Use of SciDBMaker as Tool for the Design of Specialized Biological Databases

2011 ◽  
pp. 251-265 ◽  
Author(s):  
Riadh Hammami ◽  
Ismail Fliss
Keyword(s):  
Molecular Biology ◽  
Best Practices ◽  
Exponential Growth ◽  
Protein Sequence ◽  
Knowledge Bases ◽  
Biological Processes ◽  
Biological Databases ◽  
Experimental Findings ◽  
Biology Research

The exponential growth of molecular biology research in recent decades has brought concomitant growth in the number and size of genomic and proteomic databases used to interpret experimental findings. Particularly, growth of protein sequence records created the need for smaller and manually annotated databases. Since scientists are continually developing new specific databases to enhance their understanding of biological processes, the authors created SciDBMaker to provide a tool for easy building of new specialized protein knowledge bases. This chapter also suggests best practices for specialized biological databases design, and provides examples for the implementation of these practices.

Use of SciDBMaker as Tool for the Design of Specialized Biological Databases

2013 ◽  
pp. 1755-1768
Author(s):  
Riadh Hammami ◽  
Ismail Fliss
Keyword(s):  
Molecular Biology ◽  
Best Practices ◽  
Exponential Growth ◽  
Protein Sequence ◽  
Knowledge Bases ◽  
Biological Processes ◽  
Biological Databases ◽  
Experimental Findings ◽  
Biology Research

The exponential growth of molecular biology research in recent decades has brought concomitant growth in the number and size of genomic and proteomic databases used to interpret experimental findings. Particularly, growth of protein sequence records created the need for smaller and manually annotated databases. Since scientists are continually developing new specific databases to enhance their understanding of biological processes, the authors created SciDBMaker to provide a tool for easy building of new specialized protein knowledge bases. This chapter also suggests best practices for specialized biological databases design, and provides examples for the implementation of these practices.

scholarly journals New chromogens for alkaline phosphatase histochemistry: salmon and magenta phosphate are useful for single- and double-label immunohistochemistry.

1994 ◽  
Vol 42 (4) ◽  
pp. 551-554 ◽  
Author(s):  
C Avivi ◽  
O Rosen ◽  
R S Goldstein
Keyword(s):  
Alkaline Phosphatase ◽  
Monoclonal Antibodies ◽  
Molecular Biology ◽  
Horseradish Peroxidase ◽  
Reaction Products ◽  
Immunocytochemical Detection ◽  
Hematoxylin Staining ◽  
Double Label ◽  
Biology Research

Two new substrate chromogens for alkaline phosphatase (ALP) detection have been recently synthesized for use in molecular biology research, salmon and magenta phosphate. We show here that these two chromogens have advantageous characteristics for immunocytochemistry as well. Their relatively delicate pink- and magenta-colored products do not mask the colors produced by other staining procedures. In addition, the reaction products of these substrates are insoluble in water, ethanol, and xylene, permitting the use of regressive hematoxylin staining procedures and coverslipping in permanent resin-based media. Most importantly, when these ALP substrates are used in double-label immunocytochemistry in combination with horseradish peroxidase-diaminobenzidine (HRP-DAB) and counterstained with hematoxylin, all three colors can be easily distinguished. An application using these substrates for simultaneous immunocytochemical detection of two monoclonal antibodies of different classes, in combination with hematoxylin staining, is illustrated.

scholarly journals Reviewer Acknowledgements for Journal of Molecular Biology Research, Vol. 9, No. 1

2019 ◽  
Vol 9 (1) ◽  
pp. 179
Author(s):  
Grace Brown
Keyword(s):  
Molecular Biology ◽  
Biology Research

Reviewer Acknowledgements for Journal of Molecular Biology Research, Vol. 9, No. 1, 2019

scholarly journals Contextually responsive and knowledge-focused teaching: disrupting the notion of ‘best practices’

2021 ◽  
Vol 9 (SI) ◽  
Author(s):  
Ceclia Jacobs ◽  
Keyword(s):  
Higher Education ◽  
Staff Development ◽  
Best Practices ◽  
Teaching And Learning ◽  
Academic Staff ◽  
Knowledge Bases ◽  
Good Teaching ◽  
Approach To Teaching ◽  
Conceptual Paper ◽  
Higher Education Teaching

The notion that universal ‘best practices’ underpin higher education teaching is problematic. Although there is general agreement in the literature that good teaching is not decontextualised but rather that it is responsive to the context in which it occurs, generic views of teaching and learning continue to inform practices at universities in South Africa. This conceptual paper considers why a decontextualised approach to higher education teaching prevails and interrogates factors influencing this view, such as: the knowledge bases informing this approach to teaching, the factors from within the higher education sector that shape this approach to teaching, as well as the practices and Discourses prevalent in the field of academic development. The paper argues that teaching needs to be both contextually responsive and knowledge- focused. Disrupting ‘best practices’ approaches require new ways of undertaking academic staff development, which are incumbent on the understandings that academic developers bring to the enterprise.

