scholarly journals Infected juvenile salmon can experience increased predation during freshwater migration

2021 ◽  
Vol 8 (3) ◽  
Author(s):  
Nathan B. Furey ◽  
Arthur L. Bass ◽  
Kristi M. Miller ◽  
Shaorong Li ◽  
Andrew G. Lotto ◽  
...  
Keyword(s):  
Predation Risk ◽  
Sockeye Salmon ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Profiles ◽  
Bull Trout ◽  
Infectious Agents ◽  
Migrant Populations ◽  
Ecological Benefit ◽  
South Central

Predation risk for animal migrants can be impacted by physical condition. Although size- or condition-based selection is often observed, observing infection-based predation is rare due to the difficulties in assessing infectious agents in predated samples. We examined predation of outmigrating sockeye salmon ( Oncorhynchus nerka ) smolts by bull trout ( Salvelinus confluentus ) in south-central British Columbia, Canada. We used a high-throughput quantitative polymerase chain reaction (qPCR) platform to screen for the presence of 17 infectious agents found in salmon and assess 14 host genes associated with viral responses. In one (2014) of the two years assessed (2014 and 2015), the presence of infectious haematopoietic necrosis virus (IHNv) resulted in 15–26 times greater chance of predation; in 2015 IHNv was absent among all samples, predated or not. Thus, we provide further evidence that infection can impact predation risk in migrants. Some smolts with high IHNv loads also exhibited gene expression profiles consistent with a virus-induced disease state. Nine other infectious agents were observed between the two years, none of which were associated with increased selection by bull trout. In 2014, richness of infectious agents was also associated with greater predation risk. This is a rare demonstration of predator consumption resulting in selection for prey that carry infectious agents. The mechanism by which this selection occurs is not yet determined. By culling infectious agents from migrant populations, fish predators could provide an ecological benefit to prey.

scholarly journals Discovery of novel mechanosensitive genes in vivo using mouse carotid artery endothelium exposed to disturbed flow

Blood ◽  
2010 ◽  
Vol 116 (15) ◽  
pp. e66-e73 ◽  
Author(s):  
Chih-Wen Ni ◽  
Haiwei Qiu ◽  
Amir Rezvan ◽  
Kihwan Kwon ◽  
Douglas Nam ◽  
...  
Keyword(s):  
Carotid Artery ◽  
Ex Vivo ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Profiles ◽  
Disturbed Flow ◽  
A Genome ◽  
Pattern Comparison

Abstract Recently, we showed that disturbed flow caused by a partial ligation of mouse carotid artery rapidly induces atherosclerosis. Here, we identified mechanosensitive genes in vivo through a genome-wide microarray study using mouse endothelial RNAs isolated from the flow-disturbed left and the undisturbed right common carotid artery. We found 62 and 523 genes that changed significantly by 12 hours and 48 hours after ligation, respectively. The results were validated by quantitative polymerase chain reaction for 44 of 46 tested genes. This array study discovered numerous novel mechanosensitive genes, including Lmo4, klk10, and dhh, while confirming well-known ones, such as Klf2, eNOS, and BMP4. Four genes were further validated for protein, including LMO4, which showed higher expression in mouse aortic arch and in human coronary endothelium in an asymmetric pattern. Comparison of in vivo, ex vivo, and in vitro endothelial gene expression profiles indicates that numerous in vivo mechanosensitive genes appear to be lost or dysregulated during culture. Gene ontology analyses show that disturbed flow regulates genes involved in cell proliferation and morphology by 12 hours, followed by inflammatory and immune responses by 48 hours. Determining the functional importance of these novel mechanosensitive genes may provide important insights into understanding vascular biology and atherosclerosis.

scholarly journals In vivo differences between endothelial transcriptional profiles of coronary and iliac arteries revealed by microarray analysis

2008 ◽  
Vol 295 (4) ◽  
pp. H1556-H1561 ◽  
Author(s):  
Ji Zhang ◽  
Kelley A. Burridge ◽  
Morton H. Friedman
Keyword(s):  
Dna Microarrays ◽  
System Development ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Profiles ◽  
Classical Pathway ◽  
Biological Pathway Analysis ◽  
Almost All ◽  
And Function

