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High-Throughput Sequencing

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https://www.readbyqxmd.com/read/29169139/analysis-of-extracellular-polymeric-substances-eps-and-ciprofloxacin-degrading-microbial-community-in-the-combined-fe-c-micro-electrolysis-ubaf-process-for-the-elimination-of-high-level-ciprofloxacin
#1
Longlong Zhang, Qinyan Yue, Kunlun Yang, Pin Zhao, Baoyu Gao
Extracellular polymeric substances (EPS) and ciprofloxacin-degrading microbial community in the combined Fe-C micro-electrolysis and up-flow biological aerated filter (UBAF) process for the treatment of high-level ciprofloxacin (CIP) were analyzed. The research demonstrated a great potential of Fe-C micro-electrolysis-UBAF for the elimination of high-level CIP. Above 90% of CIP removal was achieved through the combined process at 100 mg L(-1) of CIP loading. In UBAF, the pollutants were mainly removed at 0-70 cm heights...
November 14, 2017: Chemosphere
https://www.readbyqxmd.com/read/29169020/biomarkers-of-antibiotic-resistance-genes-during-seasonal-changes-in-wastewater-treatment-systems
#2
Ya-Nan Jiao, Zhen-Chao Zhou, Tao Chen, Yuan-Yuan Wei, Ji Zheng, Rui-Xia Gao, Hong Chen
To evaluate the seasonal distribution of antibiotic resistance genes (ARGs) and explore the reason for their patterns in different seasons and different systems, two wastewater treatment systems were selected and analyzed using high-throughput qPCR. Linear discriminant analysis (LDA) effect size (LEfSe) was used to discover the differential ARGs (biomarkers) and estimate the biomarkers' effect size. We found that the total absolute abundances of ARGs in inflows and excess sludge samples had no obvious seasonal fluctuations, while those in winter outflow samples decreased in comparison with the inflow samples...
November 20, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29167000/-study-on-genetype-in-lung-squamous-carcinoma-by-high-throughput-of-%C3%A2-transcriptome-sequence
#3
Ying Xiong, Mingzhen Li, Panpan Zhang, Liyi Zhang, Yue Yang
BACKGROUND: Recently, there is no effective targeted drug for to the lung squamous carcinoma, the targeted drug for the adenocarcinoma does not benefit for the patients with squamous lung cancer, and researchers have known less targets for this type of patients. The main study herein is to screen and identify the specific key genes for the lung squamous carcinoma that will provide potential novel targets to describe pathogenesis of lung cancer. METHODS: Transcript sequence was used to detect the five pairs lung squamous carcinoma and normal lung tissues and bioinformatics was performed to investigate the differential coding genes between them and quantitative PCR was done to validate the key genes expression in lung cancer cell lines...
November 20, 2017: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
https://www.readbyqxmd.com/read/29166861/comprehensive-transcriptome-analysis-reveals-distinct-regulatory-programs-during-vernalization-and-floral-bud-development-of-orchardgrass-dactylis-glomerata-l
#4
Guangyan Feng, Linkai Huang, Ji Li, Jianping Wang, Lei Xu, Ling Pan, Xinxin Zhao, Xia Wang, Ting Huang, Xinquan Zhang
BACKGROUND: Vernalization and the transition from vegetative to reproductive growth involve multiple pathways, vital for controlling floral organ formation and flowering time. However, little transcription information is available about the mechanisms behind environmental adaption and growth regulation. Here, we used high-throughput sequencing to analyze the comprehensive transcriptome of Dactylis glomerata L. during six different growth periods. RESULTS: During vernalization, 4689 differentially expressed genes (DEGs) significantly increased in abundance, while 3841 decreased...
November 22, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29165730/what-else-is-in-salviae-officinalis-folium-comprehensive-species-identification-of-plant-raw-material-by-dna-metabarcoding
#5
Corinna Schmiderer, Brigitte Lukas, Joana Ruzicka, Johannes Novak
Quality control of drugs consists of identifying the raw material to avoid unwanted admixtures or exchange of material as well as looking for abiotic and biotic contaminations. So far, identity and microbial contamination are analyzed by separate processes and separate methods. Species identification by their DNA ("DNA barcoding") has the potential to supplement existing methods of identification. The introduction of next-generation sequencing methods offers completely new approaches like the identification of whole communities in one analysis, termed "DNA metabarcoding"...
