Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants

Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants

Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

Uniparental DNA markers and forensic genetics in Finland

Over the years, a wide range of methods to verify identity have been developed. Molecular markers have been used for identification since the 1920s, commencing with blood types and culminating with the advent of DNA techniques in the 1980s. Identification is required by authorities in many occasions, e.g. in disputed paternity cases, identification of deceased, or crime investigation. To clarify maternal and paternal lineages, uniparental DNA markers in mtDNA and Y-chromosome can be utilized. These markers have several advantages: male specific Y-chromosome can be used to identify a male from a mixture of male and female cells, e.g. in rape cases. MtDNA is durable and has a high copy number, allowing analyses even from old or degraded samples. However, both markers are lineage-specific, not individualizing, and susceptible to genetic drift. Prior to the application of any DNA marker in forensic casework, it is of utmost importance to investigate its qualities and peculiarities in the target population. Earlier studies on the Finnish population have shown reduced variation in the Y-chromosome, but in mtDNA results have been ambiguous. The obtained results confirmed the low diversity in Y-chromosome in Finland. Detailed population analysis revealed large regional differences, and extremely reduced diversity especially in East Finland. Analysis of the qualities affecting Y-chromosomal short tandem repeat (Y-STR) variation and mutation frequencies, and search of new polymorphic markers resulted a set of Y-STRs with especially high diversity in Finland. Contrary to Y-chromosome, neither reduced diversity nor regional differences were found in mtDNA within Finland. In fact, mtDNA diversity was found similar to other European populations. The revealed peculiarities in the uniparental markers are a legacy of the Finnish population history. The obtained results challenge the traditional explanation which emphasizes relatively recent founder effects creating the observed east-west patterns. Uniparentally inherited markers, both mtDNA and Y-chromosome, are applicable for identification purposes in Finland. By adjusting the analysed Y marker set to meet the characteristics of Finnish population, Y-chromosomal diversity increases and the regional differentiation decreases, resulting increase in discrimination power and thus usefulness of Y-chromosomal analysis in forensic casework.

Expression of drug resistance markers by spheroplasts ofMycobacterium smegmatis after fusion

Mycobacterial spheroplasts were prepared by treatment of the glycinesensitized cells with a combination of lipase and lysozyme. They were stable for several hours at room temperature but were lysed on treatment with 0.1% sodium dodecyl sulfate. The spheroplasts could be regenerated on a suitable medium. Fusion and regeneration of the spheroplasts were attempted using drug resistant mutant strains ofM. smegmalis. Recombinants were obtained from spheroplast fusion mediated by polyethylene glycol and dimethyl sulfoxide. Simultaneous expression of rccombinant properties was observed only after an initial lag in the isolated clones. This has been explained as due to “chromosome inactivation” in the fused product.

Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

10 p.

Running Pace Decrease during a Marathon Is Positively Related to Blood Markers of Muscle Damage

Background: Completing a marathon is one of the most challenging sports activities, yet the source of running fatigue during this event is not completely understood. The aim of this investigation was to determine the cause(s) of running fatigue during a marathon in warm weather. Methodology/Principal Findings: We recruited 40 amateur runners (34 men and 6 women) for the study. Before the race, body core temperature, body mass, leg muscle power output during a countermovement jump, and blood samples were obtained. During the marathon (27 uC; 27% relative humidity) running fatigue was measured as the pace reduction from the first 5-km to the end of the race. Within 3 min after the marathon, the same pre-exercise variables were obtained. Results: Marathoners reduced their running pace from 3.5 6 0.4 m/s after 5-km to 2.9 6 0.6 m/s at the end of the race (P,0.05), although the running fatigue experienced by the marathoners was uneven. Marathoners with greater running fatigue (. 15% pace reduction) had elevated post-race myoglobin (1318 6 1411 v 623 6 391 mg L21; P,0.05), lactate dehydrogenase (687 6 151 v 583 6 117 U L21; P,0.05), and creatine kinase (564 6 469 v 363 6 158 U L21; P = 0.07) in comparison with marathoners that preserved their running pace reasonably well throughout the race. However, they did not differ in their body mass change (23.1 6 1.0 v 23.0 6 1.0%; P = 0.60) or post-race body temperature (38.7 6 0.7 v 38.9 6 0.9 uC; P = 0.35). Conclusions/Significance: Running pace decline during a marathon was positively related with muscle breakdown blood markers. To elucidate if muscle damage during a marathon is related to mechanistic or metabolic factors requires further investigation.

