A strategy for predicting gene functions from genome and metagenome sequences on the basis of oligopeptide frequency distance.

As a result of the extensive decoding of a massive amount of genomic and metagenomic sequence data, a large number of genes whose functions cannot be predicted by sequence similarity searches are accumulating, and such genes are of little use to science or industry. Current genome and metagenome sequencing largely depend on high-throughput and low-cost methods. In the case of genome sequencing for a single species, high-density sequencing can reduce sequencing errors. For metagenome sequences, however, high-density sequencing does not necessarily increase the sequence quality because multiple and unknown genomes, including those of closely related species, are likely to exist in the sample. Therefore, a function prediction method that is robust against sequence errors becomes an increased need. Here, we present a method for predicting protein gene function that does not depend on sequence similarity searches. Using an unsupervised machine learning method called BLSOM (batch-learning self-organizing map) for short oligopeptide frequencies, we previously developed a sequence alignment-free method for clustering bacterial protein genes according to clusters of orthologous groups of proteins (COGs), without using information from COGs during machine learning. This allows function-unknown proteins to cluster with function-known proteins, based solely on similarity with respect to oligopeptide frequency, although the method required high-performance supercomputers (HPCs). Based on a wide range of knowledge obtained with HPCs, we have now developed a strategy to correlate function-unknown proteins with COG categories, using only oligopeptide frequency distances (OPDs), which can be conducted with PC-level computers. The OPD strategy is suitable for predicting the functions of proteins with low sequence similarity and is applied here to predict the functions of a large number of gene candidates discovered using metagenome sequencing.

Studying anti-oxidative properties of inclusion complexes of α-lipoic acid with γ-cyclodextrin in single living fission yeast by confocal Raman microspectroscopy.

α-lipoic acid (ALA) is an essential cofactor for many enzyme complexes in aerobic metabolism, especially in mitochondria of eukaryotic cells where respiration takes place. It also has excellent anti-oxidative properties. The acid has two stereo-isomers, R- and S- lipoic acid (R-LA and S-LA), but only the R-LA has biological significance and is exclusively produced in our body. A mutant strain of fission yeast, Δdps1, cannot synthesize coenzyme Q10, which is essential during yeast respiration, leading to oxidative stress. Therefore, it shows growth delay in the minimal medium. We studied anti-oxidant properties of ALA in its free form and their inclusion complexes with γ-cyclodextrin using this mutant yeast model. Both free forms R- and S-LA as well as 1:1 inclusion complexes with γ-cyclodextrin recovered growth of Δdps1 depending on the concentration and form. However, it has no effect on the growth of wild type fission yeast strain at all. Raman microspectroscopy was employed to understand the anti-oxidant property at the molecular level. A sensitive Raman band at 1602cm-1 was monitored with and without addition of ALAs. It was found that 0.5mM and 1.0mM concentrations of ALAs had similar effect in both free and inclusion forms. At 2.5mM ALAs, free forms inhibited the growth while inclusion complexes helped in recovered. 5.0mM ALA showed inhibitory effect irrespective of form. Our results suggest that the Raman band at 1602cm-1 is a good measure of oxidative stress in fission yeast.

Infectivity of Cryptosporidium andersoni and Cryptosporidium muris to normal and immunosuppressive cynomolgus monkeys.

Cryptosporidium andersoni and Cryptosporidium muris infections have been found in the mice and/or cattle. The oocysts of C. andersoni and C. muris have been sporadically detected in human feces, but the infectious capacity and features have been unknown, because of the scarcity of reports involving human infections. To assess the infectivity and the clinical and pathological features of C. andersoni and C. muris in primates, an experimental infectious study was conducted using cynomolgus monkeys. The monkeys were orally inoculated with oocysts of two different C. andersoni Kawatabi types and C. muris RN-66 under normal and immunosuppressive conditions. The feces of the monkeys were monitored for about 40 days after the administration of oocysts using the flotation method, but no shedding oocysts were observed under either both normal or immunosuppressive conditions. Gross and histopathological examinations were performed on the immunosuppressive monkeys, but these revealed no evidence of Cryptosporidium infections, even though the monkeys were subjected to immunosuppressive conditions. It is hypothesized that C. andersoni and C. muris pose little danger of infection in primates even under immunosuppressive conditions.