scholarly journals Network Analysis of Local Gene Regulators in Arabidopsis thaliana under Spaceflight Stress

Computers ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 18
Author(s):  
Vidya Manian ◽  
Harshini Gangapuram ◽  
Jairo Orozco ◽  
Heeralal Janwa ◽  
Carlos Agrinsoni
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Response ◽  
Network Analysis ◽  
Target Genes ◽  
Carbon Fixation ◽  
Reduction Process ◽  
Centrality Measures ◽  
Lasso Regression ◽  
Gene Expressions ◽  
Stress Response Genes

Spaceflight microgravity affects normal plant growth in several ways. The transcriptional dataset of the plant model organism Arabidopsis thaliana grown in the international space station is mined using graph-theoretic network analysis approaches to identify significant gene transcriptions in microgravity essential for the plant’s survival and growth in altered environments. The photosynthesis process is critical for the survival of the plants in spaceflight under different environmentally stressful conditions such as lower levels of gravity, lesser oxygen availability, low atmospheric pressure, and the presence of cosmic radiation. Lasso regression method is used for gene regulatory network inferencing from gene expressions of four different ecotypes of Arabidopsis in spaceflight microgravity related to the photosynthetic process. The individual behavior of hub-genes and stress response genes in the photosynthetic process and their impact on the whole network is analyzed. Logistic regression on centrality measures computed from the networks, including average shortest path, betweenness centrality, closeness centrality, and eccentricity, and the HITS algorithm is used to rank genes and identify interactor or target genes from the networks. Through the hub and authority gene interactions, several biological processes associated with photosynthesis and carbon fixation genes are identified. The altered conditions in spaceflight have made all the ecotypes of Arabidopsis sensitive to dehydration-and-salt stress. The oxidative and heat-shock stress-response genes regulate the photosynthesis genes that are involved in the oxidation-reduction process in spaceflight microgravity, enabling the plant to adapt successfully to the spaceflight environment.

Hot1 factor recruits co-activator Sub1 and elongation complex Spt4/5 to osmostress genes

2016 ◽  
Vol 473 (19) ◽  
pp. 3065-3079 ◽  
Author(s):  
M. Gomar-Alba ◽  
M. del Olmo
Keyword(s):  
Transcription Factor ◽  
Stress Response ◽  
Rna Polymerase Ii ◽  
Target Genes ◽  
Coding Region ◽  
Elongation Complex ◽  
Direct Role ◽  
Coding Regions ◽  
Stress Response Genes ◽  
Rule Out

Hyperosmotic stress response involves the adaptative mechanisms needed for cell survival. Under high osmolarity conditions, many stress response genes are activated by several unrelated transcription factors that are controlled by the Hog1 kinase. Osmostress transcription factor Hot1 regulates the expression of several genes involved in glycerol biosynthesis, and the presence of this transcription factor in their promoters is essential for RNApol II recruitment. The physical association between Hog1 and Hot1 activates this transcription factor and directs the RNA polymerase II localization at these promoters. We, herein, demonstrate that physical and genetic interactions exist between Hot1 and several proteins involved in transcriptional and posttranscriptional processes: for example, transcription co-activator Sub1 and elongation complex Spt4/5. The results presented in this work demonstrate that Hot1 enrichment is not detected through the coding regions of its target genes and rule out a direct role in transcription elongation. Instead, other data presented herein indicate a key function of the Hot1 transcription factor in the recruitment of these proteins to the promoter or the 5′-coding region of the genes under its control.

scholarly journals The effects of high gravitational stress on the expression of stress response genes in Arabidopsis thaliana

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Sophia Alessandra Zappia
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Stress Response ◽  
Plant Growth ◽  
Stress Response Genes ◽  
Gravitational Stress ◽  
Model Plant Arabidopsis Thaliana ◽  
Small Model ◽  
Pathogen Response ◽  
Plant Arabidopsis Thaliana

