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https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#1
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28447132/high-throughput-analysis-of-sub-visible-mab-aggregate-particles-using-automated-fluorescence-microscopy-imaging
#2
Albert Jesuran Paul, Fabian Bickel, Martina Röhm, Lisa Hospach, Bettina Halder, Nina Rettich, René Handrick, Eva Maria Herold, Hans Kiefer, Friedemann Hesse
Aggregation of therapeutic proteins is a major concern as aggregates lower the yield and can impact the efficacy of the drug as well as the patient's safety. It can occur in all production stages; thus, it is essential to perform a detailed analysis for protein aggregates. Several methods such as size exclusion high-performance liquid chromatography (SE-HPLC), light scattering, turbidity, light obscuration, and microscopy-based approaches are used to analyze aggregates. None of these methods allows determination of all types of higher molecular weight (HMW) species due to a limited size range...
April 27, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28446598/the-histone-variant-h2a-z-promotes-efficient-cotranscriptional-splicing-in-s-cerevisiae
#3
Lauren T Neves, Stephen Douglass, Roberto Spreafico, Srivats Venkataramanan, Tracy L Kress, Tracy L Johnson
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28446532/next-generation-sequencing-ngs-analysis-on-single-circulating-tumor-cells-ctcs-with-no-need-of-whole-genome-amplification-wga
#4
Raffaele Palmirotta, Domenica Lovero, Erica Silvestris, Claudia Felici, Davide Quaresmini, Paola Cafforio, Franco Silvestris
BACKGROUND: Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS)...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28445765/in-line-monitoring-and-optimization-of-powder-flow-in-a-simulated-continuous-process-using-transmission-near-infrared-spectroscopy
#5
Md Anik Alam, Zhenqi Shi, James K Drennen, Carl A Anderson
In-line monitoring of continuous powder flow is an integral part of the continuous manufacturing process of solid oral dosage forms in the pharmaceutical industry. Specifically, monitoring downstream from loss-in-weight (LIW) feeders and/or continuous mixers provides important data about the state of the process. Such measurements support control of the process and thereby enhance product quality. Near Infrared Spectroscopy (NIRS) is a potential PAT tool to monitor the homogeneity of a continuous powder flow stream in pharmaceutical manufacturing...
April 23, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28444630/new-synthetic-methods-for-phosphate-labeling
#6
REVIEW
Amit K Dutta, Ilya Captain, Henning Jacob Jessen
The complexity of phosphorylation pathways and their downstream effects is vast. Synthetic chemistry has been working side by side with biology to develop phosphate labels for biological processes involving phosphorylated compounds. This chapter discusses recently employed methods for the preparation of several phosphate labels. Synthesis of biomolecules and their analogs and other useful or potentially useful phosphate derivatives is discussed.
June 2017: Topics in Current Chemistry (Journal)
https://www.readbyqxmd.com/read/28444370/identification-of-hda15-pif1-as-a-key-repression-module-directing-the-transcriptional-network-of-seed-germination-in-the-dark
#7
Dachuan Gu, Chia-Yang Chen, Minglei Zhao, Linmao Zhao, Xuewu Duan, Jun Duan, Keqiang Wu, Xuncheng Liu
Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated transcription regulation remains largely unclear. Here, we identified that histone deacetylase15 (HDA15) is a negative component of PHYB-dependent seed germination. Overexpression of HDA15 in Arabidopsis inhibits PHYB-dependent seed germination, whereas loss of function of HDA15 increases PHYB-dependent seed germination...
April 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28444222/feronia-receptor-kinase-at-the-crossroad-of-hormone-signaling-and-stress-responses
#8
Hongdong Liao, Renjie Tang, Xin Zhang, Sheng Luan, Feng Yu
Plant receptor-like kinases (RLKs) are involved in nearly all aspects of plant life including growth, development and stress response. Recent studies show that FERONIA (FER), a CrRLK1L subfamily member, is a versatile regulator of cell expansion and serves as a signaling node mediating crosstalks among multiple phytohormones. As a receptor for the RALF (Rapid Alkalinization Factor) peptide ligand, FER triggers a downstream signaling cascade that leads to a rapid cytoplasmic calcium increase and inhibition of cell elongation in plants...
April 19, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28444127/hla-class-i-binding-prediction-via-convolutional-neural-networks
#9
Yeeleng S Vang, Xiaohui Xie
Motivation: Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases...
