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At least 19 recordsLinked to original sources
PubMed2005

Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework.

The resolution of higher level phylogeny of the coleoid cephalopods (octopuses, squids, and cuttlefishes) has been hindered by homoplasy among morphological characters in conjunction with a very poor fossil record. Initial molecular studies, based primarily on small fragments of single mitochondrial genes, have produced little resolution of the deep relationships amongst coleoid cephalopod families. The present study investigated this issue using 3415 base pairs (bp) from three nuclear genes (octopine dehydrogenase, pax-6, and rhodopsin) and three mitochondrial genes (12S rDNA, 16S rDNA, and cytochrome oxidase I) from a total of 35 species (including representatives of each of the higher level taxa). Bayesian analyses were conducted on mitochondrial and nuclear genes separately and also all six genes together. Separate analyses were conducted with the data partitioned by gene, codon/rDNA, gene+codon/rDNA or not partitioned at all. In the majority of analyses partitioning the data by gene+codon was the appropriate model with partitioning by codon the second most selected model. In some instances the topology varied according to the model used. Relatively high posterior probabilities and high levels of congruence were present between the topologies resulting from the analysis of all Octopodiform (octopuses and vampire "squid") taxa for all six genes, and independently for the datasets of mitochondrial and nuclear genes. In contrast, the highest levels of resolution within the Decapodiformes (squids and cuttlefishes) resulted from analysis of nuclear genes alone. Different higher level Decapodiform topologies were obtained through the analysis of only the 1st+2nd codon positions of nuclear genes and of all three codon positions. It is notable that there is strong evidence of saturation among the 3rd codon positions within the Decapodiformes and this may contribute spurious signal. The results suggest that the Decapodiformes may have radiated earlier and/or had faster rates of evolution than the Octopodiformes. The following taxonomic conclusions are drawn from our analyses: (1) the order Octopoda and suborders Cirrata, Incirrata, and Oegopsida are monophyletic groups; (2) the family Spirulidae (Ram's horn squids) are the sister taxon to the family Sepiidae (cuttlefishes); (3) the family Octopodidae, as currently defined, is paraphyletic; (4) the superfamily Argonautoidea are basal within the suborder Incirrata; and (5) the benthic octopus genera Benthoctopus and Enteroctopus are sister taxa.

Animals↗
PubMed2004

Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes.

The complete nucleotide sequences of the mitochondrial (mt) genomes of three cephalopods, Octopus vulgaris (Octopodiformes, Octopoda, Incirrata), Todarodes pacificus (Decapodiformes, Oegopsida, Ommastrephidae), and Watasenia scintillans (Decapodiformes, Oegopsida, Enoploteuthidae), were determined. These three mt genomes encode the standard set of metazoan mt genes. However, W. scintillans and T. pacificus mt genomes share duplications of the longest noncoding region, three cytochrome oxidase subunit genes and two ATP synthase subunit genes, and the tRNA(Asp) gene. Southern hybridization analysis of the W. scintillans mt genome shows that this single genome carries both duplicated regions. The near-identical sequence of the duplicates suggests that there are certain concerted evolutionary mechanisms, at least in cephalopod mitochondria. Molecular phylogenetic analyses of mt protein genes are suggestive, although not statistically significantly so, of a monophyletic relationship between W. scintillans and T. pacificus.

Animals↗
PubMed2000

Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda).

