Prediction of enzymes and non-enzymes from protein sequences based on sequence derived features and PSSM matrix using artificial neural network

The problem of predicting the enzymes and non-enzymes from the protein sequence information is still an open problem in bioinformatics. It is further becoming more important as the number of sequenced information grows exponentially over time. We describe a novel approach for predicting the enzymes and non-enzymes from its amino-acid sequence using artificial neural network (ANN). Using 61 sequence derived features alone we have been able to achieve 79 percent correct prediction of enzymes/non-enzymes (in the set of 660 proteins). For the complete set of 61 parameters using 5-fold cross-validated classification, ANN model reveal a superior model (accuracy = 78.79 plus or minus 6.86 percent, Q(pred) = 74.734 plus or minus 17.08 percent, sensitivity = 84.48 plus or minus 6.73 percent, specificity = 77.13 plus or minus 13.39 percent). The second module of ANN is based on PSSM matrix. Using the same 5-fold cross-validation set, this ANN model predicts enzymes/non-enzymes with more accuracy (accuracy = 80.37 plus or minus 6.59 percent, Q(pred) = 67.466 plus or minus 12.41 percent, sensitivity = 0.9070 plus or minus 3.37 percent, specificity = 74.66 plus or minus 7.17 percent).     

N-(1,3-Diaryl-3-oxopropyl)amides as a new template for xanthine oxidase inhibitors

A series of forty two N-(1,3-diaryl-3-oxopropyl)amides were synthesized via an efficient, modified Dakin-West reaction and were evaluated for in vitro xanthine oxidase inhibitory activity for the first time. Structure-activity relationship analyses have been presented. Selected active xanthine oxidase inhibitors (3r, 3s, and 3zh) were assessed in vivo to study their anti-hyperuricemic effect in potassium oxonate induced hyperuricemic mice model. Compound 3s emerged as the most potent xanthine oxidase inhibitor (IC(50)=2.45 μM) as well as the most potent anti-hyperuricemic agent. The basis of significant inhibition of xanthine oxidase by 3s was rationalized by its molecular docking into catalytic site of xanthine oxidase.     

In vitro fibrolytic potential of anaerobic rumen fungi from ruminants and non-ruminant herbivores

In the present study, anaerobic fungi were isolated from different ruminants and non-ruminants; i.e., cattle, buffalo, sheep, goats, wild bluebulls, elephants, deer, and zebras; and were identified as Anaeromyces, Orpinomyces, Caecomyces, Piromyces, and Neocallimastix sp., based on their morphological characteristics. These isolates possessed significant in vitro hydrolytic enzyme activities; however, an isolate of Caecomyces sp. from elephant was found to exhibit maximum activity, i.e., filter paper cellulase (Fpase; 21.4 mIU/ml), carboxymethyl cellulose (CMCase; 15.1 mIU/ml), cellobiase (37.4 mIU/ml), and xylanase (26.0 mIU/ml). Besides, this isolate also showed the significantly highest ability to digest plant cell-wall contents in vitro. The in vitro dry matter digestibility increased from 45.1 to 48.9% after 48 h of incubation, and the plant cell-wall contents, in terms of neutral detergent fiber and acid detergent fiber, decreased from 64.2 to 61.3% and from 31.3 to 29.6%, respectively. These results indicate that such fibrolytic ruminal fungal strains are prevalent in wild herbivores such as elephants, as well as in other ruminants and non-ruminants, and could be exploited as microbial feed additives for improved nutrition and productivity in domesticated ruminants.     

Upregulation of human mitochondrial NADH dehydrogenase subunit 5 in intestinal epithelial cells is modulated by Vibrio cholerae pathogenesis

