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1.
PLoS Comput Biol ; 16(9): e1008269, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32941419

RESUMO

We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping enables visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Subtyping thereby advances the development of effective containment strategies and, potentially, therapeutic and vaccine strategies. However, identifying viral subtypes in real-time is challenging: SARS-CoV-2 is a novel virus, and the pandemic is rapidly expanding. Viral subtypes may be difficult to detect due to rapid evolution; founder effects are more significant than selection pressure; and the clustering threshold for subtyping is not standardized. We propose to identify mutational signatures of available SARS-CoV-2 sequences using a population-based approach: an entropy measure followed by frequency analysis. These signatures, Informative Subtype Markers (ISMs), define a compact set of nucleotide sites that characterize the most variable (and thus most informative) positions in the viral genomes sequenced from different individuals. Through ISM compression, we find that certain distant nucleotide variants covary, including non-coding and ORF1ab sites covarying with the D614G spike protein mutation which has become increasingly prevalent as the pandemic has spread. ISMs are also useful for downstream analyses, such as spatiotemporal visualization of viral dynamics. By analyzing sequence data available in the GISAID database, we validate the utility of ISM-based subtyping by comparing spatiotemporal analyses using ISMs to epidemiological studies of viral transmission in Asia, Europe, and the United States. In addition, we show the relationship of ISMs to phylogenetic reconstructions of SARS-CoV-2 evolution, and therefore, ISMs can play an important complementary role to phylogenetic tree-based analysis, such as is done in the Nextstrain project. The developed pipeline dynamically generates ISMs for newly added SARS-CoV-2 sequences and updates the visualization of pandemic spatiotemporal dynamics, and is available on Github at https://github.com/EESI/ISM (Jupyter notebook), https://github.com/EESI/ncov_ism (command line tool) and via an interactive website at https://covid19-ism.coe.drexel.edu/.


Assuntos
Betacoronavirus/classificação , Betacoronavirus/genética , Infecções por Coronavirus , Genômica/métodos , Pandemias , Pneumonia Viral , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Evolução Molecular , Marcadores Genéticos/genética , Genoma Viral/genética , Humanos , Mutação/genética , Filogenia , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , RNA Viral/genética , Alinhamento de Sequência , Análise de Sequência de RNA , Análise Espaço-Temporal
2.
PLoS Comput Biol ; 16(9): e1008269, 2020 09.
Artigo em Inglês | MEDLINE | ID: covidwho-771817

RESUMO

We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping enables visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Subtyping thereby advances the development of effective containment strategies and, potentially, therapeutic and vaccine strategies. However, identifying viral subtypes in real-time is challenging: SARS-CoV-2 is a novel virus, and the pandemic is rapidly expanding. Viral subtypes may be difficult to detect due to rapid evolution; founder effects are more significant than selection pressure; and the clustering threshold for subtyping is not standardized. We propose to identify mutational signatures of available SARS-CoV-2 sequences using a population-based approach: an entropy measure followed by frequency analysis. These signatures, Informative Subtype Markers (ISMs), define a compact set of nucleotide sites that characterize the most variable (and thus most informative) positions in the viral genomes sequenced from different individuals. Through ISM compression, we find that certain distant nucleotide variants covary, including non-coding and ORF1ab sites covarying with the D614G spike protein mutation which has become increasingly prevalent as the pandemic has spread. ISMs are also useful for downstream analyses, such as spatiotemporal visualization of viral dynamics. By analyzing sequence data available in the GISAID database, we validate the utility of ISM-based subtyping by comparing spatiotemporal analyses using ISMs to epidemiological studies of viral transmission in Asia, Europe, and the United States. In addition, we show the relationship of ISMs to phylogenetic reconstructions of SARS-CoV-2 evolution, and therefore, ISMs can play an important complementary role to phylogenetic tree-based analysis, such as is done in the Nextstrain project. The developed pipeline dynamically generates ISMs for newly added SARS-CoV-2 sequences and updates the visualization of pandemic spatiotemporal dynamics, and is available on Github at https://github.com/EESI/ISM (Jupyter notebook), https://github.com/EESI/ncov_ism (command line tool) and via an interactive website at https://covid19-ism.coe.drexel.edu/.


