keyword
MENU ▼
Read by QxMD icon Read
search

Throughput

keyword
https://www.readbyqxmd.com/read/27926367/molecular-genetics-of-pancreatic-neoplasms
#1
REVIEW
Waki Hosoda, Laura D Wood
Pancreatic neoplasms have a wide range of histologic types with distinct clinical outcomes. Recent advances in high-throughput sequencing technologies have greatly deepened our understanding of pancreatic neoplasms. Now, the exomes of major histologic types of pancreatic neoplasms have been sequenced, and their genetic landscapes have been revealed. This article reviews the molecular changes underlying pancreatic neoplasms, with a special focus on the genetic changes that characterize the histologic types of pancreatic neoplasms...
December 2016: Surgical Pathology Clinics
https://www.readbyqxmd.com/read/27925593/a-review-of-machine-learning-and-statistical-approaches-for-detecting-snp-interactions-in-high-dimensional-genomic-data
#2
Suneetha Uppu, Aneesh Krishna, Raj Gopalan
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature...
December 2, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27925498/behavior-of-tetracycline-and-sulfamethoxazole-and-their-corresponding-resistance-genes-in-three-dimensional-biofilm-electrode-reactors-with-low-current
#3
Shuai Zhang, Hai L Song, Xiao L Yang, Xi Z Long, Xi Liu, Tong Q Chen
Antibiotics and antibiotic resistance genes (ARGs) have become major health concerns. In this study, three-dimensional biofilm-electrode reactors (3D-BERs) under low current were designed to assess their performance in removing tetracycline (TC) and sulfamethoxazole (SMX) from synthetic wastewater. In addition, the fates of the corresponding ARGs in microbial communities were investigated. The mass removal ratios of TC and SMX by the 3D-BERs were 82.6-97.3% and 72.2-93.2%, respectively. There were obvious increases in the relative abundances of all target genes after ∼2 months...
December 7, 2016: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/27925216/light-regulation-of-alternative-pre-mrna-splicing-in-plants
#4
Hangxiao Zhang, Chentao Lin, Lianfeng Gu
Alternative splicing (AS) is a major post-transcriptional mechanism to enhance the diversity of proteome in response to environmental signals. Among the numerous external signals perceived by plants, light is the most crucial one. Plants utilize complex photoreceptor signaling networks to sense different light conditions and adjust their growth and development accordingly. Although light-mediated gene expression has been widely investigated, little is known regarding the mechanism of light affecting AS to modulate mRNA at the post-transcriptional level...
December 7, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27924981/hts-ftir-spectroscopy-allows-the-classification-of-polyphenols-according-to-their-differential-effects-on-the-mda-mb-231-breast-cancer-cell-line
#5
A Mignolet, V Mathieu, E Goormaghtigh
Breast cancer is a major public health issue among women in the world. Meanwhile new anticancer treatments struggle more and more to be accepted in the pharmaceutical market and research costs still increase. There is therefore a need to find new treatments and new screening methods to test them more quickly and efficiently. Among natural compounds, an increasing interest has been given to polyphenols as they can take action at the different stages of carcinogenesis, from tumour initiation to metastasis formation, by disturbing multiple cellular signalling pathways...
December 7, 2016: Analyst
https://www.readbyqxmd.com/read/27924944/platform-construction-and-extraction-mechanism-study-of-magnetic-mixed-hemimicelles-solid-phase-extraction
#6
Deli Xiao, Chan Zhang, Jia He, Rong Zeng, Rong Chen, Hua He
Simple, accurate and high-throughput pretreatment method would facilitate large-scale studies of trace analysis in complex samples. Magnetic mixed hemimicelles solid-phase extraction has the power to become a key pretreatment method in biological, environmental and clinical research. However, lacking of experimental predictability and unsharpness of extraction mechanism limit the development of this promising method. Herein, this work tries to establish theoretical-based experimental designs for extraction of trace analytes from complex samples using magnetic mixed hemimicelles solid-phase extraction...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924926/identification-of-protein-structural-elements-responsible-for-the-diversity-of-sequence-preferences-among-mini-iii-rnases
#7
Dawid Głów, Małgorzata Kurkowska, Justyna Czarnecka, Krzysztof Szczepaniak, Dariusz Pianka, Verena Kappert, Janusz M Bujnicki, Krzysztof J Skowronek
Many known endoribonucleases select their substrates based on the presence of one or a few specific nucleotides at or near the cleavage site. In some cases, selectivity is also determined by the structural features of the substrate. We recently described the sequence-specific cleavage of double-stranded RNA by Mini-III RNase from Bacillus subtilis in vitro. Here, we characterized the sequence specificity of eight other members of the Mini-III RNase family from different bacterial species. High-throughput analysis of the cleavage products of Φ6 bacteriophage dsRNA indicated subtle differences in sequence preference between these RNases, which were confirmed and characterized by systematic analysis of the cleavage kinetics of a set of short dsRNA substrates...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924604/exploring-genome-wide-expression-profiles-using-machine-learning-techniques
