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"high throughput sequencing"

Franck Carbonero, Alba C Mayta-Apaza, Jiang-Zhou Yu, Matt Lindeblad, Alex Lyubimov, Flavia Neri, Erzsebet Szilagyi, Amelia Bartholomew
In rodent studies, the gut microbiota has been implicated in facilitating both radioresistance, by protecting the epithelium from apoptotic responses and radiosensitivity, inducing endothelial apoptotic responses. Despite the observation that large animal models, such as the Chinese Rhesus macaque and the Gottingen Minipig, demonstrate similarity to human physiologic responses to radiation, little is known about radiation-induced changes of the gut microbiome in these models. To compare the two models, we used bioequivalent radiation doses which resulted in an LD50 for Gottingen Minipigs and Chinese Rhesus macaques, 1...
October 20, 2018: Radiation and Environmental Biophysics
Mareen Matz, Frederik Heinrich, Qiang Zhang, Christine Lorkowski, Evelyn Seelow, Kaiyin Wu, Nils Lachmann, Richard Kwasi Addo, Pawel Durek, Mir-Farzin Mashreghi, Klemens Budde
CONTEXT: Antibody-mediated rejection (ABMR) after kidney transplantation (KTx) remains the crucial obstacle to successful long-term graft function. The identification of gene signatures involved in ABMR could grant the basis for better prevention and treatment strategies. OBJECTIVE: The identification of gene signatures in whole blood cells specific for ABMR after kidney transplantation. MATERIAL AND METHODS: Total RNA from blood cells of 16 kidney transplanted patients with ABMR, stable graft function (SGF) and with T-cell mediated rejection (TCMR) was isolated...
October 20, 2018: Clinical Transplantation
Weigang Wang, Yuan Yan, Chengkang Song, Mianli Pan, Yayi Wang
In anaerobic ammonium oxidation (anammox) systems, temperature may regulate the activity of functional bacteria (e.g., anammox bacteria) and the composition of the microbial population, ultimately determining the performance of the anammox reactor. Knowledge of the dynamic changes in nitrogen removal rates and the microbial anammox community at low and/or ambient temperature is still limited. This study explored the response of an anammox sequencing batch reactor (SBR) to a gradient of decreasing temperature (33, 25, 20, 15, 10 °C), followed by recovery to 22 °C, over 360 days...
October 19, 2018: Environmental Science and Pollution Research International
Cicera R Lazzarotto, Nhu T Nguyen, Xing Tang, Jose Malagon-Lopez, Jimmy A Guo, Martin J Aryee, J Keith Joung, Shengdar Q Tsai
Circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq) is a sensitive and unbiased method for defining the genome-wide activity (on-target and off-target) of CRISPR-Cas9 nucleases by selective sequencing of nuclease-cleaved genomic DNA (gDNA). Here, we describe a detailed experimental and analytical protocol for CIRCLE-seq. The principle of our method is to generate a library of circularized gDNA with minimized numbers of free ends. Highly purified gDNA circles are treated with CRISPR-Cas9 ribonucleoprotein complexes, and nuclease-linearized DNA fragments are then ligated to adapters for high-throughput sequencing...
October 19, 2018: Nature Protocols
Ye Liu, Jen-Chien Chang, Chung-Chau Hon, Naoshi Fukui, Nobuho Tanaka, Zhenya Zhang, Ming Ta Michael Lee, Aki Minoda
Osteoarthritis (OA) is a common joint disorder with increasing impact in an aging society. While genetic and transcriptomic analyses have revealed some genes and non-coding loci associated to OA, the pathogenesis remains incompletely understood. Chromatin profiling, which provides insight into gene regulation, has not been reported in OA mainly due to technical difficulties. Here, we employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients...
October 19, 2018: Scientific Reports
Yanjie Wang, Lin Li, Ren Xiong, Xuesong Guo, Junxin Liu
The generation and emission of airborne bacteria from a biochemical reaction tank (BRT) for wastewater treatment was investigated by altering the aeration rate. The levels of bioaerosols increased from 715 ± 69 to 1597 ± 135 CFU/m3 (total airborne bacteria) and from 78 ± 6 to 359 ± 18 CFU/m3 (intestinal bacteria) as the aeration rate increased from 0.3 to 1.2 m3 /h. Most airborne bacteria were attached to particles smaller than 4.7 μm at an aeration rate of 0.3 m3 /h. They were found attached to larger particles (>4...
