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Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers 2016 The Graduate Center, City University of New York

Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers

All Graduate Works by Year: 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 ...


Rna2dnalign: Nucleotide Resolution Allele Asymmetries Through Quantitative Assessment Of Rna And Dna Paired Sequencing Data., Mercedeh Movassagh, Nawaf Alomran, Prakriti Mudvari, Merve Dede, Cem Dede, Kamran Kowsari, Paula Restrepo, Edmund Cauley, Sonali Bahl, Muzi Li, Wesley Waterhouse, Krasimira Tsaneva-Atanasova, Nathan Edwards, Anelia Horvath 2016 George Washington University

Rna2dnalign: Nucleotide Resolution Allele Asymmetries Through Quantitative Assessment Of Rna And Dna Paired Sequencing Data., Mercedeh Movassagh, Nawaf Alomran, Prakriti Mudvari, Merve Dede, Cem Dede, Kamran Kowsari, Paula Restrepo, Edmund Cauley, Sonali Bahl, Muzi Li, Wesley Waterhouse, Krasimira Tsaneva-Atanasova, Nathan Edwards, Anelia Horvath

Biochemistry and Molecular Medicine Faculty Publications

We introduce RNA2DNAlign, a computational framework for quantitative assessment of allele counts across paired RNA and DNA sequencing datasets. RNA2DNAlign is based on quantitation of the relative abundance of variant and reference read counts, followed by binomial tests for genotype and allelic status at SNV positions between compatible sequences. RNA2DNAlign detects positions with differential allele distribution, suggesting asymmetries due to regulatory/structural events. Based on the type of asymmetry, RNA2DNAlign outlines positions likely to be implicated in RNA editing, allele-specific expression or loss, somatic mutagenesis or loss-of-heterozygosity (the first three also in a tumor-specific setting). We applied RNA2DNAlign on 360 ...


Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager 2016 University of Wisconsin-La Crosse

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by ...


Data Development And Analysis Pathways For Marine Mammals And Turtles: Creating A User Interface, Sarina Fernandez, Warren Asfazadour, Eric Archer, Lisa Komoroske 2016 California Polytechnic State University, San Luis Obispo

Data Development And Analysis Pathways For Marine Mammals And Turtles: Creating A User Interface, Sarina Fernandez, Warren Asfazadour, Eric Archer, Lisa Komoroske

STAR (STEM Teacher and Researcher) Program Posters

A major obstacle in genetic research is developing streamlined methods for analyzing large amounts of data. The statistical computer programming language R provides users with the ability to develop packages containing specific functions in order to create more accessible data analysis pipelines. However, writing code in R can still be intimidating to those with little to no coding experience. Fortunately, the R package shiny provides a framework for developing web applications based on R functions. Using shiny, we developed a user-friendly web application containing functions of the R package strataG. The strataG package contains several functions for summarizing genetic data ...


Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. McCool Ms., Nick Hum, Gabriela G. Loots 2016 California State University, Chico

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR (STEM Teacher and Researcher) Program Posters

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few ...


End Sequence Analysis Toolkit (Esat) Expands The Extractable From Single Cell Rna-Seq Experiments, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim Artyomov, Manuel Garber 2016 University of Massachusetts Medical School

End Sequence Analysis Toolkit (Esat) Expands The Extractable From Single Cell Rna-Seq Experiments, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim Artyomov, Manuel Garber

Open Access Articles

RNA-seq protocols that focus on transcript termini are well-suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3'-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1,000 ...


Metabolic Network Rewiring Of Propionate Flux Compensates Vitamin B12 Deficiency In C. Elegans, Emma Watson, Viridiana Olin-Sandoval, Michael J. Hoy, Chi-Hua Li, Timo Louisse, Victoria Yao, Akihiro Mori, Amy D. Holdorf, Olga G. Troyanskaya, Markus Ralser, Albertha J. M. Walhout 2016 University of Massachusetts Medical School Worcester

Metabolic Network Rewiring Of Propionate Flux Compensates Vitamin B12 Deficiency In C. Elegans, Emma Watson, Viridiana Olin-Sandoval, Michael J. Hoy, Chi-Hua Li, Timo Louisse, Victoria Yao, Akihiro Mori, Amy D. Holdorf, Olga G. Troyanskaya, Markus Ralser, Albertha J. M. Walhout

Open Access Articles

Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked ...


Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson 2016 University of Nebraska-Lincoln

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and ...


