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PubMed1999

Chordate origins of the vertebrate central nervous system.

Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord. In contrast, the telencephalon, a midbrain-hindbrain boundary region with organizer properties, and the definitive neural crest appear to be vertebrate innovations.

Animals↗
PubMed1991

Specification of neurepithelium and surface epithelium in avian transplantation chimeras.

Previous studies of the avian blastoderm have revealed that extensive displacements occur within the epiblast during gastrulation and neurulation. The present study had two main purposes: (1) to map the origin and movement of prospective surface epithelial cells, and (2) to ask whether neurepithelial and surface epithelial cell fates are determined prior to cell movement, or whether they arise later as a result of the ultimate position attained by cells through their movement. Our results show that the rostral and lateral intraembryonic and extraembryonic surface epithelium originates as far laterally as at the area pellucida-area opaca interface of the early epiblast. Intraembryonic surface epithelial cells rearrange relative to one another, extending medially to contribute to the formation of the neural folds, whereas extraembryonic surface epithelial cells maintain their lateral positions, spreading uniformly as the epiblast expands. Our results further show that surface epithelial and neurepithelial cell fates are labile at the onset of neurulation, suggesting that cell fate is specified following cell movement.

Animals↗
PubMed1985

Structural analysis of the myeloma-associated membrane antigen KMA.

kappa-Myeloma antigen (KMA) was immunoprecipitated from lactoperoxidase-radioiodinated HMy2 lymphoblastoid cells by using monoclonal antibody K-1-21 and was analyzed by SDS-PAGE. Under reducing conditions, two major subunits of Mr approximately 26,000 and Mr approximately 42,000, and minor components of Mr approximately 28,000, 31,000, and 36,000 were observed. The Mr approximately 26,000 subunit was identical to kappa-light chains from HMy2 surface IgG in apparent m.w., isoelectric point, and staphylococcal V-8 protease peptide map, but was not precipitated in association with Ig heavy chain. The Mr approximately 42,000 component was homologous to rabbit skeletal muscle actin by peptide mapping with staphylococcal V-8 protease. The cell surface origin of the immunoprecipitated antigen was confirmed by demonstrating lactoperoxidase dependence of iodination and complete removal from the cell surface after pronase treatment of viable cells. Thus, cell surface expression of KMA is the result of membrane association of non-heavy chain-linked kappa-light chains, possibly in noncovalent association with actin.

Actins↗
PubMed1973

Rapid mapping of conditional and auxotrophic mutations in Escherichia coli K-12.

The approximate genetic map locations of auxotrophic and conditional lethal mutations of Escherichia coli can be rapidly determined with replica plating techniques. A set of patches of 15 streptomycin-sensitive (Str(S)) Hfr strains with points of origin distributed around the map is replica plated onto a recombinant-selective plate with a lawn of Str(R) cells which carry an unmapped mutation. The map interval defined by the Hfr points of origin which are closest to the mutant locus is seen by the presence or absence of heavy patches of recombinants produced by transfer of early wild-type genes from the Hfrs. An alternative method is to replicate patches of different mutant strains (100 per plate) onto Hfr lawns; in this case more than 1,000 different mutants can be mapped in a single experiment in a few days. In this way, many types of mutations with similar phenotypes can be grouped as to approximate location on the genetic map. For ordering mutations within groups, the same replica plating methods can be used to cross F-prime derivatives of mutants with other mutants of the same group. Relative merits of these and other mapping methods of E. coli are discussed.

Chromosome Mapping↗
PubMed2001

Mapping of 13 horse genes by fluorescence in-situ hybridization (FISH) and somatic cell hybrid analysis.

We report fluorescence in-situ hybridization (FISH) and somatic cell hybrid mapping data for 13 different horse genes (ANP, CD2, CLU, CRISP3, CYP17, FGG, IL1RN, IL10, MMP13, PRM1, PTGS2, TNFA and TP53). Primers for PCR amplification of intronic or untranslated regions were designed from horse-specific DNA or mRNA sequences in GenBank. Two different horse bacterial artificial chromosome (BAC) libraries were screened with PCR for clones containing these 13 Type I loci, nine of which were found in the libraries. BAC clones were used as probes in dual colour FISH to confirm their precise chromosomal origin. The remaining four genes were mapped in a somatic cell hybrid panel. All chromosomal assignments except one were in agreement with human-horse ZOO-FISH data and revealed new and more detailed information on the equine comparative map. CLU was mapped by synteny to ECA2 while human-horse ZOO-FISH data predicted that CLU would be located on ECA9. The assignment of IL1RN permitted analysis of gene order conservation between HSA2 and ECA15, which identified that an event of inversion had occurred during the evolution of these two homologous chromosomes.

