Genetics and Molecular Biology最新文献_第2页

Genetic associations with disease in populations with Indigenous American ancestries. 美洲原住民血统人群中疾病的遗传关联。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-09 DOI: 10.1590/1678-4685-gmb-2023-0024

Lucas Vicuña

{"title":"Genetic associations with disease in populations with Indigenous American ancestries.","authors":"Lucas Vicuña","doi":"10.1590/1678-4685-gmb-2023-0024","DOIUrl":"https://doi.org/10.1590/1678-4685-gmb-2023-0024","url":null,"abstract":"The genetic architecture of complex diseases affecting populations with Indigenous American ancestries is poorly understood due to their underrepresentation in genomics studies. While most of the genetic diversity associated with disease trait variation is shared among worldwide populations, a fraction of this component is expected to be unique to each continental group, including Indigenous Americans. Here, I describe the current state of knowledge from genome-wide association studies on Indigenous populations, as well as non-Indigenous populations with partial Indigenous ancestries from the American continent, focusing on disease susceptibility and anthropometric traits. While some studies identified risk alleles unique to Indigenous populations, their effects on trait variation are mostly small. I suggest that the associations rendered by many inter-population studies are probably inflated due to the absence of socio-cultural-economic covariates in the association models. I encourage the inclusion of admixed individuals in future GWAS studies to control for inter-ancestry differences in environmental factors. I suggest that some complex diseases might have arisen as trade-off costs of adaptations to past evolutionary selective pressures. Finally, I discuss how expanding panels with Indigenous ancestries in GWAS studies is key to accurately assess genetic risk in populations from the American continent, thus decreasing global health disparities.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"9 1","pages":"e20230024"},"PeriodicalIF":2.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Expression profile of inflammasome genes in individuals with Down syndrome. 唐氏综合征患者炎症小体基因的表达谱。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-09 DOI: 10.1590/1678-4685-gmb-2023-0339

Juliana Vieira de Barros Arcoverde,Carla Fernandes Dos Santos,Maria Cecília Magalhães Luckwu,Raysa Samanta Moraes Laranjeira,Aldianne Milene Dos Santos Barbosa,Thays Maria Costa de Lucena,Jaqueline de Azevêdo Silva,Neide Santos

{"title":"Expression profile of inflammasome genes in individuals with Down syndrome.","authors":"Juliana Vieira de Barros Arcoverde,Carla Fernandes Dos Santos,Maria Cecília Magalhães Luckwu,Raysa Samanta Moraes Laranjeira,Aldianne Milene Dos Santos Barbosa,Thays Maria Costa de Lucena,Jaqueline de Azevêdo Silva,Neide Santos","doi":"10.1590/1678-4685-gmb-2023-0339","DOIUrl":"https://doi.org/10.1590/1678-4685-gmb-2023-0339","url":null,"abstract":"Down syndrome (DS), affecting 1 in 700 live births, is the most prevalent chromosomal disorder among newborns. Recognizable by classical clinical features, patients with DS are susceptible to various immunological misbalances. Inflammasome is (mis)activated in several immune-mediated diseases, however studies on individuals with DS are lacking. The present study evaluated the gene expression of NLRP1, NLRP3 and IL-1β in individuals with DS, aiming to understand their susceptibility to immune-mediated diseases. In addition, we assessed whether the individuals with DS present a differential inflammatory response after in vitro infection using PBMCs. For the gene expression assay, 20 individuals with DS and 15 healthy individuals for the control group (CT) were included, while the in vitro infection assay included 10 subjects. mRNA levels from individuals with DS group showed 1.9-fold change (FC) downregulation for NLRP1 (p=0.0001), but no differences for NLRP3 and IL1β. We did not observe significant differences between lipopolysaccharide (LPS)-treated and untreated cells in our in vitro assays. The differential expression of NLRP1 in individuals with DS suggests a potential association with susceptibility to the development of immune-mediated diseases, but further analysis is needed to confirm this relationship.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"74 1","pages":"e20230339"},"PeriodicalIF":2.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The complete chloroplast genome sequences of three Pedicularis species (Orobanchaceae). 三个 Pedicularis 物种（大戟科）的完整叶绿体基因组序列。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0010

