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Spermatogenesis in the Drosophila male germline proceeds through a unique transcriptional program controlled both by germline-specific transcription factors and by testis-specific versions of core transcriptional machinery. This program includes the activation of genes on the heterochromatic Y chromosome, and reduced transcription from the X chromosome, but how expression from these sex chromosomes is regulated has not been defined. To resolve this, we profiled active chromatin features in the testes from wildtype and meiotic arrest mutants and integrate this with single-cell gene expression data from the Fly Cell Atlas. These data assign the timing of promoter activation for genes with germline-enriched expression throughout spermatogenesis, and general alterations of promoter regulation in germline cells. By profiling both active RNA polymerase II and histone modifications in isolated spermatocytes, we detail widespread patterns associated with regulation of the sex chromosomes. Our results demonstrate that the X chromosome is not enriched for silencing histone modifications, implying that sex chromosome inactivation does not occur in the Drosophila male germline. Instead, a lack of dosage compensation in spermatocytes accounts for the reduced expression from this chromosome. Finally, profiling uncovers dramatic ubiquitinylation of histone H2A and lysine-16 acetylation of histone H4 across the Y chromosome in spermatocytes that may contribute to the activation of this heterochromatic chromosome. [ABSTRACT FROM AUTHOR]

The abstract from the BMC Proceedings journal provides an overview of the 5th B Chromosome Conference and the research topics related to B chromosomes. B chromosomes are extra chromosomes found in some species, and the conference will focus on various aspects of B chromosome research. The abstract discusses the presence and characteristics of B chromosomes in different species, as well as the use of high-throughput sequencing to study their genetic content. It also highlights specific studies on B chromosomes in various organisms, including the Pachón cavefish, voles, Sorghum purpureosericeum, maize, and yellow-necked mice. The abstract concludes by discussing the role of B chromosomes in sex differentiation in fish, their presence in bird germline cells, and the drive mechanism and genomic conflict of B chromosomes in maize and rye. The goal of the research is to gain insights into the mechanism of B chromosome drive in plants and the genetic content and function of the germline-restricted chromosome in passerine birds. [Extracted from the article]

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When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using morphological features is unreliable, and molecular genetic methods were applied in this study. Eighty-three ancient skeletons were used as models for poorly preserved DNA. Three sex-informative markers on the Y and X chromosome were used for sex identification: a qPCR test using the PowerQuant Y target included in PowerQuant System (Promega), the amelogenin test included in ESI 17 Fast STR kit (Promega), and a Y-STR amplification test using the PowerPlex Y-23 kit (Promega). Sex was successfully determined in all but five skeletons. Successful PowerQuant Y-target, Y-amelogenin, and Y-chromosomal STR amplifications proved the presence of male DNA in 35 skeletons, and in 43 subadults female sex was established. No match was found between the genetic profiles of subadult skeletons, and the elimination database and negative control samples produced no profiles, indicating no contamination issue. Our study shows that genetic sex identification is a very successful approach for biological sexing of subadult skeletons whose sex cannot be assessed by anthropological methods. The results of this study are applicable for badly preserved subadult skeletons from routine forensic casework. [ABSTRACT FROM AUTHOR]

Introduction: Determination of the fetal gender in the first trimester is important in twin pregnancy cases of familial X-linked genetic syndromes and helps determine chorionicity. We assessed and compared the accuracy of first-trimester ultrasound scans, and cell-free fetal DNA (CfDNA) in determining fetal gender in the first trimester of twin pregnancies. Methods: Women with twin pregnancies were recruited prospectively during the first trimester. Fetal gender was determined using both ultrasound scans and CfDNA screening. Both results were compared to the newborn gender after delivery. Results: A total of 113 women with twin pregnancies were enrolled. There was 100% sensitivity and specificity in Y chromosome detection using CfDNA. Gender assignment using ultrasound in any first-trimester scans was 79.7%. Accuracy level increased from 54.2% in CRL 45-54 mm to 87.7% in CRL 55-67 mm and 91.5% in CRL 67-87 mm. Male fetuses had significantly higher chances of a gender assignment error compared to female fetuses, odds ratio = 23.574 (CI 7.346 - 75.656). Conclusions: CfDNA is highly sensitive and specific in determining the presence of the Y chromosome in twin pregnancies in the first trimester. Between CRL 55-87 mm, ultrasound scanning offers a highly accurate determination of fetal gender in twin pregnancies. [ABSTRACT FROM AUTHOR]

Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa. [ABSTRACT FROM AUTHOR]

The Hui people are the second-largest ethnic minority in China, and they are distributed throughout the country. A previous study explored the paternal genetic structure of the Hui population in nine different regions of China, but it overlooked the Liaoning province. In this study, we examined the paternal genetic makeup and forensic traits of the Hui population in Liaoning province by analyzing 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 26 short tandem repeats (Y-STRs). We successfully genotyped 282 unrelated male individuals from the Hui population of Liaoning province using the SNaPshot® single base extension assay and Goldeneye™ Y26 system kit (PEOPLESPOT R&D, Beijing, China). The results revealed high haplotypic diversity (0.9998) and identified 46 terminal haplogroups for the Hui population. Additional analyses, such as heat maps, principal component analysis (PCA), genetic distance (FST), Multidimensional scaling (MDS) analysis, and median-joining network (MJ) analysis, showed that the Hui population could be classified into three groups: Northwest Hui populations (NWH), including Liaoning, Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, and Henan; Hui populations from Sichuan and Shandong (SSH); and Yunnan Hui populations (YNH). Pairwise genetic distance (Rst) comparisons with other Chinese populations revealed that the Hui population displayed genetic affinity with the Han population. The comprehensive understanding of the Hui population in Liaoning province, explored by Y-SNPs and Y-STRs, can be utilized to interpret their genetic structure and enhance the accuracy of forensic databases. [ABSTRACT FROM AUTHOR]

Objective: PIWIL1 polymorphisms' role in pediatric acute lymphoblastic leukemia (ALL) relapse susceptibility remains undiscovered. Methods: A case-control designed and multiple logistic regression model was performed to evaluate the overall risk of pediatric ALL and five single-nucleotide polymorphisms (SNPs) of PIWIL1 gene (rs35997018 C>T, rs1106042 A>G, rs7957349 C>G, rs10773771 C>T, and rs10848087 A>G) in 785 cases and 1,323 controls, which were genotyped by TaqMan assay. The odds ratio (OR) and its 95% confidence interval (CI) were used to estimate the relationship. Stratified analysis was used to investigate the correlation of rs1106042 and rs10773771 genotypes and pediatric ALL relapse susceptibility in terms of age, sex, number of white blood cells (WBC), immunophenotyping, gene fusion type, karyotype, primitive/naïve lymphocytes, and minimal residual disease (MRD) in bone marrow. Finally, the haplotype analysis was performed to appraise the relationship between inferred haplotypes of PIWIL1 and pediatric ALL risk. Results: Among the five analyzed SNPs, rs1106042 A>G was related to increased ALL risk, and rs10773771 C>T was related to decreased ALL risk. Compared to the GG genotype, the rs1106042 GA/AA had a deleterious effect on children of age <120 months, who were female and male, had high or average number of WBC, pro-B ALL, pre-B ALL, T-ALL, low- and middle-risk ALL, E2A-PBX fusion gene, non-gene fusion, abnormal diploid, high hyperdiploid, hypodiploid, and normal diploid. Moreover, rs1106042 A>G harmfully affected primitive/naïve lymphocytes and MRD on days 15-19, day 33, and week 12. On the contrary, rs10773771 TC/CC exhibited a protective effect on ALL children with the TEL- AML fusion gene. Haplotype analysis demonstrated that haplotypes CAGT, TACC, TACT, and TAGT were significantly associated with increased pediatric ALL relapse susceptibility. Conclusion: PIWIL1 rs1106042 A>G was related to increased ALL risk, and rs10773771 C>T was linked to decreased ALL risk in eastern Chinese children. Rs1106042 GA/AA may predict poor prognosis. [ABSTRACT FROM AUTHOR]

