{"title":"Genetic analysis and preliminary mapping by BSA-seq of the CmSR gene regulating the spotted rind trait in melon (Cucumis melo L.).","authors":"Weiyan Zhang, Huijun Zhang, Xiuxiu Zhu, Yahui Li, Guoliang Yuan, Jian Ma","doi":"10.1590/1678-4685-GMB-2024-0062","DOIUrl":"10.1590/1678-4685-GMB-2024-0062","url":null,"abstract":"<p><p>Melon (Cucumis melo L.) is an economically important horticultural crop. Spotted rind at maturity is an important appearance quality trait in melons. However, the gene controlling this trait remains unknown. In this study, the inheritance pattern of this trait was explored, and the candidate gene underlying this trait was also successfully identified. Genetic analysis showed that a single dominant gene, Cucumis melo Spotted Rind (CmSR), regulates the spotted rind trait. A preliminary genetic mapping analysis was conducted based on a BSA-seq approach. The CmAPRR2 gene was identified to be linked with the spotted rind trait and was located on the short arm of chromosome 4. It harbored two single-nucleotide mutations (chr4: 687014 G/A and chr4: 687244 C/A) in the non-spotted line 'Yellow 2', which may result in the alternative splicing of the transcript and an amino acid change in the respective protein, from proline to glutamine, respectively. Moreover, marker SNP687014-G/A was developed and co-segregated with the spotted rind trait. Therefore, it is speculated that the CmAPRR2 gene may be involved in the regulation of the spotted rind trait in melon. This study provides a theoretical foundation for further research on the gene regulatory mechanism of the rind color in melon.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20240062"},"PeriodicalIF":1.7,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Janaelia Ferreira Vasconcelos Rodrigues, Jessica Maria Leite Dos Santos, Gracielle Araújo Frota, Luiz da Silva Vieira, Marcel Teixeira, Magaly Sales Monteiro, Jomar Patrício Monteiro
{"title":"Expression of transporter genes in anthelmintic resistant isolates of Haemonchus contortus.","authors":"Janaelia Ferreira Vasconcelos Rodrigues, Jessica Maria Leite Dos Santos, Gracielle Araújo Frota, Luiz da Silva Vieira, Marcel Teixeira, Magaly Sales Monteiro, Jomar Patrício Monteiro","doi":"10.1590/1678-4685-GMB-2023-0350","DOIUrl":"10.1590/1678-4685-GMB-2023-0350","url":null,"abstract":"<p><p>ATP-binding cassette (ABC) transporters, including P-glycoproteins (PGP), have been implicated in drug resistance in different organisms including Haemonchus contortus. This study confirmed the resistance status of H. contortus isolates selected for ivermectin (IVM) and oxfendazole (OXF) resistances using the fecal egg count reduction test and evaluated the gene expression of seven ABC transporters using RT-qPCR for two biological scenarios: the effect of selection for anthelmintic resistance and the effect of drug exposure on gene expression. Gene expression results showed that selection for IVM resistance led to the significant upregulation of Hco-pgp-9a (1.5-fold), Hco-pgp-11 (3-fold) and Hco-haf-9 (1.5-fold) (p < 0.05). Similarly, selection for OXF resistance led to the significant upregulation of Hco-pgp-9a (3-fold), Hco-pgp-11 (4-fold) and Hco-haf-9 (2-fold) when comparing with the unselected ISE isolate (p < 0.05). Exposure of selected isolates to anthelmintics lead to no significant upregulation of the studied transporter genes. We also observed instances where there was strong intragroup variation regarding samples originating from parasites obtained from different individual hosts pointing that the interactions of the animal host with the tested anthelmintics may also play a role in the expression of the studied nematode genes.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230350"},"PeriodicalIF":1.7,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Erratum: Investigating the shared genetic architecture between breast and ovarian cancers.","authors":"","doi":"10.1590/1678-4685-GMB-2023-0181er","DOIUrl":"10.1590/1678-4685-GMB-2023-0181er","url":null,"abstract":"<p><p>[This corrects the article doi: 10.1590/1678-4685-GMB-2023-0181].</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230181er"},"PeriodicalIF":1.7,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lucas Alexandre Barbosa de Oliveira Santos, Tales de Albuquerque Leite Feitosa, Marcus Vinicius de Aragão Batista
