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1.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 37(1): 71-74, 2020 Jan 10.
Artigo em Chinês | MEDLINE | ID: mdl-31922602

RESUMO

OBJECTIVE: To explore the molecular basis for an individual with ABO subtype. METHODS: The ABO phenotype of the proband was determined by convention serological testing. Exons 6 and 7 of the ABO gene were subjected to PCR amplification and bi-directional Sanger sequencing. Haplotypes for exons 6 and 7 of the proband was determined using an ABO haplotype-specific amplification and sequencing technique. RESULTS: Red blood cells of the proband showed a 4+ agglutination strength with anti-A or anti-H, no agglutination reaction with anti-A1, and a 3+ agglutination strength with anti-B. His serum had no reaction with standard A cells, O cells or self cells, but was weakly reactive with B cells at 4℃. The proband was assigned as an ABO subtype based on his serological features. Bi-directional sequencing of the ABO gene revealed heterozygosity of 261 G/del, 297AG, 526CG, 657CT, 703GA, 803GC and 930GA, and homozygosity of 796CC in the proband. Haplotype-specific amplification and sequencing showed that one of his alleles was ABO*O.01.01, and another contained a c.796A>C variation compared with the ABO*B.01 allele, which led to replacement of methionine by leucine at position 266. Searching the ABO allele database of International Society of Blood Transfusion suggested the variation to be a novel one. CONCLUSION: The c.796A>C variation in the ABO*B.01 allele probably underlies the CisAB subtype. Accurate identification of the ABO subtype requires combined use of serological method and genetic testing.


Assuntos
Sistema do Grupo Sanguíneo ABO , Variação Genética , Sistema do Grupo Sanguíneo ABO/genética , Alelos , Éxons , Genótipo , Humanos , Masculino , Fenótipo , Análise de Sequência de DNA
2.
J Forensic Sci ; 65(1): 295-303, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30859587

RESUMO

A set of historic murders, known as the "Jack the Ripper murders," started in London in August 1888. The killer's identity has remained a mystery to date. Here, we describe the investigation of, to our knowledge, the only remaining physical evidence linked to these murders, recovered from one of the victims at the scene of the crime. We applied novel, minimally destructive techniques for sample recovery from forensically relevant stains on the evidence and separated single cells linked to the suspect, followed by phenotypic analysis. The mtDNA profiles of both the victim and the suspect matched the corresponding reference samples, fortifying the link of the evidence to the crime scene. Genomic DNA from single cells recovered from the evidence was amplified, and the phenotypic information acquired matched the only witness statement regarded as reliable. To our knowledge, this is the most advanced study to date regarding this case.


Assuntos
Vestuário , Impressões Digitais de DNA/métodos , Genética Forense/métodos , Homicídio/história , Manchas de Sangue , Vestuário/história , Vítimas de Crime , Criminosos , DNA Mitocondrial/genética , DNA Mitocondrial/isolamento & purificação , Fluorescência , História do Século XIX , Humanos , Raios Infravermelhos , Microdissecção e Captura a Laser , Reação em Cadeia da Polimerase , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Análise de Célula Única , Reino Unido , Sequenciamento Completo do Genoma
3.
Gene ; 726: 144154, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-31589962

RESUMO

In this work the complete chloroplast DNAs of Allium paradoxum and Allium ursinum, two edible species of Allium subg. Amerallium (the first lineage), were sequenced, assembled, annotated, and compared with complete Allium plastomes of the second and third evolutionary lines from GenBank database. The A. ursinum plastome contains 90 predicted genes (81 unique) including 5 pseudogenes, while A. paradoxum has 88 predicted genes (79 unique) including 19 pseudogenes. The comparative analysis has revealed that the A. paradoxum plastome differs markedly from those of other species. Due to many deletions, the A. paradoxum plastome is the shortest of known for Allium species, being only 145,819 bp long. The most prominent distinctions are (1) a 4825 bp long local inversion that spans from the ndhE to the rpl32 gene in the small single copy region and (2) pseudogenization, or the loss of all NADH-genes. In contrast, the plastome of A. ursinum - a species from the first evolutionary line (as well as A. paradoxum) - resembles the Allium species of the second and third evolutionary lines, showing no large rearrangements or discrepancies in gene content. It is unclear yet whether only A. paradoxum was affected by some evolutionary events or its close relatives from both sect. Briseis and other sections of Amerallium were altered as well. We speculate the sunlight-intolerant, shade-loving nature of A. paradoxum and the impairment of the ndh genes in its plastome could be interrelated phenomena.


