scholarly journals Differential gene expression in Drosophila melanogaster and D. nigrosparsa infected with the same Wolbachia strain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Matsapume Detcharoen ◽  
Martin P. Schilling ◽  
Wolfgang Arthofer ◽  
Birgit C. Schlick-Steiner ◽  
Florian M. Steiner
Keyword(s):  
Gene Expression ◽  
Reduction Process ◽  
The Novel ◽  
Arthropod Species ◽  
Oxidation Reduction ◽  
Expression Of Genes ◽  
Novel Host ◽  
Differential Gene ◽  
Locomotor Activities ◽  
Potassium Channel Activity

AbstractWolbachia are maternally inherited endosymbionts that infect nearly half of all arthropod species. Wolbachia manipulate their hosts to maximize their transmission, but they can also provide benefits such as nutrients and resistance against viruses to their hosts. The Wolbachia strain wMel was recently found to increase locomotor activities and possibly trigger cytoplasmic incompatibility in the transinfected fly Drosophilanigrosparsa. Here, we investigated, in females of both D.melanogaster and D.nigrosparsa, the gene expression between animals uninfected and infected with wMel, using RNA sequencing to see if the two Drosophila species respond to the infection in the same or different ways. A total of 2164 orthologous genes were used. The two fly species responded to the infection in different ways. Significant changes shared by the fly species belong to the expression of genes involved in processes such as oxidation–reduction process, iron-ion binding, and voltage-gated potassium-channel activity. We discuss our findings also in the light of how Wolbachia survive within both the native and the novel host.

scholarly journals Differential gene expression in Drosophila melanogaster and D. nigrosparsa infected with the same Wolbachia strain

2020 ◽  
Author(s):  
Matsapume Detcharoen ◽  
Martin P. Schilling ◽  
Wolfgang Arthofer ◽  
Birgit C. Schlick-Steiner ◽  
Florian M. Steiner
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Differential Gene Expression ◽  
Expression Patterns ◽  
Specific Gene ◽  
Positive Effects ◽  
Arthropod Species ◽  
Expression Of Genes ◽  
Novel Host ◽  
Differential Gene

AbstractWolbachia, maternally inherited endosymbionts, infect nearly half of all arthropod species. Wolbachia manipulate their hosts to maximize their transmission, but they can also provide benefits such as nutrients and resistance to viruses for their hosts. The Wolbachia strain wMel was recently found to increase locomotor activities and possibly trigger cytoplasmic incompatibility in the fly Drosophila nigrosparsa. Here, we compared differential gene expression in Drosophila melanogaster (original host) and D. nigrosparsa (novel host), both uninfected and infected with wMel, using RNA sequencing to see if the two Drosophila species respond to the infection in the same or different ways. A total of 2164 orthologous genes were used. We found species-specific gene expression patterns. Significant changes shared by the fly species were confined to the expression of genes involved in heme binding and oxidation-reduction; the two host species differently changed the expression of genes when infected. Some of the genes were down-regulated in the infected D. nigrosparsa, which might indicate small positive effects of Wolbachia. We discuss our findings also in the light of how Wolbachia survive within both the native and the novel host.

scholarly journals Identification of Differential Gene Expression in Bacteria Associated with Coral Black Band Disease by Using RNA-Arbitrarily Primed PCR

2004 ◽  
Vol 70 (6) ◽  
pp. 3687-3694 ◽  
Author(s):  
Jorge Frias-Lopez ◽  
George T. Bonheyo ◽  
Bruce W. Fouke
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Black Band Disease ◽  
Expression Of Genes ◽  
Black Band ◽  
Differential Gene ◽  
Apoprotein A1 ◽  
Arbitrarily Primed Pcr ◽  
Transporter Systems ◽  
First Time

ABSTRACT RNA-arbitrarily primed PCR techniques have been applied for the first time to identify differential gene expression in black band disease (BBD), a virulent coral infection that affects reef ecosystems worldwide. The gene activity for the BBD mat on infected surfaces of the brain coral Diploria strigosa was compared with that for portions of the BBD mat that were removed from the coral and suspended nearby in the seawater column. The results obtained indicate that three genes (DD 95-2, DD 95-4, and DD 99-9) were up-regulated in the BBD bacterial mat on the coral surface compared to the transcript base levels observed in the BBD mat suspended in seawater. Clone DD 95-4 has homology with known amino acid ABC transporter systems in bacteria, while clone DD 99-9 exhibits homology with chlorophyll A apoprotein A1 in cyanobacteria. This protein is essential in the final conformation of photosystem I P700. DD 95-2, the only gene that was fully repressed in the BBD mat samples suspended in seawater, exhibited homology with the AraC-type DNA binding domain-containing proteins. These transcriptional activators coordinate the expression of genes essential for virulence in many species of gram-negative bacteria.

