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Biomedical subjects

R J Britten

Publications and source records attributed to R J Britten.

At least 37 records · Page 2Linked to original sources
PubMed1995

SpZ12-1, a negative regulator required for spatial control of the territory-specific CyIIIa gene in the sea urchin embryo.

The CyIIIa cytoskeletal actin gene of the sea urchin Strongylocentrotus purpuratus is activated in late cleavage and expressed exclusively in the aboral ectoderm territory of the embryo. Previous gene transfer studies defined a 2.3 kb cis-regulatory region that is necessary and sufficient for correct temporal and spatial expression of a CyIIIa.CAT fusion gene. In this paper, a negative regulatory element within this region was identified that is required for repression of the CyIIIa gene in skeletogenic mesenchyme cells. The repression mediated by this regulatory element takes place after initial territorial specification. A cDNA clone encoding a DNA-binding protein with twelve Zn fingers (SpZ12-1) was isolated by probing an expression library with this cis-element. Deletion analysis of the SpZ12-1 protein confirmed that a DNA-binding domain is located within the Zn finger region. SpZ12-1 is the only DNA-binding protein in embryo nuclear extract that interacts with the specific cis-target sites required for repression of CyIIIa.CAT in skeletogenic mesenchyme and is likely to be the trans factor that mediates this repression.

Actins↗
PubMed1995

Cis-regulatory control of the SM50 gene, an early marker of skeletogenic lineage specification in the sea urchin embryo.

The SM50 gene encodes a minor matrix protein of the sea urchin embryo spicule. We carried out a detailed functional analysis of a cis-regulatory region of this gene, extending 440 bp upstream and 120 bp downstream of the transcription start site, that had been shown earlier to confer accurate skeletogenic expression of an injected expression vector. The distal portion of this fragment contains elements controlling amplitude of expression, while the region from -200 to +105 contains spatial control elements that position expression accurately in the skeletogenic lineages of the embryo. A systematic mutagenesis analysis of this region revealed four adjacent regulatory elements, viz two copies of a positively acting sequence (element D) that are positioned just upstream of the transcription start site; an indispensable spatial control element (element C) that is positioned downstream of the start site; and further downstream, a second positively acting sequence (element A). We then constructed a series of synthetic expression constructs. These contained oligonucleotides representing normal and mutated versions of elements D, C, and A, in various combinations. We also changed the promoter of the SM50 gene from a TATA-less to a canonical TATA box form, without any effect on function. Perfect spatial regulation was also produced by a final series of constructs that consisted entirely of heterologous enhancers from the CyIIIa gene, the SV40 early promoter, and synthetic D, C, and A elements. We demonstrate that element C exercises the primary spatial control function of the region we analyzed. We term this a 'locator' element. This differs from conventional 'tissue-specific enhancers' in that while it is essential for expression, it has no transcriptional activity on its own, and it requires other, separable, positive regulatory elements for activity. In the normal configuration these ancillary positive functions are mediated by elements A and D. Only positively acting control elements were observed in the SM50 regulatory domain throughout this analysis.

Animals↗
PubMed1995

Maternal and embryonic provenance of a sea urchin embryo transcription factor, SpZ12-1.

SpZ12-1 is a zinc-finger transcription factor. Previous work has indicated that this factor functions late in embryogenesis as a spatial transcriptional repressor. We show here that this factor is present in significant quantities even in unfertilized egg cytoplasm, and in similar quantities in mesenchyme blastula-stage embryo cytoplasm. Taken together with earlier measurements of Calzone and associates, our observations indicate that SpZ12-1 enters the embryonic nuclei between late cleavage and mesenchyme blastula stages. A low-prevalence mRNA encoding SpZ12-1 is also present throughout development. Translation of this mRNA could, however, easily account for the complete complement of SpZ12-1 protein in the embryo, as estimated from its DNA binding activity. SpZ12-1 probably functions at several developmental stages and is evidently of both maternal and embryonic provenance.

Animals↗
PubMed1994

Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes.

Mutations have been examined in the 1500 interspersed Alu repeats of human DNA that have been sequenced and are nearly full length. There is a set of particular changes at certain positions that rarely occur (termed suppressed changes) compared to the average of identical changes of identical nucleotides in the rest of the sequence. The suppressed changes occur in positions that are clustered together in what appear to be sites for protein binding. There is a good correlation of the suppression in different positions, and therefore the joint probability of absence of mutation at many pairs of such positions is significantly higher than that expected at random. The suppression of mutation appears to result from selection that is not due to requirements for Alu sequence replication. The implication is that hundreds of thousands of Alu sequences have sequence-dependent functions in the genome that are selectively important for primates. In a few known cases Alu inserts have been adapted to function in the regulation of gene transcription.

