Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis

Ascidians are primitive chordates. Their fertilized egg develops quickly into a tadpole-type larva, which consists of a small number but distinct types of cells, including those of epidermis, central nervous system with two sensory organs, endoderm and mesenchyme in the trunk, and notochord and muscle in the tail. This configuration of the ascidian tadpole is thought to represent the most simplified and primitive chordate body plan. In addition, the free-swimming and non-feeding larvae metamorphose into sessile and filter-feeding adults. The genome size of Ciona intestinalis is estimated to be about 160 Mb, and the number of genes approximately 15,500. The present Ciona cDNA projects focused on gene expression profiles of fertilized eggs, 32-110-cell stage embryos, tailbud embryos, larvae, and young adults. Expressed sequence tags (ESTs) of the 5'-most end and 3'-most end of more than 3000 clones were determined at each developmental stage, and the clones were categorized into independent clusters using the 3'-end sequences. Nearly 1000 clusters of them were then analyzed in detail of their sequences against a BLASTX search. This analysis demonstrates that, on average, half of the clusters showed proteins with sequence similarities to known proteins and the other half did not show sequence similarities to known proteins. Genes with sequence similarities were further categorized into three major subclasses, depending on their functions. Furthermore, the expression profiles of all of the clusters were analyzed by whole-mount in situ hybridization. This analysis highlights gene expression patterns characteristic to each developmental stage. As a result, the present study provides many new molecular markers for each of the tissues and/or organs that constitutes the Ciona tailbud embryo. This sequence information will be used for further comparative genome studies to explore molecular mechanisms involved in the formation of one of the most primitive chordate body plans. All of the data fully characterized may be viewed at the web site http://ghost.zool.kyoto-u.ac.jp.     

Chemical characterization of sialyl oligosaccharides in milk of the Japanese black bear, Ursus thibetanus japonicus

Sialyl oligosaccharides were separated from two samples of Japanese black bear milk by extraction with chloroform/methanol, gel filtration on Bio Gel P-2, ion exchange chromatography on DEAE-Sephadex A-50 and high-performance liquid chromatography (HPLC) on a TSK gel Amido-80 column. They were characterized by ¹H-NMR spectroscopy. The structures of four sialyl oligosaccharides separated from the milk were the following:

Neu5Ac(α2-3)Gal(β1-4)Glc

Neu5Ac(α2-6)Gal(β1-4)GlcNAc(β1-3) Gal(α1-3)Gal(β1-4)[Fuc(α1-3)]GlcNAc(β1-6) Gal(β1-4)Glc

Neu5Ac(α2-6)Gal(β1-4)GlcNAc(β1-3) Gal(α1-3)[Fuc(α1-2)]Gal(β1-4)[Fuc(α1-3)]GlcNAc(β1-6) Gal(β1-4)Glc

Neu5Ac(α2-6)Gal(β1-4)GlcNAc(β1-3)[Neu5Ac(α2-6)Gal(β1-4)GlcNAc(β1-6)]Gal(β1-4)Glc

Capillary affinity electrophoresis using lectins for the analysis of milk oligosaccharide structure and its application to bovine colostrum oligosaccharides

Animal colostrum and milk contain complex mixtures of oligosaccharides, which have species-specific profiles. Milk oligosaccharides have various types of structure related to the core structures of glycolipids and N- and O-glycans of glycoproteins and provide a good library to examine the binding of oligosaccharides to various lectins. Recently, we reported a capillary affinity electrophoresis (CAE) method for analyzing the interactions between lectins and complex mixtures of N-linked oligosaccharides prepared from serum glycoproteins. The present paper reports the interactions between 24 milk oligosaccharides and six lectins (PA-I, RCA(120), SBA, WGA, UEA-I, and AAL) analyzed using CAE. Based on the resulting data, we constructed a library that enables us to determine nonreducing terminal monosaccharides, such as Gal, GalNAc, GlcNAc, and Fuc, and to differentiate Gal- or Fuc-linked isomers, such as lacto-N-tetraose, lacto-N-neotetraose, and lacto-N-fucopentaose II and III. In addition, using the library, we show that a combination of the lectins can characterize the neutral oligosaccharides derived from bovine colostrum.     

