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1.
Trends Genet ; 40(1): 15-16, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37968205

RESUMO

We may never understand the function of all genes, findings by Freeman, Munro and colleagues suggest, unless we rethink our approaches. They make a thorough attempt at quantifying the unknownness of protein-coding genes and experimentally prove that many neglected genes hold the seed of important discoveries.


Assuntos
Genes
2.
Nucleic Acids Res ; 52(D1): D938-D949, 2024 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-38000386

RESUMO

Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.


Assuntos
Bases de Dados Factuais , Doença , Genes , Fenótipo , Humanos , Internet , Bases de Dados Factuais/normas , Software , Genes/genética , Doença/genética
3.
Nature ; 622(7981): 41-47, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37794265

RESUMO

Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.


Assuntos
Genes , Genoma Humano , Anotação de Sequência Molecular , Isoformas de Proteínas , Humanos , Genoma Humano/genética , Anotação de Sequência Molecular/normas , Anotação de Sequência Molecular/tendências , Isoformas de Proteínas/genética , Projeto Genoma Humano , Pseudogenes , RNA/genética
4.
Cambios rev. méd ; 22 (2), 2023;22(2): 919, 16 octubre 2023. ilus, tabs
Artigo em Espanhol | LILACS | ID: biblio-1516520

RESUMO

El envejecimiento y la longevidad son procesos que involucran una serie de factores genéticos, bioquímicos y ambientales. En esta revisión se tratan algunas cuestiones sobre estos dos procesos biológicos y epigenéticos. Se presentan los genes más importantes en estos procesos, así como se ejemplifican enfermedades que presentan un aceleramiento o falla en la longevidad y el envejecimiento. Se usa el análisis inteligente de datos para hallar interacciones de proteínas/genes que expliquen estos dos fenómenos biológicos.


Aging and longevity are processes that involve a series of genetic, biochemical and environmental factors. This review addresses some issues about these two biological and epigenetic processes. The most important genes in these processes are presented, as well as diseases that present an acceleration or failure in longevity and aging. Intelligent data analysis is used to find protein/gene interactions that explain these two biological phenomena.


Assuntos
Humanos , Masculino , Feminino , Idoso , Idoso de 80 Anos ou mais , Fenômenos Biológicos , Envelhecimento , Senescência Celular , Genes , Genética , Longevidade , Qualidade de Vida , Expectativa de Vida , Apoptose , Estresse Oxidativo , Telomerase , Senilidade Prematura , Equador , Sistema Imunitário , Metabolismo
5.
Mol Biol Evol ; 40(8)2023 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-37498582

RESUMO

Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is closer to the target of natural selection but gene expression is typically measured as the amount of mRNA. The broad assumption that mRNA levels are good proxies for protein levels has been undermined by a number of studies reporting moderate or weak correlations between the two measures across species. One biological explanation for this discrepancy is that there has been compensatory evolution between the mRNA level and regulation of translation. However, we do not understand the evolutionary conditions necessary for this to occur nor the expected strength of the correlation between mRNA and protein levels. Here, we develop a theoretical model for the coevolution of mRNA and protein levels and investigate the dynamics of the model over time. We find that compensatory evolution is widespread when there is stabilizing selection on the protein level; this observation held true across a variety of regulatory pathways. When the protein level is under directional selection, the mRNA level of a gene and the translation rate of the same gene were negatively correlated across lineages but positively correlated across genes. These findings help explain results from comparative studies of gene expression and potentially enable researchers to disentangle biological and statistical hypotheses for the mismatch between transcriptomic and proteomic data.


