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A Tissue Specific Transcriptomic, Proteomic And Phospho-Proteomic Atlas Of The Translational Machinery Of Arabidopsis Thaliana, Abdullah Salim 2021 University of Tennessee, Knoxville

A Tissue Specific Transcriptomic, Proteomic And Phospho-Proteomic Atlas Of The Translational Machinery Of Arabidopsis Thaliana, Abdullah Salim

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Gene expression encompasses the flow of genetic information from DNA to mRNA (transcription) and from mRNA to protein (translation) along with the regulatory mechanisms underlying these processes. Omics technologies offer a powerful toolset with which to study gene expression at each of these stages. A recently published dataset integrating transcriptomic, proteomic and phospho-proteomic measurements from 30 Arabidopsis thaliana tissues provides a unique resource to explore gene expression.1 The translational machinery (the ribosome, and its initiation, elongation, and termination factors) are a core component in gene expression. Defects in translation can be lethal or lead to major developmental defects and ...


Systemic Tissue And Cellular Disruption From Sars-Cov-2 Infection Revealed In Covid- 19 Autopsies And Spatial Omics Tissue Maps, Jiwoon Park, Jonathan Foox, Tyler Hether, Afshin Beheshti, Amanda Saravia-Butler, Urminder Singh, Eve Syrkin Wurtele, et al. 2021 Weill Cornell Medicine

Systemic Tissue And Cellular Disruption From Sars-Cov-2 Infection Revealed In Covid- 19 Autopsies And Spatial Omics Tissue Maps, Jiwoon Park, Jonathan Foox, Tyler Hether, Afshin Beheshti, Amanda Saravia-Butler, Urminder Singh, Eve Syrkin Wurtele, Et Al.

Genetics, Development and Cell Biology Publications

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney ...


The Mycobacterium Tuberculosis Transposon Sequencing Database (Mtbtndb): A Large-Scale Guide To Genetic Conditional Essentiality [Preprint], Adrian Jinich, Anisha Zaveri, Michael A. DeJesus, Emanuel Flores-Bautista, Clare M. Smith, Christopher M. Sassetti, Jeremy M. Rock, Sabine Ehrt, Dirk Schnappinger, Thomas R. Ioerger, Kyu Rhee 2021 Weill-Cornell Medical College

The Mycobacterium Tuberculosis Transposon Sequencing Database (Mtbtndb): A Large-Scale Guide To Genetic Conditional Essentiality [Preprint], Adrian Jinich, Anisha Zaveri, Michael A. Dejesus, Emanuel Flores-Bautista, Clare M. Smith, Christopher M. Sassetti, Jeremy M. Rock, Sabine Ehrt, Dirk Schnappinger, Thomas R. Ioerger, Kyu Rhee

University of Massachusetts Medical School Faculty Publications

Characterization of gene essentiality across different conditions is a useful approach for predicting gene function. Transposon sequencing (TnSeq) is a powerful means of generating genome-wide profiles of essentiality and has been used extensively in Mycobacterium tuberculosis (Mtb) genetic research. Over the past two decades, dozens of TnSeq screens have been published, yielding valuable insights into the biology of Mtb in vitro, inside macrophages, and in model host organisms. However, these Mtb TnSeq profiles are distributed across dozens of research papers within supplementary materials, which makes querying them cumbersome and assembling a complete and consistent synthesis of existing data challenging. Here ...


Stategra: Multi-Omics Data Integration - A Conceptual Scheme With A Bioinformatics Pipeline, Nuria Planell, Vincenzo Lagani, Patricia Sebastian-Leon, Frans van der Kloet, Ewoud Ewing, Nestoras Karathanasis, Arantxa Urdangarin, Imanol Arozarena, Maja Jagodic, Ioannis Tsamardinos, Sonia Tarazona, Ana Conesa, Jesper Tegner, David Gomez-Cabrero 2021 Universidad Pública de Navarra (UPNA)

Stategra: Multi-Omics Data Integration - A Conceptual Scheme With A Bioinformatics Pipeline, Nuria Planell, Vincenzo Lagani, Patricia Sebastian-Leon, Frans Van Der Kloet, Ewoud Ewing, Nestoras Karathanasis, Arantxa Urdangarin, Imanol Arozarena, Maja Jagodic, Ioannis Tsamardinos, Sonia Tarazona, Ana Conesa, Jesper Tegner, David Gomez-Cabrero

Computational Medicine Center Faculty Papers

Technologies for profiling samples using different omics platforms have been at the forefront since the human genome project. Large-scale multi-omics data hold the promise of deciphering different regulatory layers. Yet, while there is a myriad of bioinformatics tools, each multi-omics analysis appears to start from scratch with an arbitrary decision over which tools to use and how to combine them. Therefore, it is an unmet need to conceptualize how to integrate such data and implement and validate pipelines in different cases. We have designed a conceptual framework (STATegra), aiming it to be as generic as possible for multi-omics analysis, combining ...


