Ecological Response Of Phytoplankton To The Oil Spills In The Oceans, 2019 Chinese Academy of Sciences
Ecological Response Of Phytoplankton To The Oil Spills In The Oceans, Danling Tang, Jing Sun, Li Zhou, Sufen Wang, Ramesh P. Singh, Gang Pan
Mathematics, Physics, and Computer Science Faculty Articles and Research
Oil spills in oceans have substantial influence on marine ecosystems. This study investigates 21 oil spills in the world. Analyzing Chlorophyll-a (Chl-a) from Moderate Resolution Imaging Spectroradiomerer (MODIS) data after Penglai oil spills on 4 June 2011, found a bloom with peak value of Chl-a (13.66 mg m−3) spread over an area of 800 km2 during 18–25 June 2011, and a pronounced increase in the monthly Chl-a concentration (6.40 mg m−3) on June 2012 in the Bohai Sea. Out of the 21 oil spills, 14 blooms were observed, while 11 ...
The Non-Canonical Smc Protein Smchd1 Antagonises Tad Formation And Compartmentalisation On The Inactive X Chromosome, Michal R. Gdula, Tatyana B. Nesterova, Greta Pintacuda, Jonathan Godwin, Ye Zhan, Hakan Ozadam, Michael Mcclellan, Daniella Moralli, Felix Krueger, Catherine M. Green, Wolf Reik, Skirmantas Kriaucionis, Edith Heard, Job Dekker, Neil Brockdorff
Open Access Articles
The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), A/B compartments and formation of two mega-domains. Here we demonstrate that the non-canonical SMC family protein, SmcHD1, which is important for gene silencing on Xi, contributes to this unique chromosome architecture. Specifically, allelic mapping of the transcriptome and epigenome in SmcHD1 mutant cells reveals the appearance of sub-megabase domains defined by gene activation, CpG hypermethylation and depletion of Polycomb-mediated H3K27me3. These domains, which correlate with sites of SmcHD1 enrichment on Xi in wild-type cells ...
The Caenorhabditis Elegans Oxidative Stress Response Requires The Nhr-49 Transcription Factor, Queenie Hu, Dayana R. D'Amora, Lesley T. Macneil, Albertha J. M. Walhout, Terrance J. Kubiseski
Open Access Articles
The overproduction of reactive oxygen species (ROS) in cells can lead to the development of diseases associated with aging. We have previously shown that C. elegans BRAP-2 (Brca1 associated binding protein 2) regulates phase II detoxification genes such as gst-4, by increasing SKN-1 activity. Previously, a transcription factor (TF) RNAi screen was conducted to identify potential activators that are required to induce gst-4 expression in brap-2(ok1492) mutants. The lipid metabolism regulator NHR-49/HNF4 was among 18 TFs identified. Here, we show that knockdown of nhr-49 suppresses the activation of gst-4 caused by brap-2 inactivation and that gain-of-function alleles of ...
The Mayfly Newsletter, 2018 Southwestern Oklahoma State University
The Mayfly Newsletter, Donna Giberson
The Mayfly Newsletter
Crabwalkers and sand minnows: Searching for psammophilic mayflies in the central and western states (& provinces)1
Greg Courtney Department of Entomology, Iowa State University, Ames, Iowa, USA
Motivated by a number of collaborative photography projects with Steve Marshall (e.g., Courtney & Marshall, 2019), I have devoted a bit of time recently to searching for non-dipteran aquatic insects. Among the ongoing projects is a book on which I am not only lead author but in charge of several chapters focused on taxa outside my usual bailiwick (e.g., Ephemeroptera!). Thankfully, Steve has already established an excellent template for such a book ...
Epidermal Growth Factor-Like Ligands Regulate Dimer Selection., 2018 University of Louisville
Epidermal Growth Factor-Like Ligands Regulate Dimer Selection., Jamie S. Rush
Electronic Theses and Dissertations
There are thirteen known endogenous EGF-like ligands. We previously reported that Betacellulin (BTC) increases ligand-mediated corneal wound healing more than Epidermal Growth Factor (EGF) [Peterson et al. (2014) IOVS 55(5):2870-80], although the molecular reason for this is unknown. Despite being better at promoting wound healing via enhanced cell migration, BTC has reduced receptor affinity and weaker induction of EGFR phosphorylation. These data indicate that BTC’s response is not due to enhanced affinity or EGFR-kinase activity. Receptor phosphorylation and proximity ligation assays indicate that BTC treatment significantly increases ErbB3 phosphorylation and EGFR:ErbB3 heterodimers. BTC traffics EGFR at ...
