Sachiyo Aburatani

Publications

4 Comparative Analysis of Soil Enzyme Activities between Laurel-Leaved and Cryptomeria japonica Forests

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

Soil enzyme activities in Kasuga-yama Hill Primeval Forest (Nara, Japan) were examined to determine levels of mineralization and metabolism. Samples were selected from the soil surrounding laurel-leaved (BB-1) and Carpinus japonica (BB-2 and Pw) trees for analysis. Cellulase, β-xylosidase, and protease activities were higher in BB-1 samples those in BB-2 samples. These activity levels corresponded to the distribution of cellulose and hemicellulose in the soil horizons. Cellulase, β-xylosidase, and chymotrypsin activities were higher in soil from the Pw forest than in that from the BB-2 forest. The relationships between the soil enzymes calculated by Spearman’s rank correlation indicate that the interactions between enzymes in BB-2 samples were more complex than those in Pw samples.

Keywords: Enzyme Activities, Forest Soil, Comparative Analysis, Spearman’s rank correlation

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3 Soil Respiration Rate of Laurel-Leaved and Cryptomeria japonica Forests

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

We assessed the ecology of the organic and mineral soil layers of laurel-leaved (BB-1) and Cryptomeria japonica (BB-2 and Pw) forests in the Kasugayama Hill Primeval Forest (Nara, Japan). The soil respiration rate was higher in the deeper horizons (F and H) of organic layers than in those of mineral soil layers, suggesting organic layers may be where active microbial metabolism occurs. Respiration rates in the soil of BB-1, BB-2 and Pw forests were closely similar at 5 and 10°C. However, the soil respiration rate increased in proportion to temperatures of 15°C or above. We therefore consider the activity of soil microorganisms to markedly decrease at temperatures below 10°C. At a temperature of 15°C or above, the soil respiration rate in the BB-1 organic layers was higher than in those of the BB-2 and Pw organic layers, due to differences in forest vegetation that appeared to influence several salient soil properties, particularly pH and the carbon (C) and nitrogen (N) content of the F and H horizons.

Keywords: Forest Soil, mineralization rate, soil respiration rate

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2 Application of KL Divergence for Estimation of Each Metabolic Pathway Genes

Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

Abstract:

Development of a method to estimate gene functions is an important task in bioinformatics. One of the approaches for the annotation is the identification of the metabolic pathway that genes are involved in. Since gene expression data reflect various intracellular phenomena, those data are considered to be related with genes’ functions. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: Machine Learning, Metabolic Pathways, Microarray, Gene Expression Data, SVM, Kullback–Leibler divergence, KL divergence, support vector machines

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1 Numbers and Biomass of Bacteria and Fungi Obtained by the Direct Microscopic Count Method

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

The soil ecology of the organic and mineral soil layers of laurel-leaved and Cryptomeria japonica forest in the Kasuga-yama Hill Primeval Forest (Nara, Japan) was assessed. The number of bacteria obtained by the dilution plate count method was less than 0.05% of those counted by the direct microscopic count. We therefore found that forest soil contains large numbers of non-culturable bacteria compared with agricultural soils. The numbers of bacteria and fungi obtained by both the dilution plate count and the direct microscopic count were larger in the deeper horizons (F and H) of the organic layer than in the mineral soil layer. This suggests that active microbial metabolism takes place in the organic layer. The numbers of bacteria and the length of fungal hyphae obtained by the direct count method were greater in the H horizon than in the F horizon. The direct microscopic count revealed numerous non-culturable bacteria and fungi in the soil. The ratio of fungal to bacterial biomass was lower in the laurel-leaved forest soil. The fungal biomass was therefore relatively low in the laurel-leaved forest soil due to differences in forest vegetation.

