Journal of biomolecular techniques : JBT最新文献

{"title":"Article Watch: April 2016.","authors":"C. Slaughter","doi":"10.7171/jbt.16-2701-006","DOIUrl":"https://doi.org/10.7171/jbt.16-2701-006","url":null,"abstract":"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.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"28 1","pages":"40-5"},"PeriodicalIF":0.0,"publicationDate":"2016-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75169353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Operational Changes in a Shared Resource Laboratory with the Use of a Product Lifecycle Management Approach: A Case Study.","authors":"P. Hexley, Victoria Smith, S. Wall","doi":"10.7171/jbt.16-2701-002","DOIUrl":"https://doi.org/10.7171/jbt.16-2701-002","url":null,"abstract":"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the Flow Cytometry Research Facility (FCRF) offered access to exceptional technology, but the methods of operation were outdated and unsustainable.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. To rectify this, at the end of 2013, we took a product lifecycle management approach to affect large operational changes and align the services offered with the SRL goal of education, as well as to provide service to researchers. These disruptive operational changes took over 10 mo to complete and allowed for independent end-user acquisition of flow cytometry data. The results have been monitored for the past 12 mo. The operational changes have had a positive impact on the quality of research, increased investigator-facility interaction, reduced stress of facility staff, and increased overall use of the resources. This product lifecycle management approach to facility operations allowed us to conceive of, design, implement, and monitor effectively the changes at the FCRF. This approach should be considered by SRL management when faced with the need for operationally disruptive measures.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"110 5 1","pages":"18-24"},"PeriodicalIF":0.0,"publicationDate":"2016-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89397866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combined RT-qPCR of mRNA and microRNA Targets within One Fluidigm Integrated Fluidic Circuit.","authors":"D. Baldwin, A. Horan, Patrick J. Hesketh, S. Mehta","doi":"10.7171/jbt.16-2702-003","DOIUrl":"https://doi.org/10.7171/jbt.16-2702-003","url":null,"abstract":"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.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"403 1","pages":"75-83"},"PeriodicalIF":0.0,"publicationDate":"2016-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79743980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"N-Terminal Amino Acid Sequence Determination of Proteins by N-Terminal Dimethyl Labeling: Pitfalls and Advantages When Compared with Edman Degradation Sequence Analysis.","authors":"Elizabeth Chang, S. Pourmal, Chun Zhou, Rupesh Kumar, M. Teplova, N. Pavletich, K. Marians, H. Erdjument-Bromage","doi":"10.7171/jbt.16-2702-002","DOIUrl":"https://doi.org/10.7171/jbt.16-2702-002","url":null,"abstract":"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. Application of this approach on protein domains, generated by limited proteolysis of overexpressed proteins, confirms that it is a universal labeling technique and is very sensitive when compared with Edman sequencing. Finally, we compared Edman sequencing and Nt-dimethylation of the same polypeptide fragments; results confirm that there is agreement in the identity of the Nt amino acid sequence between these 2 methods.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"8 1","pages":"61-74"},"PeriodicalIF":0.0,"publicationDate":"2016-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89705273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metrics for Success: Strategies for Enabling Core Facility Performance and Assessing Outcomes.","authors":"P. Turpen, P. Hockberger, Susan M. Meyn, Connie Nicklin, D. Tabarini, J. Auger","doi":"10.7171/jbt.16-2701-001","DOIUrl":"https://doi.org/10.7171/jbt.16-2701-001","url":null,"abstract":"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. For each category, we provide lessons learned that we believe contribute to the effective and efficient overall management of core facilities. If done well, we believe that encouraging best practices and evaluating performance in core facilities will demonstrate and reinforce the importance of core facilities in the research and educational mission of institutions. It will also increase job satisfaction of those working in core facilities and improve the likelihood of sustainability of both facilities and personnel.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"4 1","pages":"25-39"},"PeriodicalIF":0.0,"publicationDate":"2016-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89470731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disaster and Contingency Planning for Scientific Shared Resource Cores.","authors":"S. Mische, A. Wilkerson","doi":"10.7171/jbt.16-2701-003","DOIUrl":"https://doi.org/10.7171/jbt.16-2701-003","url":null,"abstract":"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. As such, protection of these assets and the ability to recover from a disaster is increasingly critical to the mission and success of the institution. Therefore, cores should develop and implement both disaster and business continuity plans and be an integral part of the institution's overall plans. Here we provide an overview of key elements required for core disaster and business continuity plans, guidance, and tools for developing these plans, and real-life lessons learned at a large research institution in the aftermath of Superstorm Sandy.