Pcr-based multiplex DNA fingerprinting techniques for the analysis of conifer genomes

We utilised fingerprinting techniques such as amplified restriction fragment polymorphism (AFLP) and selective amplification of microsatellite polymorphic loci (SAMPL) in order to identify molecular markers in the conifer species Norway spruce (Picea abies K). A total of 366 polymorphic AFLP and 20 polymorphic SAMPL bands were scored, with an average of 12.6 polymorphic bands obtained per primer combination. Of the bands, 94% segregated in a Mendelian fashion, and 14% of the AFLP bands behaved as codominant markers. Norway spruce, as well as other conifers, has a very large genome (1.5–2.5 × 10¹⁰ bp) which is thought to be largely composed of repetitive sequences of different origin, either organised in tandem or interspersed in the genome. The high complexity of these genomes has so far hindered the efficient use of multiplexed fingerprinting techniques for their analysis. The use of the methylation-sensitive restriction enzyme PstI as 6 bp cutter allows a reduction in pattern complexity as compared to EcoRI. We thus demonstrated that high-throughput PCR-based multiplex fingerprinting techniques such as AFLP and SAMPL, when opportunely modified, can be effectively applied also to these species and be useful for mapping purposes.     

Inhibition of procollagen cell-free synthesis by amino-terminal extension peptides

Peptides prepared from the amino termini of pro alpha 1(I) and pro alpha 1(III) collagen chains inhibit the production of pro alpha 1(I) and pro alpha 2 by rat calvaria rna in a reticulocyte cell-free system. The synthesis of other proteins was not altered, suggesting a specific effect on collagen production. Various peptides from the helical region of the alpha 1(I) chain did not alter translation. These studies, taken together with earlier studies showing inhibition of collagen synthesis by cells in culture receiving the amino-terminal peptides, are consistent with a regulatory function in collagen synthesis for the amino-terminal peptides from procollagen.     

Nonmedical drug use among adolescent students: highlights from the 1999 Ontario Student Drug Use Survey

BACKGROUND: During the 1990s, rates of nonmedical drug use among adolescents escalated. We assessed data from 5 cycles of the Ontario Student Drug Use Survey for overall trends in the proportion of students reporting illegal drug use between 1991 and 1999. METHODS: The survey is a repeated, cross-sectional, 2-stage cluster-design survey of students enrolled in grades 7, 9, 11 and 13. Outcome measures were prevalence of use of 17 drugs, including alcohol and tobacco, over the 12 months preceding the survey. RESULTS: The rates of drug use increased between 1993 and 1999. The 95% confidence intervals (CIs) for the differences in proportions between 1997 and 1999 indicated significant increases in the overall use of 6 drugs: alcohol (95% CIdiff 6.1, 1.9-10.3), cannabis (95% CIdiff 46.3, 0.2-8.4), glue (95% CIdiff 2.3, 1.3-3.3), other solvents (95% CIdiff 5.0, 3.1-6.3), barbiturates (95% CIdiff 1.9, 0.4-3.4) and hallucinogens such as mescaline and psilocybin (95% CIdiff 3.5, 0.8-6.9). Fewer grade 7 students in 1999 than in earlier cohorts reported using alcohol or cigarettes by age 9. INTERPRETATION: The public health implications of the findings are mixed. On the positive side, there is no evidence of increases in early onset of drug use. On the negative side, the overall proportion of students reporting illegal drug use has continued to rise.     

Trinucleotide microsatellites in Norway spruce ( Picea abies): their features and the development of molecular markers

Trinucleotide microsatellites have proven to be the markers of choice in human genetic analysis because they are easier to genotype than dinucleotides. Their development can be more time-consuming due to their lower abundance in the genome. We isolated trinucleotide microsatellites in Norway spruce ( Picea abies K.) using an enrichment procedure for the genomic-library construction. Here we report on the characterisation of 85 ATC microsatellite-containing clones, from which 39 markers were developed. Many of the clones showed the occurrence of tandem repeats of higher order than the trinucleotide ones, often resembling minisatellite repeats. The sequencing of a sample of the alleles at one of the loci revealed size homoplasy due to base substitutions within the microsatellite region. The presence of ATC motifs within repetitive sequence families was observed. We found a significant relationship between the level of polymorphism and the length of the microsatellite. The levels of variability for ATC trinucleotide markers were lower than those for dinucleotides, both when tested on all loci in a set of six individuals and on a subset of loci in four natural populations. This difference is most likely attributable to lower mutation rates for trinucleotide than for dinucleotide loci. The availability of markers with different mutation rates allows one to select the proper marker set to investigate population processes on different time scales.     