Assuntos
Betacoronavirus/classificação , Betacoronavirus/genética , Infecções por Coronavirus , Genômica/métodos , Pandemias , Pneumonia Viral , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Evolução Molecular , Marcadores Genéticos/genética , Genoma Viral/genética , Humanos , Mutação/genética , Filogenia , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , RNA Viral/genética , Alinhamento de Sequência , Análise de Sequência de RNA , Análise Espaço-Temporal
3.
Plant Mol Biol ; 104(1-2): 173-185, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32734417

RESUMO

KEY MESSAGE: A novel and major QTL for the effective tiller number was identified on chromosomal arm 1BL and validated in two genetic backgrounds The effective tiller number (ETN) substantially influences plant architecture and the wheat yield improvement. In this study, we constructed a genetic map of the 2SY (20828/SY95-71) recombinant inbred line population based on the Wheat 55K array as well as the simple sequence repeat (SSR) and Kompetitive Allele Specific PCR (KASP) markers. A comparison between the genetic and physical maps indicated the marker positions were consistent in the two maps. Additionally, we identified seven tillering-related quantitative trait locus (QTLs), including Qetn-sau-1B.1, which is a major QTL localized to a 6.17-cM interval flanked by markers AX-89635557 and AX-111544678 on chromosome 1BL. The Qetn-sau-1B.1 QTL was detected in eight environments and explained 12.12-55.71% of the phenotypic variance. Three genes associated with the ETN were detected in the physical interval of Qetn-sau-1B.1. We used a tightly linked KASP marker, KASP-AX-110129912, to further validate this QTL in two other populations with different genetic backgrounds. The results indicated that Qetn-sau-1B.1 significantly increased the ETN by up to 23.5%. The results of this study will be useful for the precise mapping and cloning of Qetn-sau-1B.1.


Assuntos
Cromossomos de Plantas , Locos de Características Quantitativas/genética , Triticum/genética , Bangladesh , Mapeamento Cromossômico , Marcadores Genéticos/genética , Genótipo , Repetições de Microssatélites , Anotação de Sequência Molecular , Fenótipo
4.
PLoS One ; 15(8): e0237405, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32817702

RESUMO

Expression of proteins in the chloroplast or mitochondria of the model green alga Chlamydomonas reinhardtii can be achieved by directly inserting transgenes into organellar genomes, or through nuclear expression and post-translational import. A number of tools have been developed in the literature for achieving high expression levels from the nuclear genome despite messy genomic integration and widespread silencing of transgenes. Here, recent advances in the field are combined and two systems of bicistronic expression, based on ribosome reinitiation or ribosomal skip induced by a viral 2A sequence, are compared side-by-side. Further, the small subunit of Rubisco (RBCS) was developed as a functional nuclear reporter for successful chloroplast import and restoration of photosynthesis: To be able to combine RBCS with a Venus fluorescent reporter without compromising photosynthetic activity, a leaky stop codon is introduced as a novel molecular tool that allows the simultaneous expression of functional and fluorescently tagged versions of the protein from a single construct.


Assuntos
Chlamydomonas reinhardtii/genética , Códon de Terminação/genética , Regulação da Expressão Gênica de Plantas , Marcadores Genéticos/genética
5.
Mutat Res ; 785: 108322, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32800273

RESUMO

Treatment with interferon beta (IFNß) is one of the first-line treatments for multiple sclerosis. In clinical practice, however, many patients present suboptimal response to IFNß, with the proportion of non-responders ranging from 20 to 50%. This variable response can be affected by genetic factors, such as polymorphisms in the genes involved in the disease state, pharmacodynamics, metabolism or in the action mechanism of IFNß, which can affect the efficacy of this drug. This review assesses the impact of pharmacogenetics studies on response to IFNß treatment among patients diagnosed with relapsing-remitting multiple sclerosis (RRMS). The results suggest that the detection of polymorphisms in several genes (CD46, CD58, FHIT, IRF5, GAPVD1, GPC5, GRBRB3, MxA, PELI3 and ZNF697) could be used in the future as predictive markers of response to IFNß treatment in patients diagnosed with RRMS. However, few studies have been carried out and they have been performed on small sample sizes, which makes it difficult to generalize the role of these genes in IFNß treatment. Studies on large sample sizes with longer term follow-up are therefore required to confirm these results.


