Genetics and Molecular Biology最新文献

Different phthalate compounds, known as emerging contaminants, such as Di-n-butyl (DBP) and di-iso-pentyl (DiPeP) phthalates, have been found in aquatic environments and are widely used as additives to increase the flexibility of plastics. This study intended to evaluate the toxicity in zebrafish embryos and larvae of DBP and DiPeP, as well as the mixture of the two compounds. Fish embryo toxicity, neurotoxicity, oxidative stress, and genotoxicity studies were carried out in Danio rerio (zebrafish) embryos and larvae. Fish were exposed to DBP and DiPeP in concentrations ranging from 0.001 to 0.125 mg/L and also a combination of compounds DBP + DiPeP (1:1 MIX). DBP caused mortality and embryo malformations from 0.062 mg/L, DiPeP at 0.125 mg/L and the mixture at 0.031 mg/L, indicating the potential toxicity of these phthalates. Isolated phthalates and in mixture induced neurotoxicity and oxidative stress, at low concentrations in zebrafish larvae. No genotoxicity was found through comet assay in larvae. DBP was more toxic than DiPeP, and the mixture was more toxic than both phthalates when tested in isolation, showing some kind of interaction.

The contemporary genetic diversity of the cheetah (Acinonyx jubatus) has been the focus of several studies, which have revealed very low levels of variation. Different hypotheses have been proposed to explain this pattern of low diversity, and require additional scrutiny. Here, we used published microsatellite data and coalescence-based analytical methods to explore the historical demography of the largest free-ranging cheetah population, aiming to assess whether present-day diversity may have been impacted by a historical demographic decline. Our results support the hypothesis of a historical (and most likely gradual) demographic decline over the past ~10,000 years, leading to a present-day N e ranging from 700 to 1,600 individuals. This decline was likely induced by climate-driven vegetational shifts affecting habitat suitability and possibly also interspecies interactions with prey and competitors. These results help clarify the demographic history of cheetahs in southern Africa and its impact on the current genetic diversity of this population.

Acute lymphoblastic leukemia (ALL) stands out as the most prevalent neoplasm during childhood, characterized by the rapid production of abnormal lymphoid cells. Chemotherapy administered to these patients may induce a substantial imbalance in the oral microbiota. A prospective pediatric study encompassing a control group (without ALL) and ALL patients at two treatment stages (pre-induction and consolidation) was conducted. Clinical and laboratory data were meticulously collected. Moreover, DNA from saliva samples was extracted for 16S rRNA sequencing. Clinical data revealed a heightened incidence of oral mucositis during the consolidation phase. Analysis of alpha biodiversity (observed taxa) exhibited a significant reduction in bacterial richness among patients in the consolidation phase. Network analysis identified key taxa during this phase, namely Neisseria flavescens, Prevotella melaninogenica and Porphyromonas. The findings underscore the substantial impact of ALL treatment on the oral microbiota composition, indicating diminished bacterial diversity and an elevated prevalence of oral mucositis.

Research has highlighted the significant role of methylated genes associated with DNA damage repair in pathogenesis of Lung adenocarcinoma (LUAD). However, the potential of DNA damage repair-related gene (DDRG) methylation as a prognostic biomarker remains underexplored. This study aimed to assess the prognostic value of methylated DDRGs in LUAD. Analysis of the TCGA-LUAD dataset revealed differentially expressed genes (DEGs) and differentially methylated genes (DE-MGs), from which methylated DE-DDRGs were identified. An independent prognostic risk model was constructed based on these methylated DE-DDRGs by integrating risk scores with clinical features. Additionally, the study examined responses to immunotherapy. Results indicated that CLU exhibited hypermethylation and elevated expression in LUAD tissues, while eight other genes (BUB1B, SHCBP1, RRM2, RPL39L, TRIP13, GAPDH, ENO1, and CENPM) showed high expression and hypomethylation. Among these, RRM2 and GAPDH were significantly linked to poorer overall survival. Furthermore, single-sample gene set enrichment analysis (ssGSEA) revealed that patients with LUAD in the high-risk group had lower immune scores and less immune cell infiltration. TIDE analysis suggested that patients in the low-risk group may exhibit greater sensitivity to immune checkpoint inhibitor therapy. In conclusion, RRM2 and GAPDH represent promising prognostic and immunotherapeutic biomarkers, offering new avenues for LUAD treatment strategies.

We report a viral metagenomic analysis of fecal samples from Bradypus crinitus (Pilosa: Bradypodidae), a recently described sloth species that occurs in the Atlantic Forest of Espírito Santo and Rio de Janeiro states, Southeast Brazil. Through Illumina sequencing, we generated a total of 2,065,344 raw reads, of which 945,386 reads (45.77%) passed the quality and size filter. The highest proportion of them was assigned to Eukarya, followed by Bacteria and only a small proportion to Virus. However, we identified 24 viral families using distinct taxonomic assignment tools, including phages and vertebrate viruses, such as retroviruses and papillomaviruses. Also, we identified four bacterial genus already associated with disease in sloths. Our study sheds light on the microbiome of a previously unexplored species, further contributing to the comprehension of metagenomic global diversity.

Neurofibromatosis type 1 (NF1) is a syndrome triggered by mutations in the NF1 gene, which alter the neurofibromin protein, a negative regulator of the RAS oncogenic pathway. Due to underreporting, the scarcity of studies on NF1 in Brazil and its importance in public health. This study aimed to assess the clinical and epidemiological characterisation of NF1 in a Reference Hospital in the country and DataSUS. The study analysed the electronic medical records of patients with NF1 and the DataSUS databases. The medical records showed a greater number of female, white and adult patients. There was a high frequency of clinical features adopted by the NIH consensus for the clinical diagnosis of the disease, such as CALMs, dermal neurofibromas and axillary/inguinal ephelides, bone and ophthalmological changes, in addition malignant and benign neoplasms and neurodevelopmental disorders. On the other hand, the data provided by DataSUS shows a disproportionate concentration of NF1 consultations between the country's regions, with a low level of diagnoses of newborn with NF1 and a NF1 mortality rate of 3.06% in the population. There is therefore a need for new public policies on access to diagnosis, treatment and information about the disease for the Brazilian population.

