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At least 991 records · Page 55Linked to original sources
PubMed1987

In vitro molecular genetics as a tool for determining the differential cleavage specificities of the poliovirus 3C proteinase.

We describe a completely in vitro system for generating defined poliovirus proteinase mutations and subsequently assaying the phenotypic expression of such mutations. A complete cDNA copy of the entire poliovirus genome has been inserted into a bacteriophage T7 transcription vector. We have introduced proteinase and/or cleavage site mutations into this cDNA. Mutant RNA is transcribed from the altered cDNA template and is subsequently translated in vitro. Employing such a system, we provide direct evidence for the bimolecular cleavage events carried out by the 3C proteinase. We show that specific genetically-altered precursor polypeptides containing authentic Q-G cleavage sites will not act as substrates for 3C either in cis or in trans. We also provide evidence that almost the entire P3 region is required to generate 3C proteinase activity capable of cleaving the P1 precursor to capsid proteins. However, only the 3C portion of P3 is required to generate 3C proteinase activity capable of cleaving P2 and its processing products.

3C Viral Proteases↗
PubMed2001

Definition of the Bacillus subtilis PurR operator using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD, and pbuO.

The expression of the pur operon, which encodes enzymes of the purine biosynthetic pathway in Bacillus subtilis, is subject to control by the purR gene product (PurR) and phosphoribosylpyrophosphate. This control is also exerted on the purA and purR genes. A consensus sequence for the binding of PurR, named the PurBox, has been suggested (M. Kilstrup, S. G. Jessing, S. B. Wichmand-Jørgensen, M. Madsen, and D. Nilsson, J. Bacteriol. 180:3900-3906, 1998). To determine whether the expression of other genes might be regulated by PurR, we performed a search for PurBox sequences in the B. subtilis genome sequence and found several candidate PurBoxes. By the use of transcriptional lacZ fusions, five selected genes or operons (glyA, yumD, yebB, xpt-pbuX, and yqhZ-folD), all having a putative PurBox in their upstream regulatory regions, were found to be regulated by PurR. Using a machine-learning algorithm developed for sequence pattern finding, we found that all of the genes identified as being PurR regulated have two PurBoxes in their upstream control regions. The two boxes are divergently oriented, forming a palindromic sequence with the inverted repeats separated by 16 or 17 nucleotides. A computerized search revealed one additional PurR-regulated gene, ytiP. The significance of the tandem PurBox motifs was demonstrated in vivo by deletion analysis and site-directed mutagenesis of the two PurBox sequences located upstream of glyA. All six genes or operons encode enzymes or transporters playing a role in purine nucleotide metabolism. Functional analysis showed that yebB encodes the previously characterized hypoxanthine-guanine permease PbuG and that ytiP encodes another guanine-hypoxanthine permease and is now named pbuO. yumD encodes a GMP reductase and is now named guaC.

Bacillus subtilis↗
PubMed1996

Cytosine deaminase gene as a potential tool for the genetic therapy of colorectal cancer.

The bacterial enzyme cytosine deaminase (CD) catalyzes the conversion of 5-fluorocytosine (5-FC) to the lethal 5-fluorouracil (5-FU) and so provides a useful system for selective killing of gene-modified mammalian tumor cells. Cloning of the CD gene from Escherichia coli and expression in human tumor cell lines enabled these cells to convert 3H-labeled 5-FC into 3H-5-FU. Two CD-expressing human tumor cell lines (adenocarcinoma cell line KM12 and glioblastoma cell line T1115) became 200-fold more sensitive to 5-FC than the nonexpressing parental cell lines. At least 90% of the cells are killed within 7 days. CD-expressing cells are able to kill nonexpressing cells when grown in the same culture flask (bystander effect). The CD gene may be used as a suicide system for in situ chemotherapy or as a safety mechanism abrogating the expression of other genes.

Base Sequence↗
PubMed2005

Genome-wide SNP arrays as a diagnostic tool: clinical description, genetic mapping, and molecular characterization of Salla disease in an Old Order Mennonite population.

