Genetic variation and relationship of alfalfa populations and their progenies based on RAPD markers

The aim of investigation was to evaluate genetic variation and relationship among alfalfa populations and their offspring, with minimal cost, by using DNA marker analysis. RAPD analysis was performed on bulked DNA samples of five alfalfa parental populations and their progenies: 20 F1 populations from reciprocal diallel crosses and five S1 populations from self-pollination. Twenty primers generated 217 bands, ranging in size from 300 to 6000 bp, with the average number of bands per primer of 10.85 and polymorphism information content of 0.246. Percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Higher diversity was observed in F1 progeny populations, while genetic variation in parental populations and S1 progenies remained similar. The genetic relatedness of alfalfa populations was analysed by UPGMA and Bayesian model-based clustering approach. In both types of analysis selfpollinated progenies were grouped. Furthermore, the hybrid offspring where Zuzana, and RSI 20 were maternal parents were placed in separate groups. The results indicate that use of RAPD markers on bulked DNA samples can be fast and cost-effective way for differentiation of alfalfa parental populations and their offspring, as well as for evaluation of their genetic relationships.     

Isolation,characterization and evaluation of significant mycoflora and mycotoxins in pig feed from Serbian farms

This paper provides a brief review of approaches for the early detection and prevention strategies which have been employed in Serbia for the control of ochratoxogenic fungi and its metabolites in feed in the context of a hazard analysis critical control point (HACCP) framework. During a mycological analysis of complete feedmixes intended for fattening swine (n = 18), a total of six genera and 14 species of moulds were identified. Penicillium was present in considerably more samples than any other genus (94.4%), followed by the genera Fusarium (55.5%) and Paecilomyces (44.4%). Other fungi from the genera Aspergillus (22%), Mucor (11.1%) and Alternaria (5.5%) were represented in a smaller amount. Total fungal counts ranged from 10⁵ to 40 × 10⁵ c.f.u./g. The mycotoxins deoxynivalenol, ochratoxin A and zearalenone were detected, while aflatoxins were not present. Deoxynivalenol was detected in 10 samples in the concentration range 0.25–2.5 mg/kg. Ochratoxin A and zaralenone were detected in nine and eight samples, respectively, in the concentration range 0.057–0.27 and 0.2–5.0 mg/kg, respectively. Isolates identified as Aspergillus and Penicillium species were subjected to molecular characterization for the presence of genes responsible for the synthesis of OTA (polyketide synthase gene-PKS) using polymerase chain reaction (PCR) applied to a set of 18 isolates. The sequences of PCR reaction products in three samples were compared with nucleotide sequences of genes for polyketide synthase (PKS) from Penicillium species and it was found that the samples possessed the PKS sequence. These findings indicate that there may be a risk of animal exposure to mycotoxins through the consumption of mouldy infected feeds.     

Assessment of genome damage in occupational exposure to ionising radiation and ultrasound

The mutagenic effects of low doses of radiation on occupationally exposed subjects were studied on lymphocyte culture using two methods: analysis of structural chromosome aberrations and micronucleus assay. The results obtained in subjects exposed to ionising radiation alone were compared to those exposed to both ionising radiation and ultrasound. A correlation between the total number of chromosome aberrations and distribution of micronuclei in the genome of somatic cells show higher deviation in the group exposed to X-ray and ultrasound than in the group exposed to X-rays alone. The degree of genome damage in occupational exposure to X-rays and ultrasound were discussed.     

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 Balkan chamois,an archipelago or a peninsula? Insights from nuclear and mitochondrial DNA

The Balkan chamois (Rupicapra rupicapra balcanica) is widespread on the Balkan Peninsula, along mountain massifs from Croatia in the north to Greece in the south and Bulgaria in the east. Knowledge on the genetic structure of Balkan chamois populations is limited and restricted to local studies. Therefore, the main objective of this study was to use nuclear (16 microsatellites) and mitochondrial (partial 376 base pairs control region) markers to investigate the genetic structure of this chamois subspecies throughout its distribution range and to obtain information on the degree of connectivity of the different (sub)populations. We extracted DNA from bone, dried skin and muscle tissue and successfully genotyped 92 individuals of Balkan chamois and sequenced the partial control region in 44 individuals. The Bayesian analysis suggested 3 genetic clusters and assigned individuals from Serbia and Bulgaria to two separate clusters, while individuals from the other countries belonged to the same cluster. Thirty new haplotypes were obtained from partial mitochondrial DNA sequences, with private haplotypes in all analyzed populations and only two haplotypes shared among populations, indicating the possibility of past translocations. The subspecies genetic composition presented here provides the necessary starting point to assess the conservation status of the Balkan chamois and allows the development of conservation strategies necessary for its sustainable management and conservation.

     

Genetic mapping of the stem rust (Puccinia graminis f. sp. tritici Eriks. & E. Henn) resistance gene Sr13 in wheat (Triticum aestivum L.)

Puccinia graminis f. sp. tritici, the causative agent of stem rust in wheat, is known for its high virulence variability and ability to evolve new virulence to resistance genes. Thus, pyramiding of several resistance genes in a single line is the best strategy for a sustainable control of wheat stem rust. Sr13 is one of the few resistance genes that are effective against wide ranging P. graminis f. sp. tritici races, including the pestilent race Ug99. Its effectiveness to Ug99 makes it a valuable source for resistance to stem rust. Molecular markers play a pivotal role in the genetic characterization of the new sources of resistance as well as in stacking two or more resistance genes in a single line. Therefore, the aim of this study was to develop molecular markers for Sr13 facilitating efficient pyramiding of Sr genes. Based on the 158 F₂ individuals derived from a cross of Khapstein/9*LMPG × Morocco and SSR analyses, the Sr13 locus was mapped on chromosome 6A of wheat, and a genetic map comprising about 90 cM was constructed with the closest marker barc37 being located 4.0 cM distally of Sr13. Of the nine mapped markers, barc37 amplified an allele specific for the presence of Sr13 as shown by testing different cultivars and breeding lines. These newly developed markers will increase the efficiency of incorporating Sr13 into cultivars that are widely adopted, but susceptible to hazardous Ug99 and/or assist for the development of new elite lines that are resistant to Ug99.     

Acute appendicitis and ileal perforation with a toothpick treated by laparoscopy

A 69-year-old man underwent an emergency laparoscopic procedure after the acute appendicitis diagnosis has been established. Laparoscopic exploration showed inflamed appendix and perforation of terminal ileum with a swallowed part of the wooden toothpick. The treatment consisted of typical laparoscopic appendectomy and laparoscopic removal of the foreign body, followed by laparoscopic closure of the perforation site and lavage of the abdominal cavity. The postoperative course was uneventful and the patient was discharged from the hospital on day 3 after the operation.     

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.