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https://www.readbyqxmd.com/read/28065881/an-integrated-transcriptomics-guided-genome-wide-promoter-analysis-and-next-generation-proteomics-approach-to-mine-factor-s-regulating-cellular-differentiation
#1
Kamal Mandal, Samuel L Bader, Pankaj Kumar, Dipankar Malakar, David S Campbell, Bhola Shankar Pradhan, Rajesh K Sarkar, Neerja Wadhwa, Souvik Sensharma, Vaibhav Jain, Robert L Moritz, Subeer S Majumdar
Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27977123/profiling-protease-specificity-combining-yeast-er-sequestration-screening-yess-with-next-generation-sequencing
#2
Qing Li, Li Yi, Kam Hon Hoi, Peter Marek, George Georgiou, Brent L Iverson
An enzyme engineering technology involving yeast endoplasmic reticulum (ER) sequestration screening (YESS) has been recently developed. Here, a new method is established, in which the YESS platform is combined with NextGen sequencing (NGS) to enable a comprehensive survey of protease specificity. In this approach, a combinatorial substrate library is targeted to the yeast ER and transported through the secretory pathway, interacting with any protease(s) residing in the ER. Multicolor FACS screening is used to isolate cells labeled with fluorophore-conjugated antibodies, followed by NGS to profile the cleaved substrates...
January 3, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/27957521/dataset-of-the-absorption-emission-and-excitation-spectra-and-fluorescence-intensity-graphs-of-fluorescent-cyanine-dyes-for-the-quantification-of-low-amounts-of-dsdna
#3
Brigitte Bruijns, Roald Tiggelaar, Han Gardeniers
This article describes data related to a research article entitled "Fluorescent cyanine dyes for the quantification of low amounts of dsDNA" (B. Bruijns, R. Tiggelaar, J. Gardeniers, 2016) [1]. Six cyanine dsDNA dyes - EvaGreen, SYBR Green, PicoGreen, AccuClear, AccuBlue NextGen and YOYO-1 - are investigated and in this article the absorption spectra, as well as excitation and emission spectra, for all six researched cyanine dyes are given, all recorded under exactly identical experimental conditions. The intensity graphs, with the relative fluorescence in the presence of low amounts of dsDNA, are also provided...
February 2017: Data in Brief
https://www.readbyqxmd.com/read/27936855/evaluating-probe-techniques-and-a-situated-theory-of-situation-awareness
#4
Dan Chiappe, Corey A Morgan, Joshua Kraut, Jason Ziccardi, Lindsay Sturre, Thomas Z Strybel, Kim-Phuong L Vu
Probe techniques for measuring situation awareness (SA) vary in whether scenarios are paused and displays visible while questions are presented. We examined which technique is least intrusive on workload and performance in air traffic control, and which is most sensitive at capturing differences in SA when automation varies. We also tested predictions from the situated SA theory, which holds that operators offload specific and low-priority information onto displays to limit internal processing. To accomplish these goals, Experiments 1 and 2 manipulated whether radar displays were visible and scenarios paused during queries...
December 2016: Journal of Experimental Psychology. Applied
https://www.readbyqxmd.com/read/27928018/expression-of-the-antisense-to-latency-transcript-long-noncoding-rna-in-kaposi-s-sarcoma-associated-herpesvirus
#5
Jason M Schifano, Kathleen Corcoran, Hemant Kelkar, Dirk P Dittmer
: The regulation of latency is central to herpesvirus biology. Recent transcriptome-wide surveys have uncovered evidence for promiscuous transcription across the entirety of the Kaposi sarcoma-associated herpesvirus genome and postulated the existence of multiple viral long noncoding RNAs (lncRNAs). NextGen sequencing studies are highly dependent on the specific experimental approach and particular algorithms of analysis, and therefore benefit from independent confirmation of the results...
December 7, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27920089/world-endometriosis-society-consensus-on-the-classification-of-endometriosis
#6
Neil P Johnson, Lone Hummelshoj, G David Adamson, Jörg Keckstein, Hugh S Taylor, Mauricio S Abrao, Deborah Bush, Ludwig Kiesel, Rulla Tamimi, Kathy L Sharpe-Timms, Luk Rombauts, Linda C Giudice
STUDY QUESTION: What is the global consensus on the classification of endometriosis that considers the views of women with endometriosis? SUMMARY ANSWER: We have produced an international consensus statement on the classification of endometriosis through systematic appraisal of evidence and a consensus process that included representatives of national and international, medical and non-medical societies, patient organizations, and companies with an interest in endometriosis...
