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https://www.readbyqxmd.com/read/28224054/variant-profiling-of-evolving-prokaryotic-populations
#1
Markus Zojer, Lisa N Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei
Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes...
2017: PeerJ
https://www.readbyqxmd.com/read/28219707/22-azidosalvinorin-a-exhibits-antidepressant-like-effect-in-mice
#2
James Oluwagbamigbe Fajemiroye, Polepally Reddy Prabhakar, Luiz Carlos da Cunha, Elson Alves Costa, Jordan K Zjawiony
The increasing cases of depression has made the searches for new drugs and understanding of the underligning neurobiology of this psychiatric disorder a necessity. Here, we modified the structure of salvinorin A (a known halucinogen) and investigated antidepressant-like activity of its four derivatives; 22-methylsulfanylsalvinorin A(SA1), 2-O-cinnamoylsalvinorin B (CSB), 22-azidosalvinorin A (SA2), and 2-O-(4(')-azidophenylsulfonyl)salvinorin B (SA3). Prior to behavioural tests (Irwin test, open field test - OFT, forced swimming test - FST and tail suspension test - TST), SA1 was prepared by reacting salvinorin B and methylthioacetic acid with 89% yield; CSB was obtained from the reaction of salvinorin B and cinnamic acid with 92% yield; SA2 was obtained from the reaction of salvinorin B and azidoacetic acid with 81% yield; and SA3 was prepared by reacting salvinorin B with 4-azidophenylsulfonyl chloride with 80% yield...
February 17, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28185557/reconstruction-of-ancestral-rna-sequences-under-multiple-structural-constraints
#3
Olivier Tremblay-Savard, Vladimir Reinharz, Jérôme Waldispühl
BACKGROUND: Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. METHODS: In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28164788/variations-in-the-bacterial-community-compositions-at-different-sites-in-the-tomb-of-emperor-yang-of-the-sui-dynasty
#4
Zhi Huang, Fei Zhao, Yonghui Li, Jianwei Zhang, Youzhi Feng
To fully understand the bacterial processes in tomb environments, it is necessary to investigate the details of the bacterial communities present under such oligotrophic conditions. Here, high-throughput sequencing based on partial 16S rRNA gene sequences was used to fully evaluate the bacterial communities at different sites in the tomb of Emperor Yang of the Sui Dynasty. We also aimed to identify the soil factors that were significant related to bacterial diversity and community composition. The results showed the presence of a broad taxonomic diversity that included nine major phyla...
March 2017: Microbiological Research
https://www.readbyqxmd.com/read/28112852/investigation-of-the-er-yag-laser-and-diamond-bur-cavity-preparation-on-the-marginal-microleakage-of-class-v-cavities-restored-with-different-flowable-composites
#5
Elif Bahar Tuna, Emre Ozel, Yelda Kasimoglu, Erhan Firatli
The purpose of this study was to evaluate the efficiency of the Er:YAG laser and diamond bur cavity preparation on the marginal microleakage of Class V cavities. Group 1: bur preparation (bp) + Vertise Flow (VF); Group 2: laser preparation (lp) + VF; Group 3: bp + Adper Easy One (AEO) + Filtek Ultimate Flowable Composite (FUFC); Group 4: lp + AEO + FUFC; Group 5: bp + Clearfil S3 Bond (CSB) + Clearfil Majesty Flow (CMF); Group 6: lp + CSB + CMF. Data were analyzed by Kruskal-Wallis and Mann-Whitney U tests (p < ...
January 23, 2017: Microscopy Research and Technique
https://www.readbyqxmd.com/read/28095775/ara-peps-a-repository-of-putative-sorf-encoded-peptides-in-arabidopsis-thaliana
#6
Rashmi R Hazarika, Barbara De Coninck, Lidia R Yamamoto, Laura R Martin, Bruno P A Cammue, Vera van Noort
BACKGROUND: Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana. RESULTS: To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www...
