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1.
Medicine (Baltimore) ; 100(36): e26983, 2021 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-34516490

RESUMO

ABSTRACT: The identification of single-nucleotide polymorphisms (SNPs) in genes putatively related to pathophysiological processes in major depressive disorder (MDD) might improve both diagnosis and personalized treatment strategies eventually leading to more effective interventions. Considering the important role of the glucocorticoid receptor and the related FK506 binding protein 51 (FKBP51) in the pathophysiology of MDD, we aimed to investigate putative associations between variants of FKBP5, the coding gene of FKBP51, with antidepressant treatment resistance and MDD susceptibility.Nine common SNPs of the FKBP5 gene prioritized based on location and, putative or known functions were genotyped in Han Chinese population, including MDD patients with or without antidepressant-treatment resistance and healthy controls. Associations of FKBP5 SNPs with MDD susceptibility and treatment response were examined in the whole group of MDD patients, as well as in subgroups stratified by antidepressant treatment resistance, compared with healthy controls.In total, 181 Han Chinese patients with MDD and 80 healthy controls were recruited. No significant SNP or haplotype associations were observed in the whole patient group. There were nominal significant differences both for the haplotype block with SNPs in strong LD (r2 > 0.8, P = .040) and haplotype block with SNPs in moderate LD (r2 > 0.1, P = .017) between the haplotype distributions of patients with antidepressant treatment resistance (n = 81) and healthy controls, but both significances did not survive multiple testing correction. Furthermore, no specific haplotype could be observed causing a significant difference in any combination between all comparisons.No associations were observed of FKBP5 variants with MDD or antidepressant treatment response. The lack of associations might be due to the relatively small sample size of this study (power ranged from 0.100 to 0.752). A follow-up study will need larger, better phenotyped, and more homogeneous samples to draw a definitive conclusion regarding the involvement of this gene in MDD.


Assuntos
Transtorno Depressivo Maior/tratamento farmacológico , Predisposição Genética para Doença , Proteínas de Ligação a Tacrolimo/genética , Adolescente , Adulto , Idoso , Grupo com Ancestrais do Continente Asiático , Estudos de Casos e Controles , China , Transtorno Depressivo Maior/genética , Feminino , Haplótipos , Humanos , Masculino , Pessoa de Meia-Idade , Fenótipo , Polimorfismo de Nucleotídeo Único , Adulto Jovem
2.
J Insect Sci ; 21(5)2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34519348

RESUMO

Islands are insular environments that are negatively impacted by invasive species. In Hawai'i, at least 21 non-native bees have been documented to date, joining the diversity of >9,000 non-native and invasive species to the archipelago. The goal of this study is to describe the persistence, genetic diversity, and natural history of the most recently established bee to Hawai'i, Megachile policaris Say, 1831 (Hymenoptera: Megachilidae). Contemporary surveys identify that M. policaris is present on at least O'ahu, Maui, and Hawai'i Island, with the earliest detection of the species in 2017. Furthermore, repeated surveys and observations by community members support the hypothesis that M. policaris has been established on Hawai'i Island from 2017 to 2020. DNA sequenced fragments of the cytochrome oxidase I locus identify two distinct haplotypes on Hawai'i Island, suggesting that at least two founders have colonized the island. In their native range, M. policaris is documented to forage on at least 21 different plant families, which are represented in Hawai'i. Finally, ensemble species distribution models (SDMs) constructed with four bioclimatic variables and occurrence data from the native range of M. policaris predicts high habitat suitability on the leeward side of islands throughout the archipelago and at high elevation habitats. While many of the observations presented in our study fall within the predicted habitat suitability on Hawai'i, we also detected the M. policaris on the windward side of Hawai'i Island suggesting that the SDMs we constructed likely do not capture the bioclimatic niche flexibility of the species.


