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https://www.readbyqxmd.com/read/28651329/high-speed-and-high-ratio-referential-genome-compression
#1
Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li
Motivation: The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28650953/de-novo-paternal-fbn1-mutation-detected-in-embryos-before-implantation
#2
Shuling Wang, Ziru Niu, Hui Wang, Minyue Ma, Wei Zhang, Shu Fang Wang, Jun Wang, Hong Yan, Yifan Liu, Na Duan, Xiandong Zhang, Yuanqing Yao
BACKGROUND Marfan syndrome (MFS) is an autosomal dominant disease caused by mutations in the Fibrillin (FBN)1 gene and characterized by disorders in the cardiovascular, skeletal, and visual systems. The diversity of mutations and phenotypic heterogeneity of MFS make prenatal molecular diagnoses difficult. In this study, we used pre-implantation genetic diagnosis (PGD) to identify the pathogenic mutation in a male patient with MFS and to determine whether his offspring would be free of the disease. MATERIAL AND METHODS The history and pedigree of the proband were analyzed...
June 26, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28649712/cross-platform-compatibility-of-de-novo-aligned-snps-in-a-non-model-butterfly-genus
#3
Erin O Campbell, Corey S Davis, Julian R Dupuis, Kevin Muirhead, Felix A H Sperling
High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in non-model systems. Using double-digest restriction site associated DNA sequencing, we sequenced a common set of 22 specimens from the butterfly genus Speyeria on two different Illumina platforms, using two variations of library preparation...
June 26, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28649474/using-high-throughput-sequencing-of-its2-to-describe-symbiodinium-metacommunities-in-st-john-us-virgin-islands
#4
Ross Cunning, Ruth D Gates, Peter J Edmunds
Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific...
2017: PeerJ
https://www.readbyqxmd.com/read/28649406/architecture-component-and-microbiome-of-biofilm-involved-in-the-fouling-of-membrane-bioreactors
#5
Tomohiro Inaba, Tomoyuki Hori, Hidenobu Aizawa, Atsushi Ogata, Hiroshi Habe
Biofilm formation on the filtration membrane and the subsequent clogging of membrane pores (called biofouling) is one of the most persistent problems in membrane bioreactors for wastewater treatment and reclamation. Here, we investigated the structure and microbiome of fouling-related biofilms in the membrane bioreactor using non-destructive confocal reflection microscopy and high-throughput Illumina sequencing of 16S rRNA genes. Direct confocal reflection microscopy indicated that the thin biofilms were formed and maintained regardless of the increasing transmembrane pressure, which is a common indicator of membrane fouling, at low organic-loading rates...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/28649403/inter-personal-diversity-and-temporal-dynamics-of-dental-tongue-and-salivary-microbiota-in-the-healthy-oral-cavity
#6
Michael W Hall, Natasha Singh, Kester F Ng, David K Lam, Michael B Goldberg, Howard C Tenenbaum, Josh D Neufeld, Robert G Beiko, Dilani B Senadheera
Oral microbes form a complex and dynamic biofilm community, which is subjected to daily host and environmental challenges. Dysbiosis of the oral biofilm is correlated with local and distal infections and postulating a baseline for the healthy core oral microbiota provides an opportunity to examine such shifts during the onset and recurrence of disease. Here we quantified the daily, weekly, and monthly variability of the oral microbiome by sequencing the largest oral microbiota time-series to date, covering multiple oral sites in ten healthy individuals...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/28649344/historical-demography-and-genetic-differentiation-of-the-giant-freshwater-prawn-macrobrachium-rosenbergii-in-bangladesh-based-on-mitochondrial-and-ddrad-sequence-variation
#7
M M Mahbub Alam, Kristen M Westfall, Snæbjörn Pálsson
Macrobrachium rosenbergii, the giant freshwater prawn, is an important source of high quality protein and occurs naturally in rivers as well as commercial farms in South and South-East Asia, including Bangladesh. This study investigated the genetic variation and population structure of M. rosenbergii sampled from four rivers in Bangladesh (sample size ranged from 19 to 20), assessing sequence variation, both in the mitochondrial cytochrome oxidase subunit 1 (CO1) gene and in 106 single nucleotide polymorphisms (SNPs) sampled randomly from the genome with double digest RAD sequencing (ddRADseq)...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649263/survey-of-high-throughput-rna-seq-data-reveals-potential-roles-for-lncrnas-during-development-and-stress-response-in-bread-wheat
