Genetics and Molecular Biology最新文献_第10页

Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis. 打破沉默：通过计算分析在人类外显子组中发现 22,841 个预测的有害同义变异。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-22 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0125

Ana Carolina Mello, Delva Leao, Luis Dias, Felipe Colombelli, Mariana Recamonde-Mendoza, Andreia Carina Turchetto-Zolet, Ursula Matte

{"title":"Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis.","authors":"Ana Carolina Mello, Delva Leao, Luis Dias, Felipe Colombelli, Mariana Recamonde-Mendoza, Andreia Carina Turchetto-Zolet, Ursula Matte","doi":"10.1590/1678-4685-GMB-2023-0125","DOIUrl":"10.1590/1678-4685-GMB-2023-0125","url":null,"abstract":"Synonymous single nucleotide variants (sSNVs) do not alter the primary structure of a protein, thus it was previously accepted that they were neutral. Recently, several studies demonstrated their significance to a range of diseases. Still, variant prioritization strategies lack focus on sSNVs. Here, we identified 22,841 deleterious synonymous variants in 125,748 human exomes using two in silico predictors (SilVA and CADD). While 98.2% of synonymous variants are classified as neutral, 1.8% are predicted to be deleterious, yielding an average of 9.82 neutral and 0.18 deleterious sSNVs per exome. Further investigation of prediction features via Heterogeneous Ensemble Feature Selection revealed that impact on amino acid sequence and conservation carry the most weight for a deleterious prediction. Thirty nine detrimental sSNVs are not rare and are located on disease associated genes. Ten distinct putatively non-deleterious sSNVs are likely to be under positive selection in the North-Western European and East Asian populations. Taken together our analysis gives voice to the so-called silent mutations as we propose a robust framework for evaluating the deleteriousness of sSNVs in variant prioritization studies.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230125"},"PeriodicalIF":1.7,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520515","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

Tailed bacteriophages (Caudoviricetes) dominate the microbiome of a diseased stingless bee. 尾部噬菌体（Caudoviricetes）在患病无刺蜂的微生物组中占主导地位。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0120

Lilian Caesar, Karen Luisa Haag

{"title":"Tailed bacteriophages (Caudoviricetes) dominate the microbiome of a diseased stingless bee.","authors":"Lilian Caesar, Karen Luisa Haag","doi":"10.1590/1678-4685-GMB-2023-0120","DOIUrl":"10.1590/1678-4685-GMB-2023-0120","url":null,"abstract":"Bacteriophages, viruses that infect bacterial hosts, are known to rule the dynamics and diversity of bacterial populations in a number of ecosystems. Bacterial communities residing in the gut of animals, known as the gut microbiome, have revolutionized our understanding of many diseases. However, the gut phageome, while of apparent importance in this context, remains an underexplored area of research. Here we identify for the first time genomic sequences from tailed viruses (Caudoviricetes) that are associated with the microbiome of stingless bees (Melipona quadrifasciata). Both DNA and RNA were extracted from virus particles isolated from healthy and diseased forager bees, the latter showing symptoms from an annual syndrome that only affects M. quadrifasciata. Viral contigs from previously sequenced metagenomes of healthy and diseased forager bees were used for the analyses. Using conserved proteins deduced from their genomes, we found that Caudoviricetes were only present in the worker bee gut microbiome from diseased stingless bees. The most abundant phages are phylogenetically related to phages that infect Gram-positive bacteria from the order Lactobacillales and Gram-negative bacteria from the genus Gilliamella and Bartonella, that are common honey bee symbionts. The potential implication of these viruses in the M. quadrifasciata syndrome is discussed.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230120"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512370","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

Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites. 位置权重矩阵或循环概率有限自动机：使用哪种模型？用于预测转录因子结合位点的决策规则推论。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0048

Guilherme Miura Lavezzo, Marcelo de Souza Lauretto, Luiz Paulo Moura Andrioli, Ariane Machado-Lima

