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1.
Cytogenet Genome Res ; 161(3-4): 213-222, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34233333

RESUMO

The genera of the tribe Triticeae (family Poaceae), constituting many economically important plants with abundant genetic resources, carry genomes such as St, H, P, and Y. The genome symbol of Roegneria C. Koch (Triticeae) is StY. The St and Y genomes are crucial in Triticeae, and tetraploid StY species participate extensively in polyploid speciation. Characterization of St and Y nonhomologous chromosomes in StY-genome species could help understand variation in the chromosome structure and differentiation of StY-containing species. However, the high genetic affinity between St and Y genome and the deficiency of a complete set of StY nonhomologous probes limit the identification of St and Y genomes and variation of chromosome structures among Roegneria species. We aimed to identify St- and Y-enhanced repeat clusters and to study whether homoeologous chromosomes between St and Y genomes could be accurately identified due to high affinity. We employed comparative genome analyses to identify St- and Y-enhanced repeat clusters and generated a FISH-based karyotype of R. grandis (Keng), one of the taxonomically controversial StY species, for the first time. We explored 4 novel repeat clusters (StY_34, StY_107, StY_90, and StY_93), which could specifically identify individual St and Y nonhomologous chromosomes. The clusters StY_107 and StY_90 could identify St and Y addition/substitution chromosomes against common wheat genetic backgrounds. The chromosomes V_St, VII_St, I_Y, V_Y, and VII_Y displayed similar probe distribution patterns in the proximal region, indicating that the high affinity between St and Y genome might result from chromosome rearrangements or transposable element insertion among V_St/Y, VII_St/Y, and I_Y chromosomes during allopolyploidization. Our results can be used to employ FISH further to uncover the precise karyotype based on colinearity of Triticeae species by using the wheat karyotype as reference, to analyze diverse populations of the same species to understand the intraspecific structural changes, and to generate the karyotype of different StY-containing species to understand the interspecific chromosome variation.


Assuntos
Cromossomos de Plantas/genética , Elymus/genética , Genoma de Planta/genética , Hibridização in Situ Fluorescente/métodos , Evolução Molecular , Marcadores Genéticos/genética , Cariótipo , Região Organizadora do Nucléolo/genética , Poliploidia , Sequências Repetitivas de Ácido Nucleico/genética , Tetraploidia , Triticum/genética
2.
Front Immunol ; 12: 615859, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34220794

RESUMO

Purpose: Systemic lupus erythematosus (SLE) is a serious autoimmune disease. Its molecular pathogenesis, especially the long non-coding RNA (lncRNA) function, remains unclear. We want to investigate the lncRNA dysregulation profile and their molecular mechanisms in SLE. Methods: In this study, we analyzed the transcriptome profiles (RNA-seq) of peripheral blood mononuclear cells (PBMCs) from SLE patients and two published transcriptome datasets to explore lncRNA profiles. The differentially expressed lncRNAs were confirmed by quantitative real-time PCR in another set of female patients. We constructed the lncRNA-mRNA regulatory networks by performing weighted gene co-expression network analysis (WGCNA). Dysregulated lncRNA AC007278.2 was repressed by short hairpin RNA (shRNA) in Jurkat cells. Dual-luciferase reporter gene assay was performed to investigate the regulatory mechanism of AC007278.2 on target gene CCR7. Results: We observed dominant up-regulation of transcripts, including mRNAs and lncRNAs, in SLE patients. By WGCNA method, we identified three modules that were highly related to SLE. We then focused on one lncRNA, AC007278.2, with a T-helper 1 lineage-specific expression pattern. We observed consistently higher AC007278.2 expression in SLE patients. Co-expression network revealed that AC007278.2 participated in the innate immune response and inflammatory bowel disease pathways. By knocking down AC007278.2 expression, we found that AC007278.2 could regulate the expression of inflammatory and cytokine stimulus response-related genes, including CCR7, AZU1, and TNIP3. AC007278.2 inhibits the functional CCR7 promoter to repress its transcription, thereby regulating autoimmunity and follicular T-helper cell differentiation. Conclusion: In summary, our study indicated the important regulatory role of lncRNAs in SLE. AC007278.2 may be treated as a novel biomarker for SLE diagnosis and treatment.