Assuntos
Allium/genética , Rearranjo Gênico/genética , Genes de Plantas/genética , Cebolas/genética , DNA de Cloroplastos/genética , DNA de Plantas/genética , Evolução Molecular , Genoma de Cloroplastos/genética , Genoma de Planta/genética , Filogenia , Folhas de Planta/genética , Pseudogenes/genética , Análise de Sequência de DNA/métodos
4.
Gene ; 726: 144162, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-31639429

RESUMO

There has been long taxonomic debate on mulberry species (genus Morus) because the classification of mulberry species has relied on morphological characteristics. Although attempts for classifying mulberry species using molecular markers have been performed, phylogenetic relationships among diploid mulberry species remain unclear. In this study, we aim to investigate the genetic relationship between 54 diploid mulberry varieties belonging to seven different Morus species (M. alba, M. indica, M. bombycis, M. acidosa, M. latifolia, M. kagayamae, and M. rotundiloba) and one unspecified Morus species ('Enbu') using genome-wide SNP discovery and phylogenetic analysis via double-digest restriction site-associated DNA sequencing (ddRAD-seq). Genome-wide 2229 homozygous SNPs of 54 mulberry varieties in the eight species were identified by ddRAD-seq. Results of the phylogenetic analysis identified only three clear monophyletic clades in two Japanese native species, M. acidosa and M. kagayamae, which are found on different geographically isolated islands and a Thai species, M. rotundiloba, whereas the other species were non-monophyletic. Varieties of M. bombycis, another Japanese native species, were roughly classified into three groups. Of these, two M. bombycis groups were monophyletic with M. acidosa and M. kagayamae, respectively, while another M. bombycis group was not monophyletic. Varieties of M. indica, an Indian native species, were classified into two different monophyletic clades. Of these, one clade was clearly monophyletic with an indigenous variety in Kenya, 'Enbu', while another clade was monophyletic with M. rotundiloba and one M. latifolia variety. There were no clear monophyletic clades within M. alba and M. latifolia varieties, which could be a result of several hybridization events after their introductions from China to Japan. Our results suggested that it was difficult to clearly classify the hybridized mulberry varieties even with genome-wide DNA markers. In addition to phylogenetic analysis, we also evaluated morphological characteristics of mulberry leaves for each variety. The results of morphological evaluation indicated that leaf tip ratio may correlate to genetic difference among the two M. bombycis groups in monophyletic clades and another M. bombycis group in non-monophyletic clades. These results suggested that leaf tip ratio might be used for evaluating hybridization of M. bombycis varieties. Over all, our results may provide new insights into taxonomic debate of mulberry species.


Assuntos
Marcadores Genéticos/genética , Morus/genética , Polimorfismo de Nucleotídeo Único/genética , China , Frutas/genética , Estudo de Associação Genômica Ampla/métodos , Japão , Filogenia , Folhas de Planta/genética , Análise de Sequência de DNA/métodos
5.
Arch Virol ; 165(1): 43-51, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31676996

