scholarly journals Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

FACETS ◽  
2017 ◽  
Vol 2 (2) ◽  
pp. 610-641 ◽  
Author(s):  
Rebekah A. Oomen ◽  
Jeffrey A. Hutchings
Keyword(s):  
Climate Change ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Environmental Variability ◽  
Global Climate ◽  
Genetic Research ◽  
Model Organisms ◽  
Rna Seq ◽  
Transcriptomic Responses ◽  
Ecological Importance

The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.

The Legal Regime of the Technologies and Products Obtained Using GMOs: Discussion Questions

Legal Concept ◽  
2021 ◽  
pp. 195-204
Author(s):  
Alexey Anisimov ◽  
◽  
Olga Popova ◽  
Keyword(s):  
Climate Change ◽  
Global Climate ◽  
Genetically Modified ◽  
Genetic Research ◽  
World Market ◽  
Legal Regulation ◽  
Legal Analysis ◽  
Legal Regime ◽  
Legal Method ◽  
The World

Introduction: the paper examines the problems associated with the definition of the legal regime of the technologies and products obtained using GMOs. The experts in the field of genetics have not yet come to an unambiguous conclusion about the degree of harm or benefit of products obtained using genetic modifications. Russia has strict restrictive measures for the production of genetically modified products. Consequently, there is virtually no market for genetically modified seeds produced in Russia. Nevertheless, the world is actively developing industries for the production of genetically modified agricultural products, and the market for the production of seeds is “captured” by a small number of foreign companies. On the other hand, climate change dictates the inevitability of using genetically modified products, the need to accelerate genetic research, and the production of GMO seeds and food. In this context, the authors set a goal to find a compromise (balanced) legal regulation of the legal regime of the technologies and products obtained using GMOs. Methods: the methodological framework for the research is a set of methods of scientific cognition, among which the formal-legal method and the method of comparative legal analysis are the leading positions. Results: the authors propose to consider the bans or support for GMO products in the context of trends in global climate change and ensuring food security. The authors have made a comparative analysis of the provisions of the international norms and the Russian legislation on the research and application of GMO technologies and products, which helped to identify an unbalanced legal regulation of the use of the GMO technologies in Russia, which reduces its competitiveness in this area on the world market. Conclusions: the Russian legislation needs to minimize this legal imbalance, which puts researchers in the field of plant genetics and producers of GMO seeds and food in unequal (worse) conditions. The legal regulation should ensure the coexistence of organic (environmentally friendly) agriculture, traditional agriculture, and the use of the GMO technologies; the introduction of special labeling of GMO products; the broadening of the powers of regional authorities in the use of GMO technologies; as well as the application of the principle of “traceability” to GMO products.

scholarly journals Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland

Marine Drugs ◽  
2020 ◽  
Vol 18 (4) ◽  
pp. 186
Author(s):  
Guoyong Yan ◽  
Jin Sun ◽  
Zishuai Wang ◽  
Pei-Yuan Qian ◽  
Lisheng He
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Lysyl Oxidase ◽  
Enrichment Analysis ◽  
Salivary Secretion ◽  
Cement Gland ◽  
Differentially Expressed ◽  
Model Organisms ◽  
Rna Seq ◽  
Secretion Pathway

Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The salivary secretion pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes, implying that the secretion of cyprid adhesive might be analogous to that of saliva. Lysyl oxidase had a higher expression level in the cement glands and was speculated to function in the curing of cyprid adhesive. Furthermore, the KEGG enrichment analysis of the 352 proteins identified in the cement gland proteome partially confirmed the comparative transcriptomic results. These results present insights into the molecular mechanisms underlying the synthesis, secretion and curing of barnacle cyprid adhesive and provide potential molecular targets for the development of environmentally friendly antifouling compounds.

