Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Biology (8)
- Ecology and Evolutionary Biology (7)
- Molecular Genetics (6)
- Genetics (4)
- Medicine and Health Sciences (4)
-
- Biochemistry, Biophysics, and Structural Biology (3)
- Biodiversity (3)
- Cell and Developmental Biology (3)
- Evolution (3)
- Animal Sciences (2)
- Bioinformatics (2)
- Cell Biology (2)
- Computational Biology (2)
- Desert Ecology (2)
- Genomics (2)
- Molecular Biology (2)
- Analytical Chemistry (1)
- Bacteriology (1)
- Biochemistry (1)
- Cancer Biology (1)
- Chemicals and Drugs (1)
- Chemistry (1)
- Health Information Technology (1)
- Integrative Biology (1)
- Medical Specialties (1)
- Microbiology (1)
- Oncology (1)
- Other Animal Sciences (1)
- Keyword
-
- Chromatin remodelers (2)
- Gene regulation (2)
- ATM and Rad3-related (ATR) kinase (1)
- Ancestral area reconstruction (1)
- Antiviral sensor (1)
-
- Arthropods (1)
- Autophagy (1)
- BEC-1 (1)
- Background (1)
- Bacteriophages (1)
- Beclin 1 (1)
- Blood feeding (1)
- C. elegans (1)
- CCTP (1)
- Cell type (1)
- Checkpoint kinase 1 (1)
- Choline (1)
- Clothing (1)
- Codon bias (1)
- Community ecology (1)
- Comparative phylogeography (1)
- DNA (1)
- DNA Profiling (1)
- DNA damage response (1)
- DNA methylation (1)
- Diversification (1)
- E. coli cytokinesis (1)
- Ecological speciation (1)
- Expression (1)
- FtsZ (1)
- Publication
- Publication Type
Articles 1 - 24 of 24
Full-Text Articles in Genetics and Genomics
A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents
A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents
Publications and Research
Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes …
Improved Genome-Scale Multitarget Virtual Screening Via A Novel Collaborative Filtering Approach To Cold-Start Problem, Hansaim Lim, Paul Gray, Lei Xie, Aleksandar Poleksic
Improved Genome-Scale Multitarget Virtual Screening Via A Novel Collaborative Filtering Approach To Cold-Start Problem, Hansaim Lim, Paul Gray, Lei Xie, Aleksandar Poleksic
Publications and Research
Conventional one-drug-one-gene approach has been of limited success in modern drug discovery. Polypharmacology, which focuses on searching for multi-targeted drugs to perturb disease-causing networks instead of designing selective ligands to target individual proteins, has emerged as a new drug discovery paradigm. Although many methods for single-target virtual screening have been developed to improve the efficiency of drug discovery, few of these algorithms are designed for polypharmacology. Here, we present a novel theoretical framework and a corresponding algorithm for genome-scale multitarget virtual screening based on the one-class collaborative filtering technique. Our method overcomes the sparseness of the protein-chemical interaction data by …
Control Of Gene Expression By Rna Binding Protein Action On Alternative Translation Initiation Sites, Angela Re, Levi Waldron, Alessandro Quattrone
Control Of Gene Expression By Rna Binding Protein Action On Alternative Translation Initiation Sites, Angela Re, Levi Waldron, Alessandro Quattrone
Publications and Research
Transcript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein. The presence of upstream translation initiation sites (uTISs) at the mRNA 5' untranslated regions was strongly associated with improvement …
Exploration Of Dna Transfer In The Nyc Subway, Sannia K. Tauqeer
Exploration Of Dna Transfer In The Nyc Subway, Sannia K. Tauqeer
Student Theses
The ability to detect “touch” DNA has complicated the interpretation of DNA profiles in the field of forensics because it leads to the introduction of the concept of DNA transfer, persistence and background into casework. This project is geared towards understanding DNA transfer in the NYC subways and has relevance in groping and attempted sexual assault cases, where garments are submitted as evidence. The study involved 10 volunteers who were asked to wear a clean jacket during their trips on the subway for one week and the DNA from these jackets was collected, extracted, quantified, amplified and typed. The results …
Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy
Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy
Publications and Research
In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it …
Ben Domain Protein Elba2 Can Functionally Substitute For Linker Histone H1 In Drosophila In Vivo, Na Xu, Xingwu Lu, Harsh Kavi, Alexander V. Emelyanov, Travis J. Bernardo, Elena Vershilova, Arthur I. Skoultchi, Dmitry V. Fyodorov
Ben Domain Protein Elba2 Can Functionally Substitute For Linker Histone H1 In Drosophila In Vivo, Na Xu, Xingwu Lu, Harsh Kavi, Alexander V. Emelyanov, Travis J. Bernardo, Elena Vershilova, Arthur I. Skoultchi, Dmitry V. Fyodorov
Publications and Research
Metazoan linker histones are essential for development and play crucial roles in organization of chromatin, modification of epigenetic states and regulation of genetic activity. Vertebrates express multiple linker histone H1 isoforms, which may function redundantly. In contrast, H1 isoforms are not present in Dipterans, including D. melanogaster, except for an embryo-specific, distantly related dBigH1. Here we show that Drosophila BEN domain protein Elba2, which is expressed in early embryos and was hypothesized to have insulator-specific functions, can compensate for the loss of H1 in vivo. Although the Elba2 gene is not essential, its mutation causes a disruption of normal internucleosomal …
Phylogeny, Systematics And Biogeography Of Short-Tailed Opossums (Didelphidae: Monodelphis), Silvia E. Pavan
Phylogeny, Systematics And Biogeography Of Short-Tailed Opossums (Didelphidae: Monodelphis), Silvia E. Pavan
Dissertations, Theses, and Capstone Projects
Short-tailed opossums (genus Monodelphis) comprise the most species-rich genus of New World marsupials, with 25 currently recognized species. Monodelphis comprise small, terrestrial species collectively widespread in South America, which makes the group potentially informative about biogeographic processes that have shaped the continental fauna. The genus exhibits striking variation in several phenotypic characters, notably pelage coloration, behavior, and reproductive strategies. This diversity is unique among Neotropical marsupials, and makes the group particularly interesting to investigate the evolution and the adaptive significance of phenotypic trait variation. Despite this potential, missing knowledge on phylogeny and basic taxonomy precludes broader studies on evolution …
Molecular Analysis Of Ftsz-Ring Assembly In E. Coli Cytokinesis, Kuo-Hsiang Huang
Molecular Analysis Of Ftsz-Ring Assembly In E. Coli Cytokinesis, Kuo-Hsiang Huang
Dissertations, Theses, and Capstone Projects
An essential first step in bacterial division is the assembly of a cytokinetic ring (Z-ring) formed by the tubulin-like FtsZ at midcell. The highly conserved core domain of FtsZ has been reported to mediate assembly of FtsZ polymers in vivo and in vitro. Species-specific differences in the FtsZ C-terminal domain such as the FtsZ CTV region and interactions with several modulatory proteins such as ZapC and ZapD, restricted to certain bacterial classes, also serve as key determinants of FtsZ protofilament bundling. Here, we characterize (i) the roles of the FtsZ CTV region in mediating both longitudinal and lateral interactions …
Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers
Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers
Dissertations, Theses, and Capstone Projects