Assuntos
Centro Germinativo/imunologia , Lúpus Eritematoso Sistêmico/genética , RNA Longo não Codificante/genética , Receptores CCR7/metabolismo , Células Th1/fisiologia , Autoimunidade/genética , Diferenciação Celular , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Marcadores Genéticos/genética , Humanos , Células Jurkat , Lúpus Eritematoso Sistêmico/diagnóstico , RNA Interferente Pequeno/genética , Receptores CCR7/genética , Transcriptoma , Regulação para Cima
3.
Sci Rep ; 11(1): 12174, 2021 06 09.
Artigo em Inglês | MEDLINE | ID: mdl-34108608

RESUMO

With many countries strapped for medical resources due to the COVID-19 pandemic, it is highly desirable to allocate the precious resources to those who need them the most. Several markers have been found to be associated with the disease severity in COVID-19 patients. However, the established markers only display modest prognostic power individually and better markers are urgently needed. The aim of this study is to investigate the potential of S100A12, a prominent marker gene for bacterial infection, in the prognosis of disease severity in COVID-19 patients. To ensure the robustness of the association, a total of 1695 samples from 14 independent transcriptome datasets on sepsis, influenza infection and COVID-19 infection were examined. First, it was demonstrated that S100A12 was a marker for sepsis and severity of sepsis. Then, S100A12 was found to be a marker for severe influenza infection, and there was an upward trend of S100A12 expression as the severity level of influenza infection increased. As for COVID-19 infection, it was found that S100A12 expression was elevated in patients with severe and critical COVID-19 infection. More importantly, S100A12 expression at hospital admission was robustly correlated with future quantitative indexes of disease severity and outcome in COVID-19 patients, superior to established prognostic markers including CRP, PCT, d-dimer, ferritin, LDH and fibrinogen. Thus, S100A12 is a valuable novel prognostic marker for COVID-19 severity and deserves more attention.


Assuntos
COVID-19/diagnóstico , COVID-19/genética , Regulação da Expressão Gênica , Proteína S100A12/genética , Índice de Gravidade de Doença , Adulto , Feminino , Marcadores Genéticos/genética , Humanos , Influenza Humana/diagnóstico , Influenza Humana/genética , Masculino , Prognóstico , RNA Mensageiro/genética
4.
Nat Commun ; 12(1): 3770, 2021 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-34145282

RESUMO

Circulating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.


Assuntos
Biomarcadores Tumorais/genética , DNA Tumoral Circulante/genética , Marcadores Genéticos/genética , Neoplasias/genética , Análise Mutacional de DNA/métodos , Frequência do Gene/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mutação/genética , Neoplasias/sangue , Neoplasias/patologia
5.
Genes (Basel) ; 12(5)2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-34069791

RESUMO

In the North Eastern Himalayan region (NEHR) of India, maize is an important food crop. The local people cultivate the maize landraces and consume them as food. However, these landraces are deficient in ß-carotene content. Thus, we aimed to incorporate the crtRB1 gene from UMI285ß+ into the genetic background of the NEHR maize landrace, Yairipok Chujak (CAUM66), and thereby enhance the ß-carotene content through marker-assisted backcrossing (MABC). In this regard, we backcrossed and screened BC1F1 and BC2F1 plants possessing the heterozygous allele for crtRB1 and then screened with 106 polymorphic simple sequence repeat (SSR) markers. The plants having maximum recurrent parent genome recovery (RPGR) were selected in each generation and selfed to produce BC2F2 seeds. In the BC2F2 generation, four plants (CAUM66-54-9-12-2, CAUM66-54-9-12-11, CAUM66-54-9-12-13, and CAUM66-54-9-12-24) having homozygous crtRB1-favorable allele with maximum RPGR (86.74-90.16%) were selected and advanced to BC2F3. The four selected plants were selfed to produce BC2F3 and then evaluated for agronomic traits and ß-carotene content. The agronomic performance of the four lines was similar (78.83-99.44%) to that of the recurrent parent, and ß-carotene content (7.541-8.711 µg/g) was on par with the donor parent. Our study is the first to improve the ß-carotene content in NEHR maize landrace through MABC. The newly developed lines could serve as potential resources to further develop nutrition-rich maize lines and could provide genetic stock for use in breeding programs.


