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Genomics review

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https://www.readbyqxmd.com/read/29458108/the-relaxin-receptor-as-a-therapeutic-target-perspectives-from-evolution-and-drug-targeting
#1
REVIEW
Ross A D Bathgate, Martina Kocan, Daniel J Scott, M Akhter Hossain, Sara V Good, Sergey Yegorov, Jan Bogerd, Paul Gooley
The peptide relaxin was first identified as an important circulating hormone during pregnancy over 90 years ago. Research over many years defined the numerous biological roles that relaxin plays throughout pregnancy in many mammalian species. These important biological actions have led to the testing of relaxin as a therapeutic agent for a number of indications. The discovery of the relaxin receptor, RXFP1, in 2002 facilitated the better understanding of the cellular targets of relaxin, its mechanism of action and enabled the development of relaxin mimetics and screening for small molecule agonists...
February 16, 2018: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/29458070/the-epigenetic-alterations-of-endogenous-retroelements-in-aging
#2
REVIEW
Maurizio Cardelli
Endogenous retroelements, transposons that mobilize through RNA intermediates, include some of the most abundant repetitive sequences of the human genome, such as Alu and LINE-1 sequences, and human endogenous retroviruses. Recent discoveries demonstrate that these mobile genetic elements not only act as intragenomic parasites, but also exert regulatory roles in living cells. The risk of genomic instability represented by endogenous retroelements is normally counteracted by a series of epigenetic control mechanisms which include, among the most important, CpG DNA methylation...
February 16, 2018: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/29457194/reproduction-in-woody-perennial-citrus-an-update-on-nucellar-embryony-and-self-incompatibility
#3
REVIEW
Siqi Zhang, Mei Liang, Nan Wang, Qiang Xu, Xiuxin Deng, Lijun Chai
Review on citrus reproduction. Citrus is one of the most important and widely grown fruit crops. It possesses several special reproductive characteristics, such as nucellar embryony and self-incompatibility. The special phenomenon of nucellar embryony in citrus, also known as the polyembryony, is a kind of sporophytic apomixis. During the past decade, the emergence of novel technologies and the construction of multiple citrus reference genomes have facilitated rapid advances to our understanding of nucellar embryony...
February 19, 2018: Plant Reproduction
https://www.readbyqxmd.com/read/29456764/integrative-analysis-of-the-epigenetic-basis-of-muscle-invasive-urothelial-carcinoma
#4
Thomas Sanford, Maxwell V Meng, Reema Railkar, Piyush K Agarwal, Sima P Porten
Background: Elucidation of epigenetic alterations in bladder cancer will lead to further understanding of the biology of the disease and hopefully improved therapies. Our aim was to perform an integrative epigenetic analysis of invasive urothelial carcinoma of the bladder to identify the epigenetic abnormalities involved in the development and progression of this cancer. Methods: Pre-processed methylation data and RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29456548/gaba-shunt-in-durum-wheat
#5
REVIEW
Petronia Carillo
Plant responses to salinity are complex, especially when combined with other stresses, and involve many changes in gene expression and metabolic fluxes. Until now, plant stress studies have been mainly dealt only with a single stress approach. However, plants exposed to multiple stresses at the same time, a combinatorial approach reflecting real-world scenarios, show tailored responses completely different from the response to the individual stresses, due to the stress-related plasticity of plant genome and to specific metabolic modifications...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29456488/exploring-the-complexity-of-cortical-development-using-single-cell-transcriptomics
#6
REVIEW
Hyobin Jeong, Vijay K Tiwari
The developing neocortex in the mammalian brain is composed of multiple cell types including apical progenitors (AP), basal progenitors (BP), and neurons that populate three different layers, the ventricular zone (VZ), the subventricular zone (SVZ), and the cortical plate (CP). Despite recent advances, the diversity of the existing cell populations including those which are differentiating and mature, their biogenesis and the underlying gene regulatory mechanisms remain poorly known. Recent studies have taken advantage of the rapidly emerging single-cell technologies to decode the heterogeneity of cell populations at the transcriptome level during cortical development and their molecular details...
2018: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29456241/ecology-and-evolution-of-mycobacterium-tuberculosis
#7
REVIEW
Sebastien Gagneux
Tuberculosis (TB) is the number one cause of human death due to an infectious disease. The causative agents of TB are a group of closely related bacteria known as the Mycobacterium tuberculosis complex (MTBC). As the MTBC exhibits a clonal population structure with low DNA sequence diversity, methods (such as multilocus sequence typing) that are applied to more genetically diverse bacteria are uninformative, and much of the ecology and evolution of the MTBC has therefore remained unknown. Owing to recent advances in whole-genome sequencing and analyses of large collections of MTBC clinical isolates from around the world, many new insights have been gained, including a better understanding of the origin of the MTBC as an obligate pathogen and its molecular evolution and population genetic characteristics both within and between hosts, as well as many aspects related to antibiotic resistance...
