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1.
BMC Genomics ; 22(1): 426, 2021 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-34107887

RESUMO

BACKGROUND: Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish that were raised in either aerated (normoxia) or non-aerated pond (nocturnal hypoxia). During grow out, fish were sampled five times to determine individual body weight (BW) gains. We applied a genome-wide association study to identify SNPs and genes associated with the hypoxic and normoxic environments in the 16th generation of a Genetically Improved Farmed Tilapia population. RESULTS: In the hypoxic environment, 36 SNPs associated with at least one of the five body weight measurements (BW1 till BW5), of which six, located between 19.48 Mb and 21.04 Mb on Linkage group (LG) 8, were significant for body weight in the early growth stage (BW1 to BW2). Further significant associations were found for BW in the later growth stage (BW3 to BW5), located on LG1 and LG8. Analysis of genes within the candidate genomic region suggested that MAPK and VEGF signalling were significantly involved in the later growth stage under the hypoxic environment. Well-known hypoxia-regulated genes such as igf1rb, rora, efna3 and aurk were also associated with growth in the later stage in the hypoxic environment. Conversely, 13 linkage groups containing 29 unique significant and suggestive SNPs were found across the whole growth period under the normoxic environment. A meta-analysis showed that 33 SNPs were significantly associated with BW across the two environments, indicating a shared effect independent of hypoxic or normoxic environment. Functional pathways were involved in nervous system development and organ growth in the early stage, and oocyte maturation in the later stage. CONCLUSIONS: There are clear genotype-growth associations in both normoxic and hypoxic environments, although genome architecture involved changed over the growing period, indicating a transition in metabolism along the way. The involvement of pathways important in hypoxia especially at the later growth stage indicates a genotype-by-environment interaction, in which MAPK and VEGF signalling are important components.


Assuntos
Ciclídeos , Estudo de Associação Genômica Ampla , Animais , Ciclídeos/genética , Ligação Genética , Genótipo , Oxigênio
2.
BMC Plant Biol ; 21(1): 255, 2021 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-34082694

RESUMO

BACKGROUND: Rice (Oryza sativa) bacterial leaf blight (BLB), caused by the hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases affecting the production of rice worldwide. The development and use of resistant rice varieties or genes is currently the most effective strategy to control BLB. RESULTS: Here, we used 259 rice accessions, which are genotyped with 2 888 332 high-confidence single nucleotide polymorphisms (SNPs). Combining resistance variation data of 259 rice lines for two Xoo races observed in 2 years, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) conferring plant resistance against BLB. The expression levels of genes, which contains in GWAS results were also identified between the resistant and susceptible rice lines by transcriptome analysis at four time points after pathogen inoculation. From that 109 candidate resistance genes showing significant differential expression between resistant and susceptible rice lines were uncovered. Furthermore, the haplotype block structure analysis predicted 58 candidate genes for BLB resistance based on Chr. 7_707158 with a minimum P-value (-log 10 P = 9.72). Among them, two NLR protein-encoding genes, LOC_Os07g02560 and LOC_Os07g02570, exhibited significantly high expression in the resistant line, but had low expression in the susceptible line of rice. CONCLUSIONS: Together, our results reveal novel BLB resistance gene resources, and provide important genetic basis for BLB resistance breeding of rice crops.


Assuntos
Regulação da Expressão Gênica de Plantas , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Oryza/genética , Doenças das Plantas/microbiologia , Transcriptoma , Regulação da Expressão Gênica de Plantas/imunologia , Genótipo , Haplótipos , Doenças das Plantas/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
3.
Biomed Environ Sci ; 34(5): 364-371, 2021 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-34059173

RESUMO

Objective: To study the polymorphism in P66 and its human B-cell epitopes of Borrelia burgdorferi strains in China. Methods: Polymerase chain reaction (PCR) and sequencing were used to obtain the P66 sequences of 59 Chinese B. burgdorferi. Then the sequences were analyzed by MEGA 5.10 software and compared with the human B-cell epitope sequences from the Immune Epitope Database (IEDB) based on the reference strain of each genotype. Results: Results showed that genetic and amino acid diversity presented in the 66 kD protein of all 59 Chinese strains, especially in Borrelia garinii ( B.g) and Borrelia afzelii ( B.a) strains. B.g strains were divided into three subclusters and two scattered strains JC1-7 and JC2-2 according to the amino acid sequences of P66. The P66 sequences of 15 Xinjiang strains represented by XI91-12 in the B.g subcluster 1, changed from CAA to TAA codon at 508aa position, resulting in early termination. Bases A and C were inserted at sequence position 1 523 bp of strains FP1, LB20, LB21, and SZ21 in the B.a genotype, which resulted to early termination at position 511 aa. G base was inserted at 438 bp of LIP94-11 strain, which led to early termination at position 172 aa. Conclusion: In P66 of 59 Chinese strains, polymorphisms were widely distributed. More importantly, the P66 amino acid sequences of B.g strains had a certain regional character. One of the characteristics of Xinjiang B.g isolates might be the variation at the 508aa location in 15 Xinjiang B.g strains, which may be related to the strains' pathogenicity in this area.