January 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28081252/corn-soy-blend-fortified-with-phosphorus-to-prevent-refeeding-hypophosphatemia-in-undernourished-piglets
#7
Anne-Louise Hother, Mikkel Lykke, Torben Martinussen, Hanne Damgaard Poulsen, Christian Mølgaard, Per Torp Sangild, André Briend, Christian Fink Hansen, Henrik Friis, Kim F Michaelsen, Thomas Thymann
BACKGROUND: Phosphorus (P) levels in refeeding diets are very important as undernourished children are at risk of hypophosphatemia during refeeding. For this reason, conventional corn-soy-blends (CSB) have been reformulated by the World Food Programme to obtain a mono-calcium-phosphate fortified product (CSB+) and a product further fortified with skim milk powder (CBS++). METHODS: Using a piglet model of undernourished children, we hypothesized that feeding of CSB+, CSB++ or CSB+ with added whey permeate (CSB+/wp) would help to prevent refeeding hypophosphatemia...
2017: PloS One
https://www.readbyqxmd.com/read/28068279/identifying-predictors-of-central-sleep-apnea-cheyne-stokes-breathing-in-chronic-heart-failure-a-pathophysiological-approach
#8
Aneliya I Draganova, Kiril V Terziyski, Stefan S Kostianev
Chronic heart failure (CHF) is a major health problem associated with increased mortality, despite modern treatment options. Central sleep apnea (CSA)/Cheyne-Stokes breathing (CSB) is a common and yet largely under-diagnosed co-morbidity, adding significantly to the poor prognosis in CHF because of a number of acute and chronic effects, including intermittent hypoxia, sympathetic overactivation, disturbed sleep architecture and impaired physical tolerance. It is characterized by repetitive periods of crescendo-decrescendo ventilatory pattern, alternating with central apneas and hypopneas...
December 1, 2016: Folia Medica
https://www.readbyqxmd.com/read/28067596/comparative-analysis-of-the-complete-mitochondrial-genomes-of-three-geographical-topmouth-culter-culter-alburnus-groups-and-implications-for-their-phylogenetics
#9
Jianwu Shi, Dexia Wang, Junhua Wang, Junqing Sheng, Kou Peng, Beijuan Hu, Liugen Zeng, Minghe Xiao, Yijiang Hong
Topmouth culter (C. alburnus) is an important commercial fish in China. We compared the nucleotide variations in the mtDNA genomes among three geographical groups of Culter alburnus: Liangzi Lake, Hubei Province (referred to as LZH); Taihu Lake, Jiangsu Province (TH); and Poyang Lake, Jiangxi Province (PYH). The similarity of whole mtDNA genomes ranged from 0.992 to 0.999. The similarity among 13 protein-coding genes, 2 rRNA genes, and the D-loop sequences was found to range from 0.982 to 0.996. This is useful data for future designing work for making specific molecular marker for distinguishing individuals of C...
January 9, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28050982/effect-of-tannic-acid-on-bond-strength-of-etch-and-rinse-and-self-etch-adhesive-systems-in-dentin-of-primary-teeth
#10
Masoumeh Ebrahimi, Alireza Sarraf Shirazi, Faraneh Abdolhoseinpour, Mojtaba Abdollahi
INTRODUCTION: One of the possible mechanisms for the gradual destruction of bond strength in dentin-resin interface, could be due to the demineralized unstable collagen matrix. Use of protease inhibitors, such as tannic acid (TA) could prevent destruction of collagen fibers. The aim of this study was to compare the TA effect on bond strength of etch and rinse and self-etch adhesive systems in the dentin of primary teeth. MATERIALS AND METHODS: This in vitro study was done on 40 extracted primary molar teeth...
January 1, 2017: Journal of Contemporary Dental Practice
https://www.readbyqxmd.com/read/28040160/isolation-molecular-and-phenotypic-characterization-and-antibiotic-susceptibility-of-cronobacter-spp-from-brazilian-retail-foods
#11
Marcelo Luiz Lima Brandão, Natália Scudeller Umeda, Emily Jackson, Stephen James Forsythe, Ivano de Filippis
Several Cronobacter species are opportunistic pathogens that cause infections in humans. The aim of this study was to detect Cronobacter spp. from 90 samples of retail foods in Brazil, and characterize the strains by phenotypic tests, molecular assays and antibiotic susceptibility. Three isolation methodologies were evaluated using different selective enrichments and the isolates were identified using Vitek 2.0, PCRs protocols, fusA allele sequencing and multilocus sequence typing (MLST). Thirty-eight samples (42...