February 19, 2018: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29455673/kinase-targeted-cancer-therapies-progress-challenges-and-future-directions
#8
REVIEW
Khushwant S Bhullar, Naiara Orrego Lagarón, Eileen M McGowan, Indu Parmar, Amitabh Jha, Basil P Hubbard, H P Vasantha Rupasinghe
The human genome encodes 538 protein kinases that transfer a γ-phosphate group from ATP to serine, threonine, or tyrosine residues. Many of these kinases are associated with human cancer initiation and progression. The recent development of small-molecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. Significantly, protein kinases are the second most targeted group of drug targets, after the G-protein-coupled receptors. Since the development of the first protein kinase inhibitor, in the early 1980s, 37 kinase inhibitors have received FDA approval for treatment of malignancies such as breast and lung cancer...
February 19, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29455671/oncogenic-fusion-proteins-adopt-the-insulin-like-growth-factor-signaling-pathway
#9
REVIEW
Haim Werner, Shilhav Meisel-Sharon, Ilan Bruchim
The insulin-like growth factor-1 receptor (IGF1R) has been identified as a potent anti-apoptotic, pro-survival tyrosine kinase-containing receptor. Overexpression of the IGF1R gene constitutes a typical feature of most human cancers. Consistent with these biological roles, cells expressing high levels of IGF1R are expected not to die, a quintessential feature of cancer cells. Tumor specific chromosomal translocations that disrupt the architecture of transcription factors are a common theme in carcinogenesis...
February 19, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29455648/mechanisms-of-receptor-tyrosine-kinase-activation-in-cancer
#10
REVIEW
Zhenfang Du, Christine M Lovly
Receptor tyrosine kinases (RTKs) play an important role in a variety of cellular processes including growth, motility, differentiation, and metabolism. As such, dysregulation of RTK signaling leads to an assortment of human diseases, most notably, cancers. Recent large-scale genomic studies have revealed the presence of various alterations in the genes encoding RTKs such as EGFR, HER2/ErbB2, and MET, amongst many others. Abnormal RTK activation in human cancers is mediated by four principal mechanisms: gain-of-function mutations, genomic amplification, chromosomal rearrangements, and / or autocrine activation...
February 19, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29455172/transmission-of-esbl-producing-enterobacteriaceae-and-their-mobile-genetic-elements-identification-of-sources-by-whole-genome-sequencing-study-protocol-for-an-observational-study-in-switzerland
#11
Tanja Stadler, Dominik Meinel, Lisandra Aguilar-Bultet, Jana S Huisman, Ruth Schindler, Adrian Egli, Helena M B Seth-Smith, Lucas Eichenberger, Peter Brodmann, Philipp Hübner, Claudia Bagutti, Sarah Tschudin-Sutter
INTRODUCTION: Extended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producing Escherichia coli was increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa...
February 17, 2018: BMJ Open
https://www.readbyqxmd.com/read/29455143/the-birth-and-death-of-effectors-in-rapidly-evolving-filamentous-pathogen-genomes
#12
REVIEW
Simone Fouché, Clémence Plissonneau, Daniel Croll
Plant pathogenic fungi and oomycetes are major risks to food security due to their evolutionary success in overcoming plant defences. Pathogens produce effectors to interfere with host defences and metabolism. These effectors are often encoded in rapidly evolving compartments of the genome. We review how effector genes emerged and were lost in pathogen genomes drawing on the links between effector evolution and chromosomal rearrangements. Some new effectors entered pathogen genomes via horizontal transfer or introgression...
February 15, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29454983/old-and-new-glycopeptide-antibiotics-from-product-to-gene-and-back-in-the-post-genomic-era
#13
REVIEW
Giorgia Letizia Marcone, Elisa Binda, Francesca Berini, Flavia Marinelli
Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics...
February 15, 2018: Biotechnology Advances
https://www.readbyqxmd.com/read/29454982/improved-genomic-resources-and-new-bioinformatic-workflow-for-the-carcinogenic-parasite-clonorchis-sinensis-biotechnological-implications
#14
REVIEW
Daxi Wang, Pasi K Korhonen, Robin B Gasser, Neil D Young
Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite...
February 15, 2018: Biotechnology Advances
https://www.readbyqxmd.com/read/29454697/symposium-review-building-a-better-cow-the-australian-experience-and-future-perspectives
#15
J E Pryce, T T T Nguyen, M Axford, G Nieuwhof, M Shaffer
Genomic selection has led to opportunities for developing new breeding values that rely on phenotypes in dedicated reference populations of genotyped cows. In Australia, it has been applied to 2 novel traits: feed efficiency, which was released in 2015 as feed saved breeding values, and heat tolerance genomic breeding values, released for the first time in 2017. Feed saved is already included in the national breeding objective, which is focused on profitability and designed to be in line with farmer preferences...