Identification Of Zika Virus And Dengue Virus Dependency Factors Using Functional Genomics, George Savidis, William M. McDougall, Paul Meraner, Jill Perreira, Jocelyn M. Portmann, Gaia Trincucci, Sinu P. John, Aaron M. Aker, Nicholas Renzette, Douglas R. Robbins, Zhiru Guo, Sharone Green, Timothy F. Kowalik, Abraham L. Brass 2016 University of Massachusetts Medical School

Identification Of Zika Virus And Dengue Virus Dependency Factors Using Functional Genomics, George Savidis, William M. Mcdougall, Paul Meraner, Jill Perreira, Jocelyn M. Portmann, Gaia Trincucci, Sinu P. John, Aaron M. Aker, Nicholas Renzette, Douglas R. Robbins, Zhiru Guo, Sharone Green, Timothy F. Kowalik, Abraham L. Brass

Sharone Green

The flaviviruses dengue virus (DENV) and Zika virus (ZIKV) are severe health threats with rapidly expanding ranges. To identify the host cell dependencies of DENV and ZIKV, we completed orthologous functional genomic screens using RNAi and CRISPR/Cas9 approaches. The screens recovered the ZIKV entry factor AXL as well as multiple host factors involved in endocytosis (RAB5C and RABGEF), heparin sulfation (NDST1 and EXT1), and transmembrane protein processing and maturation, including the endoplasmic reticulum membrane complex (EMC). We find that both flaviviruses require the EMC for their early stages of infection. Together, these studies generate a high-confidence, systems-wide view of ...


Identification Of Zika Virus And Dengue Virus Dependency Factors Using Functional Genomics, George Savidis, William M. McDougall, Paul Meraner, Jill Perreira, Jocelyn M. Portmann, Gaia Trincucci, Sinu P. John, Aaron M. Aker, Nicholas Renzette, Douglas R. Robbins, Zhiru Guo, Sharone Green, Timothy F. Kowalik, Abraham L. Brass 2016 University of Massachusetts Medical School

Identification Of Zika Virus And Dengue Virus Dependency Factors Using Functional Genomics, George Savidis, William M. Mcdougall, Paul Meraner, Jill Perreira, Jocelyn M. Portmann, Gaia Trincucci, Sinu P. John, Aaron M. Aker, Nicholas Renzette, Douglas R. Robbins, Zhiru Guo, Sharone Green, Timothy F. Kowalik, Abraham L. Brass

Microbiology and Physiological Systems Publications and Presentations

The flaviviruses dengue virus (DENV) and Zika virus (ZIKV) are severe health threats with rapidly expanding ranges. To identify the host cell dependencies of DENV and ZIKV, we completed orthologous functional genomic screens using RNAi and CRISPR/Cas9 approaches. The screens recovered the ZIKV entry factor AXL as well as multiple host factors involved in endocytosis (RAB5C and RABGEF), heparin sulfation (NDST1 and EXT1), and transmembrane protein processing and maturation, including the endoplasmic reticulum membrane complex (EMC). We find that both flaviviruses require the EMC for their early stages of infection. Together, these studies generate a high-confidence, systems-wide view of ...


Using Hadoop To Identify False Positives In Bacterial Strain Typing From Dna Fingerprints, Colin C. Adams 2016 California Polytechnic State University, San Luis Obispo

Using Hadoop To Identify False Positives In Bacterial Strain Typing From Dna Fingerprints, Colin C. Adams

Computer Science

Pyroprinting is a novel technique used by the Department of Biological Sciences to obtain “fingerprints” from the DNA of E. coli isolates in order to categorize them into strains. To determine the number of false positives that occur in the pyroprinting process, isolates with the same pyroprints needed to be sequenced to see if their underlying alleles match. If they do match, this shows they are indeed the same strain and are a true positive. If the alleles don’t match, they are different strains and are a false positive. To do this 100 isolates with nucleotide identifiers were sequenced ...


Whole Exome Sequencing Links Dental Tumor To An Autosomal-Dominant Mutation In Ano5 Gene Associated With Gnathodiaphyseal Dysplasia And Muscle Dystrophies, T. V. Andreeva, T. V. Tyazhelova, V. N. Rykalina, F. E. Gusev, Andrey Y. Goltsov, O. I. Zolotareva, M. P. Aliseichik, T. A. Borodina, Anastasia P. Grigorenko, Denis Reshetov, E. K. Ginter, S. S. Amelina, R A. Zinchenko, Evgeny I. Rogaev 2016 Russian Academy of Sciences