Integrating Node Embeddings And Biological Annotations For Genes To Predict Disease-Gene Associations, 2018 Singapore Management University
Integrating Node Embeddings And Biological Annotations For Genes To Predict Disease-Gene Associations, Sezin Kircali Ata, Le Ou-Yang, Yuan Fang, Chee-Keong Kwoh, Min Wu, Xiao-Li Li
Research Collection School Of Information Systems
Background: Predicting disease causative genes (or simply, disease genes) has played critical roles in understandingthe genetic basis of human diseases and further providing disease treatment guidelines. While various computationalmethods have been proposed for disease gene prediction, with the recent increasing availability of biologicalinformation for genes, it is highly motivated to leverage these valuable data sources and extract useful information foraccurately predicting disease genes. Results: We present an integrative framework called N2VKO to predict disease genes. Firstly, we learn the nodeembeddings from protein-protein interaction (PPI) network for genes by adapting the well-known representationlearning method node2vec. Secondly, we combine the learned node ...
Examining Patterns In Nest Predation Using Artificial Nests, 2018 University of Nebraska-Lincoln
Examining Patterns In Nest Predation Using Artificial Nests, Victoria L. Simonsen
Dissertations & Theses in Natural Resources
The use of artificial nests to study the predation of avian nests has faced disregard by ecologists due to inconsistencies found between the survival rates of real and artificial nests across studies and reviews. The negative perception of artificial nests providing an inconsistent assessment of survival has thus fostered the perception that artificial nests are a secondary option to be used to overcome logistical hurdles associated with achieving sufficient sample sizes in systems where study species are rare or elusive, or as merely a preliminary method to study predation across gradients. We argue that the greatest mistake ecologists have made ...
Using Canalization For The Control Of Discrete Networks, 2018 University of Kentucky
Using Canalization For The Control Of Discrete Networks, David Murrugarra
Annual Symposium on Biomathematics and Ecology: Education and Research
No abstract provided.
Tumor-Stroma Interactions Differentially Alter Drug Sensitivity Based On The Origin Of Stromal Cells, 2018 University of Massachusetts Medical School
Tumor-Stroma Interactions Differentially Alter Drug Sensitivity Based On The Origin Of Stromal Cells, Benjamin D. Landry, Thomas Leete, Ryan Richards, Peter Cruz-Gordillo, Hannah R. Schwartz, Megan E. Honeywell, Gary Ren, Alyssa D. Schwartz, Shelly R. Peyton, Michael J. Lee
Program in Systems Biology Publications and Presentations
Due to tumor heterogeneity, most believe that effective treatments should be tailored to the features of an individual tumor or tumor subclass. It is still unclear, however, what information should be considered for optimal disease stratification, and most prior work focuses on tumor genomics. Here, we focus on the tumor microenvironment. Using a large-scale coculture assay optimized to measure drug-induced cell death, we identify tumor-stroma interactions that modulate drug sensitivity. Our data show that the chemo-insensitivity typically associated with aggressive subtypes of breast cancer is not observed if these cells are grown in 2D or 3D monoculture, but is manifested ...
Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle
Electronic Theses and Dissertations
Background: Human arylamine N-acetyltransferase 1 (NAT1) is a phase II xenobiotic metabolizing enzyme found in almost all tissues. NAT1 can additionally hydrolyze acetyl-coenzyme A (acetyl-CoA) in the absence of an arylamine substrate. NAT1 expression varies inter-individually and is elevated in several cancers including estrogen receptor positive (ER+) breast cancers. Additionally, multiple studies have shown the knockdown of NAT1, by both small molecule inhibition and siRNA methods, in breast cancer cells leads to decreased invasive ability and proliferation and decreased anchorage-independent colony formation. However, the exact mechanism by which NAT1 expression affects cancer risk and progression remains unclear. Additionally, consequences ...
Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., 2018 University of Louisville
Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor
Electronic Theses and Dissertations
Metabolomics, the study of small molecules in biological systems, has enjoyed great success in enabling researchers to examine disease-associated metabolic dysregulation and has been utilized for the discovery biomarkers of disease and phenotypic states. In spite of recent technological advances in the analytical platforms utilized in metabolomics and the proliferation of tools for the analysis of metabolomics data, significant challenges in metabolomics data analyses remain. In this dissertation, we present three of these challenges and Bayesian methodological solutions for each. In the first part we develop a new methodology to serve a basis for making higher order inferences in metabolomics ...
A Persistence Detector For Metabolic Network Rewiring In An Animal, 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., 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, 2018 Dartmouth College
Drosophila Species Learn Dialects Through Communal Living, Balint Z. Kacsoh, Julianna Bozler, Giovanni Bosco
Open Dartmouth: Faculty Open Access Articles
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, 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
Program in Bioinformatics and Integrative Biology Publications and Presentations
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
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, 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 and Presentations
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, 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., 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, 2018 Bryant University