December 5, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27915271/changes-in-renal-gene-expression-associated-with-induced-ochratoxicosis-in-chickens-activation-and-deactivation-of-transcripts-after-varying-durations-of-exposure
#7
Cynthia P Zeferino, Kevin D Wells, Ana Silvia A M T Moura, George E Rottinghaus, David R Ledoux
Exposure to ochratoxin A (OTA) can lead to changes in global gene expression. This study investigated the individual expression of genes turned on and off in renal cells of chicks after different durations of exposure to dietary OTA. One hundred and eighty day-old male broiler chicks (Ross 308) were randomly assigned to a 3 × 3 factorial arrangement of treatments (3 levels of OTA: 0, 1 and 2 mg OTA/kg diet and 3 time periods: 7, 14 and 21 d). Birds were allocated to 36 pens (4 replicate pens of 5 birds each per treatment)...
December 3, 2016: Poultry Science
https://www.readbyqxmd.com/read/27801969/high-performance-computation-of-landscape-genomic-models-including-local-indicators-of-spatial-association
#8
S Stucki, P Orozco-terWengel, B R Forester, S Duruz, L Colli, C Masembe, R Negrini, E Landguth, M R Jones, M W Bruford, P Taberlet, S Joost
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics-i.e. the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present Samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental datasets...
November 1, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27598793/transcriptomic-changes-associated-with-pregnancy-in-a-marsupial-the-gray-short-tailed-opossum-monodelphis-domestica
#9
Victoria Leigh Hansen, Faye Dorothy Schilkey, Robert David Miller
Live birth has emerged as a reproductive strategy many times across vertebrate evolution; however, mammals account for the majority of viviparous vertebrates. Marsupials are a mammalian lineage that last shared a common ancestor with eutherians (placental mammals) over 148 million years ago. Marsupials are noted for giving birth to highly altricial young after a short gestation, and represent humans' most distant viviparous mammalian relatives. Here we ask what insight can be gained into the evolution of viviparity in mammals specifically and vertebrates in general by analyzing the global uterine transcriptome in a marsupial...
2016: PloS One
https://www.readbyqxmd.com/read/27537694/evaluating-imputation-algorithms-for-low-depth-genotyping-by-sequencing-gbs-data
#10
Ariel W Chan, Martha T Hamblin, Jean-Luc Jannink
Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordable, datasets derived from HTS methods suffer from sequencing error, alignment errors, and missing data, all of which introduce noise and uncertainty to variant discovery and genotype calling. Under such circumstances, meaningful analysis of the data is difficult...
2016: PloS One
https://www.readbyqxmd.com/read/27507117/fluorescent-cyanine-dyes-for-the-quantification-of-low-amounts-of%C3%A2-dsdna
#11
B B Bruijns, R M Tiggelaar, J G E Gardeniers
In this research six cyanine fluorophores for the quantification of dsDNA in the pg-ng range, without amplification, are compared under exactly identical conditions: EvaGreen, SYBR Green, PicoGreen, AccuClear, AccuBlue NextGen and YOYO-1. The fluorescence intensity as a function of the amount of dsDNA is measured at the optimal wavelengths for excitation and emission and for each dye the limit of detection and the response linearity at low levels of dsDNA are determined. No linear range was found for SYBR Green and YOYO-1 for pg-ng quantities of dsDNA...
October 15, 2016: Analytical Biochemistry
https://www.readbyqxmd.com/read/27504789/an-old-culprit-but-a-new-story-bisphenol-a-and-nextgen-bisphenols
#12
REVIEW
Caroline V Sartain, Patricia A Hunt
The concept that developmental events shape adult health and disease was sparked by the recognition of a link between maternal undernutrition and coronary disease in adults. From that beginning, a new field-the developmental origins of health and disease-emerged, and attention has focused on the effects of a wide array of developmental perturbations. Exposure to endocrine-disrupting chemicals has been of particular interest, and a ubiquitous environmental contaminant bisphenol A (BPA) has become the endocrine-disrupting chemical poster child...
September 15, 2016: Fertility and Sterility
https://www.readbyqxmd.com/read/27452320/excessive-reversal-of-epidermal-growth-factor-receptor-and-ephrin-signaling-following-tracheal-occlusion-in-rabbit-model-of-congenital-diaphragmatic-hernia
#13
Brian M Varisco, Lourenco Sbragia, Jing Chen, Federico Scorletti, Rashika Joshi, Hector R Wong, Rebecca Lopes-Figueira, Marc Oria, Jose Peiro
Congenital diaphragmatic hernia (CDH) causes severe pulmonary hypoplasia from herniation of abdominal contents into the thorax. Tracheal occlusion (TO) for human CDH improves survival, but morbidity and mortality remain high, and we do not fully understand the cellular pathways and processes most severely impacted by CDH and TO. We created a left diaphragmatic hernia (DH) in rabbit fetuses with subsequent TO and collected left lung sections for NextGen mRNA sequencing. DH, TO, and DHTO fetuses had comparable body and organ growth to control except for lower lung weights in DH (p<0...
