Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation

The cichlids of Lake Victoria are a textbook example of adaptive radiation, as >500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments—Haplochromis chilotes, H. sauvagei, and Lithochromis rufus—to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.     

B chromosomes have a functional effect on female sex determination in Lake Victoria cichlid fishes

The endemic cichlid fishes in Lake Victoria are a model system for speciation through adaptive radiation. Although the evolution of the sex-determination system may also play a role in speciation, little is known about the sex-determination system of Lake Victoria cichlids. To understand the evolution of the sex-determination system in these fish, we performed cytogenetic analysis in 11 cichlid species from Lake Victoria. B chromosomes, which are present in addition to standard chromosomes, were found at a high prevalence rate (85%) in these cichlids. In one species, B chromosomes were female-specific. Cross-breeding using females with and without the B chromosomes demonstrated that the presence of the B chromosomes leads to a female-biased sex ratio in this species. Although B chromosomes were believed to be selfish genetic elements with little effect on phenotype and to lack protein-coding genes, the present study provides evidence that B chromosomes have a functional effect on female sex determination. FISH analysis using a BAC clone containing B chromosome DNA suggested that the B chromosomes are derived from sex chromosomes. Determination of the nucleotide sequences of this clone (104.5 kb) revealed the presence of several protein-coding genes in the B chromosome, suggesting that B chromosomes have the potential to contain functional genes. Because some sex chromosomes in amphibians and arthropods are thought to be derived from B chromosomes, the B chromosomes in Lake Victoria cichlids may represent an evolutionary transition toward the generation of sex chromosomes.     

Difference in cesium accumulation among rice cultivars grown in the paddy field in Fukushima Prefecture in 2011 and 2012

After the accident of the Fukushima 1 Nuclear Power Plant in March 2011, radioactive cesium was released and paddy fields in a wide area including Fukushima Prefecture were contaminated. To estimate the levels of radioactive Cs accumulation in rice produced in Fukushima, it is crucial to obtain the actual data of Cs accumulation levels in rice plants grown in the actual paddy field in Fukushima City. We herein conducted a two-year survey in 2011 and 2012 of radioactive and non-radioactive Cs accumulation in rice using a number of rice cultivars grown in the paddy field in Fukushima City. Our study demonstrated a substantial variation in Cs accumulation levels among the cultivars of rice.     

Microstructures of bread dough and the effects of shortening on frozen dough

Three types of straight doughs different in combination of yeast and shortenings (RLS20, FTS20, and FTS80) were prepared, and the structure of the frozen doughs was examined under a microscope after staining protein or lipid droplets. Even after 2 months of frozen storage, distinct changes were not found in the gluten network of FTS80, although significant damages in the dough structures of FTS20 and RLS20 appeared after only one month of frozen storage. These results suggest that the gluten networks loosen and decrease in the water retention ability, and it may be concluded that the lipid is removed from the gluten protein due to the decrease in water in the continuous protein phase. The resulting product from the damage to the gluten matrix gave rise to fusion of lipid droplets and an increase in their size. Because of the difference in fatty acid composition, the lipids of shortening S80 are presumed to interact more strongly with gluten proteins and to keep the gluten matrix from damage in comparison with the lipids of shortening S20.     

Breed differences in growth hormone and insulin secretion between lactating Japanese Black cows (beef type) and Holstein cows (dairy type)

This study was performed to clarify the levels of growth hormone (GH) and insulin (INS) secretions and the glucose response to INS during lactation in a representative beef breed in Japan, Japanese Black cows, and to compare them with their counterparts in a dairy breed, Holstein cows. Six Japanese Black and seven Holstein primiparous cows received a single intravenous injection of GH-releasing factor (GRF; 0.25 microg/kg), glucose (112.5 mg/kg), or INS (0.2 U/kg) from late pregnancy (2 weeks antepartum) to mid-lactation (6 months postpartum). Japanese Black cows had one-tenth of the total milk yield of Holstein cows during lactation, and significantly lower GRF-induced GH and higher glucose-induced INS secretions than Holstein cows at all stages. In Japanese Black cows, even with lactation, these secretions remained essentially unchanged, whilst Holstein cows showed higher GH and lower INS secretions after the onset of lactation as compared with cows in late pregnancy. Both breeds had similar glucose response to INS at the respective stages. These results suggest that, during lactation, Japanese Black cows may minimize the catabolic effects of GH and sustain the anabolic effects of INS, in contrast with Holstein cows, but have similar ability to inhibit INS-mediated glucose utilization in peripheral tissues to Holstein cows.     

Conformational change of cytochrome P-450 indicated by the measurement of fluorescence-energy transfer

The conformation of cytochrome P-450 was studied in relation to the interaction with its substrate by the measurement of fluorescence energy transfer. Cytochrome P-450 I-c and cytochrome P-450 II-d, both obtained from the hepatic microsome of polychlorinated biphenyl-treated rats, were used as P-450 type and P-448 type, respectively, and benzo[a]pyrene and 7-ethoxycoumarin were used as substrate. The distance between the donor and acceptor, which was described by the F?rster equation, was calculated on the basis of the fluorescence-energy transfer between the substrate as a donor and the heme of the enzyme as an acceptor. The distance was apparently changed by incorporation of the enzyme into phospholipid or by reduction of the heme, indicating that the treatments changed the conformation of the enzyme. Differences in the conformational change were observed between the two enzymes, and the conformational change of cytochrome P-450 II-d using benzo[a]pyrene as a substrate was different from that using 7-ethoxycoumarin. The results suggest that the substrate-binding sites of the two enzymes differ in position toward the heme, and that there are at least two different substrate sites in cytochrome P-450 II-d, one for benzo[a]pyrene and another for 7-ethoxycoumarin.     

The primary structure of omega-amino acid:pyruvate aminotransferase.

The complete amino acid sequence of bacterial omega-amino acid:pyruvate aminotransferase (omega-APT) was determined from its primary structure. The enzyme protein was fragmented by CNBr cleavage, trypsin, and Staphylococcus aureus V8 digestions. The peptides were purified and sequenced by Edman degradation. omega-ATP is composed of four identical subunits of 449 amino acids each. The calculated molecular weight of the enzyme subunit is 48,738 and that of the enzyme tetramer is 194,952. No disulfide bonds or bound sugar molecules were found in the enzyme structure, although 6 cysteine residues were determined per enzyme subunit. Sequence homologies were found between an omega-aminotransferase, i.e. mammalian and yeast ornithine delta-aminotransferases, fungal gamma-aminobutyrate aminotransferase and 7,8-diaminoperalgonate aminotransferase, and 2,2-dialkylglycine decarboxylase. The enzyme structure is not homologous to those of aspartate aminotransferases (AspATs) including the enzymes of Escherichia coli and Sufolobus salfactaricus, though significant homology in the three-dimensional structures around the cofactor binding site has been found between omega-APT and AspATs (Watanabe, N., Sakabe, K., Sakabe, N., Higashi, T., Sasaki, K., Aibara, S., Morita, Y., Yonaha, K., Toyama, S., and Fukutani, H. (1989) J. Biochem. 105, 1-3).     

On optimal associative recall by an incomplete key

A new association scheme is proposed. The fundamental principle of the conventional associative memory models is to solve the matrix equation which is made by the complete (memorized) keys and responses. Therefore, when an incomplete key pattern which is a fraction of memorized key is given to the models as a key, these models can not have an optimal association except for a special case. Analyzing the property of the incomplete key pattern, in this paper, we propose a new association model which behaves optimally for an incomplete key pattern. From the result of the computer simulation, we understand that this model has the expected ability.