Keywords: Forest Soil, Bacterial number, Dilution plate count, Direct microscopic count

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Abstracts

10 Network Analysis to Reveal Microbial Community Dynamics in the Coral Reef Ocean

Authors: Keigo Ide, Toru Maruyama, Michihiro Ito, Hiroyuki Fujimura, Yoshikatu Nakano, Shoichiro Suda, Sachiyo Aburatani, Haruko Takeyama

Abstract:

Understanding environmental system is one of the important tasks. In recent years, conservation of coral environments has been focused for biodiversity issues. The damage of coral reef under environmental impacts has been observed worldwide. However, the casual relationship between damage of coral and environmental impacts has not been clearly understood. On the other hand, structure/diversity of marine bacterial community may be relatively robust under the certain strength of environmental impact. To evaluate the coral environment conditions, it is necessary to investigate relationship between marine bacterial composition in coral reef and environmental factors. In this study, the Time Scale Network Analysis was developed and applied to analyze the marine environmental data for investigating the relationship among coral, bacterial community compositions and environmental factors. Seawater samples were collected fifteen times from November 2014 to May 2016 at two locations, Ishikawabaru and South of Sesoko in Sesoko Island, Okinawa. The physicochemical factors such as temperature, photosynthetic active radiation, dissolved oxygen, turbidity, pH, salinity, chlorophyll, dissolved organic matter and depth were measured at the coral reef area. Metagenome and metatranscriptome in seawater of coral reef were analyzed as the biological factors. Metagenome data was used to clarify marine bacterial community composition. In addition, functional gene composition was estimated from metatranscriptome. For speculating the relationships between physicochemical and biological factors, cross-correlation analysis was applied to time scale data. Even though cross-correlation coefficients usually include the time precedence information, it also included indirect interactions between the variables. To elucidate the direct regulations between both factors, partial correlation coefficients were combined with cross correlation. This analysis was performed against all parameters such as the bacterial composition, the functional gene composition and the physicochemical factors. As the results, time scale network analysis revealed the direct regulation of seawater temperature by photosynthetic active radiation. In addition, concentration of dissolved oxygen regulated the value of chlorophyll. Some reasonable regulatory relationships between environmental factors indicate some part of mechanisms in coral reef area.

Keywords: Network Analysis, Marine Microbiology, coral environment, omics data analysis

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9 Gene Expression Analysis for Corals / Zooxanthellae under High Seawater Temperature Stress

Authors: Haruka Ito, Toru Maruyama, Michihiro Ito, Chuya Shinzato, Hiroyuki Fujimura, Yoshikatsu Nakano, Shoichiro Suda, Sachiyo Aburatani, Haruko Takeyama

Abstract:

Clarifying symbiotic relationships is one of the most important theme for understanding the marine eco-system. Coral reef has been regarded as an important environmental resource. Coral holobiont composed by coral, symbiotic microalgae zooxanthellae, and bacteria have complexed relationship. Zooxanthellae mainly supply organic matter to the host corals through their photosynthetic activity. The symbiotic relationship is indispensable for corals but may easily collapses due to the rise of seawater temperature. However, the molecular mechanism how seawater temperature influences their relationships still remain unclear. In this study, the transcriptomic analysis has applied to elucidate the coral-zooxanthellae relationships under high seawater temperature stress. To observe reactions of corals and zooxanthellae against the rise of seawater temperature, meta-gene expression in coral have been analyzed. The branches from six different colonies of a stony coral, Acropora tenuis, were sampled at nine times by 2016 at two locations, Ishikawabaru and South of Sesoko Island, Okinawa, Japan. The mRNAs extracted from the branches including zooxanthellae were sequenced by illumina HiSeq. Gene Set Enrichment Analysis (GSEA) based on hyper geometric distribution was performed. The seawater temperature at 2016 summer was unusually high, which was caused by El Niño event, and the number of zooxanthellae in coral was decreased in August. GSEA derived the several specific genes expressed in A. tenuis under heat stress conditions. The upregulated genes under heat stress highly related with infection immunity. The downregulated genes significantly contained cell cycle related genes. Thu, it is considered that heat stress cause disorder in cell metabolism of A. tenuis, resulting in serious influence to coral holobiont.

