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Molecular biology

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https://www.readbyqxmd.com/read/27933533/systems-genetics-as-a-tool-to-identify-master-genetic-regulators-in-complex-disease
#1
Aida Moreno-Moral, Francesco Pesce, Jacques Behmoaras, Enrico Petretto
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933430/structural-dynamics-of-nucleosome-mediated-by-acetylations-at-h3k56-and-h3k115-122
#2
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Ilya Ioshikhes, Amutha Ramaswamy
Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level...
December 8, 2016: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27933370/doxorubicin-induced-chronic-dilated-cardiomyopathy-the-apoptosis-hypothesis-revisited
#3
REVIEW
Cynthia Kankeu, Kylie Clarke, Egle Passante, Heinrich J Huber
The chemotherapeutic agent doxorubicin (DOX) has significantly increased survival rates of pediatric and adult cancer patients. However, 10% of pediatric cancer survivors will 10-20 years later develop severe dilated cardiomyopathy (DCM), whereby the exact molecular mechanisms of disease progression after this long latency time remain puzzling. We here revisit the hypothesis that elevated apoptosis signaling or its increased likelihood after DOX exposure can lead to an impairment of cardiac function and cause a cardiac dilation...
December 8, 2016: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/27933271/functional-significance-of-aurora-kinases-p53-protein-family-interactions-in-cancer
#4
REVIEW
Kaori Sasai, Warapen Treekitkarnmongkol, Kazuharu Kai, Hiroshi Katayama, Subrata Sen
Aurora kinases play critical roles in regulating spindle assembly, chromosome segregation, and cytokinesis to ensure faithful segregation of chromosomes during mitotic cell division cycle. Molecular and cell biological studies have revealed that Aurora kinases, at physiological levels, orchestrate complex sequential cellular processes at distinct subcellular locations through functional interactions with its various substrates. Aberrant expression of Aurora kinases, on the other hand, cause defects in mitotic spindle assembly, checkpoint response activation, and chromosome segregation leading to chromosomal instability...
2016: Frontiers in Oncology
https://www.readbyqxmd.com/read/27933213/molecular-pathology-of-cancer-how-to-communicate-with-disease
#5
REVIEW
Peter Birner, Gerald Prager, Berthold Streubel
: Recent technical advances have brought insights into the biology of cancer in human, establishing it as a disease driven by genetic mutations. Beside inherited family tumour syndromes caused by germline mutations, somatic genetic alterations occur early in tumourigenesis, which accumulate during the progression of the disease and its treatment. Based on these observations, medical oncology has started to enter an era of stratified medicine, where treatment selection is becoming tailored to drugable molecular pathways...
2016: ESMO Open
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/27933047/diazotroph-diversity-in-the-sea-ice-melt-ponds-and-surface-waters-of-the-eurasian-basin-of-the-central-arctic-ocean
#7
Mar Fernández-Méndez, Kendra A Turk-Kubo, Pier L Buttigieg, Josephine Z Rapp, Thomas Krumpen, Jonathan P Zehr, Antje Boetius
The Eurasian basin of the Central Arctic Ocean is nitrogen limited, but little is known about the presence and role of nitrogen-fixing bacteria. Recent studies have indicated the occurrence of diazotrophs in Arctic coastal waters potentially of riverine origin. Here, we investigated the presence of diazotrophs in ice and surface waters of the Central Arctic Ocean in the summer of 2012. We identified diverse communities of putative diazotrophs through targeted analysis of the nifH gene, which encodes the iron protein of the nitrogenase enzyme...
2016: Frontiers in Microbiology
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/27932790/motor-neurons-derived-from-als-related-mouse-ips-cells-recapitulate-pathological-features-of-als
#9
Ju-Hwang Park, Hang-Soo Park, Sunghoi Hong, Seongman Kang
Amyotrophic lateral sclerosis (ALS) is a late-onset progressive neurodegenerative disease characterized by the loss of motor neurons in the spinal cord and brain. Mutations in Cu/Zn superoxide dismutase 1 (SOD1) are known to induce ALS. Although many research models have been developed, the exact pathological mechanism of ALS remains unknown. The recently developed induced pluripotent stem (iPS) cell technology is expected to illuminate the pathological mechanisms and new means of treatment for neurodegenerative diseases...
