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1.
Electron J Biotechnol ; 49: 72-81, Jan. 2021. tab, graf
Article in English | LILACS | ID: biblio-1291929

ABSTRACT

BACKGROUND: Persimmon (Diospyros kaki Thunb.) is the most widely cultivated species of the genus Diospyros. In this study, genetic diversity and variations in persimmon genotypes were investigated using single nucleotide polymorphism (SNP) markers identified by genotyping-by-sequencing (GBS) analysis. RESULTS: Ninety-five persimmon accessions grown in the Pear Research Institute, National Institute Horticultural and Herbal Science, were sequenced using the Illumina Hiseq2500 platform and polymorphic SNPs were detected to develop molecular markers. These reliable SNPs were analyzed using the Kompetitive Allele Specific PCR (KASP) assay to discriminate among persimmon genotypes. GBS generated a total of 447,495,724 trimmed reads, of which 89.7% were raw reads. After demultiplexing and sequence quality trimming, 108,876,644 clean reads were mapped to the reference transcriptome. An average of 1,146,070 genotype reads were mapped. Filtering of raw SNPs in each sample led to selection of a total of 1,725,401 high-quality SNPs. The number of homozygous and heterozygous SNPs ranged from 1,933 to 6,834 and from 846 to 5,927, respectively. CONCLUSIONS: Of the 49 SNPs selected for development of an identification system for persimmons, 15 SNPs were used in the KASP assay to analyze 32 persimmon accessions. These KASP markers discriminated among all accessions.


Subject(s)
Polymerase Chain Reaction/methods , Diospyros/genetics , Genetic Variation , Genetic Markers , Chromosome Mapping , Polymorphism, Single Nucleotide/genetics , Alleles , Genotyping Techniques , Homozygote
2.
Braz. j. med. biol. res ; 54(2): e10098, 2021. tab, graf
Article in English | LILACS, ColecionaSUS | ID: biblio-1142576

ABSTRACT

We aimed to present an overview of the literature regarding the interaction between physical exercise and APOE gene polymorphism on cognitive function, particularly in patients with Alzheimer's disease (AD). Firstly, this review focused on the effect of the physical exercise on cognitive function, regardless of APOE gene polymorphism. Some studies have shown that a high level of cardiorespiratory fitness is associated with less neuronal damage with an improvement in memory score tests whereas other studies failed to detect any association between physical exercise and cognitive improvement either in healthy individuals or patients with AD. Taken together, standardized protocols and more longitudinal studies are required to provide a better insight into the effects of physical exercise on cognitive function. Although there is no agreement in the literature regarding the effects of physical exercise on cognitive function, it is well established that it improves social interaction and the feeling of well-being, thereby positively contributing to the quality of life of the elderly. Regarding the influence of physical exercise on cognitive function in APOE ε4 allele carriers, the data trend shows that the carriers of allele ε4 for APOE gene were more responsive to the beneficial effects of physical exercise on cognitive function compared with non-carriers. Nevertheless, studies with larger sample sizes will provide more accuracy about this relationship.


Subject(s)
Humans , Aged , Aged, 80 and over , Apolipoproteins E/genetics , Exercise , Cognition , Polymorphism, Genetic , Quality of Life , Alleles , Alzheimer Disease/genetics , Genotype
3.
Article in Chinese | WPRIM | ID: wpr-879633

ABSTRACT

OBJECTIVE@#To study the distribution of KIR3DL2 alleles among ethnic Han Chinese from Zhejiang.@*METHODS@#Genomic DNA was extracted by using a magnetic bead method. The full sequence of the KIR3DL2 gene was amplified with four pairs by PCR primers. The coding regions of 208 unrelated ethnic Han Chinese blood donors were analyzed using a BigDye Terminator v3.1 Sequencing Kit. The genotypes were assigned based on the nucleotide polymorphism of the KIR3DL2 gene.@*RESULTS@#Among the 208 samples, 133 were KIR3DL2 heterozygotes and 75 were homozygotes. Forty six KIR3DL2 genotypes were detected. Respectively, 70, 33 and 23 individuals were found to have a KIR3DL2*00201/KIR3DL2*00201, KIR3DL2*00201/KIR3DL2*00701, and KIR3DL2*00201/KIR3DL2*01001 genotype. Twenty-two KIR3DL2 alleles were discovered, and the frequencies of KIR3DL2*00201, KIR3DL2*00701 and KIR3DL2*01001 were 57.45%, 13.46% and 9.13%, respectively.@*CONCLUSION@#The distribution of KIR3DL2 alleles among ethnic Han Chinese in Zhejiang has been determined and fits the criteria for genetic polymorphism.