A Benchmark And An Algorithm For Detecting Germline Transposon Insertions And Measuring De Novo Transposon Insertion Frequencies, Tianxiong Yu, Xiao Huang, Shengqian Dou, Xiaolu Tang, Shiqi Luo, William E. Theurkauf, Jian Lu, Zhiping Weng 2021 Tongji University

A Benchmark And An Algorithm For Detecting Germline Transposon Insertions And Measuring De Novo Transposon Insertion Frequencies, Tianxiong Yu, Xiao Huang, Shengqian Dou, Xiaolu Tang, Shiqi Luo, William E. Theurkauf, Jian Lu, Zhiping Weng

University of Massachusetts Medical School Faculty Publications

Transposons are genomic parasites, and their new insertions can cause instability and spur the evolution of their host genomes. Rapid accumulation of short-read whole-genome sequencing data provides a great opportunity for studying new transposon insertions and their impacts on the host genome. Although many algorithms are available for detecting transposon insertions, the task remains challenging and existing tools are not designed for identifying de novo insertions. Here, we present a new benchmark fly dataset based on PacBio long-read sequencing and a new method TEMP2 for detecting germline insertions and measuring de novo 'singleton' insertion frequencies in eukaryotic genomes. TEMP2 achieves ...


Pfred: A Computational Platform For Sirna And Antisense Oligonucleotides Design, Simone Sciabola, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert V. Stanton 2021 Biogen

Pfred: A Computational Platform For Sirna And Antisense Oligonucleotides Design, Simone Sciabola, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert V. Stanton

Open Access Publications by UMMS Authors

PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred ...


Molecular Mechanisms Regulating Optic Fissure Fusion During Zebrafish Eye Development, Megan Weaver 2021 University of Kentucky

Molecular Mechanisms Regulating Optic Fissure Fusion During Zebrafish Eye Development, Megan Weaver

Theses and Dissertations--Biology

Vertebrate retinal development requires timely and precise fusion of the optic fissure. Failure of this event leads to congenital vision impairment in the form of coloboma. Recent studies have suggested hyaloid vasculature to be involved in OF fusion. In order to examine this link, we analyzed optic fissure fusion and hyaloid vasculogenesis in the zebrafish pax2a noi mutant line. We first determined that pax2a-/- embryos fail to accumulate F-actin in the optic fissure prior to basement membrane (BM) degradation. Furthermore, using 3D and live imaging we observed reduced OF hyaloid vascularization in pax2a-/- embryos. When examining the connection between pax2a ...


Fmri Feature Extraction Model For Adhd Classification Using Convolutional Neural Network, Senuri De Silva, Sanuwani Udara Dayarathna, Gangani Ariyarathne, Dulani Meedeniya, Sampath Jayarathna 2021 Old Dominion University

Fmri Feature Extraction Model For Adhd Classification Using Convolutional Neural Network, Senuri De Silva, Sanuwani Udara Dayarathna, Gangani Ariyarathne, Dulani Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

Biomedical intelligence provides a predictive mechanism for the automatic diagnosis of diseases and disorders. With the advancements of computational biology, neuroimaging techniques have been used extensively in clinical data analysis. Attention deficit hyperactivity disorder (ADHD) is a psychiatric disorder, with the symptomology of inattention, impulsivity, and hyperactivity, in which early diagnosis is crucial to prevent unwelcome outcomes. This study addresses ADHD identification using functional magnetic resonance imaging (fMRI) data for the resting state brain by evaluating multiple feature extraction methods. The features of seed-based correlation (SBC), fractional amplitude of low-frequency fluctuation (fALFF), and regional homogeneity (ReHo) are comparatively applied to ...


Identification And Optimization Of Mirna Biomarkers For Body Mass Index (Bmi) Estimation In Forensic Samples, Jennifer J. Shealy 2021 Virginia Commonwealth University

Identification And Optimization Of Mirna Biomarkers For Body Mass Index (Bmi) Estimation In Forensic Samples, Jennifer J. Shealy

Theses and Dissertations

DNA profiles do not provide as much evidentiary value when either all known samples can be excluded or when there is no known suspect. DNA phenotyping is a technique used for investigative purposes to predict externally visible characteristics (EVCs) based on specific markers found in the genome. Most phenotyping panels are currently restricted to markers stable over a lifetime within an individual and are not able to predict environmental or metabolic impacts on EVCs. It is known that miRNA expression levels change due to environmental and metabolic factors, such as BMI, and research has proven associations between circulating plasma miRNAs ...