Keywords: Symbiosis, coral, thermal stress response, transcriptome analysis

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8 Elucidation of the Sequential Transcriptional Activity in Escherichia coli Using Time-Series RNA-Seq Data

Authors: Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani

Abstract:

Functional genomics and gene regulation inference has readily expanded our knowledge and understanding of gene interactions with regards to expression regulation. With the advancement of transcriptome sequencing in time-series comes the ability to study the sequential changes of the transcriptome. This method presented here works to augment existing regulation networks accumulated in literature with transcriptome data gathered from time-series experiments to construct a sequential representation of transcription factor activity. This method is applied on a time-series RNA-Seq data set from Escherichia coli as it transitions from growth to stationary phase over five hours. Investigations are conducted on the various metabolic activities in gene regulation processes by taking advantage of the correlation between regulatory gene pairs to examine their activity on a dynamic network. Especially, the changes in metabolic activity during phase transition are analyzed with focus on the pagP gene as well as other associated transcription factors. The visualization of the sequential transcriptional activity is used to describe the change in metabolic pathway activity originating from the pagP transcription factor, phoP. The results show a shift from amino acid and nucleic acid metabolism, to energy metabolism during the transition to stationary phase in E. coli.

Keywords: Network, Gene Regulation, Escherichia coli, time-series

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7 Neutral Sugars in Two-Step Hydrolysis of Laurel-Leaved and Cryptomeria japonica Forests

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

Soil neutral sugar contents in Kasuga-yama Hill Primeval Forest, which is a World Heritage Site in Nara, Japan consisting of lowland laurel-leaved forest where natural conditions have been preserved for more than 1,000 years, were examined using the two-step hydrolysis to clarify the source of the neutral sugar and relations with the neutral sugar constituted the soil organic matter and the microbial biomass. Samples were selected from the soil (L, F, H and A horizons) surrounding laurel-leaved (BB-1) and Carpinus japonica (BB-2 and PW) trees for analysis. The neutral sugars were one factor of increasing the fungal and bacterial biomass in the laurel-leaved forest soil (BB-1). The more neutral sugar contents in the Cryptomeria japonica forest soil (PW) contributed to the growth of the bacteria and fungi than those of in the Cryptomeria japonica forest soil (BB-2). The neutral sugars had higher correlation with the numbers of bacteria and fungi counted by the dilution plate count method than by the direct microscopic count method. The numbers of fungi had higher correlation with those of bacteria by the dilution plate method.

Keywords: Soil Organic Matter, Forest Soil, neutral sugars, two-step hydrolysis

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6 Seasonal and Monthly Field Soil Respiration Rate and Litter Fall Amounts of Kasuga-Yama Hill Primeval Forest

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

The seasonal (January, April, July and October) and monthly soil respiration rate and the monthly litter fall amounts were examined in the laurel-leaved (B_B-1) and Cryptomeria japonica (B_B-2 and PW) forests in the Kasugayama Hill Primeval Forest (Nara, Japan). The change of the seasonal soil respiration rate corresponded to that of the soil temperature. The soil respiration rate was higher in October when fresh organic matter was supplied in the forest floor than in April in spite of the same temperature. The seasonal soil respiration rate of B_B-1 was higher than that of B_B-2, which corresponded to more numbers of bacteria and fungi counted by the dilution plate method and by the direct count method by microscopy in B_B-1 than that of B_B-2. The seasonal soil respiration rate of B_B-2 was higher than that of PW, which corresponded to more microbial biomass by the direct count method by microscopy in B_B-2 than that of PW. The correlation coefficient with the seasonal soil respiration and the soil temperature was higher than that of the monthly soil respiration. The soil respiration carbon was more than the litter fall carbon. It was suggested that the soil respiration included in the carbon dioxide which was emitted by the plant root and soil animal, or that the litter fall supplied to the forest floor included in animal and plant litter.

Keywords: Forest Soil, mineralization rate, field soil respiration rate, litter fall

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5 Neutral Sugar Contents of Laurel-leaved and Cryptomeria japonica Forests

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

Soil neutral sugar contents in Kasuga-yama Hill Primeval Forest (Nara, Japan) were examined using the Waksman’s approximation analysis to clarify relations with the neutral sugar constituted the soil organic matter and the microbial biomass. Samples were selected from the soil surrounding laurel-leaved (BB-1) and Carpinus japonica (BB-2) trees for analysis. The water and HCl soluble neutral sugars increased microbial biomass of the laurel-leaved forest soil. Arabinose, xylose, and galactose of the HCl soluble fraction were used immediately in comparison with other neutral sugars. Rhamnose, glucose, and fructose of the HCl soluble fraction were re-composed by the microbes.