Assuntos
Abelhas , Espécies Introduzidas , Distribuição Animal , Animais , Abelhas/genética , Abelhas/fisiologia , Ecossistema , Complexo IV da Cadeia de Transporte de Elétrons/genética , Genes de Insetos , Haplótipos , Hawaii , Modelos Estatísticos , Polinização , Dinâmica Populacional
3.
Zhongguo Ying Yong Sheng Li Xue Za Zhi ; 37(3): 225-229, 2021 May.
Artigo em Chinês | MEDLINE | ID: mdl-34374231

RESUMO

Objective: To investigate the relationship between mitochondrial DNA (mtDNA) variation and high altitude essential hypertension(HAEH) in the Chinese Tajik population. Methods: Fifty-three patients with HAEH and 46 healthy subjects were enrolled from the Chinese Tajik population. The mtDNA fragments were amplificated by polymerase chain reaction, and products were sequenced to acquire full sequence of mtDNA. The mtDNA sequences of all subjects were compared to the Cambridge sequence to explore mtDNA variations and analyze difference between HAEH and healthy controls. Online softwares were applied to predict function changes caused by positive associated mtDNA variations. Results: Compared to the control group, the frequency of haplogroup U4b was significant higher in HAEH group(P=0.023,OR=7.062,CI(95%)=1.306-38.182), and the frequencies of 8 mutations from haplogroup U4b showed a significant difference between the HAEH group and control group (all with P values below 0.05). The mt DNA15693T>C mutation was the only missense mutation, which affected amino acid 316 in mitochondrial cytochrome b (MTCYB) by changing it from methionine to threonine. Bioinformatics analysis indicated that the mutation in MTCYB may play a biological role through affecting the second structure of protein. Conclusion: MtDNA subhaplogroup U4b is a genetic factor for HAEH in the Chinese Tajik population, and mtDNA15693T>C mutation may be an important molecular mechanism of HAEH.


Assuntos
DNA Mitocondrial , Predisposição Genética para Doença , Altitude , Grupo com Ancestrais do Continente Asiático/genética , China , DNA Mitocondrial/genética , Hipertensão Essencial/genética , Haplótipos , Humanos , Mutação
4.
Viruses ; 13(8)2021 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-34452390

RESUMO

To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylogeographic, haplotype, and genomic analysis were effectively implemented. We estimated the Time to the Most Recent Common Ancestor (TMRCA) in reference to the Algerian pandemic and highlighted the multiple introductions of the disease and the missing data depicted in the transmission loop. In addition, we emphasized the significant role played by local and international travels in disease dissemination. Most importantly, we unveiled mutational patterns, the effect of unique mutations on corresponding proteins, and the relatedness regarding the Algerian sequences to other sequences worldwide. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Similarly, successful tracing could be established, such as Algeria/G37318-8849/2020|EPI_ISL_766863, which was imported from Saudi Arabia during the pilgrimage. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.


Assuntos
COVID-19/virologia , Evolução Molecular , SARS-CoV-2/genética , Argélia/epidemiologia , COVID-19/epidemiologia , COVID-19/transmissão , Genoma Viral , Genômica , Haplótipos , Humanos , Mutação , Pandemias , Filogenia , Filogeografia , SARS-CoV-2/classificação , SARS-CoV-2/isolamento & purificação , Arábia Saudita/epidemiologia , Viagem
5.
PLoS One ; 16(8): e0255608, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34352002

RESUMO

BACKGROUND: The diversity in the clinical course of COVID-19 has been related to differences in innate and adaptative immune response mechanisms. Natural killer (NK) lymphocytes are critical protagonists of human host defense against viral infections. It would seem that reduced circulating levels of these cells have an impact on COVID-19 progression and severity. Their activity is strongly regulated by killer-cell immuno-globulin-like receptors (KIRs) expressed on the NK cell surface. The present study's focus was to investigate the impact of KIRs and their HLA Class I ligands on SARS-CoV-2 infection. METHODS: KIR gene frequencies, KIR haplotypes, KIR ligands and combinations of KIRs and their HLA Class I ligands were investigated in 396 Sardinian patients with SARS-CoV-2 infection. Comparisons were made between 2 groups of patients divided according to disease severity: 240 patients were symptomatic or paucisymptomatic (Group A), 156 hospitalized patients had severe disease (Group S). The immunogenetic characteristics of patients were also compared to a population group of 400 individuals from the same geographical areas. RESULTS: Substantial differences were obtained for KIR genes, KIR haplotypes and KIR-HLA ligand combinations when comparing patients of Group S to those of Group A. Patients in Group S had a statistically significant higher frequency of the KIR A/A haplotype compared to patients in Group A [34.6% vs 23.8%, OR = 1.7 (95% CI 1.1-2.6); P = 0.02, Pc = 0.04]. Moreover, the KIR2DS2/HLA C1 combination was poorly represented in the group of patients with severe symptoms compared to those of the asymptomatic-paucisymptomatic group [33.3% vs 50.0%, OR = 0.5 (95% CI 0.3-0.8), P = 0.001, Pc = 0.002]. Multivariate analysis confirmed that, regardless of the sex and age of the patients, the latter genetic variable correlated with a less severe disease course [ORM = 0.4 (95% CI 0.3-0.7), PM = 0.0005, PMC = 0.005]. CONCLUSIONS: The KIR2DS2/HLA C1 functional unit resulted to have a strong protective effect against the adverse outcomes of COVID-19. Combined to other well known factors such as advanced age, male sex and concomitant autoimmune diseases, this marker could prove to be highly informative of the disease course and thus enable the timely intervention needed to reduce the mortality associated with the severe forms of SARS-CoV-2 infection. However, larger studies in other populations as well as experimental functional studies will be needed to confirm our findings and further pursue the effect of KIR receptors on NK cell immune-mediated response to SARS-Cov-2 infection.


