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The Trauma Of Head Injury, 2020 DePaul University

The Trauma Of Head Injury

DePaul Magazine

Thanks to the vision and leadership of Vincent de Paul Professor of Biological Sciences Dorothy Kozlowski, who has teamed with scientists and researchers across the country, DePaul is playing an instrumental role in advancing our understanding of the speci­fic causes and e‑ffects of traumatic brain injury (TBI). In collaboration with colleagues at DePaul partner institution Rosalind Franklin University of Medicine and Science, Kozlowski developed a novel animal model to study the connection between repeat concussions and long-term health problems. Some of the research includes looking at learning and memory on the cellular level for those with Alzheimer’s ...


Biofilm Structure Promotes Coexistence Of Phage-Resistant And Phage-Susceptible Bacteria, Emilia L. Simmons, Matthew C. Bond, Britt Koskella, Knut Drescher, Vanni Bucci, Carey D. Nadell 2020 Dartmouth College

Biofilm Structure Promotes Coexistence Of Phage-Resistant And Phage-Susceptible Bacteria, Emilia L. Simmons, Matthew C. Bond, Britt Koskella, Knut Drescher, Vanni Bucci, Carey D. Nadell

Open Access Articles

Encounters among bacteria and their viral predators (bacteriophages) are among the most common ecological interactions on Earth. These encounters are likely to occur with regularity inside surface-bound communities that microbes most often occupy in natural environments. Such communities, termed biofilms, are spatially constrained: interactions become limited to near neighbors, diffusion of solutes and particulates can be reduced, and there is pronounced heterogeneity in nutrient access and physiological state. It is appreciated from prior theoretical work that phage-bacteria interactions are fundamentally different in spatially structured contexts, as opposed to well-mixed liquid culture. Spatially structured communities are predicted to promote the protection ...


Genome Diversity And The Origin Of The Arabian Horse, Elissa J. Cosgrove, Raheleh Sadeghi, Florencia Schlamp, Heather M. Holl, Mohammad Moradi-Shahrbabak, Seyed Reza Miraei-Ashtiani, Salma Abdalla, Ben Shykind, Mats H. T. Troedsson, Monika Stefaniuk-Szmukier, Anil Prabhu, Stefania Bucca, Monika Bugno-Poniewierska, Barbara Wallner, Joel Malek, Donald C. Miller, Andrew G. Clark, Douglas F. Antczak, Samantha A. Brooks 2020 Cornell University

Genome Diversity And The Origin Of The Arabian Horse, Elissa J. Cosgrove, Raheleh Sadeghi, Florencia Schlamp, Heather M. Holl, Mohammad Moradi-Shahrbabak, Seyed Reza Miraei-Ashtiani, Salma Abdalla, Ben Shykind, Mats H. T. Troedsson, Monika Stefaniuk-Szmukier, Anil Prabhu, Stefania Bucca, Monika Bugno-Poniewierska, Barbara Wallner, Joel Malek, Donald C. Miller, Andrew G. Clark, Douglas F. Antczak, Samantha A. Brooks

Veterinary Science Faculty Publications

The Arabian horse, one of the world's oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region ...


A Synthesis Of Bacterial And Archaeal Phenotypic Trait Data., Joshua S Madin, Daniel A Nielsen, Maria Brbic, Ross Corkrey, David Danko, Kyle Edwards, Martin K M Engqvist, Noah Fierer, Jemma L Geoghegan, Michael Gillings, Nikos C Kyrpides, Elena Litchman, Christopher E Mason, Lisa Moore, Søren L Nielsen, Ian T Paulsen, Nathan D Price, T B K Reddy, Matthew A Richards, Eduardo P C Rocha, Thomas M Schmidt, Heba Shaaban, Maulik Shukla, Fran Supek, Sasha G Tetu, Sara Vieira-Silva, Alice R Wattam, David A Westfall, Mark Westoby 2020 Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA.

