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Robert D Burke

Publications and source records attributed to Robert D Burke.

16 recordsLinked to original sources
PubMed2006

Identification and structural basis of binding to host lung glycogen by streptococcal virulence factors.

The ability of pathogenic bacteria to recognize host glycans is often essential to their virulence. Here we report structure-function studies of previously uncharacterized glycogen-binding modules in the surface-anchored pullulanases from Streptococcus pneumoniae (SpuA) and Streptococcus pyogenes (PulA). Multivalent binding to glycogen leads to a strong interaction with alveolar type II cells in mouse lung tissue. X-ray crystal structures of the binding modules reveal a novel fusion of tandem modules into single, bivalent functional domains. In addition to indicating a structural basis for multivalent attachment, the structure of the SpuA modules in complex with carbohydrate provides insight into the molecular basis for glycogen specificity. This report provides the first evidence that intracellular lung glycogen may be a novel target of pathogenic streptococci and thus provides a rationale for the identification of the streptococcal alpha-glucan-metabolizing machinery as virulence factors.

Amino Acid Sequence↗
PubMed2006

The genome of the sea urchin Strongylocentrotus purpuratus.

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Animals↗
PubMed2006

Sp-Smad2/3 mediates patterning of neurogenic ectoderm by nodal in the sea urchin embryo.

Nodal functions in axis and tissue specification during embryogenesis. In sea urchin embryos, Nodal is crucial for specification of oral ectoderm and is thought to pattern neurogenesis in the animal plate. To determine if Nodal functions directly in suppressing neuron differentiation we have prepared mutant forms of Sp-Smad2/3. Expressing an activated form produces embryos similar to embryos overexpressing Nodal, but with fewer neurons. In chimeras in which Nodal is suppressed, cells expressing activated Sp-Smad2/3 form oral ectoderm, but not neurons. In embryos with vegetal signaling blocked, neurons do not form if activated Smad2/3 is co-expressed. Expression of dominant negative mutants produces embryos identical to those resulting from blocking Nodal expression. In chimeras overexpressing Nodal, cells expressing dominant negative Sp-Smad2/3 form aboral ectoderm and give rise to neurons. In permanent blastula chimeras dominant negative Sp-Smad2/3 is able to suppress the effects of Nodal permitting neuron differentiation. In these chimeras Nodal expression in one half suppresses neural differentiation across the interface. Anti-phospho-Smad3 reveals that the cells adjacent to cells expressing Nodal have nuclear immunoreactivity. We conclude Sp-Smad2/3 is a component of the Nodal signaling pathway in sea urchins and that Nodal diffuses short distances to suppress neural differentiation.

Animals↗
PubMed2006

Blood group antigen recognition by a Streptococcus pneumoniae virulence factor.

The Streptococcus pneumoniae fucose utilization operon includes a gene encoding a virulence factor that belongs to family 98 in the glycoside hydrolase classification. This protein contains a C-terminal triplet of fucose binding modules that have significant amino acid sequence identity with the Anguilla anguilla fucolectin. Functional studies of these fucose binding modules reveal binding to fucosylated oligosaccharides and suggest the importance of multivalent binding. The high resolution crystal structures of ligand bound forms of one fucose binding module uncovers the molecular basis of fucose, ABH blood group antigen, and Lewisy antigen binding. These studies are extended by fluorescence microscopy to show specific binding to mouse lung tissue. These modules define a new family of carbohydrate binding modules now classified as family 47.

Amino Acid Sequence↗
PubMed2006

A functional genomic and proteomic perspective of sea urchin calcium signaling and egg activation.

The sea urchin egg has a rich history of contributions to our understanding of fundamental questions of egg activation at fertilization. Within seconds of sperm-egg interaction, calcium is released from the egg endoplasmic reticulum, launching the zygote into the mitotic cell cycle and the developmental program. The sequence of the Strongylocentrotus purpuratus genome offers unique opportunities to apply functional genomic and proteomic approaches to investigate the repertoire and regulation of Ca(2+) signaling and homeostasis modules present in the egg and zygote. The sea urchin "calcium toolkit" as predicted by the genome is described. Emphasis is on the Ca(2+) signaling modules operating during egg activation, but the Ca(2+) signaling repertoire has ramifications for later developmental events and adult physiology as well. Presented here are the mechanisms that control the initial release of Ca(2+) at fertilization and additional signaling components predicted by the genome and found to be expressed and operating in eggs at fertilization. The initial release of Ca(2+) serves to coordinate egg activation, which is largely a phenomenon of post-translational modifications, especially dynamic protein phosphorylation. Functional proteomics can now be used to identify the phosphoproteome in general and specific kinase targets in particular. This approach is described along with findings to date. Key outstanding questions regarding the activation of the developmental program are framed in the context of what has been learned from the genome and how this knowledge can be applied to functional studies.