Animals↗
PubMed1994

Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago.

The primate Alu interspersed repeats can be subdivided into classes on the basis of shared nucleotides at a set of diagnostic positions. Each of the classes of Alu sequences is apparently the result of past retrotransposition of transcripts of highly conserved class-specific source genes that differed from each other at the diagnostic positions. The nucleotides at the majority of positions are identical among the source genes and therefore were identical among all of the Alu sequences at the time of their insertion. These CONSBI (conserved before insertion) positions are useful because the changes that have occurred after insertion are recognizable and the divergence resulting from nucleotide substitutions, insertions, and deletions is informative. The divergence of Alu sequences at the CONSBI positions is a measure of the time since a class was inserted. The greatest majority of Alu sequences are in one class (identified as class II), and it is particularly suitable for such examination, since nearly full-length sequences are now known for nearly a thousand members of this class. The average divergence of class II members indicates that the class has an average age of about 40 million years. The distribution in divergence of class II accurately fits a sum of two Poisson distributions. The implication is that class II Alu sequences were derived from two massive past events of insertion of many Alu sequences. In this model the younger subset of class II sequences (corresponding to about 300,000 copies in the genome) has an average divergence of 5% at CONSBI positions. The older set of class II sequences (corresponding to about 150,000 genomic copies) has a 9% average divergence. Based on the drift rate of primate DNA sequences, the events of insertion probably occurred 30-50 million years ago. The goodness of the fit to the Poisson distribution indicates that no significant number of members of class II have been inserted since 30 million years ago.

Animals↗
PubMed1994

Repeated sequence target sites for maternal DNA-binding proteins in genes activated in early sea urchin development.

This communication concerns a very highly conserved inverted repeat sequence element that serves as a target site for a sea urchin maternal DNA-binding factor. The maternal factor is present in relatively large amounts in unfertilized eggs, but is about 100 x less prevalent per embryo in 24-hr embryo nuclear extract. The inverted repeat target site is found in the regulatory domain of the CyIIIa cytoskeletal actin gene and also in two upstream genes encoding transcription factors that bind to a functionally important cis-regulatory element of the CyIIIa gene. There are about 460 copies of the inverted repeat target site per genome. About 15% of these sites occur in a nested arrangement together with a second inverted repeat that binds another previously characterized maternal transcription factor. This arrangement is the same as that which occurs in the CyIIIa gene, and it may be of regulatory significance with respect to activation of certain genes in oogenesis and early embryogenesis.

Actins↗
PubMed1994

The sea urchin profilin gene is specifically expressed in mesenchyme cells during gastrulation.

Eggs and embryos of the purple sea urchin (Strongylocentrotus purpuratus) contain profilin that is partly supplied from maternal sources and partly produced by the gastrula. The maternal profilin protein content is about 13 microM and it persists in the embryo at least through gastrulation. Transcript quantitation from probe excess titrations show that very few profilin gene transcripts are present in the embryo during cleavage, but that they increase at the onset of gastrulation. By in situ hybridization, the newly synthesized profilin transcripts are localized in mesenchyme cells. Profilin gene expression increases when mesenchyme cells initiate migration and filopodial extension and retraction. We show that there are three isoforms of maternal profilin protein produced from the single copy gene during oogenesis. However, the blastula stage embryo only produces the major isoform, whereas the acidic isoform is produced in the early stages of gastrulation and the basic isoform appears by the end of gastrulation. Based on transcript prevalence and protein production rates, our calculations indicate that the amount of new protein produced in the mesenchyme cells in 12 hr is at maximum < 2% of that supplied from maternal sources. Because of the large amount of maternally supplied profilin present in the egg and embryo, we suggest that it may be used in the cytokinetic processes of cleavage. Alternatively, because of the small amount of embryonically produced profilin, we suggest that it may function in the cytoskeletal shape changes required for filopodial extension and motility in the mesenchyme cells during gastrulation.

Animals↗
PubMed1994

Development of sibling inbred sea urchins: normal embryogenesis, but frequent postembryonic malformation, arrest and lethality.