An Old Order Mennonite child was evaluated for gross motor delay, truncal ataxia, and slow linear growth. The diagnostic evaluation, which included sub-specialty consultations, neuroimaging, and metabolic testing, was long, costly, and did not yield a diagnosis. Recognition of a similarly affected second cousin prompted a genome-wide homozygosity mapping study using high-density single nucleotide polymorphism (SNP) arrays. SNP genotypes from two affected individuals and their parents were used to localize the disease locus to a 14.9 Mb region on chromosome 6. This region contained 55 genes, including SLC17A5, the gene encoding the lysosomal N-acetylneuraminic acid transport protein. Direct sequencing of SLC17A5 in the proband revealed homozygosity for the 115C --> T (R39C) sequence variant, the common cause of Salla disease in Finland. Three additional affected Mennonite individuals, ages 8 months to 50 years, were subsequently identified by directed molecular genetic testing. This small-scale mapping study was rapid, inexpensive, and analytically simple. In families with shared genetic heritage, genome-wide SNP arrays with relatively high marker density allow disease gene mapping studies to be incorporated into routine diagnostic evaluations.

Agenesis of Corpus Callosum↗
PubMed1978

Chromosome mobilization by the R plasmid R68.45: a tool in Pseudomonas genetics.

The conjugative plasmid R68.45 mobilizes the chromosome of Pseudomonas aeruginosa strain PAO from multiple sites located in different chromosome regions. In interrupted matings on the plate, selection for any single marker tested resulted in entry times of 3-5 min. When selection was imposed for two markers linked in R68.45-mediated conjugation, double recombinants appeared after a delay which corresponded approximately to the map distance between the two markers as measured by the sex factor FP2. Thus, R68.45 and FP2 appear to promote chromosome transfer at similar rates, but R68.45, unlike FP2, seems to give non-polarized transfer. R68.45 may be used to estimate map distances between linked markers located in those chromosome regions where other sex factors do not produce enough recombinants to permit accurate measurement of entry times. In R68.45 matings on the plate, most recombinants inherited short donor chromosome fragments (usually less than 10 min long) and lost the R plasmid during purification. Used like a "large" generalized transducing phage, R68.45 has proved valuable in construction of PAO strains with desired genotypes.

Chromosomes, Bacterial↗
PubMed1992

New tools for mitochondrial genetics of Chlamydomonas reinhardtii: manganese mutagenesis and cytoduction.

A novel and efficient genetic procedure is described for generating mitochondrial mutants of the green alga Chlamydomonas reinhardtii. The development of a mutagenesis procedure using manganese cations and the application of cytoduction techniques resulted in a combined approach for the generation and analysis of mitochondrial mutants. Although mitochondrial mutations are inherited in sexual crosses from the minus mating type parent, the cytoduction technique can be used to transfer mitochondrial mutations into recipient strains with different genetic backgrounds, irrespective of their mating type. Cytoduction allows the transfer of mitochondrial markers from diploid to haploid cells also, which is of great benefit since diploid cells do not germinate in C. reinhardtii. We report here the isolation and characterisation of eight mutants, which are resistant to the antibiotics myxothiazol and mucidin. The mutants all have point mutations in the mitochondrial gene for apocytochrome b. Using in vitro-amplified cytb gene fragments as probes for direct DNA sequencing, three different types of single base pair substitutions were revealed in all mutants tested. In particular, amino acid substitutions in the mutant apocytochrome b polypeptide have been identified at residues 129, 132 and 137, which have been implicated in forming part of an antibiotic-binding niche. The amino acid substitution at position 132 has not been so far described for mutant apocytochrome b in any other organism, prokaryotic or eukaryotic. The genetic approach presented here confirms C. reinhardtii as a model system that is unique among plant cells.

Amino Acid Sequence↗
PubMed1997

Ribosomal DNA ITS-1 and ITS-2 sequence comparisons as a tool for predicting genetic relatedness.

The determination of the secondary structure of the internal transcribed spacer (ITS) regions separating nuclear ribosomal RNA genes of Chlorophytes has improved the fidelity of alignment of nuclear ribosomal ITS sequences from related organisms. Application of this information to sequences from green algae and plants suggested that a subset of the ITS-2 positions is relatively conserved. Organisms that can mate are identical at all of these 116 positions, or differ by at most, one nucleotide change. Here we sequenced and compared the ITS-1 and ITS-2 of 40 green flagellates in search of the nearest relative to Chlamydomonas reinhardtii. The analysis clearly revealed one unique candidate, C. incerta. Several ancillary benefits of the analysis included the identification of mislabelled cultures, the resolution of confusion concerning C. smithii, the discovery of misidentified sequences in GenBank derived from a green algal contaminant, and an overview of evolutionary relationships among the Volvocales, which is congruent with that derived from rDNA gene sequence comparisons but improves upon its resolution. The study further delineates the taxonomic level at which ITS sequences, in comparison to ribosomal gene sequences, are most useful in systematic and other studies.

