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https://www.readbyqxmd.com/read/28432951/microbial-communities-in-the-functional-areas-of-a-biofilm-reactor-with-anaerobic-aerobic-process-for-oily-wastewater-treatment
#1
Jianhua Li, Shanshan Sun, Ping Yan, Li Fang, Yang Yu, Yangdong Xiang, Di Wang, Yejing Gong, Yanjun Gong, Zhongzhi Zhang
Microbial communities in the functional areas of biofilm reactors with large height-diameter ratio using the anaerobic-aerobic (A/O) reflux process was investigated to treat heavy oil refinery wastewater without pretreatment. In the process, chemical oxygen demand (COD) and total nitrogen (TN) removal reached 93.2% and 82.8%, and the anaerobic biofilm reactor was responsible for 95% and 99%, respectively. Areas for hydrolysis acidification and acetic acid production, methane production, and COD recovery were obvious in the anaerobic reactor...
April 10, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28432689/viscosity-based-droplet-size-controlling-in-negative-pressure-driven-droplets-generator-for-large-scale-particle-synthesis
#2
Hanlin Li, Yijun Xue, Meng Xu, Wenfeng Zhao, Chenghua Zong, Xiaojun Liu, Qingquan Zhang
The poor control and regulation of droplets limit the applications of negative-pressure-driven-droplet-generator (NPDDG). Here, we present a simple method to control droplet size in NPDDG via varying the oil viscosity. Depending on the infinite inter-solubility of high viscous mineral oil and low viscous hexadecane, we obtain a series of oils with kinematic viscosities linearly varied from 4.2 mm(2) /s to 194.6 mm(2) /s. By using these oils as continuous phases, mono-disperse droplets are fabricated with controllable size in NPDDG...
April 22, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28432618/the-identification-of-key-genes-and-pathways-in-hepatocellular-carcinoma-by-bioinformatics-analysis-of-high-throughput-data
#3
Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28432352/low-cost-low-bias-and-low-input-rna-seq-with-high-experimental-verifiability-based-on-semiconductor-sequencing
#4
Zhibiao Mai, Chuanle Xiao, Jingjie Jin, Gong Zhang
Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here we demonstrate a simple, low-cost, low-bias and low-input RNA-seq with ion torrent semiconductor sequencing (LIEA RNA-seq). We also developed highly accurate and error-tolerant spliced mapping algorithm FANSe2splice to accurately map the single-ended reads to the reference genome with better experimental verifiability than the previous spliced mappers...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432350/enhancing-the-throughput-and-multiplexing-capabilities-of-next-generation-sequencing-for-efficient-implementation-of-pooled-shrna-and-crispr-screens
#5
Md Fahmid Islam, Atsushi Watanabe, Lai Wong, Conor Lazarou, Frederick S Vizeacoumar, Omar Abuhussein, Wayne Hill, Maruti Uppalapati, C Ronald Geyer, Franco J Vizeacoumar
Next generation sequencing is becoming the method of choice for functional genomic studies that use pooled shRNA or CRISPR libraries. A key challenge in sequencing these mixed-oligo libraries is that they are highly susceptible to hairpin and/or heteroduplex formation. This results in polyclonal, low quality, and incomplete reads and reduces sequencing throughput. Unfortunately, this challenge is significantly magnified in low-to-medium throughput bench-top sequencers as failed reads significantly perturb the maximization of sequence coverage and multiplexing capabilities...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431999/novel-method-to-rapidly-and-efficiently-lyse-escherichia-coli-for-the-isolation-of-recombinant-protein
#6
Himanshu Joshi, Vikas Jain
Rapid and high-throughput protein purification methods are required to explore structure and function of several uncharacterized proteins. Isolation of recombinant protein expressed in Escherichia coli strain BL21 (DE3) depends largely on the efficient and speedy bacterial cell lysis, which is considered as the bottleneck during protein purification. Cells are usually lysed by either sonication or high pressure homogenization, both of which are slow, require special equipment, lead to heat generation, and may result in loss of protein's biological activity...
April 18, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28431925/analysis-of-pm2-5-induced-cytotoxicity-in-human-hacat-cells-based-on-a-microfluidic-system
#7
Yuxiao Zhang, Lulu Zheng, Jiang Tuo, Qi Liu, Xinlian Zhang, Zhixuan Xu, Sixiu Liu, Guodong Sui
Human exposure to PM2.5 causes several adverse health effects. Skin is the first barrier against harmful environmental substances and can has direct contact with PM2.5, but there is no study about PM2.5-induced cytotoxicity in human skin cells on the molecular level partially due to the shortcomings of traditional research methods. In present study, we established a microfluidic system including a cell culture chip integrated with a high-throughput protein microarray chip to investigate the mechanism of PM2...
