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Tadkb:Family Classification And A Knowledge Base Of Topologically Associating Domains, Tong Liu, Jacob Porter, Chenguang Zhao, Hao Zhu, Nan Wang, Zheng Sun, Yin-Yuan Mo, Zheng Wang Mar 2019

Tadkb:Family Classification And A Knowledge Base Of Topologically Associating Domains, Tong Liu, Jacob Porter, Chenguang Zhao, Hao Zhu, Nan Wang, Zheng Sun, Yin-Yuan Mo, Zheng Wang

Faculty Publications

Background

Topologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can obtain family classifications and detailed information about TADs.

Results

We built an online knowledge base TADKB integrating knowledge for TADs in eleven cell types of human and mouse. For each TAD, TADKB provides the predicted three-dimensional (3D) structures of chromosomes and TADs, and detailed annotations about the protein-coding genes and long non-coding RNAs (lncRNAs) existent in each TAD. Besides the 3D chromosomal structures inferred by population Hi-C, the ...


The Receptor Protein Tyrosine Phosphatase Clr-1 Is Required For Synaptic Partner Recognition, Aruna Varshney, Kelli Benedetti, Katherine Watters, Raakhee Shankar, David Tatarakis, Doris Coto Villa, Khristina Magallanes, Venia Agenor, William Wung, Fatima Farah, Nebat Ali, Nghi Le, Jacqueline Pyle, Amber Farooqi, Zanett Kieu, Martina Bremer, Miri Vanhoven May 2018

The Receptor Protein Tyrosine Phosphatase Clr-1 Is Required For Synaptic Partner Recognition, Aruna Varshney, Kelli Benedetti, Katherine Watters, Raakhee Shankar, David Tatarakis, Doris Coto Villa, Khristina Magallanes, Venia Agenor, William Wung, Fatima Farah, Nebat Ali, Nghi Le, Jacqueline Pyle, Amber Farooqi, Zanett Kieu, Martina Bremer, Miri Vanhoven

Faculty Publications

During neural circuit formation, most axons are guided to complex environments, coming into contact with multiple potential synaptic partners. However, it is critical that they recognize specific neurons with which to form synapses. Here, we utilize the split GFP-based marker Neuroligin-1 GFP Reconstitution Across Synaptic Partners (NLG-1 GRASP) to visualize specific synapses in live animals, and a circuit-specific behavioral assay to probe circuit function. We demonstrate that the receptor protein tyrosine phosphatase (RPTP) clr-1 is necessary for synaptic partner recognition (SPR) between the PHB sensory neurons and the AVA interneurons in C. elegans. Mutations in clr-1/RPTP result in reduced ...


Developmental Ethanol Exposure Causes Reduced Feeding And Reveals A Critical Role For Neuropeptide F In Survival, Amanda Guevara, Hillary Gates, Brianna Urbina, Rachael French Mar 2018

Developmental Ethanol Exposure Causes Reduced Feeding And Reveals A Critical Role For Neuropeptide F In Survival, Amanda Guevara, Hillary Gates, Brianna Urbina, Rachael French

Faculty Publications

Food intake is necessary for survival, and natural reward circuitry has evolved to help ensure that animals ingest sufficient food to maintain development, growth, and survival. Drugs of abuse, including alcohol, co-opt the natural reward circuitry in the brain, and this is a major factor in the reinforcement of drug behaviors leading to addiction. At the junction of these two aspects of reward are alterations in feeding behavior due to alcohol consumption. In particular, developmental alcohol exposure (DAE) results in a collection of physical and neurobehavioral disorders collectively referred to as Fetal Alcohol Spectrum Disorder (FASD). The deleterious effects of ...