Subject(s)
Alleles , China , Ethnic Groups , Gene Frequency , Humans , Polymorphism, Genetic , Receptors, KIR3DL2
4.
Article in Chinese | WPRIM | ID: wpr-879613

ABSTRACT

OBJECTIVE@#To study the serological, molecular and genetic characteristics of an individual with para-Bombay blood group.@*METHODS@#Serological method was used to detect the presence of A, B, H antigens in red blood cells and saliva, and Sanger sequencing was used to analyze the FUT1 gene of the proband and her family members. Genetic mechanism of the blood group was analyzed by pedigree analysis.@*RESULTS@#Forward and reverse typing of the ABO blood group were inconsistent for the proband. A, B and H antigens were not found on erythrocytes, while B and H antigens were found in saliva, in addition with unexpected antibodies. The proband was found to have a genotype of ABO*B.01/ABO*O.01.04 caused by homozygous variant of c.948C>A (p.Tyr316Ter) of the FUT1 gene.@*CONCLUSION@#A novel para-Bombay blood group was identified, which was due to the missense variant of c.948C>A in the coding region of the FUT1 gene, which has probably resulted in inability to synthesis active H antigen transferase.


Subject(s)
ABO Blood-Group System/genetics , Alleles , Female , Fucosyltransferases/genetics , Genotype , Homozygote , Humans , Phenotype
5.
Article in Chinese | WPRIM | ID: wpr-879612

ABSTRACT

OBJECTIVE@#To delineate the serological and molecular profiles of a patient with A(w)37B subtype.@*METHODS@#The ABO bloodtypes of the proband, his wife and daughter were determined with a standard serological method. Their ABO genotypes were determined by sequence-specific primer polymerase chain reaction (PCR-SSP). All exons of the ABO gene were directly sequenced. Exons 6 and 7 of the ABO gene were further analyzed by cloning and sequencing.@*RESULTS@#The red blood cells of the proband showed a weak B phenotype. His serum sample contained weak reactive anti-A antibody, which was defined as A(w)B blood group based on the serological characteristics. The A and B alleles were detected by blood group genotyping. Gene cloning and sequencing have identified a characteristic c.940A>G variant (ABO*AW.37) in exon 7 of the ABO gene, which resulted in substitution of Lysine by Glutamate at position 314. The proband's daughter has inherited the ABO*AW.37 allele.@*CONCLUSION@#The c.940A>G variant in exon 7 of the ABO gene probably underlay the decreased activity of GTA transferase and resulted in the Aw37 phenotype.


Subject(s)
ABO Blood-Group System/genetics , Alleles , Genotype , Humans , Pedigree , Phenotype
6.
Article in Chinese | WPRIM | ID: wpr-879611

ABSTRACT

OBJECTIVE@#To explore the molecular basis of two individuals with weak D variant of the Rh blood type.@*METHODS@#Routine serological testing was carried out to detect the D, C, c, E and e antigens of the Rh blood group. The D antigen was further detected with an indirect antiglobulin test. The presence of Rhesus box was detected by PCR to determine the homozygosity of the RHD gene.@*RESULTS@#Both samples were determined as weak D phenotype by the indirect antiglobulin test. DNA sequencing revealed that case 1 harbored a heterozygous 208C>T variant in exon 2 and a heterozygous 1227G>A variant in exon 9; while case 2 harbored homozygous 779A>G variants of exon 5 of the RHD gene. Case 1 was determined as RHD+/RHD+, while case 2 was determined as RHD+/RHD-. The two samples were respectively named as weak D type 122 and weak D type 149 based on the rules of Rhesus Base Nomenclature.@*CONCLUSION@#D negative blood donors should subject to indirect antiglobulin testing and molecular analysis for safer transfusion.


