Suppressor Mutants: History and Today’s Applications

EcoSal Plus ◽  
2021 ◽  
Vol 9 (2) ◽  
Author(s):  
David E. Bautista ◽  
Joseph F. Carr ◽  
Angela M. Mitchell
Keyword(s):  
Biological Systems ◽  
Biological Processes ◽  
Gene Products ◽  
Genetic Tools ◽  
Suppressor Mutants ◽  
Suppressor Analysis

For decades, biologist have exploited the near boundless advantages that molecular and genetic tools and analysis provide for our ability to understand biological systems. One of these genetic tools, suppressor analysis, has proven invaluable in furthering our understanding of biological processes and pathways and in discovering unknown interactions between genes and gene products.

scholarly journals Annotating proteins with generalized functional linkages

2008 ◽  
Vol 105 (46) ◽  
pp. 17700-17705 ◽  
Author(s):  
Richard Llewellyn ◽  
David S. Eisenberg
Keyword(s):  
Protein Function ◽  
Biological Process ◽  
Computational Method ◽  
Majority Voting ◽  
Target Protein ◽  
Biological Processes ◽  
Gene Products ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

As genome sequencing outstrips the rate of high-quality, low-throughput biochemical and genetic experimentation, accurate annotation of protein function becomes a bottleneck in the progress of the biomolecular sciences. Most gene products are now annotated by homology, in which an experimentally determined function is applied to a similar sequence. This procedure becomes error-prone between more divergent sequences and can contaminate biomolecular databases. Here, we propose a computational method of assignment of function, termed Generalized Functional Linkages (GFL), that combines nonhomology-based methods with other types of data. Functional linkages describe pairwise relationships between proteins that work together to perform a biological task. GFL provides a Bayesian framework that improves annotation by arbitrating a competition among biological process annotations to best describe the target protein. GFL addresses the unequal strengths of functional linkages among proteins, the quality of existing annotations, and the similarity among them while incorporating available knowledge about the cellular location or individual molecular function of the target protein. We demonstrate GFL with functional linkages defined by an algorithm known as zorch that quantifies connectivity in protein–protein interaction networks. Even when using proteins linked only by indirect or high-throughput interactions, GFL predicts the biological processes of many proteins in Saccharomyces cerevisiae, improving the accuracy of annotation by 20% over majority voting.

scholarly journals Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Open Biology ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 200149 ◽  
Author(s):  
Valerie Wood ◽  
Seth Carbon ◽  
Midori A. Harris ◽  
Antonia Lock ◽  
Stacia R. Engel ◽  
...  
Keyword(s):  
Quality Control ◽  
Gene Ontology ◽  
Biological Processes ◽  
Gene Products ◽  
Model Species ◽  
Ontology Term ◽  
Protein Coding ◽  
Ontology Structure ◽  
Exclusive Processes ◽  
Annotation Quality

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

Integrating the whole from the sum of the parts: vignettes in computational biology

2017 ◽  
Vol 1 (3) ◽  
pp. 241-243
Author(s):  
Jeffrey Skolnick
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Synthetic Biology ◽  
Personalized Medicine ◽  
Computational Biology ◽  
Biological Systems ◽  
Deep Understanding ◽  
Biological Processes ◽  
Practical Applications ◽  
Biological Variables

As is typical of contemporary cutting-edge interdisciplinary fields, computational biology touches and impacts many disciplines ranging from fundamental studies in the areas of genomics, proteomics transcriptomics, lipidomics to practical applications such as personalized medicine, drug discovery, and synthetic biology. This editorial examines the multifaceted role computational biology plays. Using the tools of deep learning, it can make powerful predictions of many biological variables, which may not provide a deep understanding of what factors contribute to the phenomena. Alternatively, it can provide the how and the why of biological processes. Most importantly, it can help guide and interpret what experiments and biological systems to study.

scholarly journals Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology

2010 ◽  
Vol 74 (4) ◽  
pp. 479-503 ◽  
Author(s):  
Trudy Torto-Alalibo ◽  
Candace W. Collmer ◽  
Michelle Gwinn-Giglio ◽  
Magdalen Lindeberg ◽  
Shaowu Meng ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Effector Proteins ◽  
Biological Processes ◽  
Gene Products ◽  
Host Defenses ◽  
Host Interactions ◽  
Microbial Associations ◽  
Bioinformatic Approaches ◽  
Go Terms ◽  
Diverse Plant

SUMMARY Microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.

scholarly journals Overview and Utilization of the NCI Thesaurus

2004 ◽  
Vol 5 (8) ◽  
pp. 648-654 ◽  
Author(s):  
Gilberto Fragoso ◽  
Sherri de Coronado ◽  
Margaret Haber ◽  
Frank Hartel ◽  
Larry Wright
Keyword(s):  
National Cancer Institute ◽  
Description Logic ◽  
Biological Processes ◽  
Gene Products ◽  
Collaborative Effort ◽  
Web Ontology Language ◽  
Ontology Language ◽  
File Formats ◽  
History Of ◽  
The Web

