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3,404 full-text articles. Page 1 of 130.

A Plasmodium‐Like Virulence Effector Of The Soybean Cyst Nematode Suppresses Plant Innate Immunity, Jason B. Noon, Mingsheng Qi, Danielle N. Sill, Usha Muppirala, Sebastian Eves-van den Akker, Thomas R. Maier, Drena Dobbs, Melissa G. Mitchum, Tarek Hewezi, Thomas J. Baum 2019 Iowa State University

A Plasmodium‐Like Virulence Effector Of The Soybean Cyst Nematode Suppresses Plant Innate Immunity, Jason B. Noon, Mingsheng Qi, Danielle N. Sill, Usha Muppirala, Sebastian Eves-Van Den Akker, Thomas R. Maier, Drena Dobbs, Melissa G. Mitchum, Tarek Hewezi, Thomas J. Baum

Thomas Baum

• Heterodera glycines, the soybean cyst nematode, delivers effector proteins into soybean roots to initiate and maintain an obligate parasitic relationship. HgGLAND18 encodes a candidate H. glycines effector and is expressed throughout the infection process.

• We used a combination of molecular, genetic, bioinformatic and phylogenetic analyses to determine the role of HgGLAND18 during H. glycines infection.

• HgGLAND18 is necessary for pathogenicity in compatible interactions with soybean. The encoded effector strongly suppresses both basal and hypersensitive cell death innate immune responses, and immunosuppression requires the presence and coordination between multiple protein domains. The N-terminal domain in HgGLAND18 contains unique sequence similarity to ...


Tal Effector-Nucleotide Targeter (Tale-Nt) 2.0: Tools For Tal Effector Design And Target Prediction, Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. VanDyk, Adam J. Bogdanove 2019 Iowa State University

Tal Effector-Nucleotide Targeter (Tale-Nt) 2.0: Tools For Tal Effector Design And Target Prediction, Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. Vandyk, Adam J. Bogdanove

Nicholas J. Booher

Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0;https://boglab.plp ...


Molecular Phylogeny Implemented In An Introductory Plant Classification Course, Chao Cai, Jo Ann Banks 2019 Purdue University

Molecular Phylogeny Implemented In An Introductory Plant Classification Course, Chao Cai, Jo Ann Banks

Libraries Faculty and Staff Presentations

Plant classification is one of the core components in undergraduate programs related to plant sciences. Traditionally plant classification courses primarily introduce morphology-based taxonomy because of practical needs in the field. However, the publication of new plant classification systems by Angiosperm Phylogeny Group (APG) using molecular phylogeny methods leads to the trends of using molecular evidence (DNA barcode) for plant identification. In our introductory plant classification course, we included a two-week module (lectures and labs) to introduce key concepts and fundamental skills in molecular phylogeny. Week 1 included concepts of evolutionary tree thinking, data mining in NCBI using BLAST search, and ...


Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun 2019 Illinois State University

Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley 2019 Illinois State University

Network Reconstruction Using Computational Algebra And Gene Knockouts, Matthew Macauley

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Loop Homology Of Bi-Secondary Structures, Andrei Bura 2019 Illinois State University

Loop Homology Of Bi-Secondary Structures, Andrei Bura

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


The Energy-Spectrum Of Bicompatible Sequences, Wenda Huang 2019 Illinois State University

The Energy-Spectrum Of Bicompatible Sequences, Wenda Huang

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


On An Enhancement Of Rna Probing Data Using Information Theory, Thomas J.X. Li, Christian M. Reidys 2019 University of Virginia

On An Enhancement Of Rna Probing Data Using Information Theory, Thomas J.X. Li, Christian M. Reidys

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Investigating The Dispersal Of Antibiotic Resistance Associated Genes From Manure Application To Soil And Drainage Waters In Simulated Agricultural Farmland Systems, Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe 2019 Iowa State University

Investigating The Dispersal Of Antibiotic Resistance Associated Genes From Manure Application To Soil And Drainage Waters In Simulated Agricultural Farmland Systems, Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe

Michelle L. Soupir

Manure from animals that have been treated with antibiotics is often used to fertilize agricultural soils and its application has previously been shown to enrich for genes associated with antibiotic resistance in agroecosystems. To investigate the magnitude of this effect, we designed a column experiment simulating manure-treated agricultural soil that utilizes artificial subsurface drainage to determine the duration and extent which this type of manure fertilization impacts the set of genes associated with antibiotic resistance in drainage water. We classified ARGs in manure-treated drainage effluent water by its source of origin. Overall, we found that 61% and 7% of the ...