Subject(s)
Alleles , Blood Donors , Blood Grouping and Crossmatching , Genotype , Humans , Molecular Biology , Phenotype , Rh-Hr Blood-Group System/genetics
7.
Article in Chinese | WPRIM | ID: wpr-879572

ABSTRACT

OBJECTIVE@#To delineate the characteristics of a novel HLA-DQB1 allele identified during routine HLA matching in a leukemia family.@*METHODS@#The mother and brother of the patient were subjected to PCR sequence-specific oligonucleotide probe (SSOP), PCR sequence-based typ1ing (SBT), as well as next-generation sequencing (NGS).@*RESULTS@#PCR-SBT revealed that the patient's mother and brother's HLA-DQB1 sequences did not fully match with any known allele combination. NGS revealed that the novel allele has differed from the closest matched DQB1*03:02 with a T>G substitution at position 233 in exon 2, which resulted in substitution of Valine at codon 46 by Glycine. Pedigree analysis confirmed that the novel HLA-DQB1 allele was inherited from his mother.@*CONCLUSION@#A novel HLA-DQB1 allele has been identified through next generation sequencing and was officially named as HLA-DQB1*03:362 by the World Health Organization HLA Factor Nomenclature Committee.


Subject(s)
Alleles , Base Sequence , HLA-DQ beta-Chains/genetics , Humans , Male , Nucleotides , Polymorphism, Single Nucleotide , Sequence Analysis, DNA
8.
Article in Chinese | WPRIM | ID: wpr-879571

ABSTRACT

OBJECTIVE@#To explore the molecular basis for an individual with Bw subtype.@*METHODS@#Routine serological reactions were used to determine the surface antigens of erythrocytes and antibodies in serum. PCR-sequence-based typing (PCR-SBT) was used to analyze the coding regions of the ABO gene and erythroid-specific regulatory element in its intron 1. Amplicons for exons 5 to 7 containing the variant site were subjected to TA cloning for the isolation of the haploid and verification of the sequence. The 3D structure of mutant protein was predicted with Pymol software. Changes of amino acid residues and structural stability were also analyzed.@*RESULTS@#Serological assay showed that the individual had weakened B antigen and anti-B antibody in his serum. His genotype was determined as ABO*B.01/ABO*O.01.01. Sequencing of the entire coding region of the ABO gene identified an additional heterozygous c.734C/T variant. No variant was found in the erythroid-specific regulatory element of intron 1. Haploid cloning and isolation has obtained an ABO*O.01.01 allele and a ABO*B.01 allele containing a c.734T variant, which has led to substitution of Thr by Ile at position 245 in the functional center of glycosyltransferase. Based on the 3D structure of the protein, the residues binding with the mutation were unchanged, but the bonding distance between the hydrogens was changed with the amino acid substitution. Meanwhile, the connections with water molecules were increased.@*CONCLUSION@#The c.734C>T variant of the GTB gene can lead to an amino acid substitution in the functional center of the enzyme, which in turn may affect the stability of glycosyltransferase B protein and reduceits enzymatic activity.


Subject(s)
ABO Blood-Group System/genetics , Alleles , Exons/genetics , Genotype , Glycosyltransferases/genetics , Humans , Male , Phenotype
9.
Article in Chinese | WPRIM | ID: wpr-879550

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a Chinese pedigree with a novel ABO subtype.@*METHODS@#The proband and his family members were subjected to serological analysis, and their genotypes were determined by fluorescence PCR and direct sequencing of the coding regions of the ABO gene. Exons 6 to 7 of the ABO gene were also subjected to clone sequencing for haplotype analysis.@*RESULTS@#The proband was determined as an AxB subtype. By fluorescence PCR, he was typed as A/B. Clone sequencing has revealed a insertional mutation c.797_798 insT in exon 7 of the ABO gene, which yielded a novel allele. Pedigree analysis confirmed that the novel ABO*A1.02 allele carried by the proband and his sister was inherited from their father. The c.797_798insT mutation has been submitted to GenBank with an accession number of MK125137.@*CONCLUSION@#The c.797_798insT mutation of exon 7 of the ABO gene probably has led to weakened expression of A antigen.


