Slower development of lower canopy beans produces better coffee

Abstract The production of high-quality coffee is being challenged by changing climates in coffee-growing regions. The coffee beans from the upper and lower canopy at different development stages of the same plants were analyzed to investigate the impact of the microenvironment on gene expression and coffee quality. Compared with coffee beans from the upper canopy, lower canopy beans displayed more intense aroma with higher caffeine, trigonelline, and sucrose contents, associated with greater gene expression in the representative metabolic pathways. Global gene expression indicated a longer ripening in the lower canopy, resulting from higher expression of genes relating to growth inhibition and suppression of chlorophyll degradation during early bean ripening. Selection of genotypes or environments that enhance expression of the genes slowing bean development may produce higher quality coffee beans, allowing coffee production in a broader range of available future environments.

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Transcriptomes reveal alterations in gravity impact circadian clocks and activate mechanotransduction pathways with adaptation through epigenetic change

Physiological Genomics ◽

10.1152/physiolgenomics.00117.2014 ◽

2015 ◽

Vol 47 (4) ◽

pp. 113-128 ◽

Cited By ~ 16

Author(s):

Theresa Casey ◽

Osman V. Patel ◽

Karen Plaut

Keyword(s):

Gene Expression ◽

Late Pregnancy ◽

Global Gene Expression ◽

Circadian Clocks ◽

Epigenetic Change ◽

Pregnant Rats ◽

Affymetrix Genechips ◽

Expression Of Genes ◽

The Impact

Few studies have investigated the impact of alterations in gravity on mammalian transcriptomes. Here, we describe the impact of spaceflight on mammary transcriptome of late pregnant rats and the effect of hypergravity exposure on mammary, liver, and adipose transcriptomes in late pregnancy and at the onset of lactation. RNA was isolated from mammary collected on pregnancy day 20 from rats exposed to spaceflight from days 11 to 20 of gestation. To measure the impact of hypergravity on mammary, liver, and adipose transcriptomes we isolated RNA from tissues collected on P20 and lactation day 1 from rats exposed to hypergravity beginning on pregnancy day 9. Gene expression was measured with Affymetrix GeneChips. Microarray analysis of variance revealed alterations in gravity affected the expression of genes that regulate circadian clocks and activate mechanotransduction pathways. Changes in these systems may explain global gene expression changes in immune response, metabolism, and cell proliferation. Expression of genes that modify chromatin structure and methylation was affected, suggesting adaptation to gravity alterations may proceed through epigenetic change. Altered gravity experiments offer insights into the role of forces omnipresent on Earth that shape genomes in heritable ways. Our study is the first to analyze the impact of alterations in gravity on transcriptomes of pregnant and lactating mammals. Findings provide insight into systems that sense gravity and the way in which they affect phenotype, as well as the possibility of sustaining life beyond Earth's orbit.

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Impact of Environmental Stressors on Gene Expression in the Embryo of the Italian Wall Lizard

Applied Sciences ◽

10.3390/app11114723 ◽

2021 ◽

Vol 11 (11) ◽

pp. 4723

Author(s):

Rosaria Scudiero ◽

Chiara Maria Motta ◽

Palma Simoniello

Keyword(s):

Gene Expression ◽

Protein Interactions ◽

Membrane Trafficking ◽

Translational Regulation ◽

Cellular Protection ◽

Terrestrial Vertebrate ◽

Expression Of Genes ◽

Stress Changes ◽

Probable Consequence ◽

The Impact

The cleidoic eggs of oviparous reptiles are protected from the external environment by membranes and a parchment shell permeable to water and dissolved molecules. As a consequence, not only physical but also chemical insults can reach the developing embryos, interfering with gene expression. This review provides information on the impact of the exposure to cadmium contamination or thermal stress on gene expression during the development of Italian wall lizards of the genus Podarcis. The results obtained by transcriptomic analysis, although not exhaustive, allowed to identify some stress-reactive genes and, consequently, the molecular pathways in which these genes are involved. Cadmium-responsive genes encode proteins involved in cellular protection, metabolism and proliferation, membrane trafficking, protein interactions, neuronal transmission and plasticity, immune response, and transcription regulatory factors. Cold stress changes the expression of genes involved in transcriptional/translational regulation and chromatin remodeling and inhibits the transcription of a histone methyltransferase with the probable consequence of modifying the epigenetic control of DNA. These findings provide transcriptome-level evidence of how terrestrial vertebrate embryos cope with stress, giving a key to use in population survival and environmental change studies. A better understanding of the genes contributing to stress tolerance in vertebrates would facilitate methodologies and applications aimed at improving resistance to unfavourable environments.

