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Summary: Structural variations (SVs) are major genetic variants that can be involved in the origin, adaptation and domestication of species. However, the identification and characterization of SVs in Spinacia species are rare due to the lack of a pan‐genome. Here, we report eight chromosome‐scale assemblies of cultivated spinach and its two wild species. After integration with five existing assemblies, we constructed a comprehensive Spinacia pan‐genome and identified 193 661 pan‐SVs, which were genotyped in 452 Spinacia accessions. Our pan‐SVs enabled genome‐wide association study identified signals associated with sex and clarified the evolutionary direction of spinach. Most sex‐linked SVs (86%) were biased to occur on the Y chromosome during the evolution of the sex‐linked region, resulting in reduced Y‐linked gene expression. The frequency of pan‐SVs among Spinacia accessions further illustrated the contribution of these SVs to domestication, such as bolting time and seed dormancy. Furthermore, compared with SNPs, pan‐SVs act as efficient variants in genomic selection (GS) because of their ability to capture missing heritability information and higher prediction accuracy. Overall, this study provides a valuable resource for spinach genomics and highlights the potential utility of pan‐SV in crop improvement and breeding programmes. [ABSTRACT FROM AUTHOR]

The PowerPlex® 35GY System (Promega, USA) is an advanced eight-dye multiplex STR kit, incorporating twenty-three autosomal STR loci, eleven Y chromosome STR loci, one sex determining marker Amelogenin, and two quality indicators. This multiplex system includes 20 CODIS loci and up to 15 mini-STR loci with sizing values less than 250 bases. In this study, validation for PowerPlex® 35GY System was conducted following the guidelines of SWGDAM, encompassing sensitivity, precision, accuracy, concordance, species specificity, stutter, mixture, stability, and degraded DNA. The results from experiments demonstrated that the PowerPlex® 35GY System could effectively amplify DNA samples, with complete allele detection achieved at 125 pg. Moreover, over 90% of alleles from minor contributors were detected at a mixed ratio of 1:4. Additionally, the system was found to yield full profiles even in the presence of hematin, humic acid, and indigo. The PowerPlex® 35GY System demonstrated superior performance in the sensitivity and degraded DNA studies compared to a six-dye STR kit. Hence, it is evident that the PowerPlex® 35GY System is well-suited for forensic practice, whether in casework or for database samples. These findings provide strong support for the efficacy and reliability of the PowerPlex® 35GY System in forensic applications. [ABSTRACT FROM AUTHOR]

The Y chromosome has long been considered to be a "genetic wasteland" harboring only few genes essentially involved in male sex development and spermatogenesis. However, the discovery of mosaic loss of the Y chromosome (mLOY) in older men has led to revisiting of the potential impact of the Y chromosome on health and the pathophysiological processes of multiple diseases such as cancer, Alzheimer's disease and cardiovascular disease. Hence, developing more sensitive techniques for the detection of mLOY has become an emergent concern. In this article, we present a comprehensive review of the literature regarding mLOY. Additionally, we discuss the emerging discoveries concerning mLOY as well as the underlying mechanisms promoting disease in men of advanced age. [ABSTRACT FROM AUTHOR]

Aim: Whether widespread gene flow among primates is emblematic of their initial radiation or resulted from secondary contactremains a long‐standing question. We address this question on 'sinica' group macaques, highlighting the origin of the white‐cheeked macaque (Macaca leucogenys). Location: Eastern Himalayan highlands of Arunachal Pradesh, India. Taxon: Macaca leucogenys Li, Zhao, Fan, 2015b (Cercopithecidae). Methods: Mitochondrial genomes and Y‐chromosomal TSPY gene sequences of WCM were obtained from two distant populations through low‐depth genome sequencing. Phylogenetic analyses were conducted along with sequences of other available species within the genus Macaca. Results: We observed the presence of a single maternal lineage but two parental lineages. Interestingly, one paternal lineage of the white‐cheeked macaque clustered with a common lineage of M. assamensis and M. munzala. The other paternal lineage clustered with the sequences of the white‐cheeked macaque from the type locality in Southeastern Tibet. Main Conclusions: The result indicates a possible historic male‐mediated introgression in the white‐cheeked macaque, which is also present in the two other species belonging to the 'sinica' group. Therefore, extensive gene flow in 'sinica' group macaques possibly came from one or more introgression events in the past that also played a role in the origin and evolution of these macaque species. [ABSTRACT FROM AUTHOR]

Cytogenetic studies were carried out on 11 species of Indian Snakes collected from Jammu region using Air Drying Technique of Gorman et al 1979. Among all E. johni and E. conicus belonging to primitive family Boidae exhibits diploid number, 2n=34 with undifferentiated sex chromosomes in both male and female. In family Colubridae (an intermediate family) there exist huge variation as far as sex chromosomes are concerned i.e Ptyas mucosus has 2n=34, Oligodon arnensis has 2n=44 with undifferentiated sex chromosomes, Lycodon arnensis and Boiga trigonata both have 2n=36 with differentiated sex chromosomes(as per literature) while Natrix stolata has 2n=36 with distinct 'ZW' female. In Family Elapidae Naja naja naja has 2n=38 with undifferentiated sex chromosomes but Bungarus caerulus has 2n=44 with 'ZW' female having submetacentric 'Z' and largest telocentric 'W' but members of family Viperidae viz. Vipera russelli and Echinis carinatus both have 2n=36 with well differentiated 'ZW' where 'W' is smaller and 'Z' larger representing final step in the evolution of sex chromosome. [ABSTRACT FROM AUTHOR]

The Four Core Genotypes (FCG) mouse model has become a valuable model to study the mechanistic basis for biological sex differences. This model allows discrimination between influences of gonadal sex (ovaries or testes) from those associated with genetic sex (presence of XX or XY chromosome complement). FCG mice have illuminated distinct effects of gonadal and chromosomal sex on traits ranging from brain structure and behavior to vulnerability to obesity, atherosclerosis, multiple sclerosis, Alzheimer's and other diseases. A recent study determined that the YSry− chromosome used in a specific line of C57BL/6J FCG mice harbors nine genes that have been duplicated from the X chromosome. This report raised concern that scores of publications that previously used the FCG model may therefore be flawed, but did not provide details regarding how studies can be evaluated for potential impact (or lack of impact) of the translocation. Here we (1) provide a practical description of the genetic translocation for researchers using the FCG model, (2) document that a majority of the studies cited in the recent report are unlikely to be affected by the translocation, (3) provide a scheme for interpreting data from studies with FCG mice harboring the YSry− translocation, and (4) delineate expression levels of the nine translocated genes across tissue/cell types as a filter for evaluating their potential involvement in specific phenotypes. [ABSTRACT FROM AUTHOR]

Stamens are vital reproductive organs in angiosperms, essential for plant growth, reproduction, and development. The genetic regulation and molecular mechanisms underlying stamen development are, however, complex and varied among different plant species. MSL-lncRNAs, a gene specific to the Y chromosome of Populus deltoides, is predominantly expressed in male flower buds. Heterologous expression of MSL-lncRNAs in Arabidopsis thaliana resulted in an increase in both stamen and anther count, without affecting pistil development or seed set. To reveal the molecular regulatory network influenced by MSL-lncRNAs on stamen development, we conducted transcriptome sequencing of flowers from both wild-type and MSL-lncRNAs-overexpressing Arabidopsis. A total of 678 differentially expressed genes were identified between wild-type and transgenic Arabidopsis. Among these, 20 were classified as transcription factors, suggesting a role for these regulatory proteins in stamen development. GO enrichment analysis revealed that the differentially expressed genes were significantly associated with processes such as pollen formation, polysaccharide catabolic processes, and secondary metabolism. KEGG pathway analysis indicated that MSL-lncRNAs might promote stamen development by upregulating genes involved in the phenylpropanoid biosynthesis pathway. The top three upregulated genes, all featuring the DUF295 domain, were found to harbor an F-box motif at their N-termini, which is implicated in stamen development. Additionally, in transgenic Arabidopsis flowers, genes implicated in tapetum formation and anther development were also observed to be upregulated, implying a potential role for MSL-lncRNAs in modulating pollen development through the positive regulation of these genes. The findings from this study establish a theoretical framework for elucidating the genetic control exerted by MSL-lncRNAs over stamen and pollen development. [ABSTRACT FROM AUTHOR]

