scholarly journals MODULARITY FACILITATES FLEXIBLE TUNING OF PLASTIC AND EVOLUTIONARY GENE EXPRESSION RESPONSES DURING EARLY DIVERGENCE

2017 ◽  
Author(s):  
Hannu Mäkinen ◽  
Tiina Sävilammi ◽  
Spiros Papakostas ◽  
Erica Leder ◽  
Leif Asbjørn Vøllestad ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Thermal Adaptation ◽  
Thermal Conditions ◽  
Model System ◽  
Neutral Evolution ◽  
Phenotypic Traits ◽  
Early Stages ◽  
Large Gene ◽  
Population Effects

AbstractGene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying co-expressed modules now enable systems genetics approaches also in non-model species for better understanding of gene expression responses during early divergence. Here, we combined gene co-expression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that co-expression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.

scholarly journals Arabidopsis sepals: A model system for the emergent process of morphogenesis

2021 ◽  
Vol 2 ◽  
Author(s):  
Adrienne H. K. Roeder
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Cell Division ◽  
Slow Growth ◽  
Expression Patterns ◽  
Giant Cells ◽  
Model System ◽  
Gene Expression Patterns ◽  
Emergent Properties ◽  
Correct Size

Abstract During development, Arabidopsis thaliana sepal primordium cells grow, divide and interact with their neighbours, giving rise to a sepal with the correct size, shape and form. Arabidopsis sepals have proven to be a good system for elucidating the emergent processes driving morphogenesis due to their simplicity, their accessibility for imaging and manipulation, and their reproducible development. Sepals undergo a basipetal gradient of growth, with cessation of cell division, slow growth and maturation starting at the tip of the sepal and progressing to the base. In this review, I discuss five recent examples of processes during sepal morphogenesis that yield emergent properties: robust size, tapered tip shape, laminar shape, scattered giant cells and complex gene expression patterns. In each case, experiments examining the dynamics of sepal development led to the hypotheses of local rules. In each example, a computational model was used to demonstrate that these local rules are sufficient to give rise to the emergent properties of morphogenesis.

scholarly journals Recapitulation of Transcriptomic Characteristics of Primary Breast Tumours in Patient-Derived 3D Cultures in Vitro

2021 ◽  
Vol 75 (1) ◽  
pp. 20-24
Author(s):  
Dina Nitiša ◽  
Nityanand Jain ◽  
Arvīds Irmejs ◽  
Valdis Pirsko ◽  
Inese Čakstiņa
Keyword(s):  
Gene Expression ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
3D Cell Culture ◽  
Model System ◽  
Gene Expression Patterns ◽  
3D Cultures ◽  
Culture Development

AbstractBreast cancer (BC) is the most common cause of cancer-related deaths among women in Europe and worldwide. Adherent (2D) cell cultures have been the routine in vitro model system employed in preclinical BC research for the last half-century. Over the past decade, new protocols have been developed allowing patient-derived three-dimensional organoid (3D) cell culture development from a range of solid tumours, including BC. These 3D models offer a promise of closer resemblance to the native tumour than the 2D cultures. To test the assumption that an in vitro 3D BC model system provides increased faithfulness to the molecular processes happening in vivo, as compared to 2D BC cultures, post-operational material from three BC patients was used to simultaneously develop 2D and 3D cultures in vitro. When analysed by quantitative polymerase chain reaction (PCR), the gene expression patterns of the cells from 3D cultures resembled the original tissues, while the gene expression patterns of the conventional 2D cultures were more distant.

scholarly journals Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba)

Polar Biology ◽  
2019 ◽  
Vol 42 (12) ◽  
pp. 2205-2217
Author(s):  
Leonie Suter ◽  
Andrea Maree Polanowski ◽  
Robert King ◽  
Chiara Romualdi ◽  
Gabriele Sales ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sex Determination ◽  
Antarctic Krill ◽  
Sex Differentiation ◽  
Expression Patterns ◽  
Keystone Species ◽  
Euphausia Superba ◽  
Specific Expression ◽  
Large Gene ◽  
Juvenile Stages

