SLC6A3 (DAT1) as a Novel Candidate Biomarker Gene for Suicidal Behavior

It has been previously shown that the serotonin and dopamine neurotransmitter systems might influence the predisposition to suicidal behavior. This study aims to estimate the contribution of 11 polymorphisms in the genes SLC6A4 (5HTT), HTR1A, HTR2A, HTR1B, SLC6A3 (DAT1), DRD4, DRD2, COMT, and BDNF to suicidal behavior and severity of symptoms of depression and anxiety in the Russian population. The study was performed on 100 patients with repeated suicide attempts and 154 controls. We first found an association between SLC6A3 (DAT1) 40 bp VNTR locus and suicidal behavior. This association was significant; when using the codominant (p = 0.006), dominant (p = 0.001), overdominant (p = 0.004), and log-additive (p = 0.004) models, LL genotype played a protective role (OR = 0.48, 0.29–0.82, p = 0.005). Difference in the distribution of COMT rs4680 genotypes was significant in the codominant (p = 0.04), dominant (p = 0.013), and log-additive (p = 0.02) models, and AA genotype might protect against suicide (OR = 0.49, 0.26–0.91, p = 0.025). SLC6A4 5-HTTLPR + rs25531 locus was significant in the recessive model (p = 0.024), and also affected the severity of symptoms of depression (p = 0.044) and personal anxiety (p = 0.029). Our results suggest that allelic variants of SLC6A3, COMT, and SLC6A4 genes might be considered as risk factors for suicidal attempts.

SLC6A3 (DAT1) as a novel candidate biomarker gene for suicidal behavior: a pilot study

Objective This study aims to estimate the contribution of 11 polymorphisms in the genes SLC6A4 (5HTT), HTR1A, HTR2A, HTR1B, SLC6A3 (DAT1), DRD4, DRD2, COMT and BDNF to suicidal behavior and severity of symptoms of depression and anxiety in Russian population.Methods The study was performed on 100 patients with repeated suicide attempts and 154 controls. The SNP and VNTR genotyping was carried out using locus-specific PCR. Logistic regression approach was applied to establish associations between gene polymorphisms and risk of suicidal attempts. Negative binomial regression was used to analyze association between genotypes and count variables: severity of depressive symptoms, personal anxiety and situational anxiety. Results We have first found an association between SLC6A3 (DAT1) 40 bp VNTR locus and suicidal behavior. This association was significant in the co-dominant (P = 0.006), dominant (P = 0.001), over-dominant (P = 0.004) and log-additive (P = 0.004) models, LL genotype played a protective role (OR = 0.48, 0.29–0.82). Difference in the genotypes distribution of COMT rs4680 was significant in the co-dominant (P = 0.04), dominant (P = 0.013) and log-additive (P = 0.02) models, and AA genotype might protect against suicide (OR = 0.49, 0.26–0.91). SLC6A4 5-HTTLPR+rs25531 locus was significant only in the recessive model (P = 0.024) and also affected the severity of symptoms of depression (P = 0.044) and personal anxiety (P = 0.029). Conclusions Our results suggest that allelic variants of SLC6A3, COMT and SLC6A4 genes might be considered as risk factors for suicidal attempts.

MIRUReader: MIRU-VNTR typing directly from long sequencing reads

Summary Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is widely used to genotype Mycobacterium tuberculosis complex in epidemiological studies for tracking tuberculosis transmission. Recent long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore Technologies can produce reads that are long enough to cover the entire repeat regions in each MIRU-VNTR locus which was previously not possible using the short reads from Illumina high-throughput sequencing technologies. We thus developed MIRUReader for MIRU-VNTR typing directly from long sequence reads. Availability and implementation Source code and documentation for MIRUReader program is freely available at https://github.com/phglab/MIRUReader. Supplementary information Supplementary data are available at Bioinformatics online.

Improvement of Multiple-Locus VNTR Analysis Typing Scheme for Helicobacter pylori

Aims: To improve a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Helicobacter pylori typing. Materials and Methods: Polymorphic VNTRs were searched by Gene Expert. The distribution and polymorphism of each VNTR locus were analyzed in 18 H. pylori genomes from the NCBI genome database by BLAST and were compared with a collection of 15 clinical H. pylori strains. The MLVA assay was compared with MLST-typing for discriminating H. pylori isolates. Results: Twelve VNTR loci were identified by bioinformatic screening of H. pylori genomes, and five of them were highly polymorphic. Therefore, an MLVA assay composed of five VNTR loci was developed with greatest discriminatory power. Conclusion: MLVA typing is a faster and more standardized method for studying the genetic relatedness of H. pylori isolates. At preliminary stage it is sufficient to use only 3 VNTR loci for the differentiation of H. pylori strains.