A female protective effect has long been postulated as the primary explanation for the four-fold increase of autism spectrum disorder (ASD) diagnoses in males versus females. However, genetic and epidemiological investigations of this hypothesis have so far failed to explain the large difference in ASD prevalence between the sexes. To address this knowledge gap, we examined sex chromosome aneuploidy in a large ASD case-control cohort to evaluate the relationship between X and Y chromosome dosage and ASD risk. From these data, we modeled three relationships between sex chromosome dosage and ASD risk: the extra Y effect, the extra X effect, and sex chromosome haploinsufficiency. We found that the extra Y effect increased ASD risk significantly more than the extra X effect. Among females, we observed a large association between 45, X and ASD, confirming sex chromosome haploinsufficiency as a strong ASD risk factor. These results provide a framework for understanding the relationship between X and Y chromosome dosage on ASD, which may inform future research investigating genomic contributors to the observed sex difference. Genetic and epidemiological investigations have yet to reveal what drives the large difference in ASD prevalence between the sexes. Here authors examine chromosome aneuploidy in a large ASD case-control cohort and report sex chromosome haploinsufficiency is a strong ASD risk factor, while the extra Y effect increases ASD risk significantly more than the extra X effect. [ABSTRACT FROM AUTHOR]

The INO80 protein is the main catalytic subunit of the INO80-chromatin remodeling complex, which is critical for DNA repair and transcription regulation in murine spermatocytes. In this study, we explored the role of INO80 in silencing genes on meiotic sex chromosomes in male mice. INO80 immunolocalization at the XY body in pachytene spermatocytes suggested a role for INO80 in the meiotic sex body. Subsequent deletion of Ino80 resulted in high expression of sex-linked genes. Furthermore, the active form of RNA polymerase II at the sex chromosomes of Ino80-null pachytene spermatocytes indicates incomplete inactivation of sex-linked genes. A reduction in the recruitment of initiators of meiotic sex chromosome inhibition (MSCI) argues for INO80-facilitated recruitment of DNA repair factors required for silencing sex-linked genes. This role of INO80 is independent of a common INO80 target, H2A.Z. Instead, in the absence of INO80, a reduction in chromatin accessibility at DNA repair sites occurs on the sex chromosomes. These data suggest a role for INO80 in DNA repair factor localization, thereby facilitating the silencing of sex-linked genes during the onset of pachynema. Author summary: Chromatin accessibility is required for many DNA-protein interactions. Chromatin remodelers are the group of protein complexes that ensure the localized and timely unpacking of DNA to ensure access of a protein to its target DNA regions. The chromatin remodeler, INO80, has been implicated in many cellular processes, including transcription and DNA repair. We report that INO80 regulates the suppression of gene expression at the sex chromosomes in meiotic germ cells during mammalian spermatogenesis. INO80 localizes at the sex chromosomes during the pachynema stage, and its absence leads to a lack of suppression of gene expression at the sex chromosomes, which is known to be detrimental to meiotic progression. These genes were actively transcribed during pachynema in Ino80-mutant spermatocytes. DNA damage repair factors such as ATR and MDC1, which are instrumental in suppressing gene expression at the sex chromosomes during pachynema, were not localized properly in Ino80-mutant spermatocytes. Chromatin accessibility was also reduced at the DNA damage sites in sex chromosomes of the Ino80 mutants, which suggests a role for INO80 in the appropriate localization of DNA damage factors at accessible target sites to aid in the silencing of sex-linked genes during pachynema. [ABSTRACT FROM AUTHOR]

The human sex ratio (fraction of males) at birth is close to 0.5 at the population level, an observation commonly explained by Fisher's principle. However, past human studies yielded conflicting results regarding the existence of sex ratio-influencing mutations—a prerequisite to Fisher's principle, raising the question of whether the nearly even population sex ratio is instead dictated by the random X/Y chromosome segregation in male meiosis. Here we show that, because a person's offspring sex ratio (OSR) has an enormous measurement error, a gigantic sample is required to detect OSR-influencing genetic variants. Conducting a UK Biobank-based genome-wide association study that is more powerful than previous studies, we detect an OSR-associated genetic variant, which awaits verification in independent samples. Given the abysmal precision in measuring OSR, it is unsurprising that the estimated heritability of OSR is effectively zero. We further show that OSR's estimated heritability would remain virtually zero even if OSR is as genetically variable as the highly heritable human standing height. These analyses, along with simulations of human sex ratio evolution under selection, demonstrate the compatibility of the observed genetic architecture of human OSR with Fisher's principle and render it plausible that multiple OSR-influencing genetic variants segregate among humans. [ABSTRACT FROM AUTHOR]

Background: 46,XX testicular disorder/difference of sex development (46,XX DSD) is a rare congenital condition, characterized by a combination of the typical female sex chromosome constitution, 46,XX, and a variable male phenotype. In the majority of individuals with 46,XX DSD, a Y chromosome segment containing the sex-determining region gene (SRY) has been translocated to the paternal X chromosome. However, the precise genomic content of the translocated segment and the genome-wide effects remain elusive. Methods: We performed long-read DNA sequencing, RNA sequencing and DNA methylation analyses on blood samples from 46,XX DSD (n = 11), male controls (46,XY; variable cohort sizes) and female controls (46,XX; variable cohort sizes), in addition to RNA sequencing and DNA methylation analysis on blood samples from males with Klinefelter syndrome (47,XXY, n = 22). We also performed clinical measurements on all 46,XX DSD and a subset of 46,XY (n = 10). Results: We identified variation in the translocated Y chromosome segments, enabling subcategorization into 46,XX DSD (1) lacking Y chromosome material (n = 1), (2) with short Yp arms (breakpoint at 2.7–2.8 Mb, n = 2), (3) with medium Yp arms (breakpoint at 7.3 Mb, n = 1), and (4) with long Yp arms (n = 7), including deletions of AMELY, TBLY1 and in some cases PRKY. We also identified variable expression of the X-Y homologues PRKY and PRKX. The Y-chromosomal transcriptome and methylome reflected the Y chromosome segment lengths, while changes to autosomal and X-chromosomal regions indicated global effects. Furthermore, transcriptional changes tentatively correlated with phenotypic traits of 46,XX DSD, including reduced height, lean mass and testicular size. Conclusion: This study refines our understanding of the genetic composition in 46,XX DSD, describing the translocated Y chromosome segment in more detail than previously and linking variability herein to genome-wide changes in the transcriptome and methylome. Plain English summary: Our sex chromosome constitution determines our sex, with the presence of a Y chromosome causing male sex determination (typically 46,XY) and the lack hereof resulting in female sex development (typically 46,XX). However, individuals can become male despite of them presenting with the classical female chromosome constitution. We term this "46,XX testicular disorder/difference of sex development" or "46,XX DSD" for short. Individuals with this condition are affected by a number of traits, such as infertility, short stature and altered hormone levels. We know that most cases of 46,XX DSD are caused by the sex-determining region of the Y chromosome being moved to one of the X chromosomes. However, we do not know the more precise size of the Y-chromosomal section or its effects on the genome. In this study we investigated 11 individuals with 46,XX DSD using novel and precise techniques than previously applied. Analyzing DNA, we found that their Y-chromosomal sections varied. This was reflected in multiple types of additional genetic analyses, investigating modifications to DNA and expression of genes. Our findings are the most accurate description of the Y-chromosomal section in 46,XX DSD to date, and indicate that the genomes of individuals with 46,XX DSD differ, with many potential mechanisms of action. Highlights: • From a cohort of 11 individuals with 46,XX testicular DSD, the profile of Y chromosome segments was described in more detail than previously and used to sub-categorize subjects into four groups; SRY-negative, short Yp (2.7–2.8 Mb), medium Yp (7.3 Mb) and long Yp. • In individuals with long Yp segments, a characteristic loss of AMELY, TBL1Y and in some cases PRKY was observed. • Variable expression of the X-Y homologous gene pair PRKX and PRKY was observed, suggesting a compensatory mechanism. • The lengths of Y chromosome segments were reflected in the transcriptome and methylome. • Differential expression and methylation of autosomes suggested genome-wide effects. [ABSTRACT FROM AUTHOR]

