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PubMed2006

Over-production of beta-carotene from metabolically engineered Escherichia coli.

To produce recombinant beta-carotene in vitro, synthetic operons encoding genes governing its biosynthesis were engineered into Escherichia coli. Constructs harboring these operons were introduced into either a high-copy or low-copy cloning vector. beta-Carotene production from these recombinant E. coli cells was either constitutive or inducible depending upon plasmid copy number. The most efficient beta-carotene production was with the low-copy based vector. The process was increased incrementally from a 5 l to a 50 l fermentor and finally into a 300 l fermentor. The maximal beta-carotene yields achieved using the 50 l and 300 l fermentor were 390 mg l(-1) and 240 mg l(-1), respectively, with overall productivities of 7.8 mg l(-1) h(-1) and 4.8 mg l(-1) h(-1).

Drug Industry↗
PubMed1987

Allele-specific complementation of an Escherichia coli leuB mutation by a Lactobacillus bulgaricus tRNA gene.

A Lactobacillus bulgaricus gene encoding a serine tRNA with the anticodon CGA was isolated from a L. bulgaricus clone bank and characterized. This gene is expressed and active in Escherichia coli. The wild-type form of the gene allele specifically complements the E. coli leuB6 mutation. This process depends on gene copy number; high copy number restores leucine prototrophy, while low copy number does not. We suggest that restoration of activity of the mutant leuB6 allele occurs by missense suppression. The L. bulgaricus tRNA(CGASer) when overproduced in E. coli is misacylated at a low frequency, leading to the insertion of an amino acid other than serine in response to the presumed mutant codon UCG in the leuB6 gene. Nucleotide (nt) sequences flanking the tRNA coding region are present in the L. bulgaricus tRNA gene, closely resembling E. coli promoter and terminator elements. A noteworthy feature of this tRNA gene is the extreme length (22 nt) of its extra arm. The 3'-terminal CCA of the tRNA is not encoded in this tRNA gene and thus must be added posttranscriptionally.

Alleles↗
PubMed2007

Nuclear transfer: preservation of a nuclear genome at the expense of its associated mtDNA genome(s).

Nuclear transfer technology has uses across theoretical and applied applications, but advances are restricted by continued poor success rates and health problems associated with live offspring. Development of reconstructed embryos is dependent upon numerous interlinking factors relating both to the donor cell and the recipient oocyte. For example, abnormalities in gene expression following somatic cell nuclear transfer (SCNT) have been linked with an inability of the oocyte cytoplasm to sufficiently epigenetically reprogram the nucleus. Furthermore, influences on the propagation of mitochondria and mitochondrial DNA (mtDNA) could be of great importance in determining the early developmental potential of NT embryos and contributing to their genetic identity. mtDNA encodes some of the subunits of the electron transfer chain, responsible for cellular ATP production. The remaining subunits and those factors required for mtDNA replication, transcription and translation are encoded by the nucleus, necessitating precise intergenomic communication. Additionally, regulation of mtDNA copy number, via the processes of mtDNA transcription and replication, is essential for normal preimplantation embryo development and differentiation. Unimaternal transmission following natural fertilization usually results in the presence of a single identical population of mtDNA, homoplasmy. Heteroplasmy can result if mixed populations of mtDNA genomes co-exist. Many abnormalities observed in NT embryos, fetuses, and offspring may be caused by deficiencies in OXPHOS, perhaps resulting in part from heteroplasmic mtDNA populations. Additionally, incompatibilities between the somatic nucleus and the cytoplast may be exacerbated by increased genetic divergence between the two genomes. It is important to ensure that the nucleus is capable of sufficiently regulating mtDNA, requiring a level of compatibility between the two genomes, which may be a function of evolutionary distance. We suggest that abnormal expression of factors such as TFAM and POLG in NT embryos will prematurely drive mtDNA replication, hence impacting on early development.

Adaptation, Biological↗
PubMed1994

Fidelity of in vitro DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase.

