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https://www.readbyqxmd.com/read/28926712/pyrophosphate-release-in-the-protein-hiv-reverse-transcriptase
#1
Murat Atiş, Kenneth A Johnson, Ron Elber
Enzymatic reactions usually occur in several steps: A step of substrate binding to the surface of the protein, a step of protein re-organization around the substrate and conduction of a chemical reaction, and a step of product release. The release of inorganic phosphate - PPi - from the matrix of the protein HIV reverse transcriptase is investigated computationally. Atomically detailed simulations with explicit solvent are analyzed to obtain the free energy profile, mean first passage time, and detailed molecular mechanisms of PPi escape...
September 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28924979/quantification-of-etoposide-hypersensitivity-a-sensitive-functional-method-for-assessing-pluripotent-stem-cell-quality
#2
Frank J Secreto, Xing Li, Alyson J Smith, Elizabeth S Bruinsma, Ester Perales-Clemente, Saji Oommen, Gresin Hawse, Sybil C L Hrstka, Bonnie K Arendt, Emma B Brandt, Dennis A Wigle, Timothy J Nelson
Human induced pluripotent stem cells (hiPSC) hold great promise in diagnostic and therapeutic applications. However, translation of hiPSC technology depends upon a means of assessing hiPSC quality that is quantitative, high-throughput, and can decipher malignant teratocarcinoma clones from normal cell lines. These attributes are lacking in current approaches such as detection of cell surface makers, RNA profiling, and/or teratoma formation assays. The latter remains the gold standard for assessing clone quality in hiPSCs, but is expensive, time-consuming, and incompatible with high-throughput platforms...
September 19, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28924252/comprehensive-analysis-of-lncrnas-and-mrnas-in-skeletal-muscle-of-rainbow-trout-oncorhynchus-mykiss-exposed-to-estradiol
#3
Jian Wang, Prasanthi P Koganti, Jianbo Yao, Shuo Wei, Beth Cleveland
Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout (Oncorhynchus mykiss), but the mechanisms directing with this response are not fully understood. To better characterize the effects of E2 in muscle, we identified differentially regulated mRNAs and lncRNAs in juvenile rainbow trout exposed to E2. Here, we performed next-generation RNA sequencing and comprehensive bioinformatics analyses to characterize the transcriptome profiles, including mRNAs and long noncoding RNAs (lncRNAs), in skeletal muscle of rainbow trout injected with E2...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28923827/mutant-ctnnb1-and-histological-heterogeneity-define-metabolic-subtypes-of-hepatoblastoma
#4
Stefania Crippa, Pierre-Benoit Ancey, Jessica Vazquez, Paolo Angelino, Anne-Laure Rougemont, Catherine Guettier, Vincent Zoete, Mauro Delorenzi, Olivier Michielin, Etienne Meylan
Hepatoblastoma is the most common malignant pediatric liver cancer. Histological evaluation of tumor biopsies is used to distinguish among the different subtypes of hepatoblastoma, with fetal and embryonal representing the two main epithelial components. With frequent CTNNB1 mutations, hepatoblastoma is a Wnt/β-catenin-driven malignancy. Considering that Wnt activation has been associated with tumor metabolic reprogramming, we characterized the metabolic profile of cells from hepatoblastoma and compared it to cells from hepatocellular carcinoma...
September 18, 2017: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/28923287/aberrant-expression-of-epithelial-leucine-rich-repeat-containing-g-protein-coupled-receptor-5-positive-cells-in-the-eutopic-endometrium-in-endometriosis-and-implications-in-deep-infiltrating-endometriosis
#5
Júlia Vallvé-Juanico, Elena Suárez-Salvador, Josep Castellví, Agustín Ballesteros, Hugh S Taylor, Antonio Gil-Moreno, Xavier Santamaria
OBJECTIVE: To characterize leucine-rich repeat containing G protein-coupled receptor 5-positive (LGR5(+)) cells from the endometrium of women with endometriosis. DESIGN: Prospective experimental study. SETTING: University hospital/fertility clinic. PATIENT(S): Twenty-seven women with endometriosis who underwent surgery and 12 healthy egg donors, together comprising 39 endometrial samples. INTERVENTION(S): Obtaining of uterine aspirates by using a Cornier Pipelle...
