Sex-specific transcriptional responses of the zebrafish (Danio rerio) brain selenoproteome to acute sodium selenite supplementation

The potential benefits of selenium (Se) supplementation are currently under investigation for prevention of certain cancers and treatment of neurological disorders. However, little is known concerning the response of the brain to increased dietary Se under conditions of Se sufficiency, despite the majority of Se supplementation trials occurring in healthy, Se sufficient subjects. We evaluated the transcriptional response of Se-dependent genes, selenoproteins and the genes necessary for their synthesis (the selenoproteome), in the zebrafish ( Danio rerio) brain to supplementation with nutritionally relevant levels of dietary Se (sodium selenite) during conditions of assumed Se sufficiency. We first used a microarray approach to analyze the response of the brain selenoproteome to dietary Se supplementation for 14 days and then assessed the immediacy and time-scale transcriptional response of the brain selenoproteome to 1, 7, and 14 days of Se supplementation by quantitative real-time PCR (qRT-PCR). The microarray approach did not indicate large-scale influences of Se on the brain transcriptome as a whole or the selenoproteome specifically; only one nonselenoproteome gene (si:ch73-44m9.2) was significantly differentially expressed. Our qRT-PCR results, however, indicate that increases of dietary Se cause small, but significant transcriptional changes within the brain selenoproteome, even after only 1 day of supplementation. These responses were dynamic over a short period of supplementation in a manner highly dependent on sex and the duration of Se supplementation. In nutritional intervention studies, it may be necessary to utilize methods such as qRT-PCR, which allow larger sample sizes, for detecting subtle transcriptional changes in the brain.

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Role of the cytoskeleton in muscle transcriptional responses to altered use

Physiological Genomics ◽

10.1152/physiolgenomics.00132.2012 ◽

2013 ◽

Vol 45 (8) ◽

pp. 321-331 ◽

Cited By ~ 7

Author(s):

Gretchen A. Meyer ◽

Simon Schenk ◽

Richard L. Lieber

Keyword(s):

Mechanical Response ◽

Fiber Type ◽

Transcriptional Response ◽

Primary Component ◽

Transcriptional Responses ◽

Expression Of Genes ◽

Elevated Expression ◽

Transcriptional Changes ◽

Type Shift ◽

Future Work

In this work, the interaction between the loss of a primary component of the skeletal muscle cytoskeleton, desmin, and two common physiological stressors, acute mechanical injury and aging, were investigated at the transcriptional, protein, and whole muscle levels. The transcriptional response of desmin knockout ( des −/−) plantarflexors to a bout of 50 eccentric contractions (ECCs) showed substantial overlap with the response in wild-type ( wt) muscle. However, changes in the expression of genes involved in muscle response to injury were blunted in adult des −/− muscle compared with wt (fold change with ECC in des −/− and wt, respectively: Mybph, 1.4 and 2.9; Xirp1, 2.2 and 5.7; Csrp3, 1.8 and 4.3), similar to the observed blunted mechanical response (torque drop: des −/− 30.3% and wt 55.5%). Interestingly, in the absence of stressors, des −/− muscle exhibited elevated expression of many these genes compared with wt. The largest transcriptional changes were observed in the interaction between aging and the absence of desmin, including many genes related to slow fiber pathway (Myh7, Myl3, Atp2a2, and Casq2) and insulin sensitivity (Tlr4, Trib3, Pdk3, and Pdk4). Consistent with these transcriptional changes, adult des −/− muscle exhibited a significant fiber type shift from fast to slow isoforms of myosin heavy chain ( wt, 5.3% IIa and 71.7% IIb; des −/−, 8.4% IIa and 61.4% IIb) and a decreased insulin-stimulated glucose uptake ( wt, 0.188 μmol/g muscle/20 min; des −/−, 0.085 μmol/g muscle/20 min). This work points to novel areas of influence of this cytoskeletal protein and directs future work to elucidate its function.