Phylogenetic analysis conducted on a 784-bp fragment of 82 actin gene sequences of 44 coleoid cephalopod taxa, along with results obtained from genomic Southern blot analysis, confirmed the presence of at least three distinct actin loci in coleoids. Actin isoforms were characteri zed through phylogenetic analysis of representative cephalopod sequences from each of the three isoforms, along with translated actin cDNA sequences from a diverse array of metazoan taxa downloaded from GenBank. One of the three isoforms found in cephalopods was closely related to actin sequences expressed in the muscular tissues of other molluscs. A second isoform was most similar to cytoplasmic-specific actin amino acid sequences. The muscle type actins of molluscs were found to be distinct from those of arthropods, suggesting at least two independent derivations of muscle actins in the protostome lineage, although statistical support for this conclusion was lacking. Parsimony and maximum-likelihood analyses of two of the isoforms from which >30 orthologous coleoid sequences had been obtained (one of the cytoplasmic actins and the muscle actin) supported the monophyly of several higher-level coleoid taxa. These included the superorders Octopodiformes and Decapodiformes, the order Octopoda, the octopod suborder Incirrata, and the teuthoid suborder Myopsida. The monophyly of several taxonomic groups within the Decapodiformes was not supported, including the orders Teuthoidea and Sepioidea and the teuthoid suborder Oegopsida. Parametric bootstrap analysis conducted on the simulated cytoplasmic actin data set provided statistical support to reject the monophyly of the Sepioidea. Although parametric bootstrap analysis of the muscle actin isoform did not reject sepioid monophyly at the 5% level, the results (rejection at P: = 0.068) were certainly suggestive of sepioid nonmonophyly.

Actins↗
PubMed2006

Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications.

We determined the complete mitochondrial genomes of five cephalopods of the Subclass Coleoidea (Suborder Oegopsida: Watasenia scintillans, Todarodes pacificus, Suborder Myopsida: Sepioteuthis lessoniana, Order Sepiida: Sepia officinalis, and Order Octopoda: Octopus ocellatus) and used them to infer phylogenetic relationships. In our Maximum Likelihood (ML) tree, sepiids (cuttlefish) are at the most basal position of all decapodiformes, and oegopsids and myopsids form a monophyletic clade, thus supporting the traditional classification of the Order Teuthida. We detected extensive gene rearrangements in the mitochondrial genomes of broad cephalopod groups. It is likely that the arrangements of mitochondrial genes in Oegopsida and Sepiida were derived from those of Octopoda, which is thought to be the ancestral order, by entire gene duplication and random gene loss. Oegopsida in particular has undergone long-range gene duplications. We also found that the mitochondrial gene arrangement of Sepioteuthis lessoniana differs from that of Loligo bleekeri, although they belong to the same family. Analysis of both the phylogenetic tree and mitochondrial gene rearrangements of coleoid Cephalopoda suggests that each mitochondrial gene arrangement was acquired after the divergence of each lineage.

Animals↗
PubMed1999

Vesicle transport: the role of actin filaments and myosin motors.

The transport of vesicles and the retention of organelles at specific locations are fundamental processes in cells. Actin filaments and myosin motors have been shown to be required for both of these tasks. Most of the organelles in cells associate with actin filaments and some of the myosin motors required for movement on actin filaments have been identified. Myosin V has been shown to transport endoplasmic reticulum (ER) vesicles in neurons, pigment granules in melanocytes, and the vacuole in yeast. Myosin I has been shown to be involved in the transport of Golgi-derived vesicles in epithelial cells. Myosin VI has been shown to be associated with Golgi-derived vesicles, and cytoplasmic vesicles in living Drosophila embryos. Myosin II may be a vesicle motor but its role in vesicle transport has not been resolved. Secretory vesicles, endosomes and mitochondria appear to be transported on actin filaments but the myosin motors on these organelles have not been identified. Mitochondria in yeast may be transported by the dynamic assembly of an actin "tail." The model that has unified all of these findings is the concept that long-range movement of vesicles occurs on microtubules and short-range movement on actin filaments. The details of how the microtubule-dependent and the actin-dependent motors are coordinated are important questions in the field. There is now strong evidence that two molecular motors, kinesin and myosin V, interact with each other and perhaps function as a complex on vesicles. An understanding of the interrelationship of microtubules and actin filaments and the motors that move cargo on them will ultimately establish how vesicles and organelles are transported to their specific locations in cells.