Investigating The Dispersal Of Antibiotic Resistance Associated Genes From Manure Application To Soil And Drainage Waters In Simulated Agricultural Farmland Systems, Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe 2019 Iowa State University

Investigating The Dispersal Of Antibiotic Resistance Associated Genes From Manure Application To Soil And Drainage Waters In Simulated Agricultural Farmland Systems, Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe

Adina Howe

Manure from animals that have been treated with antibiotics is often used to fertilize agricultural soils and its application has previously been shown to enrich for genes associated with antibiotic resistance in agroecosystems. To investigate the magnitude of this effect, we designed a column experiment simulating manure-treated agricultural soil that utilizes artificial subsurface drainage to determine the duration and extent which this type of manure fertilization impacts the set of genes associated with antibiotic resistance in drainage water. We classified ARGs in manure-treated drainage effluent water by its source of origin. Overall, we found that 61% and 7% of the ...


Genome-Wide Discovery Of Missing Genes In Biological Pathways Of Prokaryotes., Yong Chen, Fenglou Mao, Guojun Li, Ying Xu 2019 Rowan University

Genome-Wide Discovery Of Missing Genes In Biological Pathways Of Prokaryotes., Yong Chen, Fenglou Mao, Guojun Li, Ying Xu

Yong Chen

BACKGROUND: Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping approaches is that the mapped pathway models are constrained by the composition of the template pathways, e.g., some genes in a target pathway may not have corresponding genes in the template pathways, the so-called "missing gene" problem.

METHODS: We present a novel pathway-expansion method for identifying additional genes that are possibly involved in a target pathway after pathway mapping, to fill holes caused by missing genes as well as to expand ...


Investigating The Dispersal Of Antibiotic Resistance Associated Genes From Manure Application To Soil And Drainage Waters In Simulated Agricultural Farmland Systems, Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe 2019 Iowa State University

Investigating The Dispersal Of Antibiotic Resistance Associated Genes From Manure Application To Soil And Drainage Waters In Simulated Agricultural Farmland Systems, Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe

Agricultural and Biosystems Engineering Publications

Manure from animals that have been treated with antibiotics is often used to fertilize agricultural soils and its application has previously been shown to enrich for genes associated with antibiotic resistance in agroecosystems. To investigate the magnitude of this effect, we designed a column experiment simulating manure-treated agricultural soil that utilizes artificial subsurface drainage to determine the duration and extent which this type of manure fertilization impacts the set of genes associated with antibiotic resistance in drainage water. We classified ARGs in manure-treated drainage effluent water by its source of origin. Overall, we found that 61% and 7% of the ...


Chromatin Digestion By The Chemotherapeutic Agent Bleomycin Produces Nucleosome And Transcription Factor Footprinting Patterns Similar To Micrococcal Nuclease, Joshua Michael Stolz 2019 Rowan University

Chromatin Digestion By The Chemotherapeutic Agent Bleomycin Produces Nucleosome And Transcription Factor Footprinting Patterns Similar To Micrococcal Nuclease, Joshua Michael Stolz

Theses and Dissertations

Bleomycin (BLM), a glycopeptide antibiotic commonly used in chemotherapeutic treatments, has been shown to produce single and double stranded DNA breaks. Subsequent analysis of DNA fragmentation patterns has demonstrated preferential digestion of chromatin in the TSS of active genes and the ability to produce nucleosome-sized fragments within intact chromatin. Nucleosome positioning plays a critical role in the regulation of gene activation. Currently, micrococcal nuclease (MNase) is used as the standard for mapping the position of nucleosomes in the genome. In order to identify whether BLM can be used as an effective nucleosome-mapping agent, BLM was used to digest chromatin in ...


Diverse Repertoire Of Human Adipocyte Subtypes Develops From Transcriptionally Distinct Mesenchymal Progenitor Cells, So Yun Min, Anand Desai, Zinger Yang, Agastya Sharma, Tiffany DeSouza, Ryan Genga, Alper Kucukural, Lawrence M. Lifshitz, Soren Nielsen, Camilla Scheele, Rene Maehr, Manuel Garber, Silvia Corvera 2019 University of Massachusetts Medical School

Diverse Repertoire Of Human Adipocyte Subtypes Develops From Transcriptionally Distinct Mesenchymal Progenitor Cells, So Yun Min, Anand Desai, Zinger Yang, Agastya Sharma, Tiffany Desouza, Ryan Genga, Alper Kucukural, Lawrence M. Lifshitz, Soren Nielsen, Camilla Scheele, Rene Maehr, Manuel Garber, Silvia Corvera

Open Access Articles

Single-cell sequencing technologies have revealed an unexpectedly broad repertoire of cells required to mediate complex functions in multicellular organisms. Despite the multiple roles of adipose tissue in maintaining systemic metabolic homeostasis, adipocytes are thought to be largely homogenous with only 2 major subtypes recognized in humans so far. Here we report the existence and characteristics of 4 distinct human adipocyte subtypes, and of their respective mesenchymal progenitors. The phenotypes of these distinct adipocyte subtypes are differentially associated with key adipose tissue functions, including thermogenesis, lipid storage, and adipokine secretion. The transcriptomic signature of "brite/beige" thermogenic adipocytes reveals mechanisms for ...


