Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Genetics and Genomics (20)
- Medicine and Health Sciences (16)
- Biochemistry, Biophysics, and Structural Biology (12)
- Medical Sciences (10)
- Biology (9)
-
- Microbiology (9)
- Cell and Developmental Biology (7)
- Medical Microbiology (7)
- Biochemistry (6)
- Genetics (6)
- Bacteriology (5)
- Molecular Biology (5)
- Physiology (5)
- Plant Sciences (5)
- Diseases (4)
- Cancer Biology (3)
- Cell Biology (3)
- Genomics (3)
- Medical Genetics (3)
- Neoplasms (3)
- Computational Biology (2)
- Medical Pharmacology (2)
- Virology (2)
- Animal Sciences (1)
- Medical Biochemistry (1)
- Medical Cell Biology (1)
- Medical Specialties (1)
- Ophthalmology (1)
- Pathogenic Microbiology (1)
Articles 1 - 30 of 52
Full-Text Articles in Life Sciences
Circnet: A Database Of Circular Rnas Derived From Transcriptome Sequencing Data, Yu-Chen Liu, Jian-Rong Li, Chuan-Hu Sun, Erik Andrews, Rou-Fang Chao, Feng-Mao Lin, Shun-Long Weng, Sheng-Da Hsu, Chieh-Chen Huang, Chao Cheng, Chun-Chi Liu, Hsien-Da Huang
Circnet: A Database Of Circular Rnas Derived From Transcriptome Sequencing Data, Yu-Chen Liu, Jian-Rong Li, Chuan-Hu Sun, Erik Andrews, Rou-Fang Chao, Feng-Mao Lin, Shun-Long Weng, Sheng-Da Hsu, Chieh-Chen Huang, Chao Cheng, Chun-Chi Liu, Hsien-Da Huang
Dartmouth Scholarship
Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), …
A Comprehensive Benchmarking Study Of Protocols And Sequencing Platforms For 16s Rrna Community Profiling, Rosalinda D’Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John G. Kenny, Richard Gregory, Alistair C. Darby, Migun Shakya
A Comprehensive Benchmarking Study Of Protocols And Sequencing Platforms For 16s Rrna Community Profiling, Rosalinda D’Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John G. Kenny, Richard Gregory, Alistair C. Darby, Migun Shakya
Dartmouth Scholarship
In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. The most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated. …
Leveraging Global Gene Expression Patterns To Predict Expression Of Unmeasured Genes, James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene S. Greene, Jennifer A. Doherty
Leveraging Global Gene Expression Patterns To Predict Expression Of Unmeasured Genes, James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene S. Greene, Jennifer A. Doherty
Dartmouth Scholarship
BackgroundLarge collections of paraffin-embedded tissue represent a rich resource to test hypotheses based on gene expression patterns; however, measurement of genome-wide expression is cost-prohibitive on a large scale. Using the known expression correlation structure within a given disease type (in this case, high grade serous ovarian cancer; HGSC), we sought to identify reduced sets of directly measured (DM) genes which could accurately predict the expression of a maximized number of unmeasured genes.
