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Journal of Biomolecular Techniques: JBT

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https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#1
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
March 10, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28260998/article-watch-april-2017
#2
Clive A Slaughter
This column highlights recently published articles that are of interest to the readership of this publication. We encourage ABRF members to forward information on articles they feel are important and useful to Clive Slaughter, MCG-UGA Medical Partnership, 1425 Prince Ave., Athens, GA 30606, USA. Tel: (706) 713-2216; Fax: (706) 713-2221; E-mail: cslaught@uga.edu, or to any member of the editorial board. Article summaries reflect the reviewer's opinions and not necessarily those of the association.
February 22, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28400709/focus-on-metagenomics
#3
Christopher E Mason, Scott Tighe
No abstract text is available yet for this article.
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28344519/assessment-of-repli-g-multiple-displacement-whole-genome-amplification-wga-techniques-for-metagenomic-applications
#4
Sofia Ahsanuddin, Ebrahim Afshinnekoo, Jorge Gandara, Mustafa Hakyemezoğlu, Daniela Bezdan, Samuel Minot, Nick Greenfield, Christopher E Mason
Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28337073/real-time-dna-sequencing-in-the-antarctic-dry-valleys-using-the-oxford-nanopore-sequencer
#5
Sarah S Johnson, Elena Zaikova, David S Goerlitz, Yu Bai, Scott W Tighe
The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#6
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28337071/international-standards-for-genomes-transcriptomes-and-metagenomes
#7
Christopher E Mason, Ebrahim Afshinnekoo, Scott Tighe, Shixiu Wu, Shawn Levy
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28260999/gut-microbiota-analysis-results-are-highly-dependent-on-the-16s-rrna-gene-target-region-whereas-the-impact-of-dna-extraction-is-minor
#8
Anniina Rintala, Sami Pietilä, Eveliina Munukka, Erkki Eerola, Juha-Pekka Pursiheimo, Asta Laiho, Satu Pekkala, Pentti Huovinen
Next-generation sequencing (NGS) is currently the method of choice for analyzing gut microbiota composition. As gut microbiota composition is a potential future target for clinical diagnostics, it is of utmost importance to enhance and optimize the NGS analysis procedures. Here, we have analyzed the impact of DNA extraction and selected 16S rDNA primers on the gut microbiota NGS results. Bacterial DNA from frozen stool specimens was extracted with 5 commercially available DNA extraction kits. Special attention was paid to the semiautomated DNA extraction methods that could expedite the analysis procedure, thus being especially suitable for clinical settings...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28100962/ctls-2016-and-the-formation-of-a-pan-european-professional-society-through-the-lens-of-an-abrf-founding-member
#9
Ronald L Niece
No abstract text is available yet for this article.
January 5, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28058039/assessment-of-il-28-rs12979860-and-rs8099917-polymorphisms-in-a-cohort-of-cuban-chronic-hcv-genotype-1b-patients
#10
Daniel Palenzuela Gardón, Isabel Alicia Guillen, Julio R Fernández, Hamlet Camacho, Zurina Cinza Estevez, Santiago Dueñas, Liz Alvares-Lajonchere, Yalena Amador, Gillian Martinez-Donato, Junsong Han, Zhiming Zhang, Xiaona Zhang, Yang Gao, Juan Roca Campaña, Lidia I Novoa
Hepatitis C virus (HCV) is a significant global public health problem with >185 million infections worldwide. A series of genome-wide association studies (GWAS) has identified IL-28B polymorphisms as a predictor of sustained virologic response (SVR), as well as spontaneous clearance in chronic HCV genotype 1 patients. The objective of this work was to evaluate the prevalence of IL-28B rs12979860 and rs8099917 polymorphisms in Cuban chronic HCV patients. The study cohort included 73 chronic HCV patients treated with concomitant administration of CIGB-230 and nonpegylated IFN-α plus ribavirin (non-pegIFN-α/R) antiviral therapy...
December 16, 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27904438/article-watch-december-2016
#11
Clive A Slaughter
This column highlights recently published articles that are of interest to the readership of this publication. We encourage ABRF members to forward information on articles they feel are important and useful to Clive Slaughter, MCG-UGA Medical Partnership, 1425 Prince Ave., Athens, GA 30606, USA. Tel: (706) 713-2216; Fax: (706) 713-2221; E-mail: cslaught@uga.edu, or to any member of the editorial board. Article summaries reflect the reviewer's opinions and not necessarily those of the association.
December 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27790076/automated-sanger-analysis-pipeline-asap-a-tool-for-rapidly-analyzing-sanger-sequencing-data-with-minimum-user-interference
#12
Aditya Singh, Prateek Bhatia
Sanger sequencing platforms, such as applied biosystems instruments, generate chromatogram files. Generally, for 1 region of a sequence, we use both forward and reverse primers to sequence that area, in that way, we have 2 sequences that need to be aligned and a consensus generated before mutation detection studies. This work is cumbersome and takes time, especially if the gene is large with many exons. Hence, we devised a rapid automated command system to filter, build, and align consensus sequences and also optionally extract exonic regions, translate them in all frames, and perform an amino acid alignment starting from raw sequence data within a very short time...
December 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27785122/core-technologies-in-life-sciences-ctls-2016-conference-summary
#13
Joshua Z Rappoport
No abstract text is available yet for this article.