{"title":"Comparative structural studies on Bovine papillomavirus E6 oncoproteins: Novel insights into viral infection and cell transformation from homology modeling and molecular dynamics simulations.","authors":"Lucas Alexandre Barbosa de Oliveira Santos, Tales de Albuquerque Leite Feitosa, Marcus Vinicius de Aragão Batista","doi":"10.1590/1678-4685-GMB-2023-0346","DOIUrl":"10.1590/1678-4685-GMB-2023-0346","url":null,"abstract":"<p><p>Bovine papillomavirus (BPV) infects cattle cells worldwide, leading to hyperproliferative lesions and the potential development of cancer, driven by E5, E6, and E7 oncoproteins along with other cofactors. E6 oncoprotein binds experimentally to various proteins, primarily paxillin and MAML1, as well as hMCM7 and CBP/p300. However, the molecular and structural mechanisms underlying BPV-induced malignant transformation remain unclear. Therefore, we have modeled the E6 oncoprotein structure from non-oncogenic BPV-5 and compared them with oncogenic BPV-1 to assess the relationship between structural features and oncogenic potential. Our analysis elucidated crucial structural aspects of E6, highlighting both conserved elements across genotypes and genotype-specific variations potentially implicated in the oncogenic process, particularly concerning primary target interactions. Additionally, we predicted the location of the hMCM7 binding site on the N-terminal of BPV-5 E6. This study enhances our understanding of the structural characteristics of BPV E6 oncoproteins and their interactions with host proteins, clarifying structural differences and similarities between high and low-risk BPVs. This is important to understand better the mechanisms involved in cell transformation in BPV infection, which could be used as a possible target for therapy.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230346"},"PeriodicalIF":1.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Glenda Nicioli da Silva, Isadora Oliveira Ansaloni Pereira, Ana Paula Braga Lima, Tamires Cunha Almeida, André Luiz Ventura Sávio, Renato Prado Costa, Kátia Ramos Moreira Leite, Daisy Maria Fávero Salvadori
{"title":"Combined expression of JHDM1D/KDM7A gene and long non-coding RNA RP11-363E7.4 as a biomarker for urothelial cancer prognosis.","authors":"Glenda Nicioli da Silva, Isadora Oliveira Ansaloni Pereira, Ana Paula Braga Lima, Tamires Cunha Almeida, André Luiz Ventura Sávio, Renato Prado Costa, Kátia Ramos Moreira Leite, Daisy Maria Fávero Salvadori","doi":"10.1590/1678-4685-GMB-2023-0265","DOIUrl":"10.1590/1678-4685-GMB-2023-0265","url":null,"abstract":"<p><p>Bladder cancer is the tenth most frequently diagnosed cancer globally. Classification of high- or low-grade tumors is based on cytological differentiation and is an important prognostic factor. LncRNAs regulate gene expression and play critical roles in the occurrence and development of cancer, however, there are few reports on their diagnostic value and co-expression levels with genes, which may be useful as specific biomarkers for prognosis and therapy in bladder cancer. Thus, we performed a marker lesion study to investigate whether gene/lncRNA expression in urothelial carcinoma tissues may be useful in differentiating low-grade and high-grade tumors. RT-qPCR was used to evaluate the expression of the JHDM1D gene and the lncRNAs CTD-2132N18.2, SBF2-AS1, RP11-977B10.2, CTD-2510F5.4, and RP11-363E7.4 in 20 histologically diagnosed high-grade and 10 low-grade tumors. A protein-to-protein interaction network between genes associated with JHDM1D gene was constructed using STRING website. The results showed a moderate (positive) correlation between CTD-2510F5.4 and CTD2132N18.2. ROC curve analyses showed that combined JHDM1D and RP11-363E7.4 predicted tumor grade with an AUC of 0.826, showing excellent accuracy. In conclusion, the results indicated that the combined expression of JHDM1D and RP11-363E7.4 may be a prognostic biomarker and a promising target for urothelial tumor therapy.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230265"},"PeriodicalIF":1.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samara Socorro Silva Pereira, Irene Plaza Pinto, Victor Cortázio do Prado Santos, Rafael Carneiro Silva, Emília Oliveira Alves Costa, Alex Silva da Cruz, Aparecido Divino da Cruz, Cláudio Carlos da Silva, Lysa Bernardes Minasi
