Timing of a mtDNA gene rearrangement and intercontinental dispersal of varanid lizards

The mitochondrial genomes of the Komodo monitor (Varanus komodoensis) and the Nile monitor (V. niloticus) were previously shown to have an extensive gene rearrangement. Here, we show that this gene arrangement widely occurs in varanid taxa originated from Africa, Asia and Australasia. Based on phylogenetic relationships of the varanids constructed using mitochondrial DNA sequences encoding the NADH dehydrogenase subunit 2 gene and seven flanking tRNA genes, we estimated their divergence times by the Bayesian method without assuming the molecular clock. The results suggested that the mitochondrial DNA gene rearrangement took place once in an ancestral varanid lineage in the Paleocene or earlier. Our results are more consistent with Cenozoic over-water dispersal of Southeast Asian varanids across the Indonesian Archipelago rather than the Cretaceous Gondwanan vicariance for the origin of Australasian varanids.     

Preparation of the Extracellular Domain of Recombinant Human Toll-like Receptor 6

Toll-like receptors (TLRs) mediate immune responses upon recognition of a variety of ligands. To further elucidate the function of TLRs, it is important to identify novel ligands and their action mechanisms including polymer assembly. In this study, we propose an efficient method for preparation of the extracellular domain of human Toll-like receptor 6 (TLR6_ED) in Escherichia coli using the bubbling cultivation method. Our preparation method improved the level of expression of TLR6_ED into a soluble fraction as compared with typical cultivation using a rotary shaker. Circular dichroism (CD) experiments confirmed the structural formation of TLR6_ED with secondary structure contents similar to leucine-rich repeat (LRR) modules. In addition, we also provided a procedure for preparing this recombinant protein using Sf9 insect cells, which ensures preservation of some key posttranslational modifications often lacking in bacteria-expressed proteins. These materials would be useful for analyzing novel molecules that bind directly to TLR6, complex formations with other regulators including TLR2 and TLR4, and the functional effects of N-linked glycosylation.     

Rapid isolation of murine primary hepatocytes for chromosomal analysis

Primary hepatocyte culture is a crucial tool for investigations of liver function and for evaluating the toxic effects of drugs. In addition, chromosomal analysis of hepatocytes could also prove useful for understanding the mechanisms of hepatocarcinogenesis. However, cultivation of primary hepatocytes for chromosome analysis has been hampered by the specific equipment and skill required to perform the in situ perfusion step necessary for isolation of primary hepatocytes. In the present study, we aimed to establish a simple and efficient method of isolating hepatocytes suitable for chromosome analysis. We performed hepatocyte isolation without using collagenase perfusion, instead digesting liver tissues using collagenase in tubes. In addition, we examined hepatocyte and bone marrow cell (BMC) co-culture and cultivation of hepatocytes with medium containing BMC culture medium supernatants. We found that hepatocyte viability and attachment rate were significantly improved, both by co-culture with BMCs and medium containing BMC culture media supernatants, with the latter also significantly increasing the mitotic index. Using this simple method of isolation and cultivation, we could successfully perform chromosomal analysis of mouse primary hepatocytes. This method has the potential to help understand the mechanisms underlying chromosomal instability-mediated hepatocarcinogenesis.     

Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics

Mitochondrial DNA sequences are often used to construct molecular phylogenetic trees among closely related animals. In order to examine the usefulness of mtDNA sequences for deep-branch phylogenetics, genes in previously reported mtDNA sequences were analyzed among several animals that diverged 20–600 million years ago. Unambiguous alignment was achieved for stem-forming regions of mitochondrial tRNA genes by virtue of their conservative secondary structures. Sequences derived from stem parts of the mitochondrial tRNA genes appeared to accumulate much variation linearly for a long period of time: nearly 100 Myr for transition differences and more than 350 Myr for transversion differences. This characteristic could be attributed, in part, to the structural variability of mitochondrial tRNAs, which have fewer restrictions on their tertiary structure than do nonmitochondrial tRNAs. The tRNA sequence data served to reconstruct a well-established phylogeny of the animals with 100% bootstrap probabilities by both maximum parsimony and neighbor joining methods. By contrast, mitochondrial protein genes coding for cytochrome b and cytochrome oxidase subunit I did not reconstruct the established phylogeny or did so only weakly, although a variety of fractions of the protein gene sequences were subjected to tree-building. This discouraging phylogenetic performance of mitochondrial protein genes, especially with respect to branches originating over 300 Myr ago, was not simply due to high randomness in the data. It may have been due to the relative susceptibility of the protein genes to natural selection as compared with the stem parts of mitochondrial tRNA genes. On the basis of these results, it is proposed that mitochondrial tRNA genes may be useful in resolving deep branches in animal phylogenies with divergences that occurred some hundreds of Myr ago. For this purpose, we designed a set of primers with which mtDNA fragments encompassing clustered tRNA genes were successfully amplified from various vertebrates by the polymerase chain reaction.Abbreviations AA stem amino acid-acceptor stem - AC stem anticodon stem - COI cytochrome oxidase subunit I - cytb cytochrome b - D stem dihydrouridine stem - MP maximum parsimony - mtDNA mitochondrial DNA - Myr million years - NJ neighbor joining - PCR polymerase chain reaction - Ti transition - T stem tC stem - Tv transversion Correspondence to: Y. Kumazawa     

