteria in that it has three nitrogenase gene clusters that encode different nitrogenases, which function under different environmental conditions. The nif1 genes encode a Mo-nitrogenase that functions only in heterocysts, …
Complete Genome Sequence Of Anabaena Variabilis Atcc 29413, Teresa Thiel, Brenda Pratte, Jinshun Zhong, Lynne Goodwin, Alex Copeland, Susan Lucas, Cliff Han, Sam Pitluck, Miriam Land, Nikos Kyrpides, Tanja Woyke
Complete Genome Sequence Of Anabaena Variabilis Atcc 29413, Teresa Thiel, Brenda Pratte, Jinshun Zhong, Lynne Goodwin, Alex Copeland, Susan Lucas, Cliff Han, Sam Pitluck, Miriam Land, Nikos Kyrpides, Tanja Woyke
Biology Department Faculty Works
Anabaena variabilis ATCC 29413 is a filamentous, heterocyst-forming cyanobacterium that has served as a model organism, with an extensive literature extending over 40 years. The strain has three distinct nitrogenases that function under different environmental conditions and is capable of photoautotrophic growth in the light and true heterotrophic growth in the dark using fructose as both carbon and energy source. While this strain was first isolated in 1964 in Mississippi and named Anabaena flos-aquae MSU A-37, it clusters phylogenetically with cyanobacteria of the genus Nostoc. The strain is a moderate thermophile, growing well at approximately 40° C. Here we provide …
Freq-Seq: A Rapid, Cost-Effective, Sequencing-Based Method To Determine Allele Frequencies Directly From Mixed Populations, Lon Chubiz, Ming-Chun Lee, Nigel Delaney, Christopher Marx
Freq-Seq: A Rapid, Cost-Effective, Sequencing-Based Method To Determine Allele Frequencies Directly From Mixed Populations, Lon Chubiz, Ming-Chun Lee, Nigel Delaney, Christopher Marx
Biology Department Faculty Works
No abstract provided.
Transcriptional Cross Talk Within The Mar-Sox-Rob Regulon In Escherichia Coli Is Limited To The Rob And Marrab Operons, Lon Chubiz, George Glekas, Christopher Rao
Transcriptional Cross Talk Within The Mar-Sox-Rob Regulon In Escherichia Coli Is Limited To The Rob And Marrab Operons, Lon Chubiz, George Glekas, Christopher Rao
Biology Department Faculty Works
Bacteria possess multiple mechanisms to survive exposure to various chemical stresses and antimicrobial compounds. In the enteric bacterium Escherichia coli, three homologous transcription factors—MarA, SoxS, and Rob—play a central role in coordinating this response. Three separate systems are known to regulate the expression and activities of MarA, SoxS, and Rob. However, a number of studies have shown that the three do not function in isolation but rather are coregulated through transcriptional cross talk. In this work, we systematically investigated the extent of transcriptional cross talk in the mar-sox-rob regulon. While the three transcription factors were found to have the potential …
Reduced Mhc And Neutral Variation In The Galápagos Hawk, An Island Endemic, Jennifer Bollmer, Joshua Hull, Holly Ernest, José Sarasola, Patricia Parker
Reduced Mhc And Neutral Variation In The Galápagos Hawk, An Island Endemic, Jennifer Bollmer, Joshua Hull, Holly Ernest, José Sarasola, Patricia Parker
Biology Department Faculty Works
BackgroundGenes at the major histocompatibility complex (MHC) are known for high levels of polymorphism maintained by balancing selection. In small or bottlenecked populations, however, genetic drift may be strong enough to overwhelm the effect of balancing selection, resulting in reduced MHC variability. In this study we investigated MHC evolution in two recently diverged bird species: the endemic Galápagos hawk (Buteo galapagoensis), which occurs in small, isolated island populations, and its widespread mainland relative, the Swainson's hawk (B. swainsoni).ResultsWe amplified at least two MHC class II B gene copies in each species. We recovered only three different sequences from 32 Galápagos …
Rna Processing Of Nitrogenase Transcripts In The Cyanobacterium Anabaena Variabilis, Justin Ungerer, Brenda Pratte, Teresa Thiel
Rna Processing Of Nitrogenase Transcripts In The Cyanobacterium Anabaena Variabilis, Justin Ungerer, Brenda Pratte, Teresa Thiel
Biology Department Faculty Works
Little is known about the regulation of nitrogenase genes in cyanobacteria. Transcription of the nifH1 and vnfH genes, encoding dinitrogenase reductases for the heterocyst-specific Mo-nitrogenase and the alternative V-nitrogenase, respectively, was studied by using a lacZ reporter. Despite evidence for a transcription start site just upstream of nifH1 and vnfH, promoter fragments that included these start sites did not drive the transcription of lacZ and, for nifH1, did not drive the expression of nifHDK1. Further analysis using larger regions upstream of nifH1 indicated that a promoter within nifU1 and a promoter upstream of nifB1 both contributed to expression of nifHDK1, …
Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao
Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao
Biology Department Faculty Works
Orthogonal ribosomes (o-ribosomes), also known as specialized ribosomes, are able to selectively translate mRNA not recognized by host ribosomes. As a result, they are powerful tools for investigating translational regulation and probing ribosome structure. To date, efforts directed towards engineering o-ribosomes have involved random mutagenesisbased approaches. As an alternative, we present here a computational method for rationally designing o-ribosomes in bacteria. Working under the assumption that base-pair interactions between the 16S rRNA and mRNA serve as the primary mode for ribosome binding and translational initiation, the algorithm enumerates all possible extended recognition sequences for 16S rRNA and then chooses those …
The Dynamic Evolutionary History Of The Bananaquit (Coereba Flaveola) In The Caribbean Revealed By A Multigene Analysis, Eva Bellemain, Eldredge Bermingham, Robert Ricklefs
The Dynamic Evolutionary History Of The Bananaquit (Coereba Flaveola) In The Caribbean Revealed By A Multigene Analysis, Eva Bellemain, Eldredge Bermingham, Robert Ricklefs
Biology Department Faculty Works
BackgroundThe bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion.ResultsPhylogenetic concordance between …
The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter Stevens, Leszek Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin Sachs, Noah Whitman, Susan Mccouch, Mary Schaeffer, Doreen Ware, Lincoln Stein, Seung Rhee
The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter Stevens, Leszek Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin Sachs, Noah Whitman, Susan Mccouch, Mary Schaeffer, Doreen Ware, Lincoln Stein, Seung Rhee
Biology Department Faculty Works
Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological …