On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data

Informatics for Integrating Biology and the Bedside (i2b2) is a database system to facilitate sharing and reuse of clinical patients' data collected in individual hospitals. The i2b2 provides an ontology based object-oriented database system with highly simple and flexible database schema which enables us to integrate clinical patients' data from different laboratories and different hospitals. 392 patients' data including carcinoma and non-carcinoma specimens from cancer patients are transported from the Integrated Clinical Omics Database (iCOD) to the i2b2 database for a feasibility study to check applicability of i2b2 ontology and database schema on Japanese clinical patients' data. No modification is required for the i2b2 data model to deal with Japanese characters. Some modification of ontology is required to integrate biomedical information extracted from the cancer patients' data. We believe that the i2b2 system will be practical infrastructure to integrate Japanese clinical databases if appropriate disease ontology for Japanese patients is provided.     

Supersaturation-limited Amyloid Fibrillation of Insulin Revealed by Ultrasonication

Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. We proposed that ultrasonication may be an effective agitation to trigger nucleation that would otherwise not occur under the persistent metastability of supersaturation. However, the roles of supersaturation and effects of ultrasonication have not been elucidated in detail except for limited cases. Insulin is an amyloidogenic protein that is useful for investigating the mechanisms underlying amyloid fibrillation with biological relevance. We studied the alcohol-induced amyloid fibrillation of insulin using various concentrations of 2,2,2-trifluoroethanol and 1,1,1,3,3,3-hexafluoro-2-propanol at pH 2.0 and 4.8. Ultrasonic irradiation effectively triggered fibrillation under conditions in which insulin retained persistent supersaturation. Structural analyses by circular dichroism, Fourier transform infrared spectroscopy, transmission electron microscopy, and atomic force microscopy revealed that the dominant structures of fibrils varied between parallel and antiparallel β-sheets depending on the solvent conditions. pH and alcohol concentration-dependent phase diagrams showed a marked difference before and after the ultrasonic treatment, which indicated that the persistent metastability of supersaturation determined the conformations of insulin. These results indicate the importance of an alternative view of amyloid fibrils as supersaturation-limited crystal-like aggregates formed above the solubility limit.     

Draft Sequences of the Radish (Raphanus sativus L.) Genome

Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.     

Intermolecular functional coupling between phosphoinositides and the potassium channel KcsA

Biological membranes are composed of a wide variety of lipids. Phosphoinositides (PIPns) in the membrane inner leaflet only account for a small percentage of the total membrane lipids but modulate the functions of various membrane proteins, including ion channels, which play important roles in cell signaling. KcsA, a prototypical K⁺ channel that is small, simple, and easy to handle, has been broadly examined regarding its crystallography, in silico molecular analysis, and electrophysiology. It has been reported that KcsA activity is regulated by membrane phospholipids, such as phosphatidylglycerol. However, there has been no quantitative analysis of the correlation between direct lipid binding and the functional modification of KcsA, and it is unknown whether PIPns modulate KcsA function. Here, using contact bubble bilayer recording, we observed that the open probability of KcsA increased significantly (from about 10% to 90%) when the membrane inner leaflet contained only a small percentage of PIPns. In addition, we found an increase in the electrophysiological activity of KcsA correlated with a larger number of negative charges on PIPns. We further analyzed the affinity of the direct interaction between PIPns and KcsA using microscale thermophoresis and observed a strong correlation between direct lipid binding and the functional modification of KcsA. In conclusion, our approach was able to reconstruct the direct modification of KcsA by PIPns, and we propose that it can also be applied to elucidate the mechanism of modification of other ion channels by PIPns.     

Cloning, nucleotide sequence and expression of the gene encoding the cellulose-binding protein 1 (CBP1) of Fibrobacter succinogenes S85

Abstract The nucleotide sequence of the gene encoding the Fibrobacter succinogenes S85 cellulose-binding protein 1 (CBP1) has been determined. The gene encodes a protein of 1054 amino acids with a molecular mass of 118614. The deduced amino acid sequence of CBPl showed an extensive similarity to the cellulose-binding domain of an endoglucanase (EGCCD) from Clostridium cellulolyticum and contained the reiterated regions. The cloned gene was inserted into an expression vector, pRSETA, and was expressed in E. coli as a fused protein with the peptide consisting of six consecutive histidine residues. The fused protein was detected by immunoblotting using antiserum against CBP1, and exhibited the cellulose-binding activities.     

Expression of a codon-optimized Aspergillus niger pectin methylesterase gene in the methylotrophic yeast Candida boidinii

A codon-optimized Aspergillus niger pectin methylesterase (PME) gene was expressed in the methylotrophic yeast Canidia boidinii. The PME-producing strains showed better growth on pectin than the wild-type strains, suggesting that the PME-producing strains could efficiently utilize methyl ester moieties of pectin. On the other hand, overproduction of PME negatively affected the proliferation of C. boidinii on leaves of Arabidopsis thaliana.     

