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https://www.readbyqxmd.com/read/28918554/genome-wide-identification-classification-evolutionary-analysis-and-gene-expression-patterns-of-the-protein-kinase-gene-family-in-wheat-and-aegilops-tauschii
#1
Jun Yan, Peisen Su, Zhaoran Wei, Eviatar Nevo, Lingrang Kong
In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes...
September 16, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28918545/increased-postharvest-life-of-tomlox-b-silenced-mutants-of-tomato-solanum-lycopersicum-var-ta234
#2
Elizabeth León-García, Gilber Vela-Gutiérrez, Oscar A Del Ángel-Coronel, Cristobal Torres-Palacios, Javier De La Cruz-Medina, Miguel A Gómez-Lim, Hugo Sergio García
A healthy lifestyle includes fruits and vegetables consumption. Tomato is one of the most consumed vegetables, although it is susceptible to physical damage through postharvest handling, thus leading to important losses. Softening is an important variable during tomato ripening; excessive softening is undesirable and leads to postharvest losses. TomloxB plays an important role in ripening, mainly in the loss of cellular integrity caused by fatty acids released from the lipid matrix of membranes that initiate oxidative deterioration, which is in turn carried into senescence...
September 16, 2017: Plant Foods for Human Nutrition
https://www.readbyqxmd.com/read/28918518/micro-rna-profiling-of-exosomes-from-marrow-derived-mesenchymal-stromal-cells-in-patients-with-acute-myeloid-leukemia-implications-in-leukemogenesis
#3
Juliana Barrera-Ramirez, Jessie R Lavoie, Harinad B Maganti, William L Stanford, Caryn Ito, Mitchell Sabloff, Marjorie Brand, Michael Rosu-Myles, Yevgeniya Le, David S Allan
Gene regulatory networks in AML may be influenced by microRNAs (miRs) contained in exosomes derived from bone marrow mesenchymal stromal cells (MSCs). We sequenced miRs from exosomes isolated from marrow-derived MSCs from patients with AML (n = 3) and from healthy controls (n = 3; not age-matched). Known targets of mIRs that were significantly different in AML-derived MSC exosomes compared to controls were identified. Of the five candidate miRs identified by differential packaging in exosomes, only miR-26a-5p and miR-101-3p were significantly increased in AML-derived samples while miR-23b-5p, miR-339-3p and miR-425-5p were significantly decreased...
September 16, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/28918420/computer-analysis-of-glioma-transcriptome-profiling-alternative-splicing-events
#4
Vladimir N Babenko, Natalya V Gubanova, Anatoly O Bragin, Irina V Chadaeva, Gennady V Vasiliev, Irina V Medvedeva, Alexey S Gaytan, Alexey L Krivoshapkin, Yuriy L Orlov
Here we present the analysis of alternative splicing events on an example of glioblastoma cell culture samples using a set of computer tools in combination with database integration. The gene expression profiles of glioblastoma were obtained from cell culture samples of primary glioblastoma which were isolated and processed for RNA extraction. Transcriptome profiling of normal brain samples and glioblastoma were done by Illumina sequencing. The significant differentially expressed exon-level probes and their corresponding genes were identified using a combination of the splicing index method...
September 18, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28918236/gene-expression-profiles-of-cell-adhesion-molecules-matrix-metalloproteinases-and-their-tissue-inhibitors-in-canine-oral-tumors
#5
Sirinun Pisamai, Anudep Rungsipipat, Chanin Kalpravidh, Gunnaporn Suriyaphol
Perturbation of cell adhesion can be essential for tumor cell invasion and metastasis, but the current knowledge on the gene expression of molecules that mediate cell adhesion in canine oral tumors is limited. The present study aimed to investigate changes in the gene expression of cell adhesion molecules (E-cadherin or CDH1, syndecan 1 or SDC1, NECTIN2 and NECTIN4), matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs), in canine oral tumors, including benign tumors, oral melanoma (OM) and non-tonsillar oral squamous cell carcinoma (OSCC), by quantitative real-time reverse transcription PCR...