#8
Moritz Kebschull, Panos N Papapanou
Although contemporary high-throughput -omics methods produce high-dimensional data, the resulting wealth of information is difficult to assess using traditional statistical procedures. Machine learning methods facilitate the detection of additional patterns, beyond the mere identification of lists of features that differ between groups.Here, we demonstrate the utility of (1) supervised classification algorithms in class validation, and (2) unsupervised clustering in class discovery. We use data from our previous work that described the transcriptional profiles of gingival tissue samples obtained from subjects suffering from chronic or aggressive periodontitis (1) to test whether the two diagnostic entities were also characterized by differences on the molecular level, and (2) to search for a novel, alternative classification of periodontitis based on the tissue transcriptomes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924603/differential-expression-and-functional-analysis-of-high-throughput-omics-data-using-open-source-tools
#9
Moritz Kebschull, Melanie Julia Fittler, Ryan T Demmer, Panos N Papapanou
Today, -omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ, or tissue sample, allow for an unbiased, comprehensive genome-level analysis of complex diseases, offering a large advantage over earlier "candidate" gene or pathway analyses. A primary goal in the analysis of these high-throughput assays is the detection of those features among several thousand that differ between different groups of samples. In the context of oral biology, our group has successfully utilized -omics technology to identify key molecules and pathways in different diagnostic entities of periodontal disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924599/tools-and-strategies-for-analysis-of-genome-wide-and-gene-specific-dna-methylation-patterns
#10
Aniruddha Chatterjee, Euan J Rodger, Ian M Morison, Michael R Eccles, Peter A Stockwell
DNA methylation is a stable epigenetic mechanism that has important roles in the normal function of a cell and therefore also in disease etiology. Accurate measurements of normal and altered DNA methylation patterns are important to understand its role in regulating gene expression and cell phenotype. Remarkable progress has been made over the last decade in developing methodologies to investigate DNA methylation. The availability of next-generation sequencing has enabled the profiling of methylation marks at an unprecedented scale...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924579/reconstructing-erk-signaling-in-the-drosophila-embryo-from-fixed-images
#11
Bomyi Lim, Carmeline J Dsilva, Ioannis G Kevrekidis, Stanislav Y Shvartsman
The early Drosophila embryo provides unique opportunities for quantitative studies of ERK signaling. This system is characterized by simple anatomy, the ease of obtaining large numbers of staged embryos, and the availability of powerful tools for genetic manipulation of the ERK pathway. Here, we describe how these experimental advantages can be combined with recently developed microfluidic devices for high throughput imaging of ERK activation dynamics. We focus on the stage during the third hour of development, when ERK activation is essential for patterning of the future nerve cord...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924563/high-throughput-in-vitro-identification-of-direct-mapk-erk-substrates
#12
Rona Grossman, Ze'ev Paroush
Phosphorylation mediated by cellular protein kinases is an effective mechanism employed by an organism to regulate central processes such as cell-cycle progression, metabolic pathways, cytoskeletal function, cell migration and differentiation. Thus, for example, various signaling pathways utilize sequential phosphorylation events to relay external cues from the cell surface to the nucleus, where eventually gene expression profiles are altered and, consequently, changes in cell fates and function are induced...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924557/high-throughput-analysis-of-mammalian-receptor-tyrosine-kinase-activation-in-yeast-cells
#13
Nobuo Yoshimoto, Shun'ichi Kuroda
Tyrosine phosphorylation is an essential posttranslational modification in intracellular signaling molecules. Since tyrosine phosphorylation occurs in less than 0.1 % of all phosphorylated amino acids in mammalian cells, it is difficult to detect the nascent phosphotyrosine at a high signal-to-noise ratio due to high intracellular backgrounds (i.e., unexpected crosstalks among endogenous signaling molecules). In order to address this issue, we reconstituted the mammalian signaling pathway involving an extracellular ligand and a receptor tyrosine kinase (RTK) in Saccharomyces cerevisiae, a lower eukaryote that lacks endogenous tyrosine kinases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924497/a-strategy-combining-higher-energy-c-trap-dissociation-with-neutral-loss-and-product-ion-based-ms-n-acquisition-for-global-profiling-and-structure-annotation-of-fatty-acids-conjugates
#14
Qi-Rui Bi, Jin-Jun Hou, Min Yang, Yao Shen, Peng Qi, Rui-Hong Feng, Zhuo Dai, Bing-Peng Yan, Jian-Wei Wang, Xiao-Jian Shi, Wan-Ying Wu, De-An Guo
Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MS(n) (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode...