Endothelial cells (ECs) from different vascular beds display a remarkable heterogeneity in both structure and function. Phenotypic heterogeneity among arterial ECs is particularly relevant to atherosclerosis since the disease occurs predominantly in major arteries, which vary in their atherosusceptibility. To explore EC heterogeneity between typical atheroprone and atheroresistant arteries, we used DNA microarrays to compare gene expression profiles of freshly harvested porcine coronary (CECs) and iliac artery (IECs) ECs. Statistical analysis revealed 51 genes that were differentially expressed in CECs relative to IECs at a false discovery rate of 5%. Seventeen of these genes are known to be involved in atherogenesis. Consistent with coronary arteries being more atherosusceptible, almost all putative atherogenic genes were overexpressed in CECs, whereas all atheroprotective genes were downregulated, relative to IECs. A subset of the identified genes was validated by quantitative polymerase chain reaction (PCR). PCR results suggest that the differences in expression levels between CECs and IECs for the HOXA10 and HOXA9 genes were >100-fold. Gene ontology (GO) and biological pathway analysis revealed a global expression difference between CECs and IECs. Genes in twelve GO categories, including complement immune activation, immunoglobulin-mediated response, and system development, were significantly upregulated in CECs. CECs also overexpressed genes involved in several inflammatory pathways, including the classical pathway of complement activation and the IGF-1-mediated pathway. The in vivo transcriptional differences between CECs and IECs found in this study may provide new insights into the factors responsible for coronary artery atherosusceptibility.

scholarly journals Microarray Analysis Shows That Recessive Resistance to Watermelon mosaic virus in Melon Is Associated with the Induction of Defense Response Genes

2012 ◽  
Vol 25 (1) ◽  
pp. 107-118 ◽  
Author(s):  
Daniel Gonzalez-Ibeas ◽  
Joaquin Cañizares ◽  
Miguel A. Aranda
Keyword(s):  
Mosaic Virus ◽  
Defense Response ◽  
Time Course ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Virus Titer ◽  
Gene Expression Profiles ◽  
Early Response ◽  
Resistant Variety ◽  
Watermelon Mosaic Virus

Resistance to Watermelon mosaic virus (WMV) in melon (Cucumis melo L.) accession TGR-1551 is characterized by a significant reduction in virus titer, and is inherited as a recessive, loss-of-susceptibility allele. We measured virus RNA accumulation in TGR-1551 plants and a susceptible control (‘Tendral’) by real-time quantitative polymerase chain reaction, and also profiled the expression of 17,443 unigenes represented on a melon microarray over a 15-day time course. The virus accumulated to higher levels in cotyledons of the resistant variety up to 9 days postinoculation (dpi) but, thereafter, levels increased in the susceptible variety while those in the resistant variety declined. Microarray experiments looking at the early response to infection (1 and 3 dpi), as well as responses after 7 and 15 dpi, revealed more profound transcriptomic changes in resistant plants than susceptible ones. The gene expression profiles revealed deep and extensive transcriptome remodeling in TGR-1551 plants, often involving genes with pathogen response functions. Overall, our data suggested that resistance to WMV in TGR-1551 melon plants is associated with a defense response, which contrasts with the recessive nature of the resistance trait.

scholarly journals A classifier driven approach to find biomarkers for affective disorders from transcription profiles in blood

2016 ◽  
Vol 1 (1) ◽  
pp. 34 ◽  
Author(s):  
Wiktor Mazin ◽  
Joseph A Tamm ◽  
Irina A Antonijevic ◽  
Aicha Abdourahman ◽  
Munish Das ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Affective Disorders ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Expression Levels ◽  
Control Subjects ◽  
Transcription Profiles

