Syntheses of cellotriose and cellotetraose analogues as transition state mimics for mechanistic studies of cellulases

Cellotriose and cellotetraose analogues carrying cyclohexene rings were developed as molecular probes which are expected to mimic the transition state conformation of hydrolysis by cellulases. The cyclohexene ring was placed at the pyranose ring being expected to locate the -1 subsite of the enzyme. In order to evaluate these probes, sulfur derivatives of cellotriose and cellotetraose were also synthesized as the enzyme tolerant analogues which mimic the stable conformations of the natural cellulose. The binding assays using differential scanning calorimetry revealed that introduction of the cyclohexene ring is effective to the complexation with an endoglucanase, NCE5 from Humicola insolens.     

Cellular uptake of covalent conjugates of oligonucleotide with membrane-modifying peptide, peptaibol

Using the membrane-modifying peptide, trichorovin-XIIa (TV-XIIa), which is an 11-residual peptaibol isolated from the fungus Trichoderma viride, we synthesized covalent conjugates of 20-mer oligonucleotide with TV-XIIa to examine the potential use of TV-XIIa in cellular delivery. The results indicated that the conjugates were progressively taken up by human lung carcinoma A549 cells. Next, the antisense effects of the conjugates on p53 protein expression were examined. The p53 expression was significantly decreased by ca. 20-50% in the presence of the conjugates upon treatment with the transfection solution at the concentration of 5 μM.     

A BAC-based integrated linkage map of the silkworm Bombyx mori

Background

In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps.

Results

We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested with different restriction enzymes, and assigned a total of 724 single copy genes to them by BLAST (basic local alignment search tool) search of the BAC end sequences and high-density BAC filter hybridization using expressed sequence tags as probes. We assigned 964 additional expressed sequence tags to linkage groups by restriction fragment length polymorphism analysis of a nonrecombining female backcross population. Altogether, 361.1 megabases of BAC contigs and singletons were integrated with a map containing 1,688 independent genes. A test of synteny using Oxford grid analysis with more than 500 silkworm genes revealed six versus 20 silkworm linkage groups containing eight or more orthologs of Apis versus Tribolium, respectively.

Conclusion

The integrated map contains approximately 10% of predicted silkworm genes and has an estimated 76% genome coverage by BACs. This provides a new resource for improved assembly of whole-genome shotgun data, gene annotation and positional cloning, and will serve as a platform for comparative genomics and gene discovery in Lepidoptera and other insects.     

Cross-linked protein complex exhibiting asymmetric oxidation activities in the absence of added cofactor

A protein complex (PC) suspension exhibits asymmetric biooxidation activities in the absence of any added cofactor such as NAD(P)⁺ or FAD. It can be extracted from pea protein (PP)‐gel (PP encapsulated with Ca²⁺ alginate gel and aerated in air for several hours) using hot water by rotary shaking and powdered by the following three steps: (1) forming precipitates from the suspension using 30% (w/v) aqueous (NH₄)₂SO₄, (2) crosslinking the precipitates with 0.25% (v/v) GA, and (3) preparing the cross‐linked powder by freeze‐drying. The cross‐linked PC (CLPC) performed asymmetric oxidation of the toward (R)‐isomers of rac‐ 1 and rac ‐2 in 50 mM glycine–NaOH (pH 9.0) buffer/DMSO cosolvent [2.07% (v/v)] with high enantioselectivity; thus, the (S)‐isomers can be obtained in greater than 99% ee from the corresponding rac‐p‐substituted naphthyl methyl carbinol (rac‐ 1 and rac ‐2 ). The CLPC activity was not only competitively inhibited by addition of either 1.0 mM ZnCl₂ or a chelating agent such as 1.0 mM EDTA but also denatured by pretreatments: autoclaving at 121°C (20 min) or using 6.0 M guanidine–HCl containing 50 mM DTT. These results indicated that the PC catalytic process may utilize an electron transfer system incorporating a redox cation (e.g., Fe²⁺ ? Fe³⁺ or Zn). Therefore, the newly introduced CLPC can asymmetrically oxidize the substrates without the addition of any cofactor resulting in a low‐cost organic method. Overall, our results show that the CLPC is an easily prepared, low‐cost reagent that can function under mild conditions and afford stereoselectivity, regioselectivity, and substrate specificity. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 28: 953–961, 2012     

Isolation and characterization of osteoclast precursors that differentiate into osteoclasts on calvarial cells within a short period of time