Assuntos
COVID-19/imunologia , Células Matadoras Naturais/imunologia , Receptores KIR/imunologia , Adulto , Idoso , COVID-19/metabolismo , Estudos de Casos e Controles , Feminino , Frequência do Gene/genética , Genes MHC Classe I/imunologia , Predisposição Genética para Doença , Antígenos HLA-C/genética , Haplótipos/genética , Humanos , Imunidade/imunologia , Imunogenética/métodos , Células Matadoras Naturais/metabolismo , Ligantes , Masculino , Pessoa de Meia-Idade , Receptores KIR/genética , Receptores KIR/metabolismo , SARS-CoV-2/patogenicidade , Índice de Gravidade de Doença
6.
Microb Pathog ; 159: 105149, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34416273

RESUMO

Genetic polymorphism in pathogen recognition receptors tends to influence infection, disease susceptibility, and progression. We analyzed the association of TLR4 and TLR9 gene polymorphisms with multiple hrHPV infections and HPV16 copy number in cervicitis and cervical cancer. A total of 440 cervical cancer, cervicitis, and healthy individuals were studied using PCR-based assays. Student t-test, chi-square test, Welch's t-test, and Fisher's Exact test were utilized to evaluate the association of HPV infection with polymorphisms. Haploview and FAMHAP were used to analyze haplotype association with HPV infection and viral load. Study results revealed HPV45 infection as the most common one in cervical cancer after HPV16, and one-fourth HPV positive cervical cancer patients possessed multiple HPV infections. Mean HPV16 copy number of 264.4 ± 58.7 and 2.1 ± 3.3 copies/cell was detected in cervical cancer and cervicitis, respectively. TLR4 rs10759931 was protective against multiple hrHPV infections. TLR4 haplotype ACAC was associated with an increased risk of multiple hrHPV infections. TLR9 SNPs rs187084, rs352140, and rs352139 were associated with decreased risk of high HPV16 copy number. Augmentation of efforts for the multivalent HPV vaccination in India is suggested. The analyzed polymorphisms were shown to modulate hrHPV co-infections and HPV16 viral load that warrants further analysis.


Assuntos
Neoplasias do Colo do Útero , Cervicite Uterina , Variações do Número de Cópias de DNA , Feminino , Haplótipos , Papillomavirus Humano 16/genética , Humanos , Receptor 4 Toll-Like/genética , Receptor Toll-Like 9/genética
7.
Gene ; 802: 145867, 2021 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-34352299

RESUMO

Genome-wide association studies (GWAS) have identified DENND1A as a potential candidate gene linked to the fertility-related phenotypes in dairy cows. However, to date, no studies have examined the association of the DENND1A insertion/deletions (indels) to bovine fertility on a large scale. Herein, two indel sites, including P4-del-26-bp and P8-ins-15-bp were identified in 1064 Holstein cows. The values of the minor allelic frequency (MAF) ranged between 0.471 (deletion) and 0.230 (deletion), respectively, and combined four different haplotypes by analyzing the haplotype combination. It is noteworthy that P4-del-26-bp is associated with the ovarian width (P = 0.0004) and corpus luteum diameter (P = 0.004). Meanwhile, P8-ins-15-bp was found to have a significant association with the ovarian width (P = 0.020), ovarian weight (P = 0.004), the number of mature follicles (P = 0.020), and diameter of the mature follicles (P = 0.016). Furthermore, the combinatorial analysis showed that the two indel combined-genotypes were significantly related to several reproductive traits (ovarian width, ovarian weight, etc.). Collectively, our findings indicated that these two novel indels and their combinations are correlated with the reproductive traits, and hence, they can serve in the marker-assisted selection (MAS) in cattle breeding. Nevertheless, further functional experiments are needed for understanding the mechanisms of these indels in cattle reproduction in a better way.