Animals↗
PubMed2006

The echinoderm adhesome.

Although the development of sea urchin embryos has been studied extensively and clearly involves both cell adhesion and cell migration, rather little is known about the adhesion receptors and extracellular matrix molecules involved. The completion of the genome of Strongylocentrotus purpuratus allows a comprehensive survey of the complement of cell-cell and cell-matrix adhesion molecules in this organism. Furthermore, the phylogenetic position of echinoderms offers the opportunity to compare the complement of adhesion proteins between protostome and deuterostome invertebrates and between invertebrate and vertebrate deuterostomes. Many aspects of development and cell interactions differ among these different taxa and it is likely that analysis of the spectrum of adhesion receptors and extracellular matrix proteins can open up new insights into which molecules have evolved to suit particular developmental processes. In this paper, we report the results of an initial analysis along these lines. The echinoderm adhesome (complement of adhesion-related genes/proteins) is similar overall to that of other invertebrates although there are significant deuterostome-specific innovations and some interesting features previously thought to be chordate or vertebrate specific.

Animals↗
PubMed2006

Neuron-specific expression of a synaptotagmin gene in the sea urchin Strongylocentrotus purpuratus.

Interest in chordate evolution has emphasized a need for a better understanding of the comparative neuroanatomy of invertebrate deuterostomes. However, molecular and genetic approaches to neurobiological studies in these groups are hampered by a lack of neuron-specific molecular markers. A monoclonal antibody, 1E11, is neuron specific and is useful in identification of neural structures in larvae and adults of echinoderms, hemichordates, and urochordates. To identify a neuron-specific gene product, we have characterized the antigen recognized by 1E11. In immunoblots and immunoprecipitations of neural tissue from adult Strongylocentrotus purpuratus, 1E11 recognizes a 57-kDa band. Tandem mass spectrometry of trypsin digests of the 57-kDa band permitted peptide mass mapping and sequencing of five peptides. All of the sequenced peptides, and 12 additional mass-mapped peptides, are found within the open reading frame of a cDNA encoding synaptotagmin B (Sp-SynB). In situ RNA hybridizations with synaptotagmin B probes with S. purpuratus larvae reveal a pattern of expression that is similar to that revealed by the antibody 1E11. Antibodies produced against a bacterially expressed Sp-SynB protein recognize a 57-kDa protein and colocalize with 1E11. When a full-length Sp-SynB cDNA is expressed in chicken embryonic cells, the cells become immunoreactive to 1E11. We conclude that synaptotagmin B is a gene expressed in neurons that has conserved epitopes in other invertebrate deuterostomes.

Amino Acid Sequence↗
PubMed2006

Specification of ectoderm restricts the size of the animal plate and patterns neurogenesis in sea urchin embryos.

The animal plate of the sea urchin embryo becomes the apical organ, a sensory structure of the larva. In the absence of vegetal signaling, an expanded and unpatterned apical organ forms. To investigate the signaling that restricts the size of the animal plate and patterns neurogenesis, we have expressed molecules that regulate specification of ectoderm in embryos and chimeras. Enhancing oral ectoderm suppresses serotonergic neuron differentiation, whereas enhancing aboral or ciliary band ectoderm increases differentiation of serotonergic neurons. In embryos in which vegetal signaling is blocked, Nodal expression does not reduce the size of the thickened animal plate; however, almost no neurons form. Expression of BMP in the absence of vegetal signaling also does not restrict the size of the animal plate, but abundant serotonergic neurons form. In chimeras in which vegetal signaling is blocked in the entire embryo, and one half of the embryo expresses Nodal, serotonergic neuron formation is suppressed in both halves. In similar chimeras in which vegetal signaling is blocked and one half of the embryo expresses Goosecoid (Gsc), serotonergic neurons form only in the half of the embryo not expressing Gsc. We propose that neurogenesis is specified by a maternal program that is restricted to the animal pole by signaling that is dependent on nuclearization of beta-catenin and specifies ciliary band ectoderm. Subsequently, neurogenesis in the animal plate is patterned by suppression of serotonergic neuron formation by Nodal. Like other metazoans, echinoderms appear to have a phase of neural development during which the specification of ectoderm restricts and patterns neurogenesis.