The NCI Thesaurus is a reference terminology covering areas of basic and clinical science, built with the goal of facilitating translational research in cancer. It contains nearly 110 000 terms in approximately 36000 concepts, partitioned in 20 subdomains, which include diseases, drugs, anatomy, genes, gene products, techniques, and biological processes, among others, all with a cancer-centric focus in content, and originally designed to support coding activities across the National Cancer Institute. Each concept represents a unit of meaning and contains a number of annotations, such as synonyms and preferred name, as well as annotations such as textual definitions and optional references to external authorities. In addition, concepts are modelled with description logic (DL) and defined by their relationships to other concepts; there are currently approximately 90 types of named relations declared in the terminology. The NCI Thesaurus is produced by the Enterprise Vocabulary Services project, a collaborative effort between the NCI Center for Bioinformatics and the NCI Office of Communications, and is part of the caCORE infrastructure stack (http://ncicb.nci.nih.gov/NCICB/core). It can be accessed programmatically through the open caBIO API and browsed via the web (http://nciterms.nci.nih.gov). A history of editing changes is also accessible through the API. In addition, the Thesaurus is available for download in various file formats, including OWL, the web ontology language, to facilitate its utilization by others.

Van der Waals forces in biological systems

1973 ◽  
Vol 6 (4) ◽  
pp. 341-387 ◽  
Author(s):  
Jacob N. Israelachvili
Keyword(s):  
Biological Systems ◽  
Van Der Waals ◽  
Van Der Waals Forces ◽  
Biological Processes ◽  
Theoretical Investigations ◽  
The Way

The theory of van der Waals forces has now developed to a stage where it constitutes a powerful tool in theoretical investigations of many biological systems. In this review we shall consider both the theoretical and conceptual aspects of these forces with the emphasis on the way they may be involved in various biological processes.

scholarly journals Cross-species comparisons and in vitro models to study tempo in development and homeostasis

2021 ◽  
Vol 11 (3) ◽  
Author(s):  
Teresa Rayon ◽  
James Briscoe
Keyword(s):  
Biological Systems ◽  
In Vitro Models ◽  
Autonomous Control ◽  
Tissue Transplantation ◽  
Biological Processes ◽  
Open Questions ◽  
Species Comparisons ◽  
Insight Into

Time is inherent to biological processes. It determines the order of events and the speed at which they take place. However, we still need to refine approaches to measure the course of time in biological systems and understand what controls the pace of development. Here, we argue that the comparison of biological processes across species provides molecular insight into the timekeeping mechanisms in biology. We discuss recent findings and the open questions in the field and highlight the use of in vitro systems as tools to investigate cell-autonomous control as well as the coordination of temporal mechanisms within tissues. Further, we discuss the relevance of studying tempo for tissue transplantation, homeostasis and lifespan.

scholarly journals Mating and blood-feeding induce transcriptome changes in the spermathecae of the yellow fever mosquito Aedes aegypti

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Carolina Camargo ◽  
Yasir H. Ahmed-Braimah ◽  
I. Alexandra Amaro ◽  
Laura C. Harrington ◽  
Mariana F. Wolfner ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Blood Meal ◽  
Transcriptional Response ◽  
Blood Feeding ◽  
Sperm Storage ◽  
Biological Processes ◽  
Gene Products ◽  
Heme Peroxidase ◽  
Males And Females

Abstract Aedes aegypti mosquitoes are the primary vectors of numerous viruses that impact human health. As manipulation of reproduction has been proposed to suppress mosquito populations, elucidation of biological processes that enable males and females to successfully reproduce is necessary. One essential process is female sperm storage in specialized structures called spermathecae. Aedes aegypti females typically mate once, requiring them to maintain sperm viably to fertilize eggs they lay over their lifetime. Spermathecal gene products are required for Drosophila sperm storage and sperm viability, and a spermathecal-derived heme peroxidase is required for long-term Anopheles gambiae fertility. Products of the Ae. aegypti spermathecae, and their response to mating, are largely unknown. Further, although female blood-feeding is essential for anautogenous mosquito reproduction, the transcriptional response to blood-ingestion remains undefined in any reproductive tissue. We conducted an RNAseq analysis of spermathecae from unfed virgins, mated only, and mated and blood-fed females at 6, 24, and 72 h post-mating and identified significant differentially expressed genes in each group at each timepoint. A blood-meal following mating induced a greater transcriptional response in the spermathecae than mating alone. This study provides the first view of elicited mRNA changes in the spermathecae by a blood-meal in mated females.

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