July 19, 2016: Molecular Medicine
https://www.readbyqxmd.com/read/27368709/the-gut-microbiome-of-the-sea-urchin-lytechinus-variegatus-from-its-natural-habitat-demonstrates-selective-attributes-of-microbial-taxa-and-predictive-metabolic-profiles
#14
Joseph A Hakim, Hyunmin Koo, Ranjit Kumar, Elliot J Lefkowitz, Casey D Morrow, Mickie L Powell, Stephen A Watts, Asim K Bej
In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbial profile comprised of Gammaproteobacteria, mainly Vibrio, and Bacteroidetes...
September 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27278669/genomic-leftovers-identifying-novel-microsatellites-over-represented-motifs-and-functional-elements-in-the-human-genome
#15
Natalie C Fonville, Karthik Raja Velmurugan, Hongseok Tae, Zalman Vaksman, Lauren J McIver, Harold R Garner
The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27154271/sensitive-and-specific-mirna-detection-method-using-splintr-ligase
#16
Jingmin Jin, Sophie Vaud, Alexander M Zhelkovsky, Janos Posfai, Larry A McReynolds
We describe a simple, specific and sensitive microRNA (miRNA) detection method that utilizes Chlorella virus DNA ligase (SplintR(®) Ligase). This two-step method involves ligation of adjacent DNA oligonucleotides hybridized to a miRNA followed by real-time quantitative PCR (qPCR). SplintR Ligase is 100X faster than either T4 DNA Ligase or T4 RNA Ligase 2 for RNA splinted DNA ligation. Only a 4-6 bp overlap between a DNA probe and miRNA was required for efficient ligation by SplintR Ligase. This property allows more flexibility in designing miRNA-specific ligation probes than methods that use reverse transcriptase for cDNA synthesis of miRNA...
July 27, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27097531/hipsc-derived-imscs-nextgen-mscs-as-an-advanced-therapeutically-active-cell-resource-for-regenerative-medicine
#17
REVIEW
Vikram Sabapathy, Sanjay Kumar
Mesenchymal stem cells (MSCs) are being assessed for ameliorating the severity of graft-versus-host disease, autoimmune conditions, musculoskeletal injuries and cardiovascular diseases. While most of these clinical therapeutic applications require substantial cell quantities, the number of MSCs that can be obtained initially from a single donor remains limited. The utility of MSCs derived from human-induced pluripotent stem cells (hiPSCs) has been shown in recent pre-clinical studies. Since adult MSCs have limited capability regarding proliferation, the quantum of bioactive factor secretion and immunomodulation ability may be constrained...
August 2016: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/27076095/predicting-air-traffic-controller-workload-trajectory-uncertainty-as-the-moderator-of-the-indirect-effect-of-traffic-density-on-controller-workload-through-traffic-conflict
#18
Sifra Christina Corver, Dana Unger, Gudela Grote
OBJECTIVE: Our study investigates whether trajectory uncertainty moderates the relationship between traffic conflict and workload. Furthermore, we examine if the indirect effect of traffic density on workload through traffic conflict is conditional on the presence of trajectory uncertainty. BACKGROUND: Although it is widely accepted that uncertainty related to the future trajectory of an aircraft impacts air traffic controller decision making, little is known about how the presence of trajectory uncertainty impacts controller workload...
June 2016: Human Factors
https://www.readbyqxmd.com/read/27075976/decoding-the-epigenetic-heterogeneity-of-human-pluripotent-stem-cells-with-seamless-gene-editing
#19
Amar M Singh, Dustin W Perry, Valeriya V Adjan Steffey, Kenneth Miller, Daniel W Allison
Pluripotent stem cells exhibit cell cycle-regulated heterogeneity for trimethylation of histone-3 on lysine-4 (H3K4me3) on developmental gene promoters containing bivalent epigenetic domains. The heterogeneity of H3K4me3 can be attributed to Cyclin-dependent kinase-2 (CDK2) phosphorylation and activation of the histone methyltransferase, MLL2 (KMT2B), during late-G1. The deposition of H3K4me3 on developmental promoters in late-G1 establishes a permissive chromatin architecture that enables signaling cues to promote differentiation from the G1 phase...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/26952545/nextgen-hiv-prevention-new-possibilities-and-questions
#20
Kenneth H Mayer
No abstract text is available yet for this article.
March 12, 2016: Lancet
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