The use of combined FISH/GISH in conjuction with DAPI counterstaining to identify chromosomes containing transgene inserts in amphidiploid tobacco

We have used combined fluorescent and genomic in situ hybridization (FISH/GISH) together with 4′,6-diamidino-2-phenylindole (DAPI) counterstaining to determine simultaneously the chromosomal integration site and subgenomic allocation of a transgene insert in amphidiploid tobacco (Nicotiana tabacum, 2n=4x=48). The procedure provides sufficient information on physical markers to identify at least 20 out of 24 chromosome pairs of two tobacco cultivars commonly used in studies on transgene expression and silencing (cv. Petit Havana SR1 and cv. Gatersleben). The chromosomes can be distinguished on the basis of diploid parental ancestry, size, morphology, the presence of rDNA loci and/or intergenomic exchanges, and the DAPI banding pattern, which is shown here for the first time forN. tabacum. From a single ISH experiment, it should now be possible in most cases to identify a tobacco chromosome carrying a transgene insert, thus permitting systematic studies of how the chromosomal location of transgenes influences expression levels. Edited by: D. Schweizer     

Rapid localization of transgenes in mouse chromosomes with a combined Spectral Karyotyping/FISH technique

We explored the feasibility of combined Spectral Karyotyping (SKY) and Fluorescence In Situ Hybridization (FISH) as means to rapidly map a chromosomally integrated renin/green fluorescent protein (GFP) fusion gene construct (Ren-GFP) in the transgenic mouse, Tg(Ren-GFP)1Kwg. A sequential hybridization with SKY probes followed by FISH gave consistently satisfactory results, demonstrating that multiple copies of the Ren-GFP transgene in this transgenic mouse line are integrated into a single chromosomal site of Chromosome (Chr) 4, most probably in the juxta-centromeric euchromatic region consisting of the A2-A3 domain. Chr 4 as a sole carrier of the transgene also was confirmed by co-hybridization to p1 BAC clone DNA containing telomeric sequences specific for mouse Chr 4 and the Ren-GFP construct in pGEM4Z vector. The hemizygosity of the Ren-GFP transgene is maintained not only in bone marrow cells, but also in lung cells proliferating in vitro, indicating that stable integration of the Ren-GFP transgene into chromosomal DNA was established at a very early embryonic stage. We conclude that the SKY/FISH technique is a reliable and facile method for establishing the integration site of a transgene. As such, this protocol has obvious advantages over traditional backcross methods in terms of time, cost and labor for determining the chromosomal location of transgenes.     

The genetic identity of alien chromosomes in potato breeding lines revealed by sequential GISH and FISH analyses using chromosome-specific cytogenetic DNA markers.

Genomic in situ hybridization (GISH) is one of the most popular and effective techniques for detecting alien chromatin introgressed into breeding lines; however, GISH analysis alone does not reveal the genetic identity of the alien chromosomes. We previously isolated a set of bacterial artificial chromosomes (BACs) specific to each of the 12 potato chromosomes. These BAC clones can be used as chromosome-specific cytogenetic DNA markers (CSCDMs) for potato chromosome identification. Here we demonstrate that GISH and fluorescence in situ hybridization (FISH), using CSCDMs, can be performed sequentially on the same chromosome preparations. Somatic metaphase chromosomes prepared using an enzymatic digestion and "flame-drying" procedure allows repeated probing up to five times without significant damage to chromosome morphology. The sequential GISH and FISH analyses reveal the genomic origin and genetic identity of the alien chromosomes in a single experiment and also determine whether an alien chromosome has been added to the genetic background of potato or is substituting for a homoeologous potato chromosome. The sequential GISH and FISH procedures should be widely applicable for germplasm characterization, especially in plant species with small-sized chromosomes.     

The impact of StuI digestion in situ on FISH to human chromosomes with satellite DNA probes

Human metaphase chromosomes were digested with StuI and subsequently hybridized in situ using chromosome 9 alphoid DNA and classical satellite III DNA as probes. The data obtained suggest that it is not possible to establish a general rule regarding the cytological effects induced by restriction enzymes in particular chromosome regions and that a number of factors, such as DNA sequences, DNA-protein interaction and enzyme structure, play a role in determining such effects.     

Identification of wheat-barley translocations by sequential GISH and two-colour FISH in combination with the use of genetically mapped barley SSR markers.

