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https://www.readbyqxmd.com/read/29146736/quantitative-high-throughput-screening-identifies-cytoprotective-molecules-that-enhance-sumo-conjugation-via-the-inhibition-of-sumo-specific-protease-senp-2
#1
Joshua D Bernstock, Daniel Ye, Jayden A Smith, Yang-Ja Lee, Florian A Gessler, Adam Yasgar, Jennifer Kouznetsova, Ajit Jadhav, Zhuoran Wang, Stefano Pluchino, Wei Zheng, Anton Simeonov, John M Hallenbeck, Wei Yang
The development of novel neuroprotective treatments for acute stroke has been fraught with failures, which supports the view of ischemic brain damage as a highly complex multifactorial process. Post-translational modifications such as small ubiquitin-like modifier (SUMO)ylation have emerged as critical molecular regulatory mechanisms in states of both homeostasis and ischemic stress, as evidenced by our previous work. Accordingly, the clinical significance of the selective control of the global SUMOylation process has become apparent in studies of ischemic pathobiology and pathophysiology...
November 16, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29145861/hybrid-de-novo-genome-assembly-and-centromere-characterization-of-the-gray-mouse-lemur-microcebus-murinus
#2
Peter A Larsen, R Alan Harris, Yue Liu, Shwetha C Murali, C Ryan Campbell, Adam D Brown, Beth A Sullivan, Jennifer Shelton, Susan J Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C Durand, Muhammad S Shamim, Erez Lieberman Aiden, Donna M Muzny, Richard A Gibbs, Anne D Yoder, Jeffrey Rogers, Kim C Worley
BACKGROUND: The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly...
November 16, 2017: BMC Biology
https://www.readbyqxmd.com/read/29144434/the-role-of-non-coding-rnas-in-cytoplasmic-male-sterility-in-flowering-plants
#3
REVIEW
Helena Štorchová
The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29143598/gwas-for-plant-growth-stages-and-yield-components-in-spring-wheat-triticum-aestivum-l-harvested-in-three-regions-of-kazakhstan
#4
Yerlan Turuspekov, Aida Baibulatova, Kanat Yermekbayev, Laura Tokhetova, Vladimir Chudinov, Grigoriy Sereda, Martin Ganal, Simon Griffiths, Saule Abugalieva
BACKGROUND: Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143457/microhaplotypes-provide-increased-power-from-short-read-dna-sequences-for-relationship-inference
#5
Diana S Baetscher, Anthony J Clemento, Thomas C Ng, Eric C Anderson, John Carlos Garza
The accelerating rate at which DNA sequence data is now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by these sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine "microhaplotypes" and then call these microhaplotypes as alleles at each locus...
November 16, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29139609/development-of-a-high-throughput-method-based-on-thin-film-microextraction-using-a-96-well-plate-system-with-a-cork-coating-for-the-extraction-of-emerging-contaminants-in-river-water-samples
#6
Lucas Morés, Adriana Neves Dias, Eduardo Carasek
In this study, a new method was developed in which a biosorbent material is used as the extractor phase in conjunction with a recently described sample preparation technique called thin-film microextraction and a 96-well plate system. The method was applied to the determination of emerging contaminants, such as 3-(4-methylbenzylidene) camphor, ethylparaben, triclocarban and bisphenol A, in water samples. The separation and detection of the analytes were performed by high-performance liquid chromatography with diode array detection...
November 15, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/29133310/convergent-origination-of-a-drosophila-like-dosage-compensation-mechanism-in-a-reptile-lineage
#7
Ray Marin, Diego Cortez, Francesco Lamanna, Madapura M Pradeepa, Evgeny Leushkin, Philippe Julien, Angélica Liechti, Jean Halbert, Thoomke Brüning, Katharina Mössinger, Timo Trefzer, Christian Conrad, Halie N Kerver, Juli Wade, Patrick Tschopp, Henrik Kaessmann
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage...
