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High throughput sequencing

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https://www.readbyqxmd.com/read/29475194/scope-and-limitations-of-carbohydrate-hydrolysis-for-de-novo-glycan-sequencing-using-a-hydrogen-peroxide-metallopeptide-based-glycosidase-mimetic
#1
Tianyuan Peng, Zachary Wooke, Nicola L B Pohl
Acidic hydrolysis is commonly used as a first step to break down oligo- and polysaccharides into monosaccharide units for structural analysis. While easy to set up and amenable to mass spectrometry detection, acid hydrolysis is not without its drawbacks. For example, ring-destruction side reactions and degradation products, along with difficulties in optimizing conditions from analyte to analyte, greatly limits its broad utility. Herein we report studies on a hydrogen peroxide/CuGGH metallopeptide-based glycosidase mimetic design for a more efficient and controllable carbohydrate hydrolysis...
February 3, 2018: Carbohydrate Research
https://www.readbyqxmd.com/read/29474909/mapping-the-mouse-cell-atlas-by-microwell-seq
#2
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Zimin Zhou, Haide Chen, Fang Ye, Daosheng Huang, Yang Xu, Wentao Huang, Mengmeng Jiang, Xinyi Jiang, Jie Mao, Yao Chen, Chenyu Lu, Jin Xie, Qun Fang, Yibin Wang, Rui Yue, Tiefeng Li, He Huang, Stuart H Orkin, Guo-Cheng Yuan, Ming Chen, Guoji Guo
Single-cell RNA sequencing (scRNA-seq) technologies are poised to reshape the current cell-type classification system. However, a transcriptome-based single-cell atlas has not been achieved for complex mammalian systems. Here, we developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we analyzed more than 400,000 single cells covering all of the major mouse organs and constructed a basic scheme for a mouse cell atlas (MCA). We reveal a single-cell hierarchy for many tissues that have not been well characterized previously...
February 22, 2018: Cell
https://www.readbyqxmd.com/read/29474379/small-rna-populations-revealed-by-blocking-rrna-fragments-in-drosophila-melanogaster-reproductive-tissues
#3
Emily K Fowler, Irina Mohorianu, Damian T Smith, Tamas Dalmay, Tracey Chapman
RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions...
2018: PloS One
https://www.readbyqxmd.com/read/29473663/long-term-clinicopathologic-observation-in-a-case-of-steroid-resistant-nephrotic-syndrome-caused-by-a-novel-crumbs-homolog-2-mutation
#4
Shojiro Watanabe, Tomomi Aizawa, Hiroyasu Tsukaguchi, Koji Tsugawa, Kazushi Tsuruga, Akemi Shono, Kandai Nozu, Kazumoto Iijima, Kensuke Joh, Hiroshi Tanaka
Recent advances in high-throughput sequencing for clinical genetic testing have revealed novel disease-causing genes, such as Crumbs homolog 2 (CRB2) for early-onset steroid-resistant nephrotic syndrome (SRNS). We report the long-term clinicopathologic observation of a Japanese female patient with SRNS caused by a newly identified compound heterozygous mutation of CRB2 (p.Arg628Cys and p.Gly839Trp located in the 10th and 11th epidermal growth factor-like domains, respectively). She was initially examined during a mass urinary mass screening for 3...
February 23, 2018: Nephrology
https://www.readbyqxmd.com/read/29473288/increasing-n-deposition-impacts-neither-diversity-nor-functions-of-deadwood-inhabiting-fungal-communities-but-adaptation-and-functional-redundancy-warrants-ecosystem-function
#5
Witoon Purahong, Tesfaye Wubet, Tiemo Kahl, Tobias Arnstadt, Björn Hoppe, Guillaume Lentendu, Kristin Baber, Tyler Rose, Harald Kellner, Martin Hofrichter, Jürgen Bauhus, Dirk Krüger, François Buscot
Nitrogen deposition can strongly affect biodiversity, but its specific effects on terrestrial microbial communities and their roles for ecosystem functions and processes are still unclear. Here, we investigated the impacts of N deposition on wood-inhabiting fungi (WIF) and their related ecological functions and processes in a highly N-limited deadwood habitat. Based on high-throughput sequencing, enzymatic activity assay and measurements of wood decomposition rates, we show that N addition has no significant effect on the overall WIF community composition or on related ecosystem functions and processes in this habitat...