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Copyright of Forensic Science & Technology is the property of Institute of Forensic Science, Ministry of Public Security and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Chromosome alignment on the metaphase plate is a conserved phenomenon and is an essential function for correct chromosome segregation for many organisms. Organisms with naturally-occurring trivalent chromosomes provide a useful system for understanding how chromosome alignment is evolutionarily regulated, as they align on the spindle with one kinetochore facing one pole and two facing the opposite pole. We studied chromosome alignment in a praying mantid that has not been previously studied chromosomally, the giant shield mantis Rhombodera megaera. R. megaera has a chromosome number of 2n = 27 in males. Males have X1, X2, and Y chromosomes that combine to form a trivalent in meiosis I. Using live-cell imaging of spermatocytes in meiosis I, we document that sex trivalent Y chromosomes associate with one spindle pole and the two X chromosomes associate with the opposing spindle pole. Sex trivalents congress alongside autosomes, align with them on the metaphase I plate, and then the component chromosomes segregate alongside autosomes in anaphase I. Immunofluorescence imaging and quantification of brightness of kinetochore–microtubule bundles suggest that the X1 and X2 kinetochores are associated with fewer microtubules than the Y kinetochore, likely explaining the alignment of the sex trivalent at the spindle equator with autosomes. These observations in R. megaera support the evolutionary significance of the metaphase alignment of chromosomes and provide part of the explanation for how this alignment is achieved. [ABSTRACT FROM AUTHOR]

Background: Do different genetic disorders impart different psychiatric risk profiles? This question has major implications for biological and translational aspects of psychiatry, but has been difficult to tackle given limited access to shared batteries of fine-grained clinical data across genetic disorders. Methods: Using a new suite of generalizable analytic approaches, we examine gold-standard diagnostic ratings, scores on 66 dimensional measures of psychopathology, and measures of cognition and functioning in two different sex chromosome aneuploidies (SCAs)—Klinefelter (XXY/KS) and XYY syndrome (n = 102 and 64 vs. n = 74 and 60 matched XY controls, total n = 300). We focus on SCAs for their high collective prevalence, informativeness regarding differential X- vs. Y-chromosome effects, and potential relevance for normative sex differences. Results: We show that XXY/KS elevates rates for most psychiatric diagnoses as previously reported for XYY, but disproportionately so for anxiety disorders. Fine-mapping across all 66 traits provides a detailed profile of psychopathology in XXY/KS which is strongly correlated with that of XYY (r =.75 across traits) and robust to ascertainment biases, but reveals: (i) a greater penetrance of XYY than KS/XXY for most traits except mood/anxiety problems, and (ii) a disproportionate impact of XYY vs. XXY/KS on social problems. XXY/KS and XYY showed a similar coupling of psychopathology with adaptive function and caregiver strain, but not IQ. Conclusions: This work provides new tools for deep-phenotypic comparisons of genetic disorders in psychiatry and uses these to detail unique and shared effects of the X- and Y-chromosome on human behavior. [ABSTRACT FROM AUTHOR]

Purpose: Non-obstructive azoospermia (NOA) represents the persistent absence of sperm in ejaculate without obstruction, stemming from diverse disease processes. This survey explores global practices in NOA diagnosis, comparing them with guidelines and offering expert recommendations. Materials and Methods: A 56-item questionnaire survey on NOA diagnosis and management was conducted globally from July to September 2022. This paper focuses on part 1, evaluating NOA diagnosis. Data from 367 participants across 49 countries were analyzed descriptively, with a Delphi process used for expert recommendations. Results: Of 336 eligible responses, most participants were experienced attending physicians (70.93%). To diagnose azoospermia definitively, 81.7% requested two semen samples. Commonly ordered hormone tests included serum follicle-stimulating hormone (FSH) (97.0%), total testosterone (92.9%), and luteinizing hormone (86.9%). Genetic testing was requested by 66.6%, with karyotype analysis (86.2%) and Y chromosome microdeletions (88.3%) prevalent. Diagnostic testicular biopsy, distinguishing obstructive azoospermia (OA) from NOA, was not performed by 45.1%, while 34.6% did it selectively. Differentiation relied on physical examination (76.1%), serum hormone profiles (69.6%), and semen tests (68.1%). Expectations of finding sperm surgically were higher in men with normal FSH, larger testes, and a history of sperm in ejaculate. Conclusions: This expert survey, encompassing 367 participants from 49 countries, unveils congruence with recommended guidelines in NOA diagnosis. However, noteworthy disparities in practices suggest a need for evidence-based, international consensus guidelines to standardize NOA evaluation, addressing existing gaps in professional recommendations. [ABSTRACT FROM AUTHOR]

This document is a letter published in the Blood Cancer Journal that discusses the global burden of Burkitt lymphoma (BL) from 1990 to 2021 and makes predictions for 2030. BL is a highly aggressive form of non-Hodgkin lymphoma that primarily affects young males. The incidence rates of BL vary significantly across different continents, with the highest rates found in equatorial Africa. Survival outcomes for BL are influenced by factors such as disease stage, geographic location, ethnicity, and treatment approaches. The document presents data on incident cases, prevalent cases, deaths, and disability-adjusted life years (DALYs) of BL, as well as age-standardized rates, and analyzes trends and shifts in these metrics. The findings show an upward trend in all metrics for BL from 1990 to 2021, with significant shifts in incidence and prevalence occurring in certain years. The document also examines the relationship between socioeconomic factors and BL rates and provides projections for BL numbers and rates until 2030. The given text provides a series of numerical values for various regions around the world, including their mortality rates, years of life lost, and disability-adjusted life years. The regions covered include Central Europe, Central Latin America, Central Sub-Saharan Africa, East Asia, Eastern Europe, Eastern Sub-Saharan Africa, High-income Asia Pacific, High-income North America, North Africa and Middle East, Oceania, South Asia, Southeast Asia, and Southern Latin America. These values can be used [Extracted from the article]

Background: Differences of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. In more than 50% of human DSD cases, a molecular diagnosis is not available. In intensively farmed pig populations, the incidence of XX DSD pigs is relatively high, leading to economic losses for pig breeders. Interestingly, in the majority of 38, XX DSD pigs, gonads still develop into testis-like structures or ovotestes despite the absence of the testis-determining gene (SRY). However, the current understanding of the molecular background of XX DSD pigs remains limited. Methods: Anatomical and histological characteristics of XX DSD pigs were analysed using necropsy and HE staining. We employed whole-genome sequencing (WGS) with 10× Genomics technology and used de novo assembly methodology to study normal female and XX DSD pigs. Finally, the identified variants were validated in 32 XX DSD pigs, and the expression levels of the candidate variants in the gonads of XX DSD pigs were further examined. Results: XX DSD pigs are characterised by the intersex reproductive organs and the absence of germ cells in the seminiferous tubules of the gonads. We identified 4,950 single-nucleotide polymorphisms (SNPs) from non-synonymous mutations in XX DSD pigs. Cohort validation results highlighted two specific SNPs, "c.218T > C" in the "Interferon-induced transmembrane protein 1 gene (IFITM1)" and "c.1043C > G" in the "Newborn ovary homeobox gene (NOBOX)", which were found exclusively in XX DSD pigs. Moreover, we verified 14 candidate structural variants (SVs) from 1,474 SVs, identifying a 70 bp deletion fragment in intron 5 of the WW domain-containing oxidoreductase gene (WWOX) in 62.5% of XX DSD pigs. The expression levels of these three candidate genes in the gonads of XX DSD pigs were significantly different from those of normal female pigs. Conclusion: The nucleotide changes of IFITM1 (c.218T > C), NOBOX (c.1043 C > G), and a 70 bp deletion fragment of the WWOX were the most dominant variants among XX DSD pigs. This study provides a theoretical basis for better understanding the molecular background of XX DSD pigs. Plain language summary: DSD are conditions affecting development of the gonads or genitalia. These disorders can happen in many different types of animals, including pigs, goats, dogs, and people. In people, DSD happens in about 0.02–0.13% of births, and in pigs, the rate is between 0.08% and 0.75%. Pigs have a common type of DSD where the animal has female chromosomes (38, XX) but no SRY gene, which is usually found on the Y chromosome in males. XX DSD pigs may look like both males and females on the outside and have testis-like or ovotestis (a mix of ovary and testis) gonads inside. XX DSD pigs often lead to not being able to have piglets, slower growth, lower chance of survival, and poorer meat quality. Here, we used a method called whole-genome de novo sequencing to look for variants in the DNA of XX DSD pigs. We then checked these differences in a larger group of pigs. Our results reveal the nucleotide changes in IFITM1 (c.218T > C), NOBOX (c.1043 C > G), and a 70 bp deletion fragment in intron 5 of the WWOX, all linked to XX DSD pigs. The expression levels of these three genes were also different in the gonads of XX DSD pigs compared to normal female pigs. These variants are expected to serve as valuable molecular markers for XX DSD pigs. Because pigs are a lot like humans in their genes, physiology, and body structure, this research could help us learn more about what causes DSD in people. Highlights: XX DSD pigs have abnormal development of reproductive organs showing both male and female characteristics and lack of germ cells in the seminiferous tubules. Whole-genome de novo sequencing was used to reveal the characteristics of genomic variants in XX DSD pigs. The nucleotide changes of IFITM1 (c.218T > C), NOBOX (c.1043 C > G), and a 70 bp deletion fragment of WWOX were the dominant variants in XX DSD pigs, and these three genes were significantly changed in the gonadal expression levels of the XX DSD pigs compared to those of normal females. [ABSTRACT FROM AUTHOR]

