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Genetic conversion

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https://www.readbyqxmd.com/read/29143279/arabidopsis-noncoding-rna-modulates-seedling-greening-during-deetiolation
#1
Yuqiu Wang, Jian Li, Xing-Wang Deng, Danmeng Zhu
Seedling greening is essential for the survival of plants emerging from the soil. The abundance of chlorophyll precursors, including protochlorophyllide (Pchlide), is precisely controlled during the dark-to-light transition, as over-accumulation of Pchlide can lead to cellular photooxidative damage. Previous studies have identified and characterized multiple regulators controlling this important process. HID1 (hidden treasure 1) is the first noncoding RNA (ncRNA) found in photomorphogenesis. Under continuous red light, HID1 has been shown to inhibit hypocotyl elongation by repressing the transcription of PIF3 (phytochrome interacting factor 3)...
October 13, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29142195/structural-basis-for-trna-dependent-cysteine-biosynthesis
#2
Meirong Chen, Koji Kato, Yume Kubo, Yoshikazu Tanaka, Yuchen Liu, Feng Long, William B Whitman, Pascal Lill, Christos Gatsogiannis, Stefan Raunser, Nobutaka Shimizu, Akira Shinoda, Akiyoshi Nakamura, Isao Tanaka, Min Yao
Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNA(Cys) followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNA(Cys), respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNA(Cys) between SepRS and SepCysS distant active sites...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29141788/interleukin-1-receptor-antagonist-and-2-5-oligoadenylate-synthetase-like-molecules-as-novel-biomarkers-for-multiple-sclerosis-patients-in-bahrain
#3
Moudi Al-Nashmi, Safa Taha, Isa Alsharoqi, Moiz Bakhiet
BACKGROUND: Multiple sclerosis (MS) is a multi-factorial disease of the Central Nervous System (CNS) affecting young adults leading to significant disabilities over time. MS is now believed to be prevalent in Arabian Gulf area with high incidence due to environmental factors and unknown genetic variations. The objectives of this study was to detect up-regulated potential genes that might be involved in neuroinflammatory process in MS patients in Bahrain and to measure the protein levels of the expressed genes...
November 2017: Multiple Sclerosis and related Disorders
https://www.readbyqxmd.com/read/29138319/frequent-nonallelic-gene-conversion-on-the-human-lineage-and-its-effect-on-the-divergence-of-gene-duplicates
#4
Arbel Harpak, Xun Lan, Ziyue Gao, Jonathan K Pritchard
Gene conversion is the copying of a genetic sequence from a "donor" region to an "acceptor." In nonallelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250 bp and a probability of [Formula: see text] per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate)...
November 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29133298/functional-redundancy-of-variant-and-canonical-histone-h3-lysine-9-modification-in-drosophila
#5
Taylor J R Penke, Daniel J McKay, Brian D Strahl, A Gregory Matera, Robert J Duronio
Histone post-translational modifications (PTMs) and differential incorporation of variant and canonical histones into chromatin are central modes of epigenetic regulation. Despite similar protein sequences, histone variants are enriched for different suites of PTMs compared to their canonical counterparts. For example, variant histone H3.3 occurs primarily in transcribed regions and is enriched for "active" histone PTMs like Lys9 acetylation (H3.3K9ac), whereas the canonical histone H3 is enriched for Lys9 methylation (H3K9me), which is found in transcriptionally silent heterochromatin...
November 13, 2017: Genetics
https://www.readbyqxmd.com/read/29130521/a-variant-in-ppp4r3a-protects-against-alzheimer-related-metabolic-decline
#6
Leigh Christopher, Valerio Napolioni, Raiyan R Khan, Summer S Han, Michael D Greicius
OBJECTIVES: A reduction in glucose metabolism in the posterior cingulate cortex (PCC) predicts conversion to Alzheimer's disease (AD) and tracks disease progression, signifying its importance in AD. We aimed to use decline in PCC glucose metabolism as a proxy for the development and progression of AD to discover common genetic variants associated with disease vulnerability. METHODS: We performed a genome-wide association study (GWAS) of decline in PCC [(18) F] FDG PET measured in Alzheimer's Disease Neuroimaging Initiative (ADNI) participants (n=606)...
