Draft genome sequence of the Aeromonas diversa type strain

We present here the first genome sequence of the Aeromonas diversa type strain (CECT 4254T). This strain was isolated from the leg wound of a patient in New Orleans (Louisiana, USA) and was originally described as Enteric Group 501 and distinguished from A. schubertii by DNADNA hybridization and phenotypical characterization.

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.

Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b.

The ability of Mycobacterium tuberculosis to establish a latent infection (LTBI) in humans confounds the treatment of tuberculosis. Consequently, there is a need to discover new therapeutic agents that can kill M. tuberculosis both during active disease and LTBI. The streptomycin-dependent strain of M. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (STR) it enters a non-replicating state that mimics latency both in vitro and in animal models. The 4.41 Mb genome sequence of M. tuberculosis 18b was determined and this revealed the strain to belong to clade 3 of the ancient ancestral lineage of the Beijing family. STR-dependence was attributable to insertion of a single cytosine in the 530 loop of the 16S rRNA and to a single amino acid insertion in the N-terminal domain of initiation factor 3. RNA-seq was used to understand the genetic programme activated upon STR-withdrawal and hence to gain insight into LTBI. This revealed reconfiguration of gene expression and metabolic pathways showing strong similarities between non-replicating 18b and M. tuberculosis residing within macrophages, and with the core stationary phase and microaerophilic responses. The findings of this investigation confirm the validity of 18b as a model for LTBI, and provide insight into both the evolution of tubercle bacilli and the functioning of the ribosome.

Analysis of TRIP expression in different types of skin tumor

TRAF-interacting protein (TRIP) is a ubiquitously expressed nucleolar E3 ubiquitin ligase. Ubiquitination of proteins is a post-translational modification, which decides on the cellular fate of the protein. TRIP in vivo substrate has not been yet identified. However, TRIP has been shown to play an important role in cellular proliferation, especially in keratinocytes. TRIP was found to be up-regulated in basal cell carcinoma (BCC) at the mRNA level. This prompted us to elucidate its role in skin proliferative diseases such as cancer by analyzing its expression in BCCs at protein level and in squamous cell carcinoma (SCC) at mRNA and protein level. To that purpose, we performed a real-time PCR (qPCR) analysis followed by an immunohistochemistry (IHC) on formalin-fixed, paraffin-embedded (FFPE) biopsies. The real-time PCR was performed on 12 RNA samples of which 6 were extracted from SCC biopsies and 6 from normal human skin. The results were statistically insignificant. Further analyses are needed on new RNA samples. The IHC assay was performed on 20 biopsies from BCCs, 21 biopsies from SCCs and on 5 tissues from normal human skin. The results obtained showed an extensive expression of TRIP in keratinocytes nuclei. Due to various limitations related to the technique and to doubts about preservation of the antigens in the tissues from normal human skin, we could not highlight a clear difference in TRIP expression between the different tissues. In conclusion, further analyses are needed on new RNA samples (qPCR) and on better preserved FFPE tissues from normal skin (IHC) to assess TRIP relative expression in BCCs and SCCs versus normal human skin.

A catalogue of Primitive Scenario-Types : The First Step to the Automation of Learning Scenarios

Peer-reviewed

Bordetella pertussis - Vaccination and Strain Variation

Pertussis or whooping cough is a highly contagious vaccine-preventable disease of the human respiratory tract caused by the Bordetella pertussis bacteria. In Finland, pertussis vaccinations were started in 1952 leading to a dramatic decrease in the morbidity and mortality. In the late 1990s, the incidence of pertussis increased despite the high vaccination coverage. Strain variation has been connected to the re-emergence of pertussis in countries with long history of pertussis vaccination. In 2005, the pertussis vaccine and the vaccination schedule were changed in Finland. The molecular epidemiology and the strain variation of the B. pertussis isolates were examined in Finland and in countries with similar (France) and different (Sweden) vaccination history. Continuous evolution of the B. pertussis population in Finland was observed since the 1950s, and the recently circulating isolates were antigenically different from the vaccine strains. Comparison of the circulating isolates from Finland, France and Sweden did not refer to significant differences. Certain type of strains noticed in France already in 1994 mainly caused the recent epidemics in Sweden (1999) and in Finland (2003-4). On several occasions, a new type of strains first appeared in Sweden and some years later in Finland. The B. pertussis isolates from the infants were shown to be similar to those from the other age groups. It is suggested that the strains originate from the same reservoir among adolescents and adults. The strain variation does not seem to have a major effect on the morbidity among recently vaccinated individuals, but it might play a role among those who are in the waning phase of immunity. The incidence of pertussis in Finland has remained low since the change of the vaccination programme. This might be related to the epidemic nature of pertussis and the near future will show the real effectiveness of the new vaccination programme. At present, many infants are infected because they are too young to be immunised with the current schedule. New strategies or vaccines are needed to protect those who are the most vulnerable.

Importance of the embedding environment on the strain within small rings in siliceous materials

The effect of the local environment on the energetic strain within small (SiO)N rings (with N=2,3) in silica materials is investigated via periodic model systems employing density functional calculations. Through comparison of the energies of various nonterminated systems containing small rings in strained and relatively unstrained environments, with alpha quartz, we demonstrate how small ring strain is affected by the nature of the embedding environment. We compare our findings with numerous previously reported calculations, often predicting significantly different small-ring strain energies, leading to a critical assessment of methods of calculating accurate localized ring energies. The results have relevance for estimates of the strain-induced response (e.g., chemical, photo, and radio) of small silica rings, and the propensity for them to form in bulk glasses, thin films, and nanoclusters.

