G-InforBIO: integrated system for microbial genomics

BACKGROUND: Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs. RESULTS: The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses. CONCLUSION: The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site

Momentum-Dependent Hybridization Gap and dispersive in-gap state of The Kondo Semiconductor SmB6

We report the temperature-dependent three-dimensional angle-resolved photoemission spectra of the Kondo semiconductor SmB$_6$. We found a difference in the temperature dependence of the peaks at the X and $\Gamma$ points, due to hybridization between the Sm 5d conduction band and the nearly localized Sm 4f state. The peak intensity at the X point has the same temperature dependence as the valence transition below 120 K, while that at the $\Gamma$ point is consistent with the magnetic excitation at Q=(0.5,0.5,0.5) below 30 K. This suggests that the hybridization with the valence transition mainly occurs at the X point, and the initial state of the magnetic excitation is located at the $\Gamma$ point.Comment: 5 pages, 3 figure

A Possible Analysis of High-Potassium Induced Contracture of Visceral Muscles

High-K induced contractures of various types of visceral muscles were analyzed. In the preparations which showed spontaneous contractions, it was required to reconstract the contrature curves using the values measured from true base line ; the true base line was determined by the removal of Ca from incubating medium in the present experiments. The reconstracted (corrected) curve of taenia coli and of ureter could be analyzed into three components of contraction; the first phasic, the second transient and the third sustained components. The curve obtained from stomach muscle was composed of two (the first phasic and the third sustained) or three components as possible analysis. Vas deferens showed a contracture composed of the first phasic and the third sustained components. The outer layer of esophagus (striated muscle) showed only a phasic contraction in response to high-K. Possible mechanisms of these components were discussed in relation to the roles of Ca

Effects of Temperature on Electrical and Mechanical Activities of Guinea Pig Ureter

The action potential and contraction of the smooth muscle at various temperatures were observed using guinea pig ureter. The contraction height was not significantly altered by the change in the temperature between 20 and 36℃, while the time course of the contraction was greately slowed at lower temperatures. The plateau potential and the number of the spike potential in the action potential decreased and the duration of the action potential and membrane resistance increased at low temperature. Though the changes in the time course of the contraction can be explained mainly by the changes in the contractile reaction of the muscle protein and by the change in the relaxing activities of the sarcoplasmic reticulum and/or of the muscle membrane, the changes in the electrical activities of the muscle membrane should also be taken into consideration

Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes

Genome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence Database Collaboration (INSDC, ) by DNA Data Bank of Japan (DDBJ), EMBL and GenBank and stored them in our system. The list of registered viruses is arranged hierarchically according to taxonomy. Keyword searches can be performed for genome/segment data or biological features of any virus stored in GIB-V. GIB-V is equipped with a BLAST search function, and search results are displayed graphically or in list form. Moreover, the BLAST results can be used online with the ClustalW feature of the DDBJ. All available virus genome/segment data can be collected by the GIB-V download function. GIB-V can be accessed at no charge at

Effect of anticomplement agent K-76 COOH in hamster-to-rat and guinea pig- to-rat xenotransplantation

In normal rats, the xenobiotic K76 inhibited the C5 and probably the C2 and C3 steps of complement and effectively depressed classical complement pathway activity, alternative complement pathway activity, and the C3 complement component during and well beyond the drug's 3-hr half-life. It was tested alone and with intramuscular tacrolimus (TAC) and/or intragastric cyclophosphamide (CP) in rat recipients of heterotopic hearts from guinea pig (discordant) and hamster (concordant) donors. Single prevascularization doses of 100 and 200 mg/kg increased the median survival time of guinea pig hearts from 0.17 hr in untreated controls to 1.7 hr and 10.2 hr, respectively; with repeated injections of the 200-mg dose every 9-12 hr, graft survival time was increased to 18.1 hr. Pretreatment of guinea pig heart recipients for 10 days with TAC and CP, with or without perioperative splenectomy or infusion of donor bone marrow, further increased median graft survival time to 24 hr. Among the guinea pig recipients, the majority of treated animals died with a beating heart from respiratory failure that was ascribed to anaphylatoxins. Hamster heart survival also was increased with monotherapy using 200 mg/kg b.i.d.i.v. K76 (limited by protocol to 6 days), but only from 3 to 4 days. Survival was prolonged to 7 days with the addition to K76 of intragastric CP at 5 mg/kg per day begun 1 day before operation (to a limit of 9 days); it was prolonged to 4.5 days with the addition of intramuscular TAC at 2 mg/kg per day beginning on the day of transplantation and continued indefinitely. In contrast to the limited efficacy of the single drugs, or any two drugs in combination, the three drugs together (K76, CP, and TAC) in the same dose schedules increased median graft survival time to 61 days. Antihamster antibodies rapidly increased during the first 5 days after transplantation, and plateaued at an abnormal level in animals with long graft survival times without immediate humoral rejection. However, rejection could not be reliably prevented, and was present even in most of the xenografts recovered from most of the animals dying (usually from infection) with a beating heart. Thus, although effective complement inhibition with K76 was achieved in both guinea pig- and hamster-to-rat heart transplant models, the results suggest that effective interruption of the complement cascade will have a limited role, if any, in the induction of xenograft acceptance

The Fragility of Cryopreserved Insulin-producing Cells Differentiated from Adipose-tissue-derived Stem Cells

The aim of our study is to determine whether insulin-producing cells (IPCs) differentiated from adipose-tissue-derived stem cells (ADSCs) can be cryopreserved. Human ADSCs were differentiated into IPCs using our two-step protocol encompassing a three-dimensional culture and xenoantigen-free method. Thereafter, IPCs were frozen using three different methods. First, IPCs were immediately frozen at −80°C (−80°C group). Second, IPCs were initially placed into a Bicell freezing container before freezing at −80°C (BICELL group). Third, a vitrification method for oocytes and embryos was used (CRYOTOP group). Cell counting kit-8 (CCK-8) assay showed that cell viability was decreased in all groups after cryopreservation (P < 0.01). Corroboratively, the amount of adenosine triphosphate was markedly decreased after cryopreservation in all groups (P < 0.01). Immunofluorescence staining showed a reduced positive staining area for insulin in all cryopreservation groups. Furthermore, 4′,6-diamidino-2-phenylindole and merged immunofluorescence images showed that cryopreserved cells appeared to be randomly reduced in the −80°C group and CRYOTOP group, while only the central region was visibly reduced in the BICELL group. Using immunohistochemical staining, IPCs after cryopreservation were shown to be positive for cleaved caspase-3 antibody in all groups. Finally, insulin secretion following glucose stimulation was significantly reduced in IPCs from all groups after cryopreservation (P < 0.01). In conclusion, IPCs may be too fragile for cryopreservation with accomplished methods and further investigations for a suitable preservation method are required