Column Stores as an IR Prototyping Tool

. We make the suggestion that instead of implementing custom index structures and query evaluation algorithms, IR researchers should simply store document representations in a column-oriented relational database and write ranking models using SQL. For rapid prototyping, this is particularly advantageous since researchers can explore new ranking functions and features by simply issuing SQL queries, without needing to write imperative code. We demonstrate the feasibility of this approach by an implementation of conjunctive BM25 using MonetDB on a part of the ClueWeb12 collection

Identification of essential cysteine residues in 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Corynebacterium glutamicum

To ascertain the functional role of cysteine residue in 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase from Corynebacterium glutamicum, site-directed mutagenesis was performed to change each of the three residues to serine. Plasmids were constructed for high-level overproduction and one-step purification of histidine-tagged DAHP synthase. Analysis of the purified wild-type and mutant enzymes by SDS-polyacrylamide gel electrophoresis showed an apparent protein band with a molecular mass of approximately 45 kDa. Cys(145)Ser mutant retained about 16% of the enzyme activity, while DAHP synthase activity was abolished in Cys(67)Ser mutant. Kinetic analysis of Cys(145)Ser mutant with PEP as a substrate revealed a marked increase in K-m with significant change in k(cat), resulting in a 13.6-fold decrease in k(cat)/K-m(PEP). Cys(334) was found to be nonessential for catalytic activity, although it is highly conserved in DAHP synthases. From these studies, Cys(67) appears important for synthase activity, while Cys(145) plays a crucial role in the catalytic efficiency through affecting the mode of substrate binding

Serine 187 is a crucial residue for allosteric regulation of Corynebacterium glutamicum 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase

Corynebacterium glutamicum 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase is sensitive to feedback inhibition by tyrosine. One feedback-insensitive mutant was obtained by in vitro chemical mutagenesis and the mutation was identified as a C-->G mutation at nucleotide 560 causing a Ser(187) to Cys(187) substitution. Replacing Ser(187) with cysteine, tyrosine or phenylalanine by site-directed mutagenesis not only reduced the enzymatic activity but also relieved its feedback inhibition by tyrosine, while Ser(187)Ala exhibited a comparable activity to that of wild-type enzyme and sensitized to allosteric regulation. The His(6)-tagged enzymes were expressed in Escherichia coli and purified to homogeneity by immobilized nickel-ion affinity chromatography. Kinetic analysis showed that tyrosine is a competitive inhibitor of phosphoenol pyruvate, one of the precursors for DAHP biosynthesis. (C) 2001 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved

First principles modelling of the ion binding capacity of finger millet

Finger millet, a cereal grain widely consumed in India and Africa, has gained more attention in recent years due to its high dietary fibre (arabinoxylan) and trace mineral content, and its climate resilience. The aim of this study was to understand the interactions between potassium (K+), calcium (Ca2+) and zinc (Zn2+) ions and the arabinoxylan structure and determine its ion-binding capacity. Three variations of a proposed model of the arabinoxylan structure were constructed and first principles Density Functional Theory calculations were carried out to determine the cation-binding capacity of the arabinoxylan complexes. Zn2+-arabinoxylan complexes were highly unstable and thermodynamically unfavourable in all three models. Ca2+ and K+ ions, however, form thermodynamically stable complexes, particularly involving two glucuronic acid residues as a binding pocket. Glucuronic acid residues are found to play a key role in stabilising the cation-arabinoxylan complex, and steric effects are more important to the stability than charge density. Our results highlight the most important structural features of the millet fibre regarding ion-storage capacity, and provide valuable preliminary data for confirmatory experimental studies and for the planning of clinical trials where the bioavailability of bound ions following digestion may be tested

Fusion of Bacillus stearothermophilus leucine aminopeptidase II with the raw-starch-binding domain of Bacillus sp strain TS-23 alpha-amylase generates a chimeric enzyme with enhanced thermostability and catalytic activity

Bacillus stearothermophilus leucine aminopeptidase 11 (LAPII) was fused at its C-terminal end with the raw-starch-binding domain of Bacillus sp. strain TS-23 alpha-amylase. The chimeric enzyme (LAPsbd), with an apparent molecular mass of approximately 61 kDa, was overexpressed in IPTG-induced Escherichia coli cells and purified to homogeneity by nickel-chelate chromatography. The purified enzyme retained LAP activity and adsorbed raw starch. LAPsbd was stable at 70degreesC for 10 min, while the activity of wild-type enzyme was completely abolished under the same environmental condition. Compared with the wild-type enzyme, the twofold increase in the catalytic efficiency for LAPsbd was due to a 218% increase in the k(cat) value

The N-terminal signal sequence and the last 98 amino acids are not essential for the secretion of Bacillus sp TS-23 alpha-amylase in Escherichia coli

A truncated Bacillus sp. TS-23 alpha -amylase gene lacking 96 and 294 bp at its 5' and 3' end respectively was prepared by polymerase chain reaction and cloned into Escherichia coli expression vector, pQE-30, under the control of T5 promoter. SDS-PAGE and activity staining analyses showed that the His(6)-tagged amylase had a molecular mass of approximately 54 kDa. Isopropyl-beta -D-thiogalactopyranoside (IPTG) induction of E. coli M15 cells bearing the recombinant plasmid resulted in the extracellular production of active amylase. Western blot analysis also revealed that the truncated amylase was present in the periplasmic space and culture medium

Fusion of Bacillus stearothermophilus leucine aminopeptidase II with the raw-starch-binding domain of Bacillus sp strain TS-23 alpha-amylase generates a chimeric enzyme with enhanced thermostability and catalytic activity

Bacillus stearothermophilus leucine aminopeptidase 11 (LAPII) was fused at its C-terminal end with the raw-starch-binding domain of Bacillus sp. strain TS-23 alpha-amylase. The chimeric enzyme (LAPsbd), with an apparent molecular mass of approximately 61 kDa, was overexpressed in IPTG-induced Escherichia coli cells and purified to homogeneity by nickel-chelate chromatography. The purified enzyme retained LAP activity and adsorbed raw starch. LAPsbd was stable at 70degreesC for 10 min, while the activity of wild-type enzyme was completely abolished under the same environmental condition. Compared with the wild-type enzyme, the twofold increase in the catalytic efficiency for LAPsbd was due to a 218% increase in the k(cat) value

Evaluation of serum sphingolipids and the influence of genetic risk factors in age-related macular degeneration

Peer reviewedPublisher PD

Identification of essential histidine residues in a recombinant alpha-amylase of thermophilic and alkaliphilic Bacillus sp strain TS-23

To understand the structure-function relationships of a truncated Bacillus sp. strain TS-23 alpha-amylase, each of His-137, His-191, His-239, His-269, His-305, His-323, His-361, His-436, and His-475 was replaced with leucine. The molecular masses of the purified wild-type and mutant enzymes were approximately 54 kDa. The specific activity of His323Leu and His436Leu was decreased by more than 52%, while His239Leu, His305Leu, and His475Leu showed activity similar to that of the wild-type enzyme. As compared with the wild-type enzyme, His323Leu and His436Leu exhibited a 62% decrease in the value of k(cat)/K-m. Alterations in His-191, His-239, His-305, and His-475 did not cause a significant change in the K-m or k(cat) values. At 70degreesC, a decreased half-life was observed in His436Leu. These results indicate that His-137, His-269, and His-361 of Bacillus sp. strain TS-23 alpha-amylase are important for proper catalytic activity and that His-436 may contribute to the thermostability of the enzyme