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| Registros recuperados: 16 | |
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| Eguiluz,Maria; Yuyama,Priscila Mary; Guzman,Frank; Rodrigues,Nureyev Ferreira; Margis,Rogerio. |
| Abstract Plinia trunciflora is a Brazilian native fruit tree from the Myrtaceae family, also known as jaboticaba. This species has great potential by its fruit production. Due to the high content of essential oils in their leaves and of anthocyanins in the fruits, there is also an increasing interest by the pharmaceutical industry. Nevertheless, there are few studies focusing on its molecular biology and genetic characterization. We herein report the complete chloroplast (cp) genome of P. trunciflora using high-throughput sequencing and compare it to other previously sequenced Myrtaceae genomes. The cp genome of P. trunciflora is 159,512 bp in size, comprising inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and 18,587 bp (SSC). The... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Jaboticaba; Myrtaceae; Chloroplast genome; Next-generation sequencing. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000500871 |
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| Malcher,Carolina; Yamamoto,Guilherme L.; Burnham,Philip; Ezquina,Suzana A.M.; Lourenço,Naila C.V.; Balkassmi,Sahilla; Antonio,David S. Marco; Hsia,Gabriella S.P.; Gollop,Thomaz; Pavanello,Rita C.; Lopes,Marco Antonio; Bakker,Egbert; Zatz,Mayana; Bertola,Débora; Vlaminck,Iwijn De; Passos-Bueno,Maria Rita. |
| Abstract Our aim was to develop and apply a comprehensive noninvasive prenatal test (NIPT) by using high-coverage targeted next-generation sequencing to estimate fetal fraction, determine fetal sex, and detect trisomy and monogenic disease without parental genotype information. We analyzed 45 pregnancies, 40 mock samples, and eight mother-child pairs to generate 35 simulated datasets. Fetal fraction (FF) was estimated based on analysis of the single nucleotide polymorphism (SNP) allele fraction distribution. A Z-score was calculated for trisomy of chromosome 21 (T21), and fetal sex detection. Monogenic disease detection was performed through variant analysis. Model validation was performed using the simulated datasets. The novel model to estimate FF was... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Cell-free DNA; Next-generation sequencing; Trisomy; Noninvasive prenatal test; Fetal fraction. |
| Ano: 2018 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000400545 |
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| Marano,Leonardo Arduino; Marcorin,Letícia; Castelli,Erick da Cruz; Mendes-Junior,Celso Teixeira. |
| Abstract The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology. Melanocortin-1 receptor (MC1R) is one of the most studied genes involved in pigmentation variation. As MC1R has already been suggested to affect melanogenesis and increase risk of developing... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Melanocortin-1 Receptor; The 1000 Genomes Project; Next-generation sequencing. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000300530 |
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| Chen,Yong; Shi,Jian-Xin; Pan,Xu-Feng; Feng,Jian; Zhao,Heng. |
| Over the past three decades, mortality from lung cancer has sharply and continuously increased in China, ascending to the first cause of death among all types of cancer. The ability to identify the actual sequence of gene mutations may help doctors determine which mutations lead to precancerous lesions and which produce invasive carcinomas, especially using next-generation sequencing (NGS) technology. In this study, we analyzed the latest lung cancer data in the COSMIC database, in order to find genomic "hotspots" that are frequently mutated in human lung cancer genomes. The results revealed that the most frequently mutated lung cancer genes are EGFR, KRAS and TP53.In recent years, EGFR and KRAS lung cancer test kits have been utilized for detecting lung... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Lung cancer; Next-generation sequencing; Somatic mutation kit; COSMIC. |
| Ano: 2013 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572013000300022 |
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| Hassan,Mariam; Essam,Tamer; Megahed,Salwa. |
| Abstract In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree)... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Bioinformatics; Method; Microbiome; Next-generation sequencing; QIIME. |
| Ano: 2018 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000500001 |
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| Krishnankutty,Sajesh Puthenpurackal; Muraleedharan,Megha; Perumal,Rajadurai Chinnasamy; Michael,Saju; Benny,Jubina; Balan,Bipin; Kumar,Pramod; Manazhi,Jishnu; Kumar,Bangaruswamy Dhinoth; Santhosh,Sam; Thomas,George; Gupta,Ravi; Zachariah,Arun. |
| Abstract Background: The oral cavities of snakes are replete with various types of bacterial flora. Culture-dependent studies suggest that some of the bacterial species are responsible for secondary bacterial infection associated with snakebite. A complete profile of the ophidian oral bacterial community has been unreported until now. Therefore, in the present study, we determined the complete bacterial compositions in the oral cavity of some snakes from India. Methods: Total DNA was isolated from oral swabs collected from three wild snake species (Indian Cobra, King Cobra and Indian Python). Next, the DNA was subjected to PCR amplification of microbial 16S rRNA gene using V3-region-specific primers. The amplicons were used for preparation of DNA... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Microbial community; Next-generation sequencing; Venomous snake; Hypervariable region. |