Subject(s)
ABO Blood-Group System/genetics , Alleles , China , Genotype , Humans , Male , Mutation , N-Acetylgalactosaminyltransferases/genetics , Pedigree
10.
Article in Chinese | WPRIM | ID: wpr-879515

ABSTRACT

OBJECTIVE@#To investigate the serological and molecular characteristics of a pedigree carrying an allele for ABO*BW.11 blood subgroup.@*METHODS@#The ABO blood type of 9 pedigree members were determined by serological methods. Exons 6 and 7 of the ABO gene were amplified by PCR and directly sequenced. The patient and her father were also subjected to clone sequencing analysis.@*RESULTS@#Serological tests demonstrated that the proband and her younger brother had an ABw subtype, whilst her father and two daughters had Bw subtype. Clone sequencing found that the exon 7 of the ABO gene of the proband had a T>C substitution at position 695, which was identified as a BW.11 allele compared with the reference sequence B.01. This BW.11 allele was also identified in the proband's father, brother and two daughters. Due to allelic competition, the A/BW.11 and BW.11/O alleles demonstrated significantly different phenotypes.@*CONCLUSION@#The c.695T>C substitution of the ABO gene may lead to allelic competition in the Bw11 subtype. Combined molecular and serological methods is helpful for precise blood grouping.


Subject(s)
ABO Blood-Group System/genetics , Alleles , Female , Genotype , Humans , Male , Pedigree , Phenotype
11.
Article in Chinese | WPRIM | ID: wpr-879514

ABSTRACT

OBJECTIVE@#To explore the molecular basis for an individual suspected as AwB subtype through DNA sequencing.@*METHODS@#ABO serology was carried out with the standard tube method. To identify the ABO gene haplotype, the amplicons of exon 7 were cloned and sequenced.@*RESULTS@#Serological results showed that the forward typing was AwB and the reverse typing was B. Sequencing analysis revealed that the sample has contained an O01 allele in addition with c.297A>G, c.657C>T, c.796C>A, c.803G>C, c.930G>A variants as compared with the A101 allele.@*CONCLUSION@#Through sequencing analysis, the sample with an AwB subtype by serological testing was identified as a novel B(A) phenotype, which was unreported previously.


Subject(s)
ABO Blood-Group System/genetics , Alleles , Base Sequence , Exons/genetics , Humans , Mutation, Missense , Phenotype
12.
Article in Chinese | WPRIM | ID: wpr-879513

ABSTRACT

OBJECTIVE@#To analyze the molecular characteristics of a recombinant allele of the ABO blood group.@*METHODS@#The ABO phenotype was determined with the tube method. The coding regions of the ABO and FUT1 genes were analyzed by PCR-sequence based typing. The ABO alleles of the proband were determined by allele-specific primer sequencing. The full sequences of the ABO gene of the proband and her mother were determined through next generation sequencing.@*RESULTS@#The red blood cells of the proband did not agglutinate with anti-H, and the sequence of the FUT1 gene was homozygous for c.551_552delAG.The proband was thereby assigned as para-Bombay. Bi-directional sequencing also found that she was heterozygous for c.261G/del,467C>T,c.526C>G,c.657C>T,c.703G>A,c.796C>A,c.803G>C and c.930G>A of the coding regions of the ABO gene. Allele-specific primer sequencing also found her to carry a ABO*A1.02 allele and a recombinant allele from ABO*O.01.01 and ABO*B.01. The recombination site was located between nucleotide c.375-269 and c.526, and the allele was maternally derived.@*CONCLUSION@#An recombinant allele of the ABO gene has been identified, which has originated from recombination of ABO*O.01.01 with the ABO*B.01 allele.