Systematic Evaluation Of Chromosome Conformation Capture Assays [Preprint], Betul Akgol-Oksuz, Liyan Yang, Sergey V. Venev, Nils Krietenstein, Krishna M. Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan M.J. Genga, Rene Maehr, Oliver J. Rando, Johan H. Gibcus, Job Dekker 2020 University of Massachusetts Medical School

Systematic Evaluation Of Chromosome Conformation Capture Assays [Preprint], Betul Akgol-Oksuz, Liyan Yang, Sergey V. Venev, Nils Krietenstein, Krishna M. Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan M.J. Genga, Rene Maehr, Oliver J. Rando, Johan H. Gibcus, Job Dekker

University of Massachusetts Medical School Faculty Publications

Chromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different ...


An Examination Of The Influence Of Multi-Scale Processes And Connectivity On The Population And Assemblage Dynamics Of Headwater Fishes, Josh P. Hubbell 2020 University of Southern Mississippi

An Examination Of The Influence Of Multi-Scale Processes And Connectivity On The Population And Assemblage Dynamics Of Headwater Fishes, Josh P. Hubbell

Dissertations

Typified by their branching pattern, headwaters are numerically abundant as the density of these habitats increases with increasing distance from the base of a dendritic river system. Connectivity among headwaters is complex, resulting in the spatial isolation of populations. Headwater specialists have evolved a suite of traits that permit these species to permanently reside within these habitats. The spatial configuration and connectivity of headwaters has repercussions for metapopulations and meta-assemblages. I investigated how multi-scale processes and connectivity influenced the patch occupancy, coexistence, movement ecology, population structure, and gene flow of headwater specialists. In chapter two, I used occupancy modeling to ...


Gene Set Testing By Distance Correlation, Sho-Hsien Su 2020 University of Arkansas, Fayetteville

Gene Set Testing By Distance Correlation, Sho-Hsien Su

Theses and Dissertations

Pathways are the functional building blocks of complex diseases such as cancers. Pathway-level studies may provide insights on some important biological processes. Gene set test is an important tool to study the differential expression of a gene set between two groups, e.g., cancer vs normal. The differential expression of a gene set could be due to the difference in mean, variability, or both. However, most existing gene set tests only target the mean difference but overlook other types of differential expression. In this thesis, we propose to use the recently developed distance correlation for gene set testing. To assess ...


Investigation Of Sulfur Cycling In Marine Sponge Cinachyrella Spp. From A South Florida Reef, Shelby K. Cain 2020 Nova Southeastern University

Investigation Of Sulfur Cycling In Marine Sponge Cinachyrella Spp. From A South Florida Reef, Shelby K. Cain

All HCAS Student Capstones, Theses, and Dissertations

Symbionts within marine sponges are actively participating in the biogeochemical cycles. Among them, the role of symbiont microbes in the sulfur cycle remains a mystery. This study measured the abundance of microbes within the genus Cinachyrella before and after exposure to hydrogen sulfide. A four-part study was conducted: a) five-hour drop experiments, b) vertical distribution experiments, c) five-hour uptake experiments, and d) long-term exposure experiments. The five-hour drop experiment utilized a microsensor to measure sulfide levels, which was lowered 1.0 mm every thirty minutes for a total of 5 hours. Three trials were performed, each with one sponge and ...


Evolved Bacterial Resistance Against Fluoropyrimidines Can Lower Chemotherapy Impact In The Caenorhabditis Elegans Host, Brittany Rosener, Serkan Sayin, Peter O. Oluoch, Aurian Garcia-Gonzalez, Hirotada Mori, Albertha J. M. Walhout, Amir Mitchell 2020 University of Massachusetts Medical School

Evolved Bacterial Resistance Against Fluoropyrimidines Can Lower Chemotherapy Impact In The Caenorhabditis Elegans Host, Brittany Rosener, Serkan Sayin, Peter O. Oluoch, Aurian Garcia-Gonzalez, Hirotada Mori, Albertha J. M. Walhout, Amir Mitchell

Open Access Publications by UMMS Authors

Metabolism of host-targeted drugs by the microbiome can substantially impact host treatment success. However, since many host-targeted drugs inadvertently hamper microbiome growth, repeated drug administration can lead to microbiome evolutionary adaptation. We tested if evolved bacterial resistance against host-targeted drugs alters their drug metabolism and impacts host treatment success. We used a model system of Caenorhabditis elegans, its bacterial diet, and two fluoropyrimidine chemotherapies. Genetic screens revealed that most of loss-of-function resistance mutations in Escherichia coli also reduced drug toxicity in the host. We found that resistance rapidly emerged in E. coli under natural selection and converged to a handful ...