| Ano: 2018 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992018000100331 |
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| Rusak,Leonardo Alves; Junqueira,Ricardo Magrani; Hofer,Ernesto; Vallim,Deyse Christina; Asensi,Marise Dutra. |
| Abstract Yersinia enterocolitica is a widespread Gram-negative bacterium that causes gastrointestinal disease and other clinical manifestations in humans. Potentially pathogenic Y. enterocolitica has been isolated in Brazil, from human, environmental, food, and animal sources. Herein we report a genome sequence of Y. enterocolitica subsp. palearctica strain YE 19, serotype O:3, biotype 4, sequence type 18, with virulence determinants isolated from human blood in Rio de Janeiro in 2005. The results corroborate other findings that this strain harbors a set of virulence determinants that could play a role in host pathoadaptation and may also justify the successful dissemination of bioserotype 4/O:3 in Brazil. The presence of strains harboring all of these... |
| Tipo: Info:eu-repo/semantics/other |
Palavras-chave: Yersinia enterocolitica; Virulence; Brazil; Next-generation sequencing. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702017000500550 |
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| Desdouits, Marion; De Graaf, Miranda; Strubbia, Sofia; Oude Munnink, Bas B.; Kroneman, Annelies; Le Guyader, Soizick; Koopmans, Marion P. G.. |
| Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application |
| Tipo: Text |
Palavras-chave: Next-generation sequencing; Metagenomics; Foodborne virus; Food virology; Human enteric virus; Norovirus. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00641/75330/75988.pdf |
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| Guerra, Juliana Mariotti; Fernandes, Natália Coelho Couto de Azevedo; Barbosa, José Eduardo de Raeffray; Taniguchi, Helena Hilomi; Hiramoto, Roberto Mitsuyoshi; Tolezano, José Eduardo; Cogliati, Bruno. |
| Next-generation sequencing (NGS) technologies are becoming widely used, and although a massive number of sequences can be generated in a single experiment, it is still important to characterize the reads. Characterizing reads may prevent undesirable outcomes in the assembly or mapping processes. Discarding low-quality reads, controlling for contamination, and trimming adaptor sequences are examples of preliminary quality control procedures that can be applied to raw reads before further analysis. Here it was applied the FastQ Quality Control Software (FastQC) in order to assess the quality of the data of next-generation sequecing for Leishmania infatum. |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Leishmania infatum; Next-generation sequencing Leishmania infatum; Next-generation sequencing. |
| Ano: 2016 |
URL: http://www.revistamvez-crmvsp.com.br/index.php/recmvz/article/view/31056 |
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| Málaga,Diana Rojas; Brusius-Facchin,Ana Carolina; Siebert,Marina; Pasqualim,Gabriela; Saraiva-Pereira,Maria Luiza; Souza,Carolina F.M de; Schwartz,Ida V.D.; Matte,Ursula; Giugliani,Roberto. |
| Abstract Lysosomal storage disorders (LSDs) constitute a heterogeneous group of approximately 50 genetic disorders. LSDs diagnosis is challenging due to variability in phenotype penetrance, similar clinical manifestations, and a high allelic heterogeneity. A powerful tool for the diagnosis of the disease could reduce the “diagnostic odyssey” for affected families, leading to an appropriate genetic counseling and a better outcome for current therapies, since enzyme replacement therapies have been approved in Brazil for Gaucher, Fabry, and Pompe diseases, and are under development for Niemann-Pick Type B. However, application of next-generation sequencing (NGS) technology in the clinical diagnostic setting requires a previous validation phase. Here, we... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Ion Torrent; Molecular diagnostics; Next-generation sequencing; Lysosomal storage disorders; Validation. |
| Ano: 2019 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000200197 |
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| Cevallos,Miguel A.; Guerrero,Gabriela; Ríos,Selma; Arroyo,Analilia; Villalobos,Miguel Angel; Porta,Helena. |
| Abstract Mosses in conjunction with hornworts and liverworts are collectively referred to as bryophytes. These seedless, nonvascular plants are the closest extant relatives of early terrestrial plants and their study is essential to understand the evolutionary first steps of land plants. Here we report the complete chloroplast (cp) genome sequence of Pseudocrossidium replicatum, a moss belonging to the Pottiaceae family that is common in the central highlands of Mexico, in South America, in southern USA, and in Kenia. The cp genome (plastome) of P. replicatum is 123,512 bp in size, comprising inverted repeats of 9,886 bp and single-copy regions of 85,146 bp (LSC) and 18,594 bp (SSC). The plastome encodes 82 different proteins, 31 different tRNAs, and 4... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Bryophytes; Pottiaceae; Chloroplast; Next-generation sequencing. |
| Ano: 2019 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000300488 |
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| Registros recuperados: 16 | |
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