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https://www.readbyqxmd.com/read/28938719/population-wide-sampling-of-retrotransposon-insertion-polymorphisms-using-deep-sequencing-and-efficient-detection
#1
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#2
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937979/molecular-genomic-characterization-of-tick-and-human-derived-severe-fever-with-thrombocytopenia-syndrome-virus-isolates-from-south-korea
#3
Seok-Min Yun, Su-Jin Park, Sun-Whan Park, WooYoung Choi, Hye Won Jeong, Young-Ki Choi, Won-Ja Lee
BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne viral disease caused by the SFTS virus (SFTSV) from Bunyaviridae that is endemic in East Asia. However, the genetic and evolutionary characteristics shared between tick- and human-derived Korean SFTSV strains are still limited. METHODOLOGY/PRINCIPAL FINDINGS: In this study we identify, for the first time, the genome sequence of a tick (Haemaphysalis longicornis)-derived Korean SFTSV strain (designated as KAGWT) and compare this virus with recent human SFTSV isolates to identify the genetic variations and relationships among SFTSV strains...
September 22, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28937734/discovery-of-oligonucleotide-signaling-mediated-by-crispr-associated-polymerases-solves-two-puzzles-but-leaves-an-enigma
#4
Eugene V Koonin, Kira S Makarova
The signature component of type III CRISPR-Cas systems is the Cas10 protein that consists of two Palm domains homologous to those of DNA and RNA polymerases, and nucleotide cyclases, and an HD nuclease domain. However, until very recently, the activity of the Palm domains and their role in CRISPR function have not been experimentally established. Most of the type III CRISPR-Cas systems and some type I systems also encompass proteins containing the CARF (CRISPR-associated Rossmann fold) domain that has been predicted to regulate CRISPR functions via nucleotide binding but its function in CRISPR-Cas remained obscure...
September 22, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28937696/chromophores-of-chromophores-a-bottom-up-h%C3%A3-ckel-picture-of-the-excited-states-of-photoactive-proteins
#5
Cate S Anstöter, Charlie R Dean, Jan R R Verlet
Many photoactive proteins contain chromophores based on para-substituted phenolate anions which are an essential component of their electronic structure. Here, we present a reductionist approach to gain fundamental insight into the evolution of electronic structure as the chromophore increases in complexity from phenolate to that in GFP. Using frequency- and angle-resolved photoelectron spectroscopy, in combination with electronic structure theory, the onset of excited states that are responsible for the characteristic spectroscopic features in biochromophores are determined...
September 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28937654/genome-wide-analysis-of-cca1-like-proteins-in-soybean-and-functional-characterization-of-gmmyb138a
#6
Shaomin Bian, Donghao Jin, Ruihua Li, Xin Xie, Guoli Gao, Weikang Sun, Yuejia Li, Lulu Zhai, Xuyan Li
Plant CIRCADIAN CLOCK ASSOCIATED1 (CCA1)-like proteins are a class of single-repeat MYELOBLASTOSIS ONCOGENE (MYB) transcription factors generally featured by a highly conserved motif SHAQK(Y/F)F, which play important roles in multiple biological processes. Soybean is an important grain legume for seed protein and edible vegetable oil. However, essential understandings regarding CCA1-like proteins are very limited in soybean. In this study, 54 CCA1-like proteins were identified by data mining of soybean genome...
September 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28936722/kinetics-of-photosystem-ii-electron-transport-a-mathematical-analysis-based-on-chlorophyll-fluorescence-induction
#7
Agu Laisk, Vello Oja
The OJDIP rise in chlorophyll fluorescence during induction at different light intensities was mathematically modeled using 24 master equations describing electron transport through photosystem II (PSII) plus ordinary differential equations for electron budgets in plastoquinone, cytochrome f, plastocyanin, photosystem I, and ferredoxin. A novel feature of the model is consideration of electron in- and outflow budgets resulting in changes in redox states of Tyrosine Z, P680, and QA as sole bases for changes in fluorescence yield during the transient...
September 21, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28935911/directing-evolution-the-next-revolution-in-drug-discovery
#8
REVIEW
Andrew M Davis, Alleyn T Plowright, Eric Valeur
The strong biological rationale to pursue challenging drug targets such as protein-protein interactions has stimulated the development of novel screening strategies, such as DNA-encoded libraries, to allow broader areas of chemical space to be searched. There has also been renewed interest in screening natural products, which are the result of evolutionary selection for a function, such as interference with a key signalling pathway of a competing organism. However, recent advances in several areas, such as understanding of the biosynthetic pathways for natural products, synthetic biology and the development of biosensors to detect target molecules, are now providing new opportunities to directly harness evolutionary pressure to identify and optimize compounds with desired bioactivities...