Five wheat-barley translocations in a wheat background were characterized through the combination of cytogenetic and molecular genetic approaches. The wheat chromosome segments involved in the translocations were identified using sequential GISH and two-colour FISH with the probes pSc119.2 and pAs1. The barley chromatin in these lines was identified using SSR markers. A total of 45 markers distributed over the total barley genome were selected from a recently published linkage map of barley and tested on the translocation lines. The following translocations were identified: 2DS.2DL-1HS, 3HS.3BL, 6BS.6BL-4HL, 4D-5HS, and 7DL.7DS-5HS. Wheat-barley disomic and ditelosomic addition lines for the chromosomes 3HS, 4H, 4HL, 5H, 5HL, and 6HS were used to determine the correct location of 21 markers and the position of the centromere. An intragenomic translocation breakpoint was detected on the short arm of the barley chromosome 5H with the help of SSR marker analysis. Physical mapping of the SSR markers on chromosomes 1H and 5H was carried out using the intragenomic and the interspecific translocation breakpoints, as well as the centromere, as physical landmarks.     

The presence of a chromatin boundary appears to shield a transgene in tobacco from RNA silencing

We present isogenic transgenic tobacco lines that carry at a given chromosomal position a beta-glucuronidase (GUS) reporter gene either with or without the presence of the matrix-associated region known as the chicken lysozyme A element. Plants were generated with the Cre-lox site-specific recombination system using heterospecific lox sites. Analysis of GUS gene expression in plant populations demonstrates that the presence of the A element can shield against RNA silencing of the GUS gene. Protection was observed in two of three independent tobacco transformants. Plants carrying an A element 5' of the GUS gene always had stable GUS activity, but upon removal of this A element, the GUS gene became silenced over time in two lines, notably when homozygous.     

The use of dimenhydrinate in conjunction with dexamethasone for induction of parturition in beef cattle

Forty-eight crossbred Chianina cows (3 to 5 years of age), with an expected gestation length of 288 days, were randomly divided into four treatment groups to evaluate the use of dimenhydrinate (an antihistamine agent) in conjunction with dexamethasone (DEX) for inducing parturition in beef cattle. Group (A) received a 20 mg dose of DEX (im) on day 282 of gestation and a carrier vehicle (iv) 24 hours later (day 283); Group (B) was given a carrier vehicle (im) on day 282 and 500 mg of dimenhy-drinate (DMH) diluted in 200 ml of 2.5% dextrose-0.9% saline solution given (iv) on day 283 and Group (C) received 20 mg of DEX (im) on day 282 and 500 mg of DMH in solution (iv) on day 283 of gestation. The remaining 12 cows assigned to Group (D) were not handled and were allowed to calve under natural conditions. The number of cows calving and percent calving within 60 hours after the first injection were: 10(91%), none(0%) and 12(100%) for the DEX, DMH and DEX plus DMH groups, respectively. The mean gestation length of the control cows in Group (D) was 288.6 days. Frequency of dystocia was: 18.2, 8.3, 0 and 0% and retained placentae (>/=24 hours) was: 72.8, 16.6, 33.3 and 0% for DEX, DMH, DEX plus DMH and control groups, respectively. In this study, a 20 mg dose of DEX (im) followed 24 hours later with 500 mg of DMH (iv) was more successful for calving induction than when DEX or DMH was used alone. The combination DEX and DMH treatment induced calving in a shorter interval from treatment (P<.05) and decreased the incidence of retained placentae (P<.01) when compared with those induced following DEX treatment.     

The use of sequence-specific antibodies to identify a secondary binding site in thrombin

The peptide comprising residues 62-73 of the B-chain of human alpha-thrombin was synthesized and polyclonal antibodies raised against it. These antibodies were found to bind to the synthetic peptide, a CNBr fragment, and a proteolytic subfragment containing this sequence, as well as the entire thrombin molecule. The purified antibodies had no effect on the hydrolysis by thrombin of D-Phe-pipecolyl-Arg-p-nitroanilide and caused only a minimal decrease (20%) in the second-order rate constant for inactivation by antithrombin III. On the other hand, the antibodies competitively inhibited the binding of hirudin over the concentration range tested (0-43 nM), and a dissociation constant of 3.4 +/- 0.5 nM was found for the antibodies. The release of fibrinopeptide A from the A alpha-chain of fibrinogen by thrombin was competitively inhibited with an inhibition constant of 11.7 +/- 0.4 nM. The activation of protein C by thrombin in the presence of thrombomodulin was also inhibited by the antibodies, and an apparent inhibition constant of 10.7 +/- 1.5 nM was found. In contrast, the antibodies had no effect on the activation of protein C in the absence of thrombomodulin. These results are discussed in relation to data obtained recently on the interaction of well defined proteolytic derivatives of human alpha-thrombin with the ligands described above.     

