Meta‐analysis of transcriptomic studies of cytokinin‐treated rice roots defines a core set of cytokinin‐response genes

2021 ◽  
Author(s):  
Joanna K. Polko ◽  
Kevin C. Potter ◽  
Christian A. Burr ◽  
G. Eric Schaller ◽  
Joseph J. Kieber
Keyword(s):  
Meta Analysis ◽  
Rice Roots ◽  
Core Set ◽  
Cytokinin Response ◽  
Transcriptomic Studies

scholarly journals Unveiling sex-based differences in the effects of alcohol abuse: a comprehensive functional meta-analysis of transcriptomic studies

2020 ◽  
Author(s):  
Franc Casanova Ferrer ◽  
María Pascual ◽  
Marta R. Hidalgo ◽  
Pablo Malmierca-Merlo ◽  
Consuelo Guerri ◽  
...  
Keyword(s):  
Alcohol Dependence ◽  
Intracellular Transport ◽  
Alcohol Intake ◽  
Meta Analysis ◽  
Subsequent Development ◽  
Social Consequences ◽  
Psychological Consequences ◽  
Biological Mechanisms ◽  
Physiological Mechanisms ◽  
Transcriptomic Studies

AbstractThe abuse of alcohol, one of the most popular psychoactive substances, can cause several pathological and psychological consequences, including alcohol use disorder (AUD). An impaired ability to stop or control alcohol intake despite adverse health or social consequences characterize AUD. While AUDs predominantly occur in men, growing evidence suggests the existence of distinct cognitive and biological consequences of alcohol dependence in women. The molecular and physiological mechanisms participating in these differential effects remain unknown. Transcriptomic technology permits the detection of the biological mechanisms responsible for such sex-based differences, which supports the subsequent development of novel personalized therapeutics to treat AUD. We conducted a systematic review and meta-analysis of transcriptomics studies regarding alcohol dependence in humans with representation from both sexes. For each study, we processed and analyzed transcriptomic data to obtain a functional profile of pathways and biological functions and then integrated the resulting data by meta-analysis to characterize any sex-based transcriptomic differences associated with AUD. Global results of the transcriptomic analysis revealed the association of decreased tissue regeneration, embryo malformations, altered intracellular transport, and increased rate of RNA and protein replacement with female AUD patients. Meanwhile, our analysis indicated that increased inflammatory response and blood pressure and a reduction in DNA repair capabilities associated with male AUD patients. In summary, our functional meta-analysis of transcriptomic studies provides evidence for differential biological mechanisms that AUD patients of differing sex.Abstract Figure

scholarly journals Meta-analysis reveals host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia

2018 ◽  
Author(s):  
Guoxin Cui ◽  
Yi Jin Liew ◽  
Yong Li ◽  
Najeh Kharbatia ◽  
Noura I Zahran ◽  
...  
Keyword(s):  
Nitrogen Availability ◽  
Meta Analysis ◽  
Model Organism ◽  
Acid Synthesis ◽  
Nitrogen Recycling ◽  
Amino Acid Synthesis ◽  
Carbon Translocation ◽  
Core Set ◽  
Experimental Parameters ◽  
Nonessential Amino Acids

AbstractThe metabolic symbiosis with photosynthetic algae of the genus Symbiodinium allows corals to thrive in the oligotrophic environments of tropical seas. Many aspects of this relationship have been investigated using transcriptomic analyses in the emerging model organism Aiptasia. However, previous studies identified thousands of putatively symbiosis-related genes, making it difficult to disentangle symbiosis-induced responses from undesired experimental parameters. Using a meta-analysis approach, we identified a core set of 731 high-confidence symbiosis-associated genes that reveal host-dependent recycling of waste ammonium and amino acid synthesis as central processes in this relationship. Combining transcriptomic and metabolomic analyses, we show that symbiont-derived carbon enables host recycling of ammonium into nonessential amino acids. We propose that this provides a regulatory mechanism to control symbiont growth through a carbon-dependent negative feedback of nitrogen availability to the symbiont. The dependence of this mechanism on symbiont-derived carbon highlights the susceptibility of this symbiosis to changes in carbon translocation, as imposed by environmental stress.

scholarly journals Convergent neural representations of acute nociceptive pain in healthy volunteers: A large-scale fMRI meta-analysis

2019 ◽  
Author(s):  
Anna Xu ◽  
Bart Larsen ◽  
Erica B. Baller ◽  
J. Cobb Scott ◽  
Vaishnavi Sharma ◽  
...  
Keyword(s):  
Acute Pain ◽  
Error Control ◽  
Large Scale ◽  
Meta Analysis ◽  
Brain Regions ◽  
Type I ◽  
List Type ◽  
Midcingulate Cortex ◽  
Core Set ◽  
Healthy Participants