Assuntos
Proteínas de Bactérias/genética , Borrelia burgdorferi/genética , Epitopos de Linfócito B/genética , Polimorfismo Genético , Porinas/genética , Borrelia burgdorferi/classificação , China , Análise por Conglomerados , Marcadores Genéticos , Genótipo , Humanos , Mutação , Reação em Cadeia da Polimerase
4.
BMC Genomics ; 22(1): 433, 2021 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-34107875

RESUMO

BACKGROUND: Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear. RESULTS: In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress. CONCLUSIONS: These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.


Assuntos
RNA Longo não Codificante , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genótipo , Fosfatos/metabolismo , RNA Longo não Codificante/genética , Soja/genética , Soja/metabolismo
5.
J Pak Med Assoc ; 71(6): 1575-1582, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-34111075

RESUMO

OBJECTIVE: To analyse mutations in precore and core promoter regions of hepatitis B virus genome in chronic hepatitis B patients. Methods: The cross-sectional prospective study was conducted at the Centre of Biotechnology and Microbiology, University of Peshawar and Pakistan Health Research Council (PHRC), Research Centre, Khyber Medical College Peshawar from June 2014 to June 2015, and comprised samples from treatment-naïve chronic hepatitis B patients aged >15 years from three cities of Pakistan. The samples included patients who were both positive and negative for hepatitis B envelope antigen. Viral load, hepatitis B envelope antigen / anti-hepatitis B envelope status, hepatitis B virus enzyme-linked immunosorbent assay and alanine aminotransferase levels were determined. Direct sequencing of basal core promoter and precore regions of hepatitis B virus genome was carried out following a nested polymerase chain reaction approach. Phylogenetic tree was constructed using Molecular Evolutionary Genetics Analysis software version 6.0. Data was analysed using SPSS 16. RESULTS: Of the 50 patients, 33(66%) were males. The overall mean age was 28.5±11.4 years. Of all the subjects, 25(50%) each were positive and negative for hepatitis B envelope antigen. Precore stop codon mutation G1896A was detected in 19 (38%) isolates; 17(34%) among negative patients and 2(4%) in positive patients. Classic A1762T/G1764A double mutation was noted in 15(30%) isolates. Mutation at position 1764 was observed in 12(48%) samples. A rare G1764T mutation was also detected in 6(12%) isolates. The CG1802-1803 mutation was detected in 47(94%) isolates, while all the 50(100%) isolates had T1858A. The GCAC Kozak sequence was present in 43(86%) isolates; CAA1817-1819 in 49(98%); and G1888 in 49(98%). Overall, 9(18%) isolates had wild-type sequences at all important loci, including positions 1762, 1764 and 1896. The pattern of sequences at genotype specific positions and phylogenetic tree speculates that majority of study isolates belonged to genotype D. Conclusion: Basal core promoter and precore regions variants along with the preponderances of genotype D-specific mutations suggested a higher risk of hepatocellular carcinoma and poor clinical outcome in such patients.


Assuntos
Hepatite B Crônica , Hepatite B , Neoplasias Hepáticas , Adolescente , Adulto , Estudos Transversais , DNA Viral/genética , Feminino , Genótipo , Vírus da Hepatite B/genética , Hepatite B Crônica/epidemiologia , Humanos , Masculino , Mutação , Paquistão , Filogenia , Regiões Promotoras Genéticas , Estudos Prospectivos , Adulto Jovem
6.
MMWR Morb Mortal Wkly Rep ; 70(23): 833-839, 2021 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-34111057