Assuntos
Evolução Molecular , Proteínas , RNA Mensageiro , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Proteínas/genética , Proteínas/metabolismo , Transcrição Gênica , Biossíntese de Proteínas , Genes , Seleção Genética , Proteômica , Perfilação da Expressão Gênica
6.
Nature ; 620(7973): 426-433, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-37468626

RESUMO

The transcriptional machinery is thought to dissociate from DNA during replication. Certain proteins, termed epigenetic marks, must be transferred from parent to daughter DNA strands in order to maintain the memory of transcriptional states1,2. These proteins are believed to re-initiate rebuilding of chromatin structure, which ultimately recruits RNA polymerase II (Pol II) to the newly replicated daughter strands. It is believed that Pol II is recruited back to active genes only after chromatin is rebuilt3,4. However, there is little experimental evidence addressing the central questions of when and how Pol II is recruited back to the daughter strands and resumes transcription. Here we show that immediately after passage of the replication fork, Pol II in complex with other general transcription proteins and immature RNA re-associates with active genes on both leading and lagging strands of nascent DNA, and rapidly resumes transcription. This suggests that the transcriptionally active Pol II complex is retained in close proximity to DNA, with a Pol II-PCNA interaction potentially underlying this retention. These findings indicate that the Pol II machinery may not require epigenetic marks to be recruited to the newly synthesized DNA during the transition from DNA replication to resumption of transcription.


Assuntos
Cromatina , Replicação do DNA , DNA , Genes , RNA Polimerase II , Transcrição Gênica , Cromatina/genética , DNA/biossíntese , DNA/genética , DNA/metabolismo , DNA Polimerase II/metabolismo , Epigênese Genética , Antígeno Nuclear de Célula em Proliferação/metabolismo , RNA Polimerase II/metabolismo , Fatores Genéricos de Transcrição/metabolismo , RNA/genética , RNA/metabolismo
7.
Nucleic Acids Res ; 51(W1): W207-W212, 2023 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-37144459

RESUMO

g:Profiler is a reliable and up-to-date functional enrichment analysis tool that supports various evidence types, identifier types and organisms. The toolset integrates many databases, including Gene Ontology, KEGG and TRANSFAC, to provide a comprehensive and in-depth analysis of gene lists. It also provides interactive and intuitive user interfaces and supports ordered queries and custom statistical backgrounds, among other settings. g:Profiler provides multiple programmatic interfaces to access its functionality. These can be easily integrated into custom workflows and external tools, making them valuable resources for researchers who want to develop their own solutions. g:Profiler has been available since 2007 and is used to analyse millions of queries. Research reproducibility and transparency are achieved by maintaining working versions of all past database releases since 2015. g:Profiler supports 849 species, including vertebrates, plants, fungi, insects and parasites, and can analyse any organism through user-uploaded custom annotation files. In this update article, we introduce a novel filtering method highlighting Gene Ontology driver terms, accompanied by new graph visualizations providing a broader context for significant Gene Ontology terms. As a leading enrichment analysis and gene list interoperability service, g:Profiler offers a valuable resource for genetics, biology and medical researchers. It is freely accessible at https://biit.cs.ut.ee/gprofiler.


Assuntos
Mapeamento Cromossômico , Biologia Computacional , Genes , Software , Animais , Mapeamento Cromossômico/instrumentação , Mapeamento Cromossômico/métodos , Bases de Dados Genéticas , Internet , Reprodutibilidade dos Testes , Interface Usuário-Computador , Biologia Computacional/instrumentação , Biologia Computacional/métodos , Genes/genética , Humanos
8.
Int. microbiol ; 26(2): 269-280, May. 2023. ilus
Artigo em Inglês | IBECS | ID: ibc-220221

RESUMO

Parasitoids, which constitute about 25% of all insects and attack arthropods of virtually all taxa, are considered the most suitable vectors for horizontal transmission of the symbiotic bacterium Wolbachia among insects. The parasitoids studied in this article develop in the larvae and pupae of ladybirds. For the first time, Wolbachia was found in parasitic wasp species of the genus Homalotylus (Hymenoptera: Encyrtidae) and from the subfamily Tetrastichinae (Hymenoptera: Eulophidae). To characterize the Wolbachia strains, six bacterial housekeeping genes were examined and compared with previously published Wolbachia gene sequences. The same bacterial strains were found in all individuals of each species of parasitic wasps collected in different places and at different times, which indicates the absence of contamination and testifies to the heritability of the symbionts in the studied chalcids. No evidence was found that the parasitic wasps were infected with Wolbachia, identical to the symbionts of their ladybirds hosts. We found one Wolbachia strain, wHom-2, which is a product of bacterial recombination from unrelated insects, including ladybirds. The lack of correspondence between the molecular phylogenies of Wolbachia strains and mitochondrial DNA of their hosts indicates horizontal transfers of Wolbachia among parasitic wasps of the genus Homalotylus and from the subfamily Tetrastichinae.(AU)


Assuntos
Humanos , Wolbachia/classificação , Filogenia , Genes , Vespas , Himenópteros , Dípteros , Insetos , Pesquisa
9.
Genet Sel Evol ; 55(1): 20, 2023 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-36959552

RESUMO

BACKGROUND: Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group. RESULTS: After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations. CONCLUSIONS: Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.


Assuntos
Adaptação Fisiológica , Galinhas , Genes , Genoma , Seleção Genética , Galinhas/classificação , Galinhas/genética , Galinhas/crescimento & desenvolvimento , Galinhas/imunologia , Animais , Genoma/genética , Adaptação Fisiológica/genética , Haplótipos , Homozigoto , Polimorfismo de Nucleotídeo Único , Itália , Predisposição Genética para Doença , Estresse Fisiológico/genética , Genética Populacional , Genômica
10.
Cells ; 12(3)2023 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-36766730

RESUMO

Genes with similar expression patterns in a set of diverse samples may be considered coexpressed. Human Gene Coexpression Analysis 2.0 (HGCA2.0) is a webtool which studies the global coexpression landscape of human genes. The website is based on the hierarchical clustering of 55,431 Homo sapiens genes based on a large-scale coexpression analysis of 3500 GTEx bulk RNA-Seq samples of healthy individuals, which were selected as the best representative samples of each tissue type. HGCA2.0 presents subclades of coexpressed genes to a gene of interest, and performs various built-in gene term enrichment analyses on the coexpressed genes, including gene ontologies, biological pathways, protein families, and diseases, while also being unique in revealing enriched transcription factors driving coexpression. HGCA2.0 has been successful in identifying not only genes with ubiquitous expression patterns, but also tissue-specific genes. Benchmarking showed that HGCA2.0 belongs to the top performing coexpression webtools, as shown by STRING analysis. HGCA2.0 creates working hypotheses for the discovery of gene partners or common biological processes that can be experimentally validated. It offers a simple and intuitive website design and user interface, as well as an API endpoint.


Assuntos
Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Genes , Humanos , RNA-Seq , Fatores de Transcrição , Genes/genética , Genes/fisiologia
11.
Braz. dent. sci ; 26(2): 1-7, 2023. ilus, tab
Artigo em Inglês | LILACS, BBO - Odontologia | ID: biblio-1427931

RESUMO

Objetivo: Evidências científicas sugerem que a deficiência de estrógeno e fatores genéticos influenciam o desenvolvimento do sistema estomatognático. Este estudo teve como objetivo avaliar a influência da deficiência de estrógeno na expressão gênica de TNF-α, IL-1ß, IL-6 e IL-10 durante o desenvolvimento dentário em modelo murino. Material e Métodos: Ratas Wistar Hannover foram divididas em dois grupos de acordo com a intervenção recebida: Grupo Hipoestrogenismo - cirurgia de ovariectomia e Grupo Controle - cirurgia fictícia. Para avaliar o desenvolvimento dentário, o incisivo inferior foi escolhido. O modelo de hipofunção dos incisivos inferiores foi realizado por ajuste incisal. O incisivo homólogo exercia hiperfunção dentária. Os animais foram avaliados durante todo o período puberal. Após a eutanásia, as hemimandíbulas foram removidas para avaliar a expressão gênica do TNF-α, IL-1ß, IL-6 e IL-10 na região odontogênica dos incisivos por meio de PCR em tempo real. Foi realizado o teste de Kruskal-Wallis e o pós-teste de Dunn. O nível de significância foi de 5%. Resultados: Houve diferenças estatisticamente significativas na expressão gênica de TNF-α e IL-1ß entre os grupos hipoestrogenismo e controle sob condição de hipofunção dentária (p=0,0084, p=0,0072, respectivamente). Conclusão: A deficiência de estrógeno influencia a expressão gênica de TNF-α e IL-1ß na região odontogênica de dentes hipofuncionais (AU)


