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951.
Fujimoto J Bando T Minoshima M Uchida S Iwasaki M Shinohara K Sugiyama H 《Bioorganic & medicinal chemistry》2008,16(11):5899-5907
Methods for sequence-specific detection in double-stranded DNA (dsDNA) are becoming increasingly useful and important as diagnostic and imaging tools. Recently, we designed and synthesized pyrrole (Py)-imidazole (Im) polyamides possessing two pyrene moieties, 1, which showed an increased excimer emission in the presence of (CAG)(12)-containing oligodeoxynucleotides (ODN) 1 and 2. In this study, we synthesized bis-pyrenyl Py-Im polyamides with rigid linkers 2, 3, and 4 to improve their fluorescence properties. Among the conjugates, 2 showed a marked increase in excimer emission, which was dependent on the concentration of the target ODN and the number of CAG repeats in the dsDNA. Unlike conjugate 1, which has flexible linkers, the excimer emission intensity of 2 was retained at over 85%, even after 4h. Py-Im polyamides have the potential to be important diagnostic molecules for detecting genetic differences between individuals. 相似文献
952.
Tanaka Y Sakamoto S Kuroda M Goda S Gao YG Tsumoto K Hiragi Y Yao M Watanabe N Ohta T Tanaka I 《Structure (London, England : 1993)》2008,16(3):488-496
The 1.1 MDa cell-wall-associated adhesion protein of staphylococci, Ebh, consists of several distinct regions, including a large central region with 52 imperfect repeats of 126 amino acid residues. We investigated the structure of this giant molecule by X-ray crystallography, circular dichroism (CD) spectrometry, and small-angle X-ray scattering (SAXS). The crystal structure of two repeats showed that each repeat consists of two distinct three-helix bundles, and two such repeats are connected along the long axis, resulting in a rod-like structure that is 120 A in length. CD and SAXS analyses of the samples with longer repeats suggested that each repeat has an identical structure, and that such repeats are connected tandemly to form a rod-like structure in solution, the length of which increased proportionately with the number of repeating units. On the basis of these results, it was proposed that Ebh is a 320 nm rod-like molecule with some plasticity at module junctions. 相似文献
953.
Yuzuru Mizukami Makoto Hado Hitoshi Kito Masahiko Kunimoto Noboru Murase 《Journal of applied phycology》2004,16(1):23-29
The transient expression of foreign genes in the protoplasts of Porphyrayezoensis was examined using three recombinant vectors, pYez-Rub-GUS, pYez-Rub-GFP and pYez-Rub-LUC, which were constructed with the
promoter sequence of the ribulose-bisphosphate-carboxylase / oxygenase (Rubisco) gene as a promoter and the bacterial β-glucuronidase
(GUS), mutant of green fluorescent protein (S65T-GFP) and firefly luciferase (LUC) genes, respectively, as reporter genes.
When the pYez-Rub-GUS was introduced into protoplasts by electroporation, cells stained dark blue by indigotin were observed
after the histochemical GUS assay. GUS activity was also detected by quantitative enzyme assays with a chemiluminescent substrate.
When the pYez-Rub-GFP was electroporated into protoplasts, the expression of GFP could be detected in vivo observations with fluorescence microscopy. However, the rates of gene expression cells to the total number of cells were
different between the GUS and GFP genes. LUC activity was also detected by assay with a chemiluminescent substrate after the
introduction of pYez-Rub-LUC into protoplasts, although the activity levels were considerably lower. Relatively high expression
rates of introduced GUS genes were observed 3 to 5 days after electroporation. These results show that the promoter sequence
of the chloroplast Rubisco gene functions as a promoter of foreign gene expression and that transient expression occurred
in protoplasts of P. yezoensis after the introduction of foreign genes.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
954.