Yeast Integral Membrane Proteins Apq12, Brl1, And Brr6 Form A Complex Important For Regulation Of Membrane Homeostasis And Nuclear Pore Complex Biogenesis, Museer A. Lone, Aaron E. Atkinson, Christine A. Hodge, Stéphanie Cottier, Fernando Martínez-Montañés, Shelley Maithel, Laurent Mène-Saffrané, Cole Cole, Roger Schneiter
Yeast Integral Membrane Proteins Apq12, Brl1, And Brr6 Form A Complex Important For Regulation Of Membrane Homeostasis And Nuclear Pore Complex Biogenesis, Museer A. Lone, Aaron E. Atkinson, Christine A. Hodge, Stéphanie Cottier, Fernando Martínez-Montañés, Shelley Maithel, Laurent Mène-Saffrané, Cole Cole, Roger Schneiter
Dartmouth Scholarship
Proper functioning of intracellular membranes is critical for many cellular processes. A key feature of membranes is their ability to adapt to changes in environmental conditions by adjusting their composition so as to maintain constant biophysical proper- ties, including fluidity and flexibility. Similar changes in the biophysical properties of membranes likely occur when intracellular processes, such as vesicle formation and fusion, require dramatic changes in membrane curvature. Similar modifications must also be made when nuclear pore complexes (NPCs) are constructed within the existing nuclear membrane, as occurs during in- terphase in all eukaryotes. Here we report on the role of …
Bypassing Iron Storage In Endodermal Vacuoles Rescues The Iron Mobilization Defect In The Natural Resistance Associated-Macrophage Protein3natural Resistance Associated-Macrophage Protein4 Double Mutant, Viviane Mary, Magali Schnell Ramos, Cynthia Gillet, Amanda L. Socha, Jerome Giraudat, Astrid Agorio, Sylvain Merlot, Colin Clairet, Sun A. Kim, Tracy Punshon, Mary Lou Guerinot, Sebastien Thomine
Bypassing Iron Storage In Endodermal Vacuoles Rescues The Iron Mobilization Defect In The Natural Resistance Associated-Macrophage Protein3natural Resistance Associated-Macrophage Protein4 Double Mutant, Viviane Mary, Magali Schnell Ramos, Cynthia Gillet, Amanda L. Socha, Jerome Giraudat, Astrid Agorio, Sylvain Merlot, Colin Clairet, Sun A. Kim, Tracy Punshon, Mary Lou Guerinot, Sebastien Thomine
Dartmouth Scholarship
To improve seed iron (Fe) content and bioavailability, it is crucial to decipher the mechanisms that control Fe storage during seed development. In Arabidopsis (Arabidopsis thaliana) seeds, most Fe is concentrated in insoluble precipitates, with phytate in the vacuoles of cells surrounding the vasculature of the embryo. NATURAL RESISTANCE ASSOCIATED-MACROPHAGE PROTEIN3 (AtNRAMP3) and AtNRAMP4 function redundantly in Fe retrieval from vacuoles during germination. When germinated under Fe-deficient conditions, development of the nramp3nramp4 double mutant is arrested as a consequence of impaired Fe mobilization. To identify novel genes involved in seed Fe homeostasis, we screened an …
Polyq-Dependent Rna–Protein Assemblies Control Symmetry Breaking, Changhwan Lee, Patricia Occhipinti, Amy S. Gladfelter
Polyq-Dependent Rna–Protein Assemblies Control Symmetry Breaking, Changhwan Lee, Patricia Occhipinti, Amy S. Gladfelter
Dartmouth Scholarship
Dendritic growth in fungi and neurons requires that multiple axes of polarity are established and maintained within the same cytoplasm. We have discovered that transcripts encoding key polarity factors including a formin, Bni1, and a polarisome scaffold, Spa2, are nonrandomly clustered in the cytosol to initiate and maintain sites of polarized growth in the fungus Ashbya gossypii. This asymmetric distribution requires the mRNAs to interact with a polyQ-containing protein, Whi3, and a Pumilio protein with a low-complexity sequence, Puf2. Cells lacking Whi3 or Puf2 had severe defects in establishing new sites of polarity and failed to localize Bni1 protein. Interaction …
Biological Significance Of Photoreceptor Photocycle Length: Vivid Photocycle Governs The Dynamic Vivid-White Collar Complex Pool Mediating Photo-Adaptation And Response To Changes In Light Intensity, Arko Dasgupta, Chen-Hui Chen, Changhwan Lee, Amy S. Gladfelter, Jay C. Dunlap, Jennifer J. Loros