November 11, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/29130143/incorporating-social-media-into-your-support-tool-box-points-to-consider-from-genetics-based-communities
#7
Heather Mae Rocha, Juliann M Savatt, Erin Rooney Riggs, Jennifer K Wagner, W Andrew Faucett, Christa Lese Martin
Patients with newly-described or rare genetic findings are turning to social media to find and connect with others. Blogs, Facebook groups, and Twitter have all been reported as tools for patients to connect with one another. However, the preferences for social media use and privacy among patients, their families, and these communities have not been well characterized. To explore preferences about privacy and membership guidelines, an online survey was administered to two web-based patient registries, Simons Variation in Individuals Project ( www...
November 13, 2017: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/29127883/metabolic-engineering-of-yeast-for-lignocellulosic-biofuel-production
#8
REVIEW
Yong-Su Jin, Jamie Hd Cate
Production of biofuels from lignocellulosic biomass remains an unsolved challenge in industrial biotechnology. Efforts to use yeast for conversion face the question of which host organism to use, counterbalancing the ease of genetic manipulation with the promise of robust industrial phenotypes. Saccharomyces cerevisiae remains the premier host for metabolic engineering of biofuel pathways, due to its many genetic, systems and synthetic biology tools. Numerous engineering strategies for expanding substrate ranges and diversifying products of S...
November 8, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29127522/common-genetic-variation-within-mir-146a-predicts-disease-onset-and-relapse-in-multiple-sclerosis
#9
Yuan Zhou, Ming Chen, Steve Simpson, Robyn M Lucas, Jac C Charlesworth, Nicholas Blackburn, Ingrid van der Mei, Anne-Louise Ponsonby, Bruce V Taylor
Despite extensive studies focusing on the changes in expression of microRNAs (miRNAs) in multiple sclerosis (MS) compared to healthy controls, few studies have evaluated the association of genetic variants of miRNAs with MS clinical course. We investigated whether a functional polymorphism in the MS associated miR-146a gene predicted clinical course (hazard of conversion to MS and of relapse, and annualized change in disability), using a longitudinal cohort study of persons with a first demyelinating event followed up to their 5-year review...
November 10, 2017: Neurological Sciences
https://www.readbyqxmd.com/read/29127119/rasa1-and-nf1-are-preferentially-co-mutated-and-define-a-distinct-genetic-subset-of-smokingassociated-non-small-cell-lung-carcinomas-sensitive-to-mek-inhibition
#10
Takuo Hayashi, Patrice Desmeules, Roger S Smith, Alexander Drilon, Romel Somwar, Marc Ladanyi
PURPOSE: Ras-GTPase activating proteins (RasGAPs), notably NF1 and RASA1, mediate negative control of the RAS/MAPK pathway. We evaluated clinical and molecular characteristics of NSCLC with RASA1 mutations in comparison with NF1-mutated cases. EXPERIMENTAL DESIGN: Large genomic datasets of NSCLC [MSK-IMPACT™ dataset at MSKCC (n=2004), TCGA combined lung cancer dataset (n=1144)] were analyzed to define concurrent mutations and clinical features of RASA1-mutated NSCLCs...
November 10, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29124862/catabolic-task-division-between-two-interchangeable-near-isogenic-subpopulations-co-existing-in-a-herbicide-degrading-bacterial-consortium-consequences-for-the-interspecies-consortium-metabolic-model
#11
Pieter Albers, Cédric Lood, Basak Özturk, Benjamin Horemans, Rob Lavigne, Vera van Noort, René De Mot, Kathleen Marchal, Aminael Sanchez-Rodriguez, Dirk Springael
Variovorax sp. WDL1 mediates hydrolysis of the herbicide linuron into 3,4-dichloroaniline (DCA) and N,O-dimethylhydroxylamine in a tripartite bacterial consortium with Comamonas testosteroni WDL7 and Hyphomicrobium sulfonivorans WDL6. Although strain WDL1 contains the dcaQTA1A2B operon for DCA oxidation, this conversion is mainly performed by WDL7. Phenotypic diversification observed in WDL1 cultures and scrutiny of the WDL1 genome suggest that WDL1 cultures consist of two dedicated subpopulations, i.e., a linuron-hydrolyzing subpopulation (Lin+DCA-) and a DCA-oxidizing subpopulation (Lin-DCA+)...