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Patterns of parent and offspring gene expression reflect canalization, not plasticity, in response to environmental stress

10.1101/2021.12.14.472162 ◽

2021 ◽

Author(s):

Jeanette B Moss ◽

Christopher B Cunningham ◽

Elizabeth C McKinney ◽

Allen J. Moore

Keyword(s):

Gene Expression ◽

Environmental Change ◽

Environmental Stress ◽

Behavioral Plasticity ◽

Transcriptional Response ◽

Transcriptional Responses ◽

Behavioral Stability ◽

The Face ◽

Transcriptional Changes ◽

Hostile Environments

Parenting buffers offspring from hostile environments, but it is not clear how or if the genes that underlie parenting change their expression under environmental stress. We recently demonstrated that for the subsocial carrion beetle, Nicrophorus orbicollis, temperature during parenting does not affect parenting phenotypes. Here, we ask if transcriptional changes associated with parenting are likewise robust to environmental stress. The absence of a transcriptional response for parenting under stress would suggest that the genetic programs for parenting and being parented are canalized. Conversely, a robust transcriptional response would suggest that plasticity of underlying gene expression is critical for maintaining behavioral stability, and that these mechanisms provide a potential target for selection in the face of environmental change. We test these alternatives by characterizing gene expression of parents and offspring with and without parent-offspring interactions under a benign and a stressful temperature. We found that parent-offspring interactions elicit distinct transcriptional responses of parents and larvae irrespective of temperature. We further detected robust changes of gene expression in beetles breeding at 24 degrees C compared to 20 degrees C irrespective of family interaction. However, no strong interaction between parent-offspring interaction and temperature was detected for either parents or larvae. We therefore conclude that canalization, not plasticity of gene expression, most likely explains the absence of behavioral plasticity under thermal stress. This result suggests that species may not have the genetic variation needed to respond to all environmental change, especially for complex phenotypes.

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An integrated approach to identify environmental modulators of genetic risk factors for complex traits

10.1101/2021.02.23.432608 ◽

2021 ◽

Author(s):

Brunilda Balliu ◽

Ivan Carcamo -Orive ◽

Michael J. Gloudemans ◽

Daniel C. Nachun ◽

Matthew G. Durrant ◽

...

Keyword(s):

Genetic Risk ◽

Complex Traits ◽

Metabolic Regulation ◽

Large Scale ◽

Integrated Approach ◽

Multiple Traits ◽

Transcriptional Responses ◽

Environmentally Responsive ◽

Transcriptional Changes ◽

Scale Characterization

AbstractComplex traits and diseases can be influenced by both genetics and environment. However, given the large number of environmental stimuli and power challenges for gene-by-environment testing, it remains a critical challenge to identify and prioritize specific disease-relevant environmental exposures. We propose a novel framework for leveraging signals from transcriptional responses to environmental perturbations to identify disease-relevant perturbations that can modulate genetic risk for complex traits and inform the functions of genetic variants associated with complex traits. We perturbed human skeletal muscle, fat, and liver relevant cell lines with 21 perturbations affecting insulin resistance, glucose homeostasis, and metabolic regulation in humans and identified thousands of environmentally responsive genes. By combining these data with GWAS from 31 distinct polygenic traits, we show that heritability of multiple traits is enriched in regions surrounding genes responsive to specific perturbations and, further, that environmentally responsive genes are enriched for associations with specific diseases and phenotypes from the GWAS catalogue. Overall, we demonstrate the advantages of large-scale characterization of transcriptional changes in diversely stimulated and pathologically relevant cells to identify disease-relevant perturbations.

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Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge

10.1101/566570 ◽

2019 ◽

Author(s):

Daria Tchessalova ◽

Natalie C. Tronson

Keyword(s):