Understanding the process of speciation is of central interest to evolutionary biologists. Speciation can be studied using a phylogeographic approach, by identifying regions that promote lineage divergence, addressing whether speciation has occurred with gene flow, and when extended to multiple taxa, addressing if the same patterns of speciation are shared across codistributed groups with different ecologies. Here I examine the comparative phylogeographic histories and population genomics of thirteen snake taxa that are widely distributed and co-occur across the arid southwest of North America. I first quantify the degree to which these species groups have a shared history of population divergence …
Metabolic Profiling And Polymer Formation Of Gene Silenced Potato Periderms, Qing Cai
Metabolic Profiling And Polymer Formation Of Gene Silenced Potato Periderms, Qing Cai
Dissertations, Theses, and Capstone Projects
Suberin is a biopolyester constituent of specialized plant periderm tissues formed within the phellem cell walls. Suberin and waxes of the periderm layer act to prevent water diffusion, mechanical breakdown and pathogenic invasion in plants. Ferulic esters, ω-hydroxyacids and α,ω-fatty diacids are considered to be the most important linkage between aliphatic and aromatic suberin domains and also linked with cell-wall polysaccharides. The potato gene FHT (fatty ω- hydroxyacid/fatty alcohol hydroxycinnamoyl transferase) esterifies ferulic acid to suberin. Diminished levels of feruloyl transferase activity have been associated with lowered amounts of feruloyl esters of fatty acids in both suberin-associated waxes and suberin …
The Regulation Of The Phosphatidate Phosphatase Gene Pah1 And Its Regulatory Role On Cell Homeostasis, Goldie Libby Sherr
The Regulation Of The Phosphatidate Phosphatase Gene Pah1 And Its Regulatory Role On Cell Homeostasis, Goldie Libby Sherr
Dissertations, Theses, and Capstone Projects
The Saccharomyces cerevisiae gene, PAH1, encodes a phosphatidate (PA) phosphatase that plays a fundamental role in lipid metabolism. PA phosphatases are key enzymes that catalyze the PA dephosphorylation reaction to form diacylglycerides, the first step in the synthesis of triacylglycerols. Pah1p, one of the main PA phosphatases in yeast, has not only emerged as a key player in lipid biosynthetic pathways, but also acts as an important regulator of nuclear membrane biogenesis, the transcriptional regulation of many inositol-sensitive upstream activating sequence (UASINO)containing genes needed for phospholipid synthesis, vacuole homeostasis, and lipid droplet formation. Due to its …
Machine Learning Meta-Analysis Of Large Metagenomic Datasets: Tools And Biological Insight, Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata
Machine Learning Meta-Analysis Of Large Metagenomic Datasets: Tools And Biological Insight, Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata
Publications and Research
Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction …
Comparative Genomics Explains The Evolutionary Success Of Reef-Forming Corals, Debashish Bhattacharya, Shobhit Agrawal, Manuel Aranda, Sebastian Baumgarten, Mahdi Belcaid, Jeana L. Drake, Douglas Erwin, Sylvian Foret, Ruth D. Gates, David F. Gruber, Bishoy Kamel, Michael P. Lesser, Oren Levy, Yi Jin Liew, Matthew Macmanes, Tali Mass, Monica Medina, Shaadi Mehr, Eli Meyer, Dana C. Price, Hollie M. Putnam, Huan Qiu, Chuya Shinzato, Eiichi Shoguchi, Alexander J. Stokes, Sylvie Tambutté, Dan Tchernov, Christian R. Voolstra, Nicole Wagner, Charles W. Walker, Andreas Pm Weber, Virginia Weis, Ehud Zelzion, Didier Zoccola, Paul G. Falkowski