The fidelity of DNA strand transfer reactions catalyzed by human immunodeficiency virus type 1 reverse transcriptase has been studied in vitro. A model system involving two sequential DNA strand transfers was developed to simulate the process of forced copy-choice recombination. A propensity for nucleotide misincorporation at the junction of the strand transfer, as determined by DNA sequencing of the reaction products, was found consistent with a model involving the addition of nontemplate-directed nucleotides prior to the transfer of nascent DNA onto the accepting RNA template [Peliska, J. A., & Benkovic, S. J. (1992) Science 258, 1112]. The kinetic and mechanistic factors that may dictate which nucleotide bases are incorporated at recombination sites during strand transfer and the possible consequences of recombination-induced mutagenesis in vivo are discussed.

Base Sequence↗
PubMed2001

Production of multiple plant hormones from a single polyprotein precursor.

Some animal and yeast hormone genes produce prohormone polypeptides that are proteolytically processed to produce multiple copies of hormones with the same or different functions. In plants, four polypeptides have been identified that can be classed as hormones (intercellular chemical messengers) but none are known to be produced as multiple copies from a single precursor. Here we describe a polyprotein hormone precursor, present in tobacco plants, that gives rise to two polypeptide hormones, as often found in animals and yeast. The tobacco polypeptides activate the synthesis of defensive proteinase-inhibitor proteins in a manner similar to that of systemin, an 18-amino-acid polypeptide found in tomato plants. The two tobacco polypeptides are derived from each end of a 165-amino-acid precursor that bears no homology to tomato prosystemin. The data show that structurally diverse polypeptide hormones in different plant species can serve similar signalling roles, a condition not found in animals or yeast.

Amino Acid Sequence↗
PubMed2003

Review article: Oral, modified-release mesalazine formulations--proprietary versus generic.

Products containing mesalazine have been used in the treatment of inflammatory bowel disease for many years. Many of the oral, modified-release products are reaching the point of patent expiration, and it is expected that several new 'generic' versions will be developed. As mesalazine acts topically, the drug needs to be available at the site of inflammation to be effective. For this reason, the currently available products have been developed with individual formulations so that physicians have a choice when matching the different release profiles to the site and extent of disease. As such, the current guidelines state that oral, delayed-release mesalazine formulations are not interchangeable and should be prescribed by their proprietary (brand) name. The standard regulatory assessment process for generic or 'copy' products, using systemic bioequivalence data, does not appear to be sufficient when evaluating topically acting, oral, modified-release products. We therefore recommend that the regulatory bodies should require that new, oral mesalazine products should be assessed by a combination of dissolution, bioequivalence and (a minimum of one) adequately powered, comparative trial to determine therapeutic equivalence. Of most importance here is that the assessment of new modified-release products is sufficiently rigorous to allow patients and physicians to be confident in their use.

Administration, Oral↗
PubMed1978

Differential expression of poly(A)-adjacent sequences of mammary tumor virus RNA in murine mammary cells.

Two DNA probes representative of either the entire mouse mammary tumor virus (MMTV) genome or the poly(A)-adjacent sequences at the 3' end of MMTV RNA were synthesized with calf thymus DNA or oligo(dT) primers, respectively. These probes were used to study the expression of endogenous MMTV sequences in several BALB/c mammary tumor cell lines, in normal lactating BALB/c tissue, and in a cloned C3H tumor cell line. Both probes were characterized with respect to their rates of hybridization with template RNA, their size as determined by alkaline sucrose gradient centrifugation, and the thermal stability of the cDNA.MMTV RNA hybrids. In addition, the ability of the calf thymus oligodeoxy-nucleotide- or oligo(dT)-primed probes to protect (125)I-labeled MMTV RNA or (125)I-labeled poly(A)-adjacent MMTV RNA sequences from S1 nuclease digestion was determined. Hybridization analysis with these two probes indicated that (i) there were approximately 20-fold more oligo(dT)-primed sequences in BALB/c lactating tissue than there were sequences representing the entire genome; (ii) in BALB/c tumor cells, the oligo(dT):random oligonucleotide-primed cDNA sequence ratio was reduced to 4:1; and (iii) in virus-producer C3H tumor cells, there was only a 2-fold excess of oligo(dT)-primed sequences over that observed with a representative cDNA. These results are consistent with the presence of subgenomic viral mRNA species, integration of partial proviral copies, or altered mRNA processing.