Osteoclasts are formed in cocultures of mouse calvarial cells and hematopoietic cells in the presence of osteotropic factors such as 1α,25-dihydroxyvitamin D₃ [1α,25(OH)₂D₃], parathyroid hormone (PTH) and prostaglandin E₂ (PGE₂). We isolated osteoclast precursors (OCPs) from the coculture and examined their characteristics. After coculture for 7 days of mouse calvarial cells and bone marrow cells in the absence of osteotropic factors, hematopoietic cells were recovered and applied to a Sephadex G-10 column. Cells which passed through the column were collected as OCPs. When OCPs were cultured on calvarial cell layers in the presence of 1α,25(OH)₂D₃, tartrate-resistant acid phosphatase (TRAP)–positive cells first appeared within 24 h, and their number increased thereafter. OCPs also differentiated into TRAP-positive cells within 48 h on the calvarial cell layer which had been pretreated with either 1α,25(OH)₂D₃, PTH, or PGE₂. Autoradiography using [¹²⁵I]-labeled calcitonin showed that TRAP-positive cells formed on the calvarial cell layer expressed calcitonin receptors. Direct contact between OCPs and calvarial cells was required for the differentiation of OCPs into TRAP-positive cells. Flow cytometric analysis revealed that OCPs were positive for Mac-1, Mac-2, and Gr-1 but negative for F4/80, B220 and CD3e. Calvarial cells obtained from macrophage-colony stimulating factor (M-CSF)–deficient osteopetrotic (op/op) mice did not support OCP formation. A cell preparation disaggregated from long bones of newborn mice contained OCPs that differentiated into TRAP-positive cells on calvarial cells within 48 h, but cell preparations of freshly isolated bone marrow cells and alveolar macrophages did not. These results suggest that OCPs are specific cells which are formed only in the bone microenvironment and that OCPs recognize a signal(s) expressed by stromal cells in response to osteotropic factors and differentiate into osteoclasts. J. Cell. Physiol. 177:26–35, 1998. © 1998 Wiley-Liss, Inc.     

CtBP1/BARS is an activator of phospholipase D1 necessary for agonist-induced macropinocytosis

Vesicular trafficking such as macropinocytosis is a dynamic process that requires coordinated interactions between specialized proteins and lipids. A recent report suggests the involvement of CtBP1/BARS in epidermal growth factor (EGF)-induced macropinocytosis. Detailed mechanisms as to how lipid remodelling is regulated during macropinocytosis are still undefined. Here, we show that CtBP1/BARS is a physiological activator of PLD1 required in agonist-induced macropinocytosis. EGF-induced macropinocytosis was specifically blocked by 1-butanol but not by 2-butanol. In addition, stimulation of cells by serum or EGF resulted in the association of CtBP1/BARS with PLD1. Finally, CtBP1/BARS activated PLD1 in a synergistic manner with other PLD activators, including ADP-ribosylation factors as demonstrated by in vitro and intact cell systems. The present results shed light on the molecular basis of how the ‘fission protein' CtBP1/BARS controls vesicular trafficking events including macropinocytosis.     

A new species ofNeosartorya from Taiwan soil

A new species ofNeosartorya, N. multiplicata (anam.Aspergillus multiplicatus), isolated from soil collected at Houli, Taichung, in Taiwan, is described and illustrated. The species is characterized by its restricted growth on Czapek agar, white ascomata, nearly globose ascospores with ribbed surface ornamentation of several linear ridges, and a limited development of conidia on common media. A key to all accepted species of the genus is provided.     

Field observations on the rhythmic up-and-down movement ofNodilittorina exigua (Gastropoda: Littorinidae)

Field observations on the activity pattern ofNodilittorina exigua were carried out in various tidal conditions in various seasons. The snails were stationary when dry on rock surface and began to move just after being splashed. On the rising tide they crawled upward aggregating in the awash zone but were not active around the time of high tide. On the receding tide they crawled predominantly downward, again in the awash zone. Position of the snails was high in spring tide and low in neap tide, changing in parallel to the change of high tide level. They were far more active in the awash condition than in the exposed or in the submerged conditions. For onset and termination of the movement, predominant influence of endogenous factors was suggested, except for onset of upward crawling. The distance of upward movement was larger when the high-tide level was higher, while that of downward movement was related to the time of high tide. Such movement patterns enable the snails to decrease the period of submergence and increase the period of their stay in the awash zone, and help them avoid long-term drying.     

Design and synthesis of regioisomerically pure unsymmetrical xanthene derivatives for staining live cells and their photochemical properties

We have demonstrated the synthesis of regioisomerically pure unsymmetrical xanthene derivatives consisting of three units which can be independently modified to control their physical properties. The photochemical properties of the synthetic unsymmetrical xanthene derivatives were investigated in solution by UV–vis absorption and fluorescence measurements, and their cell imaging properties were examined by confocal laser-scanning microscopy.