September 15, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28923134/%C3%A3-1-3-galactosyl-o-glycosyl-glycoprotein-%C3%A3-1-6-n-acetylglucosaminyltransferase-3-increases-mcam-stability-which-enhances-s100a8-a9-mediated-cancer-motility
#6
I Wayan Sumardika, Chen Youyi, Eisaku Kondo, Yusuke Inoue, I Made Winarsa Ruma, Hitoshi Murata, Rie Kinoshita, Ken-Ichi Yamamoto, Shuta Tomida, Kazuhiko Shien, Hiroki Satoh, Akira Yamauchi, Junichiro Futami, Endy Widya Putranto, Toshihiko Hibino, Shinichi Toyooka, Masahiro Nishibori, Masakiyo Sakaguchi
We previously identified novel S100A8/A9 receptors, Extracellular Matrix Metalloproteinase Inducer (EMMPRIN), MelanomaCell Adhesion Molecule (MCAM), Activated Leukocyte Cell Adhesion Molecule (ALCAM) and Neuroplastin (NPTN) ß, that are critically involved in S100A8/A9-mediated cancer metastasis and inflammation when expressed at high levels. However, little is known about the presence of any cancerspecific mechanism(s) that modifies these receptors, further inducing upregulation at protein levels without any transcriptional regulation...
September 18, 2017: Oncology Research
https://www.readbyqxmd.com/read/28922755/root-transcriptomic-responses-of-grafted-grapevines-to-heterogeneous-nitrogen-availability-depend-on-rootstock-genotype
#7
Noé Cochetel, Frédéric Escudié, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre-François Bert, Mindy Stephania Muñoz, Serge Delrot, Christophe Klopp, Nathalie Ollat, Virginie Lauvergeat
In many fruit species, including grapevine, grafting is used to improve scion productivity and quality and to adapt the plant to environmental conditions. However, the mechanisms underlying the rootstock control of scion development are still poorly understood. The ability of rootstocks to regulate nitrogen uptake and assimilation may contribute to this control. A split-root system was used to grow heterografted grapevines and to investigate the molecular responses to changes in nitrate availability of two rootstocks known to affect scion growth differently...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922749/unraveling-additional-o-methylation-steps-in-benzylisoquinoline-alkaloid-biosynthesis-in-california-poppy-eschscholzia-californica
#8
Ratmoyo Purwanto, Kentaro Hori, Yasuyuki Yamada, Fumihiko Sato
California poppy (Eschscholzia californica), a member of the Papaveraceae family, produces many biologically active benzylisoquinoline alkaloids (BIAs), such as sanguinarine, macarpine and chelerythrine. Sanguinarine biosynthesis has been elucidated at the molecular level, and its biosynthetic genes have been isolated and used in synthetic biology approaches to produce BIAs in vitro. However, several genes involved in the biosynthesis of macarpine and chelerythrine have not yet been characterized. In this study, we report the isolation and characterization of a novel O-methyltransferase (OMT) involved in the biosynthesis of partially characterized BIAs, especially chelerythrine...
September 1, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28922540/ape1-ref-1-knockdown-in-pancreatic-ductal-adenocarcinoma-characterizing-gene-expression-changes-and-identifying-novel-pathways-using-single-cell-rna-sequencing
#9
Fenil Shah, Emery Goossens, Nadia M Atallah, Michelle Grimard, Mark R Kelley, Melissa L Fishel
Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1 or APE1) is a multifunctional protein that regulates numerous transcription factors associated with cancer-related pathways. Because APE1 is essential for cell viability, generation of APE1 knockout cell lines and determining a comprehensive list of genes regulated by APE1 has not been possible. To circumvent this challenge, we utilized single-cell RNA Sequencing to identify differentially expressed genes in relation to APE1 protein levels within the cell...
September 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28921546/neuroblastoma-cells-undergo-transcriptomic-alterations-upon-dissemination-into-the-bone-marrow-and-subsequent-tumor-progression
#10
Fikret Rifatbegovic, Christian Frech, M Reza Abbasi, Sabine Taschner-Mandl, Tamara Weiss, Wolfgang M Schmidt, Iris Schmidt, Ruth Ladenstein, Inge M Ambros, Peter F Ambros
Neuroblastoma is the most common extracranial solid tumor in childhood. The vast majority of metastatic (M) stage patients present with disseminated tumor cells (DTCs) in the bone marrow (BM) at diagnosis and relapse. Although these cells represent a major obstacle in the treatment of neuroblastoma patients, insights into their expression profile remained elusive. The present RNA-Seq study of stage 4/M primary tumors, enriched BM-derived diagnostic and relapse DTCs, as well as the corresponding BM-derived mononuclear cells (MNCs) from 53 patients revealed 322 differentially expressed genes in DTCs as compared to the tumors (q < 0...
