Biomedical subjects

Joji M Otaki

Publications and source records attributed to Joji M Otaki.

9 recordsLinked to original sources

PubMed2005

Availability of short amino acid sequences in proteins.

Much attention is being paid to protein databases as an important information source for proteome research. Although used extensively for similarity searches, protein databases themselves have not fully been characterized. In a systematic attempt to reveal protein-database characters that could contribute to revealing how protein chains are constructed, frequency distributions of all possible combinatorial sets of three, four, and five amino acids ("triplets," "quartets," and "pentats"; collectively called constituent sequences) have been examined in the nonredundant (nr) protein database, demonstrating the existence of nonrandom bias in their "availability" at the population level. Nonexistent short sequences of pentats were found that showed low availability in biological proteins against their expected probabilities of occurrence. Among them, six representative ones were successfully synthesized as peptides with reasonably high yields in a conventional Fmoc method, excluding the possibility that a putative physicochemical energy barrier in forming them could be a direct cause for the low availability. They were also expressed as soluble fusion proteins in a conventional Escherichia coli BL21Star(DE3) system with reasonably high yield, again excluding a possible difficulty in their biological synthesis. Together, these results suggest that information on three-dimensional structures and functions of proteins exists in the context of connections of short constituent sequences, and that proteins are composed of evolutionarily selected constituent sequences, which are reflected in their availability differences in the database. These results may have biological implications for protein structural studies.

Amino Acid Sequence↗

PubMed2005

The proto-oncogene BCL-6 is expressed in olfactory sensory neurons.

Mammalian olfactory sensory neurons harbor a large repertoire of odorant receptors. Yet, each cell chooses a single odorant receptor gene to express, which may then serve as the molecular identification of that cell. This process of differentiation or receptor gene regulation of olfactory sensory neurons has largely been enigmatic. Here, we showed that the important proto-oncogene in B lymphocyte terminal differentiation, B-Cell Leukemia/Lymphoma 6 (BCL-6), which codes for a sequence-specific transcription repressor, is expressed in olfactory sensory neurons in the mouse. We detected BCL-6 mRNA in most, if not all, mature olfactory sensory neurons by in situ hybridization histochemistry. Western blot analysis also revealed the presence of BCL-6 protein in the olfactory epithelium, but immunohistochemical analysis using anti-BCL-6 antibodies showed that only a subset of olfactory sensory neurons highly expressed BCL-6 protein. BCL-6 mRNA was detected as early as embryonic day 14 (E14) in most olfactory sensory neurons as in adults, and at E15, BCL-6 protein was detected in most cells that were likely to be differentiating into mature olfactory sensory neurons. Artificial induction of apoptosis of olfactory sensory neurons resulted in the decrease of BCL-6 mRNA, but during the subsequent phase of regeneration and differentiation, it markedly increased. Taken together, our results suggest the possibility that BCL-6 plays an important role in terminal differentiation not only in B lymphocytes but also in olfactory sensory neurons.

Animals↗

PubMed2005

Morphological comparison of pupal wing cuticle patterns in butterflies.

Butterfly wing color-patterns are determined in the prospective wing tissues during the late larval and early pupal stages. To study the cellular differentiation process of wings, morphological knowledge on pupal wings is prerequisite. Here we systematically examined morphological patterns of the pupal wing cuticular surface in a wide variety of nymphalid butterflies in relation to adult color-patterns. Several kinds of pupal wing patterns corresponding to particular adult color-pattern elements were widely observed in many species. Especially noteworthy were the pupal "focal" spots corresponding to the adult border ocelli system, which were detected in many species of Nymphalinae, Apaturinae, Argynninae, Satyrinae, and Danainae. Striped patterns on the pupal wing cuticle seen in some species of Limenitinae, Ariadnae, and Marpesiinae directly corresponded to those of the adult wings. In Vanessa cardui, eyespot-like pattern elements were tentatively produced during development in the wing tissue underneath the pupal spots and subsequently erased, suggesting a mechanism for producing novel color-patterns in the course of development and evolution. The pupal focal spots reasonably correlated with the adult eyespots in size in Precis orithya and Ypthima argus. We physically damaged the pupal focal spots and their corresponding cells underneath in these species, which abolished or inhibited the formation of the adult eyespots. Taken together, our results clarified that pupal cuticle patterns were often indicative of the adult color-patterns and apparently reflect molecular activity of organizing centers for the adult color-pattern formation at least in nymphalid butterflies.