Animals↗
PubMed1993

Cell binding specificity of mouse R-cadherin and chromosomal mapping of the gene.

R-cadherin was originally identified as a chicken cadherin expressed by the retina. Here, we describe the identification of a mouse homologue of R-cadherin. We isolated mouse cDNAs encoding a cadherin with 94% identity in amino acid sequence to the chicken R-cadherin, and defined this molecule as mouse R-cadherin. L cells transfected with the mouse R-cadherin cDNA acquired a cadherin-mediated cell-cell adhesiveness as found for other cadherins. To examine the binding specificity of mouse R-cadherin, L cells expressing this cadherin (mRL) were mixed with L cells expressing chicken R-cadherin (cRL), mouse N-cadherin (mNL), mouse E-cadherin (mEL) and mouse P-cadherin (mPL). While mRL cells randomly intermixed with cRL cells, those cells aggregated separately from mEL or mPL cells. Mixing of mRL with mNL cells gave an intermediate result; that is, they formed both separate and chimeric aggregates, suggesting that R- and N-cadherin can interact with each other although each has a preference to bind to its own type. Similar properties were previously found for chicken R-cadherin. Thus, the cell binding specificity of R-cadherin is entirely conserved between the two species, suggesting a conserved role for this protein in morphogenesis. We also located the mouse R-cadherin gene to chromosome 2.

Amino Acid Sequence↗
PubMed1997

Temporal order of replication of mouse ribosomal RNA genes during the cell cycle.

The timing of replication of mouse ribosomal RNA (rRNA) genes was determined in cultured cells by using 5-bromodeoxyuridine labeling of DNA coupled with synchronization. Two subclasses of rRNA genes were characterized that differ in their temporal order of replication during S-phase. Approximately half of the rDNA repeat units replicated primarily during the first half of S-phase and the other 50% preferentially in the second half. This difference in replication timing was consistently observed for the approximately 400 rDNA repeat units of NIH3T3 fibroblasts, but not for plasmid DNA containing fragments of rRNA genes that had been stably transfected into the genome of these cells. The rDNA fragments inserted into these transfection vectors contained the recently mapped origin of bidirectional replication with or without amplification-promoting sequences, or none of the above. Since the plasmid DNA that was integrated into the host cell genome replicated randomly during S-phase we conclude that the integrated plasmid DNA is either replicated from a chromosomal origin in the neighborhood of its integration site or that inserts are replicated from their own origins and the timing of replication is determined by flanking sequences.

3T3 Cells↗
PubMed1998

Molecular cloning, structural characterization, and chromosomal mapping of the human LECT2 gene.

We originally isolated LECT2 (leukocyte cell-derived chemotaxin 2) as a 16-kDa secreted protein having a human neutrophil chemotactic activity, then cloned human and bovine LECT2 cDNAs and demonstrated the liver-specific expression of the protein. LECT2 is thought to be a multifunctional protein, because it was recently found to be identical to chondromodulin-II a growth stimulator of chondrocyte cells. We report here the cloning and the structural analysis of the human LECT2 gene. The gene spans approximately 8 kb and consists of four exons and three introns. Primer extension analysis revealed that several transcription initiation sites occur within 70-230 nucleotides upstream of the translation initiation codon. Several transcriptional control sequences relevant to the liver-specific expression have been identified at the 5' untranslated region of the human LECT2 gene. The human LECT2 gene was mapped to chromosome 5q31.1-q32 by fluorescence in situ hybridization. This region contains a cluster of cytokine genes including IL-4, IL-5, and IL-9.

Base Sequence↗
PubMed2006

Cell evolution and Earth history: stasis and revolution.

This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (= Chloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this 'chlorobacterial age' of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic 'age of cyanobacteria' and, as the ozone layer grew, the rise of plankton; immensely later, probably as recently as ca 0.9 Gyr ago, the neomuran revolution ushered in the 'age of eukaryotes', Archaebacteria (arguably the youngest bacterial phylum), and morphological complexity. Diversification of glycobacteria ca 2.8 Gyr ago, predominantly inhabiting stratified benthic mats, I suggest caused serial depletion of 13C by ribulose 1,5-bis-phosphate caboxylase/oxygenase (Rubisco) to yield ultralight late Archaean organic carbon formerly attributed to methanogenesis plus methanotrophy. The late origin of archaebacterial methanogenesis ca 720 Myr ago perhaps triggered snowball Earth episodes by slight global warming increasing weathering and reducing CO2 levels, to yield runaway cooling; the origin of anaerobic methane oxidation ca 570 Myr ago reduced methane flux at source, stabilizing Phanerozoic climates. I argue that the major cellular innovations exhibit a pattern of quantum evolution followed by very rapid radiation and then substantial stasis, as described by Simpson. They yielded organisms that are a mosaic of extremely conservative and radically novel features, as characterized by De Beer's phrase 'mosaic evolution'. Evolution is not evenly paced and there are no real molecular clocks.

