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1.
Medicine (Baltimore) ; 99(5): e18731, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32000376

RESUMEN

Miscarriage is the spontaneous loss of a clinically established intrauterine pregnancy before the fetus has reached viability. In order to compare the performance of traditional G banding karyotyping with next-generation sequencing (NGS) for detecting common trisomies in products of conception (POC). Chromosome abnormalities were detected by high-resolution G banding karyotyping and NGS. A total of 48 miscarriage samples, including 20 samples without karyotype result and 28 with karyotype results were selected and coded for analysis by NGS. The multiplex PCR analysis of maternal and miscarriage DNA for single nucleotide polymorphism (SNP) markers were used to simultaneously monitor maternal cell contamination (MCC), chromosomal status, and sex of the miscarriage tissue. NGS detection results of 21 chromosome abnormalities were consisted with that in karyotyping examination. These chromosome abnormalities samples included 9 chromosome 16 trisomies, 3 chromosome 22 trisomies, 2 chromosome 7 trisomies, 2 chromosome 18 trisomies, 1 chromosome 4 trisomies, one chromosome 10 trisomies, 1 chromosome 13 trisomies, 1 chromosome 15 trisomies and 1 sex chromosomal aneuploidies (45, X). Meanwhile, NGS analysis of seven chromosome normalities was adapted to the karyotyping examination. Therefore, NGS combined with multiplex PCR is an effective method to test trisomies in POC. The results mentioned above will contribute to a detailed understanding of the first-trimester spontaneous miscarriages.


Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento/estadística & datos numéricos , Trisomía/diagnóstico , Aborto Espontáneo/genética , Femenino , Humanos , Embarazo
3.
Medicine (Baltimore) ; 99(4): e18887, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31977897

RESUMEN

INTRODUCTION: MYH9-related disease (MYH9-RD) is a rare autosomal dominant disorder caused by mutations in MYH9, which is responsible for encoding nonmuscle myosin heavy chains IIA (NMMHCIIA). MYH9-RD is clinically characterized by congenital macrothrombocytopenia, granulocyte inclusions variably associated with the risk of developing progressive sensorineural deafness, cataracts and nephropathy. PATIENT CONCERNS: A 5-year-old boy had a history of a mild bleeding tendency and chronic thrombocytopenia, first identified at four months of age. No other family members were noted to have similar clinical features or hematologic disorders. DIAGNOSES: The boy was diagnosed with MYH9-RD. Light microscopic examination of peripheral blood films (Wright-Giemsa stain) showed marked platelet macrocytosis with giant platelets and basophilic Döhle-like inclusions in 83% of the neutrophils. Immunofluorescence analysis disclosed a type II pattern, manifested by neutrophils which contained several circle-to-oval shaped cytoplasmic NMMMHCA-positive granules. Sequencing analysis of MYH9-RD genes was carried out and revealed a novel missense mutation of c.97T>G (p.W33G) in the patient but not in his parents. INTERVENTION: No treatment is necessary. Recognition of MYH9-RD is important to Avoiding unnecessary and potentially harmful treatments. OUTCOMES: The patient's condition remained stable during the follow-up. CONCLUSIONS: As a result of identifying this missense mutation in this particular case, we have added c.97T>G (p.W33G) to the broad spectrum of potential MYH9 mutations.


Asunto(s)
Pérdida Auditiva Sensorineural/genética , Trombocitopenia/congénito , Preescolar , Técnica del Anticuerpo Fluorescente , Pérdida Auditiva Sensorineural/diagnóstico , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Mutación Missense , Neutrófilos/patología , Trombocitopenia/diagnóstico , Trombocitopenia/genética
4.
Anticancer Res ; 40(1): 101-107, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31892558