Mingcheng Wang, Shuqiao Zhang, Lei Zhang

{"title":"The complete chloroplast genome sequences of three Pedicularis species (Orobanchaceae).","authors":"Mingcheng Wang, Shuqiao Zhang, Lei Zhang","doi":"10.1590/1678-4685-GMB-2024-0010","DOIUrl":"10.1590/1678-4685-GMB-2024-0010","url":null,"abstract":"Pedicularis L., a generally bothersome genus of hemiparasitic plants, is primarily native to southwestern China. The phylogenetic relationship and evolutionary history of this genus have not yet been fully resolved. In this study, we sequenced and assembled chloroplast genomes of three Pedicularis species, P. chinensis, P. melampyriflora, and P. striata using high-throughput Illumina sequencing. The assembled plastomes were 142,059 bp (P. chinensis) to 152,146 bp (P. striata) in size, containing 110 (P. chinensis) to 117 (P. striata) genes. Moreover, we identified 13-15 pseudogenes within the three plastomes, nine of which were pseudogenized in all three species. The three plastomes exhibited a similar codon usage pattern. Moreover, the plastomes contained abundant simple sequence repeats and long repeats, which showed slight variations between the three species. A maximum likelihood analysis was performed to elucidate the phylogenetic positions of the three species within the Pedicularis genus. The plastomes presented in our study can be used as valuable genomic resources for further genetic and genomic studies of the Pedicularis genus.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20240010"},"PeriodicalIF":1.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11641048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361410","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}

引用次数: 0

Pioneering role of RNA in the early evolution of life. RNA 在生命早期进化中的先锋作用。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0028

Israel Muñoz-Velasco, Adrián Cruz-González, Ricardo Hernández-Morales, José Alberto Campillo-Balderas, Wolfgang Cottom-Salas, Rodrigo Jácome, Alberto Vázquez-Salazar

引用次数: 0

DNA copy number profiles and systems biology connect chromatin remodeling and DNA repair in high-risk neuroblastoma. DNA拷贝数图谱和系统生物学将高危神经母细胞瘤中的染色质重塑和DNA修复联系起来。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0007

Thatyanne Gradowski F da C do Nascimento, Joice de Faria Poloni, Mateus Eduardo de Oliveira Thomazini, Luciane R Cavalli, Selene Elifio-Esposito, Bruno César Feltes

{"title":"DNA copy number profiles and systems biology connect chromatin remodeling and DNA repair in high-risk neuroblastoma.","authors":"Thatyanne Gradowski F da C do Nascimento, Joice de Faria Poloni, Mateus Eduardo de Oliveira Thomazini, Luciane R Cavalli, Selene Elifio-Esposito, Bruno César Feltes","doi":"10.1590/1678-4685-GMB-2024-0007","DOIUrl":"10.1590/1678-4685-GMB-2024-0007","url":null,"abstract":"Neuroblastoma (NB) is a solid tumor that accounts for 15% of all pediatric oncological deaths, and much is due to the low response to therapy in relapsed tumors. High-risk NB may present deletions in chromosome 11q, which may be associated with other chromosomal alterations and a poor response to therapy, but this association is still poorly understood. Using a systems biology network approach, we studied three patients with high-risk NB with deleted 11q stage 4 to highlight the connections between treatment resistance and copy number alterations in distinct cases. We built different protein-protein interaction networks for each patient based on protein-coding genes mapped at the cytobands pre- and post-chemotherapy from distinct copy number alterations data. In the post-chemotherapy networks, we identified five common regulatory nodes corresponding to the gained region located in ch17q:BIRC5, BRCA1, PRKCA, SUMO2, andGPS1. A crosslink between DNA damage and chromatin remodeling proteins was also found - a connection still poorly understood in NB. We identified a potential connection between XPB gain and chemoresistance of NB. The findings help elucidate the molecular profiles of high-risk NB with 11q deletion in pre- and post-chemotherapy tumor samples, which may reflect unique profiles in poor response to treatment.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20240007"},"PeriodicalIF":1.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559672/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361409","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}

引用次数: 0

Accuracy of genotype imputation of a low-density SNP array for the Amazon fish Colossoma macropomum. 低密度 SNP 阵列对亚马逊鱼类 Colossoma macropomum 基因型估算的准确性。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0364

John F G Agudelo, Vito A Mastrochirico-Filho, Baltasar F Garcia, Raquel B Ariede, José M Yáñez, Gustavo M R Valladão, Diogo T Hashimoto