May 2017: Food Microbiology
https://www.readbyqxmd.com/read/28036256/uv-induced-proteolysis-of-rna-polymerase-ii-is-mediated-by-vcp-p97-segregase-and-timely-orchestration-by-cockayne-syndrome-b-protein
#12
Jinshan He, Qianzheng Zhu, Gulzar Wani, Altaf A Wani
RNA polymerase II (RNAPII) acts as a damage sensor for transcription-coupled nucleotide excision repair (TC-NER) and undergoes proteolytic clearance from damaged chromatin by the ubiquitin-proteasome system (UPS). Here, we report that Valosin-containing protein (VCP)/p97, a druggable oncotarget, is essential for RNAPII's proteolytic clearance in mammalian cells. We show that inhibition of VCP/p97, or siRNA-mediated ablation of VCP/p97 and its cofactors UFD1 and UBXD7 severely impairs ultraviolet radiation (UVR)-induced RNAPII degradation...
December 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27910283/feeding-behaviors-during-home-based-treatment-of-moderate-acute-malnutrition-using-corn-soy-blends-or-lipid-based-nutrient-supplements
#13
Ann-Sophie Iuel-Brockdorf, Albertine Ouedraogo, Christian Ritz, Tania Aase Draebel, Per Ashorn, Suzanne Filteau, Kim F Michaelsen
Feeding behaviors have an important impact on children's nutritional status and are essential to consider when implementing nutrition programs. The objective of this study was to explore and compare feeding behaviors related to supplementary feeding with corn-soy blends (CSB) and lipid-based nutrient supplements (LNS) based on best practice feeding behaviors. The study was conducted as part of a randomized controlled trial assessing the effectiveness of new formulations of CSB and LNS and comprised 1,546 children from 6 to 23 months...
December 2, 2016: Maternal & Child Nutrition
https://www.readbyqxmd.com/read/27906014/acceptability-and-use-of-ready-to-use-supplementary-food-compared-to-corn-soy-blend-as-a-targeted-ration-in-an-hiv-program-in-rural-haiti-a-qualitative-study
#14
Anne G Beckett, Debbie Humphries, J Gregory Jerome, Jessica E Teng, Patrick Ulysse, Louise C Ivers
BACKGROUND: Ready-to-use supplementary food (RUSF) is increasingly used as a component of food rations for adults with HIV. METHODS: We undertook a qualitative study to evaluate the acceptability and use of peanut-based RUSF compared to corn-soy blend (CSB) among adults living with HIV in rural Haiti who had been enrolled in a prospective, randomized trial comparing the impact of those rations. A total of 13 focus groups were conducted with 84 participants-42 selected from the RUSF arm of the study, and 42 from the CSB arm-using a guide with pre-designated core topics and open-ended questions...
February 17, 2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27862282/a-non-redundant-protein-rna-docking-benchmark-version-2-0
#15
Chandran Nithin, Sunandan Mukherjee, Ranjit Prasad Bahadur
We present an updated version of the protein-RNA docking benchmark, which we first published four years back. The non-redundant protein-RNA docking benchmark version 2.0 consists of 126 test cases, a threefold increase in number compared to its previous version. The present version consists of 21 unbound-unbound cases, of which, in 12 cases, the unbound RNAs are taken from another complex. It also consists of 95 unbound-bound cases where only the protein is available in the unbound state. Besides, we introduce 10 new bound-unbound cases where only the RNA is found in the unbound state...