RESUMO

In 2005, the Regional Committee of the World Health Organization (WHO) European Region (EUR) passed a resolution calling for the regional elimination of measles, rubella, and congenital rubella syndrome (CRS) (1). In 2010, all 53 countries in EUR* reaffirmed their commitment to eliminating measles, rubella, and CRS (2); this goal was included in the European Vaccine Action Plan 2015-2020 (3,4). Rubella, which typically manifests as a mild febrile rash illness, is the leading vaccine-preventable cause of birth defects. Rubella infection during pregnancy can result in miscarriage, fetal death, or a constellation of malformations known as CRS, which usually includes one or more visual, auditory, or cardiac defects (5). The WHO-recommended measles and rubella elimination strategies in EUR include 1) achieving and maintaining ≥95% coverage with 2 doses of measles- and rubella-containing vaccine (MRCV) through routine immunization services; 2) providing measles and rubella vaccination opportunities, including supplementary immunization activities (SIAs), to populations susceptible to measles or rubella; 3) strengthening surveillance by conducting case investigations and confirming suspected cases and outbreaks with laboratory results; and 4) improving the availability and use of evidence to clearly communicate the benefits and risks of preventing these diseases through vaccination to health professionals and the public (6). This report updates a previous report and describes progress toward rubella and CRS elimination in EUR during 2005-2019 (7). In 2000, estimated coverage with the first dose of a rubella-containing vaccine (RCV1) in EUR was 60%, and 621,039 rubella cases were reported (incidence = 716.9 per 1 million population). During 2005-2019, estimated regional coverage with RCV1 was 93%-95%, and in 2019, 31 (58%) countries achieved ≥95% coverage with the RCV1. During 2005-2019, approximately 38 million persons received an RCV during SIAs in 20 (37%) countries. Rubella incidence declined by >99%, from 234.9 cases per 1 million population (206,359 cases) in 2005 to 0.67 cases per 1 million population (620 cases) by 2019. CRS cases declined by 50%, from 16 cases in 2005 to eight cases in 2019. For rubella and CRS elimination in EUR to be achieved and maintained, measures are needed to strengthen immunization programs by ensuring high coverage with an RCV in every district of each country, offering supplementary rubella vaccination to susceptible adults, maintaining high-quality surveillance for rapid case detection and confirmation, and ensuring effective outbreak preparedness and response.


Assuntos
Erradicação de Doenças , Vigilância da População , Rubéola (Sarampo Alemão)/epidemiologia , Rubéola (Sarampo Alemão)/prevenção & controle , Adolescente , Criança , Pré-Escolar , Europa (Continente)/epidemiologia , Genótipo , Humanos , Incidência , Lactente , Vacina contra Rubéola/administração & dosagem , Vírus da Rubéola/genética , Vírus da Rubéola/isolamento & purificação , Cobertura Vacinal/estatística & dados numéricos , Organização Mundial da Saúde
7.
Viruses ; 13(6)2021 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-34072981

RESUMO

Infectious bronchitis virus (IBV) was first identified in the 1930s and it imposes a major economic burden on the poultry industry. In particular, GI-19 lineage has spread globally and has evolved constantly since it was first detected in China. In this study, we analyzed S1 gene sequences from 60 IBVs isolated in South Korea. Two IBV lineages, GI-15 and GI-19, were identified in South Korea. Phylogenetic analysis suggested that there were six distinct subgroups (KM91-like, K40/09-like, and QX-like I to IV) of the South Korean GI-19 IBVs. Among them, QX-type III and IV subgroups, which are phylogenetically different from those reported in South Korea in the past, accounted for more than half of the total. Moreover, the phylogeographic analysis of the QX-like subgroups indicated at least four distinct introductions of GI-19 IBVs into South Korea during 2001-2020. The efficacy of commercialized vaccines against the recently introduced QX-like subgroups should be verified, and continuous international surveillance efforts and quarantine procedures should be enhanced to prevent the incursion of viruses.


Assuntos
Infecções por Coronavirus/veterinária , Vírus da Bronquite Infecciosa/genética , Doenças das Aves Domésticas/virologia , Animais , Galinhas , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Genômica , Genótipo , Vírus da Bronquite Infecciosa/classificação , Vírus da Bronquite Infecciosa/isolamento & purificação , Filogenia , Doenças das Aves Domésticas/epidemiologia , República da Coreia/epidemiologia , Análise de Sequência de RNA , Homologia de Sequência , Glicoproteína da Espícula de Coronavírus/genética
8.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 29(3): 690-695, 2021 Jun.
Artigo em Chinês | MEDLINE | ID: mdl-34105458

