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W Gilbert

Publications and source records attributed to W Gilbert.

At least 37 records · Page 2Linked to original sources
PubMed1990

DNA trapping electrophoresis.

Attempts to improve the size separation of single-stranded DNA in polyacrylamide gels by field-inversion gel electrophoresis (FIGE) have met with limited success. Here we show that attaching a neutral globular protein, streptavidin, to one end of a single-stranded DNA molecule profoundly alters the DNA mobility pattern and increases the band separation manyfold within a size range controlled by voltage and pulse cycle. In constant field, short modified fragments are only slightly retarded but long molecules are retarded dramatically above a 'threshold size' of 0.6 kilobases at 60 V per cm. At this voltage, molecules above a 1.2-kilobase 'cut-off' do not enter the gel. Both the threshold and the cut-off sizes decrease as the voltage increases. In FIGE, the longer the reverse pulse, the larger the modified fragments that enter the gel. We interpret these results as the trapping by the gel matrix of the protein attached to the DNA. The probability of release then depends on the balance between the electric field and thermal motion: the larger the DNA and the higher the voltage, the harder it is to release.

DNA↗
PubMed1990

Factors released by ciliary neurons and spinal cord explants induce acetylcholine receptor mRNA expression in cultured muscle cells.

The nuclei of cultured noninnervated muscle cells are heterogeneous with respect to production of mRNA for the nicotinic acetylcholine receptor (AChR). Some nuclei actively express AChR mRNA while others have a low level of activity or are inactive. To determine if innervation, or a factor released by neurons, influences nuclear expression of AChR mRNA, we examined mRNA at a single cell level via in situ hybridization and autoradiography with an alpha-subunit AChR genomic probe. Four days after plating, we co-cultured chicken primary muscle cells with spinal cord explants, ciliary neurons, or dorsal root ganglia (DRG) cells. In situ hybridization of the spinal-cord and muscle-cell co-cultures with the AChR alpha-subunit probe revealed a high density of silver grains on muscle cells, which were within two explant diameters of the spinal cord explant, and a graded decrease in silver grain density as the distance from the explant increased, as well as the appearance of a strikingly nonhomogenous distribution of active and inactive muscle cell nuclei. When ciliary neurons were uniformly distributed over the muscle cells, a high level of AChR mRNA was induced, but no gradients appeared. Neither an increased mRNA level nor a gradient was observed when DRG cells were co-cultured with muscle cells. When ciliary neurons are cultured within Costar permeable inserts, which prevent any contact between the neurons and the underlying muscle cells, AChR messenger RNA is still induced, showing that diffusible factors are responsible. Our results indicate that molecules released by cholinergic neurons regulate the expression of AChR mRNA in the myotubes and raise the possibility that AChR expression depends on both neuronal signals and on intracellular information from the muscle cell.

Animals↗
PubMed1990

Pioneer neurons in the mouse trigeminal sensory system.

Pioneer neurons establish preliminary nerve pathways that are followed by later-growing axons. The existence of pioneers and their importance is well documented in invertebrate systems. In mammals, early neuronal development has generally been difficult to study because of the size and complexity of the embryos, and the lack of adequate markers. Here we look at the time of earliest axonal outgrowth in the mouse embryo by using specific monoclonal antibodies to stain wholemount preparations. During the period of formation and closure of the neuropore beginning at embryonic day 8.5, we can follow the earliest trigeminal sensory neurons extending axons along stereotyped pathways. In the trigeminal ganglion, an early wave of neurogenesis gives rise to a small number of neurons whose axons pioneer the different trigeminal tracts in the periphery. After a brief pause (12 hr), these primary axons branch out to innervate individual targets. Emerging a day later, secondary fibers extend along the pioneers. By contrast, in the central nervous system, neurons of the mesencephalic trigeminal nucleus extend toward the rhombencephalon independently, ignoring preexisting fibers. These results show the existence of an early set of axonal tracts in the mouse peripheral nervous system that may be used for the guidance of later-differentiating neurons.

Animals↗
PubMed1990

Simultaneous visualization of neuronal protein and receptor mRNA.

We describe a combined immunocytochemistry/in situ hybridization technique which allows for the simultaneous localization of protein and mRNA in a single cell. We have carried out these studies either on non-innervated skeletal myotubes or on myotubes which we have innervated with spinal cord explants or ciliary neurons. Our methods allowed us to detect acetylcholine receptor gene mRNA sequences which are expressed in low abundance within the cells and to determine the intracellular and intranuclear domains where these sequences are concentrated, as well as to identify neurons and their processes. The isotopic detection of RNA in combination with fluorescence microscopy produces high-resolution double-label images, with little background and good preservation of morphology, providing a powerful tool for detection of gene expression and protein content at the single-cell level.

Animals↗
PubMed1989

One-sided polymerase chain reaction: the amplification of cDNA.

