Diversity and selective sweep in the OsAMT1;1 genomic region of rice

<p>Abstract</p> <p>Background</p> <p>Ammonium is one of the major forms in which nitrogen is available for plant growth. <it>OsAMT1;1 </it>is a high-affinity ammonium transporter in rice (<it>Oryza sativa </it>L.), responsible for ammonium uptake at low nitrogen concentration. The expression pattern of the gene has been reported. However, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. In this study, nucleotide diversity of the gene <it>OsAMT1;1 </it>and the diversity pattern of seven gene fragments spanning a genomic region approximately 150 kb long surrounding the gene were surveyed by sequencing a panel of 216 rice accessions including both cultivated rice and wild relatives.</p> <p>Results</p> <p>Nucleotide polymorphism (Pi) of <it>OsAMT1;1 </it>was as low as 0.00004 in cultivated rice (<it>Oryza sativa</it>), only 2.3% of that in the common wild rice (<it>O. rufipogon</it>). A single dominant haplotype was fixed at the locus in <it>O. sativa</it>. The test values for neutrality were significantly negative in the entire region stretching 5' upstream and 3' downstream of the gene in all accessions. The value of linkage disequilibrium remained high across a 100 kb genomic region around <it>OsAMT1;1 </it>in <it>O. sativa</it>, but fell rapidly in <it>O. rufipogon </it>on either side of the promoter of <it>OsAMT1;1</it>, demonstrating a strong natural selection within or nearby the ammonium transporter.</p> <p>Conclusions</p> <p>The severe reduction in nucleotide variation at <it>OsAMT1;1 </it>in rice was caused by a selective sweep around <it>OsAMT1;1</it>, which may reflect the nitrogen uptake system under strong selection by the paddy soil during the domestication of rice. Purifying selection also occurred before the wild rice diverged into its two subspecies, namely <it>indica </it>and <it>japonica</it>. These findings would provide useful insights into the processes of evolution and domestication of nitrogen uptake genes in rice.</p

Principles of Hand Fracture Management

The hand is essential in humans for physical manipulation of their surrounding environment. Allowing the ability to grasp, and differentiated from other animals by an opposing thumb, the main functions include both fine and gross motor skills as well as being a key tool for sensing and understanding the immediate surroundings of their owner

Inefficient cell cycle checkpoints allow errors at multiple stages of oogenesis to cause aneuploidy in mouse oocytes.

Chromosome segregation errors during meiosis pose a significant threat to the survival of a species, because aneuploidy that arises due to segregation errors can lead to the demise of any resulting embryos. Therefore, production of aneuploid gametes is strongly suppressed in many organisms. Surprisingly, human females are the rare exception. It is estimated at least 10% of all human pregnancies are aneuploid, with a majority of errors originating during female meiosis. Importantly, the rate of errors increases exponentially with advancing maternal age and may exceed 50% for women nearing the end of their reproductive lifespan. Many causative factors have been proposed to explain the high incidence of aneuploidy and the effect of advancing maternal age, but the basis of human aneuploidy has remained elusive. Central to the prevention of chromosome segregation errors is the presence of a cell cycle checkpoint that stops chromosomally abnormal cells from further development. We hypothesized that the checkpoint mechanism is not stringent in the oocyte in eliminating cells with errors, therefore increasing the likelihood of generating aneuploid gametes. In my research, I tested the stringency of meiotic checkpoints in response to errors that arise at multiple stages of oogenesis by utilizing mutant mice defective in homologous chromosome synapsis and/or meiotic crossover formation.The results from studies presented in this thesis show that cell cycle checkpoints in the oocyte are inefficient at halting meiotic progression of cells with errors. Specifically, checkpoints fail to arrest meiotic progression when errors occur at two distinct developmental time points: 1) when homologous chromosomes fail to synapse properly in prophase, and 2) when chromosomes fail to align at metaphase I. Consequently, the inability of these checkpoints to halt progression of defective cells increases the likelihood of chromosome segregation errors. Importantly, these findings provide vital contributions in understanding the origin of human aneuploidy. Accumulating evidence suggests that the genesis of human aneuploidy involves errors at multiple developmental time points, and the presence of inefficient checkpoints allows the survival of cells with errors, ultimately leading to the genesis of aneuploidy

Oocyte-Specific Differences in Cell-Cycle Control Create an Innate Susceptibility to Meiotic Errors

Segregation of homologs at the first meiotic division (MI) is facilitated by crossovers and by a physical constraint imposed on sister kinetochores that facilitates monopolar attachment to the MI spindle. Recombination failure or premature separation of homologs results in univalent chromosomes at MI, and univalents constrained to form monopolar attachments should be inherently unstable and trigger the spindle assembly checkpoint (SAC) [1]. Although univalents trigger cell-cycle arrest in the male [2–5], this is not the case in mammalian oocytes [6, 7]. Because the spindle assembly portion of the SAC appears to function normally [8–10], two hypotheses have been proposed to explain the lack of response to univalents: (1) reduced stringency of the oocyte SAC to aberrant chromosome behavior [7], and (2) the ability of univalents to satisfy the SAC by forming bipolar attachments [6]. The present study of Mlh1 mutant mice demonstrates that metaphase alignment is not a prerequisite for anaphase onset and provides strong evidence that MI spindle stabilization and anaphase onset require stable bipolar attachment of a critical mass—but not all—of chromosomes. We postulate that subtle differences in SAC-mediated control make the human oocyte inherently error prone and contribute to the age-related increase in aneuploidy. ► Metaphase alignment is not a prerequisite for anaphase onset in the mouse oocyte ► Chromosome behavior influences MI spindle formation and stabilization ► Insensitivity to misaligned chromosomes renders the oocyte error pron

