Stress levels over time in the introduced ascidian Styela plicata: the effects of temperature and salinity variations on hsp70 gene expression

Cardiac hypertrophy is a growth process that occurs in response to stress stimuli or injury, and leads to the induction of several pathways to alter gene expression. Under hypertrophic stimuli, sarcomeric structure is disrupted, both as a consequence of gene expression and local changes in sarcomeric proteins. Cardiac-restricted ankyrin repeat protein (CARP) is one such protein that function both in cardiac sarcomeres and at the transcriptional level. We postulate that due to this dual nature, CARP plays a key role in maintaining the cardiac sarcomere. GATA4 is another protein detected in cardiomyocytes as important in hypertrophy, as it is activated by hypertrophic stimuli, and directly binds to DNA to alter gene expression. Results of GATA4 activation over time were inconclusive; however, the role of CARP in mediating hypertrophic growth in cardiomyocytes was clearly demonstrated. In this study, Neonatal Rat Ventricular Myocytes were used as a model to detect changes over time in CARP and GATA4 under hypertrophic stimulation by phenylephrine and high serum media. Results were detected by analysis of immunoblotting. The specific role that CARP plays in mediating cellular growth under hypertrophic stimuli was studied through immunofluorescence, which demonstrated that cardiomyocyte growth with hypertrophic stimulation was significantly blunted when NRVMs were co-treated with CARP siRNA. These data suggest that CARP plays an important role in the hypertrophic response in cardiomyocytes.

Download Full-text

Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

BMC Genomics ◽

10.1186/s12864-020-07329-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Melanie Lindner ◽

Irene Verhagen ◽

Heidi M. Viitaniemi ◽

Veronika N. Laine ◽

Marcel E. Visser ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Environmental Conditions ◽

Brain Regions ◽

Temporal Changes ◽

Egg Laying ◽

Gene Body ◽

Cpg Site ◽

Repeated Sampling ◽

Over Time

Abstract Background DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n = 6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled. Results We simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10 kb up- and downstream regions adjacent to the gene body. Conclusion Temporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.

Download Full-text

Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab021 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Hitoshi Iuchi ◽

Michiaki Hamada

Keyword(s):

Gene Expression ◽

Time Series ◽

Time Course ◽

Time Series Data ◽

Expression Patterns ◽

Detection Methods ◽

Series Data ◽

Expression Levels ◽

Over Time ◽

Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

Download Full-text

Changes in genetic parameters for milk yield and heat tolerance in the Thai Holstein crossbred dairy population under different heat stress levels and over time

Journal of Dairy Science ◽

10.3168/jds.2021-20151 ◽

2021 ◽

Author(s):

P. Sungkhapreecha ◽

I. Misztal ◽

J. Hidalgo ◽

Y. Steyn ◽

S. Buaban ◽

...

Keyword(s):

Heat Stress ◽

Milk Yield ◽

Heat Tolerance ◽

Genetic Parameters ◽

Stress Levels ◽

Over Time

Download Full-text

Comparative study on the non-specific immune response and hsp70 gene expression among three strains of koi (Cyprinus carpio) under acute heat stress

Aquaculture Reports ◽

10.1016/j.aqrep.2020.100461 ◽

2020 ◽

Vol 18 ◽

pp. 100461

Author(s):

Huanhuan Yu ◽

Chongying Zhang ◽

Wei Xing ◽

Tieliang Li ◽

Guanling Xu ◽

...

Keyword(s):

Gene Expression ◽

Immune Response ◽

Heat Stress ◽

Comparative Study ◽

Cyprinus Carpio ◽

Specific Immune Response ◽

Hsp70 Gene ◽

Acute Heat Stress

Download Full-text

Enabling out-of-clinic human immunity studies via single-cell profiling of capillary blood

10.1101/2020.07.25.210468 ◽

2020 ◽

Author(s):

Tatyana Dobreva ◽

David Brown ◽

Jong Hwee Park ◽

Matt Thomson

Keyword(s):

