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PubMed1994

The use of a hybrid genetic system to study the functional relationship between prokaryotic and plant multi-enzyme fatty acid synthetase complexes.

Fatty acid synthesis in bacteria and plants is catalysed by a multi-enzyme fatty acid synthetase complex (FAS II) which consists of separate monofunctional polypeptides. Here we present a comparative molecular genetic and biochemical study of the enoyl-ACP reductase FAS components of plant and bacterial origin. The putative bacterial enoyl-ACP reductase gene (envM) was identified on the basis of amino acid sequence similarities with the recently cloned plant enoyl-ACP reductase. Subsequently, it was unambiguously demonstrated by overexpression studies that the envM gene encodes the bacterial enoyl-ACP reductase. An anti-bacterial agent called diazaborine was shown to be a specific inhibitor of the bacterial enoyl-ACP reductase, whereas the plant enzyme was insensitive to this synthetic antibiotic. The close functional relationship between the plant and bacterial enoyl-ACP reductases was inferred from genetic complementation of an envM mutant of Escherichia coli. Ultimately, envM gene-replacement studies, facilitated by the use of diazaborine, demonstrated for the first time that a single component of the plant FAS system can functionally replace its counterpart within the bacterial multienzyme complex. Finally, lipid analysis of recombinant E. coli strains with the hybrid FAS system unexpectedly revealed that enoyl-ACP reductase catalyses a rate-limiting step in the elongation of unsaturated fatty acids.

Amino Acid Sequence↗
PubMedDate not supplied

Discovering gene networks with a neural-genetic hybrid.

Recent advances in biology (namely, DNA arrays) allow an unprecedented view of the biochemical mechanisms contained within a cell. However, this technology raises new challenges for computer scientists and biologists alike, as the data created by these arrays is often highly complex. One of the challenges is the elucidation of the regulatory connections and interactions between genes, proteins and other gene products. In this paper, a novel method is described for determining gene interactions in temporal gene expression data using genetic algorithms combined with a neural network component. Experiments conducted on real-world temporal gene expression data sets confirm that the approach is capable of finding gene networks that fit the data. A further repeated approach shows that those genes significantly involved in interaction with other genes can be highlighted and hypothetical gene networks and circuits proposed for further laboratory testing.

Algorithms↗
PubMed1976

Genetic hybridization of the leu-ilv region in bacilli.

Two auxotrophic strains of Bacillus subtilis 168 served as recipients for DNA extracted from various wild-type strains of B. subtilis and wild-type species of the genus Bacillus. Depending upon the DNA source, heterologous transformations of the linked try-his-tyr loci were either as efficient as those observed with donor DNA obtained from the wild type B. subtilis 168 strain or were undetectable. The order and relative distances of the three gene loci were the same for all active DNA preparations. Similar results were obtained in heterologous transformations of the linked leu-ilv loci, except that DNA preparations from the Bacillus globigii and B. subtilis var. niger species exhibited a reduced but detectable frequency of transformation. With the latter preparations a marked polarity of integration favouring the leu+ gene was observed, an effect not seen with homologous DNA. Six independent hybrid lines were obtained from transformation of B. subtilis leu- ilv- with DNA from B. subtilis var. niger leu+ ilv+. DNA extracted from these lines fell into two classes on the basis of activity in transforming the parental recipient strain: (i) indistinguishable from homologous DNA, and (ii) intermediate between homologous DNA and DNA from the original donor strain. With either class, polarity of integration was no longer observed in the leu-ilv region. The intermediate type of hybrid demonstrates that at least some of the inefficiency of heterospecific transformation must be due to heterology in nucleotide sequence between the different species at the leu-ilv loci.

Bacillus↗
PubMed2000

Subtractive hybridization--genetic takeaways and the search for meaning.

