Genetics and Molecular Biology最新文献

Many countries lack their guidelines for best practices in genomic medicine, whether for clinical practice or research. For the construction of these national guidelines or institutional policies in human genomics research several key criteria must be observed. The determination of variant pathogenicity has become more refined, with specific global recommendations being adopted. A well-conducted consent process, managed by qualified professionals, ensures the protection of research participants' rights. Pre-established sequencing and data analysis parameters are crucial for ensuring reliable results, and clear guidelines must be provided on whether or not to disclose findings to participants. Data storage remains a challenge due to both the size and sensitivity of the generated files. This work discusses these critical aspects and represents an initiative to propose the best practice recommendations for genomic medicine in human research. These recommendations were developed by a working group of experts and were further refined through discussions with members of the scientific community in genetics and genomic medicine.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) system constitutes a crucial adaptive defense mechanism in prokaryotes against foreign genetic elements. Although CRISPR-Cas systems have been characterized in numerous bacteria, the architecture and function of these systems in the Haemophilus genus remain poorly understood. This study aims to analyze CRISPR-Cas systems in 138Haemophilusstrains and investigate their function, particularly in relation to virulence factors. Results revealed that CRISPR-Cas systems were identified in 31.88% of the Haemophilusstrains. Subtype I-C was the most prevalent, followed by subtypes II-C and III-A. Repeat sequences and thecas1gene were highly conserved within the same subtype. 29.62% of spacer sequences exhibited homology to plasmids or bacteriophages. phiMHaA1 was an important target of the CRISPR-Cas system in Haemophilusgenus. The protospacer adjacent motif sequences (PAM) were determined to be 5'-TTC-3' for subtype I-C and 5'-TTT-3' for subtype II-C. Comparative analysis of virulence genes showed that CRISPR-positive strains carried more ompP2 than CRISPR-negative strains, while the distribution of hmw2C and hmw1C exhibited an opposite trend. These findings provide novel insights into the diversity and function of CRISPR-Cas systems inHaemophilusgenus and propose potential strategies for attenuating the impact ofHaemophilusvirulence factors.

This article explores the historical development of evolutionary biology-from Natural Theology to the Modern Synthesis (MS)-and the ongoing debate around the Extended Evolutionary Synthesis (EES). Over the past 2,500 years, evolutionary thinking has emerged from the interplay between empirical discoveries and dominant philosophical paradigms. Beginning with Aristotle and Saint Augustine, we trace how Darwin and Wallace introduced a scientific framework grounded in natural mechanisms. In the early 20th century, the MS unified Mendelian genetics and Darwinian selection, forming a gene-centered model of evolution focused on mutations and population dynamics. In recent decades, discoveries in epigenetics, phenotypic plasticity, symbiosis, niche construction, and cultural inheritance have challenged the explanatory scope of MS. The EES seeks to incorporate these processes not by discarding Darwinian principles, but by reinterpreting them through a systems biology lens. This mostly represents a conceptual shift in focus: from linear, gene-driven causality to multilevel, reciprocal, and environmentally embedded dynamics. While gaining traction, the EES has been criticized for its lack of formal models and predictive frameworks, remaining a contested proposal. Ultimately, evolutionary biology continues to evolve as a powerful scientific tradition, driven by humanity's enduring quest to understand the origins and evolution of life on Earth.

Soybean like other commodities brings important income to producer countries. In Brazil, the picture is not different. Thus, due to its economic significance and considering all field challenges, that impose abiotic and biotic constraints to improve yield, research efforts have focused on solving problems by applying biotechnological tools. In this review, a description of genetic engineering being developed in Brazil for soybean crop is addressed, including research in tolerance to abiotic conditions such as drought; to biotic factors such as insects, nematodes and fungal among other categories; as well as the use of soybean as bio-factories. All commercially available soybean events in Brazil and South American countries, for insect resistance and herbicide tolerance are also discussed. An overview of the Brazilian regulatory framework and South American countries for Biotech products is presented as well as the future perspectives for soybean genetic engineering in Brazil. In addition, a list of papers, from 2008 to the present, showing the state of the art of genetic engineering of soybean and by-products in Brazil is made available. The same search on the literature for South American countries did not return papers published on the genetic engineering of soybean and by-products. Although South American countries did not develop science on GM soybean, a search on GM varieties being sowed indicated that these countries adopted GM technology, due to all the advantages that these lines offer.

Phylogeographic and genetic structure studies involving Drosophilids have clarified numerous processes that have shaped the evolution of biodiversity over time. In this review, we aim to (i) assess the main biases, gaps, and advances in the scientific literature on this topic; (ii) synthesize the major findings emerging from these studies; and (iii) identify congruencies and discrepancies in the phylogeographical histories of different species and regions. To achieve these goals, we conducted a comprehensive review of peer-reviewed literature on phylogeographic and genetic structure studies of Drosophilidae published between 1987 and 2024. After identifying and filtering relevant studies, we extracted and analyzed key information related to each topic. Overall, we have detected a straightforward predominance of studies involving species of the Drosophila genus, especially within the melanogaster, obscura, and repleta groups. Interestingly, most studies employed nuclear DNA markers, either alone or in combination with mitochondrial markers, and were conducted across more than one biogeographical region, primarily in the Palearctic and Nearctic. Thus, our synthesis underscores the importance of broader taxonomic sampling and increased attention to understudied regions to enhance our understanding of biodiversity dynamics in response to environmental changes at both local and global scales.