Comparative transcriptome profiling in human bicuspid aortic valve disease using RNA sequencing

2015 ◽  
Vol 47 (3) ◽  
pp. 75-87 ◽  
Author(s):  
Ratnasari Padang ◽  
Richard D. Bagnall ◽  
Tatiana Tsoutsman ◽  
Paul G. Bannon ◽  
Christopher Semsarian
Keyword(s):  
Aortic Valve ◽  
Rna Sequencing ◽  
Bicuspid Aortic Valve ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Common Complication ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Calcific Aortic Stenosis ◽  
Phenotype Heterogeneity

Intrinsic valvular degeneration and dysfunction is the most common complication of bicuspid aortic valve (BAV) disease. Phenotypically, it ranges from calcific aortic stenosis to redundant or prolapsing regurgitant leaflets. The underlying molecular mechanism underpinning phenotype heterogeneity of valvular degeneration in BAV is poorly understood. We used RNA sequencing (RNA-seq) to identify genes and pathways responsible for the development of valvular degeneration in BAV, compared with tricuspid aortic valve (TAV). Comparative transcriptome analysis was performed on total RNA of aortic valve tissues of patients with diseased BAV ( n = 5) and calcified TAV ( n = 3). RNA-seq findings were validated by RT-qPCR. A total of 59 and 177 genes were significantly up- and downregulated, respectively, in BAV compared with TAV. Hierarchical clustering indicated heterogeneity within the BAV group, separating those with heavy calcification (BAVc) from those with redundant leaflets and/or minimal calcification (BAVr). Interestingly, the gene expression profile of the BAVc group closely resembled the TAV, with shared up- and downregulation of inflammatory and NOTCH1 signaling pathways, respectively. Downregulation of matrix protease ADAMTS9 and protein aggrecan were observed in BAVr compared with TAV. Dysregulation of fetal gene programs were also present, with notable downregulation of SEMA6B and SEMA3F in BAVr and BAVc compared with TAV, respectively. Upregulation of TBX20 was observed exclusively in BAVr compared with BAVc. In conclusion, diverging molecular mechanisms underpin phenotype heterogeneity of valvular degeneration in BAV and data from the present study suggest that there may be shared mechanisms leading to calcification in BAV and TAV. Recognition of these pathways is fundamental to improve our understanding of the molecular basis of human BAV disease.

scholarly journals Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

2013 ◽  
Vol 80 (5) ◽  
pp. 1777-1786 ◽  
Author(s):  
Chengwei Luo ◽  
Luis M. Rodriguez-R ◽  
Eric R. Johnston ◽  
Liyou Wu ◽  
Lei Cheng ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Molecular Mechanisms ◽  
Cellulose Degradation ◽  
Global Climate ◽  
Soil Microbial Communities ◽  
Predictive Ability ◽  
Metagenomic Data ◽  
Data Sets ◽  
Soil Microbial

ABSTRACTSoil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO2production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.

scholarly journals Environmental Variability Of The Ponto-Caspian And Mediterranean Basins During The Last Climatic Macrocycle

2020 ◽  
Vol 13 (4) ◽  
pp. 6-23
Author(s):  
Tamara A. Yanina
Keyword(s):  
Climate Change ◽  
Late Pleistocene ◽  
Global Climate Change ◽  
Environmental Variability ◽  
Global Climate ◽  
Caspian Basin ◽  
Single System ◽  
Different Types ◽  
Mediterranean Regions ◽  
Basin System

This paper reviews reconstructions of the the evolution of the Ponto-Caspian basin system to certain parts of the Pontian-Mediterranean system in order to analyze their correlation and response of the systems to the global climate change. The Ponto–Caspian and Mediterranean basins belong to different types of water basins and evolved differently in the Late Pleistocene responding in different ways to the global climate change. The paleogeographic reconstructions and correlation analysis of the Late Pleistocene events (within the last climatic macrocycle) made it possible to view the evolution of the basins as parts of a single system allowing to identify certain specific features and patterns in their functioning. The study is based on the analysis and integration of the data published by numerous researchers including the author of the paper and numerous colleagues from many countries who have been studying the paleogeography of the Ponto-Caspian and Mediterranean regions in the Late Pleistocene.

scholarly journals Environmental variability during the last three millennia in the rain shadows of central Mexico