RESUMO

OBJECTIVE: To investigate the relationship between single nucleotide polymorphisms (SNPs) of IKAROS family Zinc finger 3 (IKZF3) gene and the risk of acute lymphoblastic leukemia (ALL) in children. METHODS: The peripheral blood samples from 286 children with ALL and 382 healthy children were collected and divided into ALL group and control group, respectively. The genotypes of IKZF3 gene at rs62066988 C > T and rs12946510 C > T were detected by quantitative PCR with TaqMan detection system, and their correlation with ALL was analyzed. RESULTS: The distribution frequencies of CC, CT and TT genotypes at rs62066988 in ALL group were 58.39%, 37.06% and 4.55%, respectively, while those in control group were 69.19%, 27.68% and 3.13%, respectively. The distribution frequencies of CC, CT and TT genotypes at rs12946510 in ALL group were 58.16%, 34.75% and 7.09%, respectively, while those in control group were 55.76%, 37.43% and 6.81%, respectively. Compared with the control group, the distribution frequency of CT/TT genotype at rs62066988 was significantly increased in the ALL group (OR=1.59, 95%CI: 1.16-2.19, P=0.004). However, there was no significant difference in the distribution of rs12946510 C > T polymorphism between ALL group and control group. CONCLUSION: The CT/TT genotype of IKZF3 at the site of rs62066988 is associated with the increased risk of ALL in children.


Assuntos
Polimorfismo de Nucleotídeo Único , Leucemia-Linfoma Linfoblástico de Células Precursoras , Alelos , Estudos de Casos e Controles , Criança , Frequência do Gene , Predisposição Genética para Doença , Genótipo , Humanos , Fator de Transcrição Ikaros/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética
9.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 29(3): 860-864, 2021 Jun.
Artigo em Chinês | MEDLINE | ID: mdl-34105484

RESUMO

OBJECTIVE: To analyze the gene defect types and distribution characteristics of α- and ß-thalassemia in Lingui District of Guilin City, Guangxi, so as to provide scientific basis for genetic consultation and prevention measures. METHODS: A total of 6 496 suspected cases for screening the thalassemia during physical examination, premarital examination, pregnancy examination and hospitalization in the Second Affiliated Hospital of Guilin Medical University from May 2016 to October 2019 were analyzed. Gap-PCR, PCR-RDB and DNA sequencing techniques were used to detect the types and constituent ratios of gene defects in α- and ß-thalassemia positive cases. RESULTS: Among 6 496 suspected patients, 1 363 were thalassemia carriers, the total positive rate was 20.98%. There were 677 cases of single-gene deletion and 26 cases of double-gene detetion on the deletional α-thalassemia, 115 cases of non-deletion α-thalassemia mutation and 4 cases of deletion plus mutation. The positive rate of α-thalassemia was 12.66%. There were 11 gene abnormalities for α-thalassemia, of which --SEA/αα (50.36%) was the most common, followed by -α3.7/αα (23.84%); the main α-gene mutation was ααCS (6.93%). There were 514 ß-thalassemia gene carriers, with a positive rate of 7.93%. In 12 types of ß-gene mutations, CD41-42 (-TTCT) (55.64%) was the most common, followed by CD17 (A→T) (20.23%). There were 25 cases of double heterozygous α and ß thalassemia (0.39%), of which -α3.7/ßCD17 (24%) and --SEA/ß41-42 (16%) were numerically dominant. Two of rare thalassemia genotypes were identified by sequencing, which were heterozygous mutations of Chinese Hong Kong type α thalassemia (HKαα/αα or HKαα/-α3.7) and ß gene mutations IVS-I (-2) or codon30 (A→G) ß0, respectively. CONCLUSION: Lingui district of Guilin city is a high incidence area of thalassemia. The mutation rate of α-thalassemia --SEA/αα type deletion is relatively high, followed by that of the right deletion type (-α3.7/αα). CD41-42 (-TTCT) has the highest mutation rate in ß-thalassemia, followed by CD17(A→T). The results of this study provide reference data for the regional screening, diagnosis and treatment of thalassemia and eugenics.


Assuntos
Talassemia alfa , Talassemia beta , China/epidemiologia , Feminino , Genótipo , Heterozigoto , Humanos , Mutação , Gravidez , Talassemia alfa/epidemiologia , Talassemia alfa/genética , Talassemia beta/epidemiologia , Talassemia beta/genética
10.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 29(3): 865-868, 2021 Jun.
Artigo em Chinês | MEDLINE | ID: mdl-34105485

