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

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 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 Light-induced indeterminacy alters shade avoiding tomato leaf morphology

2015 ◽  
Author(s):  
Daniel H. Chitwood ◽  
Ravi Kumar ◽  
Aashish Ranjan ◽  
Julie Pelletier ◽  
Brad Townsley ◽  
...  
Keyword(s):  
Gene Expression ◽  
Leaf Morphology ◽  
Meta Analysis ◽  
Leaf Shape ◽  
Leaf Size ◽  
Leaf Primordia ◽  
Leaf Mass Per Area ◽  
Shade Avoidance ◽  
Canonical Pathways ◽  
Induced Changes

Plants sense foliar shade of competitors and alter their developmental programs through the shade avoidance response. Internode and petiole elongation, and changes in overall leaf area and leaf mass per area, are the stereotypical architectural responses to foliar shade in the shoot. However, changes in leaf shape and complexity in response to shade remain incompletely, and qualitatively, described. Using a meta-analysis of >18,000 previously published leaflet outlines, we demonstrate that shade avoidance alters leaf shape in domesticated tomato and wild relatives. The effects of shade avoidance on leaf shape are subtle with respect to individual traits, but are combinatorially strong. We then seek to describe the developmental origins of shade-induced changes in leaf shape by swapping plants between light treatments. Leaf size is light-responsive late into development, but patterning events, such as stomatal index, are irrevocably specified earlier. Observing that shade induces increases in shoot apical meristem size, we then describe gene expression changes in early leaf primordia and the meristem using laser microdissection. We find that in leaf primordia shade avoidance is not mediated through canonical pathways described in mature organs, but rather the expression of KNOX and other indeterminacy genes, altering known developmental pathways responsible for patterning leaf shape. We also demonstrate that shade-induced changes in leaf primordium gene expression largely do not overlap with those found in successively initiated leaf primordia, providing evidence against classic hypotheses that shaded leaf morphology results from prolonged production of juvenile leaf types.

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 Meta-Analysis of Dilated Cardiomyopathy Using Cardiac RNA-Seq Transcriptomic Datasets

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 60 ◽  
Author(s):  
Ahmad Alimadadi ◽  
Patricia B. Munroe ◽  
Bina Joe ◽  
Xi Cheng
Keyword(s):  
Dilated Cardiomyopathy ◽  
Meta Analysis ◽  
Rna Seq ◽  
Upstream Regulator ◽  
Core Set ◽  
Common Causes ◽  
Significant Pathway ◽  
Human Left Ventricle ◽  
Upregulated Genes ◽  
Cardiovascular Functions

Dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. Several studies have used RNA-sequencing (RNA-seq) to profile differentially expressed genes (DEGs) associated with DCM. In this study, we aimed to profile gene expression signatures and identify novel genes associated with DCM through a quantitative meta-analysis of three publicly available RNA-seq studies using human left ventricle tissues from 41 DCM cases and 21 control samples. Our meta-analysis identified 789 DEGs including 581 downregulated and 208 upregulated genes. Several DCM-related genes previously reported, including MYH6, CKM, NKX2–5 and ATP2A2, were among the top 50 DEGs. Our meta-analysis also identified 39 new DEGs that were not detected using those individual RNA-seq datasets. Some of those genes, including PTH1R, ADAM15 and S100A4, confirmed previous reports of associations with cardiovascular functions. Using DEGs from this meta-analysis, the Ingenuity Pathway Analysis (IPA) identified five activated toxicity pathways, including failure of heart as the most significant pathway. Among the upstream regulators, SMARCA4 was downregulated and prioritized by IPA as the top affected upstream regulator for several DCM-related genes. To our knowledge, this study is the first to perform a transcriptomic meta-analysis for clinical DCM using RNA-seq datasets. Overall, our meta-analysis successfully identified a core set of genes associated with DCM.

The effects of low-ratio n-6/n-3 PUFA on biomarkers of inflammation: a systematic review and meta-analysis

2021 ◽  
Author(s):  
Yali Wei ◽  
Yan Meng ◽  
Na Li ◽  
Qian Wang ◽  
Liyong Chen
Keyword(s):  
Systematic Review ◽  
Fatty Acid ◽  
Polyunsaturated Fatty Acid ◽  
Meta Analysis ◽  
Chain Polyunsaturated Fatty Acid ◽  
Inflammation Markers ◽  
Pufa Supplementation ◽  
Long Chain

The purpose of the systematic review and meta-analysis was to determine if low-ratio n-6/n-3 long-chain polyunsaturated fatty acid (PUFA) supplementation affects serum inflammation markers based on current studies.

A meta-analysis of individualized instruction in dental education

1992 ◽  
Vol 56 (3) ◽  
pp. 183-189 ◽  
Author(s):  
LS Dacanay ◽  
PA Cohen
Keyword(s):  
Dental Education ◽  
Meta Analysis ◽  
Individualized Instruction
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