Animals↗
PubMed1990

Stable transformation of plastids in higher plants.

Stable genetic transformation of the plastid genome is reported in a higher plant, Nicotiana tabacum. Plastid transformation was obtained after bombardment of leaves with tungsten particles coated with pZS148 plasmid DNA. Plasmid pZS148 (9.6 kilobases) contains a 3.7-kilobase plastid DNA fragment encoding the 16S rRNA. In the 16S rRNA-encoding DNA (rDNA) a spectinomycin resistance mutation is flanked on the 5' side by a streptomycin resistance mutation and on the 3' side by a Pst I site generated by ligating an oligonucleotide in the intergenic region. Transgenic lines were selected by spectinomycin resistance and distinguished from spontaneous mutants by the flanking, cotransformed streptomycin resistance and Pst I markers. Regenerated plants are homoplasmic for the spectinomycin resistance and the Pst I markers and heteroplasmic for the unselected streptomycin resistance trait. Transgenic plastid traits are transmitted to the seed progeny. The transgenic plastid genomes are products of a multistep process, involving DNA recombination, copy correction, and sorting out of plastid DNA copies.

Journal Article↗
PubMed1995

Simple tandem DNA repeats and human genetic disease.

The human genome contains many repeated DNA sequences that vary in complexity of repeating unit from a single nucleotide to a whole gene. The repeat sequences can be widely dispersed or in simple tandem arrays. Arrays of up to 5 or 6 nt are known as simple tandem repeats, and these are widely dispersed and highly polymorphic. Members of one group of the simple tandem repeats, the trinucleotide repeats, can undergo an increase in copy number by a process of dynamic mutation. Dynamic mutations of the CCG trinucleotide give rise to one group of fragile sites on human chromosomes, the rare folate-sensitive group. One member of this group, the fragile X (FRAXA) is responsible for the most common familial form of mental retardation. Another member of the group FRAXE is responsible for a rarer mild form of mental retardation. Similar mutations of AGC repeats give rise to a number of neurological disorders. The expanded repeats are unstable between generations and somatically. The intergenerational instability gives rise to unusual patterns of inheritance--particularly anticipation, the increasing severity and/or earlier age of onset of the disorder in successive generations. Dynamic mutations have been found only in the human species, and possible reasons for this are considered. The mechanism of dynamic mutation is discussed, and a number of observations of simple tandem repeat mutation that could assist in understanding this phenomenon are commented on.

Chromosome Mapping↗
PubMed1997

Fusion genes resulting from alternative chromosomal translocations are overexpressed by gene-specific mechanisms in alveolar rhabdomyosarcoma.

Chromosomal translocations identified in hematopoietic and solid tumors result in deregulated expression of protooncogenes or creation of chimeric proteins with tumorigenic potential. In the pediatric solid tumor alveolar rhabdomyosarcoma, a consistent t(2;13)(q35;q14) or variant t(1;13)(p36;q14) translocation generates PAX3-FKHR or PAX7-FKHR fusion proteins, respectively. In this report, we demonstrate that in addition to functional alterations these translocations are associated with fusion product overexpression. Furthermore, PAX3-FKHR and PAX7-FKHR overexpression occurs by distinct mechanisms. Transcription of PAX3-FKHR is increased relative to wild-type PAX3 by a copy number-independent process. In contrast, PAX7-FKHR overexpression results from fusion gene amplification. Thus, gene-specific mechanisms were selected to overexpress PAX3-FKHR and PAX7-FKHR in alveolar rhabdomyosarcoma, presumably due to differences in regulation between the wild-type loci. We postulate that these overexpression mechanisms ensure a critical level of gene product for the oncogenic effects of these fusions.

