The atRA-responsive gene neuron navigator 2 functions in neurite outgrowth and axonal elongation

Neuron navigator 2 (Nav2) was first identified as an all-trans retinoic acid (atRA)-responsive gene in human neuroblastoma cells (retinoic acid-induced in neuroblastoma 1, RAINB1) that extend neurites after exposure to atRA. It is structurally related to the Caenorhabditis elegans unc-53 gene that is required for cell migration and axonal outgrowth. To gain insight into NAV2 function, the full-length human protein was expressed in C. elegans unc-53 mutants under the control of a mechanosensory neuron promoter. Transgene expression of NAV2 rescued the defects in unc-53 mutant mechanosensory neuron elongation, indicating that Nav2 is an ortholog of unc-53. Using a loss-of-function approach, we also show that Nav2 induction is essential for atRA to induce neurite outgrowth in SH-SY5Y cells. The NAV2 protein is located both in the cell body and along the length of the growing neurites of SH-SY5Y cells in a pattern that closely mimics that of neurofilament and microtubule proteins. Transfection of Nav2 deletion constructs in Cos-1 cells reveals a region of the protein (aa 837-1065) that directs localization with the microtubule cytoskeleton. Collectively, this work supports a role for NAV2 in neurite outgrowth and axonal elongation and suggests this protein may act by facilitating interactions between microtubules and other proteins such as neurofilaments that are key players in the formation and stability of growing neurites.     

Development and Validation of a Risk Score for Predicting Death after Pneumonectomy

Pneumonectomy is associated with significant postoperative mortality. This study was undertaken to develop and validate a risk model of mortality following pneumonectomy. We reviewed our prospective database and identified 774 pneumonectomies from a total of 7792 consecutive anatomical lung resections in the years 2003 to 2010 (rate of pneumonectomy: 9.9%). Based on data from 542 pneumonectomies between 2003 and 2007 (i.e., the "discovery set"), a penalized multivariable logistic regression analysis was performed to identify preoperative risk factors. A risk model was developed and validated in an independent data set of 232 pneumonectomies that were performed between 2008 and 2010 (i.e., the "validation set"). Of the 542 patients in the discovery set (DS), 35 patients (6.5%) died after pneumonectomy during the same admission. We developed a risk prediction model for in-hospital mortality following pneumonectomy; that model included age, current alcohol use, coronary artery disease, preoperative leukocyte count and palliative indication as possible risk factors. The risk model was subsequently successfully validated in an independent data set (n = 232) in which 18 patients (7.8%) died following pneumonectomy. For the validation set, the sensitivity of the model was 53.3% (DS: 54.3%), the specificity was 88.0% (DS: 87.4%), the positive predictive value was 26.7% (DS: 22.9%) and the negative predictive value was 95.8% (DS: 96.5%). The Brier score was 0.062 (DS: 0.054). The prediction model is statistically valid and clinically relevant.     

Inhibition of dynamin‐2 confers endothelial barrier dysfunctions by attenuating nitric oxide production

Hypoxia induces barrier dysfunctions in endothelial cells. Nitric oxide is an autacoid signalling molecule that confers protection against hypoxia‐mediated barrier dysfunctions. Dyn‐2 (dynamin‐2), a large GTPase and a positive modulator of eNOS (endothelial nitric oxide synthase), plays an important role in maintaining vascular homeostasis. The present study aims to elucidate the role of dyn‐2 in hypoxia‐mediated leakiness of the endothelial monolayer in relation to redox milieu. Inhibition of dyn‐2 by transfecting the cells with K44A, a dominant negative construct of dyn‐2, elevated leakiness of the endothelial monolayer under hypoxia. Sodium nitroprusside (nitric oxide donor) and uric acid (peroxynitrite quencher) were used to evaluate the role of nitric oxide and peroxynitrite in maintaining endothelial barrier functions under hypoxia. Administration of nitric oxide and uric acid recovered hypoxia‐mediated leakiness of K44A‐overexpressed endothelial monolayer. Our study confirms that inhibition of dyn‐2 induces leakiness in the endothelial monolayer by increasing the load of peroxynitrite under hypoxia.     

Influence of alkali-treated cornsteep liquor containing medium on protein A production byStaphylococcus aureus

Staphylococcus aureus cultivated in liquid media containing untreated cornsteep liquor (CSL) and alkali-treated CSL produced similar biomass yields (6.5–6.9 g/L). However, contents of protein A in the biomass was 0.5% and 1.56% for untreated CSL and treated CSL, respectively. Addition of treated CSL at 20 g/L achieved optimal enhancement of protein A production (0.11 g/L). Probable factors associated in treated CSL for the enhanced protein A production are discussed.     

Studies on the breeding habits and development of the brood-pouch of a viviparous prosobranch; Melania scabra

Studie son the breeding habits and development of the brood-pouch of a freshwater prosobranch, Melania scabra, have revealed that the snail is ovoviviparous, showing parthenogenetic reproduction. The embryos complete their development in a special incubatory pouch called the brood-pouch or brood chamber, and hatch out in a form completely resembling that of the adult. The snail was found to be a continuous breeder, showing gravid condition throughout the year. General structure, development and functions of the brood-pouch were studied in detail. The brood-pouch was found to contain a slightly alkaline albuminous fluid with a pH 7.2, Qualitative and histochemical studies of the brood-pouch revealed the presence of glycogen, fat and protein as the major constituents. These probably play an important role in the nutrition of embryos.     