Abstract Antarctic krill (Euphausia superba) is a highly abundant keystone species of the Southern Ocean ecosystem, directly connecting primary producers to high-trophic level predators. Sex ratios of krill vary remarkably between swarms and this phenomenon is poorly understood, as identification of krill sex relies on external morphological differences that appear late during development. Sex determination mechanisms in krill are unknown, but could include genetic, environmental or parasitic mechanisms. Similarly, virtually nothing is known about molecular sex differentiation. The krill genome has to date not been sequenced, and due to its enormous size and large amount of repetitive elements, it is currently not feasible to develop sex-specific DNA markers. To produce a reliable molecular marker for sex in krill and to investigate molecular sex differentiation we therefore focused on identifying sex-specific transcriptomic differences. Through transcriptomic analysis, we found large gene expression differences between testes and ovaries and identified three genes exclusively expressed in female whole krill from early juvenile stages onwards. The sex-specific expression of these three genes persisted through sexual regression, although our regressed samples originated from a krill aquarium and may differ from wild-regressed krill. Two slightly male-biased genes did not display sufficient expression differences to clearly differentiate sexes. Based on the expression of the three female-specific genes we developed a molecular test that for the first time allows the unambiguous sex determination of krill samples lacking external sex-specific features from juvenile stages onwards, including the sexually regressed krill we examined.

scholarly journals BEST: A Novel Computational Approach for Comparing Gene Expression Patterns From Early Stages of Drosophila melanogaster Development

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 2037-2047
Author(s):  
Sudhir Kumar ◽  
Karthik Jayaraman ◽  
Sethuraman Panchanathan ◽  
Rajalakshmi Gurunathan ◽  
Ana Marti-Subirana ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Biology ◽  
Drosophila Melanogaster ◽  
Expression Pattern ◽  
Early Stage ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Computational Approach ◽  
Gene Expression Patterns ◽  
Early Stages

Abstract Embryonic gene expression patterns are an indispensable part of modern developmental biology. Currently, investigators must visually inspect numerous images containing embryonic expression patterns to identify spatially similar patterns for inferring potential genetic interactions. The lack of a computational approach to identify pattern similarities is an impediment to advancement in developmental biology research because of the rapidly increasing amount of available embryonic gene expression data. Therefore, we have developed computational approaches to automate the comparison of gene expression patterns contained in images of early stage Drosophila melanogaster embryos (prior to the beginning of germ-band elongation); similarities and differences in gene expression patterns in these early stages have extensive developmental effects. Here we describe a basic expression search tool (BEST) to retrieve best matching expression patterns for a given query expression pattern and a computational device for gene interaction inference using gene expression pattern images and information on the associated genotypes and probes. Analysis of a prototype collection of Drosophila gene expression pattern images is presented to demonstrate the utility of these methods in identifying biologically meaningful matches and inferring gene interactions by direct image content analysis. In particular, the use of BEST searches for gene expression patterns is akin to that of BLAST searches for finding similar sequences. These computational developmental biology methodologies are likely to make the great wealth of embryonic gene expression pattern data easily accessible and to accelerate the discovery of developmental networks.

scholarly journals De Novo Transcriptome Analysis Reveals Potential Thermal Adaptation Mechanisms in the Cicada Hyalessa fuscata

Animals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2785
Author(s):  
Hoa Quynh Nguyen ◽  
Yuseob Kim ◽  
Yikweon Jang
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Heat Shock ◽  
Thermal Tolerance ◽  
De Novo ◽  
Expression Patterns ◽  
Thermal Adaptation ◽  
Urban Heat Islands ◽  
Cellular Damage ◽  
Acute Heat Stress

In metropolitan Seoul, populations of the cicada Hyalessa fuscata in hotter urban heat islands (“high UHIs”) exhibit higher thermal tolerance than those in cooler UHIs (“low UHIs”). We hypothesized that heat stress may activate the expression of genes that facilitate greater thermal tolerance in high-UHI cicadas than in those from cooler areas. Differences in the transcriptomes of adult female cicadas from high-UHI, low-UHI, and suburban areas were analyzed at the unheated level, after acute heat stress, and after heat torpor. No noticeable differences in unheated gene expression patterns were observed. After 10 min of acute heat stress, however, low-UHI and suburban cicadas expressed more heat shock protein genes than high-UHI counterparts. More specifically, remarkable changes in the gene expression of cicadas across areas were observed after heat torpor stimulus, as represented by a large number of up- and downregulated genes in the heat torpor groups compared with the 10 min acute heat stress and control groups. High-UHI cicadas expressed the most differentially expressed genes, followed by the low-UHI and suburban cicadas. There was a notable increase in the expression of heat shock, metabolism, and detoxification genes; meanwhile, immune-related, signal transduction, and protein turnover genes were downregulated in high-UHI cicadas versus the other cicada groups. These results suggested that under heat stress, cicadas inhabiting high-UHIs could rapidly express genes related to heat shock, energy metabolism, and detoxification to protect cells from stress-induced damage and to increase their thermal tolerance toward heat stress. The downregulation of apoptosis mechanisms in high-UHI cicadas suggested that there was less cellular damage, which likely contributed to their high tolerance of heat stress.