Inbred lines of Strongylocentrotus purpuratus descended from a single pair of wild animals were constructed by sibling mating. We describe results from a systematic series of crosses in which eggs from F2 and from F3 females were fertilized respectively with sperm from their sibling males. Observations were also made on self-fertilized cultures derived from several naturally occurring hermaphrodites. Morphological development, survival efficiency, and expression of three territorial embryonic markers were assayed in the embryos developing from these crosses. Unexpectedly, out of > 90 controlled crosses, we observed no developmental failures whatsoever, up to the end of embryogenesis (i.e., onset of feeding) that could be attributed to homozygous, zygotically acting recessive genes. However, during postembryonic larval development, lethality, morphological malformation, and arrest are observed in inbred cultures at a high frequency. The incidence of these zygotic developmental failures is such that it appears that there is at least one recessive genetic defect affecting larval development per haploid parental genome. The relative imperviousness of the basic embryonic process to defects arising from homozygosity is consistent with other evidence implying that territorial specification in sea urchin embryogenesis is controlled by maternally rather than zygotically expressed gene products.

Animals↗
PubMed1994

Ligand-dependent stimulation of introduced mammalian brain receptors alters spicule symmetry and other morphogenetic events in sea urchin embryos.

Zygotes of S. purpuratus were injected with synthetic mRNAs encoding rodent brain neurotransmitter receptors, and specific developmental phenotypes were produced on addition to the sea water of the respective ligands. Most of these experiments were carried out with a mouse serotonin receptor (5HT-R) mRNA, though exactly comparable results were obtained with a rat muscarinic acetylcholine receptor (MAChR) mRNA; these receptors are expected to couple to the same endogenous signal transduction system. We show by whole mount in situ hybridization that the injected mRNAs diffuse to all of the early blastomeres, and that they are translated in vivo. Three specific phenotypes were reproducibly observed. The most severe, occurring at highest levels of injected mRNA, was a cleavage arrest phenotype in which no overtly differentiated cells ever appear, though the embryos remain alive for at least 72 h. A gastrular arrest (GA) phenotype is generated in appreciable fractions of embryos developing from eggs injected with lower levels of mRNA. In GA embryos the blastocoel is filled with disorganized mesenchyme cells, including pigment cells and skeletogenic cells; there is no archenteron; and the entire ectoderm expresses an oral ectoderm cell surface marker. The least severe phenotype that we recognized displays an altered arrangement of spiculogenic foci (RSE phenotype), generating a ring of extra spicules that are properly positioned with respect to the animal/vegetal axis, but that lack any reference to the oral/aboral axis. However, use of cytological and molecular markers demonstrates that RSE embryos retain normal spatial patterns of aboral and oral ectoderm. They develop a fully formed archenteron, but fail to form either a stomodaeum or a ciliated band. RSE embryos can be produced in embryos expressing the 5HT-R by exposure to serotonin, beginning as late as 12 h postfertilization (pf). All of the morphogenetic processes affected in RSE embryos depend in normal embryos on intercellular interactions occurring at the blastula-gastrula stages of development.

Animals↗
PubMed1994

Complexity and organization of DNA-protein interactions in the 5'-regulatory region of an endoderm-specific marker gene in the sea urchin embryo.

This study concerns the organization of sites of specific DNA/protein interaction within the regulatory domain of the Endo16 gene of Strongylocentrotus purpuratus. Earlier work had displayed a complex pattern of expression of this gene during embryogenesis. Endo16 transcripts are confined to the definitive vegetal plate in blastula stage embryos; at gastrula stage this gene is expressed throughout the archenteron, but later only in the midgut. In this work we exploited the exceptional experimental accessibility of the sea urchin embryo, with respect to both functional assays of gene regulatory systems and to characterization of transcription factors, in order to approach a complete description of potential Endo16 regulatory interactions. Accurate expression of an Endo16 fusion gene was obtained with a 2200-nucleotide (nt) upstream fragment of the gene. We present a map locating high specificity target sites for DNA-binding proteins within the 2200-nt Endo16 regulatory domain, and an assessment of the complexity of the set of putative Endo16 transcription factors that we have been able to recover from 24-h (blastula stage) nuclear extract. Protein binding sites were initially mapped by gel shift reactions carried out on nested sets of end-labeled restriction fragments, and then to finer resolution by oligonucleotide gel shift competitions. Thirty-eight sites of high specificity DNA-protein interaction were thus identified. Appropriate oligonucleotides were then used for partial purification of the DNA-binding proteins by affinity chromatography. DNA-binding proteins specific for each target site were identified by molecular weight, using southwestern blotting procedures and two-dimensional gel shift separations, and by directly renaturing and reacting with oligonucleotide probes specific proteins that had been resolved by SDS-PAGE from selected affinity column fractions. A complete series of gel shift cross-competitions amongst the target sites was carried out. We conclude that nine different protein factors are bound at unique sites within the Endo16 regulatory domain. Multiple target sites for five other proteins account for the remaining binding site locations. The target sites appear to be organized in a sequence of clusters, focused on the unique factors. The high complexity of the Endo16 gene regulatory system may be characteristic for genes that are spatially regulated in early embryonic development.