Assuntos
Marcadores Genéticos/genética , Interferon beta/farmacocinética , Esclerose Múltipla Recidivante-Remitente/genética , Polimorfismo Genético/genética , Humanos , Esclerose Múltipla Recidivante-Remitente/tratamento farmacológico
6.
PLoS One ; 15(7): e0236273, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32722687

RESUMO

Creating a homologous restorer line for Ogura cytoplasmic male sterility (Ogu-CMS) in Brassica napus is meaningful for the wider application of Ogu-CMS system in rapeseed production. Previously, an independent development of a new Ogu-CMS restorer line (CLR650) was reported locally from crossing between Raphanobrassica (AACCRR, 2n = 56) and B. napus and a new version of Ogu CMS lines CLR6430 derived from CLR650 was characterized in this study. The results showed that the fertility restoration gene in CLR6430 presented a distorted segregation in different segregating populations. However, the majority of somatic cells from roots had a regular chromosome number (2n = 38) and no radish signal covered a whole chromosome was detected using GISH. Thirty-two specific markers derived from the introgressed radish fragments were developed based on the re-sequencing results. Unique radish insertions and differences between CLR6430 and R2000 were also identified through both radish-derived markers and PCR product sequences. Further investigations on the genetic behaviors, interactions between the fertility restoration and other traits and specific molecular markers to the introgression in CLR6430 were also conducted in this study. These results should provide the evidence of nucleotide differences between CLR6430 and R2000, and the specific markers will be helpful for breeding new Ogura restore lines in future.


Assuntos
Brassica napus/genética , Marcadores Genéticos/genética , Infertilidade das Plantas/genética , Brassica rapa/genética , Mapeamento Cromossômico , Cromossomos de Plantas , DNA de Plantas/química , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , Repetições de Microssatélites/genética , Raphanus/genética
7.
Cytogenet Genome Res ; 160(5): 225-237, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32659775

RESUMO

Loss of chromosome Y (LOY) is a mosaic aneuploidy that can be detected mainly in blood samples of male individuals. Usually, LOY occurrence increases with chronological age in healthy men. Moreover, recently LOY has been reported in association with several diseases, such as cancer, where its frequency is even higher. The Y chromosome is one of the shortest chromosomes of the human karyotype, and it is crucial for correct male development. This chromosome has functions beyond the male reproductive system, and loss of its genes or even LOY can have consequences for the male body that are yet to be elucidated. Analyses of the Y chromosome are largely applied in forensic contexts such as paternity testing, ancestry studies, and sexual assault cases, among others. Thus, LOY can be a disadvantage, limiting laboratory methods and result interpretation. However, as an advantage, LOY detection could be used as a biological age biomarker due to its association with the aging process. The potential application of LOY as biomarker highlights the necessity to clarify the molecular mechanism behind its occurrence and its possible applications in both health and forensic studies.


Assuntos
Aneuploidia , Cromossomos Humanos Y/genética , Medicina Legal , Marcadores Genéticos/genética , Saúde , Mosaicismo , Envelhecimento/genética , Haplótipos/genética , Humanos , Masculino , Paternidade , Delitos Sexuais
8.
Parasitol Res ; 119(10): 3221-3231, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32671541

RESUMO

Members of the genus Lueheia Travassos, 1919, are endoparasites of birds, particularly passerines, throughout the Americas. Adults of Lueheia sp., (Plagiorhynchidae Golvan, 1960; Porrorchinae Golvan, 1956) were recovered from the intestine of the American robin (Turdus migratorius phillipsi Bangs) in Mexico City, and two other species of acanthocephalans identified as Porrorchis nickoli, (Plagiorhynchidae: Porrorchinae) Salgado-Maldonado and Cruz-Reyes, 2002 and Centrorhynchus microcephalus (Bravo-Hollis, 1947) Golvan, 1956 (Centrorhynchidae Van Cleave, 1916), were recovered from the Virginia opossum (Didelphis virginiana Allen) and groove-billed ani (Crotophaga sulcirostris Swainson), respectively in southeastern Mexico. Specimens of three species were sequenced at two molecular markers, the small subunit (SSU) and large subunit (LSU) of the nuclear rDNA and compared with other sequences available in GenBank. Maximum likelihood and Bayesian inference analyses of the combined (LSU + SSU) dataset and each individual dataset revealed that the specimens of Lueheia sp. formed an independent lineage, which is recognized herein as a new species, Lueheia aztecae n. sp., representing the fifth species of the genus in the Americas, and the second in the Nearctic region. The new species can be morphologically distinguished from the other five species in the genus by having a cylindrical proboscis, armed with 24-26 longitudinal rows with 9-10 hooks each. Phylogenetic inference performed with the combined dataset consisting of two genes (LSU + SSU) revealed that Lueheia aztecae n. sp. and P. nickoli belonging to subfamily Porrorchinae, formed two independent lineages, indicating that the subfamily is paraphyletic. Porrorchis nickoli and C. microcephalus formed a clade with other species of the genus Centrorhynchus, suggesting that P. nickoli should be transferred to genus Centrorhynchus, to form C. nickoli n. comb. In addition, we briefly discuss the ecological associations between the members of the families Plagiorhynchidae and Centrorhynchidae.


