scholarly journals Evolution and developmental diversity of skin spines in pufferfish

2018 ◽  
Author(s):  
Takanori Shono ◽  
Alexandre P. Thiery ◽  
Daisuke Kurokawa ◽  
Ralf Britz ◽  
Gareth J. Fraser
Keyword(s):  
Gene Network ◽  
Gene Interactions ◽  
Teleost Fishes ◽  
Scale Type ◽  
Ocean Sunfish ◽  
Skin Appendage ◽  
Appendage Formation ◽  
Conserved Gene ◽  
Extreme Scale ◽  
Huge Variety

AbstractTeleost fishes develop a huge variety of skin ornaments. How these diverse skin structures develop in fishes is unknown. The teleost fish order Tetraodontiformes includes some of the most unusual fishes such as the ocean sunfish, triggerfish and pufferfish, and they all can develop a vast assortment of scale derivatives that cover their bodies. Pufferfish have some of the most extreme scale derivatives, dermal spines, which are erected during their characteristic puffing behavior. Here we show that pufferfish spines develop through conserved gene interactions essential for other vertebrate skin appendage formation, like hair and feathers. However, pufferfish spines form without EDA (ectodysplasin), an essential molecule for the development of most vertebrate skin appendages. Modifying signaling pathways lead to loss or reduction of spine coverage in pufferfish, suggesting a mechanism for skin appendage diversification. We suggest that pufferfish skin spines evolved from a basic teleost scale-type through derived gene network modification in Tetraodontiformes.

scholarly journals Neofunctionalization of embryonic head patterning genes facilitates the positioning of novel traits on the dorsal head of adult beetles

2016 ◽  
Vol 283 (1834) ◽  
pp. 20160824 ◽  
Author(s):  
Eduardo E. Zattara ◽  
Hannah A. Busey ◽  
David M. Linz ◽  
Yoshinori Tomoyasu ◽  
Armin P. Moczek
Keyword(s):  
Rna Interference ◽  
Embryonic Development ◽  
Gene Network ◽  
Evolutionary Novelty ◽  
Developmental Evolution ◽  
Flour Beetles ◽  
Novel Traits ◽  
Adult Head ◽  
Conserved Gene ◽  
Embryonic Head

The origin and integration of novel traits are fundamental processes during the developmental evolution of complex organisms. Yet how novel traits integrate into pre-existing contexts remains poorly understood. Beetle horns represent a spectacular evolutionary novelty integrated within the context of the adult dorsal head, a highly conserved trait complex present since the origin of insects. We investigated whether otd1/2 and six3 , members of a highly conserved gene network that instructs the formation of the anterior end of most bilaterians, also play roles in patterning more recently evolved traits. Using ablation-based fate-mapping, comparative larval RNA interference (RNAi) and transcript sequencing, we found that otd1/2 , but not six3 , play a fundamental role in the post-embryonic formation of the adult dorsal head and head horns of Onthophagus beetles. By contrast, neither gene appears to pattern the adult head of Tribolium flour beetles even though all are expressed in the dorsal head epidermis of both Onthophagus and Tribolium . We propose that, at least in beetles, the roles of otd genes during post-embryonic development are decoupled from their embryonic functions, and that potentially non-functional post-embryonic expression in the dorsal head facilitated their co-option into a novel horn-patterning network during Onthophagus evolution.

DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes

2020 ◽  
Author(s):  
Peifeng Ruan ◽  
Shuang Wang
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Gene Network ◽  
Gene Interactions ◽  
Specific Gene ◽  
Comparison Methods ◽  
Cancer Types ◽  
Disease Associated Genes ◽  
Methylation Signal ◽  
Disease Specific