ABSTRACTCharacterizing a reliable, pain-related neural signature is critical for translational applications. Many prior fMRI studies have examined acute pain-related brain activation in healthy participants. However, synthesizing these data to identify convergent patterns of activation can be challenging due to the heterogeneity of experimental designs and samples. To address this challenge, we conducted a comprehensive meta-analysis of fMRI studies of stimulus-induced pain in healthy participants. Following pre-registration, two independent reviewers evaluated 4,927 abstracts returned from a search of 8 databases, with 222 fMRI experiments meeting inclusion criteria. We analyzed these experiments using Activation Likelihood Estimation with rigorous type I error control (voxel height p < 0.001, cluster p < 0.05 FWE-corrected) and found a convergent, largely bilateral pattern of pain-related activation in the secondary somatosensory cortex, insula, midcingulate cortex, and thalamus. Notably, these regions were consistently recruited regardless of stimulation technique, location of induction, and participant sex. These findings suggest a highly-conserved core set of pain-related brain areas, encouraging applications as a biomarker for novel therapeutics targeting acute pain.HIGHLIGHTSPain stimulation recruits a core set of pain-related brain regions.This core set includes thalamus, SII, insula and mid-cingulate cortex.These regions were recruited regardless of stimulus modality and stimulus location.

scholarly journals Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging

Aging Cell ◽  
2013 ◽  
Vol 13 (2) ◽  
pp. 216-225 ◽  
Author(s):  
Erik B. van den Akker ◽  
Willemijn M. Passtoors ◽  
Rick Jansen ◽  
Erik W. van Zwet ◽  
Jelle J. Goeman ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Meta Analysis ◽  
Human Aging ◽  
Protein Protein Interaction ◽  
Transcriptomic Studies

Meta-Analysis of the Transcriptome Reveals a Core Set of Shade-Avoidance Genes in Arabidopsis

2017 ◽  
Vol 93 (3) ◽  
pp. 692-702 ◽  
Author(s):  
Romina Sellaro ◽  
Manuel Pacín ◽  
Jorge J. Casal
Keyword(s):  
Meta Analysis ◽  
Shade Avoidance ◽  
Core Set

scholarly journals Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
José F. Català-Senent ◽  
Marta R. Hidalgo ◽  
Marina Berenguer ◽  
Gopanandan Parthasarathy ◽  
Harmeet Malhi ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Meta Analysis ◽  
Interleukin 2 ◽  
Premenopausal Women ◽  
Functional Results ◽  
Gene Expression Omnibus ◽  
Negative Regulation ◽  
Neural Tube Closure ◽  
Alcoholic Fatty Liver ◽  
Transcriptomic Studies

Abstract Background Previous studies have described sex-based differences in the epidemiological and clinical patterns of non-alcoholic fatty liver disease (NAFLD); however, we understand relatively little regarding the underlying molecular mechanisms. Herein, we present the first systematic review and meta-analysis of NAFLD transcriptomic studies to identify sex-based differences in the molecular mechanisms involved during the steatosis (NAFL) and steatohepatitis (NASH) stages of the disease. Methods Transcriptomic studies in the Gene Expression Omnibus database were systematically reviewed following the PRISMA statement guidelines. For each study, NAFL and NASH in premenopausal women and men were compared using a dual strategy: gene-set analysis and pathway activity analysis. Finally, the functional results of all studies were integrated into a meta-analysis. Results We reviewed a total of 114 abstracts and analyzed seven studies that included 323 eligible patients. The meta-analyses identified significantly altered molecular mechanisms between premenopausal women and men, including the overrepresentation of genes associated with DNA regulation, vinculin binding, interleukin-2 responses, negative regulation of neuronal death, and the transport of ions and cations in premenopausal women. In men, we discovered the overrepresentation of genes associated with the negative regulation of interleukin-6 and the establishment of planar polarity involved in neural tube closure. Conclusions Our meta-analysis of transcriptomic data provides a powerful approach to identify sex-based differences in NAFLD. We detected differences in relevant biological functions and molecular terms between premenopausal women and men. Differences in immune responsiveness between men and premenopausal women with NAFLD suggest that women possess a more immune tolerant milieu, while men display an impaired liver regenerative response. Graphical abstract

The flourishing diversity of models in theoretical morphology: from current practices to future macroevolutionary and bioenvironmental challenges

