Origins of Atlantic Salmon (Salmo salar) Determined Using a Hybridization Assay of Mitochondrial DNA on a Microfluidic Biochip.

The single nucleotide polymorphism (SNP) site within the aquaporin (AQP)-4 gene exons and its possible role in the pathogenesis of neuromyelitis optica (NMO) were studied. From March 2010 to June 2012, 72 patients with NMO from Xiangyang No. 1 People's Hospital, Hubei University of Medicine were enrolled in the NMO group. At the same time, 80 patients with multiple sclerosis (MS) were enrolled in our study as the MS group. Blood samples were collected and DNA was extracted for analysis of SNP sites of AQP4 gene. Specific site-directed mutagenesis method was used for site-directed mutagenesis on plasmid enhanced green fluorescence protein carrying AQP4 gene. Mutant plasmids were constructed and used for transfecting cell lines. The differences of anti-AQP4 antibody level in the cell line were analyzed. The possible correlation between AQP4 gene SNP sites and the pathogenesis of NMO were analyzed. In the NMO group, 6 SNP sites in AQP4 gene were located in exons 2 and 5. These included R108T, I110N, E280R, D281R, P295R and E317M. There was no SNP site in exons 1, 3 and 4. In the MS group, no SNP site was found in AQP4 gene. R108T, I110N, R108T/I110N, E280R/D281R, P295R and E317M cell lines were constructed in the NMO group, and anti-AQP4 antibody in the serum was compared between R108T/I110N, E280R/D281R and E317M cell lines and the original HEK293T cell line. The difference was statistically significant (P<0.05). The positive rate of anti-AQP4 antibody titer in serum was compared between R108T, I110N, R108T/I110N, E280R/D281R, P295R and E317M cell lines in the NMO group and the original cell line in the MS group. In conclusion, SNP sites in AQP4 gene in patients with NMO may lead to some conformational changes in AQP4 protein. This affects the antigenicity of AQP4 protein. The different intensity of antigen-antibody reaction may cause the differences of titer observed between the different mutant cell lines.

Objective To investigate the relationship between NINJ2 gene polymorphism and stroke, and the differences of serum levels of tumor necrosis factor-αt (TNF-α), NGF, interleukin-6 (IL-6)and P-Selectin in healthy controls and patients under recovery stage. Methods Fifty-two patients with large-artery atherosclerosis (LAA) infarction, 85 patients with small-artery occlusion lacunar (SAO)infarction, 50 patients with intracerebral hemorrhage (ICH) and 66 healthy controls were included in this study. Genotypes of the 2 single nucleotide polymorphism (SNP) sites (rs12425791 and rs11833579) in NINJ2 gene were examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RLFP) method. The differences of genotypes and alleles frequencies of the 2 SNP sites between each 2 different groups were analyzed and compared. Multinomial logistic regression was used to calculate the odds ratio (OR) of genotypes in each patient group, and 95% confidential interval (95% CI)was given. The serum levels ofTNF-α, NGF, IL-6 and P-Selectin were tested by ELISA method, and compared between groups and within group classified by genotypes. Results In regard to rs12425791 site, the frequencies of AG and AA+AG genotypes in LAA and SAO groups were significantly higher than those in control group (P＜0.05), while this difference was not found between the ICH group and control group (P＞0.05); the frequency of A allele in the SAO group was significantly higher than that in the control group (P＜0.05), while this difference was not found between the control group and both the LAA and ICH groups (P＞0.05). In regard to rs11833579 site, no significant differences in the genotypes and alleles were noted between all the patient groups and control group (P＞0.05). After adjusting the influence of other risk factors, the multinomial logistic regression analysis showed that the onset of stroke was still significantly associated with the AG genotype at rs12425791 site in the LAA group (OR=4.298,95%CI=1.430-12.922) and AG, AG+AA genotypes at rs12425791 site in the SAO group (OR=3.923 and 2.937, 95%CI= 1.417- 10.860 and 1.119-7.710). Neither genotypes in rs 11833579 site were significantly associated with the onset of stroke. No significant differences of serum levels of TNF-α, NGF, IL-6 and P-Selectin were noted between each patient group under recovery stage and control group (P＞0.05); in regard to rs12425791 site, the serum level of TNF in LAA group with different genotypes was significantly different (P＜0.05) and the serum level of P-Selectin in ICH group with different genotypes was significantly different (P＜0.05); in regard to rs11833579 site, the serum level of NGF in LAA group with different genotypes was statistically different (P＜0.05). Conclusion This SNP site (rs12425791)is significantly associated with ischemia stroke and the A allele increases the risk of being susceptible to this disease in Chinese Han population. That SNP site (rs1 1833579) is not significantly associated with stroke. No significant differences of TNF-α, NGF, IL-6, P-Selectin serum levels are noted between patients under recovery stage and controls. Key words: NINJ2 gene; Polymorphism; single nucleotide; Stroke; Tumor necrosis factor-α; NGF; Interleukin-6; P-Selectin