Biological Significance Of Photoreceptor Photocycle Length: Vivid Photocycle Governs The Dynamic Vivid-White Collar Complex Pool Mediating Photo-Adaptation And Response To Changes In Light Intensity, Arko Dasgupta, Chen-Hui Chen, Changhwan Lee, Amy S. Gladfelter, Jay C. Dunlap, Jennifer J. Loros
Dartmouth Scholarship
Most organisms on earth sense light through the use of chromophore-bearing photoreceptive proteins with distinct and characteristic photocycle lengths, yet the biological significance of this adduct decay length is neither understood nor has been tested. In the filamentous fungus Neurospora crassa VIVID (VVD) is a critical player in the process of photoadaptation, the attenuation of light-induced responses and the ability to maintain photosensitivity in response to changing light intensities. Detailed in vitro analysis of the photochemistry of the blue light sensing, FAD binding, LOV domain of VVD has revealed residues around the site of photo-adduct formation that influence the stability …
Highly Constrained Intergenic Drosophila Ultraconserved Elements Are Candidate Ncrnas, Andrew D. Kern, Daniel A. Barbash, Joshua Chang Mell, Daniel Hupalo, Amanda Jensen
Highly Constrained Intergenic Drosophila Ultraconserved Elements Are Candidate Ncrnas, Andrew D. Kern, Daniel A. Barbash, Joshua Chang Mell, Daniel Hupalo, Amanda Jensen
Dartmouth Scholarship
Eukaryotes contain short (∼80–200 bp) regions that have few or no substitutions among species that represent hundreds of millions of years of evolutionary divergence. These ultraconserved elements (UCEs) are candidates for containing essential functions, but their biological roles remain largely unknown. Here, we report the discovery and characterization of UCEs from 12 sequenced Drosophilaspecies. We identified 98 elements ≥80 bp long with very high conservation across the Drosophila phylogeny. Population genetic analyses reveal that these UCEs are not present in mutational cold spots. Instead we infer that they experience a level of selective constraint almost 10-fold higher compared with …
The Formin Fmnl3 Assembles Plasma Membrane Protrusions That Participate In Cell–Cell Adhesion, Timothy J. Gauvin, Lorna E. Young, Henry N. Higgs
The Formin Fmnl3 Assembles Plasma Membrane Protrusions That Participate In Cell–Cell Adhesion, Timothy J. Gauvin, Lorna E. Young, Henry N. Higgs
Dartmouth Scholarship
FMNL3 is a vertebrate-specific formin protein previously shown to play a role in angiogenesis and cell migration. Here we define the cellular localization of endogenous FMNL3, the dynamics of GFP-tagged FMNL3 during cell migration, and the effects of FMNL3 suppression in mammalian culture cells. The majority of FMNL3 localizes in a punctate pattern, with >95% of these puncta being indistinguishable from the plasma membrane by fluorescence microscopy. A small number of dynamic cytoplasmic FMNL3 patches also exist, which enrich near cell–cell contact sites and fuse with the plasma membrane at these sites. These cytoplasmic puncta appear to be part of …
Quantitative And Functional Characterization Of The Hyper-Conserved Protein Of Prochlorococcus And Marine Synechococcus, Caroline E. Whidden, Katrina G. Dezeeuw, Jackie K. Zorz, Andrew P. Joy, David A. Barnett, Milo S. Johnson, Olga Zhaxybayeva, Amanda M. Cockshutt
Quantitative And Functional Characterization Of The Hyper-Conserved Protein Of Prochlorococcus And Marine Synechococcus, Caroline E. Whidden, Katrina G. Dezeeuw, Jackie K. Zorz, Andrew P. Joy, David A. Barnett, Milo S. Johnson, Olga Zhaxybayeva, Amanda M. Cockshutt
Dartmouth Scholarship
A large fraction of any bacterial genome consists of hypothetical protein-coding open reading frames (ORFs). While most of these ORFs are present only in one or a few sequenced genomes, a few are conserved, often across large phylogenetic distances. Such conservation provides clues to likely uncharacterized cellular functions that need to be elucidated. Marine cyanobacteria from the Prochlorococcus/marine Synechococcus clade are dominant bacteria in oceanic waters and are significant contributors to global primary production. A Hyper Conserved Protein (PSHCP) of unknown function is 100% conserved at the amino acid level in genomes of Prochlorococcus/marine Synechococcus, but lacks …