Objective: Scientific evidence suggests that estrogen deficiency and genetic factors have an influence on the development of the stomatognathic system. This study aimed to evaluate the influence of estrogen deficiency on the gene expression of TNF-α, IL-1ß, IL-6 and IL-10 during dental development in a murine model. Material and Methods: Wistar Hannover rats were divided into two groups according to the intervention received: Hypoestrogenism Group - ovariectomy surgery and Control Group - fictitious surgery. To evaluate the dental development, the lower incisor was chosen. The mandibular incisor hypofunction model was performed by incisal adjustment. The homologous incisor exerted a hyperfunction. The animals were evaluated throughout the pubertal period. After euthanasia, the hemimandibles were removed to evaluate the gene expression of the TNF-α, IL-1ß, IL-6 and IL-10 in the odontogenic region of the incisors through real time PCR. Kruskal-Wallis test and Dunn's posttest were performed. The level of significance was 5%. Results: There were statistically significant differences of TNF-α and IL-1ß gene expression between the hypoestrogenism and control groups under hypofunction condition (p=0.0084, p=0.0072, respectively). Conclusion: Estrogen deficiency influences TNF-α and IL-1ß gene expression in the odontogenic region of the hypofunctional teeth. (AU)


Assuntos
Animais , Ratos , Osteogênese , Expressão Gênica , Citocinas , Estrogênios , Genes
12.
Afr. J. Clin. Exp. Microbiol ; 24(2): 1-8, 2023. tables
Artigo em Inglês | AIM (África) | ID: biblio-1427757

RESUMO

Artemisinin drug resistance is one of the major reasons for malaria treatment failures in the sub-Saharan African countries where artemisinin-based combination therapy (ACT) is the first-line treatment for uncomplicated malaria. The occurrence of single nucleotide polymorphisms (SNPs) is found to correlate with antimalarial drug resistance. With artemisinin, the SNPs occurs at the Kelch 13-propeller gene locus on chromosome 13. The artemisinin drug resistance surveillance strategy involves continuous monitoring of Kelch 13-propeller biomarker to detect emergence of mutations which could herald drug resistance in the region. In this narrative review paper, we examined existing literature to bridge the knowledge gap and accentuate the importance of routine surveillance for artemisinin resistance in sub-Saharan Africa. We conducted our search on PubMed database and Google Scholar to identify peer-reviewed articles, reports, and abstracts on artemisinin drug resistance using the following keywords; 'artemisinin drug resistance', 'antimalarial drug resistance', 'artemisinin-based combination therapy', 'Kelch 13-propeller', 'K13- propeller gene', and 'K13 molecular marker'. The review provided pertinent information on artemisinin derivatives, artemisinin-based combination therapy, molecular action of artemisinin, definition of artemisinin resistance, genetic basis of artemisinin drug resistance and discovery of Kelch 13, and the importance of artemisinin resistance surveillance. Molecular surveillance can provide healthcare policy makers a forecast of impending threats to malaria treatment. This is more so when drugs are in combination therapy, for instance, molecular surveillance can give a hint that one drug is failing despite the fact that in combination, it is still apparently clinically effective.