January 15, 2019: Science of the Total Environment
Yonglei An, Xueming Qin
The presence of antibiotics in municipal wastewater is bound to affect the anoxic denitrifying process in anoxic activated sludge (AAS). This study investigated the effects of sulfamethoxazole (SMZ) on the denitrifying process in AAS and the responses of denitrifying microorganisms. The results showed that SMZ could decrease the speed of nitrate removal significantly when the concentration of SMZ was lower than 10 mg/L, and the removal of nitrate would be completely inhibited when SMZ concentration was higher than 100 mg/L...
October 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Lisa N Barrow, Alan R Lemmon, Emily Moriarty Lemmon
Comparative phylogeography provides the necessary framework to examine the factors influencing population divergence, persistence, and change over time. Avise (2000) outlined four aspects of concordance that result when data exhibit significant phylogeographic signal: concordance among sites within a locus, among multiple loci within a species, among multiple species within a region, and between genetic patterns and established biogeographic provinces. To fully address each aspect of concordance, we combined target capture of a set of orthologous loci with targeted geographic sampling of multiple species, thus removing any variability introduced by using different genetic markers and heterogeneous sampling distributions...
November 1, 2018: Systematic Biology
Xi Li, Yuyuan Li, Yong Li, Jinshui Wu
Managing waste produced from swine farming operations is a significant agricultural and environmental challenge. Confined animal feeding operations continually generate large amounts of animal waste, which necessitates adequate waste management systems. This study examines the use of multistage surface flow constructed wetlands (SFCWs) to treat pig farm sewage. The wastewater removal rate, sediment deposits, physicochemical properties, and microbial community compositions of each segment of a SFCW were examined...
October 18, 2018: Applied Microbiology and Biotechnology
Ozgul Calicioglu, Michael J Shreve, Tom L Richard, Rachel A Brennan
Background: Duckweeds (Lemnaceae) are efficient aquatic plants for wastewater treatment due to their high nutrient-uptake capabilities and resilience to severe environmental conditions. Combined with their rapid growth rates, high starch, and low lignin contents, duckweeds have also gained popularity as a biofuel feedstock for thermochemical conversion and alcohol fermentation. However, studies on the acidogenic anaerobic digestion of duckweed into carboxylic acids, another group of chemicals which are precursors of higher-value chemicals and biofuels, are lacking...
2018: Biotechnology for Biofuels
Xiao Yang, Hao Zhang, Yuting Jiang, Hongguo Zhang, Xiaonan Hu, Dongliang Zhu, Dongfeng Geng, Ruizhi Liu
BACKGROUND: Non-obstructive azoospermia (NOA) is an important factor leading to male infertility and the genetic mechanism is not yet clear. It requires investigation to reveal its occurrence based on sequencing technology from the genetic level. Our previous genome wide association study (GWAS) using targeted high-throughput sequencing technology has identified suspected genetic variants including rs162036, rs161870, rs1677016R and rs1106042R associated with non-obstructive azoospermia (data not published)...
October 1, 2018: Clinical Laboratory
A Vieira, C F Galinha, A Oehmen, G Carvalho
Few attempts have been made in previous studies to link the microbial community structure and function with nitrous oxide (N2 O) emissions at full-scale wastewater treatment plants (WWTPs). In this work, high-throughput sequencing and reverse transcriptase-qPCR (RT-qPCR) was applied to activated sludge samples from three WWTPs for two seasonal periods (winter and summer) and linked with the N2 O emissions and wastewater characteristics. The total N2 O emissions ranged from 7.2 to 937.0 g N-N2 O/day, which corresponds to an emission factor of 0...
October 11, 2018: Science of the Total Environment
Zhiping Li, Xiwen Wang, Man Chen, Qianxue Li, Han Qu, Ting Shao, Rui Sun, Yandong Zhang, Zhiping Xia
Complement factor 5a is a potent proinflammatory mediator that contributes to the pathogenesis of numerous inflammatory diseases. Protein-based C5a inhibitors have proven to be clinically valuable. Aptamers, which are oligonucleic acid chains or polypeptides, can bind to target molecules and hence have the potential to be used for detection and blockade of targets. Here, we describe the discovery that the single-stranded DNA aptamer S1 can bind specifically to swine C5a, which can then be quickly selected for with capillary electrophoresis for high-throughput sequencing...