2021 ◽  
Vol 73 (1) ◽  
pp. A171220
Author(s):  
Gustavo Olivares-Casillas ◽  
Alex Correa-Metrio ◽  
Edyta Zawisza ◽  
Marta Wojewódka-Przybył ◽  
Maarten Blaauw ◽  
...  
Keyword(s):  
Climate Change ◽  
El Niño ◽  
High Frequency ◽  
Environmental Variability ◽  
El Nino ◽  
Global Climate ◽  
Anthropogenic Activities ◽  
Climatic Variability ◽  
Sea Surface ◽  
Ice Age

The last three millennia have been characterized by global temperature oscillations of around one Celsius degree, and high frequency variability on precipitation. Two main temperature anomalies have been reported worldwide, the Medieval Warm Period (MWP) and the Little Ice Age (LIA), characterized by higher and lower than average temperatures, respectively. Precipitation variability has been mostly associated with El Niño anomalies in the Equatorial Pacific. These global variability modes have been modulated by regional factors such as sea surface temperatures and their interaction with continental landmasses. Understanding regional responses to these anomalies would shed light on ecosystem response to environmental variability, a paramount tool for conservation purposes on the light of modern climate change. Here we present a 3,000-year sedimentary record from Lake Metztitlán, located in a Biosphere Reserve under the rain shadow of the Sierra Madre Oriental. Cladoceran and geochemical analyses were used to reconstruct lacustrine dynamics through the time period encompassed by the record. Our record points to highly dynamic lacustrine systems, coupled with global and regional climatic variability. In Metztitlán, the MWP was associated with low lake levels and a high torrentiality of the precipitation reflected in high-frequency peaks of detrital material. The LIA was associated with an enlarged water body, probably as a result of lower evapotranspiration. Overall, global climatic variability resulted in high variability of regional precipitation and detrital input in the Metztitlán region, in turn associated with changes in lake morphometry and depth. Our record highlights the vulnerability of the area to changes in sea surface temperature of the Gulf of Mexico, and to changes in the frequency of El Niño events. Although the effects of global climate change in the region are inescapable, our results emphasize the importance of controlling anthropogenic activities as an additional source of pressure on the regional ecosystems.

scholarly journals RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

2018 ◽  
Vol 143 (3) ◽  
pp. 194-206 ◽  
Author(s):  
Takanori Takeuchi ◽  
Miwako Cecile Matsushita ◽  
Soichiro Nishiyama ◽  
Hisayo Yamane ◽  
Kiyoshi Banno ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Selection Strategy ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Screening Criteria ◽  
Physiological Processes ◽  
Transcription Factor Genes

Endodormancy release and the fulfillment of the chilling requirement (CR) are critical physiological processes that enable uniform blooming in fruit tree species, including apple (Malus ×domestica). However, the molecular mechanisms underlying these traits have not been fully characterized. The objective of this study was to identify potential master regulators of endodormancy release and the CR in apple. We conducted RNA-Sequencing (RNA-seq) analyses and narrowed down the number of candidates among the differentially expressed genes (DEGs) based on the following two strict screening criteria: 1) the gene must be differentially expressed between endodormant and ecodormant buds under different environmental conditions and 2) the gene must exhibit chill unit (CU)–correlated expression. The results of our cluster analysis suggested that global expression patterns varied between field-grown buds and continuously chilled buds, even though they were exposed to similar amounts of chilling and were expected to have a similar dormancy status. Consequently, our strict selection strategy resulted in narrowing down the number of possible candidates and identified the DEGs strongly associated with the transition between dormancy stages. The genes included four transcription factor genes, PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), FLOWERING LOCUS C (FLC)-LIKE, APETALLA2 (AP2)/ETHYLENE-RESPONSIVE 113 (ERF113), and MYC2. Their expressions were upregulated during endodormancy release, and were correlated with the CU, suggesting that these transcription factors are closely associated with chilling-mediated endodormancy release in apple.

scholarly journals Combining Multiple RNA-Seq Data Analysis Algorithms Using Machine Learning Improves Differential Isoform Expression Analysis

2021 ◽  
Vol 4 (4) ◽  
pp. 68
Author(s):  
Alexandros C. Dimopoulos ◽  
Konstantinos Koukoutegos ◽  
Fotis E. Psomopoulos ◽  
Panagiotis Moulos
Keyword(s):  
Machine Learning ◽  
Data Analysis ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Performance Metrics ◽  
Machine Learning Techniques ◽  
Integrative Approach ◽  
Rna Seq ◽  
Isoform Expression ◽  
Differential Isoform Expression

