Effect of feeding habits of fish on the characteristics of collagenolytic proteases isolated from the visceral waste.

In this study, influence of feeding habits of fish on the activity of collagenolytic proteases (CP) has been investigated. CP from the visceral waste of freshwater fish (Pangas, Rohu and Common carp) of different feeding habits was isolated and partially purified by 2-steps, (NH4)2SO4 fractionation and dialysis. Enzymatic activity and purification fold was determined in each step. The molecular mass of the enzymes were close to that of serine collagenases. Enzyme was assayed for temperature and pH optima, effect of sodium chloride and inhibitors. Optimum temperature and pH was 40 °C and 7-8 respectively. Soybean trypsin inhibitor inhibited the enzyme activity, whereas, EDTA exerted no effect, led to confirmation of serine collagenases. CP of carnivore was more active over a wide range of temperature and pH compared to herbivore and omnivore. The study revealed that the feeding habit of fish play decides the optimal physiological conditions for maximum activity of CP.

Isolation, identification and characterization of Staphylococcus sp. from Indian ethnic fermented fish product.

Staphylococci from Sheedal of Northeast India was isolated, identified and characterized. All the isolated staphylococci were found to be coagulase negative. Based on the rpoB gene sequences followed by analysis using NCBI-BLAST software, seven species of Staphylococcus namely, S. piscifermentans, S. condimenti, S. arlettae, S. sciuri, S. warneri, S. nepalensis and S. hominis were recognized. Phylogenetic analyses revealed three major cluster groups. All the seven Staphylococcus showed their NaCl tolerance from 2 to 8%. No species was able to grow at 55°C. Except S. arlettae and S. sciuri, all the isolated staphylococcal species exhibited growth at pH 4-8. No isolated species was able to ferment mannitol, sucrose and arabinose. All the species exhibited moderate to maximum proteolytic and lipolytic activities. All the seven species were found to be sensitive to the antibiotics, namely, erythromycin, norfloxacin, ampicillin, streptomycin and vancomycin, whereas all were resistant to co-trimoxazole. Only S. piscifermentans was found antagonist to Salmonella enterica, Escherichia coli and Bacillus subtilis, although the clear zone was minimal. All the staphylococcal species except S. arlettae and S. sciuri exhibited hydrophobicity ranging from 25 to 66%. The observed characteristics of isolated Staphylococci from Sheedal revealed their role in fish fermentation.

Quality characteristics of fortified silver carp surimi with soluble dietary fiber: Effect of apple pectin and konjac glucomannan.

The study focused on assessing quality parameters of the surimi incorporated with soluble dietary fibers apple pectin and konjac glucomannan at different levels. The results showed that apple pectin at 0.025% and konjac glucomannan at a 2% level exhibited improved gel-forming ability significantly (p < 0.05). SDS- PAGE revealed high molecular weight protein crosslinks in apple pectin treated surimi gels and disappearance of myosin bands in konjac glucomannan treated surimi gels. The water holding capacity of surimi was the highest when 0.075 g/100 g of apple pectin was added. Konjac glucomannan treated gels exhibited superior whiteness values. The analysis of soluble protein revealed that hydrophobic bonds increased in both the treatments. The hardness values of pectin gels enhanced as the level increased. Other TPA parameters are shown an inconsistent trend. It can be demonstrated that the incorporation of apple pectin and konjac glucomannan at a level of 0.025 and 2.0% may be a novel strategy to improve the gel strength of the surimi.

Physical characterization of polyethylene glycols by thermal analytical technique and the effect of humidity and molecular weight.

Polyethylene glycols (PEGs) are well known as excipients in tablet dosage formulations. PEGs are generally known to be inert and have very few interactions with other components in the solid dosage forms. However, the physical nature of PEGs and how they affect the disintegration of tablets is not very well understood for the different molecular weights of PEGs. The knowledge of the effect of molecular weight of PEGs on their physical properties and the effect of humidity on the physical properties of PEGs are important parameters for the choice of a PEG to be acceptable as an excipient in pharmaceutical formulations. This study was done to determine the precision of the DSC physical properties for a wide range of PEGs with varying molecular weights from 194 to 23000 daltons. Nine different molecular weights of PEGs were examined in a DSC controlled Heat-Cool-Heat-Cool-Heat (HCHCH) cycle and the observed reproducible values of melting temperature, heat of fusion, crystallization temperature and the heat of crystallization were compared with values obtained from the literature and the observed percent crystallinity was again cross-checked by X-ray Diffraction (XRD) studies. The comparison values indicated acceptable precision. This study was also done to check the effect of humidity on the DSC physical properties for the entire range of PEGs. The results indicated that humidity probably has a higher effect on the physical properties of the low molecular weight PEGs as compared to the high molecular weight PEGs.