Assuntos
Acantocéfalos/anatomia & histologia , Acantocéfalos/classificação , Helmintíase Animal/parasitologia , Aves Canoras/parasitologia , Acantocéfalos/genética , Animais , Sequência de Bases , Teorema de Bayes , DNA Ribossômico/genética , Marcadores Genéticos/genética , Intestinos/parasitologia , México , Filogenia
9.
Arch Virol ; 165(8): 1803-1813, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32474688

RESUMO

In recent years, the availability of reverse genetics systems for porcine reproductive and respiratory syndrome virus (PRRSV) has created new perspectives for the use of recombinant viruses as expression vectors. Most of these recombinant PRRSV vectors express foreign genes through either an independent transcription unit inserted in ORF1b and ORF2, or in ORF7 and the 3' UTR. The aim of this study was to find an alternative site for foreign gene insertion into the PRRSV genome. Here, we constructed an infectious cDNA clone for a cell-adapted PRRSV strain, GXNN1396-P96. This cDNA-clone-derived recombinant virus (rGXAM) was comparable in its growth kinetics in MARC-145 cells to the parental virus, GX1396-P96. Using the infectious cDNA-clone, we inserted an independent transcription unit in ORF4 and ORF5a to generate a novel PRRSV-based recombinant virus expressing the green fluorescent protein (GFP) gene. Biological characterization of the recombinant virus, rGX45BSTRS-GFP, showed that it maintained similar growth characteristics but produced fewer infectious virions than the parental PRRSV. These data demonstrate that the ORF4 and ORF5a site is able to tolerate the insertion of foreign genes.


Assuntos
Marcadores Genéticos/genética , Fases de Leitura Aberta/genética , Síndrome Respiratória e Reprodutiva Suína/virologia , Vírus da Síndrome Respiratória e Reprodutiva Suína/genética , Animais , Linhagem Celular , Proteínas de Fluorescência Verde/genética , Suínos , Replicação Viral/genética
10.
J Biosci Bioeng ; 130(3): 227-232, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32487497

RESUMO

Marker genes are essential for gene modification and genome editing of microorganisms. In Aspergillus oryzae, a widely used host for enzyme production, only a few marker genes can be used for positive selection. One of these genes, the pyrithiamine (PT) resistance marker gene thiA, is not useful for CRISPR/Cas9 genome editing because of its unique resistance-conferring mechanism. In this study, a novel PT resistance marker was investigated considering its potential applications in genome editing. A mutant resistant to PT was selected from UV-mutagenized A. oryzae RIB40. Whole genome analysis was conducted on the mutants, and a novel candidate gene for PT resistance was identified. This candidate gene exhibited similarity to the thiamine transporter gene thi9 of Schizosaccharomyces pombe and was designated as thiI. A thiI loss-of-function mutant was generated using the CRISPR/Cas9 genome editing system to investigate its effect on PT resistance. This mutant showed PT resistance and exhibited no growth defect or auxotrophy. The thiI gene was further investigated for its use as a selection marker in genome co-editing. Ribonucleoprotein complex comprising recombinant Cas9 nuclease and sgRNA targeting thiI or another target gene (wA or sreA) was prepared and simultaneously introduced into A. oryzae RIB40. thiI and target gene double loss-of-function mutants were efficiently selected on PT-containing medium. thiI was shown to be a useful marker gene in A. oryzae for use in genome editing. This study is expected to provide insights, which will promote basic research and industrial applications of A. oryzae.


Assuntos
Aspergillus oryzae/efeitos dos fármacos , Aspergillus oryzae/genética , Farmacorresistência Fúngica/genética , Edição de Genes , Genes Fúngicos/genética , Marcadores Genéticos/genética , Piritiamina/farmacologia , Sistemas CRISPR-Cas/genética
11.
DNA Cell Biol ; 39(6): 1051-1063, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32379494

