Definition of a second dimeric subfamily of human alpha satellite DNA

We describe a new human subfamily of alpha satellite DNA. The restriction endonuclease XbaI cleaves this subfamily into a collection of fragments which are heterogeneous with respect to size. We compared the sequences of 6 clones from four different XbaI size classes. Clones from a single size class were not necessarily more related than clones from different classes. Clones from different size classes were found to produce almost identical hybridization patterns with XbaI-digested human genomic DNA. All clones were found to share a common dimeric repeat organization, with dimers exhibiting about 84% sequence identities, indicating that the clones evolved from a common progenitor alphoid dimer. We show that this subfamily, and the EcoRI dimer subfamily originally described by Wu and Manuelidis, evolved from different progenitor alphoid dimers, and therefore represent distinct human alphoid subfamilies.     

Evidence for clonal attenuation of growth potential in hela cells

Summary The growth of primary clones and serial subclones of HeLa cells and of diploid human fibroblast-like cells were compared both in the presence and absence of feeder layers; the latter had no significant effects upon the results. Clones and subclones of both cell types displayed great heterogeneity in growth rates, typically with a bimodality of growth distributions. Serial passages of clones selected on the basis of superior rates of proliferation showed attentuation of growth potentials; the extent of such attentuations was much less in the case of HeLa cells, suggesting at least one possible basis for the differences in long-term growth potential between these two classes of cell lines. This research was supported by Grants AG 00257 and AG 00592 from NIH. Dr. Martinez was supported by Postdoctoral Fellowship AG/HD 02765 from NIH.     

Pseudomonas syringae pv. phaseolicola genomic clones harboring heterologous DNA sequences suppress the same phaseolotoxin-deficient mutants

Cosmid cloning and mutagenesis were used to identify genes involved in the production of phaseolotoxin, the chlorosis-inducing phytotoxin of Pseudomonas syringae pv. phaseolicola, the causal agent of halo blight of bean (Phaseolus vulgaris L.). Eight stable clones were isolated from a genomic cosmid library by en masse mating to 10 ethyl methanesulfonate (EMS)-induced Tox- mutants. In cross-matings, each suppressed all 10 mutants as well as an additional 70 EMS-induced Tox- mutants (and one UV-induced Tox- mutant). On the basis of restriction endonuclease analysis and hybridization studies, the clones were grouped into three classes. Clones in a particular class shared common fragments, whereas clones in different classes did not. Clones from class I (but not classes II and III) also suppressed Tn5-induced Tox- mutants. Interposon mutagenesis and marker exchange of a representative clone from class III into the wild-type genome did not alter its Tox+ phenotype, indicating that this clone does not harbor structural or regulatory genes involved in phaseolotoxin production. We suggest that the genome of P. syringae pv. phaseolicola contains a "hot spot" in one of the functions involved in toxin production which is affected by EMS and UV and that heterologous clones are able to suppress the Tox- phenotype because their inserts encode products that are able to substitute for the product of the mutated gene. Alternatively, the inserts may contain sequences which titrate a repressor protein. In either case, the data suggest that suppression of EMS- and UV-induced mutants occurs when heterologous clones are present in multiple copies.     

Identificaton and characterization of stamen- and tapetum-specific genes from tomato

Summary Differential screening of a tomato cDNA library produced from pre-anthesis stamens resulted in the isolation of 25 cDNA clones that hybridized to probes made from stamen RNA and showed no hybridization to probes made from RNA of vegetative organs. The 25 clones were found to represent 11 noncross-hybridizing classes. The majority of these clones were derived from genes that were single or low copy in the tomato genome. Northern RNA blotting experiments of vegetative and floral organs at several stages of development demonstrated that expression in all 11 classes was confined to floral organs. Of the 11 classes 9 were found to be expressed exclusively in stamens prior to anthesis. Two classes showed expression in immature stamens and in petals, with one of these two additionally being expressed in mature stamens at anthesis. Clones from three of the classes that were expressed exclusively in stamens were used as probes for in situ localization of RNA in floral organs. These experiments demonstrated that expression of the genes corresponding to these clones was confined to the tapetal cells of the anthers. Expression of one of the three genes was found to be limited to a single cell type during the 5–6 day period from late meiosis to immature pollen formation.     