Subject(s)
ABO Blood-Group System/genetics , Alleles , Blood Grouping and Crossmatching , Female , Fucosyltransferases/genetics , Genotype , Humans , Phenotype , Recombination, Genetic
13.
Protein & Cell ; (12): 39-56, 2021.
Article in English | WPRIM | ID: wpr-880896

ABSTRACT

Gene expression labeling and conditional manipulation of gene function are important for elaborate dissection of gene function. However, contemporary generation of pairwise dual-function knockin alleles to achieve both conditional and geno-tagging effects with a single donor has not been reported. Here we first developed a strategy based on a flipping donor named FoRe to generate conditional knockout alleles coupled with fluorescent allele-labeling through NHEJ-mediated unidirectional targeted insertion in zebrafish facilitated by the CRISPR/Cas system. We demonstrated the feasibility of this strategy at sox10 and isl1 loci, and successfully achieved Cre-induced conditional knockout of target gene function and simultaneous switch of the fluorescent reporter, allowing generation of genetic mosaics for lineage tracing. We then improved the donor design enabling efficient one-step bidirectional knockin to generate paired positive and negative conditional alleles, both tagged with two different fluorescent reporters. By introducing Cre recombinase, these alleles could be used to achieve both conditional knockout and conditional gene restoration in parallel; furthermore, differential fluorescent labeling of the positive and negative alleles enables simple, early and efficient real-time discrimination of individual live embryos bearing different genotypes prior to the emergence of morphologically visible phenotypes. We named our improved donor as Bi-FoRe and demonstrated its feasibility at the sox10 locus. Furthermore, we eliminated the undesirable bacterial backbone in the donor using minicircle DNA technology. Our system could easily be expanded for other applications or to other organisms, and coupling fluorescent labeling of gene expression and conditional manipulation of gene function will provide unique opportunities to fully reveal the power of emerging single-cell sequencing technologies.


Subject(s)
Alleles , Animals , CRISPR-Cas Systems , DNA End-Joining Repair , DNA, Circular/metabolism , Embryo, Nonmammalian , Gene Editing/methods , Gene Knock-In Techniques , Gene Knockout Techniques , Genes, Reporter , Genetic Loci , Genotyping Techniques , Green Fluorescent Proteins/metabolism , Integrases/metabolism , Luminescent Proteins/metabolism , Mutagenesis, Insertional , Single-Cell Analysis , Zebrafish/metabolism
14.
Article in Chinese | WPRIM | ID: wpr-880168

ABSTRACT

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: Se@*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.


Subject(s)
ABO Blood-Group System , Alleles , Blood Transfusion , Fucosyltransferases/genetics , Genotype , Humans , Phenotype
15.
Article in Chinese | WPRIM | ID: wpr-880134

ABSTRACT

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.


Subject(s)
Alleles , Case-Control Studies , Child , Gene Frequency , Genetic Predisposition to Disease , Genotype , Humans , Ikaros Transcription Factor/genetics , Polymorphism, Single Nucleotide , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
16.
Rev. colomb. cardiol ; 27(6): 501-510, nov.-dic. 2020. tab, graf
Article in Spanish | LILACS | ID: biblio-1289265

