keyword
MENU ▼
Read by QxMD icon Read
search

high throughput

keyword
https://www.readbyqxmd.com/read/29166086/focused-conformational-sampling-in-proteins
#1
Marco Bacci, Cassiano Langini, Jiří Vymětal, Amedeo Caflisch, Andreas Vitalis
A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166018/discovery-of-small-molecule-inhibitors-of-ubiquitin-specific-protease-7-usp7-using-integrated-nmr-and-in-silico-techniques
#2
Paola Di Lello, Richard Pastor, Jeremy M Murray, Robert A Blake, Frederick Cohen, Terry D Crawford, Joy Drobnick, Jason Drummond, Lorna Kategaya, Tracy Kleinheinz, Till Maurer, Lionel Rouge, Xianrui Zhao, Ingrid Wertz, Chudi Ndubaku, Vickie Tsui
USP7 is a deubiquitinase implicated in destabilizing the tumor suppressor p53 and for this reason it has gained increasing attention as a potential oncology target for small molecule inhibitors. Herein we describe the biophysical, biochemical and computational approaches that led to the identification of 4-(2-aminopyridin-3-yl)-phenol compounds described by Kategaya et al.1 as specific inhibitors of USP7. Fragment based lead discovery (FBLD) by NMR combined with virtual screening and re-mining of biochemical high-throughput screening (HTS) hits led to the discovery of a series of ligands that bind in the "palm" region of the catalytic domain of USP7 and inhibit its catalytic activity...
November 22, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29165984/on-chip-lipid-extraction-using-super-absorbent-polymers-for-mass-spectrometry
#3
Geul Bang, Young Hwan Kim, Junghyo Yoon, Yeong Jun Yu, Seok Chung, Jeong Ah Kim
Pre-treatment of samples is the one of most important steps in analytical methods for efficient and accurate results. Typically, an extraction method used for lipid analysis with mass spectrometry is accompanied by complex liquid-liquid extraction. We have devised a simple, rapid, and efficient lipid extraction method using super absorbent polymers (SAPs) and developed a high-throughput lipid extraction platform based on a microfluidic system. Since SAPs can rapidly absorb an aqueous solution from a raw sample and convert it into the gel, the lipid extraction process can be remarkably simplified...
November 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29165730/what-else-is-in-salviae-officinalis-folium-comprehensive-species-identification-of-plant-raw-material-by-dna-metabarcoding
#4
Corinna Schmiderer, Brigitte Lukas, Joana Ruzicka, Johannes Novak
Quality control of drugs consists of identifying the raw material to avoid unwanted admixtures or exchange of material as well as looking for abiotic and biotic contaminations. So far, identity and microbial contamination are analyzed by separate processes and separate methods. Species identification by their DNA ("DNA barcoding") has the potential to supplement existing methods of identification. The introduction of next-generation sequencing methods offers completely new approaches like the identification of whole communities in one analysis, termed "DNA metabarcoding"...
November 17, 2017: Planta Medica
https://www.readbyqxmd.com/read/29165648/structure-modeling-of-rna-using-sparse-nmr-constraints
#5
Benfeard Williams, Bo Zhao, Arpit Tandon, Feng Ding, Kevin M Weeks, Qi Zhang, Nikolay V Dokholyan
RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165646/development-and-application-of-a-recombination-based-library-versus-library-high-throughput-yeast-two-hybrid-rll-y2h-screening-system
#6
Fang Yang, Yingying Lei, Meiling Zhou, Qili Yao, Yichao Han, Xiang Wu, Wanshun Zhong, Chenghang Zhu, Weize Xu, Ran Tao, Xi Chen, Da Lin, Khaista Rahman, Rohit Tyagi, Zeshan Habib, Shaobo Xiao, Dang Wang, Yang Yu, Huanchun Chen, Zhenfang Fu, Gang Cao
Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165544/rna-methylation-and-diseases-experimental-results-databases-web-servers-and-computational-models
#7
Xing Chen, Ya-Zhou Sun, Hui Liu, Lin Zhang, Jian-Qiang Li, Jia Meng
Ribonucleic acid (RNA) methylation is a type of posttranscriptional modifications occurring in all kingdoms of life. It is strongly related to important biological process, thus making it linked to a number of human diseases. Owing to the development of high-throughput sequencing technology, plenty of achievement had been obtained in RNA methylation research recently. Meanwhile, various computational models have been developed to analyze and mining increasing RNA methylation data. In this review, we first made a brief introduction about eight types of most popular RNA methylation, the biological functions of RNA methylation, the relationship between RNA methylation and disease and five important RNA methylation-related diseases...
