Protein dynamics from time resolved UV Raman spectroscopy

Raman spectroscopy can provide unique information on the evolution of structure in proteins over a wide range of time scales; the picosecond to millisecond range can be accessed with pump-probe techniques. Specific parts of the molecule are interrogated by tuning the probe laser to a resonant electronic transition, including the UV transitions of aromatic residues and of the peptide bond. Advances in laser technology have enabled the characterization of transient species at an unprecedented level of structural detail. Applications to protein unfolding and allostery are reviewed.     

Biotin and Zn2+ Increase Xylitol Production by Candida tropicalis

In this study, the medium requirements to increase the production of xylitol by using Candida tropicalis (CT) have been investigated. The technique of single addition or omission of medium components was applied to determine the nutritional requirements. The addition of amino acids such as Asp, Glu, Gln, Asn, Thr, and Gly had no significant effect on CT growth. However, in the absence of other metal ions, there was a higher concentration of cell growth and xylitol production when only Zn²⁺ was present in the medium. The analysis of various vitamins unveiled that biotin and thiamine were the only vitamins required for the growth of CT. Surprisingly, when only biotin was present in the medium as a vitamin, there was less growth of CT than when the medium was complete, but the amount of xylitol released was significantly higher. Overall, this study will increase the xylitol production using the single omission or addtion technique.     

Cost-Effectiveness Analysis of Endoscopic Ultrasound versus Magnetic Resonance Cholangiopancreatography in Patients with Suspected Common Bile Duct Stones

Background

Patients with suspected common bile duct (CBD) stones are often diagnosed using endoscopic retrograde cholangiopancreatography (ERCP), an invasive procedure with risk of significant complications. Using endoscopic ultrasound (EUS) or Magnetic Resonance CholangioPancreatography (MRCP) first to detect CBD stones can reduce the risk of unnecessary procedures, cut complications and may save costs.

Aim

This study sought to compare the cost-effectiveness of initial EUS or MRCP in patients with suspected CBD stones.

Methods

This study is a model based cost-utility analysis estimating mean costs and quality-adjusted life years (QALYs) per patient from the perspective of the UK National Health Service (NHS) over a 1 year time horizon. A decision tree model was constructed and populated with probabilities, outcomes and cost data from published sources, including one-way and probabilistic sensitivity analyses.

Results

Using MRCP to select patients for ERCP was less costly than using EUS to select patients or proceeding directly to ERCP ($1299 versus $1753 and $1781, respectively), with similar QALYs accruing to each option (0.998, 0.998 and 0.997 for EUS, MRCP and direct ERCP, respectively). Initial MRCP was the most cost-effective option with the highest monetary net benefit, and this result was not sensitive to model parameters. MRCP had a 61% probability of being cost-effective at $29,000, the maximum willingness to pay for a QALY commonly used in the UK.

Conclusion

From the perspective of the UK NHS, MRCP was the most cost-effective test in the diagnosis of CBD stones.     

Application of artificial neural network model for the development of optimized complex medium for phenol degradation using <Emphasis Type="Italic">Pseudomonas pictorum</Emphasis> (NICM 2074)

Biodegradation of phenol using Pseudomonas pictorum (NICM 2074) a potential biodegradant of phenol was investigated for its degrading potential under different operating conditions. The neural network input parameter set consisted of the same set of four levels of maltose (0.025, 0.05, 0.075 g/l), phosphate (3, 12.5, 22 g/l), pH (7, 8, 9) and temperature (30°C, 32°C, 34°C) on phenol degradation was investigated and a Artificial Neural Network (ANN) model was developed to predict the extent of degradation. The learning, recall and generalization characteristic of neural networks was studied using phenol degradation system data. The efficiency of the model generated by the ANN, was tested and compared with the results obtained from an established second order polynomial multiple regression analysis (MRA). Further, the two models (ANN and MRA) were used to predict the percentage of degradation of phenol for blind test data. Performance of both the models were validated in the cases of training and test data, ANN was recommended based on the following higher coefficient of determination R ²; lower standard error of residuals and lower mean absolute percentage deviation.     

Biosorption of Zn(II) on the different Ca-alginate beads from aqueous solution

The performance of a new biosorbent system, consisting of a fungal biomass immobilized within an orange peel cellulose absorbent matrix, for the removal of Zn(2+) heavy metal ions from an aqueous solution was tested. The amount of Zn(II) ion sorption by the beads was as follows; orange peel cellulose with Phanerochaete chrysosporium immobilized Ca-alginate beads (OPCFCA) (168.61 mg/g) > orange peel cellulose immobilized Ca-alginate beads (OPCCA) (147.06 mg/g) > P. chrysosporium (F) (125.0 mg/g) > orange peel cellulose (OPC) (108.70 mg/g) > plain Ca-alginate bead (PCA) (98.26 mg/g). The Zn(2+) concentration was 100 to 1000 mg/L. The widely used Langmuir and Freundlich isotherm models were utilized to describe the biosorption equilibrium process. The isotherm parameters were estimated using linear and non-linear regression analysis. The Box-Behnken model was found to be in close agreement with the experimental values, as indicated by the correlation coefficient value of 0.9999.     