Background: Female sex is a known risk factor of brain disorders with raised intracranial pressure (ICP) and sex hormones have been suggested to alter cerebrospinal fluid (CSF) dynamics, thus impairing ICP regulation in CSF disorders such as idiopathic intracranial hypertension (IIH). The choroid plexus (CP) is the tissue producing CSF and it has been hypothesized that altered hormonal composition could affect the activity of transporters involved in CSF secretion, thus affecting ICP. Therefore, we aimed to investigate if expression of various transporters involved in CSF secretion at CP were different between males and females and between females in different estrous cycle states. Steroid levels in serum was also investigated. Methods: Female and male rats were used to determine sex-differences in the genes encoding for the transporters Aqp1 and 4, NKCC1, NBCe2, NCBE; carbonic anhydrase enzymes II and III (CA), subunits of the Na+/K+-ATPase including Atp1a1, Atp1b1 and Fxyd1 at CP. The estrous cycle stage metestrus (MET) and estrous (ES) were determined before euthanasia. Serum and CP were collected and subjected to RT-qPCR analysis and western blots. Serum was used to measure steroid levels using liquid chromatography tandem mass spectrometry (LC–MS/MS). Results: Significant differences in gene expression and steroid levels between males and ES females were found, while no differences were found between male and MET females. During ES, expression of Aqp1 was lower (p < 0.01) and NKCC1 was higher in females compared to males. CAII was lower while CAIII was higher in ES females (p < 0.0001). Gene expression of Atp1a1 was lower in ES compared to male (p = 0.0008). Several of these choroidal genes were also significantly different in MET compared to females in ES. Differences in gene expression during the estrus cycle were correlated to serum level of steroid hormones. Protein expression of AQP1 (p = 0.008) and CAII (p = 0.035) was reduced in ES females compared to males. Conclusions: This study demonstrates for the first time that expression at CP is sex-dependent and markedly affected by the estrous cycle in female rats. Further, expression was related to hormone levels in serum. This opens a completely new avenue for steroid regulation of the expression of CSF transporters and the close link to the understanding of CSF disorders such as IIH. [ABSTRACT FROM AUTHOR]

Transitions in the heterogamety of sex chromosomes (e.g., XY to ZW or vice versa) fundamentally alter the genetic basis of sex determination, however the details of these changes have been studied in only a few cases. In an XY to ZW transition, the X is likely to give rise to the W because they both carry feminizing genes and the X is expected to harbour less genetic load than the Y. Here, using a new reference genome for Salix exigua, we trace the X, Y, Z, and W sex determination regions during the homologous transition from an XY system to a ZW system in willow (Salix). We show that both the W and the Z arose from the Y chromosome. We find that the new Z chromosome shares multiple homologous putative masculinizing factors with the ancestral Y, whereas the new W lost these masculinizing factors and gained feminizing factors. The origination of both the W and Z from the Y was permitted by an unexpectedly low genetic load on the Y and this indicates that the origins of sex chromosomes during homologous transitions may be more flexible than previously considered. Investigation of heterogametic transitions in sex chromosomes is challenging but fascinating from an evolutionary perspective. Here, Hu et al. have identified a transition from an XY to a ZW system in the genus Salix (willows) where both the Z and W chromosomes have originated from the ancestral Y. [ABSTRACT FROM AUTHOR]

Uniparental disomy (UPD) is a rare chromosomal condition, which apart from its importance in medical genetics can affect an outcome of parentage DNA testing, often causing pseudo exclusions. We describe a case of trio paternity test using 24 informative STR loci with potential exclusion at 2 systems located on chromosome 21. Consequent genotyping of an additional 25 autosomal and 27 Y-specific STRs revealed one other inconsistency, also located on this chromosome. All three inconsistent markers had the same heteroallelic state between the child and the biological mother providing evidence for maternal heterodisomy of chromosome 21. The case highlights the importance of considering UPD as a cause of genetic inconsistencies, especially when the inconsistent marker systems are located on the same chromosome. [ABSTRACT FROM AUTHOR]

Chromosome stability is a key point in genome evolution, particularly that of the Y chromosome. The Y chromosome loss in blood and tumor cells is well established. Through processes that are common to other chromosomes too, the Y chromosome undergoes degradation and fragmentation in the blood stream before elimination. This process gives rise to circulating DNA (cirDNA) fragments, whose examination may provide potential insight into the role of DNA fragmentation in blood for the Y chromosome elimination. In this study, we employed shallow whole genome sequencing (sWGS) to comprehensively assess the total cirDNA and the individual chromosome fragment size profiles in the plasma of healthy male individuals. Here, we show that (i) the fragment size profiles of total circulating DNA (cirDNA) and DNA fragments originating from autosomes and the X chromosome in blood plasma are homogeneous, and have a remarkably low variability (mean CV = 7%) among healthy individuals, (ii) the Y chromosome has a distinct fragment size profile with the accumulation of the fragment < 145 bp and depletion of the dinucleosome-associated fragments (290–390 bp), and its fragment fraction in blood decreases with age. These results indicate a higher fragmentation of the Y chromosome compared to other chromosomes and this in turn might be due to its increased susceptibility to degradation. Our findings pave the way for an elucidation of the impact of chromosomal origin on DNA degradation and the Y chromosome biology. [ABSTRACT FROM AUTHOR]

Background: The scientific and clinical communities now recognize that sperm DNA integrity is crucial for successful fertilization, good embryo development, and offspring quality of life. Despite the apparent unanimity, this criterion is rarely evaluated in clinical practice. We evaluated the sperm DNA fragmentation index of nearly 1200 sperm samples and its connections based on the patient's age, body mass index, the season of sperm collection, geographical location, medical history, and addictive behaviors. Methods: A cohort of 1503 patients who were referred to the Royan Institute between July 2018 and March 2020 was examined. Only 1191 patient records with demographic data, complete semen analysis, and DNA fragmentation index measurements were included in the final cohort. Documents were classified, incorporated into statistical models, and analyzed. Results: The results confirmed previous findings that the sperm DNA fragmentation index was significantly higher in aging men. The sperm DNA fragmentation index and high DNA stainability levels were significantly higher in spring and summer samples than in those of other seasons. No correlation was found between semen DNA fragmentation index and patient body mass index, although the study cohort was significantly overweight. Contrary to what might be expected, we observed that the sperm DNA fragmentation index was higher in rural than in urban patients. Intriguingly, epileptic patients exhibited significantly higher sperm DNA fragmentation index levels. Discussion and conclusion: Age is the factor that is most strongly associated with sperm DNA fragmentation index levels. Our analysis of 1191 samples indicates that between the ages of 19 and 59, the sperm DNA fragmentation index increases by an average of 2% each year. Intriguingly, from an epidemiological perspective, the warm season (spring/summer) is associated with a higher sperm DNA fragmentation index in the study population, possibly due to the deleterious effect of temperature on sperm quality. Some neurological diseases, such as epilepsy, are associated with decreased sperm DNA integrity. This observation could be related to the iatrogenic effects of associated therapies. In the study cohort, body mass index did not appear to be correlated with the DNA fragmentation index. [ABSTRACT FROM AUTHOR]

