Occurrence of organochlorine pesticides, polychlorinated biphenyls and polybrominated diphenyl ethers in deep-sea fishes from the Sulu Sea.
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Animals↗
Biomedical subjects
Shuhei Nishida
Publications and source records attributed to Shuhei Nishida.
Organization of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca).
We determined the nearly complete DNA sequence of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca), one of the most ecologically and commercially important zooplankters in Antarctic waters. All of the genome sequences were purified by gene amplification using long polymerase chain reaction (PCR), and the products were subsequently used as templates for either direct sequencing using a primer-walking strategy or nested PCR with crustacea-versatile primers. Although we were unable to determine a portion of the genome owing to technical difficulties, the sequenced position, 14,606 bp long, contained all of the 13 protein-coding genes, 19 of the 22 transfer RNA genes, and the large subunit as well as a portion of the small subunit ribosomal RNA genes. Gene rearrangement was observed for 3 transfer RNA genes (tRNACys, tRNATyr, and tRNATrp) and the 2 leucine tRNA genes.
Amino Acid Sequence↗
Large-scale gene rearrangements in the mitochondrial genomes of two calanoid copepods Eucalanus bungii and Neocalanus cristatus (Crustacea), with notes on new versatile primers for the srRNA and COI genes.
Partial sequences of the mitochondrial genomes were determined for two calanoid copepods, Eucalanus bungii [9530 bp (base pairs)] and Neocalanus cristatus (7965 bp), using an approach that employs a long polymerase chain reaction (PCR) technique and primer walking. In contrast to Tigriopus japonicus (Harpacticoida), in which the complete mitochondrial genome has been determined, genes are encoded on both strands of the genome. In spite of the close relationship between E. bungii and N. cristatus, the gene orders of these calanoid copepods differed greatly from each other. From the sequence we obtained, new copepod-specific versatile primers were designed for the cytochrome c oxidase I (COI) gene (1200 bp). These primer pairs, as well as the previously designed primer pairs for the small ribosomal RNA (srRNA) gene (500 bp), were applied for 20 species representing four orders of both calanoid and non-calanoid copepods and amplification of sequences from at least one species from each order was successful.
Animals↗
Nano-mechanical methods in biochemistry using atomic force microscopy.
The atomic force microscope has been extensively used not only to image nanometer-sized biological samples but also to measure their mechanical properties by using the force curve mode of the instrument. When the analysis based on the Hertz model of indentation is applied to the approach part of the force curve, one obtains information on the stiffness of the sample in terms of Young's modulus. Mapping of local stiffness over a single living cell is possible by this method. The retraction part of the force curve provides information on the adhesive interaction between the sample and the AFM tip. It is possible to functionalize the AFM tip with specific ligands so that one can target the adhesive interaction to specific pairs of ligands and receptors. The presence of specific receptors on the living cell surface has been mapped by this method. The force to break the co-operative 3D structure of globular proteins or to separate a double stranded DNA into single strands has been measured. Extension of the method for harvesting functional molecules from the cytosol or the cell surface for biochemical analysis has been reported. There is a need for the development of biochemical nano-analysis based on AFM technology.
Animals↗
Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda).
The complete nucleotide sequence of the mitochondrial genome was determined for a harpacticoid copepod, Tigriopus japonicus (Crustacea), using an approach that employs a long polymerase chain reaction technique and primer walking. Although the genome (14,628 bp) contained the same set of 37 genes (2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) as found in other metazoan animals, none of the previously reported gene orders were comparable to that of T. japonicus. Furthermore, all genes were encoded on one strand, unlike the mitochondrial genomes of most metazoan animals. Size reductions were notable for tRNA and rRNA genes, resulting in one of the smallest mitochondrial genomes in the arthropod lineage. Although it appears that such large-scale gene rearrangements have occurred in the ancestral species of T. japonicus, none of the proposed mechanisms parsimoniously account for this eccentric gene arrangement.
Journal Article↗
Combination of AFM with an objective-type total internal reflection fluorescence microscope (TIRFM) for nanomanipulation of single cells.
A new instrument was constructed by combining an objective-type total internal reflection fluorescence microscope with an atomic force microscope (AFM). Our purpose of constructing such an instrument is to detect and confirm the result of cellular level manipulations made with the AFM part through the detection system of the highly sensitive fluorescence microscope part. In this combination, manipulations are now possible from the nanometer to the micrometer scales and the fluorescence detection system is sensitive enough even for localizing single molecules. In this paper, we applied the system as a precise intracellular injector (nanoplanter). Fluorescent beads were first chemically immobilized onto a ZnO whisker that was glued to an AFM tip and were injected into a living BALB/3T3 cell together with the whisker. It was demonstrated that the system could clearly show the result of injection, that is, the presence of a small number of fluorescent beads in the cell.
3T3 Cells↗
Chiral separation of enantiomeric 1,2-diamines using molecular imprinting method and selectivity enhancement by addition of achiral primary amines into eluents.
The imprinted polymers based on a transient complex formation between methacrylic acid and template molecules were prepared by using methacrylic acid and ethylene dimethacrylate as a cross-linking agent. The template molecules used were (R,R)-cyclohexanediamine (1), (S,S)-1,2-diphenylethylenediamine (2) and (S)-1,1'-binaphthyl-2,2'-diamine (3). Another group of templates were those in which the amino group of these templates had been substituted by the hydroxy group: (R,R)-1,2-cyclohexanediol (4) and (S,S)-hydrobenzoin (5). Racemic 2 was separated by the polymer prepared with template 2 (P2) and that with template 1 (P1). Template 2 is larger than template 1 in steric bulkiness, but P1 was effective for the enantiomer separation of racemic 2. P1 was not effective for the separation of racemic 4. Enantioselectivity observed in racemic 2 in P2 was higher than that in racemic 1 in P1. P2 has no definite predetermined shape for solute 1, but it was capable of separating racemic 1. This separation should be thus ascribed to the orientation of at least two carbonyl groups reflecting the conformation of template 2 in P2 cavity. Racemic 5, having the same configuration of the two bulky phenyl groups as that of solute 2, was separated in P2. When the primary amines such as propylamine, cyclohexylamine and 1-adamantanamine were added into the acetic acid-methanol mixtures as eluents, both enantioselectivity and retentivity for racemic 2 were enhanced along with the remarkable peak tailing.
Amines↗