scholarly journals Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Sebastián Moschen ◽  
Johanna Marino ◽  
Salvador Nicosia ◽  
Janet Higgins ◽  
Saleh Alseekh ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Crop Yield ◽  
Leaf Senescence ◽  
Metabolic Pathways ◽  
Gene Networks ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Inbred Lines ◽  
Strong Impact ◽  
The Impact

Abstract Background Leaf senescence is a complex process, controlled by multiple genetic and environmental variables. In sunflower, leaf senescence is triggered abruptly following anthesis thereby limiting the capacity of plants to keep their green leaf area during grain filling, which subsequently has a strong impact on crop yield. Recently, we performed a selection of contrasting sunflower inbred lines for the progress of leaf senescence through a physiological, cytological and molecular approach. Here we present a large scale transcriptomic analysis using RNA-seq and its integration with metabolic profiles for two contrasting sunflower inbred lines, R453 and B481–6 (early and delayed senescence respectively), with the aim of identifying metabolic pathways associated to leaf senescence. Results Gene expression profiles revealed a higher number of differentially expressed genes, as well as, higher expression levels in R453, providing evidence for early activation of the senescence program in this line. Metabolic pathways associated with sugars and nutrient recycling were differentially regulated between the lines. Additionally, we identified transcription factors acting as hubs in the co-expression networks; some previously reported as senescence-associated genes in model species but many are novel candidate genes. Conclusions Understanding the onset and the progress of the senescence process in crops and the identification of these new candidate genes will likely prove highly useful for different management strategies to mitigate the impact of senescence on crop yield. Functional characterization of candidate genes will help to develop molecular tools for biotechnological applications in breeding crop yield.

scholarly journals Identification of Regulatory circRNAs Involved in the Pathogenesis of Acute Myocardial Infarction

2021 ◽  
Vol 11 ◽  
Author(s):  
Cuimei Zhao ◽  
Jingjing Liu ◽  
Wen Ge ◽  
Zhi Li ◽  
Mengwei Lv ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Acute Myocardial Infarction ◽  
Coronary Arteries ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Functional Characterization ◽  
High Morbidity ◽  
The Impact ◽  
Runx1 Expression

BackgroundAcute myocardial infarction (AMI) has high morbidity and mortality worldwide. However, the pathogenesis of AMI is still unclear, and the impact of circular RNAs (circRNAs) on AMI has rarely been recognized and needs to be explored.Materials and MethodsThe circRNA array was applied to investigate the expression level of circRNAs in the blood samples of coronary arteries of three AMI patients and three normal persons. Principal component analysis (PCA) and unsupervised clustering analysis were performed to reveal the distinguished expression patterns of circRNAs. The miRNA expression profiles of AMI patients were identified from a public dataset from the Gene Expression Omnibus (GEO) database (GSE31568). The miRNA binding sites on the circRNAs were predicted by miRanda. The miRNA enrichment analysis and annotation tool were used to explore the pathways that the dysregulated circRNAs may participate in.ResultsIn total, 142 differentially expressed circRNAs, including 89 upregulated and 53 downregulated in AMI samples, were identified by the differential expression analysis. AMI patients had quite different circRNA expression profiles to those of normal controls. Functional characterization revealed that circRNAs that had the potential to regulate miRNAs were mainly involved in seven pathways, such as the Runt-related transcription factor-1 (RUNX1) expression and activity-related pathway. Specifically, hsa_circRNA_001654, hsa_circRNA_091761, hsa_circRNA_405624, and hsa_circRNA_406698 were predicted to sponge four miRNAs including hsa-miR-491-3p, hsa-miR-646, hsa-miR-603, and hsa-miR-922, thereby regulating RUNX1 expression or activity.ConclusionWe identified dysregulated blood circRNAs in the coronary arteries of AMI patients and predicted that four upregulated circRNAs were involved in the regulation of RUNX1 expression or activity through sponging four miRNAs.

scholarly journals A WRKY transcription factor, TaWRKY42-B, facilitates initiation of leaf senescence by promoting jasmonic acid biosynthesis

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ming-Ming Zhao ◽  
Xiao-Wen Zhang ◽  
Yong-Wei Liu ◽  
Ke Li ◽  
Qi Tan ◽  
...  
Keyword(s):  
Leaf Senescence ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Wrky Transcription Factor ◽  
Positive Role ◽  
Environmental Signals ◽  
Source To Sink ◽  
Age Dependent ◽  
Functional Investigation