A functional single nucleotide polymorphism site detected in nasopharyngeal carcinoma-associated transforming gene Tx

Establish a multiplex PCR targeted sequencing technology to detect the single nucleotide polymorphism (SNP) sites of disease-related genes in children with autism spectrum disorder, and explore its application value as a diagnostic biomarker for autism spectrum disorder. Through a literature review, 357 candidate risk genes and their 603 mutation sites highly associated with the occurrence of autism spectrum disorder (ASD) were selected. The MFEprimer software was used to design a multiplex PCR primer library. Using this primer library and targeted gene sequencing technology, SNP polymorphisms in ASD-related risk genes were screened in 105 children with ASD and 71 healthy controls from the outpatient department of Rehabilitation Medicine in Huangshi Maternity and Children's Health Hospital from January to August 2024. The selected polymorphic SNP sites were then validated by Sanger sequencing, in order to assess the clinical application value of the multiplex PCR-based targeted sequencing technology established in this study. The results showed that analysis of the multiplex PCR-based targeted sequencing results showed that, among the 105 children with ASD, 42 individuals carried the RELN (rs12666897) mutation site, with a mutation frequency of 40.00%; 22 individuals carried the AUTS2 (rs3735260) mutation site, with a mutation frequency of 20.95%. In contrast, among the 71 healthy controls, the mutation frequencies of RELN (rs12666897) and AUTS2 (rs3735260) were 18.31%(13 cases) and 5.63%(4 cases), respectively. The differences in mutation frequencies of these two SNPs between the ASD patients and healthy controls were statistically significant (respectively 0.002 7, 0.004 7, P<0.01). Sanger sequencing validation of the genotypes at these two sites showed complete concordance with the multiplex PCR-based targeted sequencing results, suggesting that these two SNPs may be associated with the risk of ASD onset. In conclusion, the multiplex PCR targeted high-throughput sequencing technology that established can screen for differentially expressed genes in children with ASD. Candidate gene polymorphism sites are closely associated with ASD in children, and have the potential to become new diagnostic biomarkers for ASD identification.

Dysregulated mRNA–miRNA profiles might have the prospective to be used for early diagnosis of gastrointestinal cancers, estimating survival, and predicting response to treatment. Here, a novel biomarker based on miRNAs binding to mRNAs in single nucleotide polymorphism (SNP) sites related to gastrointestinal cancers is introduced that could act as an early diagnosis. The electronic databases used for the recruiting published articles included EMBASE, SCOPUS, Web of Science, and PubMed, based on MESH keywords and PRISMA methodology. Based on the considered criteria, different experimental articles were reviewed, during which 15 studies with the desired criteria were collected. Accordingly, novel biomarkers in prediction, early prognosis, and diagnosis of gastrointestinal cancers were highlighted. Moreover, it was found that 20 SNP sites and 16 miRNAs were involved in gastrointestinal cancers, with altered expression patterns associated with clinicopathological and demographic data. The results of this systematic study revealed that SNPs could affect the binding of miRNAs in the SNP sites that might play a principal role in the progression, invasion, and susceptibility of gastrointestinal cancers. In addition, it was found that the profiles of SNPs and miRNAs could serve as a convenient approach for the prognosis and diagnosis of gastric and colorectal cancers.