April 18, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28431796/lessons-learned-from-twins-in-autoimmune-and-chronic-inflammatory-diseases
#8
REVIEW
Elena Generali, Angela Ceribelli, Maria Antonietta Stazi, Carlo Selmi
Autoimmunity and chronic inflammation recognize numerous shared factors and, as a result, the resulting diseases frequently coexist in the same patients or respond to the same treatments. Among the convenient truths of autoimmune and chronic inflammatory diseases, there is now agreement that these are complex conditions in which the individual genetic predisposition provides a rate of heritability. The concordance rates in monozygotic and dizygotic twins allows to estimate the weight of the environment in determining disease susceptibility, despite recent data supporting that only a minority of immune markers depend on hereditary factors...
April 18, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28431639/advances-in-molecular-diagnosis-of-malaria
#9
Zhi Zheng, Zhibin Cheng
Malaria is a mosquito-borne disease caused by five species of Plasmodium parasites. Accurate diagnosis of malaria plays an essential part in malaria control. With traditional diagnostic methodologies, malaria control programs have achieved remarkable success during the past decade, and are now heading toward malaria elimination in many areas. This new situation, however, calls for novel diagnostics with improved sensitivity, throughput, and reduced cost for active screening of malaria parasites, as all transfected individuals have to be identified in order to block transmission...
2017: Advances in Clinical Chemistry
https://www.readbyqxmd.com/read/28431358/molecular-ecological-perspective-of-methanogenic-archaeal-community-in-rice-agroecosystem
#10
REVIEW
Singh Alpana, P Vishwakarma, T K Adhya, K Inubushi, S K Dubey
Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO2). Rice fields represent the major source of methane (CH4) emission as the recent estimates range from 34 to 112 Tg CH4 per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH4 emission from rice fields...
April 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28431310/characterization-of-bacterial-communities-of-donkey-milk-by-high-throughput-sequencing
#11
Maria de Los Dolores Soto Del Rio, Alessandra Dalmasso, Tiziana Civera, Maria Teresa Bottero
The interest in donkey milk (DM) is growing because of its functional properties and nutritional value, especially for children with allergies and food intolerances. However, most of the available reports of DM microbiota are based on culture-dependent methods to investigate food safety issues and the presence of lactic acid bacteria (LAB). The aim of this study was to determine the composition of DM bacterial communities using a high-throughput sequencing (HTS) approach. Bulk milk samples from Italian donkey dairy farms from two consecutive years were analysed using the MiSeq Illumina platform...
March 30, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28431251/tunable-expression-tools-enable-single-cell-strain-distinction-in-the-gut-microbiome
#12
Weston R Whitaker, Elizabeth Stanley Shepherd, Justin L Sonnenburg
Applying synthetic biology to engineer gut-resident microbes provides new avenues to investigate microbe-host interactions, perform diagnostics, and deliver therapeutics. Here, we describe a platform for engineering Bacteroides, the most abundant genus in the Western microbiota, which includes a process for high-throughput strain modification. We have identified a novel phage promoter and translational tuning strategy and achieved an unprecedented level of expression that enables imaging of fluorescent-protein-expressing Bacteroides stably colonizing the mouse gut...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431245/host-microbe-co-metabolism-dictates-cancer-drug-efficacy-in-c-%C3%A2-elegans
#13
Timothy A Scott, Leonor M Quintaneiro, Povilas Norvaisas, Prudence P Lui, Matthew P Wilson, Kit-Yi Leung, Lucia Herrera-Dominguez, Sonia Sudiwala, Alberto Pessia, Peter T Clayton, Kevin Bryson, Vidya Velagapudi, Philippa B Mills, Athanasios Typas, Nicholas D E Greene, Filipe Cabreiro
Fluoropyrimidines are the first-line treatment for colorectal cancer, but their efficacy is highly variable between patients. We queried whether gut microbes, a known source of inter-individual variability, impacted drug efficacy. Combining two tractable genetic models, the bacterium E. coli and the nematode C. elegans, we performed three-way high-throughput screens that unraveled the complexity underlying host-microbe-drug interactions. We report that microbes can bolster or suppress the effects of fluoropyrimidines through metabolic drug interconversion involving bacterial vitamin B6, B9, and ribonucleotide metabolism...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431229/functional-enhancer-screening-in-single-cells
#14
Joris van Arensbergen, Bas van Steensel
In this issue of Molecular Cell, Xie et al. (2017) introduce Mosaic-seq, a powerful technology that combines CRISPRi and single-cell RNA-seq. This method enables the high-throughput assessment of contributions of enhancers to gene regulation.