ZGLP1 is a determinant for the oogenic fate in mice

生殖細胞が卵母細胞へと分化する仕組みを解明. 京都大学プレスリリース. 2020-02-14.Mammalian sexual reproduction relies on the dichotomy of male and female germ cell development. However, the underlying mechanisms remain unclear. Here, we show that ZGLP1, a conserved transcriptional regulator with GATA-like zinc fingers, determines the oogenic fate in mice. ZGLP1 acts downstream of bone morphogenetic protein (BMP), but not retinoic acid (RA), and is essential for the oogenic program and meiotic entry. ZGLP1 overexpression induces differentiation of in vitro primordial germ cell-like cells (PGCLCs) into fetal oocytes by activating the oogenic programs repressed by Polycomb activities, whereas RA signaling contributes to the oogenic program maturation and PGC program repression. Our findings elucidate the mechanism for mammalian oogenic fate determination, providing a foundation for promoting in vitro gametogenesis and reproductive medicine

Inactivation of Retinoblastoma Protein (Rb1) in the Oocyte: Evidence That Dysregulated Follicle Growth Drives Ovarian Teratoma Formation in Mice

The origin of most ovarian tumors is undefined. Here, we report development of a novel mouse model in which conditional inactivation of the tumor suppressor gene Rb1 in oocytes leads to the formation of ovarian teratomas (OTs). While parthenogenetically activated ooctyes are a known source of OT in some mutant mouse models, enhanced parthenogenetic propensity in vitro was not observed for Rb1-deficient oocytes. Further analyses revealed that follicle recruitment and growth is disrupted in ovaries of mice with conditional inactivation of Rb1, leading to abnormal accumulation of secondary/preantral follicles. These findings underpin the concept that miscues between the germ cell and somatic compartments cause premature oocyte activation and the formation of OTs. Furthermore, these results suggest that defects in folliculogenesis and a permissive genetic background are sufficient to drive OT development, even in the absence of enhanced parthenogenetic activation. Thus, we have discovered a novel role of Rb1 in regulating the entry of primordial oocytes into the pool of growing follicles and signaling between the oocyte and granulosa cells during the protracted process of oocyte growth. Our findings, coupled with data from studies of other OT models, suggest that defects in the coordinated regulation between growth of the oocyte and somatic components in follicles are an underlying cause of OT formation

High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis

High-quality, straightforward single-cell RNA sequencing (RNA-seq) with spatial resolution remains challenging. Here, we developed DRaqL (direct RNA recovery and quenching for laser capture microdissection), an experimental approach for efficient cell lysis of tissue sections, directly applicable to cDNA amplification. Single-cell RNA-seq combined with DRaqL allowed transcriptomic profiling from alcohol-fixed sections with efficiency comparable with that of profiling from freshly dissociated cells, together with effective exon-exon junction profiling. The combination of DRaqL with protease treatment enabled robust and efficient single-cell transcriptome analysis from formalin-fixed tissue sections. Applying this method to mouse ovarian sections, we were able to predict the transcriptome of oocytes by their size and identified an anomaly in the size-transcriptome relationship relevant to growth retardation of oocytes, in addition to detecting oocyte-specific splice isoforms. Furthermore, we identified differentially expressed genes in granulosa cells in association with their proximity to the oocytes, suggesting distinct epigenetic regulations and cell-cycle activities governing the germ-soma relationship. Thus, DRaqL is a versatile, efficient approach for high-quality single-cell RNA-seq from tissue sections, thereby revealing histological heterogeneity in folliculogenic transcriptome.identifier:Life Science Alliance, Vol.6 No.11 Article No.e202301929 (2023 Sep)identifier:25751077identifier:http://ginmu.naramed-u.ac.jp/dspace/handle/10564/4338identifier:Life science alliance, 6(11): e20230192

Evidence for paternal age-related alterations in meiotic chromosome dynamics in the mouse

Increasing age in a woman is a well-documented risk factor for meiotic errors, but the effect of paternal age is less clear. Although it is generally agreed that spermatogenesis declines with age, the mechanisms that account for this remain unclear. Because meiosis involves a complex and tightly regulated series of processes that include DNA replication, DNA repair, and cell cycle regulation, we postulated that the effects of age might be evident as an increase in the frequency of meiotic errors. Accordingly, we analyzed spermatogenesis in male mice of different ages, examining meiotic chromosome dynamics in spermatocytes at prophase, at metaphase I, and at metaphase II. Our analyses demonstrate that recombination levels are reduced in the first wave of spermatogenesis in juvenile mice but increase in older males. We also observed age-dependent increases in XY chromosome pairing failure at pachytene and in the frequency of prematurely separated autosomal homologs at metaphase I. However, we found no evidence of an age-related increase in aneuploidy at metaphase II, indicating that cells harboring meiotic errors are eliminated by cycle checkpoint mechanisms, regardless of paternal age. Taken together, our data suggest that advancing paternal age affects pairing, synapsis, and recombination between homologous chromosomes--and likely results in reduced sperm counts due to germ cell loss--but is not an important contributor to aneuploidy