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https://www.readbyqxmd.com/read/27933714/development-of-chemical-tools-to-monitor-and-control-isoaspartyl-peptide-methyltransferase-activity
#1
Yusuke Kimura, Toru Komatsu, Kouichi Yanagi, Kenjiro Hanaoka, Tasuku Ueno, Takuya Terai, Hirotatsu Kojima, Takayoshi Okabe, Tetsuo Nagano, Yasuteru Urano
We have established a coupled assay system targeting protein l-isoaspartyl methyltransferase (PIMT), a key enzyme in the metabolism of isoaspartyl peptides and proteins. The system utilizes a fluorogenic peptide probe containing an isoaspartyl residue at the P1' position of the caspase-3 recognition sequence. Following PIMT-catalyzed methyl transfer reaction, the methylated probe is specifically cleaved by caspase-3 to give fluorescence activation. High-throughput screening of our chemical library with this assay system identified PIMT inhibitors that may be useful as leads in the design of chemical probes for controlling PIMT activity...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27933702/multiparameter-particle-display-mppd-a-quantitative-screening-method-for-the-discovery-of-highly-specific-aptamers
#2
Jinpeng Wang, Jingwen Yu, Qin Yang, John McDermott, Alexander Scott, Matthew Vukovich, Remy Lagrois, Qiang Gong, William Greenleaf, Michael Eisenstein, B Scott Ferguson, H Tom Soh
Aptamers are a promising class of affinity reagents because they are chemically synthesized, thus making them highly reproducible and distributable as sequence information rather than a physical entity. Although many high-quality aptamers have been previously reported, it is difficult to routinely generate aptamers that possess both high affinity and specificity. One of the reasons is that conventional aptamer selection can only be performed either for affinity (positive selection) or for specificity (negative selection), but not both simultaneously...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27933681/evaluating-a-primary-care-psychology-service-in-ireland-a-survey-of-stakeholders-and-psychologists
#3
Mark Corcoran, Michael Byrne
Primary care psychology services (PCPS) represent an important resource in meeting the various health needs of our communities. This study evaluated the PCPS in a two-county area within the Republic of Ireland. The objectives were to (i) examine the viewpoints of the service for both psychologists and stakeholders (healthcare professionals only) and (ii) examine the enactment of the stepped care model of service provision. Separate surveys were sent to primary care psychologists (n = 8), general practitioners (GPs; n = 69) and other stakeholders in the two counties...
December 8, 2016: Health & Social Care in the Community
https://www.readbyqxmd.com/read/27933524/a-suite-of-tools-for-biologists-that-improve-accessibility-and-visualization-of-large-systems-genetics-datasets-applications-to-the-hybrid-mouse-diversity-panel
#4
Christoph D Rau, Mete Civelek, Calvin Pan, Aldons J Lusis
In this chapter we address the recent explosion in large multilevel population studies such as the METSIM study in humans as well as large panels of animal models such as the Hybrid Mouse Diversity Panel or the BXD set of recombinant inbred strains. These studies have harnessed the increasing affordability of large-scale high-throughput profiling to gather massive quantities of data. These datasets, spread across different -omics levels (genome, transcriptome, etc.), different tissues (e.g. heart, plasma, bone) and different environmental factors (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933318/global-analysis-and-comparison-of-the-transcriptomes-and-proteomes-of-group-a-streptococcus-biofilms
#5
Jeffrey A Freiberg, Yoann Le Breton, Bao Q Tran, Alison J Scott, Janette M Harro, Robert K Ernst, Young Ah Goo, Emmanuel F Mongodin, David R Goodlett, Kevin S McIver, Mark E Shirtliff
To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GAS. Using high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics, we found distinct expression profiles in the transcriptome and proteome. A total of 46 genes and 41 proteins showed expression across the majority of biofilm time points that was consistently higher or consistently lower than that seen across the majority of planktonic time points...
November 2016: MSystems
https://www.readbyqxmd.com/read/27933070/transcriptional-responses-in-root-and-leaf-of-prunus-persica-under-drought-stress-using-rna-sequencing
#6
Najla Ksouri, Sergio Jiménez, Christina E Wells, Bruno Contreras-Moreira, Yolanda Gogorcena
Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27932994/comparative-mrna-and-microrna-profiling-during-acute-myocardial-infarction-induced-by-coronary-occlusion-and-ablation-radio-frequency-currents
#7
Eduardo T Santana, Regiane Dos Santos Feliciano, Andrey J Serra, Eduardo Brigidio, Ednei L Antonio, Paulo J F Tucci, Lubov Nathanson, Mariana Morris, José A Silva
The ligation of the left anterior descending coronary artery is the most commonly used experimental model to induce myocardial infarction (MI) in rodents. A high mortality in the acute phase and the heterogeneity of the size of the MI obtained are drawbacks recognized in this model. In an attempt to solve the problem, our group recently developed a new MI experimental model which is based on application of myocardial ablation radio-frequency currents (AB-RF) that yielded MI with homogeneous sizes and significantly reduce acute mortality...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27932801/dna-encoded-chemistry-enabling-the-deeper-sampling-of-chemical-space
#8
Robert A Goodnow, Christoph E Dumelin, Anthony D Keefe
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces...