Cholera still remains an important global predicament especially in India and other developing countries. Vibrio cholerae, the etiologic agent of cholera, colonizes the small intestine and produces an enterotoxin that is largely responsible for the watery diarrheal symptoms of the disease. Using RNA arbitrarily primed PCR, ND5 a mitochondria encoded subunit of complex I of the mitochondrial respiratory chain was found to be upregulated in the human intestinal epithelial cell line Int407 following exposure to V. cholerae. The upregulation of ND5 was not observed when Int407 was infected with Escherichia coli strains. Incubation with heat-killed V. cholerae or cholera toxin or culture supernatant also showed no such upregulation indicating the involvement of live bacteria in the process. Infection of the monolayer with aflagellate non-motile mutant of V. cholerae O395 showed a very significant (59-fold) downregulation of ND5. In contrast, a remarkable upregulation of ND5 expression (200-fold) was observed in a hyperadherent icmF insertion mutant with reduced motility. V. cholerae cheY4 null mutant defective in adherence and motility also resulted in significantly reduced levels of ND5 expression while mutant with the cheY4 gene duplicated showing increased adherence and motility resulted in increased expression of ND5. These results clearly indicate that both motility and adherence to intestinal epithelial cells are possible triggering factors contributing to ND5 mRNA expression by V. cholerae. Interestingly infection with insertion mutant in the gene coding for ToxR, the master regulator of virulence in V. cholerae resulted in significant downregulation of ND5 expression. However, infection with ctxA or toxT insertion mutants did not show any significant changes in ND5 expression compared to wild-type. Almost no expression of ND5 was observed in case of mutation in the gene coding for OmpU, a ToxR activated protein. Thus, infection of Int407 with virulence mutant strains of V. cholerae revealed that the ND5 expression is modulated by the virulence of V. cholerae in a ToxT independent manner. Although no difference in the mitochondrial copy number could be detected between infected and uninfected cells, the modulation of the expression of other mitochondrial genes were also observed. Incidentally, upon V. cholerae infection, complex I activity was found to increase about 3-folds after 6 h. This is the first report of alteration in mitochondrial gene expression upon infection of a non-invasive enteric bacterium like V. cholerae showing its modulation with adherence, motility and virulence of the organism.     

Data on the push–out bond strength of three different root canal treatment sealers

It is of interest to document data on the push – out bond strength of three different root canal treatment sealers such as MTA Fillapex (MTA based), AH plus (Epoxy Resin based) and Apexit plus (Calcium hydroxide based). Forty-five freshly extracted human maxillary central incisors with closed apices were selected randomly. All the teeth were sectioned at cement-enamel junction using a diamond disc before starting the root canal preparation to obtain root length of 12 mm. All teeth were instrumented using ProTaper rotary instruments. 5.25% sodium hypochlorite was used for irrigation between instrumentation followed by 17% EDTA, and final rinse by saline. Obturation procedures were done using the gutta-percha single cone technique. 45 roots were randomly assigned to 3 groups of 15 for obturation with gutta-percha cones and 1 of the 3 sealers (n=15). Group 1 = MTA Fillapex sealer + gutta-percha: Group 2 = AH plus sealer + gutta-percha:Group 3 = Apexit plus sealer + gutta-percha. The roots were sectioned horizontally to its canal into 3 sections: Coronal, Mid-root and Apical-thirds using a precision cutting machine, with a thickness of 3 mm. The specimens were subjected to push-out test using a universal testing machine that carried a plunger. The loading speed was 1mm/min until the dislodgment of the material occurred. The independent t- test was used to compare the mean scores among the study groups. The level of significance was set at 5% for all tests. After the push-out bond strength test, each sample was evaluated under stereomicroscope (40x) to determine the mode of failure and recorded as one of the following categories: adhesive, cohesive or mixed. The observations thus obtained were subjected to statistical analysis using Student - t test. AH Plus showed significantly higher values than MTA Fillapex and Apexit plus (p < 0.05). Amongst the push-out bond strength AH Plus sealer showed significant difference from MTA Fillapex and Apexit plus groups. There was no significant difference between MTA Fillapex and Apexit plus however (p>0.05). Microscopic analysis displayed that the majority of the modes were cohesive failures for AH Plus, adhesive failures for MTA Fillapex and mixed failures for Apexit Plus. . Thus, AH Plus had the highest bond strength and MTA Fillapex had the lowest bond strength to root dentin. Mean push-out bond strength values were ranked as follows; AH Plus >Apexit Plus > MTA Fillapex. Microscopic analysis displayed that the majority of the modes were cohesive failures of AH Plus, adhesive failures for MTA Fillapex and mixed failures for Apexit Plus.     

Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development

DNA methylation and histone methylation are two key epigenetic modifications that help govern heterochromatin dynamics. The roles for these chromatin-modifying activities in directing tissue-specific development remain largely unknown. To address this issue, we examined the roles of DNA methyltransferase 1 (Dnmt1) and the H3K9 histone methyltransferase Suv39h1 in zebra fish development. Knockdown of Dnmt1 in zebra fish embryos caused defects in terminal differentiation of the intestine, exocrine pancreas, and retina. Interestingly, not all tissues required Dnmt1, as differentiation of the liver and endocrine pancreas appeared normal. Proper differentiation depended on Dnmt1 catalytic activity, as Dnmt1 morphants could be rescued by active zebra fish or human DNMT1 but not by catalytically inactive derivatives. Dnmt1 morphants exhibited dramatic reductions of both genomic cytosine methylation and genome-wide H3K9 trimethyl levels, leading us to investigate the overlap of in vivo functions of Dnmt1 and Suv39h1. Embryos lacking Suv39h1 had organ-specific terminal differentiation defects that produced largely phenocopies of Dnmt1 morphants but retained wild-type levels of DNA methylation. Remarkably, suv39h1 overexpression rescued markers of terminal differentiation in Dnmt1 morphants. Our results suggest that Dnmt1 activity helps direct histone methylation by Suv39h1 and that, together, Dnmt1 and Suv39h1 help guide the terminal differentiation of particular tissues.     

Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover

Nitroalkane oxidase (NAO) from Fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of H(2)O(2) and nitrite. The flavoenzyme is a new member of the acyl-CoA dehydrogenase (ACAD) family, but it does not react with acyl-CoA substrates. We present the 2.2 A resolution crystal structure of NAO trapped during the turnover of nitroethane as a covalent N5-FAD adduct (ES*). The homotetrameric structure of ES* was solved by MAD phasing with 52 Se-Met sites in an orthorhombic space group. The electron density for the N5-(2-nitrobutyl)-1,5-dihydro-FAD covalent intermediate is clearly resolved. The structure of ES was used to solve the crystal structure of oxidized NAO at 2.07 A resolution. The c axis for the trigonal space group of oxidized NAO is 485 A, and there are six subunits (1(1)/(2) holoenzymes) in the asymmetric unit. Four of the active sites contain spermine (EI), a weak competitive inhibitor, and two do not contain spermine (E(ox)). The active-site structures of E(ox), EI, and ES* reveal a hydrophobic channel that extends from the exterior of the protein and terminates at Asp402 and the N5 position on the re face of the FAD. Thus, Asp402 is in the correct position to serve as the active-site base, where it is proposed to abstract the alpha proton from neutral nitroalkane substrates. The structures for NAO and various members of the ACAD family overlay with root-mean-square deviations between 1.7 and 3.1 A. The homologous region typically spans more than 325 residues and includes Glu376, which is the active-site base in the prototypical member of the ACAD family. However, NAO and the ACADs exhibit differences in hydrogen-bonding patterns between the respective active-site base, substrate molecules, and FAD. These likely differentiate NAO from the homologues and, consequently, are proposed to result in the unique reaction mechanism of NAO.     

Microtubule stability, Golgi organization, and transport flux require dystonin-a2-MAP1B interaction

Loss of function of dystonin cytoskeletal linker proteins causes neurodegeneration in dystonia musculorum (dt) mutant mice. Although much investigation has focused on understanding dt pathology, the diverse cellular functions of dystonin isoforms remain poorly characterized. In this paper, we highlight novel functions of the dystonin-a2 isoform in mediating microtubule (MT) stability, Golgi organization, and flux through the secretory pathway. Using dystonin mutant mice combined with isoform-specific loss-of-function analysis, we found dystonin-a2 bound to MT-associated protein 1B (MAP1B) in the centrosomal region, where it maintained MT acetylation. In dt neurons, absence of the MAP1B-dystonin-a2 interaction resulted in altered MAP1B perikaryal localization, leading to MT deacetylation and instability. Deacetylated MT accumulation resulted in Golgi fragmentation and prevented anterograde trafficking via motor proteins. Maintenance of MT acetylation through trichostatin A administration or MAP1B overexpression mitigated the observed defect. These cellular aberrations are apparent in prephenotype dorsal root ganglia and primary sensory neurons from dt mice, suggesting they are causal in the disorder.