To investigate the distribution of the single nucleotide polymorphism (SNP) sites in TBX1 gene and the distribution of related haplotypes in the patients with conotruncal defects (CTD) and normal people. The genotypes of the 3 selected SNPs: G2857C (rs737868), G2963A (rs28649236), and A6571T (rs28939675) in TBX1 gene were analyzed by PCR-RFLP among 130 patients with CTD and 200 normal people. Contingency table was applied to analyze the frequencies of these SNP genotypes and related alleles. PHASE software was used to construct the haplotypes and analyze the haplotype frequencies in these 2 groups. There were no significant differences in the allele frequency and genotype rates of the SNPs G2587C and A6571T between the CTD patients and normal controls (all P > 0.05). However, the allele frequency and genotype rates of the SNP G2963A were significant different between he CTD patients and normal controls: the G allele frequency in the CTD patients was 53.8%, significantly higher than that in the normal controls (42.5%, chi(2) = 8.14, P < 0.005); and the AA genotype rate of the CTD patients was 21.6%, significantly lower than that of the controls (38.0%), and the GA genotype rate in the CTD patients was 49.2%, significantly higher than that in the controls (39.0%) (both chi(2) = 9.9, P < 0.05). The haplotype frequencies of G2587/G2963/A6571 and G2587/A2963/T6571 of the CTD patients were 49.2% and 14.6% respectively, both significantly higher than those of the normal controls (36.3% and 9.5% respectively), and the haplotype frequencies of G2587/G2963/T6571 and G2587/A2963/A6571 in the CTD patients were 34.6% and 3% respectively, both significantly lower than those in the normal controls (48.3% and 18% respectively) (chi(2) = 22.39, P < 0.005). The SNP site G2963A located in the coding-region of TBX1 gene is associated with CTD. The persons with G2963 have higher risk of CTD than those with A2963. The haplotypes constructed with these 3 SNP sites may be linked with the susceptibility gene of CTD.

&lt;p&gt;Two unknown single nucleotide polymorphism (SNP) sites in exons 1 (c.194C&amp;gt;T) and 2 (c.445T&amp;gt;A) of meat-type rabbit &lt;em&gt;MSTN&lt;/em&gt; gene were identified in the study. Our objective was to analyse the population genetics structure of the two novel SNP sites in 230 individuals from six breeds and their associations with carcass traits of rabbits. We found that live body weight (BW), cold carcass weight (CCW), reference carcass weight (RCW), CCW percentage (P&lt;sub&gt;CCW&lt;/sub&gt;) and RCW percentage (P&lt;sub&gt;RCW&lt;/sub&gt;) of the rabbits with the genotype CC at the c.194C&amp;gt;T of exon 1 or AA at the c.445T&amp;gt;A of exon 2 were significantly higher than those with other genotypes. Diplotype significantly affected BW, RCW, CCW, P&lt;sub&gt;RCW&lt;/sub&gt; (&lt;em&gt;P&lt;/em&gt;&amp;lt;0.01) and P&lt;sub&gt;CCW&lt;/sub&gt; and P&lt;sub&gt;CM&lt;/sub&gt; (&lt;em&gt;P&lt;/em&gt;&amp;lt;0.05). CC/AA was the advantageous diplotype for BW, RCW, CCW and P&lt;sub&gt;CM&lt;/sub&gt;, and TT/AA was the advantageous diplotype for P&lt;sub&gt;CCW&lt;/sub&gt; and P&lt;sub&gt;RCW&lt;/sub&gt;. In contrast, TT/TT was the negative diplotype for BW, CCW, RCW, P&lt;sub&gt;CCW&lt;/sub&gt; and P&lt;sub&gt;RCW&lt;/sub&gt;, and TT/AA was the negative diplotype for P&lt;sub&gt;CM&lt;/sub&gt;. The results suggest that the two new mutations of &lt;em&gt;MSTN&lt;/em&gt; gene significantly affected BW, CCW, RCW, P&lt;sub&gt;CCW&lt;/sub&gt; and P&lt;sub&gt;RCW&lt;/sub&gt; of rabbits, and &lt;em&gt;MSTN&lt;/em&gt; may be an important candidate gene of carcass traits in meat-type rabbits.&lt;/p&gt;