{"title":"Analysis of parental origin of de novo pathogenic CNVs in patients with intellectual disability.","authors":"Samara Socorro Silva Pereira, Irene Plaza Pinto, Victor Cortázio do Prado Santos, Rafael Carneiro Silva, Emília Oliveira Alves Costa, Alex Silva da Cruz, Aparecido Divino da Cruz, Cláudio Carlos da Silva, Lysa Bernardes Minasi","doi":"10.1590/1678-4685-GMB-2023-0313","DOIUrl":"10.1590/1678-4685-GMB-2023-0313","url":null,"abstract":"<p><p>Chromosomal Microarray Analysis (CMA) has increased the comprehension of the mechanisms of copy number variation (CNV) formation, classification of these rearrangements, type of recurrence, and its origin, and has also been a powerful approach to identifying CNVs in individuals with intellectual disability. The aim of this study was to establish the parental origin of de novo pathogenic CNV in a cohort of patients with intellectual disability from the public health system of Goiás-Brazil. CMA was done in 76 trios and we identified 15 de novo pathogenic CNVs in 12 patients with intellectual disability. In a total of 15 de novo pathogenic CNV, 60% were derived from the maternal germline and 40% from the paternal germline. CNV flanked by low copy repeats (LCR) were identified in 46.7% and most of them were of maternal origin. No significant association was observed between paternal age and the mutation rate of de novo CNVs. The presence of high-identity LCRs increases the occurrence of CNV formation mediated by non-allelic homologous recombination and the majority of paternal CNVs are non-recurrent. The mechanism of formation of these CNV may have been by microhomology-mediated break-induced replication or non-homologous end joining.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230313"},"PeriodicalIF":1.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jean Carlo Pedroso de Oliveira, Gustavo Sebastián Cabanne, Fabrício Rodrigues Santos
{"title":"Phylogenomics of the gray-breasted sabrewing (Campylopterus largipennis) species complex in the Amazonia and Cerrado biomes.","authors":"Jean Carlo Pedroso de Oliveira, Gustavo Sebastián Cabanne, Fabrício Rodrigues Santos","doi":"10.1590/1678-4685-GMB-2023-0331","DOIUrl":"10.1590/1678-4685-GMB-2023-0331","url":null,"abstract":"<p><p>The Neotropics are one of the most biodiverse regions of the world, where environmental dynamics, climate and geology resulted in a complex diversity of fauna and flora. In such complex and heterogeneous environments, widely distributed species require deep investigation about their biogeographic history. The gray-breasted sabrewing hummingbird Campylopterus largipennis is a species complex that occurs in forest and open ecosystems of South America, including also high-altitude grasslands. It has been recently split into four distinct species distributed in Amazonia (rainforest) and Cerrado (savanna) biomes with boundaries marked by ecological barriers. Here, we investigated the evolutionary dynamics of population lineages within this neotropical taxon to elucidate its biogeographical history and current lineage diversity. We used a reduced-representation sequencing approach to perform fine-scale population genomic analyses of samples distributed throughout Amazonia and Cerrado localities, representing all four recently recognized species. We found a deep genetic structure separating species from both biomes, and a more recent divergence between species within each biome and from distinct habitats. The population dynamics through time was shown to be concordant with known vicariant events, isolation by distance, and altitudinal breaks, where the Amazon River and the Espinhaço Mountain Range worked as important barriers associated to speciation.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230331"},"PeriodicalIF":1.7,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11308382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetic and epigenetic landscape of early-onset oral squamous cell carcinoma: Insights of genomic underserved and underrepresented populations.","authors":"Daniela Adorno-Farias, Sebastián Morales-Pisón, Guilherme Gischkow-Rucatti, Sonia Margarit, Ricardo Fernández-Ramires","doi":"10.1590/1678-4685-GMB-2024-0036","DOIUrl":"10.1590/1678-4685-GMB-2024-0036","url":null,"abstract":"<p><p>Oral squamous cell carcinoma (OSCC) has a poor prognosis and the treatment employed generates significant physical deformity in patients. In recent years, an increase in the incidence of cases of OSCC has been observed in adult patients up to 45 years old in several genetic underrepresented and underserved countries. The increase in OSCC cases in young people is very relevant because it shows that OSCC does not make exceptions and hereditarily must play an important role. This fact has not been associated with an evident