Gene expression profiles in blood are increasingly being used to identify biomarkers for different affective disorders. We have selected a set of 29 genes to generate expression profiles for healthy control subjects as well as for patients diagnosed with acute post-traumatic stress disorder (PTSD) and with borderline personality disorder (BPD). Measurements were performed by quantitative polymerase chain reaction (qPCR). Using the actual data in an anonym-ous form we constructed a series of artificial data sets with known gene expression profiles. These sets were used to test 14 classification algorithms and feature selection methods for their ability to identify the correct expression patterns. Application of the three most effective algorithms to the actual expression data showed that control subjects can be dis-tinguished from BPD patients based on differential expression levels of the gene transcripts Gi2, GR and MAPK14, targets that may have links to stress related diseases. Controls can also be distinguished from acute PTSD patients by differential expression levels of the transcripts for ERK2 and RGS2 that are known to be associated with mood disord-ers and social anxiety. We conclude that it is possible to identify informative transcription profiles in blood samples from individuals with affective disorders.

scholarly journals High expression of RRM2 promotes the pathogenesis of malignant ovarian endometriosis.

2021 ◽  
Author(s):  
Binkai Yang ◽  
Yuanjing Hu ◽  
Tian Wang ◽  
Na Li ◽  
Wenwen Zhang
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Malignant Transformation ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Profiles ◽  
High Expression ◽  
Ovarian Endometriosis ◽  
Ki 67 ◽  
Significant Difference

Abstract Objective: Our objective was to investigate the upregulated expression of ribonucleotide reductase M2 (RRM2) in the ectopic endometrium (EC) of ovarian endometriosis (OE) patients that may indicate malignant transformation. RRM2 may be used as a marker of OE, which contribute to the research of the mechanism of the malignant transformation of OE.Methods: The gene expression profiles of ovarian cancer and OE were downloaded from Gene Expression Omnibus (GEO), and a common hub gene, RRM2, was identified. The expression of RRM2 was low in OE and high in ovarian cancer. A total of 44 patients with endometriosis-associated ovarian cancers (EAOC) and 44 with OE were enrolled in this study. Immunohistochemistry (IHC) and real-time quantitative polymerase chain reaction (RT-qPCR) were used to detect the expression of RRM2, while the relationship between RRM2 and Ki-67 was analyzed by IHC co-localization. Results: There was no significant difference in the expression of RRM2 in the eutopic endometrium (EU), EC, and cancer tissues of EAOC patients. Compared with OE patients, the mRNA and protein expression levels of RRM2 were higher in the EC of EAOC patients (p＜0.01). Moreover, the high expression of RRM2 was consistent with the expression of Ki-67 in EC of EAOC patients.Conclusions: The upregulated expression of RRM2 in the EC of OE patients may indicate malignant transformation. RRM2 may be used as a marker of OE, which allows the investigation of the mechanism of the malignant transformation of OE.

scholarly journals A distinguishing gene signature shared by tumor-infiltrating Tie2-expressing monocytes, blood “resident” monocytes, and embryonic macrophages suggests common functions and developmental relationships

Blood ◽  
2009 ◽  
Vol 114 (4) ◽  
pp. 901-914 ◽  
Author(s):  
Ferdinando Pucci ◽  
Mary Anna Venneri ◽  
Daniela Biziato ◽  
Alessandro Nonis ◽  
Davide Moi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Profiles ◽  
Tissue Remodeling ◽  
Suppressor Cells ◽  
Gene Signature ◽  
Blood Monocytes ◽  
Inflammatory Monocytes

Abstract We previously showed that Tie2-expressing monocytes (TEMs) have nonredundant proangiogenic activity in tumors. Here, we compared the gene expression profile of tumor-infiltrating TEMs with that of tumor-associated macrophages (TAMs), spleen-derived Gr1+Cd11b+ neutrophils/myeloid-derived suppressor cells, circulating “inflammatory” and “resident” monocytes, and tumor-derived endothelial cells (ECs) by quantitative polymerase chain reaction–based gene arrays. TEMs sharply differed from ECs and Gr1+Cd11b+ cells but were highly related to TAMs. Nevertheless, several genes were differentially expressed between TEMs and TAMs, highlighting a TEM signature consistent with enhanced proangiogenic/tissue-remodeling activity and lower proinflammatory activity. We validated these findings in models of oncogenesis and transgenic mice expressing a microRNA-regulated Tie2-GFP reporter. Remarkably, resident monocytes and TEMs on one hand, and inflammatory monocytes and TAMs on the other hand, expressed coordinated gene expression profiles, suggesting that the 2 blood monocyte subsets are committed to distinct extravascular fates in the tumor microenvironment. We further showed that a prominent proportion of embryonic/fetal macrophages, which participate in tissue morphogenesis, expressed distinguishing TEM genes. It is tempting to speculate that Tie2+ embryonic/fetal macrophages, resident blood monocytes, and tumor-infiltrating TEMs represent distinct developmental stages of a TEM lineage committed to execute physiologic proangiogenic and tissue-remodeling programs, which can be coopted by tumors.

