Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes

The jawless vertebrates (lamprey and hagfish) are the closest extant outgroups to all jawed vertebrates (gnathostomes) and can therefore provide critical insight into the evolution and basic biology of vertebrate genomes. As such, it is notable that the genomes of lamprey and hagfish possess a capacity for rearrangement that is beyond anything known from the gnathostomes. Like the jawed vertebrates, lamprey and hagfish undergo rearrangement of adaptive immune receptors. However, the receptors and the mechanisms for rearrangement that are utilized by jawless vertebrates clearly evolved independently of the gnathostome system. Unlike the jawed vertebrates, lamprey and hagfish also undergo extensive programmed rearrangements of the genome during embryonic development. By considering these fascinating genome biologies in the context of proposed (albeit contentious) phylogenetic relationships among lamprey, hagfish, and gnathostomes, we can begin to understand the evolutionary history of the vertebrate genome. Specifically, the deep shared ancestry and rapid divergence of lampreys, hagfish and gnathostomes is considered evidence that the two versions of programmed rearrangement present in lamprey and hagfish (embryonic and immune receptor) were present in an ancestral lineage that existed more than 400 million years ago and perhaps included the ancestor of the jawed vertebrates. Validating this premise will require better characterization of the genome sequence and mechanisms of rearrangement in lamprey and hagfish.     

X-ray diffraction evidence for the extensibility of actin and myosin filaments during muscle contraction.

To clarify the extensibility of thin actin and thick myosin filaments in muscle, we examined the spacings of actin and myosin filament-based reflections in x-ray diffraction patterns at high resolution during isometric contraction of frog skeletal muscles and steady lengthening of the active muscles using synchrotron radiation as an intense x-ray source and a storage phosphor plate as a high sensitivity, high resolution area detector. Spacing of the actin meridional reflection at approximately 1/2.7 nm-1, which corresponds to the axial rise per actin subunit in the thin filament, increased about 0.25% during isometric contraction of muscles at full overlap length of thick and thin filaments. The changes in muscles stretched to approximately half overlap of the filaments, when they were scaled linearly up to the full isometric tension, gave an increase of approximately 0.3%. Conversely, the spacing decreased by approximately 0.1% upon activation of muscles at nonoverlap length. Slow stretching of a contracting muscle increased tension and increased this spacing over the isometric contraction value. Scaled up to a 100% tension increase, this corresponds to a approximately 0.26% additional change, consistent with that of the initial isometric contraction. Taken together, the extensibility of the actin filament amounts to 3-4 nm of elongation when a muscle switches from relaxation to maximum isometric contraction. Axial spacings of the layer-line reflections at approximately 1/5.1 nm-1 and approximately 1/5.9 nm-1 corresponding to the pitches of the right- and left-handed genetic helices of the actin filament, showed similar changes to that of the meridional reflection during isometric contraction of muscles at full overlap. The spacing changes of these reflections, which also depend on the mechanical load on the muscle, indicate that elongation is accompanied by slight changes of the actin helical structure possibly because of the axial force exerted by the actomyosin cross-bridges. Additional small spacing changes of the myosin meridional reflections during length changes applied to contracting muscles represented an increase of approximately 0.26% (scaled up to a 100% tension increase) in the myosin periodicity, suggesting that such spacing changes correspond to a tension-related extension of the myosin filaments. Elongation of the myosin filament backbone amounts to approximately 2.1 nm per half sarcomere. The results indicate that a large part (approximately 70%) of the sarcomere compliance of an active muscle is caused by the extensibility of the actin and myosin filaments; 42% of the compliance resides in the actin filaments, and 27% of it is in the myosin filaments.     

Dissociation and auto-oxidation of hemerythrin induced by SH-modification: a kinetic study

Hemerythrin from Siphonosoma cumanense has a trimeric structure consisting of identical subunits, which have no cooperativity nor Bohr effect on oxygen-binding. The trimer was dissociated into its monomers by the modification of the SH group of its cysteines with p-chloromercuriphenylsulfonic acid (PCMPS), which was monitored by stopped-flow of both spectrophotomeric and small angle X-ray scattering methods. The results showed that the process involved sequential modification of the SH groups, dissociation into monomers, and auto-oxidation of ferrous iron in the active center. The modification of the SH groups with PCMPS followed second-order kinetics with a rate constant of 1.8 M-1.s-1. The dissociation and auto-oxidation followed first-order kinetics with rate constants of 4 X 10(-3) s-1 and 5 X 10(-4) s-1, respectively. The obtained rate of auto-oxidation was much faster than that in the native state. These findings lead to the conclusion that the trimeric state of S. cumanense hemerythrin is necessary to prevent auto-oxidation.     