Assuntos
Doenças dos Bovinos/genética , Mutação INDEL , Proteínas de Membrana Transportadoras/genética , Síndrome do Ovário Policístico/genética , Animais , Bovinos , Feminino , Fertilidade/genética , Frequência do Gene , Estudo de Associação Genômica Ampla/veterinária , Haplótipos , Reprodução/genética
8.
Medicine (Baltimore) ; 100(29): e26614, 2021 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-34398016

RESUMO

ABSTRACT: Cytochrome P450 enzymes play a central role in the phase I biotransformation process of a wide range of compounds, including xenobiotics, drugs, hormones and vitamins. It is noteworthy that these enzymes are highly polymorphic and, depending on the genetic makeup, an individual may have impaired enzymatic activity. Therefore, the identification of genetic variants in these genes could facilitate the implementation of pharmacogenetic studies and genetic predisposition to multifactorial diseases. We have established the frequencies of CYP2B6 (rs3745274; rs2279343) and CYP3A4 (rs2740574) alleles and genotypes in 209 healthy Malian subjects using TaqMan drug metabolism genotyping assays for allelic discrimination. Allele frequencies were 37% for CYP2B6 rs3745274; 38% for CYP2B6 rs2279343; and 75% for CYP3A4 rs2740574 respectively. Overall, the frequencies observed in Mali are statistically comparable to those reported across Africa except North Africa. The major haplotypes in CYP2B6 rs3745274 and CYP2B6 rs2279343 were represented by GA (60.24%) followed by TG (35.36%). We noted a strong linkage disequilibrium between CYP2B6 rs3745274 and CYP2B6 rs2279343 with D' = 0.91 and r2 = 0.9. The frequencies of the genotypic combinations were 43.5% (GT/AG), 37.3% (GG/AA) and 11.5% (TT/GG) in the combination of CYP2B6-rs3745274 and CYP2B6-rs2279343; 26.8% (GT/CC), 25.4%, (GT/CT), 17.2% and GG/CT in the combination CYP2B6-rs3745274-CYP3A4-rs2740574; 26.8% (AG/CC), 23.9% (AA/CC), 19.1% (AG/CT), and 11% (AA/CT) in the combination CYP2B6-rs2279343-CYP3A4-rs2740574, respectively. The most common triple genotype was GT/AG/CC with 24.9%, followed by GG/AA/CC with 23.9%, GT/AG/CT with 16.7%, and GG/AA/CT with 10%. Our results provide new insights into the distribution of these pharmacogenetically relevant genes in the Malian population. Moreover, these data will be useful for studies of individual genetic variability to drugs and genetic predisposition to diseases.


Assuntos
Alelos , Genótipo , Haplótipos/genética , Adolescente , Adulto , Idoso , Citocromo P-450 CYP2B6/genética , Citocromo P-450 CYP3A/genética , Feminino , Humanos , Malásia/etnologia , Masculino , Pessoa de Meia-Idade , Farmacogenética/métodos
9.
Fa Yi Xue Za Zhi ; 37(3): 358-365, 2021 Jun.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-34379905