Region-specific cell clones in the developing spinal cord of the zebrafish

 To analyse the proliferative abilities of cells within particular regions of the zebrafish neural plate, injections of fluorescein-dextran were made into single cells at either medial or intermediary positions in the neural plate region of two-somite stage embryos. The resulting cell clones were analysed in 3.5-day-old embryos. Clones with similar compositions were found among those derived from injections in both regions, and these were grouped into classes. 78 clones 29 obtained following injections in the medial region, and 22 of 59 cell clones derived from injections in the intermediary region, were classifiable into 9 and 10 different classes, respectively, each comprising a variable number of clones. Several identified cell types, as well as each of the clone classes themselves, were specific for the regions of the neural plate from which they derived, i.e. they were not represented among the clones derived from the other region. These results suggest that the composition of the lineages derived from particular cells is constant in different animals. Received: 13 July 1998 / Accepted: 20 October 1998     

Evolution of life histories and yields in experimental populations of Daphnia magna

An experiment on life-history evolution is described in which replicated populations of the Cladoceran Daphnia magna , made up of a standard mixture of clones, were subjected to two contrasting culling regimes, involving removal of small or large individuals. After approximately 150 days of culling, analysis of the life histories showed that genetic differences had emerged between culling regimes. Clones selected by culling small sized individuals grew rapidly through small size classes, whereas those selected by culling large sizes grew slowly through small size classes, with the result that the age at which they became vulnerable to harvesting was delayed. In addition, there was some redistribution of reproduction towards size classes that were not culled. This evolution is consistent with a major decline observed in the yield from populations in which large individuals were culled. We argue that changes of this general kind are likely to take place in exploited populations and that serious consideration should be given to evolutionary aspects of the management of such populations.     

Cytogenetically marked clones in human fibroblasts cultured from normal subjects.

Clones of cytogenetically abnormal cells have been recognized in fibroblasts cultured from normal human adult skin. No such clones have been observed in human embryo skin fibroblasts cultured in the same way. Although the culture conditions may have played some part in the emergence of these clones, it is possible that the abnormal cells from which the clones were derived were present in vivo.     

Mutation of the endogenous p53 gene in cells transformed by HPV-16 E7 and EJ c-ras confers a growth advantage involving an autocrine mechanism.

Rat embryo fibroblasts transformed with the HPV-16 E7 gene and the activated c-H-ras gene fall into two distinct phenotypic classes. At high cell density, clones of one class form colonies in methylcellulose supplemented with low serum; at low cell density, these cells display responsiveness to mitogenic factors present in serum-free conditioned medium from rat embryo fibroblasts. In contrast, clones of the second class exhibit an absolute dependency on growth factors present in serum at all cell densities in the methylcellulose colony assay and fail to respond to conditioned medium. We find that the status of the endogenous p53 gene is tightly correlated with these two classes of clones. Clones of the first class contain missense mutations in the p53 gene and have lost the wild-type allele. Clones of the second class express wild-type p53 protein. The importance of mutant p53 expression in reducing the growth factor dependency of transformed clones was confirmed in a separate series of experiments in which rat embryo fibroblasts were transformed with three genes, E7 + ras + mutant p53. The growth behaviour of these triply transfected clones was similar to that of the E7 + ras clones expressing endogenous mutant p53. We demonstrate that the enhanced proliferation of E7 + ras clones expressing mutant p53 protein involves an autocrine mechanism.     