Kotaro Ishii Ryuji Sugiyama Megumi Onuki Yusuke Kazama Sachihiro Matsunaga Shigeyuki Kawano 《Génome》2008,51(4):251-260
Sex determination in Silene latifolia uses the XX/XY system. The recent evolution of dioecy in S. latifolia provides a unique opportunity to study the early stages of Y chromosome evolution. However, the current Y chromosome map still contains many large gaps with no available markers. In this study, a sequence tagged site (STS) marker, MS2, was isolated and mapped to the same locus as L8 on the Y chromosome. To investigate the peripheral regions of MS2, a bacterial artificial chromosome (BAC) library was constructed from a male plant, and the BAC clone containing MS2 (MS2-9d12F) was isolated from 32 640 clones with an average insert size of 115 kb. A 109-kb insert of the BAC clone was analyzed. BLASTX analysis showed 11 sequences similar to some known proteins, most of which are retrotransposon-like elements. The ORF Finder predicted 9 ORFs within MS2-9d12F. RT-PCR analyses revealed that only 4 of the 9 predicted ORFs are expressed in both male and female plants. These 4 ORFs are candidates for genes having counterparts on both the X and Y chromosomes. Dot-matrix plot analysis and a BLASTN search revealed LTR-like sequences close to the retrotransposon-like elements and high similarity to 3 known genomic sequences of S. latifolia. These results suggest an accumulation of retrotransposons and segmental duplications in peripheral regions of MS2 during the early stage of sex chromosome evolution. 相似文献
955.
Morita T Tanabe H Ito H Sugiyama K Kiriyama S 《Bioscience, biotechnology, and biochemistry》2008,72(3):767-772
We reexamined the hypothesis that increased mucin secretion by the ingestion of insoluble dietary fiber (IDF) could affect small intestinal nutrient absorption. Polystyrene foam (PSF) was used as IDF. Rats were fed a diet with or without 90 g of PSF/kg for 1, 2 and 4 wk. At the end of each period, a glucose and ovalbumin (OVA) solution was intubated after 12 h of food depletion, and the changes in serum concentrations of these components were monitored. Luminal mucin was measured as O-linked oligosaccharide chains and also determined by ELISA. In all periods, the luminal mucin content was greater in the PSF-fed group than in the fiber-free control. However, the changes in serum glucose and OVA concentrations were comparable between the groups at any time during any period. These results show that the enhancement of luminal mucin secretion lasted even after chronic ingestion of IDF, but that the increased luminal mucin content had no effect on the rate of luminal nutrient absorption. 相似文献
956.
Toshiya Katano Shin-ichi Nakano Osamu Mitamura Haruko Yoshida Hisayuki Azumi Yoshiki Matsuura Yuji Tanaka Hiraku Maezono Yasuhiro Satoh Takeshi Satoh Yuko Sugiyama Yasunori Watanabe Tetsuro Mimura Yuki Akagashi Hiroshi Machida Valentin V. Drucker Irina Tikhonova Olga Belykh Vladimir A. Fialkov Myung-Soo Han Sung-Ho Kang Masahito Sugiyama 《Limnology》2008,9(2):105-114
In Lake Baikal, picocyanobacteria are the most important primary producers during the summer. Freshwater picocyanobacteria
are discriminated into either the phycoerythrin (PE)-rich or the phycocyanin (PC)-rich types according to their pigment composition.
The distributions of these two types of picocyanobacteria were investigated in Barguzin Bay. The PC-rich type accounted for
>98% of the total picocyanobacteria at the station near the shore of the bay where river water flows directly in. In the offshore
area of the lake, all of the picocyanobacteria cells were of the PE-rich type. In addition, the occurrence of the PC-rich
type was restricted to the station, where the attenuation coefficient exceeded 0.25 m−1. Near the shore, where the turbidity was high (>1 NTU), the cell densities of both the PE- and PC-rich types increased away
from the river mouth. This indicates that the PC-rich type cells grow near the shore of the bay where turbidity is high. Since
the PC-rich type could not grow well when cells were incubated in offshore lake water, restricted distribution of the PC-rich
type could also be explained by their growth capability. The present study clearly demonstrated the shift in the pigment type
composition of picocyanobacteria from the coastal to the pelagic zone of Lake Baikal. The co-existence of the two pigment
types probably enables the abundance of the picocyanobacterial community to be stable over a broader range of environmental
conditions than would be possible for a single pigment type. 相似文献
957.