RESUMO

OBJECTIVE: To understand the genotypes and distribution characteristics of thalassemia in Baise, Guangxi Zhuang Autonomous Region, to provide references for the prevention and diagnosis of thalassemia in the region and improve the quality of eugenics. METHODS: 3 482 pregnant women and their spouses from January 2019 to August 2019 in Baise Maternal and Child Health Hospital for prenatal genetic diagnosis were selected, α, ß- thalassemia genes were detected by Gap-PCR, PCR and DNA reverse dot hybridization, cases carrying thalassemia gene were confirmed and statistical analyzed. RESULTS: 2 260 samples (64.90%) carrying thalassemia gene were found, among which 1 459 cases (64.56%) were diagnosed as α- thalassemia, 617 cases (27.30%) as ß- thalassemia, 184 cases (8.14%) as α complex ß- thalassemia. Among 1 459 α- thalassemia genes, --SEA /αα(637 cases, 43.66%), -α3.7 /αα (306 cases, 20.97%), -αCS /αα(143 cases, 9.80%), -α4.2 /αα(124 cases, 8.50%) and -αWS /αα(77 cases, 5.27%) were the most common, while among 617 ß- thalassemia genes, CD17 (229 cases, 37.12%), CD41-42 (213 cases, 34.52%), IVS-I-1 (41 cases, 6.65%), ßE (38 cases, 6.16%) and CD71-72 (34 cases, 5.51%) were the most common. And --SEA /αα/ CD17 (24 cases, 13.04%), -α4.2 /αα/ CD17 (13 cases, 7.07%), -α3.7 /αα/ CD41-42 (12 cases, 6.52% ) and --SEA /αα/ CD41-42 (12 cases, 6.52%) were mainly found in 184 cases of α complex ß - thalassemia. CONCLUSION: Genotyes of thalassemia in Baise, Guangxi Zhuang Autonomous Region are complex and diverse. The prenatal screening and diagnosis of thalassemia in the region should be strengthened in accordance with the characteristics of genetypes in the region, in order to reduce birth defects and improve eugenics quality.


Assuntos
Talassemia alfa , Talassemia beta , Criança , China , Feminino , Genótipo , Humanos , Mutação , Gravidez , Diagnóstico Pré-Natal , Talassemia alfa/diagnóstico , Talassemia alfa/epidemiologia , Talassemia alfa/genética , Talassemia beta/diagnóstico , Talassemia beta/genética
11.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 29(3): 910-916, 2021 Jun.
Artigo em Chinês | MEDLINE | ID: mdl-34105493

RESUMO

OBJECTIVE: To investigate the indentification method of samples mistyped as O phenotype and to explore the precision transfusion strategy. METHODS: The blood samples from donors and patients admitted in our center from 2018 to 2019 was collected. The samples with O phenotype suspected subtypes were further determined by tube test, adsorption-elution test, etc. Molecular testing was used to sequence the related blood type genes of the subjects. RESULTS: Among 14 subjects misjudged as O, 11 different genotypes were identified, in which 3 blood donors were Ael02/O02, Bel03/O02, and one para-Bombay with B101/O02 (FUT1: h3h3; FUT2: Se357Se357); the genotypes of 11 patients were Ael02/O01, 2 cases with Ael02/O02, Ael08/O01, Aw37/O02, Aw43/O02, Bel03/O01, 3 cases with Bel03/O02, and one case was para-Bombay with A102/B101 (FUT1: h3h3; FUT2: Se357Se357). CONCLUSION: The phenotypes of Ael, Bel, Aw and para-Bombay subtypes are easily misjudged as type O. Molecular technology is helpful to identify the genotype of subtypes, and the corresponding transfusion strategies could be reasonably performed.


Assuntos
Sistema ABO de Grupos Sanguíneos , Transfusão de Sangue , Alelos , Fucosiltransferases/genética , Genótipo , Humanos , Fenótipo
12.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 29(3): 917-923, 2021 Jun.
Artigo em Chinês | MEDLINE | ID: mdl-34105494

RESUMO

OBJECTIVE: To explore the distribution characteristics of main antigen gene frequencies of Duffy,Diego,Kidd,Dombrock,MNS,Lutheran,Kell,Colton,Scianna,Yt,Knops and Indian in red blood cell blood group system of Li nationality in Hainan Province. METHODS: Antigens in twelve rare blood group systems of 214 Li people in Hainan Province were genotyped and analyzed by polymerase chain reaction-sequence specific primers (PCR-SSP). RESULTS: The gene frequency of antigens in twelve rare blood group systems of 214 Li people in Hainan Province including: the gene frequency of Duffy blood group system: fya=0.9556,fyb=0.0444;the gene frequency of Diego blood group system: Dia=0.0678,Dib=0.9322;the gene frequency of Kidd blood group system:JKa=0.4533,JKb=0.5467;the gene frequency of Dombrock blood group system:DOa=0.1051,DOb=0.8949;the gene frequency of MNS blood group system:M=0.8131,N=0.1869,S=0.0327,s=0.9673,Mur+=0.5748,Mur-=0.4252;the gene frequency of Lutheran blood group system:AUa=0.8318,AUb=0.1682;the Kell, Colton, Scianna, Yt, Knops and Indian blood type systems showed a monomorph and the genotype was kk, coacoa, Sc1Sc1, YtaYta, KnaKna and InbInb. The observed and expected genotype values in twelve rare blood group systems of Li nationality in Hainan province were obeyed by the Hardy-Weinberg genitic rules. The difference between the observed and expectated values of the Kidd blood group system showed significant differences(χ2=17.1946,P=0.0002). CONCLUSION: The genetic distribution and genetic status in twelve rare blood group systems of Li nationality in Hainan Province are relatively stable. The gene distribution of Duffy, Diego, Kidd, Drombrock, MNS and Lutheran blood group systems are polymorphic and show unique distribution characteristics compared with other regions and different nationalities. The gene frequency distribution of Kell、Colton、Scianna、Yt、Knops、Indian blood group systems are monomorphic.