The role of VNTR aggrecan gene polymorphism in the development of osteoarthritis in women

Osteoarthritis (OA) is a common multifactorial joint disease. Undifferentiated connective tissue dysplasia (uCTD) is a genetically determined lesion of the connective tissue structures, including joints, and it can be one of the factors predisposing to development of OA. Solving the problem of comorbidity of OA and uCTD signs will contribute to the early diagnosis and prophylactics of OA. Aggrecan is one of the major structural components of cartilage and it provides the ability to resist compressive loads throughout life. We examined 316 women (mean age 50.5 ± 4.77) for signs of uCTD and OA. A study of the aggrecan gene (ACAN) VNTR polymorphism, which is represented by a variable number of 57 nucleotide repeats, was performed. We searched for associations between the VNTR locus and OA in general and with an account of the localization of the pathological process, as well as with the presence of uCTD signs. Twelve allelic variants and 24 genotypes of the VNTR polymorphism of the aggrecan gene (ACAN) were identified, the most frequent variants were alleles with 27, 28 and 26 repeats. A significance of allele *27 (х2= 6.297, p = 0.012, odds ratio (OR) = 1.50; 95 % confidence interval (CI) 1.09-2.05) in the development of OA in general, knee OA (х2= 4.613, p = 0.031, OR = 1.52; 95 % CI 1.04-2.23), and multiple OA (х2= 4.181, p = 0.04, OR = 1.68; 95 % CI 1.02-2.78) was revealed. Homozygous genotype *27*27 was associated with OA (х2= 3.921, р = 0.047, OR = 1.72; 95 % CI 1-2.96), and OA with uCTD signs in women (х2= 5.415, p = 0.019, OR = 2.34; 95 % CI 1.13-4.83).

Evaluation of multiple-locus variable-number tandem repeat analysis (MLVA) for genotyping of Escherichia coli isolated from Karaj River

Most microbiological water quality regulations rely upon the detection of indicators of fecal pollution, such as coliform bacteria, or more specifically Escherichia coli. In order to further understand the source, fate, and implications for water quality regulation, environmental E. coli isolates should be assessed genetically to observe various levels of genotypic diversity. Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a novel, simple and inexpensive polymerase chain reaction (PCR) based genotyping method which relies on the detection of different copy numbers inside each VNTR locus. In this study, we evaluated MLVA as a tool for the genotyping of E. coli strains of water samples collected from the Karaj River, Iran. Overall, high genetic diversity was observed among environmental E. coli isolates. We also proved the feasibility of MLVA as a complementary or even future replacement genotyping method for the average routine laboratory.

An insulin-like growth factor homologue of Singapore grouper iridovirus modulates cell proliferation, apoptosis and enhances viral replication

Insulin-like growth factors (IGFs) play crucial roles in regulating cell differentiation, proliferation and apoptosis. In this study, a novel IGF homologue gene (IGF-like) encoded by Singapore grouper iridovirus (SGIV) ORF062R (termed SGIV–IGF), was cloned and characterized. The coding region of SGIV–IGF is 771 bp in length, with a variable number of tandem repeats (VNTR) locus at the 3′-end. We cloned one isoform of this novel gene, 582 bp in length, containing the predicted IGF domain and 3.6 copy numbers of the 27 bp repeat unit. SGIV–IGF was an early transcribed gene during viral infection, and SGIV–IGF was distributed predominantly in the cytoplasm with a diffused granular appearance. Intriguingly, overexpression of SGIV–IGF was able to promote the growth of grouper embryonic cells (GP cells) by promoting G1/S phase transition, which was at least partially dependent on its 3′-end VNTR locus. Furthermore, viral titre assay and real-time quantitative PCR (RT-qPCR) analysis proved that SGIV–IGF could promote SGIV replication in grouper cells. In addition, overexpression of SGIV–IGF mildly facilitated apoptosis in SGIV-infected non-host fathead minnow (FHM) cells. Together, our study demonstrated a novel functional gene of SGIV which may regulate viral replication and cellular processes through multiple mechanisms that appear to be cell type-dependent.

Investigation of the population structure of Legionella pneumophila by analysis of tandem repeat copy number and internal sequence variation

The population structure of the species Legionella pneumophila was investigated by multilocus variable number of tandem repeats (VNTR) analysis (MLVA) and sequencing of three VNTRs (Lpms01, Lpms04 and Lpms13) in selected strains. Of 150 isolates of diverse origins, 136 (86 %) were distributed into eight large MLVA clonal complexes (VACCs) and the rest were either unique or formed small clusters of up to two MLVA genotypes. In spite of the lower degree of genome-wide linkage disequilibrium of the MLVA loci compared with sequence-based typing, the clustering achieved by the two methods was highly congruent. The detailed analysis of VNTR Lpms04 alleles showed a very complex organization, with five different repeat unit lengths and a high level of internal variation. Within each MLVA-defined VACC, Lpms04 was endowed with a common recognizable pattern with some interesting exceptions. Evidence of recombination events was suggested by analysis of internal repeat variations at the two additional VNTR loci, Lpms01 and Lpms13. Sequence analysis of L. pneumophila VNTR locus Lpms04 alone provides a first-line assay for allocation of a new isolate within the L. pneumophila population structure and for epidemiological studies.