RESUMEN

BACKGROUND: Mitochondria are energy-producing organelles, and dysfunction in these organelles causes various types of disease. Although several studies have identified mutations in nuclear DNA that are associated with the etiology of ulcerative colitis (UC), information regarding mitochondrial DNA (mtDNA) in UC is limited. This study aimed to investigate the mitochondrial DNA polymorphism underlying the etiology of UC and UC-associated colorectal cancer. MATERIALS AND METHODS: Next-generation sequencing was performed to assess mitochondrial DNA mutations in 12 patients with UC-associated cancer. The mtDNA mutations in the non-neoplastic mucosa, tumor tissues, and healthy controls were compared. RESULTS: The incidence of mutations of nicotinamide adenine dinucleotide phosphate ubiquinone oxidase subunit, ATP synthetase, and tRNA was higher in non-neoplastic mucosa in those with UC compared with the healthy controls. However, no statistically significant differences were observed in mutations between the tumor tissues and non-neoplastic mucosa in UC. CONCLUSION: Significant mutations in mtDNA were observed in the non-neoplastic mucosa of patients with UC-associated cancer.


Asunto(s)
Colitis Ulcerosa/complicaciones , Colitis Ulcerosa/genética , Neoplasias Colorrectales/etiología , Genes Mitocondriales , Polimorfismo Genético , Transformación Celular Neoplásica/genética , Colitis Ulcerosa/metabolismo , Colitis Ulcerosa/patología , Neoplasias Colorrectales/metabolismo , Neoplasias Colorrectales/patología , Susceptibilidad a Enfermedades , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Mucosa Intestinal/metabolismo , Mucosa Intestinal/patología , Masculino , Mutación
5.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 37(1): 21-24, 2020 Jan 10.
Artículo en Chino | MEDLINE | ID: mdl-31922589

RESUMEN

OBJECTIVE: To identify potential variant in a child diagnosed as infantile neuroaxonal dystrophy. METHODS: Genomic DNA was extracted from peripheral blood samples from the patient and his parents and subjected to next generation sequencing. Suspected variant was verified by PCR and Sanger sequencing. Pathogenicity of the mutation was predicted by using bioinformatic software including SIFT and PolyPhen-2. RESULTS: The child was found to carry compound heterozygous variations c.668C>A (p.Pro223Gln) and c.2266C>T (p.Gln756Ter) of the PLA2G6 gene, which were respectively inherited from his father and mother. c.2266C>T has changed codon 756 (glutamine) into a stop codon, resulting premature termination of peptide chain synthesis. c.2266C>T has not been reported previously and was predicted to be harmful. CONCLUSION: The compound variants of c.668C>A (p.Pro223Gln) and c.2266C>T (p.Gln756Ter) of the PLA2G6 gene probably underlies the disease in the child. Above finding has enriched the variant spectrum of the PLA2G6 gene.


Asunto(s)
Fosfolipasas A2 Grupo VI , Distrofias Neuroaxonales , Niño , Fosfolipasas A2 Grupo VI/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Mutación , Distrofias Neuroaxonales/genética
6.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 37(1): 57-59, 2020 Jan 10.
Artículo en Chino | MEDLINE | ID: mdl-31922598

RESUMEN

OBJECTIVE: To explore the genetic basis of a child with idiopathic mental retardation. METHODS: Clinical data and peripheral blood sample of the child were collected. Genomic DNA was extracted and subjected to copy number analysis using single nucleotide polymrophism array comparative genome hybridization (SNP-aCGH) and targeted capture and next generation sequencing (NGS). RESULTS: No microdeletion/microduplication were detected by SNP-aCGH. NGS has detected homozygous c.722delA (p.Asp241fs) variant of the LISN1 gene, which is known to underlie autosomal recessive mental retardation-27 (MRT 27). Both parents are carriers of the variant, conforming to the autosomal recessive inheritance. CONCLUSION: A novel pathogenic variant of the LINS1 gene has been identified, which probably underlies the MRT 27 in the patient.


