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PLoS Pathogens Jun 2024Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction....
Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains-LT2 and 14028S-for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.
PubMed: 38913753
DOI: 10.1371/journal.ppat.1012301 -
PLoS Genetics Jun 2024Precise regulation of chromosome dynamics in the germline is essential for reproductive success across species. Yet, the mechanisms underlying meiotic chromosomal events...
Precise regulation of chromosome dynamics in the germline is essential for reproductive success across species. Yet, the mechanisms underlying meiotic chromosomal events such as homolog pairing and chromosome segregation are not fully understood in many species. Here, we employ Oligopaint DNA FISH to investigate mechanisms of meiotic homolog pairing and chromosome segregation in the holocentric pantry moth, Plodia interpunctella, and compare our findings to new and previous studies in the silkworm moth, Bombyx mori, which diverged from P. interpunctella over 100 million years ago. We find that pairing in both Bombyx and Plodia spermatogenesis is initiated at gene-rich chromosome ends. Additionally, both species form rod shaped cruciform-like bivalents at metaphase I. However, unlike the telomere-oriented chromosome segregation mechanism observed in Bombyx, Plodia can orient bivalents in multiple different ways at metaphase I. Surprisingly, in both species we find that kinetochores consistently assemble at non-telomeric loci toward the centers of chromosomes regardless of where chromosome centers are located in the bivalent. Additionally, sister kinetochores do not seem to be paired in these species. Instead, four distinct kinetochores are easily observed at metaphase I. Despite this, we find clear end-on microtubule attachments and not lateral microtubule attachments connecting these separated kinetochores to the meiotic spindle. These findings challenge the classical view of segregation where paired, poleward-facing kinetochores are required for accurate homolog separation in meiosis I. Our studies here highlight the importance of exploring fundamental processes in non-model systems, as employing novel organisms can lead to the discovery of novel biology.
PubMed: 38913752
DOI: 10.1371/journal.pgen.1011329 -
PloS One 2024Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy and a major cause of blindness. RP is caused by several variants of multiple genes, and genetic...
Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy and a major cause of blindness. RP is caused by several variants of multiple genes, and genetic diagnosis by identifying these variants is important for optimizing treatment and estimating patient prognosis. Next-generation sequencing (NGS), which is currently widely used for diagnosis, is considered useful but is known to have limitations in detecting copy number variations (CNVs). In this study, we re-evaluated CNVs in EYS, the main causative gene of RP, identified via NGS using multiplex ligation-dependent probe amplification (MLPA). CNVs were identified in NGS samples of eight patients. To identify potential CNVs, MLPA was also performed on samples from 42 patients who were undiagnosed by NGS but carried one of the five major pathogenic variants reported in Japanese EYS-RP cases. All suspected CNVs based on NGS data in the eight patients were confirmed via MLPA. CNVs were found in 2 of the 42 NGS-undiagnosed RP cases. Furthermore, results showed that 121 of the 661 patients with RP had EYS as the causative gene, and 8.3% (10/121 patients with EYS-RP) had CNVs. Although NGS using the CNV calling criteria utilized in this study failed to identify CNVs in two cases, no false-positive results were detected. Collectively, these findings suggest that NGS is useful for CNV detection during clinical diagnosis of RP.
Topics: Humans; Retinitis Pigmentosa; DNA Copy Number Variations; High-Throughput Nucleotide Sequencing; Female; Male; Eye Proteins; Middle Aged; Adult; Multiplex Polymerase Chain Reaction
PubMed: 38913662
DOI: 10.1371/journal.pone.0305812 -
The Canadian Journal of Urology Jun 2024Prostate cancer is the second most common malignancy in men worldwide. Genomic VPAC receptors are expressed on malignant prostate cancer cells and can be targeted and...