As humans venture farther into space, we are increasingly interested in how plants respond to the unique conditions of spaceflight. This experiment focuses on how gene expression in the model plant Arabidopsis thaliana is affected by high-gravitational stress that is comparable to the amount experienced on a small model rocket. The genes chosen have been studied previously for their roles in mechanical stress and pathogen response. Our results showed an increase in expression of the genes TCH2, TCH3, and MPK3, no change in the expression of CBP60g, and a decrease in the expression of RCI3 and ICS1. These results are largely consistent with spaceflight data and warrant further investigation into the effects of rocket launch on plant growth.

scholarly journals AITRL, an evolutionarily conserved plant specific transcription repressor regulates ABA response in Arabidopsis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yanxing Ma ◽  
Hainan Tian ◽  
Rao Lin ◽  
Wei Wang ◽  
Na Zhang ◽  
...  
Keyword(s):  
Stress Response ◽  
Protein Phosphatase ◽  
Aba Signaling ◽  
Response Gene ◽  
Stress Response Genes ◽  
Arabidopsis Protein ◽  
Evolutionarily Conserved ◽  
Increased Sensitivity ◽  
Aba Response ◽  
Transcription Repressors

AbstractExpression of stress response genes can be regulated by abscisic acid (ABA) dependent and ABA independent pathways. Osmotic stresses promote ABA accumulation, therefore inducing the expression of stress response genes via ABA signaling. Whereas cold and heat stresses induce the expression of stress response genes via ABA independent pathway. ABA induced transcription repressors (AITRs) are a family of novel transcription factors that play a role in ABA signaling, and Drought response gene (DRG) has previously been shown to play a role in regulating plant response to drought and freezing stresses. We report here the identification of DRG as a novel transcription factor and a regulator of ABA response in Arabidopsis. We found that the expression of DRG was induced by ABA treatment. Homologs searching identified AITR5 as the most closely related Arabidopsis protein to DRG, and homologs of DRG, including the AITR-like (AITRL) proteins in bryophytes and gymnosperms, are specifically presented in embryophytes. Therefore we renamed DRG as AITRL. Protoplast transfection assays show that AITRL functioned as a transcription repressor. In seed germination and seedling greening assays, the aitrl mutants showed an increased sensitivity to ABA. By using qRT-PCR, we show that ABA responses of some ABA signaling component genes including some PYR1-likes (PYLs), PROTEIN PHOSPHATASE 2Cs (PP2Cs) and SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASES 2s (SnRK2s) were reduced in the aitrl mutants. Taken together, our results suggest that AITRLs are a family of novel transcription repressors evolutionally conserved in embryophytes, and AITRL regulates ABA response in Arabidopsis by affecting ABA response of some ABA signaling component genes.

scholarly journals Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guiomar Martín ◽  
Yamile Márquez ◽  
Federica Mantica ◽  
Paula Duque ◽  
Manuel Irimia
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Alternative Splicing ◽  
Stress Responses ◽  
Target Genes ◽  
Intron Retention ◽  
Single Gene ◽  
Exon Skipping ◽  
Environmental Response ◽  
Biotic Stresses

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

scholarly journals Time to Intervene: A Continuous-Time Approach to Network Analysis and Centrality

Psychometrika ◽  
2021 ◽  
Author(s):  
Oisín Ryan ◽  
Ellen L. Hamaker
Keyword(s):  
Network Analysis ◽  
Discrete Time ◽  
Continuous Time ◽  
Centrality Measures ◽  
Time Interval ◽  
Direct Effects ◽  
Network Approach ◽  
Var Models ◽  
Auto Regressive ◽  
Conceptual Shift

AbstractNetwork analysis of ESM data has become popular in clinical psychology. In this approach, discrete-time (DT) vector auto-regressive (VAR) models define the network structure with centrality measures used to identify intervention targets. However, VAR models suffer from time-interval dependency. Continuous-time (CT) models have been suggested as an alternative but require a conceptual shift, implying that DT-VAR parameters reflect total rather than direct effects. In this paper, we propose and illustrate a CT network approach using CT-VAR models. We define a new network representation and develop centrality measures which inform intervention targeting. This methodology is illustrated with an ESM dataset.