Background: Sarcandra glabra (Thunb.) Nakai is one of the most popular and valuable plant species in the oriental medicinal herb market. Chloranthus (Chloranthaceae) species are the most widely used adulterants, but they are known to have hepatotoxicity effects and different medicinal values. Objective: The aim of this study is to develop a robust and accurate DNA marker for the qualitative and quantitative analyses of their products. Materials and methods: Four single nucleotide polymorphism (SNP) sites specific to Sarcandra glabra, Chloranthus spicatus, Chloranthus serratus and Chloranthus henryi were exploited from the trnL-F region in chloroplast DNA, which have a higher copy number in the products than the nuclear DNA. Based on the SNP sites, specific primers were designed to identify the products of Sarcandra glabra, Chloranthus spicatus, Chloranthus serratus and Chloranthus henryi in mixed solutions via multiplexed PCR. The primers were also used to quantitatively analyse the ratio of chloroplast DNA in the mixed products using real-time PCR. Results: The established multiplexed-PCR and real-time PCR methods were determined to be effective for the authentication and relative quantitative assessments of the products of Sarcandra glabra, its adulterants, and their mixtures. Conclusion: We therefore present an effective method for monitoring the quality of these products.

ObjectiveThe objective of this study was to unravel the genetic traits of Guanling cattle, pinpoint genes advantageous for muscle growth, and lay a foundation for the preservation of genetic diversity and further analysis of regulation mechanism of important economic traits in local cattle breed.MethodsIn this study, we sequenced the whole genome of 3 Guanling cattle in Guizhou province using the Illumina HiSeq cBo sequencing platform. And, high-multiplex polymerase chain reaction technology was employed to detect high-quality single nucleotide polymorphism (SNP) sites of other 55 Guanling cattle.ResultsOur study identified 166,411 non-synonymous SNPs (nsSNPs) and 42,423 insertions and deletions (indels). Through SNP annotation, gene function enrichment analysis, and comparing with Simmental, Angus, and Limousin cattle, we identified six genes (LEPR, AKAP9, SIX4, SPIDR, PRG4, FASN) which are potentially influential on meat quality traits, playing crucial roles in muscle growth, fat metabolism, and bodily support. We also examined polymorphisms at seven SNP sites in Guanling cattle and found that all seven were in Hardy–Weinberg equilibrium.ConclusionThese findings suggested that these gene sites are stable and widespread in the Guanling cattle population. Our research lays the groundwork for future genetic enhancement and variety identification of Guanling cattle.