scholarly journals Differential gene expression is associated with degeneration of mating-type chromosomes in the absence of sexual antagonism

2019 ◽  
Author(s):  
Wen-Juan Ma ◽  
Fantin Carpentier ◽  
Tatiana Giraud ◽  
Michael Hood
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Mating Type ◽  
Mating Types ◽  
Antagonistic Selection ◽  
Expression Of Genes ◽  
Sexually Antagonistic Selection ◽  
Differential Gene ◽  
Anther Smut

AbstractIn animals and plants, differential expression of genes on sex chromosomes is widespread and it is usually considered to result from sexually antagonistic selection; however differential expression can also be caused by asymmetrical sequence degeneration in non-recombining sex chromosomes, which has been very little studied. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal to investigate the extent to which differential gene expression is associated with sequence degeneration because: 1) separate haploid cultures of opposite mating types help identify differential expression, 2) its mating-type chromosomes display multiple evolutionary strata reflecting successive events of gene linkage to the mating-type loci, and 3) antagonistic selection is unlikely between isogamous haploid mating types. We therefore tested the hypothesis that differential gene expression between mating types resulted from sequence degeneration. We found that genes showing differential expression between haploid mating types were enriched only on the oldest evolutionary strata of the mating-type chromosomes and were associated with multiple signatures of sequence degeneration. We found that differential expression between mating types was associated with elevated differences between alleles in non-synonymous substitution rates, indels and premature stop codons, transposable element insertions, and altered intron and GC content. Our findings strongly suggest that degenerative mutations are important in the evolution of differential expression in non-recombining regions. Our results are relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions of recombination suppression, showing that differential expression should not be taken as necessarily arising from antagonistic selection.Author SummaryDifferences between males and females, from morphology to behavior and physiology, are considered to largely reflect differential expression of genes that maximize fitness benefits relative to costs that are specific to one sex. However, there is an unexplored alternative to such ‘sexually antagonistic selection’ to explain differential expression. Reproductive compatibility is often determined by genes located in large non-recombining chromosomal regions, where degenerative mutations are expected to accumulate and may separately affect the expression of alternate alleles of genes. We tested the role of genetic degeneration in determining differential expression between the isogamous haploid mating types of the anther-smut fungus, Microbotryum lychnidis-dioicae, where sexually antagonistic selection is not a confounding factor. We show that differentially expressed genes are highly enriched in the non-recombining mating-type chromosomes, and that they are associated with various forms of degenerative mutations, some of which indicate that the less expressed allele suffers greater mutational effects. Our finding of the role for degenerative mutations in the evolution of differential expression is relevant for a broad range of organisms where reproductive compatibility or sex is determined by genes in regions of suppressed recombination, and shows that differential expression should not be taken as necessarily arising from antagonistic selection.

scholarly journals Gene expression of settled and metamorphosed Orbicella faveolata during establishment of symbiosis

2017 ◽  
Author(s):  
Aubrie O'Rourke ◽  
Aki Ohdera ◽  
Shinichi Sunagawa ◽  
Erika M Diaz-Almeyda ◽  
Michael K DeSalvo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nutrient Metabolism ◽  
Transcriptomic Response ◽  
Tropical Oceans ◽  
Expression Of Genes ◽  
Expression Studies ◽  
Genome Wide ◽  
Orbicella Faveolata ◽  
Algal Symbiosis ◽  
Differential Gene

Corals rely on a symbiosis with dinoflagellate algae (Symbiodinium spp.) to thrive in nutrient poor tropical oceans. However, the coral-algal symbiosis can break down during bleaching events, potentially leading to coral death. While genome-wide expression studies have shown the genes associated with the breakdown of this partnership, the full conglomerate of genes responsible for the establishment and maintenance of a healthy symbiosis remains unknown. Results from previous studies suggested little transcriptomic change associated with the establishment of symbiosis. We examined the transcriptomic response of the coral Orbicella faveolata in the presence (symbiotic) and absence (aposymbiotic) of Symbiodinium minutum, one of its associated symbionts. 9 days post-metamorphic aposymbiotic coral polyps of O. faveolata were compared to symbiotic coral polyps and the subsequent differential gene expression between control and treatment was quantified using cDNA microarray technology. Coral polyps exhibited differential expression of genes associated with nutrient metabolism and development, providing insight into control of pathways as a result of symbiosis driving early polyp growth. Furthermore, genes associated with lysosomal fusion were also upregulated, suggesting host regulation of symbiont densities soon after infection.