Assuntos
Humanos , Polimorfismo de Nucleotídeo Único , Malária , Resistência Capilar , Artemisininas , Genes , Conformação Molecular
13.
Braz. J. Pharm. Sci. (Online) ; 59: e21025, 2023. tab, graf
Artigo em Inglês | LILACS | ID: biblio-1439501

RESUMO

Abstract The present study investigated the effects of valerian methanolic extract and valerenic acid on the expression of LL-37 gene and protein in A549 and MRC5 line cells. After preparing Valerian seeds, sowing them in March 2020, and harvesting the rhizome in October 2020, the extract was prepared from the valerian rhizome by maceration method. Valerian acid content was determined using high performance liquid chromatography (HPLC). Two cell lines (A549 and MRC-5) were used to study the effects of valerian extract, and the MTT test was used to evaluate cell viability. The expression of LL-37 mRNA and protein was assessed by Real-Time PCR and western blot, respectively. In vivo safety assessments and histopathological analysis were also conducted. Data was analyzed by Graphpad Prism 8 software. Valerian methanolic extract and valerenic acid upregulated the LL-37 mRNA and protein expression in both treated cell lines. Valerenic acid showed a greater effect on upregulating LL-37 expression than valerian methanolic extract. A549 cells were more sensitive to valerian methanolic extract compared to MRC5 cells, and its cell viability was reduced. Furthermore, liver and kidney-related safety assessments showed that valerian methanolic extract had no toxic effects. In general, it was concluded that the methanolic extract of valerian as well as the resulting valerenic acid as the most important component of the extract has the ability to upregulate LL-37expression. Therefore, methanolic extract of valerian and valerenic acid can be considered for improving the immune system.


Assuntos
Valeriana/efeitos adversos , Extratos Vegetais/efeitos adversos , Catelicidinas/efeitos adversos , Western Blotting/instrumentação , Cromatografia Líquida de Alta Pressão/métodos , Peptídeos Catiônicos Antimicrobianos/agonistas , Células A549/classificação , Genes/genética , Fígado/anormalidades
14.
Biomédica (Bogotá) ; 42(4): 623-632, oct.-dic. 2022. tab, graf
Artigo em Inglês | LILACS | ID: biblio-1420311

RESUMO

Introduction: Amyotrophic lateral sclerosis is a neurodegenerative disease with a possible multifactorial origin characterized by the progressive degeneration of motor neurons. There is a relatively high prevalence of this disease in Antioquia; however, there is no published genetic study to date in Colombia. Despite its unknown etiopathogenesis, more genetic risk factors possibly involved in the development of this disease are constantly found. Objetives: To evaluate G93A and D90A mutations in SOD1 gene and a short tandem repeat in C9orf72 within a cohort of amyotrophic lateral sclerosis patients from Antioquia, Colombia. Materials y methods: Thirty-four patients previously diagnosed with amyotrophic lateral sclerosis were included in the study. Peripheral blood samples were used for DNA extraction and genotyping. Results: No mutations were found in SOD1 (G93A and D90A) in any of the patients, while C9orf72 exhibited an allele with a statistically significant high prevalence in the study sample (8 hexanucleotide repeats of CAGCAG). Conclusions: These results suggest an association between this short tandem repeat (STR) in C9orf72 and the presence of amyotrophic lateral sclerosis in the studied population. However, this association should be established in a larger sample size and with controls from the same population. In addition, there also seems to be a genetic anticipation effect for the disease regarding this locus, since patients with this genotype present an earlier onset.


Introducción. La esclerosis lateral amiotrófica es una enfermedad neurodegenerativa con un posible origen multifactorial, caracterizado por una degeneración progresiva de las neuronas motoras. Hay una gran prevalencia relativa de esta enfermedad en Antioquia; sin embargo, no hay publicaciones de estudios genéticos en Colombia. A pesar de su etiopatogénesis desconocida, hay varios factores de riesgo genético que se encuentran constantemente en el desarrollo de esta enfermedad. Objetivo. Evaluar las mutaciones G93A y D90A del gen SOD1 y una repetición corta en tándem (Short Tandem Repeat, STR) en el locus C9orf72, en una cohorte de pacientes con esclerosis lateral amiotrófica en Antioquia, Colombia. Materiales y métodos. Se incluyeron 34 pacientes previamente diagnosticados en el estudio. Una muestra de sangre periférica se usó para extraer el ADN y, posteriormente, genotipificarlo. Resultados. No se encontraron mutaciones en el gen SOD1 (G93A y D90A), mientras que el C9orf72 exhibe un alelo con una significativa prevalencia en los pacientes del estudio (8 repeticiones del hexanucleótido G4C2). Conclusiones. Se sugiere una asociación entre la repetición en tándem en C9orf72 y la presencia de la esclerosis lateral amiotrófica en la población estudiada. Sin embargo, se sugiere hacer estudios adicionales e incluir un grupo control de la misma población. Además, se detecta un fenómeno de anticipación genética de la enfermedad, dado que los pacientes con el alelo de 8 repeticiones en C9orf72 presentan una edad temprana de aparición de los síntomas.