A Synthesis Of Bacterial And Archaeal Phenotypic Trait Data., Joshua S Madin, Daniel A Nielsen, Maria Brbic, Ross Corkrey, David Danko, Kyle Edwards, Martin K M Engqvist, Noah Fierer, Jemma L Geoghegan, Michael Gillings, Nikos C Kyrpides, Elena Litchman, Christopher E Mason, Lisa Moore, Søren L Nielsen, Ian T Paulsen, Nathan D Price, T B K Reddy, Matthew A Richards, Eduardo P C Rocha, Thomas M Schmidt, Heba Shaaban, Maulik Shukla, Fran Supek, Sasha G Tetu, Sara Vieira-Silva, Alice R Wattam, David A Westfall, Mark Westoby

Articles, Abstracts, and Reports

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures ...


Portable Fluorescence Illuminator, Katherine Hui, Emran Baryal, Emmett Lambert 2020 California Polytechnic State University, San Luis Obispo

Portable Fluorescence Illuminator, Katherine Hui, Emran Baryal, Emmett Lambert

Mechanical Engineering

This Final Design Review (FDR) document outlines the senior design project implemented by a team of three mechanical engineering students at California Polytechnic State University, San Luis Obispo for a professor in the biochemistry and chemistry department, Dr. Javin Oza. The project involved designing and manufacturing a portable ultraviolet fluorescence illuminator that will indicate the fluorescent glow of biomaterials for viewing purposes. The goal was to create a portable product out of recyclable material that can be used in field applications and increase accessibility to affordable science equipment. The initial sponsor and user interviews, technical background research, product research, and ...


Dynamics Of The 4d Genome During In Vivo Lineage Specification And Differentiation, A. Marieke Oudelaar, Daniel Hidalgo, Merav Socolovsky, Douglas R. Higgs, Jim R. Hughes 2020 University of Oxford

Dynamics Of The 4d Genome During In Vivo Lineage Specification And Differentiation, A. Marieke Oudelaar, Daniel Hidalgo, Merav Socolovsky, Douglas R. Higgs, Jim R. Hughes

Open Access Articles

Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of ...


Interdisciplinary Profile: An Established Chemist Journeys Into Different Disciplines., James R Heath 2020 Institute for Systems Biology, Seattle, WA, USA

Interdisciplinary Profile: An Established Chemist Journeys Into Different Disciplines., James R Heath

Articles, Abstracts, and Reports

No abstract provided.


Sequential Wnt Agonist Then Antagonist Treatment Accelerates Tissue Repair And Minimizes Fibrosis., Xiao-Jun Tian, Dong Zhou, Haiyan Fu, Rong Zhang, Xiaojie Wang, Sui Huang, Youhua Liu, Jianhua Xing 2020 Institute for Systems Biology, Seattle, Washington, USA.

Sequential Wnt Agonist Then Antagonist Treatment Accelerates Tissue Repair And Minimizes Fibrosis., Xiao-Jun Tian, Dong Zhou, Haiyan Fu, Rong Zhang, Xiaojie Wang, Sui Huang, Youhua Liu, Jianhua Xing

Articles, Abstracts, and Reports

Tissue fibrosis compromises organ function and occurs as a potential long-term outcome in response to acute tissue injuries. Currently, lack of mechanistic understanding prevents effective prevention and treatment of the progression from acute injury to fibrosis. Here, we combined quantitative experimental studies with a mouse kidney injury model and a computational approach to determine how the physiological consequences are determined by the severity of ischemia injury and to identify how to manipulate Wnt signaling to accelerate repair of ischemic tissue damage while minimizing fibrosis. The study reveals that memory of prior injury contributes to fibrosis progression and ischemic preconditioning reduces ...


From Tank To Treatment: Modeling Melanoma In Zebrafish, William Tyler Frantz, Craig J. Ceol 2020 University of Massachusetts Medical School

From Tank To Treatment: Modeling Melanoma In Zebrafish, William Tyler Frantz, Craig J. Ceol

Open Access Articles

Melanoma is the deadliest form of skin cancer and one of few cancers with a growing incidence. A thorough understanding of its pathogenesis is fundamental to developing new strategies to combat mortality and morbidity. Zebrafish-due in large part to their tractable genetics, conserved pathways, and optical properties-have emerged as an excellent system to model melanoma. Zebrafish have been used to study melanoma from a single tumor initiating cell, through metastasis, remission, and finally into relapse. In this review, we examine seminal zebrafish studies that have advanced our understanding of melanoma.


