Co s námi bude? Kam spěje lidstvo? – jsou otázky, které si klademe snad od chvíle, kdy se počítáme mezi druh označovaný jako moudrý. Někdy právem, jindy neprávem. Lidský druh se osamostatnil v pleistocénu a vyvíjel se do dnešních dob jak po stránce živočišné, tak duševní; snad vzletnější by bylo říkat jak fyzické, tak kulturní. V naší úvaze se zabýváme otázkami o stabilitě hmoty, z níž se naše fyzické já odvozuje – naším genomem a jeho vývojem, který v pohledu nazpět lze částečně rekonstruovat, pohledem do budoucnosti jen tušit. Popisujeme zákonitosti vývoje lidského genomu a vlivy, které na něj působí; pokoušíme se je i modelovat, a porovnávat s výsledky výzkumů na zvířatech, kde máme možnost i experimentovat. To, že často docházíme k protichůdným závěrům, svědčí o tom, na jak obtížném terénu se pohybujeme, a proto i naše vývody musíme brát s velkou opatrností, neboť se velice snadno můžeme svými představami nechat zavést. Z definovaných vlivů, které působí na naše genomy jako na součásti celkového genofondu lidstva, se pokoušíme hodnotit stav mutability, mutační zátěže, kvality genů/alel, efektivní velikosti populace, a míry migrace.
Where do we go and what will happen with our genomes? Viewed as a reflection of what we know about our origin as Homo sapiens, history and forecast. Archeogenetics tries to find our sourcing place and to explain how humans occupied the globe. One of the first theories based on mtDNA polymorphisms@ studies stressed on our African origin followed by stepwise dispersal all over the world which took approximately 80 000 years. But not all findings agreed with this assumption if based on nuclear loci and supported multifocal origin of humans. The process of establishing a new species – Homo sapiens, is still not fully understood and many questions remained unanswered. From the point of view of population genetics we can assume that: 1. Mutability (natural or from internal causes) does not change though we cannot neglect suspicion that environment could influence its increase. The content of harming mutations in our genome, due to the protective effect of health care, which blocks natural selection, is increasing and moreover changes of our life style opened the door for manifestation of week deleterious alleles accumulated during foregoing period of evolution. Also prolongation of our life span is accompanied with effects of genotypes positively selected because of their positive effect on our reproductive period but which could be harmful during postreproductive stage – antagonistic pleiotropy. 2. According traditional assumption on the quality of new mutations is that they are either neutral or harming. Changes which are drift-dependent are becoming reduced. 3. Effective population size (steady state could be supposed or some increase due to more intensive local migration). 4. Migration (In spite of absence of corresponding demographic data) seems to be nowadays more intensive than it was in the past.
Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR's divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.
... Kozubek 62 -- Dynamics of HPl transgene loci movement and silencing in living cells -- V. ...
1st ed. 82 s. : il., tab., grafy ; 30 cm
- MeSH
- Biophysics MeSH
- Chromatin MeSH
- DNA MeSH
- Genome MeSH
- Colorectal Neoplasms diagnosis MeSH
- Methylation MeSH
- Flow Cytometry utilization methods MeSH
- Publication type
- Congress MeSH
- Collected Work MeSH
- Conspectus
- Biochemie. Molekulární biologie. Biofyzika
- NML Fields
- biologie
- biochemie
We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.
- MeSH
- Chromosomes, Plant genetics MeSH
- Fabaceae classification genetics MeSH
- Phenotype MeSH
- Phylogeny MeSH
- Genetic Variation MeSH
- Genome, Plant * MeSH
- Genomics MeSH
- Pisum sativum genetics MeSH
- Quantitative Trait Loci * MeSH
- Chromosome Mapping MeSH
- Evolution, Molecular * MeSH
- Reference Standards MeSH
- Gene Expression Regulation, Plant MeSH
- Repetitive Sequences, Nucleic Acid MeSH
- Plant Proteins genetics MeSH
- Whole Genome Sequencing MeSH
- Seed Storage Proteins genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
Viruses from the genus Enterovirus are important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles to an activated state that is required for genome release. However, the mechanism of enterovirus uncoating is not well understood. Here, we use cryo-electron microscopy to visualize virions of human echovirus 18 in the process of genome release. We discover that the exit of the RNA from the particle of echovirus 18 results in a loss of one, two, or three adjacent capsid-protein pentamers. The opening in the capsid, which is more than 120 Å in diameter, enables the release of the genome without the need to unwind its putative double-stranded RNA segments. We also detect capsids lacking pentamers during genome release from echovirus 30. Thus, our findings uncover a mechanism of enterovirus genome release that could become target for antiviral drugs.