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28431188/t-cell-receptor-%C3%AE-chain-repertoire-analysis-reveals-the-association-between-neoantigens-and-tumour-infiltrating-lymphocytes-in-multifocal-papillary-thyroid-carcinoma
#15
Zheming Lu, Chaoting Zhang, Jindong Sheng, Jing Shen, Baoguo Liu
To explore whether a few non-synonymous somatic mutations could induce activation and proliferation of neoantigen-specific tumour-infiltrating lymphocytes (TILs) in tumours with low mutation rates, we analysed a patient with multifocal papillary thyroid carcinoma (seven non-contiguous cancer foci) to investigate the relationship between neoantigens and TILs. These seven foci had a few or no non-synonymous somatic mutations; moreover, multiple loci had similar or different spectra of mutations. We used high-throughput sequencing of the rearranged genes in T cell receptor β-chain (TCRβ) to reveal the basic characteristics of T cells in seven tumour foci and matched adjacent normal tissue...
April 21, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28431173/programmatic-access-to-bioinformatics-tools-from-embl-ebi-update-2017
#16
Szymon Chojnacki, Andrew Cowley, Joon Lee, Anna Foix, Rodrigo Lopez
Since 2009 the EMBL-EBI provides free and unrestricted access to several bioinformatics tools via the user's browser as well as programmatically via Web Services APIs. Programmatic access to these tools, which is fundamental to bioinformatics, is increasingly important as more high-throughput data is generated, e.g. from proteomics and metagenomic experiments. Access is available using both the SOAP and RESTful approaches and their usage is reviewed regularly in order to ensure that the best, supported tools are available to all users...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28431096/a-new-rapid-resazurin-based-microdilution-assay-for-antimicrobial-susceptibility-testing-of-neisseria-gonorrhoeae
#17
Sunniva Foerster, Valentino Desilvestro, Lucy J Hathaway, Christian L Althaus, Magnus Unemo
Objectives: Rapid, cost-effective and objective methods for antimicrobial susceptibility testing of Neisseria gonorrhoeae would greatly enhance surveillance of antimicrobial resistance. Etest, disc diffusion and agar dilution methods are subjective, mostly laborious for large-scale testing and take ∼24 h. We aimed to develop a rapid broth microdilution assay using resazurin (blue), which is converted into resorufin (pink fluorescence) in the presence of viable bacteria. Methods: The resazurin-based broth microdilution assay was established using 132 N...
April 19, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28431082/compositional-differences-among-female-associated-and-embryo-associated-microbiota-of-the-viviparous-pacific-beetle-cockroach-diploptera-punctata
#18
Paul A Ayayee, George Keeney, Zakee L Sabree, Agustí Muñoz-Garcia
All cockroach species, except one, harbor the endosymbiont Blattabacterium, transmitted from females to embryos. Adult cockroaches acquire non-Blattabacterium bacteria as part of their gut microbiota over time, but our knowledge of the possible transmission of these non-Blattabacterium bacteria from females to embryos is rudimentary. We characterized the gut microbiota of gravid viviparous Diploptera punctata females and the non-Blattabacterium microbiota of associated developing embryos, as well as the gut microbiota of non-gravid females, and the microbiota of orphan embryos (females not included), following high-throughput sequencing of the 16S rRNA gene to assess bacterial transference...
April 18, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28431045/water-table-drawdown-shapes-the-depth-dependent-variations-in-prokaryotic-diversity-and-structure-in-zoige-peatlands
#19
Qiuping Zhong, Huai Chen, Liangfeng Liu, Yixin He, Dan Zhu, Lin Jiang, Wei Zhan, Ji Hu
Microbial communities are important to ecosystem function and sensitive to hydrological dynamics. However, we lack predictable knowledge about how soil microorganisms respond to water table drawdown in different depths. This research used high-throughput sequencing method to determine the responses of prokaryotic communities to the changes of water table and depth on Zoige peatlands. Our results showed that water table drawdown reduced alpha diversity indices (observed species, Shannon diversity and Chao1 richness) of prokaryotic communities...
April 18, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#20
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
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