Organic carbon and nutrient (P, N) concentrations of water and sediment in several aquatic environment types of a Mediterranean coastal wetland (Empordà Wetlands, NE Iberian Peninsula)

Total sediment and water organic carbon and nutrient (nitrogen and phosphorus) concentrations of different environment types of a Mediterranean coastal wetland (temporary and brackish, temporary and freshwater, semi-permanent and brackish, and permanent and brackish basins) were analysed during two hydroperiods. A nitrogen limitation was found for both sediment and water. The total organic carbon concentration of the water was significantly related to the water level, which varies throughout the hydroperiods. In contrast, the total organic carbon concentration of the sediment was not related to water level. However, significant differences in total organic carbon of the sediment were found between hydroperiods. On the other hand, total organic carbon of the sediment varied spatially, being higher in temporary brackish basins with lower sand content, and lower in permanent and semi-permanent brackish basins with higher sand content

On the Rule of Mixtures for Predicting Stress-Softening and Residual Strain Effects in Biological Tissues and Biocompatible Materials

In this work, we use the rule of mixtures to develop an equivalent material model in which the total strain energy density is split into the isotropic part related to the matrix component and the anisotropic energy contribution related to the fiber effects. For the isotropic energy part, we select the amended non-Gaussian strain energy density model, while the energy fiber effects are added by considering the equivalent anisotropic volumetric fraction contribution, as well as the isotropized representation form of the eight-chain energy model that accounts for the material anisotropic effects. Furthermore, our proposed material model uses a phenomenological non-monotonous softening function that predicts stress softening effects and has an energy term, derived from the pseudo-elasticity theory, that accounts for residual strain deformations. The model’s theoretical predictions are compared with experimental data collected from human vaginal tissues, mice skin, poly(glycolide-co-caprolactone) (PGC25 3-0) and polypropylene suture materials and tracheal and brain human tissues. In all cases examined here, our equivalent material model closely follows stress-softening and residual strain effects exhibited by experimental data

Quantification of the bond-angle dispersion by Raman spectroscopy and the strain energy of amorphous silicon

A thorough critical analysis of the theoretical relationships between the bond-angle dispersion in a-Si, Δθ, and the width of the transverse optical Raman peak, Γ, is presented. It is shown that the discrepancies between them are drastically reduced when unified definitions for Δθ and Γ are used. This reduced dispersion in the predicted values of Δθ together with the broad agreement with the scarce direct determinations of Δθ is then used to analyze the strain energy in partially relaxed pure a-Si. It is concluded that defect annihilation does not contribute appreciably to the reduction of the a-Si energy during structural relaxation. In contrast, it can account for half of the crystallization energy, which can be as low as 7 kJ/mol in defect-free a-Si

Biochemical characterisation of lipase from a new strain of Bacillus sp. ITP-001

Lipases are characterised mainly by catalytic versatility and application in different industrial segments. The aim of this study was to biochemically characterise a lipase from a new strain of Bacillus sp. ITP-001. The isoelectric point and molecular mass were 3.12 and 54 kDa, respectively. The optima lipase activity was 276 U g-1 at pH 7.0 and a temperature of 80 ºC, showing greater stability at pH 5.0 and 37 ºC. Enzymatic activity was stimulated by various ions and pyridine, and inhibited by Cu+ and ethanol. The values of Km and v max were 105.26 mmol and 0.116 mmol min-1 g-1, respectively determined by the Eadie-Scatchard method.

Mosaic in Senna occidentalis in southern Brazil induced by a new strain of Soybean mosaic virus

Plants of Senna occidentalis (sin. Cassia occidentalis) with mosaic symptoms were collected near a soybean (Glycine max) field where some plants exhibited symptoms of mosaic and blistering. A preliminary examination of leaf tissue from diseased S. occidentalis by electron microscopy revealed the presence of pinwheel inclusions as well as long flexuous particles, indicating the presence of a potyvirus. Host range, serology, and amino acid sequence from this potyvirus were similar to those from other Brazilian isolates of Soybean mosaic virus (SMV). The 3'- terminal region of the genomic RNA was cloned and a cDNA sequence of 1.9 kb upstream of the poly (A) tract was determined. The sequence contains a single open reading frame and a 3'- non-translated region (NTR) of 259 bp. The nucleotide sequence of the CP gene of SMV-Soc was 98% identical to that of Brazilian isolates SMV-B, SMV-L, and SMV-FT10. The percentage of nucleotide identity of their 3'-NTR's was 91, 98, and 99% in relation to SMV-L, SMV-B, and SMV-FT10, respectively. In contrast to other Brazilian SMV isolates studied, SMV-Soc was able to infect sunflower (Helianthus annuus). Based on these results, the S. occidentalis isolate was identified as a new strain of SMV belonging to the SMV strain, group G5 and was named SMV-Soc. This is the first report of naturaly occurring SMV infecting plants of S. occidentalis in Brazil, adding this weed as a new source of SMV in the field.

National Library – Service Centre for All Types of Libraries in Finland

Kristiina Hormia-Poutasen esitys Jerusalemissa Israelin kansalliskirjastossa 8.9.2011