Comparative Genomics Explains The Evolutionary Success Of Reef-Forming Corals, Debashish Bhattacharya, Shobhit Agrawal, Manuel Aranda, Sebastian Baumgarten, Mahdi Belcaid, Jeana L. Drake, Douglas Erwin, Sylvian Foret, Ruth D. Gates, David F. Gruber, Bishoy Kamel, Michael P. Lesser, Oren Levy, Yi Jin Liew, Matthew Macmanes, Tali Mass, Monica Medina, Shaadi Mehr, Eli Meyer, Dana C. Price, Hollie M. Putnam, Huan Qiu, Chuya Shinzato, Eiichi Shoguchi, Alexander J. Stokes, Sylvie Tambutté, Dan Tchernov, Christian R. Voolstra, Nicole Wagner, Charles W. Walker, Andreas Pm Weber, Virginia Weis, Ehud Zelzion, Didier Zoccola, Paul G. Falkowski
Publications and Research
Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals …
Epigenetic Profiles Signify Cell Fate Plasticity In Unipotent Spermatogonial Stem And Progenitor Cells, Ying Liu, Eugenia G. Giannopoulou, Duacheng Wen, Ilaria Falciatori, Oliver Elemento, C. David Allis, Shahin Rafii, Marco Seandel
Epigenetic Profiles Signify Cell Fate Plasticity In Unipotent Spermatogonial Stem And Progenitor Cells, Ying Liu, Eugenia G. Giannopoulou, Duacheng Wen, Ilaria Falciatori, Oliver Elemento, C. David Allis, Shahin Rafii, Marco Seandel
Publications and Research
Spermatogonial stem and progenitor cells (SSCs) generate adult male gametes. During in vitro expansion, these unipotent murine cells spontaneously convert to multipotent adult spermatogonial-derived stem cells (MASCs). Here we investigate this conversion process through integrative transcriptomic and epigenomic analyses. We find in SSCs that promoters essential to maintenance and differentiation of embryonic stem cells (ESCs) are enriched with histone H3-lysine4 and -lysine 27 trimethylations. These bivalent modifications are maintained at most somatic promoters after conversion, bestowing MASCs an ESC-like promoter chromatin. At enhancers, the core pluripotency circuitry is activated partially in SSCs and completely in MASCs, concomitant with loss of …
Comparative Error-Free And Error-Prone Translesion Synthesis Of N2‑2′-Deoxyguanosine Adducts Formed By Mitomycin C And Its Metabolite, 2,7-Diaminomitosene, In Human Cells, Arindam Bose, Chaitra Surugihalli, Paritosh Pande, Elise Champeil, Ashis K. Basu
Comparative Error-Free And Error-Prone Translesion Synthesis Of N2‑2′-Deoxyguanosine Adducts Formed By Mitomycin C And Its Metabolite, 2,7-Diaminomitosene, In Human Cells, Arindam Bose, Chaitra Surugihalli, Paritosh Pande, Elise Champeil, Ashis K. Basu
Publications and Research
Mitomycin C (MC) is a cytotoxic and mutagenic antitumor agent that alkylates DNA upon reductive activation. 2,7-Diaminomitosene (2,7-DAM) is a major metabolite of MC in tumor cells, which also alkylates DNA. MC forms seven DNA adducts, including monoadducts and inter- and intrastrand cross-links, whereas 2,7-DAM forms two monoadducts. Herein, the biological effects of the dG-N2 adducts formed by MC and 2,7-DAM have been compared by constructing single-stranded plasmids containing these adducts and replicating them in human embryonic kidney 293T cells. Translesion synthesis (TLS) efficiencies of dG-N2-MC and dG-N2-2,7-DAM were 38 ± 3 and 27 …
Effects Of Choline On Dna Methylation And Macronutrient Metabolic Gene Expression In In Vitro Models Of Hyperglycemia, Xinyin Jiang, Esther Greenwald, Chauntelle Jack-Roberts
Effects Of Choline On Dna Methylation And Macronutrient Metabolic Gene Expression In In Vitro Models Of Hyperglycemia, Xinyin Jiang, Esther Greenwald, Chauntelle Jack-Roberts
Publications and Research
Choline is an essential nutrient that plays an important role in lipid metabolism and DNA methylation. Studies in rodents suggest that choline may adversely affect glycemic control, yet studies in humans are lacking. Using the human hepatic and placental cells, HepG2 and BeWo, respectively, we examined the interaction between choline and glucose treatments. In HepG2 cells, choline supplementation (1 mM) increased global DNA methylation and DNA methyltransferase expression in both low-glucose (5 mM) and high-glucose (35 mM) conditions. Choline supplementation increased the expression of peroxisomal acyl-coenzyme A oxidase 1 (ACOX1), which mediates fatty acid β-oxidation, especially in the high-glucose condition. …