November 13, 2017: Genome Research
https://www.readbyqxmd.com/read/29130757/international-barcode-of-life-focus-on-big-biodiversity-in-south-africa
#8
Sarah J Adamowicz, Peter M Hollingsworth, Sujeevan Ratnasingham, Michelle van der Bank
Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20-24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-access special issue of Genome. Hosted for the first time on the African continent, the 7th Conference places special emphasis on the evolutionary origins, biogeography, and conservation of African flora and fauna...
November 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29130189/identifying-the-m-6-a-methylome-by-affinity-purification-and-sequencing
#9
Phillip J Hsu, Chuan He
N (6)-methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic mRNA, and is newly emerging as a key posttranscriptional mRNA regulator. Recent research has uncovered insight into the location and function of m(6)A sites on a large scale, in part due to the transcriptome-wide identification of m(6)A sites by high-throughput sequencing (m(6)A-seq). Here, we present a protocol for m(6)A-seq, which maps the m(6)A methylome by affinity purification and sequencing.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29130187/the-secret-life-of-rna-lessons-from-emerging-methodologies
#10
Caroline Medioni, Florence Besse
The last past decade has witnessed a revolution in our appreciation of transcriptome complexity and regulation. This remarkable expansion in our knowledge largely originates from the advent of high-throughput methodologies, and the consecutive discovery that up to 90% of eukaryotic genomes are transcribed, thus generating an unanticipated large range of noncoding RNAs (Hangauer et al., 15(4):112, 2014). Besides leading to the identification of new noncoding RNA species, transcriptome-wide studies have uncovered novel layers of posttranscriptional regulatory mechanisms controlling RNA processing, maturation or translation, and each contributing to the precise and dynamic regulation of gene expression...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29129969/statistical-contributions-to-bioinformatics-design-modeling-structure-learning-and-integration
#11
Jeffrey S Morris, Veerabhadran Baladandayuthapani
The advent of high-throughput multi-platform genomics technologies providing whole-genome molecular summaries of biological samples has revolutionalized biomedical research. These technologiees yield highly structured big data, whose analysis poses significant quantitative challenges. The field of Bioinformatics has emerged to deal with these challenges, and is comprised of many quantitative and biological scientists working together to effectively process these data and extract the treasure trove of information they contain...
2017: Statistical Modelling
https://www.readbyqxmd.com/read/29129061/a-highly-sensitive-and-high-throughput-method-for-the-analysis-of-bisphenol-analogues-and-their-halogenated-derivatives-in-breast-milk
#12
Yumin Niu, Bin Wang, Yunfeng Zhao, Jing Zhang, Bing Shao
The structural analogs of bisphenol A (BPA) and their halogenated derivatives (together referred as BPs) have been found in environment, food and even human. Limited research showed that some of them exhibited similar to or even greater toxicities than BPA. Therefore, adverse effects on humans with low-dose in early life exposure were expected for BPs. Breast milk is an excellent matrix could reflect fetus and babies exposure to contaminants. Some of the emerging BPs may present with trace or ultra-trace levels in human...
November 13, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29126572/functionally-relevant-morphological-profiling-a-tool-to-assess-cellular-heterogeneity
#13
REVIEW
Ross A Marklein, Johnny Lam, Murat Guvendiren, Kyung E Sung, Steven R Bauer
Heterogeneity in cell function has presented a significant hurdle to the successful clinical translation of many cellular therapies. Current techniques for assessing cell quality and the effects of microenvironmental cues and manufacturing processes on cell behavior often inadequately address heterogeneity due to issues such as population versus single-cell measurements and the therapeutic relevance and throughput/robustness of the assay. Due to the well-established relationship between morphology and cellular function, morphological profiling has become increasingly utilized to better understand functional heterogeneity and its impact on therapeutic development...
November 7, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/29126559/outcomes-of-a-simplified-ultrasound-guided-intravenous-training-course-for-emergency-nurses
#14
Sarah Feinsmith, Ryan Huebinger, Michael Pitts, Emily Baran, Sheila Haas
INTRODUCTION: Various medical or anatomical conditions can lead to difficult intravenous access (DIVA) in the emergency department. It was hypothesized that developing an emergency nurse-training program could reduce IV attempts in the emergency department, improving throughput and patient care. METHODS: Emergency nurses completed a 4-hour ultrasound-guided intravenous (USGIV) access course and achieved competency after 10 successful supervised USGIV insertions on patients...
