Design and synthesis of biotinylated inositol 1,3,4,5-tetrakisphosphate targeting Grp1 pleckstrin homology domain

A bifunctional molecule containing biotin and d-myo-inositol 1,3,4,5-tetrakisphosphate was synthesized. This molecule was designed on the basis of X-ray structure of the complex of d-myo-inositol 1,3,4,5-tetrakisphosphates, Ins(1,3,4,5)P(4), and Grp1 PH (general receptor of phosphoinositides pleckstrin homology) domain for the application to the widely employed biotin-avidin techniques. The building block of inositol moiety was synthesized starting with myo-inositol and assembled with the biotin-linker moiety through a phosphate linkage. The equilibrium dissociation constant K(D) of biotinylated Ins(1,3,4,5)P(4) binding of original Grp1 PH domain was 0.14 μM in pull-down analysis, which was comparable to that of unmodified Ins(1,3,4,5)P(4). Furthermore, biotinylated Ins(1,3,4,5)P(4) had an ability to distinguish Grp1 PH domain from PLCδ(1) PH domain. Thus, biotinylated Ins(1,3,4,5)P(4) retained the binding affinity and selectivity of original Grp1 PH domain, and realized the intracellular Ins(1,3,4,5)P(4) despite a tethering at the 1-phosphate group of inositol.     

A heuristic method for discovering biomarker candidates based on rough set theory

We apply a combined method of heuristic attribute reduction and evaluation of relative reducts in rough set theory to gene expression data analysis. Our method extracts as many relative reducts as possible from the gene-expression data and selects the best relative reduct from the viewpoint of constructing useful decision rules. Using a breast cancer dataset and a leukemia dataset, we evaluated the classification accuracy for the test samples and biological meanings of the rules. As a result, our method presented superior classification accuracy comparable to existing salient classifiers. Moreover, our method extracted interesting rules including a novel biomarker gene identified in recent studies. These results indicate the possibility that our method can serve as a useful tool for gene expression data analysis.     

Construction of Flocculent Yeast Cells (Saccharomyces cerevisiae) by Mating or Protoplast Fusion Using a Yeast Cell Containing the Flocculation Gene FL05

In the yeast Saccharomyces cerevisiae, the gene FL01 and the gene FL05 are dominant flocculation genes. In diploid cells heterozygous for MAT, however, expression of the FL01 gene was greatly diminished as far as we examined, as seen in the FL08 gene. On the other hand, expression of the FL05 gene was not affected by the mating-type locus. Several brewer’s and wine flocculent yeast cells showed the flocculence phenotype defined as the FL05 type. These results suggested the usefulness of the FL05 gene in improvement of the flocculation properties of industrial strains.     

Metallo-β-lactamase inhibitory activity of 3-alkyloxy and 3-amino phthalic acid derivatives and their combination effect with carbapenem

3-Alkyloxy and 3-amino phthalic acid derivatives were found to have metallo-β-lactamase inhibitory activity. Among them, 3-amino phthalic acid derivatives showed both potent activity against metallo-β-lactamase, IMP-1 inhibitory activity and a strong combination effect with biapenem (BIPM), carbapenem antibiotic. In particular, the 4′-hydroxy-piperidine derivative showed strong IMP-1 inhibitory activity and a combination effect with various antibiotics.     

Maternal provisioning and possible joint breeding in the burrower bug Adomerus triguttulus (Heteroptera: Cydnidae)

Subsocial burrower bugs (Heteroptera: Cydnidae) provide unique opportunities to investigate evolutionary ecological questions regarding parental provisioning and family dynamics. Observations and marked nutlet‐setting experiments in the field showed that Adomerus triguttulus females progressively delivered mint nutlets into nests harbouring nymphs under the litter. More than one female often attended nymphs, but not eggs, in a nest in the field. The number of nymphs aggregating in a nest with a single female was usually smaller than that in a nest with two females, suggesting the joining of different families and facultative joint parental care. There was a positive correlation between the number of nutlets delivered and the number of nymphs in a nest. The number of attendant females also affected the amount of provisioning; more nutlets were found for second‐instar broods with more females. The effect of brood size on provisioning was confirmed for families under laboratory rearing. Maternal provisioning also varied with the developmental stage of offspring; second‐instar broods received more nutlets than first‐instar broods, with a temporal decrease in provisioning during the moulting of nymphs. Considering the growing evidence of food solicitation signals of young in subsocial insects, the observed finely tuned supply of food by the female could be induced by begging signals from the nymphs.     