Abstract Background Leaf senescence comprises numerous cooperative events, integrates environmental signals with age-dependent developmental cues, and coordinates the multifaceted deterioration and source-to-sink allocation of nutrients. In crops, leaf senescence has long been regarded as an essential developmental stage for productivity and quality, whereas functional characterization of candidate genes involved in the regulation of leaf senescence has, thus far, been limited in wheat. Results In this study, we analyzed the expression profiles of 97 WRKY transcription factors (TFs) throughout the progression of leaf senescence in wheat and subsequently isolated a potential regulator of leaf senescence, TaWRKY42-B, for further functional investigation. By phenotypic and physiological analyses in TaWRKY42-B-overexpressing Arabidopsis plants and TaWRKY42-B-silenced wheat plants, we confirmed the positive role of TaWRKY42-B in the initiation of developmental and dark-induced leaf senescence. Furthermore, our results revealed that TaWRKY42-B promotes leaf senescence mainly by interacting with a JA biosynthesis gene, AtLOX3, and its ortholog, TaLOX3, which consequently contributes to the accumulation of JA content. In the present study, we also demonstrated that TaWRKY42-B was functionally conserved with AtWRKY53 in the initiation of age-dependent leaf senescence. Conclusion Our results revealed a novel positive regulator of leaf senescence, TaWRKY42-B, which mediates JA-related leaf senescence via activation of JA biosynthesis and has the potential to be a target gene for molecular breeding in wheat.

scholarly journals Relationship between Delayed Leaf Senescence (Stay-Green) and Agronomic and Physiological Characters in Maize (Zea mays L.)

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 276
Author(s):  
Nadia Chibane ◽  
Marlon Caicedo ◽  
Susana Martinez ◽  
Purificación Marcet ◽  
Pedro Revilla ◽  
...  
Keyword(s):  
Leaf Senescence ◽  
Dry Matter ◽  
Grain Filling ◽  
Inbred Lines ◽  
Kernel Weight ◽  
Stay Green ◽  
Delayed Senescence ◽  
Yield And Quality ◽  
Stover Yield ◽  
The Impact

Stay-green (SG) is a term used to describe genotypes that have delayed leaf senescence as compared to reference genotypes. SG could be favorable for grain yield, silage yield and quality, double exploitation (grain for feed and stover for bioenergy), stress resistance, etc. However, some studies show contradictory results regarding the influence of senescence or SG in the uptake and remobilization of nutrients and the yield and moisture of stover and grain. This experiment is aimed to study the impact of senescence in grain and stover yield and moisture in inbred lines of maize and assess the potential of SG genotypes for double exploitation. We also study the influence of senescence in the uptake of N and remobilization of dry matter and N from stover to grain. We evaluated 16 maize inbred lines with contrasting expression of senescence in the field at two locations in Galicia in 2017. We confirmed that SG is functional, meaning that the SG genotypes maintained photosynthesis activity for a lengthy period. Coordinated with a delayed senescence, the grain filling of the SG genotypes was 9 days longer than NSG genotypes. SG genotypes took up more N after flowering, although the remobilization of N and, in general, of dry matter from stover to kernels was less efficient. However, the higher uptake compensated the poor remobilization, and the final effect of SG on the N content of the kernels was favorable. SG was also favorable for kernel weight and the kernels of SG genotypes were 20% heavier than for NSG. The stover yield was also higher in the SG genotypes, indicating a potential of SG for breeding for double purpose (grain for feed and stover for bioenergy).

scholarly journals A Hidden Structural Variation in a Known IRD Gene: A Cautionary Tale of Two New Disease Candidate Genes

2021 ◽  
pp. mcs.a006131
Author(s):  
Hilary A Scott ◽  
Anna Larson ◽  
Shi Song Rong ◽  
Sudeep Mehrotra ◽  
Rossano Butcher ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Vision Loss ◽  
Sequence Data ◽  
Functional Characterization ◽  
Genetic Diagnosis ◽  
Cone Dystrophy ◽  
Potential Candidate ◽  
New Disease ◽  
Functional Assays ◽  
The Impact

