scholarly journals The Case for Standardising Gene Nomenclature Across Vertebrates

2021 ◽  
Author(s):  
Fiona M. McCarthy ◽  
Tamsin E.M. Jones ◽  
Anne E. Kwitek ◽  
Cynthia L. Smith ◽  
Peter D. Vize ◽  
...  
Keyword(s):  
Arginine Vasopressin ◽  
Comparative Studies ◽  
Evolutionary History ◽  
Scientific Literature ◽  
Gene Nomenclature ◽  
Journal Editors ◽  
Novel Gene ◽  
Genes Encoding ◽  
Current Guidelines

Standardized gene nomenclature supports unambiguous communication and identification of the scientific literature associated with genes. To support the increasing number of annotated genomes that are now available for comparative studies, gene nomenclature authorities coordinate the assignment of approved gene names that can be readily propagated across species without losing their sense of meaning. Theofanopoulou et al (Theofanopoulou et al. 2021) propose nomenclature changes to the genes encoding oxytocin and arginine vasopressin and their receptors which would hinder comparative studies and literature identification. Instead, we propose minor updates to the current approved nomenclature of these vertebrate genes to better reflect their evolutionary history, without confusing the literature that already exists around these well-studied genes. We encourage authors to work with nomenclature committees to ensure any novel gene names fit current guidelines so that their publications can be readily indexed and made accessible. Moreover, we call on journal editors and reviewers to help support communication and indexing of gene-related publications by ensuring that standardized gene nomenclature is routinely used.

Working with psychology journal editors to correct problems in the scientific literature.

2020 ◽  
Vol 61 (4) ◽  
pp. 342-348
Author(s):  
Harris L. Friedman ◽  
Douglas A. MacDonald ◽  
James C. Coyne
Keyword(s):  
Scientific Literature ◽  
Journal Editors

A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 613-621 ◽  
Author(s):  
Douglas R Dorer ◽  
Jamie A Rudnick ◽  
Etsuko N Moriyama ◽  
Alan C Christensen
Keyword(s):  
Phylogenetic Analysis ◽  
Drosophila Melanogaster ◽  
Anopheles Gambiae ◽  
Evolutionary History ◽  
Codon Bias ◽  
Good Target ◽  
The Family ◽  
Genes Encoding ◽  
And Function ◽  
Gambiae Genome

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

scholarly journals Identification of Genes Encoding Antimicrobial Proteins in Langerhans Cells

2021 ◽  
Vol 12 ◽  
Author(s):  
Aislyn Oulee ◽  
Feiyang Ma ◽  
Rosane M. B. Teles ◽  
Bruno J. de Andrade Silva ◽  
Matteo Pellegrini ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Host Defense ◽  
Langerhans Cells ◽  
Scientific Literature ◽  
Inflammatory Responses ◽  
Microbial Pathogens ◽  
Anatomical Location ◽  
Skin Infections ◽  
Antimicrobial Proteins ◽  
Genes Encoding

Langerhans cells (LCs) reside in the epidermis where they are poised to mount an antimicrobial response against microbial pathogens invading from the outside environment. To elucidate potential pathways by which LCs contribute to host defense, we mined published LC transcriptomes deposited in GEO and the scientific literature for genes that participate in antimicrobial responses. Overall, we identified 31 genes in LCs that encode proteins that contribute to antimicrobial activity, ten of which were cross-validated in at least two separate experiments. Seven of these ten antimicrobial genes encode chemokines, CCL1, CCL17, CCL19, CCL2, CCL22, CXCL14 and CXCL2, which mediate both antimicrobial and inflammatory responses. Of these, CCL22 was detected in seven of nine transcriptomes and by PCR in cultured LCs. Overall, the antimicrobial genes identified in LCs encode proteins with broad antibacterial activity, including against Staphylococcus aureus, which is the leading cause of skin infections. Thus, this study illustrates that LCs, consistent with their anatomical location, are programmed to mount an antimicrobial response against invading pathogens in skin.