Actins↗
PubMed1997

n-ethylmaleimide and ethacrynic acid inhibit kinesin binding to microtubules in a motility assay.

Treatment of proteins in vitro with sulfhydryl (SH)-reactive compounds has been used successfully to determine protein regions critical for normal function. To probe structure-function relationships in the microtubule (MT) motor kinesin, the motor was treated with two SH reactive compounds, n-ethylmaleimide and ethacrynic acid, and its function was assayed by motility and co-sedimentation techniques. In the motility assay, treatment of kinesin either before or after adsorption to the glass surfaces of a flow cell was found to inhibit the ability of coverslip-bound kinesin to bind to MTs. Inactivation of MT binding was slow, required high molar excess of the SH-reactive drug, and was very sensitive to temperature. Inhibition of MT binding occurred well after complete modification of kinesin light chain, but paralleled modification of the kinesin heavy chain. The results point to a model in which one critical cysteine per kinesin heavy chain is relatively inaccessible to solvent. Surprisingly, when the interaction between modified kinesin and MTs was examined by a co-sedimentation assay, kinesin retained the ability to bind MTs. These contrasting results may be due to conformational differences in the kinesin molecule that exist in the two assays.

Animals↗
PubMed1999

Protein synthesis in presynaptic endings from squid brain: modulation by calcium ions.

Previous biochemical, autoradiographic, and ultrastructural data have shown that, in the synaptosomal fraction of the squid optic lobe, protein synthesis is largely due to the presynaptic terminals of the retinal photoreceptor neurons (Crispino et al. [1993a] Mol. Cell. Neurosci. 4:366-374; Crispino et al. [1993b] J. Neurochem. 61:1144-1146; Crispino et al. [1997] J. Neurosci. 17:7694-7702). We now report that this process is close to its maximum at the basal concentration of cytosolic Ca++, and is markedly inhibited when the concentration of this ion is either decreased or increased. This conclusion is supported by the results of experiments with: 1) compounds known to increase the level of cytosolic Ca++, such as A23187, ionomycin, thapsigargin, and caffeine; 2) compounds sequestering cytosolic calcium ions such as BAPTA-AM; and 3) agents that block the role of Ca++ as second messenger, such as TFP and W7, which inhibit calmodulin, and calphostin, which inhibits protein kinase C. We conclude that variations in the level of cytosolic Ca++ induced in presynaptic terminals by neuronal activity may contribute to the modulation of the local synthesis of protein.

Animals↗
PubMed1999

Topographic regulation of cytoskeletal protein phosphorylation by multimeric complexes in the squid giant fiber system.

In mammalian and squid nervous systems, the phosphorylation of neurofilament proteins (NFs) seems to be topographically regulated. Although NFs and relevant kinases are synthesized in cell bodies, phosphorylation of NFs, particularly in the lys-ser-pro (KSP) repeats in NF-M and NF-H tail domains, seem to be restricted to axons. To explore the factors regulating the cellular compartmentalization of NF phosphorylation, we separated cell bodies (GFL) from axons in the squid stellate ganglion and compared the kinase activity in the respective lysates. Although total kinase activity was similar in each lysate, the profile of endogenous phosphorylated substrates was strikingly different. Neurofilament protein 220 (NF220), high-molecular-weight NF protein (HMW), and tubulin were the principal phosphorylated substrates in axoplasm, while tubulin was the principal GFL phosphorylated substrate, in addition to highly phosphorylated low-molecular-weight proteins. Western blot analysis showed that whereas both lysates contained similar kinases and cytoskeletal proteins, phosphorylated NF220 and HMW were completely absent from the GFL lysate. These differences were highlighted by P13(suc1) affinity chromatography, which revealed in axoplasm an active multimeric phosphorylation complex(es), enriched in cytoskeletal proteins and kinases; the equivalent P13 GFL complex exhibited six to 20 times less endogenous and exogenous phosphorylation activity, respectively, contained fewer cytoskeletal proteins and kinases, and expressed a qualitatively different cdc2-like kinase epitope, 34 kDa rather than 49 kDa. Cell bodies and axons share a similar repertoire of molecular consitutents; however, the data suggest that the cytoskeletal/kinase phosphorylation complexes extracted from each cellular compartment by P13 are fundamentally different.