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"34 1","pages":"4-17"},"PeriodicalIF":0.0,"publicationDate":"2016-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81652116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid, Effective DNA Isolation from Osmanthus via Modified Alkaline Lysis.","authors":"L. Alexander","doi":"10.7171/jbt.16-2702-001","DOIUrl":"https://doi.org/10.7171/jbt.16-2702-001","url":null,"abstract":"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. Methods were ranked in order, based on total quantity, quality, and performance points as the following: 1) solid-phase extraction (SPE), 2) modified alkaline lysis (SDS), 3) cetyltrimethylammonium bromide (CTAB) with chloroform (CHL), and 4) CTAB with phenol/chloroform (PHE). Total DNA, isolated via SPE, showed the least contamination but the lowest mean quantity (9.6 ± 3.4 μg) and highest cost. The highest quantity of DNA was isolated via SDS (117 ± 54.1 μg). SPE and SDS resolved the most individuals on agarose gel, whereas the 2 CTAB methods had poorly resolved gels. All methods except PHE performed well in PCR. Additions to the modified alkaline lysis method increased A260:A230 by up to 59% without affecting yield. With the use of SDS, an average of 1000 μg/g DNA was isolated from fresh leaf tissue of 18 samples in ∼1.5 h at a cost of 0.74 U.S. dollars (USD)/sample. We recommend improved alkaline lysis as a rapid, effective, and cost-efficient method of isolating DNA from Osmanthus species.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"36 1","pages":"53-60"},"PeriodicalIF":0.0,"publicationDate":"2016-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81432180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sharing Core Facilities and Research Resources--An Investment in Accelerating Scientific Discoveries.","authors":"Michael C Chang, F. Grieder","doi":"10.7171/jbt.16-2701-004","DOIUrl":"https://doi.org/10.7171/jbt.16-2701-004","url":null,"abstract":"Each year, the U.S. National Institutes of Health (NIH) invests substantial resources in core facilities that provide access to advanced cutting-edge technologies, expert consultation, and other services to scientific investigators. The facilities offer a number of services, ranging from systematic analysis and data processing, using specialized instrumentation, to access and expert advice on experimental design and evaluation needs, such as biostatistics, patient outreach, and clinical regulatory issues. The largest fraction of support for cores comes from the institutes and centers of the NIH, for example, through the National Cancer Institute (NCI) and National Center for Advancing Translational Sciences (NCATS). Significant NIH investment is spent on Center Core grants, particularly the NCI Cancer Centers, and the Clinical Translational Sciences Award Program supported by NCATS. The Office of the NIH Director’s Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI) also has a substantial investment in animal and biologic resource centers that provide models of human biology and disease for basic to clinical studies to researchers around the world. Many of these centers function like cores, as they provide the following: 1) high-quality, disease-free animals; 2) access to sophisticated technologies and facilities, as well as specialized animals; and 3) expert training by professional staff and consultation services. As an example, the NIH-supported National Primate Research Centers provide facilities, animals, and expertise for investigators who use nonhuman primates for biomedical research, facilitating >1000 individual research projects annually. The DPCPSI investment in core facilities also includes support through its Shared Instrument Grant program to purchase or upgrade expensive, specialized, commercially available instruments or integrated systems. This program promotes cost effectiveness; encourages optimal sharing among investigators, research groups, and departments; and fosters a collaborative, multidisciplinary environment. In many settings, the instrument is integrated in a centralized core facility. Through these investments and many other programs not listed, NIH’s annual support for research cores is estimated conservatively at $900 million. Given this large investment, it is critical that both NIH and the research institutions receiving support for these resources identify and implement approaches that enhance core resource efficiencies.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"37 1","pages":"2-3"},"PeriodicalIF":0.0,"publicationDate":"2016-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87737375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"JBT Special Issue on Core Management.","authors":"S. Mische","doi":"10.7171/jbt.16-2701-005","DOIUrl":"https://doi.org/10.7171/jbt.16-2701-005","url":null,"abstract":"Progress in biomedical research is largely driven by improvements, innovations, and breakthroughs in technology, an increasingly complex collaboration among basic, preclinical, and clinical science. Unfortunately, this increasing sophistication correlates with both growing research costs and a shrinking federal research budget. Taken together, it makes a strong argument for investing in core facilities. Cores are not new, having been a part of the research landscape for decades. Cores leverage expertise and state-of-the-art technology in centralized facilities and support institutional research in a cost-effective and efficient manner. There is a growing recognition that centralized administration of cores ensures best practices for institutional investment, financial and resource management, and core scientist professional and career development. Centralization maximizes institutional research capabilities by providing state-of-the-art instrumentation and multidisciplinary expertise for the entire research community, establishing a culture of collaboration integrated and aligned with institutional strategic goals and success in a highly competitive playground. However, to be successful, cores requires funding agencies and partners who identify opportunities and provide financial support, scientists who embrace team science, core scientists who personify the ethos of collaborative sharing, and committed institutions and policies that make it happen.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"5 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2016-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87481198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Article Watch: December 2015.","authors":"C. Slaughter","doi":"10.7171/jbt.15-2604-004","DOIUrl":"https://doi.org/10.7171/jbt.15-2604-004","url":null,"abstract":"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, GRU-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.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"8 1","pages":"150-6"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91101606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}