Background: Sperm DNA fragmentation was hypothesized to have a role in the pathogenesis of recurrent pregnancy loss. Unfortunately, the quality of already published evidence is low. Objectives: To investigate the association between sperm DNA fragmentation and idiopathic recurrent pregnancy loss by limiting, as much as possible, the interference of confounding factors. Materials and methods: This was a retrospective multicenter case–control study conducted in two Italian University Hospitals (i.e., Policlinico Gemelli, Rome and Humanitas S. Pio X, Milan) from July 2020 to March 2022. Cases were men belonging to couples affected by first trimester idiopathic recurrent pregnancy loss, defined as the previous loss of two or more pregnancies. Two control groups were selected: (i) men belonging to couples with proven fertility (i.e., at least two previous full‐term pregnancies) (control group A); (ii) men belonging to couples with proven infertility (i.e., the failure to achieve a pregnancy after 12 months or more of regular unprotected sexual intercourse) (control group B). The sperm DNA fragmentation index was measured by the terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Results: We included 74 cases, 37 men with proven fertility (control group A) and 100 men belonging to infertile couples (control group B). The median sperm DNA fragmentation index was significantly lower in control group A (17%, interquartile range: 14.3%–20.6%) compared to both case group (24.5%, interquartile range: 17%–32%; p < 0.0001) and control group B (24%, interquartile range: 18.9%–30%; p = 0.001). The rate of subjects with sperm DNA fragmentation index greater than 30% was significantly higher in both case groups (28%, 95% confidence interval [18%–40%]) and control group B (26%, 95% confidence interval [18%, 36%]) compared to control group A (0%, 95% confidence interval [0%–10%]) (p < 0.001). Multivariate regression models yielded a significant association between sperm DNA fragmentation index and recurrent pregnancy loss (adjusted odds ratio 1.13, 95% confidence interval [1.04–1.23], p = 0.006), but failed to show an association between sperm DNA fragmentation index and infertility (adjusted odds ratio 1.13, 95% CI [1–1.29], p = 0.05). Conclusions: Men within couples affected by recurrent pregnancy loss or infertility had a significantly higher rate of sperm DNA fragmentation compared to fertile controls. However, after adjusting for covariates, sperm DNA fragmentation index was associated only with recurrent pregnancy loss. [ABSTRACT FROM AUTHOR]

Intracytoplasmic sperm injection (ICSI) using surgically retrieved spermatozoa outside the classic context of azoospermia has been increasingly used to overcome infertility. The primary indications include high levels of sperm DNA damage in ejaculated spermatozoa and severe oligozoospermia or cryptozoospermia, particularly in couples with ICSI failure for no apparent reason. Current evidence suggests that surgically retrieved spermatozoa for ICSI in the above context improves outcomes, mainly concerning pregnancy and miscarriage rates. The reasons are not fully understood but may be related to the lower levels of DNA damage in spermatozoa retrieved from the testis compared with ejaculated counterparts. These findings are consistent with the notion that excessive sperm DNA damage can be a limiting factor responsible for the failure to conceive. Using testicular in preference of low‐quality ejaculated spermatozoa bypasses post‐testicular sperm DNA damage caused primarily by oxidative stress, thus increasing the likelihood of oocyte fertilization by genomically intact spermatozoa. Despite the overall favorable results, data remain limited, and mainly concern males with confirmed sperm DNA damage in the ejaculate. Additionally, information regarding the health of ICSI offspring resulting from the use of surgically retrieved spermatoa of non‐azoospermic males is still lacking. Efforts should be made to improve the male partner's reproductive health for safer ICSI utilization. A comprehensive andrological evaluation aiming to identify and treat the underlying male infertility factor contributing to sperm DNA damage is essential for achieving this goal. [ABSTRACT FROM AUTHOR]

Eif2s3y (eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked, Eif2s3y) is an essential gene for spermatogenesis. Early studies have shown that Eif2s3y can promote the proliferation of spermatogonial stem cells (SSCs) and can replace the Y chromosome together with sex-determining region Y (Sry) to transform SSCs into round spermatozoa. We injected lentiviral particles into the seminiferous tubules of mouse testes by sterile surgery surgically to establish overexpressing Eif2s3y testes. And then the mice were intraperitoneally injected with LPS to established the model of testis inflammation. Through RNA sequencing, qRT–PCR analysis, Western blot, co-culture etc., we found that Eif2s3y alleviated LPS-induced damage in mouse testes and maintained spermatogenesis. In testes with Eif2s3y overexpression, the seminiferous tubules were more regularly organized after exposure to LPS compared with the control. Eif2s3y performs its function by negatively regulating Adamts5 (a disintegrin and metalloproteinase containing a thrombospondin-1 motif), an extracellular matrix-degrading enzyme. ADAMTS5 shows a disruptive effect when the testis is exposed to LPS. Overexpression of Eif2s3y inhibited the TLR4/NFκB signaling pathway in the testis in response to LPS. Generally, our research shows that Eif2s3y protects the testis from LPS and maintains spermatogenesis by negatively regulating A damts5. • Overexpression of Eif2s3y alleviates testicular injury induced by LPS. • Eif2s3y is a negative regulator of Adamts5. • Eif2s3y alleviates LPS-induced germ cell damage by negatively regulating Adamts5. • Eif2s3y maintains testicular immune homeostasis through negative regulation of Adamts5. [ABSTRACT FROM AUTHOR]

Sex chromosomes are havens for intragenomic conflicts. The absence of recombination between sex chromosomes creates the opportunity for the evolution of segregation distorters: selfish genetic elements that hijack different aspects of an individual's reproduction to increase their own transmission. Biased (non-Mendelian) segregation, however, often occurs at a detriment to their host's fitness, and therefore can trigger evolutionary arms races that can have major consequences for genome structure and regulation, gametogenesis, reproductive strategies and even speciation. Here, we review an emerging feature from comparative genomic and sex chromosome evolution studies suggesting that meiotic drive is pervasive: the recurrent evolution of paralogous sex-linked gene families. Sex chromosomes of several species independently acquire and co-amplify rapidly evolving gene families with spermatogenesis-related functions, consistent with a history of intragenomic conflict over transmission. We discuss Y chromosome features that might contribute to the tempo and mode of evolution of X/Y co-amplified gene families, as well as their implications for the evolution of complexity in the genome. Finally, we propose a framework that explores the conditions that might allow for recurrent bouts of fixation of drivers and suppressors, in a dosage-sensitive fashion, and therefore the co-amplification of multigene families on sex chromosomes. [ABSTRACT FROM AUTHOR]

To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community. [ABSTRACT FROM AUTHOR]

Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes; however, the diversity of splicing variants remains unexplored. Here, we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2 , CDY , DAZ , HSFY , PRY , RBMY , TSPY , VCY , and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this data set resulted in several findings. First, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Second, our results suggest that BPY2 transcripts and proteins originate from separate genomic regions in bonobo versus human, which is possibly facilitated by acquiring new promoters. Third, our analysis indicates that the PRY gene family, having the highest representation of noncoding transcripts, has been undergoing pseudogenization. Fourth, we have not detected signatures of selection in the five YAG families shared among great apes, even though we identified many species-specific protein-coding transcripts. Fifth, we predicted consensus disorder regions across most gene families and species, which could be used for future investigations of male infertility. Overall, our work illuminates the YAG isoform landscape and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes. [ABSTRACT FROM AUTHOR]

Satellite DNAS (satDNA) have long been recognized as a major driving force in karyotypic repatterning, owing to their ability to recombine between non-homologous chromosomes. A quite extensively studied model is the Repetitive PvuII Ctenomys Sequence (RPCS), the main component of constitutive heterochromatin in rodents of the genus Ctenomys (Rodentia, Ctenomyidae). At the genus level, fluctuations in RPCS copy number have been previously associated with karyotypic instability. However, when a microevolutionary approach was assayed in the most karyotypically variable lineage of the genus, the vast population-level copy number variation precluded any possibility of analyzing it in a phylogenetic framework. The existence of sex-related differences as a source of variability was not considered until later, when chromosomal banding suggested that the Y chromosome may be a significant reservoir of RPCS. This study aimed to investigate the bias associated with the presence of the Y chromosome in RPCS copy number variation in the Corrientes group of Ctenomys. The results revealed that the Y chromosome harbors almost twice the amount of RPCS compared to the rest of the chromosome complement, explaining the high levels of intrapopulation variation. The evolution of RPCS copy number in males and females showed independent patterns, attributable to the presence/absence of the Y chromosome. The correlation between RPCS dynamics and diploid number fluctuations was also investigated, concluding that some karyotypic repatterning events could be explained by satDNA amplification/deletion, but not all of them. This study highlights the importance of considering differences resulting from the differential accumulation of satDNA in the heterogametic chromosome. [ABSTRACT FROM AUTHOR]

In the sample of male residents of St. Petersburg, Y-chromosome haplogroups were determined by genotyping 18 STRs of the Y-chromosome (DYS389I, DYS389II, DYS390, DYS19, DYS385A, DYS385B, DYS456, DYS437, DYS438, DYS447, DYS448, DYS449, DYS391, DYS392, DYS393, DYS439, DYS635, and DYS576), and data on genetic demography were collected by means of a questionnaire. The distribution of Y‑chromosome haplogroups in St. Petersburg residents generally corresponds to the published data on Russian gene pool, with the most frequent haplogroups R1a, R1b, E1b1b1, N, T, I1, I2, J1, and J2, and with the predominance of haplogroup R1a. The presence of "Southern origin" haplogroups (C3, G2a, G2c, J1, J2, L, O2, O3, Q, R2, and T) entering the megalopolis with a flow of migrants, with a total frequency of 16% (in Moscow—18%) was noted. A comparative analysis of the frequency distributions of Y-chromosome haplogroups in residents of St. Petersburg and Moscow revealed statistically significant differences in the frequency of haplogroup E1b1b1 and differences in the ratio of I1 and I2 which may be due to geographical location of megalopolises. On the basis of the survey data, a sample of Russian men who had no ancestors of another ethnicity in the male line in the two previous generations was formed. Significant differences in the frequency of "Southern origin" haplogroups were established between the initial sample of residents of St. Petersburg (16%) and the sample of men with Russian ancestors in two previous generations (4%). The obtained result confirms the spectrum of haplogroups of "Southern origin" as penetrating into the gene pool of the population of a megalopolis with migrant flows and indicates the need for genetic and demographic questionnaires when forming reference databases for a megalopolis, as well as for their timely updating due to changes in the gene pool under the influence of migration. [ABSTRACT FROM AUTHOR]

Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system. [ABSTRACT FROM AUTHOR]

Background: While ageing is associated with increased insulin resistance (IR), the molecular mechanisms underlying increased IR in the muscle, the primary organ for glucose clearance, have yet to be elucidated in older individuals. As epigenetic processes are suggested to contribute to the development of ageing-associated diseases, we investigated whether differential DNA methylation was associated with IR in human primary muscle stem cells (myoblasts) from community-dwelling older individuals. Methods: We measured DNA methylation (Infinium HumanMethylationEPIC BeadChip) in myoblast cultures from vastus lateralis biopsies (119 males/females, mean age 78.24 years) from the Hertfordshire Sarcopenia Study extension (HSSe) and examined differentially methylated cytosine phosphate guanine (CpG) sites (dmCpG), regions (DMRs) and gene pathways associated with HOMA2-IR, an index for the assessment of insulin resistance, and levels of glycated hemoglobin HbA1c. Results: Thirty-eight dmCpGs (false discovery rate (FDR) < 0.05) were associated with HOMA2-IR, with dmCpGs enriched in genes linked with JNK, AMPK and insulin signaling. The methylation signal associated with HOMA2-IR was attenuated after the addition of either BMI (6 dmCpGs), appendicular lean mass index (ALMi) (7 dmCpGs), grip strength (15 dmCpGs) or gait speed (23 dmCpGs) as covariates in the model. There were 8 DMRs (Stouffer < 0.05) associated with HOMA2-IR, including DMRs within T-box transcription factor (TBX1) and nuclear receptor subfamily-2 group F member-2 (NR2F2); the DMRs within TBX1 and NR2F2 remained associated with HOMA2-IR after adjustment for BMI, ALMi, grip strength or gait speed. Forty-nine dmCpGs and 21 DMRs were associated with HbA1c, with cg13451048, located within exoribonuclease family member 3 (ERI3) associated with both HOMA2-IR and HbA1c. HOMA2-IR and HbA1c were not associated with accelerated epigenetic ageing. Conclusions: These findings suggest that insulin resistance is associated with differential DNA methylation in human primary myoblasts with both muscle mass and body composition making a significant contribution to the methylation changes associated with IR. [ABSTRACT FROM AUTHOR]

Background: The Kazakhs are one of the biggest Turkic-speaking ethnic groups, controlling vast swaths of land from the Altai to the Caspian Sea. In terms of area, Kazakhstan is ranked ninth in the world. Northern, Eastern, and Western Kazakhstan have already been studied in relation to genetic polymorphism 27 Y-STR. However, current information on the genetic polymorphism of the Y-chromosome of Southern Kazakhstan is limited only by 17 Y-STR and no geographical study of other regions has been studied at this variation. Results: The Kazakhstan Y-chromosome Haplotype Reference Database was expanded with 468 Kazakh males from the Zhambyl and Turkestan regions of South Kazakhstan by having their 27 Y-STR loci and 23 Y-SNP markers analyzed. Discrimination capacity (DC = 91.23%), haplotype match probability (HPM = 0.0029) and haplotype diversity (HD = 0.9992) are defined. Most of this Y-chromosome variability is attributed to haplogroups C2a1a1b1-F1756 (2.1%), C2a1a2-M48 (7.3%), C2a1a3-F1918 (33.3%) and C2b1a1a1a-M407 (6%). Median-joining network analysis was applied to understand the relationship between the haplotypes of the three regions. In three genetic layer can be described the position of the populations of the Southern region of Kazakhstan—the geographic Kazakh populations of Kazakhstan, the Kazakh tribal groups, and the people of bordering Asia. Conclusion: The Kazakhstan Y-chromosome Haplotype Reference Database was formed for 27 Y-STR loci with a total sample of 1796 samples of Kazakhs from 16 regions of Kazakhstan. The variability of the Y-chromosome of the Kazakhs in a geographical context can be divided into four main clusters—south, north, east, west. At the same time, in the genetic space of tribal groups, the population of southern Kazakhs clusters with tribes from the same region, and genetic proximity is determined with the populations of the Hazaras of Afghanistan and the Mongols of China. [ABSTRACT FROM AUTHOR]