Animals↗
PubMed1998

Glutamate metabolism by squid nerve fiber sheaths.

The extrasynaptic region of the squid giant nerve fiber exhibits neuron-Schwann cell interactions that appear to involve glutamate as a mediator. In an earlier work, it was demonstrated that the periaxonal sheaths of such nerves (where the Schwann cells are located) possess the capacity to transport glutamate. However there was no information available about the possible fate of the glutamate incorporated into the sheaths. In this study, it is demonstrated that the periaxonal sheaths of the extrasynaptic region of squid giant nerves are capable of metabolizing glutamate. Sheaths incubated with 10 microM [1-14C] glutamate produced [14C] O2 in a manner proportional to time and estimated cell water volume. At least 45% of this CO2 production was determined to be independent of transaminase catalyzed isotopic exchange, thus reflecting real degradation (decarboxylation) of glutamate. It was also demonstrated that the sheaths were capable of glutamine synthesis. Taken together, the findings of our laboratory indicate not only that the Schwann cells of the sheaths fulfil the requirements for a site for the uptake and metabolism of transmitter glutamate in the squid giant nerve but also that certain metabolic characteristics associated with the neuro-glial unit around synapses are also found in non-synaptic areas of nerve fibers.

Animals↗
PubMedDate not supplied

The widespread occurrence and tissue distribution of the imidazolopyrazine luciferins.

Bioluminescence has been reported to occur in 17 phyla and at least 700 genera. However, the luciferin chemistry of the majority of luminous organisms has yet to be determined. The most common chemistry which is known to occur in deep sea bioluminescence is imidazolopyrazine bioluminescence. The main aim of this study was to examine the phyletic and tissue distribution of imidazolopyrazine luciferins. This will facilitate analysis of imidazolopyrazine bioluminescence at the cellular and molecular levels and, in particular, how and when its chemistry is controlled and expressed in vivo. Assays for both known imidazolopyrazines were established and a range of fresh organisms and tissue were analysed, i.e. fish, cephalopods, copepods, ostracods, amphipods and euphausiids. The main findings were that the number of genera in which coelenterazine has been detected has been increased from 52 to about 90. Also, for the first time, the other known imidazolopyrazine luciferin, Vargula-type luciferin, was quantified in the ostracod Cypridina dentata, but was not detected in any of its potential predators. Neither imidazolopyrazine luciferin was found in several luminous stomiiform fish assayed. Coelenterazine was measured in the livers and photophores of a number of cephalopods and it is apparent that coelenterazine is responsible for both modes of luminescence.

Animals↗
PubMed1998

Host-microbial symbiosis in the mammalian intestine: exploring an internal ecosystem.

The mammalian intestine contains a complex, dynamic, and spatially diversified society of nonpathogenic bacteria. Very little is known about the factors that help establish host-microbial symbiosis in this open ecosystem. By introducing single genetically manipulatable components of the microflora into germfree mice, simplified model systems have been created that will allow conversations between host and microbe to be heard and understood. Other paradigms of host-microbial symbiosis suggest that these interactions will involve an exchange of biochemical signals between host and symbionts as well as among the bacteria themselves. The integration of molecular microbiology, cell biology, and gnotobiology should provide new insights about how we adapt to a microbial world and reveal the roles played by our indigenous, 'nonpathogenic' flora.

Adaptation, Physiological↗
PubMed2000

Sequence and phylogenetic analysis of squid myosin-V: a vesicle motor in nerve cells.