biological basis, and a large majority of these patients do not present the classic principal risk factors association. OSCC is the result of accumulation of genetic and epigenetic alterations and this information is still fragmented in the literature, mainly in the young group. Conducting studies with a comprehensive analysis of genetic and epigenetic data is crucial, to provide greater understanding of the underlying biology of OSCC, because this information can be decisive to determine targets for therapeutic treatment. We review the main germline and somatic aspects of genetic and genomic variation in OSCC considering the absence of genomic data from developing countries such as Chile and the rest of Hispano-America.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47Suppl 1 Suppl 1","pages":"e20240036"},"PeriodicalIF":1.7,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11309523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adjanny Estela Santos de Souza, Caio Henrique Silva da Silva, Rita de Cássia Silva de Oliveira, Ana Paula Araújo Guimarães, Aylla Núbia Lima Martins da Silva, Isabela Guerreiro Diniz, Haiala Soter Silva de Oliveira, Diego Sarmento de Sousa, Fernanda Andreza de Pinho Lott Figueiredo, Greice de Lemos Cardoso Costa, João Farias Guerreiro
{"title":"Investigation of genetic markers associated to type 2 diabetes mellitus in Santarém-Pará.","authors":"Adjanny Estela Santos de Souza, Caio Henrique Silva da Silva, Rita de Cássia Silva de Oliveira, Ana Paula Araújo Guimarães, Aylla Núbia Lima Martins da Silva, Isabela Guerreiro Diniz, Haiala Soter Silva de Oliveira, Diego Sarmento de Sousa, Fernanda Andreza de Pinho Lott Figueiredo, Greice de Lemos Cardoso Costa, João Farias Guerreiro","doi":"10.1590/1678-4685-GMB-2023-0107","DOIUrl":"10.1590/1678-4685-GMB-2023-0107","url":null,"abstract":"<p><p>Genetic, epigenetic and environmental factors play an important role in the genesis of Type 2 Diabetes Mellitus (T2D). In the genetic context, one of the strategies used to investigate possible associations with diabetes is the search for Single Nucleotide Polymorphisms (SNPs), involving the comparison of alelle frequencies, the phenotypic variations and other relevant factors, such as environmental influences and lifestyle choices, Thus, the aim of this study was to find the relationship of risk variants for T2D in SNPs (rs4994) in the ADRB3 gene; (rs1799854) in the ABCC8 gene; (rs7901695 and rs12255372) in the TCF7L2 gene; and (rs8050136) in the FTO gene in a sample of the population of the municipality of Santarém (PA), Brazilian Amazon, in the northern region of Brazil. ABCC8 (rs1799854 C>T) showed a statistically significant association with T2D. Each chosen gene and SNP has been previously implicated in T2D risk according to existing scientific literature, owing to their roles in glucose regulation and body fat.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230107"},"PeriodicalIF":1.7,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11308377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomic characterization of SNW-1, a novel prophage of the deep-sea vent chemolithoautotroph Sulfurimonas indica NW79.","authors":"Xiaofeng Li, Ruolin Cheng, Chuanxi Zhang, Zongze Shao","doi":"10.1590/1678-4685-GMB-2023-0355","DOIUrl":"10.1590/1678-4685-GMB-2023-0355","url":null,"abstract":"<p><p>The globally widespread genus Sulfurimonas are playing important roles in different habitats, including the deep-sea hydrothermal vents. However, phages infecting Sulfurimonas have never been isolated and characterized to date. In the present study, a novel prophage SNW-1 was identified from Sulfurimonas indica NW79. Whole genome sequencing resulted in a circular, double-stranded DNA molecule of 37,096 bp with a mol% G+C content of 37. The genome includes 64 putative open reading frames, 33 of which code for proteins with predicted functions. Presence of hallmark genes associated with Caudoviricetes and genes involved in lysis and lysogeny indicated that SNW-1 should be a temperate, tailed phage. Phylogenetic and comparative proteomic analyses suggested that Sulfurimonas phage SNW-1 was distinct from other double stranded DNA phages and might represent a new viral genus.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 2","pages":"e20230355"},"PeriodicalIF":1.7,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11290706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141878632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}