ABSTRACT

Resumen Introducción: La hipercolesterolemia familiar homocigótica (HFHo) se caracteriza por niveles muy elevados de cLDL y por enfermedad aterosclerótica temprana. Aunque la frecuencia es baja (1/300.000), las complicaciones son muy severas y pueden ser evitadas. Encontrar y tratar esta población de manera temprana podría reducir la mortalidad. Se describen 36 casos en Colombia, en donde se calcula que haya entre 160 y 200 casos. Resultados: Un total de 36 pacientes con fenotipo sugestivo de HFHo fueron identificados y tratados en un período de observación de cuatro años. La media de edad fue 27 años (24 mujeres). 34 pacientes tuvieron un puntaje según la Red de Clínicas de Lípidos de Holanda (RCLH) mayor de 8 (diagnóstico definitivo) y los restantes 2 tenían puntaje equivalente a diagnóstico probable. Un cuarto de los casos procedían de la costa norte colombiana. En las pruebas genéticas, 14 fueron homocigóticos verdaderos para mutación del gen que codifica para el receptor de LDL (LDLR), 12 heterocigóticos compuestos, 2 heterocigóticos dobles y uno autosómico recesivo (LDLRAP1); 5 pacientes fueron heterocigóticos simples (LDLR) y 2 pacientes no autorizaron la prueba. En los homocigóticos verdaderos, la variante más frecuente encontrada fue la c.11G>A. 14 pacientes cursaron con enfermedad coronaria, 9 con estenosis carotídea, 8 con estenosis aórtica y 2 tuvieron ataques cerebrovasculares (ACV). 34 pacientes recibían estatinas (24 rosuvastatina), 30 recibían ezetimibe, 2 recibían evolocumab y 20 recibían lomitapide (dosis promedio 12,7mg). Ninguno recibió aféresis de cLDL. Los medicamentos, en general, fueron bien tolerados y la reducción promedio de cLDL con la terapia fue de 533,7mg/dl a 245,1mg/dl (54%). Conclusiones: Todos los pacientes recibieron tratamiento hipolipemiante y se encontraron alteraciones genéticas diagnósticas en todos aquellos que autorizaron el examen. Los niveles elevados de cLDL conllevan tanto riesgo que el tratamiento debe establecerse aún sin conocer el diagnóstico genético.


Abstract Background: Homozygous familial hypercholesterolemia (HoFH) is characterized for very high levels of cLDL and early cardiovascular disease. Although incidence is low (1/300 000), complications are very severe and can be avoided. Finding and treating this population promptly could reduce mortality. We describe 36 cases in Colombia, where 160 to 200 cases are expected. Results: 36 patients with phenotype of HoHF were identified and treated in a follow-up of 4 years. The mean age was 27 years (24 women). 34 of them had at least 8 points in the FH Dutch Lipid Clinic Criteria (definitive diagnosis) and two had probable diagnosis. A quarter of the cases came from the Colombian North Coast. In molecular tests, 14 were true homozygous for LDLR, 12 were compound heterozygous for LDLR, 2 double heterozygous and one was autosomal recessive; 5 were heterozygous and 2 patients did not authorized genetic test. In true homozygous subjects, the most frequent variant was c.11G>A. 14 patients had coronary disease, 9 carotid stenosis, 8 aortic stenosis and 2 had stroke. 34 patients were on statins (25 rosuvastatin), 30 were receiving ezetimibe, 2 were receiving a PSCK9 inhibitor (evolocumab) and 20 were on lomitapide with mean doses of 12.7mg. None received lipoprotein apheresis. Medications were very well tolerated. Changes in cLDL after therapy was from 533.7 mg/dL to 245 mg/dL, (54%). Conclusions: Treatment was started in all patients. We found genetic mutations in all patients with genetic tests. The high levels of cLDL mean such a high risk that treatment must be started promptly, even without a genetic test.


Subject(s)
Humans , Male , Female , Adult , Hypercholesterolemia , Alleles , Genetics , Hyperlipoproteinemia Type II , Lipids , Cholesterol, LDL , Mutation
17.
Electron. j. biotechnol ; 48: 23-28, nov. 2020. tab, ilus
Article in English | LILACS | ID: biblio-1254683

ABSTRACT

BACKGROUND: Meretrix petechialis is one of the commercially important marine bivalves. In this study, we selected six highly polymorphic EST-derived microsatellite markers to assess the genetic diversity and population differentiation on nine wild populations of Meretrix petechialis. RESULTS: The number of alleles detected per-locus ranged from 4 to 30 (mean NA = 27.5) with a total of 165 alleles. The mean value of observed and expected heterozygosities varied from 0.717 to 0.861 and from 0.797 to 0.856, respectively. Meanwhile, the result of Neighbor-joining and overall FST = 0.214 (P < 0.01) reveled that M. petechialis populations from GX are the farthest populations, a certain degree of genetic variation among individuals in each population and the genetic differentiation is significant. CONCLUSIONS: GX population has high genetic diversity among individual, and there are certain differences in genetic characteristics among different populations. This study will provide a basis for the domestication and cultivation of genetic diversity of M. petechialis population and the protection of clam germplasm resources.