RESUMO

Inclusion body hepatitis (IBH), hydropericardium syndrome (HS), and gizzard erosion (GE) are all economically important diseases in the poultry industry worldwide and are all caused by fowl aviadenovirus (FAdV). It is important to identify the serotype of the virus to differentiate these diseases. In the present study, a total of six recent FAdV serotypes were isolated and identified in broiler and broiler-breeder flocks in Izmir, Manisa, and Aydin provinces of the Aegean region of Turkey between January and March 2019. The viruses were isolated from livers and pooled organs of chickens using primary chicken embryo kidney cell cultures (CEKC). Virus isolates were identified by PCR amplification of the loop 1 (L1) variable region of the hexon gene followed by Sanger sequencing. Sequence analysis revealed the presence of both FAdV-D (serotype 11) and FAdV-E (serotype 8b). The viruses that were isolated were associated with IBH, which is typically characterized by gross lesions such as enlarged and pale yellow liver with multiple petechial hemorrhages. Histopathological examination also showed necrotizing hepatitis with intranuclear inclusion bodies in hepatocytes. This study is the first report of the isolation and identification of FAdV serotypes associated with IBH in commercial broilers and broiler-breeder flocks in Turkey. The results of sequence analysis showed that FAdV-8b and FAdV-11 were the circulating serotypes that caused recent field outbreaks of IBH in the Aegean region between January and March, 2019.


Assuntos
Infecções por Adenoviridae/virologia , Aviadenovirus/classificação , Doenças das Aves Domésticas/virologia , Análise de Sequência de DNA/métodos , Animais , Aviadenovirus/genética , Aviadenovirus/isolamento & purificação , Células Cultivadas , Galinhas , Corpos de Inclusão/virologia , Rim/citologia , Rim/virologia , Fígado/virologia , Filogenia , Sorotipagem , Turquia
6.
J Forensic Sci ; 65(1): 283-287, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31436852

RESUMO

Species identification of necrophagous insects found on a dead body is an essential key in applying medicolegal entomology to the estimation of postmortem interval (PMI). Due to limited morphological identification of insect evidence, several studies have identified species using molecular information such as DNA markers. While considerable cytochrome c oxidase subunit I (COI) gene sequence data of necrophagous fly species have been collected and annotated, those of necrophagous beetle species have not. Since necrophagous beetles such as Dermestes species have a larval period longer than that of flies, beetles are useful in even the late decomposition phase in estimating minimum PMI. To obtain the full-length COI gene sequences of six Dermestes species collected from South Korea, we designed primers for polymerase chain reaction amplification and sequencing. The obtained full COI nucleotide sequences were used for performing phylogenic analysis and comparison with previously reported sequences. The results demonstrated that the COI gene sequences could be used to identify forensically important Dermestes species in South Korea.


Assuntos
Besouros/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Análise de Sequência de DNA , Animais , Primers do DNA , Larva , Filogenia , Reação em Cadeia da Polimerase , República da Coreia , Especificidade da Espécie
7.
J Forensic Sci ; 65(1): 259-265, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31411746

RESUMO

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.


Assuntos
Cannabis/genética , Genomas de Plastídeos , Plastídeos/genética , DNA de Plantas , Bases de Dados de Ácidos Nucleicos , Ciências Forenses , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Análise de Sequência de DNA
8.
APMIS ; 128(1): 3-9, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31628675

RESUMO

Biliary tract cancers (BTC) are a rare heterogeneous disease group with a dismal prognosis and limited treatment options. The mutational landscape consists of genetic aberrations both shared by and characteristic for anatomical location. Here, we present exome sequencing data on 22 genes from a phase 2 trial using a clinically validated panel used in patients with colorectal cancer. A total of 56 patients were included in a one-armed phase 2 trial investigating the treatment combination of capecitabine, gemcitabine, oxaliplatin, and cetuximab. Tissue DNA yield and quality allowed analysis of 30 patients on our panel including 22 genes. ARID1A (33%) and TP53 (33%) were found to be most frequently mutated followed by KRAS mutations found in 20% of the patients. Mutational aberrations in ARID1A were found more prevalent than expected, whereas TP53 and KRAS were in concordance with earlier reported data. Mutation in CTNNB1 was significantly associated with poor prognosis. Our panel is clinically validated and suitable for a high volume of samples to detect mutations in patients with BTC. However, it is reasonable to assume that the clinical utility could be optimized in this patient group by extending the panel to include BTC specific mutations with potential therapeutic consequences such as IDH1/2, FGFR fusions, ERBB3, and BRCA1/2.


