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A Persistence Detector For Metabolic Network Rewiring In An Animal, Jote T. Bulcha, Gabrielle E. Giese, Zulfikar Ali, Yong-Uk Lee, Melissa D. Walker, Amy D. Holdorf, L. Safak Yilmaz, Robert C. Brewster, Albertha J. M. Walhout 2018 University of Massachusetts Medical School

A Persistence Detector For Metabolic Network Rewiring In An Animal, Jote T. Bulcha, Gabrielle E. Giese, Zulfikar Ali, Yong-Uk Lee, Melissa D. Walker, Amy D. Holdorf, L. Safak Yilmaz, Robert C. Brewster, Albertha J. M. Walhout

University of Massachusetts Medical School Faculty Publications

Persistence detection is a mechanism that ensures a physiological output is only executed when the relevant input is sustained. Gene regulatory network circuits known as coherent type 1 feed forward loops (FFLs) with an AND-logic gate have been proposed to generate persistence detection. In such circuits two transcription factors (TFs) are both required to activate target genes and one of the two TFs activates the other. While numerous FFLs have been identified, examples of actual persistence detectors have only been described for bacteria. Here, we discover a transcriptional persistence detector in Caenorhabditis elegans involving the nuclear hormone receptors nhr-10 and ...


Computational Analysis Of Genomic Variants Affecting Predicted Microrna:Target Interactions In Prostate Cancer., Angélica Paola Hernández Pérez 2018 Keck Graduate Institute, KGI

Computational Analysis Of Genomic Variants Affecting Predicted Microrna:Target Interactions In Prostate Cancer., Angélica Paola Hernández Pérez

KGI Theses and Dissertations

Prostate cancer (PCa) is the most common cancer of men in the United States and is third only to lung and colon as a cause of cancer death. Clinical behavior of the disease is variable and the combination of prostate-specific antigen (PSA) screening and Gleason score staging are currently the best available molecular and pathology tools to predict outcomes. Cancer biology research establishes microRNAs (miRNAs) as key molecular components in both normal and pathological states. Thus, elucidating miRNAs perturbed by genomic alterations will expand our understanding of the molecular taxonomy of PCa with the aim to complement current practices in ...


Drosophila Species Learn Dialects Through Communal Living, Balint Z. Kacsoh, Julianna Bozler, Giovanni Bosco 2018 Dartmouth College

Drosophila Species Learn Dialects Through Communal Living, Balint Z. Kacsoh, Julianna Bozler, Giovanni Bosco

Open Dartmouth: Published works by Dartmouth faculty

Many species are able to share information about their environment by communicating through auditory, visual, and olfactory cues. In Drosophila melanogaster, exposure to para- sitoid wasps leads to a decline in egg laying, and exposed females communicate this threat to naïve flies, which also depress egg laying. We find that species across the genus Drosophila respond to wasps by egg laying reduction, activate cleaved caspase in oocytes, and communicate the presence of wasps to naïve individuals. Communication within a species and between closely related species is efficient, while more distantly related species exhibit partial communication. Remarkably, partial communication between some ...


Elimination Of Pcr Duplicates In Rna-Seq And Small Rna-Seq Using Unique Molecular Identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, Zhiping Weng 2018 University of Massachusetts Medical School

Elimination Of Pcr Duplicates In Rna-Seq And Small Rna-Seq Using Unique Molecular Identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, Zhiping Weng

Open Access Articles

BACKGROUND: RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules.

RESULTS: We have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species ...


Validating The Accuracy Of Neatwork, A Rural Gravity Fed Water Distribution System Design Program, Using Field Data In The Comarca Ngöbe-Bugle, Panama, Maria Briones 2018 University of South Florida

Validating The Accuracy Of Neatwork, A Rural Gravity Fed Water Distribution System Design Program, Using Field Data In The Comarca Ngöbe-Bugle, Panama, Maria Briones

Graduate Theses and Dissertations

Despite the sustainable development goals to increase access to improved water there are still 884 million people in the world without access to an improved water source (WHO, 2017). One method to improve access to water in rural, mountainous areas, is through construction of gravity fed water distribution systems. These systems should be designed based upon fundamental principles of hydraulics. One method of doing so in a time efficient manner with minimal engineering knowledge is to utilize a downloadable computer program such as Neatwork, which aids in design of rural, gravity fed water distribution systems and has been used by ...