RESUMO

Triple-negative breast cancer (TNBC) is a high-risk subtype of breast cancer defined by negative expression of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Accumulating evidence indicates that alternative splicing (AS) events are correlated with the prognosis of cancer. RNA sequencing data and AS event data were manually curated from The Cancer Genome Atlas (TCGA) dataset and TCGA Splice Seq, respectively. Univariate and multivariate Cox regression analyses were applied to screen AS events associated with TNBC survival and to establish a prognostic model. A receiver operating characteristic (ROC) curve was used to evaluate the performance of the prognostic model. Differentially expressed gene analysis and functional enrichment analysis were harnessed to reveal the functional role of gene sets and to screen novel biomarkers. By integrated bioinformatics analysis of AS events and gene expression in TNBC, our study is the first to generate specific AS event profiles, prognostic AS event interaction networks, and splice factor-AS interaction networks for TNBC. Surprisingly, we found that the performance of the AS-based prognostic model was encouraging with a mean area under the ROC curve of 0.957 at 2-10 years. We also found that chemokine (C-C motif) ligand 16 (CCL16) expression was correlated with TNBC grade and could be a potential novel biomarker. In conclusion, this study provided a systematic analysis of prognostic AS event profiles and gene expression in TNBC. A novel prognostic model based on AS events may establish a foundation for future research investigating the diagnosis and treatment of TNBC.


Assuntos
Processamento Alternativo , Neoplasias de Mama Triplo Negativas/genética , Marcadores Genéticos/genética , Humanos , Prognóstico , RNA Mensageiro/genética , Análise de Sobrevida , Neoplasias de Mama Triplo Negativas/diagnóstico
12.
Nat Commun ; 11(1): 2410, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-32415110

RESUMO

The current trends of crop yield improvements are not expected to meet the projected rise in demand. Genomic selection uses molecular markers and machine learning to identify superior genotypes with improved traits, such as growth. Plant growth directly depends on rates of metabolic reactions which transform nutrients into the building blocks of biomass. Here, we predict growth of Arabidopsis thaliana accessions by employing genomic prediction of reaction rates estimated from accession-specific metabolic models. We demonstrate that, comparing to classical genomic selection on the available data sets for 67 accessions, our approach improves the prediction accuracy for growth within and across nitrogen environments by 32.6% and 51.4%, respectively, and from optimal nitrogen to low carbon environment by 50.4%. Therefore, integration of molecular markers into metabolic models offers an approach to predict traits directly related to metabolism, and its usefulness in breeding can be examined by gathering matching datasets in crops.


Assuntos
Arabidopsis/genética , Marcadores Genéticos/genética , Genoma de Planta , Agricultura/métodos , Biomassa , Carbono , Produtos Agrícolas , Genômica , Genótipo , Aprendizado de Máquina , Modelos Estatísticos , Nitrogênio , Fenótipo , Melhoramento Vegetal , Reprodutibilidade dos Testes , Seleção Genética
13.
Gene ; 753: 144794, 2020 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-32464245

RESUMO

Novel microsatellite markers were developed to investigate the genetic diversity and DNA fingerprinting of bougainvillea cultivars. Total of 175 SSRs were designed from over 50,000 SSRs identified in the whole genome sequence data, 33 highly polymorphic markers were identified. These selected SSRs produced a total of 165 alleles with 2 (BOUG-3 and BOUG-50) to 9 (BOUG-69) alleles per loci with an average of 5 alleles per locus. The overall size of the amplified products ranged from 90 bp (BOUG-51 and BOUG-81) to 320 bp (BOUG-162). The gene diversity per locus ranged from 0.13 to 0.91 with a mean of 0.71. Primer BOUG-73 and BOUG-124 exhibited highest gene diversity with greater number of alleles. The mean Nei's genetic diversity index was 0.678 with range of 0.134 (BOUG-77) to 0.958 (BOUG-69). The UPGMA based dendrogram divided the cultivars into seven major clusters. Clustering pattern was more distinct for bract types and variegated cultivars which were also confirmed by PCA scatter plot diagram. The pair-wise genetic distance estimates ranged from 0.089 to 0.86 with an average of 0.56. Each of the 125 cultivar profiled had unique marker profile indicating that the SSR markers identified are useful for identification and differentiation of bougainvillea cultivars. These informative markers identified from the study will be of great utility to assess the genetic diversity, understanding the population structure and in marker assisted breeding for improvement of bougainvillea.


