An Infertile Azoospermic Male with 45, X T(Yp;15) Karyotype

Objective: 45, X is a very rare condition that usually results from Y/autosomal translocations or insertions. Here we present an infertile azoospermic man who had 45, X t(Yp;15) karyotype and deletion of AZF (azoospermia factor) gene region. Case report: A 35-year-old infertile azoospermic man with a typical male appearance came for infertility genetic counseling. He was infertile for more than ten years and had short height. High-resolution of metaphase chromosomes of 50 peripheral white blood cells were analyzed for karyotyping. Fluorescence in situ hybridization (FISH) analysis and Polymerase chain reaction (PCR) were done for SRY and AZF gene localization. Karyotyping and FISH analysis revealed 45, X t(Yp;15) karyotype and no mosaicism. More investigation on the Y chromosome revealed no deletion in the SRY region, but AZF a/b/c were deleted. It was revealed that Yp's subtelomeric region but not Yq was translocated to chromosome 15. Conclusion: This study shows that despite the lack of a complete Y chromosome in this person, the occurrence of secondary male traits is a result of the short arm translocation of the Y chromosome, which contains the (ex-determining region Y) SRY gene. Infertility is also due to the Y chromosomes long arm's deletion containing the AZF gene region.

Distribution of Immune Cells Including Macrophages in the Human Cochlea

Background: The human cochlea was earlier believed to lack capacity to mount specific immune responses. Recent studies established that the human cochlea holds macrophages. The cells appear to surveil, dispose of, and restore wasted cells to maintain tissue integrity. Macrophage activities are believed to be the central elements in immune responses and could swiftly defuse invading microbes that enter via adjacent infection-prone areas. This review updates recent human studies in light of the current literature and adds information about chemokine gene expression.Materials and Methods: We analyzed surgically obtained human tissue using immunohistochemistry, confocal microscopy, and multichannel super-resolution structured illumination microscopy. The samples were considered representative of steady-state conditions. Antibodies against the ionized calcium-binding adaptor molecule 1 were used to identify the macrophages. CD68 and CD11b, and the major histocompatibility complex type II (MHCII) and CD4 and CD8 were analyzed. The RNAscope technique was used for fractalkine gene localization.Results: Many macrophages were found around blood vessels in the stria vascularis but not CD4 and CD8 lymphocytes. Amoeboid macrophages were identified in the spiral ganglion with surveilling “antennae” projecting against targeted cells. Synapse-like contacts were seen on spiral ganglion cell bodies richly expressing single CXC3CL gene transcripts. Branching neurite-like processes extended along central and peripheral axons. Active macrophages were occasionally found near degenerating hair cells. Some macrophage-interacting T lymphocytes were observed between the scala tympani wall and Rosenthal's canal. CD4 and CD8 cells were not found in the organ of Corti.Conclusions: The results indicate that the human cochlea is equipped with macrophages and potentially lymphocytes, suggesting both an innate and adaptive immune capacity. A rich expression of fractalkine gene transcripts in spiral ganglion neurons suggest an essential role for auditory nerve protection, as has been demonstrated experimentally. The findings provide further information on the important role of the immune machinery present in the human inner ear and its potential to carry adverse immune reactions, including cytotoxic and foreign body responses. The results can be used to form a rationale for therapies aiming to modulate these immune activities.

POLYMORPHISMS OF INSULIN RECEPTOR SUBSTRATE 1 AS A RISK FACTOR FOR TYPE 2 DIABETES MELLITUS, OBESITY AND CHRONIC PANCREATITIS AMONG POPULATION OF TERNOPIL REGION

Background. The course of type 2 diabetes mellitus (T2DM), obesity and chronic pancreatitis (CP) in most cases is not isolated, so it requires broadening the knowledge about the pathogenetic links at their combined course. Despite significant advances in genome research, most of the genetic factors that cause development of T2DM are still unclear. Objective. The aim of the study was to establish the prevalence of IRS1 gene polymorphism in the patients with T2DM as well as obesity and CP. Methods. The study involved 34 patients with T2DM who were hospitalized in the endocrinology department of Ternopil University Hospital in 2019-2020 and 10 apparently healthy patients. Analysis of IRS1 gene polymorphism (SNP in the promoter region - rs2943640; gene localization 2q36.3) was performed on the basis of polymerase chain reaction data using specific primers. Results. It was found that the frequencies of the genotype responsible for C/A polymorphism of IRS1 gene in T2DM, T2DM with obesity and in the combined course of T2DM with obesity and CP did not deviate significantly from the Hardy-Weinberg equilibrium (p>0.05). The patients with combined course of T2DM, obesity and chronic pancreatitis experienced a probable influence of genotypes C/C and C/A of IRS1 gene on the development of the studied comorbidity (p<0.05), which is confirmed by a probable difference in the dominant model of IRS1 gene inheritance only when T2DM was combined with obesity and CP compared to the control group (p<0.001). Conclusions. The presence of the C allele in both homozygous and heterozygous states may increase the risk of T2DM comorbidity, obesity and CP in the population of Ternopil region.