Radiation as a carcinogen

2019 ◽  
pp. 91-102
Author(s):  
Yan-Qun Xiang ◽  
Chao-Nan Qian
Keyword(s):  
Molecular Biology ◽  
Cancer Incidence ◽  
Dose Response ◽  
Past Century ◽  
Response Relationship ◽  
Radiation Carcinogenesis ◽  
Pathway Activation ◽  
Biology Research ◽  
Chromosome Alterations ◽  
Abscopal Effects

The data from animals, cell lines, and humans have led to the consensus of induction of carcinogenesis by ionizing radiation, especially at low-level doses, and that there is a dose–response relationship between radiation and cancer incidence. However, additional factors, including radiation type, dose rate, specific tissues, and animal species, also provide a contribution. The development of molecular biology research has helped explain the mechanism of radiation carcinogenesis, including pathway activation and chromosome alterations. Bystander effects and abscopal effects are additionally characteristics of radiation carcinogenesis. This chapter takes a look at how radiation, from both environment and industry, has contributed to cancer incidence over the past century.

Verification of Uncurated Protein Annotations

2010 ◽  
pp. 301-314
Author(s):  
Francisco M. Couto ◽  
Mário J. Silva ◽  
Vivian Lee ◽  
Emily Dimmer ◽  
Evelyn Camon ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Molecular Biology ◽  
Domain Knowledge ◽  
Text Processing ◽  
The Other ◽  
Research Projects ◽  
Evidence Text ◽  
Biological Sources ◽  
Biology Research ◽  
Automatic Text

Molecular Biology research projects produced vast amounts of data, part of which has been preserved in a variety of public databases. However, a large portion of the data contains a significant number of errors and therefore requires careful verification by curators, a painful and costly task, before being reliable enough to derive valid conclusions from it. On the other hand, research in biomedical information retrieval and information extraction are nowadays delivering Text Mining solutions that can support curators to improve the efficiency of their work to deliver better data resources. Over the past decades, automatic text processing systems have successfully exploited biomedical scientific literature to reduce the researchers’ efforts to keep up to date, but many of these systems still rely on domain knowledge that is integrated manually leading to unnecessary overheads and restrictions in its use. A more efficient approach would acquire the domain knowledge automatically from publicly available biological sources, such as BioOntologies, rather than using manually inserted domain knowledge. An example of this approach is GOAnnotator, a tool that assists the verification of uncurated protein annotations. It provided correct evidence text at 93% precision to the curators and thus achieved promising results. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

scholarly journals Ian Read Gibbons. 30 October 1931—30 January 2018

2019 ◽  
Vol 66 ◽  
pp. 201-223
Author(s):  
Wendy E. Gibbons ◽  
Ronald D. Vale ◽  
Winfield S. Sale
Keyword(s):  
Molecular Biology ◽  
Mitotic Spindle ◽  
Molecular Motor ◽  
Experimental Methods ◽  
Vital Role ◽  
Biological Processes ◽  
Scientific Career ◽  
Innovative Solutions ◽  
Cilia And Flagella ◽  
The Right

Ian Read Gibbons is best known for discovering dynein, a molecular motor that powers the motion of cilia and flagella, is involved in assembling the mitotic spindle and moves chromosomes as well as other cargoes inside cells. Gibbons devoted his career in the lab of more than 50 years to understanding the mechanism of how dynein works in driving motility. In doing so, he built a life-long reputation as a creative, collaborative and tenacious researcher with an unusual gift for crafting innovative solutions to tricky experimental problems. His experimental methods spanned electron as well as light microscopy, biochemistry, molecular biology, crystallography and molecular modelling. He perceived the right set of experimental moves that would allow him to dissect and observe the physical underpinnings of minute biological processes such as the delicate movements of dynein. Gibbons traced his success to the ability to envision how pieces of a scientific puzzle might fit together to make a coherent story: ‘My own approach to research has always emphasized intuition over logic. Perhaps for that reason, I get attracted to questions with aesthetic appeal.’ Even though dynein holds much promise for helping to engineer ways to fight disease, Gibbons' focus was always on the intrinsic grace of understanding nature's workings. Gibbons’ marriage to his biochemist wife Barbara played a particularly vital role in his life. Barbara and Ian worked frequently together as she built her own scientific career through their partnership in the study of dynein. Ian's many scientific accomplishments as well as his dedication to his friends and family represent enduring gifts to us all.

Advances in visualizing transcription factor-DNA interactions

Genome ◽  
2020 ◽  
Author(s):  
Rachel M. Price ◽  
Marek A Budzynski ◽  
Shivani Kundra ◽  
Sheila S. Teves
Keyword(s):  
Molecular Biology ◽  
Dna Sequences ◽  
Imaging Techniques ◽  
Specific Interaction ◽  
Dna Interactions ◽  
Dynamic Information ◽  
Transcription Process ◽  
Target Dna ◽  
Biology Research

At the heart of the transcription process is the specific interaction between transcription factors (TFs) and their target DNA sequences. Decades of molecular biology research have led to unprecedented insights into how TFs access the genome to regulate transcription. In the last 20 years, advances in microscopy have enabled scientists to add imaging as a powerful tool in probing two specific aspects of TF-DNA interactions: structure and dynamics. In this review, we examine how applications of diverse imaging technologies can provide structural and dynamic information that complements insights gained from molecular biology assays. As a case study, we discuss how applications of advanced imaging techniques have reshaped our understanding of TF behavior across the cell cycle, leading to a rethinking in the field of mitotic bookmarking.

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