Subject(s)
Animals , Genetic Variation , Bivalvia/genetics , Microsatellite Repeats , Expressed Sequence Tags , Population , Alleles
18.
Rev. Assoc. Med. Bras. (1992) ; 66(10): 1396-1401, Oct. 2020. tab, graf
Article in English | LILACS, SES-SP | ID: biblio-1136166

ABSTRACT

SUMMARY OBJECTIVE: The relationship between the clinicopathological and sociodemographics characteristics of acral melanomas diagnosed at BACKGROUND: This study aimed to investigate the frequency of VEGF gene insertion (I) / deletion (D) polymorphism (rs35569394) in patients with Polycystic Ovarian Syndrome (PCOS) and to compare with a control population to verify its association with the pathology. METHODS: 206 women participated in this study, 103 with PCOS (group of patients) and 103 without the disease (control group). After extraction of genomic DNA from the samples, molecular analysis was performed by Polymerase Chain Reaction (PCR) and electrophoresis in polycrylamide. Descriptive analysis, univariate analysis and logistic regression model were used. Results were presented in odds ratio (OR) and 95% confidence interval (95% CI), considering the significance of p <0.05. RESULTS: There were no statistical differences between patients and controls for allele frequencies (χ2 = 1.16, p = 0.56). The genotypic frequency distribution was in Hardy Weinberg equilibrium for the patients (χ2 = 2.42; p <0.05), but not for the control group (χ2 = 7.26; p <0.05). Regarding risk factors for the syndrome, a history of familial PCOS is more frequent among women with the syndrome. CONCLUSIONS: In the present study, there is no association between VEGF gene I / D polymorphism and PCOS.


RESUMO OBJETIVO: Este estudo teve como objetivo investigar a frequência do polimorfismo de inserção (I)/ deleção (D) do gene VEGF (rs35569394) em pacientes com Síndrome dos Ovários Policísticos (SOP) e comparar com uma população controle para verificar sua associação com a patologia. MÉTODOS: Participaram desse estudo 206 mulheres sendo 103 com SOP (grupo de pacientes) e 103 sem a doença (grupo controle). Após extração do DNA genômico das amostras, a análise molecular foi realizada por Reação em Cadeia da Polimerase e eletroforese em gel de poliacrilamida. Utilizou-se análise descritiva, análise univariada e modelo de regressão logística. Os resultados foram apresentados em odds ratio (OR) e intervalo de confiança de 95% (IC-95%), considerando a significância de p < 0,05. RESULTADOS: Não houve diferenças estatísticas entre as pacientes e controles para as frequências alélicas (χ2 = 1,16, p = 0,56). A distribuição da frequência genotípica estava em equilíbrio de Hardy Weinberg para as pacientes (χ2= 2,42; p<0,12), mas não para o grupo controle (χ2= 7,26; p<0,05). Em relação aos fatores de risco para a síndrome, a história de SOP familiar é mais frequente entre as mulheres com a síndrome. CONCLUSÕES: Na casuística estudada, não há associação entre o polimorfismo I/D do gene da VEGF e a SOP.


