Combined method of whole mount and block-face imaging: Acquisition of 3D data of gene expression pattern from conventional in situ hybridization

Visualization of spatiotemporal expression of a gene of interest is a fundamental technique for analyzing the involvements of genes in organ development. In situ hybridization (ISH) is one of the most popular methods for visualizing gene expression. When conventional ISH is performed on sections or whole-mount specimens, the gene expression pattern is represented in 2-dimensional (2D) microscopic images or in the surface view of the specimen. To obtain 3-dimensional (3D) data of gene expression from conventional ISH, the “serial section method” has traditionally been employed. However, this method requires an extensive amount of time and labor because it requires researchers to collect a tremendous number of sections, label all sections by ISH, and image them before 3D reconstruction. Here, we proposed a rapid and low-cost 3D imaging method that can create 3D gene expression patterns from conventional ISH-labeled specimens. Our method consists of a combination of whole-mount ISH and Correlative Microscopy and Blockface imaging (CoMBI). The whole-mount ISH-labeled specimens were sliced using a microtome or cryostat, and all block-faces were imaged and used to reconstruct 3D images by CoMBI. The 3D data acquired using our method showed sufficient quality to analyze the morphology and gene expression patterns in the developing mouse heart. In addition, 2D microscopic images of the sections can be obtained when needed. Correlating 2D microscopic images and 3D data can help annotate gene expression patterns and understand the anatomy of developing organs. These results indicated that our method can be useful in the field of developmental biology.     

On-line melting of double-stranded DNA for analysis of single-stranded DNA using capillary electrophoresis

Capillary electrophoresis (CE) is a convenient, fast and non-radioactive method with possibilities for automatization. To analyse single-stranded DNA molecules in a more automated way, we developed a heating device to melt double-stranded DNA fragments in the capillary during electrophoresis. In this study we used this device to obtain single-stranded DNA, necessary for the detection of point mutations in DNA using the single-strand conformation polymorphism technique. Results show that double-stranded DNA molecules can be melted on-line into single-stranded DNA molecules, although not for 100%. In an attempt to find universal electrophoretic conditions for the analysis of single-stranded DNA, we investigated the influence of several parameters on the yield of single-stranded DNA molecules and on the resolution of the single-stranded DNA peaks. We demonstrate that this heating device is a technical adjustment of CE which contributes to more automated analyses of DNA fragments.     

A preliminary study on relationships among selected Australian members of the tribe Spilomelini (Lepidoptera: Crambidae: Pyraustinae)

A preliminary study was conducted on phylogenetic relationships among some selected genera of the Australian Spilomelini, focusing on relationships among the Australian Glyphodes group (Glyphodes Guenée, 1854, Dysallacta Lederer, 1863, Talanga Moore, 1885 and Agrioglypta Meyrick, 1932) and the 17 genera which are morphologically similar to it. Representatives of three genera of the Pyarustini were used as outgroups. Cladistic analysis of morphological data from the adult moths produced 10 equally MP trees (length = 221, CI=0.294, and RI=0.608). The clade formed by the 21 selected genera of the Australian Spilomelini had low bootstrap support even though a good apomorphy supported the monophyly of this group, namely, a strong, bilobed praecinctorium of abdominal tympanal organs. The analysis showed that the Glyphodes group is not monophyletic because the genus Chrysothyridia Snellen appears within it in the 10 MP trees. The concept of the Glyphodes group should be expanded to include Chrysothyridia and also the Synclera Zeller and Didymostoma (Walker) since the Synclera + Didymostoma clade, as the hypothesised sister group of the Glyphodes group, is not sufficiently supported as a separate monophyletic group. The analysis also showed that genus Glyphodes is not a monophyletic group, while Metallarcha Meyrick is a monophyletic group.     