December 9, 2016: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/27932576/mammalian-synthetic-biology-for-studying-the-cell
#10
REVIEW
Melina Mathur, Joy S Xiang, Christina D Smolke
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes...
December 8, 2016: Journal of Cell Biology
https://www.readbyqxmd.com/read/27932498/harnessing-molecular-motors-for-nanoscale-pulldown-in-live-cells
#11
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/27932441/trophoblast-cells-inhibit-neutrophil-extracellular-trap-formation-and-enhance-apoptosis-through-vasoactive-intestinal-peptide-mediated-pathways
#12
Guillermina Calo, Florencia Sabbione, Daiana Vota, Daniel Paparini, Rosanna Ramhorst, Analía Trevani, Claudia Pérez Leirós
STUDY QUESTION: Do human trophoblast cells modulate neutrophil extracellular trap (NET) formation, reactive oxygen species (ROS) synthesis and neutrophil apoptosis through mechanisms involving vasoactive intestinal peptide (VIP)? SUMMARY ANSWER: Trophoblast cells inhibited NET formation and ROS synthesis and enhanced neutrophil apoptosis through VIP-mediated pathways in a model of maternal-placental interaction. WHAT IS KNOWN ALREADY: Immune homeostasis maintenance at the maternal-placental interface is mostly coordinated by trophoblast cells...
December 7, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27932423/integrated-genomic-analysis-of-survival-outliers-in-glioblastoma
#13
Sen Peng, Harshil Dhurv, Brock Armstrong, Bodour Salhia, Christophe Legendre, Jeffrey Kiefer, Julianna Parks, Selene Virk, Andrew E Sloan, Quinn T Ostrom, Jill S Barnholtz-Sloan, Nhan L Tran, Michael E Berens
BACKGROUND: To elucidate molecular features associated with disproportionate survival of glioblastoma (GB) patients, we conducted deep genomic comparative analysis of a cohort of patients receiving standard therapy (surgery plus concurrent radiation and temozolomide); "GB outliers" were identified: long-term survivor of 33 months (LTS; n = 8) versus short-term survivor of 7 months (STS; n = 10). METHODS: We implemented exome, RNA, whole genome sequencing, and DNA methylation for collection of deep genomic data from STS and LTS GB patients...
December 8, 2016: Neuro-oncology
https://www.readbyqxmd.com/read/27932416/a-phase-ii-trial-of-dovitinib-in-bcg-unresponsive-urothelial-carcinoma-with-fgfr3-mutations-or-over-expression-hoosier-cancer-research-network-trial-hcrn-12-157
#14
Noah M Hahn, Trinity J Bivalacqua, Ashley E Ross, George J Netto, Alexander S Baras, Jong Chul Park, Carolyn Chapman, Timothy A Masterson, Michael O Koch, Richard Bihrle, Richard S Foster, Thomas A Gardner, Liang Cheng, David R Jones, Kyle McElyea, George E Sandusky, Timothy Breen, Ziyue Liu, Costantine Albany, Marietta L Moore, Rhoda A Loman, Angela Reed, Scott A Turner, Francine B de Abreu, Torrey L Gallagher, Gregory J Tsongalis, Elizabeth R Plimack, Richard E Greenberg, Daniel M Geynisman
PURPOSE: To assess the clinical and pharmacodynamic activity of dovitinib in a treatment resistant, molecularly enriched NMIUC population. EXPERIMENTAL DESIGN: A multi-site pilot phase 2 trial was conducted. Key eligibility criteria included: BCG unresponsive NMIUC (> 2 prior intravesical regimens) with increased phosphorylated FGFR3 (pFGFR3) expression by centrally analyzed immunohistochemistry (IHC+) or FGFR3 mutations (Mut+) assessed in a CLIA-licensed laboratory...