#8
Shumayla, Shailesh Sharma, Mehak Taneja, Shivi Tyagi, Kashmir Singh, Santosh K Upadhyay
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28649234/ecological-succession-pattern-of-fungal-community-in-soil-along-a-retreating-glacier
#9
Jianqing Tian, Yuchen Qiao, Bing Wu, Huai Chen, Wei Li, Na Jiang, Xiaoling Zhang, Xingzhong Liu
Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2-188 years of deglaciation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28648749/transcriptome-profiling-of-3d-co-cultured-cardiomyocytes-and-endothelial-cells-under-oxidative-stress-using-a-photocrosslinkable-hydrogel-system
#10
Xiaoshan Yue, Aylin Acun, Pinar Zorlutuna
Myocardial infarction (MI) is one of the most common among cardiovascular diseases. Endothelial cells (ECs) are considered to have protective effects on cardiomyocytes (CMs) under stress conditions such as MI; however, the paracrine CM-EC crosstalk and the resulting endogenous cellular responses that could contribute to this protective effect are not thoroughly investigated. Here we created biomimetic synthetic tissues containing CMs and human induced pluripotent stem cell (hiPSC)-derived ECs (iECs), which showed improved cell survival compared to single cultures under conditions mimicking the aftermath of MI, and performed high-throughput RNA-sequencing to identify target pathways that could govern CM-iEC crosstalk and the resulting improvement in cell viability...
June 22, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28648677/cell-type-specific-transcriptome-profiling-in-c-elegans-using-the-translating-ribosome-affinity-purification-technique
#11
Xicotencatl Gracida, John A Calarco
Organs and specific cell types execute specialized functions in multicellular organisms, in large part through customized gene expression signatures. Thus, profiling the transcriptomes of specific cell and tissue types remains an important tool for understanding how cells become specialized. Methodological approaches to detect gene expression differences have utilized samples from whole animals, dissected tissues, and more recently single cells. Despite these advances, there is still a challenge and a need in most laboratories to implement less invasive yet powerful cell-type specific transcriptome profiling methods...
June 22, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28648489/pyrosequencing-analysis-of-cryogenically-ground-samples-from-primary-and-secondary-persistent-endodontic-infections
#12
Cangül Keskin, Ebru Özsezer Demiryürek, Ertan Emek Onuk
INTRODUCTION: This study aimed to characterize the microbial communities of primary and secondary/persistent endodontic infections using high-throughput pyrosequencing from the pulverized samples. METHODS: The roots of 20 extracted human teeth with primary endodontic infection and 20 teeth with secondary/persistent endodontic infection were collected. The outer surfaces of the roots were disinfected, and whole roots were cryopulverized. 16S amplicon pyrosequencing data from the DNA extracted from the pulverized root powders were obtained, and microorganism abundance and diversity were calculated...
June 22, 2017: Journal of Endodontics
https://www.readbyqxmd.com/read/28648286/yeast-diversity-during-the-fermentation-of-andean-chicha-a-comparison-of-high-throughput-sequencing-and-culture-dependent-approaches
#13
Lucía M Mendoza, Alexander Neef, Graciela Vignolo, Carmela Belloch
Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Five hundred and ninety six yeasts were isolated by classical microbiological methods and 16 species identified by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns...
October 2017: Food Microbiology
https://www.readbyqxmd.com/read/28647779/transcriptome-profiling-and-digital-gene-expression-analysis-of-the-skin-of-dybowski-s-frog-rana-dybowskii-exposed-to-aeromonas-hydrophila
#14
Yi-Gang Xu, Long-Hui Chai, Wen Shi, Dan-Dan Wang, Jing-Yu Zhang, Xiang-Hong Xiao
Recently, populations of Rana dybowskii, an important amphibian species in Northeast China, have decreased, mainly owing to the disease caused by Aeromonas hydrophila. However, effective control methods have not yet been developed. In order to explore the immune responses of R. dybowskii upon exposure to A. hydrophila infection, Illumina high-throughput transcriptome sequencing and digital gene expression (DGE) technology were employed to investigate transcriptomic changes in the skin of R. dybowskii exposed to A...
