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229 results for “meiosis”
Recombination and aneuploidy data for: Insights about variation in meiosis from 31,228 human sperm genomes
<p>This repository holds crossover and aneuploidy data for 31,228 human sperm genomes sequenced with Sperm-seq. Data are described in the preprint/paper "Insights about variation in meiosis from 31,228 human sperm genomes." Several levels of data are available, e.g., each crossover (allcrossovers_hg38.txt.gz) and the numbers of crossovers detected per sperm cell (numbercrossoverspercell.txt.gz). Each data file is described in its own readme, so README_allgainsdivisionoforigin.txt explains the data present in allgainsdivisionoforigin.txt. All files are either text files or text files compressed via gzip. All data was generated as described in the preprint/paper, using scripts available in the companion repository (most recent version DOI: 10.5281/zenodo.3561080).</p> <p>This new version has updated sex chromosome ploidies after identifying a minor coding error affecting ~24 cells (sexchromosomeploidy.txt.gz) and includes more detail about possible crossover error modes (README_allcrossovers_hg38.txt.gz).</p>
Figure 5 in Cytological evidence for automictic thelytoky in parthenogenetic oribatid mites (Acari, Oribatida): Synaptonemal complexes confirm meiosis in Archegozetes longisetosus
Figure 5 Archegozetes longisetosus. Peripheral oocyte of a tritonymph, showing oocyte extension and dense bundle of microtubuli passing the vicinity of the nuclear envelope. Nuclear envelope with numerous nuclear pores. Abbreviations: MT: microtubuli, NP: nuclear pores.
Figure 4 in Cytological evidence for automictic thelytoky in parthenogenetic oribatid mites (Acari, Oribatida): Synaptonemal complexes confirm meiosis in Archegozetes longisetosus
Figure 4 Archegozetes longisetosus.Ovary of a 5 day old tritonymph: a – Overview, parasagittal plane; b – detail of central region; c – detail
Figure 3 in Cytological evidence for automictic thelytoky in parthenogenetic oribatid mites (Acari, Oribatida): Synaptonemal complexes confirm meiosis in Archegozetes longisetosus
Figure 3 Archegozetes longisetosus.Synaptonemal complexes in oocytes of a two day old tritonymph: a-c: Three pachytene nuclei; d-g details: Synaptonemal complexes in longitudinal (d), (e), and transversal (f), (g) section. Abbreviations: CE: central element, LE: lateral element, SC: synaptonemal complex, TE: transversal element.
Figure 2 in Cytological evidence for automictic thelytoky in parthenogenetic oribatid mites (Acari, Oribatida): Synaptonemal complexes confirm meiosis in Archegozetes longisetosus
Figure 2 Archegozetes longisetosus.Germ cells in meiotic prophase of a two day old tritonymph: a – Pachytene cell with SC attached to the nuclear envelope; b – putative later stage with prominent nucleoli, from more peripheral region of the ovary. Abbreviations: AP: attachment
Figure 6 in Cytological evidence for automictic thelytoky in parthenogenetic oribatid mites (Acari, Oribatida): Synaptonemal complexes confirm meiosis in Archegozetes longisetosus
Figure 6 Archegozetes longisetosus: a – Vitellogenetic oocyte from the ovary of an adult female; b – Nuclear envelope with numerous nuclear
Figure 1 in Cytological evidence for automictic thelytoky in parthenogenetic oribatid mites (Acari, Oribatida): Synaptonemal complexes confirm meiosis in Archegozetes longisetosus
Figure 1 Archegozetes longisetosus.Overview of the arrangement of germ cells and somatic tissue in the ovary of a two day old tritonymph: a – Rostro-medially; b – centrally in the ovary. Abbreviations: BL: basal lamina, NP: nuclear pores, OE: oocyte extension, SC: synaptonemal complex, ST: somatic tissue.