The phylogenetic positioning of the non-pathogenic genusSpiromastix in the Onygenales was studied based on large subunit rDNA (LSU rDNA) partial sequences (ca. 570 bp.). FourSpiromastix species and 28 representative taxa of the Onygenales were newly sequenced. Phylogenetic trees were constructed by the neighbor-joining
(NJ) method and evaluated by the maximum parsimony (MP) method with the data of 13 taxa retrieved from DNA databases.Spiromastix and dimorphic systemic pathogens,Ajellomyces andParacoccidioides, appear to be a monophyletic group with 74% bootstrap probability (BP) in the NJ tree constructed with the representative
taxa of the Onygenales. The tree topology was concordant with the NJ tree based on SSU rDNA sequences of our previous work
and corresponded to the classification system of the Onygenales by Currah (1985) and its minor modification by Udagawa (1997)
with the exception of the classification of the Onygenaceae. The Onygeneceae sensu Udagawa may still be polyphyletic, since
three independent lineages were recognized. The taxa forming helicoid peridial appendages were localized to two clades on
the tree. The topology of the NJ tree constructed withSpiromastix and its close relatives suggested that the helicoid peridial appendages were apomorphic and acquired independently in the
two clades of the Onygenales. 相似文献
958.
During the period from July 1992 to March 1995, suspended particulate matter in Lake Biwa was collected at 1-month intervals,
and the contents of Al, Si, and P were determined. Based on the analytical data, the particulate matter was fractionated by
calculation into three types of particles of different origins: particles of terrigenous origin, particles of diatom origin,
and particles due to microorganisms except for diatoms. The relative abundance of the respective particles was featured in
water depth-time (month) diagrams, with contours in terms of weight per liter of lake water. As a result, the characteristic
distributions of the particles were revealed, and their inherent roles in natural purification were distinguished from each
other. Of the three types of particles, the particles of diatom origin were anticipated to be the principal scavengers not
only of nutritious elements of silicon and phosphorus, but also of various metal ions dissolved in the lake.
Received: October 5, 2000 / Accepted: June 6, 2001 相似文献
959.
Rina Yogo Saeko Yanaka Hirokazu Yagi Anne Martel Linoel Porcar Yutaro Ueki Rintaro Inoue Nobuhiro Sato Masaaki Sugiyama Koichi Kato 《Biochemistry and Biophysics Reports》2017
A recently developed integrative approach combining varied types of experimental data has been successfully applied to three-dimensional modelling of larger biomacromolecular complexes. Deuteration-assisted small-angle neutron scattering (SANS) plays a unique role in this approach by making it possible to observe selected components in the complex. It enables integrative modelling of biomolecular complexes based on building-block structures typically provided by X-ray crystallography. In this integrative approach, it is important to be aware of the flexible properties of the individual building blocks. Here we examine the ability of SANS to detect a subtle conformational change of a multidomain protein using the Fc portion of human immunoglobulin G (IgG) interacting with a soluble form of the low-affinity Fcγ receptor IIIb (sFcγRIIIb) as a model system. The IgG-Fc glycoprotein was subjected to SANS in the absence and presence of 75%-deuterated sFcγRIIIb, which was matched out in D2O solution. This inverse contrast-matching technique enabled selective observation of SANS from IgG-Fc, thereby detecting its subtle structural deformation induced by the receptor binding. The SANS data were successfully interpreted by considering previously reported crystallographic data and an equilibrium between free and sFcγRIIIb-bound forms. Our SANS data thus demonstrate the applicability of SANS in the integrative approach dealing with biomacromolecular complexes composed of weakly associated building blocks with conformational plasticity. 相似文献
960.
Yuko Shimamura Chikako Hirai Yuka Sugiyama Masaharu Shibata Junya Ozaki Masatsune Murata 《Bioscience, biotechnology, and biochemistry》2017,81(12):2346-2352
In this study, we examined the inhibitory effects of 14 food additives derived from polyphenol samples on staphylococcal enterotoxin A (SEA) production and biofilm formation by Staphylococcus aureus. Tannic acid AL (TA), Purephenon 50 W (PP) and Polyphenon 70A (POP) at 0.25 mg/mL and Gravinol®-N (GN), Blackcurrant polyphenol AC10 (BP), and Resveratrol-P5 (RT) at 1.0 mg/mL significantly decreased SEA production by S. aureus C-29 (p < 0.05). TA, GN, BP, and RT significantly inhibited the expression of the sea gene in S. aureus C-29 (p < 0.05), while suppression attempts by PP and POP proved unsuccessful. After result analysis, it can be derived that TA, GN, BP, and RT inhibit the production of SEA. Of the six samples, each one significantly inhibited biofilm formation (p < 0.05). Food additives derived from polyphenols have viability to be used as a means to inhibit the enterotoxin production and control the biofilm formation of foodborne pathogens. 相似文献