How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple reference-quality genome assemblies. Here we show the existence of a positive correlation between Sdic copy number and total expression, plus vast intrastrain differences in mRNA abundance among paralogs, using RNA-sequencing from testis of four strains with variable paralog composition. Single cell and nucleus RNA-sequencing data expose paralog expression differentiation in meiotic cell types within testis from third instar larva and adults. Additional RNA-sequencing across synthetic strains only differing in their Y chromosomes reveal a tissue-dependent trans-regulatory effect on Sdic: upregulation in testis and downregulation in male accessory gland. By leveraging paralog-specific expression information from tissue- and cell-specific data, our results elucidate the intraspecific functional diversification of a recently expanded tandem gene family. RNA-seq in fly lines with different Sdic paralog composition reveals paralog expression differentiation within and between lines, and across spermatogenesis stages, showing early functional diversification of recently expanded tandem gene families. [ABSTRACT FROM AUTHOR]

Summary: The sex‐determining‐region (SDR) may offer the best prospects for studying sex‐determining gene, recombination suppression, and chromosome heteromorphism. However, current progress of SDR identification and cloning showed following shortcomings: large near‐isogenic lines need to be constructed, and a relatively large population is needed; the cost of whole‐genome sequencing and assembly is high.Herein, the X/Y chromosomes of Spinacia oleracea L. subsp. turkestanica were successfully microdissected and assembled using single‐chromosome sequencing.The assembly length of X and Y chromosome is c. 192.1 and 195.2 Mb, respectively. Three large inversions existed between X and Y chromosome. The SDR size of X and Y chromosome is c. 13.2 and 24.1 Mb, respectively. MSY region and six male‐biased genes were identified. A Y‐chromosome‐specific marker in SDR was constructed and used to verify the chromosome assembly quality at cytological level via fluorescence in situ hybridization. Meanwhile, it was observed that the SDR located on long arm of Y chromosome and near the centromere.Overall, a technical system was successfully established for rapid cloning the SDR and it is also applicable to rapid assembly of specific chromosome in other plants. Furthermore, this study laid a foundation for studying the molecular mechanism of sex chromosome evolution in spinach. [ABSTRACT FROM AUTHOR]

Aim and Objective: Intellectual disability (ID) is a heterogeneous condition affecting brain development, function, and/or structure. The X-linked mode of inheritance of ID (X-linked intellectual disability; XLID) has a prevalence of 1 out of 600 to 1000 males. In the last decades, exome sequencing technology has revolutionized the process of disease-causing gene discovery in XLIDs. Nevertheless, so many of them still remain with unknown etiology. This study investigated four families with severe XLID to identify deleterious variants for possible diagnostics and prevention aims. Methods: Nine male patients belonging to four pedigrees were included in this study. The patients were studied genetically for Fragile X syndrome, followed by whole exome sequencing and analysis of intellectual disability-related genes variants. Sanger sequencing, co-segregation analysis, structural modeling, and in silico analysis were done to verify the causative variants. In addition, we collected data from previous studies to compare and situate our work with existing knowledge. Results: In three of four families, novel deleterious variants have been identified in three different genes, including ZDHHC9 (p. Leu189Pro), ATP2B3 (p. Asp847Glu), and GLRA2 (p. Arg350Cys) and also with new clinical features and in another one family, a reported pathogenic variant in the L1CAM (p. Glu309Lys) gene has been identified related to new clinical findings. Conclusion: The current study's findings expand the existing knowledge of variants of the genes implicated in XLID and broaden the spectrum of phenotypes associated with the related conditions. The data have implications for genetic diagnosis and counseling. [ABSTRACT FROM AUTHOR]

The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia. The phylogeographic patterns of Mycobacterium tuberculosis lineages in East Asia mirror those of human Y-chromosome haplogroups, supporting the Two Layer hypothesis, and a Paleolithic emergence scenario for the Mycobacterium tuberculosis complex. [ABSTRACT FROM AUTHOR]

The article focuses on the concept of fetal microchimerism, where fetal cells from pregnancies are retained by mothers for extended periods post-delivery, and the recent publication by Úbeda & Wild regarding the potential function of these cells. The commentary discusses the hypothesis that these microchimeric cells serve as indicators of kinship, affecting resource allocation to the fetus based on the mother's mating behavior and the genetic diversity of her microchiome.

Uniparental-inherited haploid genetic marker of Y-chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/μL tannic acid, 20 ng/μL humic acid, or 37.5 μM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications. [ABSTRACT FROM AUTHOR]

Background: Lung cancer is more common in posttransplant recipients than in the general population. The objective of this study was to examine the chimerism donor/recipient cell origin of graft cancer in recipients of lung transplant. Methods: A retrospective chart review was conducted at Foch Hospital for all lung transplantations from 1989 to 2020. Short tandem repeat PCR (STR-PCR) analysis, the gold standard technique for chimerism quantification, was used to determine the donor/recipient cell origin of lung cancers in transplant patients. Results: Fourteen (1.4%) of the 1,026 patients were found to have graft lung cancer after lung transplantation, and one developed two different lung tumors in the same lobe. Among the 15 lung tumors, 10 (67%) presented with adenocarcinoma, four (27%) with squamous cell carcinoma and one with small cell lung cancer. STR analysis showed that the origin of the cancer was the donor in 10 patients (71%), the recipient in three patients (21%), and was undetermined in one patient. Median time to diagnosis was 62 months. Conclusion: The prevalence of lung cancer in lung transplant recipients is very low. However, the results of our study showed heterogeneity of genetic alterations, with 21% being of recipient origin. Our results highlight the importance of donor selection and medical supervision after lung transplantation. [ABSTRACT FROM AUTHOR]

Jade perch (Scortum barcoo) has an XX/XY sex-determination system (SDS); however, its sex chromosomes and sex-determining region remain unknown. The recent availability of the jade perch chromosome-level genomic data provides a valuable resource for pinpointing the location of functional genes and the whole genomic structure. In this study, we conducted. In silico chromosome mapping of male-specific/linked loci of jade perch and identified a potential 11.18 Mb male-linked region localized on chromosome 19 (SBA19). Repeat annotations of the male-linked region revealed an abundance of transposable elements, particularly Ty3/Gypsy and novel repeats. Sequence analysis of this region identified a remnant of amh gene, which is considered a potential candidate for SDS in many teleosts. A duplicate copy of amh remnant was located at SBA6. These duplicated amh copies were highly similar to those of XX/XY SDS in teleosts, in which one copy of amh was identified on the Y sex chromosome. Taken all together, we hypothesize SBA19 as the putative sex chromosome and the 11.18 Mb male-linked region to be a potential male-determining region. [ABSTRACT FROM AUTHOR]