All-atom Molecular Dynamics Simulations of Meiosis 1-associated protein (M1AP) to Investagate the Impact of Known Missense Mutations Associated with Male Infertility through Non-obstructive Azoospermia
<p>Protein structure of meiosis 1-associated protein (M1AP) was modelled by using GalaxyWeb (from Seok Lab). We used this model to investigate the impact of variants (i.e., S50P, R266Q, P389L, G317R, and L430P) in M1AP which were recently associated with non-obstructive azoospermia (NOA). NOA is a male infertility-related condition causing absence of sperm in the seminal fluid due to meiosis failure. We aimed to elucidate the pathogenicity mechanisms of these five missense NOA-related mutations on M1AP by performing molecular modeling and molecular dynamics (MD) simulations. This dataset includes the results of 1000 ns MD simulations (two repeats, each 500 ns) for each of the mutant and wild-type systems.</p> <p>Systems were prepared in Visual Molecular Dynamics (VMD 1.9.3) by placing them in a TIP3P water box with approximately 20 Å thickness from the protein surface and neutralizing the system charge with 0.15 M KCl. Of note, only protein parts were kept for the submission to reduce the size of files. Nanoscale Molecular Dynamics (NAMD 2.13-CUDA) was used to perform MD simulations with CHARMM36m force field. For pressure and temperature controls, Nosé-Hoover Langevin barostat and Langevin thermostat were used. ShakeH algorithm of NAMD was applied for water molecule constraints. 12 Å cut-off distance was used for van der Waals interactions. Switching function starts at 10 Å and reaches zero at 14 Å. Integration time-step was 2 fs. To compute the long-range Coulomb interactions, the particle-mash Ewald method was used. NPT ensemble was applied for whole simulations. Two step minimization & equilibration procedure was performed: (1) 5,000-step minimization and 1 ns equilibrium with constraints on the protein; (2) 5,000-step minimization and 1 ns equilibrium without the constraints on the protein. All related configuration files for wild-type system were also included to the dataset. Production simulations were run twice along 500 ns by using different random seeds to assign the velocities from Boltzmann distribution (total simulation time for each system was 1000 ns, which are given as 500 ns repeat 1, and 500 ns repeat 2). The production simulations were supplied in the dataset. "out" and "log" files were used for energy analysis.</p> <p>For all analysis scripts, see https://github.com/ugerlevik/M1AP_analysis.</p>
Establishment of a Spermatogonial Stem Cell Line with Potential of Meiosis in a Hermaphroditic Fish, Epinephelus coioides
<p>Figure S1. Cell localization of ly75, thy1, and dmc1 in adult testis of orange-spotted grouper. (A-C) Antisense probe signals of ly75, thy1, and dmc1. (D-F) Sense probe signals of ly75, thy1, and dmc1. Sg, Spermatogonium; Sc, Spermatocyte; St, spermatid. Scale Bars: 20 μm.</p> <p>Figure S2. Fluorescent immunostaining of antibodies in adult testis of orange-spotted grouper. (A-D and M-O) Fluorescence signals of Piwi, Dazl, Ssea1, Nanog, PCNA, Sycp3, and Dmc1. (E-H and P-R) Nuclei are counterstained with PI. (I-L and S-U) Merge images. Sg, Spermatogonium; Sc, Spermatocyte; St, spermatid; Sz, spermatozoa. Scale Bars: 20 μm.</p> <p>Figure S3. Derivation of a single colony from a single cell of GPT line. (A) A small colony after five days of culture. (B) A distinct colony after 10 days of culture. (C) A large colony containing hundreds of cells after 20 days of culture. Scale Bars: 20 μm in A; 50 μm in B; 200 μm in C.</p> <p>Figure S4. Prolonged cultivation of GPT cells under the lack of bFGF. (A-D) All GPT cells would differentiate into large epithelial-like cells and gradually die out during 25 days of culture under the lack of bFGF, LIF, and SCF (-/-). (E-H, J-M, and O-R) GPT cells consisted of some polygonal-like cells and many epithelial-like cells during 25 days of culture in the ESM media containing SCF and/or LIF. (I, N and S) All GPT cells transformed into very large epithelial-like cells and gradually died after 35 days of culture in the ESM media containing SCF and/or LIF. Scale Bars: 50 μm.</p> <p>Figure S5. Morphology of GPT cells under a condition of high cell confluence. (A) GPT cells were cultured for 14 days without subculture and (B) generated a few spherical cells (Arrows). Scale Bars: 50 μm in A; 20 μm in B.</p> <p>Figure S6. Establishment of a GPT cell line stably expressing green fluorescence protein. (A-C) Bright-field image, fluorescent image, and merged image of GPT cells after 48 hours of culture following electrotransfection with pEGFP-N3 plasmid. (D-F) Bright-field image, fluorescent image, and merged image of GPT cells after G418 resistance screening. Scale Bars: 200 μm in A-C; 100 μm in D-F.</p>
Cytoplasmic components of the machinery mediating telomere-led rapid chromosome movements in mouse meiosis
<p>Telomere-led rapid chromosome movements (RPMs) are a prominent characteristic of chromosome dynamics during meiosis. Although of crucial importance in maintaining germ cell integrity, the extranuclear portion of the machinery supporting RPMs in mammals is poorly understood. Using an unbiased proteomic approach to identify motor proteins associated to microtubules in mouse meiotic cells, complemented with co-immunoprecipitation confirmation, we uncovered kinesins as candidate of the machinery mediating RPMs in mouse spermatocytes. Further biochemical, microscopy, and functional analysis shows that KIF5B and KIF2B interact with KASH5 and act as motor proteins mediating the LINC complex-microtubule interactions. Our results show that member of the kinesin family of molecular motors act as novel critical modules of the machinery promoting complex dynamic chromosomes in mammals.</p>
RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" in Journal of Evolutionary Biology
<p>This a data set from the paper RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" to be published in Journal of Evolutionary Biology</p>
Fig. 17. Meiosis metaphase I in Taxonomy, larval morphology and cytogenetics of Lihelophorus, the Tibetan endemic subgenus of Helophorus (Coleoptera: Hydrophiloidea)
Fig. 17. Meiosis metaphase I from testes of Helophorus (Lihelophorus) species from Qinghai: Zuimatan. a – H. lamicola Zaitzev, 1908; b – H. ser Zaitzev, 1908; c – H. yangae sp. nov.