Deep Experimental Profiling Of Microrna Diversity, Deployment, And Evolution Across The Drosphila Genus, Jaaved Mohammed, Alex S. Flynt, Alexandra M. Panzarino, Md Mosharrof Hossain Mondal, Matthew De Cruz, Adam Siepel, Eric C. Lai Jan 2018

Deep Experimental Profiling Of Microrna Diversity, Deployment, And Evolution Across The Drosphila Genus, Jaaved Mohammed, Alex S. Flynt, Alexandra M. Panzarino, Md Mosharrof Hossain Mondal, Matthew De Cruz, Adam Siepel, Eric C. Lai

Faculty Publications

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death ...


Deep Experimental Profiling Of Microrna Diversity, Deployment, And Evolution Across The Drosophila Genus, Jaaven Mohammed, Alex S. Flynt, Alexandra M. Panzarino, Md Mosharrof Hossain Mondal, Matthew Decruz, Adam Siepel, Eric C. Lai Dec 2017

Deep Experimental Profiling Of Microrna Diversity, Deployment, And Evolution Across The Drosophila Genus, Jaaven Mohammed, Alex S. Flynt, Alexandra M. Panzarino, Md Mosharrof Hossain Mondal, Matthew Decruz, Adam Siepel, Eric C. Lai

Faculty Publications

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death ...


An Undergraduate Laboratory Manual For Analyzing A Crispr Mutant With A Predicted Role In Regeneration, Susan Walsh, Ashley Becker, Paxton S. Sickler, Damian G. Clarke, Erin Jimenez Nov 2017

An Undergraduate Laboratory Manual For Analyzing A Crispr Mutant With A Predicted Role In Regeneration, Susan Walsh, Ashley Becker, Paxton S. Sickler, Damian G. Clarke, Erin Jimenez

Faculty Publications

Exposing students to undergraduate research has reportedly improved students’ development of knowledge and skills in the laboratory, self-efficacy, satisfaction with their research, retention, and perseverance when faced with obstacles. Furthermore, utilizing authentic course-based undergraduate research experiences (CUREs) includes all students enrolled in the class, giving those who may not otherwise have access to an independent undergraduate research project an opportunity to engage in the scientific process in context of an original, unanswered question. In the fall of 2016, second semester introductory biology students conducted a semester-long research project on the transcription factor Lin28a to determine the effect of Lin28a on ...


In Vivo Cloning Of Up To 16 Kb Plasmids In E. Coli Is As Simple As Pcr, Faqing Huang, Joseph Rankin Spengler, Allen Yang Huang Aug 2017

In Vivo Cloning Of Up To 16 Kb Plasmids In E. Coli Is As Simple As Pcr, Faqing Huang, Joseph Rankin Spengler, Allen Yang Huang

Faculty Publications

The precise assembly of defined DNA sequences into plasmids is an essential task in bioscience research. While a number of molecular cloning techniques have been developed, many methods require specialized expensive reagents or laborious experimental procedure. Not surprisingly, conventional cloning techniques based on restriction digestion and ligation are still commonly used in routine DNA cloning. Here, we describe a simple, fast, and economical cloning method based on RecA- and RecET-independent in vivo recombination of DNA fragments with overlapping ends using E. coli. All DNA fragments were prepared by a 2-consecutive PCR procedure with Q5 DNA polymerase and used directly for ...


Rolling Circle Mutagenesis Of Gst-Mcherry To Understand Mutation, Gene Expression, And Regulation, Jessica Cole, Amanda Ferguson, Veronica A. Segarra, Susan Walsh Apr 2017

Rolling Circle Mutagenesis Of Gst-Mcherry To Understand Mutation, Gene Expression, And Regulation, Jessica Cole, Amanda Ferguson, Veronica A. Segarra, Susan Walsh

Faculty Publications

Undergraduates are often familiar with textbook examples of human mutations that affect coding regions and the subsequent disorders, but they may struggle with understanding the implications of mutations in the regulatory regions of genes. We have designed a laboratory sequence that will allow students to explore the effect random mutagenesis can have on protein function, expression, and ultimately phenotype. Students design and perform a safe and time-efficient random mutagenesis experiment using error-prone rolling circular amplification of a plasmid expressing the inducible fusion protein glutathione S-transferase (GST)-mCherry. Mutagenized and wild-type control plasmid DNA, respectively, are then purified and transformed into ...