Whole Exome Sequencing Links Dental Tumor To An Autosomal-Dominant Mutation In Ano5 Gene Associated With Gnathodiaphyseal Dysplasia And Muscle Dystrophies, T. V. Andreeva, T. V. Tyazhelova, V. N. Rykalina, F. E. Gusev, Andrey Y. Goltsov, O. I. Zolotareva, M. P. Aliseichik, T. A. Borodina, Anastasia P. Grigorenko, Denis Reshetov, E. K. Ginter, S. S. Amelina, R A. Zinchenko, Evgeny I. Rogaev

Open Access Articles

Tumors of the jaws may represent different human disorders and frequently associate with pathologic bone fractures. In this report, we analyzed two affected siblings from a family of Russian origin, with a history of dental tumors of the jaws, in correspondence to original clinical diagnosis of cementoma consistent with gigantiform cementoma (GC, OMIM: 137575). Whole exome sequencing revealed the heterozygous missense mutation c.1067G > A (p.Cys356Tyr) in ANO5 gene in these patients. To date, autosomal-dominant mutations have been described in the ANO5 gene for gnathodiaphyseal dysplasia (GDD, OMIM: 166260), and multiple recessive mutations have been described in the gene ...


Phylogenetic Analysis Of Human Cytomegalovirus Pus27 And Pus28: Ascertaining An Independent Or Linked Evolutionary History, Jessica A. Scarborough 2016 University of San Francisco

Phylogenetic Analysis Of Human Cytomegalovirus Pus27 And Pus28: Ascertaining An Independent Or Linked Evolutionary History, Jessica A. Scarborough

Undergraduate Honors Theses

Human cytomegalovirus (HCMV) is a widespread pathogen that is particularly skilled at evading immune detection and defense mechanisms, largely due to extensive co-evolution with its host’s immune system. One aspect of this co-evolution involves the acquisition of four virally encoded GPCR chemokine receptor homologs, products of the US27, US28, UL33 and UL78 genes. G protein-coupled receptors (GPCR) are the largest family of cell surface proteins, found in organisms from yeast to humans. In this research, phylogenetic analysis was used to investigate the origins of the US27 and US28 genes, which are adjacent in the viral genome. The results indicate ...


Accurate Mutation Annotation And Functional Prediction Enhance The Applicability Of -Omics Data In Precision Medicine, Tenghui Chen 2016 The University of Texas Graduate School of Biomedical Sciences at Houston

Accurate Mutation Annotation And Functional Prediction Enhance The Applicability Of -Omics Data In Precision Medicine, Tenghui Chen

UT GSBS Dissertations and Theses (Open Access)

Clinical sequencing has been recognized as an effective approach for enhancing the accuracy and efficiency of cancer patient management and therefore achieve the goals of personalized therapy. However, the accuracy of large scale sequencing data in clinics has been constrained by many different aspects, such as clinical detection, annotation and interpretation of the variants that are observed in clinical sequencing data. In my Ph.D thesis work, I mainly investigated how to comprehensively and efficiently apply high dimensional -omics data to enhance the capability of precision cancer medicine. Following this motivation, my dissertation has been focused on two important topics ...


In Silico Driven Metabolic Engineering Towards Enhancing Biofuel And Biochemical Production, Richard Adam Thompson 2016 University of Tennessee - Knoxville

In Silico Driven Metabolic Engineering Towards Enhancing Biofuel And Biochemical Production, Richard Adam Thompson

Doctoral Dissertations

The development of a secure and sustainable energy economy is likely to require the production of fuels and commodity chemicals in a renewable manner. There has been renewed interest in biological commodity chemical production recently, in particular focusing on non-edible feedstocks. The fields of metabolic engineering and synthetic biology have arisen in the past 20 years to address the challenge of chemical production from biological feedstocks. Metabolic modeling is a powerful tool for studying the metabolism of an organism and predicting the effects of metabolic engineering strategies. Various techniques have been developed for modeling cellular metabolism, with the underlying principle ...


Diverse Human Extracellular Rnas Are Widely Detected In Human Plasma, Jane E. Freedman, Eric Mick, Lea M. Beaulieu, Selim E. Tanriverdi, Milka Koupenova-Zamor, Ekaterina Mikhalev, Kahraman Tanriverdi 2016 University of Massachusetts Medical School

Diverse Human Extracellular Rnas Are Widely Detected In Human Plasma, Jane E. Freedman, Eric Mick, Lea M. Beaulieu, Selim E. Tanriverdi, Milka Koupenova-Zamor, Ekaterina Mikhalev, Kahraman Tanriverdi

Open Access Articles

There is growing appreciation for the importance of non-protein-coding genes in development and disease. Although much is known about microRNAs, limitations in bioinformatic analyses of RNA sequencing have precluded broad assessment of other forms of small-RNAs in humans. By analysing sequencing data from plasma-derived RNA from 40 individuals, here we identified over a thousand human extracellular RNAs including microRNAs, piwi-interacting RNA (piRNA), and small nucleolar RNAs. Using a targeted quantitative PCR with reverse transcription approach in an additional 2,763 individuals, we characterized almost 500 of the most abundant extracellular transcripts including microRNAs, piRNAs and small nucleolar RNAs. The presence ...