Changes in Differential Gene and Protein Expression Patterns during Development of Cord Blood (CB) Versus Adult Peripheral Blood (APB) Monocyte (Mo) into Mature Dendritic Cells (mDC): Insight into Immaturity of CB DC Immunity.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 5204-5204
Author(s):  
Hong Jiang ◽  
Cheryl Wade-Harris ◽  
Megan Lim ◽  
Laxmi Baxi ◽  
Mitchell S. Cairo
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Oligonucleotide Microarray ◽  
Differentially Expressed ◽  
Expression Of Genes ◽  
Differential Gene ◽  
Hla Dqa1 ◽  
Antigen Presenting

Abstract It has been recognized that dysfunction of CB immune system is in part due to the immaturity of CB cellular immunity (Cairo, Blood,1997). The molecular mechanisms associated with the immaturity of CB cellular immunity including DC subset remain to be defined. The maturation status of DC greatly influences its antigen presentation capacity. Recently, we have utilized oligonucleotide microarray to demonstrate differential gene expression profiles of CB vs APB Mo (Jiang/Cairo, JI, 2004). In the current study, differential expressed genes and proteins were examined in Mo-derived CB vs. APB DC during DC developmental stages: Mo, immature DC (iDC) and mDC, by utilizing oligonucleotide microarray and proteomics. Briefly, Mo isolated from CB or APB and cultured for 8 days with GM-CSF/IL-4 (iDC) and further stimulated with LPS (mDC). Oligonucleotide microarray was carried out using U133A gene chip (Affymetrix). The representative differentially expressed genes resulted from microarray analysis were selected and analyzed by quantitative RT-PCR (Roche). The proteomic technique was conducted by liquid chromatography (LC) and mass spectrometry (MS) (Lim, Mol Cell Proteomics, 2006). The differentially expressed proteins were compared in CB vs. APB for iDC and mDC. We identified different gene expression patterns that were significantly lower in CB vs. APB in different stages during DC differentiation: Mo, iDC and mDC. These differentially expressed genes included RELA (5F), JUNB (6F), IRF-1 (3F) in Mo; CREB5 (3F), MAP7 (5F), IL1R2 (6F) in iDC; and HLA-DQA1 (4F), CD80 (3F), IRF-5 (3F) in mDC. The proteomic studies demonstrated Tyrosine Kinase Fer (12.5F), Actin regulator 3 (2.5F), Rap guanine nucleotide exchange factor 1 (2.4F) and Myeloid cell nuclear differentiation antigen (1.5F) were expressed higher in APB vs.CB iDC, while MAX binding protein MNT (5.5F), IRS2 (2.2F) and Zinc-Finger Proteins (514, 212, 462) (3–14F) were expressed higher in CB vs. APB iDC. Further, the proteomic results also indicated other Zinc-Finger Proteins (292, 221, 474) (2–5F), Fibrillin 1 precursor (2.5F) and interleukin-4 (7.7F) were expressed higher in APB vs. CB mDC. In contrast, cyclin I (3F), Rb-like protein 2 (4.35 F) and PKC theta (2F) were significantly lower in APB vs. CB DC. Moreover, the comparison of CB vs. APB DC antigen presenting activity by ELISPOT was performed and the influenza-peptide loaded CB-mDC demonstrated weaker ability to induce T cells to produce IFNg compared with APB-mDC. In summary, these differentially expressed genes in Mo (RELA, JUN) may play key roles in initiating Mo differentiation toward DC. The increased expression of genes in APB vs. CB iDC, like CREB5, IL1R2, may be involved in mediating maturation process of iDC to mDC. Lastly, the elevated expression of genes in APB vs. CB mDC, such as HLA-DQA1, CD80, IRF5 among others, may be likely to control mDC functionality as demonstrated by weaker antigen presenting activity of CB vs. APB mDC. We postulate that decreased expression of specific genes in CB vs. APB DC during DC developmental stages may in part be responsible for the lack of maturity of CB, and ultimately may partially be responsible for differential CB vs. APB innate and adaptive immunity.