Myeloid Derived Hypoxia Inducible Factor 1-Alpha Is Required For Protection Against Pulmonary Aspergillus Fumigatus Infection, Kelly M. Shepardson, Anupam Jhingran, Alayna Caffrey, Joshua J. Obar, Benjamin T. Suratt, Brent L. Berwin, Tobias M. Hohl, Robert A. Cramer
Myeloid Derived Hypoxia Inducible Factor 1-Alpha Is Required For Protection Against Pulmonary Aspergillus Fumigatus Infection, Kelly M. Shepardson, Anupam Jhingran, Alayna Caffrey, Joshua J. Obar, Benjamin T. Suratt, Brent L. Berwin, Tobias M. Hohl, Robert A. Cramer
Dartmouth Scholarship
Hypoxia inducible factor 1α (HIF1α) is the mammalian transcriptional factor that controls metabolism, survival, and innate immunity in response to inflammation and low oxygen. Previous work established that generation of hypoxic microenvironments occurs within the lung during infection with the human fungal pathogen Aspergillus fumigatus. Here we demonstrate that A. fumigatus stabilizes HIF1α protein early after pulmonary challenge that is inhibited by treatment of mice with the steroid triamcinolone. Utilizing myeloid deficient HIF1α mice, we observed that HIF1α is required for survival and fungal clearance early following pulmonary challenge with A. fumigatus. Unlike previously reported research with bacterial …
Orthoclust: An Orthology-Based Network Framework For Clustering Data Across Multiple Species, Koon-Kiu Yan, Daifeng Wang, Joel Rozowsky, Henry Zheng, Chao Cheng, Mark Gerstein Gerstein
Orthoclust: An Orthology-Based Network Framework For Clustering Data Across Multiple Species, Koon-Kiu Yan, Daifeng Wang, Joel Rozowsky, Henry Zheng, Chao Cheng, Mark Gerstein Gerstein
Dartmouth Scholarship
Increasingly, high-dimensional genomics data are becoming available for many organisms.Here, we develop OrthoClust for simultaneously clustering data across multiple species. OrthoClust is a computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific. We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium. A potential application of cross-species modules is to infer putative analogous functions of uncharacterized elements like non-coding RNAs based on guilt-by-association.
Microbial Diversity Of A Mediterranean Soil And Its Changes After Biotransformed Dry Olive Residue Amendment, José A. Siles, Caio T.C.C Rachid, Inmaculada Sampedro, Inmaculada García-Romera, James M. Tiedje
Microbial Diversity Of A Mediterranean Soil And Its Changes After Biotransformed Dry Olive Residue Amendment, José A. Siles, Caio T.C.C Rachid, Inmaculada Sampedro, Inmaculada García-Romera, James M. Tiedje
Dartmouth Scholarship
The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a …
Gene Expression Studies For The Analysis Of Domoic Acid Production In The Marine Diatom Pseudo-Nitzschia Multiseries, Katie Boissonneault, Brooks M. Henningsen, Stephen S. Bates, Deborah L. Robertson, Sean Milton, Jerry Pelletier, Deborah A. Hogan, David E. Housman
Gene Expression Studies For The Analysis Of Domoic Acid Production In The Marine Diatom Pseudo-Nitzschia Multiseries, Katie Boissonneault, Brooks M. Henningsen, Stephen S. Bates, Deborah L. Robertson, Sean Milton, Jerry Pelletier, Deborah A. Hogan, David E. Housman
Dartmouth Scholarship
Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated intensely, the characterization of the genes and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference genes for Ps-n RNA expression analysis under these conditions.
Identification Of Cell Cycle–Regulated Genes Periodically Expressed In U2os Cells And Their Regulation By Foxm1 And E2f Transcription Factors, Gavin D. Grant, Lionel Brooks Iii, Xiaoyang Zhang, J. Matthew Mahoney, Viktor Martyanov, Tammara A. Wood, Gavin Sherlock, Chao Cheng, Michael L. Whitfield
Identification Of Cell Cycle–Regulated Genes Periodically Expressed In U2os Cells And Their Regulation By Foxm1 And E2f Transcription Factors, Gavin D. Grant, Lionel Brooks Iii, Xiaoyang Zhang, J. Matthew Mahoney, Viktor Martyanov, Tammara A. Wood, Gavin Sherlock, Chao Cheng, Michael L. Whitfield