Asunto(s)
Discapacidad Intelectual , Proteínas , Niño , Hibridación Genómica Comparativa , Secuenciación de Nucleótidos de Alto Rendimiento , Homocigoto , Humanos , Discapacidad Intelectual/genética , Proteínas/genética
7.
Zhonghua Wai Ke Za Zhi ; 58(1): 37-41, 2020 Jan 01.
Artículo en Chino | MEDLINE | ID: mdl-31902168

RESUMEN

Pancreatic cancer is the most lethal malignancy with an overall 5-year survival rate less than 9%, mainly due to late diagnosis and lack of effective therapeutic options.In the last decade, post-operative survival has been enhanced with advent of neoadjuvant therapy and combined adjuvant therapy.Furthermore, the information gained from the omics data, including next generation sequencing data, hasn't yet begun to affect treatment of pancreatic cancer patients.However, in terms of precision medicine, pancreatic cancer has always lagged behind other tumors.Therefore, combined with practical experience, summary of the latest development and research progress of precise medical treatment of pancreatic cancer, especially from the fields of molecular biology and experimental models, is of critical importance. Further development of precise medicine for pancreatic cancer based on platforms using PDX and organoid model would promisingly help in effective improvement of clinical treatment.


Asunto(s)
Neoplasias Pancreáticas/terapia , Medicina de Precisión , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Terapia Neoadyuvante
9.
Sichuan Da Xue Xue Bao Yi Xue Ban ; 51(1): 97-101, 2020 Jan.
Artículo en Chino | MEDLINE | ID: mdl-31950797

RESUMEN

Objective: To analyse potential genetic cause of a family affected with hereditary elliptocytosis (HE). Methods: Peripheral blood samples from this HE family were collected. Targeted capture and high-throughput sequencing of 4 813 genetic disease-associated genes was performed in four members of the family. Possible causative genetic variation was obtained and further confirmed by Sanger sequencing. Fifty healthy control subjects were recruited for detection of the candidate variation. Results: High-throughput sequencing detected a nonsense mutation c.1215G>A(p.Trp405Ter)in exon 13 of the EPB41 gene in the proband and his mother presenting with moderate anemia. The pathogenicity of this loss-of-function mutation is very strong, because the G→A transition leads to introduce the premature stop codon instead of tryptophan codon at position 405, which producing a truncating protein with loss of important functional domains. This causative mutation is extremely rare in the population, and it has not yet been reported. The grandmother of the proband was heterozygous for the same mutation. Genotype-phenotype cosegregation was observed in this family. This mutation was not found in the 50 unrelated healthy controls. Conclusion: The c.1215G>A mutation of the EPB41 gene probably accounts for the disease in this HE family. This study reports a pathogenic EPB41 mutation in a Chinese HE family for the first time.


Asunto(s)
Proteínas del Citoesqueleto , Eliptocitosis Hereditaria , Proteínas de la Membrana , Mutación , Proteínas del Citoesqueleto/genética , Eliptocitosis Hereditaria/genética , Heterocigoto , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Proteínas de la Membrana/genética , Linaje
10.
Forensic Sci Int ; 306: 110052, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31778923

RESUMEN

Metabarcoding through Next Generation Sequencing (NGS) has revolutionized environmental biological studies. The availability of this technical approach has opened the opportunity for a systematic implementation of fungal metabarcoding analysis in forensics, where standardized, sensitive and reproducible protocols are highly desirable. In the present paper, a pipeline including a semi-automated molecular protocol and user-friendly bioinformatics tools are applied to several kinds of environmental samples and forensic caseworks. The identification of fungi that characterize specific environments (like Aspergillus for indoor walls, or Penicillium, Debaryomices and Wickerhamomyces for food storage) can be informative for the provenance of samples. In some situations, fungal analysis cannot allow the identification of a defined environment but seems useful to cluster samples with similar provenance. Based on these considerations, fungal analysis can be included in a wider process of non-human DNA identification in order to provide clues on sample provenance.


