Arsenic in Agricultural Soils of a Historically Mined and Industrial Region of Southern Serbia and Northern Kosovo: Bioavailability and Uptake by Plants Species Zea mays L. and Solanum tuberosum L.

This article reports the results of a study focused on the presence and bioavailability of arsenic in agricultural soil in the mining and industrial regions of northern Kosovo and southern Serbia, as well as uptake and bioaccumulation of arsenic in two commonly cultivated plant species (Zea mays L. and Solanum tuberosum L.). This area was one of the most important mining districts in Europe. The collected soil samples were subjected to a modified BCR three-step sequential extraction procedure in order to investigate the chemical partitioning of arsenic in the soils. The general distribution of arsenic in various fractions was: exchangeable < reducible < oxidizable fractions. Highest concentrations of total arsenic in soil were found close to industrial facilities and tailing ponds. In addition, fluvisols were significantly more enriched with arsenic than soils at a distance from the river flows. The edible parts of the plant specimen showed different As contents, suggesting that these plant species have different propensities for the uptake and bioaccumulation of arsenic from soil.     

An Efficient Approach for the Development of Locus Specific Primers in Bread Wheat (Triticum aestivum L.) and Its Application to Re-Sequencing of Genes Involved in Frost Tolerance

Recent declines in costs accelerated sequencing of many species with large genomes, including hexaploid wheat (Triticum aestivum L.). Although the draft sequence of bread wheat is known, it is still one of the major challenges to developlocus specific primers suitable to be used in marker assisted selection procedures, due to the high homology of the three genomes. In this study we describe an efficient approach for the development of locus specific primers comprising four steps, i.e. (i) identification of genomic and coding sequences (CDS) of candidate genes, (ii) intron- and exon-structure reconstruction, (iii) identification of wheat A, B and D sub-genome sequences and primer development based on sequence differences between the three sub-genomes, and (iv); testing of primers for functionality, correct size and localisation. This approach was applied to single, low and high copy genes involved in frost tolerance in wheat. In summary for 27 of these genes for which sequences were derived from Triticum aestivum, Triticum monococcum and Hordeum vulgare, a set of 119 primer pairs was developed and after testing on Nulli-tetrasomic (NT) lines, a set of 65 primer pairs (54.6%), corresponding to 19 candidate genes, turned out to be specific. Out of these a set of 35 fragments was selected for validation via Sanger''s amplicon re-sequencing. All fragments, with the exception of one, could be assigned to the original reference sequence. The approach presented here showed a much higher specificity in primer development in comparison to techniques used so far in bread wheat and can be applied to other polyploid species with a known draft sequence.     

Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative,Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA

Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing^TM is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient’s cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.     

Novel benzothiophene H1-antihistamines for the treatment of insomnia

SAR of lead benzothiophene H₁-antihistamine 2 was explored to identify backup candidates with suitable pharmacokinetic profiles for an insomnia program. Several potent and selective H₁-antihistamines with a range of projected half-lives in humans were identified. Compound 16d had a suitable human half-life as demonstrated in a human microdose study, but variability in pharmacokinetic profile, attributed to metabolic clearance, prevented further development of this compound. Compound 28b demonstrated lower predicted clearance in preclinical studies, and may represent a more suitable backup compound.     

Identification of a novel selective H1-antihistamine with optimized pharmacokinetic properties for clinical evaluation in the treatment of insomnia

Analogs of the known H₁-antihistamine R-dimethindene with suitable selectivity for key GPCRs, P450 enzymes and hERG channel were assessed for metabolism profile and in vivo properties. Several analogs were determined to exhibit diverse metabolism. One of these compounds, 10a, showed equivalent efficacy in a rat EEG/EMG model to a previously identified clinical candidate and a potentially superior pharmacokinetic profile as determined from a human microdose study.     