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Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1807796115 ◽

2018 ◽

Vol 115 (48) ◽

pp. E11321-E11330 ◽

Cited By ~ 11

Author(s):

Jie Hou ◽

Xiaowen Shi ◽

Chen Chen ◽

Md. Soliman Islam ◽

Adam F. Johnson ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Transcription Factors ◽

Leaf Tissue ◽

Global Gene Expression ◽

Published Data ◽

Chromosomal Imbalance ◽

Regulatory Processes ◽

Expression Of Genes ◽

Global Impacts

Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.

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Global transcriptome analysis of rat hypothalamic arcuate nucleus demonstrates reversal of hypothalamic gliosis following surgically and diet induced weight loss

Scientific Reports ◽

10.1038/s41598-019-52257-8 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Pernille Barkholt ◽

Kristoffer T. G. Rigbolt ◽

Mechthilde Falkenhahn ◽

Thomas Hübschle ◽

Uwe Schwahn ◽

...

Keyword(s):

Gene Expression ◽

Weight Loss ◽

Molecular Mechanisms ◽

Arcuate Nucleus ◽

Gene Expression Signature ◽

Global Gene Expression ◽

Metabolic Effects ◽

Expression Of Genes ◽

Hypothalamic Arcuate Nucleus ◽

Laser Capture

Abstract The central mechanisms underlying the marked beneficial metabolic effects of bariatric surgery are unclear. Here, we characterized global gene expression in the hypothalamic arcuate nucleus (Arc) in diet-induced obese (DIO) rats following Roux-en-Y gastric bypass (RYGB). 60 days post-RYGB, the Arc was isolated by laser-capture microdissection and global gene expression was assessed by RNA sequencing. RYGB lowered body weight and adiposity as compared to sham-operated DIO rats. Discrete transcriptome changes were observed in the Arc following RYGB, including differential expression of genes associated with inflammation and neuropeptide signaling. RYGB reduced gene expression of glial cell markers, including Gfap, Aif1 and Timp1, confirmed by a lower number of GFAP immunopositive astrocyte profiles in the Arc. Sham-operated weight-matched rats demonstrated a similar glial gene expression signature, suggesting that RYGB and dietary restriction have common effects on hypothalamic gliosis. Considering that RYGB surgery also led to increased orexigenic and decreased anorexigenic gene expression, this may signify increased hunger-associated signaling at the level of the Arc. Hence, induction of counterregulatory molecular mechanisms downstream from the Arc may play an important role in RYGB-induced weight loss.

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Global gene expression analysis of Escherichia coli K-12 DH5α after exposure to 2.4 GHz wireless fidelity radiation

Scientific Reports ◽

10.1038/s41598-019-51046-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Ilham H. Said-Salman ◽