Asunto(s)
Código de Barras del ADN Taxonómico , ADN de Hongos/genética , Hongos/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Microbiología Ambiental , Ciencias Forenses , Análisis de Componente Principal , Análisis de Secuencia de ADN , Programas Informáticos
11.
Forensic Sci Int ; 306: 110050, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31790892

RESUMEN

In 1995, the historical shipwreck of La Belle was discovered off the coast of Texas. One partial human skeleton was recovered from alongside cargo in the rear portion of the ship; a second (complete) skeleton was found atop coiled anchor rope in the bow. In late 2015, comprehensive forensic genetic testing began on multiple samplings from each set of remains. For the partial skeleton recovered from the ship's rear cargo area, results were obtained for 26/27 Y-STRs using traditional CE; with MPS technology, results were obtained for 18/24 Y-STRs, 56/56 ancestry-informative SNPs (aiSNPs), 22/22 phenotype-informative SNPs (piSNPs), 22/27 autosomal STRs, 4/7 X-STRs, and 94/94 identity-informative SNPs (iiSNPs). For the complete skeleton of the second individual, results were obtained for 7/17 Y-STRs using traditional CE; with MPS technology, results were obtained for 5/24 Y-STRs, 49/56 aiSNPs, 18/22 piSNPs, 15/27 autosomal STRs, 1/7 X-STRs, and 66/94 iiSNPs. Biogeographic ancestry for each set of skeletal remains was predicted using the ancestry feature and metapopulation tool of the Y-STR Haplotype Reference Database (YHRD), Haplogroup Predictor, and the Forensic Research/Reference on Genetics knowledge base (FROG-kb). Phenotype prediction was performed using piSNP data and the HIrisplex eye color and hair color DNA phenotyping webtool. mtDNA whole genome sequencing also was performed successfully. This study highlights the sensitivity of current forensic laboratory methods in recovering DNA from historical and archaeological human remains. Using advanced sequencing technology provided by MiSeq™ FGx (Verogen) and Ion S5™ (Thermo Fisher Scientific) instrumentation, degraded skeletal remains can be characterized using a panel of diverse and highly informative markers, producing data which can be useful in both forensic and genealogical investigations.


Asunto(s)
Restos Mortales , Dermatoglifia del ADN , Genética Forense , Fenotipo , Navíos/historia , Accidentes/historia , Cromosomas Humanos Y , Grupos de Población Continentales/genética , ADN Mitocondrial/genética , Electroforesis Capilar , Francia , Haplotipos , Secuenciación de Nucleótidos de Alto Rendimiento , Historia del Siglo XVII , Humanos , Masculino , Repeticiones de Microsatélite , Reacción en Cadena de la Polimerasa , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN , Texas , Secuenciación Completa del Genoma
12.
Forensic Sci Int ; 306: 110056, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31765883

RESUMEN

The killings during the Second World War, with nearly one hundred thousand victims, is one of the greatest losses of life in Slovenia's modern history. This article presents the genetic identification of the victims of the largest family massacre that occurred in Slovenia, in which 10 members of the same family were killed. Seven of them were buried in a hidden mass grave and only two children survived. In 2015 and 2016, two graves were found and three incomplete female skeletons and at least three incomplete male skeletons were exhumed. A total of 12 bones and teeth were analysed and compared to two living relatives. Extracted DNA was quantified using the PowerQuant kit, and various autosomal and Y-STR kits were used for STR typing. Up to 2.7 ng DNA/g of powder was acquired from the samples analysed. We managed to obtain nuclear DNA for successful STR typing from seven bones and one molar. From the female grave, autosomal profiles were obtained only from one skeleton, and from the male grave from five out of six femurs. The relationships between the males were additionally confirmed by analyses of Y-STRs. STR profiles made possible the identification of four family members; one of the aunts from the female grave, and two uncles and the father of the surviving children, who were used as family references, from the male grave. The product rule was used to calculate a combined likelihood ratio for autosomal and Y-STRs, and statistical analyses showed high confidence of correct identification with posterior probability (PP) greater than 99.9 % for three out of four victims identified. For identifying the aunt, the PP obtained after ESI-17 and NGM STR typing was too low. To increase the PP, the next-generation sequencing Precision ID GlobalFiler NGS STR Panel was used and, after the analysis of additional STR loci, the statistical analysis showed a PP greater than 99.9 %, indicating that a sufficient number of genetic markers had been investigated in identifying the skeletal remains of the aunt. An elimination database containing the genetic profiles of all individuals that had been in contact with the bones was created to ensure traceability in case of contamination, and no matches were found. After more than 70 years, the skeletal remains were returned to the surviving children, who buried their relatives in a family grave.