Distribution of TRPVs,P2X3, and Parvalbumin in the Human Nodose Ganglion

Immunohistochemistry for several neurochemical substances, the transient receptor potential cation channel subfamily V member 1 (TRPV1) and 2 (TRPV2), P2X3 receptor, and parvalbumin (PV), was performed on the nodose ganglion, pharynx, and epiglottis in human cadavers. The nodose ganglion was situated beneath the jugular foramen, and had a spindle shape with the long rostrocaudal axis. The pharyngeal branch (PB) issued from a rostral quarter of the nodose ganglion, whereas the superior laryngeal nerve (SLN) usually originated from a caudal half of the ganglion. In the nodose ganglion, sensory neurons were mostly immunoreactive for TRPV1 (89 %) or P2X3 (93.9 %). About 30 % of nodose neurons contained TRPV2 (35.7 %)—or PV (29.9 %)—immunoreactivity (-IR). These neurons mainly had small to medium-sized cell bodies, and were distributed throughout the ganglion. Neurodegenerative profiles such as shrinkage or pyknosis could not be detected in the examined ganglion. Occasionally, TRPV2-IR nerve fibers surrounded blood vessels in the epiglottis as well as in the nasal and oral parts of the pharynx. Isolated TRPV2-IR nerve fibers were also located beneath the epithelium. TRPV1-, P2X3-, or PV-IR nerve endings could not be detected in the pharynx or epiglottis. In the PB and SLN, however, numerous nerve fibers contained TRPV1-, TRPV2-, P2X3-, and PV-IR. The present study suggests that TRPV1-, TRPV2-, P2X3-, and PV-IR neurons in the human nodose ganglion innervate the pharynx and epiglottis through the PB and SLN. These neurons may respond to chemical, thermal, and mechanical stimuli during respiration and swallowing.     

Chemical structures of oligosaccharides in milks of the American black bear (Ursus americanus americanus) and cheetah (Acinonyx jubatus)

The milk oligosaccharides were studied for two species of the Carnivora: the American black bear (Ursus americanus, family Ursidae, Caniformia), and the cheetah, (Acinonyx jubatus, family Felidae, Feliformia). Lactose was the most dominant saccharide in cheetah milk, while this was a minor saccharide and milk oligosaccharides predominated over lactose in American black bear milk. The structures of 8 neutral saccharides from American black bear milk were found to be Gal(β1–4)Glc (lactose), Fuc(α1–2)Gal(β1–4)Glc (2′-fucosyllactose), Gal(α1–3)Gal(β1–4)Glc (isoglobotriose), Gal(α1–3)[Fuc(α1–2)]Gal(β1–4)Glc (B-tetrasaccharide), Gal(α1–3)[Fuc(α1–2)]Gal(β1–4)[Fuc(α1–3)]Glc (B-pentasaccharide), Fuc(α1–2)Gal(β1–4)[Fuc(α1–3)]GlcNAc(β1–3)Gal(β1–4)Glc (difucosyl lacto-N-neotetraose), Gal(α1–3)Gal(β1–4)[Fuc(α1–3)]GlcNAc(β1–3)Gal(β1–4)Glc (monogalactosyl monofucosyl lacto-N-neotetraose) and Gal(α1–3)Gal(β1–4)GlcNAc(β1–3)Gal(β1–4)Glc (Galili pentasaccharide). Structures of 5 acidic saccharides were also identified in black bear milk: Neu5Ac(α2–3)Gal(β1–4)Glc (3′-sialyllactose), Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3)[Fuc(α1–2)Gal(β1–4)GlcNAc(β1–6)]Gal(β1–4)Glc (monosialyl monofucosyl lacto-N-neohexaose), Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3)[Gal(α1–3)Gal(β1–4)GlcNAc(β1–6)]Gal(β1–4)Glc (monosialyl monogalactosyl lacto-N-neohexaose), Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3){Gal(α1–3)Gal(β1–4)[Fuc(α1–3)]GlcNAc(β1–6)}Gal(β1–4)Glc (monosialyl monogalactosyl monofucosyl lacto-N-neohexaose), and Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3){Gal(α1–3)[Fuc(α1–2)]Gal(β1–4)[Fuc(α1–3)]GlcNAc(β1–6)}Gal(β1–4)Glc (monosialyl monogalactosyl difucosyl lacto-N-neohexaose). A notable feature of some of these milk oligosaccharides is the presence of B-antigen (Gal(α1–3)[Fuc(α1–2)]Gal), α-Gal epitope (Gal(α1–3)Gal(β1–4)Glc(NAc)) and Lewis x (Gal(β1–4)[Fuc(α1–3)]GlcNAc) structures within oligosaccharides. By comparison to American black bear milk, cheetah milk had a much smaller array of oligosaccharides. Two cheetah milks contained Gal(α1–3)Gal(β1–4)Glc (isoglobotriose), while another cheetah milk did not, but contained Gal(β1–6)Gal(β1–4)Glc (6′-galactosyllactose) and Gal(β1–3)Gal(β1–4)Glc (3′-galactosyllactose). Two cheetah milks contained Gal(β1–4)GlcNAc(β1–3)[Gal(β1–4)GlcNAc(β1–6)]Gal(β1–4)Glc (lacto-N-neohexaose), and one cheetah milk contained Gal(β1–4)Glc-3’-O-sulfate. Neu5Ac(α2–8)Neu5Ac(α2–3)Gal(β1–4)Glc (disialyllactose) was the only sialyl oligosaccharide identified in cheetah milk. The heterogeneity of milk oligosaccharides was found between both species with respect of the presence/absence of B-antigen and Lewis x. The variety of milk oligosaccharides was much greater in the American black bear than in the cheetah. The ratio of milk oligosaccharides-to-lactose was lower in cheetah (1:1–1:2) than American black bear (21:1) which is likely a reflection of the requirement for a dietary supply of N-acetyl neuraminic acid (sialic acid), in altricial ursids compared to more precocial felids, given the role of these oligosaccharides in the synthesis of brain gangliosides and the polysialic chains on neural cell adhesion.