September 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28920956/biotin-tagging-of-mecp2-in-mice-reveals-contextual-insights-into-the-rett-syndrome-transcriptome
#11
Brian S Johnson, Ying-Tao Zhao, Maria Fasolino, Janine M Lamonica, Yoon Jung Kim, George Georgakilas, Kathleen H Wood, Daniel Bu, Yue Cui, Darren Goffin, Golnaz Vahedi, Tae Hoon Kim, Zhaolan Zhou
Mutations in MECP2 cause Rett syndrome (RTT), an X-linked neurological disorder characterized by regressive loss of neurodevelopmental milestones and acquired psychomotor deficits. However, the cellular heterogeneity of the brain impedes an understanding of how MECP2 mutations contribute to RTT. Here we developed a Cre-inducible method for cell-type-specific biotin tagging of MeCP2 in mice. Combining this approach with an allelic series of knock-in mice carrying frequent RTT-associated mutations (encoding T158M and R106W) enabled the selective profiling of RTT-associated nuclear transcriptomes in excitatory and inhibitory cortical neurons...
September 18, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28920417/effects-of-deoxynivalenol-and-zearalenone-contaminated-feed-on-the-gene-expression-profiles-in-the-kidneys-of-piglets
#12
Kondreddy Eswar Reddy, Woong Lee, Jin Young Jeong, Yookyung Lee, Hyun-Jeong Lee, Min Seok Kim, Dong-Woon Kim, Dongjo Yu, Ara Cho, Young Kyoon Oh, Sung Dae Lee
Objective: Fusarium mycotoxins deoxynivalenol (DON) and zearalenone (ZEN), common contaminants in the feed of farm animals, cause immune function impairment and organ inflammation. Consequently, the main objective of this study was to elucidate DON and ZEN effects on the mRNA expression of pro-inflammatory cytokines and other immune related genes in the kidneys of piglets. Methods: Fifteen 6-week-old piglets were randomly assigned to three dietary treatments for 4 weeks: control diet, and diets contaminated with either 8 mg DON/kg feed or 0...
September 18, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28920148/differential-gene-expression-profiles-and-alternative-isoform-regulations-in-gill-of-nile-tilapia-in-response-to-acute-hypoxia
#13
Hong Lian Li, Hao Ran Lin, Jun Hong Xia
Fish often encounters exposures to acute environmental hypoxia either spatially or temporally. Gill organ plays important roles in response to hypoxic stress in fish. Few studies focus on the molecular regulation mechanisms of gills under hypoxic stress. In this study, we investigated the transcriptomic response to 12-h acute hypoxia in gill of a hypoxia tolerant fish, Nile tilapia Oreochromis niloticus through RNA sequencing (RNA-Seq). We sequenced messenger RNA from three control samples and three hypoxia-treated samples...
September 18, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28919899/emerging-roles-and-landscape-of-translating-mrnas-in-plants
#14
REVIEW
Gaurav Sablok, Jonathan J Powell, Kemal Kazan
Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28919018/de-novo-transcriptome-assembly-of-the-calanoid-copepod-neocalanus-flemingeri-a-new-resource-for-emergence-from-diapause
#15
Vittoria Roncalli, Matthew C Cieslak, Stephanie A Sommer, Russell R Hopcroft, Petra H Lenz
Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N...
September 14, 2017: Marine Genomics
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
#16
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
#17
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/28918047/long-noncoding-rna-bc032913-as-a-novel-therapeutic-target-for-colorectal-cancer-that-suppresses-metastasis-by-upregulating-timp3
#18
Jiaxin Lin, Xin Tan, Lin Qiu, Long Huang, Yi Zhou, Zhizhong Pan, Ranyi Liu, Shuai Chen, Rong Geng, Jiangxue Wu, Wenlin Huang
Long noncoding RNAs (lncRNAs) have been shown to play critical roles in the biology of various cancers. However, their expression patterns and biological functions in human colorectal cancer (CRC) remain largely unknown. The aim of this study was to explore lncRNA profiles in CRC and investigate key lncRNAs involved in CRC tumorigenesis and progression. The microarray data of six CRC and matched non-cancerous tissues revealed distinct lncRNA profiles, including 899 upregulated and 1,646 downregulated lncRNAs (p < 0...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28918038/strategies-for-in%C3%A2-vivo-screening-and-mitigation-of-hepatotoxicity-associated-with-antisense-drugs
#19
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/28917040/studying-selenoprotein-mrna-translation-using-rna-seq-and-ribosome-profiling
#20
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
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