Asunto(s)
Huesos/química , Dermatoglifia del ADN , Familia , Diente/química , Restos Mortales , Entierro , Cromosomas Humanos Y , ADN/aislamiento & purificación , Exhumación , Femenino , Genética Forense , Secuenciación de Nucleótidos de Alto Rendimiento , Historia del Siglo XX , Humanos , Masculino , Repeticiones de Microsatélite , Linaje , Reacción en Cadena de la Polimerasa , Análisis de Secuencia de ADN , Eslovenia , Segunda Guerra Mundial
14.
Arch Virol ; 165(1): 227-231, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31659444

RESUMEN

Three viral contig sequences, which represented complete genome of a novel virus with three dsRNAs of 1,712 nucleotides (nt) (dsRNA1), 1,504 nt (dsRNA2) and 1,353 nt (dsRNA3), were found in tea-oil camellia plants by high-throughput sequencing analysis. The three dsRNAs were re-sequenced by RT-PCR cloning. The largest dsRNA, dsRNA1, had a single open reading frame (ORF) that encoded a putative 52.7-kDa protein of a putative viral RNA-dependent RNA polymerase (RdRp). DsRNA2 and dsRNA3 were predicted to encode putative capsid proteins (CPs) of 40.47 kDa and 40.59 kDa, respectively. The virus, which is provisionally named "tea-oil camellia deltapartitivirus 1",  shared amino acid sequence itentities of 36.09-69.18% with members of the genus Deltapartitivirus on RdRp. Phylogenetic analysis based on RdRp also placed the new virus and other deltapartitiviruses together in a group, suggesting that this virus should be considered a new member of the genus Deltapartitivirus.


Asunto(s)
Camellia/virología , Virus ARN/genética , Secuenciación Completa del Genoma/métodos , Mapeo Contig , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Sistemas de Lectura Abierta , Filogenia , Virus ARN/clasificación , ARN Bicatenario/genética
15.
Arch Virol ; 165(1): 241-244, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31701224

RESUMEN

A novel virus was discovered in a Rosa wichuraiana Crep. by high-throughput sequencing and tentatively named "rose virus A" (RVA). Based on sequence identity and phylogenetic analysis, RVA represents a new member of the genus Carlavirus (family Betaflexiviridae). The genome of RVA is 8,849 nucleotides long excluding the poly(A) tail and contains six open reading frames (ORFs). The predicted ORFs code for a replicase, triple gene block (TGB), coat protein, and nucleic acid binding protein, as in a typical carlavirus. RVA is the first carlavirus identified in rose and has the highest nucleotide sequence similarity to poplar mosaic virus. Reverse transcription-PCR-based assays were developed to confirm the presence of RVA in the original source and to screen additional rose plants.


Asunto(s)
Carlavirus/genética , Rosa/virología , Secuenciación Completa del Genoma/métodos , Carlavirus/clasificación , Tamaño del Genoma , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento , Sistemas de Lectura Abierta , Filogenia
16.
Arch Virol ; 165(1): 87-96, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31707455