RESUMO

Abstract: Objective To study the genetic polymorphism of whole mitochondrial DNA (mtDNA) genomes in She population in Zhejiang and to explore the maternal genetic structure of the She population. Methods Whole mtDNA genomes of 231 unrelated individuals from She population in Zhejiang Province were sequenced. The number of mutations and population genetics parameters such as, the haplotype diversity (HD), discrimination power (DP), and random match probabilities (RMP) were analyzed. The mtDNA haplogroups of Zhejiang She population were classified, and the maternal genetic relationships between She and nine other Chinese populations were estimated. Results In 231 Zhejiang She samples, 8 507 mutations (702 types) were observed and the samples were classified into 94 haplogroups. The HD, DP and RMP values were 0.998 6, 0.994 2 and 0.005 8, respectively. The lowest genetic differentiation degree (Fst=0.006 89) was detected between Zhejiang She population and southern Han population. Principal component analysis (PCA) and median-joining network analysis showed that the genetic distance of Zhejiang She population with Guangxi Yao, Yunnan Dai and Southern Han populations was relatively close, but the population still had some unique genetic characteristics. Conclusion The whole mtDNA genomes are highly polymorphic in Zhejiang She population. The Zhejiang She population contains complex and diverse genetic components and has a relatively close maternal genetic relationship with Guangxi Yao, Yunnan Dai and Southern Han populations. Meanwhile, Zhejiang She population has kept its unique maternal genetic components.


Assuntos
DNA Mitocondrial , Sequenciamento de Nucleotídeos em Larga Escala , Grupo com Ancestrais do Continente Asiático/genética , China , DNA Mitocondrial/genética , Grupos Étnicos/genética , Feminino , Genética Populacional , Haplótipos , Humanos , Polimorfismo Genético
10.
Clin Lab ; 67(8)2021 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-34383420

RESUMO

BACKGROUND: Sickle cell disease (SCD) is a common hematological genetic disorder in Saudi Arabia, Africa, the Mediterranean region, and India. The present study aimed to characterize ßS haplotypes found in the Jazan region, Saudi Arabia. METHODS: One hundred sickle cell trait (SCT) individuals, diagnosed during their visit to the premarital screening clinic at King Fahad Central Hospital, were included in the study. Molecular analysis was carried out by polymerase chain reaction (PCR) and six polymorphic sites of the ß-globin gene were analyzed using restriction endonucleases Hind II, Xmn-I, Hind III, and Ava II. RESULTS: The results of the current study revealed the presence of five typical haplotypes in which Benin, Bantu, and Senegal were found in homozygous state with 29%, 3% and 1% frequencies, respectively. Interestingly, 29% of the studied population showed atypical haplotypes in heterozygous state and 2% in homozygous state for the first time in Jazan region. CONCLUSIONS: In addition to the typical haplotypes, high frequency of atypical haplotypes in this study indicates a diverse genetic mechanism that might have a crucial effect on the severity of SCD in this region. Therefore, considering this study in a cohort population with SCD in Jazan region may provide more indepth details about the correlation between haplotypes and the clinical manifestation of the disease.


Assuntos
Anemia Falciforme , Globinas beta , Anemia Falciforme/diagnóstico , Anemia Falciforme/epidemiologia , Anemia Falciforme/genética , Haplótipos , Hemoglobina Falciforme/genética , Humanos , Prevalência , Arábia Saudita/epidemiologia , Globinas beta/genética
11.
BMC Genomics ; 22(1): 582, 2021 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-34332539

RESUMO

BACKGROUND: Single cell Strand-seq is a unique tool for the discovery and phasing of genomic inversions. Conventional methods to discover inversions with Strand-seq data are blind to known inversion locations, limiting their statistical power for the detection of inversions smaller than 10 Kb. Moreover, the methods rely on manual inspection to separate false and true positives. RESULTS: Here we describe "InvertypeR", a method based on a Bayesian binomial model that genotypes inversions using fixed genomic coordinates. We validated InvertypeR by re-genotyping inversions reported for three trios by the Human Genome Structural Variation Consortium. Although 6.3% of the family inversion genotypes in the original study showed Mendelian discordance, this was reduced to 0.5% using InvertypeR. By applying InvertypeR to published inversion coordinates and predicted inversion hotspots (n = 3701), as well as coordinates from conventional inversion discovery, we furthermore genotyped 66 inversions not previously reported for the three trios. CONCLUSIONS: InvertypeR discovers, genotypes, and phases inversions without relying on manual inspection. For greater accessibility, results are presented as phased chromosome ideograms with inversions linked to Strand-seq data in the genome browser. InvertypeR increases the power of Strand-seq for studies on the role of inversions in phenotypic variation, genome instability, and human disease.


