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PubMed2003

Two Corbicula (Corbiculidae: Bivalvia) mitochondrial lineages are widely distributed in Asian freshwater environment.

We investigated the biogeography of Asian Corbicula using mitochondrial gene sequence variation for Corbicula members sampled from 24 localities of eight Asian regions. A total of 210 individuals were genetically characterized by examining sequence variations of a 614 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene. Phylogenetic analyses of the COI dataset revealed that Corbicula members are subdivided into two well-supported clades: estuarine and freshwater. A robust dichotomy between the Japanese/Korean (Corbicula japonica) and Chinese (Corbicula fluminalis) estuarine forms was evident, suggesting that these two regional populations represent a deep phylogeographic split. Our mitochondrial gene tree showed that among the freshwater members, two Corbicula mitochondrial lineages are the most common, having attained extensive geographic distribution in the Asian freshwater environment. While the present study provides significant biogeographic information on Asian Corbicula, a comprehensive phylogenetic study by cross-referencing the mitochondrial-based Corbicula phylogeny with nuclear gene data is required to fully understand the evolutionary origin(s) of triploidy/clonality in this genus.

Animals↗
PubMed1996

Immunolocalization of an inwardly rectifying K+ channel, K(AB)-2 (Kir4.1), in the basolateral membrane of renal distal tubular epithelia.

Immunolocalization of K(AB)-2 (Kir4.1), an inwardly rectifying K+ channel with a putative ATP-binding domain, was examined in rat kidney where expression of K(AB)-2 mRNA was previously shown. Anti-K(AB)-2 antibody was raised in rabbit and then affinity-purified. An immunohistochemical study revealed that K(AB)-2 immunoreactivity was detected specifically in the basolateral membrane of distal tubular epithelia. Therefore, K(AB)-2 is the first K+ channel shown to be localized in the basolateral membrane of renal epithelia. The finding suggests that K(AB)-2 may contribute to supplying K+ to the Na(+)-K+ pump, which is abundant in the basolateral membrane of distal tubular epithelia, as well as to maintenance of the deep negative membrane potential of these cells.

Amino Acid Sequence↗
PubMed2005

Neuroacanthocytosis: new developments in a neglected group of dementing disorders.

Neurological abnormalities associated with spiculated, "acanthocytic" red cells in blood have been summarized as neuroacanthocytosis. This is a heterogeneous group of conditions that can now be clearly subdivided on the basis of genetic discoveries. The core neuroacanthocytosis syndromes are autosomal recessive chorea-acanthocytosis (ChAc) and the X-linked McLeod syndrome (MLS). Huntington's disease-like 2 (HLD2) and pantothenate kinase associated neurodegeneration (PKAN) can now also be included. All of these share dyskinesias, cognitive deterioration and progressive neurodegeneration mainly of the basal ganglia, but they are sufficiently distinct to permit a specific working diagnosis on the basis of clinical, laboratory and imaging findings. In addition, the VPS13A (formerly called CHAC), XK, JPH3 and PANK2 genes, respectively, may be examined for mutations. Unfortunately, little is yet known about the normal and abnormal physiology of the protein products of these genes, but they appear to be involved in membrane function and intracellular protein sorting. Since no cures are yet available, development and study of disease models in experimental animals (mouse, C. elegans) is a priority for current research. From a clinical point of view, the common occurrence of cardiomyopathy in MLS, the transfusion hazards due to the McLeod Kell phenotype and the possibility of improving the violent trunk spasms and orofacial dyskinesias typical for ChAc (with subsequent lip or tongue mutilations and feeding dystonia) by deep brain surgery or stimulation should be considered in patient management.

Amino Acid Sequence↗
PubMed1995

Sequestration of the membrane-targeting myristoyl group of recoverin in the calcium-free state.

Recoverin, a retinal calcium-binding protein of relative molecular mass (M(r)) 23K, participates in the recovery phase of visual excitation and in adaptation to background light. The Ca(2+)-bound form of recoverin prolongs the photoresponse, probably by blocking phosphorylation of photoexcited rhodopsin. Retinal recoverin contains a covalently attached myristoyl group or related acyl group at its amino terminus and two Ca(2+)-binding sites. Ca2+ binding to myristoylated, but not unmyristoylated, recoverin induces its translocation to bilayer membranes, indicating that the myristoyl group is essential to the read-out of calcium signals (calcium-myristoyl switch). Here we present the solution structure of Ca(2+)-free, myristoylated recombinant recoverin obtained by heteronuclear multidimensional NMR spectroscopy. The myristoyl group is sequestered in a deep hydrophobic pocket formed by many aromatic and other hydrophobic residues from five flanking helices.