December 6, 2016: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/27924486/surface-plasmon-resonance-a-useful-strategy-for-the-identification-of-small-molecule-argonaute-2-protein-binders
#15
Elena Poser, Ilaria Genovese, Silvia Masciarelli, Teresa Bellissimo, Francesco Fazi, Gianni Colotti
Surface plasmon resonance (SPR) is one of the most important techniques for the detection and the characterization of molecular interactions. SPR technology is a label-free approach for monitoring biomolecular interactions in real time. The binding of analytes to molecules immobilized on a thin metal film (ligand) determines a change in the refractive index and, therefore in the angle of extinction of light, is reflected when polarized light hits the film, monitored in real time as a change in the position of the dip in reflected intensity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924483/rapid-generation-of-mirna-inhibitor-leads-by-bioinformatics-and-efficient-high-throughput-screening-methods
#16
Christopher L Haga, Sai Pradeep Velagapudi, Jessica L Childs-Disney, Jacqueline Strivelli, Matthew D Disney, Donald G Phinney
The discovery of microRNAs (miRNAs) has opened an entire new avenue for drug development. These short (15-22 nucleotides) noncoding RNAs, which function in RNA silencing and posttranscriptional regulation of gene expression, have been shown to critically affect numerous pathways in both development and disease progression. Current miRNA drug development focuses on either reintroducing the miRNA into cells through the use of a miRNA mimic or inhibiting its function via use of a synthetic antagomir. Although these methods have shown some success as therapeutics, they face challenges particularly with regard to cellular uptake and for use as systemic reagents...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924481/machine-learning-approaches-toward-building-predictive-models-for-small-molecule-modulators-of-mirna-and-its-utility-in-virtual-screening-of-molecular-databases
#17
Vinita Periwal, Vinod Scaria
The ubiquitous role of microRNAs (miRNAs) in a number of pathological processes has suggested that they could act as potential drug targets. RNA-binding small molecules offer an attractive means for modulating miRNA function. The availability of bioassay data sets for a variety of biological assays and molecules in public domain provides a new opportunity toward utilizing them to create models and further utilize them for in silico virtual screening approaches to prioritize or assign potential functions for small molecules...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924474/quantification-of-oligonucleotide-association-with-mirna-argonaute-complexes-in-vitro
#18
Dimitrios G Zisoulis
A major challenge in the development of oligonucleotide-based microRNA (miRNA) inhibitors for therapeutic applications is the identification of candidate designs with strong affinity for the target miRNA in the context of the Argonaute complex. To this effect, distinct chemical modifications are employed along the length of the oligonucleotide aimed at strengthening the interactions with the target miRNA. However, the modification chemistry and placement can inadvertently affect the intrinsic ability of the oligonucleotide to pair with its target in the context of Argonaute...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924402/age-related-response-of-rumen-microbiota-to-mineral-salt-and-effects-of-their-interactions-on-enteric-methane-emissions-in-cattle
#19
C Liu, X H Li, Y X Chen, Z H Cheng, Q H Duan, Q H Meng, X P Tao, B Shang, H M Dong
Mineral salt bricks are often used in cow raising as compensation for mineral losses to improve milk yield, growth, and metabolic activity. Generally, effects of minerals are partially thought to result from improvement of microbial metabolism, but their influence on the rumen microbiota has rarely been documented to date. In this study, we investigated the response of microbiota to mineral salt in heifer and adult cows and evaluated ruminal fermentation and enteric methane emissions of cows fed mineral salts...
December 6, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27924345/chemoenzymatic-synthesis-of-para-nitrophenol-pnp-tagged-%C3%AE-2-8-sialosides-and-high-throughput-substrate-specificity-studies-of-%C3%AE-2-8-sialidases
#20
Nova Tasnima, Hai Yu, Yanhong Li, Abhishek Santra, Xi Chen
para-Nitrophenol (pNP)-tagged α2-8-linked sialosides containing different sialic acid forms were chemoenzymatically synthesized using an efficient one-pot three-enzyme α2-8-sialylation system. The resulting compounds allowed high-throughput substrate specificity studies of the α2-8-sialidase activity of a recombinant human cytosolic sialidase hNEU2 and various bacterial sialidases. The sialoside substrate profiles obtained can be used to guide the selection of suitable sialidases for sialylglycan analysis and for cell and tissue surface glycan modification...
December 7, 2016: Organic & Biomolecular Chemistry
keyword
keyword
24928
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"