Developmental Ethanol Exposure Leads To Dysregulation Of Lipid Metabolism And Oxidative Stress In Drosophila, Theresa Logan-Garbisch, Anthony Bortolazzo, Peter Luu, Audrey Ford, David Do, Payam Khodabakhshi, Rachael French Jan 2015

Developmental Ethanol Exposure Leads To Dysregulation Of Lipid Metabolism And Oxidative Stress In Drosophila, Theresa Logan-Garbisch, Anthony Bortolazzo, Peter Luu, Audrey Ford, David Do, Payam Khodabakhshi, Rachael French

Faculty Publications

Ethanol exposure during development causes an array of developmental abnormalities, both physiological and behavioral. In mammals, these abnormalities are collectively known as Fetal Alcohol Effects (FAE) or Fetal Alcohol Spectrum Disorder (FASD). We have established a Drosophila melanogaster model of FASD, and have previously shown that developmental ethanol exposure in flies leads to reduced expression of insulin like peptides (dILPs) and their receptor. In this work, we link that observation to dysregulation of fatty acid metabolism and lipid accumulation. Further, we show that developmental ethanol exposure in Drosophila causes oxidative stress, that this stress is a primary cause of the ...


An Asian Origin Of Virulent Aeromonas Hydrophila Responsible For Disease Epidemics In United States-Farmed Catfish, Mohammad J. Hossain, Dawei Sun, Donald J. Mcgarey, Shannon Wrenn Jun 2014

An Asian Origin Of Virulent Aeromonas Hydrophila Responsible For Disease Epidemics In United States-Farmed Catfish, Mohammad J. Hossain, Dawei Sun, Donald J. Mcgarey, Shannon Wrenn

Faculty Publications

Unlabelled: Since 2009, catfish farming in the southeastern United States has been severely impacted by a highly virulent and clonal population of Aeromonas hydrophila causing motile Aeromonas septicemia (MAS) in catfish. The possible origin of this newly emerged highly virulent A. hydrophila strain is unknown. In this study, we show using whole-genome sequencing and comparative genomics that A. hydrophila isolates from diseased grass carp in China and catfish in the United States have highly similar genomes. Our phylogenomic analyses suggest that U.S. catfish isolates emerged from A. hydrophila populations of Asian origin. Furthermore, we identified an A. hydrophila strain ...


Drosophila Snap-29 Is An Essential Snare That Binds Multiple Proteins Involved In Membrane Traffic, Hao Xu, Mahmood Mohtashami, Bryan Stewart, Gabrielle Boulianne, William S. Trimble Mar 2014

Drosophila Snap-29 Is An Essential Snare That Binds Multiple Proteins Involved In Membrane Traffic, Hao Xu, Mahmood Mohtashami, Bryan Stewart, Gabrielle Boulianne, William S. Trimble

Faculty Publications

Each membrane fusion event along the secretory and endocytic pathways requires a specific set of SNAREs to assemble into a 4-helical coiled-coil, the so-called trans-SNARE complex. Although most SNAREs contribute one helix to the trans-SNARE complex, members of the SNAP-25 family contribute two helixes. We report the characterization of the Drosophila homologue of SNAP-29 (dSNAP-29), which is expressed throughout development. Unlike the other SNAP-25 like proteins in fruit fly (i.e., dSNAP-25 and dSNAP-24), which form SDS-resistant SNARE complexes with their cognate SNAREs, dSNAP-29 does not participate in any SDS-resistant complexes, despite its interaction with dsyntaxin1 and dsyntaxin 16 in ...