Background: Extra Y chromosome was found to cause more aggression with a ratio 1:28 in case of violent and aggressive males. The present study was done to see the level of aggression and number of Y chromosomes in the taller male prisoners of Ambala Central Jail. Material & Methods: The Buss and Perry questionnaire along with certain demographic factors was used to estimate the level of aggression in the male prisoners. Buccal smear staining and conventional karyotyping method was used to see the presence of extra Y chromosome. Results: The aggression score was found highest in the tallest group of males and no extra Y chromosome was found in the prisoners. Conclusions: The aggression score was found increasing with the height. So, a correlation was found between height and aggression. [ABSTRACT FROM AUTHOR]

Background: Although male factor accounts for 40%–50% of unintended childlessness, we are far from fully understanding the detailed causes. Usually, affected men cannot even be provided with a molecular diagnosis. Objectives: We aimed at a higher resolution of the human sperm proteome for better understanding of the molecular causes of male infertility. We were particularly interested in why reduced sperm count decreases fertility despite many normal‐looking spermatozoa and which proteins might be involved. Material and methods: Applying mass spectrometry analysis, we qualitatively and quantitatively examined the proteomic profiles of spermatozoa from 76 men differing in fertility. Infertile men had abnormal semen parameters and were involuntarily childless. Fertile subjects exhibited normozoospermia and had fathered children without medical assistance. Results: We discovered proteins from about 7000 coding genes in the human sperm proteome. These were mainly known for involvements in cellular motility, response to stimuli, adhesion, and reproduction. Numbers of sperm proteins showing at least threefold deviating abundances increased from oligozoospermia (N = 153) and oligoasthenozoospermia (N = 154) to oligoasthenoteratozoospermia (N = 368). Deregulated sperm proteins primarily engaged in flagellar assembly and sperm motility, fertilization, and male gametogenesis. Most of these participated in a larger network of male infertility genes and proteins. Discussion: We expose 31 sperm proteins displaying deviant abundances under infertility, which already were known before to have fertility relevance, including ACTL9, CCIN, CFAP47, CFAP65, CFAP251 (WDR66), DNAH1, and SPEM1. We propose 18 additional sperm proteins with at least eightfold differential abundance for further testing of their diagnostic potential, such as C2orf16, CYLC1, SPATA31E1, SPATA31D1, SPATA48, EFHB (CFAP21), and FAM161A. Conclusion: Our results shed light on the molecular background of the dysfunctionality of the fewer spermatozoa produced in oligozoospermia and syndromes including it. The male infertility network presented may prove useful in further elucidating the molecular mechanism of male infertility. [ABSTRACT FROM AUTHOR]

Testicular dysfunction has been associated with genetic properties. Azoospermia factors (AZF) located on the Y chromosome are very important for spermatogenesis. Male fertility is directly dependent on a successful spermatogenesis process in which several genes participate. We investigated to determine the frequency of region-specific Y chromosome microdeletions in patients diagnosed with infertility and to reveal the relationships between them with gonadal hormone, sperm concentration and sperm count. Karyotype analysis was performed by standard G band in peripheral blood lymphocytes and Y microdeletions was determined by multiplex PCR in 562 patients who applied with the diagnosis of infertility. After determining the distribution of AZF regions, the relationship between this distribution and chromosomal anomaly, gonadal hormone levels, sperm concentration and sperm count was examined. In patients without Y gene microdeletion but with chromosomal anomaly, gonadal hormone LH and FSH levels were higher than those without chromosomal anomaly (p < 001). In the group with AZF gene deletion, there was no difference between gonadal hormone levels in those with and without chromosomal anomaly (p > 0.05). Sperm count and concentration of these patients were examined, no changes were observed in the group with AZF gene deletion. In the group without AZF gene deletion, the sperm concentration (p = 0.006) and sperm count (p = 0.006) due to chromosomal anomaly was lower. Right and left testicular volumes were found to be significantly lower in patients with AZF gene deletion (p = 0.001) compared to those without (p = 0.001). We think that FSH, LH, testosterone levels, sperm count and concentration are more affected by chromosomal anomaly than AZF gene deletions. [ABSTRACT FROM AUTHOR]

Objectives: From an anthropological genetic perspective, little is known about the ethnogenesis of African descendants in Puerto Rico. Furthermore, historical interactions between Indigenous Caribbean and African descendant peoples that may be reflected in the ancestry of contemporary populations are understudied. Given this dearth of genetic research and the precedence for Afro‐Indigenous interactions documented by historical, archeological, and other lines of evidence, we sought to assess the biogeographic origins of African descendant Puerto Ricans and to query the potential for Indigenous ancestry within this community. Materials and Methods: Saliva samples were collected from 58 self‐identified African descendant Puerto Ricans residing in Puerto Rico. We sequenced whole mitochondrial genomes and genotyped Y chromosome haplogroups for each male individual (n = 25). Summary statistics, comparative analyses, and network analysis were used to assess diversity and variation in haplogroup distribution between the sample and comparative populations. Results: As indicated by mitochondrial haplogroups, 66% had African, 5% had European, and 29% had Indigenous American matrilines. Along the Y chromosome, 52% had African, 28% had Western European, 16% had Eurasian, and, notably, 4% had Indigenous American patrilines. Both mitochondrial and Y chromosome haplogroup frequencies were significantly different from several comparative populations. Discussion: Biogeographic origins are consistent with historical accounts of African, Indigenous American, and European ancestry. However, this first report of Indigenous American paternal ancestry in Puerto Rico suggests distinctive features within African descendant communities on the island. Future studies expanding sampling and incorporating higher resolution genetic markers are necessary to more fully understand African descendant history in Puerto Rico. [ABSTRACT FROM AUTHOR]

Hematological diseases are characterized by changes such as chromosomal abnormalities, the activation of proto-oncogenes and inactivation of tumor suppressor genes in hematopoietic cells. The loss of chromosome Y (LOY) is frequent in the hematopoietic cells of older men. It has been accepted that LOY is related to the normal aging process for many years. However, some studies have shown that LOY in blood cells may be related to disease processes. We aimed to show whether LOY in patients with hematological malignancy is due to aging or a somatic chromosomal mutation seen in hematological malignancy. We conducted cytogenetic analysis on bone marrow samples obtained from 247 male patients between 2001 and 2021. Genetic test results for pre-diagnosed patients in the hematology department were conducted at the Genetic Diseases Assessment Center at Akdeniz University Faculty of Medicine. Patients are grouped into acute lymphoblastic leukemia (ALL) (n= 8), acute myeloid leukemia (AML) (n= 19), chronic lymphocytic leukemia (CLL) (n= 15), lymphoma (n= 49), myelodysplastic syndrome (MDS) (n= 54), multiple myeloma (MM) (n= 65) and myeloproliferative neoplasms (MPN) (n= 12). The 100% LOY was observed in 31,81% (n= 7) AML, 27.27% (n= 6) MM, 18,18% (n= 4) MDS, 9.09% (n= 3) ALL, 9,09% (n= 2) MPN, and 4.54% (n=1) lymphoma. The percentage of LOY in AML patients was significantly higher than that in lymphoma, CLL, MM, MDS patients, and control groups (p< 0.01). However, we found no statistically significant relationship between the percentage of LOY and advanced age in patients. Our data revealed that LOY was not associated with age, but rather with the disease, and it might be a chromosomal marker for AML. Further studies are needed to support our suggestion. [ABSTRACT FROM AUTHOR]