Dartmouth Scholarship
We identify the cell cycle–regulated mRNA transcripts genome-wide in the osteosarcoma-derived U2OS cell line. This results in 2140 transcripts mapping to 1871 unique cell cycle–regulated genes that show periodic oscillations across multiple synchronous cell cycles. We identify genomic loci bound by the G2/M transcription factor FOXM1 by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and associate these with cell cycle–regulated genes. FOXM1 is bound to cell cycle–regulated genes with peak expression in both S phase and G2/M phases. We show that ChIP-seq genomic loci are responsive to FOXM1 using a real-time luciferase assay in live cells, showing that FOXM1 strongly …
Identification Of Cytokinin-Responsive Genes Using Microarray Meta-Analysis And Rna-Seq In Arabidopsis, Apurva Bhargava, Ivory Clabaugh, Jenn P. To, Bridey B. Maxwell, Yi-Hsuan Chiang, G. Eric Schaller, Ann Loraine, Joseph J. Kieber
Identification Of Cytokinin-Responsive Genes Using Microarray Meta-Analysis And Rna-Seq In Arabidopsis, Apurva Bhargava, Ivory Clabaugh, Jenn P. To, Bridey B. Maxwell, Yi-Hsuan Chiang, G. Eric Schaller, Ann Loraine, Joseph J. Kieber
Dartmouth Scholarship
Cytokinins are N6-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin as well as to query the response of genes not represented on microarrays. To this end, we performed a meta-analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Microarray meta-analysis using 13 microarray experiments combined with empirically defined filtering criteria identified a set of 226 genes differentially regulated by cytokinin, a subset of which has previously been …
Insights Into Mrnp Biogenesis Provided By New Genetic Interactions Among Export And Transcription Factors, Francisco Estruch, Christine Hodge, Natalia Gómez-Navarro, Lorena Peiró-Chova, Catherine V. Heath, Charles N. Cole
Insights Into Mrnp Biogenesis Provided By New Genetic Interactions Among Export And Transcription Factors, Francisco Estruch, Christine Hodge, Natalia Gómez-Navarro, Lorena Peiró-Chova, Catherine V. Heath, Charles N. Cole
Dartmouth Scholarship
The various steps of mRNP biogenesis (transcription, processing and export) are interconnected. It has been shown that the transcription machinery plays a pivotal role in mRNP assembly, since several mRNA export factors are recruited during transcription and physically interact with components of the transcription machinery. Although the shuttling DEAD-box protein Dbp5p is concentrated on the cytoplasmic fibrils of the NPC, previous studies demonstrated that it interacts physically and genetically with factors involved in transcription initiation. We investigated the effect of mutations affecting various components of the transcription initiation apparatus on the phenotypes of mRNA export mutant strains. Our results show …
Pv1 Down-Regulation Via Shrna Inhibits The Growth Of Pancreatic Adenocarcinoma Xenografts, Sophie J. Deharvengt, Dan Tse, Olga Sideleva, Caitlin Mcgarry, Jason R. Gunn, Daniel S. Longnecker, Catherine Carriere, Radu V. Stan
Pv1 Down-Regulation Via Shrna Inhibits The Growth Of Pancreatic Adenocarcinoma Xenografts, Sophie J. Deharvengt, Dan Tse, Olga Sideleva, Caitlin Mcgarry, Jason R. Gunn, Daniel S. Longnecker, Catherine Carriere, Radu V. Stan
Dartmouth Scholarship
PV1 is an endothelial-specific protein with structural roles in the formation of diaphragms in endothelial cells of normal vessels. PV1 is also highly expressed on endothelial cells of many solid tumours. On the basis of in vitro data, PV1 is thought to actively participate in angiogenesis. To test whether or not PV1 has a function in tumour angiogenesis and in tumour growth in vivo, we have treated pancreatic tumour-bearing mice by single-dose intratumoural delivery of lentiviruses encoding for two different shRNAs targeting murine PV1. We find that PV1 down-regulation by shRNAs inhibits the growth of established tumours derived from two …
