Genetics and Molecular Biology最新文献_第3页

Erratum: 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? 勘误：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 : 2024-11-22 DOI: 10.1590/1678-4685-GMB-2023-0127er

引用次数: 0

Phylogenomic Analysis of Dichrocephala benthamii and Comparative Analysis within Tribe Astereae (Asteraceae). Dichrocephala benthamii 的系统发生组分析和菊科（Asteraceae）内的比较分析。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-10-21 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0340

Hui Chen, Tingyu Li, Xinyu Chen, Xinyi Zheng, Tianmeng Qu, Bo Li, Zhixi Fu

{"title":"Phylogenomic Analysis of Dichrocephala benthamii and Comparative Analysis within Tribe Astereae (Asteraceae).","authors":"Hui Chen, Tingyu Li, Xinyu Chen, Xinyi Zheng, Tianmeng Qu, Bo Li, Zhixi Fu","doi":"10.1590/1678-4685-GMB-2023-0340","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2023-0340","url":null,"abstract":"Dichrocephala benthamii C. B. Clarke has long been used as traditional Chinese medicine. However, the chloroplast (cp) genome of D. benthamii is poorly understood so far. In this study, we sequenced and analyzed the cp genome of D. benthamii. The results showed that the cp genome is 152,350 bp in length, with a pair of inverted repeat regions (IRa and IRb, each 24,982 bp), a large single-copy (LSC) region comprising 84,136 bp, and a small single-copy (SSC) region comprising 18,250 bp. The GC content of the cp genome was 37.3%. A total of 134 genes were identified, including 87 protein-coding genes (CDS), 38 tRNA genes, 8 rRNA genes, and 1 pseudogene (ycf1). Expansion or contraction of IR regions were detected in D. benthamii and other species of the tribe Astereae. Additionally, our analyses showed the types of sequence repeats and the highly variable regions discovered by analyzing the border regions, sequence divergence, and hot spots. The phylogenetic analysis revealed D. benthamii is the basal group of Astereae. The results of this study will be a significant contribution to the genetics and species identification related to D. benthamii.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 4","pages":"e20230340"},"PeriodicalIF":1.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11495966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498597","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

The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system. 具有 ZZ/ZW 性染色体系统的新热带鱼 Apareiodon sp.

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-10-11 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0098

Ivan Rodrigo Wolf, Michelle Orane Schemberger, Matheus Azambuja, Fernanda Souza de Oliveira, Viviane Nogaroto, Guilherme Targino Valente, Cesar Martins, Marcelo Ricardo Vicari

{"title":"The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system.","authors":"Ivan Rodrigo Wolf, Michelle Orane Schemberger, Matheus Azambuja, Fernanda Souza de Oliveira, Viviane Nogaroto, Guilherme Targino Valente, Cesar Martins, Marcelo Ricardo Vicari","doi":"10.1590/1678-4685-GMB-2024-0098","DOIUrl":"10.1590/1678-4685-GMB-2024-0098","url":null,"abstract":"Neotropical fishes emerge as an extremely diverse group of vertebrates where genomic strategies to evaluate structural and functional features are still beginning. Here, we present a second draft genome of Apareiodon sp. (2n=54, ZZ/ZW), adding PacBio technology whole genome sequencing, and assembling by combining two technologies (long and short reads). Using a detailed strategy for genome assembly with fish genomes of Pygocentrus nattereri, Carassius auratus, and Astyanax mexicanus as references, the final assembly of the Apareiodon sp. genome generated 93 scaffolds, an N50 of 37,200,078 bases, and a size estimate considering 28 scaffolds (26 autosomes+ZW) of ~945 Mb. In Apareiodon sp., this second genome draft confirmed that ~36% of the genome is composed of repetitive DNA. Furthermore, the new draft genome has improved genomic quality assessments, allowing the annotation of 36,290 genes and 15,683 proteins, which presented similarities to reference genomes. The second draft genome of Apareiodon sp. will be useful for research on integrative cytogenetic and genomic data. It will open perspectives for analyzing sex-determining genes in Neotropical fish with a ZZ/ZW sex chromosome system.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 4","pages":"e20240098"},"PeriodicalIF":1.7,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11468460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406322","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

What we know so far and what we can expect next: A molecular investigation of plant parasitism. 我们目前所知道的和我们可以期待的下一步：植物寄生的分子研究。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-30 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0051