scholarly journals The acute transcriptional responses to dietary methionine restriction are triggered by inhibition of ternary complex formation and linked to Erk1/2, mTOR, and ATF4

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kirsten P. Stone ◽  
Sujoy Ghosh ◽  
Jean Paul Kovalik ◽  
Manda Orgeron ◽  
Desiree Wanders ◽  
...  
Keyword(s):  
Stress Response ◽  
Complex Formation ◽  
Ternary Complex ◽  
Target Genes ◽  
Bioinformatic Analysis ◽  
Transcriptional Responses ◽  
Metabolomics Data ◽  
Ternary Complex Formation ◽  
Methionine Restriction

AbstractThe initial sensing of dietary methionine restriction (MR) occurs in the liver where it activates an integrated stress response (ISR) that quickly reduces methionine utilization. The ISR program is regulated in part by ATF4, but ATF4’s prototypical upstream regulator, eIF2α, is not acutely activated by MR. Bioinformatic analysis of RNAseq and metabolomics data from liver samples harvested 3 h and 6 h after initiating MR shows that general translation is inhibited at the level of ternary complex formation by an acute 50% reduction of hepatic methionine that limits formation of initiator methionine tRNA. The resulting ISR is induced by selective expression of ATF4 target genes that mediate adaptation to reduced methionine intake and return hepatic methionine to control levels within 4 days of starting the diet. Complementary in vitro experiments in HepG2 cells after knockdown of ATF4, or inhibition of mTOR or Erk1/2 support the conclusion that the early induction of genes by MR is partially dependent on ATF4 and regulated by both mTOR and Erk1/2. Taken together, these data show that initiation of dietary MR induces an mTOR- and Erk1/2-dependent stress response that is linked to ATF4 by the sharp, initial drop in hepatic methionine and resulting repression of translation pre-initiation.

scholarly journals Visualization of clinical teaching citations using social network analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hakimeh Hazrati ◽  
Shoaleh Bigdeli ◽  
Seyed Kamran Soltani Arabshahi ◽  
Vahideh Zarea Gavgani ◽  
Nafiseh Vahed
Keyword(s):  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Research Collaboration ◽  
Clinical Teaching ◽  
Clustering Coefficient ◽  
Knowledge Network ◽  
Research Network ◽  
Centrality Measures ◽  
The Usa

Abstract Background Analyzing the previous research literature in the field of clinical teaching has potential to show the trend and future direction of this field. This study aimed to visualize the co-authorship networks and scientific map of research outputs of clinical teaching and medical education by Social Network Analysis (SNA). Methods We Identified 1229 publications on clinical teaching through a systematic search strategy in the Scopus (Elsevier), Web of Science (Clarivate Analytics) and Medline (NCBI/NLM) through PubMed from the year 1980 to 2018.The Ravar PreMap, Netdraw, UCINet and VOSviewer software were used for data visualization and analysis. Results Based on the findings of study the network of clinical teaching was weak in term of cohesion and the density in the co-authorship networks of authors (clustering coefficient (CC): 0.749, density: 0.0238) and collaboration of countries (CC: 0.655, density: 0.176). In regard to centrality measures; the most influential authors in the co-authorship network was Rosenbaum ME, from the USA (0.048). More, the USA, the UK, Canada, Australia and the Netherlands have central role in collaboration countries network and has the vertex co-authorship with other that participated in publishing articles in clinical teaching. Analysis of background and affiliation of authors showed that co-authorship between clinical researchers in medicine filed is weak. Nineteen subject clusters were identified in the clinical teaching research network, seven of which were related to the expected competencies of clinical teaching and three related to clinical teaching skills. Conclusions In order to improve the cohesion of the authorship network of clinical teaching, it is essential to improve research collaboration and co-authorship between new researchers and those who have better closeness or geodisk path with others, especially those with the clinical background. To reach to a dense and powerful topology in the knowledge network of this field encouraging policies to be made for international and national collaboration between clinicians and clinical teaching specialists. In addition, humanitarian and clinical reasoning need to be considered in clinical teaching as of new direction in the field from thematic aspects.

Sign in / Sign up

Export Citation Format

Share Document