scholarly journals Dissecting the Transcriptomic Basis of Phenotypic Evolution in an Aquatic Keystone Grazer

2019 ◽  
Vol 37 (2) ◽  
pp. 475-487 ◽  
Author(s):  
Dagmar Frisch ◽  
Dörthe Becker ◽  
Marcin W Wojewodzic
Keyword(s):  
Gene Networks ◽  
Fine Tuning ◽  
Transcriptional Networks ◽  
Phenotypic Traits ◽  
P Availability ◽  
Phenotypic Evolution ◽  
Before And After ◽  
Coexpression Networks ◽  
Phenotypic Responses ◽  
Genomic Model

Abstract Knowledge of the molecular basis of phenotypic responses to environmental cues is key to understanding the process of adaptation. Insights to adaptation at an evolutionary time scale can be gained by observing organismal responses before and after a shift in environmental conditions, but such observations can rarely be made. Using the ecological and genomic model Daphnia, we linked transcriptomic responses and phosphorus (P)-related phenotypic traits under high and low P availability. We mapped weighted gene coexpression networks to traits previously assessed in resurrected ancient (600 years old) and modern Daphnia pulicaria from a lake with a historic shift in P-enrichment. Subsequently, we assessed evolutionary conservation or divergence in transcriptional networks of the same isolates. We discovered highly preserved gene networks shared between ancient genotypes and their modern descendants, but also detected clear evidence of transcriptional divergence between these evolutionarily separated genotypes. Our study highlights that phenotypic evolution is a result of molecular fine-tuning on different layers ranging from basic cellular responses to higher order phenotypes. In a broader context, these findings advance our understanding how populations are able to persist throughout major environmental shifts.

scholarly journals The underestimated role of the microphthalmia-associated transcription factor (MiTF) in normal and pathological haematopoiesis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alessia Oppezzo ◽  
Filippo Rosselli
Keyword(s):  
Stem Cells ◽  
Gene Networks ◽  
Bone Marrow Failure ◽  
Phenotypic Traits ◽  
Expression Of Genes ◽  
Specific Setting ◽  
Haematopoietic System ◽  
Abnormal Pigmentation ◽  
In Cells

AbstractHaematopoiesis, the process by which a restrained population of stem cells terminally differentiates into specific types of blood cells, depends on the tightly regulated temporospatial activity of several transcription factors (TFs). The deregulation of their activity or expression is a main cause of pathological haematopoiesis, leading to bone marrow failure (BMF), anaemia and leukaemia. TFs can be induced and/or activated by different stimuli, to which they respond by regulating the expression of genes and gene networks. Most TFs are highly pleiotropic; i.e., they are capable of influencing two or more apparently unrelated phenotypic traits, and the action of a single TF in a specific setting often depends on its interaction with other TFs and signalling pathway components. The microphthalmia-associated TF (MiTF) is a prototype TF in multiple situations. MiTF has been described extensively as a key regulator of melanocyte and melanoma development because it acts mainly as an oncogene. Mitf-mutated mice show a plethora of pleiotropic phenotypes, such as microphthalmia, deafness, abnormal pigmentation, retinal degeneration, reduced mast cell numbers and osteopetrosis, revealing a greater requirement for MiTF activity in cells and tissue. A growing amount of evidence has led to the delineation of key roles for MiTF in haematopoiesis and/or in cells of haematopoietic origin, including haematopoietic stem cells, mast cells, NK cells, basophiles, B cells and osteoclasts. This review summarizes several roles of MiTF in cells of the haematopoietic system and how MiTFs can impact BM development.

scholarly journals Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Erik M Quandt ◽  
Jimmy Gollihar ◽  
Zachary D Blount ◽  
Andrew D Ellington ◽  
George Georgiou ◽  
...  
Keyword(s):  
Citrate Synthase ◽  
Fine Tuning ◽  
Ecological Niches ◽  
Glta Gene ◽  
Evolutionary Changes ◽  
Before And After ◽  
Evolution Experiment ◽  
History Of ◽  
Second Wave

Evolutionary innovations that enable organisms to colonize new ecological niches are rare compared to gradual evolutionary changes in existing traits. We discovered that key mutations in the gltA gene, which encodes citrate synthase (CS), occurred both before and after Escherichia coli gained the ability to grow aerobically on citrate (Cit+ phenotype) during the Lenski long-term evolution experiment. The first gltA mutation, which increases CS activity by disrupting NADH-inhibition of this enzyme, is beneficial for growth on the acetate and contributed to preserving the rudimentary Cit+ trait from extinction when it first evolved. However, after Cit+ was refined by further mutations, this potentiating gltA mutation became deleterious to fitness. A second wave of beneficial gltA mutations then evolved that reduced CS activity to below the ancestral level. Thus, dynamic reorganization of central metabolism made colonizing this new nutrient niche contingent on both co-opting and overcoming a history of prior adaptation.