Rod cone dystrophy (RCD), also known as retinitis pigmentosa, is an inherited condition leading to vision loss, affecting 1/3500 people. Over 270 genes are known to be implicated in the inherited retinal degenerations (IRDs), yet genetic diagnosis for ~30% IRD of patients remains elusive despite advances in sequencing technologies. The goal of this study was to determine the genetic causality in a family with Rod-cone dystrophy (RCD). Family members were given a full ophthalmic exam at the Retinal Service at MEE and consented to genetic testing. Whole exome sequencing (WES) was performed and variants of interest were Sanger validated. Functional assays were conducted in zebrafish along with splicing assays in relevant cell lines to determine the impact on retinal function. WES identified variants in two potential candidate genes that segregated with disease: GNL3 (G Protein Nucleolar 3) c.1187+3A>C and c.1568-8C>A; and PDE4DIP (Phosphodiester 4D Interacting Protein) c.3868G>A (p.Glu1290Lys) and c.4603G>A (p.Ala1535Thr). Both genes were promising candidates based on their retinal involvement (development and interactions with IRD-associated proteins), however the functional assays did not validate either gene. Subsequent WES reanalysis with an updated bioinformatics pipeline and widened search parameters led to the detection of a 94bp duplication in PRPF31 (pre-mRNA Processing Factor 31) c.73_266dup (p.Asp56GlyfsTer33) as the causal variant. Our study demonstrates the importance of thorough functional characterization of new disease candidate genes, and the value of reanalyzing NGS sequence data, which in our case led to identification of a hidden pathogenic variant in a known IRD gene.

scholarly journals Mammalian meiosis is more conserved by sex than by species: conserved co-expression networks of meiotic prophase

Reproduction ◽  
2011 ◽  
Vol 142 (5) ◽  
pp. 675-687 ◽  
Author(s):  
Yongchun Su ◽  
Yunfei Li ◽  
Ping Ye
Keyword(s):  
Germ Cell ◽  
Candidate Genes ◽  
Meiotic Prophase ◽  
Gene Networks ◽  
Expression Profiles ◽  
Mammalian Species ◽  
Human Reproduction ◽  
Cell Populations ◽  
Disease Genes ◽  
Clustering Methods

Despite the importance of meiosis to human reproduction, we know remarkably little about the genes and pathways that regulate meiotic progression through prophase in any mammalian species. Microarray expression profiles of mammalian gonads provide a valuable resource for probing gene networks. However, expression studies are confounded by mixed germ cell and somatic cell populations in the gonad and asynchronous germ cell populations. Further, widely used clustering methods for analyzing microarray profiles are unable to prioritize candidate genes for testing. To derive a comprehensive understanding of gene expression in mammalian meiotic prophase, we constructed conserved co-expression networks by linking expression profiles of male and female gonads across mouse and human. We demonstrate that conserved gene co-expression dramatically improved the accuracy of detecting known meiotic genes compared with using co-expression in individual studies. Interestingly, our results indicate that meiotic prophase is more conserved by sex than by species. The co-expression networks allowed us to identify genes involved in meiotic recombination, chromatin cohesion, and piRNA metabolism. Further, we were able to prioritize candidate genes based on quantitative co-expression links with known meiotic genes. Literature studies of these candidate genes suggest that some are human disease genes while others are associated with mammalian gonads. In conclusion, our co-expression networks provide a systematic understanding of cross-sex and cross-species conservations observed during meiotic prophase. This approach further allows us to prioritize candidate meiotic genes for in-depth mechanistic studies in the future.

scholarly journals Functional Genomics in Chickens: Development of Integrated-Systems Microarrays for Transcriptional Profiling and Discovery of Regulatory Pathways

2004 ◽  
Vol 5 (3) ◽  
pp. 253-261 ◽  
Author(s):  
L. A. Cogburn ◽  
X. Wang ◽  
W. Carre ◽  
L. Rejto ◽  
S. E. Aggrey ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Metabolic Pathways ◽  
Gene Networks ◽  
Broiler Chickens ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Transcriptional Profiling ◽  
Gene Expression Profiles ◽  
New Era ◽  
Regulatory Pathways

The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.

scholarly journals A Hidden Structural Variation in a Known IRD Gene: A Cautionary Tale of Two New Disease Candidate Genes