{"title":"Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites.","authors":"Guilherme Miura Lavezzo, Marcelo de Souza Lauretto, Luiz Paulo Moura Andrioli, Ariane Machado-Lima","doi":"10.1590/1678-4685-GMB-2023-0048","DOIUrl":"10.1590/1678-4685-GMB-2023-0048","url":null,"abstract":"Prediction of transcription factor binding sites (TFBS) is an example of application of Bioinformatics where DNA molecules are represented as sequences of A, C, G and T symbols. The most used model in this problem is Position Weight Matrix (PWM). Notwithstanding the advantage of being simple, PWMs cannot capture dependency between nucleotide positions, which may affect prediction performance. Acyclic Probabilistic Finite Automata (APFA) is an alternative model able to accommodate position dependencies. However, APFA is a more complex model, which means more parameters have to be learned. In this paper, we propose an innovative method to identify when position dependencies influence preference for PWMs or APFAs. This implied using position dependency features extracted from 1106 sets of TFBS to infer a decision tree able to predict which is the best model - PWM or APFA - for a given set of TFBSs. According to our results, as few as three pinpointed features are able to choose the best model, providing a balance of performance (average precision) and model simplicity.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 4","pages":"e20230048"},"PeriodicalIF":2.1,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10945726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570329","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

Adaptive strategies of aquatic mammals: Exploring the role of the HIF pathway and hypoxia tolerance. 水生哺乳动物的适应策略：探索 HIF 通路和耐缺氧性的作用。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0140

Yuri Yépez, Mariana Marcano-Ruiz, Maria Cátira Bortolini

{"title":"Adaptive strategies of aquatic mammals: Exploring the role of the HIF pathway and hypoxia tolerance.","authors":"Yuri Yépez, Mariana Marcano-Ruiz, Maria Cátira Bortolini","doi":"10.1590/1678-4685-GMB-2023-0140","DOIUrl":"10.1590/1678-4685-GMB-2023-0140","url":null,"abstract":"Aquatic mammals (marine and freshwater species) share significant and similar adaptations, enabling them to tolerate hypoxia during regular breath-hold diving. Despite the established importance of HIF1A, a master regulator in the molecular mechanism of hypoxia response, and other associated genes, their role in the evolutionary adaptation of aquatic mammals is not fully understood. In this study, we investigated this topic by employing a candidate gene approach to analyze 11 critical genes involved in the HIF1A signaling pathway in aquatic mammals. Our gene analyses included evaluating positive and negative selection, relaxation or constriction of selection, and molecular convergence compared to other terrestrial mammals, including subterranean mammals. Evidence of selection suggested a significant role of negative selection, as well as relaxation of the selective regime in cetaceans for most of these genes. We found that the glutamine 68 variant in the HIF3α protein is unique to cetaceans and initial evaluations indicated a destabilizing effect on protein structure. However, further analyses are necessary to evaluate its functional impact and adaptive relevance in this taxon.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230140"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512324","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

Gene-environment interactions and preterm birth predictors: A Bayesian network approach. 基因-环境相互作用与早产预测因素：贝叶斯网络方法

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0090

Dario E Elias, Maria R Santos, Hebe Campaña, Fernando A Poletta, Silvina L Heisecke, Juan A Gili, Julia Ratowiecki, Viviana R Cosentino, Rocio Uranga, Diana Rojas Málaga, Alice Brinckmann Oliveira Netto, Ana Carolina Brusius-Facchin, César Saleme, Mónica Rittler, Hugo B Krupitzki, Jorge S Lopez Camelo, Lucas G Gimenez

{"title":"Gene-environment interactions and preterm birth predictors: A Bayesian network approach.","authors":"Dario E Elias, Maria R Santos, Hebe Campaña, Fernando A Poletta, Silvina L Heisecke, Juan A Gili, Julia Ratowiecki, Viviana R Cosentino, Rocio Uranga, Diana Rojas Málaga, Alice Brinckmann Oliveira Netto, Ana Carolina Brusius-Facchin, César Saleme, Mónica Rittler, Hugo B Krupitzki, Jorge S Lopez Camelo, Lucas G Gimenez","doi":"10.1590/1678-4685-GMB-2023-0090","DOIUrl":"10.1590/1678-4685-GMB-2023-0090","url":null,"abstract":"Preterm birth (PTB) is the main condition related to perinatal morbimortality worldwide. The aim of this study was to identify gene-environment interactions associated with spontaneous PTB or its predictors. We carried out a retrospective case-control study including parental sociodemographic and obstetric data as well as newborn genetic variants of 69 preterm and 61 at term newborns born at a maternity hospital from Tucumán, Argentina, between 2005 and 2010. A data-driven Bayesian network including the main PTB predictors was created where we identified gene-environment interactions. We used logistic regressions to calculate the odds ratios and confidence intervals of the interactions. From the main PTB predictors (nine exposures and six genetic variants) we identified an interaction between low neighbourhood socioeconomic status and rs2074351 (PON1, genotype GG) variant that was associated with an increased risk of toxoplasmosis (odds ratio 12.51, confidence interval 95%: 1.71 - 91.36). The results of this exploratory study suggest that structural social disparities could influence the PTB risk by increasing the frequency of exposures that potentiate the risk associated with individual characteristics such as genetic traits. Future studies with larger sample sizes are necessary to confirm these findings.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 4","pages":"e20230090"},"PeriodicalIF":2.1,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570318","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

