Microsatellite inferred genetic diversity and structure of Western Balkan grapevines (Vitis vinifera L.)

A collection of 196 grapevine samples from five countries of the Western Balkan region, representing local and traditional cultivars, was genotyped with 22 SSR markers. Identity analysis revealed 125 unique genotypes, which were further used for diversity assessment. The average number of alleles per locus detected was 11?±?3.53, ranging from 6 to 21. The low cumulative probability of identical genotypes (2.96?×?10^?20) shown in this study implies an even distribution of alleles within the analyzed set of grapevines and a sufficient number of loci. On the basis of the discriminatory power of each SSR, a set of five markers (VVMD5, VVMD7, VVMD28, VChr3a, and VChr8b) was determined as sufficient for high-throughput discrimination of the target cultivars. The maximum discriminating power was evidenced for loci VVMD28 and Vchr8b (0.96, 0.94, respectively). A core collection covering the entire genetic diversity resulted in a set of 60 genotypes representing approximately 50 % of the samples from each country. Structure clustering of Balkan and West European cultivars resulted in four well distinct groups identified according to the classification of Negrul (1946). The lowest level of admixed genotypes was assigned for grapevines from Bosnia and Herzegovina (61 %) and the highest for Serbian (87 %) grapevines. In terms of grape use, the wine cultivars were divided into three groups and the fourth group was intermixed, with half wine and half table grapes. The highest Nei’s genetic distance (0.22) was discovered between Slovenian and Macedonian cultivars, while the lowest (0.09) was between Slovenian and Serbian cultivars. Macedonian cultivars were genetically most distant from the others (0.17). A similar pattern of differentiation among populations is seen with distance-based clustering. Analysis of molecular variance revealed only 1 % of genetic variation among groups of different origin, while the variation among individuals within geographical groups and within individuals explained 13 and 86 % of the total variation, respectively.     

Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates

Background

Multiplex ligation-dependent probe amplification (MLPA) is a powerful tool to identify genomic polymorphisms. We have previously developed a single nucleotide polymorphism (SNP) and large sequence polymorphisms (LSP)-based MLPA assay using a read out on a liquid bead array to screen for 47 genetic markers in the Mycobacterium tuberculosis genome. In our assay we obtain information regarding the Mycobacterium tuberculosis lineage and drug resistance simultaneously. Previously we called the presence or absence of a genotypic marker based on a threshold signal level. Here we present a more elaborate data analysis method to standardize and streamline the interpretation of data generated by MLPA. The new data analysis method also identifies intermediate signals in addition to classification of signals as positive and negative. Intermediate calls can be informative with respect to identifying the simultaneous presence of sensitive and resistant alleles or infection with multiple different Mycobacterium tuberculosis strains.

Results

To validate our analysis method 100 DNA isolates of Mycobacterium tuberculosis extracted from cultured patient material collected at the National TB Reference Laboratory of the National Center for Tuberculosis and Lung Diseases in Tbilisi, Republic of Georgia were tested by MLPA. The data generated were interpreted blindly and then compared to results obtained by reference methods. MLPA profiles containing intermediate calls are flagged for expert review whereas the majority of profiles, not containing intermediate calls, were called automatically. No intermediate signals were identified in 74/100 isolates and in the remaining 26 isolates at least one genetic marker produced an intermediate signal.

Conclusion

Based on excellent agreement with the reference methods we conclude that the new data analysis method performed well. The streamlined data processing and standardized data interpretation allows the comparison of the Mycobacterium tuberculosis MLPA results between different experiments. All together this will facilitate the implementation of the MLPA assay in different settings.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-572) contains supplementary material, which is available to authorized users.     

A differential response to chemical elicitors in Catharanthus roseus in vitro cultures

The effects of methyl jasmonate, salicylic acid and ethylene on alkaloid accumulation in in vitro cell suspension, hairy roots and rootless shoot cultures of Catharanthus roseus were analyzed. Ajmalicine, but not catharanthine, accumulation was promoted by jasmonate and ethylene treatments in cell suspensions. In hairy roots, jasmonate induced the accumulation of both alkaloids, whereas ethylene only induced catharanthine accumulation. In shoot cultures, positive effects of jasmonate and ethylene were recorded only in vindoline accumulation. Ethylene diminished catharanthine accumulation in these cultures. No effect of salicylic acid was observed in any of the studied in vitro culture systems. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Influence of instability and muscular weakness in ethiopathogenesis of hip fractures

