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Search Results: 1 - 10 of 4073 matches for " Haruo Suzuki "
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Measure of synonymous codon usage diversity among genes in bacteria
Haruo Suzuki, Rintaro Saito, Masaru Tomita
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-167
Abstract: The application of Dmean to 268 bacterial genomes shows that in bacteria with extremely biased genomic G+C compositions there is little diversity in synonymous codon usage among genes. Furthermore, our findings contradict previous reports. For example, a low level of diversity in codon usage among genes has been reported for Helicobacter pylori, but based on Dmean, the diversity level of this species is higher than those of more than half of bacteria tested here. The discrepancies between our findings and previous reports are probably due to differences in the methods used for measuring codon usage diversity.We recommend that Dmean be used to measure the diversity level of codon usage among genes. This measure can be applied to other compositional features such as amino acid usage and dinucleotide relative abundance as a genomic signature.Most amino acids can be encoded by more than one codon (i.e., a triplet of nucleotides); such codons are described as being synonymous, and usually differ by one nucleotide in the third position. In most bacteria, alternative synonymous codons are not used with equal frequencies. Grantham et al. [1] showed that genes from same species often show similar patterns of codon usage, and proposed the 'genome hypothesis' that there exists a species-specific pattern of codon usage. Then, it was shown that in many organisms there are also considerable differences in codon usage among genes within a genome [2]. Previous analyses of codon usage diversity in bacteria have mostly focused on individual genomes, with no quantitative attempt to compare the diversity levels among different genomes. For comparative genomic analysis, it is desirable to quantify the level of codon usage diversity among genes in such a way that the estimates could be compared among genomes.Different factors have been proposed to explain the preferential usage of a subset of synonymous codons, including biased mutation pressure (genome-wide mutational bias toward G/C or
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria
Haruo Suzuki, Rintaro Saito, Masaru Tomita
EURASIP Journal on Bioinformatics and Systems Biology , 2007, DOI: 10.1155/2007/61374
Abstract: [1234567891011121314151617181920212223]
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index
Kazuharu Arakawa, Haruo Suzuki, Masaru Tomita
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-640
Abstract: Here we discuss a quantitative index for the measurement of GC skew strength, named the generalised GC skew index (gGCSI), which is applicable to genomes of any length, including bacterial chromosomes and plasmids. We demonstrate that gGCSI is independent of the window size and can thus be used to compare genomes with different sizes, such as bacterial chromosomes and plasmids. It can suggest the existence of different replication mechanisms in archaea and of rolling-circle replication in plasmids. Correlation of gGCSI values between plasmids and their corresponding host chromosomes suggests that within the same strain, these replicons have reproduced using the same replication machinery and thus exhibit similar strengths of replication strand skew.gGCSI can be applied to genomes of any length and thus allows comparative study of replication-related mutation and selection pressures in genomes of different lengths such as bacterial chromosomes and plasmids. Using gGCSI, we showed that replication-related mutation or selection pressure is similar for replicons with similar machinery.DNA replication makes up a significant proportion of the bacterial cell cycle, especially in fast-growing bacteria where chromosomes undergo multiple rounds of replication in order to compensate for a short generation time [1]. Therefore, bacterial chromosomes are structured by the requirement to be an efficient medium for replication [2]. Eubacterial species typically have circular chromosomes that are partitioned into two replichores by one finite set of a symmetrically located replication origin and terminus [3]. Accordingly, many genomic features exhibit characteristic replication-related organisation, including the nucleotide compositional bias, distribution of signal oligonucleotides such as Chi sites [4,5] and KOPS motifs [6,7], as well as gene positioning and strand preference [8]. Nucleotide compositional asymmetry in the leading and lagging strands has been extensively studied us
A Statistical Method for Selecting Pattern Descriptors of Textured 3D Models
Motofumi T. Suzuki,Yoshitomo Yaginuma,Haruo Kodama
Lecture Notes in Engineering and Computer Science , 2010,
Abstract:
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria
Suzuki Haruo,Saito Rintaro,Tomita Masaru
EURASIP Journal on Bioinformatics and Systems Biology , 2007,
Abstract: G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from 0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.
Natural Forest Biomass Estimation Based on Plantation Information Using PALSAR Data
Ram Avtar, Rikie Suzuki, Haruo Sawada
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086121
Abstract: Forests play a vital role in terrestrial carbon cycling; therefore, monitoring forest biomass at local to global scales has become a challenging issue in the context of climate change. In this study, we investigated the backscattering properties of Advanced Land Observing Satellite (ALOS) Phased Array L-band Synthetic Aperture Radar (PALSAR) data in cashew and rubber plantation areas of Cambodia. The PALSAR backscattering coefficient (σ0) had different responses in the two plantation types because of differences in biophysical parameters. The PALSAR σ0 showed a higher correlation with field-based measurements and lower saturation in cashew plants compared with rubber plants. Multiple linear regression (MLR) models based on field-based biomass of cashew (C-MLR) and rubber (R-MLR) plants with PALSAR σ0 were created. These MLR models were used to estimate natural forest biomass in Cambodia. The cashew plant-based MLR model (C-MLR) produced better results than the rubber plant-based MLR model (R-MLR). The C-MLR-estimated natural forest biomass was validated using forest inventory data for natural forests in Cambodia. The validation results showed a strong correlation (R2 = 0.64) between C-MLR-estimated natural forest biomass and field-based biomass, with RMSE = 23.2 Mg/ha in deciduous forests. In high-biomass regions, such as dense evergreen forests, this model had a weaker correlation because of the high biomass and the multiple-story tree structure of evergreen forests, which caused saturation of the PALSAR signal.
Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae
Haruo Suzuki, Tristan Lefébure, Paulina Bitar, Michael J Stanhope
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-38
Abstract: We determined a Roche/454 draft genome sequence for S. simiae and included it in comparative genomic analyses with 11 other Staphylococcus species including S. aureus. A genome based phylogeny of the genus confirms that S. simiae is the sister group to S. aureus and indicates that the most basal Staphylococcus lineage is Staphylococcus pseudintermedius, followed by Staphylococcus carnosus. Given the primary niche of these two latter taxa, compared to the other species in the genus, this phylogeny suggests that human adaptation evolved after the split of S. carnosus. The two coagulase-positive species (S. aureus and S. pseudintermedius) are not phylogenetically closest but share many virulence factors exclusively, suggesting that these genes were acquired by horizontal transfer. Enrichment in genes related to mobile elements such as prophage in S. aureus relative to S. simiae suggests that pathogenesis in the S. aureus group has developed by gene gain through horizontal transfer, after the split of S. aureus and S. simiae from their common ancestor.Comparative genomic analyses across 12 Staphylococcus species provide hypotheses about lineages in which human adaptation has taken place and contributions of horizontal transfer in pathogenesis.Staphylococcus belongs to the Gram-positive low G + C content group of the Firmicutes division of bacteria. Staphylococcus aureus is an important human and veterinary pathogen that causes a broad spectrum of diseases, and has developed important multidrug resistant forms such as methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) [1-3]. Despite emergence of MRSA in human and various animal species, mechanisms of host adaptation are poorly understood [4]. Comparative genomic analyses of phylogenetically closely related bacteria with different phenotypes (e.g. host specificity and pathogenicity) can provide information relevant to understanding adaptation to host environment and mechanisms of pathogenicit
Changes in Acid Invertase Activity and Sugar Distribution During Postharvest Senescence in Broccoli
Bimal Kumar Pramanik,Toshiyuki Matsui,Haruo Suzuki,Yusuke Kosugi
Pakistan Journal of Biological Sciences , 2004,
Abstract: Changes in acid invertase activity and sugar distribution were studied during postharvest senescence of broccoli (Brassica oleracea L. cvs. `Hartland` and `Sairin`) stored at 20 C. Broccoli head began to degreen after 3 days of storage and the degree of yellowing gradually increased at the end of the storage period. Respiration rate decreased markedly during the first 24 h of postharvest storage and increased slightly thereafter. In both cultivars and portions, the invertase activity increased gradually at the end of the storage time. The acid invertase in cell wall-bound fraction (CWBF) showed a higher activity than that in soluble fraction (SF). Again, the branchlets showed a significantly higher invertase activity than that of florets. Of the two cultivars, `Sairin` showed a higher invertase activity in both portions. Sucrose content gradually decreased in both portions of the two cultivars with time. It was negatively correlated with the acid invertase activity in both portions accounting well for the relation between the substrate and the activity. Fructose content was higher than glucose and sucrose in the florets as well as branchlets in both cultivars. Comparing the two cultivars, `Sairin` showed higher enzyme activities, sugar content and respiration rate than `Hartland`.
Classification of Oriental Melon by RAPD Analysis
Toshiyuki Matsui,Yusuke Kosugi,Tomohiro Yanagi,Haruo Suzuki
Pakistan Journal of Biological Sciences , 2002,
Abstract: The genetic relationship of 13 oriental melon (Cucumis melo L.) was determined using random amplified polymorphic DNA (RAPD) analysis with 12 dodecamer oligonucleotide primers. Representative cultivars could be divided into two major groups at 0.756 similarity value. One group included 7 makuwa melons namely, " Nara-1-gou ", " Tiger-melon ", " Kinpyou ", " Kiku-melon ", " Nashi-makuwa ", " Shouwa-melon " and 4 conomon melons namely, " Numame-shirouri ", " Katsura-ohoshirouri ", " Tokyo-ohoshirouri ", " Kuromonao-ohoshirouri ". The other major group included 2 makuwa cultivars namely " Ginsen " and " Wasegin ". The RAPD showed that conomon melon belonged to same species as makuwa melon. It seemed that, makuwa melon is an allogamous plant which hybridizes easily with table-melons and conomon melon and it might have hybridized with conomon melon in the distant past.
Effects of Mulching on the Activity of Acid Invertase and Sugar Contents in Japanese Radish
Teerasak Pongsa-Anutin,Haruo Suzuki,Toshiyuki Matsui
Asian Journal of Plant Sciences , 2007,
Abstract: The effects of mulching on soil moisture and temperature and sugar metabolism in Japanese radish (Raphanus sativus L.) were studied. Soil moisture content and temperature were higher in mulched plots than the none-mulched plots throughout the experimental period. Radish roots grown in plots with mulch were heavier than those without one. Acid invertase activities in soluble fraction (SF) and cell wall-bound fraction (CWBF) of the roots grown in plots with and without mulch showed the same pattern. However, the enzyme activity was higher in roots grown in mulched plots. The acid invertase activity in SF gradually increased during growth and development while no specific inclining or declining pattern was found in CWBF. Mulching did not significantly affect the amount of fructose (Fru) and glucose (Glc) contents during growth and development. However, sucrose (Suc) content in roots grown in plots with mulch was higher than those grown without mulch throughout the experimental period. Fru and Glc contents in the bottom portion of the root were also found to have same pattern as the top portion. Present results suggest that mulching could increase crop yield by producing heavier root weight and improve product quality such as sweetness due to higher Suc content of the roots.
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