scholarly journals An Emiliania huxleyi pan-transcriptome reveals basal strain specificity in gene expression patterns

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ester Feldmesser ◽  
Shifra Ben-Dor ◽  
Assaf Vardi
Keyword(s):  
Gene Expression ◽  
Viral Infection ◽  
Expression Patterns ◽  
Protein Translation ◽  
Biogeochemical Cycles ◽  
Emiliania Huxleyi ◽  
Strain Specificity ◽  
Bloom Formation ◽  
Resistant Strains ◽  
Ecological Importance

AbstractEmiliania huxleyi is a cosmopolitan coccolithophore widespread in temperate oceans. This unicellular photoautotroph forms massive recurring blooms that play an important role in large biogeochemical cycles of carbon and sulfur, which play a role in climate change. The mechanism of bloom formation and demise, controlled by giant viruses that routinely infect these blooms, is poorly understood. We generated a pan-transcriptome of E. huxleyi, derived from three strains with different susceptibility to viral infection. Expression profiling of E. huxleyi sensitive and resistant strains showed major basal differences, including many genes that are induced upon viral infection. This suggests that basal gene expression can affect the host metabolic state and the susceptibility of E. huxleyi to viruses. Due to its ecological importance, the pan-transcriptome and its protein translation, applicable to many E. huxleyi strains, is a powerful resource for investigation of eukaryotic microbial communities.

scholarly journals Gene expression patterns in synchronized islet populations

2018 ◽  
Author(s):  
Nikita Mukhitov ◽  
Michael G. Roper
Keyword(s):  
Gene Expression ◽  
Environmental Changes ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Protein Translation ◽  
Gene Set Enrichment Analysis ◽  
Gene Expression Patterns ◽  
Insulin Synthesis

AbstractIn vivo levels of insulin are oscillatory with a period of ~5-10 minutes, implying that the numerous islets of Langerhans within the pancreas are synchronized. While the synchronizing factors are still under investigation, one result of this behavior is expected to be coordinated intracellular [Ca2+] ([Ca2+]i) oscillations throughout the islet population. The role that coordinated [Ca2+]i oscillations have on controlling gene expression within pancreatic islets was examined by comparing gene expression levels in islets that were synchronized using a low amplitude glucose wave and an unsynchronized population. The [Ca2+]i oscillations in the synchronized population were homogeneous and had a significantly lower drift in their oscillation period as compared to unsynchronized islets. This reduced drift in the synchronized population was verified by comparing the drift of in vivo and in vitro profiles from published reports. Microarray profiling indicated a number of Ca2+-dependent genes were differentially regulated between the two islet populations. Gene set enrichment analysis revealed that the synchronized population had reduced expression of gene sets related to protein translation, protein turnover, energy expenditure, and insulin synthesis, while those that were related to maintenance of cell morphology were increased. It is speculated that these gene expression patterns in the synchronized islets results in a more efficient utilization of intra-cellular resources and response to environmental changes.

scholarly journals Regulation of gene expression during the fasting-feeding cycle of the liver displays mouse strain specificity

2020 ◽  
Vol 295 (15) ◽  
pp. 4809-4821 ◽  
Author(s):  
Yuling Chi ◽  
Dou Yeon Youn ◽  
Alus M. Xiaoli ◽  
Li Liu ◽  
Jacob B. Pessin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lipid Metabolism ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Nutrient Status ◽  
Mouse Strains ◽  
Strain Specificity ◽  
Biological Regulation ◽  
Lipogenic Genes ◽  
Feeding Cycle

The liver maintains metabolic homeostasis by integrating the regulation of nutrient status with both hormonal and neural signals. Many studies on hepatic signaling in response to nutrients have been conducted in mice. However, no in-depth study is currently available that has investigated genome-wide changes in gene expression during the normal physiological fasting-feeding cycle in nutrient-sensitive and -insensitive mice. Using two strains of mice, C57BL/6J and BALB/cJ, and deploying deep RNA-Seq complemented with quantitative RT-PCR, we found that feeding causes substantial and transient changes in gene expression in the livers of both mouse strains. The majority of significantly changed transcripts fell within the areas of biological regulation and cellular and metabolic processes. Among the metabolisms of three major types of macronutrients (i.e. carbohydrates, proteins, and lipids), feeding affected lipid metabolism the most. We also noted that the C57BL/6J and BALB/cJ mice significantly differed in gene expression and in changes in gene expression in response to feeding. In both fasted and fed states, both mouse strains shared common expression patterns for about 10,200 genes, and an additional 400–600 genes were differentially regulated in one strain but not the other. Among the shared genes, more lipogenic genes were induced upon feeding in BABL/cJ than in C57BL/6J mice. In contrast, in the population of differentially enriched genes, C57BL/6J mice expressed more genes involved in lipid metabolism than BALB/cJ mice. In summary, these results reveal that the two mouse strains used here exhibit several differences in feeding-induced hepatic responses in gene expression, especially in lipogenic genes.