Multiple Roles For Hoxa3 In Regulating Thymus And Parathyroid Differentiation And Morphogenesis In Mouse, Jena L. Chojnowski, Kyoko Masuda, Heidi A. Trau, Kirk Thomas, Mario Capeechi, Nancy R. Manley Jan 2014

Multiple Roles For Hoxa3 In Regulating Thymus And Parathyroid Differentiation And Morphogenesis In Mouse, Jena L. Chojnowski, Kyoko Masuda, Heidi A. Trau, Kirk Thomas, Mario Capeechi, Nancy R. Manley

Faculty Publications

Hoxa3 was the first Hox gene to be mutated by gene targeting in mice and is required for the development of multiple endoderm and neural crest cell (NCC)-derived structures in the pharyngeal region. Previous studies have shown that the Hoxa3 null mutant lacks third pharyngeal pouch derivatives, the thymus and parathyroids by E18.5, and organ-specific markers are absent or downregulated during initial organogenesis. Our current analysis of the Hoxa3 null mutant shows that organ-specific domains did undergo initial patterning, but the location and timing of key regional markers within the pouch, including Tbx1, Bmp4 and Fgf8, were altered ...


A Small Subset Of Fruitless Subesophageal Neurons Modulate Early Courtship In Drosophila, David Tran, Geoffrey Meissner, Rachael French, Bruce Baker Jan 2014

A Small Subset Of Fruitless Subesophageal Neurons Modulate Early Courtship In Drosophila, David Tran, Geoffrey Meissner, Rachael French, Bruce Baker

Faculty Publications

We show that a small subset of two to six subesophageal neurons, expressing the male products of the male courtship master regulator gene products fruitlessMale (fruM), are required in the early stages of the Drosophila melanogaster male courtship behavioral program. Loss of fruM expression or inhibition of synaptic transmission in these fruM(+) neurons results in delayed courtship initiation and a failure to progress to copulation primarily under visually-deficient conditions. We identify a fruM-dependent sexually dimorphic arborization in the tritocerebrum made by two of these neurons. Furthermore, these SOG neurons extend descending projections to the thorax and abdominal ganglia. These anatomical ...


A Course-Based Research Experience: How Benefits Change With Increased Investment In Instructional Time, Christopher D. Shaffer, Consuelo J. Alvarez, April E. Bednarski, David Dunbar, Anya L. Goodman, Catherine Reinke, Anne G. Rosenwald, Michael J. Wolyniak, Cheryl Bailey, Daron Barnard, Christopher Bazinet, Dale L. Beach, James E.J. Bedard, Satish Bhalla, John Braverman, Martin Burg, Vidya Chandrasekaran, Hui-Min Chung, Kari Clase, Randall J. Dejong, Justin R. Diangelo, Chunguang Du, Todd T. Eckdahl, Heather Eisler, Julia A. Emerson, Amy Frary, Donald Frohlich, Yuying Gosser, Shubha Govind, Adam Haberman, Amy T. Hark, Charles Hauser, Arlene Hoogewerf, Laura L.M. Hoopes, Carina E. Howell, Diana Johnson, Christopher J. Jones, Lisa Kadlec, Marian Kaehler, S. Catherine Silver Key, Adam Kleinschmit, Nighat P. Kokan, Olga Kopp, Gary Kuleck, Judith Leatherman, Jane Lopilato, Christy Mackinnon, Juan Carlos Martinez-Cruzado, Gerard Mcneil, Stephanie Mel, Hemlata Mistry, Alexis Nagengast, Paul Overvoorde, Don W. Paetkau, Susan Parrish, Celeste N. Peterson, Mary Preuss, Laura K. Reed, Dennis Revie, Srebrenka Robic, Jennifer Roecklein-Canfield, Michael R. Rubin, Kenneth Saville, Stephanie Schroeder, Karim Sharif, Mary Shaw, Gary Skuse, Christopher D. Smith, Mary A. Smith, Sheryl T. Smith, Eric Spana, Mary Spratt, Aparna Sreenivasan, Joyce Stamm, Paul Szauter, Jeffrey S. Thompson, Matthew Wawersik, James Youngblom, Leming Zhou, Elaine R. Mardis, Jeremy Buhler, Wilson Leung, David Lopatto, Sarah C.R. Elgin Jan 2014