Subject(s)
Humans , Female , Polycystic Ovary Syndrome/genetics , Vascular Endothelial Growth Factor A/genetics , Case-Control Studies , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Alleles , Gene Frequency , Genotype
19.
Braz. j. infect. dis ; 24(4): 296-303, Jul.-Aug. 2020. tab
Article in English | LILACS, ColecionaSUS, SES-SP, CONASS, HANSEN, SESSP-ILSLPROD, SES-SP, SESSP-ILSLACERVO, SES-SP | ID: biblio-1132457

ABSTRACT

The frequencies of the Human leukocyte antigen (HLA) alleles in the Puyanawa indigenous reserve population and their association with the NDO-LID and ELISA PGL-1 rapid serological test was assessed. This was a cross-sectional study with an epidemiological clinical design conducted in two indigenous communities in the state of Acre, Brazil. Blood was collected in a tube with EDTA to identify HLA alleles and perform serological tests. DNA was obtained using the salting out procedure. The LabType™ technique (One-Lambda-USA) was used for HLA class I (loci A*, B* and C*) and II (loci DRB1*, DQA1* and DQB1*) typing. Allele frequency was obtained by direct count, and the chi-square test was used to assess the association with the NDO-LID and PGL-1 tests. The most frequent alleles in the two communities were: HLA-A*02:01, HLA-B*40:02, HLA-DRB1*16:02, HLA-DQA1*05:05 and HLA-DQB1*03:01. The allele HLA-C*04:01 was the most common in the Barão community, and the allele HLA-C*07:01 in Ipiranga. Among individuals who presented seropositivity to the NDO-LID test, the association with alleles HLA-A*02 (43.18% vs 24.8%, p = 0.03, OR = 2.35) and HLA-B*53 (6.83% vs 0.0%, p = 0.03, OR = 8.95) was observed in the Barão community. HLA-B*15 was associated with non-seroconversion to the NDO-LID test in Ipiranga. In both communities, HLA-B*40 and HLA-C*03 were associated with positive serological response to ELISA PGL-1. The HLA class I and II alleles most frequently found in this study have already been described among Terena indigenous groups, and HLA class I contributes to seroconversion to NDO-LID and PGL-1 tests in inhabitants of the Barão and Ipiranga communities(AU).


Subject(s)
Humans , Male , Female , Alleles , Health of Indigenous Peoples , HLA-DRB1 Chains , Gene Frequency , Leprosy/epidemiology , Brazil/epidemiology , Serologic Tests , Indians, South American , Cross-Sectional Studies , Risk Factors
20.
Electron. j. biotechnol ; 46: 1-7, jul. 2020. ilus, graf, tab
Article in English | LILACS | ID: biblio-1223252

ABSTRACT

BACKGROUND: Fragrance is one of the most important quality traits in rice, and the phenotype is attributed to the loss-of-function betaine aldehyde dehydrogenase (BADH2) gene. At least 12 allelic variations of BADH2 have been identified, and some of these have been applied to rice fragrance breeding using traditional molecular markers and Sanger sequencing techniques. However, these traditional methods have several limitations, such as being very expensive, imprecise, inefficient, and having security issues. Thus, a new molecular marker technology must be developed to improve rice fragrance breeding. RESULTS: In this study, more than 95% of the cultivated fragrant rice varieties belonged to a 7-bp deletion in exon 2 (badh2-E2) or an 8-bp deletion and 3-bp variation in exon 7 (badh2-E7). Both allelic variations resulted in the loss of function of the badh2 gene. We developed two novel SNP molecular markers, SNP_badh2-E2 and SNP_badh2- E7, related to the alleles. Their genotype and phenotype were highly cosegregated in the natural variation of rice accessions, with 160 of the 164 fragrant rice varieties detected with the two markers. These markers cosegregated with the fragrance phenotype in the F2 population. CONCLUSIONS: Two functional SNP molecular markers of badh2-E2 and badh2-E7 allelic variations were developed. These functional SNP molecular markers can be used for genotype and genetic improvement of rice fragrance through marker-assisted selection and will significantly improve the efficiency of fragrant rice breeding and promote commercial molecular breeding of rice in the future.


Subject(s)
Oryza/enzymology , Oryza/genetics , Betaine-Aldehyde Dehydrogenase/metabolism , Genetic Markers , Alleles , Genotyping Techniques/methods , Genotype , Odorants
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