New genetic markers for treatment personalization in pediatric acute lymphoblastic leukemia

La Leucemia Linfoblástica Aguda (LLA) es el cáncer pediátrico más común. Es un desorden de las células linfoblásticas, que son las precursoras de las células linfáticas, y se caracteriza por la acumulación en médula ósea y sangre de pequeñas células blásticas con poco citoplasma y cromatina dispersa. En las últimas décadas, se ha conseguido aumentar la supervivencia del 10% al 80% pero todavía hay un 20% de pacientes que no responden al tratamiento. Esta mejoría se ha conseguido mediante la implantación de terapias combinadas y la adecuación de la terapia a grupos de riesgo. Los pacientes se separan en tres grupos de riesgo, Riesgo Estándar (RE), Alto Riesgo (AR) y Muy Alto Riesgo (MAR), en base a marcadores pronósticos, entre los que se incluyen alteraciones citogenéticas. Sin embargo, a lo largo del tratamiento, nos encontramos con dos problemas:1) Por un lado, algunos de los pacientes incluidos en el grupo de RE y AR no responden bien al tratamiento y pasan AR y MAR respectivamente. Esto quiere decir que los grupos de riesgo no están bien definidos. Por lo tanto, sería de interés poder caracterizar los pacientes que realmente son RE y AR y aquéllos que desde un principio deberían haber sido considerados como de mayor riesgo.2) Por otro lado, un alto porcentaje de pacientes experimenta toxicidad, que puede llegar a ser muy grave en algunos casos, siendo necesario parar el tratamiento. Por este motivo, sería altamente beneficioso poder reconocer a los pacientes que van a ser más sensibles al tratamiento para, de ese modo, poder ajustar la dosis.Por todo esto, creemos que una mejor asignación de los pacientes de LLA a grupos de riesgo y la personalización de la dosis, mediante nuevos marcadores genéticos, permitiría mejorar la respuesta al tratamiento.En este estudio nos planteamos, por lo tanto, dos objetivos: 1) Llevar a cabo la identificación de nuevas alteraciones genéticas presentes en el tumor para una mejor caracterización del riesgo y 2) Realizar una caracterización genética del individuo que permita predecir la respuesta al tratamiento.

Association between dietary phylloquinone intake and peripheral metabolic risk markers related to insulin resistance and diabetes in elderly subjects at high cardiovascular risk

Background: Vitamin K has been related to glucose metabolism, insulin sensitivity and diabetes. Because inflammation underlies all these metabolic conditions, it is plausible that the potential role of vitamin K in glucose metabolism occurs through the modulation of cytokines and related molecules. The purpose of the study was to assess the associations between dietary intake of vitamin K and peripheral adipokines and other metabolic risk markers related to insulin resistance and type 2 diabetes mellitus. Methods: Cross-sectional and longitudinal assessments of these associations in 510 elderly participants recruited in the PREDIMED centers of Reus and Barcelona (Spain). We determined 1-year changes in dietary phylloquinone intake estimated by food frequency questionnaires, serum inflammatory cytokines and other metabolic risk markers. Results: In the cross-sectional analysis at baseline no significant associations were found between dietary phylloquinone intake and the rest of metabolic risk markers evaluated, with exception of a negative association with plasminogen activator inhibitor-1. After 1-year of follow-up, subjects in the upper tertile of changes in dietary phylloquinone intake showed a greater reduction in ghrelin (-15.0%), glucose-dependent insulinotropic peptide (-12.9%), glucagon-like peptide-1 (-17.6%), IL-6 (-27.9%), leptin (-10.3%), TNF (-26.9%) and visfatin (-24.9%) plasma concentrations than those in the lowest tertile (all p<0.05). Conclusion: These results show that dietary phylloquinone intake is associated with an improvement of cytokines and other markers related to insulin resistance and diabetes, thus extending the potential protection by dietary phylloquinone on chronic inflammatory diseases.

Evidence for classification of c.1852_1853AA > GC in MLH1 as a neutral variant for Lynch syndrome

Background: Lynch syndrome (LS) is an autosomal dominant inherited cancer syndrome characterized by early onset cancers of the colorectum, endometrium and other tumours. A significant proportion of DNA variants in LS patients are unclassified. Reports on the pathogenicity of the c.1852_1853AA>GC (p.Lys618Ala) variant of the MLH1 gene are conflicting. In this study, we provide new evidence indicating that this variant has no significant implications for LS. Methods: The following approach was used to assess the clinical significance of the p.Lys618Ala variant: frequency in a control population, case-control comparison, co-occurrence of the p.Lys618Ala variant with a pathogenic mutation, co-segregation with the disease and microsatellite instability in tumours from carriers of the variant. We genotyped p.Lys618Ala in 1034 individuals (373 sporadic colorectal cancer [CRC] patients, 250 index subjects from families suspected of having LS [revised Bethesda guidelines] and 411 controls). Three well-characterized LS families that fulfilled the Amsterdam II Criteria and consisted of members with the p.Lys618Ala variant were included to assess co-occurrence and co-segregation. A subset of colorectal tumour DNA samples from 17 patients carrying the p.Lys618Ala variant was screened for microsatellite instability using five mononucleotide markers. Results: Twenty-seven individuals were heterozygous for the p.Lys618Ala variant; nine had sporadic CRC (2.41%), seven were suspected of having hereditary CRC (2.8%) and 11 were controls (2.68%). There were no significant associations in the case-control and case-case studies. The p.Lys618Ala variant was co-existent with pathogenic mutations in two unrelated LS families. In one family, the allele distribution of the pathogenic and unclassified variant was in trans, in the other family the pathogenic variant was detected in the MSH6 gene and only the deleterious variant co-segregated with the disease in both families. Only two positive cases of microsatellite instability (2/17, 11.8%) were detected in tumours from p.Lys618Ala carriers, indicating that this variant does not play a role in functional inactivation of MLH1 in CRC patients. Conclusions: The p.Lys618Ala variant should be considered a neutral variant for LS. These findings have implications for the clinical management of CRC probands and their relatives.

