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On The Inadequacy Of Species Distribution Models For Modelling The Spread Of Sars-Cov-2: Response To Araújo And Naimi, Joseph D. Chipperfield, Blas M. Benito, Robert B. O'Hara, Richard J. Telford, Colin J. Carlson 2020 Norwegian Institute for Nature Research

On The Inadequacy Of Species Distribution Models For Modelling The Spread Of Sars-Cov-2: Response To Araújo And Naimi, Joseph D. Chipperfield, Blas M. Benito, Robert B. O'Hara, Richard J. Telford, Colin J. Carlson

Public Health Resources

The ongoing pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing significant damage to public health and economic livelihoods, and is putting significant strains on healthcare services globally. This unfolding emergency has prompted the preparation and dissemination of the article “Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate” by Araújo and Naimi (2020). The authors present the results of an ensemble forecast made from a suite of species distribution models (SDMs), where they attempt to predict the suitability of the climate for the spread of SARS-CoV-2 over the coming months. They argue that climate is ...


Evaluation Of Pre-Processing On The Meta-Analysis Of Dna Methylation Data From The Illumina Humanmethylation450 Beadchip Platform, Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini 2020 University of Bologna

Evaluation Of Pre-Processing On The Meta-Analysis Of Dna Methylation Data From The Illumina Humanmethylation450 Beadchip Platform, Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini

Open Access Articles

INTRODUCTION: Meta-analysis is a powerful means for leveraging the hundreds of experiments being run worldwide into more statistically powerful analyses. This is also true for the analysis of omic data, including genome-wide DNA methylation. In particular, thousands of DNA methylation profiles generated using the Illumina 450k are stored in the publicly accessible Gene Expression Omnibus (GEO) repository. Often, however, the intensity values produced by the BeadChip (raw data) are not deposited, therefore only pre-processed values -obtained after computational manipulation- are available. Pre-processing is possibly different among studies and may then affect meta-analysis by introducing non-biological sources of variability.

MATERIAL AND ...


Evaluation Of Pre-Processing On The Meta-Analysis Of Dna Methylation Data From The Illumina Humanmethylation450 Beadchip Platform, Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini 2020 University of Bologna

Evaluation Of Pre-Processing On The Meta-Analysis Of Dna Methylation Data From The Illumina Humanmethylation450 Beadchip Platform, Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini

Infectious Diseases and Immunology Publications

INTRODUCTION: Meta-analysis is a powerful means for leveraging the hundreds of experiments being run worldwide into more statistically powerful analyses. This is also true for the analysis of omic data, including genome-wide DNA methylation. In particular, thousands of DNA methylation profiles generated using the Illumina 450k are stored in the publicly accessible Gene Expression Omnibus (GEO) repository. Often, however, the intensity values produced by the BeadChip (raw data) are not deposited, therefore only pre-processed values -obtained after computational manipulation- are available. Pre-processing is possibly different among studies and may then affect meta-analysis by introducing non-biological sources of variability.

MATERIAL AND ...


Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer 2020 New Mexico State University

Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer

Poisonous Plant Research (PPR)

Locoweeds are the most widespread poisonous plant problem in the world and have been reported in the Western United States since the 1800s, causing tremendous losses in livestock. Consumption of locoweeds by grazing animals stimulates the neurological disease, locoism, characterized by weight loss, ataxia, and lack of muscular coordination. The name locoweed is used for Astragalus and Oxytropis species known to contain swainsonine, the toxic principle produced by the plant endophytic fungus Undifilum. Astragalus includes 2,500-3,000 species and many varieties that have almost identical morphological characteristics that overlap among species, leading to improper identification. Therefore, the aim of ...