We have shown that vesicles in the axoplasm of the squid giant axon move on actin filaments and that movement is inhibited by myosin V-specific antibodies [Tabb et al., 1998]. In the study reported in this article, experiments were performed to clone and sequence the cDNA for squid brain myosin V. Five proteolytic fragments of purified squid brain myosin V were analyzed by direct protein sequencing [Tabb et al., 1998]. Based on this sequence information, degenerate primers were constructed and used to isolate cDNA clones by PCR. Five clones, representing overlapping segments of the gene, were sequenced. The sequence data and the previous biochemical characterization of the molecule support the classification of this vesicle-associated myosin as a member of the class V myosins. Motif analysis of the head, neck, and tail domains revealed that squid MyoV has consensus sequences for all the motifs found in vertebrate members of the myosin V family of motor proteins. A phylogenetic tree was constructed from a sequence alignment by the neighbor-joining method, using Megalign (DNAStar, Madison, WI); the resulting phylogenetic tree showed that squid MyoV is more closely related to vertebrate MyoV (mouse dilute, chicken dilute, rat myr6, and human myo5a) than Drosophila and yeast (myo2, and myo4) myosins V. These new data on the phylogenetic relationships of squid myosin V to vertebrate myosin V strengthens the argument that myosin V functions as a vesicle motor in vertebrate neurons.

Amino Acid Motifs↗
PubMed2000

Ca(2+) dynamics in synaptosomes isolated from the squid optic lobe.

Synaptosomes from the optic lobes of squid (Loligo forbesi) were prepared by homogenization and allowed to settle onto glass coverslips. Synaptosomes were loaded with Ca(2+) sensitive dyes (Fura-2 AM, Calcium Green-1 AM and Calcium Green-5N AM), visualized by light microscopy and Ca(2+) sensitive fluorescence signals recorded and analyzed. With Fura-2, resting Ca(2+) was found to be 80 nM (n = 10, SEM 5.7). Addition of K(+) (30 mM), caffeine (3 mM) and thapsigargin (10 microM) evoked transient increases in cytoplasmic Ca(2+). Addition of BAPTA-AM (20 microM) decreased intrasynaptosomal free Ca(2+). Similar results were obtained with Calcium Green-1 AM but not with Calcium Green-5N AM. We conclude that synaptosomes from the squid optic lobe posses intact membranes and mechanisms to regulate intrasynaptosomal free [Ca(2+)], as well as caffeine sensitive Ca(2+) stores. The results of this study are discussed with respect to the role of Ca(2+) in presynaptic protein synthesis.

Animals↗
PubMed2000

Axolemmal repair requires proteins that mediate synaptic vesicle fusion.

A damaged cell membrane is repaired by a seal that restricts entry or exit of molecules and ions to that of the level passing through an undamaged membrane. Seal formation requires elevation of intracellular Ca(2+) and, very likely, protein-mediated fusion of membranes. Ca(2+) also regulates the interaction between synaptotagmin (Syt) and syntaxin (Syx), which is thought to mediate fusion of synaptic vesicles with the axolemma, allowing transmitter release at synapses. To determine whether synaptic proteins have a role in sealing axolemmal damage, we injected squid and crayfish giant axons with an antibody that inhibits squid Syt from binding Ca(2+), or with another antibody that inhibits the Ca(2+)-dependent interaction of squid Syx with the Ca(2+)-binding domain of Syt. Axons injected with antibody to Syt did not seal, as assessed at axonal cut ends by the exclusion of extracellular hydrophilic fluorescent dye using confocal microscopy, and by the decay of extracellular injury current compared to levels measured in uninjured axons using a vibrating probe technique. In contrast, axons injected with either denatured antibody to Syt or preimmune IgG did seal. Similarly, axons injected with antibody to Syx did not seal, but did seal when injected with either denatured antibody to Syx or preimmune IgG. These results indicate an essential involvement of Syt and Syx in the repair (sealing) of severed axons. We suggest that vesicles, which accumulate and interact at the injury site, re-establish axolemmal continuity by Ca(2+)-induced fusions mediated by proteins such as those involved in neurotransmitter release.

