scholarly journals InvestigatinghspGene Expression in Liver ofChanna striatusunder Heat Stress for Understanding the Upper Thermal Acclimation

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Gopal Krishna Purohit ◽  
Arabinda Mahanty ◽  
Mrutyunjay Suar ◽  
Anil Prakash Sharma ◽  
Bimal Prasanna Mohanty ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Hot Spring ◽  
Expression Profiles ◽  
Transcript Level ◽  
Thermal Acclimation ◽  
Farmed Fish ◽  
Term Survival ◽  
Spring Runoff

Changes inhspgene expression profiles in murrelChanna striatusexperimentally exposed to temperature stress (36°C) for 4, 15, and 30 days were investigated; fish collected from aquaculture ponds and maintained in laboratory at the pond temperature (25 ± 1°C) served as control.Channacollected from a hot spring runoff (36°C) was included in the study to examine thehspprofiles beyond 30 days of exposure. Gene expression analyses of a battery ofhspsin liver tissues were carried out by quantitative RT-PCR and protein expressions were analyzed by immunoblotting.hspscould be grouped into three clusters based on similarity in response to heat stress:hsp70, hsp78,andhsp60, whose transcript level continued to increase with duration of exposure;hsp90andhsp110that increased to a much higher level and then decreased;hsp27andhsp47that did not significantly vary as compared to control. The results suggest that Hsp70, Hsp78, and Hsp60 are involved in thermal acclimation and long term survival at high temperature. Fish living in the hot spring runoff appears to continuously expresshspsthat can be approximated by long term induction ofhspsin farmed fish if temperature of their environment is raised to 36°C.

scholarly journals Transcriptome dynamics predict thermotolerance in Caenorhabditis elegans

2019 ◽  
Author(s):  
Katharina Jovic ◽  
Jacopo Grilli ◽  
Mark G. Sterken ◽  
Basten L. Snoek ◽  
Joost A. G. Riksen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Caenorhabditis Elegans ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Intrinsic Property ◽  
Recovery Process ◽  
Term Outcome ◽  
Term Survival ◽  
Long Term Outcome

AbstractBackgroundThe detrimental effects of a short bout of stress can persist, and potentially turn lethal, long after the return to normal conditions. Thermotolerance, which is the capacity of an organism to withstand relatively extreme temperatures, is influenced by the response during stress exposure, as well as the recovery process afterwards. While heat-shock response mechanisms have been studied intensively, predicting thermal tolerance remains a challenge.ResultsHere, we use the nematode Caenorhabditis elegans to measure transcriptional resilience to heat stress and predict thermotolerance. Using high dimensionality reduction techniques in combination with genome-wide gene expression profiles collected in three high resolution time-series during control, heat stress and recovery conditions, we infer a quantitative scale capturing the extent of stress-induced transcriptome dynamics in a single value. This scale provides a basis for evaluating transcriptome resilience, defined here as the ability to depart from stress-expression dynamics during recovery. Independent replication across multiple highly divergent genotypes reveals that the transcriptional resilience parameter measured after a spike in temperature is quantitatively linked to long-term survival after heat stress.ConclusionOur findings imply that thermotolerance is an intrinsic property that pre-determines long term outcome of stress and can be predicted by the transcriptional resilience parameter. Inferring the transcriptional resilience parameters of higher organisms could aid in evaluating rehabilitation strategies after stresses such as disease and trauma.

scholarly journals Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Katharina Jovic ◽  
Jacopo Grilli ◽  
Mark G. Sterken ◽  
Basten L. Snoek ◽  
Joost A. G. Riksen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Caenorhabditis Elegans ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Principal Component ◽  
Intrinsic Property ◽  
Term Outcome ◽  
Term Survival ◽  
Long Term Outcome