Chromosomes, Human, Pair 1↗
PubMed1985

Association of a truncated cytochrome c processed pseudogene with a similarly truncated member from a long interspersed repeat family of rat.

The cytochrome c multigene family of rat contains approximately 30 processed pseudogenes that represent genomic DNA copies of three alternate mRNAs. Here, the DNA sequence of an unusual processed pseudogene reveals that it has a complete 3' noncoding region including a short poly A tail but unlike the others is abruptly truncated at its 5' end, 19 amino acid codons from the translation terminator. At this position the pseudogene is fused through 17 consecutive adenylic acid residues to a 1.3 kb repetitive sequence. This repetitive element is flanked by direct repeats and represents a truncated member from a major long interspersed repeat family. The rat element is a composite of sequences observed in long interspersed repeats from both rodents and primates. Comparison to the equivalent mouse sequences shows that the 5' half of the repeat distal to the pseudogene has an open reading frame and is highly conserved whereas the half adjacent to the pseudogene is evolutionarily unstable. The proportion of cytochrome c pseudogene recombinant clones containing this repetitive DNA is 3 fold greater than observed in random isolates and may reflect a general tendency of processed pseudogenes to associate with other repetitive sequences in the genome.

Animals↗
PubMed2002

Detection and quantification of mitochondrial DNA deletions in individual cells by real-time PCR.

Defects of mitochondrial DNA (mtDNA) are an important cause of disease and play a role in the ageing process. There are multiple copies of the mitochondrial genome in a single cell. In many patients with acquired or inherited mtDNA mutations, there exists a mixture of mutated and wild type genomes (termed heteroplasmy) within individual cells. As a biochemical and clinical defect is only observed when there are high levels of mutated mtDNA, a crucial investigation is to determine the level of heteroplasmic mutations within tissues and individual cells. We have developed an assay to determine the relative amount of deleted mtDNA using real-time fluorescence PCR. This assay detects the vast majority of deleted molecules, thus eliminating the need to develop specific probes. We have demonstrated an excellent correlation with other techniques (Southern blotting and three- primer competitive PCR), and have shown this technique to be sensitive to quantify the level of deleted mtDNA molecules in individual cells. Finally, we have used this assay to investigate patients with mitochondrial disease and shown in individual skeletal muscle fibres that there exist different patterns of abnormalities between patients with single or multiple mtDNA deletions. We believe that this technique has significant advantages over other methods to quantify deleted mtDNA and, employed alongside our method to sequence the mitochondrial genome from single cells, will further our understanding of the role of mtDNA mutations in human disease and ageing.

DNA, Mitochondrial↗
PubMed2001

World Wide Web scaling exponent from Simon's 1955 model.

The statistical properties of the World Wide Web have attracted considerable attention recently since self-similar regimes were first observed in the scaling of its link structure. One characteristic quantity is the number of (in-)links k that point to a particular web page. Its probability distribution P(k) shows a pronounced power-law scaling P(k) approximately k(-gamma) that is not readily explained by standard random graph theory. Here, we recall a simple and elegant model for scaling phenomena in general copy- and growth-processes as proposed by Simon in 1955. When combined with an experimental measurement of network growth in the World Wide Web, this classical model is able to model the in-link dynamics and predicts the scaling exponent gamma=2.1 in accordance with observation.

Journal Article↗
PubMed1996

Subtle pulmonary disease: detection with computed radiography versus conventional chest radiography.