Archaea↗
PubMed1993

Locations of the ectodermal and nonectodermal subdivisions of the epiblast at stages 3 and 4 of avian gastrulation and neurulation.

A prospective fate map of the avian epiblast at late gastrula and early neurula stages has been generated through the construction of quail/chick transplantation chimeras. This map shows the subdivisions of the prospective ectoderm, mesoderm, and endoderm, both within the epiblast prior to their ingression and within the primitive streak. The map demarcates the locations and extents of the prospective surface ectoderm, otic placodes, neural crest, and neural plate--including its postnodal levels--in prospective ectoderm of the epiblast; prospective foregut, within the prospective endoderm of the epiblast and primitive streak; and prospective notochord, somites, intermediate mesoderm, lateral plate mesoderm, and extraembryonic mesoderm in the prospective mesoderm of the epiblast and/or primitive streak. Prospective cardiogenic cells are apparently absent from the primitive streak at these stages, and contributions of the epiblast to the heart are relatively scant and inconsistent with the expected timing and directions of migrations of prospective cardiogenic cells. Mapping of the primitive streak at earlier stages in another study (García-Martinez and Schoenwolf: Developmental Biology, in press) reveals that the ingression of cardiogenic cells through the primitive streak occurs prior to late gastrula stages, suggesting that contributions of epiblast to the heart at later stages are artifactual. Tests of prospective potency, based on the projected locations of origin of various cell groups provided by the new prospective fate map, are underway.

Animals↗
PubMed1991

A prespore gene, Dd31, expressed during culmination of Dictyostelium discoideum.

During culmination of Dictyostelium fruiting bodies, prespore and prestalk cells undergo terminal differentiation to form spores and a cellular stalk. A genomic fragment was isolated by random cloning that hybridizes to a 1.4-kb mRNA present during culmination. Cell type separations at culmination showed that the mRNA is present in prespore cells and spores, but not in prestalk or stalk cells. After genomic mapping, an additional 3 kb of DNA surrounding the original 1-kb fragment was cloned. The gene was sequenced and named Dd31 after the size of the predicted protein product in kilodaltons. Accumulation of Dd31 mRNA occurs immediately prior to sporulation. Addition of 20 mM 8-Br-cAMP to cells dissociated from Mexican hat stage culminants induced sporulation and the accumulation of Dd31 mRNA, while 20 mM cAMP did not. Dd31 mRNA does not accumulate in the homeotic mutant stalky in which prespore cells are converted to stalk cells rather than spores. Characterization of Dd31 extends the known temporal dependent sequence of molecular differentiations to sporulation.

Amino Acid Sequence↗
PubMed1993

Identification of novel sequences in the repertoire of hypervariable TRE17 genes from immortalized nonmalignant and malignant human keratinocytes.

The TRE17 oncogene, originally cloned from transfected DNA of Ewing's sarcoma cells, maps to chromosome 17q and is expressed in a wide variety of human cancer cells. We recently detected the variants of this gene by using the polymerase chain reaction (PCR) and sequencing from the first exon to the third intron. Based on sequence homology scores, the variants could be grouped into three families, denoted alpha, beta, and gamma. Here, we used human keratinocytes from healthy skin which had been spontaneously immortalized and then rendered malignant by serum privation in vitro. Both immortalized and malignant cells expressed TRE17 sequences to the same extent, and, according to the restriction site analysis of cloned PCR products, both contained common and rare TRE17 variants in similar proportions. These variants, one of each from both cell types, were then sequenced and compared with those from the previous study. In the phylogenetic tree, they clustered with alpha and gamma at the most distant tree positions. The overall fraction of conserved sites in the whole TRE17 repertoire was 80%. An unexpected feature of the observed variability was that intronic sites were significantly better conserved than exonic sites. Members of TRE17 gamma detected in immortalized and malignant keratinocytes differed one from another, and both differed from the TRE17 gamma already identified in Ewing's sarcoma. No TRE17 gamma has been found so far in healthy tissues, thus leaving open the possibility of its origin from TRE17 beta by somatic changes during tumor progression.

Base Sequence↗
PubMed1997

Mapping of replication origins and termination sites in the Duchenne muscular dystrophy gene.

