[Genetic type of Helicobacter pylori and the efficacy of eradication therapy]. / Typ genetyczny Helicobacter pylori a skutecznosc leczenia eradykacyjnego.

UNLABELLED: Helicobacter pylori is one of the most popular bacteria in the world. The H. pylori infection is an etiological factor of permanent changes in inflammatory of stomach mucous membrane, peptic ulcer of the stomach and duodenum disease and stomach cancer or mucosa associated lymphoid tissue from lymphoid tissue of mucous membrane. The strain bacteria which produce the protein CagA and cytotoxin VacA belong to the more pathogenic strains. The most successful method of treatment for H. pylori infection is an eradication of the bacteria. THE AIM OF THE STUDY: Was an evaluation of the influence which H. pylori genetic type (type I: CagA-positive, CagA-negative, VacA-positive, VacA-negative) has on efficacy of eradication therapy. MATERIAL AND METHODS: 214 of patients over the third year of life with symptoms of dyspepsia, of the upper part of the gastrointestinal tract was performed and H. pylori infection was proved in histopathological or (and) urease test and urea breath test. H. pylori identification was performed using PCR method for biopsy specimens of the gastric mucosa, estimating genetic type of the bacteria (CagA-positive, CagA-negative, VacA-positive, VacA-negative). Triple-drug eradication therapy was introduced. The efficiency of this treatment was checked after 6 weeks with the breath test. RESULTS: The H. pylori infection was found in 101 patients (47.2%), 33 patients were infected with the strain type I (32.7%) and 68 patients (67.3%) with the strain type II. After the treatment the eradication of the infection was found at 71 patients (70.3%), lack of efficacy in H. pylori infection treatment was found at 30 patients (29.7%). Considerably higher percentage of eradicative infection was shown in the group of patients infected with the type II of H. pylori (76.5% vs. 58.8%, p < 0.04). CONCLUSIONS: The effectiveness of eradication can be influenced by the genetic type of H. pylori. The better effects of eradicative treatment can be expected if one is infected with the strains of smaller virulence.

[Identification of semen in bloodstains with the use of alternative light source and biochemical screening tests]. / Identyfikacja nasienia w zaplamieniach krwawych z uzyciem alternatywnego zródla swiatta i przesiewowych testów biochemicznych.

The objective of the investigation was the verification of the presence of semen in stains constituting mixtures of semen and blood employing alternative light source (ALS) and commercially available biochemical screening tests based on the activity of acid phosphatase (AP) and prostate-specific antigen (PSA). The tests demonstrated that discrimination between particular components of a blood-semen mixture was impossible either with the naked eye, as well as with the use of ALS. White fluorescence was observed only in stains consisting of pure semen and semen-blood mixtures at a ratio of 100:1. The assay for PSA was positive in the case of all the examined semen dilutions and semen-blood mixtures, whereas the sensitivity of the AP-based test assay was lower by one order of magnitude.

[Correlations between haplogroup membership and Y-STR haplotype as a potential measure of quality control in forensic examinations]. / Zaleznosci pomiedzy przynaleznoscia haplogrupowa a haplotypem Y-STR jako potencjalny element kontroli poprawnosci analiz w medycynie sadowej.

A correlation between particular Y-STR alleles from the so-called "minimal haplotype" and haplogroup membership of the Y chromosome was tested. We collected 146 Y chromosomes from haplogroups R1*, R1a1* and 1* and estimated the frequency of Y-STR alleles in each haplogroup. We then used different algorithms to assign a haplogroup to a haplotype, and tested their accuracy. Generally, a method based on calculation of haplotype similarity using the highest allele frequencies as modal values and assigning a score to each locus based on a ratio of allele frequencies turned out to give the most precise matches. However, using the same rules for Y chromosomes from other populations did not allow for precise estimation of their Y chromosome haplogroup frequencies. Possible explanations for this failure include interpopulation differences in haplotypes correlated with particular haplogroups, as well as a relatively small number of chromosomes analyzed. Potential uses for the presented method in forensics were also described.

[A comparison of the Bluestar and luminol effectiveness in bloodstain detection]. / Porównanie efektywnosci odczynnika Bluestar i luminolu w wykrywaniu sladów krwawych.