Cloning of eukaryotic genes in single-strand phage vectors: the human interferon genes

Using oligonucleotide probes with defined sequences, we have selected clones from a human lymphocyte cDNA library which represent human leukocyte (HuIFN-α) and fibroblast (HuIFN-β) interferon gene sequences. Double-stranded f1 phage DNA was used as the vector for initial cloning of cDNA. Clones carrying interferon gene sequences were identified by hybridization with the oligonucleotide probes. The same oligonucleotide probes were used as primers for dideoxy chain termination sequencing of the clones. One HuIFN-α clone, 201, has a nucleotide sequence different from published HuIFN-α sequences. Under control of the lacUV5 promoter, the 201 gene has been used to express biologically active HuIFN-α in Escherichia coli.     

Monoclonal antibodies to red cell cytoskeletal proteins

Monoclonal antibodies to human red cell cytoskeletal proteins were produced following immunization of mice with Triton shells produced from intact red cells. Two lines producing antibodies binding to spectrin and actin, respectively, were subcloned and further characterized. Clones producing the anti-spectrin antibody were stable. The antibody was monoclonal and specific for spectrin band 2. The anti-actin clones were unstable.     

Evolution and heterogeneity of the alpha-/beta-type and gamma-type gliadin DNA sequences

Near full length cDNA clones for both alpha-/beta- and gamma-type gliadins were isolated and studied for sequence diversity. Based on restriction site polymorphism and cross-hybridization studies, alpha-/beta- and gamma-type clones could be divided into five and three homology classes, respectively. Clones representing each of the different classes were sequenced and compared. Sequence divergence between the classes was due to single-base substitutions and to duplications or deletions within or near direct repeats. Thus, through numerous duplications and subsequent divergence, the gliadin multigene family encodes a polymorphic set of polypeptides differing in both isoelectric point and molecular size. Southern blot analysis of wheat DNA suggested that the number of genes encoding the alpha-/beta-type gliadins was extremely large (greater than 100 copies/haploid genome). Inasmuch as hybridization patterns were the same using DNA isolated from seeds or leaves, amplification or rearrangement of DNA does not occur during development. The complete coding sequence of a gamma-gliadin was similar to that observed for the alpha-/beta-gliadins, but with several notable differences. Comparison of gamma-type gliadin cDNA sequences showed that, unlike the conserved dodecamer repeat common to all the alpha-/beta-gliadins, the tandem repeat unit differed among gamma-gliadin clones.     

Use of a recombinant parvovirus to facilitate screening for human melanoma cell clones expressing tetracycline-responsive transactivators.

The tetracycline regulatory (TET) system provides a useful means of controlling foreign gene expression in mammalian cells. Exploiting this system in cultured cells requires the prior isolation, from the cells of interest, of transfectant clones expressing the necessary TET transactivator, tTA, or reverse transactivator, rtTA. We describe a simple screening procedure for identifying transfectant clones expressing a properly regulated transactivator, and the application of this method to isolating clones of human melanoma cells expressing either tTA or rtTA. Clones in multi-well plates are transduced by exposure to a recombinant parvovirus containing a luciferase reporter, under control of a promoter responsive to the TET system transactivators. Transactivation of reporter expression in the presence or absence of doxycycline (DOXY) is determined after one to two days, using a rapid luciferase assay. Screening is easier and more reproducible with this transduction method than with conventional transient transfection of analogous reporter plasmids. Clones of two human melanoma cell lines showing >100-200-fold transactivation after transfection with either tTA or rtTA were readily identified using this method.     

Expression in Escherichia coli cells of mutant human interferon alpha2

cDNA library was obtained from mRNA isolated from human leukocytes induced by Newcastle disease virus. Clones containing cDNA for alpha 2-interferons were identified by colony hybridization with two synthetic hexadecanucleotides. One of the positive clones contained a NH2-terminal part of cDNA of human interferon identical to cDNA for IFN-alpha 2. The only difference between these two clones was the Ser-8 leads to Asn-8 substitution in deduced sequenced of mature interferons. This mutant interferon, named alpha 2, was expressed in E. coli and its properties were compared with those of interferon alpha 2.     