Amino Acid Sequence↗
PubMed1995

A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA.

A 17-amino acid arginine-rich peptide from the bovine immunodeficiency virus Tat protein has been shown to bind with high affinity and specificity to bovine immunodeficiency virus transactivation response element (TAR) RNA, making contacts in the RNA major groove near a bulge. We show that, as in other peptide-RNA complexes, arginine and threonine side chains make important contributions to binding but, unexpectedly, that one isoleucine and three glycine residues also are critical. The isoleucine side chain may intercalate into a hydrophobic pocket in the RNA. Glycine residues may allow the peptide to bind deeply within the RNA major groove and may help determine the conformation of the peptide. Similar features have been observed in protein-DNA and drug-DNA complexes in the DNA minor groove, including hydrophobic interactions and binding deep within the groove, suggesting that the major groove of RNA and minor groove of DNA may share some common recognition features.

Amino Acid Sequence↗
PubMed2005

Molecular phylogenetics of the siphonophora (Cnidaria), with implications for the evolution of functional specialization.

Siphonophores are a group of pelagic colonial hydrozoans (Cnidaria) that have long been of general interest because of the division of labor between the polyps and medusae that make up these "superorganisms." These polyps and medusae are each homologous to free living animals but are generated by an incomplete asexual budding process that leaves them physiologically integrated. They are functionally specialized for different tasks and are precisely organized within each colony. The number of functional types of polyps and medusae varies across taxa, and different authors have used this character to construct phylogenies polarized in opposite directions, depending on whether they thought siphonophore evolution proceeded by a reduction or an increase in functional specialization. We have collected taxa across all major groups of siphonophores, many of which are found exclusively in the deep sea, using remotely operated underwater vehicles (ROVs) and by SCUBA diving from ships in the open ocean. We have used 52 siphonophores and four outgroup taxa to estimate the siphonophore phylogeny with molecular data from the nuclear small subunit ribosomal RNA gene (18S) and the mitochondrial large subunit ribosomal RNA gene (16S). Parsimony reconstructions indicate that functionally specialized polyps and medusae have been gained and lost across the phylogeny. Maximum likelihood and Bayesian analyses of morphological data suggest that the transition rate for decreased functional specialization is greater than the transition rate for increased functional specialization for three out of the four investigated categories of polyps and medusae. The present analysis also bears on several long-standing questions about siphonophore systematics. It indicates that the cystonects are sister to all other siphonophores, a group that we call the Codonophora. We also find that the Calycophorae are nested within the Physonectae, and that the Brachystelia, a historically recognized grouping of short-stemmed taxa, are polyphyletic. [Cnidaria; colonial animals; deep sea; division of labor; functional specialization; Hydrozoa; phylogenetics; Siphonophores.].

Animals↗
PubMed2001

Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies.

Jakobids are free-living, heterotrophic flagellates that might represent early-diverging mitochondrial protists. They share ultrastructural similarities with eukaryotes that occupy basal positions in molecular phylogenies, and their mitochondrial genome architecture is eubacterial-like, suggesting a close affinity with the ancestral alpha-proteobacterial symbiont that gave rise to mitochondria and hydrogenosomes. To elucidate relationships among jakobids and other early-diverging eukaryotic lineages, we characterized alpha- and beta-tubulin genes from four jakobids: Jakoba libera, Jakoba incarcerata, Reclinomonas americana (the "core jakobids"), and Malawimonas jakobiformis. These are the first reports of nuclear genes from these organisms. Phylogenies based on alpha-, beta-, and combined alpha- plus beta-tubulin protein data sets do not support the monophyly of the jakobids. While beta-tubulin and combined alpha- plus beta-tubulin phylogenies showed a sister group relationship between J. libera and R. americana, the two other jakobids, M. jakobiformis and J. incarcerata, had unclear affinities. In all three analyses, J. libera, R. americana, and M. jakobiformis emerged from within a well-supported large "plant-protist" clade that included plants, green algae, cryptophytes, stramenopiles, alveolates, Euglenozoa, Heterolobosea, and several other protist groups, but not animals, fungi, microsporidia, parabasalids, or diplomonads. A preferred branching order within the plant-protist clade was not identified, but there was a tendency for the J. libera-R. americana lineage to group with a clade made up of the heteroloboseid amoeboflagellates and euglenozoan protists. Jakoba incarcerata branched within the plant-protist clade in the beta- and the combined alpha- plus beta-tubulin phylogenies. In alpha- tubulin trees, J. incarcerata occupied an unresolved position, weakly grouping with the animal/fungal/microsporidian group or with amitochondriate parabasalid and diplomonad lineages, depending on the phylogenetic method employed. Tubulin gene phylogenies were in general agreement with mitochondrial gene phylogenies and ultrastructural data in indicating that the "jakobids" may be polyphyletic. Relationships with the putatively deep-branching amitochondriate diplomonads remain uncertain.