Assuntos
Genes de Plantas/genética , Marcadores Genéticos/genética , Zea mays/genética , beta Caroteno/genética , Alelos , Endogamia/métodos , Índia , Repetições de Microssatélites/genética , Fenótipo , Melhoramento Vegetal/métodos , Polimorfismo Genético/genética
6.
Int J Infect Dis ; 107: 234-241, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33940188

RESUMO

BACKGROUND: Recent studies showed the first emergence of the R561H artemisinin-associated resistance marker in Africa, which highlights the importance of continued molecular surveillance to assess the selection and spread of this and other drug resistance markers in the region. METHOD: In this study, we used targeted amplicon deep sequencing of 116 isolates collected in two areas of Cameroon to genotype the major drug resistance genes, k13, crt, mdr1, dhfr, and dhps, and the cytochrome b gene (cytb) in Plasmodium falciparum. RESULTS: No confirmed or associated artemisinin resistance markers were observed in Pfk13. In comparison, both major and minor alleles associated with drug resistance were found in Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps. Notably, a high frequency of other nonsynonymous mutations was observed across all the genes, except for Pfcytb, suggesting continued selection pressure. CONCLUSIONS: The results from this study supported the continued use of artemisinin-based combination therapy and administration of sulfadoxine-pyrimethamine for intermittent preventive therapy in pregnant women, and for seasonal chemoprevention in these study sites in Cameroon.


Assuntos
Antimaláricos/farmacologia , Resistência a Medicamentos/genética , Marcadores Genéticos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Plasmodium falciparum/efeitos dos fármacos , Plasmodium falciparum/genética , Alelos , Camarões , Feminino , Genótipo , Humanos , Mutação , Plasmodium falciparum/isolamento & purificação , Gravidez
7.
Am J Surg ; 221(6): 1159-1163, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33849710

RESUMO

INTRODUCTION: The use of restricted versus expanded panel genetic testing in breast cancer is controversial, with some institutions offering predominantly abbreviated gene panel testing. Our community program has offered larger panel testing for several years. We sought to evaluate the outcomes of large panel genetic testing and understand their impact on patient care. METHODS: A retrospective review of our multi-institutional tumor registry was performed from 2015 to 2018 for patients undergoing surgery for breast cancer. Referral to genetic counseling and outcomes of panel testing were examined. RESULTS: 2237 patients met study criteria. Median age was 63 years (range 22-99). Eight hundred and thirty-eight patients (37.4%) were referred for genetic counseling. Of these patients, 509 (60.7%) had negative results, 108 (12.8%) had deleterious mutations (37 not included in abbreviated panels), and 221 (26.3%) had variants of undetermined significance (VUS). Bilateral mastectomy rates for patients with deleterious mutations were 53.7%, versus 31% for negative and 32.6% for VUS. DISCUSSION: Large panel testing finds a significant number of actionable mutations. The increased identification of VUS did not result in higher mastectomy rates.


Assuntos
Neoplasias da Mama/genética , Testes Genéticos , Mastectomia/estatística & dados numéricos , Academias e Institutos , Adulto , Idoso , Idoso de 80 Anos ou mais , Neoplasias da Mama/cirurgia , Serviços de Saúde Comunitária , Feminino , Aconselhamento Genético/métodos , Aconselhamento Genético/estatística & dados numéricos , Marcadores Genéticos/genética , Predisposição Genética para Doença/genética , Testes Genéticos/métodos , Humanos , Pessoa de Meia-Idade , Mutação/genética , Sistema de Registros , Estudos Retrospectivos , Resultado do Tratamento , Adulto Jovem
8.
Cancer Med ; 10(10): 3177-3187, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33838014

RESUMO

OBJECTIVE: Accumulating evidence from recent molecular diagnostic studies has indicated the prognostic significance of various genetic markers for patients with glioblastoma (GBM). To evaluate the impact of such genetic markers on prognosis, we retrospectively analyzed the outcomes of patients with IDH-wildtype GBM in our institution. In addition, to assess the impact of bevacizumab (BEV) treatment, we compared overall survival (OS) between the pre- and post-BEV eras. METHODS: We analyzed the data of 100 adult patients (over 18 years old) with IDH-wildtype GBM from our database between February 2006 and October 2018. Genetic markers, such as MGMT methylation status, EGFR amplification, CDKN2A homozygous deletion, and clinical factors were analyzed by evaluating the patients' OS. RESULTS: CDKN2A homozygous deletion showed no significant impact on OS in patients with methylated MGMT status (p = 0.5268), whereas among patients with unmethylated MGMT status, there was a significant difference in OS between patients with and without CDKN2A homozygous deletion (median OS: 14.7 and 16.9 months, respectively, p = 0.0129). This difference was more evident in the pre-BEV era (median OS: 10.1 and 15.6 months, respectively, p = 0.0351) but has become nonsignificant in the post-BEV era (median OS: 16.0 and 16.9 months, respectively, p = 0.1010) due to OS improvement in patients with CDKN2A homozygous deletion. However, these findings could not be validated in The Cancer Genome Atlas cohort. CONCLUSIONS: MGMT and CDKN2A status subdivided our cohort into three race-specific groups with different prognoses. Our findings indicate that BEV approval in Japan led to OS improvement exclusively for patients with concurrent unmethylated MGMT status and CDKN2A homozygous deletion.