November 17, 2017: Planta Medica
https://www.readbyqxmd.com/read/29165646/development-and-application-of-a-recombination-based-library-versus-library-high-throughput-yeast-two-hybrid-rll-y2h-screening-system
#6
Fang Yang, Yingying Lei, Meiling Zhou, Qili Yao, Yichao Han, Xiang Wu, Wanshun Zhong, Chenghang Zhu, Weize Xu, Ran Tao, Xi Chen, Da Lin, Khaista Rahman, Rohit Tyagi, Zeshan Habib, Shaobo Xiao, Dang Wang, Yang Yu, Huanchun Chen, Zhenfang Fu, Gang Cao
Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165544/rna-methylation-and-diseases-experimental-results-databases-web-servers-and-computational-models
#7
Xing Chen, Ya-Zhou Sun, Hui Liu, Lin Zhang, Jian-Qiang Li, Jia Meng
Ribonucleic acid (RNA) methylation is a type of posttranscriptional modifications occurring in all kingdoms of life. It is strongly related to important biological process, thus making it linked to a number of human diseases. Owing to the development of high-throughput sequencing technology, plenty of achievement had been obtained in RNA methylation research recently. Meanwhile, various computational models have been developed to analyze and mining increasing RNA methylation data. In this review, we first made a brief introduction about eight types of most popular RNA methylation, the biological functions of RNA methylation, the relationship between RNA methylation and disease and five important RNA methylation-related diseases...
November 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29165344/high-throughput-identification-of-antimicrobial-peptides-from-amphibious-mudskippers
#8
Yunhai Yi, Xinxin You, Chao Bian, Shixi Chen, Zhao Lv, Limei Qiu, Qiong Shi
Widespread existence of antimicrobial peptides (AMPs) has been reported in various animals with comprehensive biological activities, which is consistent with the important roles of AMPs as the first line of host defense system. However, no big-data-based analysis on AMPs from any fish species is available. In this study, we identified 507 AMP transcripts on the basis of our previously reported genomes and transcriptomes of two representative amphibious mudskippers, Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM)...
November 22, 2017: Marine Drugs
https://www.readbyqxmd.com/read/29164062/preleukemic-hematopoietic-stem-cells-in-human-acute-myeloid-leukemia
#9
REVIEW
M Ryan Corces, Howard Y Chang, Ravindra Majeti
Acute myeloid leukemia (AML) is an aggressive malignancy of the bone marrow characterized by an uncontrolled proliferation of undifferentiated myeloid lineage cells. Decades of research have demonstrated that AML evolves from the sequential acquisition of genetic alterations within a single lineage of hematopoietic cells. More recently, the advent of high-throughput sequencing has enabled the identification of a premalignant phase of AML termed preleukemia. Multiple studies have demonstrated that AML can arise from the accumulation of mutations within hematopoietic stem cells (HSCs)...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29164055/micrornas-and-acute-myeloid-leukemia-chemoresistance-a-mechanistic-overview
#10
REVIEW
Martino Marco Gabra, Leonardo Salmena
Up until the early 2000s, a functional role for microRNAs (miRNAs) was yet to be elucidated. With the advent of increasingly high-throughput and precise RNA-sequencing techniques within the last two decades, it has become well established that miRNAs can regulate almost all cellular processes through their ability to post-transcriptionally regulate a majority of protein-coding genes and countless other non-coding genes. In cancer, miRNAs have been demonstrated to play critical roles by modifying or controlling all major hallmarks including cell division, self-renewal, invasion, and DNA damage among others...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29163701/high-levels-of-depdc1b-predict-shorter-biochemical-recurrence-free-survival-of-patients-with-prostate-cancer
#11
Shoumin Bai, Ting Chen, Tao Du, Xianju Chen, Yiming Lai, Xiaoming Ma, Wanhua Wu, Chunhao Lin, Leyuan Liu, Hai Huang
DEP domain-containing protein 1B (DEPDC1B) has been reported to serve important functions in breast cancer and non-small cell lung cancer. However, its involvement in the development of prostate cancer (PCa) remains unclear. Therefore, the present study aimed to investigate the expression and clinical significance of DEPDC1B in tumor tissues from patients diagnosed with PCa. A total of 80 prostate tissue samples were collected following prostatectomy to generate a tissue microarray for immunohistochemical analysis of DEPDC1B protein expression...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29163636/a-pipeline-for-high-throughput-concentration-response-modeling-of-gene-expression-for-toxicogenomics
#12
John S House, Fabian A Grimm, Dereje D Jima, Yi-Hui Zhou, Ivan Rusyn, Fred A Wright
Cell-based assays are an attractive option to measure gene expression response to exposure, but the cost of whole-transcriptome RNA sequencing has been a barrier to the use of gene expression profiling for in vitro toxicity screening. In addition, standard RNA sequencing adds variability due to variable transcript length and amplification. Targeted probe-sequencing technologies such as TempO-Seq, with transcriptomic representation that can vary from hundreds of genes to the entire transcriptome, may reduce some components of variation...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29163601/genome-wide-constitutively-expressed-gene-analysis-and-new-reference-gene-selection-based-on-transcriptome-data-a-case-study-from-poplar-canker-disease-interaction
#13
Jiaping Zhao, Fan Yang, Jinxia Feng, Yanli Wang, Barbara Lachenbruch, Jiange Wang, Xianchong Wan