RESUMEN

In May 2017, high mortality of chickens and Muscovy ducks due to the H5N8 highly pathogenic avian influenza virus (HPAIV) was reported in the Democratic Republic of Congo (DR Congo). In this study, we assessed the molecular, antigenic, and pathogenic features in poultry of the H5N8 HPAIV from the 2017 Congolese outbreaks. Phylogenetic analysis of the eight viral gene segments revealed that all 12 DR Congo isolates clustered in clade 2.3.4.4B together with other H5N8 HPAIVs isolated in Africa and Eurasia, suggesting a possible common origin of these viruses. Antigenically, a slight difference was observed between the Congolese isolates and a representative virus from group C in the same clade. After intranasal inoculation with a representative DR Congo virus, high pathogenicity was observed in chickens and Muscovy ducks but not in Pekin ducks. Viral replication was higher in chickens than in Muscovy duck and Pekin duck organs; however, neurotropism was pronounced in Muscovy ducks. Our data confirmed the high pathogenicity of the DR Congo virus in chickens and Muscovy ducks, as observed in the field. National awareness and strengthening surveillance in the region are needed to better control HPAIVs.


Asunto(s)
Antígenos Virales/metabolismo , Subtipo H5N8 del Virus de la Influenza A/clasificación , Subtipo H5N8 del Virus de la Influenza A/patogenicidad , Gripe Aviar/inmunología , Enfermedades de las Aves de Corral/virología , África , Animales , Asia , Pollos , República Democrática del Congo , Patos/clasificación , Patos/virología , Europa (Continente) , Secuenciación de Nucleótidos de Alto Rendimiento , Subtipo H5N8 del Virus de la Influenza A/genética , Subtipo H5N8 del Virus de la Influenza A/aislamiento & purificación , Gripe Aviar/virología , Filogenia , Filogeografía , Enfermedades de las Aves de Corral/inmunología , Especificidad de la Especie , Replicación Viral
17.
Water Res ; 169: 115246, 2020 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-31710918

RESUMEN

In a one-year (October 2014-October 2015) pilot study, we assessed wastewater monitoring with sustained sampling for analysis of global enterovirus (EV) infections in an urban community. Wastewater was analysed by ultra-deep sequencing (UDS) after PCR amplification of the partial VP1 capsid protein gene. The nucleotide sequence analysis showed an unprecedented diversity of 48 EV types within the community, which were assigned to the taxonomic species A (n = 13), B (n = 23), and C (n = 12). During the same period, 26 EV types, of which 22 were detected in wastewater, were identified in patients referred to the teaching hospital serving the same urban population. Wastewater surveillance detected a silent circulation of 26 EV types including viruses reported in clinically rare respiratory diseases. Wastewater monitoring as a supplementary procedure can complement clinical surveillance of severe diseases related to non-polio EVs and contribute to the final stages of poliomyelitis eradication.


Asunto(s)
Infecciones por Enterovirus , Enterovirus , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Filogenia , Proyectos Piloto , Aguas Residuales
18.
Arch Virol ; 165(1): 105-114, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31741095

RESUMEN

Piwi-interacting RNAs (piRNAs) play pivotal roles in spermatogenesis and are widely distributed among somatic tissues. However, little is known about piRNAs in HeLa cells infected with coxsackievirus B3 (CVB3). In this study, we systematically investigated changes in piRNA expression in HeLa cells infected with CVB3 using high-throughput sequencing technology. piRNA expression profiles in CVB3-infected HeLa cells were examined at 3, 6 and 9 h postinfection (pi). Of the 32,826 piRNAs that were annotated in the NCBI database, 151,571, 89,698 and 76,626 piRNAs were detected in CVB3-infected HeLa cells at 3, 6 and 9 h pi, respectively. Compared with normal cells, 211, 72 and 94 piRNAs were differentially expressed in CVB3-infected HeLa cells at 3, 6 and 9 h pi, respectively. Thirteen piRNAs, including four novel piRNAs, exhibited concurrent changes in CVB3-infected HeLa cells. The changes in the expression of these 13 piRNAs was confirmed in CVB3-infected HeLa cells and 293T cells by stem-loop RT-qPCR at 3, 6 and 9 h pi. The target genes of 13 piRNAs were predicted. The four novel piRNAs were associated with LTR/ERV, LINE/L1 and LTR/ERVK repetitive elements located on different chromosomes. These findings may promote a better understanding of the regulatory mechanism of pathophysiological changes induced by CVB3 infection.


