Evidence for late Pleistocene origin of Astyanax mexicanus cavefish

BMC Evolutionary Biology, Journal Year: 2018, Volume and Issue: 18(1)

Published: April 4, 2018

Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models study tempo and mode of adaptation a radical environmental change. They currently assigned two main groups, so-called "old" "new" lineages, which would have populated several caves independently at different times. However, we do not yet accurate estimations time frames evolution these populations.We reanalyzed geographic distribution mitochondrial nuclear DNA polymorphisms found that data support existence cavefish lineages. Using IMa2, program allows dating population divergence in addition demographic parameters, microsatellite polymorphism strongly supports very recent origin cave (< 20,000 years). We identified large number single-nucleotide (SNPs) transcript sequences pools embryos (Pool-seq) Pachón surface from Texas. Based on summary statistics can be computed with this SNP set together simulations recently isolated populations, looked for sets parameters allow computation simulated similar ones sampled populations. In most could find good fit between observed data, best occurred when was less than 30,000 years.Although it is often assumed some ancient origin, supported by our analyses independent polymorphism. Moreover, observation divergent haplogroups genes distributions admixture before isolation If indeed only thousand years old, many phenotypic changes thus mainly involved fixation genetic variants present fish within short period time.

Language: Английский

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Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes

PLoS Computational Biology, Journal Year: 2016, Volume and Issue: 12(8), P. e1004972 - e1004972

Published: Aug. 18, 2016

Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable to the cell-cycle length, randomness cell-division times generates additional intercellular levels. Moreover, many mRNA/protein species are expressed at low-copy numbers, errors incurred partitioning molecules between two daughter cells significant. We derive analytical formulas for total levels when duration follows a general class probability distributions. Using novel hybrid approach decomposed into components arising from i) expression; ii) time cell division iii) random events. These reveal that not only generate extrinsic noise, but also critically affect mean numbers intrinsic components. Counter intuitively, some parameter regimes, decrease become more stochastic. Computations extended consider genome duplication, where transcription rate increased point cycle. systematically investigate how timing duplication influences different Intriguingly, results show contribution minimized an optimal genome-duplication time. Our theoretical motivate new experimental methods decomposing synchronized asynchronized single-cell data. Characterizing contributions mechanisms will lead precise estimates gene parameters techniques altering stochasticity change phenotype cells.

Language: Английский

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Single-cell transcriptomic evidence for dense intracortical neuropeptide networks

eLife, Journal Year: 2019, Volume and Issue: 8

Published: Nov. 11, 2019

Seeking new insights into the homeostasis, modulation and plasticity of cortical synaptic networks, we have analyzed results from a single-cell RNA-seq study 22,439 mouse neocortical neurons. Our analysis exposes transcriptomic evidence for dozens molecularly distinct neuropeptidergic modulatory networks that directly interconnect all This begins with discovery transcripts one or more neuropeptide precursor (NPP) neuropeptide-selective G-protein-coupled receptor (NP-GPCR) genes are highly abundant in all, very nearly Individual neurons express diverse subsets NP signaling palettes encoding 18 NPPs 29 NP-GPCRs. These 47 comprise 37 cognate NPP/NP-GPCR pairs, implying likelihood local signaling. Here, use neuron-type-specific patterns gene expression to offer specific, testable predictions regarding peptidergic neuromodulatory may play prominent roles homeostasis plasticity.

Language: Английский

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Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii

GigaScience, Journal Year: 2018, Volume and Issue: 7(4)

Published: Feb. 26, 2018

Abstract Background As one of the most popular and valuable commercial marine fishes in China East Asian countries, Chinese black porgy (Acanthopagrus schlegelii), also known as blackhead seabream, has some attractive characteristics such fast growth rate, good meat quality, resistance to diseases, excellent adaptability various environments. Furthermore, is a model for investigating sex changes fish due its protandrous hermaphroditism. Here, we obtained high-quality genome assembly this interesting teleost species performed genomic survey on potential genes associated with sex-change phenomenon. Findings We generated 175.4 gigabases (Gb) clean sequence reads using whole-genome shotgun sequencing strategy. The final approximately 688.1 megabases (Mb), accounting 93% estimated size (739.6 Mb). achieved scaffold N50 7.6 Mb, reaching relatively high level among sequenced species. identified 19 465 protein-coding genes, which had an average transcript length 17.3 kb. By performing comparative analysis, found 3 types potentially change, are useful studying genetic basis Conclusions provide draft discuss mechanisms change. These data important resource biology facilitating breeding economically fish.

Language: Английский

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Roles of pH in control of cell proliferation

Acta Physiologica, Journal Year: 2018, Volume and Issue: 223(3)

Published: March 25, 2018

Precise spatiotemporal regulation of intracellular pH (pHi ) is a prerequisite for normal cell function, and changes in pHi or pericellular (pHe exert important signalling functions. It well established that proliferation mammalian cells dependent on permissive the slightly alkaline range (7.0-7.2). also clear mitogen nominal absence HCO3- associated with an alkalinization (~0.3 unit above steady-state ), which secondary to activation Na+ /H+ exchange. However, it remains controversial whether this increase part mitogenic signal cascade leading cycle entry progression, relevant under physiological conditions. Furthermore, essentially all studies have focused mitogen-induced G0-G1 transition, roles during remain poorly understood. The aim review summarize critically discuss possible pHe progression. While focus cycle, insights from lower eukaryotes are discussed. We current evidence links between progression - sensors pathways control. possibility may be integral checkpoint control machinery explored. Finally, we relevance context perturbed homoeostasis acidic microenvironment solid tumours.