Auf1/Hnrnp D Represses Expression Of Vegf In Macrophages, Abigail Fellows, Mary E. Griffin, Brenda L. Petrella, Lihui Zhong, Fatemeh P. Parvin-Nejad, Roy Fava, Peter Morganelli, R. Brooks Robey, Ralph C. Nichols
Auf1/Hnrnp D Represses Expression Of Vegf In Macrophages, Abigail Fellows, Mary E. Griffin, Brenda L. Petrella, Lihui Zhong, Fatemeh P. Parvin-Nejad, Roy Fava, Peter Morganelli, R. Brooks Robey, Ralph C. Nichols
Dartmouth Scholarship
Vascular endothelial growth factor (VEGF) is a regulator of vascularization in development and is a key growth factor in tissue repair. In disease, VEGF contributes to vascularization of solid tumors and arthritic joints. This study examines the role of the mRNA-binding protein AUF1/heterogeneous nuclear ribonucleoprotein D (AUF1) in VEGF gene expression. We show that overexpression of AUF1 in mouse macrophage-like RAW-264.7 cells suppresses endogenous VEGF protein levels. To study 3′ untranslated region (UTR)–mediated regulation, we introduced the 3′ UTR of VEGF mRNA into a luciferase reporter gene. Coexpression of AUF1 represses VEGF-3′ UTR reporter expression in RAW-264.7 cells and in …
Morpholino Gene Knockdown In Adult Fundulus Heteroclitus: Role Of Sgk1 In Seawater Acclimation, Emily G. Notch, Joseph R. Shaw, Bonita A. Coutermarsh, Marisa Dzioba, Bruce A. Stanton
Morpholino Gene Knockdown In Adult Fundulus Heteroclitus: Role Of Sgk1 In Seawater Acclimation, Emily G. Notch, Joseph R. Shaw, Bonita A. Coutermarsh, Marisa Dzioba, Bruce A. Stanton
Dartmouth Scholarship
The Atlantic killifish (Fundulus heteroclitus) is an environmental sentinel organism used extensively for studies on environmental toxicants and salt (NaCl) homeostasis. Previous research in our laboratory has shown that rapid acclimation of killifish to seawater is mediated by trafficking of CFTR chloride channels from intracellular vesicles to the plasma membrane in the opercular membrane within the first hour in seawater, which enhances chloride secretion into seawater, thereby contributing to salt homeostasis. Acute transition to seawater is also marked by an increase in both mRNA and protein levels of serum glucocorticoid kinase 1 (SGK1) within 15 minutes of transfer. …
Variations In Mre11/Rad50/Nbs1 Status And Dna Damage-Induced S-Phase Arrest In The Cell Lines Of The Nci60 Panel, Kristen M. K. Garner, Alan Eastman
Variations In Mre11/Rad50/Nbs1 Status And Dna Damage-Induced S-Phase Arrest In The Cell Lines Of The Nci60 Panel, Kristen M. K. Garner, Alan Eastman
Dartmouth Scholarship
The Mre11/Rad50/Nbs1 (MRN) complex is a regulator of cell cycle checkpoints and DNA repair. Defects in MRN can lead to defective S-phase arrest when cells are damaged. Such defects may elicit sensitivity to selected drugs providing a chemical synthetic lethal interaction that could be used to target therapy to tumors with these defects. The goal of this study was to identify these defects in the NCI60 panel of cell lines and identify compounds that might elicit selective cytotoxicity.
Genetic And Molecular Characterization Of A Cryptochrome From The Filamentous Fungus Neurospora Crassa, Allan C. Froehlich, Chen-Hui Chen, William J. Belden, Cornelia Madeti
Genetic And Molecular Characterization Of A Cryptochrome From The Filamentous Fungus Neurospora Crassa, Allan C. Froehlich, Chen-Hui Chen, William J. Belden, Cornelia Madeti
Dartmouth Scholarship
In plants and animals, cryptochromes function as either photoreceptors or circadian clock components. We have examined the cryptochrome from the filamentous fungus Neurospora crassa and demonstrate that Neurospora cry encodes a DASH-type cryptochrome that appears capable of binding flavin adenine dinucleotide (FAD) and methenyltetrahydrofolate (MTHF). The cry transcript and CRY protein levels are strongly induced by blue light in a wc-1-dependent manner, and cry transcript is circadianly regulated, with a peak abundance opposite in phase to frq. Neither deletion nor overexpression of cry appears to perturb the free-running circadian clock. However, cry disruption knockout mutants show a small phase delay …