Animals↗
PubMed2006

Bioconjugation of Ln3+-doped LaF3 nanoparticles to avidin.

The binding of Eu3+-doped LaF3 nanoparticles with biotin moieties at the surface of the stabilizing ligand layer to avidin, immobilized on cross-linked aragose beads, is described. The biotin moieties were attached to the nanoparticles by reaction of an activated ester with the amino groups on the surface of the nanoparticles resulting from the 2-aminoethyl phosphate ligands that were coordinated to the surface through the phosphate end. This strategy of employing the reactions of amines with activated esters provides a general platform to modify the surface of the 2-aminophosphate stabilized Ln3+-doped LaF3 nanoparticles with biologically relevant groups. Significant suppression of nonspecific binding to the avidin modified aragose beads has been realized by the incorporation of poly(ethylene glycol) units via the same reaction of a primary amine with an activated ester. The particle size distribution of the functionalized nanoparticles was within 10-50 nm, with a quantum yield of 19% in H2O for the LaF3 nanoparticles codoped with Ce3+ and Tb3+. A discreet, 4 unit poly(ethylene glycol) spaced heterobifunctional cross-linker, functionalized with biotin and N-hydroxysuccinimide at opposite termini, was covalently linked to the 2-aminoethyl phosphate ligand via the N-hydroxysuccinimide activated ester, making an amide bond, imparting biological activity to the particle. Modification of the remaining unreacted amino groups of the stabilizing ligands was done with Me(OCH2CH2)3CH2CH2(C=O)-NHS (NHS = N-hydroxysuccinimide).

Avidin↗
PubMed2006

Embryonic expression of engrailed in sea urchins.

Neural patterning genes that are expressed along the anterior-posterior axis of deuterostomes are expressed late in larval development in echinoderms and are thought to function in establishing the highly-derived, adult body plan. We have used genomic resources to clone an engrailed gene (SpEn) from Strongylocentrotus purpuratus, and with this we have developed an antibody specific for SpEn. SpEn is expressed late in embryogenesis in the developing larval nervous system. At the prism stage, a small number of neuroblasts in the oral ectoderm on the edge of the larval mouth begin expressing SpEn. The cells are in bilaterally symmetric positions. The expression of SpEn precedes the expression of the neural markers, synaptotagmin and serotonin in the SpEn immunoreactive cells. The SpEn cells are located on the margin of the domain of cells expressing SpNK2.1, but they do not have nuclear SpNK2.1. Expression of engrailed in a pair of bilateral neural structures in early development appears to be a shared feature of bilaterians.

Amino Acid Sequence↗
PubMed2006

Virulence of Francisella spp. in chicken embryos.

We examined the utility of infecting chicken embryos as a means of evaluating the virulence of different Francisella sp. strains and mutants. Infection of 7-day-old chicken embryos with a low dose of F. novicida or F. tularensis subsp. holarctica live vaccine strain (LVS) resulted in sustained growth for 6 days. Different doses of these two organisms were used to inoculate chicken embryos to determine the time to death. These experiments showed that wild-type F. novicida was at least 10,000-fold more virulent than the LVS strain. We also examined the virulence of several attenuated mutants of F. novicida, and they were found to have a wide range of virulence in chicken embryos. Fluorescent microscopic examination of infected chicken embryo organs revealed that F. tularensis grew in scattered foci of infections, and in all cases the F. tularensis appeared to be growing intracellularly. These results demonstrate that infection of 7-day-old chicken embryos can be used to evaluate the virulence of attenuated F. tularensis strains.

Animals↗
PubMed2004

Expression of an NK2 homeodomain gene in the apical ectoderm defines a new territory in the early sea urchin embryo.