Assuntos
Esclerose Amiotrófica Lateral/genética , Mutação , Doenças Neurodegenerativas , Genes
15.
An. pediatr. (2003. Ed. impr.) ; 97(4): 247-254, Oct. 2022. tab, ilus
Artigo em Espanhol | IBECS | ID: ibc-210023

RESUMO

Introducción: El hipogonadismo hipogonadotropo congénito (HHC) puede presentarse de manera aislada o acompañado de anosmia o de malformaciones congénitas. Más de 30 genes han sido implicados en la patogénesis de HHC; además, se han descrito varios patrones de herencia asociados a esta entidad. La creciente disponibilidad de técnicas de secuenciación masiva (NGS) ha permitido que aumente el rendimiento diagnóstico del estudio de esta patología. Pacientes y métodos: Evaluamos el rendimiento diagnóstico del estudio mediante NGS de pacientes con HHC, usando la secuenciación del exoma clínico filtrado por paneles virtuales. Además, se analizó si el diseño de estos paneles, basándose en la presencia/ausencia de microsmia/anosmia aumentaban este rendimiento diagnóstico. Resultados: Usando un panel virtual compuesto de 34 genes pudimos confirmar el diagnóstico de HHC en cinco de nueve pacientes (55%). En dos de nueve individuos (22%) estudiados se obtuvieron resultados no concluyentes. La ausencia/presencia de microsmia para la elección de genes a estudiar no mejora el rendimiento diagnóstico. Conclusiones: El abordaje del estudio genético de pacientes con HHC puede variar en función de las técnicas disponibles en cada centro, por lo que la sensibilidad del test utilizado variará, dependiendo si se utiliza secuenciación de paneles, exoma clínico o exoma completo. El análisis de todos los genes relacionados con HHC independientemente de la presencia/ausencia de microsmia pareciera el abordaje con mejor rendimiento. (AU)


Introduction: Congenital hypogonadotropic hypogonadism (CHH) can present alone or in association with anosmia or other congenital malformations. More than 30 genes have been identified as being involved in the pathogenesis of CHH with different patterns of inheritance, and the increasing availability of next generation sequencing (NGS) has increased the diagnostic yield. Methods: We analysed the diagnostic yield of NGS in patients with CHH using the clinical exome filtered with virtual panels. We also assessed whether designing panels based on the presence/absence of microsmia increased the diagnostic yield. Results: The use of a 34-gene virtual panel confirmed the diagnosis of CHH in 5 out of 9 patients (55%). In 2 out of 9 (22%), the findings were inconclusive. Applying the presence/absence of microsmia criterion to choose genes for analysis did not improve the diagnostic yield. Conclusions: The approach to the genetic study of patients with CHH varies depending on the resources of each healthcare facility, so the sensitivity of testing may vary substantially depending on whether panels, clinical exome sequencing or whole exome sequencing (WES) are used. The analysis of every genes related to CHH regardless of the presence/absence of microsmia seems to be the best approach. (AU)


Assuntos
Humanos , História do Século XXI , Hipogonadismo/congênito , Hipogonadismo/diagnóstico , Hipogonadismo/genética , Epidemiologia Descritiva , Genes , Síndrome de Kallmann
16.
Nat Commun ; 13(1): 5488, 2022 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-36123336