Prostate cancer (PCa) is one of the most common and prevalent cancers in men worldwide. The majority of PCa-related deaths result from metastasis rather than primary tumors. Several studies have focused on the relationship between male-specific genes encoded on the Y chromosome and PCa metastasis; however, the relationship between the male specific protein encoded on the Y chromosome and tumor suppression has not been fully clarified. Here, we report a male specific protein of this type, the histone H3 lysine 4 (H3K4) demethylase JARID1D, which has the ability to inhibit the gene expression program related to cell invasion, and can thus form a phenotype that inhibits the invasion of PCa cells. However, JARID1D exhibits low expression level in advanced PCa, and which is related to rapid invasion and metastasis in patients with PCa. Curcumin, as a multi-target drug, can enhance the expression and demethylation activity of JARID1D, affect the androgen receptor (AR) and epithelial-mesenchymal transition (EMT) signaling cascade, and inhibit the metastatic potential of castration resistant cancer (CRPC). These findings suggest that using curcumin to increase the expression and demethylation activity of JARID1D may be a feasible strategy to inhibit PCa metastasis by regulating EMT and AR. Highlights: Knockdown of JARID1D can enhance the invasion and metastasis ability of prostate cancer cells. Curcumin improves the expression and demethylation activity of JARID1D. Curcumin can stimulate the JARID1D/AR/EMT signaling cascade through demethylation to inhibit the metastatic potential of castration-resistant prostate cancer. [ABSTRACT FROM AUTHOR]

Simple Summary: The process of acquiring sexed sperm involves the separation of sperm with X and Y chromosomes, allowing for the production of offspring of the desired sex. However, this process can negatively affect the quality of semen due to biochemical and physical stresses. ProAKAP4 is a major component of the sperm flagellum structure. In this study, sexed bull semen samples were evaluated using the proAKAP4 biomarker for the first time. Based on CASA and flow cytometry analysis of spermatozoa after thawing and incubation for 3 h, proAKAP4 is considered a practical biomarker for estimating the longevity of sexed sperm quality. ProAKAP4 is a sperm structural protein that regulates motility through the PKA-dependent cAMP signaling pathway, which is synthesized as an X chromosome-linked member of the gene family. This study aims to determine the optimal level of proAKAP4 for evaluating sexed semen through investigating its relationship with the longevity of sperm quality in sexed Holstein bull sperm. A total of 30 sexed sperm samples (bearing X chromosomes) from 30 distinct Holstein bulls (n = 30) were analyzed. The frozen bull sperm samples were assessed for their proAKAP4 levels, mitochondrial membrane potential, plasma membrane and acrosome integrity (PMAI), and spermatozoa movement parameters at hours 0 and 3 after thawing. The proAKAP4 levels in the sexed sperm samples ranged from 16.35 to 72.10 ng/10 M spz, with an average of 37.18 ± 15.1 ng/10 M spz. A strong positive correlation was observed between proAKAP4 levels and total motility, progressive motility, PMAI, high mitochondrial membrane potential, VAP, and VCL values after 3 h of incubation, when compared to post-thaw analyses. The results also reveal that spermatozoa with proAKAP4 levels of ≥40 ng/10 M spz exhibit higher quality. In conclusion, the level of proAKAP4 in sexed sperm aligns with previous studies and shows potential as a biomarker for assessing the longevity of sexed sperm quality. [ABSTRACT FROM AUTHOR]

Mixed gonadal dysgenesis (MGD) is a disorder of sex development caused by mosaicism of the Y chromosome, represented by 45,X/46,XY. Prophylactic gonadectomy is recommended as soon as possible after its diagnosis, owing to a high risk of malignancy. In the present case, a 21-year-old woman presented with primary amenorrhea. Although the patient's external genitalia were female, the patient exhibited a hypoplastic uterus, wherein the ovaries were difficult to identify. The patient's height was 146 cm; they had cubitus valgus and webbing of the neck, leading to the consideration of a disorder of sex development. Chromosomal examination revealed 45,X/46,XY mosaicism. Thus, the patient was diagnosed with MGD. After thorough counseling, laparoscopic bilateral gonadectomy was performed. Pathological examination revealed a gonadoblastoma of the left gonad. Postoperatively, the patient had no recurrence and continued on Kaufmann therapy. In conclusion, prophylactic gonadectomy is recommended immediately following a diagnosis of MGD; however, the timing of the surgery should be carefully considered and adequate counseling should be conducted by a multidisciplinary team. [ABSTRACT FROM AUTHOR]

Background: Non‐obstructive azoospermia is the most severe form of male infertility. A testicular biopsy is required for the diagnosis of non‐obstructive azoospermia, and the causal factors for non‐obstructive azoospermia remain unknown. Objectives: To reduce the risk of multiple biopsies and identify factors that contribute to non‐obstructive azoospermia, we proposed an integrated approach for the preoperative diagnosis and clinical management of non‐obstructive azoospermia by applying the chromosome‐spreading technique and whole‐exome sequencing. Materials and Methods: Between July 2020 and December 2022, after ruling out definitive obstructive azoospermia and non‐obstructive azoospermia patients with testicular volume < 6 mL, 20 patients with non‐obstructive azoospermia who underwent preoperative testicular diagnostic biopsy using testicular sperm aspiration were subjected to retrospective analysis. Results: Microscopic examination identified four patients with sperm cells, and 16 without sperm cells. Routine pathological analysis classified one patient as normal spermatogenesis, three as hypospermatogenesis, five as maturation arrest, nine as Sertoli cell‐only, and two as unable to judge. With chromosome‐spreading technology using routine cell suspension samples for microscopic examination, 18 patient diagnoses were validated, and two patients without a definitive diagnosis were supplemented. Detection of the Y chromosome and a well‐organized whole‐exome sequencing analysis revealed potential genetic factors. Discussion and Conclusion: The full use of testicular biopsy is beneficial for the diagnosis of azoospermia, as it avoids the risk of multiple biopsies. Moreover, in combination with whole‐exome sequencing, clinicians can obtain more information regarding the pathogenesis of non‐obstructive azoospermia, which may guide treatment. [ABSTRACT FROM AUTHOR]

A total of 154 Emirati infertile patients were included in this study of which a cohort of 18 infertile males undergoing fertility counseling were recruited from Dubai Fertility Center (DFC) and University Hospital of Sharjah (UHS), in addition to136 azoospermic Emirati infertile patients who performed AZF-deletion screening as counselled and recorded by DFC during the period of January 2011 and January 2021. Diagnostic screening was conducted to investigate the frequency of microdeletion in the Azoospermia Factor (AZFa, AZFb, AZFc, AZFd) gene cluster of the Y-chromosome among Emirati infertile male patients using the Sequences-Tagged-Sites (STS)-Multiplex PCR diagnostic technology. The frequency of the AZF microdeletions was 2.2% as detected in three patients with azoospermia (n=3/136). There were two complete deletions in the AZFc region as shown by deletion of the two STS; SY254 (380 bp) and SY255 (124 bp). Our findings are similar to those reported in regional and global range, which appeared to vary across genealogical-lineages in different geographical landscape. This article is the first to profile AZF microdeletions in Emirati Azospermic males, offering valuable insights into male infertility genomics worldwide. The novelty and importance of the findings are especially relevant for improved healthcare and male infertility in Gulf countries due to shared tribal genetic lineage. This highlights the importance of the screening for the AZF-deletion for male infertility diagnosis for better management and treatments in the fertility clinics and hospitals in the UAE. [ABSTRACT FROM AUTHOR]

Sex-ratio meiotic drivers are selfish genes or gene complexes that bias the transmission of sex chromosomes resulting in skewed sex ratios. Existing theoretical models have suggested the maintenance of a four-chromosome equilibrium (with driving and standard X and suppressing and susceptible Y) in a cyclic dynamic, but studies of natural populations have failed to capture this pattern. Although there are several plausible explanations for this lack of cycling, interference from autosomal suppressors has not been studied using a theoretical population genetic framework even though autosomal suppressors and Y-linked suppressors coexist in natural populations of some species. In this study, we use a simulation-based approach to investigate the influence of autosomal suppressors on the cycling of sex chromosomes. Our findings demonstrate that the presence of an autosomal suppressor can hinder the invasion of a Y-linked suppressor under some parameter space, thereby impeding the cyclic dynamics, or even the invasion of Y-linked suppression. Even when a Y-linked suppressor invades, the presence of an autosomal suppressor can prevent cycling. Our study demonstrates the potential role of autosomal suppressors in preventing sex chromosome cycling and provides insights into the conditions and consequences of maintaining both Y-linked and autosomal suppressors. [ABSTRACT FROM AUTHOR]

