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https://www.readbyqxmd.com/read/28636268/high-throughput-sequencing-reveals-drosophila-suzukii-responses-to-insecticides
#1
Ruchir Mishra, Joanna C Chiu, Gang Hua, Nilesh R Tawari, Michael J Adang, Ashfaq A Sial
Global climate change and acquired resistance to insecticides are threats to world food security. Drosophila suzukii, a devastating invasive pest in many parts of the world, causes substantial economic losses to fruit production industries, forcing farmers to apply broad-spectrum insecticides frequently. This could lead to the development of insecticide resistance. We determined the Lethal Concentration50 (median lethal concentration) values of zeta-cypermethrin, spinosad, and malathion insecticides against D...
June 21, 2017: Insect Science
https://www.readbyqxmd.com/read/28634762/rapid-preconcentration-of-viable-bacteria-using-magnetic-ionic-liquids-for-pcr-amplification-and-culture-based-diagnostics
#2
Kevin D Clark, Jeffrey A Purslow, Stephen A Pierson, Omprakash Nacham, Jared L Anderson
In this study, a series of magnetic ionic liquids (MILs) were investigated for the extraction and preconcentration of bacteria from aqueous samples. By dispersing small volumes (e.g., 15 μL) of MIL within an aqueous cell suspension, bacteria were rapidly extracted and isolated using a magnetic field. Of the seven hydrophobic MILs examined, the trihexyl(tetradecyl)phosphonium Ni(II) hexafluoroacetylacetonate ([P66614(+)][Ni(hfacac)3(-)]) MIL exhibited the greatest enrichment of viable Escherichia coli K12 when coupled with microbiological culture as the detection method...
June 20, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28634756/a-high-throughput-targeted-and-non-targeted-method-for-the-analysis-of-microcystins-and-anatoxin-a-using-on-line-solid-phase-extraction-coupled-to-liquid-chromatography-quadrupole-time-of-flight-high-resolution-mass-spectrometry
#3
Xavier Ortiz, Eva Korenkova, Karl J Jobst, Karen A MacPherson, Eric J Reiner
Microcystins are cyclic heptapeptide hepatotoxins produced by cyanobacteria in freshwater. Sample preparation for the analysis of these cyanotoxins in water from algal blooms can take up to several days due to the matrix complexity and the low detection limits required to comply with current legislation. Moreover, there is a large number of unknown microcystins that could potentially exist in the environment resulting from different amino acid substitutions into the microcystin skeletal structure. To tackle these problems, the present study involved the development of a high throughput method based on on-line solid phase extraction coupled to liquid chromatography that could provide quantitative results for 12 microcystin variants (LR, YR, RR, HtyR, HilR, WR, LW, LA, LF, LY, Dha(7)-LR, and Dha(7)-RR) and anatoxin-A in less than 3 h with detection limits between 0...
June 20, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28634607/a-high-throughput-microfluidic-platform-for-size-selective-enrichment-of-cell-populations-in-tissue-and-blood-samples
#4
Nivedita Nivedita, Neha Garg, Abraham P Lee, Ian Papautsky
Numerous applications in biology and medicine require the efficient and reliable separation of cells for disease diagnosis, genetic analysis, drug screening, and therapeutics. In this work, we demonstrate a novel technology that integrates a passive and an active device to separate, enrich and release cells on-demand from a complex blood sample, or cancer cells derived from a tissue biopsy. We exploit the high throughput (>1 mL min(-1)), size-based sorting capability of the passive spiral inertial microfluidic (iMF) device to focus particles/cells towards an active lateral cavity acoustic transducer (LCAT) device for size-selective enrichment...
June 21, 2017: Analyst
https://www.readbyqxmd.com/read/28634339/effective-synthesis-of-highly-oxidized-graphene-oxide-that-enables-wafer-scale-nanopatterning-preformed-acidic-oxidizing-medium-approach
#5
Chun-Hu Chen, Shin Hu, Jyun-Fu Shih, Chang-Ying Yang, Yun-Wen Luo, Ren-Huai Jhang, Chao-Ming Chiang, Yung-Jr Hung
Demand for rapid and massive-scale exfoliation of bulky graphite remains high in graphene commercialization and property manipulation. We report a procedure utilizing "preformed acidic oxidizing medium (PAOM)" as a modified version of the Hummers' method for fast and reliable synthesis of graphene oxide. Pre-mixing of KMnO4 and concentrated H2SO4 prior to the addition of graphite flakes enables the formation of effectively and efficiently oxidized graphene oxide (EEGO) featured by its high yields and suspension homogeneity...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634292/monte-carlo-sampling-for-stochastic-weight-functions
#6
Daan Frenkel, K Julian Schrenk, Stefano Martiniani
Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here, we consider the case that the weight determining the acceptance probability itself is fluctuating. This situation is common in many numerical studies. We show that it is possible to construct a rigorous Monte Carlo algorithm that visits points in state space with a probability proportional to their average weight...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28634160/high-throughput-characterization-of-cascade-type-i-e-crispr-guide-efficacy-reveals-unexpected-pam-diversity-and-target-sequence-preferences
#7
Becky Xu Hua Fu, Michael Wainberg, Anshul Kundaje, Andrew Z Fire
Interactions between Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs and CRISPR-associated (Cas) proteins form an RNA-guided adaptive immune system in prokaryotes. The adaptive immune system utilizes segments of the genetic material of invasive foreign elements in the CRISPR locus. The loci are transcribed and processed to produce small CRISPR RNAs (crRNAs), with degradation of invading genetic material directed by a combination of complementarity between RNA and DNA and in some cases recognition of adjacent motifs called PAMs (Protospacer Adjacent Motifs)...
