Do you do text?

Retrieving information from text has become an important areain bioinformatics, and not too surprisingly, this journal haspublished more than 30 papers on this topic since the firstarticle published by the journal in 1998. In addition, ISCB(International Society for Computational Biology) (www.iscb.org)has organized special sessions in the ISMB conferences (IntelligentSystems for Molecular Biology, see www.iscb.org/ismb2005) anda specialized interest group (www.pdg.cnb.uam.es/BioLink/) forthe last five years. In parallel, major computer science conferencesin related areas have begun     

Localization of RecA in Escherichia coli K-12 using RecA-GFP

RecA is important in recombination, DNA repair and repair of replication forks. It functions through the production of a protein-DNA filament. To study the localization of RecA in live Escherichia coli cells, the RecA protein was fused to the green fluorescence protein (GFP). Strains with this gene have recombination/DNA repair activities three- to tenfold below wild type (or about 1000-fold above that of a recA null mutant). RecA-GFP cells have a background of green fluorescence punctuated with up to five foci per cell. Two types of foci have been defined: 4,6-diamidino-2-phenylindole (DAPI)-sensitive foci that are bound to DNA and DAPI-insensitive foci that are DNA-less aggregates/storage structures. In log phase cells, foci were not localized to any particular region. After UV irradiation, the number of foci increased and they localized to the cell centre. This suggested colocalization with the DNA replication factory. recA, recB and recF strains showed phenotypes and distributions of foci consistent with the predicted effects of these mutations.     

Pro-oxidative effect of beta-carotene and the interaction with flavonoids on UVA-induced DNA strand breaks in mouse fibroblast C3H10T1/2 cells

It has been suggested that β-carotene itself is unstable under certain conditions and that a combination of antioxidants may prevent the pro-oxidative effects of β-carotene. Thus, the present study aimed to investigate the interaction of β-carotene with three flavonoids—naringin, rutin and quercetin—on DNA damage induced by ultraviolet A (UVA) in C3H10T1/2 cells, a mouse embryo fibroblast. The cells were preincubated with β-carotene and/or flavonoid for 1 h followed by UVA irradiation, and DNA damage was measured using comet assay. We showed that β-carotene at 20 μM enhanced DNA damage (by 35%; P<.05) induced by UVA (7.6 kJ/m²), whereas naringin, rutin and quercetin significantly decreased UVA-induced DNA damage. When each flavonoid was combined with β-carotene during preincubation, UVA-induced cellular DNA damage was significantly suppressed and the effects were in the order of naringin≥rutin>quercetin. The flavonoids decreased UVA-induced oxidation of preincorporated β-carotene in the same order. Using electron spin resonance spectroscopy, we showed that the ability of these flavonoids to quench singlet oxygen was consistent with protection against DNA damage and β-carotene oxidation. All three flavonoids had some absorption at the UVA range (320–380 nm), but the effects were opposite to those on DNA damage and β-carotene oxidation. Taken together, this cell culture study demonstrates an interaction between flavonoids and β-carotene in UVA-induced DNA damage, and the results suggest that a combination of β-carotene with naringin, rutin or quercetin may increase the safety of β-carotene.     

A proatherogenic role for C-reactive protein in vivo

PURPOSE OF REVIEW: We have selectively reviewed some of the latest papers on the mechanistic role of C-reactive protein in atherosclerotic cardiovascular disease. RECENT DEVELOPMENTS: C-reactive protein is known to activate the classic pathway of the complement system. One paper examined the role of C-reactive protein in complement activation by enzymatically remodeled LDL proteins. Enzymatically remodeled LDL was found to induce complement activation with or without C-reactive protein, but in the presence of C-reactive protein the activation of complement halted before its terminal sequence. Complement activation by C-reactive protein in atherogenesis remains controversial. Different laboratories have reported the multi-organ origin of C-reactive protein. The atherosclerotic lesion itself is another place where C-reactive protein could be produced. Numerous studies have continued to dissect the potential diverse proatherogenic actions of C-reactive protein on cultured vascular cells. Caution must be exercised in inadequately controlled studies that have unwittingly used commercial C-reactive protein preparations contaminated by other bioactive components. In contrast to in-vitro experiments, in-vivo studies that support a proatherogenic role of C-reactive protein are less likely to be subject to misinterpretation. SUMMARY: Evidence suggests that C-reactive protein is a proatherogenic molecule that plays an active role. The amount of C-reactive protein in lesions is determined by its plasma levels and its local production. The biological effect of C-reactive protein on atherosclerosis development seems to encompass a complex network of interactions with other players in immunity and inflammation, such as the complement system, as well as a direct effect of C-reactive protein on the cells involved in lesion growth and development.     

Syntheses, characterization and crystal structures of copper(I) o-(diphenylphosphino)benzaldehyde complexes

The complexes [Cu(PCHO)₂(NCMe)][BF₄] (1) and [Cu(PCHO)₃][BF₄] (2) have been prepared by treating [Cu(NCMe)₄][BF₄] with two and three equivalents of Ph₂P(o-C₆H₄)C(O)H (abbreviated as PCHO) at room temperature, respectively. The reaction of 1 and (Ph₂PC₅H₄)₂Fe (abbreviated as DPPF) affords [Cu(PCHO)(DPPF)][BF₄] (3). The molecular structures of 1-3 have been determined by an X-ray diffraction study. The aldehyde groups in 1 are pendant, while one of the formyl groups in 2 is weakly coordinated to the copper ion through the oxygen atom. On the other hand, the copper atom in 3 is strongly chelated by both DPPF and PCHO ligands.     