Gene expression profiling relies on mRNA extraction from defined cell systems, which in the case of pathological processes necessarily results in the use of small quantities of tissues, sometimes as little as a few cells. This obviates the use of many systems of gene expression profiling and is best carried out using cDNA amplified by poly(A) reverse transcription polymerase chain reaction, which is capable of generating material representative of all the expressed genes in samples as small as one cell. Analysis of this material using subtractive hybridization compares the genes expressed at different stages of a biological/pathological process allowing identification of the all the genes upregulated during the process. The identification of the genes present is not dependent on their prior description or on the choice of genes used in a screen and as such the method is ideal for identifying novel genes or unsuspected genes. We have used the method to identify genes involved in normal osteoblastic differentiation and in Paget's disease of bone and it has been widely used to study normal differentiation and pathological processes in a number of systems. The method, its applications and its relationship with the other methods of gene expression profiling are reviewed.

Cell Differentiation↗
PubMed2004

Development of hybrid genetic algorithms for product line designs.

In this paper, we investigate the efficacy of artificial intelligence (AI) based meta-heuristic techniques namely genetic algorithms (GAs), for the product line design problem. This work extends previously developed methods for the single product design problem. We conduct a large scale simulation study to determine the effectiveness of such an AI based technique for providing good solutions and bench mark the performance of this against the current dominant approach of beam search (BS). We investigate the potential advantages of pursuing the avenue of developing hybrid models and then implement and study such hybrid models using two very distinct approaches: namely, seeding the initial GA population with the BS solution, and employing the BS solution as part of the GA operator's process. We go on to examine the impact of two alternate string representation formats on the quality of the solutions obtained by the above proposed techniques. We also explicitly investigate a critical managerial factor of attribute importance in terms of its impact on the solutions obtained by the alternate modeling procedures. The alternate techniques are then evaluated, using statistical analysis of variance, on a fairy large number of data sets, as to the quality of the solutions obtained with respect to the state-of-the-art benchmark and in terms of their ability to provide multiple, unique product line options.

Journal Article↗
PubMedDate not supplied

A novel multipurpose Excel tool for equilibrium speciation based on Newton-Raphson method and on a hybrid genetic algorithm.

A new algorithm for simulation of chemical equilibria is developed, based on classical Newton-Raphson method applied to mass balance. This tool, named EST (Equilibrium Speciation Tool), is improved by using a robust Genetic Algorithm. In addition, EST works by using Excel spreadsheets and therefore offers the innovation of a great simplicity and versatility. In fact, it allows the users to simulate, or to obtain from experimental data, desired chemical-physical parameters as well as to interact with other available or freely created Excel tools. The reliability of this utility is here proved by comparison with some published data by other authors, concerning both complicated homogeneous and heterogeneous equilibria. In addiction its flexibility is tested computing thermodynamic parameters by using experimental calorimetric data referred to the complex formation of cobalt(II) with a macrocyclic ligand. A brief review and comparison of the relative robustness and quickness of main numerical methods are also reported.

Algorithms↗
PubMed2000

Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids.

Nucleolar dominance is a phenomenon in hybrids or allopolyploids in which nucleoli form on chromosomes inherited from only one of the two parents. The molecular basis for nucleolar dominance is the transcription by RNA polymerase I of only one parental set of ribosomal RNA genes (rRNA genes). These rRNA genes are clustered by the hundreds, or thousands, of copies, often spanning tens of millions of basepairs of chromosomal DNA at loci known as nucleolus organizer regions (NORs). Enforcement of nucleolar dominance appears to be accomplished by selectively silencing one set of rRNA genes via chemical modifications of chromatin. However, the mechanisms responsible for initially discriminating among the parental sets of rRNA genes and establishing nucleolar dominance remain unclear. Possibilities include mechanisms that act on each rRNA gene or mechanisms that affect whole NORs or even larger chromosomal domains. This review provides a historical perspective of nucleolar dominance research, explores the most popular hypotheses and their shortcomings, and offers some speculations concerning alternative hypotheses to be considered.

Chimera↗
PubMed1994

Polioviruses containing picornavirus type 1 and/or type 2 internal ribosomal entry site elements: genetic hybrids and the expression of a foreign gene.