Abstract Background The detrimental effects of a short bout of stress can persist and potentially turn lethal, long after the return to normal conditions. Thermotolerance, which is the capacity of an organism to withstand relatively extreme temperatures, is influenced by the response during stress exposure, as well as the recovery process afterwards. While heat-shock response mechanisms have been studied intensively, predicting thermal tolerance remains a challenge. Results Here, we use the nematode Caenorhabditis elegans to measure transcriptional resilience to heat stress and predict thermotolerance. Using principal component analysis in combination with genome-wide gene expression profiles collected in three high-resolution time series during control, heat stress, and recovery conditions, we infer a quantitative scale capturing the extent of stress-induced transcriptome dynamics in a single value. This scale provides a basis for evaluating transcriptome resilience, defined here as the ability to depart from stress-expression dynamics during recovery. Independent replication across multiple highly divergent genotypes reveals that the transcriptional resilience parameter measured after a spike in temperature is quantitatively linked to long-term survival after heat stress. Conclusion Our findings imply that thermotolerance is an intrinsic property that pre-determines long-term outcome of stress and can be predicted by the transcriptional resilience parameter. Inferring the transcriptional resilience parameters of higher organisms could aid in evaluating rehabilitation strategies after stresses such as disease and trauma.

scholarly journals Whole blood gene expression within days after total-body irradiation predicts long term survival in Gottingen minipigs

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sunita Chopra ◽  
Maria Moroni ◽  
Jaleal Sanjak ◽  
Laurel MacMillan ◽  
Bernadette Hritzo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Total Body Irradiation ◽  
Whole Blood ◽  
Radiation Effects ◽  
Expression Profiles ◽  
Mass Casualty ◽  
Machine Learning Algorithms ◽  
Term Survival ◽  
Blood Gene Expression ◽  
Total Body

AbstractGottingen minipigs mirror the physiological radiation response observed in humans and hence make an ideal candidate model for studying radiation biodosimetry for both limited-sized and mass casualty incidents. We examined the whole blood gene expression profiles starting one day after total-body irradiation with increasing doses of gamma-rays. The minipigs were monitored for up to 45 days or time to euthanasia necessitated by radiation effects. We successfully identified dose- and time-agnostic (over a 1–7 day period after radiation), survival-predictive gene expression signatures derived using machine-learning algorithms with high sensitivity and specificity. These survival-predictive signatures fare better than an optimally performing dose-differentiating signature or blood cellular profiles. These findings suggest that prediction of survival is a much more useful parameter for making triage, resource-utilization and treatment decisions in a resource-constrained environment compared to predictions of total dose received. It should hopefully be possible to build such classifiers for humans in the future.

Predictive value of gene expression profiling for long-term survival after heart transplantation

2017 ◽  
Vol 41 ◽  
pp. 27-31 ◽  
Author(s):  
Buntaro Fujita ◽  
Emir Prashovikj ◽  
Uwe Schulz ◽  
Jochen Börgermann ◽  
Jakub Sunavsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heart Transplantation ◽  
Gene Expression Profiling ◽  
Predictive Value ◽  
Expression Profiling ◽  
Term Survival ◽  
Long Term Survival

scholarly journals Transcriptome-wide gene expression plasticity in Stipa grandis in response to grazing intensity differences

2020 ◽  
Author(s):  
Zhenhua Dang ◽  
Yuanyuan Jia ◽  
Yunyun Tian ◽  
Jiabin Li ◽  
Yanan Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Pathways ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Grazing Intensity ◽  
Glycolate Oxidase ◽  
Bisphosphate Carboxylase ◽  
Grazing Intensities

Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is one of the widespread dominant species on the typical steppe of the Inner Mongolian Plateau, and is regarded as a suitable species for studying the effects of grazing in this region. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Accordingly, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. A total of 2,357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified that indicated modulation of Calvin–Benson cycle and photorespiration metabolic pathways. The key gene´expression profiles encoding various proteins (e.g., Ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection, and identify important questions to address in future transcriptome studies.

scholarly journals Cloning and evaluation of reference genes for quantitative real-time PCR analysis inAmorphophallus