April 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28443119/parsing-the-regulatory-network-between-small-rnas-and-target-genes-in-ethylene-pathway-in-tomato
#10
Yunxiang Wang, Qing Wang, Lipu Gao, Benzhong Zhu, Zheng Ju, Yunbo Luo, Jinhua Zuo
Small RNAs are a class of short non-coding endogenous RNAs that play essential roles in many biological processes. Recent studies have reported that microRNAs (miRNAs) are also involved in ethylene signaling in plants. LeERF1 is one of the ethylene response factors (ERFs) in tomato that locates in the downstream of ethylene signal transduction pathway. To elucidate the intricate regulatory roles of small RNAs in ethylene signaling pathway in tomato, the deep sequencing and bioinformatics methods were combined to decipher the small RNAs landscape in wild and sense-/antisense-LeERF1 transgenic tomato fruits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442548/keratin-8-18-regulation-of-insulin-receptor-signaling-and-trafficking-in-hepatocytes-through-a-concerted-phosphoinositide-dependent-akt-and-rab5-modulation
#11
Alexandra Roux, Anne Loranger, Josée N Lavoie, Normand Marceau
Keratins (Ks) are epithelial cell intermediate filament (IF) proteins that are expressed as pairs in a differentiation-regulated manner. Hepatocyte IFs are made only of K8/K18 pairs, which means that a K8 loss in K8-null mice leads to degradation of K18. Functionally, there is accumulating evidence that IFs contribute to signaling platforms. Here, we investigate the role of K8/K18 IFs in the regulation of insulin receptor (IR) signaling and trafficking in hepatocytes. We find that the IR substrate 1 (IRS1)/PI3K/Akt signaling cascade-downstream of IR-display prolonged activation in K8-null compared with wild-type hepatocytes...
April 25, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28442327/sample-preservation-transport-and-processing-strategies-for-honeybee-rna-extraction-influence-on-rna-yield-quality-target-quantification-and-data-normalization
#12
Eva Forsgren, Barbara Locke, Emilia Semberg, Ane T Laugen, Joachim R de Miranda
Viral infections in managed honey bees are numerous, and most of them are caused by viruses with an RNA genome. Since RNA degrades rapidly, appropriate sample management and RNA extraction methods are imperative to get high quality RNA for downstream assays. This study evaluated the effect of various sampling-transport scenarios (combinations of temperature, RNA stabilizers, and duration) of transport on six RNA quality parameters; yield, purity, integrity, cDNA synthesis efficiency, target detection and quantification...
April 22, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28441870/protein-nanocellulose-interactions-in-paper-filters-for-advanced-separation-applications
#13
Simon Johan Gustafsson, Levon Manukyan, Albert Mihranyan
Protein-based pharmaceutics are widely explored for healthcare applications, and six out of ten best selling drugs today are biologicals. The goal of this work was to evaluate the protein nanocellulose interactions in paper filter for advanced separation applications such as virus removal filtration and bioprocessing. The protein recovery was measured for bovine serum albumin (BSA), γ-Globulin and Lysozyme using biuret total protein reagent and polyacrylamide gel electrophoresis (SDS-PAGE), and the throughput was characterized in terms of flux values from fixed volume filtrations at various protein concentrations and under worst-case experimental conditions...
April 26, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28440206/role-of-foxm1-in-the-progression-and-epithelial-to-mesenchymal-transition-of-gastrointestinal-cancer
#14
Jing Zhang, Yangyang Niu, Chen Huang
Background and Objective:Gastrointestinal (GI) cancer, characterized by its leading mortality, is one of the most common cancers worldwide. The underlying mechanisms contributing to epithelial to mesenchymal transition (EMT) and metastasis of GI cancer is poorly understood. It is well known that a great number of transcription factors including FoxM1, KLF4, STAT3 and so forth, are associated with the process of EMT and have also been strongly implicated in the proliferation, migration, and invasion of GI cancer cells...
April 24, 2017: Recent Patents on Anti-cancer Drug Discovery
https://www.readbyqxmd.com/read/28440186/the-double-roles-of-the-prostaglandin-e2-ep2-receptor-in-intracerebral-hemorrhage
#15
Xu Luo, Qiquan Zhu, Jie Zhang, Qin Huang, Zongyi Xie, Yuan Cheng
Intracerebral hemorrhage (ICH), a subtype of stroke, brings high morbidity and mortality to human beings. Multiple studies indicate that neuroinflammation, excitotoxicity, oxidative stress, cytotoxicity resulted from the degradation products of blood clot play vital roles in ICH-induced secondary brain injury, which contributes to deterioration of neurological outcome. Prostaglandin E2 (PGE2), a type of prostanoids commonly up-regulated in these progresses, is known to modulate numerous cellular and molecular processes and involve in various diseases, including ICH, cerebral ischemic, Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS) etc...
