scholarly journals Use of Heat Stress Responsive Gene Expression Levels for Early Selection of Heat Tolerant Cabbage (Brassica oleracea L.)

2013 ◽  
Vol 14 (6) ◽  
pp. 11871-11894 ◽  
Author(s):  
Hyun Park ◽  
Won Jung ◽  
Sang Lee ◽  
Jun Song ◽  
Suk-Yoon Kwon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Brassica Oleracea ◽  
Early Selection ◽  
Expression Levels ◽  
Heat Tolerant ◽  
Responsive Gene ◽  
Brassica Oleracea L ◽  
Gene Expression Levels ◽  
Selection Of

scholarly journals Targeted reduction of highly abundant transcripts with pseudo-random primers

2015 ◽  
Author(s):  
Ophélie Arnaud ◽  
Sachi Kato ◽  
Stéphane Poulain ◽  
Charles Plessy
Keyword(s):  
Gene Expression ◽  
Reverse Transcription ◽  
Flexible Tool ◽  
Expression Levels ◽  
Random Primers ◽  
Sequencing Cost ◽  
Transcriptome Diversity ◽  
Gene Expression Levels ◽  
Selection Of

Transcriptome studies based on quantitative sequencing estimate gene expression levels by measuring the abundance of target RNAs in libraries of sequence reads. The sequencing cost is proportional to the total number of sequenced reads. Therefore, in order to cover rare RNAs, considerable quantities of abundant and identical reads have to be sequenced. This major limitation can be lifted by strategies used to deplete the library from some of the most abundant sequences. However, these strategies involve either an extra handling of the input RNA sample, or the use of a large number of reverse-transcription primers (termed "not-so-random primers"), which are costly to synthetize and customize. Here, we demonstrate that with a precise selection of only 40 "pseudo-random" reverse-transcription primers, it is possible to decrease the rate of undesirable abundant sequences within a library without affecting the transcriptome diversity. "Pseudo-random" primers are simple to design, and therefore are a flexible tool for enriching transcriptome libraries in rare transcripts sequences.

scholarly journals Gene Expression and Photophysiological Changes in Pocillopora acuta Coral Holobiont Following Heat Stress and Recovery

2020 ◽  
Vol 8 (8) ◽  
pp. 1227
Author(s):  
Rosa Celia Poquita-Du ◽  
Yi Le Goh ◽  
Danwei Huang ◽  
Loke Ming Chou ◽  
Peter A. Todd
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Target Genes ◽  
Differential Expression Analysis ◽  
Heat Exposure ◽  
Small Heat Shock Protein ◽  
Expression Levels ◽  
Chl A ◽  
Coral Holobiont ◽  
Gene Expression Levels

The ability of corals to withstand changes in their surroundings is a critical survival mechanism for coping with environmental stress. While many studies have examined responses of the coral holobiont to stressful conditions, its capacity to reverse responses and recover when the stressor is removed is not well-understood. In this study, we investigated among-colony responses of Pocillopora acuta from two sites with differing distance to the mainland (Kusu (closer to the mainland) and Raffles Lighthouse (further from the mainland)) to heat stress through differential expression analysis of target genes and quantification of photophysiological metrics. We then examined how these attributes were regulated after the stressor was removed to assess the recovery potential of P. acuta. The fragments that were subjected to heat stress (2 °C above ambient levels) generally exhibited significant reduction in their endosymbiont densities, but the extent of recovery following stress removal varied depending on natal site and colony. There were minimal changes in chl a concentration and maximum quantum yield (Fv/Fm, the proportion of variable fluorescence (Fv) to maximum fluorescence (Fm)) in heat-stressed corals, suggesting that the algal endosymbionts’ Photosystem II was not severely compromised. Significant changes in gene expression levels of selected genes of interest (GOI) were observed following heat exposure and stress removal among sites and colonies, including Actin, calcium/calmodulin-dependent protein kinase type IV (Camk4), kinesin-like protein (KIF9), and small heat shock protein 16.1 (Hsp16.1). The most responsive GOIs were Actin, a major component of the cytoskeleton, and the adaptive immune-related Camk4 which both showed significant reduction following heat exposure and subsequent upregulation during the recovery phase. Our findings clearly demonstrate specific responses of P. acuta in both photophysiological attributes and gene expression levels, suggesting differential capacity of P. acuta corals to tolerate heat stress depending on the colony, so that certain colonies may be more resilient than others.