The XX/XY sex chromosome system is deeply conserved in therian mammals, as is the role of Sry in testis determination, giving the impression of stasis relative to other taxa. However, the long tradition of cytogenetic studies in mammals documents sex chromosome karyotypes that break this norm in myriad ways, ranging from fusions between sex chromosomes and autosomes to Y chromosome loss. Evolutionary conflict, in the form of sexual antagonism or meiotic drive, is the primary predicted driver of sex chromosome transformation and turnover. Yet conflict-based hypotheses are less considered in mammals, perhaps because of the perceived stability of the sex chromosome system. To address this gap, we catalog and characterize all described sex chromosome variants in mammals, test for family-specific rates of accumulation, and consider the role of conflict between the sexes or within the genome in the evolution of these systems. We identify 152 species with sex chromosomes that differ from the ancestral state and find evidence for different rates of ancestral to derived transitions among families. Sex chromosome-autosome fusions account for 79% of all variants whereas documented sex chromosome fissions are limited to three species. We propose that meiotic drive and drive suppression provide viable explanations for the evolution of many of these variant systems, particularly those involving autosomal fusions. We highlight taxa particularly worthy of further study and provide experimental predictions for testing the role of conflict and its alternatives in generating observed sex chromosome diversity. [ABSTRACT FROM AUTHOR]

Advances in genome sequencing have greatly accelerated the identification of sex chromosomes in a variety of species. Many of these species have experienced structural rearrangements that reduce recombination between the sex chromosomes, allowing the accumulation of sequence differences over many megabases. Identification of the genes that are responsible for sex determination within these sometimes large regions has proved difficult. Here, we identify an XY sex chromosome system on LG19 in the West African cichlid fish Chromidotilapia guntheri in which the region of differentiation extends over less than 400 kb. We develop high-quality male and female genome assemblies for this species, which confirm the absence of structural variants, and which facilitate the annotation of genes in the region. The peak of differentiation lies within rin3, which has experienced several debilitating mutations on the Y chromosome. We suggest two hypotheses about how these mutations might disrupt endocytosis, leading to Mendelian effects on sexual development. [ABSTRACT FROM AUTHOR]

Background: Chromoanagenesis is an umbrella term used to describe catastrophic "all at once" cellular events leading to the chaotic reconstruction of chromosomes. It is characterized by numerous rearrangements involving a small number of chromosomes/loci, copy number gains in combination with deletions, reconstruction of chromosomal fragments with improper order/orientation, and preserved heterozygosity in copy number neutral regions. Chromoanagesis is frequently described in association with cancer; however, it has also been described in the germline. The clinical features associated with constitutional chromoanagenesis are typically due to copy number changes and/or disruption of genes or regulatory regions. Case presentation: We present an 8-year-old male patient with complex rearrangements of the Y chromosome including a ring Y chromosome, a derivative Y;21 chromosome, and a complex rearranged Y chromosome. These chromosomes were characterized by G-banded chromosome analysis, SNP microarray, interphase FISH, and metaphase FISH. The mechanism(s) by which these rearrangements occurred is unclear; however, it is evocative of chromoanagenesis. Conclusion: This case is a novel example of suspected germline chromoanagenesis leading to large copy number changes that are well-tolerated, possibly because only the sex chromosomes are affected. [ABSTRACT FROM AUTHOR]

In order to identify the genetic stability in biology of bovine small intestinal epithelial cell line (BIECs-21), BIECs-21 cells were cultured in vitro by using adherent culture, and chromosome and G-band samples were prepared to analyze the chromosome karyotype and G-band of BIECs-21 cells. The results show that the number of chromosomes in BIECs-21 cells is 2n = 60, including 29 pairs of autosomes and 1 pair of sex chromosomes (X and Y chromosomes). Among them, 29 pairs of autosomes are all terminal centromere chromosomes, with X chromosome being the larger centromere chromosome and Y chromosome being the smaller centromere chromosome in the sex chromosome. There is no significant difference in the number and position of G-bands pattern on the autosomes of BIECs-21 cells, except for X and Y sex chromosome. Compared with the normal chromosome karyotype of Holstein cattle, there is no significant change in the number and morphological structure of chromosomes in BIECs-21 cells, indicating that the genetic characteristics of the cell line are stable, and it can be used for the research on the molecular mechanisms of bovine intestinal related diseases. [ABSTRACT FROM AUTHOR]

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow. How different parental sex chromosome systems affect allopolyploidization is yet unknown. Here, the authors assemble the genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii, and explore the transition from XY system to ZW system following allopolyploidization. [ABSTRACT FROM AUTHOR]

With the widespread use of the Y chromosome in genetics, a lot of commercially available Y chromosome kits were developed, validated, and applied to forensic science practice. The AGCU YNFS Y Kit is a new Y chromosome system containing forty-four preferred Y short tandem repeats (Y-STRs) and five common Y-InDels. In this study, the AGCU YNFS Y system was validated to verify its performance by following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM). A series of validation experiments included the following parameters: PCR-based studies, sensitivity studies, species specificity studies, stability studies, mixture studies, precision studies, stutter calculation, mutation and statistical analysis, population study, and case samples and degradation studies. The results suggested that appropriately changing PCR amplification conditions did not affect genotyping; the kit had good sensitivity for trace amounts of DNA (0.0625 ng), mixtures of multiple male individuals (minor: major = 1: 9), and three PCR inhibitors (more than 250 μM hematin, 250 ng/μL humic acid and 50 ng/μL tannic acid). The maximum standard deviation of allele size did not exceed 0.1552 reflecting the high accuracy of the system. By this, 87 DNA-confirmed pairs of father-son pairs were also analyzed for mutations. A total of 18 loci were mutated, with mutation rates ranging from 11.5×10−3 to 34.5×10−3 (95% CI 7.2×10−3–97.5×10−3, DYS627 and DYF404S1). In the population study, the haplotype diversity of 87 unrelated individuals was 0.9997, and discrimination capacity was 0.9885. Degradation studies have demonstrated that UV-C light exposure for up to 120 hours has no effect on male blood and semen-vaginal secretion mixtures. However, complete typing could no longer be obtained after 48 hours of UV exposure in single male saliva and in male saliva and female blood mixed samples. Collectively, the AGCU YNFS Y Kit is sensitive and accurate and can play its application value in forensic science practice. [ABSTRACT FROM AUTHOR]

Primate‐specific DAZ (deleted in azoospermia) has evolved in the azoospermia factor c (AZFc) locus on the Y chromosome. Loss of DAZ is associated with azoospermia in patients with deletion of the AZFc region (AZFc_del). However, the molecular mechanisms of DAZ in spermatogenesis remain uncertain. In this study, the molecular mechanism of DAZ is identified, which is unknown since it is identified 40 years ago because of the lack of a suitable model. Using clinical samples and cell models, it is shown that DAZ plays an important role in spermatogenesis and that loss of DAZ is associated with defective proliferation of c‐KIT‐positive spermatogonia in patients with AZFc_del. Mechanistically, it is shown that knockdown of DAZ significantly downregulated global translation and subsequently decreased cell proliferation. Furthermore, DAZ interacted with PABPC1 via the DAZ repeat domain to regulate global translation. DAZ targeted mRNAs that are involved in cell proliferation and cell cycle phase transition. These findings indicate that DAZ is a master translational regulator and essential for the maintenance of spermatogonia. Loss of DAZ may result in defective proliferation of c‐KIT‐positive spermatogonia and spermatogenic failure. [ABSTRACT FROM AUTHOR]