Assuntos
Neoplasias Encefálicas/genética , Inibidor p16 de Quinase Dependente de Ciclina/genética , Metilases de Modificação do DNA/genética , Enzimas Reparadoras do DNA/genética , Glioblastoma/genética , Isocitrato Desidrogenase/genética , Deleção de Sequência/genética , Proteínas Supressoras de Tumor/genética , Idoso , Antineoplásicos Imunológicos/uso terapêutico , Bevacizumab/uso terapêutico , Neoplasias Encefálicas/tratamento farmacológico , Metilação de DNA/genética , Feminino , Marcadores Genéticos/genética , Glioblastoma/tratamento farmacológico , Homozigoto , Humanos , Masculino , Pessoa de Meia-Idade , Prognóstico , Estudos Retrospectivos
9.
Methods Mol Biol ; 2250: 207-218, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33900607

RESUMO

Transposable elements (TEs) are mobile, recurring DNA sequences scattered throughout genome and have a large impact on genome structure and function. Several genetic marker techniques were developed to exploit their ubiquitous nature. Sequence-specific amplified polymorphism (SSAP) is a TE-based genetic marker system that has been used in various purposes such as measuring genetic relatedness between species, deciphering the population structures, molecular tagging for agronomic development in marker-assisted breeding (MAS). In addition to SSAP, sequence characterized amplified region (SCAR) from the SSAP markers provides an added advantage in identifying qualitative traits. Once developed SCAR markers are efficient, fast, and reliable method for genetic evaluations. These methods can be useful especially for the crops which have no genetic sequence information. With improved discriminatory ability they offer access to dynamic and polymorphic regions of genome. These techniques can be useful in breeding programs to improve or develop high yielding crops.


Assuntos
Elementos de DNA Transponíveis/genética , Marcadores Genéticos/genética , Polimorfismo Genético , Técnica de Amplificação ao Acaso de DNA Polimórfico/métodos , Zea mays/genética , DNA de Plantas/análise , DNA de Plantas/genética , Eletroforese em Gel de Poliacrilamida/métodos , Variação Genética , Genoma de Planta , Melhoramento Vegetal/métodos
10.
Viruses ; 13(2)2021 02 12.
Artigo em Inglês | MEDLINE | ID: mdl-33673082

RESUMO

Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.


Assuntos
Cipriniformes/virologia , Doenças dos Peixes/virologia , Variação Genética/genética , Genoma Viral/genética , Vírus da Hepatite B/genética , Alberta , Animais , Marcadores Genéticos/genética , Great Lakes Region , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Filogeografia , Internalização do Vírus , Replicação Viral/genética
11.
Genet Test Mol Biomarkers ; 25(3): 211-217, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33734895

