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PubMedDate not supplied

Bayesian predictiveness, exchangeability and sufficientness in bacterial taxonomy.

We present a theory of classification and predictive identification of bacteria. Bacterial strains are characterized by a binary vector and the taxonomy is specified by attaching a label to each vector. The theory is developed from only two basic assumptions, viz. that the sequence of pairs of feature vectors and the attached labels is judged (infinitely) exchangeable and predictively sufficient. We derive expressions for the training error and the probability of identification error and show that latter is an affine function of the former. We prove the law of large numbers for identification matrices, which contain the fundamental information of bacterial data. We prove the Bayesian risk consistency of the predictive identification rule given by the theory and show that the training error is a consistent estimate of the generalization error.

Bacteria↗

PubMed2002

Alkaloid production in Duboisia hybrid hairy root cultures overexpressing the pmt gene.

Putrescine:SAM N-methyltransferase (PMT) catalyses the N-methylation of the diamine putrescine to form N-methylputrescine, the first specific precursor of both tropane and pyridine-type alkaloids, which are present together in the roots of Duboisia plants. The pmt gene of Nicotiana tabacum was placed under the regulation of the CaMV 35S promoter and introduced into the genome of a scopolamine-rich Duboisia hybrid by a binary vector system using the disarmed Agrobacterium tumefaciens strain C58C1 carrying the rooting plasmid pRiA4. The presence of the foreign gene in kanamycin-resistant hairy roots and its overexpression were confirmed by polymerase chain reaction and Northern blot analysis respectively. The N-methylputrescine levels of the resulting engineered hairy roots increased (2-4-fold) compared to wild type roots, but there was no significant increase in either tropane or pyridine-type alkaloids.

Agrobacterium tumefaciens↗

PubMed2001

Green fluorescent protein as a secretory reporter and a tool for process optimization in transgenic plant cell cultures.

Green fluorescent protein (GFP) is an attractive reporter for bioprocess monitoring. Although expression of GFP in plants has been widely reported, research on the use of GFP in plant cell cultures for bioprocess applications has been limited. In this study, the suitability of GFP as a secretory reporter and a useful tool in plant cell bioprocess optimization was demonstrated. GFP was produced and secreted from suspension cells derived from tobacco that was transformed with a binary vector containing mgfp5-ER cDNA, a modified GFP for efficient sorting to the endoplasmic reticulum, under control of the CaMV 35S promoter. For cell line gfp-13, extracellular and intracellular GFP accumulated to 15.4 and 29.4 mg x 1(-1), respectively. Extracellular GFP accounted for 30.9% of the total extracellular protein. The molecular mass of extracellular GFP was nearly identical to that of a recombinant GFP standard, indicating cleavage of the signal sequence. Neomycin phosphotransferase II, a cytosolic selection marker, was found almost exclusively in cellular extracts with less than 2% in the extracellular medium. These results suggest that extracellular GFP is most likely the result of secretion rather than nonspecific leakage from cells. Furthermore, medium fluorescence intensity correlated nicely with extracellular GFP concentration supporting the use of GFP as a quantitative secretory reporter. During the batch cultivation, culture GFP fluorescence also followed closely with cell growth. A medium feeding strategy was then developed based on culture GFP fluorescence that resulted in improved biomass as well as GFP production in a fed-batch culture.

Biotechnology↗

PubMed2000

Analysis of transgenic grapevine (Vitis rupestris) and Nicotiana benthamiana plants expressing an Arabis mosaic virus coat protein gene.