In-Silico and In-Vitro Analysis of Human SOS1 Protein Causing Noonan Syndrome - A Novel Approach to Explore the Molecular Pathways

AimsPerform in-silico analysis of human SOS1 mutations to elucidate their pathogenic role in Noonan syndrome (NS).BackgroundNS is an autosomal dominant genetic disorder caused by single nucleotide mutation in PTPN11, SOS1, RAF1, and KRAS genes. NS is thought to affect approximately 1 in 1000. NS patients suffer different pathogenic effects depending on the mutations they carry. Analysis of the mutations would be a promising predictor in identifying the pathogenic effect of NS.MethodsWe performed computational analysis of the SOS1 gene to identify the pathogenic nonsynonymous single nucleotide polymorphisms (nsSNPs) th a t cause NS. SOS1 variants were retrieved from the SNP database (dbSNP) and analyzed by in-silico tools I-Mutant, iPTREESTAB, and MutPred to elucidate their structural and functional characteristics.ResultsWe found that 11 nsSNPs of SOS1 that were linked to NS. 3D modeling of the wild-type and the 11 nsSNPs of SOS1 showed that SOS1 interacts with cardiac proteins GATA4, TNNT2, and ACTN2. We also found that GRB2 and HRAS act as intermediate molecules between SOS1 and cardiac proteins. Our in-silico analysis findings were further validated using induced cardiomyocytes (iCMCs) derived from NS patients carrying SOS1 gene variant c.1654A>G (NSiCMCs) and compared to control human skin fibroblast-derived iCMCs (C-iCMCs). Our in vitro data confirmed that the SOS1, GRB2 and HRAS gene expressions as well as the activated ERK protein, were significantly decreased in NS-iCMCs when compared to C-iCMCs.ConclusionThis is the first in-silico and in vitro study demonstrating that 11 nsSNPs of SOS1 play deleterious pathogenic roles in causing NS.     

Efficient solubilization buffers for two-dimensional gel electrophoresis of acidic and basic proteins extracted from wheat seeds

Plant tissues are made up of a broad range of proteins with a variety of properties. After extraction, solubilization of a diverse range of plant proteins for efficient proteomic analysis using two-dimensional electrophoresis is a challenging process. We tested the efficiency of 12 solubilization buffers in dissolving acidic and basic proteins extracted from mature seeds of wheat. The buffer containing two chaotropes (urea and thiourea), two detergents (3-[(3-cholamidopropyl) dimethyl-ammonio]-1-propane-sulfonate and N-decyl-N,N-dimethyl-3-ammonio-1-propane-sulfonate), two reducing agents (dithiothreitol and tris (2-carboxyethyl) phosphine hydrochloride) and two types of carrier ampholytes (BioLyte pH 4-6 and pH 3-10) solubilized the most acidic proteins in the pH range between 4 and 7. The buffer made up of urea, thiourea, 3-[(3-cholamidopropyl) dimethyl-ammonio]-1-propane-sulfonate, DeStreak reagent (Amersham Biosciences, Uppsala, Sweden) and immobilized pH gradient buffer, pH 6-11 (Amersham Biosciences) solubilized the most basic proteins in the pH range between 6 and 11. These two buffers produced two-dimensional gels with high resolution, superior quality and maximum number of detectable protein (1425 acidic protein and 897 basic protein) spots.     

Genetic inactivation of the allograft inflammatory factor‐1 locus

Allograft inflammatory factor‐1 (Aif‐1) is a 17 kDa EF hand motif‐bearing protein expressed primarily in developing spermatids and cells of monocyte/macrophage lineage. Increased Aif‐1 expression has been identified in clinically important conditions, including rheumatoid arthritis, systemic sclerosis, endometriosis, and transplant‐associated arteriosclerosis. Largely similar gene products arising from the same locus are known as ionized Ca²⁺ binding adapter‐1 (Iba1), microglial response factor‐1 (MRF1), and daintain; Iba1 in particular has emerged as a histologic marker of microglia and their activation in pathologic CNS conditions, including the response to facial nerve axotomy and stroke, uveitis, and experimental autoimmune neuritis and encephalomyelitis. Nevertheless, how aif‐1 gene products affect cellular function is only partly understood, and the physiologic significance of these products for male fertility, immune system development, and inflammation has not been described. To permit such investigations, we generated a mouse line with targeted deletion of the coding regions of the aif‐1 gene. Here we report that mice lacking Aif‐1 breed well and show normal post‐natal growth, but show resistance to disease in a model of collagen‐induced arthritis. We anticipate that these mice will be useful for studies of Aif‐1 function in a variety of immune and inflammatory disease models. genesis 51:734–740. © 2013 Wiley Periodicals, Inc.