RESUMO

Background: The Wnt/ß catenin pathway promotes bone mineralization stimulating proliferation, differentiation, and survival of osteoblasts; it also inhibits osteoclast differentiation and osteocyte activity. Sclerostin (SOST) and Dickkopf 1 (DKK1) are Wnt/ß catenin pathway inhibitors. Genetic variability in the expression of SOST and DKK1 might be involved in the development of postmenopausal osteoporosis (OP). Aim: To determine whether the SOST rs851056 and DKK1 rs1569198 polymorphisms are associated with OP in Mexican-Mestizo postmenopausal women. Materials and Methods: Two hundred and eighty Mexican-Mestizo postmenopausal women were assessed for their bone mineral density by dual-energy X-ray absorptiometry (DXA). Patients were classified as OP or non-OP. Genomic DNA was extracted from peripheral blood leukocytes. Genetic polymorphisms were analyzed by quantitative polymerase chain reaction using TaqMan probes. Results: The frequency of OP was 40% among the study population. Osteoporotic patients were older (p < 0.001), had a higher frequency of smoking (p = 0.01), and lower body mass index (p < 0.001) compared with the non-osteoporotic patients. The genotypic frequencies of the rs851056 locus of the SOST gene were GG 19%, GC 45%, and CC 35%, whereas the genotypic frequencies of the rs1569198 locus of the DKK1 gene were GG 15%, GA 40%, and AA 44%. In relation to rs851056 locus of the SOST gene, no differences were observed between the OP and non-OP cohorts in the frequencies of the GC polymorphism (48.7% vs. 43.1%). Similarly, analyses of the DKK1 rs1569198 does not demonstrate differences in the GA genotypic frequencies between the OP and non-OP cohorts (42.5% vs. 38.9%). Conclusion: Polymorphisms SOST rs851056 and DKK1 rs1569198 polymorphisms are not associated with OP in Mexican-Mestizo postmenopausal women.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/genética , Peptídeos e Proteínas de Sinalização Intercelular/genética , Osteoporose Pós-Menopausa/genética , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Densidade Óssea/genética , Estudos de Casos e Controles , Grupos Étnicos/genética , Feminino , Marcadores Genéticos/genética , Genótipo , Humanos , Peptídeos e Proteínas de Sinalização Intercelular/metabolismo , México/epidemiologia , Pessoa de Meia-Idade , Osteoporose Pós-Menopausa/fisiopatologia , Polimorfismo de Nucleotídeo Único/genética , Pós-Menopausa/genética , Via de Sinalização Wnt/genética
12.
Malar J ; 20(1): 144, 2021 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-33706773

RESUMO

BACKGROUND: The national policy for malaria treatment of the Democratic Republic of Congo recommends two first-line artemisinin-based combinations for the treatment of uncomplicated malaria: artesunate-amodiaquine and artemether-lumefantrine. This study investigated the presence of markers associated with resistance to the current first-line artemisinin-based combination therapy (ACT) in isolates of Plasmodium falciparum from treatment failure patients in the Democratic Republic of Congo. METHODS: From November 2018 to November 2019, dried blood spots were taken from patients returning to health centres for fever within 28 days after an initial malaria treatment in six sentinel sites of the National Malaria Control Programme across Democratic Republic of Congo. The new episode of malaria was first detected by a rapid diagnostic test and then confirmed by a real-time PCR assay to define treatment failure. Fragments of interest in pfk13 and pfcrt genes were amplified by conventional PCR before sequencing and the Pfmdr1 gene copy number was determined by a TaqMan real-time PCR assay. RESULTS: Out of 474 enrolled patients, 364 (76.8%) were confirmed positive by PCR for a new episode of P. falciparum malaria, thus considered as treatment failure. Of the 325 P. falciparum isolates obtained from 364 P. falciparum-positive patients and successfully sequenced in the pfk13-propeller gene, 7 (2.2%) isolates carried non-synonymous mutations, among which 3 have been previously reported (N498I, N554K and A557S) and 4 had not yet been reported (F506L, E507V, D516E and G538S). Of the 335 isolates successfully sequenced in the pfcrt gene, 139 (41.5%) harboured the K76T mutation known to be associated with chloroquine resistance. The SVMNT haplotype associated with resistance to amodiaquine was not found. None of the isolates carried an increased copy number of the pfmdr1 gene among the 322 P. falciparum isolates successfully analysed. CONCLUSION: No molecular markers currently known to be associated with resistance to the first-line ACT in use were detected in isolates of P. falciparum from treatment failure patients. Regular monitoring through in vivo drug efficacy and molecular studies must continue to ensure the effectiveness of malaria treatment in Democratic Republic of Congo.