A disarmed LBA4404 strain of Agrobacterium tumefaciens harboring a binary vector which contained chimeric genes encoding the neomycin phosphotransferase (npt II) and the coat protein (CP) of Arabis mosaic nepovirus (ArMV) was used in co-cultivation experiments with leaf discs of Nicotiana benthamiana and somatic embryos of the grapevine rootstock cultivar Vitis rupestris. Transgenic N. benthamiana expressing the ArMV CP gene were regenerated and six independent lines were characterized. Enzyme-linked immunosorbent assay (ELISA) performed on leaf tissue demonstrated the accumulation of the ArMV CP in five of the six lines analyzed. Immunosorbent electron microscopy (ISEM) studies revealed the presence of virion-like isometric particles (VLPs) reacting to a rabbit antiserum specific to ArMV virions. ArMV-CP expressing transgenic N. benthamiana lines showed protection against ArMV expressed as a delay in infection and a reduction of the percentage of infected plants. Four independent transgenic lines of V. rupestris transformed with the ArMV CP gene were regenerated and characterized. In contrast to N. benthamiana, transgenic V. rupestris did not accumulate the ArMV CP at levels detectable by ELISA and no VLPs could be observed by ISEM. Northern blot analysis showed that the ArMV CP mRNA was expressed at lower level in V. rupestris compared with N. benthamiana. The reason for this difference in transgene expression and/or mRNA stability between grapevine and N. benthamiana is unclear, but the genetic state of the transgene(s) (homozygous in N. benthamiana versus hemizygous in V. rupestris) may have an effect on gene expression.

Journal Article↗

PubMed2000

An efficient method for the production of transgenic plants of peanut (Arachis hypogaea L.) through Agrobacterium tumefaciens-mediated genetic transformation.

Cotyledon explants from mature peanut seeds (Arachis hypogaea L.) were optimized to obtain adventitious shoot buds with high frequencies (>90%). Efficient transformation of these cotyledons by using Agrobacterium tumefaciens strain C58 carrying neomycin phosphotransferase II (nptII) and ß-glucuronidase (GUS; uidA), or coat protein gene of the Indian peanut clump virus (IPCVcp) and nptII on binary vectors (pBI121; pROKII:IPCVcp) led to the production of a large percentage (55%) of transgenic plants. Transformed individuals were obtained through selection on medium containing 125 mg l(-1) kanamycin. A large number of independently transformed plants (over 75) were successfully transplanted to the glasshouse. Integration of the transgenes and stable genetic transformants in the progeny were assessed by PCR amplification of 700-bp fragment of nptII and 585-bp of IPCVcp genes, and Southern blot hybridizations in the T1 generation of transgenic plants. Analysis of 35 transgenic plants of T1 generation from the progeny of a single transformation event suggested the segregation of a single copy insert in a 3:1 Mendelian ratio. On an average, 120-150 days were required between the initiation of explant transformation and transfer of rooted plants to the greenhouse. The cotyledon regeneration system proved to be an excellent vehicle for the production of a large number of independently transformed peanut plants. Shoot formation was rapid and prolific, and a large proportion of these shoots developed into fertile plants. The method reported here provides new opportunities for the crop improvement of peanut via genetic transformation.

Journal Article↗

PubMed2001

Effects of ipt gene expression on the physiological and chemical characteristics of Artemisia annua L.

An isopentenyl transferase gene (ipt) from T-DNA was transferred into Artemisia annua L. via Agrobacterium tumefaciens. The ipt gene was placed in a binary vector under the control of the CaMV 35S promoter. Leaf explants were infected with A. tumefaciens LBA4404 containing pBIipt to induce the buds. Nineteen shoot lines were selected, which were resistant to kanamycin. Polymerase chain reactions and Southern blotting confirmed that at least five shoot lines contained the foreign gene. The results of RT-PCR and Northern blotting analyses suggested that the foreign ipt gene of the transgenic shoot was expressed. Cytokinins, chlorophyll and artemisinin contents were found increased at different degree. Content of cytokinins (iPA and iP) was elevated 2- to 3-fold, chlorophyll increased 20-60% and artemisinin increased 30-70% compared with the control plants, respectively. A direct correlation was found between the contents of cytokinins, chlorophyll and artemisinin. This may be the first report on the relationship between endogenous cytokinin content and the production of secondary metabolites in plants.

Journal Article↗

PubMed2001

Mikimopine synthase (mis) gene on pRi1724.