Simultaneous monitoring of excitatory postsynaptic potentials and extracellular L-glutamate in mouse hippocampal slices

Simultaneous monitoring of amperometric currents at a glass capillary sensor based on recombinant GluOx and field excitatory postsynaptic potentials (fEPSPs) were performed in region CA1 of mouse hippocampal slices. A transient increase in the glutamate current relative to the basal one at control stimulation (0.052Hz) was evoked by stimulation at 2 Hz for 2 min. The magnitude of the glutamate current was dependent on the intensity (current) of a 2 Hz stimulus and reflected the slope of the fEPSP. The in situ calibration of the L-glutamate sensor revealed that the extracellular concentration of L-glutamate released by 2 Hz stimulation before tetanus is in the range from 0.8 to 2.2 μM and it is enhanced after tetanic stimulation. The L-glutamate level at a test stimulus (0.052 Hz) was estimated to be 32 nM. The recombinant GluOx-based sensor exhibited weak responses to glutamine above 300 μM and L-aspartic acid above 200 μM. The potential use of a glass capillary sensor in combination with fEPSP measurements for electrophysiological study is discussed.     

Convergence of reference frequencies by multiple CF–FM bats (Rhinolophus ferrumequinum nippon) during paired flights evaluated with onboard microphones

The constant frequency component of the second harmonic (CF(2)) of echolocation sounds in Rhinolophus ferrumequinum nippon were measured using onboard telemetry microphones while the bats exhibited Doppler-shift compensation during flights with conspecifics. (1) The CF(2) frequency of pulses emitted by individual bats at rest (F (rest)) showed a long-term gradual decline by 0.22?kHz on average over a period of 3?months. The mean neighboring F (rest) (interindividual differences in F (rest) between neighboring bats when the bats were arranged in ascending order according to F (rest)) ranged from 0.08 to 0.11?kHz among 18 bats in a laboratory colony. (2) The standard deviation of observed echo CF(2) (reference frequency) for bats during paired flights ranged from 50 to 90?Hz, which was not significantly different from that during single flights. This finding suggests that during paired flights, bats exhibit Doppler-shift compensation with the same accuracy as when they fly alone. (3) In 60?% (n?=?29) of the cases, the difference in the reference frequency between two bats during paired flights significantly decreased compared to when the bats flew alone. However, only 15?% of the cases (n?=?7) showed a significant increase during paired flights. The difference in frequency between two bats did not increase even when the reference frequencies of the individuals were not statistically different during single flights.     

Studies of the Active Principles of Leucothoe grayana MAX.

Amides, IVa and IVb, which were derived from Grayanotoxin-II reacted very easily under a mild acidic condition to give a product, the structure of which has been established to be Va.     

Studies on CN--insensitive respiration in plant roots III. Induction of CN--insensitive respiration with low concentrations of respiratory inhibitors

Induction of CN^–-insensitive respiration with low concentrationsof respiratory inhibitors was studied. If roots were treatedwith 10^–3 M CN^– for 96 hr, the plants died, whilethose treated with 10^–4 M CN^– showed healthy growth. O₂ uptake in untreated rice and wheat roots showed a negativeresponse to 10^–2 M CN^– to a considerable extent.On the other hand, pretreatment with 10^–4 M CN^–for more than 6 hr did not greatly affect respiratory rate,but made respiration insensitive to 10^–2 M CN^–.A similar induction of CN^–-insensitivity was also broughtabout with 10^–4 and 10^–3 M H₂S and 10^–4 MNaN₃. (Received July 6, 1971; )     

Rearrangements of mitochondrial transfer RNA genes in marsupials

Summary The nucleotide sequences of the mitochondrial origin of light-strand replication and the five tRNA genes surrounding it were determined for three marsupials. The region was found to be rearranged, leaving only the tRNA^Tyr gene at the same position as in placental mammals andXenopus. Distribution of the same rearranged genotype among two marsupial families indicates that the events causing the rearrangements took place in an early marsupial ancestor. The putative mitochondrial light-strand origin of replication in marsupials contains a hairpin structure similar to other vertebrate origins and, in addition, extensive flanking sequences that are not found in other vertebrates. Sequence comparisons among the marsupials as well as placentals indicate that the tRNA^Tyr gene has been evolving under more constraints than the other tRNA genes.Deceased July 21, 1991     

Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes

Summary The gene organization of starfish mitochondrial DNA is identical with that of the sea urchin counterpart except for a reported inversion of an approximately 4.6-kb segment containing two structural genes for NADH dehydrogenase subunits 1 and 2 (ND 1 and ND 2). When the codon usage of each structural gene in starfish, sea urchin, and vertebrate mitochondrial DNAs is examined, it is striking that codons ending in T and G are preferentially used more for heavy strand-encoded genes, including starfish ND 1 and ND 2, than for light strand-encoded genes, including sea urchin ND 1 and ND 2. On the contrary, codons ending in A and Care preferentially used for the light strand-encoded genes rather than for the heavy strand-encoded ones. Moreover, G-U base pairs are more frequently found in the possible secondary structures of heavy strandencoded tRNAs than in those of light strand-encoded tRNAs. These observations suggest the existence of a certain constraint operating on mitochondrial genomes from various animal phyla, which results in the accumulation of G and T on one strand, and A and C on the other.