Correction To: Small Molecule Kras Agonist For Mutant Kras Cancer Therapy., Ke Xu, Dongkyoo Park, Andrew T Magis, Jun Zhang, Wei Zhou, Gabriel L Sica, Suresh S Ramalingam, Walter J Curran, Xingming Deng 2020 Institute for Systems Biology, Seattle, WA, 98109, USA.

Correction To: Small Molecule Kras Agonist For Mutant Kras Cancer Therapy., Ke Xu, Dongkyoo Park, Andrew T Magis, Jun Zhang, Wei Zhou, Gabriel L Sica, Suresh S Ramalingam, Walter J Curran, Xingming Deng

Articles, Abstracts, and Reports

An amendment to this paper has been published and can be accessed via the original article.


Status Of The Blackstripe (Fundulus Notatus) And Blackspotted (F. Olivaceus) Topminnows In The Ozark Uplands Of Central Missouri, Nathaniel Steffensmeier, Naznin Sultana Remex, Robert Hrabik, David D. Duvernell 2020 The Ohio State University

Status Of The Blackstripe (Fundulus Notatus) And Blackspotted (F. Olivaceus) Topminnows In The Ozark Uplands Of Central Missouri, Nathaniel Steffensmeier, Naznin Sultana Remex, Robert Hrabik, David D. Duvernell

Southeastern Fishes Council Proceedings

The topminnow species Fundulus notatus and F. olivaceus have broadly overlapping geographic distributions that extend throughout much of the central and southern United States. In the northern portion of their respective ranges, in Missouri, the regional distributions of the two species coincide largely with recognized ecoregions. In the unglaciated southern half of Missouri, F. olivaceus is distributed throughout Ozark upland habitats while F. notatus is abundant in marginal large river and prairie habitats along the Ozark borders. An exception to this partitioning is the historical report of abundant F. notatus in the Bourbeuse and upper Meramec River drainages within the ...


A Cas9 With Pam Recognition For Adenine Dinucleotides, Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo 2020 Massachusetts Institute of Technology

A Cas9 With Pam Recognition For Adenine Dinucleotides, Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo

Open Access Articles

CRISPR-associated (Cas) DNA-endonucleases are remarkably effective tools for genome engineering, but have limited target ranges due to their protospacer adjacent motif (PAM) requirements. We demonstrate a critical expansion of the targetable sequence space for a type II-A CRISPR-associated enzyme through identification of the natural 5[Formula: see text]-NAAN-3[Formula: see text] PAM preference of Streptococcus macacae Cas9 (SmacCas9). To achieve efficient editing activity, we graft the PAM-interacting domain of SmacCas9 to its well-established ortholog from Streptococcus pyogenes (SpyCas9), and further engineer an increased efficiency variant (iSpyMac) for robust genome editing activity. We establish that our hybrids can target all ...


Combinatorial Pharmacogenomic Algorithm Is Predictive Of Citalopram And Escitalopram Metabolism In Patients With Major Depressive Disorder, Richard C. Shelton, Anthony J. Rothschild 2020 University of Alabama, Birmingham

Combinatorial Pharmacogenomic Algorithm Is Predictive Of Citalopram And Escitalopram Metabolism In Patients With Major Depressive Disorder, Richard C. Shelton, Anthony J. Rothschild

Psychiatry Publications

Pharmacogenomic tests used to guide clinical treatment for major depressive disorder (MDD) must be thoroughly validated. One important assessment of validity is the ability to predict medication blood levels, which reflect altered metabolism. Historically, the metabolic impact of individual genes has been evaluated; however, we now know that multiple genes are often involved in medication metabolism. Here, we evaluated the ability of individual pharmacokinetic genes (CYP2C19, CYP2D6, CYP3A4) and a combinatorial pharmacogenomic test (GeneSight Psychotropic(R); weighted assessment of all three genes) to predict citalopram/escitalopram blood levels in patients with MDD. Patients from the Genomics Used to Improve DEpression ...


Statistical Inference Of Adaptation At Multiple Genomic Scales Using Supervised Classification And A Hidden Markov Model, Lauren A. Sugden 2020 Duquesne University

Statistical Inference Of Adaptation At Multiple Genomic Scales Using Supervised Classification And A Hidden Markov Model, Lauren A. Sugden

Biology and Medicine Through Mathematics Conference

No abstract provided.