2021 ◽  
Author(s):  
Hilary A Scott ◽  
Anna Larson ◽  
Shisong Rong ◽  
Sudeep Mehrotra ◽  
Rossano Butcher ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Vision Loss ◽  
Sequence Data ◽  
Functional Characterization ◽  
Genetic Diagnosis ◽  
Cone Dystrophy ◽  
Potential Candidate ◽  
New Disease ◽  
Functional Assays ◽  
The Impact

Rod cone dystrophy (RCD), also known as retinitis pigmentosa, is an inherited condition leading to vision loss, affecting 1/3500 people. Over 270 genes are known to be implicated in the inherited retinal degenerations (IRDs), yet genetic diagnosis for ~30% IRD of patients remains elusive despite advances in sequencing technologies. The goal of this study was to determine the genetic causality in a family with Rod-cone dystrophy (RCD). Family members were given a full ophthalmic exam at the Retinal Service at MEE and consented to genetic testing. Whole exome sequencing (WES) was performed and variants of interest were Sanger validated. Functional assays were conducted in zebrafish along with splicing assays in relevant cell lines to determine the impact on retinal function. WES identified variants in two potential candidate genes that segregated with disease: GNL3 (G Protein Nucleolar 3) c.1187+3A>C and c.1568-8C>A; and PDE4DIP (Phosphodiester 4D Interacting Protein) c.3868G>A (p.Glu1290Lys) and c.4603G>A (p.Ala1535Thr). Both genes were promising candidates based on their retinal involvement (development and interactions with IRD-associated proteins), however the functional assays did not validate either gene. Subsequent WES reanalysis with an updated bioinformatics pipeline and widened search parameters led to the detection of a 94bp duplication in PRPF31 (pre-mRNA Processing Factor 31) c.73_266dup (p.Asp56GlyfsTer33) as the causal variant. Our study demonstrates the importance of thorough functional characterization of new disease candidate genes, and the value of reanalyzing NGS sequence data, which in our case led to identification of a hidden pathogenic variant in a known IRD gene.

Uveal Melanoma—Where are We Going?

2011 ◽  
Vol 04 (01) ◽  
pp. 105 ◽  
Author(s):  
Miguel A Materin ◽  
Bertil Damato ◽  
◽  
Keyword(s):  
Uveal Melanoma ◽  
Chromosomal Abnormalities ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Lymphocytic Infiltration ◽  
Tumor Control ◽  
Strong Impact ◽  
Sampling Errors ◽  
Tumor Biopsy ◽  
The Impact

Despite good local tumor control, about 50% of patients affected by uveal melanoma die of their disease. Poor prognosis has been related to increased patient age, larger tumor size, ciliary body involvement, epithelioid cell type, extraocular extension, lymphocytic infiltration and high mitotic rate. In recent years, cytogenetic analysis has shown a strong impact on the management of these patients. Since monosomy of chromosome 3 proved to be a high predictive factor for metastatic disease, more ocular oncologists perform tumor biopsy almost routinely. However, there are still controversies regarding these results, such as sampling errors, mainly of disomy 3 results; the impact on quality of life; and the presence of other chromosomal abnormalities that correlate with prognosis as recently described in the literature (e.g. chromosomes 6, 8, 15 and 18). New classification of uveal melanomas as class 1 or class 2 tumors, indicating low and high risk for metastasis, respectively, has also been proposed using gene expression profiles.

When Do Psychopathic Traits Affect Cooperative Behavior?: An Iterated Prisoner's Dilemma Experimental Study

2020 ◽  
Author(s):  
M Testori ◽  
M Kempf ◽  
RB Hoyle ◽  
Hedwig Eisenbarth
Keyword(s):  
Prisoner's Dilemma ◽  
Cooperative Behavior ◽  
Prisoner’S Dilemma ◽  
Selection Procedure ◽  
Psychopathic Traits ◽  
Strong Impact ◽  
Iterated Prisoner's Dilemma ◽  
Human Decision ◽  
The Impact ◽  
Iterated Prisoner’S Dilemma

© 2019 Hogrefe Publishing. Personality traits have been long recognized to have a strong impact on human decision-making. In this study, a sample of 314 participants took part in an online game to investigate the impact of psychopathic traits on cooperative behavior in an iterated Prisoner's dilemma game. We found that disinhibition decreased the maintenance of cooperation in successive plays, but had no effect on moving toward cooperation after a previous defection or on the overall level of cooperation over rounds. Furthermore, our results underline the crucial importance of a good model selection procedure, showing how a poor choice of statistical model can provide misleading results.

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