Cadmium reduces nitric oxide production by impairing phosphorylation of endothelial nitric oxide synthase.

Cadmium (Cd) perturbs vascular health and interferes with endothelial function. However, the effects of exposing endothelial cells to low doses of Cd on the production of nitric oxide (NO) are largely unknown. The objective of the present study was to evaluate these effects by using low levels of CdCl2 concentrations, ranging from 10 to 1000 nmol/L. Cd perturbations in endothelial function were studied by employing wound-healing and MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assays. The results suggest that a CdCl2 concentration of 100 nmol/L maximally attenuated NO production, cellular migration, and energy metabolism in endothelial cells. An egg yolk angiogenesis model was employed to study the effect of Cd exposure on angiogenesis. The results demonstrate that NO supplementation restored Cd-attenuated angiogenesis. Immunofluorescence, Western blot, and immuno-detection studies showed that low levels of Cd inhibit NO production in endothelial cells by blocking eNOS phosphorylation, which is possibly linked to processes involving endothelial function and dysfunction, including angiogenesis.     

Evaluation of Physical and Functional Protein-Protein Interaction Prediction Methods for Detecting Biological Pathways

Background

Cellular activities are governed by the physical and the functional interactions among several proteins involved in various biological pathways. With the availability of sequenced genomes and high-throughput experimental data one can identify genome-wide protein-protein interactions using various computational techniques. Comparative assessments of these techniques in predicting protein interactions have been frequently reported in the literature but not their ability to elucidate a particular biological pathway.

Methods

Towards the goal of understanding the prediction capabilities of interactions among the specific biological pathway proteins, we report the analyses of 14 biological pathways of Escherichia coli catalogued in KEGG database using five protein-protein functional linkage prediction methods. These methods are phylogenetic profiling, gene neighborhood, co-presence of orthologous genes in the same gene clusters, a mirrortree variant, and expression similarity.

Conclusions

Our results reveal that the prediction of metabolic pathway protein interactions continues to be a challenging task for all methods which possibly reflect flexible/independent evolutionary histories of these proteins. These methods have predicted functional associations of proteins involved in amino acids, nucleotide, glycans and vitamins & co-factors pathways slightly better than the random performance on carbohydrate, lipid and energy metabolism. We also make similar observations for interactions involved among the environmental information processing proteins. On the contrary, genetic information processing or specialized processes such as motility related protein-protein linkages that occur in the subset of organisms are predicted with comparable accuracy. Metabolic pathways are best predicted by using neighborhood of orthologous genes whereas phyletic pattern is good enough to reconstruct central dogma pathway protein interactions. We have also shown that the effective use of a particular prediction method depends on the pathway under investigation. In case one is not focused on specific pathway, gene expression similarity method is the best option.     

Validation of a blood protein signature for non-small cell lung cancer

Background

CT screening for lung cancer is effective in reducing mortality, but there are areas of concern, including a positive predictive value of 4% and development of interval cancers. A blood test that could manage these limitations would be useful, but development of such tests has been impaired by variations in blood collection that may lead to poor reproducibility across populations.

Results

Blood-based proteomic profiles were generated with SOMAscan technology, which measured 1033 proteins. First, preanalytic variability was evaluated with Sample Mapping Vectors (SMV), which are panels of proteins that detect confounders in protein levels related to sample collection. A subset of well collected serum samples not influenced by preanalytic variability was selected for discovery of lung cancer biomarkers. The impact of sample collection variation on these candidate markers was tested in the subset of samples with higher SMV scores so that the most robust markers could be used to create disease classifiers. The discovery sample set (n = 363) was from a multi-center study of 94 non-small cell lung cancer (NSCLC) cases and 269 long-term smokers and benign pulmonary nodule controls. The analysis resulted in a 7-marker panel with an AUC of 0.85 for all cases (68% adenocarcinoma, 32% squamous) and an AUC of 0.93 for squamous cell carcinoma in particular. This panel was validated by making blinded predictions in two independent cohorts (n = 138 in the first validation and n = 135 in the second). The model was recalibrated for a panel format prior to unblinding the second cohort. The AUCs overall were 0.81 and 0.77, and for squamous cell tumors alone were 0.89 and 0.87. The estimated negative predictive value for a 15% disease prevalence was 93% overall and 99% for squamous lung tumors. The proteins in the classifier function in destruction of the extracellular matrix, metabolic homeostasis and inflammation.

Conclusions

Selecting biomarkers resistant to sample processing variation led to robust lung cancer biomarkers that performed consistently in independent validations. They form a sensitive signature for detection of lung cancer, especially squamous cell histology. This non-invasive test could be used to improve the positive predictive value of CT screening, with the potential to avoid invasive evaluation of nonmalignant pulmonary nodules.     

Embryology and development of a freshwater prosobranch,Melania scabra

Embryology and development of the snail, Melania scabra was studied. The embryos complete their development in a special incubatory pouch called the broodpouch and hatch out in a form completely resembling that of the adult. The embryonic development of the snail represents specialized features like precocious development of the statocyst, presence of a well developed velar retractor muscle and torsion.