Single nucleotide polymorphisms (SNPs) in the HLA DR/DQ region have the greatest impact on susceptibility to type 1 diabetes mellitus (T1DM). Non-HLA SNPs interact with the HLA, influencing the risk for T1DM. The aim of this study was to develop a genetic risk score (GRS) based on HLA DR/DQ and non-HLA SNPs to discriminate patients with T1DM. The sample comprised 466 patients with T1DM and 469 controls. The rs689/INS, rs2476601/PTPN22, rs231775/CTLA-4, rs2304256/TYK2, rs2292239/ERBB3, and HLA DR/DQ SNPs were genotyped using real-time PCR. The unweighted GRS (uGRS) was calculated by summing the risk alleles of each SNP and the weighted GRS (wGRS) by multiplying the risk alleles by their odds ratios. The uGRS was higher in T1DM patients than in non-diabetic controls (0.34 ± 0.14 vs. 0.26 ± 0.13, P <0.0001), being positively correlated with HbA1c levels (P <0.0001). wGRSs exhibited higher AUCs than uGRSs. The wGRS containing only HLA DR/DQ SNPs showed an AUC of 0.75 (95% CI 0.72 - 0.78). The wGRS containing both HLA DR/DQ and non-HLA SNPs, adjusted for race, demonstrated the best discriminative power [AUC 0.91 (95% CI 0.89 - 0.93)]. The race adjusted-wGRS, including all SNPs, seems to be a useful genetic tool for assessing individual's predisposition to T1DM.

The genome of Corynebacterium pseudotuberculosis, etiologic agent of Caseous Lymphadenitis (CLA), was sequenced to comprehend its genetics, pathogenicity, and virulence mechanisms due to its economic importance. A focus was placed on the G/U mismatch-specific DNA glycosylase (Mug), an enzyme vital for base excision repair in DNA that can play an important role in uracil repair, since the high G+C content of C. pseudotuberculosis makes it prone to deamination events, accentuating the potential significance of Mug. Through in silico and in vitro analyses, the Corynebacterium pseudotuberculosis Mug protein (CpMug) was characterized to confirm its DNA glycosylase activity and lesion affinity. The mug gene was identified in both pathogenic and non-pathogenic Corynebacterium species, lacking a discernible ancestry pattern. Bioinformatics analyses revealed the preservation of essential uracil DNA glycosylase catalytic residues in CpMug. The 3D structure of CpMug was constructed, and molecular docking analysis demonstrated its interaction with DNA containing uracil and other lesions. Comparative analyses revealed a higher affinity of CpMug's catalytic residues for uracil over other DNA lesions and enzymatic assays with purified CpMug affirmed its uracil DNA glycosylase activity, while it exhibited no activity on 8-oxoguanine, tetrahydrofuran, or thymine glycol, consistent with computational simulations.

Tumor necrosis factor-alpha (TNF-α), is partly attributed to pathogenesis of end-stage renal disease (ESRD). Inconsistency of reported associations between TNF-α G-308A polymorphism (rs1800629) and ESRD prompted a meta-analysis to obtain more precise estimates. Eleven case-control studies from 11 articles were included. Pooled odds ratios (OR) and 95% confidence intervals (95% CIs) were estimated to evaluate the association. Subgroup analysis was based on ethnicity (Caucasian and Asian). Multiple comparisons were Bonferroni-corrected. Trial sequential analysis (TSA) was implemented to ascertain the reliability of results. Sensitivity analyses and publication bias tests were performed on significant results. There were no significant association (pa >0.05) in the overall and ethnic subgroup. Indians, three significant pool ORs (pa < 0.01-0.03) showed increased susceptibility to ESRD in homozygous (OR, 6.57; 95% CI, 1.45 to 29.75; pa = 0.01), recessive (OR, 6.75; 95% CI, 1.44 to 31.56; pa = 0.02), and codominant (OR, 2.06; 95% CI, 1.08 to 3.94; pa = 0.03) models. TSA indicated the robustness of such association in the Indian population. The main outcomes were robust without evidence of publication bias. This study showed associations between TNF-α G-308A and ESRD are confined to Indians, which are susceptible to ESRD up to approximately 7 times.

Aging is a significant risk factor for male fertility and can lead to severe developmental disorders in offspring. It disrupts testicular function and spermatogenesis, resulting in sperm abnormalities and DNA fragmentation. Male aging alters the genome and epigenome of germ cells due to persistent oxidative stress caused by the cumulative effects of environmental factors over a lifetime. At the molecular level, DNA damage occurs and is poorly repaired due to impaired DNA repair pathways, leading to unrepaired lesions and de novo mutations. Aging also creates distinct epigenetic landscapes that modify gene expression in germ cells, affect the DNA damage response, and generate de novo DNA and epigenetic mutations that are transmitted to the sperm and inherited by the offspring. This review discusses current knowledge on the age-associated effects on male germ cells and the genomic and epigenomic mechanisms contributing to altered male reproductive health and outcomes in progeny. We propose a male reproductive aging threshold, where cumulative exposure to risk factors leads to oxidative stress, impaired spermatogenesis, and altered reproductive outcomes. Finally, we discuss novel interventions to prevent premature testicular aging and emphasize the need for public health policies and counseling guidelines for men seeking paternity.