February 23, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29472946/heavy-chronic-intermittent-ethanol-exposure-alters-small-noncoding-rnas-in-mouse-sperm-and-epididymosomes
#6
Gregory R Rompala, Anais Mounier, Cody M Wolfe, Qishan Lin, Iliya Lefterov, Gregg E Homanics
While the risks of maternal alcohol abuse during pregnancy are well-established, several preclinical studies suggest that chronic preconception alcohol consumption by either parent may also have significance consequences for offspring health and development. Notably, since isogenic male mice used in these studies are not involved in gestation or rearing of offspring, the cross-generational effects of paternal alcohol exposure suggest a germline-based epigenetic mechanism. Many recent studies have demonstrated that the effects of paternal environmental exposures such as stress or malnutrition can be transmitted to the next generation via alterations to small noncoding RNAs in sperm...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29471815/glucocorticosteroids-and-ciclosporin-do-not-significantly-impact-canine-cutaneous-microbiota
#7
Giovanni Widmer, Lluís Ferrer, Claude Favrot, Judy Paps, Kevin Huynh, Thierry Olivry
BACKGROUND: As prednisone and ciclosporin can have immunosuppressive effects and have been considered potential predisposing factors for skin infections, we investigated the impact of these drugs on the diversity of the cutaneous microbiota, the abundance of Malassezia and infection with Papillomaviruses. RESULTS: Six atopic, asymptomatic Maltese-beagle dogs were treated with ciclosporin for one month and then with prednisone for another month, with a one-month wash-out between treatments...
February 23, 2018: BMC Veterinary Research
https://www.readbyqxmd.com/read/29471801/a-maximum-likelihood-algorithm-for-reconstructing-3d-structures-of-human-chromosomes-from-chromosomal-contact-data
#8
Oluwatosin Oluwadare, Yuxiang Zhang, Jianlin Cheng
BACKGROUND: The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics and computational biology. Aided by high-throughput next generation sequencing techniques, the Hi-C technique can generate genome-wide, large-scale intra- and inter-chromosomal interaction data capable of describing in details the spatial interactions within a genome. These data can be used to reconstruct 3D structures of chromosomes that can be used to study DNA replication, gene regulation, genome interaction, genome folding, and genome function...
February 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29471546/longitudinal-analyses-of-blood-transcriptome-during-conversion-to-psychosis
#9
Boris Chaumette, Oussama Kebir, Juliette Pouch, Bertrand Ducos, Fekrije Selimi, Raphael Gaillard, Marie-Odile Krebs
The biological processes associated with the onset of schizophrenia remain largely unknown. Current hypotheses favor gene × environment interactions as supported by our recent report about DNA methylation changes during the onset of psychosis. Here, we conducted the first longitudinal transcriptomic analysis of blood samples from 31 at-risk individuals who later converted to psychosis and 63 at-risk individuals who did not. Individuals were followed for a maximum of 1 year. Blood samples were collected at baseline and at the end of follow-up and individuals served as their own controls...
February 17, 2018: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29471361/microbial-community-composition-along-a-50-000-year-lacustrine-sediment-sequence
#10
Aurèle Vuillemin, Daniel Ariztegui, Fabian Horn, Jens Kallmeyer, William D Orsi
For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high resolution climate intervals covering the last 50,000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial...