Mitochondrial genome variation is a risk factor for Parkinson's disease, but its role in levodopa-induced dyskinesia remains incompletely understood. This study examines the mitochondrial mutation repertoire as a potential biomarker for levodopa-induced dyskinesia in patients with Parkinson's disease. We analyzed the mitogenome using next-generation sequencing data from 42 controls and 45 people with Parkinson's (25 without dyskinesia and 20 with dyskinesia). The mtDNA-server 2 workflow was applied for variant calling analysis. Transition and transversion rates vary during disease progression, especially in patients without levodopa-induced dyskinesia. Although the occurrence of these mutations does not follow a linear pattern, the frequency of transitions modestly increases with age. Specific coding regions (CO1, CO2, CO3, ND4, ND5, and ND6) and the regulatory region (RNR2) exhibited an enrichment of transitions and transversions in patients without dyskinesia. Additionally, we have upgraded the mtDNA-network tool (https://apps.lghm.ufpa.br/mtdna) with an integrated visual component that summarizes the mitochondrial profile in Parkinson's disease. The study highlights dynamic shifts in the mitochondrial mutation repertoire, with clinical implications for underrepresented populations, underscoring the importance of accounting for genetic characteristics across diverse groups.

Staphylococcus species include both well-known pathogens and overlooked reservoirs of antimicrobial resistance. With rising resistance rates and limited treatment options, especially for methicillin-resistant strains, interest in alternative therapies has resurged. Among them, bacteriophages (phages) are promising biological agents due to their high specificity, low toxicity, ability to disrupt biofilms, and co-evolution with bacterial hosts. This review explores the biology, pan-genomics, diversity, and therapeutic relevance of staphylococcal phages. We revisit their historical discovery and re-emergence as tools against multidrug-resistant infections, highlighting morphological features, replication strategies, and recent taxonomic updates. Genomic analyses reveal distinct clusters of genome sizes, rare presence of resistance genes, and implications of transduction, bacterial defense systems, and phage-encoded anti-defense mechanisms. Preclinical studies show broad host range and synergistic activity with diverse antimicrobial agents, while engineered phage enzymes expand therapeutic possibilities. Clinical evidence, though limited, supports safety and efficacy in compassionate-use cases and early trials targeting Staphylococcus. Finally, we examine business models translating phage innovation into applied therapies, emphasizing regulatory, logistical, and financial challenges. In this broader context, phage technologies are not just alternatives to antibiotics-they represent an opportunity for innovation in global health. Their full potential depends on coordinated actions across science, industry, and policy.

Bardet-Biedl syndrome (BBS) is a rare ciliopathic disorder that segregates in an autosomal recessive manner. Genetic studies have so far identified 26 BBS-associated genes worldwide. This study analyzed a multiplex consanguineous Pakistani family with Bardet-Biedl syndrome. Genetic analysis was performed using whole-exome sequencing and Sanger sequencing. Additionally, in silico predictions were performed for functional characterization of the identified mutation. Whole exome analysis of this family identified a novel nonsense mutation [(NM_144596: exon11:c.C1047G: p.(Tyr349*)] in the 11th exon of TTC8 gene. The identified mutation presumably leads to removal of four TPR domains and C-terminus portion. Structural analyses of mutant TTC8 protein showed substantial morphologic and interactional variations, suggesting a defective role of the TTC8 protein in BBSome complex and thus its involvement in disease progression. Identification of novel mutation has expanded the mutational spectrum of TTC8. Moreover, these findings will help in genotype-phenotype association, prenatal diagnosis and genetic counseling of families at risk of BBS syndrome.

Paracidovorax citrulli is the causative agent of bacterial fruit blotch in melons and watermelons. This study used comparative genomic approaches of 17 Brazilian P. citrulli strains obtained from melons and watermelons to classify them into groups I and II and try to understand their genomic differences. The genomes of P. citrulli presented general characteristics similar to those shown for the genomes of the type strain of P. citrulli and reference strains of groups I and II. A phylogenomic analysis revealed two distinct groups of P. citrulli, in which most Brazilian P. citrulli strains were grouped with the strain representing group I. CRISPR-Cas analysis revealed the presence of two proteins, Cas3 and Cas10, in all Brazilian P. citrulli genomes. In addition, we observed the presence of two plasmids (pAMC6 and pAC53) in three Brazilian P. citrulli strains, all closely related to group I. The prediction of effector proteins revealed the XopE/AvrPphe protein as a differential between the strains of groups I and II. The present study will contribute to a more detailed understanding of aspects of host-pathogen interactions and will help improve the detection of strains from these groups, thus elucidating the population dynamics of Brazilian strains of P. citrulli.

Evolutionary analyses of mitogenomes have provided insights into species evolution and conservation. Studies on snakes revealed a higher diversity especially involving variation in tRNA clusters. However, despite the increase in assemblies in databases, the available information for Brazilian species remains scarce in mitogenomic surveys. Based on this, we sequenced and provided the first description of the mitogenome of Bothrops insularis, a critically endangered taxon. We also used the B. insularis assembly and 128 molecules available in databases up to March 2022 to explore rearrangements and evolution of the mtDNA under a phylogenomic perspective. Comparative analyses revealed 24 mitotypes due to rearrangements within four tRNA clusters and within control regions. Mitotype 1 (M1) and Mitotype 2 (M2) are restricted to Scolecophidia and M3 is highly distributed within Alethinophidia. In addition, the M3 is suggested as the most likely ancestral mitotype during the mitogenome evolution. Regarding Bothrops, we recovered the same mitotype for B. jararaca and B. insularis, which structure differs from other Bothrops species. Nucleotide variation suggests 1.5% divergence between B. jararaca and B. insularis. Therefore, we suggest that B. insularis can be considered an evolutionary significant unit, and the data generated herein can be valuable for insights into genome evolution and conservation.