Animals↗
PubMed2002

An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks.

A unified understanding of >390 Myr of insect evolution requires insight into their origin. Molecular clocks are widely applied for evolutionary dating, but clocks for the class Insecta have remained elusive. We now define a robust nucleotide and amino acid mitochondrial molecular clock encompassing five insect orders, including the Blattaria (cockroaches), Orthoptera (crickets and locusts), Hemiptera (true bugs), Diptera, and Lepidoptera (butterflies and moths). Calibration of the clock using one of the earliest, most extensive fossil records for insects (the early ancestors of extant Blattaria) was congruent with all available insect fossils, with biogeographic history, with the Cambrian explosion, and with independent dating estimates from Lepidopteran families. In addition, dates obtained from both nucleotide and amino acid clocks were congruent with each other. Of particular interest to vector biology is the early date of the emergence of triatomine bugs (99.8-93.5 MYA), coincident with the formation of the South American continent during the breakup of Gondwanaland. More generally, we reveal the insects arising from a common ancestor with the Anostraca (fairy shrimps) at around the Silurian-Ordovician boundary (434.2-421.1 MYA) coinciding with the earliest plant megafossil. We explore Tilyard's theory proposing that the terrestrial transition of the aquatic arthropod ancestor to the insects is associated with a particular plant group (early vascular plants). The major output of the study is a comprehensive series of dates for deep-branching points within insect evolution that can act as calibration points for further dating studies within insect families and genera.

Animals↗
PubMed1996

Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans.

A gene lineage (SAR406) related to Chlorobium and Fibrobacter species was found in 16S rRNA gene clone libraries prepared from samples from two oceans. The clone libraries were constructed from total picoplankton genomic DNA to assess bacterial diversity in the lower surface layer. The samples were collected by filtration from a depth of 80 m at a site in the western Sargasso Sea and from a depth of 120 m at a site in the Pacific Ocean, approximately 70 km from the Oregon coast. The PCR and primers which amplified nearly full-length 16S rRNA genes were used to prepare the clone libraries. Among the diverse gene clones in these libraries were two related clones (SAR406 and OCS307) which could not be assigned to any of the major bacterial phyla. Phylogenetic analyses demonstrated that these genes were distant relatives of the genus Fibrobacter and the green sulfur bacterial phylum, which includes the genus Chlorobium. The inclusion of SAR406 in phylogenetic trees inferred by several methods resulted in support from bootstrap replicates for the conclusion that Fibrobacter and Chlorobium species and SAR406 are a monophyletic group. An oligonucleotide probe that selectively hybridized to clone SAR406 was used to examine the distribution of this gene lineage in vertical profiles from the Atlantic and Pacific Oceans and in monthly time series at 0 and 200 m in the Atlantic Ocean. During stratified periods, the genes were most abundant slightly below the deep chlorophyll layer. Seasonal changes in the surface abundance of SAR406 rDNA were highly correlated with chlorophyll a levels (r = 0.75).

Bacteria↗
PubMed2001

Cortical upper layer neurons derive from the subventricular zone as indicated by Svet1 gene expression.

The cerebral cortex is composed of a large variety of different neuron types. All cortical neurons, except some interneurons, are born in two proliferative zones, the cortical ventricular (VZ) and subventricular (SVZ) zones. The relative contribution of both proliferative zones to the generation of the diversity of the cortical neurons is not well understood. To further dissect the underlying mechanism, molecular markers specific for the SVZ are required. Towards this end we performed a subtraction of cDNA libraries, generated from E15.5 and E18.5 mouse cerebral cortex. A novel cDNA, Svet1, was cloned which was specifically expressed in the proliferating cells of the SVZ but not the VZ. The VZ is marked by the expression of the Otx1 gene. Later in development, Svet1 and Otx1 were expressed in subsets of cells of upper (II-IV) and deep (V-VI) layers, respectively. In the reeler cortex, where the layers are inverted, Svet1 and Otx1 label precursors of the upper and deeper layers, respectively, in their new location. Interestingly, in the Pax6/small eye mutant, Svet1 activity was abolished in the SVZ and in the upper part of the cortical plate while the Otx1 expression domain remained unchanged. Therefore, using Svet1 and Otx1 as cell-type-specific molecular markers for the upper and deep cortical layers we conclude that the Sey mutation affects predominantly the differentiation of the SVZ cells that fail to migrate into the cortical plate. The abnormality of the SVZ coincides with the absence of upper layer cells in the cortex. Taken together our data suggest that while the specification of deep cortical layers occurs in the ventricular zone, the SVZ is important for the proper specification of upper layers.