A Course-Based Research Experience: How Benefits Change With Increased Investment In Instructional Time, Christopher D. Shaffer, Consuelo J. Alvarez, April E. Bednarski, David Dunbar, Anya L. Goodman, Catherine Reinke, Anne G. Rosenwald, Michael J. Wolyniak, Cheryl Bailey, Daron Barnard, Christopher Bazinet, Dale L. Beach, James E.J. Bedard, Satish Bhalla, John Braverman, Martin Burg, Vidya Chandrasekaran, Hui-Min Chung, Kari Clase, Randall J. Dejong, Justin R. Diangelo, Chunguang Du, Todd T. Eckdahl, Heather Eisler, Julia A. Emerson, Amy Frary, Donald Frohlich, Yuying Gosser, Shubha Govind, Adam Haberman, Amy T. Hark, Charles Hauser, Arlene Hoogewerf, Laura L.M. Hoopes, Carina E. Howell, Diana Johnson, Christopher J. Jones, Lisa Kadlec, Marian Kaehler, S. Catherine Silver Key, Adam Kleinschmit, Nighat P. Kokan, Olga Kopp, Gary Kuleck, Judith Leatherman, Jane Lopilato, Christy Mackinnon, Juan Carlos Martinez-Cruzado, Gerard Mcneil, Stephanie Mel, Hemlata Mistry, Alexis Nagengast, Paul Overvoorde, Don W. Paetkau, Susan Parrish, Celeste N. Peterson, Mary Preuss, Laura K. Reed, Dennis Revie, Srebrenka Robic, Jennifer Roecklein-Canfield, Michael R. Rubin, Kenneth Saville, Stephanie Schroeder, Karim Sharif, Mary Shaw, Gary Skuse, Christopher D. Smith, Mary A. Smith, Sheryl T. Smith, Eric Spana, Mary Spratt, Aparna Sreenivasan, Joyce Stamm, Paul Szauter, Jeffrey S. Thompson, Matthew Wawersik, James Youngblom, Leming Zhou, Elaine R. Mardis, Jeremy Buhler, Wilson Leung, David Lopatto, Sarah C.R. Elgin

Faculty Publications

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant ...


Relationships Between The Weedy (Amaranthaceae) And The Grain Amaranths [Abstract], Kiel D. Kielinski, Felix Jimenez, Eric N. Jellen, Peter J. Maughan, Scott M. Smith, Donald B. Pratt Jan 2014

Relationships Between The Weedy (Amaranthaceae) And The Grain Amaranths [Abstract], Kiel D. Kielinski, Felix Jimenez, Eric N. Jellen, Peter J. Maughan, Scott M. Smith, Donald B. Pratt

Faculty Publications

No abstract provided.


A Path To Success? A Review Of Evolution, Development, And The Predictable Genome By David L. Stern, Hope Hollocher, Charles H. Pence, Grant Ramsey, Michelle M. Wirth Jan 2013

A Path To Success? A Review Of Evolution, Development, And The Predictable Genome By David L. Stern, Hope Hollocher, Charles H. Pence, Grant Ramsey, Michelle M. Wirth

Faculty Publications

No abstract provided.


Staffan Müller-Wille And Hans-Jörg Rheinberger, A Cultural History Of Heredity, Charles H. Pence Jan 2013

Staffan Müller-Wille And Hans-Jörg Rheinberger, A Cultural History Of Heredity, Charles H. Pence

Faculty Publications

No abstract provided.