We report a rapid technique, based on the polymerase chain reaction (PCR), for the direct targeting, enhancement, and sequencing of previously uncharacterized cDNAs. This method is not limited to previously sequenced transcripts, since it requires only two adjacent or partially overlapping specific primers from only one side of the region to be amplified. These primers can be located anywhere within the message. The specific primers are used in conjunction with nonspecific primers targeted either to the poly(A)+ region of the message or to an enzymatically synthesized d(A) tail. Pairwise combinations of specific and general primers allow for the amplification of regions both 3' and 5' to the point of entry into the message. The amplified PCR products can be cloned, sequenced directly by genomic sequencing, or labeled for sequencing by amplifying with a radioactive primer. We illustrate the power of this approach by deriving the cDNA sequences for the skeletal muscle alpha-tropomyosins of European common frog (Rana temporaria) and zebrafish (Brachydanio rerio) using only 300 ng of a total poly(A)+ preparation. In these examples, we gained initial entry into the tropomyosin messages by using heterologous primers (to conserved regions) derived from the rat skeletal muscle alpha-tropomyosin sequence. The frog and zebrafish sequences are used in an analysis of tropomyosin evolution across the vertebrate phylogenetic spectrum. The results underscore the conservative nature of the tropomyosin molecule and support the notion of a constrained heptapeptide unit as the fundamental structural motif of tropomyosin.

Animals↗
PubMed1989

Direct genomic sequencing of bacterial DNA: the pyruvate kinase I gene of Escherichia coli.

The genomic sequencing procedure is applied to the direct sequencing of uncharacterized regions of bacterial DNA by a "multiplex walking" approach. Samples of bulk Escherichia coli DNA are cut with various restriction enzymes, subjected to chemical sequencing degradations, run in a sequencing gel, and transferred to nylon membranes. When a labeled oligomer is hybridized to a membrane, a sequence ladder appears wherever the probe lies near a restriction cut. New probes, based on sequence that lies beyond other restriction sites, are then synthesized, and the membranes are reprobed to reveal new sequence. Repeated cycles of oligomer probe synthesis and subsequent reprobing permit rapid sequence walking along the genome. This oligomer walking technique was used to sequence the pyruvate kinase (EC 2.7.1.40) gene in E. coli without resorting to cloning or to library construction. The sequenced region was amplified by the polymerase chain reaction and subsequently transcribed and translated using both in vivo and in vitro systems, and the resultant gene product characterized to show that the gene encodes the type I isoform of pyruvate kinase.

Base Sequence↗
PubMed1989

Differential expression of acetylcholine receptor mRNA in nuclei of cultured muscle cells.

Muscle cells in vitro and in vivo are multinucleated and express acetylcholine receptors (AcChoRs). On innervated cells, the AcChoRs form clusters which lie under the nerve terminals. However, noninnervated cells in culture also express clusters of AcChoR. Both in vivo and in vitro the AcChoR clusters appear to be associated with clusters of nuclei. We have used in situ hybridization to determine whether all the nuclei in cultured chicken embryo myotubes are equally active in expressing the AcChoR alpha subunit message. Cells were hybridized with 35S-labeled probes that contained either both an exon and an intron region or only exon sequences. Control cultures were hybridized with a labeled actin DNA probe or poly(U). The hybrids were detected by emulsion autoradiography; simultaneously, the nuclei were visualized with bisbenzamide. Cells hybridized with the intron/exon probe showed a striking preferential silver grain localization in and around some of the myotube nuclei, whereas those hybridized with the exon probe gave a rather homogeneous grain distribution in the cytoplasm. These results show that myotube nuclei possess differential activation capacities for the expression of AcChoR alpha subunit mRNA and that this difference is due to differential rates of transcription.

Animals↗
PubMed1989

The monoclonal antibody B30 recognizes a specific neuronal cell surface antigen in the developing mesencephalic trigeminal nucleus of the mouse.

A monoclonal antibody, B30, obtained with whole cells from embryonic brain as an immunogen, recognizes a neuronal cell surface antigen that appears only in 2 distinct systems in the developing mouse brain: the trigeminal system and the cerebellum. In the trigeminal system, B30 labels the surface of neurons, including their axons and their transient dendrites, in 2 groups of cells: the centrally located mesencephalic trigeminal nucleus and the peripheral trigeminal ganglion. Immunoreactivity is detectable during axon outgrowth, peaks around the seventh postnatal day, and disappears around 2 weeks after birth. In the cerebellum, B30 labels 2 layers of cells during development. Perinatally, and for about a week after birth, the layer of premigratory granule cells stains. After their maturation, Purkinje cells start to stain and by 12 d postnatally all the Purkinje cell bodies, their axons, and their dendritic trees show strong immunoreactivity. Subsequently, and in the adult, this staining is lost from some cells to reveal bands of antigen positive and negative Purkinje cells. Initial biochemical characterization of the epitope shows that it is carried on 2 minor gangliosides.

Animals↗
PubMed1988

Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis.