INTRODUCTION
Prostate cancer is the second most common malignancy in men worldwide. Genomic VPAC receptors are expressed on malignant prostate cancer cells and can be targeted and imaged optically by a peptide labeled fluorophore. The objective of our study was to assess the feasibility of detecting cancer of the prostate using a voided urine sample.
MATERIALS AND METHODS
Patients ≥ 40 years old, with lower urinary tract symptoms and serum PSA > 4 ng/mL formed the study group. The first 50 mL of voided urine sample was collected and processed. The cells that were shed in the voided urine were fixed and stained with a peptide TP4303 and incubated. The slide was then stained with DAPI which binds with the DNA in the nucleus. All patients underwent a standard 12-core TRUS-guided prostate biopsy.
RESULTS
A total of 318 patients were included in the study, of these 158 were histologically confirmed cancers. Voided urine samples were positive for VPAC receptors in 154 (97.46%) of these. The remaining 160 patients had no cancer on the HPR examination and none of these patients were positive for VPAC receptors.
CONCLUSIONS
This study validates our belief that patients with prostate cancer shed malignant cells in the urine that can be identified by targeting the VPAC receptors. If these results are further validated by multicentric studies, then this could form the basis for indications for a preliminary prostate biopsy in patients with elevated serum PSA but normal digital examination or in patients needing a repeat biopsy.
Topics: Humans; Male; Prostatic Neoplasms; Middle Aged; Aged; Feasibility Studies; Adult; Lower Urinary Tract Symptoms; Aged, 80 and over
PubMed: 38912942
DOI: No ID Found -
Parasite (Paris, France) 2024Wild rodents are key carriers of various human pathogens, including Blastocystis spp. Our study aimed to assess the prevalence and genetic characteristics of...
Molecular investigation of Blastocystis sp. infections in wild rodents from the Inner Mongolian Autonomous Region and Liaoning province, China: High prevalence and dominance of ST4.
Wild rodents are key carriers of various human pathogens, including Blastocystis spp. Our study aimed to assess the prevalence and genetic characteristics of Blastocystis among wild rodents in the Inner Mongolian Autonomous Region and Liaoning Province of China. From November 2023 to February 2024, 486 rodents were captured in these regions. Fresh feces were collected from the intestines of each rodent for the isolation of DNA and PCR amplification of the vertebrate cytochrome b (cytb) gene to identify rodent species. Subsequently, PCR analysis and sequencing of the partial small subunit of the ribosomal RNA (rRNA) gene were utilized to detect Blastocystis in all fecal samples. Of the total samples, 27.4% (133/486) were found to be Blastocystis positive. The results revealed the presence of four species of rodents infected with Blastocystis, 32.3% (63/195) in Rattus norvegicus, 15.1% (16/106) in Mus musculus, 20.2% (18/89) in Apodemus agrarius, and 37.5% (36/96) in Cricetulus barabensis. Sequence analysis confirmed the existence of five Blastocystis subtypes: ST1 (n = 4), ST2 (n = 2), the ST4 (n = 125, the dominant subtype), ST10 (n = 1), and a novel ST (n = 1). The identified zoonotic subtypes (ST1, ST2, ST4, and ST10) highlight the possible role played by wild rodents in the transmission of Blastocystis to humans, thereby elevating the chances of human infection. Meanwhile, the discovery of novel sequences also provides new insights into the genetic diversity of this parasite.
Topics: Animals; Blastocystis; Blastocystis Infections; China; Prevalence; Feces; Rodent Diseases; Rats; Mice; Rodentia; Animals, Wild; Cytochromes b; Phylogeny; DNA, Protozoan; Polymerase Chain Reaction; Murinae
PubMed: 38912917
DOI: 10.1051/parasite/2024031 -
Journal of Applied Biomedicine Jun 2024Diffuse large B-cell lymphoma (DLBCL) stands out as the most common type of malignant cancer, representing the majority of cases of non-Hodgkin's lymphoma. Ethyl...