November 7, 2017: Journal of Emergency Nursing: JEN: Official Publication of the Emergency Department Nurses Association
https://www.readbyqxmd.com/read/29123481/development-in-assay-methods-for-in-vitro-antimalarial-drug-efficacy-testing-a-systematic-review
#15
REVIEW
Shweta Sinha, Phulen Sarma, Rakesh Sehgal, Bikash Medhi
The emergence and spread of drug resistance are the major challenges in malaria eradication mission. Besides various strategies laid down by World Health Organization, such as vector management, source reduction, early case detection, prompt treatment, and development of new diagnostics and vaccines, nevertheless the need for new and efficacious drugs against malaria has become a critical priority on the global malaria research agenda. At several screening stages, millions of compounds are screened (1,000-2,000,000 compounds per screening campaign), before pre-clinical trials to select optimum lead...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29119352/using-physics-based-pose-predictions-and-free-energy-perturbation-calculations-to-predict-binding-poses-and-relative-binding-affinities-for-fxr-ligands-in-the-d3r-grand-challenge-2
#16
Christina Athanasiou, Sofia Vasilakaki, Dimitris Dellis, Zoe Cournia
Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands...
November 8, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29118424/methods-for-scarless-selection-free-generation-of-human-cells-and-allele-specific-functional-analysis-of-disease-associated-snps-and-variants-of-uncertain-significance
#17
Nicole B Coggins, Jacob Stultz, Henriette O'Geen, Luis G Carvajal-Carmona, David J Segal
With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29118095/nmr-in-structure-based-drug-design
#18
REVIEW
Marta G Carneiro, Eiso Ab, Stephan Theisgen, Gregg Siegal
NMR spectroscopy is a powerful technique that can provide valuable structural information for drug discovery endeavors. Here, we discuss the strengths (and limitations) of NMR applications to structure-based drug discovery, highlighting the different levels of resolution and throughput obtainable. Additionally, the emerging field of paramagnetic NMR in drug discovery and recent developments in approaches to speed up and automate protein-observed NMR data collection and analysis are discussed.
November 8, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/29117239/novel-viruses-in-salivary-glands-of-mosquitoes-from-sylvatic-cerrado-midwestern-brazil
#19
Andressa Zelenski de Lara Pinto, Michellen Santos de Carvalho, Fernando Lucas de Melo, Ana Lúcia Maria Ribeiro, Bergmann Morais Ribeiro, Renata Dezengrini Slhessarenko
Viruses may represent the most diverse microorganisms on Earth. Novel viruses and variants continue to emerge. Mosquitoes are the most dangerous animals to humankind. This study aimed at identifying viral RNA diversity in salivary glands of mosquitoes captured in a sylvatic area of Cerrado at the Chapada dos Guimarães National Park, Mato Grosso, Brazil. In total, 66 Culicinae mosquitoes belonging to 16 species comprised 9 pools, subjected to viral RNA extraction, double-strand cDNA synthesis, random amplification and high-throughput sequencing, revealing the presence of seven insect-specific viruses, six of which represent new species of Rhabdoviridae (Lobeira virus), Chuviridae (Cumbaru and Croada viruses), Totiviridae (Murici virus) and Partitiviridae (Araticum and Angico viruses)...
2017: PloS One
https://www.readbyqxmd.com/read/29115357/measuring-biotherapeutic-viscosity-and-degradation-on-chip-with-particle-diffusometry
#20
K N Clayton, D Lee, S T Wereley, T L Kinzer-Ursem
In the absence of efficient ways to test drug stability and efficacy, pharmaceuticals that have been stored outside of set temperature conditions are destroyed, often at great cost. This is especially problematic for biotherapeutics, which are highly sensitive to temperature fluctuations. Current platforms for assessing the stability of protein-based biotherapeutics in high throughput and in low volumes are unavailable outside of research and development laboratories and are not efficient for use in production, quality control, distribution, or clinical settings...
November 8, 2017: Lab on a Chip
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