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez
Publications and Research
Rattlesnakes (Crotalus and Sistrurus) represent a radiation of approximately 42 species distributed throughout the New World from southern Canada to Argentina. Interest in this enigmatic group of snakes continues to accrue due, in part, to their ecomorphological diversity, contributions to global envenomations, and potential medicinal importance. Although the group has garnered substantial attention from systematists and evolutionary biologists for decades, little is still known regarding patterns of lineage diversification. In addition, few studies have statistically quantified broad-scale biogeographic patterns in rattlesnakes to ascertain how dispersal occurred throughout the New World, particularly among the different major biomes of the …
Genome Assembly And Geospatial Phylogenomics Of The Bed Bug Cimex Lectularius, Jeffrey A. Rosenfeld, Darryl Reeves, Mercer R. Brugler, Apurva Narechania, Sabrina Simon, Russell Durrett, Jonathan Foox, Kevin Shianna, Michael C. Schatz, Jorge Gandara, Ebrahim Afshinnekoo, Ernest T. Lam, Alex R. Hastie, Saki Chan, Han Cao, Michael Saghbini, Alex Kentsis, Paul J. Planet, Vladyslav Kholodovych, Michael Tessler, Richard Baker, Rob Desalle, Louis N. Sorkin, Sergios-Orestis Kolokotronis, Mark E. Siddall, George Amato, Christopher E. Mason
Genome Assembly And Geospatial Phylogenomics Of The Bed Bug Cimex Lectularius, Jeffrey A. Rosenfeld, Darryl Reeves, Mercer R. Brugler, Apurva Narechania, Sabrina Simon, Russell Durrett, Jonathan Foox, Kevin Shianna, Michael C. Schatz, Jorge Gandara, Ebrahim Afshinnekoo, Ernest T. Lam, Alex R. Hastie, Saki Chan, Han Cao, Michael Saghbini, Alex Kentsis, Paul J. Planet, Vladyslav Kholodovych, Michael Tessler, Richard Baker, Rob Desalle, Louis N. Sorkin, Sergios-Orestis Kolokotronis, Mark E. Siddall, George Amato, Christopher E. Mason
Publications and Research
The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug’s basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on …
The Evolution Of The Viral Rna Sensor Oas1 In Old World Monkeys And Cetartiodactyls, Ian Fish
The Evolution Of The Viral Rna Sensor Oas1 In Old World Monkeys And Cetartiodactyls, Ian Fish
Dissertations, Theses, and Capstone Projects
Animals produce an array of sensors patrolling the intracellular environment poised to detect and respond to viral infection. The oligoadenylate synthetase family of enzymes comprises a crucial part of this innate immune response, directly signaling endonuclease activity responsible for inhibiting viral replication. Oligoadenylate synthetase 1 plays a vital role in animal susceptibility to pathogens including flaviviruses such as dengue, West Nile, and hepatitis c virus. This thesis includes a population level analysis of OAS1 diversity within macaque and baboon species followed by a broader survey of the gene in nineteen Old World monkeys. My research found that at the species …
The Implications Of Chromatin Remodelers' Acetylation In Ino1 Activation, Michelle M. Esposito
The Implications Of Chromatin Remodelers' Acetylation In Ino1 Activation, Michelle M. Esposito
Dissertations, Theses, and Capstone Projects
It is known that histone acetylases (HATs) regulate gene expression, but only recently have new functional implications about remodelers’ acetylation emerged. For instance, the HAT, Gcn5p, is capable of acetylating the catalytic subunit of the nucleosome remodeling complex SWI/SNF, Snf2p, which results in the dissociation of the complex from chromatin. The implications of this acetylation and subsequent dissociation have yet to be explored with regard to transcriptional regulation and other possible mechanisms. To further understand the implications of remodeler acetylation, I used a yeast model system examining the expression of the inositol-3-phosphate synthase gene INO1. Through chromatin immunoprecipitation (ChIP) …