Attenuated accumulation of regulatory T cells and reduced production of interleukin 10 lead to the exacerbation of tissue injury in a mouse model of acute respiratory distress syndrome

Acute respiratory distress syndrome (ARDS) is a pathological condition that involves diffuse lung injury and severe hypoxemia caused by pulmonary and systemic diseases. We have established a mouse model of severe ARDS, developed by intratracheal injection of α‐galactosylceramide (α‐GalCer), an activator of natural killer T (NKT) cells, followed by LPS. In the present study, we used this model to investigate the regulatory mechanism in the early inflammatory response during acute lung injury. In α‐GalCer/LPS‐treated mice, the number of CD4⁺CD25⁺Foxp3⁺ regulatory T (Treg) cells and the expression of a Treg cell‐tropic chemokine, secondary lymphoid‐tissue chemokine (SLC), in the lungs was significantly lower than in mice treated with LPS alone. Giving recombinant (r)SLC increased the number of Treg cells in α‐GalCer/LPS‐treated mice. Treatment with anti‐IFN‐γ mAb enhanced the expression of SLC and the accumulation of Treg cells in the lungs of α‐GalCer/LPS‐treated mice, whereas giving recombinant (r)IFN‐γ reduced the number of Treg cells in mice treated with LPS alone. IL‐10 production was significantly lower in α‐GalCer/LPS‐treated mice than in mice treated with LPS alone. Giving rIL‐10 prolonged survival and attenuated lung injury as a result of reduced production of inflammatory cytokines (such as IL‐1β, IL‐6, TNF‐α, and IFN‐γ) and chemokines (including MCP‐1, RANTES, IP‐10, Mig, MIP‐2, and KC) in α‐GalCer/LPS‐treated mice. Treatment with anti‐IFN‐γ mAb enhanced IL‐10 production in α‐GalCer/LPS‐treated mice. These results suggest that the attenuated accumulation of Treg cells may be involved in the development of severe ARDS through a reduction in the synthesis of IL‐10.

     

Characterization of a Protease from a Psychrotroph, Pseudomonas fluorescens 114

A psychrotrophic bacterium isolated from river sediment was identified as Pseudomonas fluorescens 114. It grew at 0°C and optimally at 20°C. The bacterium produced a protease with a molecular weight of 47,000, which was stable in the pH range of 5 to 9 and worked optimally between pH 6.5 and 10. Activity was optimal at 35°C and was lost immediately at 50°C and after 5 min at 45°C. At 0, 10, and 20°C, 24, 38, and 57% of optimal activity were observed, respectively.     

Cloning, expression, and nucleotide sequence of the alpha-amylase gene from the haloalkaliphilic archaeon Natronococcus sp. strain Ah-36.

The alpha-amylase gene of a Natronococcus sp. (1,512 bp) contained a signal peptide of 43 amino acids. Haloferax volcanii expressed the gene and cleaved the signal peptide accurately. The signal peptide shared an extremely high amino acid sequence identity with that of a protease from the halophilic archaeon 172P1.     

Construction of a Fibrobacter succinogenes Genomic Map and Demonstration of Diversity at the Genomic Level

The genomic cleavage map of the type strain Fibrobacter succinogenes S85 was constructed. The restriction enzymes AscI, AvrII, FseI, NotI, and SfiI generated DNA fragments of suitable size distribution that could be resolved by pulsed-field gel electrophoresis (PFGE). An average genome size of 3.6 Mb was obtained by summing the total fragment sizes. The linkages between the 15 AscI fragments of the genome were determined by combining two approaches: isolation of linking clones and cross-hybridization of restriction fragments. The genome of F. succinogenes was found to be represented by the single circular DNA molecule. Southern hybridization with specific probes allowed the eight genetic markers to be located on the restriction map. The genome of this bacterium contains at least three rRNA operons. PFGE of the other three strains of F. succinogenes gave estimated genome sizes close to that of the type strain. However, RFLP patterns of these strains generated by AscI digestion are completely different. Pairwise comparison of the genomic fragment distribution between the type strain and the three isolates showed a similarity level in the region of 14.3% to 31.3%. No fragment common to all of these F. succinogenes strains could be detected by PFGE. A marked degree of genomic heterogeneity among members of this species makes genomic RFLP a highly discriminatory and useful molecular typing tool for population studies. Received: 23 October 1996 / Accepted: 31 December 1996