Animals↗
PubMed1993

The embryonic ciliated band of the sea urchin, Strongylocentrotus purpuratus derives from both oral and aboral ectoderm.

The ciliated band of the Strongylocentrotus purpuratus embryo consists of a columnar epithelium, 3-5 cells wide, which gives rise to a small number of neuroblasts. It arises late in development, as a border separating the squamous epithelial cells of the oral and aboral ectoderm. To determine the lineage origins of this structure, we performed double labeling experiments at the 2-cell stage and the 16-cell stage, which were designed to reveal clonal boundaries in the ciliated band. The ciliated band forms in a region of the ectoderm derived from descendants of the following blastomeres: No, VO, Na1u, Na2u, right and left NL1u, and right and left NL2u. In contrast to the lineage contributions of the embryonic territories established early in development, lineage origins of the ciliated band are variable. Specification of the ciliated band thus depends on intercellular interaction rather than lineage.

Animals↗
PubMed1993

Whole mount in situ hybridization shows Endo 16 to be a marker for the vegetal plate territory in sea urchin embryos.

We have used whole mount in situ hybridization to analyze the pattern of expression of the gene Endo 16 in S. purpuratus embryos. The mRNA is first detectable at 18 h post-fertilization in the cytoplasm of blastomeres derived from the Veg2 6th cleavage tier. The number of Endo 16 positive cells increases gradually through the beginning of gastrulation, and these cell numbers are in agreement with estimates of the number of cells that should be in the vegetal plate at these stages. We conclude that Endo 16 expression is indeed an early vegetal plate marker and that this gene is expressed by all Veg2 tier derivatives while they are part of the vegetal plate. The progressive regionalization of Endo 16 expression that occurs in normal embryos is also seen in lithium chloride induced exogastrulae, leading to the conclusion that genetic regulation of endoderm differentiation is programmed into the vegetal plate cells once they have been specified. Finally, we report a reproducible phenomenon seen in cultures of LiCl exogastrulae, in which the tips of the everted archenterons fuse, followed by the induction of supernumerary pigment cells.

Animals↗
PubMed1993

Species-specific inhibition of fertilization by a peptide derived from the sperm protein bindin.

The sperm protein bindin is responsible for the species-specific adhesion of the sperm to the egg. The regions of the bindin molecule responsible for forming the contact between the sperm and the egg were investigated by measuring the ability of peptides representing various regions of the bindin sequence to inhibit fertilization. Twenty-four peptides were studied: 7 based on the Strongylocentrotus purpuratus bindin sequence, 11 based on the S. franciscanus bindin sequence, and 6 control peptides. Values for the concentration of peptide required to inhibit 50% of the productive sperm contacts (IC50) were extracted from experimental measurements of the extent of fertilization in the presence of various concentrations. of these peptides. The IC50 value averaged 220 microM for the control peptides. Active peptides representing certain specific subregions of the bindin sequence displayed IC50 values < 10% of the average value for control peptides, and the IC50 for the most potent of the peptides tested was only approximately 1% of the control peptide value (IC50 = 2.2 microM). Furthermore, we found that a peptide representing a particular region of the S. franciscanus bindin sequence that differs from the S. purpuratus bindin sequence inhibits fertilization species specifically. For the reaction of S. purpuratus sperm and eggs, the IC50 of this peptide was approximately 120 microM, whereas for the reaction of S. franciscanus sperm and eggs it was only 8.6 microM. These results demonstrate that a few specific regions of the bindin molecule are involved in the sperm-egg contact and that certain of these regions mediate the species specificity of the interaction in a sequence-specific manner.

Amino Acid Sequence↗
PubMed1993

Forbidden synonymous substitutions in coding regions.

In the evolution of highly conserved genes, a few "synonymous" substitutions at third bases that would not alter the protein sequence are forbidden or very rare, presumably as a result of functional requirements of the gene or the messenger RNA. Another 10% or 20% of codons are significantly less variable by synonymous substitution than are the majority of codons. The changes that occur at the majority of third bases are subject to codon usage restrictions. These usage restrictions control sequence similarities between very distant genes. For example, 70% of third bases are identical in calmodulin genes of man and trypanosome. Third-base similarities of distant genes for conserved proteins are mathematically predicted, on the basis of the G+C composition of third bases. These observations indicate the need for reexamination of methods used to calculate synonymous substitutions.