Pirscan: A Webserver To Predict Pirna Targeting Sites And To Avoid Transgene Silencing In C. Elegans, Wei-Sheng Wu, Wei-Che Huang, Jordan S. Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, Heng-Chi Lee 2018 National Cheng Kung University

Pirscan: A Webserver To Predict Pirna Targeting Sites And To Avoid Transgene Silencing In C. Elegans, Wei-Sheng Wu, Wei-Che Huang, Jordan S. Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, Heng-Chi Lee

Program in Bioinformatics and Integrative Biology Publications

pirScan is a web-based tool for identifying C. elegans piRNA-targeting sites within a given mRNA or spliced DNA sequence. The purpose of our tool is to allow C. elegans researchers to predict piRNA targeting sites and to avoid the persistent germline silencing of transgenes that has rendered many constructs unusable. pirScan fulfills this purpose by first enumerating the predicted piRNA-targeting sites present in an input sequence. This prediction can be exported in a tabular or graphical format. Subsequently, pirScan suggests silent mutations that can be introduced to the input sequence that would allow the modified transgene to avoid piRNA targeting ...


Studying Egfr Signaling Through Single Molecule Imaging And Computational Modeling, Emanuel Salazar Cavazos 2018 University of New Mexico

Studying Egfr Signaling Through Single Molecule Imaging And Computational Modeling, Emanuel Salazar Cavazos

Biomedical Sciences ETDs

Signaling through the Epidermal Growth Factor Receptor (EGFR) plays an important role in both physiological and cancer-related processes. In this work, single-molecule microscopy measurements and computational modeling were closely integrated to better understand the mechanisms that regulate EGFR signaling. Technical improvements were made over the previously described Single-Molecule Pull-down (SiMPull) assay to facilitate direct detection of the phosphorylation state of thousands of individual receptors, and thereby estimate both the fraction of receptors phosphorylated at specific tyrosine residues and the frequency of multisite phosphorylation. These improvements enabled the first direct detection of multisite phosphorylation on full-length Epidermal Growth Factor Receptor (EGFR ...


Sources And Fates Of Carbamyl Phosphate: A Labile Energy-Rich Molecule With Multiple Facets., Dashuang Shi, Ljubica Caldovic, Mendel Tuchman 2018 George Washington University

Sources And Fates Of Carbamyl Phosphate: A Labile Energy-Rich Molecule With Multiple Facets., Dashuang Shi, Ljubica Caldovic, Mendel Tuchman

Genomics and Precision Medicine Faculty Publications

Carbamyl phosphate (CP) is well-known as an essential intermediate of pyrimidine and arginine/urea biosynthesis. Chemically, CP can be easily synthesized from dihydrogen phosphate and cyanate. Enzymatically, CP can be synthesized using three different classes of enzymes: (1) ATP-grasp fold protein based carbamyl phosphate synthetase (CPS); (2) Amino-acid kinase fold carbamate kinase (CK)-like CPS (anabolic CK or aCK); and (3) Catabolic transcarbamylase. The first class of CPS can be further divided into three different types of CPS as CPS I, CPS II, and CPS III depending on the usage of ammonium or glutamine as its nitrogen source, and whether


Obat Aborsi Penajam 081901222272 Jual Obat Cytotec Asli Di Penajam, Apotik Cytotec 2018 Bryant University

Obat Aborsi Penajam 081901222272 Jual Obat Cytotec Asli Di Penajam, Apotik Cytotec

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Multi-Behavioral Endpoint Testing Of An 87-Chemical Compound Library In Freshwater Planarians, S. Zhang, D. Hagstrom, P. Hayes, A. Graham, Eva-Maria S. Collins 2018 Swarthmore College

Multi-Behavioral Endpoint Testing Of An 87-Chemical Compound Library In Freshwater Planarians, S. Zhang, D. Hagstrom, P. Hayes, A. Graham, Eva-Maria S. Collins

Biology Faculty Works

There is an increased recognition in the field of toxicology of the value of medium-to-high-throughput screening methods using in vitro and alternative animal models. We have previously introduced the asexual freshwater planarian Dugesia japonica as a new alternative animal model and proposed that it is particularly well-suited for the study of developmental neurotoxicology. In this paper, we discuss how we have expanded and automated our screening methodology to allow for fast screening of multiple behavioral endpoints, developmental toxicity, and mortality. Using an 87-compound library provided by the National Toxicology Program (NTP), consisting of known and suspected neurotoxicants, including drugs, flame ...