A picornavirus hybrid genome was constructed in which the internal ribosomal entry site (IRES) of encephalomyocarditis virus was inserted between the 5' non-translated region and the open reading frame of poliovirus (PV), type 1 (Mahoney). Upon transfection into HeLa cells, the hybrid RNA replicated and yielded a derivative of PV (W1-PNENPO). The PV IRES could be removed from pPNENPO, which resulted in a hybrid picornavirus (W1-P108ENPO) in which the translation of the PV open reading frame normally promoted by the type 1 IRES of PV was promoted by the type 2 IRES of encephalomyocarditis virus. This result indicates that these elements are not likely to contain cis-acting elements necessary for PV replication or encapsidation. A foreign gene (bacterial chloramphenicol acetyltransferase, CAT) was inserted into pPNENPO cDNA between the PV and encephalomyocarditis virus IRES elements. The dicistronic RNA replicated in HeLa cells and yielded a derivative of PV (W1-DICAT) with a genome 17% longer than that of wild-type PV. CAT assays and immunoblot analyses showed that the viral RNA efficiently expressed the foreign gene in cell culture. The CAT activity diminished somewhat with each passage of the dicistronic virus, an observation which suggested that the inserted gene had a deleterious effect on viral replication. However, even after five virus passages, a significant quantity of the foreign gene was still expressed. Insertion of the open reading frame of luciferase (67 kDa) resulted in an RNA species that replicated and expressed luciferase for up to 20 hr after transfection. However, this elongated RNA was not encapsidated.

Base Sequence↗
PubMedDate not supplied

A genetic hybrid of the Campylobacter jejuni flaA gene with LT-B of Escherichia coli and assessment of the efficacy of the hybrid protein as an oral chicken vaccine.

The objectives of this study were to produce Campylobacter jejuni flagellin fused to the B-subunit of the labile toxin (LT-B) of Escherichia coli and to assess the efficacy of the hybrid protein as a chicken vaccine. Part of the flaA gene (780 base pairs) was cloned in plasmid pBEB downstream and in frame with the LT-B to allow expression of a hybrid protein. Transformed E. coli chi 6097 expressed the hybrid protein (43 kdaltons) in inclusion bodies at mid log phase. The inclusion bodies were isolated, and the identity of the protein was verified by western blot. This hybrid protein was administered as a vaccine to chickens either orally (0, 250, 500, or 1000 micrograms total protein) or intramuscularly (250 or 1000 micrograms). Alimentary secretions were collected, and specific antibodies were assayed by western blot analyses. Seventy-two percent of the birds vaccinated orally with 1000 micrograms protein showed detectable antibodies against C. jejuni flagellin in the excreta. None of the control birds produced detectable antibody to this antigen. For trials to demonstrate clearance of Campylobacter, groups of chickens were vaccinated with the hybrid protein at 2 and 4 wk of age and challenged at 3 wk with an excess of C.jejuni. The number of birds that remained colonized at 5 wk of age was significantly lower among the vaccinated birds than among controls.

Administration, Oral↗
PubMed1999

Introgression through rare hybridization: A genetic study of a hybrid zone between red and sika deer (genus Cervus) in Argyll, Scotland.

In this article we describe the structure of a hybrid zone in Argyll, Scotland, between native red deer (Cervus elaphus) and introduced Japanese sika deer (Cervus nippon), on the basis of a genetic analysis using 11 microsatellite markers and mitochondrial DNA. In contrast to the findings of a previous study of the same population, we conclude that the deer fall into two distinct genetic classes, corresponding to either a sika-like or red-like phenotype. Introgression is rare at any one locus, but where the taxa overlap up to 40% of deer carry apparently introgressed alleles. While most putative hybrids are heterozygous at only one locus, there are rare multiple heterozygotes, reflecting significant linkage disequilibrium within both sika- and red-like populations. The rate of backcrossing into the sika population is estimated as H = 0.002 per generation and into red, H = 0.001 per generation. On the basis of historical evidence that red deer entered Kintyre only recently, a diffusion model evaluated by maximum likelihood shows that sika have increased at approximately 9.2% yr-1 from low frequency and disperse at a rate of approximately 3.7 km yr-1. Introgression into the red-like population is greater in the south, while introgression into sika varies little along the transect. For both sika- and red-like populations, the degree of introgression is 30-40% of that predicted from the rates of current hybridization inferred from linkage disequilibria; however, in neither case is this statistically significant evidence for selection against introgression.