Pyrpipe: A Python Package For Rna-Seq Workflows, Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele 2020 Iowa State University

Pyrpipe: A Python Package For Rna-Seq Workflows, Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele

Genetics, Development and Cell Biology Publications

Implementing RNA-Seq analysis pipelines is challenging as data gets bigger and more complex. With the availability of terabytes of RNA-Seq data and continuous development of analysis tools, there is a pressing requirement for frameworks that allow for fast and efficient development, modification, sharing and reuse of workflows. Scripting is often used, but it has many challenges and drawbacks. We have developed a python package, python RNA-Seq Pipeliner (pyrpipe) that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in python, in an object-oriented manner. pyrpipe provides high level APIs to popular RNA-Seq tools. Pipelines can be customized by ...


High-Throughput Sequencing Pipeline Tool Analysis - Staphylococcus Aureus, Justin Fay 2020 University of Nebraska at Omaha

High-Throughput Sequencing Pipeline Tool Analysis - Staphylococcus Aureus, Justin Fay

Student Research and Creative Activity Fair

In this project, I compared the tools used at each step of the high-throughput sequencing pipeline used to detect single-nucleotide polymorphisms (SNP’s). There are 11 sequences I utilized from my mentor, Dr. Kate Cooper, on this project (pertaining to Staphylococcus aureus) and I used those in the sequencing pipeline. I evaluated different tools by using different ones at different steps of the pipeline. By doing this, I was able to see how close or far the outputs are by only changing one factor. It is also important to note that, with each online tool comes its own sets of ...


Comprehensive Identification Of Alternative Back-Splicing In Human Tissue Transcriptomes, Peng Zhang, Xiao-Ou Zhang, Tingting Jiang, Lingling Cai, Xiao Huang, Qi Liu, Dan Li, Aiping Lu, Yan Liu, Wen Xue, Peng Zhang, Zhiping Weng 2020 Tongji University

Comprehensive Identification Of Alternative Back-Splicing In Human Tissue Transcriptomes, Peng Zhang, Xiao-Ou Zhang, Tingting Jiang, Lingling Cai, Xiao Huang, Qi Liu, Dan Li, Aiping Lu, Yan Liu, Wen Xue, Peng Zhang, Zhiping Weng

Open Access Articles

Circular RNAs (circRNAs) are covalently closed RNAs derived from back-splicing of genes across eukaryotes. Through alternative back-splicing (ABS), a single gene produces multiple circRNAs sharing the same back-splice site. Although many ABS events have recently been discovered, to what extent ABS involves in circRNA biogenesis and how it is regulated in different human tissues still remain elusive. Here, we reported an in-depth analysis of ABS events in 90 human tissue transcriptomes. We observed that ABS occurred for about 84% circRNAs. Interestingly, alternative 5' back-splicing occurs more prevalently than alternative 3' back-splicing, and both of them are tissue-specific, especially enriched in ...


Adaptive Evolution Targets A Pirna Precursor Transcription Network, Swapnil Parhad, Tianxiong Yu, Gen Zhang, Nicholas P. Rice, Zhiping Weng, William E. Theurkauf 2020 University of Massachusetts Medical School

Adaptive Evolution Targets A Pirna Precursor Transcription Network, Swapnil Parhad, Tianxiong Yu, Gen Zhang, Nicholas P. Rice, Zhiping Weng, William E. Theurkauf

Open Access Articles

In Drosophila, transposon-silencing piRNAs are derived from heterochromatic clusters and a subset of euchromatic transposon insertions, which are bound by the Rhino-Deadlock-Cutoff complex. The HP1 homolog Rhino binds to Deadlock, which recruits TRF2 to promote non-canonical transcription from both genomic strands. Cuff function is less well understood, but this Rai1 homolog shows hallmarks of adaptive evolution, which can remodel functional interactions within host defense systems. Supporting this hypothesis, Drosophila simulans Cutoff is a dominant-negative allele when expressed in Drosophila melanogaster, in which it traps Deadlock, TRF2, and the conserved transcriptional co-repressor CtBP in stable complexes. Cutoff functions with Rhino and ...