By determination of the nucleotide sequence adjacent to the right border of T-DNA of the mikimopine-type Ri plasmid (pRi1724) in Agrobacterium rhizogenes, a new open reading frame (ORF) encoding 318 amino acids was found. A transcript of 1.35 kb derived from this ORF was observed in hairy roots of Ajuga reptans by northern blotting analysis. Including its own promoter and terminator, this ORF was isolated from the pRi1724 T-DNA and introduced into tobacco plants by the Agrobacterium-binary vector system. Since mikimopine, an opine and a stereoisomer of cucumopine, was accumulated in all organs of the transgenic tobacco plants, the new ORF was deduced to be the mikimopine synthase gene. For comparison, the nucleotide sequence of cucumopine synthase encoded on pRi2659 was also determined. No homology was found between mikimopine synthase and cucumopine synthase at the nucleotide, but partial homology was found at the amino acid level. Mikimopine synthase and cucumopine synthase produced by a protein expression system using E. coli catalyzed the synthesis of mikimopine and cucumopine from L-histidine and alpha-ketoglutaric acid, requiring NADH as a cofactor. These synthesized opines were identified by paper electrophoresis, TLC and HPLC analyses. The synthesized mikimopine or cucumopine could be degraded by A. rhizogenes strains harboring Ri plasmids encoding the respective catabolic enzyme.

Amino Acid Sequence↗

PubMed2001

Targeted expression of a synthetic codon optimized gene, encoding the spruce budworm antifreeze protein, leads to accumulation of antifreeze activity in the apoplasts of transgenic tobacco.

A synthetic gene based on the primary sequence of the mature spruce budworm antifreeze protein (sbwAFP) was constructed by primer overlap extension. The amino acid codons were chosen to mimic those of a highly expressed tobacco nuclear gene. A DNA sequence encoding the amino-terminal leader sequence from the tobacco pathogen related protein 1b (PR), which targets the protein to the apoplastic space, was fused in frame to the synthetic sbwAFP gene. This fusion was placed downstream of the cauliflower mosaic virus 35S promoter and upstream of the nopaline synthase terminator in a T-DNA binary vector. Transgenic tobacco lines transcribing PR-sbwAFP were selected by RT-PCR. The apoplastic protein fractions of sbwAFP expressing tobacco lines exhibited enhanced antifreeze activity as demonstrated by the ability to inhibit ice re-crystallization and increased thermal hysteresis.

Adaptation, Physiological↗

PubMed2000

M-31 mutant (virA::Tn5) of Agrobacterium tumefaciens is capable of transferring its T-DNA into the nucleus of host cell, but incapable of integrating it into the chromosome.

An avirulent mutant (M-31 strain) was produced by the transposon (Tn5) mutagenesis of Agrobacterium tumefaciens (A-208 strain). A binary vector, pIG121-Hm, containing a kanamycin resistance gene (nptII) and beta-glucuronidase (GUS) gene with an intron, was introduced into M-31 and A-208 strains. The resultant Agrobacteria were inoculated onto leaves of Kalanchoe daigremontiana and to tobacco BY-2 cells to assay GUS activity to monitor the T-DNA transfer into the nuclei of host cells. The results indicated that T-DNA was transferred into the nuclei of cells of both host plants inoculated with the M-31 mutant. The M-31 mutant strain had an insertion of Tn5 in the virA gene on its Ti plasmid. The introduction of the virA gene in the M-31 mutant complemented its avirulent phenotype. No kanamycin-resistant cells were observed when the M-31 mutant harboring the pIG121-Hm was inoculated to tobacco BY-2 cells. The M-31 mutant (virA::Tn5) seems to transfer T-DNA into the nucleus of the host cell, but is unable to integrate it to the chromosome.

Journal Article↗

PubMed2004

In planta transformation of kenaf plants (Hibiscus cannabinus var. aokawa No. 3) by Agrobacterium tumefaciens.

Kenaf was transformed by inoculation of Agrobacterium tumefaciens onto the meristems of young plants in pots. The transformation was demonstrated by three lines of evidence: a phenotypic inheritance from T(0) to T(1) plants, detection of the transgene in both T(0) and T(1) plants, and rescue of plasmids composed of T-DNA of the binary vector and flanking plant genomic DNA from T(1) plants.

Journal Article↗

PubMed2003

Agrobacterium and PEG-mediated transformation of the phytopathogen Venturia inaequalis.

We report the development of two new transformation systems, polyethylene glycol (PEG)-mediated transformation of protoplasts and Agrobacterium tumefaciens-mediated transformation of mycelium, for the filamentous ascomycete Venturia inaequalis. New binary vectors have been created for the latter. Although transformation was initially achieved using a PEG-mediated method, this was superseded by the A. tumefaciens-mediated approach. The advantages of the latter include: ease of the protocol, no requirement for protoplasts; higher transformation efficiency; and single-site integration. A comparison between the two transformation methods is presented.