Temperature dependence of the ripple structure in dimyristoylphosphatidylcholine studied by synchrotron X-ray small-angle diffraction

The ripple structure of 1,2-dimyristoyl-L-phosphatidylcholine (DMPC) multibilayer containing excess water (60 wt%) was studied by synchrotron X-ray small-angle diffraction. The (0,1) spacing which corresponds to the ripple repeat distance depends on temperature: At 13 degrees C the (0,1) spacing is 14.15 nm, the spacing decreases at higher temperatures and reaches 12.1 nm at 23.5 degrees C, just below the main transition temperature. The spacing is in good agreement between heating process and cooling process except for the supercooling region. The result suggests that the rearrangement of the ripple structure takes place during temperature change successively. The Landau-de Gennes free energy equation explains well the temperature dependence of the ripple repeat distance.     

A two-dimensional YAC pooling strategy for library screening via STS and Alu-PCR methods.

We have developed a simple two-dimensional YAC pooling strategy to facilitate YAC library screening via STS and Alu-PCR approaches. The method has been implemented using the human total genomic YAC library of Olson and coworkers, and its validity tested by isolation of many chromosomes 19- and 21-specific YACs. The Alu-PCR approach is notable in that it is hybridization-based, such that PCR primer pairs do not need to be repeatedly synthesized and tested for each screening step.     

A BAC library of the East African haplochromine cichlid fish Astatotilapia burtoni

A BAC library was constructed from Astatotilapia burtoni, a haplochromine cichlid that is found in Lake Tanganyika, East Africa, and its surrounding rivers. The library was generated from genomic DNA of blood cells and comprises 96,768 individual clones. Its median insert size is 150 kb and the coverage is expected to represent about 14 genome equivalents. The coverage evaluation was based on genome size estimates that were obtained by flow cytometry. In addition, hybridization screens with five probes largely corroborate the above coverage estimate, although the number of clones ranged from 5 to 22 authenticated clones per single copy probe. The BAC library described here is expected to be useful to the scientific community interested in cichlid genomics as an important resource to gain new insights into the rapid evolution of the great species diversity of haplochromine cichlid fishes.     

RNA interference for the organizer-specific gene Xlim-1 in Xenopus embryos

Double-stranded RNA (dsRNA) interferes with gene expression in various species, a phenomenon known as RNA interference (RNAi). We show here that RNAi is also effective in modifying gene expression in Xenopus embryos. First, expression of an exogenous luciferase gene as a reporter in embryos was reduced by coinjection with dsRNA corresponding to the luciferase gene. Next, injection of dsRNA for Xlim-1, a homeobox gene suggested to be involved in Spemann organizer functions, reduced the endogenous level of Xlim-1 mRNA and produced embryos with reduced eyes or anterior truncation at high efficiency. In addition, injection of an antisense expression construct of Xlim-1 elicited phenotypes very similar to those of Xlim-1 dsRNA-injected embryos. These results indicate the effectiveness of RNAi for loss of function studies in Xenopus embryos, and the importance of Xlim-1 in head formation.     

Differential effects of sublethal ischemia and chemical preconditioning with 3-nitropropionic acid on protein expression in gerbil hippocampus

Pretreatment with a low dose of 3-nitropropionic acid (3-NPA) has been shown to induce ischemic tolerance in the gerbil hippocampus. It is well known that sublethal (2-min) ischemia also induces ischemic tolerance. To investigate the acquisition of ischemic tolerance with 3-NPA, we examined the protein expression after 3-NPA treatment in comparison with sublethal ischemia. Immunohistochemical studies revealed intense expression of Bcl-2 and Bcl-xL in the hippocampal CA1 area after 3-NPA treatment. Furthermore, the time course of the expression of Bcl-xL showed a similar pattern to the acquisition of ischemic tolerance by 3-NPA treatment. The induction of Bcl-xL occurred in the hippocampal CA1 area at 24 h after 3-NPA treatment, and significant induction was observed at 48 h. Western blot analysis of hippocampus harvested 48 h after the pretreatment, showed that the expression of Bcl-2 and Bcl-xL was significantly increased by either 3-NPA treatment or 2-min ischemia. However, PMCA1 and HSP70 protein expression increased only in the sublethal ischemia treated group. The difference between 3-NPA treated group and control group was not statistically significant. These results suggest that Bcl-2 and Bcl-xL are essential for acquisition of ischemic tolerance, while HSP70 and PMCA1 play important roles in the enhancement of ischemic tolerance.     

Hippocampal Theta-Gamma Coupling Reflects State-Dependent Information Processing in Decision Making

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