Characterization of Two Members among the Five ADP-Forming Acyl Coenzyme A (Acyl-CoA) Synthetases Reveals the Presence of a 2-(Imidazol-4-yl)Acetyl-CoA Synthetase in Thermococcus kodakarensis

The genome of Thermococcus kodakarensis, along with those of most Thermococcus and Pyrococcus species, harbors five paralogous genes encoding putative α subunits of nucleoside diphosphate (NDP)-forming acyl coenzyme A (acyl-CoA) synthetases. The substrate specificities of the protein products for three of these paralogs have been clarified through studies on the individual enzymes from Pyrococcus furiosus and T. kodakarensis. Here we have examined the biochemical properties of the remaining two acyl-CoA synthetase proteins from T. kodakarensis. The TK0944 and TK2127 genes encoding the two α subunits were each coexpressed with the β subunit-encoding TK0943 gene. In both cases, soluble proteins with an α₂β₂ structure were obtained and their activities toward various acids in the ADP-forming reaction were examined. The purified TK0944/TK0943 protein (ACS III_Tk) accommodated a broad range of acids that corresponded to those generated in the oxidative metabolism of Ala, Val, Leu, Ile, Met, Phe, and Cys. In contrast, the TK2127/TK0943 protein exhibited relevant levels of activity only toward 2-(imidazol-4-yl)acetate, a metabolite of His degradation, and was thus designated 2-(imidazol-4-yl)acetyl-CoA synthetase (ICS_Tk), a novel enzyme. Kinetic analyses were performed on both proteins with their respective substrates. In T. kodakarensis, we found that the addition of histidine to the medium led to increases in intracellular ADP-forming 2-(imidazol-4-yl)acetyl-CoA synthetase activity, and 2-(imidazol-4-yl)acetate was detected in the culture medium, suggesting that ICS_Tk participates in histidine catabolism. The results presented here, together with those of previous studies, have clarified the substrate specificities of all five known NDP-forming acyl-CoA synthetase proteins in the Thermococcales.     

One-year spinal bone change in pre- and perimenopausal Japanese women. A prospective observational study

BACKGROUND: This prospective observational study was designed to determine whether the bone mineral density (BMD) of the lumbar spine decreases before menopause. METHODS: The change in BMD of the second through fourth lumbar vertebrae (delta%L2-4BMD) over the course of 12 months was measured in 197 pre- and perimenopausal Japanese women aged 48.2 +/- 2.3 (mean +/- SD) years. RESULTS: Overall, delta%L2-4BMD decreased significantly, with a greater decrease seen in perimenopausal women. This group also had a significantly higher level of FSH (p < 0.05, t = 7.356), a significantly lower level of estradiol (p < 0.05, t = 4.245), and significantly higher levels of the bone metabolic markers, alkaline phosphatase (p < 0.05, t = 3.841), calcium (p < 0.05, t = 3.939), and osteocalcin (p < 0.05, t = -3.295). Overall, there was a significant positive correlation between osteocalcin and delta%L2-4BMD (r = -0.194, p = 0.0479). CONCLUSION: A subset of perimenopausal women with transient decreases in ovarian function that do not respond to increased FSH may be at increased risk for abnormally low BMD, and may benefit from early management of bone mass.     

Ca(2+) channels activated by endothelin-1 in CHO cells expressing endothelin-A or endothelin-B receptors

We comparedthe Ca²⁺ channels activated by endothelin-1 (ET-1) inChinese hamster ovary (CHO) cells stably expressing endothelin type A(ET_A) or endothelin type B (ET_B) receptorsusing the Ca²⁺ channel blockers LOE-908 and SK&F-96365. Inboth CHO-ET_A and CHO-ET_B, ET-1 at 0.1 nMactivated the Ca²⁺-permeable nonselective cation channel-1(NSCC-1), which was sensitive to LOE-908 and resistant to SK&F-96365.ET-1 at 1 nM activated NSCC-2 in addition to NSCC-1; NSCC-2 wassensitive to both LOE-908 and SK&F-96365. ET-1 at 10 nM activated thesame channels as 1 nM ET-1 in both cell types, but inCHO-ET_A, it additionally activated the store-operatedCa²⁺ channel (SOCC), which was resistant to LOE-908 andsensitive to SK&F-96365. Up to 1 nM ET-1, the level of the formation of inositol phosphates (IPs) was low and similar in both cell types, but,at 10 nM ET-1, it was far greater in CHO-ET_A than inCHO-ET_B. These results show that, in CHO-ET_Aand CHO-ET_B, ET-1 up to 10 nM activated the sameCa²⁺ entry channels: 0.1 nM ET-1 activated NSCC-1, andET-1  1 nM activated NSCC-1 and NSCC-2. Notably, inCHO-ET_A, 10 nM ET-1 activated SOCCs because of the higherformation of IPs.

     

Grafting of material-binding function into antibodies Functionalization by peptide grafting

Quite recently, a few antibodies against bulk material surface have been selected from a human repertoire antibody library, and they are attracting immense interest in the bottom-up integration of nanomaterials. Here, we constructed antibody fragments with binding affinity and specificity for nonbiological inorganic material surfaces by grafting material-binding peptides into loops of the complementarity determining region (CDR) of antibodies. Loops were replaced by peptides with affinity for zinc oxide and silver material surfaces. Selection of CDR loop for replacement was critical to the functionalization of the grafted fragments; the grafting of material-binding peptide into the CDR2 loop functionalized the antibody fragments with the same affinity and selectivity as the peptides used. Structural insight on the scaffold fragment used implies that material-binding peptide should be grafted onto the most exposed CDR loop on scaffold fragment. We show that the CDR-grafting technique leads to a build-up creation of the antibody with affinity for nonbiological materials.