Agrobacterium tumefaciens↗

PubMedDate not supplied

Direct Agrobacterium tumefaciens-mediated transformation of Hyoscyamus muticus hairy roots using green fluorescent protein.

Hyoscyamus muticus hairy root segments were infected with Agrobacterium tumefaciens ASE containing the binary vector pCGN1548 with a green fluorescent protein (GFP) reporter gene under the control of the CaMV 35S promoter. The roots were incubated on callus-inducing medium to generate transformed cells. Transformants were selected on medium containing 50 and 100 mg/L kanamycin and screened by visual inspection for GFP expression. Highly fluorescent cells were incubated on phytohormone-free medium for regeneration of the hairy root phenotype. This infection technique can be applied directly to existing hairy root cultures which have been previously characterized and selected for desirable physiological traits. These studies also indicate that GFP is not toxic to H. muticus plant tissue and that H. muticus hairy roots have minimal autofluorescence which allows for clear observation of GFP.

Cell Culture Techniques↗

PubMed1979

Using bibliometric analyses of patent literature for predicting the clinical fates of developing drugs.

Certain bibliometric features of the early literatures of developing drugs can be used to predict their ultimate clinical fates. The chronological sequence of publications is expressed as a binary vector with 1 for a patent and 0 for a nonpatent. The decimal equivalents for standardized vector lengths provide scalar values for comparing one drug with another. In order to incorporate concordant patents, fuzzy subsets are employed, with the number of attempts required to achieve transitive closure being the values for comparison. The methods involved are described using minoxidil as an example.

Bibliographies as Topic↗

PubMed2000

The ternary transformation system: constitutive virG on a compatible plasmid dramatically increases Agrobacterium-mediated plant transformation.

This paper describes a so-called ternary transformation system for plant cells. We demonstrate that Agrobacterium tumefaciens strain LBA4404 supplemented with a constitutive virG mutant gene (virGN54D) on a compatible plasmid is capable of very efficient T-DNA transfer to a diverse range of plant species. For the plant species Catharanthus roseus it is shown that increased T-DNA transfer results in increased stable transformation frequencies. Analysis of stably transformed C. roseus cell lines showed that, although the T-DNA transfer frequency is greatly enhanced by addition of virGN54D, only one or a few T-DNA copies are stably integrated into the plant genome. Thus, high transformation frequencies of different plant species can be achieved by introduction of a ternary plasmid carrying a constitutive virG mutant into existing A. tumefaciens strains in combination with standard binary vectors.

Acetophenones↗

PubMed2001

Functional expression and subcellular localization of the Nectria haematococca Mak1 phytoalexin detoxification enzyme in transgenic tobacco.

Medicarpin and maackiain are antifungal pterocarpan phytoalexins produced by many legumes, and are thought to be important components of the defense response of these legumes to certain fungal pathogens. The Mak1 gene from the fungal pathogen Nectria haematococca encodes an FAD-dependent mono-oxygenase, known to specifically hydroxylate the phytoalexins medicarpin and maackiain, converting them to less fungitoxic derivatives. Two binary vector constructs were made containing the coding regions from two fungal clones, a Mak1 cDNA (intronless) and a genomic (including three fungal introns) clone, regulated by an enhanced cauliflower mosaic virus 35S promoter. The constructs were introduced into tobacco to check for expression of active fungal enzyme in plant cells and for splicing of fungal introns. Leaves of tobacco plants transformed with the Mak1 cDNA construct readily metabolized infiltrated medicarpin to 1a-hydroxymedicarpin, indicating high levels of active enzyme. RT-PCR analysis of tobacco plants transformed with the Mak1 genomic construct indicated no processing of Mak1 introns, and no Mak1 activity was detected in these plants. When using plants containing the Mak1 cDNA construct, immunolocalization with a Mak1-specific antibody together with cellular fractionation indicated that Mak1 protein accumulated in the plant cytoplasm, associated with endoplasmic reticulum membranes; medicarpin biosynthetic enzymes have been localized to the same subcellular region. The Mak1 cDNA construct is therefore suitable for use in studies to selectively eliminate medicarpin accumulation to assess the relative importance of medicarpin in the antifungal defense mechanisms of alfalfa and other legumes.