Abstract 133: A Systems Genetics Approach to Identify Genetic Pathways and Key Drivers of Isoproterenol-induced Cardiac Hypertrophy and Cardiomyopathy in Mice

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Christoph D Rau ◽  
Milagros Romay ◽  
Jessica Wang ◽  
Aldons J Lusis ◽  
Yibin Wang
Keyword(s):  
Heart Failure ◽  
Cardiac Hypertrophy ◽  
Gene Networks ◽  
Complex Disease ◽  
Left Ventricular ◽  
Causal Modeling ◽  
Neonatal Rat ◽  
Mouse Strains ◽  
Phenotypic Traits ◽  
Systems Genetics

Heart Failure (HF) is a complex disease involving numerous environmental and genetic factors. We previously reported a genetic analysis of HF traits in a population of inbred mouse strains treated with isoproterenol, a β-adrenergic agonist used to mimic catecholamine-driven cardiac hypertrophy. We now present a systems genetics analysis in which we have used left ventricular transcript levels from these mice to perform co-expression network modeling. We constructed gene networks composed of 8,126 genes and 20 modules using the wMICA algorithm. In the wMICA network generated from treated hearts, we identified a module with significant correlations to several HF-related phenotypic traits. Further analysis of this module showed significant over-representation of genes known to contribute to the development of HF. Using the causal modeling algorithm NEO, we identified the gene Adamts2 as a putative master regulator of the module. We then validated the role of this gene through siRNA-mediated knockdown in neonatal rat ventricular myocytes (NRVM). Consistent with our model, Adamts2 silencing was able to regulate the expression of the genes residing within the module as well as impairing isoproterenol-induced cell size changes . Our results provide a view of higher order interactions in heart failure with potential to facilitate diagnostic and therapeutic approaches.

scholarly journals Impact of transition to a subterranean lifestyle on morphological disparity and integration in talpid moles (Mammalia, Talpidae)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Gabriele Sansalone ◽  
Paolo Colangelo ◽  
Anna Loy ◽  
Pasquale Raia ◽  
Stephen Wroe ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Morphological Variability ◽  
Phenotypic Integration ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Morphological Disparity ◽  
Morphological Diversification ◽  
Phylogenetic Conservatism ◽  
Selective Forces ◽  
Subterranean Species

Abstract Background Understanding the mechanisms promoting or constraining morphological diversification within clades is a central topic in evolutionary biology. Ecological transitions are of particular interest because of their influence upon the selective forces and factors involved in phenotypic evolution. Here we focused on the humerus and mandibles of talpid moles to test whether the transition to the subterranean lifestyle impacted morphological disparity and phenotypic traits covariation between these two structures. Results Our results indicate non-subterranean species occupy a significantly larger portion of the talpid moles morphospace. However, there is no difference between subterranean and non-subterranean moles in terms of the strength and direction of phenotypic integration. Conclusions Our study shows that the transition to a subterranean lifestyle significantly reduced morphological variability in talpid moles. However, this reduced disparity was not accompanied by changes in the pattern of traits covariation between the humerus and the mandible, suggesting the presence of strong phylogenetic conservatism within this pattern.

scholarly journals Regulostat Inferelator: a novel network biology platform to uncover molecular devices that predetermine cellular response phenotypes

2019 ◽  
Vol 47 (14) ◽  
pp. e82-e82
Author(s):  
Choong Yong Ung ◽  
Mehrab Ghanat Bari ◽  
Cheng Zhang ◽  
Jingjing Liang ◽  
Cristina Correia ◽  
...  
Keyword(s):  
Cellular Response ◽  
Expression Patterns ◽  
Fine Tuning ◽  
Molecular Devices ◽  
Proof Of Concept ◽  
Genetic Circuits ◽  
Continuous Response ◽  
Context Specific ◽  
First Time ◽  
Phenotypic Responses

Abstract With the emergence of genome editing technologies and synthetic biology, it is now possible to engineer genetic circuits driving a cell's phenotypic response to a stressor. However, capturing a continuous response, rather than simply a binary ‘on’ or ‘off’ response, remains a bioengineering challenge. No tools currently exist to identify gene candidates responsible for predetermining and fine-tuning cell response phenotypes. To address this gap, we devised a novel Regulostat Inferelator (RSI) algorithm to decipher intrinsic molecular devices or networks that predetermine cellular phenotypic responses. The RSI algorithm is designed to extract gene expression patterns from basal transcriptomic data in order to identify ‘regulostat’ constituent gene pairs, which exhibit rheostat-like mode-of-cooperation capable of fine-tuning cellular response. Our proof-of-concept study provides computational evidence for the existence of regulostats and that these networks predetermine cellular response prior to exposure to a stressor or drug. In addition, our work, for the first time, provides evidence of context-specific, drug–regulostat interactions in predetermining drug response phenotypes in cancer cells. Given RSI-inferred regulostat networks offer insights for prioritizing gene candidates capable of rendering a resistant phenotype sensitive to a given drug, we envision that this tool will be of great value in bioengineering and medicine.

