Ovarian cancer detection by logical analysis of proteomic data

A new type of efficient and accurate proteomic ovarian cancer diagnosis systems is proposed. The system is developed using the combinatorics and optimization-based methodology of logical analysis of data (LAD) to the Ovarian Dataset 8-7-02 (http://clinicalproteomics.steem.com), which updates the one used by Petricoin et al. in The Lancet 2002, 359, 572-577. This mass spectroscopy-generated dataset contains expression profiles of 15 154 peptides defined by their mass/charge ratios (m/z) in serum of 162 ovarian cancer and 91 control cases. Several fully reproducible models using only 7-9 of the 15 154 peptides were constructed, and shown in multiple cross-validation tests (k-folding and leave-one-out) to provide sensitivities and specificities of up to 100%. A special diagnostic system for stage I ovarian cancer patients is shown to have similarly high accuracy. Other results: (i) expressions of peptides with relatively low m/z values in the dataset are shown to be better at distinguishing ovarian cancer cases from controls than those with higher m/z values; (ii) two large groups of patients with a high degree of similarities among their formal (mathematical) profiles are detected; (iii) several peptides with a blocking or promoting effect on ovarian cancer are identified.     

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

The helical hairpin is one of the most ubiquitous and elementary secondary structural motifs in nucleic acids, capable of serving functional roles and participating in long-range tertiary contacts. Yet the self-assembly of these structures has not been well-characterized at the atomic level. With this in mind, the dynamics of nucleic acid hairpin formation and disruption have been studied using a novel computational tool: large-scale, parallel, atomistic molecular dynamics simulation employing an inhomogeneous distributed computer consisting of more than 40,000 processors. Using multiple methodologies, over 500 micro s of atomistic simulation time has been collected for a large ensemble of hairpins (sequence 5'-GGGC[GCAA]GCCU-3'), allowing characterization of rare events not previously observable in simulation. From uncoupled ensemble dynamics simulations in unperturbed folding conditions, we report on 1), competing pathways between the folded and unfolded regions of the conformational space; 2), observed nonnative stacking and basepairing traps; and 3), a helix unwinding-rewinding mode that is differentiated from the unfolding and folding dynamics. A heterogeneous transition state ensemble is characterized structurally through calculations of conformer-specific folding probabilities and a multiplexed replica exchange stochastic dynamics algorithm is used to derive an approximate folding landscape. A comparison between the observed folding mechanism and that of a peptide beta-hairpin analog suggests that although native topology defines the character of the folding landscape, the statistical weighting of potential folding pathways is determined by the chemical nature of the polymer.     

Proximal Tubule Dysfunction Is Associated with Podocyte Damage Biomarkers Nephrin and Vascular Endothelial Growth Factor in Type 2 Diabetes Mellitus Patients: A Cross-Sectional Study

Background

There is an ongoing debate as to whether early diabetic nephropathy in Type 2 diabetes mellitus may be attributed to the glomerulus or to the proximal tubule. Urinary excretion of nephrin and vascular endothelial growth factor may increase even in the normoalbuminuria stage. In the course of diabetic nephropathy, the proximal tubule may be involved in the uptake of urinary nephrin and vascular endothelial growth factor.

Materials and Methods

Two groups of consecutive Type 2 diabetes mellitus outpatients (38 normo-, 32 microalbuminuric) and 21 healthy subjects were enrolled in a cross-sectional study and evaluated concerning the relation of proximal tubule dysfunction with the podocyte biomarkers excretion, assessed by ELISA methods. The impact of advanced glycation end-products on this relation was also queried.

Results

Urinary alpha₁-microglobulin and kidney injury molecule-1 correlated with urinary albumin:creatinine ratio (R² = 0.269; p<0.001; R² = 0.125; p<0.001), nephrinuria (R² = 0.529; p<0.001; R² = 0.203; p<0.001), urinary vascular endothelial growth factor (R² = 0.709; p<0.001; R² = 0.360; p<0.001), urinary advanced glycation end-products (R² = 0.578; p<0.001; R² = 0.405; p<0.001), serum cystatin C (R² = 0.130; p<0.001; R² = 0.128; p<0.001), and glomerular filtration rate (R² = 0.167; p<0.001; R² = 0.166; p<0.001); nephrinuria and urinary vascular endothelial growth factor correlated with urinary albumin:creatinine ratio (R² = 0.498; p<0.001; R² = 0.227; p<0.001), urinary advanced glycation end-products (R² = 0.251; p<0.001; R² = 0.308; p<0.001), serum cystatin C (R² = 0.157; p<0.001; R² = 0.226; p<0.001), and glomerular filtration rate (R² = 0.087; p = 0.007; R² = 0.218; p<0.001).

Conclusions

In Type 2 diabetes mellitus there is an association of proximal tubule dysfunction with podocyte damage biomarkers, even in the normoalbuminuria stage. This observation suggests a potential role of the proximal tubule in urinary nephrin and urinary vascular endothelial growth factor processing in early diabetic nephropathy, a fact which could be related to advanced glycation end-products intervention. Podocyte damage and proximal tubule dysfunction biomarkers could be validated as a practical approach to the diagnosis of early diabetic nephropathy by further studies on larger cohorts.     

Sendai virus vectors as an emerging negative-strand RNA viral vector system

The power to manipulate the genome of negative-strand RNA viruses, including the insertion of additional non-viral genes, has led to the development of a new class of viral vectors for gene transfer approaches. The murine parainfluenza virus type I, or Sendai virus (SeV), has emerged as a prototype virus of this vector group, being employed in numerous in vitro as well as animal studies over the last few years. Extraordinary features of SeV are the remarkably brief contact time that is necessary for cellular uptake, a strong but adjustable expression of foreign genes, efficient infection in the respiratory tract despite a mucus layer, transduction of target cells being independent of the cell cycle, and an exclusively cytoplasmic replication cycle without any risk of chromosomal integration. In this review we describe the current knowledge of Sendai virus vector (SeVV) development as well as the results of first-generation vector applications under both in vitro and in vivo conditions. So far, Sendai virus vectors have been identified to be a highly efficient transduction tool for a broad range of different tissues and applications. Future directions in vector design and development are discussed.     