Bovine hepatic differential gene expression in response to perennial ryegrass staggers

2015 ◽  
Vol 8 (3) ◽  
pp. 351-360 ◽  
Author(s):  
L. Li ◽  
D.D. Tanaree ◽  
Y. Di ◽  
C.T. Estill ◽  
J.M. Duringer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Perennial Ryegrass ◽  
Extended Period ◽  
Double Blind Study ◽  
Double Blind ◽  
Oxidation Reduction ◽  
Differential Gene ◽  
Lolitrem B ◽  
Pathway Analyses

>‘Perennial ryegrass staggers’ is a neurological condition characterised by muscular tremors and ataxia in livestock that ingest the indole diterpene lolitrem B from endophyte-infected perennial ryegrass. While the neurotoxic mechanism of action of ryegrass staggers has been defined, little is known about metabolic and other molecular processes that lolitrem B may affect in livestock. The objective of this study was to characterise differential gene expression in the liver of animals fed lolitrem B-containing feed over an extended period of time. Eighteen steers were fed one of three rations (n=6/group) containing lolitrem B (247, 1,554 or 2,256 μg/kg (dry matter basis)) over 64 days in a double-blind study. Microarray and confirmatory qPCR were performed to evaluate the hepatic gene expression profile from biopsies taken on days 0 and 64. Widespread perturbation of gene expression was observed in all groups receiving lolitrem B, with a total of 152 differential genes identified (false discovery rate ≤0.05). This suggests that chronic exposure to lolitrem B, even at levels below the current threshold of toxicity (2,000 μg/kg lolitrem B), can perturb many genes, biological processes and pathways. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that many of these genes were categorised under lipid/steroid biosynthesis/metabolism and oxidation-reduction. Specifically, genes involved in the biosynthesis pathway of ceramide, a sphingolipid molecule (ACSS2, LASS6 and SCD) and changes in neurosignaling through alteration of nitric oxide synthase activity (ARG1 and GPX4) were up-regulated. Future work should focus on the overall balance between ceramide and its metabolites and antioxidants/oxidants in a variety of body matrices in animals with perennial ryegrass staggers, to determine how these compounds contribute to the overall etiology of this disease.

scholarly journals Changes in Nuclear Shape and Gene Expression in Response to Simulated Microgravity Are LINC Complex-Dependent

2020 ◽  
Vol 21 (18) ◽  
pp. 6762
Author(s):  
Srujana Neelam ◽  
Brian Richardson ◽  
Richard Barker ◽  
Ceasar Udave ◽  
Simon Gilroy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Simulated Microgravity ◽  
Focal Adhesions ◽  
Nuclear Shape ◽  
Microgravity Environment ◽  
Dependent Manner ◽  
Linc Complex ◽  
Expression Of Genes ◽  
Differential Gene

Microgravity is known to affect the organization of the cytoskeleton, cell and nuclear morphology and to elicit differential expression of genes associated with the cytoskeleton, focal adhesions and the extracellular matrix. Although the nucleus is mechanically connected to the cytoskeleton through the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, the role of this group of proteins in these responses to microgravity has yet to be defined. In our study, we used a simulated microgravity device, a 3-D clinostat (Gravite), to investigate whether the LINC complex mediates cellular responses to the simulated microgravity environment. We show that nuclear shape and differential gene expression are both responsive to simulated microgravity in a LINC-dependent manner and that this response changes with the duration of exposure to simulated microgravity. These LINC-dependent genes likely represent elements normally regulated by the mechanical forces imposed by gravity on Earth.