December 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27672352/monitoring-error-rates-in-illumina-sequencing
#14
Leigh J Manley, Duanduan Ma, Stuart S Levine
Guaranteeing high-quality next-generation sequencing data in a rapidly changing environment is an ongoing challenge. The introduction of the Illumina NextSeq 500 and the depreciation of specific metrics from Illumina's Sequencing Analysis Viewer (SAV; Illumina, San Diego, CA, USA) have made it more difficult to determine directly the baseline error rate of sequencing runs. To improve our ability to measure base quality, we have created an open-source tool to construct the Percent Perfect Reads (PPR) plot, previously provided by the Illumina sequencers...
December 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27672351/establishment-of-a-simple-and-quick-method-for-detecting-extended-spectrum-%C3%AE-lactamase-esbl-genes-in-bacteria
#15
Song-Tao Han, Ying Fei, Jin-You Huang, Mei Xu, Li-Chan Chen, D Joshua Liao, Yu-Jie Tan
Extended-spectrum β-lactamase (ESBL) genes that render bacteria resistant to antibiotics are commonly detected using phenotype testing, which is time consuming and not sufficiently accurate. To establish a better method, we used phenotype testing to identify ESBL-positive bacterial strains and conducted PCR to screen for TEM (named after the patient Temoneira who provided the first sample), sulfhydryl reagent variable (SHV), cefotaxime (CTX)-M-1, and CTX-M-9, the 4 most common ESBL types and subtypes. We then performed multiplex PCR with 1 primer containing a biotin and hybridized the PCR products with gene-specific probes that were coupled with microbeads and coated with a specific fluorescence...
December 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27582640/article-watch-september-2016
#16
Clive A Slaughter
This column highlights recently published articles that are of interest to the readership of this publication. We encourage ABRF members to forward information on articles they feel are important and useful to Clive Slaughter, AU-UGA Medical Partnership, 1425 Prince Ave., Athens, GA 30606, USA. Tel: (706) 713-2216; Fax: (706) 713-2221; E-mail: cslaught@uga.edu, or to any member of the editorial board. Article summaries reflect the reviewer's opinions and not necessarily those of the association.
September 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27582639/effects-of-reusing-gel-electrophoresis-and-electrotransfer-buffers-on-western-blotting
#17
Ghanshyam D Heda, Oluwabukola B Omotola, Rajiv P Heda, Jamie Avery
SDS-PAGE and Western blotting are 2 of the most commonly used biochemical methods for protein analysis. Proteins are electrophoretically separated based on their MWs by SDS-PAGE and then electrotransferred to a solid membrane surface for subsequent protein-specific analysis by immunoblotting, a procedure commonly known as Western blotting. Both of these procedures use a salt-based buffer, with the latter procedure consisting of methanol as an additive known for its toxicity. Previous reports present a contradictory view in favor or against reusing electrotransfer buffer, also known as Towbin's transfer buffer (TTB), with an aim to reduce the toxic waste...
September 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27582638/resolving-isomeric-glycopeptide-glycoforms-with-hydrophilic-interaction-chromatography-hilic
#18
Yining Huang, Yongxin Nie, Barry Boyes, Ron Orlando
The ability to resolve glycans while attached to tryptic peptides would greatly facilitate glycoproteomics, as this would enable site-specific glycan characterization. Peptide/glycopeptide separations are typically performed using reversed-phase liquid chromatography (RPLC), where retention is driven by hydrophobic interaction. As the hydrophilic glycans do not interact significantly with the RPLC stationary phase, it is difficult to resolve glycopeptides that differ only in their glycan structure, even when these differences are large...
September 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27382362/pcr-conditions-for-16s-primers-for-analysis-of-microbes-in-the-colon-of-rats
#19
I A Guillen, H Camacho, A D Tuero, D Bacardí, D O Palenzuela, A Aguilera, J A Silva, R Estrada, O Gell, J Suárez, J Ancizar, E Brown, A B Colarte, J Castro, L I Novoa
The study of the composition of the intestinal flora is important to the health of the host, playing a key role in maintaining intestinal homeostasis and the evolution of the immune system. For these studies, various universal primers of the 16S rDNA gene are used in microbial taxonomy. Here, we report an evaluation of 5 universal primers to explore the presence of microbial DNA in colon biopsies preserved in RNAlater solution. The DNA extracted was used for the amplification of PCR products containing the variable (V) regions of the microbial 16S rDNA gene...
September 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27182204/a-practical-approach-to-quantitative-processing-and-analysis-of-small-biological-structures-by-fluorescent-imaging
#20
Crystal M Noller, Maria Boulina, George McNamara, Angela Szeto, Philip M McCabe, Armando J Mendez
Standards in quantitative fluorescent imaging are vaguely recognized and receive insufficient discussion. A common best practice is to acquire images at Nyquist rate, where highest signal frequency is assumed to be the highest obtainable resolution of the imaging system. However, this particular standard is set to insure that all obtainable information is being collected. The objective of the current study was to demonstrate that for quantification purposes, these correctly set acquisition rates can be redundant; instead, linear size of the objects of interest can be used to calculate sufficient information density in the image...
September 2016: Journal of Biomolecular Techniques: JBT
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