Lim Protein Ajuba Participates In The Repression Of Atr-Mediated Dna Damage Response In Human Cells, Sampada Kalan
Lim Protein Ajuba Participates In The Repression Of Atr-Mediated Dna Damage Response In Human Cells, Sampada Kalan
Dissertations, Theses, and Capstone Projects
LIM proteins constitute a superfamily characterized by the presence of specialized domains called LIM. LIM domain is a unique double-zinc finger motif found in a variety of proteins and is mainly involved in protein-protein interactions. Previous work has implicated that members of the Zyxin subfamily of LIM proteins, namely TRIP6 and LPP are involved in the repression of the DNA damage response (DDR) at telomeres. We further explore if another member from this family has an influence on DDR prevention in the cells. Here, we describe a novel role for Ajuba, a Zyxin family LIM protein, in repressing inappropriate activation …
Role Of Bec-1/Beclin 1 And Autophagy Genes In C.Elegans Germline Cell Proliferation, Kristina Ames
Role Of Bec-1/Beclin 1 And Autophagy Genes In C.Elegans Germline Cell Proliferation, Kristina Ames
Dissertations, Theses, and Capstone Projects
Autophagy is an evolutionary conserved process involved in the cellular adaptation to stress and basal levels of autophagy are crucial for cellular metabolism and homeostasis. Cellular recycling by autophagy is characterized by the formation of distinctive double-membrane vesicles (autophagosomes) that engulf unnecessary cytoplasmic components, such as organelles and long-lived proteins. Failure to remove protein aggregates and/or damaged organelles, via autophagy, has been implicated in various medical conditions such as liver disease, neurodegenerative diseases and cancer. Autophagy may suppress or promote cellular proliferation in tumors, depending on the type and metabolic state of the cell, where autophagy is generally believed to …
Cellmapper: Rapid And Accurate Inference Of Gene Expression In Difficult-To-Isolate Cell Types, Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer
Cellmapper: Rapid And Accurate Inference Of Gene Expression In Difficult-To-Isolate Cell Types, Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer
Publications and Research
We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.
The Mitogenome Of The Bed Bug Cimex Lectularius (Hemiptera: Cimicidae), Sergios-Orestis Kolokotronis, Jonathan Foox, Jeffrey A. Rosenfeld, Mercer R. Brugler, Darryl Reeves, Joshua B. Benoit, Warren Booth, Grant Robison, Michael Steffen, Zoe Sakas, Subba R. Palli, Coby Schal, Stephen Richards, Apurva Narechania, Richard H. Baker, Louis N. Sorkin, George Amato, Christopher E. Mason, Mark E. Siddall, Rob Desalle
The Mitogenome Of The Bed Bug Cimex Lectularius (Hemiptera: Cimicidae), Sergios-Orestis Kolokotronis, Jonathan Foox, Jeffrey A. Rosenfeld, Mercer R. Brugler, Darryl Reeves, Joshua B. Benoit, Warren Booth, Grant Robison, Michael Steffen, Zoe Sakas, Subba R. Palli, Coby Schal, Stephen Richards, Apurva Narechania, Richard H. Baker, Louis N. Sorkin, George Amato, Christopher E. Mason, Mark E. Siddall, Rob Desalle
Publications and Research
We report the extraction of a bed bug mitogenome from high-throughput sequencing projects originally focused on the nuclear genome of Cimex lectularius. The assembled mitogenome has a similar AT nucleotide composition bias found in other insects. Phylogenetic analysis of all protein-coding genes indicates that C. lectularius is clearly a member of a paraphyletic Cimicomorpha clade within the Order Hemiptera.