Aggregation of Microtubule Binding Repeats of Tau Protein is Promoted by Cu2.

Understanding the factors that give rise to tau aggregation and reactive oxygen species (ROS) is the key aspect in Alzheimer's disease pathogenesis. Microtubule (MT) binding repeats of tau protein were suggested to play a critical role in tau aggregation. Here, we show that the interaction of Cu2+ with full-length MT binding repeats R1-R4 leads to the aggregation, and a Cys-based redox chemistry is critically involved in tau aggregation leading to disulfide-bridge dimerization of R2 and R3 and further aggregation into a fibrillar structure. Notably, ascorbate and glutathione, the most abundant antioxidants in neurons, cannot prevent the effect of Cu2+ on R2 and R3 aggregation. Detailed ESI-MS and NMR experiments demonstrate the interaction of Cu2+ with MT binding repeats. We show that redox activity of copper increases when bound to the MT repeats leading to ROS formation, which significantly contribute to cellular damage and neuron death. Results presented here provide new insights into the molecular mechanism of tau aggregation and ROS formation and suggest a new target domain for tau aggregation inhibitors.

A Gene Expression Classifier from Whole Blood Distinguishes Benign from Malignant Lung Nodules Detected by Low-Dose CT.

Low-dose CT (LDCT) is widely accepted as the preferred method for detecting pulmonary nodules. However, the determination of whether a nodule is benign or malignant involves either repeated scans or invasive procedures that sample the lung tissue. Noninvasive methods to assess these nodules are needed to reduce unnecessary invasive tests. In this study, we have developed a pulmonary nodule classifier (PNC) using RNA from whole blood collected in RNA-stabilizing PAXgene tubes that addresses this need. Samples were prospectively collected from high-risk and incidental subjects with a positive lung CT scan. A total of 821 samples from 5 clinical sites were analyzed. Malignant samples were predominantly stage 1 by pathologic diagnosis and 97% of the benign samples were confirmed by 4 years of follow-up. A panel of diagnostic biomarkers was selected from a subset of the samples assayed on Illumina microarrays that achieved a ROC-AUC of 0.847 on independent validation. The microarray data were then used to design a biomarker panel of 559 gene probes to be validated on the clinically tested NanoString nCounter platform. RNA from 583 patients was used to assess and refine the NanoString PNC (nPNC), which was then validated on 158 independent samples (ROC-AUC = 0.825). The nPNC outperformed three clinical algorithms in discriminating malignant from benign pulmonary nodules ranging from 6-20 mm using just 41 diagnostic biomarkers. Overall, this platform provides an accurate, noninvasive method for the diagnosis of pulmonary nodules in patients with non-small cell lung cancer. SIGNIFICANCE: These findings describe a minimally invasive and clinically practical pulmonary nodule classifier that has good diagnostic ability at distinguishing benign from malignant pulmonary nodules.

Functional consequences of substitution of the active site (phospho)histidine residue of Escherichia coli succinyl-CoA synthetase.

Succinyl-CoA synthetase (EC 6.2.1.5, succinate:CoA ligase (ADP-forming] of Escherichia coli is an alpha 2 beta 2 tetramer, with the active site believed to be located at the point of contact between the two subunit types. It has been previously established that the reaction involves the intermediate participation of a phosphorylated enzyme form in the process of catalysis. The site of phosphorylation (His-246) and the binding sites for the substrates ADP and ATP are located in the alpha subunit, and the succinate and CoA binding sites are in beta. A mutant form of this enzyme, with the active site histidine residue replaced by aspartate, has been produced in large quantities and purified to homogeneity. This form appears to be indistinguishable from the native enzyme with respect to its subunit assembly, but has no ability to catalyze the overall reaction. As expected, the His-246 alpha----Asp mutant is incapable of undergoing phosphorylation. We have developed an assay based upon the arsenolysis of succinyl-CoA that effectively isolates the partial reaction that occurs in the portion of the active site contributed by the beta subunit; this reaction does not involve covalent participation of His-246 alpha. We have found that the His-246 alpha----Asp mutant is also devoid of activity in this arsenolysis reaction, indicating that an intact His-246 alpha is required for the establishment of the microenvironment in this portion of the active site that is required for the corresponding step of the overall reaction.