Assuntos
Antígenos de Grupos Sanguíneos , Grupos Étnicos , Antígenos de Grupos Sanguíneos/genética , Frequência do Gene , Genótipo , Humanos , Sistema do Grupo Sanguíneo Kidd , Polimorfismo Genético
13.
Int J Mol Sci ; 22(10)2021 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-34065289

RESUMO

Genome-wide association studies (GWAS) found locus 3p21.31 associated with severe COVID-19. CCR5 resides at the same locus and, given its known biological role in other infection diseases, we investigated if common noncoding and rare coding variants, affecting CCR5, can predispose to severe COVID-19. We combined single nucleotide polymorphisms (SNPs) that met the suggestive significance level (P ≤ 1 × 10-5) at the 3p21.31 locus in public GWAS datasets (6406 COVID-19 hospitalized patients and 902,088 controls) with gene expression data from 208 lung tissues, Hi-C, and Chip-seq data. Through whole exome sequencing (WES), we explored rare coding variants in 147 severe COVID-19 patients. We identified three SNPs (rs9845542, rs12639314, and rs35951367) associated with severe COVID-19 whose risk alleles correlated with low CCR5 expression in lung tissues. The rs35951367 resided in a CTFC binding site that interacts with CCR5 gene in lung tissues and was confirmed to be associated with severe COVID-19 in two independent datasets. We also identified a rare coding variant (rs34418657) associated with the risk of developing severe COVID-19. Our results suggest a biological role of CCR5 in the progression of COVID-19 as common and rare genetic variants can increase the risk of developing severe COVID-19 by affecting the functions of CCR5.


Assuntos
COVID-19/genética , COVID-19/metabolismo , Predisposição Genética para Doença , Receptores CCR5/genética , Receptores CCR5/metabolismo , Alelos , Brônquios/metabolismo , Brônquios/patologia , Brônquios/virologia , COVID-19/fisiopatologia , Cromossomos Humanos/genética , Estudos de Coortes , Biologia Computacional , Bases de Dados Genéticas , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Pulmão/metabolismo , Pulmão/patologia , Pulmão/virologia , Polimorfismo de Nucleotídeo Único , Sequenciamento Completo do Exoma
14.
Ann Saudi Med ; 41(3): 141-146, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34085542

RESUMO

BACKGROUND: Angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism may play a role in the pathogenesis of coronavirus-19 disease (COVID-19). OBJECTIVES: Investigate the relationship between ACE I/D polymorphism and the clinical severity of COVID-19. DESIGN: Prospective cohort study. SETTING: Tertiary care hospital. PATIENTS AND METHODS: The study included COVID-19 patients with asymptomatic, mild, and severe disease with clinical data and whole blood samples collected from 1 April 2020 to 1 July 2020. ACE I/D genotypes were determined by polymerase chain reaction and agarose gel electrophoresis. MAIN OUTCOME MEASURE: ACE DD, DI and II genotypes frequencies. SAMPLE SIZE: 90 cases, 30 in each disease severity group. RESULTS: Age and the frequency of general comorbidity increased significantly from the asymptomatic disease group to the severe disease group. Advanced age, diabetes mellitus and presence of ischemic heart disease were independent risk factors for severe COVID-19 [OR and 95 % CI: 1.052 (1.021-1.083), 5.204 (1.006-26.892) and 5.922 (1.109-31.633), respectively]. The ACE II genotype was the dominant genotype (50%) in asymptomatic patients, while the DD genotype was the dominant genotype (63.3 %) in severe disease. The ACE II geno-type was protective against severe COVID-19 [OR and 95% CI: .323 (.112-.929)]. All nine patients (8.9%) who died had severe disease. CONCLUSIONS: The clinical severity of COVID-19 infection may be associated with the ACE I/D polymorphism. LIMITATIONS: Small sample size and single center. CONFLICT OF INTEREST: None.


