Linking adaptation, delimitation of evolutionarily significant units (ESUs), and gene function: a case study using hemlock looper ecotypes

2013 ◽  
Vol 38 (2) ◽  
pp. 428-439 ◽  
Author(s):  
LISA M. LUMLEY ◽  
MICHEL CUSSON
Keyword(s):  
Gene Function ◽  
Evolutionarily Significant Units ◽  
Hemlock Looper

A Case Study - NeuBase Therapeutics, Inc.

2021 ◽  
Vol 26 (2) ◽  
Author(s):  
Dietrich A. Stephan
Keyword(s):  
Gene Function ◽  
Genetic Defects ◽  
New Class ◽  
Genetic Revolution

NeuBase is accelerating the genetic revolution by developing a new class of precision genetic medicines which can be designed to increase, decrease, or change gene function, as appropriate, to resolve genetic defects that drive disease.

Hierarchical multi-label classification with SVMs: A case study in gene function prediction

2014 ◽  
Vol 18 (4) ◽  
pp. 717-738 ◽  
Author(s):  
Peerapon Vateekul ◽  
Miroslav Kubat ◽  
Kanoksri Sarinnapakorn
Keyword(s):  
Gene Function ◽  
Function Prediction ◽  
Gene Function Prediction

scholarly journals Functional genomics in the wild: a case study with paper wasps shows challenges and prospects for RNA interference in ecological systems

Genome ◽  
2018 ◽  
Vol 61 (4) ◽  
pp. 266-272 ◽  
Author(s):  
S.A. Weiner ◽  
A.G. Geffre ◽  
A.L. Toth
Keyword(s):  
Rna Interference ◽  
Functional Genomics ◽  
Gene Function ◽  
Ecological Model ◽  
Model Organisms ◽  
Natural Environments ◽  
Paper Wasps ◽  
Fatty Acid Binding ◽  
In The Wild

RNA interference (RNAi) is a useful tool to assess gene function by knocking down expression of a target gene and has been used successfully in domestic and laboratory organisms. However, the use of RNAi for functional genomics has not fully extended into ecological model organisms in natural environments. Assessment of gene function in the wild is important because gene function can be environmentally and context dependent. Here, we present a case study using RNAi to assess gene function in wild paper wasps Polistes metricus, to test roles for two candidate genes (NADH dehydrogenase (NADHdh) and retinoid and fatty acid binding protein (RfaBp)) in the development of reproductive castes. Previous studies have shown that these genes are upregulated in larvae that become queens compared to workers, but this pattern was reversed in the laboratory, making field-based studies necessary. We orally administered dsRNA to larvae in field colonies and found evidence of a short-term knockdown followed by a compensatory rebound in expression for RfaBp. We also observed the predicted worker-like decrease in lipid stores in NADHdh dsRNA treated wasps, suggesting a possible role for NADHdh in caste development. We discuss our results in the context of challenges for using RNAi for functional genomics in ecological model organisms in the field.

scholarly journals LSTrAP-Cloud: A User-friendly Cloud Computing Pipeline to Infer Co-functional and Regulatory Networks

2020 ◽  
Author(s):  
Qiao Wen Tan ◽  
William Goh ◽  
Marek Mutwil
Keyword(s):  
Rna Sequencing ◽  
Gene Function ◽  
Regulatory Networks ◽  
Large Scale ◽  
Function Prediction ◽  
Sequencing Data ◽  
Gene Function Prediction ◽  
Analysis Pipeline ◽  
User Friendly

AbstractAs genomes become more and more available, gene function prediction presents itself as one of the major hurdles in our quest to extract meaningful information on the biological processes genes participate in. In order to facilitate gene function prediction, we show how our user-friendly pipeline, Large-Scale Transcriptomic Analysis Pipeline in Cloud (LSTrAP-Cloud), can be useful in helping biologists make a shortlist of genes that they might be interested in. LSTrAP-Cloud is based on Google Colaboratory and provides user-friendly tools that process and quality-control RNA sequencing data streamed from the European Sequencing Archive. LSTRAP-Cloud outputs a gene co-expression network that can be used to identify functionally related genes for any organism with a sequenced genome and publicly available RNA sequencing data. Here, we used the biosynthesis pathway of Nicotiana tabacum as a case study to demonstrate how enzymes, transporters and transcription factors involved in the synthesis, transport and regulation of nicotine can be identified using our pipeline.

scholarly journals Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

Database ◽  
2016 ◽  
Vol 2016 ◽  
pp. baw155 ◽  
Author(s):  
Marc Feuermann ◽  
Pascale Gaudet ◽  
Huaiyu Mi ◽  
Suzanna E. Lewis ◽  
Paul D. Thomas
Keyword(s):  
Gene Ontology ◽  
Gene Function ◽  
Large Scale ◽  
Cellular Processes

The Genesis and Internal Dynamics of El Salvador's People's Revolutionary Army, 1970–1976

2014 ◽  
Vol 38 (01) ◽  
pp. 102-129
Author(s):  
ALBERTO MARTÍN ÁLVAREZ ◽  
EUDALD CORTINA ORERO
Keyword(s):  
Latin America ◽  
El Salvador ◽  
Early Years ◽  
Left Wing ◽  
Internal Dynamics ◽  
Internal Coherence ◽  
The 1960S

AbstractUsing interviews with former militants and previously unpublished documents, this article traces the genesis and internal dynamics of the Ejército Revolucionario del Pueblo (People's Revolutionary Army, ERP) in El Salvador during the early years of its existence (1970–6). This period was marked by the inability of the ERP to maintain internal coherence or any consensus on revolutionary strategy, which led to a series of splits and internal fights over control of the organisation. The evidence marshalled in this case study sheds new light on the origins of the armed Salvadorean Left and thus contributes to a wider understanding of the processes of formation and internal dynamics of armed left-wing groups that emerged from the 1960s onwards in Latin America.

Culture and the plasticity of perception

2020 ◽  
Vol 43 ◽  
Author(s):  
Michael Lifshitz ◽  
T. M. Luhrmann
Keyword(s):  
Cultural Context ◽  
Sensory Experience ◽  
Cultural Learning ◽  
The World

Abstract Culture shapes our basic sensory experience of the world. This is particularly striking in the study of religion and psychosis, where we and others have shown that cultural context determines both the structure and content of hallucination-like events. The cultural shaping of hallucinations may provide a rich case-study for linking cultural learning with emerging prediction-based models of perception.

Dual systems for all: Higher-order, role-based relational reasoning as a uniquely derived feature of human cognition

2019 ◽  
Vol 42 ◽  
Author(s):  
Daniel J. Povinelli ◽  
Gabrielle C. Glorioso ◽  
Shannon L. Kuznar ◽  
Mateja Pavlic
Keyword(s):  
Temporal Reasoning ◽  
Higher Order ◽  
Important Case ◽  
Human Cognition ◽  
Relational Reasoning ◽  
Dual Systems ◽  
First Order ◽  
Reasoning System ◽  
Role Based

Abstract Hoerl and McCormack demonstrate that although animals possess a sophisticated temporal updating system, there is no evidence that they also possess a temporal reasoning system. This important case study is directly related to the broader claim that although animals are manifestly capable of first-order (perceptually-based) relational reasoning, they lack the capacity for higher-order, role-based relational reasoning. We argue this distinction applies to all domains of cognition.

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