Determination Of Ubiquitin Fitness Landscapes Under Different Chemical Stresses In A Classroom Setting, David Mavor, Benjamin P. Roscoe, Daniel N. Bolon, James S. Fraser 2016 University of California, San Francisco

Determination Of Ubiquitin Fitness Landscapes Under Different Chemical Stresses In A Classroom Setting, David Mavor, Benjamin P. Roscoe, Daniel N. Bolon, James S. Fraser

Open Access Articles

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover 'shared sensitized positions' localized to areas around the hydrophobic patch and the C-terminus. In addition, we ...


Genomic Access To Monarch Migration Using Talen And Crispr/Cas9-Mediated Targeted Mutagenesis, Matthew J. Markert, Ying Zhang, Metewo Selase Enuameh, Steven M. Reppert, Scot A. Wolfe, Christine Merlin 2016 Texas A&M University

Genomic Access To Monarch Migration Using Talen And Crispr/Cas9-Mediated Targeted Mutagenesis, Matthew J. Markert, Ying Zhang, Metewo Selase Enuameh, Steven M. Reppert, Scot A. Wolfe, Christine Merlin

Open Access Articles

The eastern North American monarch butterfly, Danaus plexippus, is an emerging model system to study the neural, molecular, and genetic basis of animal long-distance migration and animal clockwork mechanisms. While genomic studies have provided new insight into migration-associated and circadian clock genes, the general lack of simple and versatile reverse-genetic methods has limited in vivo functional analysis of candidate genes in this species. Here, we report the establishment of highly efficient and heritable gene mutagenesis methods in the monarch butterfly using transcriptional activator-like effector nucleases (TALENs) and CRISPR-associated RNA-guided nuclease Cas9 (CRISPR/Cas9). Using two clock gene loci, cryptochrome 2 ...


Functional Analysis Of Girardia Tigrina Transcriptome Seeds Pipeline For Anthelmintic Target Discovery, Nicholas Wheeler, Prince Agbedanu, Michael Kimber, Paula Ribeiro, Timothy Day, Mostafa Zamanian 2016 Iowa State University

Functional Analysis Of Girardia Tigrina Transcriptome Seeds Pipeline For Anthelmintic Target Discovery, Nicholas Wheeler, Prince Agbedanu, Michael Kimber, Paula Ribeiro, Timothy Day, Mostafa Zamanian

Michael Kimber

Background Neglected diseases caused by helminth infections impose a massive hindrance to progress in the developing world. While basic research on parasitic flatworms (platyhelminths) continues to expand, researchers have yet to broadly adopt a free-living model to complement the study of these important parasites. Methods We report the high-coverage sequencing (RNA-Seq) and assembly of the transcriptome of the planarian Girardia tigrina across a set of dynamic conditions. The assembly was annotated and extensive orthology analysis was used to seed a pipeline for the rational prioritization and validation of putative anthelmintic targets. A small number of targets conserved between parasitic and ...


Development Of An In Vivo Rnai Protocol To Investigate Gene Function In The Filarial Nematode, Brugia Malayi, Chuanzhe Song, Jack Gallup, Timothy Day, Lyric Bartholomay, Michael Kimber 2016 Iowa State University

Development Of An In Vivo Rnai Protocol To Investigate Gene Function In The Filarial Nematode, Brugia Malayi, Chuanzhe Song, Jack Gallup, Timothy Day, Lyric Bartholomay, Michael Kimber

Michael Kimber

Our ability to control diseases caused by parasitic nematodes is constrained by a limited portfolio of effective drugs and a paucity of robust tools to investigate parasitic nematode biology. RNA interference (RNAi) is a reverse-genetics tool with great potential to identify novel drug targets and interrogate parasite gene function, but present RNAi protocols for parasitic nematodes, which remove the parasite from the host and execute RNAi in vitro, are unreliable and inconsistent. We have established an alternative in vivo RNAi protocol targeting the filarial nematode Brugia malayi as it develops in an intermediate host, the mosquito Aedes aegypti. Injection of ...


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