Abstract Biological network-based strategies are useful in prioritizing genes associated with diseases. Several comprehensive human gene networks such as STRING, GIANT and HumanNet were developed and used in network-assisted algorithms to identify disease-associated genes. However, none of these networks are disease-specific and may not accurately reflect gene interactions for a specific disease. Aiming to improve disease gene prioritization using networks, we propose a Disease-Specific Network Enhancement Prioritization (DiSNEP) framework. DiSNEP first enhances a comprehensive gene network specifically for a disease through a diffusion process on a gene–gene similarity matrix derived from disease omics data. The enhanced disease-specific gene network thus better reflects true gene interactions for the disease and may improve prioritizing disease-associated genes subsequently. In simulations, DiSNEP that uses an enhanced disease-specific network prioritizes more true signal genes than comparison methods using a general gene network or without prioritization. Applications to prioritize cancer-associated gene expression and DNA methylation signal genes for five cancer types from The Cancer Genome Atlas (TCGA) project suggest that more prioritized candidate genes by DiSNEP are cancer-related according to the DisGeNET database than those prioritized by the comparison methods, consistently across all five cancer types considered, and for both gene expression and DNA methylation signal genes.

scholarly journals Early Events in Skin Appendage Formation: Induction of Epithelial Placodes and Condensation of Dermal Mesenchyme

1999 ◽  
Vol 4 (3) ◽  
pp. 302-306 ◽  
Author(s):  
Randall B. Widelitz ◽  
Cheng-Ming Chuong
Keyword(s):  
Skin Appendage ◽  
Appendage Formation

scholarly journals Gene network modeling via TopNet reveals robust epistatic interactions between functionally diverse tumor critical mediator genes

2020 ◽  
Author(s):  
Helene R. McMurray ◽  
Aslihan Ambeskovic ◽  
Laurel A. Newman ◽  
Jordan Aldersley ◽  
Vijaya Balakrishnan ◽  
...  
Keyword(s):  
Network Architecture ◽  
Gene Network ◽  
Cell Transformation ◽  
Network Modeling ◽  
Malignant Cell ◽  
Gene Interactions ◽  
Novel Approach ◽  
Genetic Perturbations ◽  
Perturbation Data ◽  
Cancer Intervention

AbstractMalignant cell transformation and the underlying genomic scale reprogramming of gene expression require cooperation of multiple oncogenic mutations. Notably, this cooperation is reflected in the synergistic regulation of downstream genes, so-called cooperation response genes (CRGs). CRGs impact diverse hallmark features of cancer cells and are not known to be functionally connected. Yet, they act as critical mediators of the cancer phenotype at an unexpectedly high frequency of >50%, as indicated by genetic perturbations. Here we demonstrate that CRGs function within a network of strong genetic interdependencies that are critical to the robustness of the malignant state. Our approach, termed TopNet, utilizes attractor-based ternary network modeling that takes the novel approach of incorporating uncertainty in the underlying gene perturbation data and is capable of identifying non-linear gene interactions. TopNet reveals topological gene network architecture that effectively predicts previously unknown, functionally relevant epistatic gene interactions, and thus, among a broad range of applications, has utility for identification of non-mutant targets for cancer intervention.

scholarly journals Eda-activated RelB recruits an SWI/SNF (BAF) chromatin-remodeling complex and initiates gene transcription in skin appendage formation

2018 ◽  
Vol 115 (32) ◽  
pp. 8173-8178 ◽  
Author(s):  
Jian Sima ◽  
Zhijiang Yan ◽  
Yaohui Chen ◽  
Elin Lehrmann ◽  
Yongqing Zhang ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Gene Transcription ◽  
Target Genes ◽  
Specific Gene ◽  
Open Chromatin ◽  
Transcription Profiling ◽  
Baf Complex ◽  
Skin Appendage ◽  
Chromatin Remodeling Complex ◽  
Appendage Formation

Ectodysplasin A (Eda) signaling activates NF-κB during skin appendage formation, but how Eda controls specific gene transcription remains unclear. Here, we find that Eda triggers the formation of an NF-κB–associated SWI/SNF (BAF) complex in which p50/RelB recruits a linker protein, Tfg, that interacts with BAF45d in the BAF complex. We further reveal that Tfg is initially induced by Eda-mediated RelB activation and then bridges RelB and BAF for subsequent gene regulation. The BAF component BAF250a is particularly up-regulated in skin appendages, and epidermal knockout of BAF250a impairs skin appendage development, resulting in phenotypes similar to those of Eda-deficient mouse models. Transcription profiling identifies several target genes regulated by Eda, RelB, and BAF. Notably, RelB and the BAF complex are indispensable for transcription of Eda target genes, and both BAF complex and Eda signaling are required to open chromatin of Eda targets. Our studies thus suggest that Eda initiates a signaling cascade and recruits a BAF complex to specific gene loci to facilitate transcription during organogenesis.