June 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28647345/cutaneous-nod2-expression-regulates-the-skin-microbiome-and-wound-healing-in-a-murine-model
#15
Helen Williams, Rachel A Crompton, Helen A Thomason, Laura Campbell, Gurdeep Singh, Andrew J McBain, Sheena M Cruickshank, Matthew J Hardman
The skin microbiome exists in dynamic equilibrium with the host but when the skin is compromised, bacteria can colonise the wound and impair wound healing. Thus the interplay between normal skin-microbial interactions versus pathogenic-microbial interactions in wound repair is important. Bacteria are recognised by innate host pattern recognition receptors (PRRs) and we previously demonstrated an important role for the PRR NOD2 (nucleotide-binding oligomerisation domains-containing protein 2) in skin wound repair...
June 21, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28647253/nano-sized-fe2o3-fe3o4-facilitate-anaerobic-transformation-of-hexavalent-chromium-in-soil-water-systems
#16
Yaxian Zhang, Hua Li, Libo Gong, Guowen Dong, Liang Shen, Yuanpeng Wang, Qingbiao Li
The purpose of this study is to investigate the effects of nano-sized or submicro Fe2O3/Fe3O4 on the bioreduction of hexavalent chromium (Cr(VI)) and to evaluate the effects of nano-sized Fe2O3/Fe3O4 on the microbial communities from the anaerobic flooding soil. The results indicated that the net decreases upon Cr(VI) concentration from biotic soil samples amended with nano-sized Fe2O3 (317.1±2.1mg/L) and Fe3O4 (324.0±22.2mg/L) within 21days, which were approximately 2-fold of Cr(VI) concentration released from blank control assays (117...
July 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/28646867/a-high-quality-annotated-transcriptome-of-swine-peripheral-blood
#17
Haibo Liu, Timothy P L Smith, Dan J Nonneman, Jack C M Dekkers, Christopher K Tuggle
BACKGROUND: High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes and/or transcriptomes. However, neither the reference genome nor the peripheral blood transcriptome of the pig have been sufficiently assembled and annotated to support such profiling assays in this emerging biomedical model organism...
June 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28646085/generation-of-a-collection-of-mutant-tomato-lines-using-pooled-crispr-libraries
#18
Thomas B Jacobs, Ning Zhang, Dhruv Patel, Gregory B Martin
The high efficiency of CRIPSR-mediated mutagenesis in plants enables the development of high-throughput mutagenesis strategies. By transforming pooled CRISPR libraries into tomato, collections of mutant lines were generated with minimal transformation attempts and in a relatively short period of time. Identification of the targeted gene(s) was easily determined by sequencing the incorporated gRNA(s) in the primary transgenic events. From a single transformation with a CRISPR library targeting the immunity-associated leucine-rich repeat subfamily XII genes, heritable mutations were recovered in 15 of the 54 genes targeted...
June 23, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28645800/high-throughput-sequencing-of-the-entire-genomic-regions-of-ccm1-krit1-ccm2-and-ccm3-pdcd10-to-search-for-pathogenic-deep-intronic-splice-mutations-in-cerebral-cavernous-malformations
#19
Matthias Rath, Sönke E Jenssen, Konrad Schwefel, Stefanie Spiegler, Dana Kleimeier, Christian Sperling, Lars Kaderali, Ute Felbor
Cerebral cavernous malformations (CCM) are vascular lesions of the central nervous system that can cause headaches, seizures and hemorrhagic stroke. Disease-associated mutations have been identified in three genes: CCM1/KRIT1, CCM2 and CCM3/PDCD10. The precise proportion of deep-intronic variants in these genes and their clinical relevance is yet unknown. Here, a long-range PCR (LR-PCR) approach for target enrichment of the entire genomic regions of the three genes was combined with next generation sequencing (NGS) to screen for coding and non-coding variants...
June 20, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28645760/effects-of-endocrine-disrupting-chemicals-edcs-on-bacterial-communities-in-mangrove-sediments
#20
Ke Yuan, Sirui Xiao, Xiaotao Jiang, Lihua Yang, Baowei Chen, Tiangang Luan, Li Lin, Nora Fung Yee Tam
The diversity and composition of bacterial communities in mudflat and mangrove sediments were investigated under the stresses of endocrine-disrupting chemicals (EDCs) using high-throughput sequencing technique. Bacterial diversity in the original sediments was highest among all samples, followed by non-sterilized and sterilized sediments after 84-day incubation. Proteobacteria were the predominant phylum in both mangrove and mudflat sediments, which accounted for 40-60% of the total tags, followed by Cyanobacteria, Chloroflexi, Planctomycetes and Acidobacteria...
June 20, 2017: Marine Pollution Bulletin
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