Fatima A. Jebaii ◽

Hoda H. Yusef ◽

Mohamed E. Moustafa

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Cell Adhesion ◽

Metabolic Pathways ◽

Enrichment Analysis ◽

Global Gene Expression ◽

Enrichment Score ◽

Pcr Analysis ◽

Radiofrequency Radiation ◽

K 12

Abstract This study investigated the non-thermal effects of Wi-Fi radiofrequency radiation of 2.4 GHz on global gene expression in Escherichia coli K-12 DH5α. High-throughput RNA-sequencing of 2.4 GHz exposed and non-exposed bacteria revealed that 101 genes were differentially expressed (DEGs) at P ≤ 0.05. The up-regulated genes were 52 while the down-regulated ones were 49. QRT-PCR analysis of pgaD, fliC, cheY, malP, malZ, motB, alsC, alsK, appB and appX confirmed the RNA-seq results. About 7% of DEGs are involved in cellular component organization, 6% in response to stress stimulus, 6% in biological regulation, 6% in localization, 5% in locomotion and 3% in cell adhesion. Database for annotation, visualization and integrated discovery (DAVID) functional clustering revealed that DEGs with high enrichment score included genes for localization of cell, locomotion, chemotaxis, response to external stimulus and cell adhesion. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis showed that the pathways for flagellar assembly, chemotaxis and two-component system were affected. Go enrichment analysis indicated that the up-regulated DEGs are involved in metabolic pathways, transposition, response to stimuli, motility, chemotaxis and cell adhesion. The down-regulated DEGs are associated with metabolic pathways and localization of ions and organic molecules. Therefore, the exposure of E. coli DH5α to Wi-Fi radiofrequency radiation for 5 hours influenced several bacterial cellular and metabolic processes.

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153 SUPPLEMENTATION WITH LINOLENIC ACID AND L-CARNITINE DURING IVM REDUCED THE EXPRESSION OF GENES RELATED TO LIPOGENESIS BUT DID NOT ALTER THE LIPID CONTENT AND CRYOTOLERANCE OF IN VITRO-PRODUCED EMBRYOS

Reproduction Fertility and Development ◽

10.1071/rdv29n1ab153 ◽

2017 ◽

Vol 29 (1) ◽

pp. 185 ◽

Cited By ~ 1

Author(s):

B. C. S. Leao ◽

N. A. S. Rocha Frigoni ◽

P. C. Dall'Acqua ◽

M. Ambrogi ◽

G. B. Nunes ◽

...

Keyword(s):

Gene Expression ◽

Linolenic Acid ◽

Lipid Content ◽

Control Group ◽

Intracellular Lipid ◽

Chi Square ◽

Sudan Black B ◽

Expression Of Genes ◽

The Impact

This study was conducted to evaluate the impact of supplementation during in vitro maturation (IVM) with linolenic acid (ALA), l-carnitine (L-car), or the combination of both supplements on the embryo intracellular lipid content and cryotolerance, as well as in the embryo expression of genes involved in lipid metabolism (lipogenesis regulation: SCD1, FASN, and SREBP1; and β-oxidation pathway: CPT1B and CPT2). Cumulus-oocyte complexes (n = 1076) were IVM for 22 h at 38.5°C and 5% CO2 in air, in TCM-199 medium with bicarbonate, hormones, and 10% FCS (control group), supplemented with 100 μM ALA (ALA group), 5 mM L-car (L-car group), or a combination of 100 μM ALA + 5 mM L-car (ALA + L-car group). After IVF, presumptive zygotes were in vitro cultured in SOFaa medium supplemented with 5 mg mL−1 BSA and 2.5% FCS, at 38.5°C and 5% CO2 in air during 7 days. Cleavage and blastocyst rates were evaluated on Day 3 and 7, respectively (IVF = Day 0). At Day 7, the blastocysts were stained with the lipophilic dye Sudan Black B (n = 60), vitrified/warmed (n = 260; Ingámed® protocol, Maringa-PR, Brazil), or collected for analysis of gene expression (n = 180). Embryonic development were analysed by ANOVA and the multiple comparisons of means were determined by Tukey’s test. The embryonic re-expansion data were subjected to chi-square test and the differences in gene expression among groups were evaluated by Duncan’s multiple range test (P < 0.05). Data are presented as means ± standard error means. There was no effect (P > 0.05) of the supplements used during IVM on cleavage (79.54 ± 2.76% to 82.16 ± 1.13%) and blastocyst rates (29.03 ± 3.07% to 30.46 ± 2.01%). Similarly, the intracellular lipid content in Day-7 blastocysts (1.03 ± 0.04 to 1.15 ± 0.07 pixels) and the embryonic cryotolerance, assessed by the re-expansion rates after 24 h (67.3 to 78.3%) hatching rates after 48 h (11.5 to 25.5%) of post-warming culture, were unaffected (P > 0.05) by the supplements of IVM medium. Although the treatments did not alter (P > 0.05) the expression of CPT1B and CPT2 genes, the expression of FASN gene was decreased (P < 0.05) in the ALA group and the expression of SREBP1 gene was decreased (P < 0.05) in the ALA and L-car groups. The expression of the gene SCD1 was reduced (P < 0.05) in all treatments compared with the control group. Thus, despite the lack of effects of the treatments performed during IVM on the intracellular lipid content and cryotolerance of the embryos derived from the treated oocytes, a reduction in the expression of genes related to lipogenesis was observed in Day-7 blastocysts. These results suggest that treatments performed in the oocytes during IVM may have prolonged effects, affecting the subsequent expression of genes in embryos. Further studies are needed to determine the mechanisms related to the differentiation of the oocyte machinery during maturation. Financial support was provided by FAPESP (#2012/10084–4 and #2013/07382–6).