Parsimony And Model-Based Analyses Of Indels In Avian Nuclear Genes Reveal Congruent And Incongruent Phylogenetic Signals, Tamaki Yuri, Rebecca T. Kimball, John Harshman, Rauri C.K. Bowie, Michael J. Braun, Jena L. Chojnowski, Kin-Lan Han, Shannon J. Hackett, Christopher J. Huddleston, William S. Moore, Sushma Reddy, Frederick H. Sheldon, David W. Steadman, Christopher C. Witt, Edward L. Braun Jan 2013

Parsimony And Model-Based Analyses Of Indels In Avian Nuclear Genes Reveal Congruent And Incongruent Phylogenetic Signals, Tamaki Yuri, Rebecca T. Kimball, John Harshman, Rauri C.K. Bowie, Michael J. Braun, Jena L. Chojnowski, Kin-Lan Han, Shannon J. Hackett, Christopher J. Huddleston, William S. Moore, Sushma Reddy, Frederick H. Sheldon, David W. Steadman, Christopher C. Witt, Edward L. Braun

Faculty Publications

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that ...


Assessment Of Genetic Diversity In Peruvian Amaranth (Amaranthus Caudatus And A. Hybridus) Germplasm Using Single Nucleotide Polymorphism Markers [Abstract], Felix Jimenez, Peter J. Maughan, Aquilino Alvarez, Kiel D. Kielinski, Scott M. Smith, Donald B. Pratt, David B. Elzinga, Eric N. Jellen Jan 2013

Assessment Of Genetic Diversity In Peruvian Amaranth (Amaranthus Caudatus And A. Hybridus) Germplasm Using Single Nucleotide Polymorphism Markers [Abstract], Felix Jimenez, Peter J. Maughan, Aquilino Alvarez, Kiel D. Kielinski, Scott M. Smith, Donald B. Pratt, David B. Elzinga, Eric N. Jellen

Faculty Publications

No abstract provided.


Genomic Characteristics Of An Environmental Microbial Community Harboring A Novel Human Uncultured Tm7 Bacterium Associated With Oral Diseases, Michael Abrams, David Barton, Eamon Vandaei, Diana Romero, Adam Caldwell, Cleber C. Ouverney Aug 2012

Genomic Characteristics Of An Environmental Microbial Community Harboring A Novel Human Uncultured Tm7 Bacterium Associated With Oral Diseases, Michael Abrams, David Barton, Eamon Vandaei, Diana Romero, Adam Caldwell, Cleber C. Ouverney

Faculty Publications

The diversity of prokaryotes associated with humans has been dominated by uncultured species (not isolated in pure culture). For instance, nearly 80% of the human gut and 68% of the human oral microbes are thought to be uncultured; some of which have been associated with human oral, digestive, vaginal, and cardiovascular diseases. The revalence of uncultured pathogens is expected to continue to increase within the near future. In fact, public databases such as GenBank have nearly quadrupled the number of candidate phyla (those made entirely of uncultured organisms) since the 1980s and currently lists many new lineages of unclassified Bacteria ...


Akirin Links Twist-Regulated Transcription With The Brahma Chromatin Remodeling Complex During Embryogenesis, Scott J. Nowak, Hitoshi Aihara, Katie Gonzalez, Yutaka Nibu, Mary K. Baylies Mar 2012

Akirin Links Twist-Regulated Transcription With The Brahma Chromatin Remodeling Complex During Embryogenesis, Scott J. Nowak, Hitoshi Aihara, Katie Gonzalez, Yutaka Nibu, Mary K. Baylies

Faculty Publications

The activities of developmentally critical transcription factors are regulated via interactions with cofactors. Such interactions influence transcription factor activity either directly through protein–protein interactions or indirectly by altering the local chromatin environment. Using a yeast double-interaction screen, we identified a highly conserved nuclear protein, Akirin, as a novel cofactor of the key Drosophila melanogaster mesoderm and muscle transcription factor Twist. We find that Akirin interacts genetically and physically with Twist to facilitate expression of some, but not all, Twist-regulated genes during embryonic myogenesis. akirin mutant embryos have muscle defects consistent with altered regulation of a subset of Twistregulated genes ...