Assuntos
Neoplasias dos Ductos Biliares/genética , Exoma , Mutação , Adulto , Idoso , Antineoplásicos/uso terapêutico , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Neoplasias dos Ductos Biliares/tratamento farmacológico , Estudos de Coortes , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Proteínas Nucleares/genética , Inclusão em Parafina , Prognóstico , Proteínas Proto-Oncogênicas p21(ras)/genética , Análise de Sequência de DNA , Fatores de Transcrição/genética , Proteína Supressora de Tumor p53/genética , beta Catenina/genética
9.
An Bras Dermatol ; 94(6): 658-663, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31789248

RESUMO

BACKGROUND: Palmoplantar pustulosis is considered to be a localized pustular psoriasis confined to the palms and soles. Mutation of the IL36RN gene, encoding interleukin-36 receptor antagonist (IL-36Ra), is associated with generalized pustular psoriasis, but IL36RN mutations in Chinese palmoplantar pustulosis patients have not previously been investigated. OBJECTIVE: The aim of this study was to evaluate the mutation of IL36RN in Chinese patients with palmoplantar pustulosis. METHODS: Fifty-one Han Chinese patients with palmoplantar pustulosis were recruited. All exons and exon-intron boundary sequences of IL36RN were amplified in polymerase chain reactions, and Sanger sequencing of the amplicons was performed. RESULTS: Among the 51 palmoplantar pustulosis patients, four different single-base substitutions were identified in nine patients. The mutations were c.140A>G/p.Asn47Ser in five patients, c.258G>A/p.Met86IIe in two patients, and c.115+6T>C and c.169G>A/p.Val57IIe in one patient each. All mutations were heterozygous. Comparison with the human genome database and reported literature suggested that these variants may not be pathogenic mutations causing palmoplantar pustulosis. Furthermore, there was no difference in disease severity, onset age, or disease duration between patients with these heterozygous IL36RN variants and those without (p>0.1). STUDY LIMITATION: Lack of the further evaluation of IL36Ra protein in palmoplantar pustulosis lesions. CONCLUSIONS: The four variants of IL36RN identified did not appear to be associated with the specific phenotypes of palmoplantar pustulosis.


Assuntos
Interleucinas/genética , Mutação , Psoríase/genética , Adulto , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Grupo com Ancestrais do Continente Asiático/genética , China , Feminino , Dermatoses do Pé/genética , Dermatoses do Pé/patologia , Estudos de Associação Genética , Dermatoses da Mão/genética , Dermatoses da Mão/patologia , Heterozigoto , Humanos , Masculino , Pessoa de Meia-Idade , Fenótipo , Psoríase/patologia , Análise de Sequência de DNA , Estatísticas não Paramétricas
10.
Zhonghua Yu Fang Yi Xue Za Zhi ; 53(12): 1271-1277, 2019 Dec 06.
Artigo em Chinês | MEDLINE | ID: mdl-31795585

