Parallel matching and sorting with TACO's distributed collections-a case study from molecular biology research

2002 ◽  
Author(s):  
J. Nolte ◽  
P. Horton
Keyword(s):  
Molecular Biology ◽  
Parallel Matching ◽  
Biology Research

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.

scholarly journals How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b

2021 ◽  
Author(s):  
Yorick Bernardus Cornelis van de Grift ◽  
Nika Heijmans ◽  
Renée van Amerongen
Keyword(s):  
Mammary Gland ◽  
In Silico ◽  
Online Tools ◽  
Mammary Gland Biology ◽  
User Friendly ◽  
In Silico Analyses ◽  
Biology Research ◽  
Selection Of

AbstractAn increasing number of ‘-omics’ datasets, generated by labs all across the world, are becoming available. They contain a wealth of data that are largely unexplored. Not every scientist, however, will have access to the required resources and expertise to analyze such data from scratch. Fortunately, a growing number of investigators is dedicating their time and effort to the development of user friendly, online applications that allow researchers to use and investigate these datasets. Here, we will illustrate the usefulness of such an approach. Using regulation of Wnt7b expression as an example, we will highlight a selection of accessible tools and resources that are available to researchers in the area of mammary gland biology. We show how they can be used for in silico analyses of gene regulatory mechanisms, resulting in new hypotheses and providing leads for experimental follow up. We also call out to the mammary gland community to join forces in a coordinated effort to generate and share additional tissue-specific ‘-omics’ datasets and thereby expand the in silico toolbox.

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

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.

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.

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