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Journal of Biomolecular Techniques: JBT

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https://www.readbyqxmd.com/read/29977167/abrf-proteome-informatics-research-group-iprg-2016-study-inferring-proteoforms-from-bottom-up-proteomics-data
#1
Joon-Yong Lee, Hyungwon Choi, Christopher M Colangelo, Darryl Davis, Michael R Hoopmann, Lukas Käll, Henry Lam, Samuel H Payne, Yasset Perez-Riverol, Matthew The, Ryan Wilson, Susan T Weintraub, Magnus Palmblad
This report presents the results from the 2016 Association of Biomolecular Resource Facilities Proteome Informatics Research Group (iPRG) study on proteoform inference and false discovery rate (FDR) estimation from bottom-up proteomics data. For this study, 3 replicate Q Exactive Orbitrap liquid chromatography-tandom mass spectrometry datasets were generated from each of 4 Escherichia coli samples spiked with different equimolar mixtures of small recombinant proteins selected to mimic pairs of homologous proteins...
June 21, 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29967569/article-watch-july-2018
#2
REVIEW
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.
June 18, 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29805321/the-cellosaurus-a-cell-line-knowledge-resource
#3
Amos Bairoch
The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research. Its scope encompasses both vertebrates and invertebrates. Currently, information for >100,000 cell lines is provided. For each cell line, it provides a wealth of information, cross-references, and literature citations. The Cellosaurus is available on the ExPASy server (https://web.expasy.org/cellosaurus/) and can be downloaded in a variety of formats. Among its many uses, the Cellosaurus is a key resource to help researchers identify potentially contaminated/misidentified cell lines, thus contributing to improving the quality of research in the life sciences...
May 10, 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29667651/-unknown-title
#4
(no author information available yet)
[This corrects the article on p. 137 in vol. 28, PMID: 29151820.].
April 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29667650/-unknown-title
#5
(no author information available yet)
[This corrects the article on p. 137 in vol. 28, PMID: 29151820.].
April 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29623005/challenges-and-opportunities-for-biological-mass-spectrometry-core-facilities-in-the-developing-world
#6
Liam Bell, Bridget Calder, Reinhard Hiller, Ashwil Klein, Nelson C Soares, Stoyan H Stoychev, Barend C Vorster, David L Tabb
The developing world is seeing rapid growth in the availability of biological mass spectrometry (MS), particularly through core facilities. As proteomics and metabolomics becomes locally feasible for investigators in these nations, application areas associated with high burden in these nations, such as infectious disease, will see greatly increased research output. This article evaluates the rapid growth of MS in South Africa (currently approaching 20 laboratories) as a model for establishing MS core facilities in other nations of the developing world...
April 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29618955/content-is-king-databases-preserve-the-collective-information-of-science
#7
John R Yates
Databases store sequence information experimentally gathered to create resources that further science. In the last 20 years databases have become critical components of fields like proteomics where they provide the basis for large-scale and high-throughput proteomic informatics. Amos Bairoch, winner of the Association of Biomolecular Resource Facilities Frederick Sanger Award, has created some of the important databases proteomic research depends upon for accurate interpretation of data.
April 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29463959/article-watch-april-2018
#8
REVIEW
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.
April 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29623006/development-of-a-membrane-based-method-for-isolation-of-genomic-dna-from-human-blood
#9
Goutam Mandal, Subhasish Das, Sriram Padmanabhan
High quality and sufficient quantity of genomic DNA (gDNA) are the primary requisites of several molecular biologic applications, including clinical studies related to genetics, genomics, gene polymorphism, and DNA fingerprinting. Whole blood is the primary source of gDNA in most of the clinical investigations. Currently, commercial kits are primarily used to achieve these goals. However, the use of kits is limited by the cost and involvement of several centrifugal steps. Other methods reported are either laborious or do not produce high quality or quantity of gDNA or both...
March 23, 2018: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29151820/name-it-store-it-protect-it-a-systems-approach-to-managing-data-in-research-core-facilities
#10
REVIEW
Matthew DeVries, Matthew Fenchel, R E Fogarty, Byong-Do Kim, Daniel Timmons, A Nicole White
As the capabilities of technology increase, so do the production of data and the need for data management. The need for data storage at many academic institutions is increasing exponentially. Technology is expanding rapidly, and institutions are recognizing the need to incorporate data management that can be available for future data sharing as a critical component of institutional services. The establishment of a process to manage the surge in data storage is complex and often hindered by not having a plan...