Paleobiology ◽  
2008 ◽  
Vol 34 (3) ◽  
pp. 301-317 ◽  
Author(s):  
Guillaume Dera ◽  
Gunther J. Eble ◽  
Pascal Neige ◽  
Bruno David
Keyword(s):  
Representative Sample ◽  
Meta Analysis ◽  
Morphological Studies ◽  
Theoretical Morphology ◽  
Core Set ◽  
Starting Point ◽  
The Future ◽  
Efficient Construction ◽  
Research Questions ◽  
Similarity And Difference

For decades, theoretical morphological studies of different groups of organisms have been successfully pursued in biological, paleontological, and computational contexts, often with distinct modeling approaches and research questions. A regular influx of new perspectives and varied expertise has contributed to the emergence of a veritable multidisciplinary outlook for theoretical morphology. The broadening of this discipline is reflected in a substantial increase in the number of models, leading to a bewildering diversity that has yet to be scrutinized. In this work, we tackle this issue in a synthetic fashion, with a quantitative meta-analysis that allows an objective comparison of theoretical morphological models treated as entities. By analogy with empirical morphospace analyses of actual organisms, we performed a multivariate ordination of a representative sample of models, producing a metaspace of models in which patterns of similarity and difference are visualized. A phenetic tree was used to characterize the relationships between models. Four major groups have been identified, and their disparity analyzed. We suggest this typology as a useful starting point to identify a core set of fundamental principles and protocols for better interpretation of the plethora of current models and for more efficient construction of models in the future. This in turn can help in diversifying the scope of macroevolutionary, developmental, and bioenvironmental questions in theoretical morphology.

scholarly journals Sex differences in the progression from NAFL to NASH: a functional meta-analysis of transcriptomic studies

2020 ◽  
Author(s):  
José F. Català-Senent ◽  
Marta R. Hidalgo ◽  
Marina Berenguer ◽  
Harmeet Malhi ◽  
Francisco García-García
Keyword(s):  
Sex Differences ◽  
Meta Analysis ◽  
Premenopausal Women ◽  
Negative Regulation ◽  
List Type ◽  
Immune Responsiveness ◽  
Biological Functions ◽  
Alcoholic Fatty Liver ◽  
Transcriptomic Data ◽  
Transcriptomic Studies

AbstractBackground & aimsSex differences in non-alcoholic fatty liver disease (NAFLD) are well known and yet, most of the studies available in the literature do not include this factor when analysing the data. Here we present a functional meta-analysis of NAFLD studies to detect the molecular mechanisms involved in its progression, distinguishing any differences relative to patient sex.MethodsWe systematically reviewed the Gene Expression Omnibus (GEO) database functional Gene Ontology (GO) terms detailed in transcriptomic studies, following the PRISMA statement guidelines. For each study, we compared the progression from steatosis (NAFL) to steatohepatitis (NASH) in premenopausal women and men using a dual strategy: a gene-set analysis and a pathway activity analysis. The functional results of all the studies were integrated in a meta-analysis used to detect functions that were differentially affected in these groups, according to these two methods.ResultsA total of 105 abstracts were reviewed and 7 studies, which included 624 patients, were finally analysed. The meta-analyses highlighted significant functions in both sexes. In premenopausal women, the overrepresented functions referred to DNA regulation, vinculin binding, interleukin 2 (IL-2) responses, negative regulation of neuronal death, and the transport of ions and cations. In men, they referred to the negative regulation of IL-6 and the establishment of planar polarity involved in neural tube closure.ConclusionsOur meta-analysis of this transcriptomic data provides a powerful approach to identify sex differences in the progression from NAFL to NASH. We detected relevant biological functions and molecular terms that were affected differently between premenopausal women and men. Changes in the immune responsiveness between men and women with NAFLD suggested that women have a more immune tolerant milieu while men have an impaired liver regenerative response. These results open the door to more pathophysiological studies into the differential role of IL-2 and IL-6 in NAFLD, and eventually to personalised treatments for this disease.Lay summaryProgression from NAFL to NASH differently affects cellular functions in women and men. Here we systematically reviewed publicly available transcriptomic data and then performed a meta-analysis to find these affected functions. Thus, we identified 13 biological functions implicated in the progression of NAFLD that were differentially affected by sex.HighlightsTranscriptomics meta-analysis detects significant sex differences in NAFLD progression.Interleukins 2 and 6 are upregulated in premenopausal women compared to men.Changes in the immune responsiveness may explain the sex-differences observed.Sex differences need to be taken into account in the NAFLD studies.Graphical abstract

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