June 20, 2017: Genetics
https://www.readbyqxmd.com/read/28634068/investigation-of-changes-in-endocannabinoids-and-n-acylethanolamides-in-biofluids-and-their-correlations-with-female-infertility
#8
Jun Ding, Xiao-Tong Luo, Yan-Ru Yao, Hua-Ming Xiao, Ming-Quan Guo
Female infertility is a worldwide medical problem, and the scarcity of infertility biomarkers has hindered the ability to launch preventive and therapeutic measures in a timely manner. Intriguingly, alterations in endocannabinoids (eCBs) and N-acylethanolamides (NAEs) have been observed in the biofluids of infertile females. Therefore, a hypothesis of using eCB and NAEs in biofluids as infertility biomarkers was proposed by several researchers; however, little evidence exists to verify the hypothesis. To investigate their correlations with female infertility, we developed a magnetic liquid microextraction-chemical derivatization (MLME-CD) method coupled with liquid chromatography-tandem mass spectrometry for the quantification of eCBs and NAEs in biofluids...
June 12, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28633993/microfluidics-as-a-strategic-player-to-decipher-single-cell-omics
#9
REVIEW
Ouriel Caen, Heng Lu, Philippe Nizard, Valerie Taly
Most cell studies are performed at a population level, relying on the assumption of a normal distribution of the function and fate of a cell among a population. However, technologies allowing single-cell analysis (SCA) have recently arisen and have led to increasing evidence of cell population heterogeneity and its importance. Tremendous amounts of new data could now be uncovered to redefine our understanding of cell omics. Microfluidics has emerged as a major technological player in this new era and is gradually increasing in use among biology laboratories, mainly due to the single-cell high-throughput handling solutions it offers...
June 17, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28633897/discovery-and-optimization-of-3-4-aryl-heteroarylsulfonyl-piperazin-1-yl-6-piperidin-1-yl-pyridazines-as-novel-cns-penetrant-pan-muscarinic-antagonists
#10
Aaron M Bender, Rebecca L Weiner, Vincent B Luscombe, Sonia Ajmera, Hyekyung P Cho, Sichen Chang, Xiaoyan Zhan, Alice L Rodriguez, Colleen M Niswender, Darren W Engers, Thomas M Bridges, P Jeffrey Conn, Craig W Lindsley
This letter describes the synthesis and structure activity relationship (SAR) studies of structurally novel M4 antagonists, based on a 3-(4-aryl/heteroarylsulfonyl)piperazin-1-yl)-6-(piperidin-1-yl)pyridazine core, identified from a high-throughput screening campaign. A multi-dimensional optimization effort enhanced potency at human M4 (hM4 IC50s<200nM), with only moderate species differences noted, and with enantioselective inhibition. Moreover, CNS penetration proved attractive for this series (rat brain:plasma Kp=2...
May 15, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28633662/orthored-a-rapid-and-accurate-orthology-prediction-tool-with-low-computational-requirement
#11
Kai Battenberg, Ernest K Lee, Joanna C Chiu, Alison M Berry, Daniel Potter
BACKGROUND: Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time, in silico orthology prediction tools often require large computational resources only available on computing clusters. Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to published tools that requires only a desktop computer...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28633659/computing-patient-data-in-the-cloud-practical-and-legal-considerations-for-genetics-and-genomics-research-in-europe-and-internationally
#12
Fruzsina Molnár-Gábor, Rupert Lueck, Sergei Yakneen, Jan O Korbel
Biomedical research is becoming increasingly large-scale and international. Cloud computing enables the comprehensive integration of genomic and clinical data, and the global sharing and collaborative processing of these data within a flexibly scalable infrastructure. Clouds offer novel research opportunities in genomics, as they facilitate cohort studies to be carried out at unprecedented scale, and they enable computer processing with superior pace and throughput, allowing researchers to address questions that could not be addressed by studies using limited cohorts...
June 20, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28633445/bpp-a-sequence-based-algorithm-for-branch-point-prediction
#13
Qing Zhang, Xiaodan Fan, Yejun Wang, Mingan Sun, Jianlin Shao, Dianjing Guo
Motivation: Although high-throughput sequencing methods have been proposed to identify splicing branch points in the human genome, these methods can only detect a small fraction of the branch points subject to the sequencing depth, experimental cost and the expression level of the mRNA. An accurate computational model for branch point prediction is therefore an ongoing objective in human genome research. Results: We here propose a novel branch point prediction algorithm that utilises information on the branch point sequence and the polypyrimidine tract...