RESUMO

Objective: The genetic characteristics of the human adenovirus type 53 (HAdV-53) strains isolated from Taiyuan city of Shanxi Province were studied to obtain the baseline data of their molecular characteristics. Methods: Conjunctival swabs (n=79) were collected from epidemic keratoconjunctivitis (EKC) patients in Shanxi eye Hospital in 2016, and five HAdV-53 strains were obtained after virus isolation and identification based on the three major capsid genes sequences including Penton base, Hexon and Fiber gene. And the corresponding sequences of global epidemic HAdV-53 strains and the strains with the same genetic origin as HAdV-53 were also downloaded from GenBank database, and then the three gene database were established, respectively. With the database, phylogenetic tree was constructed, and the genetic and molecular evolutionary characteristics were analyzed with bioinformatics software. Results: Five HAdV-53 strains in Shanxi Province in 2016 showed high consistency with the HAdV-53 strains prevalent in other countries in 1996-2014 (>99.8%). All HAdV-53 strains were in the same evolutionary branch with their recombinant source genotypes (HAdV-37 and HAdV-8) in Penton base and Fiber gene, respectively, and maintained a high degree of consistency in gene sequences. In Hexon gene, HAdV-53 strains were more closed to its recombinant source genotype HAdV-22, the nucleotide and amino acid sequences between two types were highly homologous, while HAdV-53 and HAdV-22 belonged to different evolutionary branches, and the evolution rate of HAdV-53 based on Hexon gene was 3.51×10(-5) substitution/site/year. Conclusion: HAdV-53 has become an important new ocular infectious pathogen of Taiyuan. HAdV-53 strain are relatively conservative and stable based on Penton base, Hexon, and Fiber gene.


Assuntos
Infecções por Adenovirus Humanos/diagnóstico , Adenovírus Humanos/genética , Adenovírus Humanos/isolamento & purificação , Infecções por Adenovirus Humanos/epidemiologia , China/epidemiologia , Humanos , Filogenia , Prevalência , Análise de Sequência de DNA
11.
Anticancer Res ; 39(12): 6595-6602, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31810925

RESUMO

BACKGROUND/AIM: Non-invasive biomarker detection using DNA from cell-free circulating DNA (cfDNA) and circulating tumor cells (ctcDNA) are emerging as they can be used for early diagnosis, prognosis and therapeutic target selection for cancer. However, cfDNA and ctcDNA from the same patient have not yet been compared extensively on how different the genetic characteristics of the two are in terms of the overlap between them. MATERIALS AND METHODS: The performance of a customized NGS panel was used to compare the variants found in the 20 pairs of cfDNA and ctcDNA from gynecological cancer patients. RESULTS: A genetic variant analysis revealed that there were only nine common overlapping variants out of 63 between the cfDNA and ctcDNA pairs, while 31 and 22 were unique to cfDNA and ctcDNA, respectively. CONCLUSION: A combinatory analysis of both cfDNA and CTCs from cancer patients can improve the sensitivity of liquid biopsies. These results are expected to provide better genetic target information for guiding clinical strategies for cancer.


Assuntos
Ácidos Nucleicos Livres/genética , DNA Tumoral Circulante/genética , Variação Genética , Neoplasias dos Genitais Femininos/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/genética , Linhagem Celular Tumoral , DNA de Neoplasias/genética , Feminino , Neoplasias dos Genitais Femininos/tratamento farmacológico , Humanos , Pessoa de Meia-Idade , Análise de Sequência de DNA/métodos
12.
Fa Yi Xue Za Zhi ; 35(5): 602-606, 2019 Oct.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31833297

RESUMO

Abstract: Single-cell sequencing is a technique that analyzes DNA and RNA sequences on the cellular level with next generation sequencing. The ultra high resolution of single-cell sequencing provides new perspectives and opens new frontiers for our understanding of many areas of life sciences, including forensic genome. This paper summarizes the recent advancements in single-cell sequencing and the prospect of its forensic application.