Exploring the frequency of a TP53 polyadenylation signal variant in tumor DNA from patients diagnosed with lung adenocarcinomas, sarcomas and uterine leiomyomas. 探索肺腺癌、肉瘤和子宫肌瘤患者肿瘤 DNA 中 TP53 多腺苷酸化信号变异的频率。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0133

Igor Araujo Vieira, Guilherme Danielski Viola, Eduarda Heidrich Pezzi, Thayne Woycinck Kowalski, Bruna Vieira Fernandes, Tiago Finger Andreis, Natascha Bom, Giulianna Sonnenstrahl, Yasminne Marinho de Araújo Rocha, Bruno da Silveira Corrêa, Luiza Mezzomo Donatti, Gabriela Dos Santos Sant'Anna, Helena von Eye Corleta, Ilma Simoni Brum, Clévia Rosset, Fernanda Sales Luiz Vianna, Gabriel S Macedo, Edenir Inez Palmero, Patricia Ashton-Prolla

{"title":"Exploring the frequency of a TP53 polyadenylation signal variant in tumor DNA from patients diagnosed with lung adenocarcinomas, sarcomas and uterine leiomyomas.","authors":"Igor Araujo Vieira, Guilherme Danielski Viola, Eduarda Heidrich Pezzi, Thayne Woycinck Kowalski, Bruna Vieira Fernandes, Tiago Finger Andreis, Natascha Bom, Giulianna Sonnenstrahl, Yasminne Marinho de Araújo Rocha, Bruno da Silveira Corrêa, Luiza Mezzomo Donatti, Gabriela Dos Santos Sant'Anna, Helena von Eye Corleta, Ilma Simoni Brum, Clévia Rosset, Fernanda Sales Luiz Vianna, Gabriel S Macedo, Edenir Inez Palmero, Patricia Ashton-Prolla","doi":"10.1590/1678-4685-GMB-2023-0133","DOIUrl":"10.1590/1678-4685-GMB-2023-0133","url":null,"abstract":"The TP53 3'UTR variant rs78378222 A>C has been detected in different tumor types as a somatic alteration that reduces p53 expression through modification of polyadenylation and miRNA regulation. Its prevalence is not yet known in all tumors. Herein, we examine tumor tissue prevalence of rs7837822 in Brazilian cohorts of patients from south and southeast regions diagnosed with lung adenocarcinoma (LUAD, n=586), sarcoma (SARC, n=188) and uterine leiomyoma (ULM, n=41). The minor allele (C) was identified in heterozygosity in 6/586 LUAD tumors (prevalence = 1.02 %) and none of the SARC and ULM samples. Additionally, next generation sequencing analysis revealed that all variant-positive tumors (n=4) with sample availability had additional pathogenic or likely pathogenic somatic variants in the TP53 coding regions. Among them, 3/4 (75 %) had the same pathogenic or likely pathogenic sequence variant (allele frequency <0.05 in tumor DNA) namely c.751A>C (p.Ile251Leu). Our results indicate a low somatic prevalence of rs78378222 in LUAD, ULM and SARC tumors from Brazilian patients, which suggests that no further analysis of this variant in the specific studied regions of Brazil is warranted. However, these findings should not exclude tumor molecular testing of this TP53 3'UTR functional variant for different populations.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230133"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512326","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

Microcephaly in South Brazil: Are cases of Congenital Zika Syndrome increasing in recent years? 南巴西的小头畸形：先天性寨卡综合征病例近年来是否有所增加？