Animals↗

PubMed2005

Tungstate-induced color-pattern modifications of butterfly wings are independent of stress response and ecdysteroid effect.

Systemic injections of sodium tungstate, a protein-tyrosine phosphatase (PTPase) inhibitor, to pupae immediately after pupation have been shown to efficiently produce characteristic color-pattern modifications on the wings of many species of butterflies. Here we demonstrated that the tungstate-induced modification pattern was entirely different from other chemically-induced ones in a species of nymphalid butterfly Junonia (Precis) orithya. In this species, the systemic injections of tungstate produced characteristic expansion of black area and shrinkage of white area together with the move of parafocal elements toward the wing base. Overall, pattern boundaries became obscure. In contrast, an entirely different modification pattern, overall darkening of wings, was observed by the injections of stress-inducing chemicals, thapsigargin, ionomycin, or geldanamycin, to pupae under the rearing conditions for the adult summer form. On the ventral wings, this darkening was due to an increase of the proportion of peppered dark scales, which was reminiscent of the natural fall form of this species. Under the same rearing conditions, the injections of ecdysteroid, which is a well-known hormone being responsible for the seasonal polyphenism of nymphalid butterflies, yielded overall expansion of orange area especially around eyespots. Taken together, we conclude that the tungstate-induced modifications are clearly distinguishable from those of stress response and ecdysteroid effect. This conclusion then suggests that the putative PTPase signaling pathway that is sensitive to tungstate uniquely contributes to the wing-wide color-pattern development in butterflies.

Animals↗

PubMed2004

Odorant receptor expression in the mouse cerebral cortex.

Mammalian odorant receptors have been known to be involved not only in odorant detection but also in neuronal development of olfactory sensory neurons. We have examined a possibility of odorant receptor expression in nonolfactory neurons in the mouse. Mouse odorant receptors (M71, C6, and OR3), two of which were already shown to be functionally activated by odorants in heterologous systems, were detected by polymerase chain reactions (PCRs) from the cerebral cortex but not from other brain tissues. Degenerate PCR further suggested that other odorant receptors were also expressed in the mouse cerebral cortex. One of these receptors showed high sequence-match with a putative chick odorant receptor OR7 transiently expressed in the notochord during development. In situ hybridization detected signals for M71 and C6 receptors in the layer II cortical pyramidal neurons located in the occipital pole. In the M71-IRES-tauLacZ mouse, in which M71 expression was genetically marked with tauLacZ, X-gal staining signals were mostly localized in the layer II neurons in the occipital pole, being consistent with the in situ hybridization result. Fluorescent immunohistochemistry using anti-beta-galactosidase antibody further detected the tauLacZ signals in the same cells. X-gal staining began at P3, peaked at P8, and continued to adults, although signals gradually decreased. These data showed that at least a few odorant receptors are expressed not only in olfactory sensory neurons but also in pyramidal neurons in the cerebral cortex, possibly playing an important role either in chemical detection of exogenous or endogenous ligands or in a developmental process such as axon guidance and target recognition.

Amino Acid Sequence↗

PubMed2004

Species-specific color-pattern modifications of butterfly wings.

We have previously shown that the systemic injection of sodium tungstate, a general protein-tyrosine phosphatase (PTPase) inhibitor, efficiently produces characteristic color-pattern modifications on the wings of the Painted Lady butterfly, Vanessa cardui. By using this method in the present study, we analyzed modification patterns of six species of Japanese butterflies. Whereas in Vanessa indica the black spots on the forewings reduced in size in response to the treatment, in Lycaena phlaeas the morphologically similar black spots enlarged in size. However, the metallic blue spots on the forewings of V. indica did enlarge in size, showing different behavior even within a single wing surface. The response patterns of Ypthima argus differed markedly from those of other species in that ectopic color-pattern elements were created. Colias erate showed minor modifications that coincidentally resembled the natural color-pattern of a closely related species, Colias palaeno. Through a comprehensive literature search, we confirmed the existence of naturally occurring aberrant color patterns with close similarities to the experimentally induced phenocopies in each of the modified species. Our results point out the possibility that a hypothetical transduction pathway with a PTPase for the scale-cell differentiation globally coordinates the wing-wide color-pattern development in butterflies.

Animals↗

PubMed2004

Color-pattern modifications and speciation in butterflies of the genus Vanessa and its related genera Cynthia and Bassaris.