Assuntos
Genética Forense , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA/métodos , DNA , Humanos
14.
Huan Jing Ke Xue ; 40(8): 3699-3705, 2019 Aug 08.
Artigo em Chinês | MEDLINE | ID: mdl-31854778

RESUMO

To better understanding the microbial composition of activated sludge (AS), unique OTUs and their indicators were examined and SourceTracker was used to identify possible source environments for AS communities to thrive in 15 cities across China, based on 16S rRNA gene sequencing. This may help reveal the underlying mechanisms of AS community composition formations in various areas. The results indicated that the dominant phyla in AS in each city were similar; Proteobacteria, Bacteroidetes, and Chloroflexi made up 94.53%-97.04% of the whole microbial communities. Geographic location and environmental conditions were identified as having an effect on microbial compositions. Cities located toward to the edge of China or along the coast tended to harbor more unique OTUs. Moreover, the composition of indicators in wastewater treatment plants (WWTPs) near the sea were more similar, while no indicators were detected in WWTPs in Chengdu and Chongqing. Source environments for AS microbial communities also depended on location and environmental conditions. Overall, microbes from 'plant' and 'soil' sources accounted for a large proportion of the AS microbial communities in each city, while bacteria from 'marine' sources were only detected in coastal AS communities. Cities with more rivers and lakes tended to have more bacteria originating from 'fresh water' sources. Since most of the WWTPs in China play a role in treating industrial wastewater, industrial wastewater was also an important source environment. However, few bacteria originating from the human digestive system were identified in the AS communities. Moreover, a large proportion of bacteria (36%-70%) originated from unknown sources not included in the source database, such as sewage infrastructure, indicating that the source database will need to be expanded in the future.


Assuntos
Microbiota , Águas Residuárias , China , Cidades , RNA Ribossômico 16S , Análise de Sequência de DNA , Esgotos , Microbiologia da Água
15.
Sheng Wu Gong Cheng Xue Bao ; 35(12): 2284-2294, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31880136

RESUMO

With the development of liquid biopsy technology, plasma cell-free DNA (cfDNA) becomes one of the research hotspots. Whole-genome bisulfite sequencing of plasma cell-free DNA has shown great potential medical applications such as cancer detection. However, the practical stability evaluation is still lacking. In this study, plasma cell-free DNA samples from two volunteers at different time were collected and prepared for sequencing in multiple laboratories. The library preparation strategies include pre-bisulfite, post-bisulfite and regular whole-genome sequencing. We established a set of quality control references for plasma cell-free DNA sequencing data and evaluated practical stability of blood collection, DNA extraction, and library preparation and sequencing depth. This work provided a technical practice guide for the application of plasma cfDNA methylation sequencing for clinical applications.


Assuntos
Sequenciamento Completo do Genoma , Ácidos Nucleicos Livres , Metilação de DNA , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Análise de Sequência de DNA , Sulfitos
16.
Pol J Microbiol ; 68(4): 527-539, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31880896

RESUMO

Ulleungdo and Dokdo are volcanic islands with an oceanic climate located off the eastern coast of South Korea. In the present study, we used barcoded Illumina MiSeq to analyze eukaryotic microalgal genera collected from Seonginbong, the highest peak on Ulleungdo, and from groundwater sites on Dongdo and Seodo Islands, which are part of Dokdo. Species richness was significantly greater in the Seonginbong samples than in the Dongdo and Seodo samples, with 834 operational taxonomic units (OTUs) identified from Seonginbong compared with 203 OTUs and 182 OTUs from Dongdo and Seodo, respectively. Taxonomic composition analysis was also used to identify the dominant microalgal phyla at each of the three sites, with Chlorophyta (green algae) the most abundant phyla on Seonginbong and Dongdo, and Bacillariophyta (diatoms) the most abundant on Seodo. These findings suggest that differences in the abundances of Chlorophyta and Bacillariophyta species in the Seonginbong, Dongdo, and Seodo samples are due to variations in species richness and freshwater resources at each sampling location. To the best of our knowledge, this is the first report to detail freshwater microalgal communities on Ulleungdo and Dokdo. As such, the number of species identified in the Seonginbong, Dongdo, and Seodo samples might be an indicator of the ecological differences among these sites and varying characteristics of their microbial communities. Information regarding the microalgal communities also provides a basis for understanding the ecological interactions between microalgae species and other eukaryotic microorganisms.Ulleungdo and Dokdo are volcanic islands with an oceanic climate located off the eastern coast of South Korea. In the present study, we used barcoded Illumina MiSeq to analyze eukaryotic microalgal genera collected from Seonginbong, the highest peak on Ulleungdo, and from groundwater sites on Dongdo and Seodo Islands, which are part of Dokdo. Species richness was significantly greater in the Seonginbong samples than in the Dongdo and Seodo samples, with 834 operational taxonomic units (OTUs) identified from Seonginbong compared with 203 OTUs and 182 OTUs from Dongdo and Seodo, respectively. Taxonomic composition analysis was also used to identify the dominant microalgal phyla at each of the three sites, with Chlorophyta (green algae) the most abundant phyla on Seonginbong and Dongdo, and Bacillariophyta (diatoms) the most abundant on Seodo. These findings suggest that differences in the abundances of Chlorophyta and Bacillariophyta species in the Seonginbong, Dongdo, and Seodo samples are due to variations in species richness and freshwater resources at each sampling location. To the best of our knowledge, this is the first report to detail freshwater microalgal communities on Ulleungdo and Dokdo. As such, the number of species identified in the Seonginbong, Dongdo, and Seodo samples might be an indicator of the ecological differences among these sites and varying characteristics of their microbial communities. Information regarding the microalgal communities also provides a basis for understanding the ecological interactions between microalgae species and other eukaryotic microorganisms.