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633424/three-dimensional-3d-heparg-spheroid-model-with-physiologically-relevant-xenobiotic-metabolism-competence-and-hepatocyte-functionality-for-liver-toxicity-screening
#14
Sreenivasa C Ramaiahgari, Suramya Waidyanatha, Darlene Dixon, Michael J DeVito, Richard S Paules, Stephen S Ferguson
Effective prediction of human responses to chemical and drug exposure is of critical importance in environmental toxicology research and drug development. While significant progress has been made to address this challenge using in vitro liver models, these approaches often fail due to inadequate tissue model functionality. Herein, we describe the development, optimization, and characterization of a novel three-dimensional (3D) spheroid model using differentiated HepaRG cells that achieve and maintain physiologically-relevant levels of xenobiotic metabolism (CYP1A2, CYP2B6, and CYP3A4/5)...
June 15, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28633418/detecting-and-removing-multiplicative-spatial-bias-in-high-throughput-screening-technologies
#15
Iurie Caraus, Bogdan Mazoure, Robert Nadon, Vladimir Makarenkov
Motivation: Considerable attention has been paid recently to improve data quality in high-throughput screening (HTS) and high-content screening (HCS) technologies widely used in drug development and chemical toxicity research. However, several environmentally- and procedurally-induced spatial biases in these screens decrease measurement accuracy, leading to increased numbers of false positives and false negatives in hit selection. Although effective bias correction methods and software have been developed over the past decades, almost all of these tools have been designed to reduce the effect of additive bias only...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633357/matter-an-r-package-for-rapid-prototyping-with-larger-than-memory-datasets-on-disk
#16
Kylie A Bemis, Olga Vitek
Summary: We introduce matter , an R package for direct interactions with larger-than-memory datasets, stored in an arbitrary number of files of any size. matter is primarily designed for datasets in new and rapidly evolving file formats, which may lack extensive software support. matter enables a wide variety of data exploration and manipulation steps, and is extensible to many bioinformatics applications. It supports reproducible research by minimizing the need of converting and storing data in multiple formats...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632966/characterizing-alzheimer-s-disease-through-metabolomics-and-investigating-anti-alzheimer-s-disease-effects-of-natural-products
#17
REVIEW
Lunzhao Yi, Wenbin Liu, Zhe Wang, Dabing Ren, Weijun Peng
Alzheimer's disease (AD) is the most common cause of dementia in elderly people and is among the greatest healthcare challenges of the 21st century. However, the etiology and pathogenesis of AD remain poorly understood, and no curative treatments are available to slow down or stop the degenerative effects of AD. As a high-throughput approach, metabolomics is gaining significant attention in AD research, because it has a powerful potential to discover novel biomarkers, unravel new therapeutic targets for AD, and identify perturbed metabolic pathways involved in AD progression...
June 20, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28632788/high-throughput-identification-and-rational-design-of-synergistic-small-molecule-pairs-for-combating-and-bypassing-antibiotic-resistance
#18
Morgan A Wambaugh, Viplendra P S Shakya, Adam J Lewis, Matthew A Mulvey, Jessica C S Brown
Antibiotic-resistant infections kill approximately 23,000 people and cost $20,000,000,000 each year in the United States alone despite the widespread use of small-molecule antimicrobial combination therapy. Antibiotic combinations typically have an additive effect: the efficacy of the combination matches the sum of the efficacies of each antibiotic when used alone. Small molecules can also act synergistically when the efficacy of the combination is greater than the additive efficacy. However, synergistic combinations are rare and have been historically difficult to identify...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28631939/a-high-throughput-screening-assay-for-nkcc1-cotransporter-using-nonradioactive-rubidium-flux-technology
#19
Sikander Gill, Rajwant Gill, Yang Wen, Thilo Enderle, Doris Roth, Dong Liang
A high-throughput screening (HTS) assay was developed for cotransporter, NKCC1, which is a potential target for the treatment of diverse disorders. This nonradioactive rubidium flux assay coupled with ion channel reader series provides a working screen for this target expressed in human embryonic kidney (HEK) cell line. An eightfold window of detection was achieved with the optimized assay. This new functional assay offered a robust working model for NKCC1 in determining reliable and concordant rank orders of the test compounds supporting its sensitivity and specificity...
May 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28631799/droplet-control-technologies-for-microfluidic-high-throughput-screening-%C3%AE-hts
#20
REVIEW
Muhsincan Sesen, Tuncay Alan, Adrian Neild
The transition from micro well plate and robotics based high throughput screening (HTS) to chip based screening has already started. This transition promises reduced droplet volumes thereby decreasing the amount of fluids used in these studies. Moreover, it significantly boosts throughput allowing screening to keep pace with the overwhelming number of molecular targets being discovered. In this review, we analyse state-of-the-art droplet control technologies that exhibit potential to be used in this new generation of screening devices...
June 20, 2017: Lab on a Chip
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