Diffuse large B-cell lymphoma (DLBCL) stands out as the most common type of malignant cancer, representing the majority of cases of non-Hodgkin's lymphoma. Ethyl pyruvate (EP) is a derivative of pyruvic acid and found to have potent anti-tumor properties. Despite its potential benefits, the impact of EP on DLBCL remains ambiguous. Our objective is to elucidate the role of EP in modulating the development of DLBCL. Analysis of cholecystokinin-8 (CCK-8) revealed that treatment with EP significantly diminished the viability of DLBCL cells. Furthermore, EP administration suppressed colony formation and hindered cell adhesion and invasion in DLBCL cells. Examination of cell cycle progression showed that EP treatment induced arrest at the G1 phase and subsequently reduced the S phase population in DLBCL cells. EP treatment consistently exhibited apoptosis-inducing properties in Annexin-V assays, and notably downregulated the expression of Bcl-2 while increasing levels of proapoptotic cleaved caspase 3 and BAX in DLBCL cells. Additionally, EP treatment decreased the overexpression of c-Jun in c-Jun-transfected DLBCL cells. Further, EP demonstrated DNA-damaging effects in TUNEL assays. In vivo, xenograft animal models revealed that EP treatment significantly mitigated DLBCL tumor growth and suppressed DLBCL cell adhesion to bone marrow stromal cells. In summary, these findings suggest that EP mitigates DLBCL progression by inducing apoptosis, inducing cell cycle arrest, and promoting DNA damage.
Topics: Pyruvates; Lymphoma, Large B-Cell, Diffuse; Humans; Animals; Cell Adhesion; Cell Proliferation; Cell Line, Tumor; Mice; Apoptosis; Proto-Oncogene Proteins c-jun; Xenograft Model Antitumor Assays
PubMed: 38912866
DOI: 10.32725/jab.2024.014 -
MBio Jun 2024We have investigated the function of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) in the replication of murine leukemia virus (MLV). While IP6 is...
We have investigated the function of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) in the replication of murine leukemia virus (MLV). While IP6 is known to be critical for the life cycle of HIV-1, its significance in MLV remains unexplored. We find that IP6 is indeed important for MLV replication. It significantly enhances endogenous reverse transcription (ERT) in MLV. Additionally, a pelleting-based assay reveals that IP6 can stabilize MLV cores, thereby facilitating ERT. We find that IP5 and IP6 are packaged in MLV particles. However, unlike HIV-1, MLV depends upon the presence of IP6 and IP5 in target cells for successful infection. This IP6/5 requirement for infection is reflected in impaired reverse transcription observed in IP6/5-deficient cell lines. In summary, our findings demonstrate the importance of capsid stabilization by IP6/5 in the replication of diverse retroviruses; we suggest possible reasons for the differences from HIV-1 that we observed in MLV.IMPORTANCEInositol hexakisphosphate (IP6) is crucial for the assembly and replication of HIV-1. IP6 is packaged in HIV-1 particles and stabilizes the viral core enabling it to synthesize viral DNA early in viral infection. While its importance for HIV-1 is well established, its significance for other retroviruses is unknown. Here we report the role of IP6 in the gammaretrovirus, murine leukemia virus (MLV). We found that like HIV-1, MLV packages IP6, and as in HIV-1, IP6 stabilizes the MLV core thus promoting reverse transcription. Interestingly, we discovered a key difference in the role of IP6 in MLV versus HIV-1: while HIV-1 is not dependent upon IP6 levels in target cells, MLV replication is significantly reduced in IP6-deficient cell lines. We suggest that this difference in IP6 requirements reflects key differences between HIV-1 and MLV replication.
PubMed: 38912776
DOI: 10.1128/mbio.01158-24 -
Iranian Journal of Immunology : IJI Jun 2024Ankylosing spondylitis (AS) is a chronic autoimmune disorder characterized by the fusion of vertebral joints and axial arthritis. The programmed death-1 (PD-1)...