Assuntos
Microalgas/isolamento & purificação , Clorófitas/classificação , Clorófitas/genética , Diatomáceas/classificação , Diatomáceas/genética , Diatomáceas/isolamento & purificação , Água Doce/análise , Ilhas , Microalgas/classificação , Microalgas/genética , Filogenia , Análise de Sequência de DNA
17.
Clin Biochem ; 74: 60-68, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31669510

RESUMO

BACKGROUND: Colorectal cancer (CRC) is one of the most common cancers worldwide, and emerging lines of evidence have implicated circular RNAs (circRNAs), a novel class of endogenous noncoding RNAs, in CRC development. However, whether plasma circRNAs might be novel diagnostic biomarkers for CRC remains unclear. METHODS: We investigated the plasma levels of selected circRNAs by quantitative real-time PCR (qRT-PCR). The presence of the candidate circRNAs was confirmed through RNase R assays, qRT-PCR and DNA sequencing, and their diagnostic value was evaluated using a receiver operating characteristic (ROC) curve. RESULTS: The plasma levels of three circRNAs (circ-CCDC66, circ-ABCC1 and circ-STIL) were significantly decreased in CRC patients (n = 45) compared with healthy controls (n = 61). The ROC curve analysis showed that the area under the ROC curve (AUC) of the three-circRNA panel was 0.780, which is higher than that of traditional protein biomarkers, such as carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9). Combining the circRNA panel with CEA and CA19-9 might improve the ability to diagnose CRC (AUC = 0.855). In addition, the plasma circ-ABCC1 level was related to tumor growth and progression, and the plasma circ-CCDC66 and circ-ABCC1 levels were decreased in precursor lesions of CRC, including colon adenomas and adenomatous polyps. More importantly, circ-CCDC66 and circ-STIL were found to be useful for diagnosing early-stage CRC, and the three-circRNA panel improved the ability to diagnose CEA-negative and CA19-9-negative CRC. CONCLUSION: Our study provides the first identification of a panel of three plasma circRNAs that could serve as a novel and independent diagnostic biomarker for CRC.