Keywords: Soil Organic Matter, Forest Soil, neutral sugaras, Waksman’s approximation analysis

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4 Application of KL Divergence for Estimation of Each Metabolic Pathway Genes

Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

Abstract:

The development of the method to annotate unknown gene functions is an important task in bioinformatics. One of the approaches for the annotation is The identification of the metabolic pathway that genes are involved in. Gene expression data have been utilized for the identification, since gene expression data reflect various intracellular phenomena. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: Machine Learning, Support Vector Machines, Metabolic Pathways, Microarray, Gene Expression Data, SVM, Kullback–Leibler divergence, KL divergence

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3 Comparative Analysis of Soil Enzyme Activities between Laurel-Leaved and Cryptomeria japonica Forests

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

Soil enzyme activities in Kasuga-yama Hill Primeval Forest (Nara, Japan) were examined to determine levels of mineralization and metabolism. Samples were selected from the soil surrounding laurel-leaved (BB-1) and Carpinus japonica (BB-2 and Pw) trees for analysis. Cellulase, β-xylosidase, and protease activities were higher in BB-1 samples those in BB-2 samples. These activity levels corresponded to the distribution of cellulose and hemicellulose in the soil horizons. Cellulase, β-xylosidase, and chymotrypsin activities were higher in soil from the Pw forest than in that from the BB-2 forest. The relationships between the soil enzymes calculated by Spearman’s rank correlation indicate that the interactions between enzymes in BB-2 samples were more complex than those in Pw samples.

Keywords: Enzyme Activities, Forest Soil, Comparative Analysis, Spearman's rank correlation

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2 Soil Respiration Rate of Laurel-Leaved and Cryptomeria japonica Forests

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

We assessed the ecology of the organic and mineral soil layers of laurel-leaved (BB-1) and Cryptomeria japonica (BB-2 and Pw) forests in the Kasugayama Hill Primeval Forest (Nara, Japan). The soil respiration rate was higher in the deeper horizons (F and H) of organic layers than in those of mineral soil layers, suggesting organic layers may be where active microbial metabolism occurs. Respiration rates in the soil of BB-1, BB-2 and Pw forests were closely similar at 5 and 10°C. However, the soil respiration rate increased in proportion to temperatures of 15°C or above. We therefore consider the activity of soil microorganisms to markedly decrease at temperatures below 10°C. At a temperature of 15°C or above, the soil respiration rate in the BB-1 organic layers was higher than in those of the BB-2 and Pw organic layers, due to differences in forest vegetation that appeared to influence several salient soil properties, particularly pH and the carbon (C) and nitrogen (N) content of the F and H horizons.

Keywords: Forest Soil, mineralization rate, heterotroph, soil respiration rate

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1 Comparative Analysis of Enzyme Activities Concerned in Decomposition of Toluene

Authors: Ayuko Itsuki, Sachiyo Aburatani

Abstract:

In recent years, pollutions of the environment by toxic substances become a serious problem. While there are many methods of environmental clean-up, the methods by microorganisms are considered to be reasonable and safety for environment. Compost is known that it catabolize the meladorous substancess in its production process, however the mechanism of its catabolizing system is not known yet. In the catabolization process, organic matters turn into inorganic by the released enzymes from lots of microorganisms which live in compost. In other words, the cooperative of activated enzymes in the compost decomposes malodorous substances. Thus, clarifying the interaction among enzymes is important for revealing the catabolizing system of meladorous substance in compost. In this study, we utilized statistical method to infer the interaction among enzymes. We developed a method which combined partial correlation with cross correlation to estimate the relevance between enzymes especially from time series data of few variables. Because of using cross correlation, we can estimate not only the associative structure but also the reaction pathway. We applied the developed method to the enzyme measured data and estimated an interaction among the enzymes in decomposition mechanism of toluene.

Keywords: Enzyme Activities, Comparative Analysis, compost, toluene

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