     

Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags

The polyploid nature of wheat is a key characteristic of the plant. Full-length complementary DNAs (cDNAs) provide essential information that can be used to annotate the genes and provide a functional analysis of these genes and their products. We constructed a full-length cDNA library derived from young spikelets of common wheat, and obtained 24056 expressed sequence tags (ESTs) from both ends of the cDNA clones. These ESTs were grouped into 3605 contigs using the phrap method, representing expressed loci from each of the three genomes. Using BLAST, 3605 contigs were grouped into 1902 gene clusters, showing that loci of the three genomes are not always expressed. A homology search of these gene clusters against a wheat EST database (15964 gene clusters) and a rice full-length cDNA database (21447 gene clusters) revealed that a quarter of the wheat full-length cDNAs were novel. A protein database of Arabidopsis was used to examine the functional classification of these gene clusters. The GC-content in the 5 -UTR region of wheat cDNAs was compared to that of rice. Forty-three genes (3.5% of wheat cDNAs homologous to those of rice) possessed distinct GC-content in the 5 -UTR region, suggesting different breeding behaviors of wheat and rice.     

Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat

In order to assess global changes in gene expression patterns in stress-induced tissues, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Twenty-one cDNA libraries derived from stress-induced tissues, such as callus, as well as liquid cultures and abiotic stress conditions (temperature treatment, desiccation, photoperiod, moisture and ABA) were constructed. Several thousand colonies were randomly selected from each of these 21 cDNA libraries and sequenced from both the 5′ and 3′ ends. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were monitored. Furthermore, the relationships between gene expression profiles among the stress-induced tissues were inferred from the gene expression patterns. Multi-dimensional analysis of EST data is analogous to microarray experiments. As an example, genes specifically induced and/or suppressed by cold acclimation and heat-shock treatments were selected in silico. Four hundred and ninety genes showing fivefold induction or 218 genes for suppression in comparison to the control expression level were selected. These selected genes were annotated with the BLAST search. Furthermore, gene ontology was conducted for these genes with the InterPro search. Because genes regulated in response to temperature treatment were successfully selected, this method can be applied to other stress-treated tissues. Then, the method was applied to screen genes in response to abiotic stresses such as drought and ABA treatments. In silico selection of screened genes from virtual display should provide a powerful tool for functional plant genomics.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Life history and group composition of melon‐headed whales based on mass strandings in Japan

We examined melon‐headed whales that mass‐stranded live in two events in Japan: (1) 171 animals at Tanegashima Island in 2001 and (2) 85 animals at Hasaki in 2002. We report here the results of life history traits and group composition of these strandings, and compare them to another mass stranding with 135 individuals at Aoshima in 1982. In the Hasaki event, most stranded animals, including those released were sexed and measured. The proportion of live males released was much higher than that of females, and larger animals, especially females, were more likely to have died. Females were estimated to attain sexual maturity at around 7 yr and give birth every 3–4 yr. The sex ratio was significantly different between the Hasaki and Aoshima events. Among dead specimens, females of various age classes were included in all strandings, while age distribution of males varied considerably among strandings. This suggests females show group fidelity while males move between groups. Asymptotic body length of females from Hasaki was significantly smaller than that from Tanegashima, suggesting that more than one population of melon‐headed whales exist off Japan.