Mtbindingsim: Simulate Protein Binding To Microtubules, Julia T. Philip, Charles H. Pence, Holly V. Goodson Jan 2012

Mtbindingsim: Simulate Protein Binding To Microtubules, Julia T. Philip, Charles H. Pence, Holly V. Goodson

Faculty Publications

Summary: Many protein–protein interactions are more complex than can be accounted for by 1:1 binding models. However, biochemists have few tools available to help them recognize and predict the behaviors of these more complicated systems, making it difficult to design experiments that distinguish between possible binding models. MTBindingSim provides researchers with an environment in which they can rapidly compare different models of binding for a given scenario. It is written specifically with microtubule polymers in mind, but many of its models apply equally well to any polymer or any protein–protein interaction. MTBindingSim can thus both help in ...


An Unbiased Approach To Identify Genes Involved In Development In A Turtle With Temperature-Dependent Sex Determination, Jena L. Chojnowski, Edward L. Braun Jan 2012

An Unbiased Approach To Identify Genes Involved In Development In A Turtle With Temperature-Dependent Sex Determination, Jena L. Chojnowski, Edward L. Braun

Faculty Publications

Many reptiles exhibit temperature-dependent sex determination (TSD). The initial cue in TSD is incubation temperature, unlike genotypic sex determination (GSD) where it is determined by the presence of specific alleles (or genetic loci). We used patterns of gene expression to identify candidates for genes with a role in TSD and other developmental processes without making a priori assumptions about the identity of these genes (ortholog-based approach). We identified genes with sexually dimorphic mRNA accumulation during the temperature sensitive period of development in the Red-eared slider turtle (Trachemys scripta), a turtle with TSD. Genes with differential mRNA accumulation in response to ...


A Systematic Genetic Screen To Dissect The Microrna Pathway In Drosophila, Sigal Pressman, Catherine A. Reinke, Xiaohong Wang, Richard W. Carthew Jan 2012

A Systematic Genetic Screen To Dissect The Microrna Pathway In Drosophila, Sigal Pressman, Catherine A. Reinke, Xiaohong Wang, Richard W. Carthew

Faculty Publications

A central goal of microRNA biology is to elucidate the genetic program of miRNA function and regulation. However, relatively few of the effectors that execute miRNA repression have been identified. Because such genes may function in many developmental processes, mutations in them are expected to be pleiotropic and thus are discarded in most standard genetic screens. Here, we describe a systematic screen designed to identify all Drosophila genes in ~40% of the genome that function in the miRNA pathway. To identify potentially pleiotropic genes, the screen analyzed clones of homozygous mutant cells in heterozygous animals. We identified 45 mutations representing ...


Genetic Control Of A Central Pattern Generator: Rhythmic Oromotor Movement In Mice Is Controlled By A Major Locus Near Atp1a2, Steven J. St. John, John D. Boughter Jr, Megan K. Mulligan, Kenichi Tokita, Lu Lu, Detlef H. Heck, Robert W. Williams Jan 2012

Genetic Control Of A Central Pattern Generator: Rhythmic Oromotor Movement In Mice Is Controlled By A Major Locus Near Atp1a2, Steven J. St. John, John D. Boughter Jr, Megan K. Mulligan, Kenichi Tokita, Lu Lu, Detlef H. Heck, Robert W. Williams

Faculty Publications

calreticulin, Animals, Chromosome Mapping, Mammalian Chromosomes, Gene Expression Regulation, Genetic Linkage, Genome-Wide Association Study. Inbred C57BL Mice, Inbred DBA Mice, Quantitative Trait Loci, Sodium-Potassium-Exchanging ATPase/genetics, Atp1a2 protein, Sodium-Potassium-Exchanging ATPase, feeding behavior, drinking behavior, mice, central pattern generator, genetic control


The Nuclear Pore Complex Mediates Binding Of The Mig1 Repressor To Target Promoters, Nayan J. Sarma, Thomas D. Buford, Terry Haley, Kellie Barbara-Haley, George M. Santangelo, Kristine A. Willis Nov 2011