scholarly journals Identification of reference genes for gene expression studies among different developmental stages of murine hearts

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jie Ren ◽  
Ningning Zhang ◽  
Xiangjie Li ◽  
Xiaogang Sun ◽  
Jiangping Song
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Heart Development ◽  
Reference Genes ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Qpcr Data

Abstract Background Real-time quantitative polymerase chain reaction (RT-qPCR) is a widely-used standard assay for assessing gene expression. RT-qPCR data requires reference genes for normalization to make the results comparable. Therefore, the selected reference gene should be highly stable in its expression throughout the experimental datasets. So far, reports about the optimal set of reference genes in murine left ventricle (LV) across embryonic and postnatal stages are few. The objective of our research was to identify the appropriate reference genes in murine LV among different developmental stages. Methods We investigated the gene expression profiles of 21 widely used housekeeping genes in murine LV from 7 different developmental stages (almost throughout the whole period of the mouse lifespan). The stabilities of the potential reference genes were evaluated by five methods: GeNorm, NormFinder, BestKeeper, Delta-Ct and RefFinder. Results We proposed a set of reliable reference genes for normalization of RT-qPCR experimental data in different conditions. Furthermore, our results showed that 6 genes (18S, Hmbs, Ubc, Psmb4, Tfrc and Actb) are not recommended to be used as reference genes in murine LV development studies. The data also suggested that the Rplp0 gene might serve as an optimal reference gene in gene expression analysis. Conclusions Our study investigated the expression stability of the commonly used reference genes in process of LV development and maturation. We proposed a set of optimal reference genes that are suitable for accurate normalization of RT-qPCR data in specific conditions. Our findings may be helpful in future studies for investigating the gene expression patterns and mechanism of mammalian heart development.

Temporal gene expression profile of human precursor B leukemia cells induced by adhesion receptor: identification of pathways regulating B-cell survival

Blood ◽  
2003 ◽  
Vol 101 (3) ◽  
pp. 1118-1127 ◽  
Author(s):  
Anne Laurence Astier ◽  
Ronghui Xu ◽  
Marek Svoboda ◽  
Esther Hinds ◽  
Olivier Munoz ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cells ◽  
Stromal Cells ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Survivin Expression ◽  
Gene Expression Profiles ◽  
Leukemia Cells ◽  
Drug Induced ◽  
Temporal Gene Expression

Abstract The physical interactions between B cells and stromal cells from the lymphoid tissue microenvironment are critical to the survival of normal and malignant B cells. They are principally mediated by integrins expressed on B cells and counterreceptors on stromal cells. Specifically, α4β1 integrin engagement rescues B cells from physiological or drug-induced apoptosis. Therefore, in order to understand the mechanisms by which integrins prevent apoptosis in leukemia B cells, we compared the temporal gene expression profiles induced by β1-integrin ligation with fibronectin (Fn) or adhesion by poly-L-Lysine in serum-starved precursor B leukemia cells. Among the 38 selected differentially expressed genes, 6 genes involved in adhesion (VAV2, EPB41L1, CORO1A), proliferation (FRAP1, CCT4), and intercellular communication (GJB3) were validated by real-time quantitative polymerase chain reaction (RT-Q-PCR). Gene expression modulation could also be validated at the protein level for 5 other genes. We show that integrin stimulation up-regulated FBI-1 expression but inhibited CD79a, Requiem, c-Fos, and caspase 7 induction when the cells underwent apoptosis. We further demonstrate that Fn stimulation also inhibits caspase 3 activation but increases XIAP and survivin expression. Moreover, integrin stimulation also prevents caspase activation induced by doxorubicin. Therefore, we identified genes modulated by adhesion of human precursor B leukemia cells that regulate proliferation and apoptosis, highlighting new pathways that might provide insights into future therapy aiming at targeting apoptosis of leukemia cells.