February 20, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29471278/intestinal-bacteria-in-bioaerosols-and-factors-affecting-their-survival-in-two-oxidation-ditch-process-municipal-wastewater-treatment-plants-located-in-different-regions
#11
Yanjie Wang, Lin Li, Yunping Han, Junxin Liu, Kaixiong Yang
Samples from two oxidation ditch process municipal wastewater treatment plants (MWTPs) (HJK and GXQ) in two regions of China were analysed for bacteria, particles, total organic carbon, and water-soluble ions in bioaerosols. Diversity and potential pathogen populations were evaluated by high-throughput sequencing. Bioaerosol sources, factors affecting intestinal bacterial survival, and the relationship between bioaerosols and water were analysed by Source tracker and partial least squares-discriminant, principal component, and canonical correspondence analyses...
February 19, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29471236/shifts-of-system-performance-and-microbial-community-structure-in-a-constructed-wetland-after-exposing-silver-nanoparticles
#12
Chong Cao, Juan Huang, Chunni Yan, Jialiang Liu, Qian Hu, Wenzhu Guan
The increasing utilization of silver nanoparticles (Ag NPs) in industry and commerce inevitably raises its release into wastewater. In this work, effects of Ag NPs on system performance and microbial community along the way of a vertical flow constructed wetland (VFCW) were investigated, along with the removal and fate of Ag NPs within the system. Results showed that the performance of control wetland kept stable during the experimental period, and the top substrate layer (soil layer) of wetland could remove most of pollutants in the influent...
February 7, 2018: Chemosphere
https://www.readbyqxmd.com/read/29471079/exploring-the-utility-of-next-generation-sequence-data-on-inferring-the-phylogeny-of-the-south-american-valeriana-valerianaceae
#13
Charles D Bell, Lauren A Gonzalez
This study aimed to investigate the phylogenetic utility of genotyping-by-sequencing (GBS) data in the southern South American subclade of Valerianaceae (Dipsacales). The variety of forms that has arisen in this clade, presumably over the past 5-10 million years, has all the signatures of an adaptive and rapid radiation. While the phylogeny of Valerianaceae has received a great deal of attention in the last decade, species relationships have been hard to resolve using traditional phylogenetic markers. Here, we collected high-throughput genomic sequence data from reduced-representation libraries obtained through GBS protocols...
February 19, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29470975/high-throughput-screening-of-t7-phage-display-and-protein-microarrays-as-a-methodological-approach-for-the-identification-of-ige-reactive-components
#14
P San Segundo-Acosta, M Garranzo-Asensio, C Oeo-Santos, A Montero-Calle, J Quiralte, J Cuesta-Herranz, M Villalba, R Barderas
Olive pollen and yellow mustard seeds are major allergenic sources with high clinical relevance. To aid with the identification of IgE-reactive components, the development of sensitive methodological approaches is required. Here, we have combined T7 phage display and protein microarrays for the identification of allergenic peptides and mimotopes from olive pollen and mustard seeds. The identification of these allergenic sequences involved the construction and biopanning of T7 phage display libraries of mustard seeds and olive pollen using sera from allergic patients to both biological sources together with the construction of phage microarrays printed with 1536 monoclonal phages from the third/four rounds of biopanning...
February 19, 2018: Journal of Immunological Methods
https://www.readbyqxmd.com/read/29470497/most-yeast-sh3-domains-bind-peptide-targets-with-high-intrinsic-specificity
#15
Tom Brown, Nick Brown, Elliott J Stollar
A need exists to develop bioinformatics for predicting differences in protein function, especially for members of a domain family who share a common fold, yet are found in a diverse array of proteins. Many domain families have been conserved over large evolutionary spans and representative genomic data during these periods are now available. This allows a simple method for grouping domain sequences to reveal common and unique/specific binding residues. As such, we hypothesize that sequence alignment analysis of the yeast SH3 domain family across ancestral species in the fungal kingdom can determine whether each member encodes specific information to bind unique peptide targets...