November 12, 2016: Proteins
https://www.readbyqxmd.com/read/27855199/the-values-of-coronary-circulating-mirnas-in-patients-with-atrial-fibrillation
#16
Guiyu Xu, Yuxia Cui, Zhenghua Jia, Yunan Yue, Shuixiang Yang
The mechanism of miRNA regulation in atrial fibrillation (AF) occurrence and development is still unclear, especially, the regulating values of coronary circulating miRNAs has not been reported. Based on our AF radiofrequency ablation clinical practice and previous miRNA study, we proposed a hypothesis that the coronary circulating miRNA might much better reflect the regulating state and metabolic level of myocardial miRNA in AF patient. To investigate the regulating values of coronary circulation miRNA, 90 AF patients were selected and compared with 90 healthy subjects, the changes of coronary circulating miRNA differential expression profile in the whole genome were observed in this study...
2016: PloS One
https://www.readbyqxmd.com/read/27797766/ymap-an-automated-method-to-map-yeast-variants-to-protein-modifications-and-functional-regions
#17
Ahmed Arslan, Vera van Noort
: Recent advances in sequence technology result in large datasets of sequence variants. For the human genome, several tools are available to predict the impact of these variants on gene and protein functions. However, for model organisms such as yeast such tools are lacking, specifically to predict the effect of protein sequence altering variants on the protein level. We present a python framework that enables users to map in a fully automated fashion large set of variants to protein functional regions and post-translationally modified residues...
October 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27791127/cockayne-syndrome-group-a-and-b-proteins-converge-on-transcription-linked-resolution-of-non-b-dna
#18
Morten Scheibye-Knudsen, Anne Tseng, Martin Borch Jensen, Karsten Scheibye-Alsing, Evandro Fei Fang, Teruaki Iyama, Sanjay Kumar Bharti, Krisztina Marosi, Lynn Froetscher, Henok Kassahun, David Mark Eckley, Robert W Maul, Paul Bastian, Supriyo De, Soumita Ghosh, Hilde Nilsen, Ilya G Goldberg, Mark P Mattson, David M Wilson, Robert M Brosh, Myriam Gorospe, Vilhelm A Bohr
Cockayne syndrome is a neurodegenerative accelerated aging disorder caused by mutations in the CSA or CSB genes. Although the pathogenesis of Cockayne syndrome has remained elusive, recent work implicates mitochondrial dysfunction in the disease progression. Here, we present evidence that loss of CSA or CSB in a neuroblastoma cell line converges on mitochondrial dysfunction caused by defects in ribosomal DNA transcription and activation of the DNA damage sensor poly-ADP ribose polymerase 1 (PARP1). Indeed, inhibition of ribosomal DNA transcription leads to mitochondrial dysfunction in a number of cell lines...
November 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27787929/compulsive-sexual-behavior-prefrontal-and-limbic-volume-and-interactions
#19
Casper Schmidt, Laurel S Morris, Timo L Kvamme, Paula Hall, Thaddeus Birchard, Valerie Voon
BACKGROUND: Compulsive sexual behaviors (CSB) are relatively common and associated with significant personal and social dysfunction. The underlying neurobiology is still poorly understood. The present study examines brain volumes and resting state functional connectivity in CSB compared with matched healthy volunteers (HV). METHODS: Structural MRI (MPRAGE) data were collected in 92 subjects (23 CSB males and 69 age-matched male HV) and analyzed using voxel-based morphometry...
October 27, 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/27760194/kingella-kingae-expresses-four-structurally-distinct-polysaccharide-capsules-that-differ-in-their-correlation-with-invasive-disease
#20
Kimberly F Starr, Eric A Porsch, Patrick C Seed, Christian Heiss, Radnaa Naran, L Scott Forsberg, Uri Amit, Pablo Yagupsky, Parastoo Azadi, Joseph W St Geme
Kingella kingae is an encapsulated gram-negative organism that is a common cause of osteoarticular infections in young children. In earlier work, we identified a glycosyltransferase gene called csaA that is necessary for synthesis of the [3)-β-GalpNAc-(1→5)-β-Kdop-(2→] polysaccharide capsule (type a) in K. kingae strain 269-492. In the current study, we analyzed a large collection of invasive and carrier isolates from Israel and found that csaA was present in only 47% of the isolates. Further examination of this collection using primers based on the sequence that flanks csaA revealed three additional gene clusters (designated the csb, csc, and csd loci), all encoding predicted glycosyltransferases...
October 2016: PLoS Pathogens
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