Objectives: Evaluate the prevalence of genetic factors in a large population of infertile subjects and define the seminological, hormonal, and ultrasonographic features for each alteration. Methods: This single-center retrospective study included male partners of infertile couples undergoing genetic investigations due to oligozoospermia or azoospermia evaluated from January 2012 to January 2022. The genetic investigations consist of karyotype, CFTR gene mutations plus variant of the IVS8-5T polymorphic trait, Y chromosome microdeletion, and Next Generation Sequencing panel to analyze genes implicated in congenital hypogonadotropic hypogonadism (CHH). Results: Overall, 15.4% (72/466) of patients received a diagnosis of genetic cause of infertility. Specifically, 23 patients (31.9%) harbor mutations in the CFTR gene, 22 (30.6%) have a 47, XXY karyotype, 14 (19.4%) patients show a Y chromosome microdeletion, 7 (9.7%) have structural chromosomal anomalies, and 6 (8.3%) have CHH. Overall, 80.6% of patients were azoospermic and 19.4% oligozoospermic (sperm concentration 3.5 ± 3.8 million/mL). Almost all patients presented hormonal alterations related to the specific genotype, while the main ultrasound alterations were testicular hypoplasia, calcifications/microcalcifications, and enlarged/hyperechoic epididymis. Conclusions: The prevalence of genetic abnormalities in males of infertile couples was 15.4% in our Center. CFTR gene disease-causing variants resulted in more frequent, with various clinical features, highlighting the complexity and heterogeneity of the presentation. Other investigations are needed to understand if conditions like ring chromosomes and other translocations are related to infertility or are incidental factors. [ABSTRACT FROM AUTHOR]

Sex chromosomes display remarkable diversity and variability among vertebrates. Compared with research on the X/Y and Z/W chromosomes, which have long evolutionary histories in mammals and birds, studies on the sex chromosomes at early evolutionary stages are limited. Here, we precisely assembled the genomes of homozygous XX female and YY male Lanzhou catfish (Silurus lanzhouensis) derived from an artificial gynogenetic family and a self-fertilized family, respectively. Chromosome 24 (Chr24) was identified as the sex chromosome based on resequencing data. Comparative analysis of the X and Y chromosomes showed an approximate 320 kb Y-specific region with a Y-specific duplicate of anti-Mullerian hormone type II receptor (amhr2y), which is consistent with findings in 2 other Silurus species but on different chromosomes (Chr24 of Silurus meridionalis and Chr5 of Silurus asotus). Deficiency of amhr2y resulted in male-to-female sex reversal, indicating that amhr2y plays a male-determining role in S. lanzhouensis. Phylogenetic analysis and comparative genomics revealed that the common sex-determining gene amhr2y was initially translocated to Chr24 of the Silurus ancestor along with the expansion of transposable elements. Chr24 was maintained as the sex chromosome in S. meridionalis and S. lanzhouensis , whereas a sex-determining region transition triggered sex chromosome turnover from Chr24 to Chr5 in S. asotus. Additionally, gene duplication, translocation, and degeneration were observed in the Y-specific regions of Silurus species. These findings present a clear case for the early evolutionary trajectory of sex chromosomes, including sex-determining gene origin, repeat sequence expansion, gene gathering and degeneration in sex-determining region, and sex chromosome turnover. [ABSTRACT FROM AUTHOR]

Introduction: Distinguishing paracentric inversions (PAIs) from chromosomal insertions has traditionally relied on fluorescent in situ hybridization (FISH) techniques, but recent advancements in high‐throughput sequencing have enabled the use of genome sequencing for such differentiation. In this study, we present a 38‐year‐old male carrier of a paracentric inversion on chromosome 2q, inv (2)(q31.2q34), whose partner experienced recurrent miscarriages. Material and Methods: FISH analysis confirmed the inversion, and genome sequencing was employed for detailed characterization. Results: Preimplantation genetic testing (PGT) revealed that all assessed embryos were balanced, consistent with the low risk of unbalanced offspring associated with PAIs. While PAI carriers traditionally exhibit low risk of producing unbalanced offspring, exceptions exist due to crossover events within the inversion loop. Although the sample size was limited, the findings align with existing sperm study data, supporting the rare occurrence of unbalanced progeny in PAI carriers. Conclusions: This study highlights the possibility of characterizing PAIs using genome sequencing to enable correct reproductive counseling and PGT decisions. Detailed characterization of a PAI is crucial for understanding potential outcomes and guiding PGT strategies, as accurate knowledge of the inversion size is essential for appropriate method selection in PGT. Given the very low risk of unbalanced offspring in PAI carriers, routine PGT may not be warranted but should be considered in specific cases with a history of unbalanced progeny or recurrent miscarriages. This study contributes to our understanding of PAI segregation and its implications for reproductive outcomes. [ABSTRACT FROM AUTHOR]

The evolution of suppressed recombination between sex chromosomes is widely hypothesized to be driven by sexually antagonistic selection (SA), where tighter linkage between the sex-determining gene(s) and nearby SA loci is favored when it couples male-beneficial alleles to the proto-Y chromosome, and female-beneficial alleles to the proto-X. Although difficult to test empirically, the SA selection hypothesis overshadows several alternatives, including an incomplete but often-repeated "sheltering" hypothesis which suggests that expansion of the sex-linked region (SLR) reduces the homozygous expression of deleterious mutations at selected loci. Here, we use population genetic models to evaluate the consequences of partially recessive deleterious mutational variation for the evolution of otherwise neutral chromosomal inversions expanding the SLR on proto-Y chromosomes. Both autosomal and SLR-expanding inversions face a race against time: lightly-loaded inversions are initially beneficial, but eventually become deleterious as they accumulate new mutations, after which their chances of fixing become negligible. In contrast, initially unloaded inversions eventually become neutral as their deleterious load reaches the same equilibrium as non-inverted haplotypes. Despite the differences in inheritance and indirect selection, SLR-expanding inversions exhibit similar evolutionary dynamics to autosomal inversions over many biologically plausible parameter conditions. Differences emerge when the population average mutation load is quite high; in this case large autosomal inversions that are lucky enough to be mutation-free can rise to intermediate to high frequencies where selection in homozygotes becomes important (Y-linked inversions never appear as homozygous karyotypes); conditions requiring either high mutation rates, highly recessive deleterious mutations, weak selection, or a combination thereof. [ABSTRACT FROM AUTHOR]

Genomic Safe Harbors (GSH) are loci used for the insertion of exogenous genetic elements, enabling exogenous gene expressing predictably without alterations of the host genome. These sites are becoming increasingly important as the gene editing technologies advance rapidly. Currently, only a few GSHs have been identified in the pig genome. In this study, a novel strategy was demonstrated for the efficient insertion of exogenous genetic material into the third exon of the UTY gene on the Y chromosome using CRISPR/Cas9-mediated homology arm-mediated end joining. The safety of the locus was verified according to the proper expression of the inserted EGFP gene without altering the expression of UTY. This approach enables the integration and expression of the exogenous gene at this locus, indicating that the UTY locus serves as a genomic safe harbor site for gene editing in the pig genome. Located on the Y chromosome, this site can be utilized for sex-biased pig breeding and developing biomedical models. [ABSTRACT FROM AUTHOR]

Genes on the Y chromosome play important roles in male sex determination and development. The identification of Y‐chromosome‐specific genes not only provides a theoretical basis for the study of male reproductive development, but also offers genetic control targets for agricultural pests. However, Y‐chromosome genes are rarely characterized due to their high repeatability and high heterochromatinization, especially in the oriental fruit fly. In this study, 1 011 Y‐chromosome‐specific candidate sequences were screened from 2 to 4 h Bactrocera dorsalis embryo datasets with the chromosome quotient method, 6 of which were identified as Y‐chromosome‐specific sequences by polymerase chain reaction, including typo‐gyf, a 19 126‐bp DNA sequence containing a 575‐amino acid open reading frame. Testicular deformation and a significant reduction in sperm number were observed after typo‐gyf knockdown with RNA interference in embryos. After typo‐gyf knockout with clustered regularly interspaced palindromic repeats (CRISPR) / CRISPR‐associated protein 9 in the embryonic stage, the sex ratio of the emergent adults was unbalanced, with far more females than males. A genotype analysis of these females with the Y‐chromosome gene MoY revealed no sex reversal. Typo‐gyf knockout led to the death of XY individuals in the embryonic stage. We conclude that typo‐gyf is an essential gene for male survival, and is also involved in testicular development and spermatogenesis. The identification of typo‐gyf and its functional verification provide insight into the roles of Y‐chromosome genes in male development. [ABSTRACT FROM AUTHOR]