Mir319a Targeting Of Tcp4 Is Critical For Petal Growth And Development In Arabidopsis, Anwesha Nag, Stacey King, Thomas Jack
Mir319a Targeting Of Tcp4 Is Critical For Petal Growth And Development In Arabidopsis, Anwesha Nag, Stacey King, Thomas Jack
Dartmouth Scholarship
In a genetic screen in a drnl-2 background, we isolated a loss-of-function allele in miR319a (miR319a129). Previously, miR319a has been postulated to play a role in leaf development based on the dramatic curled-leaf phenotype of plants that ectopically express miR319a (jaw-D). miR319a129 mutants exhibit defects in petal and stamen development; petals are narrow and short, and stamens exhibit defects in anther development. The miR319a129 loss-of-function allele contains a single-base change in the middle of the encoded miRNA, which reduces the ability of miR319a to recognize targets. Analysis of the expression patterns of the …
Chronic Exposure To Arsenic In The Drinking Water Alters The Expression Of Immune Response Genes In Mouse Lung, Courtney D. Kozul, Thomas H. Hampton, Jennifer C. Davey, Julie A. Gosse, Athena P. Nomikos, Phillip L. Eisenhauer, Daniel J. Weiss, Jessica E. Thorpe, Michael A. Ihnat, Joshua W. Hamilton
Chronic Exposure To Arsenic In The Drinking Water Alters The Expression Of Immune Response Genes In Mouse Lung, Courtney D. Kozul, Thomas H. Hampton, Jennifer C. Davey, Julie A. Gosse, Athena P. Nomikos, Phillip L. Eisenhauer, Daniel J. Weiss, Jessica E. Thorpe, Michael A. Ihnat, Joshua W. Hamilton
Dartmouth Scholarship
Background:
Chronic exposure to drinking water arsenic is a significant worldwide environmental health concern. Exposure to As is associated with an increased risk of lung disease, which may make it a unique toxicant, because lung toxicity is usually associated with inhalation rather than ingestion.
Objectives:
The goal of this study was to examine mRNA and protein expression changes in the lungs of mice exposed chronically to environmentally relevant concentrations of As in the food or drinking water, specifically examining the hypothesis that As may preferentially affect gene and protein expression related to immune function as part of its mechanism of …
Overexpression Of Mazfsa In Staphylococcus Aureus Induces Bacteriostasis By Selectively Targeting Mrnas For Cleavage, Zhibiao Fu, Sandeep Tamber, Guido Memmi, Niles P. Donegan, Ambrose L. Cheung
Overexpression Of Mazfsa In Staphylococcus Aureus Induces Bacteriostasis By Selectively Targeting Mrnas For Cleavage, Zhibiao Fu, Sandeep Tamber, Guido Memmi, Niles P. Donegan, Ambrose L. Cheung
Dartmouth Scholarship
The role of chromosomally encoded toxin-antitoxin (TA) loci in bacterial physiology has been under debate, with the toxin proposed as either an inducer of bacteriostasis or a mediator of programmed cell death (PCD). We report here that ectopic expression of MazFSa, a toxin of the TA module from Staphylococcus aureus, led to a rapid decrease in CFU counts but most cells remained viable as determined by differential Syto 9 and propidium iodide staining after MazFSa induction. This finding suggested that the toxin MazFSa induced cell stasis rather than cell death. We also showed that MazFSa selectively cleaves cellular mRNAs in …
Systems Approach Identifies An Organic Nitrogen-Responsive Gene Network That Is Regulated By The Master Clock Control Gene Cca1, Rodrigo A. Gutierrez, Trevor L. Stokes, Karen Thum, Xiaodong Xu, Mariana Obertello, Manpreet S. Katari, Milos Tanurdzic, Alexis Dean, Damion C. Nero, C Robertson Mcclung, Gloria M. Coruzzi
Systems Approach Identifies An Organic Nitrogen-Responsive Gene Network That Is Regulated By The Master Clock Control Gene Cca1, Rodrigo A. Gutierrez, Trevor L. Stokes, Karen Thum, Xiaodong Xu, Mariana Obertello, Manpreet S. Katari, Milos Tanurdzic, Alexis Dean, Damion C. Nero, C Robertson Mcclung, Gloria M. Coruzzi
Dartmouth Scholarship
Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of …
Genome-Wide Transcriptional Profiling Of The Cyclic Amp-Dependent Signaling Pathway During Morphogenic Transitions Of Candida Albicans, Yong-Sun Bahn, Matthew Molenda, Janet F. Staab, Courtney A. Lyman, Laura J. Gordon, Paula Sundstrom