November 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29165344/high-throughput-identification-of-antimicrobial-peptides-from-amphibious-mudskippers
#8
Yunhai Yi, Xinxin You, Chao Bian, Shixi Chen, Zhao Lv, Limei Qiu, Qiong Shi
Widespread existence of antimicrobial peptides (AMPs) has been reported in various animals with comprehensive biological activities, which is consistent with the important roles of AMPs as the first line of host defense system. However, no big-data-based analysis on AMPs from any fish species is available. In this study, we identified 507 AMP transcripts on the basis of our previously reported genomes and transcriptomes of two representative amphibious mudskippers, Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM)...
November 22, 2017: Marine Drugs
https://www.readbyqxmd.com/read/29165063/high-throughput-screening-strategies-for-the-development-of-anti-virulence-inhibitors-against-staphylococcus-aureus
#9
Xiaodan Cai, Weihao Zheng, Zigang Li
The increasing threats of antibiotic resistance urge the need for developing new approaches to combat bacterial infections. Unlike conventional antibiotics that aim to kill bacteria or inhibit their growth, targeting bacterial virulence may be a promising alternative approach, which imposes weaker selective pressure for the generation of resistance. Here, we review the pathways related to staphylococcal virulence, summarize the high-throughput screening strategies used to identify novel anti-virulence inhibitors, and discuss the advantages and disadvantages of these strategies...
November 20, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29164775/high-throughput-phase-field-design-of-high-energy-density-polymer-nanocomposites
#10
Zhong-Hui Shen, Jian-Jun Wang, Yuanhua Lin, Ce-Wen Nan, Long-Qing Chen, Yang Shen
Understanding the dielectric breakdown behavior of polymer nanocomposites is crucial to the design of high-energy-density dielectric materials with reliable performances. It is however challenging to predict the breakdown behavior due to the complicated factors involved in this highly nonequilibrium process. In this work, a comprehensive phase-field model is developed to investigate the breakdown behavior of polymer nanocomposites under electrostatic stimuli. It is found that the breakdown strength and path significantly depend on the microstructure of the nanocomposite...
November 22, 2017: Advanced Materials
https://www.readbyqxmd.com/read/29164709/identification-of-pyridoxal-phosphate-modified-proteins-using-mass-spectrometry
#11
Yue Wu, Jin Chen, Zheyi Liu, Fangjun Wang
RATIONALE: Pyridoxal 5'-phosphate (PLP) cooperates with a variety of enzymes in all organisms for many important biological processes. The development of mass-spectrometry-based methodology for high throughput modification analyses could provide an alternative way for PLP identification. The present study aims to identify PLP modification. METHODS: More PLP site-determining information was obtained by introducing multistage activation (MSA) assisted collision induced dissociation (CID)...
November 22, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29164416/high-throughput-and-direct-measurement-of-androgen-levels-using-turbulent-flow-chromatography-liquid-chromatography-triple-quadrupole-mass-spectrometry-tfc-lc-tqms-to-discover-chemicals-that-modulate-dihydrotestosterone-production-in-human-prostate-cancer-cells
#12
Kyungsu Kang, Lei Peng, Yu-Jin Jung, Joo Yeon Kim, Eun Ha Lee, Hee Ju Lee, Sang Min Kim, Sang Hyun Sung, Cheol-Ho Pan, Yongsoo Choi
OBJECTIVES: To develop a high-throughput screening system to measure the conversion of testosterone to dihydrotestosterone (DHT) in cultured human prostate cancer cells using turbulent flow chromatography liquid chromatography-triple quadrupole mass spectrometry (TFC-LC-TQMS). RESULTS: After optimizing the cell reaction system, this method demonstrated a screening capability of 103 samples, including 78 single compounds and 25 extracts, in less than 12 h without manual sample preparation...