September 8, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28918173/edited-course-of-biomedical-research-leaping-forward-with-crispr
#6
REVIEW
Patrick J Collins, Christopher M Hale, Han Xu
Within the short few years since the report of its application in precise genome editing, CRISPR technology has become the method of choice to modify and modulate gene expression in biomedical research and therapeutic development. Subsequently, a variety of research, diagnostic, and therapeutic tools have been developed based upon CRISPR's mechanism of action. Such tools have helped to deepen the understanding of fundamental biology and broaden the horizon in the search for treatments for diseases that have been considered hard or impossible to cure...
September 13, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28918157/differential-proteomic-profiling-of-endometrium-and-plasma-indicate-the-importance-of-hydrolysis-in-bovine-endometritis
#7
Shi-Dong Zhang, Shu-Wei Dong, Dong-Sheng Wang, Chike F Oguejiofor, Ali A Fouladi-Nashta, Zhi-Qiang Yang, Zuo-Ting Yan
Endometritis is an important disease of dairy cows that leads to significant economic losses in the dairy cattle industry. To investigate the alteration of proteins associated with endometritis in the dairy cow, the isobaric tags for relative and absolute quantification (iTRAQ) technique was applied to quantitatively identify differentially expressed proteins (DEP) in the endometrium and peripheral plasma of Chinese Holstein cows with endometritis. Compared with the normal (control) group, 159 DEP in the endometrium and 137 DEP in the plasma were identified in cows with endometritis...
September 13, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28918038/strategies-for-in%C3%A2-vivo-screening-and-mitigation-of-hepatotoxicity-associated-with-antisense-drugs
#8
Piotr J Kamola, Klio Maratou, Paul A Wilson, Kay Rush, Tanya Mullaney, Tom McKevitt, Paula Evans, Jim Ridings, Probash Chowdhury, Aude Roulois, Ann Fairchild, Sean McCawley, Karen Cartwright, Nigel J Gooderham, Timothy W Gant, Kitty Moores, Stephen A Hughes, Mark R Edbrooke, Kenneth Clark, Joel D Parry
Antisense oligonucleotide (ASO) gapmers downregulate gene expression by inducing enzyme-dependent degradation of targeted RNA and represent a promising therapeutic platform for addressing previously undruggable genes. Unfortunately, their therapeutic application, particularly that of the more potent chemistries (e.g., locked-nucleic-acid-containing gapmers), has been hampered by their frequent hepatoxicity, which could be driven by hybridization-mediated interactions. An early de-risking of this liability is a crucial component of developing safe, ASO-based drugs...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28918017/efficacy-and-safety-profile-of-tricyclo-dna-antisense-oligonucleotides-in-duchenne-muscular-dystrophy-mouse-model
#9
Karima Relizani, Graziella Griffith, Lucía Echevarría, Faouzi Zarrouki, Patricia Facchinetti, Cyrille Vaillend, Christian Leumann, Luis Garcia, Aurélie Goyenvalle
Antisense oligonucleotides (AONs) hold promise for therapeutic splice-switching correction in many genetic diseases. However, despite advances in AON chemistry and design, systemic use of AONs is limited due to poor tissue uptake and sufficient therapeutic efficacy is still difficult to achieve. A novel class of AONs made of tricyclo-DNA (tcDNA) is considered very promising for the treatment of Duchenne muscular dystrophy (DMD), a neuromuscular disease typically caused by frameshifting deletions or nonsense mutations in the gene-encoding dystrophin and characterized by progressive muscle weakness, cardiomyopathy, and respiratory failure in addition to cognitive impairment...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917323/seroprevalence-and-first-multilocus-microsatellite-genotyping-of-neospora-caninum-in-dairy-cattle-in-henan-central-china
#10
Weifeng Qian, Tianqi Wang, Wenchao Yan, Min Zhang, Lifang Han, Rui Xue, Shaofu Song, Chaochao Lv
Neospora caninum is one of the important causes of abortion in cattle worldwide, and losses due to neosporosis to the cattle industry are considerable. However, the knowledge of genetic characterization of this parasite is limited. The aim of the present study is to determine the prevalence and genetic characterization of N. caninum from dairy cows in Henan Province, central China. A total of 510 blood samples and 7 aborted fetuses were collected from 8 dairy farms in Henan Province. Serum antibodies to N. caninum were examined by ELISA using a recombinant tNcSRS2 protein as the coating antigen...