Assuntos
Amodiaquina/farmacologia , Antimaláricos/farmacologia , Combinação Arteméter e Lumefantrina/farmacologia , Artemisininas/farmacologia , Resistência a Medicamentos/genética , Proteínas de Membrana Transportadoras/genética , Proteínas Associadas à Resistência a Múltiplos Medicamentos/genética , Plasmodium falciparum/genética , Proteínas de Protozoários/genética , Adolescente , Adulto , Idoso , Criança , Pré-Escolar , República Democrática do Congo , Combinação de Medicamentos , Feminino , Marcadores Genéticos/genética , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Falha de Tratamento , Adulto Jovem
13.
Acta Trop ; 217: 105880, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33662336

RESUMO

The cat flea Ctenocephalides felis (Siphonaptera: Pulicidae) is the most important ectoparasite in cats and dogs worldwide. Over the years, there has been much dispute regarding the taxonomic and systematic status of C. felis. Mitochondrial (mt) genome sequences are useful genetic markers for the identification and differentiation of ectoparasites, but the mt genome of C. felis and its subspecies has not yet been entirely characterized. In the present study, the entire mt genome of C. f. felis from China was sequenced and compared with that of C. felis from the USA. Both contain 37 genes and a long non-coding region of >6 kbp. The molecular identity between the Chinese and American isolates was 99%, except for the non-coding region. The protein-coding genes showed differences at both the nucleotide (1.2%) and amino acid (1%) levels. Interestingly, the cox1 gene of the Chinese isolate had an unusual putative start codon (TTT). Taken together, our analyses strongly support the hypothesis that C. felis isolates from China and the USA were the same C. f. felis subspecies. The mt genome sequence of the C. f. felis China isolate presented in this study provides useful molecular markers to further address the taxonomy and systematics of C. felis.


Assuntos
Ctenocephalides/classificação , Ctenocephalides/genética , Genoma Mitocondrial/genética , Análise de Sequência , Animais , Gatos , China , Cães , Marcadores Genéticos/genética , Estados Unidos
14.
J Med Virol ; 93(7): 4382-4391, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33782990

RESUMO

The coronavirus disease 2019 (COVID-19) pandemic has spread around the globe very rapidly. Previously, the evolution pattern and similarity among the COVID-19 causative organism severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causative organisms of other similar infections have been determined using a single type of genetic marker in different studies. Herein, the SARS-CoV-2 and related ß coronaviruses Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV,  bat coronavirus (BAT-CoV) were comprehensively analyzed using a custom-built pipeline that employed phylogenetic approaches based on multiple types of genetic markers including the whole genome sequences, mutations in nucleotide sequences, mutations in protein sequences, and microsatellites. The whole-genome sequence-based phylogeny revealed that the strains of SARS-CoV-2 are more similar to the BAT-CoV strains. The mutational analysis showed that on average MERS-CoV and BAT-CoV genomes differed at 134.21 and 136.72 sites, respectively, whereas the SARS-CoV genome differed at 26.64 sites from the reference genome of SARS-CoV-2. Furthermore, the microsatellite analysis highlighted a relatively higher number of average microsatellites for MERS-CoV and SARS-CoV-2 (106.8 and 107, respectively), and a lower number for SARS-CoV and BAT-CoV (95.8 and 98.5, respectively). Collectively, the analysis of multiple genetic markers of selected ß viral genomes revealed that the newly born SARS-COV-2 is closely related to BAT-CoV, whereas, MERS-CoV is more distinct from the SARS-CoV-2 than BAT-CoV and SARS-CoV.


Assuntos
Alphacoronavirus/genética , Genoma Viral/genética , Repetições de Microssatélites/genética , Coronavírus da Síndrome Respiratória do Oriente Médio/genética , Vírus da SARS/genética , SARS-CoV-2/genética , Animais , Sequência de Bases/genética , Quirópteros/virologia , Análise Mutacional de DNA , Marcadores Genéticos/genética , Variação Genética/genética , Humanos , Filogenia , Alinhamento de Sequência , Homologia de Sequência do Ácido Nucleico , Sequenciamento Completo do Genoma
15.
Zhongguo Zhong Yao Za Zhi ; 46(4): 931-937, 2021 Feb.
Artigo em Chinês | MEDLINE | ID: mdl-33645099