Assuntos
Biomarcadores Tumorais/sangue , Neoplasias Colorretais/sangue , Neoplasias Colorretais/diagnóstico , /sangue , Adenoma/sangue , Pólipos Adenomatosos/sangue , Idoso , Antígenos Glicosídicos Associados a Tumores/sangue , Biomarcadores Tumorais/genética , Antígeno Carcinoembrionário/sangue , Estudos de Coortes , Neoplasias do Colo/sangue , Detecção Precoce de Câncer , Feminino , Humanos , Modelos Logísticos , Metástase Linfática , Masculino , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Curva ROC , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de DNA
18.
Int J Syst Evol Microbiol ; 69(12): 3702-3709, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31671048

RESUMO

Strain YZ-8T, isolated from soil sampled at Fildes Peninsula, Antarctica, was found to be a Gram-stain-negative, yellow-pigmented, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain YZ-8T grewoptimally at pH 7.0 and 20 °C. Tolerance to NaCl was up to 0.3 % (w/v) with optimum growth in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YZ-8T belonged to the family Sphingomonas. Strain YZ-8T showed the highest sequence similarities to Sphingomonas molluscorum KMM 3882T (94.4 %), Sphingomonas oligophenolica JCM 12082T (94.4 %), Sphingomonas gotjawalisoli SN6-9T (94.3 %) and Sphingomonas aquatica W1-2-1T (94.3 %). The predominant respiratory isoprenoid quinone and polyamine components were identified as ubiquinone Q-10 and sym-homospermidine, respectively. In addition, carotenoid were also found. The polar lipid profile of the strain YZ-8T was found to contain one phosphatidylethanolamine, an unidentified phospholipid, one diphosphatidylglycerol, one phosphatidylglycerol, two sphingophosphonolipids, one phosphatidylcholine and two unidentified alkali-stable lipids. The G+C content of the genomic DNA was determined to be 58.8 mol%. The main fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 35.4 %), summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c; 32.6 %) and C14 : 0 2-OH (7.7 %). On the basis of the evidence presented in this study, a novel species of the genus Sphingomonas, Sphingomonaspaeninsulae sp. nov., is proposed, with the type strain YZ-8T (=CCTCC AB 2017137T=LMG 31027T).


Assuntos
Filogenia , Microbiologia do Solo , Sphingomonas/classificação , Regiões Antárticas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espermidina/análogos & derivados , Espermidina/química , Sphingomonas/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
20.
Parasit Vectors ; 12(1): 518, 2019 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-31685017

RESUMO

BACKGROUND: Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular C. trachomatis previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia (A/SA1). No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan. METHODS: This study sequenced twenty ocular C. trachomatis isolates to improve understanding of pathogen diversity in North-East Africa and examine for genomic variation specific to Sudan, possibly related to the persistence of trachoma in surveyed communities. High quality, whole genome sequences were obtained from 12/20 isolates. RESULTS: All isolates were serovar A and had tarP and trpA sequences typical of classical, ocular C. trachomatis isolates. The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of C. trachomatis phylogeny distinct from geographically disparate ocular isolates, with little intra-population diversity. We found 333 SNPs that were conserved in Sudanese ocular isolates but rare compared to other ocular C. trachomatis populations, which were focused in two genomic loci (CTA0172-CTA0173 and CTA0482). CONCLUSIONS: Limited intra-population diversity and geographical clustering of ocular C. trachomatis suggests minimal transmission between and slow diversification within trachoma-endemic communities. However, diversity may have been higher pre-treatment in these communities. Over-representation of Sudan-specific SNPs in three genes suggests they may have an impact on C. trachomatis growth and transmission in this population.


Assuntos
Chlamydia trachomatis/genética , Genoma Bacteriano , Tracoma/microbiologia , Sequenciamento Completo do Genoma , Antibacterianos/administração & dosagem , Azitromicina/administração & dosagem , Pré-Escolar , Chlamydia trachomatis/classificação , Chlamydia trachomatis/isolamento & purificação , Túnica Conjuntiva/microbiologia , Estudos Transversais , DNA Bacteriano/química , Frequência do Gene , Variação Estrutural do Genoma/genética , Humanos , Lactente , Funções Verossimilhança , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA , Sudão/epidemiologia , Tracoma/tratamento farmacológico , Tracoma/epidemiologia
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