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.

Considering RNAi experimental design in parasitic helminths

Parasitology ◽  
2012 ◽  
Vol 139 (5) ◽  
pp. 589-604 ◽  
Author(s):  
JOHNATHAN J. DALZELL ◽  
NEIL D. WARNOCK ◽  
PAUL MCVEIGH ◽  
NIKKI J. MARKS ◽  
ANGELA MOUSLEY ◽  
...  
Keyword(s):  
Rna Interference ◽  
Experimental Design ◽  
Gene Function ◽  
Experimental Validation ◽  
Parasite Species ◽  
Model Organisms ◽  
Helminth Parasites ◽  
Parasitic Helminth ◽  
Parasitic Helminths ◽  
Parasite Biology

SUMMARYAlmost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.

scholarly journals RNA Interference of Dual Oxidase in the Plant Nematode Meloidogyne incognita

2005 ◽  
Vol 18 (10) ◽  
pp. 1099-1106 ◽  
Author(s):  
Manjula Bakhetia ◽  
Wayne Charlton ◽  
Howard J. Atkinson ◽  
Michael J. McPherson
Keyword(s):  
Rna Interference ◽  
Gene Function ◽  
Meloidogyne Incognita ◽  
Feeding Strategy ◽  
Model Organisms ◽  
Parasitic Nematodes ◽  
In Planta ◽  
Oxidase Gene ◽  
Dual Oxidase

RNA interference (RNAi) is a powerful tool for the analysis of gene function in model organisms such as the nematode Caenorhabditis elegans. Recent demonstrations of RNAi in plant parasitic nematodes provide a stimulus to explore the potential of using RNAi to investigate disruption of gene function in Meloidogyne incognita, one of the most important nematode pests of global agriculture. We have used RNAi to examine the importance of dual oxidases (peroxidase and NADPH oxidase), a class of enzyme associated with extracellular matrix cross-linking in C. elegans. RNAi uptake by M. incognita juveniles is highly efficient. In planta infection data show that a single 4-h preinfection treatment with double-stranded RNA derived from the peroxidase region of a dual oxidase gene has effects on gene expression that are phenotypically observable 35 days postinfection. This RNAi effect results in a reduction in egg numbers at 35 days of up to 70%. The in vitro feeding strategy provides a powerful tool for identifying functionally important genes, including those that are potential targets for the development of new agrochemicals or transgenic resistance strategies.

Functional Genomics in Xenopus laevis: Towards Transgene-Driven RNA Interference and Cell-Specific Transgene Expression

2003 ◽  
Vol 4 (8) ◽  
pp. 699-711 ◽  
Author(s):  
Ron Dirks ◽  
Gerrit Bouw ◽  
Rick Huizen ◽  
Eric Jansen ◽  
Gerard Martens
Keyword(s):  
Rna Interference ◽  
Xenopus Laevis ◽  
Functional Genomics ◽  
Transgene Expression

scholarly journals A Genome Scan for Quantitative Trait Loci in a Wild Population of Red Deer (Cervus elaphus)

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1863-1873 ◽  
Author(s):  
J Slate ◽  
P M Visscher ◽  
S MacGregor ◽  
D Stevens ◽  
M L Tate ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Cervus Elaphus ◽  
Quantitative Trait ◽  
Red Deer ◽  
Wild Population ◽  
Additive Genetic Variance ◽  
Model Organisms ◽  
A Genome ◽  
Trait Loci ◽  
In The Wild

Abstract Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

scholarly journals Functional genomics and proteomics of the cellular osmotic stress response in `non-model' organisms

2007 ◽  
Vol 210 (9) ◽  
pp. 1593-1601 ◽  
Author(s):  
D. Kultz ◽  
D. Fiol ◽  
N. Valkova ◽  
S. Gomez-Jimenez ◽  
S. Y. Chan ◽  
...  
Keyword(s):  
Stress Response ◽  
Osmotic Stress ◽  
Functional Genomics ◽  
Model Organisms ◽  
Genomics And Proteomics ◽  
Osmotic Stress Response

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.

Genome-Wide RNA Interference: Functional Genomics in the Postgenomics Era

2017 ◽  
Vol 2017 (9) ◽  
pp. pdb.top097550 ◽  
Author(s):  
Katerina Politi ◽  
Narendra Wajapeyee
Keyword(s):  
Rna Interference ◽  
Functional Genomics ◽  
Genome Wide

RNA Interference and Wheat Functional Genomics

2011 ◽  
pp. 285-308
Author(s):  
Pradeep Sharma ◽  
Rajender Singh
Keyword(s):  
Rna Interference ◽  
Functional Genomics
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