Book Reviews: Force Of Nature: George Fell, Founder Of The Natural Areas Movement. Arthur Melville Pearson., James R. Herkert 2018 Illinois Audubon Society

Book Reviews: Force Of Nature: George Fell, Founder Of The Natural Areas Movement. Arthur Melville Pearson., James R. Herkert

The Prairie Naturalist

Arthur Melville Pearson’s Force of Nature is a book that tells two very interesting and intertwined stories. One is a story of how perseverance and determination can drive an individual to accomplish great things. And the other is a story of how the modern day natural areas movement came to be. Fortunately for those interested in conservation and natural areas protection, those two stories were combined in the life of George Fell (1916-1994). In Fell’s home state of Illinois, where his impact is widely known, his name is synonymous with conservation. In other places where his impact is ...


Age And Growth Of Cottonwood Trees Along The Missouri River, North Dakota, Jonathan M. Friedman, Fisher R. Ankney, J. Marshall Wolf 2018 U.S. Geological Survey Fort Collins Science Center

Age And Growth Of Cottonwood Trees Along The Missouri River, North Dakota, Jonathan M. Friedman, Fisher R. Ankney, J. Marshall Wolf

The Prairie Naturalist

The relict plains cottonwood (Populus deltoides subsp. monilifera) forest along the Missouri River between Lakes Sakakawea and Oahe includes trees as large as two meters in diameter. We cored 24 of these trees to determine their age and suitability for flow reconstruction. Because most of the trees were rotten in the center, we developed a method to estimate the date of the center ring that accounts for the increase in ring width toward the center. Estimated center ring dates were as early as 1806. Cottonwood growth at a dry site was correlated with April–August flow prior to construction of ...


Spatiotemporal Distribution Of Waterfowl Disease Outbreaks In Kansas, Usa, Thomas A. Becker, Adam A. Ahlers, Shane Hesting, David A. Haukos 2018 Kansas Cooperative Fish and Wildlife Research Unit

Spatiotemporal Distribution Of Waterfowl Disease Outbreaks In Kansas, Usa, Thomas A. Becker, Adam A. Ahlers, Shane Hesting, David A. Haukos

The Prairie Naturalist

Causes and impacts of disease outbreaks in wild bird populations are rarely studied beyond documentation of large epizootic events. In Kansas, USA, a central disease surveillance and reporting protocol currently does not exist within the Kansas Department of Wildlife, Parks and Tourism, which has led to a lack of available knowledge of disease occurrences that could be used to predict and manage future outbreaks. We compiled historic records of documented waterbird disease outbreaks in Kansas from 1967–2014 and related the frequency of outbreaks with light geese (Ross’s goose [Anser rossii]; Snow goose [A. caerulescens]) populations from 1970–2014 ...


Lekking Behavior Of A Sharp-Tailed Grouse In South-Central Nebraska, Kelsey C. King, Andrew J. Caven, Keith Geluso 2018 Crane Trust

Lekking Behavior Of A Sharp-Tailed Grouse In South-Central Nebraska, Kelsey C. King, Andrew J. Caven, Keith Geluso

The Prairie Naturalist

Sharp-tailed grouse (Tympanuchus phasianellus; STGR) occur throughout much of the northern Great Plains, and historically were suspected to have ranged as far south as Kansas (Connelly et al. 1998). Sharp-tailed grouse were the dominant grouse in Nebraska 200 years ago, but early settlers and their associated agricultural practices extirpated STGR from much of their former range, including Kansas and southern Nebraska (Sisson 1976, Johnsgard 2016). During the period of initial land conversion, the greater prairie-chicken (T. cupido; GRPC) filled the void, benefiting from small plots of cropland providing winter forage, and outcompeting the STGR (Johnsgard and Wood 1968, Svedarsky et ...


A Short Narrative For Writing For The Prairie Naturalist, Christopher N. Jacques 2018 Western Illinois University

A Short Narrative For Writing For The Prairie Naturalist, Christopher N. Jacques

The Prairie Naturalist

The abstract should be written upon completion of the paper. A well-written abstract is a single short (≤1 line/page of text), concise, and includes 1) an introductory sentence justifying why the study was conducted, 2) a statement of the principal objectives or hypotheses tested during the study, 3) a brief description of pertinent methods, 4) a summary of significant results, 5) a punchy conclusion, and 6) management implications (i.e., utility of results explaining how, when, where, and by whom data or interpretations can be applied; Krausman and Cox 2017). Keep in mind that abstracts are read more than ...