- MeSH
- Chlorocebus aethiops MeSH
- RNA, Double-Stranded chemistry genetics MeSH
- Cryoelectron Microscopy MeSH
- Enterovirus B, Human genetics ultrastructure MeSH
- Epithelial Cells ultrastructure virology MeSH
- Genome, Viral * MeSH
- Capsid chemistry ultrastructure MeSH
- Hydrogen-Ion Concentration MeSH
- Humans MeSH
- RNA, Viral chemistry genetics MeSH
- Molecular Dynamics Simulation MeSH
- Virus Uncoating genetics MeSH
- Virion genetics ultrastructure MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Nuclear genome size is an inherited quantitative trait of eukaryotic organisms with both practical and biological consequences. A detailed analysis of major families is a promising approach to fully understand the biological meaning of the extensive variation in genome size in plants. Although Orchidaceae accounts for ∼10% of the angiosperm diversity, the knowledge of patterns and dynamics of their genome size is limited, in part due to difficulties in flow cytometric analyses. Cells in various somatic tissues of orchids undergo extensive endoreplication, either whole-genome or partial, and the G1-phase nuclei with 2C DNA amounts may be lacking, resulting in overestimated genome size values. Interpretation of DNA content histograms is particularly challenging in species with progressively partial endoreplication, in which the ratios between the positions of two neighboring DNA peaks are lower than two. In order to assess distributions of nuclear DNA amounts and identify tissue suitable for reliable estimation of nuclear DNA content, we analyzed six different tissue types in 48 orchid species belonging to all recognized subfamilies. Although traditionally used leaves may provide incorrect C-values, particularly in species with progressively partial endoreplication, young ovaries and pollinaria consistently yield 2C and 1C peaks of their G1-phase nuclei, respectively, and are, therefore, the most suitable parts for genome size studies in orchids. We also provide new DNA C-values for 22 orchid genera and 42 species. Adhering to the proposed methodology would allow for reliable genome size estimates in this largest plant family. Although our research was limited to orchids, the need to find a suitable tissue with dominant 2C peak of G1-phase nuclei applies to all endopolyploid species.
Mitochondria, the powerhouse and the vital signaling hub of the cell, participate in a variety of biological processes, such as apoptosis, redox responses, cell senescence, autophagy, and iron homeostasis. Mitochondria form a mostly tubular network, made up of an outer and a cristeae-forming inner membrane. The network undergoes dynamic fusion and fission that change its morphological structure according to the functional needs. Approximately 1500 mitochondrial proteins encoded by nuclear genome plus over 10 proteins encoded by mitochondrial DNA are folded and assembled in the mitochondria under a high-fidelity control system. These proteins are involved in oxidative phosphorylation, metabolism, network and cristae dynamics, mitophagy, import machinery, ion channels, and mitochondrial DNA maintenance. This Collection gathers original research that advances our understanding of the monitoring techniques and pathophysiological significance of mitochondrial dynamics in health and disease.
- MeSH
- Humans MeSH
- Mitochondrial Dynamics * MeSH
- Mitochondria * metabolism MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Editorial MeSH
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1.2-1.4 Mbp) and low genomic GC content. Genome reduction in these bacteria might have led to auxotrophy for various vitamins, amino acids and reduced sulphur sources, thus creating dependencies to co-occurring organisms (the 'Black Queen' hypothesis). Genome analyses, moreover, revealed a surprising degree of inter- and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands. The striking genotype microdiversification of acI Actinobacteria might explain their global success in highly dynamic freshwater environments with complex seasonal patterns of allochthonous and autochthonous carbon sources. We propose a new order within Actinobacteria ('Candidatus Nanopelagicales') with two new genera ('Candidatus Nanopelagicus' and 'Candidatus Planktophila') and nine new species.
- MeSH
- Actinobacteria classification genetics isolation & purification MeSH
- Biodiversity MeSH
- DNA, Bacterial chemistry MeSH
- Phylogeny MeSH
- Genome, Bacterial * MeSH
- Metabolic Networks and Pathways genetics MeSH
- Fresh Water microbiology MeSH
- Base Composition MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Telomeres and genes encoding 45S ribosomal RNA (rDNA) are frequently located adjacent to each other on eukaryotic chromosomes. Although their primary roles are different, they show striking similarities with respect to their features and additional functions. Both genome domains have remarkably dynamic chromatin structures. Both are hypersensitive to dysfunctional histone chaperones, responding at the genomic and epigenomic levels. Both generate non-coding transcripts that, in addition to their epigenetic roles, may induce gross chromosomal rearrangements. Both give rise to chromosomal fragile sites, as their replication is intrinsically problematic. However, at the same time, both are essential for maintenance of genomic stability and integrity. Here we discuss the structural and functional inter-connectivity of telomeres and rDNA, with a focus on recent results obtained in plants.
- MeSH
- Chromatin chemistry metabolism MeSH
- DNA, Plant chemistry metabolism MeSH
- Epigenesis, Genetic MeSH
- Histones genetics metabolism MeSH
- Genomic Instability MeSH
- DNA Replication MeSH
- DNA, Ribosomal chemistry metabolism MeSH
- Plants genetics MeSH
- Telomere genetics metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