September 15, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28917045/radioactive-75-se-labeling-and-detection-of-selenoproteins
#11
Sun Hee Yim, Ryuta Tobe, Anton A Turanov, Bradley A Carlson
The trace element selenium (Se) is incorporated into proteins as the amino acid selenocysteine (Sec), which is cotranslationally inserted into specific proteins in response to a UGA codon. Proteins containing Sec at these specific positions are called selenoproteins. Most selenoproteins function as oxidoreductases, while some serve other important functions. There are 25 known selenoprotein genes in humans and 24 in mice. The use of Sec allows selenoproteins to be detected by a convenient method involving metabolic labeling with (75)Se...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28917040/studying-selenoprotein-mrna-translation-using-rna-seq-and-ribosome-profiling
#12
Brian K Dalley, Lisa Baird, Michael T Howard
Deep sequencing of ribosome protected mRNA footprints, also called ribosome profiling or Ribo-Seq, is a relatively new methodology well suited to address questions regarding the mechanisms and efficiency of protein expression. Specifically, the ability of this technique to quantify ribosome abundance with codon resolution enables experiments aimed at studying many aspects of translation, including gene-specific translational efficiency, translation of regulatory upstream short open reading frames, sites of ribosome pausing, and most importantly for selenoproteins, the efficiency by which UGA codons are redefined to encode selenocysteine...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28917034/selenoprofiles-a-computational-pipeline-for-annotation-of-selenoproteins
#13
Didac Santesmasses, Marco Mariotti, Roderic Guigó
Selenoproteins contain selenocysteine (Sec or U), the 21st amino acid, inserted in response to an in-frame UGA codon. UGA normally terminates translation, but in selenoprotein mRNAs it is recoded to specify Sec insertion. For this reason, standard gene prediction programs fail to predict Sec codons, and selenoproteins are usually misannotated in protein databases and genome projects. Selenoprofiles is a computational pipeline able to correctly annotate selenoprotein genes in genomic sequences. This program uses a SECIS-independent approach, based on homology searches, and employs curated built-in profile alignments for all known selenoprotein families...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28916981/expression-of-a-novel-bi-directional-brassica-napus-promoter-in-soybean
#14
Siva Chennareddy, Toby Cicak, Lauren Clark, Sean Russell, Michiyo Skokut, Jeffrey Beringer, Xiaozeng Yang, Yi Jia, Manju Gupta
The expression profile of a natural bi-directional promoter, derived from the Brassica napus EPSPS-A gene, was studied in transgenic soybean (Glycine max C.V. Maverick) lines. Two constructs, pDAB100331 and pDAB100333, were assembled to test the bi-directionality of the promoter. Two reporter genes, gfp and gusA, were employed and they were interchangeably placed in both constructs, one on each end of the promoter such that both proteins expressed divergently in each construct. In the T0 generation, GUS expression was more uniform throughout the leaf of pDAB100333 transgenic plants, where the gusA gene was expressed from the downstream or EPSPS-A end of the bi-directional promoter...
September 15, 2017: Transgenic Research
https://www.readbyqxmd.com/read/28916833/inhibition-of-wnt-%C3%AE-catenin-pathway-and-histone-acetyltransferase-activity-by-rimonabant-a-therapeutic-target-for-colon-cancer
#15
Maria Chiara Proto, Donatella Fiore, Chiara Piscopo, Silvia Franceschelli, Valentina Bizzarro, Chiara Laezza, Gianluigi Lauro, Alessandra Feoli, Alessandra Tosco, Giuseppe Bifulco, Gianluca Sbardella, Maurizio Bifulco, Patrizia Gazzerro
In a high percentage (≥85%) of both sporadic and familial adenomatous polyposis forms of colorectal cancer (CRC), the inactivation of the APC tumor suppressor gene initiates tumor formation and modulates the Wnt/β-Catenin transduction pathways involved in the control of cell proliferation, adhesion and metastasis. Increasing evidence showed that the endocannabinoids control tumor growth and progression, both in vitro and in vivo. We evaluated the effect of Rimonabant, a Cannabinoid Receptor 1 (CB1) inverse agonist, on the Wnt/β-Catenin pathway in HCT116 and SW48 cell lines carrying the genetic profile of metastatic CRC poorly responsive to chemotherapies...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916729/identification-of-differential-plasma-mirna-profiles-in-chinese-workers-with-occupational-lead-exposure
#16
Ming Xu, Zhengmin Yu, Feifei Hu, Hongbing Zhang, Lixin Zhong, Lei Han, Yan An, Baoli Zhu, Hengdong Zhang
Elevated lead absorptions are hazardous factor in lead-related workers. Previous studies have found its toxic impacts on nervous, circulatory, and metabolic systems. We hypothesized that alteration of miRNAs profile in plasma was closely associated with lead exposure. We analyzed to identify lead-related miRNAs of workers occupationally exposed to lead. Microarray assay was performed to detect plasma miRNA between workers with high and minimal lead exposure in the discovery stage. The following prediction of miRNAs' candidate target genes was carried out by using miRecords, STRING and KEGG databases...
