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Journal of Biomolecular Techniques: JBT

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https://www.readbyqxmd.com/read/27904438/article-watch-december-2016
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/27257408/article-watch-july-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.
July 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27006647/n-terminal-amino-acid-sequence-determination-of-proteins-by-n-terminal-dimethyl-labeling-pitfalls-and-advantages-when-compared-with-edman-degradation-sequence-analysis
#12
Elizabeth Chang, Sergei Pourmal, Chun Zhou, Rupesh Kumar, Marianna Teplova, Nikola P Pavletich, Kenneth J Marians, Hediye Erdjument-Bromage
In recent history, alternative approaches to Edman sequencing have been investigated, and to this end, the Association of Biomolecular Resource Facilities (ABRF) Protein Sequencing Research Group (PSRG) initiated studies in 2014 and 2015, looking into bottom-up and top-down N-terminal (Nt) dimethyl derivatization of standard quantities of intact proteins with the aim to determine Nt sequence information. We have expanded this initiative and used low picomole amounts of myoglobin to determine the efficiency of Nt-dimethylation...
July 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/27006646/next-generation-sequencing-based-hpv-genotyping-assay-validated-in-formalin-fixed-paraffin-embedded-oropharyngeal-and-cervical-cancer-specimens
#13
Nicholas P Ambulos, Lisa M Schumaker, Trevor J Mathias, Ruth White, Jennifer Troyer, David Wells, Kevin J Cullen
Available clinical human papilloma virus (HPV) diagnostics for head and neck cancer have limited sensitivity and/or fail to define the HPV genotype. Common HPV genotyping assays are costly and labor intensive. We sought to develop a next-generation sequencing (NGS)-based HPV genotyping assay that was sensitive enough to work on formalin-fixed paraffin-embedded (FFPE) samples. We developed an ion torrent NGS HPV genotyping assay using barcoded HPV PCR broad-spectrum general primers 5(+)/6(+) (BSGP)5(+)/6(+)...
July 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/26977138/combined-rt-qpcr-of-mrna-and-microrna-targets-within-one-fluidigm-integrated-fluidic-circuit
#14
Don A Baldwin, Annamarie D Horan, Patrick J Hesketh, Samir Mehta
The ability to profile expression levels of a large number of mRNAs and microRNAs (miRNAs) within the same sample, using a single assay method, would facilitate investigations of miRNA effects on mRNA abundance and streamline biomarker screening across multiple RNA classes. A protocol is described for reverse transcription of long RNA and miRNA targets, followed by preassay amplification of the pooled cDNAs and quantitative PCR (qPCR) detection for a mixed panel of candidate RNA biomarkers. The method provides flexibility for designing custom target panels, is robust over a range of input RNA amounts, and demonstrated a high assay success rate...
July 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/26816495/rapid-effective-dna-isolation-from-osmanthus-via-modified-alkaline-lysis
#15
Lisa Alexander
Variability of leaf structure and presence of secondary metabolites in mature leaf tissue present a challenge for reliable DNA extraction from Osmanthus species and cultivars. The objective of this study was to develop a universal rapid, effective, and cost-efficient method of DNA isolation for Osmanthus mature leaf tissue. Four different methods were used to isolate DNA from 8 cultivars of Osmanthus. Absorbance spectra, DNA concentration, appearance on agarose gel, and performance in PCR were used to analyze quality, quantity, and integrity of isolated DNA...
July 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/26848285/disaster-and-contingency-planning-for-scientific-shared-resource-cores
#16
Sheenah Mische, Amy Wilkerson
Progress in biomedical research is largely driven by improvements, innovations, and breakthroughs in technology, accelerating the research process, and an increasingly complex collaboration of both clinical and basic science. This increasing sophistication has driven the need for centralized shared resource cores ("cores") to serve the scientific community. From a biomedical research enterprise perspective, centralized resource cores are essential to increased scientific, operational, and cost effectiveness; however, the concentration of instrumentation and resources in the cores may render them highly vulnerable to damage from severe weather and other disasters...
April 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/26848284/metrics-for-success-strategies-for-enabling-core-facility-performance-and-assessing-outcomes
#17
Paula B Turpen, Philip E Hockberger, Susan M Meyn, Connie Nicklin, Diane Tabarini, Julie A Auger
Core Facilities are key elements in the research portfolio of academic and private research institutions. Administrators overseeing core facilities (core administrators) require assessment tools for evaluating the need and effectiveness of these facilities at their institutions. This article discusses ways to promote best practices in core facilities as well as ways to evaluate their performance across 8 of the following categories: general management, research and technical staff, financial management, customer base and satisfaction, resource management, communications, institutional impact, and strategic planning...
April 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/26766928/jbt-special-issue-on-core-management
#18
EDITORIAL
Sheenah Mische
No abstract text is available yet for this article.
April 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/26763487/sharing-core-facilities-and-research-resources-an-investment-in-accelerating-scientific-discoveries
#19
EDITORIAL
Michael Chang, Franziska B Grieder
No abstract text is available yet for this article.
April 2016: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/26681929/operational-changes-in-a-shared-resource-laboratory-with-the-use-of-a-product-lifecycle-management-approach-a-case-study
#20
Philip Hexley, Victoria Smith, Samantha Wall
Shared Resource Laboratories (SRLs) provide investigators access to necessary scientific and resource expertise to leverage complex technologies fully for advancing high-quality biomedical research in a cost-effective manner. At the University of Nebraska Medical Center, the Flow Cytometry Research Facility (FCRF) offered access to exceptional technology, but the methods of operation were outdated and unsustainable. Whereas technology has advanced and the institute has expanded, the operations at the facility remained unchanged for 35 yr...
April 2016: Journal of Biomolecular Techniques: JBT
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