Human Y‐chromosome short tandem repeats: A tale of acculturation and migrations as mechanisms for the diffusion of agriculture in the Balkan Peninsula

Southeastern Europe and, particularly, the Balkan Peninsula are especially useful when studying the mechanisms responsible for generating the current distribution of Paleolithic and Neolithic genetic signals observed throughout Europe. In this study, 404 individuals from Montenegro and 179 individuals from Serbia were typed for 17 Y‐STR loci and compared across 9 Y‐STR loci to geographically targeted previously published collections to ascertain the phylogenetic relationships of populations within the Balkan Peninsula and beyond. We aim to provide information on whether groups in the region represent an amalgamation of Paleolithic and Neolithic genetic substrata, or whether acculturation has played a critical role in the spread of agriculture. We have found genetic markers of Middle Eastern, south Asian and European descent in the area, however, admixture analyses indicate that over 80% of the Balkan gene pool is of European descent. Altogether, our data support the view that the diffusion of agriculture into the Balkan region was mostly a cultural phenomenon although some genetic infiltration from Africa, the Levant, the Caucasus, and the Near East has occurred. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

DNA bending by charged peptides: electrophoretic and spectroscopic analyses

We are testing the idea that placement of fixed charges near one face of the DNA double helix can induce DNA bending by a purely electrostatic mechanism. If stretching forces between DNA phosphates are significant, fixed charges should induce DNA bending by asymmetrically modulating these forces. We have previously tested this hypothesis by adding charged residues to small bZIP DNA binding peptides and monitoring DNA bending using electrophoretic phasing assays. Our results were consistent with an electrostatic model of DNA bending in predicted directions. We now confirm these observations with fluorescence resonance energy transfer (FRET). Using a "U"-shaped DNA probe, we report that DNA bending by charged bZIP peptides is readily detected by FRET. We further show that charged bZIP peptides cause DNA bending rather than DNA twisting.     

The impact of age, sex, body mass index and menstrual cycle phase on gastric myoelectrical activity characteristics in a healthy Croatian population

The aim of the study was to determine the impact of demographic and anthropometric parameters on the gastric myoelectrical activity characteristics in a healthy Croatian population. The influence of age, sex, body mass index (BMI) and menstrual cycle phase on the gastric myoelectrical activity characteristics was assessed. The study included 120 healthy subjects of both sexes (60 male and 60 female), divided into four age groups (18-35, 36-50, 51-65 and > 65 years) and three BMI groups (BMI < 25, 25-30 and > 30). Female subjects of reproductive age were divided into three groups according to menstrual cycle phase (day 1-3, day 4-8 and day 9-20 of menstruation). All study subjects underwent percutaneous electrogastrography (EGG) for 60 min before and 60 min after a test meal. The following parameters of the gastric myoelectrical activity were observed: dominant frequency (DF); dominant frequency within normal range (DFNR, %); coefficient of variation for dominant frequency (CVDF); dominant strength (DS. mV); postprandial increase intensity in dominant strength (PPIIDS, %); bradygastria (BG, c/min, %); tachygastria (TG, c/min, %); and arrhythmia (AR). Age was found to influence preprandial but not postprandial DFNR, CVDF and AR. Sex influenced preprandial DF, CVDF, DS and BG, and postprandial DF, CVDF, PPIIDS and TG. BMI exerted an impact on preprandial TG and AR, and postprandial DF, CVDF and AR. The phase of menstrual cycle influenced DF in preprandial period and none of EGG parameters in postprandial period.     

Laboratory and sonographic findings in dialyzed patients with bilateral chronic knee pain versus dialyzed asymptomatic patients

The aim of this study is to evaluate connection of plasma level of beta2-microglobulin, C-reactive protein and uric acid as well as sonographic parameters like thickness of synovial membrane, thickness of femoral condylar cartilage and presence of joint effusion and Baker's cysts with bilateral knee pain in dialyzed patients, comparing them with parameters in asymptomatic dialyzed patients. Plasma levels of beta2-microglobulin and C-reactive protein were significantly higher in symptomatic patients while uric acid level showed no difference among the groups. In symptomatic patients synovial membrane was thicker and in those patients there were more knee effusions and Baker's cysts. Thickness of femoral condylar cartilage showed no difference between groups. That suggests that inflammatory mechanisms developing from beta2-microglobulin accumulation could be important factor in bilateral knee pain in dialyzed patients even in shorter duration dialysis.