Gene Expression ◽

Large Scale ◽

Transcriptional Response ◽

Neural Function ◽

Immune Challenge ◽

Memory Decline ◽

Memory Impairments ◽

Differential Gene ◽

The Brain ◽

Neuroimmune Activation

AbstractMajor illnesses, including heart attack and sepsis, can cause cognitive impairments, depression, and progressive memory decline that persist long after recovery from the original illness. In rodent models of sepsis or subchronic immune challenge, memory deficits also persist for weeks or months, even in the absence of ongoing neuroimmune activation. This raises the question of what mechanisms in the brain mediate such persistent changes in neural function. Here, we used RNA-sequencing as a large-scale, unbiased approach to identify changes in hippocampal gene expression long after a subchronic immune challenge previously established to cause persistent memory impairments in both males and females. We observed enduring dysregulation of gene expression three months after the end of a subchronic immune challenge, Surprisingly, we also found striking sex differences in both the magnitude of changes and the specific genes and pathways altered, where males showed persistent changes in both immune- and plasticity-related genes three months after immune challenge, whereas females showed few such changes. In contrast, females showed striking differential gene expression in response to a subsequent immune challenge. Thus, immune activation has enduring and sex-specific consequences for hippocampal gene expression and the transcriptional response to subsequent stimuli. Together with findings of long-lasting memory impairments after immune challenge, these data suggest that illnesses can cause enduring vulnerability to, cognitive decline, affective disorders, and memory impairments via dysregulation of transcriptional processes in the brain.

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Seasonally hibernating phenotype assessed through transcript screening

Physiological Genomics ◽

10.1152/physiolgenomics.00301.2004 ◽

2006 ◽

Vol 24 (1) ◽

pp. 13-22 ◽

Cited By ~ 95

Author(s):

Daryl R. Williams ◽

L. Elaine Epperson ◽

Weizhong Li ◽

Margaret A. Hughes ◽

Ruth Taylor ◽

...

Keyword(s):

Large Scale ◽

Cardiac Tissue ◽

Rna Binding ◽

Transcriptional Responses ◽

Spermophilus Lateralis ◽

Cellular Processes ◽

New Genes ◽

Molecular Events ◽

Unbiased Gene ◽

Transcriptional Changes

Hibernation is a seasonally entrained and profound phenotypic transition to conserve energy in winter. It involves significant biochemical reprogramming, although our understanding of the underpinning molecular events is fragmentary and selective. We have conducted a large-scale gene expression screen of the golden-mantled ground squirrel, Spermophilus lateralis, to identify transcriptional responses associated specifically with the summer-winter transition and the torpid-arousal transition in winter. We used 112 cDNA microarrays comprising 12,288 probes that cover at least 5,109 genes. In liver, the profiles of torpid and active states in the winter were almost identical, although we identified 102 cDNAs that were differentially expressed between winter and summer, 90% of which were downregulated in the winter states. By contrast, in cardiac tissue, 59 and 115 cDNAs were elevated in interbout arousal and torpor, respectively, relative to the summer active condition, but only 7 were common to both winter states, and during arousal none was downregulated. In brain, 78 cDNAs were found to change in winter, 44 of which were upregulated. Thus transcriptional changes associated with hibernation are qualitatively modest and, since these changes are generally less than twofold, also quantitatively modest. Unbiased Gene Ontology profiling of the transcripts suggests a winter switch to β-oxidation of lipids in liver and heart, a reduction in metabolism of toxic compounds and the urea cycle in liver, and downregulated electron transport in the brain. We identified just one strongly winter-induced transcript common to all tissues, namely an RNA-binding protein, RBM3. This analysis clearly differentiates responses of the principal tissues, identifies a large number of new genes undergoing regulation, and broadens our understanding of affected cellular processes that, in part, account for the winter-adaptive hibernating phenotype.

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Metatranscriptomic Analysis of the Response of River Biofilms to Pharmaceutical Products, Using Anonymous DNA Microarrays

Applied and Environmental Microbiology ◽

10.1128/aem.00873-10 ◽

2010 ◽

Vol 76 (16) ◽

pp. 5432-5439 ◽

Cited By ~ 34

Author(s):

Etienne Yergeau ◽

John R. Lawrence ◽

Marley J. Waiser ◽

Darren R. Korber ◽

Charles W. Greer

Keyword(s):