October 15, 2018: Analytical Biochemistry
Ming Jiang, Hui Li
High-throughput sequencing is an effective approach to analyse the bioinformation on the molecular biological and whole genome levels, especially in non-model plants for which reference genome sequences are unavailable. In this study, high-throughput sequencing analysis of Euphorbia fischeriana Steud was conducted on the Illumina HiSeq 2000 platform. A total of 9,6481,893 raw reads were generated and assembled into 304,217 transcripts and 186,384 unigenes. Of the 186,384 unigenes, 77.45% were annotated in at least one database, and some pathways involved in the biosynthesis of the terpenoid backbone were closely linked to the main anticancer components...
October 2018: 3 Biotech
Alexander Dimitri Yermanos, Andreas Kevin Dounas, Tanja Stadler, Annette Oxenius, Sai T Reddy
Antibody evolution studies have been traditionally limited to either tracing a single clonal lineage (B cells derived from a single V-(D)-J recombination) over time or examining bulk functionality changes (e.g., tracing serum polyclonal antibody proteins). Studying a single B cell disregards the majority of the humoral immune response, whereas bulk functional studies lack the necessary resolution to analyze the co-existing clonal diversity. Recent advances in high-throughput sequencing (HTS) technologies and bioinformatics have made it possible to examine multiple co-evolving antibody monoclonal lineages within the context of a single repertoire...
2018: Frontiers in Immunology
Yunjian Xu, Suwen Zhu, Fang Liu, Wei Wang, Xuewen Wang, Guomin Han, Beijiu Cheng
Maize can form symbiotic relationships with arbuscular mycorrhiza (AM) fungus to increase productivity and resistance, but the miRNAs in maize responsible for this process have not been discovered. In this study, 155 known and 28 novel miRNAs were identified by performing high-throughput sequencing of sRNA in maize roots colonized by AM fungi. Similar to the profiles in other AM-capable plants, a large proportion of identified maize miRNAs were 24 nt in length. Fourteen and two miRNAs were significantly down- and up-regulated in response to AM fungus Glomus intraradices inoculation, respectively, suggesting potential roles of these miRNAs in AM symbiosis...
October 16, 2018: International Journal of Molecular Sciences
Siemon H Ng, Cassandra Braxton, Marc Eloit, Szi Fei Feng, Romain Fragnoud, Laurent Mallet, Edward T Mee, Sarmitha Sathiamoorthy, Olivier Vandeputte, Arifa S Khan
A key step for broad viral detection using high-throughput sequencing (HTS) is optimizing the sample preparation strategy for extracting viral-specific nucleic acids since viral genomes are diverse: They can be single-stranded or double-stranded RNA or DNA, and can vary from a few thousand bases to over millions of bases, which might introduce biases during nucleic acid extraction. In addition, viral particles can be enveloped or non-enveloped with variable resistance to pre-treatment, which may influence their susceptibility to extraction procedures...
October 16, 2018: Viruses
Wenhui Wei, Gan Li, Xiaoling Jiang, Yuquan Wang, Zhihui Ma, Zhipeng Niu, Zhiwei Wang, Xinxin Geng
MicroRNAs (miRNAs) play a prominent role in post-transcriptional gene expression regulation and have been involved in various biological and metabolic processes to regulate gene expression. For Brassica napus, improving seed-weight and oil-content is the main breeding goal. In order to better understand the regulation mechanism of miRNAs during seed-weight formation and oil-content accumulation in B. napus, in this study, a high-throughput sequencing technology was used to profile miRNAs expression of Brassica napus immature seeds from one to six weeks after flowering...
2018: PloS One
Siv Nam Khang Hoff, Helle T Baalsrud, Ave Tooming-Klunderud, Morten Skage, Todd Richmond, Gregor Obernosterer, Reza Shirzadi, Ole Kristian Tørresen, Kjetill S Jakobsen, Sissel Jentoft
Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years...
October 17, 2018: Molecular Ecology Resources
Sihyung Park, Seung Hyun Ahn, Eun Sol Cho, You Kyung Cho, Eun-Sook Jang, Sung Wook Chi
High-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP, also called CLIP-Seq) has been used to map global RNA-protein interactions. However, a critical caveat of HITS-CLIP results is that they contain non-linear background noise-different extent of non-specific interactions caused by individual transcript abundance-that has been inconsiderately normalized, resulting in sacrifice of sensitivity. To properly deconvolute RNA-protein interactions, we have implemented CLIPick, a flexible peak calling pipeline for analyzing HITS-CLIP data, which statistically determines the signal-to-noise ratio for each transcript based on the expression-dependent background simulation...
October 17, 2018: Nucleic Acids Research
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