Actins↗
PubMed1993

Phylogenetic relationships of reverse transcriptase and RNase H sequences and aspects of genome structure in the gypsy group of retrotransposons.

The gypsy group of long-terminal-repeat retrotransposons contains elements having the same order of enzyme domains in the pol gene as do retroviruses. Elements in the gypsy group are now known from yeast, filamentous fungi, plants, insects, and echinoids. Reverse transcriptase and RNase H amino acid sequences from elements in the gypsy group--including the recently described SURL elements, TED, Cft1, and Ulysses,--were aligned and analyzed by using parsimony and bootstrapping methods, with plant caulimoviruses and/or retroviruses as outgroups. Clades supported at the 95% level after bootstrapping include (1) 17.6 with 297 and (2) all of the SURL elements together. Other likely relationships supported at lower bootstrap confidence intervals include (1) SURL elements with mag, (2) 17.6 and 297 with TED, and this collective group with 412 and gypsy, (3) Tf1 with Cft1, (4) IFG7 with Del, and (5) all of the retrotransposons in the gypsy group together, to the exclusion of Ty3. In contrast with an earlier analysis, our results place mag within the gypsy group rather than outside of a cluster that contains gypsy group retrotransposons and plant caulimoviruses. Several features of retrotransposon genomes provide further support for some of the aforementioned relationships. The union of SURL elements with mag is supported by the presence of two RNA binding sites in the nucleocapsid protein. Location of the tRNA primer binding site and the presence of a long open reading frame 3' to the pol gene support the 17.6-297-TED-412-gypsy cluster.

Amino Acid Sequence↗
PubMed1992

Complexity of sea urchin embryo nuclear proteins that contain basic domains.

We describe a quantitative two-dimensional gel electrophoretic analysis of nuclear extract from 24-hr sea urchin embryos. The extract was fractionated by using a weak cation-exchange resin, and eight known DNA-binding proteins were shown to be entirely included in a salt eluate that releases proteins containing basic domains. This fraction and a lower-salt fraction containing the majority of the protein species were mapped two-dimensionally by using new algorithms that permit reproducible spot identification, storage of intensity and map-position data, and subtractive comparison of one pattern with respect to another. By reference to a previously characterized DNA-binding factor, spot intensity could be interpreted in terms of the number of molecules per embryo nucleus. A map was constructed displaying all nuclear proteins containing basic domains that are present within the concentration range per nucleus of a set of known DNA-binding factors of the sea urchin embryo. The map includes 265 spots that fulfill both of these criteria, probably representing about 100 different protein species.

Animals↗
PubMed1992

Graviton scattering and matter distribution.

In this model gravitation results from the emission and absorption of quanta (gravitons) that are scattered a few times in crossing a typical galaxy. Many features of the universe can be explained in terms of this model, although theoretical justification for the scattering of gravitons is lacking. Gravitons follow a random walk and diffuse through the outer regions of a galaxy. As a result the force of attraction follows a 1/R law, matching observed galactic rotation curves and explaining galactic dynamics without the need of dark matter. The model makes predictions regarding early stages in the expansion of the universe and the establishment of the mass distribution. It may be assumed that a nearly uniform expanding cloud of gas was present that was subject to collapse under gravitational forces. The 1/R law of attraction due to graviton diffusion is orders of magnitude more effective for initiation of collapse than the inverse square law, and it applies to blocks of gas larger than the graviton mean free path. Delay in the spread of gravitational attraction by diffusion sets a time-dependent range beyond which the attractive force is zero. In the model this causes arrays of matter to collapse locally into zones with a spacing set by the length of the range of the attractive force. An initial examination indicates that under these conditions the background radiation could have been released from a nearly uniform distribution at the time of decoupling of radiation and matter, followed by gravitational collapse into blocks of galactic mass. In the model the diffusion of gravitons continued and collapse became possible on a larger scale, initiating the formation of galactic clusters and still larger structures. The slow rate of diffusion then prevented the largest structures from attracting each other and permitted the formation of the voids on a very large scale. The model predicts that on the largest scale there is a three-dimensional repeated array of structures separated by voids. Ultimately structures larger than galactic clusters outran the diffusion of the gravitons and have since been freely expanding.

Journal Article↗