Purification and characterization of chitinase B from moderately thermophilic bacterium Ralstonia sp. A-471

Chitinase B was purified from a culture medium of Ralstonia sp. A-471 by precipitation with (NH4)2SO4 and column chromatography with DEAE-Toyopearl 650 M and Sephacryl S-200. The purified enzyme was homogeneous on SDS-PAGE. The molecular weight was 45,000 by SDS-PAGE. The optimum pH was 5.0 and stable pH was from 5.0 to 10.0. In the early stage of the reaction, chitinase B produced beta-anomer of (GlcNAc)2 from the substrate (GlcNAc)6, whereas (GlcNAc)4 produced almost at equilibrium, indicating that the enzyme predominantly hydrolyzes the second glycosidic linkage from the nonreducing end of (GlcNAc)6.     

Estimates and implications of the costs of compliance with biosafety regulations in developing countries

Estimating the cost of compliance with biosafety regulations is important as it helps developers focus their investments in producer development. We provide estimates for the cost of compliance for a set of technologies in Indonesia, the Philippines and other countries. These costs vary from US $100,000 to 1.7 million. These are estimates of regulatory costs and do not include product development or deployment costs. Cost estimates need to be compared with potential gains when the technology is introduced in these countries and the gains in knowledge accumulate during the biosafety assessment process. Although the cost of compliance is important, time delays and uncertainty are even more important and may have an adverse impact on innovations reaching farmers.     

Influence of Forest Seasonality on Gibbon Food Choice in the Rain Forests of Barito Ulu,Central Kalimantan

We describe the diet of two hybrid gibbon groups (Hylobates mulleri x H. agilis) in relation to forest seasonality. We collected data over 12 mo in lowland dipterocarp forest in the Barito Ulu research area, Central Kalimantan, Indonesia. Although non-fig fruit was the main dietary item (52–64% of diet), gibbon diet was most strongly influenced by the availability of flowers. During periods when flowers were most abundant and the gibbons increased consumption of them, they also ate figs or young leaves more often. We suggest that although flowers are nutritionally rich sources of food, providing relatively high levels of protein compared to fruit, they are unlikely to satiate gibbon hunger and they seek dietary bulk from figs or young leaves, because they are easily obtained. Rainfall also influenced food choice, and non-fig fruit availability had a weak influence on fruit selection for one group. The group concentrated feeding on the fruit of a few species when fruit was most abundant and ate a greater diversity of species when fruit was scarce. Gibbon diet appeared not to be influenced by changes in availability of figs, young leaves and diversity of fruiting species.     

Revision of the Australian species of Hyalobathra Meyrick (Lepidoptera: Pyraloidea: Crambidae: Pyraustinae) based on adult morphology and with description of a new species

Abstract The genus Hyalobathra Meyrick is redefined based on five Australian species including the type  species. The four named Australian species, H. archeleuca Meyrick, H. unicolor (Warren) , H. miniosalis (Guenée) and H. minialis (Warren), are redescribed and a new species, H. crenulata sp. n., is described . Hyalobathra unicolor is removed from synonymy with H. illectalis (Walker), and lectotypes are designated for H. archeleuca , H. minialis and for H. rhodoplecta Turner, a synonym of H. miniosalis . The presence of H. paupellalis (Lederer) in Australia could not be confirmed, but its genitalia are figured. Two previously included species, ' Hyalobathra ' aequalis (Lederer) and ' H .'  brevialis (Walker), are excluded from Hyalobathra, as they lack its generic apomorphies, but cannot at present be assigned to any other genus.     