RESUMO

Single-cell gene expression data with positional information is critical to dissect mechanisms and architectures of multicellular organisms, but the potential is limited by the scalability of current data analysis strategies. Here, we present scGCO, a method based on fast optimization of hidden Markov Random Fields with graph cuts to identify spatially variable genes. Comparing to existing methods, scGCO delivers a superior performance with lower false positive rate and improved specificity, while demonstrates a more robust performance in the presence of noises. Critically, scGCO scales near linearly with inputs and demonstrates orders of magnitude better running time and memory requirement than existing methods, and could represent a valuable solution when spatial transcriptomics data grows into millions of data points and beyond.


Assuntos
Genes
17.
Nature ; 609(7929): 1038-1047, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-36171374

RESUMO

Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate-early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.


Assuntos
Proteínas de Ciclo Celular , Dano ao DNA , Reparo do DNA , Estresse Oxidativo , Regiões Promotoras Genéticas , Proteínas de Ciclo Celular/metabolismo , Cromatina/genética , Genes , Teste de Complementação Genética , Mitose , Mutação , Estresse Oxidativo/genética , Diester Fosfórico Hidrolases/metabolismo , Poli ADP Ribosilação , Regiões Promotoras Genéticas/genética , RNA/biossíntese , RNA/genética , RNA Polimerase II/metabolismo , Fuso Acromático/metabolismo , Sítio de Iniciação de Transcrição
18.
Science ; 377(6608): 802, 2022 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-35981035

RESUMO

Embryonic tissue samples reveal how pelvis shape-primed for bipedalism-comes to life.


Assuntos
Evolução Biológica , Genes , Pelve , Humanos , Locomoção , Pelve/anatomia & histologia , Pelve/embriologia
19.
Nature ; 609(7928): 747-753, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-36002568

RESUMO

Animals and fungi have radically distinct morphologies, yet both evolved within the same eukaryotic supergroup: Opisthokonta1,2. Here we reconstructed the trajectory of genetic changes that accompanied the origin of Metazoa and Fungi since the divergence of Opisthokonta with a dataset that includes four novel genomes from crucial positions in the Opisthokonta phylogeny. We show that animals arose only after the accumulation of genes functionally important for their multicellularity, a tendency that began in the pre-metazoan ancestors and later accelerated in the metazoan root. By contrast, the pre-fungal ancestors experienced net losses of most functional categories, including those gained in the path to Metazoa. On a broad-scale functional level, fungal genomes contain a higher proportion of metabolic genes and diverged less from the last common ancestor of Opisthokonta than did the gene repertoires of Metazoa. Metazoa and Fungi also show differences regarding gene gain mechanisms. Gene fusions are more prevalent in Metazoa, whereas a larger fraction of gene gains were detected as horizontal gene transfers in Fungi and protists, in agreement with the long-standing idea that transfers would be less relevant in Metazoa due to germline isolation3-5. Together, our results indicate that animals and fungi evolved under two contrasting trajectories of genetic change that predated the origin of both groups. The gradual establishment of two clearly differentiated genomic contexts thus set the stage for the emergence of Metazoa and Fungi.


Assuntos
Evolução Molecular , Fungos , Genoma , Genômica , Filogenia , Animais , Fungos/genética , Transferência Genética Horizontal , Genes , Genoma/genética , Genoma Fúngico/genética , Metabolismo/genética
20.
Medicina UPB ; 41(2): 133-144, julio-diciembre 2022.
Artigo em Inglês | LILACS, COLNAL | ID: biblio-1392154