Large Scale ◽

Dna Microarrays ◽

Domestic Wastewater ◽

Microarray Platform ◽

Pharmaceutical Products ◽

Ecosystem Dynamics ◽

Transcriptional Responses ◽

Domestic Wastewater Treatment ◽

Low Concentrations ◽

Transcriptional Changes

ABSTRACT Pharmaceutical products are released at low concentrations into aquatic environments following domestic wastewater treatment. Such low concentrations have been shown to induce transcriptional responses in microorganisms, which could have consequences on aquatic ecosystem dynamics. In order to test if these transcriptional responses could also be observed in complex river microbial communities, biofilm reactors were inoculated with water from two rivers of differing trophic statuses and subsequently treated with environmentally relevant doses (ng/liter to μg/liter range) of four pharmaceuticals (erythromycin [ER], gemfibrozil [GM], sulfamethazine [SN], and sulfamethoxazole [SL]). To monitor functional gene expression, we constructed a 9,600-feature anonymous DNA microarray platform onto which cDNA from the biofilms was hybridized. Pharmaceutical treatments induced both positive and negative transcriptional responses from biofilm microorganisms. For instance, ER induced the transcription of several stress, transcription, and replication genes, while GM, a lipid regulator, induced transcriptional responses from several genes involved in lipid metabolism. SN caused shifts in genes involved in energy production and conversion, and SL induced responses from a range of cell membrane and outer envelope genes, which in turn could affect biofilm formation. The results presented here demonstrate for the first time that low concentrations of small molecules can induce transcriptional changes in a complex microbial community. The relevance of these results also demonstrates the usefulness of anonymous DNA microarrays for large-scale metatranscriptomic studies of communities from differing aquatic ecosystems.

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Murine Macrophage Transcriptional Responses to Bacillus anthracis Infection and Intoxication

Infection and Immunity ◽

10.1128/iai.73.2.1069-1080.2005 ◽

2005 ◽

Vol 73 (2) ◽

pp. 1069-1080 ◽

Cited By ~ 37

Author(s):

Nicholas H. Bergman ◽

Karla D. Passalacqua ◽

Renee Gaspard ◽

Lynne M. Shetron-Rama ◽

John Quackenbush ◽

...

Keyword(s):

Bacillus Anthracis ◽

Bacterial Species ◽

Expression Patterns ◽

Transcriptional Response ◽

Anthrax Lethal Toxin ◽

Transcriptional Responses ◽

Transcriptional Changes ◽

Infected Cells ◽

Induced Apoptosis

ABSTRACT Interactions between Bacillus anthracis and host macrophages represent critical early events in anthrax pathogenesis, but their details are not clearly understood. Here we report the first genomewide characterization of the transcriptional changes within macrophages infected with B. anthracis and the identification of several hundred host genes that were differentially expressed during this intracellular stage of infection. These loci included both genes that are known to be regulated differentially in response to many other bacterial pathogens and those that appear to be differentially regulated in response to B. anthracis but not other bacterial species that have been tested. These data provide a transcriptional basis for a variety of physiological changes observed during infection, including the induction of apoptosis caused by the infecting bacteria. The expression patterns underlying B. anthracis-induced apoptosis led us to test further the importance of one very highly induced macrophage gene, that for ornithine decarboxylase. Our data show that this enzyme plays an important and previously unrecognized role in suppressing apoptosis in B. anthracis-infected cells. We have also characterized the transcriptional response to anthrax lethal toxin in activated macrophages and found that, following toxin treatment, many of the host inflammatory response pathways are dampened. These data provide insights into B. anthracis pathogenesis as well as potential leads for the development of new diagnostic and therapeutic options.

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Transcriptional responses to hyperplastic MRL signalling in Drosophila

Open Biology ◽

10.1098/rsob.160306 ◽

2017 ◽

Vol 7 (2) ◽

pp. 160306 ◽

Cited By ~ 1

Author(s):

Vincent Jonchère ◽

Nada Alqadri ◽

John Herbert ◽

Lauren Dodgson ◽

David Mason ◽

...