Aquaculture Asia, Vol.14, No.2, pp.1-40, April-June 2009

Sustainable aquaculture GLOBALG.A.P. standard in Thai shrimp farms: Mission (im)possible? p.4 Leepaisomboon, T., Chuchird, N., Limsuwan, C., Steenbruggen, E.R., and Mungkung, R. The Victorian trout industry & the bushfires p.6 Mosig, J. Small-scale aquaculture in the Ayeyarwady Delta, Myanmar p.10 Edwards, P. The history, status, and future prospects of monosex tilapia culture in Thailand p.18 Belton, B., Turongruang, D., Bhujel, R. and Little, D.C. Mangroves of Nakhon Si Thammarat Province in southern Thailand: Species diversity, community structure and current status p.20 By Amarasinghe, M.D., Dulyapurk, V., Taparhudee, W., Yoonpundh, R. and Jumnongsong, S. Research and farming techniques Induced breeding of pacu (Piaractus brachypomus) in captivity with pituitary extract p.23 Chattarjee, N.R. and Mazumdar, B. Aquatic animal health Fumonisins - mycotoxins of increasing importance in fish! p. 24 Griessler, K. and Encarnação, P. Genetics and biodiversity Microsatellite DNA markers, a fisheries perspective. Part 1: The nature of microsatellites p.27 Sekar, M., Suresh, E., Kumar, N.S., Nayak, S.K., Balakrishna, C. Asia-Pacific Marine Finfi sh Aquaculture Magazine Formulated feed for tiger grouper grow-out p.30 Rachmansyah, Usman, Palinggi, N.N. and Williams, K. NACA Newsletter 36

Detection of hepatitis B virus markers using a biosensor based on imaging ellipsometry

A biosensor based on imaging ellipsometry (BIE) has been developed and validated in 169 patients for detecting five markers of hepatitis B virus (HBV) infection. The methodology has been established to pave the way for clinical diagnosis, including ligand screening, determination of the sensitivity, set-up of cut-off values (CoVs) and comparison with other clinical methods. A matrix assay method was established for ligand screening. The CoVs of HBV markers were derived with the help of receiver operating characteristic curves. Enzyme-linked immunosorbent assay (ELISA) was the reference method. Ligands with high bioactivity were selected and sensitivities of 1 ng/mL and 1 IU/mL for hepatitis B surface antigen (HBsAg) and surface antibody (anti-HBs) were obtained respectively. The CoVs of HBsAg, anti-HBs, hepatitis B e antigen, hepatitis B e antibody and core antibody were as follows: 15%, 18%, 15%, 20% and 15%, respectively, which were the percentages over the values of corresponding ligand controls. BIE can simultaneously detect up to five markers within 1 h with results in acceptable agreement with ELISA, and thus shows a potential for diagnosing hepatitis B with high throughput.

Surface markers of regionalization in the vertebrate nervous system

In order to identify new molecules that might play a role in regional specification of the nervous system, we generated and characterized monoclonal antibodies (mAbs) that have positionally-restricted labeling patterns.

The FORSE-1 mAb was generated using a strategy designed to produce mAbs against neuronal cell surface antigens that might be regulated by regionally-restricted transcription factors in the developing central nervous system (CNS). FORSE-1 staining is enriched in the forebrain as compared to the rest of the CNS until E18. Between E11.5-E13.5, only certain areas of the forebrain are labeled. There is also a dorsoventrally-restricted region of labeling in the hindbrain and spinal cord. The mAb labels a large proteoglycan-like cell-surface antigen (>200 kD). The labeling pattern of FORSE-1 is conserved in various mammals and in chick.

To determine whether the FORSE-1 labeling pattern is similar to that of known transcription factors, the expression of BF-1 and Dlx-2 was compared with FORSE-1. There is a striking overlap between BF-1 and FORSE-1 in the telencephalon. In contrast, FORSE-1 and Dlx-2 have very different patterns of expression in the forebrain, suggesting that regulation by Dlx-2 alone cannot explain the distribution of FORSE-1. They do, however, share some sharp boundaries in the diencephalon. In addition, FORSE-1 identifies some previously unknown boundaries in the developing forebrain. Thus, FORSE-1 is a new cell surface marker that can be used to subdivide the embryonic forebrain into regions smaller than previously described, providing further complexity necessary for developmental patterning.

I also studied the expression of the cell surface protein CD9 in the developing and adult rat nervous system. CD9 is implicated in intercellular signaling and cell adhesion in the hematopoetic system. In the nervous system, CD9 may perform similar functions in early sympathetic ganglia, chromaffin cells, and motor neurons, all of which express the protein. The presence of CD9 on the surfaces of Schwann cells and axons at the appropriate time may allow the protein to participate in the cellular interactions involved in myelination.