A number of transcriptome datasets for differential expression (DE) genes have been widely used for understanding organismal biology, but these datasets also contain untapped information that can be used to develop more precise analytical tools. With the use of transcriptome data generated from poplar/canker disease interaction system, we describe a methodology to identify candidate reference genes from high-throughput sequencing data. This methodology will improve the accuracy of RT-qPCR and will lead to better standards for the normalization of expression data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163600/plastome-rearrangements-in-the-adenocalymma-neojobertia-clade-bignonieae-bignoniaceae-and-its-phylogenetic-implications
#14
Luiz H M Fonseca, Lúcia G Lohmann
The chloroplast is one of the most important organelles of plants. This organelle has a circular DNA with approximately 130 genes. The use of plastid genomic data in phylogenetic and evolutionary studies became possible with high-throughput sequencing methods, which allowed us to rapidly obtain complete genomes at a reasonable cost. Here, we use high-throughput sequencing to study the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). More specifically, we use Hi-Seq Illumina technology to sequence 10 complete plastid genomes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163567/soil-type-has-a-stronger-role-than-dipterocarp-host-species-in-shaping-the-ectomycorrhizal-fungal-community-in-a-bornean-lowland-tropical-rain-forest
#15
Adam L Essene, Katherine L Shek, J D Lewis, Kabir G Peay, Krista L McGuire
The role that mycorrhizal fungal associations play in the assembly of long-lived tree communities is poorly understood, especially in tropical forests, which have the highest tree diversity of any ecosystem. The lowland tropical rain forests of Southeast Asia are characterized by high levels of species richness within the family Dipterocarpaceae, the entirety of which has been shown to form obligate ectomycorrhizal (ECM) fungal associations. Differences in ECM assembly between co-occurring species of dipterocarp have been suggested, but never tested in adult trees, as a mechanism for maintaining the coexistence of closely related tree species in this family...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163494/reproducibility-and-reuse-of-adaptive-immune-receptor-repertoire-data
#16
Felix Breden, Eline T Luning Prak, Bjoern Peters, Florian Rubelt, Chaim A Schramm, Christian E Busse, Jason A Vander Heiden, Scott Christley, Syed Ahmad Chan Bukhari, Adrian Thorogood, Frederick A Matsen Iv, Yariv Wine, Uri Laserson, David Klatzmann, Daniel C Douek, Marie-Paule Lefranc, Andrew M Collins, Tania Bubela, Steven H Kleinstein, Corey T Watson, Lindsay G Cowell, Jamie K Scott, Thomas B Kepler
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1-3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29163432/stratified-bacterial-and-archaeal-community-in-mangrove-and-intertidal-wetland-mudflats-revealed-by-high-throughput-16s-rrna-gene-sequencing
#17
Zhichao Zhou, Han Meng, Yang Liu, Ji-Dong Gu, Meng Li
The stratified distribution of bacterial and archaeal communities has been detected in many sediment profiles from various natural environments. A better understanding of microbial composition and diversity pattern in coastal mangrove wetlands in relation to physicochemical and spatial-temporal influences could provide more insights into the ecological functions of microbes in coastal wetlands. In this study, seasonal variations of microbial communities within sediment profiles from two sediment types (mangrove forest and intertidal mudflats) at three sampling locations in coastal Mai Po wetland were characterized using MiSeq high throughput sequencing and 16S rRNA quantitative PCR methods...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163420/microbial-diversity-and-community-structure-of-sulfate-reducing-and-sulfur-oxidizing-bacteria-in-sediment-cores-from-the-east-china-sea
#18
Yu Zhang, Xungong Wang, Yu Zhen, Tiezhu Mi, Hui He, Zhigang Yu
Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163336/two-novel-mutations-associated-with-ataxia-telangiectasia-identified-using-an-ion-ampliseq-inherited-disease-panel
#19
Maria V Kuznetsova, Dmitry Yu Trofimov, Ekaterina S Shubina, Taisiya O Kochetkova, Natalia A Karetnikova, Ilya Yu Barkov, Vladimir A Bakharev, Oleg A Gusev, Gennady T Sukhikh
Ataxia-telangiectasia (A-T), or Louis-Bar syndrome, is a rare neurodegenerative disorder associated with immunodeficiency. For families with at least one affected child, timely A-T genotyping during any subsequent pregnancy allows the parents to make an informed decision about whether to continue to term when the fetus is affected. Mutations in the ATM gene, which is 150 kb long, give rise to A-T; more than 600 pathogenic variants in ATM have been characterized since 1990 and new mutations continue to be discovered annually...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/29162694/an-endogenous-retroviral-envelope-syncytin-and-its-cognate-receptor-identified-in-the-viviparous-placental-mabuya-lizard
#20
Guillaume Cornelis, Mathis Funk, Cécile Vernochet, Francisca Leal, Oscar Alejandro Tarazona, Guillaume Meurice, Odile Heidmann, Anne Dupressoir, Aurélien Miralles, Martha Patricia Ramirez-Pinilla, Thierry Heidmann
Syncytins are envelope genes from endogenous retroviruses that have been captured during evolution for a function in placentation. They have been found in all placental mammals in which they have been searched, including marsupials. Placental structures are not restricted to mammals but also emerged in some other vertebrates, most frequently in lizards, such as the viviparous Mabuya Scincidae. Here, we performed high-throughput RNA sequencing of a Mabuya placenta transcriptome and screened for the presence of retroviral env genes with a full-length ORF...
November 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
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