December 9, 2016: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/27932698/identification-of-inhibitors-of-the-association-of-zap-70-with-the-t-cell-receptor-by-high-throughput-screen
#9
Patrick R Visperas, Christopher G Wilson, Jonathan A Winger, Qingrong Yan, Kevin Lin, Michelle R Arkin, Arthur Weiss, John Kuriyan
ZAP-70 is a critical molecule in the transduction of T cell antigen receptor signaling and the activation of T cells. Upon activation of the T cell antigen receptor, ZAP-70 is recruited to the intracellular ζ-chains of the T cell receptor, where ZAP-70 is activated and colocalized with its substrates. Inhibitors of ZAP-70 could potentially function as treatments for autoimmune diseases or organ transplantation. In this work, we present the design, optimization, and implementation of a screen for inhibitors that would disrupt the interaction between ZAP-70 and the T cell antigen receptor...
December 8, 2016: Journal of Biomolecular Screening
https://www.readbyqxmd.com/read/27932553/normalization-matters-tracking-the-best-strategy-for-sperm-mirna-quantification
#10
Celia Corral-Vazquez, Joan Blanco, Albert Salas-Huetos, Francesca Vidal, Ester Anton
STUDY QUESTION: What is the most reliable normalization strategy for sperm microRNA (miRNA) quantitative Reverse Transcription Polymerase Chain Reactions (qRT-PCR) using singleplex assays? SUMMARY ANSWER: The use of the average expression of hsa-miR-100-5p and hsa-miR-30a-5p as sperm miRNA qRT-PCR data normalizer is suggested as an optimal strategy. WHAT IS KNOWN ALREADY: Mean-centering methods are the most reliable normalization strategies for miRNA high-throughput expression analyses...
December 8, 2016: Molecular Human Reproduction
https://www.readbyqxmd.com/read/27932544/improving-the-identification-of-phenotypic-abnormalities-and-sexual-dimorphism-in-mice-when-studying-rare-event-categorical-characteristics
#11
Natasha A Karp, Ruth Heller, Shay Yaacoby, Jacqueline K White, Yoav Benjamini
Biological research frequently involves the study of phenotyping data. Many of these studies focus on rare event categorical data, and in functional genomics typically study the presence or absence of an abnormal phenotype. With the growing interest in the role of sex, there is a need to assess the phenotype for sexual dimorphism. The identification of abnormal phenotypes for downstream research is challenged by the small sample size, the rare event nature, and the multiple testing problem, as many variables are monitored simultaneously...
December 7, 2016: Genetics
https://www.readbyqxmd.com/read/27932498/harnessing-molecular-motors-for-nanoscale-pulldown-in-live-cells
#12
Jonathan E Bird, Melanie Barzik, Meghan C Drummond, Daniel C Sutton, Spencer M Goodman, Eva L Morozko, Stacey M Cole, Alexandra K Boukhvalova, Jennifer Skidmore, Diana Syam, Elizabeth A Wilson, Tracy Fitzgerald, Atteeq U Rehman, Donna M Martin, Erich T Boger, Inna A Belyantseva, Thomas B Friedman
Protein-protein interactions (PPIs) regulate assembly of macromolecular complexes, yet these remain challenging to study within the native cytoplasm where they normally exert their biological effect. Here, we miniaturize the concept of affinity pulldown, a gold-standard in vitro PPI interrogation technique, to perform nanoscale pulldowns (NanoSPD) within living cells. NanoSPD hijacks the normal process of intracellular trafficking by myosin motors to forcibly pull fluorescently-tagged protein complexes along filopodial actin filaments...
December 8, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27932479/progress-in-understanding-the-genetics-of-calcium-containing-nephrolithiasis
#13
John A Sayer
Renal stone disease is a frequent condition, causing a huge burden on health care systems globally. Calcium-based calculi account for around 75% of renal stone disease and the incidence of these calculi is increasing, suggesting environmental and dietary factors are acting upon a preexisting genetic background. The familial nature and significant heritability of stone disease is known, and recent genetic studies have successfully identified genes that may be involved in renal stone formation. The detection of monogenic causes of renal stone disease has been made more feasible by the use of high-throughput sequencing technologies and has also facilitated the discovery of novel monogenic causes of stone disease...
December 8, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27932461/structural-characterization-and-ligand-inhibitor-identification-provide-functional-insights-into-the-mycobacterium-tuberculosis-cytochrome-p450-cyp126a1
#14
Jude T Chenge, Duyet Van Le, Shalini Swami, Kirsty J McLean, Madeline E Kavanagh, Anthony G Coyne, Stephen E J Rigby, Myles R Cheesman, Hazel M Girvan, Colin W Levy, Bernd Rupp, Jens P von Kries, Chris Abell, David Leys, Andrew W Munro
The Mycobacterium tuberculosis (Mtb) H37Rv genome encodes 20 cytochromes P450, including P450s crucial to infection and bacterial viability. Many Mtb P450s remain uncharacterized, suggesting their further analysis may provide new insights into Mtb metabolic processes and new targets for drug discovery. CYP126A1 is representative of a P450 family widely distributed in mycobacteria and other bacteria. Here we explore the biochemical and structural properties of CYP126A1, including its interactions with new chemical ligands...