Keyword(s):

Serum Response Factor ◽

Transcriptional Response ◽

Size Control ◽

Actin Dynamics ◽

Transcriptional Responses ◽

Rna Profiling ◽

Related Transcription Factor ◽

Transcriptional Changes ◽

Wing Discs

Recent work has implicated the actin cytoskeleton in tissue size control and tumourigenesis, but how changes in actin dynamics contribute to hyperplastic growth is still unclear. Overexpression of Pico, the only Drosophila Mig-10/RIAM/Lamellipodin adapter protein family member, has been linked to tissue overgrowth via its effect on the myocardin-related transcription factor (Mrtf), an F-actin sensor capable of activating serum response factor (SRF). Transcriptional changes induced by acute Mrtf/SRF signalling have been largely linked to actin biosynthesis and cytoskeletal regulation. However, by RNA profiling, we find that the common response to chronic mrtf and pico overexpression in wing discs was upregulation of ribosome protein and mitochondrial genes, which are conserved targets for Mrtf/SRF and are known growth drivers. Consistent with their ability to induce a common transcriptional response and activate SRF signalling in vitro , we found that both pico and mrtf stimulate expression of an SRF-responsive reporter gene in wing discs. In a functional genetic screen, we also identified deterin , which encodes Drosophila Survivin, as a putative Mrtf/SRF target that is necessary for pico -mediated tissue overgrowth by suppressing proliferation-associated cell death. Taken together, our findings raise the possibility that distinct targets of Mrtf/SRF may be transcriptionally induced depending on the duration of upstream signalling.

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Tomato Whole Genome Transcriptional Response to Tetranychus urticae Identifies Divergence of Spider Mite-Induced Responses Between Tomato and Arabidopsis

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-09-14-0291-fi ◽

2015 ◽

Vol 28 (3) ◽

pp. 343-361 ◽

Cited By ~ 47

Author(s):

Catherine Martel ◽

Vladimir Zhurov ◽

Marie Navarro ◽

Manuel Martinez ◽

Marc Cazaux ◽

...

Keyword(s):

Tetranychus Urticae ◽

Spider Mite ◽

Transcriptional Response ◽

Defense Responses ◽

Induced Responses ◽

Transcriptional Responses ◽

Transcriptional Changes ◽

Mite Feeding ◽

Two Spotted Spider Mite ◽

Ja Signaling

The two-spotted spider mite Tetranychus urticae is one of the most significant mite pests in agriculture, feeding on more than 1,100 plant hosts, including model plants Arabidopsis thaliana and tomato, Solanum lycopersicum. Here, we describe timecourse tomato transcriptional responses to spider mite feeding and compare them with Arabidopsis in order to determine conserved and divergent defense responses to this pest. To refine the involvement of jasmonic acid (JA) in mite-induced responses and to improve tomato Gene Ontology annotations, we analyzed transcriptional changes in the tomato JA-signaling mutant defenseless1 (def-1) upon JA treatment and spider mite herbivory. Overlay of differentially expressed genes (DEG) identified in def-1 onto those from the timecourse experiment established that JA controls expression of the majority of genes differentially regulated by herbivory. Comparison of defense responses between tomato and Arabidopsis highlighted 96 orthologous genes (of 2,133 DEG) that were recruited for defense against spider mites in both species. These genes, involved in biosynthesis of JA, phenylpropanoids, flavonoids, and terpenoids, represent the conserved core of induced defenses. The remaining tomato DEG support the establishment of tomato-specific defenses, indicating profound divergence of spider mite–induced responses between tomato and Arabidopsis.

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Some comments about observations and image processing of comet 29P/Schwassmann-Wachmann 1

International Astronomical Union Colloquium ◽

10.1017/s0252921100031493 ◽

1999 ◽

Vol 173 ◽

pp. 243-248

Author(s):

D. Kubáček ◽

A. Galád ◽

A. Pravda

Keyword(s):

Image Processing ◽

Large Scale ◽

Harvard College ◽

Oak Ridge ◽

Large Scale Structures ◽

Short Period Comet ◽

Short Period ◽

Scale Structures ◽

Harvard College Observatory ◽

Period Comet

AbstractUnusual short-period comet 29P/Schwassmann-Wachmann 1 inspired many observers to explain its unpredictable outbursts. In this paper large scale structures and features from the inner part of the coma in time periods around outbursts are studied. CCD images were taken at Whipple Observatory, Mt. Hopkins, in 1989 and at Astronomical Observatory, Modra, from 1995 to 1998. Photographic plates of the comet were taken at Harvard College Observatory, Oak Ridge, from 1974 to 1982. The latter were digitized at first to apply the same techniques of image processing for optimizing the visibility of features in the coma during outbursts. Outbursts and coma structures show various shapes.

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