LINKS BETWEEN MOLECULAR BIOLOGY RESEARCH, EDUCATION AND LEARNING BY INTEGRATING WET LAB AND IN SILICO LAB

2017 ◽  
Author(s):  
Rosanna del Gaudio
Keyword(s):  
Molecular Biology ◽  
In Silico ◽  
Research Education ◽  
Wet Lab ◽  
Biology Research

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 Integrating Molecular Biology and Bioinformatics Education

2018 ◽  
Author(s):  
Boas Pucker ◽  
Hanna Marie Schilbert ◽  
Sina Franziska Schumacher
Keyword(s):  
Molecular Biology ◽  
Cooperative Learning ◽  
Peer Review ◽  
High Throughput ◽  
Teaching Method ◽  
Integrated Education ◽  
High Throughput Data ◽  
Wet Lab ◽  
Bioinformatics Education ◽  
Increasing Demand

Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand for scientists with a combined background in both fields, the education in dry lab and wet lab is often separated. This work describes an example of integrated education with focus on genomics and transcriptomics. Participants learn computational and molecular biology methods in the same practical course. Peer-review is applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. Evaluation results indicate acceptance and appreciation of this approach.

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 Integrating Molecular Biology and Bioinformatics Education

2018 ◽  
Author(s):  
Boas Pucker ◽  
Hanna Marie Schilbert ◽  
Sina Franziska Schumacher
Keyword(s):  
Molecular Biology ◽  
Cooperative Learning ◽  
Peer Review ◽  
High Throughput ◽  
Teaching Method ◽  
Integrated Education ◽  
High Throughput Data ◽  
Wet Lab ◽  
Bioinformatics Education ◽  
Increasing Demand

Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand for scientists with a combined background in both fields, the education in dry lab and wet lab is often separated. This work describes an example of integrated education with focus on genomics and transcriptomics. Participants learn computational and molecular biology methods in the same practical course. Peer-review is applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. Evaluation results indicate acceptance and appreciation of this approach.

IN SILICO CHARACTERIZATION, MOLECULAR DOCKING, AND IN VITRO EVALUATION OF TRIAZOLE DERIVATIVES AS POTENTIAL ANTICANCER AGENTS

2021 ◽  
pp. 22-28
Author(s):  
HARSHITHA T ◽  
VINAY KUMAR T ◽  
VINEETHA T
Keyword(s):  
Molecular Docking ◽  
Anticancer Activity ◽  
Anticancer Agents ◽  
In Silico ◽  
Docking Studies ◽  
Pharmacokinetic Parameters ◽  
Pancreatic Cell ◽  
Triazole Derivatives ◽  
Wet Lab

Objective: The objective of the study was to perform in silico molecular docking and in vitro anticancer studies of proposed 1,2,4-triazole derivatives for the determination of their anticancer activity. Methods: A series of 10 triazole compounds with different substituents were drawn in ACD Lab ChemSketch software. Molecular and biological properties were identified using Molinspiration software. The compounds that obeyed Lipinski rule of five are subjected for pharmacokinetic parameters prediction and docking analysis. SwissDock ADME software is used for the prediction of absorption, distribution, metabolism, and elimination. Then, the compounds are docked with target enzymes in Chimera software 1.14 version. The molecular docking studies revealed favorable molecular interactions and binding energies. The compounds that showed good docking results were synthesized through wet lab synthesis and further preceded for in vitro anticancer studies. Results: Three compounds are selected for wet lab synthesis due to their good docking results compared to other compounds. The synthesized compounds are subjected to different in vitro anticancer studies and found to be having potential anticancer activity. Conclusion: The pharmacokinetic and docking studies conclude that the triazole compounds have potential as anticancer agents. The in vitro anticancer studies revealed that the triazole derivatives are having high potency of anticancer activity against pancreatic cell lines.

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.

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/.

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