RESUMO

Based on the characteristics and ISSR molecular marker technology, the study is aimed to compare and perform genetic diversity analysis on Sparganium stoloniferum from 7 regions. Molecular identification method was established for S. stoloniferum from Hunan province. Differences among Sparganii Rhizoma samples from seven habitats were analyzed via measuring weight, length, width and thickness of them. Genetic diversity of S. stoloniferum from 7 regions was analyzed by screening out primers amplifying clear band and showing rich polymorphism, then a cultivars dendrogram was built. The target primer was screened out, and the specific band was sequenced. Nine ISSR primers were selected to amplified clear band, rich polymorphism. A total of 73 bands were amplified by nine ISSR primers selected from 27 ISSR primers. On average, each primer produced 8.0 bands. A total of 38 bands were polymorphic, which occupied 52.8% of all bands. The cultivars dendrogram showed the genetic similarity was 0.54-0.94. Genetic similarity coefficient of S. stoloniferum from Jiangsu province, Anhui province and Jiangxi province was big, indicating the differences among them were slight on genetic level. S. stoloniferum from Hunan province is quite different from samples from the other six habitats on appea-rance and genetic level. A specific band(327 bp) in S. stoloniferum from Hunan province was obtained via ISSR-857 primer, and was sequenced. According BLASTn database, there were few sequences similar to the gene fragment and had little correlation with the growth process of plant. ISSR molecular marker technology provides a new idea for the identification of S. stoloniferum. This result confirmed the particularity of S. stoloniferum from ancient Jingzhou.


Assuntos
Medicamentos de Ervas Chinesas , Variação Genética , Polimorfismo Genético , China , Marcadores Genéticos/genética , Repetições de Microssatélites , Filogenia
16.
Medicine (Baltimore) ; 100(8): e24825, 2021 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-33663102

RESUMO

ABSTRACT: Voltage-gated Ca2+ channels play a key role in the regulation of arterial tone and blood pressure. The aim of this study was to determine whether the association of calcium voltage-gated channel subunit alpha1 C (CACNA1C) rs1006737 with essential hypertension (EH) exists in both Chinese Han and ethnic Russian populations of Northeast Asia. We used a case-control study of 2 ethnic groups in the same latitude geographical area to investigate the association between the susceptibility of EH and rs1006737 polymorphism. A total of 1512 EH patients and 1690 controls in Chinese Han people (Heilongjiang Provence, China), 250 EH patients, and 250 controls in ethnic Russian people (Chita, Russia), participated in this study. All participants were genotyped using the TaqMan SNP genotyping assay (Agena Company). Baseline characteristics and the minor allele frequencies of rs1006737 vary substantially among common Chinese Han and ethnic Russian people. Allele A was found to be a risk factor for EH in Chinese Han [(odds ratio) OR 1.705, (confidence interval) 95% CI: 1.332-2.182, P < .001] and ethnic Russian (OR 1.437; 95% CI: 1.110-1.860, P = .006). The GA genotype was significantly associated with an increased risk of hypertension (OR 1.538, 95% CI: 1.188-1.991, P = .001) for Chinese Han people, and the AA genotype (OR 2.412, 95% CI: 1.348-4.318, P = .003) for ethnic Russian people. The results of this study indicate that the A allele of the variant rs1006737 in the CACNA1C gene may be a useful genetic marker for EH risk prediction in Chinese Han and ethnic Russian populations.


Assuntos
Canais de Cálcio Tipo L , Hipertensão Essencial/genética , Adulto , Alelos , Grupo com Ancestrais do Continente Asiático , Estudos de Casos e Controles , China , Grupo com Ancestrais do Continente Europeu , Feminino , Marcadores Genéticos/genética , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Fatores de Risco , Federação Russa
17.
Medicine (Baltimore) ; 100(11): e24769, 2021 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-33725943

RESUMO

ABSTRACT: Several genetic loci have been reported to be significantly associated with coronary artery disease (CAD) by multiple genome-wide association studies (GWAS). Nevertheless, the biological and functional effects of these genetic variants on CAD remain largely equivocal. In the current study, we performed an integrative genomics analysis by integrating large-scale GWAS data (N = 459,534) and 2 independent expression quantitative trait loci (eQTL) datasets (N = 1890) to determine whether CAD-associated risk single nucleotide polymorphisms (SNPs) exert regulatory effects on gene expression. By using Sherlock Bayesian, MAGMA gene-based, multidimensional scaling (MDS), functional enrichment, and in silico permutation analyses for independent technical and biological replications, we highlighted 4 susceptible genes (CHCHD1, TUBG1, LY6G6C, and MRPS17) associated with CAD risk. Based on the protein-protein interaction (PPI) network analysis, these 4 genes were found to interact with each other. We detected a remarkably altered co-expression pattern among these 4 genes between CAD patients and controls. In addition, 3 genes of CHCHD1 (P = .0013), TUBG1 (P = .004), and LY6G6C (P = .038) showed significantly different expressions between CAD patients and controls. Together, we provide evidence to support that these identified genes such as CHCHD1 and TUBG1 are indicative factors of CAD.