Proteomic And Transcriptional Profiles Of Human Stem Cell-Derived Beta Cells Following Enteroviral Challenge, Julius O. Nyalwidhe, Agata Jurczyk, Basanthi Satish, Sambra D. Redick, Natasha Qaisar, Melanie I. Trombly, Pranitha Vangala, Riccardo Racicot, Rita Bortell, David M. Harlan, Dale L. Greiner, Michael A. Brehm, Jerry L. Nadler, Jennifer P. Wang 2020 Eastern Virginia Medical School

Proteomic And Transcriptional Profiles Of Human Stem Cell-Derived Beta Cells Following Enteroviral Challenge, Julius O. Nyalwidhe, Agata Jurczyk, Basanthi Satish, Sambra D. Redick, Natasha Qaisar, Melanie I. Trombly, Pranitha Vangala, Riccardo Racicot, Rita Bortell, David M. Harlan, Dale L. Greiner, Michael A. Brehm, Jerry L. Nadler, Jennifer P. Wang

Open Access Articles

Enteroviral infections are implicated in islet autoimmunity and type 1 diabetes (T1D) pathogenesis. Significant beta-cell stress and damage occur with viral infection, leading to cells that are dysfunctional and vulnerable to destruction. Human stem cell-derived beta (SC-beta) cells are insulin-producing cell clusters that closely resemble native beta cells. To better understand the events precipitated by enteroviral infection of beta cells, we investigated transcriptional and proteomic changes in SC-beta cells challenged with coxsackie B virus (CVB). We confirmed infection by demonstrating that viral protein colocalized with insulin-positive SC-beta cells by immunostaining. Transcriptome analysis showed a decrease in insulin gene expression following ...


A Chromosomal Connectome For Psychiatric And Metabolic Risk Variants In Adult Dopaminergic Neurons, Sergio Espeso-Gil, Tyler M. Borrman, Zhiping Weng, Schahram Akbarian 2020 Icahn School of Medicine at Mount Sinai

A Chromosomal Connectome For Psychiatric And Metabolic Risk Variants In Adult Dopaminergic Neurons, Sergio Espeso-Gil, Tyler M. Borrman, Zhiping Weng, Schahram Akbarian

Open Access Articles

BACKGROUND: Midbrain dopaminergic neurons (MDN) represent 0.0005% of the brain's neuronal population and mediate cognition, food intake, and metabolism. MDN are also posited to underlay the neurobiological dysfunction of schizophrenia (SCZ), a severe neuropsychiatric disorder that is characterized by psychosis as well as multifactorial medical co-morbidities, including metabolic disease, contributing to markedly increased morbidity and mortality. Paradoxically, however, the genetic risk sequences of psychosis and traits associated with metabolic disease, such as body mass, show very limited overlap.

METHODS: We investigated the genomic interaction of SCZ with medical conditions and traits, including body mass index (BMI), by exploring ...


Hiv-1 Did Not Contribute To The 2019-Ncov Genome, Chuan Xiao, Xiaojun Li, Shuying Liu, Yongming Sang, Shou-Jiang Gao, Feng Gao 2020 University of Texas at El Paso

Hiv-1 Did Not Contribute To The 2019-Ncov Genome, Chuan Xiao, Xiaojun Li, Shuying Liu, Yongming Sang, Shou-Jiang Gao, Feng Gao

Coronavirus COVID-19 Publications by UMMS Authors

When a new pathogen that causes a global epidemic in humans, one key question is where it comes from. This is especially important for a zoonotic infectious disease that jumps from animals to humans. Knowing the origin of such a pathogen is critical to develop means to block further transmission and to develop vaccines. Discovery of the origin of a newly human pathogen is a sophisticated process that requires extensive and vigorous scientific validations and generally takes many years, such as the cases for HIV-1, SARS and MERS. Unfortunately, before the natural sources of new pathogens are clearly defined, conspiracy ...