The Prairie Naturalist: The Journal Of The Great Plains Natural Science Society Volume 50 No. 1, 2018 University of Nebraska - Lincoln

The Prairie Naturalist: The Journal Of The Great Plains Natural Science Society Volume 50 No. 1

The Prairie Naturalist

TABLE OF CONTENTS

1 EDITOR’S NOTE

RESEARCH ARTICLES

3 Spatiotemporal Distribution of Waterfowl Disease Outbreaks in Kansas, USA Thomas A. Becker, Adam A. Ahlers, Shane Hesting, and David A. Haukos

14 Wild Turkey Occupancy in a Prairie Landscape Joshua C. Courlas and R. Scott Lutz

24 Age and Growth of Cottonwood Trees along the Missouri River, North Dakota Jonathan M. Friedman, Fisher R. Ankeny, and Marshall Wolf

NOTES

34 Hoary Bat Impaled on Barbed Wire Fence

37 Lekking Behavior of a Sharp-Tailed Grouse in South-Central Nebraska

BOOK REVIEWS

40 Force of Nature: George Fell, Founder of The Natural Areas ...


Wild Turkey Occupancy In A Prairie Landscape, Joshua C. Courlas, R. Scott Lutz 2018 University of Wisconsin-Madison

Wild Turkey Occupancy In A Prairie Landscape, Joshua C. Courlas, R. Scott Lutz

The Prairie Naturalist

We investigated wild turkey (Meleagris gallopavo) distribution in prairie landscapes in North Dakota using occupancy modeling in two stages. In 2012, we extensively surveyed ecoregions across the state and in 2013, intensively surveyed the ecoregion with the highest probability of occupancy. Occupancy models from the statewide survey indicated wild turkeys were sparse in ecoregions with primarily agricultural landscapes, were found associated with wooded riparian cover, and found most frequently in the Missouri River Plateau ecoregion. In the Missouri River Plateau, our occupancy models identified that an additive model including mean patch area of cropland fields and spatial aggregation of forest ...


Generation Of Nonlinear-Differential-Equations System From A Model Of Boolean Relationships In Arabidopsis Salt Stress Network, Renee Dale 2018 Louisiana State University and Agricultural and Mechanical College

Generation Of Nonlinear-Differential-Equations System From A Model Of Boolean Relationships In Arabidopsis Salt Stress Network, Renee Dale

Biology and Medicine Through Mathematics Conference

No abstract provided.


Transcriptional Profiling Reveals Extraordinary Diversity Among Skeletal Muscle Tissues, Erin E. Terry, Xiping Zhang, Christy Hoffmann, Laura D. Hughes, Scott A. Lewis, Jiajia Li, Matthew J. Wallace, Lance A. Riley, Collin M. Douglas, Miguel A. Gutierrez-Monreal, Nicholas F. Lahens, Ming C. Gong, Francisco H. Andrade, Karyn A. Esser, Michael E. Hughes 2018 Washington University in St. Louis

Transcriptional Profiling Reveals Extraordinary Diversity Among Skeletal Muscle Tissues, Erin E. Terry, Xiping Zhang, Christy Hoffmann, Laura D. Hughes, Scott A. Lewis, Jiajia Li, Matthew J. Wallace, Lance A. Riley, Collin M. Douglas, Miguel A. Gutierrez-Monreal, Nicholas F. Lahens, Ming C. Gong, Francisco H. Andrade, Karyn A. Esser, Michael E. Hughes

Physiology Faculty Publications

Skeletal muscle comprises a family of diverse tissues with highly specialized functions. Many acquired diseases, including HIV and COPD, affect specific muscles while sparing others. Even monogenic muscular dystrophies selectively affect certain muscle groups. These observations suggest that factors intrinsic to muscle tissues influence their resistance to disease. Nevertheless, most studies have not addressed transcriptional diversity among skeletal muscles. Here we use RNAseq to profile mRNA expression in skeletal, smooth, and cardiac muscle tissues from mice and rats. Our data set, MuscleDB, reveals extensive transcriptional diversity, with greater than 50% of transcripts differentially expressed among skeletal muscle tissues. We detect ...


Radical Social Ecology As Deep Pragmatism: A Call To The Abolition Of Systemic Dissonance And The Minimization Of Entropic Chaos, Arielle Brender 2018 Fordham University

Radical Social Ecology As Deep Pragmatism: A Call To The Abolition Of Systemic Dissonance And The Minimization Of Entropic Chaos, Arielle Brender

Student Theses 2015-Present

This paper aims to shed light on the dissonance caused by the superimposition of Dominant Human Systems on Natural Systems. I highlight the synthetic nature of Dominant Human Systems as egoic and linguistic phenomenon manufactured by a mere portion of the human population, which renders them inherently oppressive unto peoples and landscapes whose wisdom were barred from the design process. In pursuing a radical pragmatic approach to mending the simultaneous oppression and destruction of the human being and the earth, I highlight the necessity of minimizing entropic chaos caused by excess energy expenditure, an essential feature of systems that aim ...


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