December 8, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27932412/universal-haplotype-based-noninvasive-prenatal-testing-for-single-gene-diseases
#15
Winnie W I Hui, Peiyong Jiang, Yu K Tong, Wing-Shan Lee, Yvonne K Y Cheng, Maria I New, Rezan A Kadir, K C Allen Chan, Tak Y Leung, Y M Dennis Lo, Rossa W K Chiu
BACKGROUND: Researchers have developed approaches for the noninvasive prenatal testing of single gene diseases. One approach that allows for the noninvasive assessment of both maternally and paternally inherited mutations involves the analysis of single nucleotide polymorphisms (SNPs) in maternal plasma DNA with reference to parental haplotype information. In the past, parental haplotypes were resolved by complex experimental methods or inferential approaches, such as through the analysis of DNA from other affected family members...
December 8, 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27932033/cellular-analysis-of-trophoblast-and-placenta
#16
Frances Wong, Brian J Cox
The placenta is composed of two lineages: the trophoblast and mesoderm. While morphological assessment of the placenta has highlighted major cell types and developmental structures, the human placenta is relatively unexplained on a molecular level. Current molecular analysis of the placenta has largely been confined to assessing whole organs that include both cell lineages and their differentiated progeny. This has confounded our understanding of the processes of placental development and function for two reasons...
November 30, 2016: Placenta
https://www.readbyqxmd.com/read/27931939/ex-situ-biogas-upgrading-and-enhancement-in-different-reactor-systems
#17
Panagiotis G Kougias, Laura Treu, Daniela Peñailillo Benavente, Kanokwan Boe, Stefano Campanaro, Irini Angelidaki
Biogas upgrading is envisioned as a key process for clean energy production. The current study evaluates the efficiency of different reactor configurations for ex-situ biogas upgrading and enhancement, in which externally provided hydrogen and carbon dioxide were biologically converted to methane by the action of hydrogenotrophic methanogens. The methane content in the output gas of the most efficient configuration was >98%, allowing its exploitation as substitute to natural gas. Additionally, use of digestate from biogas plants as a cost efficient method to provide all the necessary nutrients for microbial growth was successful...
December 2, 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27931803/the-rat-pig-a-assay-using-an-erythroid-his49-antibody-in-a-single-dose-study-of-isopropyl-p-toluenesulfonate
#18
Satsuki Chikura, Yuki Okada, Takafumi Kimoto, Hideshi Kaneko, Daishiro Miura, Yoshinori Kasahara
As part of a collaborative study in the Mammalian Mutagenicity Study group of the Japanese Environmental Mutagen Society, we evaluated the in vivo mutagenicity of isopropyl p-toluenesulfonate (IPTS) using a peripheral blood Pig-a assay in rats. Pig-a mutant frequency (MF) data was obtained for both red blood cells (RBCs) and reticulocytes (RETs) at 1, 2 and 4 weeks after a single oral administration of IPTS at doses of 125, 250, or 500mg/kg. The results of the RBC Pig-a assay demonstrated that both the 250 and 500mg/kg treatment groups showed significant increases in Pig-a MF only at 4 weeks after IPTS treatment...
November 15, 2016: Mutation Research
https://www.readbyqxmd.com/read/27931360/molecular-biological-methods-in-environmental-engineering
#19
Guocai Zhang, Li Wei, Chein-Chi Chang, Yuhua Zhang, Dong Wei
Bacteria, acting as catalysts, perform the function of degrading pollutants. Molecular biological techniques play an important role in research on the community analysis, the composition and the functions of complex microbial communities. The development of secondary high-throughput pyrosequencing techiniques enhances the understanding of the composition of the microbial community. The literatures of 2015 indicated that 16S rDNA gene as genetic tag is still the important method for bacteria identification and classification...
October 2016: Water Environment Research: a Research Publication of the Water Environment Federation
https://www.readbyqxmd.com/read/27931010/impact-and-influence-of-omics-technology-on-hyper-tension-studies
#20
REVIEW
Alzenira Costa, Octavio Luiz Franco
BACKGROUND: Hypertension is an important risk factor for cardiovascular diseases. Pathophysiology and molecular mechanisms involved in hypertension regulation are not very well known. Recently, high-throughput Next-Generation Sequencing (NGS) technology has identified hundreds of gene loci associated with multiple cardiovascular pathologies, including blood pressure (BP), generating new expectations in hypertension studies, revealing new pathways and genetic mechanisms underlying BP regulation...
November 23, 2016: International Journal of Cardiology
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