scholarly journals The Gene Coexpression Analysis Identifies Functional Modules Dynamically Changed After Traumatic Brain Injury

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Zhi-jie Zhao ◽  
Dong-po Wei ◽  
Rui-zhe Zheng ◽  
Tinghua Peng ◽  
Xiang Xiao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Cell Activation ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Translation ◽  
Functional Modules ◽  
Coexpression Analysis ◽  
Gene Coexpression

Traumatic brain injury (TBI) is a major cause of morbidity and mortality, both in adult and pediatric populations. However, the dynamic changes of gene expression profiles following TBI have not been fully understood. In this study, we identified the differentially expressed genes (DEGs) following TBI. Remarkably, Serpina3n, Asf1b, Folr1, LOC100366216, Clec12a, Olr1, Timp1, Hspb1, Lcn2, and Spp1 were identified as the top 10 with the highest statistical significance. The weighted gene coexpression analysis (WGCNA) identified 12 functional modules from the DEGs, which showed specific expression patterns over time and were characterized by enrichment analysis. Specifically, the black and turquoise modules were mainly involved in energy metabolism and protein translation. The green yellow and yellow modules including Hmox1, Mif, Anxa2, Timp1, Gfap, Cd9, Gja1, Pdpn, and Gpx1 were related to response to wounding, indicating that expression of these genes such as Hmox1, Anxa2, and Timp1 could protect the brains from brain injury. The green yellow module highlighted genes involved in microglial cell activation such as Tyrobp, Cx3cr1, Grn, Trem2, C1qa, and Aif1, suggesting that these genes were responsible for the inflammatory response caused by TBI. The upregulation of these genes has been validated in an independent dataset. These results indicated that the key genes in microglia cell activation may serve as a promising therapeutic target for TBI. In summary, the present study provided a full view of the dynamic gene expression changes following TBI.

scholarly journals Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi

2006 ◽  
Vol 72 (1) ◽  
pp. 252-260 ◽  
Author(s):  
Sonya T. Dyhrman ◽  
Sheean T. Haley ◽  
Shanda R. Birkeland ◽  
Louie L. Wurch ◽  
Michael J. Cipriano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expressed Sequence Tag ◽  
Marine Organism ◽  
Sequence Data ◽  
Expression Patterns ◽  
Gene Discovery ◽  
Emiliania Huxleyi ◽  
Transcriptional Analysis ◽  
Transcriptional Level ◽  
Gene Sequences

ABSTRACT The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism.

scholarly journals Maternal stress has divergent effects on gene expression patterns in the brains of male and female threespine stickleback

2016 ◽  
Vol 283 (1839) ◽  
pp. 20161734 ◽  
Author(s):  
David C. H. Metzger ◽  
Patricia M. Schulte
Keyword(s):  
Gene Expression ◽  
Maternal Stress ◽  
Expression Patterns ◽  
Protein Translation ◽  
Threespine Stickleback ◽  
Synaptic Function ◽  
Male And Female ◽  
Brain Transcriptome ◽  
The Brain

Maternal stress can have long-term effects on neurodevelopment that can influence offspring performance and population evolutionary trajectories. To examine the mechanistic basis for these neurodevelopmental effects of maternal stress, we used RNA-seq to assess differential gene expression across the brain transcriptome of adult male and female threespine stickleback ( Gasterosteus aculeatus ) from stressed and unstressed mothers. We identified sexually divergent effects of maternal stress on the brain transcriptome. In males, genes that were upregulated by maternal stress were enriched for processes involved in synaptic function and organization and steroid hormone-mediated signalling pathways, whereas in females genes that were upregulated by maternal stress were enriched for processes involved in protein translation and metabolic functions. The expression of several genes involved in the hypothalamic–pituitary–interrenal response to stress and epigenetic processes such as the regulation of DNA methylation patterns and miRNAs increased in males and not in females. These data suggest that maternal stress has markedly different effects on cellular pathways in the brains of male and female offspring of mothers that are exposed to stress, which could have important implications when assessing the long-term ecological and evolutionary impacts of stress across generations.

Gene expression patterns in blood predict future severe endpoints in community acquired pneumonia

Pneumologie ◽  
2018 ◽  
Vol 72 (S 01) ◽  
pp. S8-S9
Author(s):  
M Bauer ◽  
H Kirsten ◽  
E Grunow ◽  
P Ahnert ◽  
M Kiehntopf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Community Acquired Pneumonia ◽  
Gene Expression Patterns
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