Animals↗
PubMed1991

Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor.

The origin of plastids by either a single or multiple endosymbiotic event(s) and the nature of the progenitor(s) of plastids have been the subjects of much controversy. The sequence of the small subunit rRNA (Ssu rRNA) from the plastid of the chlorophyll c-containing alga Cryptomonas phi is presented, allowing for the first time a comparison of this molecule from all of the major land plant and algal lineages. Using a distance matrix method, the phylogenetic relationships among representatives of these lineages have been inferred and the results indicate a common origin of plastids from a cyanobacterium-like ancestor. Within the plastid line of descent, there is a deep dichotomy between the chlorophyte/land plant lineage and the rhodophyte/chromophyte lineage, with the cyanelle of Cyanophora paradoxa forming the deepest branch in the latter group. Interestingly, Euglena gracilis and its colorless relative Astasia longa are more related to the chromophytes than to the chlorophytes, raising once again the question of the origin of the euglenoid plastids.

Base Sequence↗
PubMed1993

Crystal structure of an anticholera toxin peptide complex at 2.3 A.

Cholera toxin peptide 3 (CTP3) is a 15-residue peptide corresponding in sequence to an immunogenic loop on the surface of the B-subunits of both cholera toxin and the heat-labile toxin from Escherichia coli. TE33 is the Fab fragment of a monoclonal antibody elicited against CTP3. The crystal structure of the TE33-CTP3 complex at 2.3 A resolution reveals an antigen-binding pocket, 13 A deep and 13 A wide, which is lined with many aromatic residues. The N-terminal portion of the peptide antigen CTP3 forms a type II beta-turn that fits snugly into this pocket. At gln7 the peptide backbone of CTP3 forms a kink followed by an extended C-terminal chain that seals off the cleft and buries the beta-turn underneath it. All six complementarity-determining regions of TE33 contribute to the binding of CTP3. The antibody-peptide contacts include, in addition to van der Waals' interactions and hydrogen bonds, also one salt bridge and one water molecule, which mediates the interaction.

Amino Acid Sequence↗
PubMed1997

Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography.

Y chromosome haplotypes are particularly useful in deciphering human evolutionary history because they accentuate the effects of drift, migration, and range expansion. Significant acceleration of Y biallelic marker discovery and subsequent typing involving heteroduplex detection has been achieved by implementing an innovative and cost-efficient method called denaturing high-performance liquid chromatography (DHPLC). The power of the method resides in its sensitivity and ability to rapidly compare amplified sequences in an automated manner. We have determined the allelic states of 22 Y polymorphisms; 19 of which are unreported, in 718 diverse extant chromosomes; established haplotype frequencies; and deduced a phylogeny. All major geographic regions, including Eurasia, are characterized by mutations reflecting episodes of genetic drift and expansion. Most biallelic markers are localized regionally. However, some show wider dispersal and designate older, core haplotypes. One transversion defines a major haplogroup that distinguishes a previously unknown deep, apparently non-African branch. It provides evidence of an ancient bottleneck event. It is now possible to anticipate the inevitable detailed reconstruction of human Y chromosome genealogy based on several tens to even hundreds of these important polymorphisms.

Alleles↗
PubMed1985

Magnetic resonance imaging of bone and soft tissue tumors: early experience in 31 patients compared with computed tomography.

In 31 patients with 21 soft tissue and 10 bone tumors, magnetic resonance imaging (MRI) and computed tomography (CT) were equally effective in delineating the margins of most soft tissue tumors, and the margins of bone tumors from fat and adjacent normal bone. However, MRI was superior to CT in delineating bone tumors from adjacent muscle, and in showing the relationships to bone of the deep margins of some soft tissue tumors. This was true because the quality of CT images around thick cortical bone often was severely degraded by streak artifact, which does not occur in MRI. Excellent anatomic detail was achieved on MRI by spin echo pulse sequences with short repetition times. Bone tumors were delineated best by spin echo 1000/30 images, and soft tissue tumors by spin echo 1000/30 or inversion recovery images.