Assuntos
COVID-19/genética , Peptidil Dipeptidase A/genética , Polimorfismo Genético , Índice de Gravidade de Doença , Adulto , Idoso , Sequência de Bases , COVID-19/diagnóstico , Feminino , Seguimentos , Marcadores Genéticos , Genótipo , Técnicas de Genotipagem , Humanos , Masculino , Pessoa de Meia-Idade , Mutagênese Insercional , Estudos Prospectivos , Deleção de Sequência
15.
Genes (Basel) ; 12(6)2021 05 28.
Artigo em Inglês | MEDLINE | ID: mdl-34071309

RESUMO

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection provides a critical host-immunological challenge. AIM: We explore the effect of host-genetic variation in interferon-lambda-3 rs12979860, Tolloid Like-1 (TLL1) rs17047200 and Discoidin domain receptor 1(DDR1) rs4618569 on host response to respiratory viral infections and disease severity that may probe the mechanistic approach of allelic variation in virus-induced inflammatory responses. METHODS: 141 COVID-19 positive patients and 100 healthy controls were tested for interferon-lambda-3 rs12979860, TLL1 rs17047200 and DDR1 rs4618569 polymorphism by TaqMan probe-based genotyping. Different genotypes were assessed regarding the COVID-19 severity and prognosis. RESULTS: There were statistically significant differences between the studied cases and control group with regard to the presence of comorbidities, total leucocytic count, lymphocytic count, CRP, serum LDH, ferritin and D-dimer (p < 0.01). The CC genotype of rs12979860 cytokine, the AA genotype of TLL1 rs17047200 and the AA genotype of the rs4618569 variant of DDR1 showed a higher incidence of COVID-19 compared to the others. There were significant differences between the rs4618569 variant of DDR and the outcome of the disease, with the highest mortality in AG genotype 29 (60.4%) in comparison to 16 (33.3%) and 3 (6.2%) in the AA and GG genotypes, respectively (p = 0.007*), suggesting that the A allele is associated with a poor outcome in the disease. CONCLUSION: Among people who carry C and A alleles of SNPs IFN-λ rs12979860 and TLL1 rs17047200, respectively, the AG genotype of the DDR1 rs4618569 variant is correlated with a COVID-19 poor outcome. In those patients, the use of anti-IFN-λ 3, TLL1 and DDR1 therapy may be promising for personalized translational clinical practice.


Assuntos
COVID-19/genética , COVID-19/virologia , Receptor com Domínio Discoidina 1/genética , Predisposição Genética para Doença , Interferons/genética , Polimorfismo de Nucleotídeo Único , SARS-CoV-2/fisiologia , Metaloproteases Semelhantes a Toloide/genética , Alelos , Biomarcadores , COVID-19/diagnóstico , COVID-19/imunologia , Estudos de Casos e Controles , Comorbidade , Citocinas/metabolismo , Feminino , Genótipo , Interações Hospedeiro-Patógeno/genética , Interações Hospedeiro-Patógeno/imunologia , Humanos , Imunidade Inata , Masculino , Prognóstico , Índice de Gravidade de Doença , Carga Viral
16.
Genes (Basel) ; 12(6)2021 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-34072181

RESUMO

The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein-protein interactions, fusion of viral and cellular membranes, and virion assembly.


Assuntos
COVID-19/virologia , Genoma Viral , Interações Hidrofóbicas e Hidrofílicas , Mutação , SARS-CoV-2/genética , Proteínas Virais/química , Proteínas Virais/genética , Desaminases APOBEC , Alelos , Substituição de Aminoácidos , Aminoácidos/química , Aminoácidos/genética , Evolução Molecular , Variação Genética , Genótipo , Interações Hospedeiro-Patógeno , Humanos , Filogenia , Polimorfismo de Nucleotídeo Único , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética
17.
An Acad Bras Cienc ; 93(2): e20200452, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34076039

RESUMO

Microsatellite primers pairs were developed for the Neotropical tree Roupala montana var. brasiliensis for use in studies on genetic diversity, mating system, and gene flow. Forty-two primer pairs were developed, resulting in 27 polymorphic loci, with two to 27 alleles per locus. The primer pairs were validated against 34 R. montana var. brasiliensis adult trees from four populations. The observed (H o) and expected (H e)heterozygosities ranged among loci from 0.061 to 0.930 (mean of 0.544) and from 0.116 to 0.950 (mean of 0.700), respectively. Null alleles were observed for ten loci. No genotypic linkage disequilibrium was detected in any pair of loci. This set of loci is suitable for population genetic studies of the species.