September 15, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28916716/deregulation-of-microrna-expression-in-purified-t-and-b-lymphocytes-from-patients-with-primary-sj%C3%A3-gren-s-syndrome
#17
Shu-Fang Wang-Renault, Saida Boudaoud, Gaétane Nocturne, Elodie Roche, Nelly Sigrist, Christian Daviaud, Andreas Bugge Tinggaard, Victor Renault, Jean-François Deleuze, Xavier Mariette, Jörg Tost
OBJECTIVE: MicroRNAs (miRNAs) play an important role in the pathogenesis of autoimmune diseases such as primary Sjögren's syndrome (pSS). This study is the first to investigate miRNA expression patterns in purified T and B lymphocytes from patients with pSS using a high-throughput quantitative PCR (qPCR) approach. METHODS: Two independent cohorts of both patients with pSS and controls, one for discovery and one for replication, were included in this study. CD4+ T cells and CD19+ B cells were isolated from peripheral blood mononuclear cells by magnetic microbeads and expression of miRNAs was profiled using the Exiqon Human miRNome panel I analysing 372 miRNAs...
September 15, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28916708/architectural-delineation-and-molecular-identification-of-extracellular-matrix-in-ascidian-embryos-and-larvae
#18
Jiankai Wei, Guilin Wang, Xiang Li, Ping Ren, Haiyan Yu, Bo Dong
The extracellular matrix (ECM) not only provides essential physical scaffolding for cellular constituents but also initiates crucial biochemical and biomechanical cues that are required for tissue morphogenesis. In this study, we utilized wheat germ agglutinin (WGA) staining to characterize the ECM architecture in ascidian embryos and larvae. The results showed three distinct populations of ECM presenting in Ciona embryogenesis: the outer layer localized at the surface of embryo, an inner layer of notochord sheath and the apical ECM secreted by the notochord...
September 15, 2017: Biology Open
https://www.readbyqxmd.com/read/28916633/systems-genetics-identifies-a-co-regulated-module-of-liver-micrornas-associated-with-plasma-ldl-cholesterol-in-murine-diet-induced-dyslipidemia
#19
Alisha R Coffey, Tangi L Smallwood, Jody Albright, Kunjie Hua, Matt Kanke, Daniel Pomp, Brian J Bennett, Praveen Sethupathy
Chronically altered levels of circulating lipids, termed dyslipidemia, is a significant risk factor for a number of metabolic and cardiovascular morbidities. MicroRNAs (miRNAs) have emerged as important regulators of lipid balance, have been implicated in dyslipidemia, and have been proposed as candidate therapeutic targets in lipid-related disorders including atherosclerosis. A major limitation of most murine studies of miRNAs in lipid metabolic disorders is that they have been performed in just one (or very few) inbred strains, such as C57BL/6...
September 15, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28916538/analysis-of-blood-based-gene-expression-in-idiopathic-parkinson-disease
#20
Ron Shamir, Christine Klein, David Amar, Eva-Juliane Vollstedt, Michael Bonin, Marija Usenovic, Yvette C Wong, Ales Maver, Sven Poths, Hershel Safer, Jean-Christophe Corvol, Suzanne Lesage, Ofer Lavi, Günther Deuschl, Gregor Kuhlenbaeumer, Heike Pawlack, Igor Ulitsky, Meike Kasten, Olaf Riess, Alexis Brice, Borut Peterlin, Dimitri Krainc
OBJECTIVE: To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples). METHODS: Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature...
September 15, 2017: Neurology
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