December 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29118677/article-watch-december-2017
#11
REVIEW
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 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29042829/kinetics-of-n-glycan-release-from-human-immunoglobulin-g-igg-by-pngase-f-all-glycans-are-not-created-equal
#12
Yining Huang, Ron Orlando
The biologic activity of IgG molecules is modulated by its crystallizable fragment N-glycosylation, and thus, the analysis of IgG glycosylation is critical. A standard approach to analyze glycosylation of IgGs involves the release of the N-glycans by the enzyme peptide N-glycosidase F, which cleaves the linkage between the asparagine residue and innermost N-acetylglucosamine (GlcNAc) of all N-glycans except those containing a 3-linked fucose attached to the reducing terminal GlcNAc residue. The importance of obtaining complete glycan release for accurate quantitation led us to investigate the kinetics of this de-glycosylation reaction for IgG glycopeptides and to determine the effect of glycan structure and amino acid sequence on the rate of glycan release from glycopeptides of IgGs...
December 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/29038641/a-method-for-mapping-glycosylation-sites-in-proteins
#13
Mark S Han, John T Simpson
The analysis of protein glycosylation by mass spectrometry (MS) has been a challenging technical problem. Quantification by HPLC of N -linked glycans can be executed by the use of peptide- N -glycosidase F to release them from the protein, followed by attachment of a fluorescent label and subsequent fluorescence detection. Similar quantification of O -linked glycans is not possible, as a result of the lack of a universal deglycosylation enzyme. Site-specific analyses by MS, such as the use of proteases to digest the glycoprotein, are difficult to use for quantification of glycans, as a result of the presence of miscleavages...
December 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28860948/outstanding-scientific-poster-awards-for-the-abrf-2017-organized-by-the-education-committee-and-sponsored-by-waters-corporation
#14
Ron Orlando
No abstract text is available yet for this article.
September 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28860947/article-watch-september-2017
#15
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.
September 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28785176/predicting-the-retention-behavior-of-specific-o-linked-glycopeptides
#16
Majors J Badgett, Barry Boyes, Ron Orlando
O -Linked glycosylation is a common post-translational modification that can alter the overall structure, polarity, and function of proteins. Reverse-phase (RP) chromatography is the most common chromatographic approach to analyze O -glycosylated peptides and their unmodified counterparts, even though this approach often does not provide adequate separation of these two species. Hydrophilic interaction liquid chromatography (HILIC) can be a solution to this problem, as the polar glycan interacts with the polar stationary phase and potentially offers the ability to resolve the peptide from its modified form(s)...
September 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28785175/evaluation-of-a-bead-free-coimmunoprecipitation-technique-for-identification-of-virus-host-protein-interactions-using-high-resolution-mass-spectrometry
#17
Stacy L DeBlasio, Michael S Bereman, Jaclyn Mahoney, Theodore W Thannhauser, Stewart M Gray, Michael J MacCoss, Michelle Cilia Heck
Protein interactions between virus and host are essential for viral propagation and movement, as viruses lack most of the proteins required to thrive on their own. Precision methods aimed at disrupting virus-host interactions represent new approaches to disease management but require in-depth knowledge of the identity and binding specificity of host proteins within these interaction networks. Protein coimmunoprecipitation (co-IP) coupled with mass spectrometry (MS) provides a high-throughput way to characterize virus-host interactomes in a single experiment...
September 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28785174/-squirrel-primer-based-pcr-assay-for-direct-and-targeted-sanger-sequencing-of-short-genomic-segments
#18
Henry O Ebili, James C Hassall, Wakkas Fadhil, Hersh Ham-Karim, Abutaleb Asiri, Teresa P Raposo, Ayodeji Johnson Agboola, Mohammad Ilyas
Currently, short DNA segments of sub-100 bp can be sequenced either directly by next-generation sequencing and pyrosequencing, which are expensive, or indirectly, via Sanger sequencing combined with the cumbersome and failure-prone plasmid cloning. To circumvent these issues, we have generated a novel sequencing-purposed PCR assay using long-tailed primers (squirrel primers) to Sanger sequence directly sub-100 bp genomic amplicons. Squirrel primers, 40-65 nt in length, were used to amplify 51-93 bp long genomic sequences of KRAS exons 2 and 3, BRAF exon 15, PI3K catalytic subunit alpha exon 20, and phosphatase and tensin homolog exon 3 from colorectal cancer (CRC) cell lines and preamplified clinical CRC samples with known mutation status by PCR...
September 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28630600/-unknown-title
#19
(no author information available yet)
[This corrects the article on p. 46 in vol. 28, PMID: 28344519.].
July 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28630599/-unknown-title
#20
(no author information available yet)
[This corrects the article on p. 40 in vol. 28, PMID: 28337072.].
July 2017: Journal of Biomolecular Techniques: JBT
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