Asunto(s)
Infecciones por Coxsackievirus/genética , Enterovirus Humano B/patogenicidad , ARN Interferente Pequeño/genética , Regulación de la Expresión Génica , Células HEK293 , Células HeLa , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Análisis de Secuencia de ARN/métodos
19.
Arch Virol ; 165(1): 127-135, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31741097

RESUMEN

In clinical virome research, whole-genome/transcriptome amplification is required when starting material is limited. An improved method, named "template-dependent multiple displacement amplification" (tdMDA), has recently been developed in our lab (Wang et al. in BioTechniques 63:21-25. https://doi.org/10.2144/000114566, 2017). In combination with Illumina sequencing and bioinformatics pipelines, its application in virome sequencing was explored using a serum sample from a patient with chronic hepatitis C virus (HCV) infection. In comparison to an amplification-free procedure, virome sequencing via tdMDA showed a 9.47-fold enrichment for HCV-mapped reads and, accordingly, an increase in HCV genome coverage from 28.5% to 70.1%. Eight serum samples from acute patients liver failure (ALF) with or without known etiology were then used for virome sequencing with an average depth at 94,913x. Both similarity-based (mapping, NCBI BLASTn, BLASTp, and profile hidden Markov model analysis) and similarity-independent methods (machine-learning algorithms) identified viruses from multiple families, including Herpesviridae, Picornaviridae, Myoviridae, and Anelloviridae. However, their commensal nature and cross-detection ruled out an etiological interpretation. Together with a lack of detection of novel viruses in a comprehensive analysis at a resolution of single reads, these data indicate that viral agents might be rare in ALF cases with indeterminate etiology.


Asunto(s)
Biología Computacional/métodos , Hepatitis C Crónica/diagnóstico , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Fallo Hepático Agudo/virología , Suero/virología , Anelloviridae/aislamiento & purificación , Anelloviridae/fisiología , Perfilación de la Expresión Génica/métodos , Hepacivirus/genética , Hepacivirus/aislamiento & purificación , Hepatitis C Crónica/sangre , Herpesviridae/aislamiento & purificación , Herpesviridae/fisiología , Humanos , Fallo Hepático Agudo/sangre , Myoviridae/aislamiento & purificación , Myoviridae/fisiología , Picornaviridae/aislamiento & purificación , Picornaviridae/fisiología , Especificidad de la Especie , Simbiosis , Secuenciación Completa del Genoma/métodos
20.
J Forensic Sci ; 65(1): 259-265, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31411746

RESUMEN

DNA is one of the fastest growing tools in forensic sciences, increasing reliability in forensic reports and judgments. The use of DNA has increased in different areas of the forensic sciences, such as investigation of plant species, where plastid DNA has been used to elucidate and generate evidence in cases of traceability of genetically modified and controlled plants. Even with several advances and the practice of using DNA in forensic investigations, there are just few studies related to the identification of genetic tools for the characterization of drug and nondrug-types of Cannabis. Herein, the whole plastomes of two drug-type Cannabis are presented and have their structures compared with other Cannabis plastomes deposited in the GenBank, focusing in the forensic use of plastome sequences. The plastomes of Cannabis sativa "Brazuka" and of the hybrid Cannabis AK Royal Automatic presented general structure that does not differs from the reported for other C. sativa cultivars. A phylogenomic analyses grouped C. sativa "Brazuka" with the nondrug C. sativa cultivars, while the hybrid Cannabis AK Royal Automatic placed isolated, basal to this group. This suggests that the analysis of plastomes is useful toward genetic identification of hybrids in relation to C. sativa.


Asunto(s)
Cannabis/genética , Genoma de Plastidios , Plastidios/genética , ADN de Plantas , Bases de Datos de Ácidos Nucleicos , Ciencias Forenses , Secuenciación de Nucleótidos de Alto Rendimiento , Filogenia , Análisis de Secuencia de ADN
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