Assuntos
Inversão Cromossômica , Genoma Humano , Teorema de Bayes , Genótipo , Haplótipos , Humanos
12.
J Int Med Res ; 49(7): 3000605211029504, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34266338

RESUMO

OBJECTIVE: Schizophrenia is a complex mental disorder with high heritability. The hypothalamic-pituitary-adrenal (HPA) axis, which is the stress system of the neuroendocrine system, is considered to impact psychotic disorders. We hypothesized that polymorphisms of HPA axis genes might be involved in the development of schizophrenia. METHODS: A case-control study comprising 234 patients with schizophrenia and 399 matched healthy controls was conducted to investigate the association between the human melanocortin 2 receptor (MC2R) gene and schizophrenia risk. Seven tag single nucleotide polymorphisms (SNPs) (rs16941303, rs16941314, rs2186944, rs28926188, rs7230126, rs948322, and rs948331) of MC2R were genotyped by direct sequencing. RESULTS: No significant associations were observed between any of the alleles, genotypes, or haplotypes examined within the MC2R gene and the risk of schizophrenia in the total group or in subgroups stratified by smoking or alcoholism. However, a subgroup analysis stratified by sex revealed that under the additive model, the C allele of the MC2R rs948331 SNP significantly decreased the risk of schizophrenia in females (odds ratio=0.18). CONCLUSION: The C allele of the MC2R rs948331 locus may be a protective factor, reducing the risk of schizophrenia in the female Han Chinese population.


Assuntos
Grupo com Ancestrais do Continente Asiático , Receptor Tipo 2 de Melanocortina , Esquizofrenia , Regiões 3' não Traduzidas , Alelos , Grupo com Ancestrais do Continente Asiático/genética , Estudos de Casos e Controles , China , Feminino , Predisposição Genética para Doença , Genótipo , Haplótipos , Humanos , Sistema Hipotálamo-Hipofisário , Sistema Hipófise-Suprarrenal , Polimorfismo de Nucleotídeo Único/genética , Receptor Tipo 2 de Melanocortina/genética , Receptor Tipo 2 de Melanocortina/metabolismo , Esquizofrenia/genética
13.
Nat Commun ; 12(1): 4377, 2021 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-34312382

RESUMO

The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.


Assuntos
Apomixia/genética , Citrus/genética , Frutas/genética , Genoma de Planta/genética , Alelos , Citrus/classificação , Extremo Oriente , Frequência do Gene , Genética Populacional , Genótipo , Geografia , Haplótipos , Hibridização Genética , Filogenia , Especificidade da Espécie
14.
Int J Mol Sci ; 22(14)2021 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-34299329

RESUMO

The low-molecular weight glutenin subunit (LMW-GS) composition of wheat (Triticum aestivum) flour has important effects on end-use quality. However, assessing the contributions of each LMW-GS to flour quality remains challenging because of the complex LMW-GS composition and allelic variation among wheat cultivars. Therefore, accurate and reliable determination of LMW-GS alleles in germplasm remains an important challenge for wheat breeding. In this study, we used an optimized reversed-phase HPLC method and proteomics approach comprising 2-D gels coupled with liquid chromatography-tandem mass spectrometry (MS/MS) to discriminate individual LMW-GSs corresponding to alleles encoded by the Glu-A3, Glu-B3, and Glu-D3 loci in the 'Aroona' cultivar and 12 'Aroona' near-isogenic lines (ARILs), which contain unique LMW-GS alleles in the same genetic background. The LMW-GS separation patterns for 'Aroona' and ARILs on chromatograms and 2-D gels were consistent with those from a set of 10 standard wheat cultivars for Glu-3. Furthermore, 12 previously uncharacterized spots in 'Aroona' and ARILs were excised from 2-D gels, digested with chymotrypsin, and subjected to MS/MS. We identified their gene haplotypes and created a 2-D gel map of LMW-GS alleles in the germplasm for breeding and screening for desirable LMW-GS alleles for wheat quality improvement.