Genome-Wide Transcriptional Profiling Of The Cyclic Amp-Dependent Signaling Pathway During Morphogenic Transitions Of Candida Albicans, Yong-Sun Bahn, Matthew Molenda, Janet F. Staab, Courtney A. Lyman, Laura J. Gordon, Paula Sundstrom
Dartmouth Scholarship
Candida albicans is an opportunistic human fungal pathogen that causes systemic candidiasis as well as superficial mucosal candidiasis. In response to the host environment, C. albicans transitions between yeast and hyphal forms. In particular, hyphal growth is important in facilitating adhesion and invasion of host tissues, concomitant with the expression of various hypha-specific virulence factors. In previous work, we showed that the cyclic AMP (cAMP) signaling pathway plays a crucial role in morphogenic transitions and virulence of C. albicans by studying genes encoding adenylate cyclase-associated protein (CAP1) and high-affinity phosphodiesterase (PDE2) (Y. S. Bahn, J. Staab, and P. Sundstrom, Mol. …
Characterization Of Mazfsa, An Endoribonuclease From Staphylococcus Aureus, Zhibiao Fu, Niles P. Donegan, Guido Memmi, Ambrose L. Cheung
Characterization Of Mazfsa, An Endoribonuclease From Staphylococcus Aureus, Zhibiao Fu, Niles P. Donegan, Guido Memmi, Ambrose L. Cheung
Dartmouth Scholarship
The mazEF homologs of Staphylococcus aureus, designated mazEF(sa), have been shown to cotranscribe with the sigB operon under stress conditions. In this study, we showed that MazEF(Sa), as with their Escherichia coli counterparts, compose a toxin-antitoxin module wherein MazF(Sa) leads to rapid cell growth arrest and loss in viable CFU upon overexpression. MazF(Sa) is a novel sequence-specific endoribonuclease which cleaves mRNA to inhibit protein synthesis. Using ctpA mRNA as the model substrate both in vitro and in vivo, we demonstrated that MazF(Sa) cleaves single-strand RNA preferentially at the 5' side of the first U or 3' side of the second …
The Small Rna Repertoire Of Dictyostelium Discoideum And Its Regulation By Components Of The Rnai Pathway, Andrea Hinas, Johan Reimegård, E. Gerhart H. Wagner, Wolfgang Nellen, Victor R. Ambros, Fredrik Soderbum
The Small Rna Repertoire Of Dictyostelium Discoideum And Its Regulation By Components Of The Rnai Pathway, Andrea Hinas, Johan Reimegård, E. Gerhart H. Wagner, Wolfgang Nellen, Victor R. Ambros, Fredrik Soderbum
Dartmouth Scholarship
Small RNAs play crucial roles in regulation of gene expression in many eukaryotes. Here, we report the cloning and characterization of 18–26 nt RNAs in the social amoeba Dictyostelium discoideum . This survey uncovered developmentally regulated microRNA candidates whose biogenesis, at least in one case, is dependent on a Dicer homolog, DrnB. Furthermore, we identified a large number of 21 nt RNAs originating from the DIRS-1 retrotransposon, clusters of which have been suggested to constitute centromeres. Small RNAs from another retrotransposon, Skipper, were significantly up-regulated in strains depleted of the second Dicer-like protein, DrnA, and a putative RNA-dependent RNA polymerase, …
A Serratia Marcescens Oxyr Homolog Mediates Surface Attachment And Biofilm Formation, Robert M. Q. Shanks, Nicholas A. Stella, Eric J. Kalivoda, Megan R. Doe
A Serratia Marcescens Oxyr Homolog Mediates Surface Attachment And Biofilm Formation, Robert M. Q. Shanks, Nicholas A. Stella, Eric J. Kalivoda, Megan R. Doe
Dartmouth Scholarship
OxyR is a conserved bacterial transcription factor with a regulatory role in oxidative stress response. From a genetic screen for genes that modulate biofilm formation in the opportunistic pathogen Serratia marcescens, mutations in an oxyR homolog and predicted fimbria structural genes were identified. S. marcescens oxyR mutants were severely impaired in biofilm formation, in contrast to the hyperbiofilm phenotype exhibited by oxyR mutants of Escherichia coli and Burkholderia pseudomallei. Further analysis revealed that OxyR plays a role in the primary attachment of cells to a surface. Similar to what is observed in other bacterial species, S. marcescens OxyR …