The subunits of succinyl-coenzyme A synthetase--function and assembly.

Succinyl-CoA synthetase is made up of two kinds of subunits, designated alpha and beta. The enzyme from Escherichia coli is an alpha 2 beta 2 tetramer (mol. mass. 142 kDa), whereas the mammalian mitochondrial species is an alpha beta dimer. By means of active enzyme centrifugation, we have shown that the active form of the bacterial enzyme is the tetramer even at very low assay concentrations, while the pig heart enzyme is a non-associating dimer over a wide concentration range. The E. coli enzyme shows distinct half-of-the-sites reactivity with respect to the phosphorylation of a histidine residue in the alpha-subunit that represents a step in catalysis. Many lines of evidence (hybrid enzyme formation, oxygen exchange kinetics, 31P-n.m.r. studies) suggest that co-operative interactions between alternatingly functional active sites on the two halves of the E. coli enzyme contribute to its catalytic efficacy. In further refining this model for catalysis, we have shown that the monothiophosphorylated E. coli enzyme does not catalyse exchange of 18O from the beta, gamma-bridge to the beta-non-bridge position of ATP, indicating that the enzyme does not undergo even transient bis-phosphorylation. As a first step in studying the in vivo synthesis and assembly of the enzyme in the mammalian mitochondrial matrix, we have cloned and sequenced a 900 bp cDNA fragment that encodes most of the alpha subunit of rat liver succinyl-CoA synthetase. The derived amino acid sequence shows an impressive degree of homology to that of the alpha subunit of the enzyme from E. coli. We have shown that the alpha subunit in rat liver is a discrete nuclear gene product, complete with cleavable signal sequence to specify mitochondrial targetting.

Evidence of two mechanisms of prostaglandin release in an in vitro model of muscle damage. Possible therapeutic implications.

In spite of recent progress, treatment of muscle disease based on specific gene therapy is not yet available. An alternative approach is to develop treatment which affords non-specific protection against general factors involved in cell damage. This approach is used effectively to prevent neuronal damage in experimental brain ischemia in animals and has been proposed for human trials. The most effective intervention is the use of mild (35 degrees C) hypothermia. An in vitro model to study muscle cell damage employs the rat epitrochlearis muscle exposed to low concentrations of 2:4-dinitrophenol, an uncoupler of oxidative phosphorylation. The efflux of prostaglandin E2 (PGE2) from the muscle is used as an indicator of muscle damage. We now show that there are two types of PGE2 release. "Basal" efflux gradually declines with decreasing temperatures and is not affected by removal of calcium from the medium. The efflux of PGE2 in response to metabolic stress is dependent on the presence of calcium and is abolished by mild hypothermia of 35 degrees C. The latter effect suggests that cell death is muscle and neurons have features in common and that muscle may be a useful tissue in which to investigate this phenomenon further.

The solubilization of platelet membrane-bound acetylcholinesterase and aryl acylamidase by exogenous or endogenous phosphatidylinositol specific phospholipase C.

Phosphatidylinositol specific phospholipase C from Staphylococcus aureus could solubilize acetylcholinesterase up to 55% from sheep platelets in the presence of ethylenediaminetetra acetic acid (EDTA). The endogenous phosphatidylinositol specific phospholipase C of platelets activated by deoxycholate (at 3-5 mM) could also solubilize the enzyme to a similar extent. The solubilized enzyme could be further purified to apparent homogeneity by affinity chromatography without the use of any detergents. It is suggested that phosphatidylinositol specific phospholipase C will be a useful tool in the solubilization of acetylcholinesterase from mammalian sources and its purification free of detergents. The present study also demonstrates the parallel behaviour of acetylcholinesterase and aryl acylamidase in platelets confirming their identity.