scholarly journals Pseudo-Location: A novel predictor for predicting pseudo-temporal gene expression patterns using spatial functional regression

2020 ◽  
Author(s):  
Kyungmin Ahn ◽  
Hironobu Fujiwara
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Functional Regression ◽  
Rna Seq ◽  
Temporal Gene Expression ◽  
Early Stages ◽  
The Future

Statement of withdrawalThe authors have withdrawn version 1 of this manuscript because a draft manuscript, which was still in the early stages of preparation and required major revisions including the replacement of the source RNA-seq datasets, was erroneously submitted. The authors do not wish this version to be cited as reference for this study. We will post a revised manuscript in the future. If you have any questions, please contact the corresponding author.

scholarly journals Robustness of the Dorsal morphogen gradient with respect to morphogen dosage

2019 ◽  
Author(s):  
Hadel Al Asafen ◽  
Prasad U. Bandodkar ◽  
Sophia Carrell-Noel ◽  
Gregory T. Reeves
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Positional Information ◽  
The Body ◽  
Morphogen Gradient ◽  
Gene Expression Patterns ◽  
Facilitated Diffusion ◽  
Uniform Field ◽  
Stages Of Development ◽  
Early Stages

AbstractIn multicellular organisms, the timing and placement of gene expression in a developing tissue assigns the fate of each cell in the embryo in order for a uniform field of cells to differentiate into a reproducible pattern of organs and tissues. This positional information is often achieved through the action of spatial gradients of morphogens. Spatial patterns of gene expression are paradoxically robust to variations in morphogen dosage, given that, by definition, gene expression must be sensitive to morphogen concentration. In this work we investigate the robustness of the Dorsal/NF-κB signaling module with respect to perturbations to the dosage of maternally-expressed dorsal mRNA. The Dorsal morphogen gradient patterns the dorsal-ventral axis of the early Drosophila embryo, and we found that an empirical description of the Dorsal gradient is highly sensitive to maternal dorsal dosage. In contrast, we found experimentally that gene expression patterns are highly robust. Although the components of this signaling module have been characterized in detail, how their function is integrated to produce robust gene expression patterns to variations in the dorsal maternal dosage is still unclear. Therefore, we analyzed a mechanistic model of the Dorsal signaling module and found that Cactus, a cytoplasmic inhibitor for Dorsal, must be present in the nucleus for the system to be robust. Furthermore, active Toll, the receptor that dissociates Cactus from Dorsal, must be saturated. Finally, the vast majority of robust descriptions of the system require facilitated diffusion of Dorsal by Cactus. Each of these three recently-discovered mechanisms of the Dorsal module are critical for robustness. Our work highlights the need for quantitative understanding of biophysical mechanisms of morphogen gradients in order to understand emergent phenotypes, such as robustness.Author SummaryThe early stages of development of an embryo are crucial for laying the foundation of the body plan. The blueprint of this plan is encoded in long-range spatial protein gradients called morphogens. This positional information is then interpreted by nuclei that begin to differentiate by expressing different genes. In fruit fly embryos, the Dorsal morphogen forms a gradient along the dorsal-ventral axis, with a maximum at the ventral midline. This gradient, and the resulting gene expression patterns are extraordinarily robust to variations in developmental conditions, even during early stages of development. Since positional information is interpreted in terms of concentration of the morphogen, one would expect that doubling or halving dosage would result in disastrous consequences for the embryo. However, we observed that development remains robust. We quantified the effect of dosage by experimentally measuring the boundaries of 2 genes, - sna and sog, expressed along the DV axis and found that variation in the boundaries of these genes was minimal, across embryos with different dosages of Dl. We then used a mathematical model to discern components of the Dl system responsible for buffering the effects of dosage and found three specific mechanisms – deconvolution, Toll saturation and shuttling

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