Single Cell Transcriptomics Reveals Dysregulated Cellular And Molecular Networks In A Fragile X Syndrome Model, Elisa Donnard, Huan Shu, Manuel Garber 2020 University of Massachusetts Medical School

Single Cell Transcriptomics Reveals Dysregulated Cellular And Molecular Networks In A Fragile X Syndrome Model, Elisa Donnard, Huan Shu, Manuel Garber

University of Massachusetts Medical School Faculty Publications

Despite advances in understanding the pathophysiology of Fragile X syndrome (FXS), its molecular bases are still poorly understood. Whole brain tissue expression profiles have proved surprisingly uninformative. We applied single cell RNA sequencing to profile a FXS mouse model. We found that FXS results in a highly cell type specific effect and it is strongest among different neuronal types. We detected a downregulation of mRNAs bound by FMRP and this effect is prominent in neurons. Metabolic pathways including translation are significantly upregulated across all cell types with the notable exception of excitatory neurons. These effects point to a potential difference ...


Mushroom Body-Specific Gene Regulation By The Swi/Snf Chromatin Remodeling Complex, Kevin CJ Nixon 2020 The University of Western Ontario

Mushroom Body-Specific Gene Regulation By The Swi/Snf Chromatin Remodeling Complex, Kevin Cj Nixon

Electronic Thesis and Dissertation Repository

Over the lifetime of an organism, neurons must establish, remodel, and maintain precise connections in order to form neural circuits that are required for proper nervous system functioning. Disruptions in these processes can lead to neurodevelopmental disorders such as intellectual disability (ID) and autism spectrum disorder. Mutations in genes encoding subunits of the SWI/SNF chromatin remodeling complex have been implicated in ID, yet the role of this complex in neurons is poorly understood. In this project, I established cell-type specific methods to examine the effect of SWI/SNF subunit knockdowns on gene transcription and chromatin structure in the memory-forming ...


On The Distribution Of Genetic Variation In Ecological Communities, Isaac Overcast 2020 The Graduate Center, City University of New York

On The Distribution Of Genetic Variation In Ecological Communities, Isaac Overcast

All Dissertations, Theses, and Capstone Projects

Biodiversity in ecological communities is structured hierarchically across spatial and temporal scales. Many open questions remain as to how this structure accumulates. For example, what are the relative contributions of dispersal versus in situ speciation? Or, how important are stochastic drift versus deterministic processes? Up to this point, these questions have been investigated by isolated disciplines (e.g. macroecology, comparative phylogeography, macroevolution) using tools and data that tend to focus on only one axis of community scale data (e.g. phylogenies, relative abundances, and/or trait information). Yet we know that there are feedbacks among processes that respond on short ...


Pseudomonas And Bacillus Soil Isolates Produce Antibiotics, Chelsea Brandt, Dr. Lori Scott 2020 Augustana College, Rock Island Illinois

Pseudomonas And Bacillus Soil Isolates Produce Antibiotics, Chelsea Brandt, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

The recent emergence of antibiotic resistance bacterial strains presents a significant challenge and threat to human healthcare. While new methods of treatment such as bacteriophage therapy and combinations of existing antibiotics are being researched, the human population is in dire need of new antibiotics to replace those that are ineffective. This research addresses this need by identifying antibiotic producing bacteria in a soil sample from Davenport, IA. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on studentsourcing antibiotic discovery from soil. Microbiology lab techniques and 16S ...


A Curated Benchmark Of Enhancer-Gene Interactions For Evaluating Enhancer-Target Gene Prediction Methods, Jill E. Moore, Henry E. Pratt, Michael J. Purcaro, Zhiping Weng 2020 University of Massachusetts Medical School

A Curated Benchmark Of Enhancer-Gene Interactions For Evaluating Enhancer-Target Gene Prediction Methods, Jill E. Moore, Henry E. Pratt, Michael J. Purcaro, Zhiping Weng

Open Access Articles

BACKGROUND: Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes.