Objective: To investigate 38 Y-chromosome short tandem repeat (Y-STR) genetic polymorphisms in Beijing Han and analyze the genetic distance with neighboring or linguistically similar populations. Materials and Methods: In the study, we selected 531 unrelated male individuals of Beijing Han, and the results were statistically analyzed by testing with GSTAR™ 41Y reagents. Results: The allele peak heights were balanced among the Y loci, the amplified fragment ranged from 100 to 500 bps. A total of 531 haplotypes were detected in 531 samples. Eight null genotypes were observed on locus DYS448. One and three double alleles were observed on single-copy locus DYS576 and DYS19, respectively. DYS385 a/b, DYF387S1 a/b, and DYS527 a/b were more common in double copies, but 3, 13, and 11 triple alleles were detected, respectively. The gene diversity values of Y-STRs except DYS391, DYS438, and DYS645 were >0.5. Twenty-seven Y-STRs of Beijing Han population were selected for genetic distance comparison with 17 populations including Changchun Han, with Rst values ranging from 0.0002 to 0.1703. Conclusion: The 38 Y-STRs in this study have strong male lineage identification ability and have great potential for individual identification, kinship identification, Y-STR database construction, and genetic relationship research. [ABSTRACT FROM AUTHOR]

Sex chromosomes are popularized as a special role in driving speciation. However, the empirical evidence from natural population processes has been limited to organisms with degenerated sex chromosomes, where hemizygosity is mainly considered to act as the driver of reproductive isolation. Here, we examined several hybrid zones of torrent frog Amolops mantzorum species complex, using an approach by mapping species‐diagnostic loci onto the reference genome to compare sex‐linked versus autosomal patterns of introgression. We find little support in sex‐linked incompatibilities for large X‐effects for these populations in hybrid zones with homomorphic sex chromosomes, due to the absence of the hemizygous effects. As expected, the large X‐effects were not found in those with heteromorphic but newly evolved sex chromosomes, owing to the absence of strong genetic differences between X and Y chromosomes. The available data so far on amphibians suggest little role for sex‐linked genes in speciation. The large X‐effects in those with nascent sex chromosomes may not be as ubiquitous as presumed across the animal kingdom. [ABSTRACT FROM AUTHOR]

Background: Several genetic mutations in female thrombotic defects have recently been shown to affect recurrent pregnancy loss (RPL); however, it is unclear which common parental mutations are involved in thrombosis-associated repeated pregnancy loss RPL. Aims: In this study, the prevalence of some combined parental thrombophilia gene mutation defects was studied in couples with RPL. Settings and Design: The observational study was done in babol infertility research center (Iran) in 2022. Materials and Methods: Sixty-two infertile women with a history of RPL and their male partners (124 individuals) participated in this study. The frequencies of common defects associated with methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C, factor V Leiden, protein C, protein S and homocysteine were analysed in these couples. Statistical analysis used: The data were statistically analysed using the Mann-Whitney test. Results: Sixty-two couples (124 individuals) were analysed. 56.2% of couples with a history of RPL had MTHFR C677T and 23.1% had MTHFR A1298C. Forty percent of couples showed homocysteine deficiency and 12.5% protein C deficiency. Other genes tested were only observed in the mother or father but not both. Conclusions: Results obtained with RPL couples demonstrate the importance of further investigating combined parental thrombophilia gene mutation defects (not only maternal). [ABSTRACT FROM AUTHOR]

Background: Turner syndrome (TS) is the most common chromosomal abnormality in females. The diagnosis of TS is based on karyotyping of 30 blood lymphocytes. This technique does not rule out tissue mosaicism or low-grade mosaicism in the blood. Because of the associated risk of gonadoblastoma, mosaicism is especially important in case this involves a Y chromosome. Aims: This study was set to determine the value of additional genetic studies such as fluorescent in situ hybridisation and the inclusion of buccal cells in search for mosaicism in TS patients. Settings and Design: This cross-sectional, descriptive study was performed in Human Genetics Department, Medical Research Institute, Alexandria University. Materials and Methods: Fluorescence in situ hybridisation technique was applied to lymphocyte cultures as well as buccal smears using centromeric probes for X and Y chromosomes. Genotype phenotype correlation was also evaluated. Statistical Analysis Used: Descriptive study where categorical variables were described using number and percentage and continuous variables were described using mean and standard deviation. Results: Fluorescence in situ hybridisation technique study detected hidden mosaicism in 60% of studied patients; 20% of patients had a cell line containing Y material, while 40% had variable degrees of X, XX mosaicism, and in the remaining 40% no second cell line was detected. Fluorescence in situ hybridisation study helped identify the origin of the marker to be Y in all patients. The introduction of an additional cell line helped in identifying mosaicism in patients with monosomy X. Virilisation signs were only observed among TS patients with Y cell line mosaicism. The clinical manifestations were more severe in patients with monosomy X than other mosaic cases. Conclusions: Molecular cytogenetic investigation for all suspected cases of TS should be considered for appropriate treatment plan and genetic counselling. [ABSTRACT FROM AUTHOR]

Purpose: To study the prevalence, subtypes, and risk markers for the development of gonadal germ cell tumors (GCT's) among disorders of sexual differentiation (DSD) patients with the Y chromosome. Materials and Method: Design: A retrospective review of the patient's case records from 2010 to 2020 in Government Medical College, Thiruvananthapuram, India was studied. The study participants included 54 subjects with DSD containing the Y chromosome. Demographic data, external masculinization scoring, associated congenital anomalies, karyotyping, intraoperative findings such as gonadal location and internal genital ducts, histopathology of the resected gonads, and its immunohistochemistry were collected. The prevalence of gonadal GCT's was estimated from paraffin-embedded gonadectomy samples (S = 82). Results: The median age of occurrence of gonadal GCT's was 18 years. The prevalence of malignant gonadal GCT's was highest among the PAIS group (19.2%) followed by gonadal dysgenesis (15.8% each in MGD and CGD) and least among CAIS (7.7%) (p < 0.01). The most common type of malignant gonadal GCT's in the descending order of frequency was dysgerminoma, seminoma, mixed GCT, and yolk sac tumor. Multivariance logistic analysis showed post-puberty and the presence of congenital anomalies were associated with the occurrence of gonadal GCT's (P < 0.01). Conclusion: The overall prevalence of gonadal GCT's (malignant and premalignant) among DSD with Y chromosomes is nearly 25%. Dysgerminoma is the most common malignant gonadal GCT's. Age at or above 18 years and the presence of congenital anomalies like renal agenesis, retroperitoneal vascular defects, and congenital diaphragmatic hernia were independent risk markers for the development of gonadal GCT's. [ABSTRACT FROM AUTHOR]