Juliane Karine Ishida, Elaine Cotrim Costa

引用次数: 0

Lack of genotoxicity of iron oxide maghemite (γ-Fe2O3) and magnetite (Fe3O4) nanoparticles to Oreochromis niloticus after acute exposures. 氧化铁磁铁矿（γ-Fe2O3）和磁铁矿（Fe3O4）纳米粒子在急性暴露后对裸鲤无遗传毒性。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-20 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB2023-0330

Maria Luiza Fascineli, Paolin Rocio Cáceres-Vélez, Willie Oliveira Pinheiro, Sacha Braun Chaves, Marcelo Henrique Sousa, Wilson Sacchi Peternella, Frederico Hillesheim Horst, Michele de Castro Fernandes, Wania Guimarães, Ricardo Bentes Azevedo, Cesar Koppe Grisolia

{"title":"Lack of genotoxicity of iron oxide maghemite (γ-Fe2O3) and magnetite (Fe3O4) nanoparticles to Oreochromis niloticus after acute exposures.","authors":"Maria Luiza Fascineli, Paolin Rocio Cáceres-Vélez, Willie Oliveira Pinheiro, Sacha Braun Chaves, Marcelo Henrique Sousa, Wilson Sacchi Peternella, Frederico Hillesheim Horst, Michele de Castro Fernandes, Wania Guimarães, Ricardo Bentes Azevedo, Cesar Koppe Grisolia","doi":"10.1590/1678-4685-GMB2023-0330","DOIUrl":"10.1590/1678-4685-GMB2023-0330","url":null,"abstract":"Iron oxide nanoparticles (FeO-NPs) are widely used in scientific and technological fields. Environmental concerns have been raised about residual FeO-NPs levels as their toxicity and bioaccumulative potential are not well understood. Oreochromis niloticus were exposed to nanoparticles of γ-Fe2O3 and Fe3O4. Micro-CT 3D image and grayscale graphic assessments revealed the accumulation of radiopaque material in the digestive tract of fish exposed to FeO-NPs. Histological analysis showed the presence of such NPs in the hepatopancreas, gills, kidneys, and muscles. No genotoxicity occurred, through micronucleus test and comet assay in peripheral erythrocytes. Body clearance was confirmed by iron-content reduction in organisms exposed to FeO-NPs after recovery period. No tissue injuries were observed in the exposed animals which may be attributed to the absence or low toxicity of iron oxide nanoparticles under the study conditions. O. niloticus showed tolerance to sublethal exposures to FeO-NPs.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230330"},"PeriodicalIF":1.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142618179","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

Expression of the C-allele of intronic rs8192675 in SLC2A2 is associated with improved glucose response to metformin. SLC2A2 内含子 rs8192675 的 C-等位基因表达与改善葡萄糖对二甲双胍的反应有关。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-20 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0281

Wanjun Wang, Suying Chen, Yilei Jiang, Jianhong Ji, Ruochen Cong

{"title":"Expression of the C-allele of intronic rs8192675 in SLC2A2 is associated with improved glucose response to metformin.","authors":"Wanjun Wang, Suying Chen, Yilei Jiang, Jianhong Ji, Ruochen Cong","doi":"10.1590/1678-4685-GMB-2023-0281","DOIUrl":"10.1590/1678-4685-GMB-2023-0281","url":null,"abstract":"Glucose is a critical nutrient for energy metabolism. The SLC2A2 gene is essential for glucose sensing and homeostasis, as it encodes the facilitated glucose transporter GLUT2. During diabetes treatment, the C-allele of rs8192675 in SLC2A2 has been found to regulate the action of metformin and reduce the absolute level of HbA1c more effectively than the T-allele. In this study, stable HEK293T cell lines carrying the CC, CT, and TT genotypes of rs8192675 in SLC2A2 were generated using CRISPR/Cas9-mediated genome editing. GLUT2 mRNA and protein levels were elevated in cell clones with the TC genotype compared to those with the CC genotype but were reduced relative to the TT genotype. Additionally, high concentrations of glucose or fructose induced more GLUT2 protein production in CT-genotype cells than that induced in CC-genotype cells, yet less than that induced in TT-genotype cells. Metformin induced a greater increase in GLUT2 expression and a smaller increase in activated AMPK protein expression in CC-genotype cells than those induced in TT-genotype cells, resulting in a remarkable reduction in activated mTOR and S6 levels. This study directly supports the biological mechanism linking the C-allele of rs8192675 with improved treatment outcomes in metformin therapy for diabetes.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 3","pages":"e20230281"},"PeriodicalIF":1.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142618166","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

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