RESULTS: To facilitate the development of computational methods for predicting target genes, we develop a Benchmark of candidate Enhancer-Gene Interactions (BENGI) by integrating the recently developed Registry of cCREs with experimentally derived genomic interactions. We use BENGI to test several published computational methods for linking enhancers with genes, including signal correlation and the TargetFinder and PEP supervised learning methods. We find that while TargetFinder is the best-performing method, it ...


Statistical Analysis Of Social Network Change, Teresa D. Schmidt 2020 Portland State University

Statistical Analysis Of Social Network Change, Teresa D. Schmidt

Systems Science Friday Noon Seminar Series

We explore two statistical methods that infer social network structures and statistically test those structures for change over time: regression-based differential network analysis (R-DNA) and information theory-based differential network analysis (I-DNA). RDNA is adapted from bioinformatics and I-DNA employs reconstructability analysis. Both methods are used to analyze Medicaid claims data from one-year periods before and after the formation of the Health Share of Oregon Coordinated Care Organization (CCO). We hypothesized that Health Share’s CCO formation would be followed by several changes in the healthcare delivery network.

Application of R-DNA and I-DNA to claims data involves three steps: (a) the ...


The Role Of Influenza Infection On Cell Metabolism, Megha Mokkapati 2020 The University of Akron

The Role Of Influenza Infection On Cell Metabolism, Megha Mokkapati

Williams Honors College, Honors Research Projects

In this particular study global metabolomics LCMS data was analyzed to determine the effect of influenza infection on host metabolic processes. Specifically, wild-type male and female mouse lung samples from mice infected with PR8 (H1N1) or both PR8 and a reinfection of X31 (H3N2) were analyzed. The LC/MS(liquid chromatography-mass spectrometry) based global metabolomics will be performed on the samples using hydrophilic interaction liquid chromatography to separate polar analytes from the tissues (Dettmer, Aronov, 2007). Metabolites impacted by influenza infection in all samples will be analyzed to compare male and female mice, as well as differences between PR8 infection ...


Interspecific Gene Flow Potentiates Adaptive Evolution In A Hybrid Zone Formed Between Pinus Strobiformis And Pinus Flexilis, Mitra Menon 2020 Virginia Commonwealth University

Interspecific Gene Flow Potentiates Adaptive Evolution In A Hybrid Zone Formed Between Pinus Strobiformis And Pinus Flexilis, Mitra Menon

Theses and Dissertations

Species range margins are often characterised by high degrees of habitat fragmentation resulting in low genetic diversity and higher gene flow from populations at the core of the species range. Interspecific gene flow from a closely related species with abutting range margins can increase standing genetic diversity and generate novel allelic combinations thereby alleviating limits to adaptive evolution in range margin populations. Hybridization driven interspecific gene flow has played a key role in the demographic history of several conifer due to their life history characteristics such as weak crossability barriers and long generation times. Nevertheless, demonstrating whether introgression is adaptive ...


De Novo Transcriptome Of Phakopsora Pachyrhizi Uncovers Putative Effector Repertoire During Infection, Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham 2020 Iowa State University

De Novo Transcriptome Of Phakopsora Pachyrhizi Uncovers Putative Effector Repertoire During Infection, Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham

Plant Pathology and Microbiology Publications

Phakopsora pachyrhizi, which causes Asian soybean rust (ASR), secretes effector proteins to manipulate host immunity and promote disease. To date, only a small number of effectors have been identified from transcriptome studies. To obtain a more comprehensive understanding of P. pachyrhizi candidate secreted effector proteins (CSEPs), we sequenced the transcriptome using two next-generation sequencing technologies. Short-read Illumina RNA-Seq data was used for reducing base-calling errors for long-read PacBio Iso-Seq. After initial de novo assemblies for RNA-seq and error correction of transcripts for Iso-Seq followed by filtering, we obtained 8,528, 27,647, 26,895, and 17,141 non-plant, non-soybean transcripts ...


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