Animals↗
PubMed2004

Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics.

The aim of the present work was to develop a microsatellite marker-based map of the Vitis vinifera genome (n=19), useful for genetic studies in this perennial heterozygous species, as SSR markers are highly transferable co-dominant markers. A total of 346 primer pairs were tested on the two parents (Syrah and Grenache) of a full sib population of 96 individuals (S x G population), successfully amplifying 310 markers. Of these, 88.4% markers were heterozygous for at least one of the two parents. A total of 292 primer pairs were then tested on Riesling, the parent of the RS1 population derived from selfing (96 individuals), successfully amplifying 299 markers among which 207 (62.9%) were heterozygous. Only 6.7% of the markers were homozygous in all three genotypes, stressing the interest of such markers in grape genetics. Four maps were constructed based on the segregation of 245 SSR markers in the two populations. The Syrah map was constructed from the segregations of 177 markers that could be ordered into 19 linkage groups (total length 1,172.2 cM). The Grenache map was constructed with the segregations of 178 markers that could be ordered into 18 linkage groups (total length 1,360.6 cM). The consensus S x G map was constructed with the segregations of 220 markers that were ordered into 19 linkage groups (total length 1,406.1 cM). One hundred and eleven markers were scored on the RS1 population, among them 27 that were not mapped using the S x G map. Out of these 111 markers, 110 allowed to us to construct a map of a total length of 1,191.7 cM. Using these four maps, the genome length of V. vinifera was estimated to be around 2,200 cM. The present work allowed us to map 123 new SSR markers on the V. vinifera genome that had not been ordered in a previous SSR-based map (Riaz et al. 2004), representing an average of 6.5 new markers per linkage group. Any new SSR marker mapped is of great potential usefulness for many applications such as the transfer of well-scattered markers to other maps for QTL detection, the use of markers in specific regions for the fine mapping of genes/QTL, or for the choice of markers for MAS.

Agriculture↗
PubMed2006

The PsEND1 promoter: a novel tool to produce genetically engineered male-sterile plants by early anther ablation.

PsEND1 is a pea anther-specific gene that displays very early expression in the anther primordium cells. Later on, PsEND1 expression becomes restricted to the epidermis, connective, endothecium and middle layer, but it is never observed in tapetal cells or microsporocytes. We fused the PsEND1 promoter region to the cytotoxic barnase gene to induce specific ablation of the cell layers where the PsEND1 is expressed and consequently to produce male-sterile plants. Expression of the chimaeric PsEND1::barnase gene in two Solanaceae (Nicotiana tabacum and Solanum lycopersicon) and two Brassicaceae (Arabidopsis thaliana and Brassica napus) species, impairs anther development from very early stages and produces complete male-sterile plants. The PsEND1::barnase gene is quite different to other chimaeric genes previously used in similar approaches to obtain male-sterile plants. The novelty resides in the use of the PsEND1 promoter, instead of a tapetum-specific promoter, to produce the ablation of specific cell lines during the first steps of the anther development. This chimaeric construct arrests the microsporogenesis before differentiation of the microspore mother cells and no viable pollen grains are produced. This strategy represents an excellent alternative to generate genetically engineered male-sterile plants, which have proved useful in breeding programmes for the production of hybrid seeds. The PsEND1 promoter also has high potential to prevent undesirable horizontal gene flow in many plant species.

Arabidopsis↗
PubMed1975

The "fetoscope"--a new clinical tool for prenatal genetic diagnosis.

Our experience in 65 patients using a "fetoscope" and local anesthesia prior to saline abortion is described. Visualization of the intrauterine contents improved with experience, was optimum at 16 to 18 weeks' gestation, and was superior to the quality of photographic records. Four fetal skin biopsies and 6 amnion biopsies were done. Six blood samples were taken from the fetal surface of the placenta. The limitations of this instrument are described. No significant complications have occurred. Current and probable future indications for fetoscopy are reviewed. Until both the safety of the procedure is proved and problems of visualization due to limitation of visual field are solved, extreme caution is urged in the employment of this instrument in genetic high-risk pregnancy.

Abortion, Therapeutic↗
PubMed1980

The recombinant inbred strains: a tool for the genetic analysis of differences observed in the self-stimulation behaviour of the mouse.