We have previously shown that the systemic injection of sodium tungstate, a protein-tyrosine phosphatase (PTPase) inhibitor, to pupae immediately after pupation efficiently produces characteristic color-pattern modifications on the wings of many species of butterflies including Vanessa indica and Cynthia cardui. In these species, the black spots reduced in size in response to the treatment. Similar modifications are occasionally seen in the field-caught aberrant individuals. Exceptionally, however, a C. cardui individual with enlarged black spots ("reversed" modification pattern) has been reported. Here we show that these modified patterns of V. indica and C. cardui are quite similar to the normal color-patterns of other Vanessa species. V. indica with tungstate-induced modifications resembled V. tameamea, V. samani, and Bassaris itea, whereas V. dilecta, V. atalanta, and V. dejeanii are similar to the "reversed" individual. Most features seen in the experimentally-modified V. indica were observed throughout the fore- and hindwings of V. samani. In contrast, the experimentally-induced color-patterns of C. cardui did not parallel variation of Cynthia butterflies. Since it has been proposed that a hypothetical transduction pathway with a PTPase for the scale-cell differentiation globally coordinates the wing-wide color-patterns, our findings suggest that spontaneous mutations in genes in this hypothetical pathway might have played a major role in creating new color-patterns and species in the Vanessa genus but not in the Cynthia genus. This evolutionary mechanism may probably be shared more widely in Lepidoptera, although this would not be a sole determinant for the color-pattern development and evolution.

Animals↗

PubMed2003

Length analyses of Drosophila odorant receptors.

Odorant receptors comprise a unique family of G-protein-coupled seven-transmembrane receptors both in mammals and insects. In the fruit fly Drosophila melanogaster, all 61 candidate odorant receptor genes have been identified based on the complete genome sequence, and their expression patterns have been examined. A given odorant receptor is expressed in the antenna or maxillary palp, or not expressed at all. Here we have applied a set of statistical analyses to the length of the extra- and intracellular loops and terminals (LTs) of Drosophila odorant receptors to examine possible inter- and intramolecular relations at the population level. We have first provided some useful statistical information such as mean length values and length histograms to depict a general nature of Drosophila odorant receptors at the population level, after focusing on discrepancy on assigning transmembrane domains between researchers. In a preferable transmembrane assignment, all extracellular LTs, especially the second extracellular loops, were relatively large in length, suggesting their functional significance. Somewhat surprisingly, principle component analysis (PCA) indicated that the maxillary palp receptors were almost as diverse as the antenna receptors despite their much smaller population size. PCA together with histograms also revealed that receptors with an abnormal length configuration tended not to be expressed, suggesting that LT length deviations are related to transcriptional silencing of odorant receptor genes. Rank transformation tests pointed out possible LTs that could have different length between differently expressed receptors at the population level. Taken together, length analyses provide us with a general picture, i.e. "length configuration," of Drosophila odorant receptors at the population level that could point out putatively important functional sites for experimental studies.

Amino Acid Sequence↗

PubMedDate not supplied

Alignment-free classification of G-protein-coupled receptors using self-organizing maps.

Proteins are classified mainly on the basis of alignments of amino acid sequences. Drug discovery processes based on pharmacologically important proteins such as G-protein-coupled receptors (GPCRs) may be facilitated if more information is extracted directly from the primary sequences. Here, we investigate an alignment-free approach to protein classification using self-organizing maps (SOMs), a kind of artificial neural network, which needs only primary sequences of proteins and determines their relative locations in a two-dimensional lattice of neurons through an adaptive process. We first showed that a set of 1397 aligned samples of Class A GPCRs can be classified by our SOM program into 15 conventional categories with 99.2% accuracy. Similarly, a nonaligned raw sequence data set of 4116 samples was categorized into 15 conventional families with 97.8% accuracy in a cross-validation test. Orphan GPCRs were also classified appropriately using the result of the SOM learning. A supposedly diverse family of olfactory receptors formed the most distinctive cluster in the map, whereas amine and peptide families exhibited diffuse distributions. A feature of this kind in the map can be interpreted to reflect hierarchical family composition. Interestingly, some orphan receptors that were categorized as olfactory were somatosensory chemoreceptors. These results suggest the applicability and potential of the SOM program to classification prediction and knowledge discovery from protein sequences.

GTP-Binding Proteins↗