scholarly journals Effects of methionine supplementation on the expression of oxidative stress-related genes in acute heat stress-exposed broilers

2015 ◽  
Vol 113 (4) ◽  
pp. 549-559 ◽  
Author(s):  
Ana Paula Del Vesco ◽  
Eliane Gasparino ◽  
Daiane de Oliveira Grieser ◽  
Vittor Zancanela ◽  
Maria Amélia Menck Soares ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Thermal Comfort ◽  
Expression Level ◽  
Glutathione Synthetase ◽  
Environment Interaction ◽  
Expression Levels ◽  
Methionine Supplementation ◽  
Stress Related Genes ◽  
Gene Expression Levels

The aim of the present study was to evaluate the effects of heat stress (HS) and methionine supplementation on the markers of stress and on the gene expression levels of uncoupling proteins (UCP), betaine–homocysteine methyltransferase (BHMT), cystathionine β-synthase (CBS), glutathione synthetase (GSS) and glutathione peroxidase 7 (GPx7). Broilers from 1 to 21 d and from 22 to 42 d of age were divided into three treatment groups related to methionine supplementation: without methionine supplementation (MD); recommended level of methionine supplementation (DL1); excess methionine supplementation (DL2). The broilers were either kept at a comfortable thermal temperature or exposed to HS (38°C for 24 h). During the starter period, we observed the effects of the interaction between diet and environment on the gene expression levels of UCP, BHMT and GSS. Higher gene expression levels of UCP and BHMT were observed in broilers that were maintained at thermal comfort conditions and received the MD diet. HS broilers fed the DL1 and DL2 diets had the highest expression level of GSS. The expression levels of the CBS and GPx7 genes were influenced by both the environment and methionine supplementation. During the grower period, the gene expression levels of BHMT, CBS, GSS and GPx7 were affected by the diet × environment interaction. A higher expression level of BHMT was observed in broilers maintained at thermal comfort conditions and on the MD diet. HS induced higher expression levels of CBS, GSS and GPx7 in broilers that received the DL1 and DL2 diets. The present results suggest that under HS conditions, methionine supplementation could mitigate the effects of stress, since methionine contributed to the increased expression levels of genes related to antioxidant activity.

scholarly journals A Sparse and Low-Rank Regression Model for Identifying the Relationships Between DNA Methylation and Gene Expression Levels in Gastric Cancer and the Prediction of Prognosis

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 854
Author(s):  
Yishu Wang ◽  
Lingyun Xu ◽  
Dongmei Ai
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Dna Methylation ◽  
Regression Model ◽  
The Cancer Genome Atlas ◽  
Low Rank ◽  
Expression Levels ◽  
Rank Regression ◽  
Prediction Of Prognosis ◽  
Gene Expression Levels

DNA methylation is an important regulator of gene expression that can influence tumor heterogeneity and shows weak and varying expression levels among different genes. Gastric cancer (GC) is a highly heterogeneous cancer of the digestive system with a high mortality rate worldwide. The heterogeneous subtypes of GC lead to different prognoses. In this study, we explored the relationships between DNA methylation and gene expression levels by introducing a sparse low-rank regression model based on a GC dataset with 375 tumor samples and 32 normal samples from The Cancer Genome Atlas database. Differences in the DNA methylation levels and sites were found to be associated with differences in the expressed genes related to GC development. Overall, 29 methylation-driven genes were found to be related to the GC subtypes, and in the prognostic model, we explored five prognoses related to the methylation sites. Finally, based on a low-rank matrix, seven subgroups were identified with different methylation statuses. These specific classifications based on DNA methylation levels may help to account for heterogeneity and aid in personalized treatments.

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