November 10, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29124769/introgression-from-populus-balsamifera-underlies-adaptively-significant-variation-and-range-boundaries-in-p-%C3%A2-trichocarpa
#12
Adriana Suarez-Gonzalez, Charles A Hefer, Christian Lexer, Carl J Douglas, Quentin C B Cronk
Introgression can be an important source of adaptive phenotypes, although conversely it can have deleterious effects. Evidence for adaptive introgression is accumulating but information on the genetic architecture of introgressed traits lags behind. Here we determine trait architecture in Populus trichocarpa under introgression from P. balsamifera using admixture mapping and phenotypic analyses. Our results reveal that admixture is a key driver of clinal adaptation and suggest that the northern range extension of P...
November 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/29124514/anaerobic-microplate-assay-for-direct-microbial-conversion-of-switchgrass-and-avicel-using-clostridium-thermocellum
#13
Gbekeloluwa B Oguntimein, Miguel Rodriguez, Alexandru Dumitrache, Todd Shollenberger, Stephen R Decker, Brian H Davison, Steven D Brown
OBJECTIVE: To develop and prototype a high-throughput microplate assay to assess anaerobic microorganisms and lignocellulosic biomasses in a rapid, cost-effective screen for consolidated bioprocessing potential. RESULTS: Clostridium thermocellum parent Δhpt strain deconstructed Avicel to cellobiose, glucose, and generated lactic acid, formic acid, acetic acid and ethanol as fermentation products in titers and ratios similar to larger scale fermentations confirming the suitability of a plate-based method for C...
November 9, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/29123542/effects-of-diet-and-genetics-on-growth-performance-of-pigs-in-response-to-repeated-exposure-to-heat-stress
#14
Wendy M Rauw, E Johana Mayorga, Soi Meng Lei, Jack C M Dekkers, John F Patience, Nicholas K Gabler, Steven M Lonergan, Lance H Baumgard
Heat stress (HS) is one of the costliest issues in the U.S. pork industry. Aims of the present study were to determine the consequences of repeated exposure to HS on growth performance, and the effects of a high fiber diet, the genetic potential for high lean tissue accretion, and the genetic potential for residual feed intake (RFI) on resilience to HS. Barrows (n = 97) from three genetic lines (commercial, high RFI, low RFI) where subjected three times to a 4-day HS treatment (HS1, HS2, and HS3) which was preceded by a 9-day neutral (TN) adaptation period (TN1) and alternated by 7-day periods of neutral temperatures (TN2, TN3, and TN4)...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29117554/downregulation-of-the-apelinergic-axis-accelerates-aging-whereas-its-systemic-restoration-improves-the-mammalian-healthspan
#15
Rahul Rai, Asish K Ghosh, Mesut Eren, Alexander R Mackie, Daniel C Levine, So-Youn Kim, Jonathan Cedernaes, Veronica Ramirez, Daniele Procissi, Layton H Smith, Teresa K Woodruff, Joseph Bass, Douglas E Vaughan
Aging drives the occurrence of numerous diseases, including cardiovascular disease (CVD). Recent studies indicate that blood from young mice reduces age-associated pathologies. However, the "anti-aging" factors in juvenile circulation remain poorly identified. Here, we characterize the role of the apelinergic axis in mammalian aging and identify apelin as an anti-aging factor. The expression of apelin (apln) and its receptor (aplnr) exhibits an age-dependent decline in multiple organs. Reduced apln signaling perturbs organismal homeostasis; mice harboring genetic deficiency of aplnr or apln exhibit enhanced cardiovascular, renal, and reproductive aging...