{"title":"Accuracy of genotype imputation of a low-density SNP array for the Amazon fish Colossoma macropomum.","authors":"John F G Agudelo, Vito A Mastrochirico-Filho, Baltasar F Garcia, Raquel B Ariede, José M Yáñez, Gustavo M R Valladão, Diogo T Hashimoto","doi":"10.1590/1678-4685-GMB-2023-0364","DOIUrl":"10.1590/1678-4685-GMB-2023-0364","url":null,"abstract":"In South America, Tambaqui (Colossoma macropomum) stands as the primary target for aquaculture, yet breeding programs for this Amazon native species are in their early stages. While high-density single nucleotide polymorphism (SNP) arrays are pivotal for aquaculture breeding, their costs can be prohibitive for non- or semi-industrial species. To overcome this, a cost-effective approach involves developing low-density SNP arrays followed by genotype imputation to higher densities. In this study, a 1K SNP array for tambaqui was created and validated, offering a balance between SNP quantity and genome representativity. The imputation accuracy from various SNP densities to a medium-density array was evaluated, with the 1K density demonstrating the best trade-off (accuracy of 0.93). This subset was further utilized to construct a commercial array through Agriseq™ targeted genotyping-by-sequencing, validated in 192 DNA samples, affirming its high quality for genotyping tambaqui. The low-density SNP array, with genome-wide coverage and high polymorphism, emerges as an effective tool for exploring genetic variation within diverse populations. Population analyses using the 1K panel proved to be an efficient tool for genetic characterization of sampled broodstocks, making it a valuable resource for genetic improvement programs targeting this Amazon native species.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230364"},"PeriodicalIF":1.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361408","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}

引用次数: 0

Variability and functional characterization of the Phakopsora pachyrhizi Egh16-like effectors. Phakopsora pachyrhizi Egh16 类效应器的变异性和功能特征。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0192

Fernanda Machado Castanho, Beatriz Lorena Comin da Costa, Valéria Yukari Abe, Alessandra Yokoyama, Luana Mieko Darben, Liliane Santana Oliveira, Everton Geraldo Capote Ferreira, Ivani de Oliveira Negrão Lopes, Mayra Costa da Cruz Gallo de Carvalho, Maria Isabel Balbi-Peña, Francismar Corrêa Marcelino-Guimarães

{"title":"Variability and functional characterization of the Phakopsora pachyrhizi Egh16-like effectors.","authors":"Fernanda Machado Castanho, Beatriz Lorena Comin da Costa, Valéria Yukari Abe, Alessandra Yokoyama, Luana Mieko Darben, Liliane Santana Oliveira, Everton Geraldo Capote Ferreira, Ivani de Oliveira Negrão Lopes, Mayra Costa da Cruz Gallo de Carvalho, Maria Isabel Balbi-Peña, Francismar Corrêa Marcelino-Guimarães","doi":"10.1590/1678-4685-GMB-2023-0192","DOIUrl":"10.1590/1678-4685-GMB-2023-0192","url":null,"abstract":"Effector proteins in Phakopsora pachyrhizi (Pp), the causative agent of Asian Soybean rust, are involved in the infection process. A previous study identified a rust effector Egh16-like family based expression profile during the interaction with soybean. Herein, we scrutinized available the Pp genomes to validate the predicted Egh16-like family of Pp and identify new family members. We described 22 members of the Egh16-like gene family in the Pp MT2006 genome and 18 in the UFV02 and K8108 genomes, highlighting a family expansion. Family members have a small signal peptide, conserved cysteine-rich R/Y/FxC motifs in the C-terminal region, and a virulence-related Egh16-like domain and were able to suppress PTI related responses in Benthamiana. Phylogenetic analysis placed the family members into eight clusters, with members induced during the early stages of rust infection. Members of clusters VI and VII are present in different copy numbers in Pp genomes and suppressed PAMP-related responses.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230192"},"PeriodicalIF":1.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11378017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139796","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}

引用次数: 0

Molecular mechanisms of cell death by parthanatos: More questions than answers. Parthanatos 导致细胞死亡的分子机制：问题多于答案。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-08-30 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0357

Rafael Dias de Moura, Priscilla Doria de Mattos, Penélope Ferreira Valente, Nícolas Carlos Hoch

引用次数: 0

From bench to in silico and backwards: What have we done on genetics of recurrent pregnancy loss and implantation failure and where should we go next? 从工作台到硅学，再从硅学到工作台：我们在复发性妊娠失败和植入失败的遗传学方面做了哪些工作？

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-08-26 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0127