The aim of our study was to, in accordance with the presented theoretical presumptions, analyze the possible reasons for hip fractures of the older population in the north-eastern part of Croatia. A group of 2,696 persons (1,936 women and 760 men) with hip fractures has been analyzed during a 12 year period (from 1993. until 2005. year) in the Clinical Hospital Osijek. The date of admittance, age, gender and fracture location were recorded. In men, the incidence of total hip fracture number on the left side was greater 23.5% (p<0.01) compared to the right side, while in women this difference does not exist. Men have a greater incidence of trochanteric fractures than fractures of femoral neck on both sides, while in women this difference could be shown on the right side only. In women, a 30.5% (p<0.001) higher fracture incidence occurred in the winter compared to the summer. It has been concluded that in men the impaired neuromuscular function on the left body side caused the greater incidence of falls on this side. The more frequent multifragmental fractures of the trochanteric massive in men indicate the possible role of preserved pelvitrochanteric muscle tension in fracture characterization. Increased incidence of falls and fractures in the older female population can be interpreted with a more pronounced weakness of pelvitrochanteric muscles and consequent walking instability. Furthermore, a smaller incidence of hip fractures was noticed in the summer compared with winter. This is explained by a reduced exhaustion of pelvic muscles in summer (primarily pelvitrochanteric) and decrease in fall frequency.     

Association of methylenetetrahydrofolate (MTHFR) and apolipoprotein E (apo E) genotypes with homocysteine, vitamin and lipid levels in carotid stenosis

The aim of the study was to investigate the association between methylenetetrahydrofolate (MTHFR) genotypes and levels of homocysteine (Hcy), folate, vitamin B12 and lipids as well as the association between apolipoprotein E (apo E) genotypes and levels of lipids in a Croatian healthy control group and a group of patients with > 70% carotid stenosis (CS). The study included 98 Croats, 38 patients with > 70% carotid stenosis and 60 age- and sex-matched controls. The MTHFR and apo E genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), Hcy by enzyme immunoassay, vitamins by immunochemiluminiscence, and lipids by spectrophotometric method. There was no difference between control subjects and CS patients in the distribution of C677T MTHFR genotypes (p=0. 786) and alleles (p=0.904), however, differences in the frequencies of apo E genotypes (p=0.012) and alleles (p=0.029) were statistically significant. The odds ratio for apo E 3/4 genotype was 3.93 (95% CI 1.23-12.61). Hyperhomocysteinemia (> or =15 micromol/L) was found in 11% of CS patients and 5% of control subjects. Total cholesterol, triglycerides, vitamin B12 and folate were statistically different in "all MTHFR genotypes" (p<0.001, p<0.01, p=0.044 and p=0.036, respectively), and in TC/TT (p<0.001, p=0.003, p=0.030 and p=0.032, respectively) groups. The levels of total cholesterol, LDL cholesterol and triglycerides in the apo E 3/3, and total cholesterol in the apo E 3/4 group yielded statistical difference. An association was found of apo E 3/4 genotype but not of MTHFR genotypes with the risk of CS. MTHFR and apo E affect blood lipid levels, which was statistically confirmed. An association was also recorded between hyperhomocysteinemia and patients with CS. Vitamin status in CS showed a statistically verified association with TC/TT MTHFR genotype. In the group of patients with TC/TT MTHFR genotype, lower vitamin B12 and higher folate values were recorded. The results of multiple logistic analysis showed that there was no statistical significance of Hcy levels (OR 2.403, p=0.334) or conventional vascular risk factors such as smoking habit (OR 0.505, p=0.149), age (OR 1.048, p=0.087) or sex (OR 2.037, p=0.112) in predicting CS.     