Alternative Splicing↗

PubMed2001

A library of Arabidopsis 35S-cDNA lines for identifying novel mutants.

We have developed a system to over-express or co-suppress random cDNAs in Arabidopsis thaliana upon Agrobacterium tumefaciens-mediated transformation. We constructed a binary vector containing a novel Arabidopsis cDNA library driven by the cauliflower mosaic virus (CaMV) 35S promoter. The vector, 35SpBARN, offers in terra selection with glufosinate ammonium (BASTA) and the ability to identify the cDNA insert using PCR with flanking primers. We introduced this overexpression library into Arabidopsis and selected over 30,000 transformants. A random sample of 50 T1 plants was analyzed to determine the quality of the cDNA library in planta. About 90% of T1 plants in the collection have inserts, the average insert size is ca. 1.1 kb, and ca. 43% of these inserts appear to encode full-length proteins. T1 plants were screened for visible abnormalities, and one mutant, V5, was chosen for further study. This mutant displays a pale green phenotype, and its transgene contains a partial petH cDNA encoding chloroplast ferredoxin-NADP+ reductase (EC 1.18.1.2). This construct co-suppresses the endogenous petH transcript. We recapitulated the mutant phenotype by expressing either the full-length or truncated petH cDNA from the CaMV 35S promoter in wild-type Arabidopsis. Our results indicate that co-suppressing endogenous genes can cause dominant phenotypes as expected. As we have also used the 35SpBARN vector to successfully over-express other transcripts in planta, we predict that this system will be generally useful for identifying genes that yield phenotypes upon over-expression as well.

Arabidopsis↗

PubMed2002

Phosphorylation of the movement protein of cucumber mosaic virus in transgenic tobacco plants.

The 3a protein of Cucumber mosaic virus is essential for the cell-to-cell movement of the viral RNA through plasmodesmata. We have introduced an epitope peptide before the stop codon of the 3a protein and cloned the tagged ORF into a binary vector for Agrobacterium-mediated transformation. The established transgenic tobacco lines produced the 3a protein, which was specifically detected with anti-3a and anti-epitope antisera. Metabolic labeling and subsequent immunoprecipitation revealed that [32P]-orthophosphate was incorporated into the 3a protein. The phosphoamino acid analysis indicated that the 3a protein contained phosphoserine but not phosphothreonine or phosphotyrosine. This is the first demonstration of the 3a protein phosphorylation in planta.

Cucumovirus↗

PubMed2002

Cotton alpha-globulin promoter: isolation and functional characterization in transgenic cotton, Arabidopsis, and tobacco.

Globulins are the most abundant seed storage proteins in cotton and, therefore, their regulatory sequences could potentially provide a good source of seed-specific promoters. We isolated the putative promoter region of cotton alpha-globulin B gene by gene walking using the primers designed from a cotton staged embryo cDNA clone. PCR amplified fragment of 1108 bp upstream sequences was fused to gusA gene in the binary vector pBI101.3 to create the test construct. This was used to study the expression pattern of the putative promoter region in transgenic cotton, Arabidopsis, and tobacco. Histochemical GUS analysis revealed that the promoter began to express during the torpedo stage of seed development in tobacco and Arabidopsis, and during cotyledon expansion stage in cotton. The activity quickly increased until embryo maturation in all three species. Fluorometric GUS analysis showed that the promoter expression started at 12 and 15 dpa in tobacco and cotton, respectively, and increased through seed maturation. The strength of the promoter expression, as reflected by average GUS activity in the seeds from primary transgenic plants, was vastly different amongst the three species tested. In Arabidopsis, the activity was 16.7% and in tobacco it was less than 1% of the levels detected in cotton seeds. In germinating seedlings of tobacco and Arabidopsis, GUS activity diminished until it was completely absent 10 days post imbibition. In addition, absence of detectable level of GUS expression in stem, leaf, root, pollen, and floral bud of transgenic cotton confirmed that the promoter is highly seed-specific. Analysis of GUS activity at individual seed level in cotton showed a gene dose effect reflecting their homozygous or hemizygous status. Our results show that this promoter is highly tissue-specific and it can be used to control transgene expression in dicot seeds.

Alpha-Globulins↗