BACKGROUND
Ankylosing spondylitis (AS) is a chronic autoimmune disorder characterized by the fusion of vertebral joints and axial arthritis. The programmed death-1 (PD-1) inhibitory receptor has a pivotal role in controlling T cell function and may have a significant impact on the pathogenesis of autoimmune diseases such as AS pathogenesis.
OBJECTIVE
To investigate PD-1 gene expression and its epigenetic regulation by detecting methylated CpG islands in the regulatory sites of the gene. This will provide insight into the mechanisms involved in the disease.
METHODS
30 AS patients and 30 healthy individuals were examined to detect the 16 CpG islands in intron 1 using bisulfite conversion and methylation-specific PCR technique. In addition, RNA samples were isolated from fresh peripheral blood mononuclear cells (PBMCs), and after complementary DNA (cDNA) synthesis, the expression level of the PD-1 gene was evaluated using Real-Time PCR.
RESULTS
The CpG islands located in the intronic zone of the PD-1 gene were hyper-methylated in both the patients with AS and the healthy controls. The gene expression of PD-1 was significantly downregulated in AS patients compared with the controls (p=0.017). A negative correlation between the Bath Ankylosing Spondylitis Disease Activity Index and PD-1 gene expression was also revealed.
CONCLUSION
The low level of PD-1 gene expression is implicated in the pathogenesis of AS. However, in both groups, the methylation level of the intron 1 CpG islands of the PD-1 gene suggests that other regulatory mechanisms are more relevant to PD-1 gene expression than methylation in the intron.
PubMed: 38912647
DOI: 10.22034/iji.2024.101565.2757 -
JCI Insight Jun 2024Spermatogenesis requires precise posttranslational control in the endoplasmic reticulum (ER), but the mechanism remains largely unknown. The protein disulfide isomerase...
Spermatogenesis requires precise posttranslational control in the endoplasmic reticulum (ER), but the mechanism remains largely unknown. The protein disulfide isomerase (PDI) family is a group of thiol oxidoreductases responsible for catalyzing the disulfide bond formation of nascent proteins. In this study, we generated 14 strains of KO mice lacking the PDI family enzymes and found that only PDI deficiency caused spermatogenesis defects. Both inducible whole-body PDI-KO (UBC-Cre/Pdifl/fl) mice and premeiotic PDI-KO (Stra8-Cre/Pdifl/fl) mice experienced a significant decrease in germ cells, testicular atrophy, oligospermia, and complete male infertility. Stra8-Cre/Pdifl/fl spermatocytes had significantly upregulated ER stress-related proteins (GRP78 and XBP1) and apoptosis-related proteins (Cleaved caspase-3 and BAX), together with cell apoptosis. PDI deletion led to delayed DNA double-strand break repair and improper crossover at the pachytene spermatocytes. Quantitative mass spectrometry indicated that PDI deficiency downregulated vital proteins in spermatogenesis such as HSPA4L, SHCBP1L, and DDX4, consistent with the proteins' physical association with PDI in normal testes tissue. Furthermore, PDI served as a thiol oxidase for disulfide bond formation of SHCBP1L. Thus, PDI plays an essential role in protein quality control for spermatogenesis in mice.
Topics: Animals; Male; Spermatogenesis; Protein Disulfide-Isomerases; Mice; Mice, Knockout; Testis; Endoplasmic Reticulum Chaperone BiP; Infertility, Male; Apoptosis; Spermatocytes; Endoplasmic Reticulum Stress; Oligospermia
PubMed: 38912589
DOI: 10.1172/jci.insight.177743 -
JCI Insight Jun 2024
Topics: Humans; DNA, Mitochondrial; Pulmonary Disease, Chronic Obstructive; Male; Female; Middle Aged; Aged; Cohort Studies; Biomarkers; Spirometry
PubMed: 38912587
DOI: 10.1172/jci.insight.181925