April 24, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28439835/the-uea-small-rna-workbench-a-suite-of-computational-tools-for-small-rna-analysis
#16
Irina Mohorianu, Matthew Benedict Stocks, Christopher Steven Applegate, Leighton Folkes, Vincent Moulton
RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439830/peptide-based-isolation-of-argonaute-protein-complexes-using-ago-app
#17
Judith Hauptmann, Gunter Meister
Argonaute (Ago) proteins bind small RNAs such as microRNAs (miRNAs) or short interfering RNAs (siRNAs), which guide them to distinct mRNAs for post-transcriptional gene silencing. Mammalian miRNA-guided gene silencing pathways mainly lead to translational repression and mRNA destabilization. To facilitate these processes, Ago proteins bind members of the GW protein family, which form central interaction platforms for the recruitment of downstream effector proteins. GW proteins use tryptophane residues (W) to bind to the surface of Ago proteins...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439080/ets-related-gene-mediated-androgen-receptor-aggregation-and-endoplasmic-reticulum-stress-in-prostate-cancer-development
#18
Taduru L Sreenath, Shiela S Macalindong, Natallia Mikhalkevich, Shashwat Sharad, Ahmed Mohamed, Denise Young, Talaibek Borbiev, Charles Xavier, Rishita Gupta, Muhammad Jamal, Kevin Babcock, Shyh-Han Tan, Marja T Nevalainen, Albert Dobi, Gyorgy Petrovics, Isabell A Sesterhenn, Inger L Rosner, Charles J Bieberich, Peter Nelson, Valeri Vasioukhin, Shiv Srivastava
Mechanistic studies of deregulated ERG in prostate cancer and other cancers continue to enhance its role in cancer biology and its utility as a biomarker and therapeutic target. Here, we show that ERG, through its physical interaction with androgen receptor, induces AR aggregation and endoplasmic reticulum stress in the prostate glands of ERG transgenic mice. Histomorphological alterations and the expression of ER stress sensors Atf6, Ire1α, Perk, their downstream effectors Grp78/BiP and eIF2α in ERG transgenic mouse prostate glands indicate the presence of chronic ER stress...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28438779/human-alternative-macrophages-populate-calcified-areas-of-atherosclerotic-lesions-and-display-impaired-rankl-induced-osteoclastic-bone-resorption-activity
#19
Giulia Chinetti-Gbaguidi, Mehdi Daoudi, Mickael Rosa, Manjula Vinod, Loïc Louvet, Corinne Copin, Melanie Fanchon, Jonathan Vanhoutte, Bruno Derudas, Loic Belloy, Stephan Haulon, Christophe Zawadzki, Sophie Susen, Ziad A Massy, Jérôme Eeckhoute, Bart Staels
Rationale: Vascular calcification is a process similar to bone formation leading to an inappropriate deposition of calcium phosphate minerals in advanced atherosclerotic plaques. Monocyte-derived macrophages, located in atherosclerotic lesions and presenting heterogeneous phenotypes, from classical pro-inflammatory M1 to alternative anti-inflammatory M2 macrophages, could potentially display osteoclast-like functions. Objective: To characterize the phenotype of macrophages located in areas surrounding the calcium deposits in human atherosclerotic plaques...
April 24, 2017: Circulation Research
https://www.readbyqxmd.com/read/28438487/processdriver-a-computational-pipeline-to-identify-copy-number-drivers-and-associated-disrupted-biological-processes-in-cancer
#20
Brittany Baur, Serdar Bozdag
Copy number amplifications and deletions that are recurrent in cancer samples harbor genes that confer a fitness advantage to cancer tumor proliferation and survival. One important challenge in computational biology is to separate the causal (i.e., driver) genes from passenger genes in large, aberrated regions. We propose a computational pipeline, called ProcessDriver, that prioritizes candidate drivers by relating cis genes within the copy number aberration to dysregulated trans genes and biological processes...
April 21, 2017: Genomics
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