RNA sequencing has become the standard technique for high resolution genome-wide monitoring of gene expression. As such, it often comprises the first step towards understanding complex molecular mechanisms driving various phenotypes, spanning organ development to disease genesis, monitoring and progression. An advantage of RNA sequencing is its ability to capture complex transcriptomic events such as alternative splicing which results in alternate isoform abundance. At the same time, this advantage remains algorithmically and computationally challenging, especially with the emergence of even higher resolution technologies such as single-cell RNA sequencing. Although several algorithms have been proposed for the effective detection of differential isoform expression from RNA-Seq data, no widely accepted golden standards have been established. This fact is further compounded by the significant differences in the output of different algorithms when applied on the same data. In addition, many of the proposed algorithms remain scarce and poorly maintained. Driven by these challenges, we developed a novel integrative approach that effectively combines the most widely used algorithms for differential transcript and isoform analysis using state-of-the-art machine learning techniques. We demonstrate its usability by applying it on simulated data based on several organisms, and using several performance metrics; we conclude that our strategy outperforms the application of the individual algorithms. Finally, our approach is implemented as an R Shiny application, with the underlying data analysis pipelines also available as docker containers.

scholarly journals The HPA stress axis shapes aging rates in long-lived, social mole-rats

2020 ◽  
Author(s):  
Arne Sahm ◽  
Steve Hoffmann ◽  
Philipp Koch ◽  
Yoshiyuki Henning ◽  
Martin Bens ◽  
...  
Keyword(s):  
Life Expectancy ◽  
Sexual Activity ◽  
Molecular Mechanisms ◽  
The Other ◽  
Model Organisms ◽  
Stress Axis ◽  
Rna Seq ◽  
Independent Evidence ◽  
Hypothalamic Pituitary Adrenal ◽  
Aging Rates

AbstractSexual activity and/or reproduction doubles life expectancy in the long-lived rodent genus Fukomys. To investigate the molecular mechanisms underlying this phenomenon, we analyzed a total of 636 RNA-seq samples across 15 tissues. This analysis suggests that the differences in life expectancy between reproductive and non-reproductive mole-rats are mainly caused by critical changes in the regulation of the hypothalamic-pituitary-adrenal stress axis, which we further substantiate with a series of independent evidence. In accordance with previous studies, the up-regulation of the proteasome and several so-called “anti-aging molecules”, such as DHEA, is also linked with enhanced life expectancy. On the other hand, several our results oppose crucial findings in short-lived model organisms. For example, we found the up-regulation of the IGF1/GH axis and several other anabolic processes to be compatible with a considerable lifespan prolongation. These contradictions question the extent to which findings from short-lived species can be transferred to longer-lived ones.

scholarly journals Towards mouse genetic-specific RNA-sequencing read mapping

2021 ◽  
Author(s):  
Nastassia Gobet ◽  
Maxime Jan ◽  
Paul Franken ◽  
Ioannis Xenarios
Keyword(s):  
Rna Sequencing ◽  
Genetic Variants ◽  
Complex Traits ◽  
Recombinant Inbred Lines ◽  
Reference Sequence ◽  
Model Organisms ◽  
Rna Seq ◽  
Genetic Population ◽  
The Impact ◽  
Mouse Genetic

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using RNA-sequencing (RNA-seq). Paradoxically, these variants between the samples are usually ignored at the beginning of RNA-seq analyses of many model organisms. This can skew the transcriptome estimates that are used later for downstream analyses, such as expression quantitative trait locus (eQTL) detection. Here, we assessed the impact of reference-based analysis on the transcriptome and eQTLs in a widely-used mouse genetic population: the BXD panel of recombinant inbred lines. We highlight existing reference bias in the transcriptome data analysis and propose practical solutions which combine available genetic variants, genotypes, and genome reference sequence. The use of custom BXD line references improved downstream analysis compared to classical genome reference. These insights would likely benefit genetic studies with a transcriptomic component and demonstrate that genome references might need to be reassessed and improved.

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