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Impact of aromatase inhibitor treatment on global gene expression and its association with antiproliferative response in ER+ breast cancer in postmenopausal patients

Breast Cancer Research ◽

10.1186/s13058-019-1223-z ◽

2019 ◽

Vol 22 (1) ◽

Cited By ~ 1

Author(s):

Qiong Gao ◽

◽

Elena López-Knowles ◽

Maggie Chon U. Cheang ◽

James Morden ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cell Proliferation ◽

Aromatase Inhibitor ◽

Breast Cancer Mortality ◽

Global Gene Expression ◽

Therapy Resistance ◽

Control Group ◽

Short Term Exposure ◽

The Impact

Abstract Background Endocrine therapy reduces breast cancer mortality by 40%, but resistance remains a major clinical problem. In this study, we sought to investigate the impact of aromatase inhibitor (AI) therapy on gene expression and identify gene modules representing key biological pathways that relate to early AI therapy resistance. Methods Global gene expression was measured on pairs of core-cut biopsies taken at baseline and at surgery from 254 patients with ER-positive primary breast cancer randomised to receive 2-week presurgical AI (n = 198) or no presurgical treatment (control n = 56) from the POETIC trial. Data from the AI group was adjusted to eliminate artefactual process-related changes identified in the control group. The response was assessed by changes in the proliferation marker, Ki67. Results High baseline ESR1 expression associated with better AI response in HER2+ tumours but not HER2− tumours. In HER2− tumours, baseline expression of 48 genes associated with poor antiproliferative response (p < 0.005) including PERP and YWHAQ, the two most significant, and the transcription co-regulators (SAP130, HDAC4, and NCOA7) which were among the top 16 most significant. Baseline gene signature scores measuring cell proliferation, growth factor signalling (ERBB2-GS, RET/GDNF-GS, and IGF-1-GS), and immune activity (STAT1-GS) were significantly higher in poor AI responders. Two weeks of AI caused downregulation of genes involved in cell proliferation and ER signalling, as expected. Signature scores of E2F activation and TP53 dysfunction after 2-week AI were associated with poor AI response in both HER2− and HER2+ patients. Conclusions There is a high degree of heterogeneity in adaptive mechanisms after as little as 2-week AI therapy; however, all appear to converge on cell cycle regulation. Our data support the evaluation of whether an E2F signatures after short-term exposure to AI may identify those patients most likely to benefit from the early addition of CDK4/6 inhibitors. Trial registration ISRCTN, ISRCTN63882543, registered on 18 December 2007.

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Circulating miRNA 887 is differentially expressed in ARDS and modulates endothelial function

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00494.2019 ◽

2020 ◽

Vol 318 (6) ◽

pp. L1261-L1269 ◽

Cited By ~ 1

Author(s):

Andrew J. Goodwin ◽

Pengfei Li ◽

Perry V. Halushka ◽

James A. Cook ◽

Aman S. Sumal ◽

...