WaterLOGSY as a method for primary NMR screening: Practical aspects and range of applicability

WaterLOGSY represents a powerful method for primary NMR screening in the identification of compounds interacting with macromolecules, including proteins and DNA or RNA fragments. Several relay pathways are used constructively in the experiment for transferring bulk water magnetization to the ligand. The method is particularly useful for the identification of novel scaffolds of micromolar affinity that can be then optimized using directed screening, combinatorial chemistry, medicinal chemistry and structure-based drug design. The practical aspects and range of applicability of the WaterLOGSY experiment are analyzed in detail here. Competition binding and titration WaterLOGSY permit, after proper correction, the evaluation of the dissociation binding constant. The high sensitivity of the technique in combination with the easy deconvolution of the mixtures for the identification of the active components, significantly reduces the amount of material and time needed for the NMR screening process.     

Silent <Emphasis Type="Italic">Orthohantavirus</Emphasis> Circulation Among Humans and Small Mammals from Central Minas Gerais,Brazil

New World orthohantaviruses are emerging RNA viruses that cause hantavirus cardiopulmonary syndrome (HCPS). These viruses are a burden to public health around the world with a lethality rate of around 60%. In South America, rodents of Sigmodontinae subfamily are the main reservoirs of orthohantaviruses. We described a serosurvey for orthohantaviruses circulation in an apparently healthy human population and small mammals from rural areas in Central Minas Gerais State, Brazil. A total of 240 individuals and 50 small mammals (26 rodents belonging to 10 different species and 24 marsupials from 4 different species) were sampled during 2012–2013. The seroprevalence rates of IgG/IgM antibodies in humans were 7.1 and 1.6%, respectively. Only one rodent, an Oligoryzomys nigripes captured in peridomestic area, tested positive for IgG antibodies and viral RNA. Our findings suggest a silent circulation of orthohantaviruses in a region of intensive agriculture production. The detection of seropositive humans in an area with a lack of previous HCPS reports highlights potential oligosymptomatic cases and the need for surveillance strategies that could reduce the risk of future outbreaks.     

Functional Metabolic Map of Faecalibacterium prausnitzii,a Beneficial Human Gut Microbe

The human gut microbiota plays a central role in human well-being and disease. In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms. We demonstrate this approach for the beneficial human gut microbe Faecalibacterium prausnitzii strain A2-165. We generated an automated draft reconstruction, which we curated against the limited biochemical data. This reconstruction modeling was used to develop in silico and in vitro a chemically defined medium (CDM), which was validated experimentally. Subsequent metabolomic analysis of the spent medium for growth on CDM was performed. We refined our metabolic reconstruction according to in vitro observed metabolite consumption and secretion and propose improvements to the current genome annotation of F. prausnitzii A2-165. We then used the reconstruction to systematically characterize its metabolic properties. Novel carbon source utilization capabilities and inabilities were predicted based on metabolic modeling and validated experimentally. This study resulted in a functional metabolic map of F. prausnitzii, which is available for further applications. The presented workflow can be readily extended to other poorly characterized and uncharacterized organisms to yield novel biochemical insights about the target organism.     

Fine-scale sites of global conservation importance in the Atlantic forest of Brazil

The Brazilian Atlantic Forest is a highly threatened biodiversity hotspot that has been the subject of several complementary conservation assessments and priority-setting initiatives in the last 30 years. Results of these initiatives have relied on distinct types of distribution data for biodiversity features and differ in the objectivity and repeatability of their methodologies. Here we refine earlier priority-setting exercises using the key biodiversity areas (KBA) approach. We evaluate how well these KBAs are represented in the existing protected areas system, prioritize among them, and analyze critical aspects of the KBA methodology in the Brazilian Atlantic Forest context, such as its ability to guide specific conservation strategies. Building upon an extensive database with 1,636 species records and 122 previously identified Important Bird Areas, we demonstrate that conservation assessments in highly fragmented landscapes may be benefited by high resolution species data as is required by the KBA process. We identify 538 KBAs for 141 globally threatened vertebrate species. Prioritizing among these KBA, we highlight the 24 most irreplaceable sites for terrestrial vertebrate species conservation in the Atlantic Forest, based on existing data.     

Structural Damage Induced by Peroxidation May Account for Functional Impairment of Heavy Synaptic Mitochondria

Coenzyme Q distribution, as well as respiratory chain features, in rat brain mitochondria depend on mitochondrial subpopulation, brain region and age. Heavy mitochondria (HM) usually display the lowest content of respiratory components and the lowest enzymatic activities and it has been suggested that they represent the oldest mitochondrial population. In this study, we confirmed that HM are considerably compromised in their structure. In fact, HM showed to have the highest hydroperoxide content and the most consistent modifications in their fatty acid pattern with wide loss of fatty acids (or part of them) in the phospholipid moiety. Such situation could explain the typical impairment of HM and could support the hypothesis that they represent an old mitochondrial population.