The Nuclear Pore Complex Mediates Binding Of The Mig1 Repressor To Target Promoters, Nayan J. Sarma, Thomas D. Buford, Terry Haley, Kellie Barbara-Haley, George M. Santangelo, Kristine A. Willis

Faculty Publications

All eukaryotic cells alter their transcriptional program in response to the sugar glucose. In Saccharomyces cerevisiae, the best-studied downstream effector of this response is the glucose-regulated repressor Mig1. We show here that nuclear pore complexes also contribute to glucose-regulated gene expression. NPCs participate in glucose-responsive repression by physically interacting with Mig1 and mediating its function independently of nucleocytoplasmic transport. Surprisingly, despite its abundant presence in the nucleus of glucose-grown nup120Δ or nup133Δ cells, Mig1 has lost its ability to interact with target promoters. The glucose repression defect in the absence of these nuclear pore components therefore appears to ...


Functional Dissection Of The Glucose Signaling Pathways That Regulate The Yeast Glucose Transporter Gene (Hxt) Repressor Rgt1, David J. Jouandot Ii, Adhiraj Roy, Jeong-Ho Kim Nov 2011

Functional Dissection Of The Glucose Signaling Pathways That Regulate The Yeast Glucose Transporter Gene (Hxt) Repressor Rgt1, David J. Jouandot Ii, Adhiraj Roy, Jeong-Ho Kim

Faculty Publications

The yeast Rgt1 repressor is a bifunctional protein that acts as a transcriptional repressor and activator. Under glucose-limited conditions, Rgt1 induces transcriptional repression by forming a repressive complex with its corepressors Mth1 and Std1. Here, we show that Rgt1 is converted from a transcriptional repressor into an activator under high glucose conditions and this occurs through two independent but consecutive events mediated by two glucose signaling pathways: (1) disruption of the repressive complex by the Rgt2/Snf3 pathway; (2) phosphorylation of Rgt1 by the cAMP-dependent protein kinase (cAMP-PKA) pathway. Rgt1 is phosphorylated by PKA at four serine residues within its ...


Drosophila Model For Fetal Alcohol Syndrome Disorders: Role For The Insulin Pathway, Rachael L. French, K D. Mcclure, U Heberlein May 2011

Drosophila Model For Fetal Alcohol Syndrome Disorders: Role For The Insulin Pathway, Rachael L. French, K D. Mcclure, U Heberlein

Faculty Publications

Prenatal exposure to ethanol in humans results in a wide range of developmental abnormalities, including growth deficiency, developmental delay, reduced brain size, permanent neurobehavioral abnormalities and fetal death. Here we describe the use of Drosophila melanogaster as a model for exploring the effects of ethanol exposure on development and behavior. We show that developmental ethanol exposure causes reduced viability, developmental delay and reduced adult body size. We find that flies reared on ethanol-containing food have smaller brains and imaginal discs, which is due to reduced cell division rather than increased apoptosis. Additionally, we show that, as in mammals, flies reared ...


Density Based Pruning For Identification Of Differentially Expressed Genes From Microarray Data, Jianjun Hu, J. Xu Jan 2010

Density Based Pruning For Identification Of Differentially Expressed Genes From Microarray Data, Jianjun Hu, J. Xu

Faculty Publications

Motivation

Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a single statistics. The false positive rate of these methods can be improved by considering other features of differentially expressed genes.

Results

We proposed a pattern recognition strategy for identifying differentially expressed genes. Genes are mapped to a two dimension feature space composed of average difference of gene expression and average expression levels. A density based pruning algorithm (DB Pruning) is developed to screen out potential differentially expressed genes usually ...


Using Jackknife To Assess The Quality Of Gene Order Phylogenies, Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang Jan 2010

Using Jackknife To Assess The Quality Of Gene Order Phylogenies, Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang

Faculty Publications

Background
In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.

Results
In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to ...