Effects of calcium channel antagonists on the release of prostaglandin E2 from metabolically stressed muscle.

Calcium influx plays a critical role in the activation of the arachidonic cascade in muscle damage. We examined the effects of L-type calcium channel antagonists on the release of prostaglandin E2 (PGE2), a bioactive metabolite of arachidonic acid metabolism, from skeletal muscle. The basal release of PGE2 was not affected by calcium channel inhibitors, such as nifedipine and verapamil. The release of PGE2 induced by dinitrophenol, an uncoupler of oxidative phosphorylation, was abolished by nifedipine and verapamil at 50 and 150 microM, respectively. It was not necessary to include the calcium channel blockers in the medium before or at the time of dinitrophenol stimulation to produce the effect on PGE2 release. The release of PGE2 was prevented for as long as calcium channel blockers were present in the medium after the dinitrophenol stress.

Serotonin-sensitive aryl acylamidase activity of platelet acetylcholinesterase.

Serotonin-sensitive aryl acylamidase (AAA, EC 3.5.1.13) was purified to apparent homogeneity from sheep platelets by affinity chromatography and it was shown to be associated with the platelet acetylcholinesterase (AChE, EC 3.1.1.7). The basis for the association of the two enzymes was the following. Both enzyme activities co-eluted from the affinity columns with constant ratios of specific activities and percentage recoveries. Both enzymes co-migrated on gel electrophoresis. Both enzymes co-eluted during sepharose 6B gel filtration. Potent inhibitors of AChE such as bis(4-allyldimethyl ammoniumphenyl) pentan-3-one dibromide (BW 284C51), neostigmine and eserine also inhibited AAA potently. Both enzymes lost significant activity on treatment with deoxycholate or taurodeoxycholate and the loss could be partly restored by a mixture of phospholipids. The platelet AAA was specifically inhibited by serotonin and to a lesser extent by tryptamine but not by several other amines. It was also inhibited by acetylcholine and several of its analogues and homologues. It is suggested that in the platelets the two enzymes (AAA and AChE) are probably identical.

Evidence of a temperature-sensitive step in the release of prostaglandin E2 in calcium ionophore-stimulated rat muscle.

Recent studies have shown that mild hypothermia (32-35 degrees C) confers striking protection against ischemic muscle and neuronal injuries, although the mechanisms are unknown. We previously demonstrated that the release of prostaglandin E2 (PGE2) from metabolically stressed muscles was dependent on calcium and was abolished at or below 35 degrees C. In this study, we examined the temperature response of the release of arachidonic acid (AA) and its cyclooxygenase metabolites, PGE2 and prostaglandin F2 alpha (PGF2 alpha) from rat skeletal muscle in the presence of calcium ionophore A23187, an agent that directly elevates intracellular calcium. Calcium ionophore markedly stimulated the release of AA, PGE2 and PGF2 alpha at 37 degrees C, as expected. Reducing the temperature to 35 degrees C and below sharply decreased PGE2 and PGF2 alpha release but not AA release. The activity of phospholipase A2 stimulated by calcium ionophore was unaffected when temperature of incubation was lowered from 37 to 32 degrees C. The results suggest that reducing temperature from 37 degrees C to 35 degrees C or below inhibits the conversion from free arachidonate to PGs in calcium ionophore-stimulated muscle.

A novel deletion mutation within the carboxyl terminus of the copper-transporting ATPase gene causes Wilson disease.

In patients with Wilson disease (WD), an autosomal recessive disorder, toxic accumulation of copper results in fatal liver disease and irreversible neuronal degeneration. ATP7B, the gene mutated in WD, contains 21 exons and encodes a copper-transporting ATPase. In this study, all exons of the ATP7B gene of nine WD patients were screened for alterations by conventional mutation detection enhancement (MDE) heteroduplex analysis, followed by direct sequencing of the regions that showed heteroduplex formation. For the first time, a novel deletion mutation (4193delC) in exon 21, causing a frameshift leading to premature truncation of the protein was detected in four of nine patients. The 4193delC removes several signals within the carboxyl terminal domain that may disrupt trafficking of ATP7B protein through trans-Golgi network at the cellular level.

Molecular analysis of the SMN and NAIP genes in Saudi spinal muscular atrophy patients.

