A genome-wide survey of changes in protein evolutionary rates across four closely related species of <Emphasis Type="Italic">Saccharomyces</Emphasis> sensu stricto group

Background  

Changes in protein evolutionary rates among lineages have been frequently observed during periods of notable phenotypic evolution. It is also known that, following gene duplication and loss, the protein evolutionary rates of genes involved in such events changed because of changes in functional constraints acting on the genes. However, in the evolution of closely related species, excluding the aforementioned situations, the frequency of changes in protein evolutionary rates is still not clear at the genome-wide level. Here we examine the constancy of protein evolutionary rates in the evolution of four closely related species of the Saccharomyces sensu stricto group (S. cerevisiae, S. paradoxus, S. mikatae and S. bayanus).     

Galectin-3 and metastasis

Galectin-3, a 31 kDa member of the β-galactoside-binding proteins, is an intracellular and extracellular lectin which interacts with intracellular glycoproteins, cell surface molecules and extracellular matrix proteins. Galectin-3 is expressed widely in epithelial and immune cells and its expression is correlated with cancer aggressiveness and metastasis. Galectin-3 is involved in various biological phenomena including cell growth, adhesion, differentiation, angiogenesis and apoptosis. Recent research revealed that galectin-3 is associated with several steps of invasion and metastasis, like angiogenesis, cell-matrix interaction, dissemination through blood flow and extravasation. Recently, we and others have shown that galectin-3 can be a reliable diagnostic marker in certain cancers and one of the target proteins of cancer treatment. In this review, we describe the involvement of galectin-3 in each steps of metastasis and clinical significance of galectin-3. Published in 2004.     

Independent domestication of Asian rice followed by gene flow from japonica to indica

Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.     

Three new species of Fancy Case caterpillars from threatened forests of Hawaii (Lepidoptera, Cosmopterigidae, Hyposmocoma)

The endemic Hawaiian moth genus Hyposmocoma includes 348 described species and perhaps twice as many that remain undescribed. The genus is unusual within Lepidoptera in that its larvae create distinctive silk cases in which they perambulate while protected and camouflaged. An extraordinary diversity of case types exists, and to date more than ten different types have been identified, each corresponding roughly to a separate evolutionary lineage. In this study, we describe three new species of Hyposmocoma: Hyposmocoma ipohapuusp. n. from Big Island, Hyposmocoma makawaosp. n. from Makawao Forest Reserve in Mauiand Hyposmocoma tantalasp. n. from Mt. Tantalus, Oahu, all of which produce tubular purse cases during their larval stage. We also describe the female of Hyposmocoma inversella Walsingham, which was previously undescribed, and re-describe two closely related species, Hyposmocoma auropurpurea Walsingham and Hyposmocoma nebulifera Walsingham, neither which have been formally described in recent years. We present for the first time, primer sequences for a 705 bp fragment of CAD, designed for Hyposmocoma and relatives. The molecular phylogeny based on mitochondrial and nuclear loci demonstrates that all are distinct species. The discovery of a new, endemic species from Mt. Tantalus, an area with many invasive species, suggests that even relatively degraded areas in Hawaii would be worthy of active conservation efforts.     

Radular mechanosensory neuron in the buccal ganglia of the terrestrial slug,Incilaria fruhstorferi

A radular mechanosensory neuron, RM, was identified in the buccal ganglia of Incilaria fruhstorferi. Fine neurites ramified bilaterally in the buccal ganglia, and main neurites entered the subradular epithelium via buccal nerve 3 (n3). When the radula was distorted by bending, RM produced an afferent spike which was preceded by an axonic spike recorded at n3. The response of RM to radular distortion was observed even in the absence of Ca²⁺, which drastically suppressed chemical synaptic interactions. Therefore, RM was concluded to be a primary radular mechanoreceptor.During rhythmic buccal motor activity induced by food or electrical stimulation of the cerebrobuccal connective, RM received excitatory input during the radular retraction phase. In the isolated buccal ganglia connected to the radula via n3s, the afferent spike, which had been evoked by electrical stimulation of the subradular epithelium, was broadened with the phasic excitatory input. Since the afferent spike was also broadened by current injection into the soma, depolarization due to the phasic input may have produced the spike broadening.Spike broadening was also observed during repetitive firing evoked by current injection. The amplitude of the excitatory postsynaptic potential in a follower neuron increased depending on the spike broadening of RM.Abbreviations CBC cerebrobuccal connective - EPSP excitatory postsynaptic potential - n1,n3 buccal nerves 1 and 3 - RBMA rhythmic buccal motor activity - RM radular mechanosensory neuron - SMT supramedian radular tensor neuron     

Proline in the Osmoregulation of Brevibacterium lactofermentum

Osmoregulation in Brevibacterium lactofermentum was studied. Proline was accumulated up to approximately 35mg/g dry cell weight in the cells of a wild strain of the bacterium grown under osmotic stress. The osmotic tolerance of a proline auxotroph mutant obtained from the bacterium was lower than that in the wild strain. The activity of pyrroline-5-carboxylate reductase, one of the enzymes in the proline biosynthetic pathway, increased about 3-fold when the cells of B. lactofermentum were grown under osmotic stress. These data indicated that proline is important in osmoregulation in the bacterium.     

Molecular heterogeneity of heat-stable toxin-producing and non-producing Escherichia coli O25 strains isolated in Japan

Escherichia coli O25 strains that produce heat-stable toxin (ST) have been recently isolated in Japan, and epidemiological study of this type of enterotoxigenic E. coli is required. In this study the heterogeneity of 16 ST-producing and non-producing strains of E. coli O25 was investigated. All eight ST-producing strains were shown to have STIb gene, and seven of them had similar profiles of plasmids, ladder-banding of LPS in SDS-polyacrylamide gel electrophoresis, and chromosomal DNA digestions in pulsed-field gel electrophoresis (PFGE). In contrast, ST-non-producing strains were more heterogeneous in all parameters examined. PFGE of the digested chromosomal DNA with several restriction enzymes was proved to be an effective procedure to compare the closely related strains of E. coli O25.     

Site-specific isotope labeling of long RNA for structural and mechanistic studies

A site-specific isotope labeling technique of long RNA molecules was established. This technique is comprised of two simple enzymatic reactions, namely a guanosine transfer reaction of group I self-splicing introns and a ligation with T4 DNA ligase. The trans-acting group I self-splicing intron with its external cofactor, 'isotopically labeled guanosine 5'-monophosphate' (5'-GMP), steadily gave a 5'-residue-labeled RNA fragment. This key reaction, in combination with a ligation of 5'-remainder non-labeled sequence, allowed us to prepare a site-specifically labeled RNA molecule in a high yield, and its production was confirmed with (15)N NMR spectroscopy. Such a site-specifically labeled RNA molecule can be used to detect a molecular interaction and to probe chemical features of catalytically/structurally important residues with NMR spectroscopy and possibly Raman spectroscopy and mass spectrometry.     

Mechanism of proliferation arrest of embryonic cells of Xenopus by diterpene compounds

Three diterpene compounds isolated from the anti-cancer herbal medicine kansui, namely, kansuinin B, 20-OD-ingenol Z, and 20-OD-ingenol E, specifically inhibited the proliferation of isolated embryonic cells from Xenopus embryos. We conducted a cytologic study to determine the mechanism underlying the arrest of the cellular proliferation by these compounds. While kansuinin B and 20-OD-ingenol Z treatment decreased the cell numbers in the S phase and the M phase substages of the cell cycle, 20-OD-ingenol E inhibited mitosis.