Assuntos
Repetições de Microssatélites/genética , Nyctaginaceae/genética , Alelos , Impressões Digitais de DNA/métodos , Marcadores Genéticos/genética , Variação Genética , Genótipo , Filogenia , Melhoramento Vegetal/métodos , Polimorfismo Genético
14.
J Bone Miner Metab ; 38(5): 631-638, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32350615

RESUMO

INTRODUCTION: Disuse-induced bone loss is caused by a suppression of osteoblastic bone formation and an increase in osteoclastic bone resorption. There are few data available for the effects of environmental conditions, i.e., atmospheric pressure and/or oxygen concentration, on osteoporosis. This study examined the effects of mild hyperbaric oxygen at 1317 hPa with 40% oxygen on unloading-induced osteoporosis. MATERIALS AND METHODS: Eighteen 8-week old male Wistar rats were randomly divided into three groups: the control for 21 days without unloading and mild hyperbaric oxygen (NOR, n = 6), the unloading for 21 days and recovery for 10 days without mild hyperbaric oxygen (HU + NOR, n = 6), and the unloading for 21 days and recovery for 10 days with mild hyperbaric oxygen (HU + MHO, n = 6). RESULTS: The cortical thickness and trabecular bone surface area were decreased in the HU + NOR group compared to the NOR group. There were no differences between the NOR and HU + MHO groups. Osteoclast surface area and Sclerostin (Sost) mRNA expression levels were decreased in the HU + MHO group compared to the HU + NOR group. These results suggested that the loss of the cortical and trabecular bone is inhibited by mild hyperbaric oxygen, because of an inhibition of osteoclasts and enhancement of bone formation with decreased Sost expression. CONCLUSIONS: We conclude that exposure to mild hyperbaric oxygen partially protects from the osteoporosis induced by hindlimb unloading.


Assuntos
Elevação dos Membros Posteriores/fisiologia , Oxigenação Hiperbárica , Osteoporose/fisiopatologia , Osteoporose/terapia , Animais , Peso Corporal , Proteínas Morfogenéticas Ósseas/genética , Proteínas Morfogenéticas Ósseas/metabolismo , Osso Esponjoso/patologia , Osso Esponjoso/fisiopatologia , Osso Cortical/patologia , Osso Cortical/fisiopatologia , Marcadores Genéticos/genética , Lâmina de Crescimento/patologia , Masculino , Osteocalcina/genética , Osteocalcina/metabolismo , Osteoclastos/patologia , Osteoporose/genética , Coativador 1-alfa do Receptor gama Ativado por Proliferador de Peroxissomo/genética , Coativador 1-alfa do Receptor gama Ativado por Proliferador de Peroxissomo/metabolismo , Ligante RANK/genética , Ligante RANK/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ratos Wistar
15.
Mem Inst Oswaldo Cruz ; 115: e190407, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32321155

RESUMO

BACKGROUND: Early diagnosis of tuberculosis (TB) and identification of strains of Mycobacterium tuberculosis resistant to anti-TB drugs are considered the main factors for disease control. OBJECTIVES: To standardise a real-time polymerase chain reaction (qPCR) assay technique and apply it to identify mutations involved in M. tuberculosis resistance to Isoniazid (INH) directly in Ziehl-Neelsen (ZN) stained slides. METHODS: Were analysed 55 independent DNA samples extracted from clinical isolates of M. tuberculosis by sequencing. For application in TB diagnosis resistance, 59 ZN-stained slides were used. The sensitivity, specificity and Kappa index, with a 95% confidence interval (CI95%), were determined. FINDINGS: The agreement between the tests was, for the katG target, the Kappa index of 0.89 (CI95%: 0.7-1.0). The sensitivity and specificity were 97.6% (CI95%: 87.7-99.9) and 91.7% (CI95%: 61.5-99.5), respectively. For inhA, the Kappa index was 0.92 (CI95%: 0.8-1.0), the sensitivity and specificity were 94.4% (CI95%: 72.7-99.8) and 97.3% (CI95%: 85.8-99.9), respectively. The use of ZN-stained slides for drug-resistant TB detection showed significant results when compared to other standard tests for drug resistance. MAIN CONCLUSIONS: qPCR genotyping proved to be an efficient method to detect genes that confer M. tuberculosis resistance to INH. Thus, qPCR genotyping may be an alternative instead of sequencing.


Assuntos
Antituberculosos/farmacologia , Farmacorresistência Bacteriana/genética , Marcadores Genéticos/genética , Isoniazida/farmacologia , Mutação/genética , Mycobacterium tuberculosis/genética , DNA Bacteriano/genética , Genótipo , Humanos , Testes de Sensibilidade Microbiana , Mycobacterium tuberculosis/efeitos dos fármacos , Reação em Cadeia da Polimerase em Tempo Real , Sensibilidade e Especificidade
16.
Biol Res ; 53(1): 15, 2020 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-32299502

RESUMO

BACKGROUND: Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. RESULTS: A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country's average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. CONCLUSIONS: We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.