The objective of the present study was to compare the effectiveness of two chemical agents--Bluestar and luminol--in detection of bloodstains. The experiments were performed to test for bloodstain detection sensitivity, chemical stability and to investigate the effect of both reagents on DNA typing. During this study, the authors prepared serial dilutions (1:2 to 1:10 000 000) of fresh blood, as well as dilutions of 25-year old blood on Whatman 3MM blotting paper. Additional dilutions of fresh blood were spotted on a glass surface. The experiments showed very similar results for both investigated reagents, although the Bluestar solution proved to be more stable (at least 7 days after the preparation) as compared to luminol (stable for not more than 24 hours). Both reagents showed a higher sensitivity for diluted bloodstains on a glass surface than for similar stains on filter paper. The investigators also demonstrated that multiplex amplification of DNA was feasible after Bluestar or luminol treatment, although the detected bloodstains might be too diluted to allow for effective DNA extraction and amplification.

[Phylogeographic approach in the interpretation of mitochondrial DNA sequencing results in forensics]. / Zastosowanie analizy filogeograficznej w interpretacji wyników sekwencjonowania mitochondrialnego DNA dla celów sadowych.

In recent years, forensic mitochondrial DNA analysis has been undertaken from an evolutionary perspective. In particular, the phylogeographic approach based on a phylogenetic analysis of the spatial distribution of mitochondrial haplotypes and haplogroups appears to be a useful tool in the interpretation of identification cases. In this study, the phylogeographic approach has been employed in the analysis of three difficult forensic cases, where single nucleotide, homoplasmic differences were found between the reference and evidentiary haplotypes. mtDNA sequence variation has been examined by the control region (HVS I and HVS II) direct sequencing. Additionally, in order to clarify the subhaplogroup status of the selected haplotypes, DNA sequences of entire mitochondrial genomes obtained from two samples representing J1b subclade have been analyzed.

No Evidence for Association of SCO2 Heterozygosity with High-Grade Myopia or Other Diseases with Possible Mitochondrial Dysfunction.

SCO2 mutations cause recessively inherited cytochrome c oxidase deficiency. Recently Tran-Viet et al. proposed that heterozygosity for pathogenic SCO2 variants, including the common E140K variant, causes high-grade myopia. To investigate the association of SCO2 mutations with myopia, ophthalmic examinations were performed on 35 E140K carriers, one homozygous infant, and on a mouse model of Sco2 deficiency. Additionally, a screen for other putative effects of SCO2 heterozygosity was carried out by comparing the prevalence of the common E140K variant in a population of patients with undiagnosed diseases compatible with SCO2-related pathogenesis to that in a general population sample. High-grade myopia was not identified in any of the studied individuals. Of the carriers, 17 were emmetropic, and 18 possessed refractive errors. Additionally, no significant axial elongation indicative of high-grade myopia was found in mice carrying E129K (corresponding to E140K in humans) knock-in mutations. The prevalence of E140K carriers in the symptomatic cohort was evaluated as 1:103 (CI: 0.44-2.09) and did not differ significantly from the population prevalence (1:147, CI: 0.45-1.04).Our study demonstrates that heterozygosity for pathogenic SCO2 variants is not associated with high-grade myopia in either human patients or in mice.

The natural history of SCO2 deficiency in 36 Polish children confirmed the genotype-phenotype correlation.

The aim of this study was to assess the natural history of the SCO2 deficiency in relation to the genotype in a cohort of 62 patients with SCO2 mutations (36 this study, 26 previous reports). A novel, milder phenotype (disease onset delayed until one year after birth, nonspecific encephalomyopathy, and 2-4 year survival period) associated with compound heterozygosity of the common p.E140K and a novel p.M177T mutations extends the range of symptoms of the SCO2 deficiency. The prevalence of SCO2 deficiency in Poland is relatively high. A search for SCO2 mutations in patients with histology resembling SMA appears to efficiently improve the detection rate.

Ensemble fits of restrained peptides' conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3.