November 7, 2017: Cell Reports
https://www.readbyqxmd.com/read/29116059/genetic-predictors-associated-with-diabetic-retinopathy-in-diabetic-foot-patients-a-preliminary-study
#16
Beata Mrozikiewicz-Rakowska, Magdalena Łukawska, Piotr Nehring, Konrad Szymański, Agnieszka Sobczyk-Kopcioł, Monika Krzyżewska, Paweł Maroszek, Rafał Płoski, Leszek Czupryniak
INTRODUCTION    Early detection of diabetic retinopathy (DR) is key for preventing irreversible blindness. Recent research has identified some of the genetic factors involved in the pathology of DR, although their precise underlying mechanisms remain unclear. OBJECTIVES    This pilot study aimed to determine genetic predictors of DR among patients with type 2 diabetes mellitus (T2DM) and diabetic foot (DF) based on pathogenetic pathways. PATIENTS AND METHODS    The study was conducted on 114 patients with T2DM and DF (64 with DR, 50 without DR) treated in the Medical University of Warsaw...
November 7, 2017: Polish Archives of Internal Medicine
https://www.readbyqxmd.com/read/29115286/genetic-predictors-associated-with-diabetic-retinopathy-in-diabetic-foot-patients
#17
Beata Mrozikiewicz-Rakowska, Magdalena Łukawska, Piotr Nehring, Konrad Szymański, Agnieszka Sobczyk-Kopcioł, Monika Krzyżewska, Paweł Maroszek, Rafał Płoski, Leszek Czupryniak
INTRODUCTION: Early detection of diabetic retinopathy (DR) is key for preventing irreversible blindness. Recent research has identified some of the genetic factors involved in the pathology of DR, although their precise underlying mechanisms remain unclear. OBJECTIVES: This pilot study aimed to determine genetic predictors of DR among patients with type 2 diabetes mellitus (T2DM) and diabetic foot (DF) based on pathogenetic pathways. PATIENTS AND METHODS: The study was conducted on 114 patients with T2DM and DF (64 with DR, 50 without DR) treated in the Medical University of Warsaw...
November 7, 2017: Polish Archives of Internal Medicine
https://www.readbyqxmd.com/read/29114997/in-vitro-modeling-of-hiv-proviral-activity-in-microglia
#18
Lee A Campbell, Christopher T Richie, Yajun Zhang, Emily J Heathward, Lamarque M Coke, Emily Y Park, Brandon K Harvey
Microglia, the resident macrophages of the brain, play a key role in the pathogenesis of HIV-associated neurocognitive disorders (HAND) due to their productive infection by HIV. This results in the release of neurotoxic viral proteins and pro-inflammatory compounds which negatively affect the functionality of surrounding neurons. Because models of HIV infection within the brain are limited, we aimed to create a novel microglia cell line with an integrated HIV provirus capable of recreating several hallmarks of HIV infection...
November 8, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29114105/neuregulin-3-signaling-mediates-nicotine-dependent-synaptic-plasticity-in-the-orbitofrontal-cortex-and-cognition
#19
Luyi Zhou, Miranda L Fisher, Robert D Cole, Thomas J Gould, Vinay Parikh, Pavel I Ortinski, Jill R Turner
Neuregulin 3 (NRG3) and ErbB4 have been linked to nicotine addiction; however, the neuronal mechanisms and behavioral consequences of NRG3-ErbB4 sensitivity to nicotine remain elusive. Recent literature suggests that relapse to smoking is due to a lack of impulsive control, which is thought to be due to altered functioning within the orbitofrontal cortex (OFC). Therefore, we examined circuitry changes within this structure following nicotine application. We report that nicotine controls synaptic plasticity in the OFC through NRG3/ErbB4-dependent regulation of GABAergic inhibition...
November 7, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29111666/switching-cyclic-nucleotide-selective-activation-of-pka-holoenzyme-reveals-distinct-roles-of-tandem-cnb-domains
#20
Daniel He, Robin Lorenz, Choel Kim, Friedrich W Herberg, Chinten James Lim
The cAMP- and cGMP-dependent protein kinases (PKA and PKG) are key effectors of cyclic nucleotide signaling. Both share structural features that include tandem cyclic nucleotide-binding (CNB) domains, CNB-A and CNB-B, yet their functions are separated through preferential activation by either cAMP or cGMP. Based on structural studies and modeling, key CNB contact residues have been identified for both kinases. In this study, we explored the requirements for conversion of PKA activation from cAMP-dependent to cGMP-dependent...
November 7, 2017: ACS Chemical Biology
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