scholarly journals River and Estuary Current Power Overview

2019 ◽  
Vol 7 (10) ◽  
pp. 365 ◽  
Author(s):  
Jorel Flambard ◽  
Yassine Amirat ◽  
Gilles Feld ◽  
Mohamed Benbouzid ◽  
Nicolas Ruiz
Keyword(s):  
Comparative Studies ◽  
Scientific Literature ◽  
River Estuary ◽  
Research Interest ◽  
Power Sector ◽  
Primary Interest ◽  
Energy Potential ◽  
Industrial Projects ◽  
River Current ◽  
Development Prospects

This paper presents a review of the stream current power sector, with a distinction made between the marine (MCP) and the river/estuary current power (RECP). Although scientific literature about MCP is actually well defined, that about RECP seems small, though this domain has some research interest. This paper has thus a special emphasis on this latter, with comparative studies done between these domains. The assessment of the academic and industrial interests for the RECP is first addressed, based on two main scientific resources and a qualitative highlight of its potential. Then, a review of actual constraints restricting its development is introduced, followed by a non-exhaustive presentation of industrial projects. Finally, some development prospects allowing constraints to be mitigated are proposed. Globally, MCP and RECP are treated unconcernedly, with a primary interest on the mechanical converter study and the location energy potential estimation. It has been highlighted that countries with RECP potential are more plentiful, and that undertaken projects can be classified mainly into two categories following the nominal power of the production unit. Furthermore, the river current power growth has been confirmed in recent years, with a majority part of patented hydrokinetic technologies, although commercial deployments are still scarce.

scholarly journals Non-trophic Functional Ecology of Vertebrate Teeth: A Review

2020 ◽  
Vol 60 (3) ◽  
pp. 665-675
Author(s):  
Courtney E Gorman ◽  
C Darrin Hulsey
Keyword(s):  
Comparative Studies ◽  
Evolutionary History ◽  
Functional Ecology ◽  
Developmental Genetics ◽  
Ecological Diversity ◽  
Functional Importance ◽  
Substantial Role ◽  
History Of

Synopsis Teeth are critical to the functional ecology of vertebrate trophic abilities, but are also used for a diversity of other non-trophic tasks. Teeth can play a substantial role in how animals move, manipulate their environment, positively interact with conspecifics, antagonistically interact with other organisms, and sense the environment. We review these non-trophic functions in an attempt to place the utility of human and all other vertebrate dentitions in a more diverse framework that emphasizes an expanded view of the functional importance and ecological diversity of teeth. In light of the extensive understanding of the developmental genetics, trophic functions, and evolutionary history of teeth, comparative studies of vertebrate dentitions will continue to provide unique insights into multi-functionality, many-to-one mapping, and the evolution of novel abilities.

scholarly journals Updated Sequence Information and Proposed Nomenclature for blaTEM Genes and Their Promoters

2000 ◽  
Vol 44 (11) ◽  
pp. 3232-3234 ◽  
Author(s):  
V. Leflon-Guibout ◽  
B. Heym ◽  
M.-H. Nicolas-Chanoine
Keyword(s):  
Genetic Variability ◽  
Nucleotide Sequences ◽  
Sequence Information ◽  
Gene Nomenclature ◽  
Different Types ◽  
Genes Encoding

ABSTRACT The nucleotide sequences of 59 bla TEM genes encoding inhibitor-resistant TEM enzymes showed great genetic variability and were associated with different types of promoters. These findings led us to suggest an updatedbla TEM gene nomenclature based on the origin of the bla TEM gene (bla TEM-1A, bla TEM-1B,bla TEM-1C, bla TEM-1D,bla TEM-1E, andbla TEM-1F) and the promoter type.

scholarly journals Common mistakes in data presentation and statistical analysis: how can the BioStat Decision Tool help?

2013 ◽  
Author(s):  
Siouxsie Wiles ◽  
Anne L Bishop
Keyword(s):  
Scientific Literature ◽  
Statistical Tests ◽  
Statistical Test ◽  
Statistical Techniques ◽  
Sample Collection ◽  
Decision Tool ◽  
Data Presentation ◽  
Journal Editors ◽  
Molecular Microbiology ◽  
User Friendly