Two variants of NMR-based conformational analyses of flexible peptides are compared using two examples meeting the formula Tyr-D-Daa-Phe-Daa-NH2 (Daa=diamino acid): 1 combining D-Dab² (α,γ-diaminobutyryl) with Lys4, and 2 -D-Dap² (α,ß-diaminopropionyl) with Orn4. The ω-amino groups of D-Daa² and Daa4 are coupled with C=O into the urea, restraining 1 and 2 with 16- and 14-membered rings and leading to potent and impotent µ/δ opioid peptides, respectively. To the current task, we took from an earlier work (Filip et al, J. Pept. Sci. 11 (2005) 347-352) the NMR NOE- and J-data in H2O/D2O; and the selection of the ensembles of 1 and 2, 822 and 788 conformational families, respectively, obtained by using the EDMC/ECEPP3 method. Here, we generated ensembles of 1 and 2 using AMBER molecular dynamics in explicit water to eventually selected 686 and 761 conformers for 1 and 2, respectively. We did numbers of fits for both types of the conformational ensembles of 1 and 2 to their NOE- and J-data using a common method i.e. maximum entropy approach (Groth et al, J. Biomol. NMR 15 (1999) 315-330). Both types of the well structurally diversified ensembles fit to quite different equilibria in regressions to common experimental NOE- and J-restraints using maximum entropy principle, which is a disappointing message. Intriguing is startlingly small standard deviation in J-couplings: σ(JNHαH) ≈ 0.01 Hz for LES-MD/AMBER ensemble, contrary to σ(JNHαH) = 0.8 - 1.1 Hz for the EDMC/ECEPP ensemble, over the wide range of entropy, i.e. relatively insensitive to it. A similar feature is not the case when comparing σ(NOE) in both methods. Hence, at minute entropy contributions, it follows that J does or does not transpose "overfitted" into the final σ(J) in the AMBER or ECEPP ensemble, respectively. Could this be an effect of softness of the AMBER flexible-valence force field compared to ECEPP rigid-geometry, and its effect on ensemble sampling? We do not know an answer.

Diversity of 15 human X chromosome microsatellite loci in Polish population.

X-STR analysis is a powerful tool in both phylogeny reconstruction and forensic investigation. Hereby, we provide new population data concerning 15 X-STR loci (included in commercially available typing kit Mentype Argus X-8 (Biotype AG, Dresden, Germany) (DXS10135, DXS8378, DXS7132, DXS10074, HPRTB, DXS10101, DXS10134 and DXS7423) and another seven (DXS6807, DXS9898, DXS101, DXS7424, DXS7133, DXS8377 and DXS10011) that were previously described by Poetsch et al. [1] obtained from a sample of 311 individuals from Poland and compared to the results previously obtained from other populations of European, Asian and African origin [2-4]. Numerous experiments seem to prove that X-STRs are valuable markers for human identification, kinship testing and even phylogenetic research - thus serving as a complement for autosomal microsatellites, Y-STRs and mtDNA [5-7].

Conformation-activity relationships of cyclo-constrained micro/delta opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin.

The N-terminal tetrapeptide segments of dermorphin (Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH(2)) and deltorphin (Tyr-D-Ala-Phe-Asp/Glu-Val-Val-Gly-NH(2)) are agonists at the opioid receptors micro and delta, respectively. [D-Arg(2), Lys(4)]-dermorphin-(1-4) amide (Tyr-D-Arg-Phe-Lys-NH(2), DALDA) and [Dmt(1)]DALDA (where Dmt is 2',6'-dimethyltyrosine) are among the most potent and selective micro-agonists reported to date, both in vitro (having picomolar micro receptor affinity) and in vivo. In this communication, conformation-activity studies of the following four cyclic analogs of DALDA are presented and discussed: the lead peptide S(2),S(4)-cyclo (Tyr-D-Cys-Phe-Cys-NH(2)), constrained by means of an S(4.2)--S(4.4) disulfide between Cys(2) and Cys(4); its two cis and trans C(4.2)--C(4.4)-olefinic dicarba analogs, and the product of saturation of them both. They are potent nonselective or moderately micro-selective opioid agonists in vitro.They have been synthesized and tested earlier [Berezowska I, Chung NN, Lemieux C, Wilkes BC, and Schiller PW, Acta Biochim Polon 53, 2006, 73-76]. We have studied their conformations using NMR and molecular dynamics. With major conformational constraints imposed by the 11-membered ring spanning residues 2-4, they show well defined conformations of this ring, while the exocylic Tyr(1) and Phe(3) side chains still have significant conformational freedom. The more active and selective micro versus delta disulfide and saturated dicarba agonists seem to have in common: (i) their ring structures more flexible than those of the other two and (ii) their ring structures similar to each other and more diverse than those in the other two. Given this and the small size of the peptides having confirmed bioactivity profiles, there is a chance that their conformations determined in solution approach receptor-bound conformations.