PURPOSE: To determine the diagnostic efficacy of hard- and soft-copy computed radiographic (CR) images versus conventional screen-film images of the chest in the detection of subtle pulmonary abnormalities. MATERIALS AND METHODS: Twenty observes compared 87 hard-copy and soft-copy CR images with hard-copy screen-film images. Of 87 test images, 45 (including two identical sets of 12 images to test intra-observer variability) were abnormal and 42 (including two identical sets of 12 images) were normal. Of the 45 abnormal images, 15 (including two sets of four identical images) showed subtle abnormalities, 15 (including two sets of four identical images) showed mild abnormalities, and 15 (including two sets of four identical images) showed obvious abnormalities. Soft-copy viewing provided three differently processed images of every radiograph. RESULTS: No statistically significant differences in receiver operating characteristic analyses were found among hard-copy screen-film images, hard-copy CR images, and soft-copy CR images, even in the group with subtle interstitial abnormalities. CONCLUSION: Hard-copy and soft-copy chest CR images are acceptable and available in place of screen-film images for primary interpretation of subtle interstitial lung diseases.

Adult↗
PubMed1998

Radiosensitive human tumour cell lines show misrepair of DNA termini.

Physical measures of the rejoining of radiation-induced breaks in DNA strands are limited in terms of sensitivity and the fact that they do not assess the fidelity with which the rejoining occurs. In this report, transfection of cleaved plasmid has been used as a probe for repair in three radiosensitive tumour cell lines and shown them to have low repair fidelity compared with resistant cells. Errors in the repair of linear plasmid were found by Southern analysis, in keeping with the measured repair fidelity. Radiosensitive tumour cells showed few errors in the uptake and integration of circular plasmid, in contrast to ataxia-telangiectasia (A-T) cells. In the neuroblastoma HX142, the repair of blunt-ended linear plasmid was associated with deletions of > 1 kb; staggered-ended linear plasmid was repaired with small insertions and circular plasmid integration was intact in > 60% of the copies. The neuroblastoma SKN.SH, processed staggered-ended plasmid by insertions of a variety of sizes, but processed circular plasmid largely error-free. In contrast, A-T cells (AT5BIVA) had the same spectrum of errors irrespective of the form of plasmid transfected. Cell fusion between HX142 and AT5BIVA showed complementation to a resistant phenotype, suggesting that misrepair in the tumour cell did not result from somatic mutation in the ATM gene. In conclusion, radiosensitive tumours show evidence of misrepair of DNA termini, with a mechanism which is functionally and genetically distinct from that in A-T cells.

Ataxia Telangiectasia↗
PubMed2004

Functional difference between Sinorhizobium meliloti NifA and Enterobacter cloacae NifA.

The nifA gene is an important regulatory gene and its product, NifA protein, regulates the expression of many nif genes involved in the nitrogen fixation process. We introduced multiple copies of the constitutively expressed Sinorhizobium meliloti (Sm) or Enterobacter cloacae (Ec) nifA gene into both the nifA mutant strain SmY and the wild-type strain Sm1021. Root nodules produced by SmY containing a constitutively expressed Sm nifA gene were capable of fixing nitrogen, while nodules produced by SmY containing the Ec nifA gene remained unable to fix nitrogen, as is the case for SmY itself. However, transfer of an additional Sm nifA gene into Sm1021 improved the nitrogen-fixing efficiency of root nodules to a greater extent than that observed upon transfer of the Ec nifA gene into Sm1021. Comparative analysis of amino acid sequences between Sm NifA and Ec NifA showed that the N-terminal domain was the least similar, but this domain is indispensable for complementation of the Fix- phenotype of SmY by Sm NifA. We conclude that more than one domain is involved in determining functional differences between Sm NifA and Ec NifA.

Amino Acid Sequence↗
PubMed2000

Rhino horns and paper cups: deceptive similarities between natural and human designs.

One cannot assume that resemblances between the mechanical devices of human technology and those produced by the evolutionary process reflect either specific copying of nature by people or some particular point of functional superiority. A third alternative is that the two mechanical contexts derive quite different advantages from a given arrangement. While this latter might appear unlikely, one can argue that it underlies such things as the use of conical shapes, helical tensile structures, spheres and cylinders, beams and columns of relatively low torsional stiffness, and geodesic shells.

Animals↗