The replication structure of the human dystrophin gene in cultured masculine erythroleukemia cells (line HEL 92.1.7) was studied using the replication direction assay. This gene is organized into at least six replicons ranging in size from 170 to more than 500 kb. One of the replicon junctions (sites of replication termination) was mapped to intron 44, i.e., roughly in the same area where the major recombination hot spot is located. A replicon junction was also found between the muscle and the brain promoters. The two replicons mapped in the present study are highly asymmetric, as the distances covered by the replication forks moving in opposite directions from the same origin differ by more than threefold.

Dystrophin↗
PubMed1997

Expression, genomic structure and high resolution mapping to 19p13.2 of the human smooth muscle cell calponin gene.

Smooth muscle cells (SMC) express a battery of cell-restricted differentiation genes, many of which are down-regulated during the course of vascular disease. Here, we present the mRNA expression, genomic structure and chromosomal mapping of the gene encoding human smooth muscle cell calponin (SMCC). Human SMCC transcripts are restricted to tissues and cells of SMC origin and, in the latter case, appear to be uniquely controlled in two distinct human SMC lines of uterine and aortic origin. Restriction mapping. Southern blot and PCR analysis of a 70-kb human bacterial artificial chromosome (BAC) revealed a genomic structure (seven exons spanning > 11 kb) very similar to that reported for the mouse SMCC gene. Using a variety of human-rodent somatic cell hybrid and radiation hybrid mapping panels, the human SMCC gene was mapped to a genomic interval of less than 1.32 Mb in 19p13.2. These results provide new information concerning the regulation of SMCC gene expression and demonstrate the utility of two human SMC lines for the further characterization of this gene's expression control. The identification of a BAC harboring the entire human SMCC locus represents an important reagent for future analysis of SMCC regulatory sequences. Finally, the localization of SMCC to a defined genomic interval will facilitate an analysis of its potential as a candidate gene for disease phenotypes mapping to 19p13.2.

Amino Acid Sequence↗
PubMed1975

Temporal genetic mapping in the blue-green alga Anacystis nidulans using ethyl methanesulphonate.

Cultures of the blue-green alga Anacytis nidulans were synchronized with respect to DNA synthesis as well as cell division. Application of ethyl methanesulphonate at different stages of replication resulted in a peak of mutation frequency for different genetic markers; this peak can be accounted for in terms of the involvement of repair processes. A temporal map of 19 markers has been constructed by this method. Comparison of gene position obtained by temporal mapping indicates that either bidirectional replication or unidirectional replication from more than one origin occurs.

Cell Division↗
PubMed1979

Epstein-Barr virus-specific RNA. III. Mapping of DNA encoding viral RNA in restringent infection.

Namalwa and Raji cells, originally obtained from a Burkitt tumor biopsy, grow as continuous cell lines in vitro and contain the Epstein-Barr virus (EBV)-related nuclear antigen EBNA (B. M. Reedman and G. Klein, Int. J. Cancer 11:499-520, 1973) and RNA homologous to at least 17 and 30% of the EBV genome, respectively (S. D. Hayward and E. Kieff, J. Virol. 18:518-525, 1976; T. Orellana and E. Kieff, J. Virol. 22:321-330, 1977). The polyribosomal and polyadenylated [poly(A)+] RNA fractions of Namalwa and Raji cells are enriched for a class of viral RNA homologous to 5 to 7% of EBV DNA (Hayward and Kieff, J. Virol. 18:518-525, 1976; Orellana and Kieff, J. Virol. 22:321-330, 1977). The objective of the experiments described in this communication was to determine the location within the map of the EBV genome (D. Given and E. Kieff, J. Virol. 28:524-542, 1978) of the DNA which encodes the viral RNA in the poly(A)+ and non-polyadenylated [poly(A)-] RNA fractions of Namalwa cells. Hybridization of labeled DNA homologous to Namalwa poly(A)+ or poly(A)- RNA to blots containing EcoRI, Hsu I, or Hsu I/EcoRI double-cut fragments of EBV (B95-8) or (W91) DNA indicated that these RNAs are encoded by DNA contained primarily in the Hsu I A/EcoRI A and Hsu I B/EcoRI A fragments and, to a lesser extent, in other fragments of the EBV genome. Hybridizations of Namalwa poly(A)+ and poly(A)- RNA in solution to denatured labeled EcoRI A or B fragments, Hsu I A, B, or D fragments, and Hsu I A/EcoRI A or Bam I S fragments and of Raji polyribosomal poly(A)+ RNA to the EcoRI A fragment indicated that (i) Namalwa poly(A)+ RNA is encoded primarily by 6 x 10(5) daltons of a 2 x 10(6)-dalton segment of DNA, Bam I S, which is tandemly reiterated, approximately 10 times, in the Hsu I A/EcoRI A fragment and is encoded to a lesser extent by DNA in the Hsu I B, EcoRI B, and Hsu I D fragments. Raji polyribosomal poly(A)+ RNA is encoded by a similar fraction of the EcoRI A fragment as that which encodes Namalwa poly(A)+ RNA. (ii) The fraction of the Bam I S fragment homologous to Namalwa poly(A)- RNA is similar to the fraction homologous to Namalwa poly(A)+ RNA. However, Namalwa poly(A)- RNA is homologous to a larger fraction of the DNA in the Hsu I B, Hsu I D, and EcoRI B fragments.