Gene Expression ◽

Immune System ◽

Environmental Factors ◽

Single Cell ◽

Immune Cell ◽

Cell Types ◽

Capillary Blood ◽

Specific Gene ◽

Human Immune ◽

Over Time

AbstractAn individual’s immune system is driven by both genetic and environmental factors that vary over time. To better understand the temporal and inter-individual variability of gene expression within distinct immune cell types, we developed a platform that leverages multiplexed single-cell sequencing and out-of-clinic capillary blood extraction to enable simplified, cost-effective profiling of the human immune system across people and time at single-cell resolution. Using the platform, we detect widespread differences in cell type-specific gene expression between subjects that are stable over multiple days.SummaryIncreasing evidence implicates the immune system in an overwhelming number of diseases, and distinct cell types play specific roles in their pathogenesis.1,2 Studies of peripheral blood have uncovered a wealth of associations between gene expression, environmental factors, disease risk, and therapeutic efficacy.4 For example, in rheumatoid arthritis, multiple mechanistic paths have been found that lead to disease, and gene expression of specific immune cell types can be used as a predictor of therapeutic non-response.12 Furthermore, vaccines, drugs, and chemotherapy have been shown to yield different efficacy based on time of administration, and such findings have been linked to the time-dependence of gene expression in downstream pathways.21,22,23 However, human immune studies of gene expression between individuals and across time remain limited to a few cell types or time points per subject, constraining our understanding of how networks of heterogeneous cells making up each individual’s immune system respond to adverse events and change over time.

Download Full-text

Quantification of HSP70 Gene Expression and Determination of Capacitation Status of Magnetically Separated Cryopreserved Bovine Spermatozoa at Different Thawing Temperature and Time

Sains Malaysiana ◽

10.17576/jsm-2018-4706-04 ◽

2018 ◽

Vol 47 (6) ◽

pp. 1101-1108

Author(s):

Syarifah Faezah Syed Mohamad ◽

Siti Fatimah Ibrahim ◽

Nur Hilwan Ismail ◽

Khairul Osman ◽

Farah Hanan Fathihah Jaafar ◽

...

Keyword(s):

Gene Expression ◽

Hsp70 Gene ◽

Bovine Spermatozoa

Download Full-text

Decreased sensitivity to the anorectic effects of leptin in mice that lack a Pomc-specific neural enhancer

PLoS ONE ◽

10.1371/journal.pone.0244793 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0244793

Author(s):

Elisa S. Na ◽

Daniel D. Lam ◽

Eva Yokosawa ◽

Jessica M. Adams ◽

David P. Olson ◽

...

Keyword(s):

Gene Expression ◽

Body Weight ◽

Knockout Mice ◽

Weight Change ◽

Body Weight Change ◽

Dynamic Regulation ◽

Adult Mice ◽

Environmental Perturbations ◽

Mild Obesity ◽

Over Time

Enhancer redundancy has been postulated to provide a buffer for gene expression against genetic and environmental perturbations. While work in Drosophila has identified functionally overlapping enhancers, work in mammalian models has been limited. Recently, we have identified two partially redundant enhancers, nPE1 and nPE2, that drive proopiomelanocortin gene expression in the hypothalamus. Here we demonstrate that deletion of nPE1 produces mild obesity while knockout of nPE2 has no discernible metabolic phenotypes. Additionally, we show that acute leptin administration has significant effects on nPE1 knockout mice, with food intake and body weight change significantly impacted by peripheral leptin treatment. nPE1 knockout mice became less responsive to leptin treatment over time as percent body weight change increased over 2 week exposure to peripheral leptin. Both Pomc and Agrp mRNA were not differentially affected by chronic leptin treatment however we did see a decrease in Pomc and Agrp mRNA in both nPE1 and nPE2 knockout calorie restricted mice as compared to calorie restricted PBS-treated WT mice. Collectively, these data suggest dynamic regulation of Pomc by nPE1 such that mice with nPE1 knockout become less responsive to the anorectic effects of leptin treatment over time. Our results also support our earlier findings in which nPE2 may only be critical in adult mice that lack nPE1, indicating that these neural enhancers work synergistically to influence metabolism.

Download Full-text