Transcriptome profiles relate to migration fate in hatchery steelhead (Oncorhynchus mykiss) smolts

2018 ◽  
Vol 75 (11) ◽  
pp. 2053-2068 ◽  
Author(s):  
Stephen J. Healy ◽  
Scott G. Hinch ◽  
Arthur L. Bass ◽  
Nathan B. Furey ◽  
David W. Welch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Oncorhynchus Mykiss ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Physiological State ◽  
Life Stage ◽  
Gene Expression Profiles ◽  
Infectious Agent ◽  
Immune Genes ◽  
Intrinsic Factors

For anadromous Pacific salmonid (Oncorhynchus spp.) smolts, the physiological state of individuals can influence migration fate. This critical life stage is typically associated with poor survival and influences population productivity, highlighting the need to identify intrinsic factors associated with outmigration fate. To better understand and identify such factors, we combined acoustic telemetry with nonlethal gill biopsies and used high-throughput real-time quantitative polymerase chain reaction to assess how infectious agents and host gene expression profiles influence migration fate for hatchery steelhead smolts (Oncorhynchus mykiss). Redundancy analyses of gene expression, infectious agent loads, and body condition highlighted gene expression profiles indicative of migratory fate. Smolts never detected after release in the river had significantly elevated expression of the immune genes Il-17D and RPL6, and lower expression of the osmoregulatory gene NKA α1b relative to other individuals. Flavobacterium psychrophilum and “Candidatus Branchiomonas cysticola” were detected in gill samples, but neither influenced survival. We demonstrate rare evidence of gene expression profiles relating to migration fate in juvenile salmonids and highlight potential mechanisms influencing fate for hatchery steelhead smolts.

High IGSF4 expression in pediatric M5 acute myeloid leukemia with t(9;11)(p22;q23)

Blood ◽  
2011 ◽  
Vol 117 (3) ◽  
pp. 928-935 ◽  
Author(s):  
Jenny E. Kuipers ◽  
Eva A. Coenen ◽  
Brian V. Balgobind ◽  
Jan Stary ◽  
Andre Baruchel ◽  
...  
Keyword(s):  
Overall Survival ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Methylation Status ◽  
Gene Expression Profiles ◽  
Promoter Hypermethylation ◽  
Acute Monoblastic Leukemia ◽  
A Cell ◽  
Polymerase Chain ◽  
French American British

Abstract Pediatric mixed-lineage leukemia (MLL)–rearranged acute monoblastic leukemia with t(9;11)(p22;q23) has a favorable outcome compared with other MLL-rearranged AML. The biologic background for this difference remains unknown. Therefore, we compared gene expression profiles (GEPs; Affymetrix HGU133 + 2.0) of 26 t(9;11)(p22;q23) patients with 42 other MLL-rearranged AML patients to identify differentially expressed genes. IGSF4, a cell-cell adhesion molecule, was found to be highly expressed in t(9;11)(p22;q23) patients, which was confirmed by real-time quantitative polymerase chain reaction and Western blot. IGSF4 expression within t(9;11)(p22;q23) patients was 4.9 times greater in French-American-British morphology classification (FAB)–M5 versus other FAB-types (P = .001). Methylation status investigation showed that high IGSF4-expressing t(9;11)(p22;q23) patients with FAB-M5 have no promoter hypermethylation, whereas all other cases do. Cell-line incubation with demethylating agent decitabine resulted in promoter demethylation and increased expression of IGSF4. Down-regulation of IGSF4 by siRNA did not affect proliferation or drug sensitivity. In a cohort of 79 MLL-rearranged AML cases, we show significant better overall survival for cases with high IGSF4 expression (5-year overall survival 0.70 vs 0.37, P = .03) In conclusion, we identified IGSF4 overexpression to be discriminative for t(9;11)(p22;q23) patients with FAB-M5, regulated partially by promoter methylation and resulting in survival benefit.

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