Gene amplification in methotrexate-resistant mouse cells. IV. Different DNA sequences are amplified in different resistant lines

DNA was purified from double minutes isolated from MTX-resistant EL4/8 mouse lymphoma cells, digested to completion with Bam H1 restriction endonuclease and cloned in lambda-1059. The properties of the library suggest that the DNA from which it was made was not detectably contaminated with non-dm chromosome material, and that the library is essentially complete for sequences contained in Bam H1 restriction fragments between 9 and 19 kb. The inserts of some selected lambda-recombinants were subcloned in pBR328 or pAT153 to separate sequences of differing repetition frequency. Clones representative of different classes of sequences were used as probes to Southern transfers of Bam H1 digested total nuclear DNAs of various MTX-resistant cell lines. The results clearly show that the amplified unit of each cell line has a unique structure, and that different amplified units differ widely in their sequence composition.     

Size and organization of a multigene family encoding phaseolin, the major seed storage protein of Phaseolus vulgaris L.

Summary Solution hybridization kinetics and genomic nitrocellulose blot hybridization analyses show that the Phaseolus vulgaris L. (French bean) storage proteins (phaseolins) are encoded as a small, homologous, multigene family consisting of approximately seven members. Restriction endonuclease site mapping (EcoRI, BamHI, and BglII) of DNA regions flanking the phaseolin genes has shown that the gene family can be divided into at least three characteristic fragment size classes. Clones representative of two of these phaseolin gene classes have been isolated from a 1059 phage library.     

Isolation and characterisation of cDNA clones for the A alpha- and gamma-chains of human fibrinogen.

cDNA clones coding for the A alpha- and gamma-chains of human fibrinogen have been isolated from an adult liver cDNA library. Clones were identified by hybridisation with mixtures of synthetic oligonucleotides 17 bases long, predicted using amino acid sequence data for each chain. The cDNA insert sizes are 1,950bp for A alpha-fibrinogen and 950bp for gamma-fibrinogen. The clones do not show any cross-hybridisation. Each cDNA hybridises to a unique sequence in the human genome. In adult human liver, Northern blots give an estimated messenger RNA size of 2.6kb for A alpha-fibrinogen and 1.8kb for gamma-fibrinogen.     

Variation in the life-span of clones derived from human diploid cell strains

The doubling potential of several hundred clones derived from WI-38 and WI-26 cell cultures has been determined. Clones were isolated at various population doubling levels (PDLs) during the finite in vitro life-span of the mass (uncloned) cultures. In all cases, there was a large variation in population doubling potential (or life-span) among the clones isolated from a single mass culture. When clones were isolated from mass cultures which had undergone eight or nine population doublings, only about 50% of the clones were capable of more than eight population doublings. This percentage was further reduced when clones were isolated from mass cultures at higher PDLs. Mass cultures appear to be composed of two subpopulation classes: one with a low population doubling potential, and the other with a higher population doubling potential. Nevertheless, the highest doubling potential observed in clones isolated from any single culture was about the same as the doubling potential of the mass culture from which single cells were taken.     

Single-chain variable fragment antibodies selected by phage display against the sporozoite surface antigen P23 Of Cryptosporidium parvum

Cryptosporidium parvum, an apicomplexan parasite transmitted via animal fecal wastes, is the causative agent of cryptosporidiosis. Clones were selected from 2 synthetic na?ve human single-chain variable fragment (scFv) phagemid libraries that bound to the recombinant P23 protein of C. parvum. Panning the Tomlinson I and J phagemid libraries resulted in 6 distinct clones. Two clones had full-length scFv sequences, while the remaining clones were either truncated or missing a section of the heavy chain. Despite these differences, all clones were able to detect both native C. parvum proteins and recombinant P23. None of the selected clones cross-reacted with Escherichia coli, Streptococcus pyogenes, Listeria monocytogenes, Bacillus cereus, Giardia lamblia (cysts or trophozoites), or with S16, another dominant surface antigen on C. parvum sporozoites. Clones expressed as the scFv-gIIIp fusion construct in soluble form detected C. parvum. Panning from na?ve libraries is a useful method for isolation and identification of recombinant antibodies that have the potential for use in pathogen detection and immunotherapy.