Sex-Biased Expression of Genes Allocated in the Autosomal Chromosomes: Lc-ms/ms Protein Profiling in Healthy Subjects

Sex and gender has large impact in human health and disease prediction. Men differ from women by a limited number of genes in Y chromosome while their phenotypes differ markedly. In this study, serum samples from healthy Bahraini men and women were analyzed by LC-MS/MS. Bioinformatics databases were used for proteins/peptides (PPs) identification and their gene localization. Results revealed that, the PPs which differed significantly (p<0.05 ANOVA) in abundance with fold change (FC) of ³1.5, were twenty, 11 were up-regulated in women (up to 8-folds), and 9 were up-regulated in men but with much lower FC, however, all PPs are encoded by genes located in autosomal chromosomes, indicative of sex-biased gene expression. The only PP related to sex, the sex hormone-binding globulin, was up-regulated in women. The remaining PPs were involved in immunity (6), lipid metabolism (5), gene expression (3) connective tissue (3), and others. The identified PPs were discussed within their physiological and pathological context, in relation to sex e.g. Apo-B100 (pathological cholesterol) was unregulated in men while the inflammatory/immunity related PPs, including Alpha-1-acid glycoproteins, were up-regulated in women. Finally, we propose proteomic as an ideal complementary tool for study of the molecular basis of the sex-biased gene expression.

Potassium content diminishes in infected cells of Medicago truncatula nodules due to the mislocation of channels MtAKT1 and MtSKOR/GORK

Root nodule-infected cells have defects in K+ balance, as compared with non-infected cells, probably due to variation in the location of K+ channel proteins MtAKT1 and MtSKOR/GORK. Abstract Rhizobia establish a symbiotic relationship with legumes that results in the formation of root nodules, where bacteria encapsulated by a membrane of plant origin (symbiosomes), convert atmospheric nitrogen into ammonia. Nodules are more sensitive to ionic stresses than the host plant itself. We hypothesize that such a high vulnerability might be due to defects in ion balance in the infected tissue. Low temperature SEM (LTSEM) and X-ray microanalysis of Medicago truncatula nodules revealed a potassium (K+) decrease in symbiosomes and vacuoles during the life span of infected cells. To clarify K+ homeostasis in the nodule, we performed phylogenetic and gene expression analyses, and confocal and electron microscopy localization of two key plant Shaker K+ channels, AKT1 and SKOR/GORK. Phylogenetic analyses showed that the genome of some legume species, including the Medicago genus, contained one SKOR/GORK and one AKT1 gene copy, while other species contained more than one copy of each gene. Localization studies revealed mistargeting and partial depletion of both channels from the plasma membrane of M. truncatula mature nodule-infected cells that might compromise ion transport. We propose that root nodule-infected cells have defects in K+ balance due to mislocation of some plant ion channels, as compared with non-infected cells. The putative consequences are discussed.

Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination

Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR. Next-generation sequencing (NGS) technologies are ideal for the detection of AMR genes; however, reliable reconstruction of plasmids is still a challenge due to large repetitive regions. This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads (Oxford Nanopore Technologies) and a combination of both (hybrid). Furthermore, the added value of conjugation of a plasmid to a known host was evaluated. As a case study, an isolate harboring a large, low-copy mcr-1-carrying plasmid (>200 kb) was used. Hybrid assemblies of NGS data obtained from whole-genome DNA extractions of the original isolates resulted in the most complete reconstruction of plasmids. The optimal workflow was successfully applied to multidrug-resistant Salmonella Kentucky isolates, where the transfer of an ESBL-gene-containing fragment from a plasmid to the chromosome was detected. This study highlights a strategy including wet and dry lab parameters that allows accurate plasmid reconstruction, which will contribute to an improved monitoring of circulating plasmids and the assessment of their risk of transfer.

Mass-spectrometry-based near-complete draft of the Saccharomyces cerevisiae proteome

Proteomics approaches designed to catalogue all open reading frames (ORFs) under a defined set of growth conditions of an organism have flourished in recent years. However, no proteome has been sequenced completely so far. Here we generate the largest yeast proteome dataset, including 5610 identified proteins using a strategy based on optimized sample preparation and high-resolution mass spectrometry. Among the 5610 identified proteins, 94.1% are core proteins, which achieves near complete coverage of the yeast ORFs. Comprehensive analysis of missing proteins in our dataset indicate that the MS-based proteome coverage has reached the ceiling. A review of protein abundance shows that our proteome encompasses a uniquely broad dynamic range. Additionally, these values highly correlate with mRNA abundance, implying a high level of accuracy, sensitivity and precision. We present examples of how the data could be used, including re-annotating gene localization, providing expression evidence of pseudogenes. Our near complete yeast proteome dataset will be a useful and important resource for further systematic studies.

Lessons from the analysis of TAD boundary deletions in normal population

Topologically Associating Domains (TAD)-boundaries induce spatial constraints, allowing interaction between regulatory elements and promoters only within their TAD. Their disruption could lead to disease, through gene-expression deregulation. This mechanism has been shown in only a relatively low number of diseases and a relatively low proportion of patients, raising the possibility of TAD boundary disruption without phenotypical consequence. We investigated, therefore, the occurrence of TAD boundaries disruption in the general population. Coordinates of 307,430 benign deletions from public databases were crossed with 36 Hi-C datasets. Differences in gene content and gene localization were compared in the TADs, according to the possible disruption of their boundaries by a deletion found in the general population. TADs with no deletion encompassing their boundaries (R-TAD) represented 38% of TADs. Enrichment in OMIM genes as well as in morbid genes was observed in R-TADs and genes in R-TADs were found to localize closer to the boundaries. Our results support recent publications tempering the impact of breaking TADs on gene expression with a majority of broken TADs in the general population. A subgroup of R-TAD emerges from this analysis with enrichment in disease genes and their coordinates could be used to annotate CNV from pangenomic approaches to enhance data interpretation.