December 8, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27932294/large-scale-structure-based-prediction-and-identification-of-novel-protease-substrates-using-computational-protein-design
#15
Manasi A Pethe, Aliza B Rubenstein, Sagar D Khare
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data...
December 5, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27932023/molecular-cloning-and-expression-analysis-of-a-fish-specific-interferon-regulatory-factor-irf11-in-orange-spotted-grouper-epinephelus-coioides
#16
Wen Shu Huang, Mei Hua Zhu, Shan Chen, Zhi Xuan Wang, Ying Liang, Bei Huang, P Nie
Interferon regulatory factors (IRFs) are transcription mediators which play vital roles in multiple biological processes, such as antiviral defense, immune response, cell growth regulation and apoptosis. A fish specific IRF, termed IRF11, has been identified in previous study through searching fish genome databases. Herein, a transcript of IRF11, EcIRF11 was cloned from orange-spotted grouper, Epinephelus coioides. The EcIRF11 cDNA sequence has 1573 bp in length, encoding a putative protein of 261 amino acids, with a high degree of similarity found between EcIRF11 and its teleost counterparts...
December 5, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27931841/new-molecular-therapies-in-patients-with-advanced-hepatocellular-cancer-in-second-line-of-treatment-is-a-real-defeat-results-from-a-literature-based-meta-analysis-of-randomized-trials
#17
REVIEW
Giandomenico Roviello, Laura Zanotti, Maria Rosa Cappelletti, Angela Gobbi, Giulia Borsella, Chiara Pacifico, Andrea Giovanni Multari, Daniele Generali
Several new biological agents have been investigated as second line of treatment in advanced Hepatocellular Cancer (HCC). We performed a meta-analysis to assess the effect of targeted therapies in advanced HCC patients beyond the first line of treatment. A literature-based metaanalysis of randomized controlled trials was undertaken. The primary outcome was the overall survival. The secondary endpoints were the progression-free survival (PFS), the response rate (RR) and disease control rate (DCR) and the safety...
December 2016: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/27931833/hyperglycemia-tumorigenesis-and-chronic-inflammation
#18
REVIEW
Shu-Chun Chang, Wei-Chung Vivian Yang
Hyperglycemia is the most prominent sign that characterizes diabetes. Hyperglycemia favors malignant cell growth by providing energy to cancer cells. Clinical studies also showed an increased risk of diabetes being associated with different types of cancers. In addition, poorly regulated glucose metabolism in diabetic patients is often found with increased levels of chronic inflammatory markers, e.g., interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α, and emerging evidence has highlighted activation of the immune response in the progression and development of cancer cells...
December 2016: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/27931609/clinical-and-biological-insights-into-combined-post-and-pre-capillary-pulmonary-hypertension
#19
Tufik R Assad, Anna R Hemnes, Emma K Larkin, Andrew M Glazer, Meng Xu, Quinn S Wells, Eric H Farber-Eger, Quanhu Sheng, Yu Shyr, Frank E Harrell, John H Newman, Evan L Brittain
BACKGROUND: Pulmonary hypertension (PH) is a common and morbid complication of left heart disease with 2 subtypes: isolated post-capillary pulmonary hypertension (Ipc-PH) and combined post-capillary and pre-capillary pulmonary hypertension (Cpc-PH). Little is known about the clinical or physiological characteristics that distinguish these 2 subphenotypes or if Cpc-PH shares molecular similarities to pulmonary arterial hypertension (PAH). OBJECTIVES: The goal of this study was to test the hypothesis that the hemodynamic and genetic profile of Cpc-PH would more closely resemble PAH than Ipc-PH...
December 13, 2016: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/27931360/molecular-biological-methods-in-environmental-engineering
#20
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
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