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0191

Anna Pires Terra, Ricardo Rohweder, Silvani Herber, Luciana Friedrich, Maria Teresa Vieira Sanseverino, Catia Favreto, Fernanda Santa Maria, Emilly de Jesus Athayde, Laércio Moreira Cardoso-Júnior, Andrea Cristina Pereira Marinho, Allanamara Pereira Marinho, Tailine Zarpelon, Lavínia Schuler-Faccini

{"title":"Microcephaly in South Brazil: Are cases of Congenital Zika Syndrome increasing in recent years?","authors":"Anna Pires Terra, Ricardo Rohweder, Silvani Herber, Luciana Friedrich, Maria Teresa Vieira Sanseverino, Catia Favreto, Fernanda Santa Maria, Emilly de Jesus Athayde, Laércio Moreira Cardoso-Júnior, Andrea Cristina Pereira Marinho, Allanamara Pereira Marinho, Tailine Zarpelon, Lavínia Schuler-Faccini","doi":"10.1590/1678-4685-GMB-2023-0191","DOIUrl":"10.1590/1678-4685-GMB-2023-0191","url":null,"abstract":"Northeast Brazil was the first region to detect a significant increase in babies born with microcephaly associated with prenatal zika virus infection in 2015. Rio Grande do Sul (RS) state was less impacted due to the temperate climate preventing the spread of the vector. This study investigated the prevalence and etiology of congenital microcephaly in RS in two different periods. This cross-sectional descriptive study included all live births with congenital microcephaly in RS from 2015 to 2022. Cases were divided into two groups: P1 \"outbreak\" (2015-16); and P2 \"endemic\" (2017-22). There were 58 cases of microcephaly (3.8/10,000) in P1 and 148 (1.97/10,000) in P2. Congenital Zika Virus infection was the etiology in 5.2% (n=3) in P1 and 6.7% (n=10) in P2. In conclusion, although the ZIKV outbreak in Brazil has receded, RS remains an area of concern, with a possible slight increase of live births with microcephaly secondary to ZIKV prenatal infection relative to the number of cases due to congenital infections. The broader distribution of the vector Aedes aegypti with warmer temperatures in our state might be linked to the increase in recent years. This study can be an alert to other regions of temperate or subtropical climates.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230191"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512369","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

Human genetic determinants of COVID-19 in Brazil: challenges and future plans. 巴西 COVID-19 的人类基因决定因素：挑战与未来计划。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-15 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0128

Bibiana S de Oliveira Fam, Marilea Furtado Feira, Nathan Araujo Cadore, Renan Sbruzzi, Tábita Hünemeier, Laurent Abel, Qian Zhang, Jean-Laurent Casanova, Fernanda Sales Luiz Vianna

{"title":"Human genetic determinants of COVID-19 in Brazil: challenges and future plans.","authors":"Bibiana S de Oliveira Fam, Marilea Furtado Feira, Nathan Araujo Cadore, Renan Sbruzzi, Tábita Hünemeier, Laurent Abel, Qian Zhang, Jean-Laurent Casanova, Fernanda Sales Luiz Vianna","doi":"10.1590/1678-4685-GMB-2023-0128","DOIUrl":"10.1590/1678-4685-GMB-2023-0128","url":null,"abstract":"COVID-19 pandemic represented a worldwide major challenge in different areas, and efforts undertaken by the scientific community led to the understanding of some of the genetic determinants that influence the different COVID-19 outcomes. In this paper, we review the studies about the role of human genetics in COVID-19 severity and how Brazilian studies also contributed to those findings. Rare variants in genes related to Inborn Errors of Immunity (IEI) in the type I interferons pathway, and its phenocopies, have been described as being causative of severe outcomes. IEI and its phenocopies are present in Brazil, not only in COVID-19 patients, but also in autoimmune conditions and severe reactions to yellow fever vaccine. In addition, studies focusing on common variants and GWAS studies encompassing worldwide patients have found several loci associated with COVID-19 severity. A GWAS study including only Brazilian COVID-19 patients identified a new locus 1q32.1 associated with COVID-19 severity. Thus, more comprehensive studies considering the Brazilian genomic diversity should be performed, since they can help to reveal not only what are the genetic determinants that contribute to the different outcomes for COVID-19 in the Brazilian population, but in the understanding of human genetics in different health conditions.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230128"},"PeriodicalIF":1.7,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10792479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139471972","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

