Nozomi Ytow

Microbial Community Analyses Using a Simple, Rapid Detection Method for DNA Fingerprints with a Fluorescence Scanner

A simple detection procedure was developed for terminal restriction fragment length polymorphism and ribosomal intergenic spacer analysis for microbial community analysis. A fluorescence scanner enables generation of fingerprinting data in these methods within 3 h of obtaining PCR products of microbial communities.

Multiple viewed search engine for an e-journal: a case study on zoological science

The multiple viewed search engine presented here retrieves documents of an indicated search area and displays a matrix of the distribution of the clustering from two aspects of the retrieval result. The search engine provides a visual and semantic birds-eye view of the entire retrieval result. In addition, the characteristic words of each cluster are displayed in the matrix, and supports narrowing of the search. Furthermore, it is possible to immediately change the analysis criteria or the number of clusters and to use a zooming function. Thus, various retrieval conditions for a query can be attempted immediately and continuously. As a case study, this paper performs several analyses on the electronic journal Zoological Science using a multiple viewed search engine.

Rough Set Approximation as formal concept

Formal Concept Analysis (FCA) defines a formal concept as a pair of sets: objects and attributes, called extent and intent respectively. A rough set, on the other hand, approximates a concept using sets of objects only (in terms of FCA). We show that 1) a formal concept can be composed using a set of objects and its complement, 2) such object-based formal concepts are isomorphic to formal concepts based on objects and attributes, 3) upper and lower approximations of rough sets give generalization of formal concept, and 4) the pair of positive and negative sets (sensu rough set theory) are isomorphic to complemental formal concepts when the equivalence of the rough set gives positive and negative sets unique to each of the formal concepts. Implications of this are discussed.

Trophodynamic structure of a swampy bog at the climax stage of limnological succession. II: Bacterioplankton dynamics

Matsumi-ike Bog is a swampy bog that has attained the climax stage of limnological succession. The dynamics of bacterioplankton were studied in relation to the influence of environment factors. The water temperature was shown primarily affect bacterial dynamics as a limiting factor throughout the year. The second most profound factor on the dynamics was the concentration of dissolved organic carbon (DOC) when dead phytoplankton were the major DOC source in the bog, whereas phosphate concentration was most important in the periods when the dead emergent plants were responsible for the DOC supply.

Dynamics of attached bacteria at the water-sediment interface in a mesotrophic swampy bog of Japan

The population dynamics of attached bacteria at the water-sediment interface were studied in a mesotrophic swampy bog, Matsumi-ike, near Tsukuba, Japan. The density of attached bacteria was higher at the sediment boundary layer than in the water column, and low inside the sediment (deeper, than 10 mm below the sediment surface) throughout the year. The density of bacteria attached on the glass slide was highest during spring when the source of organic matter in the water column was mainly withered cattail, and gradually decreased toward summer, while the phytoplankton became the dominant source of organic matter in the water column. The epibacterial populations in the water column and at the boundary showed almost the same seasonal fluctuation in attachment and detachment rates. However, bacterial growth rates did not show the same seasonal fluctuation, and annual average growth rates on the glass slides were all lower than that of bacterioplankton (free-living bacteria in water) in the water column.

Trophodynamic structure of a swampy bog at the clymax stage of limnological succssion I. Prmary production dynamics

Effect of emergent vegetation on the population dynamics of phytoplankton community in Matsumi-ike Bog, a typical bog at the climax stage of limnological succession, was studied. The emergent vegetation grew until August and then withered and collapsed mainly during December and January, supplying the debris of emergent plants into the water column. Population density of the predominant phytoplankton showed sinusoidal fluctuation affected primarily by the water temperature, with various lag phases due to the function of other environmental factors. Shading by the emergent vegetation shifted the initiation of phytoplankton fluctuation earlier. This fluctuation patterns was most obvious among those phytoplankton contain chlorophyll-a and -b, but non -a and-c. The population dynamics were also compared with that of Matsumi-ike Bog at premature stages without (8 yr ago) or with littoral vegetations (3 yr ago). The population density of phytoplankton with chlorophyll-b decreased but those with chlorophyll-c increased, due to the shading effect of the emergent vegetation with the limnological succession of the bog. At the climax of succession, the dynamic state of phytoplankton community has become more stable.

UV spectrometry for measuring particulate organic matter in natural water

Ultraviolet (UV) spectra were measured to characterize the dissolved and particulate organic matter in a bog and to investigate the seasonal fluctuation of this organic matter. The optical density spectra in the UV region of dissolved organic matter (DOM) were proportional toλ−4, whereλ is the wavelength of incident light. There was also small absorption on theλ−4 spectra. The optical density at a wavelength of 280 nm was proportional to the concentration of dissolved organic carbon (DOC). The spectra and the dependency of optical density on DOC did not vary throughout the investigation period. The UV spectra of acid extractions of particulate organic matter (POM) showed two absorption peaks at the wavelengths of 220 nm and 335 nm. These peaks are well represented by the sum of two Lorentz functions. The ratio of the absorbances,A280/A335, was dependent on the nitrogen/carbon ratio of POM and the chlorophyll fraction in particulate organic carbon (POC), and not dependent on POC itself. The dependency of POC absorption at 280 nm varied with this ratio which fluctuated seasonally.

Microcolonization mechanism of attached bacteria in a natural water-column

AbstractA mathematical model of attached bacterial dynamics based on microcolonization was devised using data obtained from a bog. Bacterial samples obtained from any natural water body can be examined by this model with the method of non-linear least squares. The model comprises three bacterial processes; i.e., (1) the attachment rate which was dependent on time after submergence by adsorption onto the substratum surface, and both (2) growth and (3) detachment rate which were dependent on the number of bacterial cells in the microcolony. The population dynamics are expressed as

Nomencurator: a nomenclatural history model to handle multiple taxonomic views

\frac{{dC_i }}{{dt}} = - g_i C_i + g_{i - 1} C_{i - 1} - b_i C_i + b_{i + 1} C_{i + 1} + a_i F_i ,