September 22, 2017: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/28935886/stepwise-evolution-improves-identification-of-diverse-peptides-binding-to-a-protein-target
#9
Victor I Lyamichev, Lauren E Goodrich, Eric H Sullivan, Ryan M Bannen, Joerg Benz, Thomas J Albert, Jigar J Patel
Considerable efforts have been made to develop technologies for selection of peptidic molecules that act as substrates or binders to a protein of interest. Here we demonstrate the combination of rational peptide array library design, parallel screening and stepwise evolution, to discover novel peptide hotspots. These hotspots can be systematically evolved to create high-affinity, high-specificity binding peptides to a protein target in a reproducible and digitally controlled process. The method can be applied to synthesize both linear and cyclic peptides, as well as peptides composed of natural and non-natural amino acid analogs, thereby enabling screens in a much diverse chemical space...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935574/taurocholate-induces-biliary-differentiation-of-liver-progenitor-cells-causing-hepatic-stellate-cell-chemotaxis-in-the-ductular-reaction-role-in-pediatric-cystic-fibrosis-liver-disease
#10
Katarzyna N Pozniak, Michael A Pearen, Tamara N Pereira, Cynthia Sm Kramer, Priyakshi Kalita-De Croft, Sujeevi K Nawaratna, Manuel A Fernandez-Rojo, Geoffrey N Gobert, Janina Ee Tirnitz-Parker, John K Olynyk, Ross W Shepherd, Peter J Lewindon, Grant A Ramm
Cystic fibrosis liver disease (CFLD) in children causes progressive fibrosis leading to biliary cirrhosis, however its cause(s) and early pathogenesis are unclear. We hypothesised that a bile acid-induced Ductular Reaction (DR) drives fibrogenesis. We evaluated the DR by cytokeratin-7 immunohistochemistry in liver biopsies, staged for fibrosis, from 60 children with CFLD and demonstrated that the DR was significantly correlated with hepatic fibrosis stage and biliary taurocholate levels. To examine the mechanisms involved in DR induction liver progenitor cells (LPCs) were treated with taurocholate and key events in DR evolution were assessed: LPC proliferation, LPC biliary differentiation and hepatic stellate cell (HSC) chemotaxis...
September 18, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28935117/the-role-of-krab-zfps-in-transposable-element-repression-and-mammalian-evolution
#11
REVIEW
Peng Yang, Yixuan Wang, Todd S Macfarlan
Kruppel-associated box zinc-finger proteins (KRAB-ZFPs) make up the largest family of transcription factors in humans. These proteins emerged in the last common ancestor of coelacanth and tetrapods, and have expanded and diversified in the mammalian lineage. Although their mechanism of transcriptional repression has been well studied for over a decade, the DNA-binding activities and the biological functions of these proteins have been largely unexplored. Recent large-scale ChIP-seq studies and loss-of-function experiments have revealed that KRAB-ZFPs play a major role in the recognition and transcriptional silencing of transposable elements (TEs), consistent with an 'arms race model' of KRAB-ZFP evolution against invading TEs...