February 14, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29454655/neurogenetic-approaches-to-stress-and-fear-in-humans-as-pathophysiological-mechanisms-for-posttraumatic-stress-disorder
#16
REVIEW
Frauke Nees, Stephanie H Witt, Herta Flor
In this review article, genetic variation associated with brain responses related to acute and chronic stress reactivity and fear learning in humans is presented as an important mechanism underlying posttraumatic stress disorder. We report that genes related to the regulation of the hypothalamic-pituitary-adrenal axis, as well as genes that modulate serotonergic, dopaminergic, and neuropeptidergic functions or plasticity, play a role in this context. The strong overlap of the genetic targets involved in stress and fear learning suggests that a dimensional and mechanistic model of the development of posttraumatic stress disorder based on these constructs is promising...
January 10, 2018: Biological Psychiatry
https://www.readbyqxmd.com/read/29454536/the-role-of-the-ovol1-ovol2-axis-in-normal-and-diseased-human-skin
#17
REVIEW
Gaku Tsuji, Takamichi Ito, Takahito Chiba, Chikage Mitoma, Takeshi Nakahara, Hiroshi Uchi, Masutaka Furue
OVOLs (OVO-like proteins) are ubiquitously conserved genes encoding a C2 H2 zinc finger transcription factor in mammals. Functional studies on OVOL1 and OVOL2 using knockout mice have suggested that these genes play a pivotal role in the development of epithelial tissues arising from germ cells; however, the role of the OVOL1-OVOL2 axis in normal and diseased tissues remains unclear. This review highlights recent advances in understanding how the OVOL1-OVOL2 axis modulates cell differentiation and proliferation in human keratinocytes, hair follicles, and benign or malignant skin tumors including squamous cell carcinoma and malignant melanoma...
February 12, 2018: Journal of Dermatological Science
https://www.readbyqxmd.com/read/29454384/applaud-access-for-patients-and-participants-to-individual-level-uninterpreted-genomic-data
#18
REVIEW
Adrian Thorogood, Jason Bobe, Barbara Prainsack, Anna Middleton, Erick Scott, Sarah Nelson, Manuel Corpas, Natasha Bonhomme, Laura Lyman Rodriguez, Madeleine Murtagh, Erika Kleiderman
BACKGROUND: There is a growing support for the stance that patients and research participants should have better and easier access to their raw (uninterpreted) genomic sequence data in both clinical and research contexts. MAIN BODY: We review legal frameworks and literature on the benefits, risks, and practical barriers of providing individuals access to their data. We also survey genomic sequencing initiatives that provide or plan to provide individual access. Many patients and research participants expect to be able to access their health and genomic data...
February 17, 2018: Human Genomics
https://www.readbyqxmd.com/read/29454225/low-power-lasers-on-genomic-stability
#19
Larissa Alexsandra da Silva Neto Trajano, Luiz Philippe da Silva Sergio, Ana Carolina Stumbo, Andre Luiz Mencalha, Adenilson de Souza da Fonseca
Exposure of cells to genotoxic agents causes modifications in DNA, resulting to alterations in the genome. To reduce genomic instability, cells have DNA damage responses in which DNA repair proteins remove these lesions. Excessive free radicals cause DNA damages, repaired by base excision repair and nucleotide excision repair pathways. When non-oxidative lesions occur, genomic stability is maintained through checkpoints in which the cell cycle stops and DNA repair occurs. Telomere shortening is related to the development of various diseases, such as cancer...
February 10, 2018: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/29453967/discovery-of-anti-viral-molecules-and-their-vital-functions-in-bombyx-mori
#20
REVIEW
Peng Lü, Ye Pan, Yanhua Yang, Feifei Zhu, Chengjun Li, Qin Yao, Keping Chen
The silkworm Bombyx mori (B. mori), a lepidopteran model organism, has become an important model for molecular biology researches with its genome completely sequenced. Silkworms confront different types of virus diseases, mainly including those caused by Bombyx mori nucleopolyhedrovirus (BmNPV), Bombyx mori densovirus type 1 (BmDNV-1), Bombyx mori bidesovirus (BmBDV) which was termed as Bombyx mori densovirus type 2 (BmDNV-2) or Bombyx mori parvo-like virus (BmPLV) before in sericulture. B. mori offers excellent models to study the molecular mechanisms of insect innate immune responses to viruses...
February 14, 2018: Journal of Invertebrate Pathology
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