Bone Neoplasms↗
PubMed1999

The root of the tree of life in the light of the covarion model.

A few duplicated genes have been found useful to root the universal tree of life. Despite controversial results, the consensus led to locate the root in the eubacterial branch. However, we demonstrated (Philippe and Forterre 1999) that all these markers were in fact unsuitable for any firm conclusion, mainly because of their high level of mutational saturation, which masks a major part of the phylogenetic signal. But then, the very persistence of signal for events as early as the separation of the three domains becomes puzzling. This paradox was studied here for translation elongation factor proteins, EF-1alpha and EF-2, which appeared to be one of the least confusing markers. We showed that these proteins do not conform to a classical rate-across-sites pattern, as those modeled by a gamma law, but rather to a covarion-based model, because the evolutionary rate of a given position often changes between taxonomic groups. Conservation of the very ancient signal can thus be better explained by the covarion model: a substitution can occur in deep branches, and the position remains constant afterward, as "fossilized" by a change of covation. As no reconstruction method has up to now taken into account this complex model, we devised a simple method for extracting the phylogenetic signal, by considering the variability of sequence positions within predefined phylogenetic groups. We showed that noise quantitatively prevailed upon signal. Parsimony will produce erroneous topologies, because it has to minimize primarily the number of steps of the noise. In contrast, our method effectively concentrated the signal and was more suitable for inferring ancient events. We consequently found the eubacterial rooting to be presumably due to a long branch attraction artifact, because of the higher evolutionary rate of Eubacteria for these proteins. Among the two other rooting possibilities, the eukaryotic rooting appeared to be more supported, although not enough to be conclusive.

Algorithms↗
PubMed2004

Leukoaraiosis and mobility decline: a high resolution magnetic resonance imaging study in older people with mild cognitive impairment.

Patterns of leukoaraiosis were analyzed on both T2-weighted fast fluid-attenuated inversion-recovery and 3D T1-weighted sequences in 23 community-dwelling older subjects with mild cognitive impairment. Mobility assessment had allowed their classification into higher and lower mobility groups (P<0.0001). Lower mobility appeared correlated with frontal subependymal lesions (P=0.0005). The absence of marked ventriculomegaly, any thick caps, deep white matter lesions curved along the ventricles bodies, large deep white matter lesions, deep grey matter leukoaraiosis was an hallmark of the higher mobility group (P<0.0001). High resolution MRI demonstrated regular patterns of the subependymal lesions and detected perivascular distribution in other forms of leukoaraiosis. It suggests that the underlying mechanism of mobility decline in the elderly may be impairment of cerebrospinal fluid dynamics with cerebral small vessel disease.

Aged↗
PubMed1998

Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA.

Telomeres are specialized protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. We have determined the crystal structure of the two-subunit Oxytricha nova telomere end binding protein (OnTEBP) complexed with single strand telomeric DNA at 2.8 A resolution. The structure reveals four oligonucleotide/oligosaccharide-binding folds, three of which form a deep cleft that binds the ssDNA, and a fourth that forms an unusual protein-protein interaction between the alpha and beta subunits. This structure provides a molecular description of how the two subunits of OnTEBP recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes.

Animals↗
PubMed2000

Identification of variants and dual promoters of murine serine/threonine kinase KKIAMRE.

KKIAMRE is a serine/threonine protein kinase whose transcripts increase in the deep cerebellar nuclei of the rabbit after eyeblink conditioning, a model of associative learning and memory. We here characterized the expression, isoforms, and promoters of murine KKIAMRE gene. The expression of KKIAMRE was detected, by in situ hybridization and immunohistochemistry, in neurons in various brain regions including deep cerebellar nuclei. The gene spans approximately 40 kb and consists of 15 exons. Analysis of cDNA clones revealed multiple variants, having diversity in the putative carboxy-terminal regulatory domain, generated by alternative splicing and intraexonal termination. Furthermore, they had alternative 5' noncoding sequences. Primer extension, RNase protection, and transient expression assays revealed that two alternative promoters linked to distinct noncoding exons direct the expression of KKIAMRE. The gene was mapped on chromosomes 5 and 4 in mouse and human, respectively.

Amino Acid Sequence↗