To investigate the frequeney of four single nucleotide polymorphism (SNP) sites (rs17300539, rs12495941, rs2241766 and rs1501299) of adiponectin gene (ADIPOQ) and to elucidate its role in the pathogenesis of polycystic ovary syndrome (PCOS). A total of 207 women with PCOS and 192 controls were recruited. Four ml whole-blood samples were collected in tubes containing ethylene diamine tetraacetic acid (EDTA) by peripheral venous puncture. Genomic DNA was extracted using a QIAamp DNA mini kit. Four SNP sites (rs17300539, rs12495941, rs2241766 and rs1501299) of ADIPOQ were amplified by PCR and then directly sequenced to screen variants. (1) The genotype frequencies of AA of rs17300539 in PCOS was significantly higher than controls [57.5% (119/207) versus 48.4% (93/192), P<0.05]. The genotype frequencies of AA of rs1501299 in PCOS was significantly lower than controls [4.8% (10/207) versus 11.5% (22/192), P<0.05]. While no significant differences were found in rs2241766 and rs12495941 (P>0.05). (2) The allele A of rs17300539 [75.8% (314/414)] and allele C frequeneies of rs1501299 [76.3% (316/414)] in PCOS were significantly higher than controls [67.7% (260/384), 69.0% (265/384), respectively; all P<0.05]. While no significant differences were found in rs2241766 and rs12495941 (P>0.05). (3) Further analysis we found rs17300539 AA genotypes had an increased risk for PCOS compared with GG genotype (OR=2.670, P=0.009), rs1501299 CC genotype had an increased risk for PCOS compared with AA genotypes (OR=2.756, P=0.012); and the difference remained significantly after adjustment for age, testosterone and body mass index (P<0.05). No significant differences were observed in genotype and allele frequencies between PCOS and controls for rs2241766 and rs12495941. However, we observed an association between rs17300539, rs1501299 and PCOS. rs17300539 and rs1501299 of ADIPOQ perhaps are the susceptibility gene locus of PCOS.

Lack of association between integrin αvβ3 gene polymorphisms and hemorrhagic fever with renal syndrome in Han Chinese from Hubei, China.

Recently, the world-wide human genome-related projects have been vigorously launched and implemented. Gene-sequencing techniques play a critical role in disease diagnosis, prediction, and population stratification relying on efficiently mining genetic features in the gene pool. Exploring the association between the sites of the genetic mutation and the disease-based population classification becomes a hot topic, which beneficially supports disease diagnosis and treatment on the molecular level. However, there are numerous variable sites even on a single chromosome in the human gene pool, and hence, the traditional classifiers are not able to dig out all single nucleotide polymorphism (SNP) sites without clearly excavating the characteristic SNP sites, termed tagSNPs, in SNP clusters. By applying big data mining techniques, in this paper, we, first of all, propose a principal component analysis-based algorithm for reducing the gene data dimension in order to cluster SNP sites in the low-dimensional space. Moreover, an oriented graph theory-based tagSNPs selection algorithm is designed. Finally, relying on the real-world 1000 Genomes Project dataset, we can achieve fewer tagSNPs than the traditional methods by invoking the complete process of our designed SNP classifier.

ABO genotyping by TaqMan assay and allele frequencies in a Japanese population

Profil étiologique des hémoptysies au service de pneumologie de l’HMIMV de Rabat

Acetylcholinesterase (AChE) plays a vital role in the nervous system of insects and other animal species and serves as the target for many chemical agents such as organophosphate and carbamate insecticides. The mosquito, Culex pipiens complex, a vector of human disease, has evolved to be resistant to insecticides by a limited number of amino acid substitutions in AChE1, which is encoded by the ace-1 gene. The aims of this study are to identify single nucleotide polymorphism (SNP) sites in the ace-1 gene of the C. pipiens complex and explore an economical high-throughput method to differentiate the genotypes of these sites in mosquitoes collected in the field. We identified 22 SNP sites in exon regions of the ace-1 gene. Four of them led to non-synonymous mutations, that is, Y163C, G247S, C677S and T682A. We used matrix-assisted laser desorption ionization - time-of-flight mass spectrometry for genotyping at these four sites and another site F416V, which was relevant to insecticide resistance, in 150 mosquitoes collected from 15 field populations. We were able to synchronize analysis of the five SNP sites in each well of a 384-well plate for each individual mosquito, thus decreasing the cost to one-fifth of the routine analysis. Heterozygous genotypes at Y163C and G247S sites were observed in one mosquito. The possible influence of the five SNP sites on the activity or function of the enzyme is discussed based on the predicted tertiary structure of the enzyme.