A large conformational change in the putative ATP pyrophosphatase PF0828 induced by ATP binding.

ATP pyrophosphatases (ATP PPases) are widely distributed in archaea and eukaryotes. They share an HUP domain at the N-terminus with a conserved PP-motif that interacts with the phosphates of ATP. The PF0828 protein from Pyrococcus furiosus is a member of the ATP PPase superfamily and it also has a 100-residue C-terminal extension that contains a strictly conserved EGG(E/D)xE(T/S) motif, which has been named the EGT-motif.

Development of a certified reference material for the determination of acrylamide in potato chips.

A certified reference material (CRM), KRISS CRM 108-10-003, has been developed for analysis of acrylamide in potato chips, as a representative of carbohydrate-rich food cooked in high-temperature oil. The material was prepared by grinding commercially available potato chips to a paste which was then homogenized, bottled in 15-g units, and stored at -70 °C. Certification, homogeneity and stability testing, were carried out by liquid chromatography-isotope-dilution mass spectrometry (ID-LC-MS).

Putative probiotic Lactobacillus spp. from porcine gastrointestinal tract inhibit transmissible gastroenteritis coronavirus and enteric bacterial pathogens.

A total of 310 bacterial strains isolated from the porcine gastrointestinal tract were tested for their activity against transmissible gastroenteritis (TGE) coronavirus and other enteric pathogens. Based on activity, the strains Probio-38 and Probio-37 were selected as potential probiotics and identified as Lactobacillus plantarum Probio-38 and Lactobacillus salivarius Probio-37 respectively by 16S rRNA gene sequencing. Supernatants of these strains inhibited TGE coronavirus in vitro in ST cells, without any cytopathic effect even after 72 h of incubation.

Bile tolerant Lactobacillus reuteri isolated from pig feces inhibits enteric bacterial pathogens and porcine rotavirus.

Lactic acid producing bacterial strain Probio-16 was isolated from the swine excrements under anaerobic conditions and characterized by morphology and biochemical characteristics. The strain was further identified by 16S rRNA gene sequencing and phylogeneitc analysis. The antimicrobial activity of the strain was assayed by testing for growth inhibition of thirteen pathogenic microorganisms.

New functional probiotic Lactobacillus sakei probio 65 alleviates atopic symptoms in the mouse.

The purpose of this study was to investigate the improvement of allergic dermatitis in chemical allergen-induced mice by Lactobacillus sakei probio 65. L. sakei probio-65 was isolated from kimchi, a traditional Korean fermented food.

Functional insights from structural genomics.

Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening.

Short-term hyperhomocysteinemia-induced oxidative stress activates retinal glial cells and increases vascular endothelial growth factor expression in rat retina.

Hyperhomocysteinemia is associated with an increase in the incidence of vascular diseases, including retinal vascular diseases. We examined the effects of high plasma levels of homocysteine on retinal glial cells and vascular endothelial growth factor (VEGF) expression. Male Sprague-Dawley rats were fed either a 3.

Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria.

The genome-probing microarray (GPM) was developed for quantitative, high-throughput monitoring of community dynamics in lactic acid bacteria (LAB) fermentation through the deposit of 149 microbial genomes as probes on a glass slide. Compared to oligonucleotide microarrays, the specificity of GPM was remarkably increased to a species-specific level. GPM possesses about 10- to 100-fold higher sensitivity (2.

Structural and functional evidence for Bacillus subtilis PaiA as a novel N1-spermidine/spermine acetyltransferase.

Bacillus subtilis PaiA has been implicated in the negative control of sporulation as well as production of degradative enzymes. PaiA shares recognizable sequence homology with N-acetyltransferases, including those that can acetylate spermidine/spermine substrates. We have determined the crystal structure of PaiA in complex with CoA at 1.

The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.

TenA (transcriptional enhancer A) has been proposed to function as a transcriptional regulator based on observed changes in gene-expression patterns when overexpressed in Bacillus subtilis. However, studies of the distribution of proteins involved in thiamine biosynthesis in different fully sequenced genomes have suggested that TenA may be an enzyme involved in thiamine biosynthesis, with a function related to that of the ThiC protein. The crystal structure of PF1337, the TenA homolog from Pyrococcus furiosus, is presented here.

Folic acid supplementation can reduce the endothelial damage in rat brain microvasculature due to hyperhomocysteinemia.

To evaluate the effects of dietary folic acid supplementation on the cerebral vascular damage induced by hyperhomocysteinemia, rats were fed a diet containing 3.0 g/kg homocystine for 2 wk and then either 3.0 g/kg homocystine or 3.

Metabolism of subtoxic level of selenite by double-perfused small intestine in rats.

Intestinal metabolism of the subtoxic level of selenite in rats was investigated using a double-perfusion system, which is an in situ, in vitro preparation in which the intestinal lumen and its vasculature are perfused simultaneously. The toxicity of sodium selenite was determined by inhibition of 3-O-methyl glucose (3MG) absorption and by histological examination. Levels of 1.

Quercetin, a flavonoid, inhibits the proliferation, differentiation, and mineralization of osteoblasts in vitro.

It is possible that the flavonoids that are found in many foods might have a protective effect against osteoclastic activity. However, little information is available about the effects of flavonoids on osteoblastogenesis. Therefore, we investigated the effects of quercetin, a flavonoid, on the metabolism of rat calvarial osteoblast-like cells (ROB cells) in culture.

A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK).

Escherichia coli YiaK catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH. It belongs to a large family of oxidoreductases that is conserved in archaea, bacteria, and eukaryotes but shows no sequence homology to other proteins. We report here the crystal structures at up to 2.

The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase.

We present here the 2.3-A crystal structure of the Escherichia coli YdiB protein, an orthologue of shikimate 5-dehydrogenase. This enzyme catalyzes the reduction of 3-dehydroshikimate to shikimate as part of the shikimate pathway, which is absent in mammals but required for the de novo synthesis of aromatic amino acids, quinones, and folate in many other organisms.