Creating, Modeling, And Visualizing Metabolic Networks, Julie A. Dickerson, Daniel Berleant, Pan Du, Jing Ding, Carol M. Foster, Ling Li, Eve Syrkin Wurtele 2019 Iowa State University

Creating, Modeling, And Visualizing Metabolic Networks, Julie A. Dickerson, Daniel Berleant, Pan Du, Jing Ding, Carol M. Foster, Ling Li, Eve Syrkin Wurtele

Ling Li

Metabolic networks combine metabolism and regulation. These complex networks are difficult to understand and create due to the diverse types of information that need to be represented. This chapter describes a suite of interlinked tools for developing, displaying, and modeling metabolic networks. The metabolic network interactions database, MetNetDB, contains information on regulatory and metabolic interactions derived from a combination of web databases and input from biologists in their area of expertise. PathBinderA mines the biological “literaturome” by searching for new interactions or supporting evidence for existing interactions in metabolic networks. Sentences from abstracts are ranked in terms of the likelihood ...


Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus 2019 University of New Orleans

Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus

University of New Orleans Theses and Dissertations

Proteins are the fundamental machinery that enables the functions of life. It is critical to understand them not just for basic biology, but also to enable medical advances. The field of protein structure prediction is concerned with developing computational techniques to predict protein structure and function from a protein’s amino acid sequence, encoded for directly in DNA, alone. Despite much progress since the first computational models in the late 1960’s, techniques for the prediction of protein structure still cannot reliably produce structures of high enough accuracy to enable desired applications such as rational drug design. Protein structure refinement ...


Response Of Early Life Stage Homarus Americanus To Ocean Warming And Acidification: An Interpopulation Comparison, Maura K. Niemisto 2019 University of Maine

Response Of Early Life Stage Homarus Americanus To Ocean Warming And Acidification: An Interpopulation Comparison, Maura K. Niemisto

Electronic Theses and Dissertations

Anthropogenic carbon released into the atmosphere is driving rapid, concurrent increases in temperature and acidity across the world’s oceans, most prominently in northern latitudes. The geographic range of the iconic American lobster (Homarus americanus) spans a steep thermal gradient and one of the most rapidly warming oceanic environments. Understanding the interactive effects of ocean warming and acidification on this species’ most vulnerable early life stages is important to predict its response to climate change on a stage-specific and population level. This study compares the responses of lobster larvae from two sub-populations spanning New England’s north-south temperature gradient (southern ...


P53r245w Mutation Elicits Metastatic Phenotype In Pten Deficient Prostate Cancer, Ky Pham 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

P53r245w Mutation Elicits Metastatic Phenotype In Pten Deficient Prostate Cancer, Ky Pham

UT GSBS Dissertations and Theses (Open Access)

Trp53 mutations are the most frequent genetic alterations in prostate cancer and are associated with more aggressive disease and worse overall survival. The majority of Trp53 mutations in prostate cancer are missense mutations, resulting in amino acid substitutions with profound effect. In addition to the loss of wild type function, missense mutations in Trp53 result in a gain-of-function (GOF) phenotype. This GOF phenotype confers biologic advantages to the tumor cells, enabling them to metastasize and invade distant organs. In this study, we generated mice carrying a conditional prostate-specific p53R245W mutant and Pten deletion to access the role of this common ...


Designing And Sample Size Calculation In Presence Of Heterogeneity In Biological Studies Involving High-Throughput Data., Sudhir Srivastava 2019 University of Louisville

Designing And Sample Size Calculation In Presence Of Heterogeneity In Biological Studies Involving High-Throughput Data., Sudhir Srivastava

Electronic Theses and Dissertations

The designing and determination of sample size are important for conducting high-throughput biological experiments such as proteomics experiments and RNA-Seq expression studies, thus leading to better understanding of complex mechanisms underlying various biological processes. The variations in the biological data or technical approaches to data collection lead to heterogeneity for the samples under study. We critically worked on the issues of technical and biological heterogeneity. The quantitative measurements based on liquid chromatography (LC) coupled with mass spectrometry (MS) often suffer from the problem of missing values (MVs) and data heterogeneity. We considered a proteomics data set generated from human kidney ...


Intron And Small Rna Localization In Mammalian Neurons, Harleen Saini 2019 University of Massachusetts Medical School

Intron And Small Rna Localization In Mammalian Neurons, Harleen Saini

GSBS Dissertations and Theses

RNA molecules are diverse in form and function. They include messenger RNAs (mRNAs) that are templates for proteins, splice products such as introns that can generate functional noncoding RNAs, and a slew of smaller RNAs such as transfer RNAs (tRNAs) that help decode mRNAs into proteins. RNAs can show distinct patterns of subcellular localization that play an important role in protein localization. However, RNA distribution in cells is incompletely understood, with prior studies focusing primarily on RNAs that are long (>200 nucleotides), fully processed, and polyadenylated. We examined the distribution of RNAs in neurons. Neuronal compartments can be separated by ...


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