Objectives: To investigate the distribution of sperm DNA fragmentation (SDF) values and their association with clinical and seminal parameters in idiopathic infertile men. Design, Patients, Measurements: Data from 3224 primary infertile men (belonging to couples having failed to conceive a pregnancy within 12 months) who underwent a thorough diagnostic work‐up were analysed. A SDF value ≥ 30% (according to Sperm Chromatin Structure Assay) was considered pathologic. We excluded: (1) men with genetic abnormalities; (2) men with history of cryptorchidism; (3) men with biochemical hypogonadism; (4) men with clinical varicocele; and (5) men with other possible known aetiological factors. Descriptive statistics and logistic regression analyses were used to describe the whole cohort. Results: Of all, 792 (23%) men with at least one abnormal WHO semen parameter but without any identified aetiologic factor for infertility, were considered as idiopathic infertile men. Of 792, 418 (52.7%) men had SDF ≥30%. Men with pathologic SDF were older (p =.02), had higher Follicle‐stimulating hormone (FSH) (p =.04) but lower total testosterone (p =.03) values than those with SDF <30%. The homoeostatic model assessment index for insulin resistance (HOMA‐IR) was higher in men with SDF ≥30% (p =.01). Idiopathic infertile men with SDF ≥30% presented with lower sperm concentration (p <.001) and lower progressive sperm motility (p <.01) than those with SDF < 30%. Logistic regression analysis revealed that older age (OR: 1.1, p =.02) and higher HOMA‐IR score (OR: 1.8, p =.03) were associated with SDF ≥ 30%, after accounting for FSH and sperm concentration values. Conclusions: Approximately half of infertile men categorized as idiopathic had pathologic SDF values. Idiopathic infertile men with pathologic SDF showed worse clinical, hormonal and semen parameters than those with normal SDF values. These results suggest that including SDF testing could be clinically relevant over the real‐life management work‐up of infertile men. [ABSTRACT FROM AUTHOR]

Objective High-grade aneuploidies of X and Y sex chromosomes (HGAs) are exceedingly rare and complex conditions. We aimed to investigate the effect of supernumerary X chromosomes (extra-Xs) on the clinical, hormonal, metabolic, and echocardiographic features of patients with HGAs. Design and Methods In a cross-sectional study, we compared 23 subjects with HGAs and 46 age-matched subjects with 47,XXY Klinefelter syndrome (KS), according to the number of extra-Xs: two (47,XXY and 48,XXYY), three (48,XXXY and 49,XXXYY), or four supernumerary Xs (49,XXXXY). A second cohort consisting of 46 pubertal stage-matched KS subjects was employed for validation. Clinical, hormonal, metabolic and ultrasonographic parameters were collected and analyzed. Results The increase in the number of extra-Xs was associated with a progressive adverse effect on height, pubertal development, testicular volume and function, adrenal steroidogenesis, and thyroid function. A progressive linear increase in ACTH and a decrease in cortisol/ACTH ratios were found. Weight and body mass index, Sertoli cell function, lipid profile, and glucose tolerance post-oral glucose tolerance test were all worse in the HGA cohort compared to KS. Cardiac evaluation revealed a linear association with reduced left and right end-diastolic diameters and reduced ejection fraction. Conclusion The increase in the number of extra-Xs is associated with a "dose-dependent" progressive impairment in steroid producing glands, thyroid function, cardiac structure, and performance. [ABSTRACT FROM AUTHOR]

During the treatment of 89 pediatric patients with Acute Myeloid Leukemia (AML) at the Hematology Department of Kunming Medical University's Children's Hospital from 2020 to 2023, three patients were identified to co-express the NUP98-NSD1, FLT3-ITD, and WT1 gene mutations. The bone marrow of these three patients was screened for high-risk genetic mutations using NGS and qPCR at the time of diagnosis. The treatment was administered following the China Children's Leukemia Group (CCLG)-AML-2019 protocol. All three patients exhibited a fusion of the NUP98 exon 12 with the NSD1 exon 6 and co-expressed the FLT3-ITD and WT1 mutations; two of the patients displayed normal karyotypes, while one presented chromosomal abnormalities. During the induction phase of the CCLG-AML-2019 treatment protocol, the DAH (Daunorubicin, Cytarabine, and Homoharringtonine) and IAH (Idarubicin, Cytarabine, and Homoharringtonine) regimens, in conjunction with targeted drug therapy, did not achieve remission. Subsequently, the patients were shifted to the relapsed/refractory chemotherapy regimen C + HAG (Cladribine, Homoharringtonine, Cytarabine, and G-CSF) for two cycles, which also failed to induce remission. One patient underwent Haploidentical Hematopoietic Stem Cell Transplantation (Haplo-HSCT) and achieved complete molecular remission during a 12-month follow-up period. Regrettably, the other two patients, who did not receive transplantation, passed away. The therapeutic conclusion is that pediatric AML patients with the aforementioned co-expression do not respond to chemotherapy. Non-remission transplantation, supplemented with tailor-made pre- and post-transplant strategies, may enhance treatment outcomes. [ABSTRACT FROM AUTHOR]

Simple Summary: Phan Rang sheep is a term used to collectively refer to the sheep raised in the central Vietnam provinces of Ninh Thuan and Binh Thuan. Given the extreme weather conditions of their habitat, Phan Rang sheep are assumed to be heat-resilient. With climate change's mounting challenges, the sheep have become a focus of government-led breeding and conservation initiatives. However, there is a critical knowledge gap regarding the sheep's genetic information, including their origins, diversity, population structure, and genetics, as well as the morphological basis of their adaptive traits. This gap has hindered the development of breeding programs and genetic resource conservation efforts. In an effort to contribute to filling this knowledge gap, we employed a two-fold approach to investigate Phan Rang sheep's morphometrics and genetic lineages. First, we collected body conformational data to facilitate the quick identification of purebred individuals. Secondly, we collected and analyzed the mitochondrial DNA control region (D-loop) and the Y chromosome SRY and SRYM18 sequences to elucidate the maternal and paternal lineages of the sheep. Of the sheep analyzed for the D-loop, approximately one-third belonged to haplogroup A, while the remainder belonged to haplogroup B. For the paternal lineage, two main Y haplotypes, H5 and H6, were identified. Overall, the findings supported the hypothesis of dual origins for the Phan Rang sheep. The Phan Rang sheep, considered the sole indigenous breed of Vietnam, are primarily concentrated in the two central provinces of Ninh Thuan and Binh Thuan, with Ninh Thuan accounting for more than 90% of the country's sheep population. These provinces are known for their high temperatures and frequent droughts. The long-standing presence of the Phan Rang sheep in these regions suggests their potential resilience to heat stress—a trait of increasing interest in the face of global climate change. Despite the breed's significance, a critical knowledge gap hinders conservation and breeding programs. To address this, our study employed a two-pronged approach. First, we collected body conformational data to aid in breed identification. Second, we analyzed mitochondrial DNA (D-loop) and Y chromosome markers (SRY and SRYM18) to elucidate the maternal and paternal lineages. Among the 68 Phan Rang sheep analyzed for their D-loop, 19 belonged to mitochondrial haplogroup A, while 49 belonged to haplogroup B. The haplogroups can be subdivided into 16 unique haplotypes. All 19 rams surveyed for their paternal lineages belonged to haplotypes H5 and H6. These findings strongly support the hypothesis of dual origins for the Phan Rang sheep. This study presents the first genetic data for the Phan Rang breed, providing crucial insights for future research and conservation efforts. [ABSTRACT FROM AUTHOR]

Objectives: Diagnosing brain tumors is critical due to their complex nature. This review explores the potential of in situ hybridization for diagnosing brain neoplasms, examining their attributes and applications in neurology and oncology. Methods: The review surveys literature and cross-references findings with the OMIM database, examining 513 records. It pinpoints mutations suitable for in situ hybridization and identifies common chromosomal and gene anomalies in brain tumors. Emphasis is placed on mutations’ clinical implications, including prognosis and drug sensitivity. Results: Amplifications in EGFR, MDM2, and MDM4, along with Y chromosome loss, chromosome 7 polysomy, and deletions of PTEN, CDKN2/p16, TP53, and DMBT1, correlate with poor prognosis in glioma patients. Protective genetic changes in glioma include increased expression of ADGRB3/1, IL12B, DYRKA1, VEGFC, LRRC4, and BMP4. Elevated MMP24 expression worsens prognosis in glioma, oligodendroglioma, and meningioma patients. Meningioma exhibits common chromosomal anomalies like loss of chromosomes 1, 9, 17, and 22, with specific genes implicated in their development. Main occurrences in medulloblastoma include the formation of isochromosome 17q and SHH signaling pathway disruption. Increased expression of BARHL1 is associated with prolonged survival. Adenomas mutations were reviewed with a focus on adenoma-carcinoma transition and different subtypes, with MMP9 identified as the main metalloprotease implicated in tumor progression. Discussion: Molecular-genetic diagnostics for common brain tumors involve diverse genetic anomalies. In situ hybridization shows promise for diagnosing and prognosticating tumors. Detecting tumor-specific alterations is vital for prognosis and treatment. However, many mutations require other methods, hindering in situ hybridization from becoming the primary diagnostic method. [ABSTRACT FROM AUTHOR]

