scholarly journals Shaping a Plant Genetics and Molecular Biology research community in Brazil

2017 ◽  
Vol 40 (1 suppl 1) ◽  
pp. I-I
Author(s):  
Marie-Anne Van Sluys
Keyword(s):  
Molecular Biology ◽  
Research Community ◽  
Plant Genetics ◽  
Biology Research

scholarly journals A recombineering pipeline to clone large and complex genes in Chlamydomonas

2021 ◽  
Author(s):  
Tom Z Emrich-Mills ◽  
Gary Yates ◽  
James Barrett ◽  
Philipp Girr ◽  
Irina Grouneva ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Bacterial Artificial Chromosome ◽  
Molecular Biology ◽  
Fluorescent Protein ◽  
Artificial Chromosome ◽  
Research Community ◽  
Mass Spectrometry Data ◽  
Parallel Cloning ◽  
Mutant Complementation ◽  
Biology Research

Abstract The ability to clone genes has greatly advanced cell and molecular biology research, enabling researchers to generate fluorescent protein fusions for localization and confirm genetic causation by mutant complementation. Most gene cloning is PCR or DNA synthesis dependent, which can become costly and technically challenging as genes increase in size, particularly if they contain complex regions. This has been a long-standing challenge for the Chlamydomonas reinhardtii research community, as this alga has a high percentage of genes containing complex sequence structures. Here we overcame these challenges by developing a recombineering pipeline for the rapid parallel cloning of genes from a Chlamydomonas bacterial artificial chromosome collection. To generate fluorescent protein fusions for localization, we applied the pipeline at both batch and high-throughput scales to 203 genes related to the Chlamydomonas CO2 concentrating mechanism (CCM), with an overall cloning success rate of 77%. Cloning success was independent of gene size and complexity, with cloned genes as large as 23 kilobases. Localization of a subset of CCM targets confirmed previous mass spectrometry data, identified new pyrenoid components, and enabled complementation of mutants. We provide vectors and detailed protocols to facilitate easy adoption of this technology, which we envision will open up new possibilities in algal and plant research.

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.

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/.

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.

Molecular biology research offers new weapons against cancer

JAMA ◽  
1990 ◽  
Vol 263 (17) ◽  
pp. 2289-2290
Author(s):  
A. Skolnick
Keyword(s):  
Molecular Biology ◽  
Biology Research
Sign in / Sign up

Export Citation Format

Share Document