Enhanced production of surfactin from Bacillus subtilis by addition of solid carriers

Addition of a small quantity of solid porous carriers (e.g., activated carbon or expanded clay) into fermentation broth significantly increased surfactin production with Bacillus subtilis ATCC 21332. Culture medium containing 25 g L(-1) of activated carbon gave an optimal surfactin yield of 3600 mg L(-1), which was approximately 36-fold higher than that obtained from carrier-free liquid culture. The marked increase in surfactin production was primarily attributed to stimulation of cell growth due to the presence of activated carbon carriers. Concentration of limiting carbon substrate (glucose) is also an important factor affecting the production of surfactin, as an initial glucose concentration of 40 g L(-1) resulted in optimal surfactin production. An appropriate agitation rate also benefited surfactin production, as the best yield appeared at an agitation rate of 200 rpm. Surfactin was purified from fermentation broth via a series of acidic precipitation and solvent extraction. The resulting product was nearly 90% pure with a recovery efficiency of ca. 72%. The purified surfactin reduced the surface tension of water from 72 to 27 mN m(-1) with a critical micelle concentration of ca. 10 mg L(-1). The surfactin product also attained an emulsion index of 70% for kerosene and diesel at a low concentration of 100 and 600 mg L(-1), respectively.     

TTK/hMps1 participates in the regulation of DNA damage checkpoint response by phosphorylating CHK2 on threonine 68

CHK2/hCds1 plays important roles in the DNA damage-induced cell cycle checkpoint by phosphorylating several important targets, such as Cdc25 and p53. To obtain a better understanding of the CHK2 signaling pathway, we have carried out a yeast two-hybrid screen to search for potential CHK2-interacting proteins. Here, we report the identification of the mitotic checkpoint kinase, TTK/hMps1, as a novel CHK2-interacting protein. TTK/hMps1 directly phosphorylates CHK2 on Thr-68 in vitro. Expression of a TTK kinase-dead mutant, TTK(D647A), interferes with the G(2)/M arrest induced by either ionizing radiation or UV light. Interestingly, induction of CHK2 Thr-68 phosphorylation and of several downstream events, such as cyclin B1 accumulation and Cdc2 Tyr-15 phosphorylation, is also affected. Furthermore, ablation of TTK expression using small interfering RNA results not only in reduced CHK2 Thr-68 phosphorylation, but also in impaired growth arrest. Our results are consistent with a model in which TTK functions upstream from CHK2 in response to DNA damage and suggest possible cross-talk between the spindle assembly checkpoint and the DNA damage checkpoint.     

Peptergents: peptide detergents that improve stability and functionality of a membrane protein, glycerol-3-phosphate dehydrogenase

Toward enhancing in vitro membrane protein studies, we have utilized small self-assembling peptides with detergent properties ("peptergents") to extract and stabilize the integral membrane flavoenzyme, glycerol-3-phosphate dehydrogenase (GlpD), and the soluble redox flavoenzyme, NADH peroxidase (Npx). GlpD is a six transmembrane spanning redox enzyme that catalyzes the oxidation of glycerol-3-phosphate to dihydroxyacetone phosphate. Although detergents such as n-octyl-beta-D-glucpyranoside can efficiently solubilize the enzyme, GlpD is inactivated within days once reconstituted into detergent micelles. In contrast, peptergents can efficiently extract and solubilize GlpD from native Escherichia coli membrane and maintain its enzymatic activity up to 10 times longer than in traditional detergents. Intriguingly, peptergents also extended the activity of a soluble flavoenzyme, Npx, when used as an additive. Npx is a flavoenzyme that catalyzes the two-electron reduction of hydrogen peroxide to water using a cysteine-sulfenic acid as a secondary redox center. The lability of the peroxidase results from oxidation of the sulfenic acid to the sulfinic or sulfonic acid forms. Oxidation of the sulfenic acid, the secondary redox center, results in inactivation, and this reaction proceeds in vitro even in the presence of reducing agents. Although the exact mechanism by which peptergents influence solution stability of Npx remains to be determined, the positive effects may be due to antioxidant properties of the peptides. Peptide-based detergents can be beneficial for many applications and may be particularly useful for structural and functional studies of membrane proteins due to their propensity to enhance the formation of ordered supramolecular assemblies.     

The role of interleukin 1 receptor-associated kinase-4 (IRAK-4) kinase activity in IRAK-4-mediated signaling

Interleukin 1 receptor (IL-1R)-associated kinase-4 (IRAK-4) is required for various responses induced by IL-1R and Toll-like receptor signals. However, the molecular mechanism of IRAK-4 signaling and the role of its kinase activity have remained elusive. In this report, we demonstrate that IRAK-4 is recruited to the IL-1R complex upon IL-1 stimulation and is required for the recruitment of IRAK-1 and its subsequent activation/degradation. By reconstituting IRAK-4-deficient cells with wild type or kinase-inactive IRAK-4, we show that the kinase activity of IRAK-4 is required for the optimal transduction of IL-1-induced signals, including the activation of IRAK-1, NF-kappaB, and JNK, and the maximal induction of inflammatory cytokines. Interestingly, we also discover that the IRAK-4 kinase-inactive mutant is still capable of mediating some signals. These results suggest that IRAK-4 is an integral part of the IL-1R signaling cascade and is capable of transmitting signals both dependent on and independent of its kinase activity.