Genetic Interactions And Maternal Genes Modulate Congenital Heart Disease Risk, Ehiole Ogboma Akhirome 2020 Washington University in St. Louis

Genetic Interactions And Maternal Genes Modulate Congenital Heart Disease Risk, Ehiole Ogboma Akhirome

Arts & Sciences Electronic Theses and Dissertations

Congenital heart disease (CHD) is the most common congenital anomaly, which makes it a leading cause of infant mortality. Congenital heart defects are a cluster of distinct developmental malformations that affect the vasculature, musculature and organization of the heart, each with varying clinical severity. Although medical and surgical advances have reduced CHD mortality in newborns and children, these patients grow up and many experience serious morbidity and early mortality. The first step toward reducing this burden is to understand the causes of CHD. Surprisingly, environmental insults and de novo mutations are estimated to explain less than one-third of CHD cases ...


Dendritic Cell Development And Function, Vivek Durai 2020 Washington University in St. Louis

Dendritic Cell Development And Function, Vivek Durai

Arts & Sciences Electronic Theses and Dissertations

Dendritic cells (DCs) are a group of immune cells that include both classical dendritic cells (cDCs) and plasmacytoid dendritic cells (pDCs). cDCs are further comprised of two distinct subsets, cDC1s and cDC2s, which play critical roles in the initiation of innate and adaptive immune responses. Understanding how these lineages develop and function is therefore paramount. All DCs require the receptor tyrosine kinase Flt3 and its ligand Flt3L for their development, but the loss of Flt3L in mice leads to a more severe DC deficiency than does the loss of Flt3. This has led to speculation that Flt3L can bind to ...


Developing Tools For Identifying Tissue-Specific Epigenetic Marks And Predicting Dna Hydroxy/Methylation, Yu He 2020 Washington University in St. Louis

Developing Tools For Identifying Tissue-Specific Epigenetic Marks And Predicting Dna Hydroxy/Methylation, Yu He

Arts & Sciences Electronic Theses and Dissertations

A single genome can derive phenotypically unique cell types through various epigenetic modifications that instruct specific gene expression patterns. Histone modifications, DNA methylation, and DNA hydroxymetylation are the most common epigenetic modifications. To understand the mechanisms how these epigenetic modifications regulate gene expression, one often needs to map these marks genome-wide through profiling methods. Firstly, for histone modifications, Roadmap Epigenomics Consortium generated The Human Reference Epigenome Map, containing thousands of genome-wide histone modification datasets that describe epigenomes of a variety of different human tissue and cell types. This map has allowed investigators to obtain a much deeper and more comprehensive ...


Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath 2020 Children's Mercy Kansas City

Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath

Research Days

No abstract provided.


Identification Of Clinically-Relevant Sequence Variants Within The Human Reference Genome, Lisa A. Lansdon 2020 Children's Mercy Kansas City

Identification Of Clinically-Relevant Sequence Variants Within The Human Reference Genome, Lisa A. Lansdon

Research Days

No abstract provided.


Tim, A Targeted Insertional Mutagenesis Method Utilizing Crispr/Cas9 In Chlamydomonas Reinhardtii, Tyler Picariello, Yuqing Hou, Tomohiro Kubo, Nathan A. McNeill, Haru-Aki Yanagisawa, Toshiyuki Oda, George B. Witman 2020 University of Massachusetts Medical School

Tim, A Targeted Insertional Mutagenesis Method Utilizing Crispr/Cas9 In Chlamydomonas Reinhardtii, Tyler Picariello, Yuqing Hou, Tomohiro Kubo, Nathan A. Mcneill, Haru-Aki Yanagisawa, Toshiyuki Oda, George B. Witman

Radiology Publications

Generation and subsequent analysis of mutants is critical to understanding the functions of genes and proteins. Here we describe TIM, an efficient, cost-effective, CRISPR-based targeted insertional mutagenesis method for the model organism Chlamydomonas reinhardtii. TIM utilizes delivery into the cell of a Cas9-guide RNA (gRNA) ribonucleoprotein (RNP) together with exogenous double-stranded (donor) DNA. The donor DNA contains gene-specific homology arms and an integral antibiotic-resistance gene that inserts at the double-stranded break generated by Cas9. After optimizing multiple parameters of this method, we were able to generate mutants for six out of six different genes in two different cell-walled strains with ...


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