MANIA: A GENE NETWORK REVERSE ALGORITHM FOR COMPOUNDS MODE-OF-ACTION AND GENES INTERACTIONS INFERENCE

2010 ◽  
Vol 13 (01) ◽  
pp. 83-94
Author(s):  
DARONG LAI ◽  
HONGTAO LU ◽  
MARIO LAURIA ◽  
DIGEO DI BERNARDO ◽  
CHRISTINE NARDINI
Keyword(s):  
Mode Of Action ◽  
Gene Network ◽  
Expression Profiles ◽  
Gene Interactions ◽  
Grand Challenge ◽  
Expression Data ◽  
Linear Ordinary Differential Equations ◽  
Cellular Machinery ◽  
High Throughput Gene Expression ◽  
I Gene

Understanding the complexity of the cellular machinery represents a grand challenge in molecular biology. To contribute to the deconvolution of this complexity, a novel inference algorithm based on linear ordinary differential equations is proposed, based solely on high-throughput gene expression data. The algorithm can infer (i) gene–gene interactions from steady state expression profiles and (ii) mode-of-action of the components that can trigger changes in the system. Results demonstrate that the proposed algorithm can identify both information with high performances, thus overcoming the limitation of current algorithms that can infer reliably only one.

Comparative genomic organization and tissue-specific transcription of the duplicated fabp7 and fabp10 genes in teleost fishes

Genome ◽  
2013 ◽  
Vol 56 (11) ◽  
pp. 691-701 ◽  
Author(s):  
Manoj B. Parmar ◽  
Jonathan M. Wright
Keyword(s):  
Genomic Organization ◽  
Genome Duplication ◽  
Comparative Genomic ◽  
Teleost Fishes ◽  
Tissue Specific ◽  
Specific Distribution ◽  
Evolutionary Trajectories ◽  
Spotted Green Pufferfish ◽  
Gene Duplicates ◽  
Conserved Gene

A whole-genome duplication (WGD) early in the teleost fish lineage makes fish ideal organisms to study the fate of duplicated genes and underlying evolutionary trajectories that have led to the retention of ohnologous gene duplicates in fish genomes. Here, we compare the genomic organization and tissue-specific transcription of the ohnologous fabp7 and fabp10 genes in medaka, three-spined stickleback, and spotted green pufferfish to the well-studied duplicated fabp7 and fabp10 genes of zebrafish. Teleost fabp7 and fabp10 genes contain four exons interrupted by three introns. Polypeptide sequences of Fabp7 and Fabp10 show the highest sequence identity and similarity with their orthologs from vertebrates. Orthology was evident as the ohnologous Fabp7 and Fabp10 polypeptides of teleost fishes each formed distinct clades and clustered together with their orthologs from other vertebrates in a phylogenetic tree. Furthermore, ohnologous teleost fabp7 and fabp10 genes exhibit conserved gene synteny with human FABP7 and chicken FABP10, respectively, which provides compelling evidence that the duplicated fabp7 and fabp10 genes of teleost fishes most likely arose from the well-documented WGD. The tissue-specific distribution of fabp7a, fabp7b, fabp10a, and fabp10b transcripts provides evidence of diverged spatial transcriptional regulation between ohnologous gene duplicates of fabp7 and fabp10 in teleost fishes.

scholarly journals Estimating network changes from lifespan measurements using a parsimonious gene network model of cellular aging

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hong Qin
Keyword(s):  
Mortality Rate ◽  
Network Model ◽  
Gene Networks ◽  
Gene Network ◽  
Cellular Aging ◽  
System Level ◽  
Gene Interactions ◽  
Virtual Age ◽  
Average Lifespan ◽  
Natural Isolates