Alleles↗
PubMed1997

The developmental genetics of hybrid inviability: a mitotic defect in Drosophila hybrids.

We report studies of the developmental basis of hybrid inviability in the Drosophila melanogaster complex. The pathology of these hybrids closely resembles that of mitotic mutants in D. melanogaster. We use mosaic and cytological analyses to show that hybrid male inviability is associated with, and probably caused by, a defect in mitotic cell division. In the mosaic study, we find that male clones produced in otherwise female hybrids are not cell lethal but are very small, probably reflecting defects in mitotic proliferation. Cytological inspection of larval neuroblasts reveals a profound mitotic defect in hybrids: chromosomes show a near-complete failure to condense even after 2 hr of incubation in colchicine. Both the defect in clonal proliferation and in chromatin condensation are rescued by mutations known to rescue normally inviable hybrid males. We present a simple model in which hybrid inviability is partly or entirely caused by a mitotic defect; this defect is, in turn, caused by an interaction between the Hybrid male rescue (Hmr) locus of D. melanogaster and autosomal gene(s) from D. melanogaster's sister species.

Animals↗
PubMed1998

Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid.

Genetic models predict that genomic rearrangement in hybrids can facilitate reproductive isolation and the formation of new species by preventing gene flow between the parent species and hybrid (sunflowers are an example). The mechanism underlying hybridization-induced chromosome remodelling is as yet unknown, although mobile element activity has been shown to be involved in DNA rearrangement in some dysgenic Drosophila hybrids. It has been proposed that DNA methylation evolved as a means of repressing the movement of mobile elements (the host defence model). If such a protective mechanism were to fail, mobile elements could be activated, and could cause major and rapid genome alterations. Here we demonstrate the occurrence of genome-wide undermethylation, retroviral element amplification and chromosome remodelling in an interspecific mammalian hybrid (Macropus eugenii x Wallabia bicolor). Atypically extended centromeres of Macropus eugenii derived autosomes in the hybrid were composed primarily of an unmethylated, amplified retroviral element not detectable in either parent species. These results, taken with the observation of deficient methylation and de novo chromosome change in other mammalian hybrids, indicate that the failure of DNA methylation and subsequent mobile-element activity in hybrids could facilitate rapid karyotypic evolution.

Animals↗
PubMed2000

Surrogate genetics: the use of bacterial hybrids as a genetic tool.

Experimental dissection of bacterial genomes requires a well-developed set of genetic tools, but many bacteria lack the essential tools required for genetic analysis. Recombination of a region of chromosomal DNA from poorly characterized donor bacteria with the chromosome of a suitable surrogate host creates a genetically malleable hybrid, providing a short-cut for the detailed genetic analysis of the substituted genes. However, recombination between closely related but nonidentical DNA sequences ("homeologous recombination") is strongly inhibited, posing a powerful barrier to gene exchange between bacteria and a major impediment to the construction of genetic hybrids. By taking advantage of mutS and recD mutant recipients, it is possible to effectively overcome the recombination barrier, allowing construction of genetic hybrids in a related surrogate host. Once stably recombined into the recipient chromosome, the donor DNA can be studied with all the genetic tools available in the surrogate host. In addition to facilitating standard genetic analysis, use of a surrogate host can provide novel approaches to study the physiological roles of unique genes from poorly characterized bacteria.

Bacteria↗
PubMed2001

A genome-wide survey of reproductive barriers in an intraspecific hybrid.