The self-stimulation behaviour (ICSS) in the lateral hypothalamus of mice was studied using 5 recombinant inbred strains having the DBA/2 and BLAB/c lines for their parental origin. Two of these recombinant inbred strains behave like the recessive parental line (BALB/c) while the three others have a performance level similar to that of the dominant (DBA/2) parent. This division suggests that there is a major gene which determines the difference in performance between the two parental lines. The mean value for the self-stimulation threshold is negatively correlated with the value of the performance. The sensitivity to convulsions, which interrupt ICSS behaviour above certain current intensities, is under the control of a genetic determinant independent, but more complex, than the one which controls the level of performance.

Animals↗
PubMedDate not supplied

Two-dimensional gel electrophoresis of proteins as a tool in wheat genetics.

In this minireview are reported several genetic investigations undertaken on wheat with the use of two-dimensional gel electrophoresis of total proteins extracted mainly from etiolated seedlings or from green leaves. Differences between developmental stages or organs of one genotype and nuclear and cytoplasmic genetic variations between genotypes are revealed by this method. We have also localized on the chromosomes structural genes coding for the proteins revealed and assigned their subcellular location to many polypeptides. We obtained new information concerning the regulation of protein amounts as well as the phylogenetic and homeology relationships between the A, B and D genomes.

Electrophoresis, Polyacrylamide Gel↗
PubMed1995

New tools for integrated genetic and physical analyses of the Escherichia coli chromosome.

Genetic and biophysical techniques have traditionally been applied to genome mapping independently of one another. We present a series of Escherichia coli mini-Tn10 insertions that contain the rare-cutting polylinker 1 (RCP1) of rare restriction sites [including BlnI/AvrII, SpeI, NheI, XbaI, NotI, PacI and SfiI; Mahillon and Kleckner, Gene 116 (1992) 69-74] which allows them to be used not just for genetic mapping, but also for rapid physical mapping and integrated physical and genetic mapping of the E. coli chromosome. Their isolation and their physical and genetic coordinates in K-12 strain MG1655 are presented. Also, their use in purifying insertion-delimited DNAs from E. coli K-12 and in macrorestriction mapping of a pathogenic strain's chromosome is demonstrated. These insertions allow integration of (i) different macrorestriction patterns of a single strain's chromosome, (ii) the physical map of a single strain's chromosome with the genetic map of the species, and (iii) the physical maps of different strains' chromosomes.

Chromosome Mapping↗
PubMed2007

Tools for the genetic analysis of Mycoplasma.

The mycoplasmas have attracted much scientific attention since they contain the smallest known genomes of any independently viable bacterial species. However, the detailed genetic analysis of these bacteria has lagged behind the well-analyzed bacterial model organisms for a long time. This is due to the use of the UGA codon for tryptophan rather than as stop codon, which had often prevented the expression of full-length Mycoplasma proteins in heterologous hosts. Additionally, insufficient efficiency of homologous recombination prevented the targeted disruption of genes in some species such as M. pneumoniae whereas homologous recombination is operative in other mycoplasmas. Only recently, efficient screening systems for the use of transposon-based mutagenesis have been developed to circumvent this problem and to allow the targeted isolation of desired transposon insertion mutants. With the availability of several Mycoplasma genome sequences, artificial plasmids based on the chromosomal origin of replication were constructed that can now be used for complementation studies and for the stable introduction of foreign genetic material. In this review, we give an overview on recent developments in Mycoplasma genetics that facilitate the genetic manipulation of these interesting organisms.

Codon↗
PubMed2004

An electrophoretic tool for the genetic characterisation and delineation of lungworms.

In the present study, PCR-based single-strand conformation polymorphism (SSCP) analysis of the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) was applied to the genetic characterisation of Dictyocaulus from red deer from New Zealand and to its differentiation from species of lungworm from cattle and other hosts. Based on SSCP profiles, Dictyocaulus individuals from red deer from different geographical localities in New Zealand could be readily distinguished from those representing other lungworms examined, irrespective of low-level sequence variability in the ITS-2 (0.4-2.6%) detectable among individuals. The ITS-2 of Dictyocaulus from red deer differed in sequence by approximately 7-35% from congeners from other cervid hosts, demonstrating that this parasite is genetically distinct from other species of Dictyocaulus for which ITS-2 sequence data are presently available. The results emphasize the need for a large-scale molecular systematic study of Dictyocaulus specimens from various species of cervid and other ruminant hosts and the usefulness of mutation scanning for taxonomic, epidemiological and population genetic investigations.

Animals↗