Assuntos
Grupos Étnicos/genética , Genética Populacional/organização & administração , Índios Sul-Americanos/genética , Polimorfismo de Nucleotídeo Único/genética , Grupos Populacionais/genética , Chile , Feminino , Frequência do Gene/genética , Marcadores Genéticos/genética , Genótipo , Técnicas de Genotipagem , Humanos , Masculino , Filogeografia , Saliva
17.
Mol Genet Genomics ; 295(4): 837-841, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32300860

RESUMO

This work presents a new method and tool to solve a common problem of molecular biologists and geneticists who use molecular markers in their scientific research and developments: curation of sequences. Omic studies conducted by molecular biologists and geneticists usually involve the use of molecular markers. AFLP, cDNA-AFLP, and MSAP are examples of markers that render information at the genomics, transcriptomics, and epigenomics levels, respectively. These three types of molecular markers use adaptors that are the template for PCR amplification. The sequences of the adaptors have to be eliminated for the analysis of the results. Since a large number of sequences are usually obtained in these studies, this clean-up of the data could demand long time and work. To automate this work, an R package, named CleanBSequences, was created that allows the sequences to be curated massively, quickly, without errors and can be used offline. The curating is performed by aligning the forward and/or reverse primers or ends of cloning vectors with the sequences to be removed. After the alignment, new subsequences are generated without biological fragments not desired by the user, i.e., sequences needed by the techniques. In conclusion, the CleanBSequences tool facilitates the work of researchers, reducing time, effort, and working errors. Therefore, the present tool would respond to the problems related to the curation of sequences obtained from the use of some types of molecular markers. In addition to the above, being an open source, CleanBSequences is a flexible tool that has the potential to be used in future improvements to respond to new problems.


Assuntos
Biologia Computacional , Marcadores Genéticos/genética , Biologia Molecular/métodos , Software , Epigenômica/métodos , Genômica/métodos , Anotação de Sequência Molecular/métodos , Alinhamento de Sequência/métodos , Análise de Sequência/métodos , Transcriptoma/genética
18.
PLoS One ; 15(3): e0230905, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32226026

RESUMO

As cancer mortality is high in most regions of the world, early screening of cancer has become increasingly important. Minimally invasive screening programs that use peripheral blood mononuclear cells (PBMCs) are a new and reliable strategy that can achieve early detection of tumors by identifying marker genes. From 797 datasets, four (GSE12771, GSE24536, GSE27562, and GSE42834) including 428 samples, 236 solid tumor cases, and 192 healthy controls were chosen according to the inclusion criteria. A total of 285 genes from among 440 reported genes were selected by meta-analysis. Among them, 4 of the top significantly differentially expressed genes (ANXA1, IFI44, IFI44L, and OAS1) were identified as marker genes of PBMCs. Pathway enrichment analysis identified, two significant pathways, the 'primary immunodeficiency' pathway and the 'cytokine-cytokine receptor interaction' pathway. Protein- protein interaction (PPI) network analysis revealed the top 27 hubs with a degree centrality greater than 23 to be hub genes. We also identified 3 modules in Molecular Complex Detection (MCODE) analysis: Cluster 1 (related to ANXA1), Cluster 2 (related to IFI44 and IFI44L) and Cluster 3 (related to OAS1). Among the 4 marker genes, IFI44, IFI44L, and OAS1 are potential diagnostic biomarkers, even though their results were not as remarkable as those for ANXA1 in our study. ANXA1 is involved in the immunosuppressive mechanism in tumor-bearing hosts and may be used in a new strategy involving the use of the host's own immunity to achieve tumor suppression.


Assuntos
Detecção Precoce de Câncer , Marcadores Genéticos/genética , Monócitos/metabolismo , Neoplasias/diagnóstico , Neoplasias/genética , Redes Reguladoras de Genes , Humanos , Anotação de Sequência Molecular , Neoplasias/sangue , Neoplasias/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos , Mapeamento de Interação de Proteínas
19.
Nat Med ; 26(4): 542-548, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32251405