Abstract Background Cellular aging is best studied in the budding yeast Saccharomyces cerevisiae. As an example of a pleiotropic trait, yeast lifespan is influenced by hundreds of interconnected genes. However, no quantitative methods are currently available to infer system-level changes in gene networks during cellular aging. Results We propose a parsimonious mathematical model of cellular aging based on stochastic gene interaction networks. This network model is made of only non-aging components: the strength of gene interactions declines with a constant mortality rate. Death of a cell occurs in the model when an essential node loses all of its interactions with other nodes, and is equivalent to the deletion of an essential gene. Stochasticity of gene interactions is modeled using a binomial distribution. We show that the exponential increase of mortality rate over time can emerge from this gene network model during the early stages of aging.We developed a maximal likelihood approach to estimate three lifespan-influencing network parameters from experimental lifespans: t0, the initial virtual age of the network system; n, the average lifespan-influencing interactions per essential node; and R, the initial mortality rate. We applied this model to yeast mutants with known effects on replicative lifespans. We found that deletion of SIR2, FOB1, and HXK2 considerably altered the initial virtual age but not the average lifespan-influencing interactions per essential node, suggesting that these mutations mainly influence the reliability of gene interactions but not the overall configurations of gene networks.We applied this model to investigate replicative lifespans of yeast natural isolates. We estimated that the average number of lifespan-influencing interactions per essential node is 7.0 (6.1–8) and the average estimated initial virtual age is 45.4 (30.6–74) cell divisions in these isolates. We also found that t0 could potentially mediate the observed Strehler-Mildvan correlation in yeast natural isolates. Conclusions Our theoretical model provides a parsimonious interpretation of experimental lifespan data from the perspective of gene networks. We hope that our work will stimulate more interest in developing network models to study aging as a pleiotropic trait.

Genetic Variation: Impact on Folate (and Choline) Bioefficacy

2010 ◽  
Vol 80 (45) ◽  
pp. 319-329 ◽  
Author(s):  
Allyson A. West ◽  
Marie A. Caudill
Keyword(s):  
Carbon Metabolism ◽  
Genetic Variants ◽  
Plasma Homocysteine ◽  
Water Soluble ◽  
Gene Interactions ◽  
Dietary Folate ◽  
Methyl Donors ◽  
Common Genetic Variants ◽  
One Carbon Metabolism ◽  
The Impact

Folate and choline are water-soluble micronutrients that serve as methyl donors in the conversion of homocysteine to methionine. Inadequacy of these nutrients can disturb one-carbon metabolism as evidenced by alterations in circulating folate and/or plasma homocysteine. Among common genetic variants that reside in genes regulating folate absorptive and metabolic processes, homozygosity for the MTHFR 677C > T variant has consistently been shown to have robust effects on status markers. This paper will review the impact of genetic variants in folate-metabolizing genes on folate and choline bioefficacy. Nutrient-gene and gene-gene interactions will be considered along with the need to account for these genetic variants when updating dietary folate and choline recommendations.

Characterization and evolution of spearfishing in Madeira archipelago, Eastern Atlantic

2020 ◽  
Vol 33 ◽  
pp. 15
Author(s):  
Roi Martínez-Escauriaza ◽  
Claudio Vieira ◽  
Lídia Gouveia ◽  
Nuno Gouveia ◽  
Margarida Hermida
Keyword(s):  
Fish Species ◽  
Young Men ◽  
Coastal Areas ◽  
Teleost Fishes ◽  
The North ◽  
Southeast Coast ◽  
Madeira Archipelago ◽  
First Time

Data obtained from licenses of spearfishers and surveys conducted in 2004 and 2017 allowed for the analysis, for the first time, of the practice of spearfishing in the Madeira archipelago. Only a small percentage of the population practices spearfishing, mostly local young men. Most of them practice the activity with a partner throughout most of the year and along most of the island's coastal areas, although preferentially along the North and Southeast coast. Results show how, in recent years, despite the population of spearfishers decreasing, the abundance in the annual catch potentially increased, probably due to the higher investment of time in this activity. It has been observed that many fishers complement their catches with manual collecting of invertebrates. Overall, 40 teleost fishes and also 4 crustaceans and 8 molluscs were identified. The most frequently captured fish species were parrotfish and white seabream, while limpets were the most collected invertebrates in both selected periods.

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