A new pearleye (Teleostei,Aulopiformes) species from the Oligocene of Romania

A new pearleye species of the alepisauroid family Scopelarchidae, Scopelarchoides neamticus sp. nov., is described herein based on two specimens from the Oligocene Lower Dysodilic Shales Formation, cropping out in the Pietricica Mountain, Romanian Eastern Carpathians. The new species described herein exhibits a unique combination of features (including head length about 25% of SL; coracoid remarkably expanded; both preorbital and postorbital lengths larger than orbit diameter; 50 or 51 vertebrae; dorsal fin with nine or ten rays; anal-fin with 28 rays; length of anal fin base about 30% of SL; preanal distance almost 60% of SL; pelvic fin insertion located just under the second dorsal fin ray; pectoral fins only slightly longer than pelvic fins; caudal fin with 19 principal rays plus 14 upper and 13 lower procurrent rays) that justifies its recognition as a new species of the genus Scopelarchoides. Both morphological and meristic features suggest a certain degree of similarity between S. neamticus sp. nov. and the extant species Scopelarchoides signifer. The fossils of the new Oligocene species described herein represent the oldest known skeletal record of Scopelarchidae.     

N-Glycosylation Determines the Abundance of the Transient Receptor Potential Channel TRPP2

Glycosylation plays a critical role in the biogenesis and function of membrane proteins. Transient receptor potential channel TRPP2 is a nonselective cation channel that is mutated in autosomal dominant polycystic kidney disease. TRPP2 has been shown to be heavily N-glycosylated, but the glycosylation sites and the biological role of N-linked glycosylation have not been investigated. Here we show, using a combination of mass spectrometry and biochemical approaches, that native TRPP2 is glycosylated at five asparagines in the first extracellular loop. Glycosylation is required for the efficient biogenesis of TRPP2 because mutations of the glycosylated asparagines result in strongly decreased protein expression of the ion channel. Wild-type and N-glycosylation-deficient TRPP2 is degraded in lysosomes, as shown by increased TRPP2 protein levels upon chemical inhibition of lysosomal degradation. In addition, using pharmacological and genetic approaches, we demonstrate that glucosidase II (GII) mediates glycan trimming of TRPP2. The non-catalytic β subunit of glucosidase II (GIIβ) is encoded by PRKCSH, one of the genes causing autosomal dominant polycystic liver disease (ADPLD). The impaired GIIβ-dependent glucose trimming of TRPP2 glycosylation in ADPLD may explain the decreased TRPP2 protein expression in Prkcsh^−/− mice and the genetic interaction observed between TRPP2 and PRKCSH in ADPLD. These results highlight the biological importance of N-linked glycosylation and GII-mediated glycan trimming in the control of biogenesis and stability of TRPP2.     

Serological survey of Neospora caninum infection in cattle herds from Western Romania

Serum samples from 376 randomly selected adult cattle, from 25 farms located in 3 counties (Arad, Bihor, and Timi?) from western Romania, were sampled for Neospora caninum antibodies using a commercial ELISA-kit. Seroprevalence values and risk factors for neosporosis (cow age, breed, herd size, farming system, previous abortion, and number of farm dogs) were examined using a generalized linear mixed model with a binomial distribution. Overall, the seroprevalence of N. caninum was 27.7% (104/376) with a prevalence of 27.9% (24/86) in Arad, 26.9% (25/93) in Bihor, and 27.9% (55/197) in Timi?. Of 25 cattle herds, 23 were seropositive with a prevalence ranging from 10.0 to 52.2%. No correlation was found between N. caninum seropositivity and age, breed, herd size, breeding system, and previous abortion. The number of farm dogs was the only factor (P(Wald) = 0.03) positively associated with seroprevalence in cows and can be considered the risk factor in the acquiring of infection. The present work is the first regarding serological evidence of N. caninum infection in cattle from western Romania.     

Identification of Salt Stress Biomarkers in Romanian Carpathian Populations of Picea abies (L.) Karst.

The Norway spruce (Picea abies), the most important tree species in European forests, is relatively sensitive to salt and does not grow in natural saline environments. Yet many trees are actually exposed to salt stress due to the common practice of de-icing of mountain roads in winter, using large amounts of NaCl. To help develop strategies for an appropriate use of reproductive seed material on reforestation sites, ensuring better chances of seedling survival in salt-affected areas, we have studied the responses of young spruce seedlings to salt treatments. The specific aim of the work was to identify the optimal salt stress biomarkers in Picea abies, using as experimental material seedlings obtained by germination of seeds with origin in seven populations from the Romanian Carpathian Mountains. These responses included general, conserved reactions such as the accumulation of ions and different osmolytes in the seedlings needles, reduction in photosynthetic pigments levels, or activation of antioxidant systems. Although changes in the contents of different compounds involved in these reactions can be associated to the degree of stress affecting the plants, we propose that the (decreasing) levels of total phenolics or total carotenoids and the (increasing) levels of Na⁺ or K⁺ ions in Picea abies needles, should be considered as the most reliable and useful biomarkers for salt stress in this species. They all show very high correlation with the intensity of salt stress, independently of the genetic background of the seeds parental population, and relatively easy, quantitative assays are available to determine their concentrations, requiring simple equipment and little amount of plant material.