Neuroimaging techniques in modern forensic psychiatry

Applied neuroscientific knowledge such as brain neuroimaging has widespread application in the medical diagnostic and treatment areas. Neuroscientific progress such as cognitive neuroscience has strong implications in specific medical fields such as forensic psychiatry. Significant progress in forensic psychiatry has affected the practice of law, in which an understanding of the complex relationship among mind, brain, and behavior is becoming necessary. Forensic psychiatry is concerned with the relationship between psychiatric abnormalities and legal violations and crimes. Due to the lack of available biological criteria, assessment, evaluation and therapy in forensic psychiatry have so far been restricted to psychosocial and mental criteria of offender personality. Recent advances in nuclear radiology such as brain imaging techniques (fMRI, DT-MRI, PET SPECT) allow a closer approach to the neural correlates of personality, moral judgments and decision-making. Introduction of neurobiological criteria (based on advanced neuroimaging techniques) in the field of forensic psychiatry and establishing the rules to what extent such biological criteria will be more reliable choice in evaluating mentally ill offenders would be of fundamental value in the modern forensic psychiatry. Psychosocial and subjective criteria in forensic evaluation will be more accomplished by biopsychosocial and objective criteria. Advances in the neuroimaging techniques bring specificity to the problems underlying the application of neuroscience to criminal law.     

Clinical characteristics of patients with spondyloarthritides and HLA-B27 positive antigen

The aim of this study was to present our experiences in diagnosing spondyloarthritides (SpA), and to list the most common clinical features of HLA-B27 positive patients. The study included 65 HLA-B27 positive patients with confirmed diagnosis of ankylosing spondylitis (AS) and psoriatic arthritis (PsA) who were analyzed between 2009 and 2010 in Clinic of Internal Medicine in Osijek. The diagnosis of seronegative spondyloarthritides was based on the ASAS (Assessment in AS Working Group) classification criteria for axial and then supplemented with ASAS criteria for peripheral SpA and was confirmed by radiological techniques. For diagnosing the ankylosing spondylitis (AS), there have been applied the modified New York criteria. Radiological criteria for definite sacroiliitis according to the modified New York criteria is bilateral sacroiliitis, grade 2-4 (> or = 2) or unilateral sacroiliitis, grade 3-4. For diagnosing the psoriatic arthritis (PsA), there were used CASPAR diagnostic criteria. Other features of SpA are defined within the existing classification criteria. HLA-B27 antigen was determined by direct immune-fluorescence technique using flow cytometer. The average age of patients was 50.34 years, of whom 27 female (41.53%), 38 male (58.46%). Duration of illness was 15.79 years on average. With 75.38% of patients, there had been determined the diagnosis of AS; 24.62% of patients had the diagnosis of PsA. The most common clinical characteristics that patients had were: inflammatory back pain (pain Inflammation along the lumbosacral spine), peripheral arthritis, intermittent pain in the gluteus, sacroiliitis, enthesitis, uveitis, dactilitis.     

Combined Species Identification, Genotyping, and Drug Resistance Detection of Mycobacterium tuberculosis Cultures by MLPA on a Bead-Based Array

The population structure of Mycobacterium tuberculosis is typically clonal therefore genotypic lineages can be unequivocally identified by characteristic markers such as mutations or genomic deletions. In addition, drug resistance is mainly mediated by mutations. These issues make multiplexed detection of selected mutations potentially a very powerful tool to characterise Mycobacterium tuberculosis. We used Multiplex Ligation-dependent Probe Amplification (MLPA) to screen for dispersed mutations, which can be successfully applied to Mycobacterium tuberculosis as was previously shown. Here we selected 47 discriminative and informative markers and designed MLPA probes accordingly to allow analysis with a liquid bead array and robust reader (Luminex MAGPIX technology). To validate the bead-based MLPA, we screened a panel of 88 selected strains, previously characterised by other methods with the developed multiplex assay using automated positive and negative calling. In total 3059 characteristics were screened and 3034 (99.2%) were consistent with previous molecular characterizations, of which 2056 (67.2%) were directly supported by other molecular methods, and 978 (32.0%) were consistent with but not directly supported by previous molecular characterizations. Results directly conflicting or inconsistent with previous methods, were obtained for 25 (0.8%) of the characteristics tested. Here we report the validation of the bead-based MLPA and demonstrate its potential to simultaneously identify a range of drug resistance markers, discriminate the species within the Mycobacterium tuberculosis complex, determine the genetic lineage and detect and identify the clinically most relevant non-tuberculous mycobacterial species. The detection of multiple genetic markers in clinically derived Mycobacterium tuberculosis strains with a multiplex assay could reduce the number of TB-dedicated screening methods needed for full characterization. Additionally, as a proportion of the markers screened are specific to certain Mycobacterium tuberculosis lineages each profile can be checked for internal consistency. Strain characterization can allow selection of appropriate treatment and thereby improve treatment outcome and patient management.