We have identified an NK2 family homeodomain transcription factor, SpNK2.1, in the sea urchin Strongylocentrotus purpuratus whose transcripts are initially detected within the apical plate ectoderm of the hatching blastula and are confined to the apical organ at least through 2 weeks of development. Protein localization studies demonstrate that SpNK2.1 is restricted to the apical plate epithelium, but is excluded from the nucleus of serotonergic neurons. The expression profile of SpNK2.1 is dictated via two separate regulatory systems. Initially, SpNK2.1 is restricted to the apical pole domain by beta-catenin-dependent processes operating along the animal-vegetal axis, as evidenced by an expansion of SpNK2.1 expression upon cadherin overexpression. Starting at gastrulation, expression in the apical plate is maintained by SpDri, the sea urchin orthologue of dead ringer. Abrogation of SpDri results in the downregulation of SpNK2.1 after gastrulation, but SpDri is not necessary for the initial activation of SpNK2.1. Loss of function experiments using SpNK2.1-specific morpholino antisense oligonucleotides and SpNK2.1 overexpression experiments do not disrupt embryonic development and have no effect upon the development of neuronal components of the apical organ. Nonetheless, SpNK2.1 defines a new early territory of the sea urchin embryo.

Animals↗
PubMed2004

Integrins on eggs: the betaC subunit is essential for formation of the cortical actin cytoskeleton in sea urchin eggs.

Eggs of several metazoans have been demonstrated to express integrins; however, their function is unclear. Previous studies have shown that the betaC integrin subunit is expressed on unfertilized sea urchin eggs and proteolytically removed at fertilization. Here we report that the betaC subunit is reexpressed on the egg surface immediately after fertilization. Using morpholino antisense oligonucleotides to block translation, we show that without betaC expression, eggs undergo cleavage resulting in loosely adherent cells that fail to develop beyond a blastula. Without betaC containing integrins, the cortical actin network of the egg does not form, yet contractile rings appear. Coinjection of RNA encoding the betaC or chicken beta1 subunit, but lacking the morpholino target sequence, rescues the cortical actin network and normal embryos result. Coinjection of RNA encoding the betaC subunit lacking the cytoplasmic domain fails to rescue. These studies demonstrate that the cortical actin cytoskeleton is anchored by betaC integrins and contractile ring actin is not. We suggest that one important function of egg integrins is to organize the actin cortex.

Actins↗
PubMed2002

SpADAM, a sea urchin ADAM, has conserved structure and expression.

ADAMs are multidomain cell surface proteins that function in receptor-ligand processing, cell adhesion and fusion, and signaling. SpADAM, a single copy sea urchin ADAM gene with a 3072 bp open reading frame, is expressed during embryonic and larval development. The deduced SpADAM protein is 1023 amino acids long and includes all domains characteristic of ADAMs. Northern blots reveal the presence of 4.4 and 2.3 kb SpADAM transcripts throughout development. Predominant SpADAM proteins are 131 and 95 kDa. The deduced primary structure of SpADAM is closely related to vertebrate ADAMs 12, 13, and 19. SpADAM is expressed during cleavage on blastomere surfaces, and later by vegetal plate cells, migrating secondary mesenchyme, skeletogenic mesenchyme, muscles, and neurons within the ciliated band. Apparently, the structure and types of cells in which ADAM 12/13/19 orthologues are expressed are conserved in deuterostomes.

Amino Acid Sequence↗
PubMedDate not supplied

Divergent patterns of neural development in larval echinoids and asteroids.

The development and organization of the nervous systems of echinoderm larvae are incompletely described. We describe the development and organization of the larval nervous systems of Strongylocentrotus purpuratus and Asterina pectinifera using a novel antibody, 1E11, that appears to be neuron specific. In the early pluteus, the antibody reveals all known neural structures: apical ganglion, oral ganglia, lateral ganglia, and an array of neurons and neurites in the ciliary band, the esophagus, and the intestine. The antibody also reveals several novel features, such as neurites that extend to the posterior end of the larva and additional neurons in the apical ganglion. Similarly, in asteroid larvae the antibody binds to all known neural structures and identifies novel features, including large numbers of neurons in the ciliary bands, a network of neurites under the oral epidermis, cell bodies in the esophagus, and a network of neurites in the intestine. The 1E11 antigen is expressed during gastrulation and can be used to trace the ontogenies of the nervous systems. In S. purpuratus, a small number of neuroblasts arise in the oral ectoderm in late gastrulae. The cells are adjacent to the presumptive ciliary bands, where they project neurites with growth cone-like endings that interconnect the neurons. In A. pectinifera, a large number of neuroblasts appear scattered throughout the ectoderm of gastrulae. The cells aggregate in the developing ciliary bands and then project neurites under the oral epidermis. Although there are several shared features of the larval nervous systems of echinoids and asteroids, the patterns of development reveal fundamental differences in neural ontogeny.

Animals↗