Assuntos
Glutens/análise , Glutens/metabolismo , Triticum/metabolismo , Alelos , Sequência de Aminoácidos , Eletroforese em Gel Bidimensional/métodos , Haplótipos , Peso Molecular , Melhoramento Vegetal/métodos , Proteômica/métodos , Espectrometria de Massas em Tandem/métodos , Triticum/química , Triticum/genética
15.
Eur Respir J ; 58(1)2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34244302
17.
Bioinformatics ; 37(Suppl_1): i161-i168, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34252973

RESUMO

MOTIVATION: The availability of human genomic data, together with the enhanced capacity to process them, is leading to transformative technological advances in biomedical science and engineering. However, the public dissemination of such data has been difficult due to privacy concerns. Specifically, it has been shown that the presence of a human subject in a case group can be inferred from the shared summary statistics of the group, e.g. the allele frequencies, or even the presence/absence of genetic variants (e.g. shared by the Beacon project) in the group. These methods rely on the availability of the target's genome, i.e. the DNA profile of a target human subject, and thus are often referred to as the membership inference method. RESULTS: In this article, we demonstrate the haplotypes, i.e. the sequence of single nucleotide variations (SNVs) showing strong genetic linkages in human genome databases, may be inferred from the summary of genomic data without using a target's genome. Furthermore, novel haplotypes that did not appear in the database may be reconstructed solely from the allele frequencies from genomic datasets. These reconstructed haplotypes can be used for a haplotype-based membership inference algorithm to identify target subjects in a case group with greater power than existing methods based on SNVs. AVAILABILITY AND IMPLEMENTATION: The implementation of the membership inference algorithms is available at https://github.com/diybu/Haplotype-based-membership-inferences.


Assuntos
Genoma Humano , Genômica , Algoritmos , Frequência do Gene , Haplótipos , Humanos
18.
Nat Genet ; 53(8): 1135-1142, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34282336

RESUMO

Birth weight is a common measure of fetal growth that is associated with a range of health outcomes. It is directly affected by the fetal genome and indirectly by the maternal genome. We performed genome-wide association studies on birth weight in the genomes of the child and parents and further analyzed birth length and ponderal index, yielding a total of 243 fetal growth variants. We clustered those variants based on the effects of transmitted and nontransmitted alleles on birth weight. Out of 141 clustered variants, 22 were consistent with parent-of-origin-specific effects. We further used haplotype-specific polygenic risk scores to directly test the relationship between adult traits and birth weight. Our results indicate that the maternal genome contributes to increased birth weight through blood-glucose-raising alleles while blood-pressure-raising alleles reduce birth weight largely through the fetal genome.


Assuntos
Peso ao Nascer/genética , Desenvolvimento Fetal/genética , Adulto , Glicemia/genética , Pressão Sanguínea/genética , Estatura/genética , Doenças Cardiovasculares/genética , Feminino , Estudo de Associação Genômica Ampla , Haplótipos , Humanos , Islândia , Recém-Nascido , Masculino , Modelos Genéticos , Polimorfismo de Nucleotídeo Único
19.
Int J Legal Med ; 135(5): 1675-1684, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34216266

RESUMO

The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.


Assuntos
Cromossomos Humanos Y/genética , Grupo com Ancestrais do Continente Europeu/genética , Variação Genética , Haplótipos , Europa (Continente)/etnologia , Migração Humana , Humanos , Repetições de Microssatélites , Filogenia , Filogeografia , Polimorfismo de Nucleotídeo Único
20.
Virology ; 562: 63-73, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34265628

RESUMO

We aimed to describe SARS-CoV-2 strains in Iranians from nine distributed cities infected during two months expanding late 2020 and early 2021 by genotyping known informative single nucleotide in five PCR amplicons. Two variants associated with haplotype H1 (clade G) and nine additional variants associated with other haplotypes were genotyped, respectively, in RNA isolates of 244 and 85 individuals. The variants associated with the H1a (GR) and H1b (GH) haplotypes were most prevalent, indicating a significant change in infection pattern with passage of time. The most important findings were that recombinant genomes and co-infection, respectively, were surmised in 44.7% and 12.9% of the samples extensively genotyped. Partners of many of the recombinations were relatively common strains. Co-existing viruses were among those currently circulating in Iran. In addition to random mutations, co-infection with different existing strains and recombination between their genomes may significantly contribute to the emergence of new SARS-CoV-2 strains.


Assuntos
COVID-19/virologia , Variação Genética , Genoma Viral , Recombinação Genética , SARS-CoV-2/genética , Coinfecção/genética , Evolução Molecular , Técnicas de Genotipagem , Haplótipos , Humanos , Mutação , Filogenia , RNA Viral/genética , SARS-CoV-2/isolamento & purificação
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