As medical and molecular microbiologists who regularly read the scientific literature, it is our impression that many published papers contain data that is inappropriately presented and/or analysed. This is borne out by a number of studies which indicate that typically at least half of published scientific articles that use statistical methods contain statistical errors. While there are an abundance of resources dedicated to explaining statistics to biologists, the evidence would suggest that they are largely ineffective. These resources tend to focus on how particular statistical tests work, with reams of complicated-looking mathematical formulae. In addition, many statisticians are unfamiliar with the application of statistical techniques to molecular microbiology, instead telling us we need more samples, which can be difficult both ethically and practically in fields that include animal work and painstaking sample collection. In an age where performing a statistical test merely requires clicking a button in a computer programme, it could be argued that what the vast majority of biologists need is not mathematical formulae but simple guidance on which buttons to click. We have developed an easy to follow decision chart that guides biologists through the statistical maze. Our practical and user friendly chart should prove useful not only to active researchers, but also to journal editors and reviewers to rapidly determine if data presented in a submitted manuscript has been correctly analysed.

scholarly journals Common mistakes in data presentation and statistical analysis: how can the BioStat Decision Tool help?

2013 ◽  
Author(s):  
Siouxsie Wiles ◽  
Anne L Bishop
Keyword(s):  
Scientific Literature ◽  
Statistical Tests ◽  
Statistical Test ◽  
Statistical Techniques ◽  
Sample Collection ◽  
Decision Tool ◽  
Data Presentation ◽  
Journal Editors ◽  
Molecular Microbiology ◽  
User Friendly

As medical and molecular microbiologists who regularly read the scientific literature, it is our impression that many published papers contain data that is inappropriately presented and/or analysed. This is borne out by a number of studies which indicate that typically at least half of published scientific articles that use statistical methods contain statistical errors. While there are an abundance of resources dedicated to explaining statistics to biologists, the evidence would suggest that they are largely ineffective. These resources tend to focus on how particular statistical tests work, with reams of complicated-looking mathematical formulae. In addition, many statisticians are unfamiliar with the application of statistical techniques to molecular microbiology, instead telling us we need more samples, which can be difficult both ethically and practically in fields that include animal work and painstaking sample collection. In an age where performing a statistical test merely requires clicking a button in a computer programme, it could be argued that what the vast majority of biologists need is not mathematical formulae but simple guidance on which buttons to click. We have developed an easy to follow decision chart that guides biologists through the statistical maze. Our practical and user friendly chart should prove useful not only to active researchers, but also to journal editors and reviewers to rapidly determine if data presented in a submitted manuscript has been correctly analysed.

scholarly journals Beyond conflict: exploring the spectrum of human–wildlife interactions and their underlying mechanisms

Oryx ◽  
2019 ◽  
Vol 54 (5) ◽  
pp. 621-628
Author(s):  
Saloni Bhatia ◽  
Stephen Mark Redpath ◽  
Kulbhushansingh Suryawanshi ◽  
Charudutt Mishra
Keyword(s):  
Evolutionary History ◽  
Scientific Literature ◽  
Influential Factors ◽  
Wild Animals ◽  
Knowledge Database ◽  
Wildlife Conflict ◽  
Nuanced Understanding ◽  
Underlying Mechanisms ◽  
Human Wildlife Conflict ◽  
Wildlife Impacts

AbstractHumans have lived alongside and interacted with wild animals throughout evolutionary history. Even though wild animals can damage property, or injure humans and domesticated animals, not all interactions between humans and wildlife are negative. Yet, research has tended to focus disproportionately on negative interactions leading to negative outcomes, labelling this human–wildlife conflict. Studies have identified several factors, ranging from gender, religion, socio-economics and literacy, which influence people's responses to wildlife. We used the ISI Web of Knowledge database to assess quantitatively how human–wildlife interactions are framed in the scientific literature and to understand the hypotheses that have been invoked to explain these. We found that the predominant focus of research was on human–wildlife conflict (71%), with little coverage of coexistence (2%) or neutral interactions (8%). We suggest that such a framing is problematic as it can lead to biases in conservation planning by failing to consider the nuances of people's relationships with wildlife and the opportunities that exist for conservation. We propose a typology of human responses to wildlife impacts, ranging from negative to positive, to help moderate the disproportionate focus on conflict. We suggest that standardizing terminology and considering interactions beyond those that are negative can lead to a more nuanced understanding of human–wildlife relations and help promote greater coexistence between people and wildlife. We also list the various influential factors that are reported to shape human–wildlife interactions and, to generate further hypotheses and research, classify them into 55 proximate (correlates) and five ultimate (mechanisms) factors.

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