Cell Line↗
PubMed1997

Rapid genotyping of mutant mice using dried blood spots for polymerase chain reaction (PCR) analysis.

Spontaneous neurologic mutations in the mouse provide powerful tools for the study of mammalian central nervous system development. The study of mouse neurologic mutants has led to a better understanding of the complex mechanisms involved in the development of the nervous system. Because few of these mutations have been identified, molecular probes distinguishing heterozygotes from homozygotes are generally unavailable. Further, most neurologic mouse mutants breed poorly as homozygotes, making it necessary to breed heterozygotes and select homozygous mutant progeny based on phenotype. The requirement for heterozygous breeding and the lack of molecular markers specific for the mutation have hampered developmental studies because the underlying neurologic perturbations occur before the mutant mice can be identified by phenotype. The recent identification and chromosomal assignment of simple sequence repeats (SSRs), repetitive sequences of DNA found at a high density throughout the mouse genome, provide the tools for mapping mutations in the mouse and for subsequent genotyping of potential mutants prior to phenotype onset. The SSRs are useful because these markers are polymorphic (for review see Weber, J.L., Human DNA polymorphisms based on length variations in simple-sequence tandem repeats. In: K.E. Davies and S.M. Tilghman (Eds.), Genetic and Physical Mapping. Genome Analysis, Vol. I, Cold Spring Harbor Laboratory Press, Plainview, NY, 1990, pp. 159-181 [16]), that is, the size of the individual SSRs differs among strains of mice. Following polymerase chain reaction (PCR) amplification of an SSR and separation of PCR products by polyacrylamide gel electrophoresis, one can easily visualize differences in the size of the PCR product between mouse strains. Many mutations in the mouse arose spontaneously on inbred strains and were subsequently backcrossed onto a different strain. After many generations of congenic backcrosses, the only DNA retained from the original mutant strain is composed of the mutant gene and closely linked regions. Thus, it is possible to cross the mutant strain to a different mouse strain and map the mutation by correlating mutant phenotype to SSRs the same size as the original mutant strain. We have mapped the tottering (tg), Purkinje cell degeneration (pcd), and nervous (nr) mutations using SSRs in backcrossed mouse strains. The SSRs distinguishing mutant from normal strains can then be used to genotype potential mutant pups before the onset of the mutant phenotype. The protocol described below can be adapted to almost any mutation congenically inbred for genotyping. Here we describe a method for selecting primers appropriate for genotyping potential mouse mutants and a rapid protocol for genotype screening. Even with SSRs distinguishing mutant from normal mice, genotyping several mice simultaneously can be a daunting task. This is primarily because the protocols available for preparing DNA for PCR amplification are time-consuming, requiring several purification steps including phenol extractions. Although kits are commercially available for DNA preparation without organic extractions, these kits tend to be expensive. The protocol described is a rapid, inexpensive method of determining the genotype of mice using PCR analysis of dried blood spots. The protocol only requires PCR primers distinguishing among alleles and is therefore ideal for the rapid identification of potential mutants for those mouse mutations which have been mapped using microsatellite markers. The DNA preparation protocol may also be used in rapid screening of potential transgenic mice.

Animals↗
PubMed1985

Human tumour cell lines established in vitro from tumours after long-term passage as nude mouse xenografts. Comparative fingerprinting of their concanavalin-A acceptor glycoproteins.

Two human colon cancer xenografts (EC and AC) were established in tissue culture only after long-term passage in nude mice. Earlier attempts to establish cell lines were unsuccessful. The epithelioid cells retain their tumourigenicity after in vitro growth, giving rise to tumours with a take rate of 60-80%. After reimplantation, the xenografts retain a similar morphology to that of the original human tumours. Both cell lines show human karyology. Comparative mapping of Concanavalin-A acceptor glycoproteins provides a fingerprint characteristic of each cell line. These glycoprotein patterns are similar to those shown by HT-29, an established colon cancer cell line.

Animals↗