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3260 ◽  
Author(s):  
Kai Wang ◽  
Yi Niu ◽  
Qijun Wang ◽  
Haili Liu ◽  
Yi Jin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Real Time ◽  
Reference Genes ◽  
Dynamic Range ◽  
Expression Profiles ◽  
Mrna Levels ◽  
Expression Stability ◽  
Degenerate Primers ◽  
Different Tissues

Quantitative real-time reverse transcription PCR (RT-qPCR) has been widely used in the detection and quantification of gene expression levels because of its high accuracy, sensitivity, and reproducibility as well as its large dynamic range. However, the reliability and accuracy of RT-qPCR depends on accurate transcript normalization using stably expressed reference genes.Amorphophallusis a perennial plant with a high content of konjac glucomannan (KGM) in its corm. This crop has been used as a food source and as a traditional medicine for thousands of years. Without adequate knowledge of gene expression profiles, there has been no report of validated reference genes inAmorphophallus. In this study, nine genes that are usually used as reference genes in other crops were selected as candidate reference genes. These putative sequences of these genesAmorphophalluswere cloned by the use of degenerate primers. The expression stability of each gene was assessed in different tissues and under two abiotic stresses (heat and waterlogging) inA. albusandA. konjac. Three distinct algorithms were used to evaluate the expression stability of the candidate reference genes. The results demonstrated thatEF1-a,EIF4A,H3andUBQwere the best reference genes under heat stress inAmorphophallus. Furthermore,EF1-a,EIF4A,TUB, andRPwere the best reference genes in waterlogged conditions. By comparing different tissues from all samples, we determined thatEF1-α,EIF4A,andCYPwere stable in these sets. In addition, the suitability of these reference genes was confirmed by validating the expression of a gene encoding the small heat shock proteinSHSP, which is related to heat stress inAmorphophallus. In sum,EF1-αandEIF4Awere the two best reference genes for normalizing mRNA levels in different tissues and under various stress treatments, and we suggest using one of these genes in combination with 1 or 2 reference genes associated with different biological processes to normalize gene expression. Our results will provide researchers with appropriate reference genes for further gene expression quantification using RT-qPCR inAmorphophallus.

scholarly journals Electrotransfer of IL-15/IL-15Rα Complex for the Treatment of Established Melanoma

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 3072
Author(s):  
Shawna A. Shirley ◽  
Cathryn G. Lundberg ◽  
Richard Heller
Keyword(s):  
Plasmid Dna ◽  
Tumor Regression ◽  
Important Determinant ◽  
Expression Profiles ◽  
Cell Infiltrate ◽  
Term Survival ◽  
Interleukin 15 ◽  
Ifn Γ ◽  
Low Levels

Gene electrotransfer (GET) is a safe, reliable, and effective method of delivering plasmid DNA (pDNA) to solid tumors. GET has been previously used to deliver interleukin-15 (IL-15) to mouse melanoma, resulting in long-term tumor regression and the survival of a percentage of treated animals after challenge. To enhance this effect, we evaluated modulating the expression levels of IL-15 and co-expressing its receptor, IL-15Rα. GET was used to deliver plasmids encoding IL-15 and IL-15Rα to established B16.F10 tumors on days 0, 4, and 7. Two delivery protocols that yielded different expression profiles were utilized. Mice that were tumor-free for 50 days were then challenged with B16.F10 cells on the opposite flank and monitored for an additional 50 days. The amount of IL-15 expressed and the presence or absence of IL-15Rα in the treated tumors did not significantly affect the tumor regression and long-term survival. Upon challenge, however, low levels of IL-15 were more protective and resulted in a greater production of anti-tumor cytokines such as IFN-γ and MIP-1β and a greater amount of CD11b+ and CD3e+ cells infiltrating tumors. While mice with high levels of IL-15 showed CD11b+ and CD3e+ cell infiltrate, there was a substantial presence of NK cells that was absent in other treated groups. We can conclude that the level of IL-15 expressed in tumors after GET is an important determinant of the therapeutic outcome, a finding that will help us finetune this type of therapy.

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