Animals↗
PubMed2000

Localization of voltage-gated K(+) channels in squid giant axons.

We have localized the classical voltage-gated K(+) channel within squid giant axons by immunocytochemistry using the Kv1 antibody of Rosenthal et al. (1996). Widely dispersed patches of intense immunofluorescence were observed in the axonal membrane. Punctate immunofluorescence was also observed in the axoplasm and was localized to approximately 25-50-microm-wide column down the length of the nerve (axon diameter approximately 500 microm). Immunoelectronmicroscopy of the axoplasm revealed a K(+) channel containing vesicles, 30-50 nm in diameter, within this column. These and other vesicles of similar size were isolated from axoplasm using a novel combination of high-speed ultracentrifugation and controlled-pore size, glass bead separation column techniques. Approximately 1% of all isolated vesicles were labeled by K(+) channel immunogold reacted antibody. Incorporation of isolated vesicle fractions within an artificial lipid bilayer revealed K(+) channel electrical activity similar to that recorded directly from the axonal membrane by Llano et al. (1988). These K(+) channel-containing vesicles may be involved in cycling of K(+) channel protein into the axonal membrane. We have also isolated an axoplasmic fraction containing approximately 150-nm-diameter vesicles that may transport K(+) channels back to the cell body.

Animals↗
PubMed1975

The ionic channels in excitable membranes.

The ionic channels in excitable membranes are of two classes: those that open and close when the membrane potential alters and those that respond to the release of an appropriate chemical transmitter. The former are responsible for the conduction of impulses in nerve and muscle fibres and the latter for synaptic transmission. It is now clear that the sodium and potassium channels in electrically excitable membranes are functionally distinct, since each can be blocked without affecting the behaviour of the other. It has recently proved possible to study, in the voltage-clamped squid giant axon, the movements of the mobile charges or dipoles that form the voltage-sensitive portion of the sodium channels, which give rise to the so-called 'gating' current. Detailed comparisons can now be made between the kinetics of the ionic conductances as described by Hodgkin & Huxley, and the steady-state distribution and kinetics of the charged controlling particles, which should lead to useful conclusions about the intramolecular organization of the sodium channels and the conformational changes that take place under the influence of the electric field. There is as yet little information about the chemical nature of the electrically excitable channels, but significant progress has been made towards the isolation and characterization of the acetylcholine receptors in muscle and electric organ.

Animals↗
PubMed1994

Immunolocalization of S-crystallins in the developing squid (Loligo opalescens) lens.

S-crystallins are the predominant soluble proteins of the squid lens. Of these, S-III crystallin is the major component and S-I and S-II crystallin are the minor lens components. The lens has a posterior and anterior segment, each derived from separate groups of ectodermal cells referred to as lentigenic cells. In the present study, the appearance of S-crystallins during the development of the lens of Loligo opalescens was followed by immuno-cytochemistry. S-crystallins of the lens and lentigenic cells were first observed at day 17 (Arnold stage 27) of embryogenesis. S-crystallins were not confined to a single region, but were present in the middle group (group 2) of lentigenic cells, the posterior lens primordium, and the processes connecting the lentigenic cells and the posterior lens primordium. Two days later (Arnold stage 28), the S-crystallins were also observed in the anterior group (group 1) of lentigenic cells, the anterior lens primordium, and the processes connecting the cells with the anterior lens primordium. Thus, during development, S-crystallins accumulate first in the posterior lens primordium and subsequently in the anterior lens primordium and their respective lentigenic cells and connecting lentigenic processes. Incubated sections of the adult lens and lentigenic cells also show specific immuno-peroxidase staining when compared with controls. This evidence in combination with a recent investigation (West [1993] Ph.D. dissertation), which indicates that the cephalopod lens continues to grow throughout adulthood, suggests that squid lens crystallins are synthesized during adulthood.

Animals↗