In this study we examined the deletion of the SMN and NAIP genes in 14 Saudi families (16 patients and 38 relatives of the patients, including parents and siblings) and six healthy Saudi volunteers. The homozygous deletions of exons 7 and 8 of the telomeric SMN gene and exon 5 of the NAIP gene were found in seven out of eight spinal muscular atrophy (SMA) type-I patients. In seven SMA type-II patients, exons 7 and 8 of telomeric SMN were deleted in six cases and exon 5 of NAIP was deleted in three cases. Three patients with SMA diagnosis did not show either of the above deletions. All control Saudi volunteers and all but two family members of the patients had both normal SMN and NAIP genes. Our results show that the incidence of NAIP deletion is higher in the more severe SMA cases and the dual deletions of the SMN and NAIP genes are more common in Saudi SMA type-I patients compared to patients of other ethnic groups.

Ligand binding isotherm for DNA in the presence of supercoil-induced non-B form: a theoretical analysis.

A binding isotherm in the form of a modified McGhee-Von Hippel equation is proposed, on the basis of thermodynamical considerations, to include the non-cooperative binding of extended ligands to supercoiled DNA, where a stretch of non-B form may be present under superhelical stress. It is then studied, on the basis of a non-linear Scatchard plot, how the presence of an intercalating ligand can relax the supercoiled molecule and thus destabilise the non-B stretch, which may be recognised by the existence of a significant kink in the Scatchard plot.

Melting characteristics of highly supercoiled DNA.

The effect of high supercoil densities on the melting characteristics of a supercoiled DNA has been studied. It is found that although the melting temperature increases abruptly on converting a linear DNA merely into the relaxed circular form, it falls back substantially at high supercoil densities. It is further predicted, in such cases, that the number of melted base pairs should be significantly enhanced even at the physiological temperature, which may facilitate the binding of other molecules to the highly supercoiled DNA.

Sequence directed flexibility of DNA and the role of cross-strand hydrogen bonds.

Persistence length and torsional rigidity for different B-DNA sequences have been calculated by analysing crystal structure database. The values of these parameters for mixed sequence DNA are in good agreement with those estimated by others. Persistence lengths for the homopolymeric sequences, namely poly(dA).poly(dT) and poly(dG).poly(dC), are significantly large compared to those of others as expected from the inability of these sequences to form nucleosome under normal conditions. The heteropolymeric sequences poly(dA-dC).poly(dG-dT) and poly(dG-dC).poly(dG-dC), on the other hand, have smaller persistence lengths. This implies larger flexibility of the d(AC).d(GT), d(CA).d(TG), d(GC).d(GC) and d(CG).d(CG) doublets, some of which constitute the genetic disease forming triplet repeats d(CTG).d(CAG) and d(CGG).d(CCG). Thus it is expected that these triplet repeat sequences are also flexible and wrap around the histone octamer efficiently. Persistence length calculations also indicate larger flexibility for these triplet repeat sequences. Furthermore, our computations reveal that the rigidity of a given DNA sequence is controlled by its ability to form cross-strand bifurcated hydrogen bonds between the successive base pairs. Molecular orbital calculations suggest that these hydrogen bonds are generally extended with bond lengths around 3A.

Nucleosomal positioning and genetic divergence study based on DNA flexibility map.

Based on worm like chain model, DNA structural parameters--tilt, roll and rise, derived from crystallographic database have been used to determine the flexibility of DNA that regulates the nucleosomal translational positioning. Theoretically derived data has been compared to the experimental values available in loshikhes and Trifonov's database. The methodology has been extended to determine the flexibility of 18S rRNA genome in eukarya, where yeast shows a distinct difference when compared with mammals like human, mouse and rabbit.

A test of the bay-region mechanism in carcinogenesis for monomethyl benz[a]anthracenes in a self-consistent-field molecular orbital theory.

The relative carcinogenic activity of the isomeric monomethyl derivatives of benz[a]anthracene has been studied on the basis of their bay-region reactivity, and the subsequent ease of carbonium ion formation, as obtained from a suitable 'self-consistent-field' molecular orbital theory for the mobile pi-electrons. The predicted order of carcinogenic activity of these molecules is compared with the available experimental data.