A novel goose-type lysozyme gene with chitinolytic activity from the moderately thermophilic bacterium <Emphasis Type="Italic">Ralstonia</Emphasis> sp. A-471: cloning,sequencing, and expression

In this study, we cloned the gene encoding goose-type (G-type) lysozyme with chitinase (Ra-ChiC) activity from Ralstonia sp. A-471 genomic DNA library. This is the first report of another type of chitinase after the previously reported chitinases ChiA (Ra-ChiA) and ChiB (Ra-ChiB) in the chitinase system of the moderately thermophilic bacterium, Ralstonia sp. A-471 and also the first such data in Ralstonia sp. G-type lysozyme gene. It consisted of 753 bp nucleotides, which encodes 251 amino acids including a putative signal peptide. This ORF was modular enzyme composed of a signal sequence, chitin-binding domain, linker, and catalytic domain. The catalytic domain of Ra-ChiC showed homologies to those of G-type lysozyme (glycoside hydrolases (GH) family 23, 16.8%) and lysozyme-like enzyme from Clostridium beijerincki (76.1%). Ra-ChiC had activities against ethylene glycol chitin, carboxyl methyl chitin, and soluble chitin but not against the cell wall of Micrococcus lysodeikticus. The enzyme produced α-anomer by hydrolyzing β-1,4-glycosidic linkage of the substrate, indicating that the enzyme catalyzes the hydrolysis through an inverting mechanism. When N-acetylglucosamine hexasaccharide [(GlcNAc)6] was hydrolyzed by the enzyme, the second and third glycosidic linkage from the non-reducing end were split producing (GlcNAc)2 + (GlcNAc)4 and (GlcNAc)3 + (GlcNAc)3 of almost the same concentration in the early stage of the reaction. The G-type lysozyme hydrolyzed (GlcNAc)6 in an endo-splitting manner, which produced (GlcNAc)3 + (GlcNAc)3 predominating over that to (GlcNAc)2 + (GlcNAc)4. Thus, Ra-ChiC was found to be a novel enzyme in its structural and functional properties. The sequence data reported in the present paper have been submitted to the DDBJ, EMBL, and NCBI databases under the accession number AB45458.     

2B4+ CD8+ T cells play an inhibitory role against constrained HIV epitopes

Cytotoxic T cells play a critical role in the control of HIV and the progression of infected individuals to AIDS. 2B4 (CD244) is a member of the SLAM family of receptors that regulate lymphocyte development and function. The expression of 2B4 on CD8⁺ T cells was shown to increase during AIDS disease progression. However, the functional role of 2B4⁺ CD8⁺ T cells against HIV infection is not known. Here, we have examined the functional role of 2B4⁺ CD8⁺ T cells during and after stimulation with HLA B14 or B27 restricted HIV epitopes. Interestingly, IFN-γ secretion and cytotoxic activity of 2B4⁺ CD8⁺ T cells stimulated with HIV peptides were significantly decreased when compared to influenza peptide stimulated 2B4⁺ CD8⁺ T cells. The expression of the signaling adaptor molecule SAP was downregulated in 2B4⁺ CD8⁺ T cells upon HIV peptide stimulation. These results suggest that 2B4⁺ CD8⁺ T cells play an inhibitory role against constrained HIV epitopes underlying the inability to control the virus during disease progression.     

Selection of Fruit by Gibbons (Hylobates muelleri × agilis) in the Rain Forests of Central Borneo

Gibbons (Hylobates spp.) are among the main frugivorous primates in Southeast Asia, yet little is known about the criteria by which they select fruit for consumption. We studied two gibbon groups for 14 mo in the lowland dipterocarp forests of Central Borneo to determine their selectivity for different fruit species and traits. Ideal gibbon fruit were yellow, large, with a juicy-soft pulp, thin skin and available in large crops. Gibbons ultimately sought seedless fruit, but when seeds were present they selected fruit with a single, well-protected seed. Given that few fruit exhibited all the desired traits, we also carried out a multiple regression using the selection ratios of the various fruit species and their associated fruit traits to determine which traits ultimately determined gibbon choice. The analysis was stratified to account for differences in fruit availability. Selection was strongest when fruit were abundant in the forest and was based on seed width (<21 mm), color (yellow-orange), and fruit weight (1–5 g). No selection is apparent when food abundance was intermediate, but when fruit were scarce they preferentially ate larger fruit (6–30 g).