Keyword(s):

Gene Expression ◽

Cell Function ◽

In Silico Analysis ◽

Leukocyte Migration ◽

Differentially Expressed ◽

Expression Of Genes ◽

Cell Gene Expression ◽

And Function ◽

The Impact

Circulating microRNAs (miRNAs) can be taken up by recipient cells and have been recently associated with the acute respiratory distress syndrome (ARDS). Their role in host predisposition to the syndrome is unknown. The objective of the study was to identify circulating miRNAs associated with the development of sepsis-related ARDS and examine their impact on endothelial cell gene expression and function. We determined miRNA levels in plasma collected from subjects during the first 24 h of admission to a tertiary intensive care unit for sepsis. A miRNA that was differentially expressed between subjects who did and did not develop ARDS was identified and was transfected into human pulmonary microvascular endothelial cells (HPMECs). RNA sequencing, in silico analysis, cytokine expression, and leukocyte migration assays were used to determine the impact of this miRNA on gene expression and cell function. In two cohorts, circulating miR-887-3p levels were elevated in septic patients who developed ARDS compared with those who did not. Transfection of miR-887-3p into HPMECs altered gene expression, including the upregulation of several genes previously associated with ARDS (e.g., CXCL10, CCL5, CX3CL1, VCAM1, CASP1, IL1B, IFNB, and TLR2), and activation of cellular pathways relevant to the response to infection. Functionally, miR-887-3p increased the endothelial release of chemokines and facilitated trans-endothelial leukocyte migration. Circulating miR-887-3p is associated with ARDS in critically ill patients with sepsis. In vitro, miR-887-3p regulates the expression of genes relevant to ARDS and neutrophil tracking. This miRNA may contribute to ARDS pathogenesis and could represent a novel therapeutic target.

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Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

Genetics ◽

10.1534/genetics.119.302978 ◽

2020 ◽

Vol 214 (3) ◽

pp. 651-667 ◽

Cited By ~ 2

Author(s):

Marco Di Stefano ◽

Francesca Di Giovanni ◽

Vasilisa Pozharskaia ◽

Mercè Gomar-Alba ◽

Davide Baù ◽

...

Keyword(s):

Gene Expression ◽

Budding Yeast ◽

Nuclear Organization ◽

Nuclear Periphery ◽

Three Dimensional ◽

Global Gene Expression ◽

3D Genome ◽

Expression Of Genes ◽

Genome Wide ◽

Chromosome Fusions

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

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Genomic dissection of the cytokine-controlled STAT5 signaling network in liver

Physiological Genomics ◽

10.1152/physiolgenomics.00048.2008 ◽

2008 ◽

Vol 34 (2) ◽

pp. 135-143 ◽

Cited By ~ 18

Author(s):

Atsushi Hosui ◽

Lothar Hennighausen

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Target Genes ◽

Global Gene Expression ◽

Specific Expression ◽

Partial Explanation ◽

Downstream Target ◽

Expression Of Genes ◽

Global Gene Expression Profiling

Growth hormone (GH) controls the physiology and pathophysiology of the liver, and its signals are conducted by two members of the family of signal transducers and activators of transcription, STAT5A and STAT5B. Mice in which the Stat5a/b locus has been inactivated specifically in hepatocytes display GH resistance, the sex-specific expression of genes associated with liver metabolism and the cytochrome P-450 system is lost, and they develop hepatosteatosis. Several groups have shown by global gene expression profiling that a cadre of STAT5A/B target genes identify genetic cascades induced by GH and other cytokines. Evidence is accumulating that in the absence of STAT5A/B GH aberrantly activates STAT1 and STAT3 and their downstream target genes and thereby offers a partial explanation of some of the physiological alterations observed in Stat5a/b-null mice and human patients. We hypothesize that phenotypic changes observed in the absence of STAT5A/B are due to two distinct molecular consequences: first, the failure of STAT5A/B target genes to be activated by GH and second, the rerouting of GH signaling to other members of the STAT family. Rerouting of GH signaling to STAT1 and STAT3 might partially compensate for the loss of STAT5A/B, but it certainly activates biological programs distinct from STAT5A/B. Here we discuss the extent to which studies on global gene expression profiling have fostered a better understanding of the biology behind cytokine-STAT5A/B networks in hepatocytes. We also explore whether this wealth of information on gene activity can be used to further understand the roles of cytokines in liver disease.

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