Polerovirus Genomic Variation And Mechanisms Of Silencing Suppression By P0 Protein, Natalie Holste 2020 University of Nebraska-Lincoln

Polerovirus Genomic Variation And Mechanisms Of Silencing Suppression By P0 Protein, Natalie Holste

Dissertations and Theses in Biological Sciences

The family Luteoviridae consists of three genera: Luteovirus, Enamovirus, and Polerovirus. The genus Polerovirus contains 32 virus species. All are transmitted by aphids and can infect a wide variety of crops from cereals and wheat to cucurbits and peppers. However, little is known about how this wide range of hosts and vectors developed. In poleroviruses, aphid transmission and virion formation is mediated by the coat protein read-through domain (CPRT) while silencing suppression and phloem limitation is mediated by Protein 0 (P0)—a protein unique to poleroviruses. P0 gives poleroviruses a great advantage amongst plant viruses and diversifies polerovirus species, but ...


Pathway-Extended Gene Expression Signatures Integrate Novel Biomarkers That Improve Predictions Of Patient Responses To Kinase Inhibitors, Ashis Jem Bagchee-Clark, Eliseos J. Mucaki, Tyson Whitehead, Peter Rogan 2020 Western University

Pathway-Extended Gene Expression Signatures Integrate Novel Biomarkers That Improve Predictions Of Patient Responses To Kinase Inhibitors, Ashis Jem Bagchee-Clark, Eliseos J. Mucaki, Tyson Whitehead, Peter Rogan

Biochemistry Publications

No abstract provided.


Measuring Stability Of 3d Chromatin Conformations And Identifying Neuron Specific Chromatin Loops Associated With Schizophrenia Risk, Tyler M. Borrman 2020 University of Massachusetts Medical School

Measuring Stability Of 3d Chromatin Conformations And Identifying Neuron Specific Chromatin Loops Associated With Schizophrenia Risk, Tyler M. Borrman

GSBS Dissertations and Theses

The 23 pairs of chromosomes comprising the human genome are intricately folded within the nucleus of each cell in a manner that promotes efficient gene regulation and cell function. Consequently, active gene rich regions are compartmentally segregated from inactive gene poor regions of the genome. To better understand the mechanisms driving compartmentalization we investigated what would occur if this system was disrupted. By digesting the genome to varying sizes and analyzing the fragmented 3D structure over time, our work revealed essential laws governing nuclear compartmentalization.

At a finer resolution within compartments, chromatin forms loop structures capable of regulating gene expression ...


Progressive Cactus Is A Multiple-Genome Aligner For The Thousand-Genome Era, Joel Armstrong, Elinor K. Karlsson, Guojie Zhang, Benedict Paten 2020 University of California, Santa Cruz

Progressive Cactus Is A Multiple-Genome Aligner For The Thousand-Genome Era, Joel Armstrong, Elinor K. Karlsson, Guojie Zhang, Benedict Paten

University of Massachusetts Medical School Faculty Publications

New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies(1-3). For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database(4) increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies(5) are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes ...


A Comparative Genomics Multitool For Scientific Discovery And Conservation, Zoonomia Consortium, Diane P. Genereux, Manuel Garber, Kerstin Lindblad-Toh, Elinor K. Karlsson 2020 Zoonomia Consortium

A Comparative Genomics Multitool For Scientific Discovery And Conservation, Zoonomia Consortium, Diane P. Genereux, Manuel Garber, Kerstin Lindblad-Toh, Elinor K. Karlsson

Open Access Publications by UMMS Authors

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia ...


Daglogo: An R/Bioconductor Package For Identifying And Visualizing Differential Amino Acid Group Usage In Proteomics Data, Jianhong Ou, Haibo Liu, Niraj K. Nirala, Alexey Stukalov, Usha Acharya, Michael R. Green, Lihua Julie Zhu 2020 University of Massachusetts Medical School

Daglogo: An R/Bioconductor Package For Identifying And Visualizing Differential Amino Acid Group Usage In Proteomics Data, Jianhong Ou, Haibo Liu, Niraj K. Nirala, Alexey Stukalov, Usha Acharya, Michael R. Green, Lihua Julie Zhu

Open Access Publications by UMMS Authors

Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. To fill this gap, we ...


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