September 18, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28935113/directed-evolution-of-glycopeptides-using-mrna-display
#12
Satoru Horiya, Jennifer K Bailey, Isaac J Krauss
Directed evolution is a useful method for the discovery of nucleic acids, peptides, or proteins that have desired binding abilities or functions. Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. However, common directed evolution platforms such as phage-, yeast-, or mammalian-cell display are limited for these applications by several factors. Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28934927/evolution-and-expression-analysis-reveal-the-potential-role-of-the-hd-zip-gene-family-in-regulation-of-embryo-abortion-in-grapes-vitis-vinifera-l
#13
Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang, Yan Xu
BACKGROUND: The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs. RESULTS: A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934386/expression-of-the-neuropathy-associated-mtmr2-gene-rescues-mtm1-associated-myopathy
#14
Matthieu A Raess, Belinda S Cowling, Dimitri L Bertazzi, Christine Kretz, Bruno Rinaldi, Jean-Marie Xuereb, Pascal Kessler, Norma B Romero, Bernard Payrastre, Sylvie Friant, Jocelyn Laporte
Myotubularins (MTMs) are active or dead phosphoinositides phosphatases defining a large protein family conserved through evolution and implicated in different neuromuscular diseases. Loss-of-function mutations in MTM1 cause the severe congenital myopathy called myotubular myopathy (or X-linked centronuclear myopathy) while mutations in the MTM1-related protein MTMR2 cause a recessive Charcot-Marie-Tooth peripheral neuropathy. Here we aimed to determine the functional specificity and redundancy of MTM1 and MTMR2, and to assess their abilities to compensate for a potential therapeutic strategy...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28934209/microbial-translocation-is-correlated-with-hiv-evolution-in-hiv-hcv-co-infected-patients
#15
Jean-Jacques Tudesq, Catherine Dunyach-Remy, Christophe Combescure, Régine Doncesco, Didier Laureillard, Jean-Philippe Lavigne, Albert Sotto
Microbial translocation (MT) is characterized by bacterial products passing into the blood through the gut barrier and is a key phenomenon in the pathophysiology of Human Immunodeficiency Virus (HIV) infection. MT is also associated with liver damage in Hepatitis C Virus (HCV) patients. The aim of the study was to assess MT in plasma of HIV-HCV co-infected patients. 16S rDNA (16 S Ribosomal DNA subunit) marker and other markers of MT such as Lipopolysaccharide (LPS)-binding protein (LBP), soluble CD14 (sCD14), intestinal fatty acid binding protein (I-FABP) were used...
2017: PloS One
https://www.readbyqxmd.com/read/28934148/tomato-leaf-curl-new-delhi-virus-an-emerging-virus-complex-threatening-vegetable-and-fiber-crops
#16
REVIEW
Enrique Moriones, Shelly Praveen, Supriya Chakraborty
The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent. However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin. Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade...
September 21, 2017: Viruses
https://www.readbyqxmd.com/read/28933119/-research-on-rat-models-of-acute-liver-injury-with-syndrome-of-liver-depression-and-spleen-deficiency
#17
Na-Na Huang, Xiao-Qian Sun, Qian Yang, Xiao-Yu Li, Rong Sun
This paper aimed to establish animal models which are suitable for the activity found, efficacy evaluation of herbs resistant to acute liver injury with syndrome of liver depression and spleen deficiency and new drug research and development based on corresponding of formula and syndrome. The symptoms that are suitable for evaluating the rat models of acute liver injury with syndrome of liver depression and spleen deficiency were extracted according to the evolution rule of the etiology and pathogenesis in traditional Chinese medicine and the modern pathological mechanism...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932624/staphylococci-on-ice-overlooked-agents-of-horizontal-gene-transfer
#18
REVIEW
Emily A Sansevere, D Ashley Robinson
Horizontal gene transfer plays a significant role in spreading antimicrobial resistance and virulence genes throughout the genus Staphylococcus, which includes species of clinical relevance to humans and animals. While phages and plasmids are the most well-studied agents of horizontal gene transfer in staphylococci, the contribution of integrative conjugative elements (ICEs) has been mostly overlooked. Experimental work demonstrating the activity of ICEs in staphylococci remained frozen for years after initial work in the 1980s that showed Tn916 was capable of transfer from Enterococcus to Staphylococcus...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28932623/proteomics-technique-opens-new-frontiers-in-mobilome-research
#19
COMMENT
Andrew D Davidson, David A Matthews, Kevin Maringer
A large proportion of the genome of most eukaryotic organisms consists of highly repetitive mobile genetic elements. The sum of these elements is called the "mobilome," which in eukaryotes is made up mostly of transposons. Transposable elements contribute to disease, evolution, and normal physiology by mediating genetic rearrangement, and through the "domestication" of transposon proteins for cellular functions. Although 'omics studies of mobilome genomes and transcriptomes are common, technical challenges have hampered high-throughput global proteomics analyses of transposons...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28932346/insights-from-the-draft-genome-into-the-pathogenicity-of-a-clinical-isolate-of-elizabethkingia-meningoseptica-em3
#20
Shicheng Chen, Marty Soehnlen, Frances P Downes, Edward D Walker
Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high mortality rate in immunocompromised patients. We report the draft genome sequence of E. meningoseptica Em3, isolated from sputum from a patient with multiple underlying diseases. The genome has a length of 4,037,922 bp, a GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide identity analysis (>95%) assigned the bacterium to the species E. meningoseptica. Genome analysis showed presence of the curli formation and assembly operon and a gene encoding hemagglutinins, indicating ability to form biofilm...
2017: Standards in Genomic Sciences
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