Family environments and leukocyte transcriptome indicators of a proinflammatory phenotype in children and parents

2017 ◽  
Vol 30 (1) ◽  
pp. 235-253 ◽  
Author(s):  
Theodore F. Robles ◽  
Rena L. Repetti ◽  
Bridget M. Reynolds ◽  
Paul J. Chung ◽  
Jesusa M. G. Arevalo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Family Conflict ◽  
Upper Respiratory Infection ◽  
Response Elements ◽  
Expression Of Genes ◽  
Children And Parents ◽  
High Conflict ◽  
Differential Gene ◽  
Upper Respiratory ◽  
Inhibitory Signaling

AbstractHigh conflict and low warmth in families may contribute to immune cells developing a tendency to respond to threats with exaggerated inflammation that is insensitive to inhibitory signaling. We tested associations between family environments and expression of genes bearing response elements for transcription factors that regulate inflammation: nuclear factor kappa B (NF-κB) and glucocorticoid receptor. The overall sample (47 families) completed interviews, questionnaires, and 8-week daily diary assessments of conflict and warmth, which were used to create composite family conflict and warmth scores. The diaries assessed upper respiratory infection (URI) symptoms, and URI episodes were clinically verified. Leukocyte RNA was extracted from whole blood samples provided by a subsample of 42 children (8–13 years of age) and 73 parents. In children, higher conflict and lower warmth were related to greater expression of genes bearing response elements for the proinflammatory transcription factor NF-κB, and more severe URI symptoms. In parents, higher conflict and lower warmth were also related to greater NF-κB–associated gene expression. Monocytes and dendritic cells were implicated as primary cellular sources of differential gene expression in the sample. Consistent with existing conceptual frameworks, stressful family environments were related to a proinflammatory phenotype at the level of the circulating leukocyte transcriptome.

Implication of clusterin in TNF-α response of rheumatoid synovitis: lesson from in vitro knock-down of clusterin in human synovial fibroblast cells

2012 ◽  
Vol 44 (3) ◽  
pp. 229-235 ◽  
Author(s):  
Géraldine Falgarone ◽  
Abdellatif Essabbani ◽  
Florent Dumont ◽  
Nicolas Cagnard ◽  
Sylvie Mistou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Molecular Signature ◽  
Expression Of Genes ◽  
Tnf Α ◽  
Genomic Gene ◽  
Differential Gene ◽  
Good Concordance

Recently clusterin (CLU) was reported to be an inhibitor of NF-κB pathway and involved in rheumatoid arthritis (RA) synovitis. This study was designed to decipher the molecular network linked to CLU expression in FLS (fibroblast-like synoviocytes) and evaluate the consequences of its low expression in conditions of TNF-α stimulation. FLS were transfected with siRNA for CLU or not and cultured for 24 and 48 h with TNF-α or not. Pan-genomic gene expression was assayed by DNA microarray. The gene network around CLU and gene interactions were analyzed with the Ingenuity Pathway Analysis software. Downregulation of CLU resulted in modification of the expression of genes known to be directly linked to CLU and for almost 5% of the tested genes (857 out of 17,225); the upregulation of a small group of gene (e.g., TIAM1) emphasizes the hypothetical role of CLU in the pseudotumoral characteristic of FLS. The comparison of gene expression with or without TNF stimulation allowed the classification of sampled with good concordance. Moreover, differential comparison showed that CLU downregulation in RA led to a profound modification of the TNF-α response as three sets of genes emerged: 497 genes modulated by siCLU transfection with TNF stimulation, 356 genes modified because of TNF stimulation only, and 484 genes modulated during TNF stimulation with CLU expression (e.g., IL-8 and Wnt signaling genes). Using a global two-way ANOVA we could identify a set of genes defining a molecular signature of TNF response directly influenced by CLU. These results (based on differential gene expression patterns) argue that CLU downregulation in FLS alters their aggressiveness in RA synovitis.

scholarly journals Assessment of the differential gene expression in anthracnose treated seedlings of yellow lupin

2021 ◽  
Vol 65 (3) ◽  
pp. 330-336
Author(s):  
E. N. Sysoliatin ◽  
V. S. Anokhina ◽  
N. V. Anisimova ◽  
O. G. Babak ◽  
A. V. Kilchevsky
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Genetic Determinants ◽  
Yellow Lupin ◽  
Expression Of Genes ◽  
Differential Gene ◽  
Colletotrichum Lupini ◽  
Yellow Lupine ◽  
Differential Expression Of Genes

Seedlings of yellow lupine treated with Colletotrichum lupini isolate were studied by the method of SRAP-analysis with the purpose to assess the differential expression of genes. As a result, the PCR fragment corresponding to tolerant seedlings was found. The genetic determinants found are likely involved in the control of the resistance (tolerance) of lupine plants to anthracnose.

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