2018: PloS One
https://www.readbyqxmd.com/read/29470465/genome-wide-mapping-of-endogenous-g-quadruplex-dna-structures-by-chromatin-immunoprecipitation-and-high-throughput-sequencing
#16
Robert Hänsel-Hertsch, Jochen Spiegel, Giovanni Marsico, David Tannahill, Shankar Balasubramanian
G-rich DNA sequences can form four-stranded G-quadruplex (G4) secondary structures and are linked to fundamental biological processes such as transcription, replication and telomere maintenance. G4s are also implicated in promoting genome instability, cancer and other diseases. Here, we describe a detailed G4 ChIP-seq method that robustly enables the determination of G4 structure formation genome-wide in chromatin. This protocol adapts traditional ChIP-seq for the detection of DNA secondary structures through the use of a G4-structure-specific single-chain antibody with refinements in chromatin immunoprecipitation followed by high-throughput sequencing...
March 2018: Nature Protocols
https://www.readbyqxmd.com/read/29470101/ebselen-reversibly-inhibits-human-glutamate-dehydrogenase-at-the-catalytic-site
#17
Yanhong Jin, Di Li, Shiying Lu, Han Zhao, Zhao Chen, Wei Hou, Benfang Helen Ruan
Human glutamate dehydrogenase (GDH) plays an important role in neurological diseases, tumor metabolism, and hyperinsulinism-hyperammonemia syndrome (HHS). However, there are very few inhibitors known for human GDH. Recently, Ebselen was reported to crosslink with Escherichia coli GDH at the active site cysteine residue (Cys321), but the sequence alignment showed that the corresponding residue is Ala329 in human GDH. To investigate whether Ebselen could be an inhibitor for human GDH, we cloned and expressed an N-terminal His-tagged human GDH in E...
February 22, 2018: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/29470090/engineering-interfacial-processes-at-mini-micro-nano-scales-using-sessile-droplet-architecture
#18
Lalit Bansal, Apratim Sanyal, Prasenjit Kabi, Binita Pathak, Saptarshi Basu
Evaporating sessile functional droplets act as the fundamental building block that control the cumulative outcome of many industrial and biological applications such as surface patterning, 3D printing, photonic crystals, DNA sequencing, to name a few. Additionally, a drying single sessile droplet forms a high throughput processing technique using low material volume which is especially suitable for medical diagnosis. Sessile droplet also provides an elementary platform to study and analyze fundamental interfacial processes at various lengthscale ranging from macroscopically observable wetting and evaporation to microfluidic transport to interparticle forces operating at a nanometric lengthscale...
February 22, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29469687/diverse-papillomaviruses-identified-in-weddell-seals
#19
Zoe E Smeele, Jennifer M Burns, Koenraad Van Doorsaler, Rafaela S Fontenele, Kara Waits, Daisy Stainton, Michelle R Shero, Roxanne S Beltran, Amy L Kirkham, Rachel Berngartt, Simona Kraberger, Arvind Varsani
Papillomaviridae is a diverse family of circular, double-stranded DNA (dsDNA) viruses that infect a broad range of mammalian, avian and fish hosts. While papillomaviruses have been characterized most extensively in humans, the study of non-human papillomaviruses has contributed greatly to our understanding of their pathogenicity and evolution. Using high-throughput sequencing approaches, we identified 7 novel papillomaviruses from vaginal swabs collected from 81 adult female Weddell seals (Leptonychotes weddellii) in the Ross Sea of Antarctica between 2014-2017...
February 22, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29469596/genome-scale-metabolic-models-as-platforms-for-identification-of-novel-genes-as-antimicrobial-drug-targets
#20
Bashir Sajo Mienda, Rabiu Salihu, Aliyu Adamu, Shehu Idris
The growing number of multidrug-resistant pathogenic bacteria is becoming a world leading challenge for the scientific community and for public health. However, advances in high-throughput technologies and whole-genome sequencing of bacterial pathogens make the construction of bacterial genome-scale metabolic models (GEMs) increasingly realistic. The use of GEMs as an alternative platforms will expedite identification of novel unconditionally essential genes and enzymes of target organisms with existing and forthcoming GEMs...
February 22, 2018: Future Microbiology
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