Assuntos
Repetições de Microssatélites , Proteaceae/genética , Genética Populacional , Genótipo , Polimorfismo Genético
18.
Wiad Lek ; 74(5): 1200-1203, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34090290

RESUMO

OBJECTIVE: The aim: The objective of the study was to analyze the frequency of Arg16Gly polymorphism in the ß2 -adrenoceptor (ß2 -АR) gene in patients with bronchial asthma (BA) and to assess the association of the polymorphism with BA risk. PATIENTS AND METHODS: Materials and methods: We examined 553 BA patients and 95 apparently healthy individuals. Arg16Gly polymorphism in the ß2 -АR gene (rs1042713) was determined using polymerase chain reaction-restriction fragment length polymorphism analysis. Statistical analysis of obtained results was performed using SPSS-17 program. RESULTS: Results: It was established that distribution of Arg/Arg, Arg/Gly, and Gly/Gly genotypes for Arg16Gly polymorphism in the ß2 -АR gene was 44.2%, 40.0%, 15.8% in the control group vs. 31.3%; 45.7% and 23.0 among BA patients, respectively (χ2 = 6.59; р = 0.037). No significant difference was observed with regards to the distribution of genotypes for Arg16Gly polymorphism in the ß2 -АR gene in men and women controls (χ2 = 4.05; р = 0.13) and BA patients (χ2 = 4.34; р = 0.11). BA risk was 1.74 times higher in the minor allele carriers (Arg/Gly + Gly/Gly genotypes) for Arg16Gly polymorphism in the ß2 -АR gene. CONCLUSION: Conclusions: Analysis of Arg16Gly polymorphic variants in the ß2-AR gene showed a statistically significant difference in the distribution of Arg/Arg, Arg/Gly, and Gly/Gly genotypes in patients with BA and apparently healthy individuals due to the higher frequency of Arg/Arg genotype in controls and higher frequency of Gly/Gly genotype in patients with asthma. No difference with regard to gender was found in the distribution of genotypes.


Assuntos
Asma , Receptores Adrenérgicos beta 2 , Alelos , Asma/genética , Feminino , Genótipo , Humanos , Masculino , Polimorfismo Genético , Receptores Adrenérgicos beta 2/genética
19.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(6): 557-560, 2021 Jun 10.
Artigo em Chinês | MEDLINE | ID: mdl-34096025

RESUMO

OBJECTIVE: To carry out genetic testing for a Chinese patient with X-linked hypohidrotic ectodermal dysplasia (XLHED) and explore its genotype-phenotype correlation. METHODS: Clinical data of the patient was collected. Peripheral blood samples were taken from the patient, his parents and 100 unrelated healthy controls. Genetic variants were detected by using next-generation sequencing using a skin-disease panel through targeted capture and next generation sequencing. Candidate variant was verified by Sanger sequencing. All literature related to genetic testing of XLHED patients in China was searched in the database, and the genotypes and phenotypes of patients in the literature and the correlation between them were statistically analyzed. RESULTS: A novel splice site variant c.655_689del was detected in the patient but not among his parents and the 100 unrelated healthy controls. So far 61 variants of the EDA gene have been identified among Chinese patients with XLHED, which suggested certain degree of genotype-phenotype correlation. CONCLUSION: A novel c.655_689del variant has been identified in the EDA gene, which has expanded the spectrum of EDA gene variant and facilitated delineation of the genotype-phenotype correlation of XLHED.


Assuntos
Displasia Ectodérmica Anidrótica Tipo 1 , Criança , China , Displasia Ectodérmica Anidrótica Tipo 1/genética , Ectodisplasinas/genética , Testes Genéticos , Genótipo , Humanos , Fenótipo
20.
BMC Res Notes ; 14(1): 216, 2021 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-34059110

RESUMO

OBJECTIVE: Helicobacter pylori is one of the most common causes of gastric infections in humans. It is estimated that approximately 50% of people around the world are infected with this bacterium. This study aimed to determine the antibiotic resistance pattern, as well as the frequency of cagA and vacA genes in H. pylori isolates obtained from patients in the clinical centers in Tabriz city, Iran. RESULTS: The culture method detected 100 (45.25%) H. pylori isolates from 221 biopsy samples during 3 years. The results showed that 63% and 81% of the isolates were positive for cagA and vacA genes, respectively. The highest resistance of isolates was seen against metronidazole (79%) and amoxicillin (36%), respectively. Also, the isolates showed the least resistance to tetracycline (8%).


Assuntos
Helicobacter pylori , Antígenos de Bactérias/genética , Proteínas de Bactérias/genética , Resistência Microbiana a Medicamentos , Genótipo , Helicobacter pylori/genética , Humanos , Irã (Geográfico)/epidemiologia
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