scholarly journals Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature

2018 ◽  
Vol 15 (4) ◽  
Author(s):  
Olga V. Saik ◽  
Pavel S. Demenkov ◽  
Timofey V. Ivanisenko ◽  
Elena Yu. Bragina ◽  
Maxim B. Freidin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Molecular Genetic ◽  
Genetic Networks ◽  
Positive Sign ◽  
Phenotypic Traits ◽  
Protein Protein Interactions ◽  
Scientific Publications ◽  
Associative Gene Networks

AbstractComorbid states of diseases significantly complicate diagnosis and treatment. Molecular mechanisms of comorbid states of asthma and hypertension are still poorly understood. Prioritization is a way for identifying genes involved in complex phenotypic traits. Existing methods of prioritization consider genetic, expression and evolutionary data, molecular-genetic networks and other. In the case of molecular-genetic networks, as a rule, protein-protein interactions and KEGG networks are used. ANDSystem allows reconstructing associative gene networks, which include more than 20 types of interactions, including protein-protein interactions, expression regulation, transport, catalysis, etc. In this work, a set of genes has been prioritized to find genes potentially involved in asthma and hypertension comorbidity. The prioritization was carried out using well-known methods (ToppGene and Endeavor) and a cross-talk centrality criterion, calculated by analysis of associative gene networks from ANDSystem. The identified genes, including IL1A, CD40LG, STAT3, IL15, FAS, APP, TLR2, C3, IL13 and CXCL10, may be involved in the molecular mechanisms of comorbid asthma/hypertension. An analysis of the dynamics of the frequency of mentioning the most priority genes in scientific publications revealed that the top 100 priority genes are significantly enriched with genes with increased positive dynamics, which may be a positive sign for further studies of these genes.

scholarly journals The genetic covariance between life cycle stages separated by metamorphosis

2014 ◽  
Vol 281 (1788) ◽  
pp. 20141091 ◽  
Author(s):  
J. David Aguirre ◽  
Mark W. Blows ◽  
Dustin J. Marshall
Keyword(s):  
Life Cycle ◽  
Life Cycle Stage ◽  
Evolutionary Change ◽  
Phenotypic Evolution ◽  
Genetic Associations ◽  
Embryo Viability ◽  
Genetic Covariance ◽  
Life Cycle Stages ◽  
Target Matrix ◽  
Before And After

Metamorphosis is common in animals, yet the genetic associations between life cycle stages are poorly understood. Given the radical changes that occur at metamorphosis, selection may differ before and after metamorphosis, and the extent that genetic associations between pre- and post-metamorphic traits constrain evolutionary change is a subject of considerable interest. In some instances, metamorphosis may allow the genetic decoupling of life cycle stages, whereas in others, metamorphosis could allow complementary responses to selection across the life cycle. Using a diallel breeding design, we measured viability at four ontogenetic stages (embryo, larval, juvenile and adult viability), in the ascidian Ciona intestinalis and examined the orientation of additive genetic variation with respect to the metamorphic boundary. We found support for one eigenvector of G ( g obs max ), which contrasted larval viability against embryo viability and juvenile viability. Target matrix rotation confirmed that while g obs max shows genetic associations can extend beyond metamorphosis, there is still considerable scope for decoupled phenotypic evolution. Therefore, although genetic associations across metamorphosis could limit that range of phenotypes that are attainable, traits on either side of the metamorphic boundary are capable of some independent evolutionary change in response to the divergent conditions encountered during each life cycle stage.

scholarly journals Phenotypic evolution is more constrained in simpler food webs

2019 ◽  
Author(s):  
Matthew A. Barbour ◽  
Christopher J. Greyson-Gaito ◽  
Arezoo Sootodeh ◽  
Brendan Locke ◽  
Jordi Bascompte
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Ecological Networks ◽  
Community Context ◽  
Relative Fitness ◽  
Adaptive Landscape ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Adaptive Landscapes ◽  
Food Web Complexity