Identification and characterization of waterlogging-responsive genes in the parental line of maize hybrid An'nong 876. 玉米杂交种 "安农 876 "亲本系水涝响应基因的鉴定和特征描述

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-08 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0026

Hongying Wu, Haitao Yu, Xingen Zhang, Yixiao Wang, Hongjia Zhu, Yang Zhao, Qing Ma

{"title":"Identification and characterization of waterlogging-responsive genes in the parental line of maize hybrid An'nong 876.","authors":"Hongying Wu, Haitao Yu, Xingen Zhang, Yixiao Wang, Hongjia Zhu, Yang Zhao, Qing Ma","doi":"10.1590/1678-4685-GMB-2023-0026","DOIUrl":"10.1590/1678-4685-GMB-2023-0026","url":null,"abstract":"Waterlogging stress is an important abiotic stress that adversely affects maize growth and yield. The mechanism regulating the early stage of the maize response to waterlogging stress is largely unknown. In this study, CM37 and cmh15 seedlings were treated with waterlogging stress and then examined in terms of their physiological changes. The results indicated that inbred line cmh15 is more tolerant to waterlogging stress and less susceptible to peroxide-based damages than CM37. The RNA sequencing analysis identified 1,359 down-regulated genes and 830 up-regulated genes in the waterlogging-treated cmh15 plants (relative to the corresponding control levels). According to the Gene Ontology analysis for the differentially expressed genes (DEGs), some important terms were identified which may play important roles in the response to waterlogging stress. Moreover, enriched Kyoto Encyclopedia of Genes and Genomes pathways were also identified for the DEGs. Furthermore, the substantial changes in the expression of 36 key transcription factors may be closely related to the maize in response to waterlogging stress. This study offers important insights into the mechanism in regulating maize tolerance to waterlogging stress, with important foundations for future research.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 4","pages":"e20230026"},"PeriodicalIF":2.1,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10789244/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139471976","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

Global DNA methylation patterns in Alcohol Use Disorder. 酒精使用障碍的全球 DNA 甲基化模式。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-08 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0139

Jaqueline B Schuch, Cibele E Bandeira, Jorge L S Junior, Diana Müller, Mariele F Charão, Bruna S da Silva, Eugenio H Grevet, Felix H P Kessler, Lisia von Diemen, Diego L Rovaris, Claiton H D Bau

{"title":"Global DNA methylation patterns in Alcohol Use Disorder.","authors":"Jaqueline B Schuch, Cibele E Bandeira, Jorge L S Junior, Diana Müller, Mariele F Charão, Bruna S da Silva, Eugenio H Grevet, Felix H P Kessler, Lisia von Diemen, Diego L Rovaris, Claiton H D Bau","doi":"10.1590/1678-4685-GMB-2023-0139","DOIUrl":"10.1590/1678-4685-GMB-2023-0139","url":null,"abstract":"Alcohol Use Disorder (AUD) is a highly prevalent condition worldwide that produces a wide range of pathophysiological consequences, with a critical impact on health and social issues. Alcohol influences gene expression through epigenetic changes mainly through DNA methylation. In this sense, levels of 5-methylcytosine (5-mC), namely Global DNA methylation (GMe), which can be influenced by environmental and hormonal effects, represent a putative biological mechanism underlying alcohol effects. Our aim was to investigate the influence of AUD diagnosis and alcohol patterns (i.e., years of addiction, use in the last 30 days, and alcohol severity) on GMe levels. The sample consisted of 256 men diagnosed with AUD and 361 men without AUD. DNA samples from peripheral blood were used to assess GMe levels, measured through the levels of 5-mC using high-performance liquid chromatography. Results from multiple linear regression analysis indicated that the presence of AUD was associated with lower GMe levels (beta=-0.155, p=0.011). Other alcohol-related outcomes were not associated with DNA methylation. Our findings are consistent with the hypothesis that the impact of chronic and heavy alcohol use in GMe could be a potential mechanism mediating the multiple organ damages related to AUD.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230139"},"PeriodicalIF":2.1,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10778554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139402558","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