November 21, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/29164062/preleukemic-hematopoietic-stem-cells-in-human-acute-myeloid-leukemia
#13
REVIEW
M Ryan Corces, Howard Y Chang, Ravindra Majeti
Acute myeloid leukemia (AML) is an aggressive malignancy of the bone marrow characterized by an uncontrolled proliferation of undifferentiated myeloid lineage cells. Decades of research have demonstrated that AML evolves from the sequential acquisition of genetic alterations within a single lineage of hematopoietic cells. More recently, the advent of high-throughput sequencing has enabled the identification of a premalignant phase of AML termed preleukemia. Multiple studies have demonstrated that AML can arise from the accumulation of mutations within hematopoietic stem cells (HSCs)...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29164055/micrornas-and-acute-myeloid-leukemia-chemoresistance-a-mechanistic-overview
#14
REVIEW
Martino Marco Gabra, Leonardo Salmena
Up until the early 2000s, a functional role for microRNAs (miRNAs) was yet to be elucidated. With the advent of increasingly high-throughput and precise RNA-sequencing techniques within the last two decades, it has become well established that miRNAs can regulate almost all cellular processes through their ability to post-transcriptionally regulate a majority of protein-coding genes and countless other non-coding genes. In cancer, miRNAs have been demonstrated to play critical roles by modifying or controlling all major hallmarks including cell division, self-renewal, invasion, and DNA damage among others...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29163701/high-levels-of-depdc1b-predict-shorter-biochemical-recurrence-free-survival-of-patients-with-prostate-cancer
#15
Shoumin Bai, Ting Chen, Tao Du, Xianju Chen, Yiming Lai, Xiaoming Ma, Wanhua Wu, Chunhao Lin, Leyuan Liu, Hai Huang
DEP domain-containing protein 1B (DEPDC1B) has been reported to serve important functions in breast cancer and non-small cell lung cancer. However, its involvement in the development of prostate cancer (PCa) remains unclear. Therefore, the present study aimed to investigate the expression and clinical significance of DEPDC1B in tumor tissues from patients diagnosed with PCa. A total of 80 prostate tissue samples were collected following prostatectomy to generate a tissue microarray for immunohistochemical analysis of DEPDC1B protein expression...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29163636/a-pipeline-for-high-throughput-concentration-response-modeling-of-gene-expression-for-toxicogenomics
#16
John S House, Fabian A Grimm, Dereje D Jima, Yi-Hui Zhou, Ivan Rusyn, Fred A Wright
Cell-based assays are an attractive option to measure gene expression response to exposure, but the cost of whole-transcriptome RNA sequencing has been a barrier to the use of gene expression profiling for in vitro toxicity screening. In addition, standard RNA sequencing adds variability due to variable transcript length and amplification. Targeted probe-sequencing technologies such as TempO-Seq, with transcriptomic representation that can vary from hundreds of genes to the entire transcriptome, may reduce some components of variation...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29163629/high-throughput-field-phenotyping-of-leaves-leaf-sheaths-culms-and-ears-of-spring-barley-cultivars-at-anthesis-and-dough-ripeness
#17
Gero Barmeier, Urs Schmidhalter
To optimize plant architecture (e.g., photosynthetic active leaf area, leaf-stem ratio), plant physiologists and plant breeders rely on destructively and tediously harvested biomass samples. A fast and non-destructive method for obtaining information about different plant organs could be vehicle-based spectral proximal sensing. In this 3-year study, the mobile phenotyping platform PhenoTrac 4 was used to compare the measurements from active and passive spectral proximal sensors of leaves, leaf sheaths, culms and ears of 34 spring barley cultivars at anthesis and dough ripeness...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163607/increasing-leaf-vein-density-via-mutagenesis-in-rice-results-in-an-enhanced-rate-of-photosynthesis-smaller-cell-sizes-and-can-reduce-interveinal-mesophyll-cell-number
#18
Aryo B Feldman, Hei Leung, Marietta Baraoidan, Abigail Elmido-Mabilangan, Irma Canicosa, William P Quick, John Sheehy, Erik H Murchie
Improvements to leaf photosynthetic rates of crops can be achieved by targeted manipulation of individual component processes, such as the activity and properties of RuBisCO or photoprotection. This study shows that simple forward genetic screens of mutant populations can also be used to rapidly generate photosynthesis variants that are useful for breeding. Increasing leaf vein density (concentration of vascular tissue per unit leaf area) has important implications for plant hydraulic properties and assimilate transport...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163601/genome-wide-constitutively-expressed-gene-analysis-and-new-reference-gene-selection-based-on-transcriptome-data-a-case-study-from-poplar-canker-disease-interaction
#19
Jiaping Zhao, Fan Yang, Jinxia Feng, Yanli Wang, Barbara Lachenbruch, Jiange Wang, Xianchong Wan
A number of transcriptome datasets for differential expression (DE) genes have been widely used for understanding organismal biology, but these datasets also contain untapped information that can be used to develop more precise analytical tools. With the use of transcriptome data generated from poplar/canker disease interaction system, we describe a methodology to identify candidate reference genes from high-throughput sequencing data. This methodology will improve the accuracy of RT-qPCR and will lead to better standards for the normalization of expression data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163600/plastome-rearrangements-in-the-adenocalymma-neojobertia-clade-bignonieae-bignoniaceae-and-its-phylogenetic-implications
#20
Luiz H M Fonseca, Lúcia G Lohmann
The chloroplast is one of the most important organelles of plants. This organelle has a circular DNA with approximately 130 genes. The use of plastid genomic data in phylogenetic and evolutionary studies became possible with high-throughput sequencing methods, which allowed us to rapidly obtain complete genomes at a reasonable cost. Here, we use high-throughput sequencing to study the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). More specifically, we use Hi-Seq Illumina technology to sequence 10 complete plastid genomes...
2017: Frontiers in Plant Science
keyword
keyword
39332
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"