AbstractGlobal change is simplifying the structure of ecological networks; however, we are currently in a poor position to predict how these simplified communities will affect the evolutionary potential of remaining populations. Theory on adaptive landscapes provides a framework for predicting how selection constrains phenotypic evolution, but often treats the community context of evolving populations as a “black box”. Here, we integrate ecological networks and adaptive landscapes to examine how changes in food-web complexity shape evolutionary constraints. We conducted a field experiment that manipulated the diversity of insect parasitoids (food-web complexity) that were able to impose selection on an insect herbivore. We then measured herbivore survival as a function of three key phenotypic traits. We found that more traits were under selection in simpler vs. more complex food webs. The adaptive landscape was more neutral in complex food webs because different parasitoid species impose different selection pressures, minimizing relative fitness differences among phenotypes. Our results suggest that phenotypic evolution becomes more constrained in simplified food webs. This indicates that the simplification of ecological communities may constrain the adaptive potential of remaining populations to future environmental change. “What escapes the eye, however, is a much more insidious kind of extinction: the extinction of ecological interactions.” Janzen (1974)

scholarly journals Cortisol, Temperament and Serotonin in Karate Combats: An Evolutionary Psychobiological Perspective

2021 ◽  
Author(s):  
Davide Ponzi ◽  
Harold Dadomo ◽  
Laura Filonzi ◽  
Paola Palanza ◽  
Annalisa Pelosi ◽  
...  
Keyword(s):  
Salivary Cortisol ◽  
Physiological Stress ◽  
Conclusive Evidence ◽  
Harm Avoidance ◽  
Phenotypic Traits ◽  
Sport Competition ◽  
Physiological Stress Response ◽  
Before And After ◽  
Cortisol Levels ◽  
S Allele

Abstract Objectives There is evidence suggesting that in martial arts competitions athletes characterized by higher anxiety and harm avoidance may be more likely to lose a fight. This psychological profile has been hypothesized to explain in part the observation that cortisol is higher in losers before and in response to a competition. An important research target that needs further exploration is the identification of phenotypic traits that can be helpful in predicting athletes’ performance. Here we present a brief description of the theoretical bases that drives our research in the evolutionary psychobiology of sports and illustrate preliminary data on the relationship between the 5HTTLPR genotype, salivary cortisol, temperament and competition. Methods Sixty-five healthy male non-professional athletes provided saliva samples 10 min before and after a kumite session and filled out the Tridimensional Personality Questionnaire. Results Salivary cortisol levels 10 min before the competition were higher in losers and in athletes with the S allele. Temperament was associated with competition outcome and cortisol: losers were characterized by higher scores of harm avoidance and harm avoidance was positively correlated with cortisol levels. Conclusions The results confirm previous findings linking temperamental traits, pre-and post- competition physiological stress response with competition outcome in kumite fight. Moreover, they indicate an association between the 5HTTLPR polymorphism and pre-competition salivary cortisol, thus providing a preliminary but non-conclusive evidence on the role played by the 5HTTLPR genotype as a vulnerability factor in sport competition.

scholarly journals Phenotype-limited distributions: short-billed birds move away during times that prey bury deeply

2015 ◽  
Vol 2 (6) ◽  
pp. 150073 ◽  
Author(s):  
Sjoerd Duijns ◽  
Jan A. van Gils ◽  
Jennifer Smart ◽  
Theunis Piersma
Keyword(s):  
Breeding Season ◽  
Resource Use ◽  
Environmental Conditions ◽  
Wadden Sea ◽  
Phenotypic Traits ◽  
Sexually Dimorphic ◽  
Phenotypic Evolution ◽  
Main Prey ◽  
Limited Distribution ◽  
Widespread Phenomenon

In our seasonal world, animals face a variety of environmental conditions in the course of the year. To cope with such seasonality, animals may be phenotypically flexible, but some phenotypic traits are fixed. If fixed phenotypic traits are functionally linked to resource use, then animals should redistribute in response to seasonally changing resources, leading to a ‘phenotype-limited’ distribution. Here, we examine this possibility for a shorebird, the bar-tailed godwit ( Limosa lapponica ; a long-billed and sexually dimorphic shorebird), that has to reach buried prey with a probing bill of fixed length. The main prey of female bar-tailed godwits is buried deeper in winter than in summer. Using sightings of individually marked females, we found that in winter only longer-billed individuals remained in the Dutch Wadden Sea, while the shorter-billed individuals moved away to an estuary with a more benign climate such as the Wash. Although longer-billed individuals have the widest range of options in winter and could therefore be selected for, counterselection may occur during the breeding season on the tundra, where surface-living prey may be captured more easily with shorter bills. Phenotype-limited distributions could be a widespread phenomenon and, when associated with assortative migration and mating, it may act as a precursor of phenotypic evolution.

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