We have discovered that single-stranded DNA containing short guanine-rich motifs will self-associate at physiological salt concentrations to make four-stranded structures in which the strands run in parallel fashion. We believe these complexes are held together by guanines bonded to each other by Hoogsteen pairing. Such guanine-rich sequences occur in immunoglobulin switch regions, in gene promoters, and in chromosomal telomeres. We speculate that this self-recognition of guanine-rich motifs of DNA serves to bring together, and to zipper up in register, the four homologous chromatids during meiosis.

Base Sequence↗
PubMed1987

Basic protein enhances the incorporation of DNA into lipid vesicles: model for the formation of primordial cells.

DNA can be encapsulated into lipid vesicles formed by sonication. The presence of a basic protein, lysozyme, enhances the incorporation 100-fold above the level expected by random trapping. This is demonstrated by the ability of the lipid vesicles to protect DNA from digestion with DNase. Such an enhancement of nuclei acid incorporation into vesicles by basic polypeptides and the sharply increased concentration of these macromolecules in the internal volume may have been advantageous in prebiotic evolution.

Biological Evolution↗
PubMed1986

Reaction energetics of a mutant triosephosphate isomerase in which the active-site glutamate has been changed to aspartate.

The essential catalytic base at the active site of the glycolytic enzyme triosephosphate isomerase is the carboxylate group of Glu-165, which directly abstracts either the 1-pro-R proton of dihydroxyacetone phosphate or the 2-proton of (R)-glyceraldehyde 3-phosphate to yield the cis-enediol intermediate. Using the methods of site-directed mutagenesis, we have replaced Glu-165 by Asp. The three enzymes chicken isomerase from chicken muscle, wild-type chicken isomerase expressed in Escherichia coli, and mutant (Glu-165 to Asp) chicken isomerase expressed in E. coli have each been purified to homogeneity. The specific catalytic activities of the two wild-type isomerases are identical, while the specific activity of the mutant enzyme is reduced by a factor of about 1000. The observed kinetic differences do not derive from a change in mechanism in which the aspartate of the mutant enzyme acts as a general base through an intervening water molecule, because the D2O solvent isotope effects and the stoichiometries of inactivation with bromohydroxyacetone phosphate are identical for the wild-type and mutant enzymes. Using the range of isotopic experiments that were used to delineate the free-energy profile of the wild-type chicken enzyme, we here derive the complete energetics of the reaction catalyzed by the mutant protein. Comparison of the reaction energetics for the wild-type and mutant isomerases shows that only the free energies of the transition states for the two enolization steps have been seriously affected. Each of the proton abstraction steps is about 1000-fold slower in the mutant enzyme. Evidently, the excision of a methylene group from the side chain of the essential glutamate has little effect on the free energies of the intermediate states but dramatically reduces the stabilities of the transition states for the chemical steps in the catalyzed reaction.

Aspartic Acid↗
PubMed1986

The triosephosphate isomerase gene from maize: introns antedate the plant-animal divergence.

We have cloned and characterized a cDNA and genomic DNA for the triosephosphate isomerase expressed in maize roots. The gene is interrupted by eight introns. If we compare this gene with that for the protein in chicken, which has six introns, we see that five of the introns are at identical places, one has shifted by three codons, and two are totally new. This great matching leads us to conclude that the introns were in place before the plant-animal divergence, and that the parental gene had at least eight introns, two of which were lost in the line that leads to animals.

Animals↗
PubMed1985

Rous sarcoma virus encodes a transcriptional activator.

Rous sarcoma virus expresses a transcriptional activator that affects the LTR as well as other promoters. We discern this activity as a stimulation of the transient expression of an LTR-promoted hybrid transcriptional unit and also of the rat preproinsulin II gene in transfected NIH 3T3 cells. We map the activity to an alternate reading frame in the p19-p10 region of the gag gene and identify a mRNA whose spliced structure would direct translation of this reading frame from the Pr76gag initiation codon. This mRNA probably differs from genomic RNA only by the 282 nucleotide splice. The predicted translation product is a 124 residue polypeptide; the first six amino acids arise from gag. The target for the action of this transcriptional modulator at the LTR lies between 111 and 620 nucleotides upstream of the cap site.

Animals↗
PubMed1985

Intron/exon structure of the chicken pyruvate kinase gene.

The chicken pyruvate kinase gene is interrupted by at least ten introns, including nine introns within the coding region. We compare the structure of this gene with the three-dimensional protein structure of the homologous cat muscle enzyme. The introns are not randomly placed--they divide the coding sequence into fairly uniformly sized pieces encoding discrete elements of secondary structure. The introns tend to fall at interruptions between stretches of alpha-helix or beta-sheet residues, and each of the six exons that contribute to the barrel-shaped central domain include one or two repeats of a simple unit, an alpha-helix plus a beta strand. This structure suggests that introns were not inserted into a previously uninterrupted coding sequence, but instead are products of the evolution of the first pyruvate kinase gene. We have found some sequence homology between a segment of pyruvate kinase and the structurally homologous mononucleotide binding fold of alcohol dehydrogenase. The superposition of these two regions aligns an intron from the maize alcohol dehydrogenase gene four nucleotides from an intron in the chicken pyruvate kinase gene.

Amino Acid Sequence↗