Flavia Gobetti Gomes, Juliano André Boquett, Thayne Woycinck Kowalski, João Matheus Bremm, Marcus Silva Michels, Luiza Pretto, Marília Körbes Rockenbach, Fernanda Sales Luiz Vianna, Lavinia Schuler-Faccini, Maria Teresa Vieira Sanseverino, Lucas Rosa Fraga

{"title":"From bench to in silico and backwards: What have we done on genetics of recurrent pregnancy loss and implantation failure and where should we go next?","authors":"Flavia Gobetti Gomes, Juliano André Boquett, Thayne Woycinck Kowalski, João Matheus Bremm, Marcus Silva Michels, Luiza Pretto, Marília Körbes Rockenbach, Fernanda Sales Luiz Vianna, Lavinia Schuler-Faccini, Maria Teresa Vieira Sanseverino, Lucas Rosa Fraga","doi":"10.1590/1678-4685-GMB-2023-0127","DOIUrl":"10.1590/1678-4685-GMB-2023-0127","url":null,"abstract":"Human reproduction goes through many challenges to its success and in many cases it fails. Cases of pregnancy loss are common outcomes for pregnancies, and implantation failures (IF) are common in assisted reproduction attempts. Although several risk factors have already been linked to adverse outcomes in reproduction, many cases remain without a definitive cause. Genetics of female reproduction is a field that may bring some pieces of this puzzle; however, there are no well-defined genes that might be related to the risk for recurrent pregnancy loss (RPL) and IF. Here, we present a literature review of the studies of genetic association in RPL and IF carried out in the Brazilian population and complemented with a database search to explore genes previously related to RPL and IF, where a search for genes previously involved in these conditions was performed in OMIM, HuGE, and CTD databases. Finally, we present the next steps for reproductive genetics investigation, through genomic sequencing analyses and discuss future plans in the study of RPL genetics. The combined strategy of looking for literature and databases is useful to raise hypotheses and to identify underexplored genes related to RPL and IF.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230127"},"PeriodicalIF":1.7,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142072459","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}

引用次数: 0

Can ploidy levels explain the variation of Herbertia lahue (Iridaceae)? 倍性水平能否解释 Herbertia lahue（鸢尾科）的变异？

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-08-23 DOI: 10.1590/1678-4685-gmb-2023-0137

Eudes Maria Stiehl-Alves,Ariane Tonetto Vieira,Caroline Trevelin,Alexandre Cristante Martins,Tatiana Teixeira de Souza-Chies,Eliane Kaltchuk-Santos

{"title":"Can ploidy levels explain the variation of Herbertia lahue (Iridaceae)?","authors":"Eudes Maria Stiehl-Alves,Ariane Tonetto Vieira,Caroline Trevelin,Alexandre Cristante Martins,Tatiana Teixeira de Souza-Chies,Eliane Kaltchuk-Santos","doi":"10.1590/1678-4685-gmb-2023-0137","DOIUrl":"https://doi.org/10.1590/1678-4685-gmb-2023-0137","url":null,"abstract":"Polyploidy is often related with phenotypic variation, as observed in Herbertia lahue, a geophyte species. This study examined the H. lahue polyploid series and departure in cytogenetic, morphometric, and pollen data. Diploids (2n=2x=14) present bimodal karyotype with two long and five short chromosome pairs, while hexaploids (2n=6x=42) and octoploids (2n=8x=56) present a gradual decrease in chromosome size. All cytotypes have CMA+/DAPI- bands co-localized with 18S rDNA sites in the satellite region (no DAPI+ bands in any cytotype). Unlike diploids and octoploids, 5S rDNA interstitial sites in hexaploids are not in a syntenic position with 18S rDNA sites. Genome size is effective as an indirect predictor of the cytotypes since 2C-values increased according to ploidy level. The reduction in the number of the rDNA sites in polyploids associated with their lower 1Cx-values compared to diploids may suggest a genome downsizing process. Morphometric analysis revealed significant differences among cytotypes, and discriminant analysis identified three morphometric groupings corresponding to the cytotypes. The phenotypic variation observed in pollen grains, bulbs, and ovary characters suggested the gigas effect. Concluding, remarkable differentiation was observed at both genomic and phenotypic characters in all the cytotypes analyzed, suggesting a possible ongoing speciation process in H. lahue.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"63 1","pages":"e20230137"},"PeriodicalIF":2.1,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0