RESUMO

While polygenic risk scores (PRSs) are poised to be translated into clinical practice through prediction of inborn health risks1, a strategy to utilize genetics to prioritize modifiable risk factors driving heath outcome is warranted2. To this end, we investigated the association of the genetic susceptibility to complex traits with human lifespan in collaboration with three worldwide biobanks (ntotal = 675,898; BioBank Japan (n = 179,066), UK Biobank (n = 361,194) and FinnGen (n = 135,638)). In contrast to observational studies, in which discerning the cause-and-effect can be difficult, PRSs could help to identify the driver biomarkers affecting human lifespan. A high systolic blood pressure PRS was trans-ethnically associated with a shorter lifespan (hazard ratio = 1.03[1.02-1.04], Pmeta = 3.9 × 10-13) and parental lifespan (hazard ratio = 1.06[1.06-1.07], P = 2.0 × 10-86). The obesity PRS showed distinct effects on lifespan in Japanese and European individuals (Pheterogeneity = 9.5 × 10-8 for BMI). The causal effect of blood pressure and obesity on lifespan was further supported by Mendelian randomization studies. Beyond genotype-phenotype associations, our trans-biobank study offers a new value of PRSs in prioritization of risk factors that could be potential targets of medical treatment to improve population health.


Assuntos
Bancos de Espécimes Biológicos/estatística & dados numéricos , Marcadores Genéticos , Estudo de Associação Genômica Ampla/métodos , Longevidade/genética , Herança Multifatorial/genética , Adulto , Fatores Etários , Idoso , Diabetes Mellitus Tipo 2/genética , Diabetes Mellitus Tipo 2/mortalidade , Feminino , Finlândia/epidemiologia , Marcadores Genéticos/genética , Predisposição Genética para Doença/epidemiologia , Estudo de Associação Genômica Ampla/estatística & dados numéricos , Humanos , Hipertensão/genética , Hipertensão/mortalidade , Japão/epidemiologia , Masculino , Pessoa de Meia-Idade , Obesidade/genética , Obesidade/mortalidade , Polimorfismo de Nucleotídeo Único , Fatores de Risco , Reino Unido/epidemiologia
20.
Nat Med ; 26(4): 549-557, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32273609

RESUMO

Polygenic risk scores (PRSs) have shown promise in predicting susceptibility to common diseases1-3. We estimated their added value in clinical risk prediction of five common diseases, using large-scale biobank data (FinnGen; n = 135,300) and the FINRISK study with clinical risk factors to test genome-wide PRSs for coronary heart disease, type 2 diabetes, atrial fibrillation, breast cancer and prostate cancer. We evaluated the lifetime risk at different PRS levels, and the impact on disease onset and on prediction together with clinical risk scores. Compared to having an average PRS, having a high PRS contributed 21% to 38% higher lifetime risk, and 4 to 9 years earlier disease onset. PRSs improved model discrimination over age and sex in type 2 diabetes, atrial fibrillation, breast cancer and prostate cancer, and over clinical risk in type 2 diabetes, breast cancer and prostate cancer. In all diseases, PRSs improved reclassification over clinical thresholds, with the largest net reclassification improvements for early-onset coronary heart disease, atrial fibrillation and prostate cancer. This study provides evidence for the additional value of PRSs in clinical disease prediction. The practical applications of polygenic risk information for stratified screening or for guiding lifestyle and medical interventions in the clinical setting remain to be defined in further studies.


Assuntos
Doenças Cardiovasculares , Predisposição Genética para Doença , Doenças Metabólicas , Herança Multifatorial , Neoplasias , Adulto , Idade de Início , Biomarcadores/análise , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/epidemiologia , Neoplasias da Mama/genética , Doenças Cardiovasculares/diagnóstico , Doenças Cardiovasculares/epidemiologia , Doenças Cardiovasculares/genética , Estudos de Casos e Controles , Diabetes Mellitus Tipo 2/diagnóstico , Diabetes Mellitus Tipo 2/epidemiologia , Diabetes Mellitus Tipo 2/genética , Feminino , Finlândia/epidemiologia , Marcadores Genéticos/genética , Predisposição Genética para Doença/epidemiologia , Estudo de Associação Genômica Ampla , Humanos , Masculino , Doenças Metabólicas/diagnóstico , Doenças Metabólicas/epidemiologia , Doenças Metabólicas/genética , Pessoa de Meia-Idade , Neoplasias/diagnóstico , Neoplasias/epidemiologia , Neoplasias/genética , Polimorfismo de Nucleotídeo Único , Valor Preditivo dos Testes , Prognóstico , Neoplasias da Próstata/diagnóstico , Neoplasias da Próstata/epidemiologia , Neoplasias da Próstata/genética , Medição de Risco , Fatores de Risco , Adulto Jovem
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