Fig. 18. Meiosis metaphase II in Taxonomy, larval morphology and cytogenetics of Lihelophorus, the Tibetan endemic subgenus of Helophorus (Coleoptera: Hydrophiloidea)
Fig. 18. Meiosis metaphase II from testes of Helophorus (Lihelophorus) species from Qinghai: Zuimatan. a–b – H. lamicola Zaitzev, 1908 (a – with y chromosome; b – with X chromosome). c – H. ser Zaitzev, 1908, with X chromosome. d–e – H. yangae sp. nov. (d – with y chromosome; e – with X chromosome).
Abb. IV. 68. Meiosis einer Pollenmutterzelle von Lycopersicon peruvianum, 2n in IV. Tropisches Obst und Gemüse
Abb. IV. 68. Meiosis einer Pollenmutterzelle von Lycopersicon peruvianum, 2n = 24 Chromosomen (Foto: M. P. Inst. f. Züchtungsforschung, Hamburg)
Supplemental Movie Files for "Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis" by Chriss et al.
<p>This set of Supplemental Information contains two movies made from the simulations from the model developed in the manuscript "<strong>Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis</strong>" by A. Chriss, G. V. Börner, and S. D. Ryan. </p> <p> </p> <p>Supplemental Movie S1: <strong>WT Chromosome Trajectories during Prophase I. </strong>The first file "movie_WT..." contains the file for the results of simulations for the wild-type chromosomes and the exact parameter values can be found in Table 1 of the manuscript. The movie shows one realization of the agent-based model. The simulation movie covers the homology search process from <em>t = 3h </em>to <em>t = 9h</em>. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii. The radius represents the attractive and non-homologous repulsive region.</p> <p> </p> <p>Supplemental Movie S2: <strong>WT Chromosome Trajectories during Prophase I with active dumbbell model. </strong> The second file "movie<em>WT</em>_activedumbbell..." contains the file for the results of the simulations for the modeling of chromosomes as active dumbbells (from polymers) to allow for the study of the effects of elongation, orientation, and flexibility. The movie shows one realization of the agent-based active dumbbell model which is closer to modeling a chromosome as a polymer. The simulation movie covers the homology search process from <em>t = 3h </em>to <em>t = 9h</em>. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii, but are allowed to change in time as the two beads expand and contract. The radius represents the attractive and non-homologous repulsive region.</p> <p> </p> <p>Supplemental Movie S3: <strong><em>spo11</em> hypomorph (30% WT DSB levels) Chromosome Trajectories during Prophase I (parameters from Fig 7B)</strong>. The third file "movie_spo11..." contains the file for the results of the simulations for the spo-11 hypomorph and the associated parameter values can be found in Table 1 of the manuscript. The movie depicts one realization of the agent-based model for the {\it spo11} hypomorphic mutant. The simulation movie covers the homology search process from <em>t = 3h</em> to <em>t = 9h</em> where mutant <em>spo11</em> is associated with a weaker attractive and repulsive force (e.g., reduction to 77% of WT values). True chromosome lengths are incorporated and scale the relevant interaction radii. Matching colors correspond to homologous pairs. The radii represent the homologous attractive and the non-homologous repulsive region. Note that the reduction in interaction strength delays homologous pairing consistent with experimental observations in [13]. </p> <p> </p> <p> </p> <p>The codes that generated these movies were written in Matlab and freely available via GitHub: <a href="https://github.com/sdryan/ChromosomeDynamicsProphase1">https://github.com/sdryan/ChromosomeDynamicsProphase1</a></p> <p> </p> <p>For questions please contact the corresponding authors: G. Valentin Börner <a href="mailto:g.boerner@csuohio.edu">g.boerner@csuohio.edu</a> (Biology) or Shawn D. Ryan <a href="mailto:s.d.ryan@csuohio.edu">s.d.ryan@csuohio.edu</a> (Math).</p>
Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation
<div class="abstract">A long-standing goal in the field of polyploid biology has been the derivation of mathematical models of gamete mode formation. These models form the basis of statistical inference and evolutionary theory. Here, we present 3-locus models of gamete mode formation in autotetraploids without and with preferential cross-over formation. The three loci are assumed to occur on one arm of the same chromosome. For preferential cross-over formation, one of the three loci affects the tendency for sets of sister chromatids to pair and therefore affects rates of recombination. The models are derived such that the process of double reduction is a function of rates of synaptic partner switches and recombination, as opposed to being independent of these processes. We assume potentially one synaptic partner switch per meiosis. We also assume the coefficient of coincidence is one, such that cross-over events are independent, given a set of cross-over rates. Illustrative cases are examined demonstrating differences in the gamete mode probabilities without and with preferential cross-over formation. Lastly, we explore the accuracy of maximum likelihood estimates of the probability of synaptic partner switches and preferential cross-over formation when the locus controlling preferences is at a proximal, middle or distal location on the chromosome arm. All Supplementary Information is available at https://github.com/ckgriswold/3-locus-autotetraploid-meiosis.</div>
Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation
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Data from: Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum
<p>Naturally occurring autopolyploid species such as the autotetraploid potato <i>Solanum tuberosum</i> face a variety of challenges during meiosis. These include proper pairing, recombination and correct segregation of multiple homologous chromosomes, which can form complex multivalent configurations at metaphase I, and in turn alter allelic segregation ratios through double reduction. Here, we present a reference map of meiotic stages in diploid and tetraploid <i>S. tuberosum</i> using fluorescence <i>in situ</i> hybridisation (FISH) to differentiate individual meiotic chromosomes 1 and 2. A diploid-like behaviour at metaphase I involving bivalent configurations was predominant in all three tetraploid varieties. The crossover frequency per bivalent was significantly reduced in the tetraploids compared with a diploid variety, which likely indicates meiotic adaptation to the autotetraploid state. Nevertheless, bivalents were accompanied by a substantial frequency of multivalents, which varied by variety and by chromosome (7-48%). We identified possible sites of synaptic partner switching, leading to multivalent formation, and found potential defects in the polymerisation and/or maintenance of the synaptonemal complex in tetraploids. These findings demonstrate the rise of <i>S. tuberosum</i> as a model for autotetraploid meiotic recombination research and highlight constraints on meiotic chromosome configurations and chiasma frequencies as an important feature of an evolved autotetraploid meiosis.</p>
Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.
<p>In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid <em>Arabidopsis lyrata</em> and <em>A</em>. <em>lyrata/A</em>. <em>arenosa</em> hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (<em>ASY1</em>, <em>ASY3</em>, <em>PDS5b</em>, <em>PRD3</em>, <em>REC8</em>, <em>SMC3</em>, <em>ZYP1a/b</em>) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20–100%) between individual tetraploid plants and associated with segregation of a novel <em>ASYNAPSIS3</em> (<em>ASY3</em>) allele derived from <em>A</em>. <em>lyrata</em>. The <em>ASY3</em> allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the <em>ASY3 TD</em> haplotype was significantly lower than in plants heterozygous for <em>ASY3 TD/ND</em> (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for <em>ASY3 TD</em> compared to a plant heterozygous for <em>ASY3 ND/TD</em>. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from <em>A</em>. <em>lyrata/A</em>. <em>arenosa</em> and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.</p>
Evidence from automixis with inverted meiosis for the maintenance of sex by loss of complementation
<p>The adaptive value of sexual reproduction is still debated. A short-term disadvantage of asexual reproduction is loss of heterozygosity, which leads to the unmasking of recessive deleterious mutations. The cost of this loss of complementation is predicted to be higher than the twofold cost of meiosis for most types of asexual reproduction. Automixis with terminal fusion of sister nuclei is especially vulnerable to the effect of loss of complementation. It is found, however, in some taxa including oribatid mites, the most prominent group of ancient asexuals. Here I show that automixis with terminal fusion is stable if it is associated with inverted meiosis, and that this appears to be the case in nature, notably in oribatid mites. The existence of automixis with terminal fusion, and its co-occurrence with inverted meiosis, therefore, is consistent with the hypothesis that loss of complementation is important in the evolution of sexual reproduction.</p>
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