Genetic study of the reproductive barriers between related species plays an essential role in understanding the process of speciation. We developed a new method for mapping all possible factors causing deviations from expected Mendelian segregation ratios in F(2) progeny, which substantially contribute to reproductive isolation. A multiresponse nonlinear regression analysis of the allele frequencies of the markers covering an entire genome in the F(2) population was performed to estimate the map position and intensity of the reproductive barriers on each chromosome. In F(2) plants from a cross between a Japonica variety of rice, Nipponbare, and an Indica variety, Kasalath, the deviations of allele frequencies were well explained by 33 reproductive barriers. Of these, 15 reproductive barriers affected the allele transmission rate through the gametophyte and in 9 of these 15 cases, an Indica allele was transmitted at a higher frequency than a Japonica allele. The other 18 reproductive barriers altered the viability of the zygote via its genotype. Two zygotic reproductive barriers showed overdominance and 5 showed underdominance. The most pronounced reproductive barrier, mapped at 62.3 +/- 0.4 cM on chromosome 3, transmitted the Indica allele by 94% through the male gametophyte. The accuracy of the barrier position in the regression analysis was confirmed by progeny analysis. The regression analysis proved to be a powerful tool for detecting and characterizing every reproductive barrier, irrespective of whether it acted on the male or female gametophyte or the zygote.

Chromosome Mapping↗
PubMed1995

Genetic changes in primary and recurrent prostate cancer by comparative genomic hybridization.

Genetic changes leading to the development of prostate cancer and factors that underlie the clinical progression of the disease are poorly characterized. Here, we used comparative genomic hybridization (CGH) to screen for DNA sequence copy number changes along all chromosomes in 31 primary and 9 recurrent uncultured prostate carcinomas. The aim of the study was to identify those chromosome regions that contain genes important for the development of prostate cancer and to identify genetic markers of tumor progression. CGH analysis indicated that 74% of primary prostate carcinoma showed DNA sequence copy number changes. Losses were 5 times more common than gains and most often involved 8p (32%), 13q (32%), 6q (22%), 16q (19%), 18q (19%), and 9p (16%). Allelic loss studies with 5 polymorphic microsatellite markers for 4 different chromosomes were done from 13 samples and showed a 76% concordance with CGH results. In local recurrences that developed during endocrine therapy, there were significantly more gains (P < 0.001) and losses (P < 0.05) of DNA sequences than in primary tumors, with gains of 8q (found in 89% of recurrences versus 6% of primary tumors), X (56% versus 0%), and 7 (56% versus 10%), as well as loss of 8p (78% versus 32%), being particularly often involved. In conclusion, our CGH results indicate that losses of several chromosomal regions are common genetic changes in primary tumors, suggesting that deletional inactivation of putative tumor suppressor genes in these chromosomal sites is likely to underlie development of prostate cancer. Furthermore, the pattern of genetic changes seen in recurrent tumors with the frequent gains of 7, 8q, and X suggests that the progression of prostate cancer and development of hormone-independent growth may have a distinct genetic basis. These chromosome aberrations may have diagnostic utility as markers of prostate cancer progression.

Chromosome Deletion↗
PubMed1999

Quantitative genetics of intraspecies hybrids.

Quantitative genetics generally is based on the properties of the randomly fertilized (RF) population or inbred derivatives of it. Simple hybrids and hybrid swarms do not conform to this model; and only some properties of hybrid means appear to have been available. In this paper, several genetical properties are derived, including genotype and allele frequencies, genotypic variance, broad-sense heritability, and outbreeding coefficient. The earlier mean is confirmed, and hybrid vigour is examined critically. These results make it possible to evaluate quantitatively both natural selection and forward selection (in plant breeding) from hybrids. An important finding is that hybrids with maximum hybrid vigour do not maximize genetic advance from forward selection, i.e. evolution is unlikely to enhance hybrid vigour. Another finding is that the concepts of additive genetic variance and narrow-sense heritability are inappropriate for hybrids, owing to the genetic disequilibrium inherent from their origin, and to the ephemeral nature of their population structure.

Alleles↗