Both sex chromosomes and gonadal hormones influence cellular metabolism to generate sex biases in cardiometabolic traits. Males and females exhibit widespread differences in gene expression across the autosomes as well as the sex chromosomes. Sex biases exist at several levels of gene regulation including epigenetic modifications and pre- and post-translational processes. X chromosome dosage has direct effects on gene expression levels through enhanced expression of specific genes that escape X chromosome inactivation. Genes that escape X chromosome inactivation include histone demethylases that regulate gene expression throughout the genome. Using mouse models that distinguish between chromosomal and gonadal sex effects, sex chromosomes have been shown to impact sex-biased diseases such as obesity, hyperlipidemia, atherosclerosis, Alzheimer's disease, autoimmunity, and pulmonary hypertension. Many aspects of metabolism are sex-biased, from gene expression in metabolic tissues to the prevalence and presentation of cardiometabolic diseases. The influence of hormones produced by male and female gonads has been widely documented, but recent studies have begun to elucidate the impact of genetic sex (XX or XY chromosomes) on cellular and organismal metabolism. XX and XY cells have differential gene dosage conferred by specific genes that escape X chromosome inactivation or the presence of Y chromosome genes that are absent from XX cells. Studies in mouse models that dissociate chromosomal and gonadal sex have uncovered mechanisms for sex-biased epigenetic, transcriptional, and post-transcriptional regulation of gene expression in conditions such as obesity, atherosclerosis, pulmonary hypertension, autoimmune disease, and Alzheimer's disease. [ABSTRACT FROM AUTHOR]

Apical periodontitis (AP) is a common consequence of root canal infection leading to periapical bone resorption. Microbial and host genetic factors and their interactions have been shown to play a role in AP development and progression. Variations in a few genes have been reported in association with AP; however, the lack of genome-wide studies has hindered progress in understanding the molecular mechanisms involved. Here, we report the first genome-wide association study of AP in a large and well-characterized population. Male and female adults (n = 932) presenting with deep caries and AP (cases), or deep caries without AP (controls) were included. Genotyping was performed using the Illumina Expanded Multi-Ethnic Genotyping Array (MEGA). Single-variant association testing was performed adjusting for sex and 5 principal components. Subphenotype association testing, analyses of genetically regulated gene expression, polygenic risk score, and phenome-wide association (PheWAS) analyses were also conducted. Eight loci reached near genome-wide significant association with AP (P < 5 × 10−6); gene-focused analyses replicated 3 previously reported associations (P < 8.9 × 10−5). Sex-specific and subphenotype-specific analyses revealed additional significant associations with variants genome-wide. Functionally oriented gene-based analyses revealed 8 genes significantly associated with AP (P < 5 × 10−5), and PheWAS analysis revealed 33 phecodes associated with AP risk score (P < 3.08 × 10−5). This study identified novel genes/loci contributing to AP and specific contributions to AP risk in men and women. Importantly, we identified additional systemic conditions significantly associated with AP risk. Our findings provide strong evidence for host-mediated effects on AP susceptibility. [ABSTRACT FROM AUTHOR]

Objective: The dysfunction of the CLCN4 gene can lead to X-linked intellectual disability and Raynaud-Claes syndrome (MRXSRC), characterized by severe cognitive impairment and mental disorders. This study aimed to investigate the genetic defects and clinical features of Chinese children with CLCN4 variants and explore the effect of mutant ClC-4 on the protein expression level and subcellular localization through in vitro experiments. Methods: A total of 401 children with intellectual disabilities were screened for genetic variability using whole-exome sequencing (WES). Clinical data, including age, sex, perinatal conditions, and environmental exposure, were collected. Cognitive, verbal, motor, and social behavioral abilities were evaluated. Candidate variants were verified using Sanger sequencing, and their pathogenicity and conservation were analyzed using in silico prediction tools. Protein expression and localization of mutant ClC-4 were measured using Western blotting (WB) and immunofluorescence microscopy. The impact of a splice site variant was assessed with a minigene assay. Results: Exome analysis identified five rare CLCN4 variants in six unrelated patients with intellectual disabilities, including two recurrent heterozygous de novo missense variants (p.D89N and p.A555V) in three female patients, and two hemizygous missense variants (p.N141S and p.R694Q) and a splicing variant (c.1390-12T > G) thatare maternally inherited in three male patients. The p.N141S variant and the splicing variant c.1390-12(T > G were novel, while p.R694Q was identified in two asymptomatic heterozygous female patients. The six children with CLCN4 variants exhibited a neurodevelopmental spectrum disease characterized by intellectual disability (ID), delayed speech, autism spectrum disorders (ASD), microcephaly, hypertonia, and abnormal imaging findings. The minigene splicing result indicated that the c.1390-12T > G did not affect the splicing of CLCN4 mRNA. In vitro experiments showed that the mutant protein level and localization of mutant protein are similar to the wild type. Conclusion: The study identified six probands with CLCN4 gene variants associated with X-linked ID. It expanded the gene and phenotype spectrum of CLCN4 variants. The bioinformatic analysis supported the pathogenicity of CLCN4 variants. However, these CLCN4 gene variants did not affect the ClC-4 expression levels and protein location, consistent with previous studies. Further investigations are necessary to investigate the pathogenetic mechanism. [ABSTRACT FROM AUTHOR]

Introduction: Neurogenesis within the dentate gyrus is thought to play an important role in cognitive processes such as reversal learning and pattern separation. The α7 nicotinic acetylcholine receptor (α7 nAChR) is expressed early in newly formed granule cells of the dentate gyrus, though its role in neurogenesis and related cognitive function is not fully understood. Methods: To better characterize relevant function of α7 nAChRs, we performed unbiased stereology to quantify hippocampal granule cells, pyramidal cells, and total volume and used a touchscreen operant spatial discrimination/reversal task to test pattern separation in a global α7 nAChR knockout mouse line. Results: The knockout resulted in an ≈22% reduction in granule cells and a ≈ 20% reduction in pyramidal cells in both sexes, with no change in total hippocampal volume. However, the knockout impaired performance in the touchscreen task for males only. The sex-dependent difference in behavioral, but not stereological, results suggest a divergence in the structure--function relationship in males versus females. Detailed analyses revealed males were more biased by the initial reversal contingency relative to females indicating a potential source of the sex-specific interaction with the loss of α7 nAChRs. Discussion: These findings argue that the α7 nAChR plays a critical role in hippocampal development, not just granule cell neurogenesis, and plays a sexdependent role in cognitive function. [ABSTRACT FROM AUTHOR]

Background: Dioecious plants have male and female flowers on separate plants. Jojoba is a dioecious plant that is drought-tolerant and native to arid areas. The genome sequence of male and female plants was recently reported and revealed an X and Y chromosome system, with two large male-specific insertions in the Y chromosome. Results: A total of 16,923 differentially expressed genes (DEG) were identified between the flowers of the male and female jojoba plants. This represented 40% of the annotated genes in the genome. Many genes, including those responsible for plant environmental responses and those encoding transcription factors (TFs), were specific to male or female reproductive organs. Genes involved in plant hormone metabolism were also found to be associated with flower and pollen development. A total of 8938 up-regulated and 7985 down-regulated genes were identified in comparison between male and female flowers, including many novel genes specific to the jojoba plant. The most differentially expressed genes were associated with reproductive organ development. The highest number of DEG were linked with the Y chromosome in male plants. The male specific parts of the Y chromosome encoded 12 very highly expressed genes including 9 novel genes and 3 known genes associated with TFs and a plant hormone which may play an important role in flower development. Conclusion: Many genes, largely with unknown functions, may explain the sexual dimorphisms in jojoba plants and the differentiation of male and female flowers. [ABSTRACT FROM AUTHOR]