Language: Английский

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Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from Crystal Structures of the Catalytic Domain of MCR-1

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: Jan. 6, 2017

The polymixin colistin is a "last line" antibiotic against extensively-resistant Gram-negative bacteria. Recently, the mcr-1 gene was identified as plasmid-mediated resistance mechanism in human and animal Enterobacteriaceae, with wide geographical distribution many producer strains resistant to multiple other antibiotics. encodes membrane-bound enzyme catalysing phosphoethanolamine transfer onto bacterial lipid A. Here we present crystal structures revealing MCR-1 periplasmic, catalytic domain be zinc metalloprotein an alkaline phosphatase/sulphatase fold containing three disulphide bonds. One structure captures phosphorylated form representing first intermediate reaction. Mutation of residues implicated or binding, activity, restores susceptibility recombinant E. coli. Zinc deprivation reduces MICs MCR-1-producing laboratory, environmental, Conversely, over-expression isomerase DsbA increases MIC laboratory Preliminary density functional theory calculations on cluster models suggest single ion may sufficient support transfer. These data demonstrate importance bonds that assays under zinc-limiting conditions represent route phenotypic identification producing coli, identify key features likely mechanism.

Language: Английский

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Re‐evaluation of insect melanogenesis research: Views from the dark side

Pigment Cell & Melanoma Research, Journal Year: 2017, Volume and Issue: 30(4), P. 386 - 401

Published: April 5, 2017

Melanins (eumelanin and pheomelanin) are synthesized in insects for several purposes including cuticle sclerotization color patterning, clot formation, organogenesis, innate immunity. Traditional views of insect immunity detail the storage pro-phenoloxidases inside specialized blood cells (hemocytes) their release upon recognition foreign bodies. Activated phenoloxidases convert monophenols into reactive quinones a two-step enzymatic reaction, until recently, mechanism tyrosine hydroxylation remained mystery. Herein, we present our interpretations these enzyme-substrate complexes. The resultant melanins deposited onto surface microbes to immobilize, agglutinate, suffocate them. Phenoloxidase activity melanin production not limited (hemolymph) or cuticle, as recent evidence points more diverse, sophisticated interactions gut with resident symbionts. This review offers insight somewhat neglected areas melanogenesis research, particularly immunity, its role beneficial such pollinators, functional versatility phenoloxidases, limitations common experimental approaches that may impede progress inadvertently.

Language: Английский

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Cavefish and the basis for eye loss

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2016, Volume and Issue: 372(1713), P. 20150487 - 20150487

Published: Dec. 23, 2016

Animals have colonized the entire world from rather moderate to harshest environments, some of these so extreme that only few animals are able survive. Cave environments present such a challenge and obligate cave adapted perpetual darkness by evolving multitude traits. The most common studied characteristics regression eyes overall reduction in pigmentation. Studying traits can provide important insights into how evolutionary forces drive convergent regressive adaptation. blind Mexican cavefish ( Astyanax mexicanus ) has emerged as useful model study evolution owing availability genetic genomic resources, amenability embryonic development different populations remain fertile with each other. In this review, we give an overview our current knowledge underlying process using eye degeneration example. This article is part themed issue ‘Evo-devo genomics era, origins morphological diversity’.

Language: Английский

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Resolving Cypriniformes relationships using an anchored enrichment approach

BMC Evolutionary Biology, Journal Year: 2016, Volume and Issue: 16(1)

Published: Nov. 9, 2016

Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular morphological characters have been incongruent. In this study we present first phylogenomic analysis anchored hybrid enrichment for 172 taxa represent order (plus three out-group taxa), which dataset date (219 loci, 315,288 bp, average locus length 1011 bp). Concatenation establishes a robust tree with 97 % nodes at 100 bootstrap support. Species was highly congruent concatenation only two major differences: monophyly Cobitoidei placement Danionidae. Most clades obtained prior studies were validated as monophyletic, provide resolution among these time. These can be used framework addressing variety evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) ideally suited.

Language: Английский

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Evolution and diversity of transposable elements in fish genomes

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: Oct. 28, 2019

Abstract Transposable elements (TEs) are genomic sequences that can move, multiply, and often form sizable fractions of vertebrate genomes. Fish belong to a unique group vertebrates, since their karyotypes genome sizes more diverse complex, with probably higher diversity evolution specificity TE. To investigate the characteristics fish TEs, we compared mobilomes 39 species, observed significant variation TE content in (from 5% pufferfish 56% zebrafish), along positive correlation between size content. In different classification hierarchies, retrotransposons (class), long terminal repeat (order), as well Helitron , Maverick Kolobok CMC DIRS P I L1 L2 5S (superfamily) were all positively correlated size. Consistent previous studies, our data suggested genomes not always be dominated by DNA transposons; interspersed nuclear also prominent many species. This study suggests CR1 distribution obviously regular, provides new clues concerning important events evolution. Altogether, results highlight importance TEs structure suggest species parallel transposon diversification.

Language: Английский

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