Assuntos
Doença da Artéria Coronariana/genética , Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla/estatística & dados numéricos , Locos de Características Quantitativas/genética , Adulto , Antígenos Ly/genética , Teorema de Bayes , Feminino , Redes Reguladoras de Genes/genética , Marcadores Genéticos/genética , Genômica , Fatores de Risco de Doenças Cardíacas , Humanos , Masculino , Proteínas Mitocondriais/genética , Proteínas Nucleares/genética , Polimorfismo de Nucleotídeo Único/genética , Mapas de Interação de Proteínas/genética , Proteínas Ribossômicas/genética , Tubulina (Proteína)/genética
18.
Medicine (Baltimore) ; 100(12): e25147, 2021 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-33761683

RESUMO

BACKGROUND: Long non-coding RNAs (LncRNAs) play important roles in the regulation of neuropathic pain (NP) development. LncRNAs dysregulations are related to the development of NP. However, a comprehensive meta-analysis has never been conducted to assess the relationship between LncRNAs and NP. To combine the results of dysregulated LncRNAs in individual NP studies and to identify potential LncRNAs biomarkers. METHODS: LncRNAs profiling studies of NP were extracted from Pubmed, Web of science, Embase, Google Scholar, and Chinese National Knowledge Infrastructure, and the Chinese Biomedical Literature Database if they met the inclusion criteria. The meta-analysis was conducted using a random effects model to identify the effect of each multiple-reported LncRNAs. We also performed subgroup analysis according to LncRNAs detecting methods and sample type. Sensitivity analysis was performed on the sample size. Bioinformatic analysis was performed to identify the potential biomatic functions. All results were represented as log10 odds ratios. RESULTS: This review will be disseminated in print by peer-review. CONCLUSION: The identified LncRNAs may be closely linked with NP and may act as potentially useful biomarkers. ETHICS AND DISSEMINATION: The private information from individuals will not publish. This systematic review also will not involve endangering participant rights. Ethical approval is not available. The results may be published in a peer- reviewed journal or disseminated in relevant conferences. OSF REGISTRATION NUMBER: DOI 10.17605/OSF.IO/ZRX7C.


Assuntos
Predisposição Genética para Doença/genética , Neuralgia/genética , RNA Longo não Codificante/genética , Estudos de Casos e Controles , Biologia Computacional , Marcadores Genéticos/genética , Humanos , Metanálise como Assunto , Projetos de Pesquisa , Revisões Sistemáticas como Assunto
19.
Genes (Basel) ; 12(2)2021 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-33669871

RESUMO

Small farm producers' sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.


Assuntos
Camelídeos Americanos/genética , Marcadores Genéticos/genética , Análise em Microsséries , Polimorfismo de Nucleotídeo Único/genética , Animais , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala
20.
PLoS One ; 16(2): e0246028, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33529261

RESUMO

The first step in managing herbicide-resistant weeds is to confirm their resistance status. It is, therefore, crucial to have a rapid, reliable and cost-effective technique to assess samples for herbicide resistance. We designed and evaluated three derived cleaved amplified polymorphic sequence (dCAPS) markers for detecting glyphosate resistance in Lolium perenne. conferred by non-synonymous mutations at codon-106 in the enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. The dCAPS markers involve amplification of the target region, digestion of the amplified products with restriction enzymes and gel-based visualisation of the digested products. The results showed that all three dCAPS markers could successfully detect mutations at codon-106 in the target enzyme. The dCAPS markers can also inform us of the zygosity state of the resistance allele and was confirmed by sequencing the target region of the EPSPS gene. The markers described here are effective quick tests for the monitoring and evaluation of the target-enzyme mechanism of glyphosate resistance in Lolium perenne.


Assuntos
Análise Mutacional de DNA , Resistência a Medicamentos/genética , Glicina/análogos & derivados , Lolium/efeitos dos fármacos , Lolium/genética , Reação em Cadeia da Polimerase , Mapeamento por Restrição , Marcadores Genéticos/genética , Glicina/farmacologia , Polimorfismo de Nucleotídeo Único
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