Chromosomal fusions play an integral role in genome remodeling and karyotype evolution. Fusions that join a sex chromosome to an autosome are particularly abundant across the tree of life. However, previous models on the establishment of such fusions have not accounted for the physical structure of the chromosomes. We predict a fusion joining an autosome to the pseudoautosomal region (PAR) of a sex chromosome will not remain stable, and the fusion will switch from the X to the Y chromosome each generation due to recombination. We have produced a forward-time population genetic simulation to explore the outcomes of fusions to both the PAR and non-PAR of sex chromosomes. The model can simulate the fusion of an autosome containing a sexually antagonistic locus to either the PAR or non-PAR end of a sex chromosome. Our model is diploid, two-locus, and biallelic. Our results show a clear pattern where fusions to the non-PAR are favored in the presence of sexual antagonism, whereas fusions to the PAR are disfavored in the presence of sexual antagonism. [ABSTRACT FROM AUTHOR]

Aim: Short tandem repeats (STRs) are repetitive DNA sequences and highly mutable in various human disorders. While the involvement of STRs in various genetic disorders has been extensively studied, their role in autism spectrum disorder (ASD) remains largely unexplored. In this study, we aimed to investigate genetic association of STR expansions with ASD using whole genome sequencing (WGS) and identify risk loci associated with ASD phenotypes. Methods: We analyzed WGS data of 634 ASD families and performed genome‐wide evaluation for 12,929 STR loci. We found rare STR expansions that exceeded normal repeat lengths in autism cases compared to unaffected controls. By integrating single cell RNA and ATAC sequencing datasets of human postmortem brains, we prioritized STR loci in genes specifically expressed in cortical development stages. A deep learning method was used to predict functionality of ASD‐associated STR loci. Results: In ASD cases, rare STR expansions predominantly occurred in early cortical layer‐specific genes involved in neurodevelopment, highlighting the cellular specificity of STR‐associated genes in ASD risk. Leveraging deep learning prediction models, we demonstrated that these STR expansions disrupted the regulatory activity of enhancers and promoters, suggesting a potential mechanism through which they contribute to ASD pathogenesis. We found that individuals with ASD‐associated STR expansions exhibited more severe ASD phenotypes and diminished adaptability compared to non‐carriers. Conclusion: Short tandem repeat expansions in cortical layer‐specific genes are associated with ASD and could potentially be a risk genetic factor for ASD. Our study is the first to show evidence of STR expansion associated with ASD in an under‐investigated population. [ABSTRACT FROM AUTHOR]

Alternative splicing is an essential post-transcriptional regulatory mechanism that diversifies gene function by generating multiple protein isoforms from a single gene and act as a crucial role in insect environmental adaptation. Olfaction, a key sense for insect adaptation, relies heavily on the antennae, which are the primary olfactory organs expressing most of the olfactory genes. Despite the extensive annotation of olfactory genes within insect antennal tissues facilitated by highthroughput sequencing technology advancements, systematic analyses of alternative splicing are still relatively less. In this study, we focused on the oriental fruit fly (Bactrocera dorsalis), a significant pest of fruit crops. We performed a detailed analysis of alternative splicing in its antennae by utilizing the full-length transcriptome of its antennal tissue and the insect’s genome. The results revealed 8600 non-redundant full-length transcripts identified in the oriental fruit fly antennal full-length transcriptome, spanning 4,145 gene loci. Over 40% of these loci exhibited multiple isoforms. Among these, 161 genes showed sex-biased isoform switching, involving seven different types of alternative splicing. Notably, events involving alternative transcription start sites (ATSS) and alternative transcription termination sites (ATTS) were the most common. Of all the genes undergoing ATSS and ATTS alternative splicing between male and female, 32 genes were alternatively spliced in protein coding regions, potentially affecting protein function. These genes were categorized based on the length of the sex-biased isoforms, with the highest difference in isoform fraction (dIF) associated with the ATSS type, including genes such as BdorABCA13, BdorCAT2, and BdorTSN3. Additionally, transcription factor binding sites for doublesex were identified upstream of both BdorABCA13 and BdorCAT2. Besides being expressed in the antennal tissues, BdorABCA13 and BdorCAT2 are also expressed in the mouthparts, legs, and genitalia of both female and male adults, suggesting their functional diversity. This study reveals alternative splicing events in the antennae of Bactrophora dorsalis from two aspects: odorant receptor genes and other types of genes expressed in the antennae. This study not only provides a research foundation for understanding the regulation of gene function by alternative splicing in the oriental fruit fly but also offers new insights for utilizing olfaction-based behavioral manipulation techniques to manage this pest. [ABSTRACT FROM AUTHOR]

This article examines the concept of sexual diversity in the natural world and its implications for our understanding of sex, gender, and biology. It provides examples of sexual diversity in various species, including a parasitic relationship between a mayfly and a worm, same-sex courtship in bighorn sheep, and polymorphism in white-throated sparrows. The article emphasizes the need to carefully navigate the similarities and differences between sex, gender, and sexuality in humans and the natural world. It also challenges traditional understandings of testosterone and the role of X and Y chromosomes in determining biological sex, highlighting the importance of recognizing and teaching about the diversity of the natural world to foster a more inclusive and accurate understanding of sex and gender. [Extracted from the article]

The widespread Palearctic rodent species gray hamster Nothocricetulus migratorius has a karyotype with a stable number of chromosomes 2n = 22 throughout the entire range of its habitat. We found gray hamsters with diploid number of chromosomes 2n = 24 locally distributed in the Qurama Ridge of the Tian Shan. A new karyotype and analysis of G- and NORs-bands of differentially stained chromosome sets were described for the first time. The described karyotype differs from the 22-chromosomal karyotype of gray hamsters by the Y-chromosome morphology and the presence of an additional pair of heteromorphic small chromosomes. Molecular genetic analysis revealed genetic divergence of 24- and 22-chromosomal forms of N. migratorius, and the differences between them in mitochondrial markers are comparable and in terms of nuclear markers exceed the differences between C. barabensis (2n = 20) and C. psevdogriseus (2n = 24). The data obtained give grounds to discuss the taxonomic status of the 24-chromosomal form of gray hamsters from the Qurama Ridge and consider the differentiation of N. migratorius karyomorphs as a stage of chromosomal speciation. [ABSTRACT FROM AUTHOR]

The phenomenon of sex chromosome loss from hematopoietic cells is an emerging indicator of biological aging. While many methods to detect this loss have been developed, enhancing the field, these existing methods often suffer from being labor‐intensive, expensive, and not sufficiently sensitive. To bridge this gap, a novel and more efficient technique is developed, named the SinChro assay. This method employs multiplexed single‐cell droplet PCR, designed to detect cells with sex chromosome loss at single‐cell resolution. Through the SinChro assay, the age‐dependent increase in Y chromosome loss in male blood is successfully mapped. The age‐dependent loss of the X chromosome in female blood is also identified, a finding that has been challenging with existing methods. The advent of the SinChro assay marks a significant breakthrough in the study of age‐related sex mosaicism. Its utility extends beyond blood analysis, applicable to a variety of tissues, and it holds the potential to deepen the understanding of biological aging and related diseases. [ABSTRACT FROM AUTHOR]

Inherited disorders are one of the reasons of infertility and economic losses for the equine industry. The detection rate of chromosomal abnormalities is rising due to the use of sex chromosome linked molecular markers. Here, a rare sterile five-year-old Arabian mare with XY male chromosomes is presented. The phenotype was corresponded to female with normal external genitalia. By transrectal ultrasound, there were hypoplastic ovaries and aplasia of uterine horns. Chromosome analysis was accomplished on blood samples using conventional, and G-banding techniques and confirmed by PCR and hormonal analysis. Although the karyotype (2n = 64, XY) revealed a typical male arrangement, it was SRY gene negative and amelogenin gene positive for X and Y chromosome. Hormonal analysis showed slight estrogenic activity of the ovary, but low progesterone and anti-mullerian hormones levels. In conclusion, this case of sex reversal mare (SRY-negative 64, XY) was recorded using cytogenetic, genetic, and hormonal analysis. Cytogenetics and molecular screening could be used as a fast approach for reproductive disorders evaluation in equine to save money, effort, and time of breeders. [ABSTRACT FROM AUTHOR]