RESUMO

The use of substances with addictive potential is a relevant health problem. Scientific evidence suggests that the underlying mechanisms that regulate behavioral processes in addictions involve a complex interplay between genetic and environmental factors. Therefore, this narrative review aims to provide a framework to synthesize the evidence on gene-environment-agent interactions from the perspective of the natural history of the disease and the stages of the addictive process for alcohol, nicotine, cannabis, psychostimulants, and opioids. In this review, we conducted an exhaustive literature search without time limits in PubMed, Ebsco, Lilacs, and SciELO, reviewing the title and abstract we selected original articles in humans or animals that addressed the etiology of addictions according to the methodological approach of gene-environment (G-E) interaction, including articles in Spanish, English, and Portuguese. Genetic studies have revealed the critical role of epigenetic modifiers (histone acetylation) in maintaining brain homeostasis in pathological conditions and focusing on G-E interactions will also allow characterizing subgroups (based on environmental factors) at high risk for addictive behaviors that can be targeted for specific interventions, Thus, treatment strategies should encompass a combination of psychosocial interventions with gene therapy involving pharmacological manipulations of histones that may contribute to design better therapies and perhaps lead to more successful management of drug dependencies.


El consumo de sustancias con potencial adictivo es un problema relevante de salud. La evidencia científica sugiere que los mecanismos subyacentes que regulan los procesos comportamentales en las adicciones involucran un complejo interjuego entre factores genéticos y ambientales. Por lo tanto, esta revisión narrativa tiene como objetivo aportar un marco de referencia que permita sintetizar la evidencia sobre interacciones genes- ambiente-agente desde la perspectiva de la historia natural de la enfermedad y los estadios del proceso adictivo para: alcohol, nicotina, cannabis, psicoestimulantes y opioides. En esta revisión realizamos una búsqueda exhaustiva de la literatura sin límites de tiempo en PubMed, Ebsco, Lilacs y SciELO, revisando el título y el resumen se seleccionaron artículos originales en humanos o animales que abordaran la etiología de las adiciones según el enfoque metodológico de interacción entre genes y ambiente (G-A), incluyendo artículos en español, inglés y portugués. Los estudios genéticos han revelado el papel crítico de los modificadores epigenéticos (acetilación de las histonas) en mantener la homeóstasis cerebral en condiciones patológicas y enfocarse en las interacciones G-A también permitirá caracterizar subgrupos (basados en los factoresambientales) de alto riesgo para conductas adictivas que pueden ser objeto de intervenciones específicas, por lo que, las estrategias de tratamiento deben englobar una combinación de intervenciones psicosociales con terapia génica que involucren las manipulaciones farmacológicas de las histonas que pueden contribuir a diseñar mejores terapias y tal vez conducir a un manejo más exitoso de las drogodependencias.


O consumo de substâncias com potencial viciante é um relevante problema de saúde. Evidências científicas sugerem que os mecanismos subjacentes que regulam os processos comportamentais em vícios envolvem uma interação complexa entre fatores genéticos e ambientais. Portanto, esta revisão narrativa visa fornecer um quadro de referência que permita sintetizar as evidências sobre interações gene-ambiente-agente sob a perspectiva da história natural da doença e as etapas do processo de dependência para: álcool, nicotina, cannabis, psicoestimulantes e opióides. Nesta revisão, realizamos uma busca exaustiva da literatura sem limites de tempo no PubMed, Ebsco , Lilacs e SciELO, revisando o título e o resumo, foram selecionados artigos originais em humanos ou animais que abordassem a etiologia dos acréscimos de acordo com a abordagem metodológica de interação entre genes e ambiente (GA), incluindo artigos em espanhol, inglês e português. Estudos genéticos revelaram o papel crítico dos modificadores epigenéticos (acetilação de histonas) na manutenção da homeostase cerebral em condições patológicas, e o direcionamento das interações GA também permitirá caracterizar subgrupos (com base em fatores ambientais) de alto risco para comportamentos aditivos que podem ser alvo de ataques específicos. intervenções, portanto, as estratégias de tratamento devem abranger uma combinação de intervenções psicossociais com terapia gênica envolvendo manipulações farmacológicas de histonas que podem contribuir para projetar melhores terapias e talvez levar a um manejo mais bem-sucedido das dependências de drogas.


Assuntos
Humanos , Animais , Comportamento Aditivo , Cannabis , Epigenômica , Genes , Analgésicos Opioides
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