The use of enzyme polymorphisms to identify genetic differences in the genus Trichinella

Seven isolates of the genus Trichinella were evaluated for their genetic identity and variability using starch gel electrophoresis. The various strains exhibited polymorphism in 8 of 11 enzyme systems tested and the strains could be segregated into at least 3 basic patterns for geographical isolates of Trichinella: pigs, wild carnivores and Trichinella spiralis var. pseudospiralis. There was also evidence for further differences between isolates from wild carnivores. The isozyme technique appears to have potential for zoogeographic studies in the genus Trichinella.     

The use of a laser microprobe to identify calcium oxalate in histological material

Summary Some birefringent renal deposits were found to give the usual histological reactions for calcium oxalate but were soluble in caustic alkalis. Comparison with known oxalate crystals using a laser microprobe mass analyser confirmed the presence of calcium oxalate. Similar crystals were found in liver tissue from a rat poisoned with ethylene glycol.     

The use of reverse immunology to identify HLA-A2 binding epitopes in Tie-2

A potential target for a cancer vaccine would be receptors, such as Tie-2 which are over expressed on tumour endothelium. Using computer aided motif predictions for possible HLA class I epitopes, we have identified peptides from Tie-2 that should bind with a range of affinities to HLA-A*0201. No direct correlation between predicted values and actual binding affinities was observed. Although, the programs did produce a number of false positives, two epitopes were predicted that bound with relatively high affinity when compared with an influenza peptide. We have previously identified a Tie-2 epitope and shown that it was only immunogenic when we substituted preferred amino acids at key anchor residues to increase binding affinity. In this study we used a similar approach to generate modified epitopes. When HLA-A2 transgenic mice were immunised with peptides, CTL killing of the target cells was only achieved when the wild type epitope was presented at moderate levels. Moreover, the efficiency of immunisation was increased when we linked CD4 epitopes to CD8 epitopes. Caution should therefore be employed in the use of both reverse immunology and anchor modification of CTL epitopes in the identification of CTL epitopes for cancer vaccines.This article is a symposium paper from the “Robert Baldwin Symposium: 50 years of Cancer Immunotherapy”, held in Nottingham, Great Britain, on 30th June 2005.     

The use of multi-frequency EPR techniques to identify the radicals produced in irradiated beta-blockers

The identification of radicals trapped in irradiated drugs can be very intricate. A multi-frequency electron paramagnetic resonance (EPR) study is proposed to resolve this problem. The Q-band (ca. 34 GHz) comparison with X-band (ca. 9 GHz) did not show significant differences for the four β-blockers studied (atenolol, esmolol, nadolol and propranolol). The use of a higher frequency (285 GHz) was required. It enabled us to determine the g-tensor values of the radicals present in atenolol and esmolol, respectively, g₁=2.0086, g₂=2.0059 and g₃=2.0021 and g₁=2.0066, g₂=2.0044 and g₃=2.0021. The latter was assigned as a phenoxyl radical, which can not be the case for the former. Therefore, radicals produced in esmolol may result from a more complex mechanism than the abstraction followed by the diffusion of an H atom inside the solid. In addition, two molecules as similar as atenolol and esmolol hydrochloride do not contain the same radicals after irradiation. These two conclusions drawn from the EPR results on β-blockers show clearly the importance of continuing the investigations on radiolytic mechanisms in solid-state drugs.     

Heterochromatin in the chromosomes of the gorilla: characterization with distamycin A/DAPI, D287/170, chromomycin A3, quinacrine, and 5-azacytidine

The chromosomes of the gorilla were extensively studied with various staining techniques labeling the different classes of heterochromatin. The chromosomal distribution of distamycin A/DAPI-, D287/170-, quinacrine-, and chromomycin A3-positive heterochromatic regions, as well as the nucleolus organizer regions, is described and compared with the karyotypes of other hominoid species. Lymphocyte cultures were treated with low doses of 5-azacytidine during the last hours of culture. This cytidine analog induces distinct undercondensation in 37 heterochromatic regions in the 24 gorilla chromosomes. The 5-azacytidine-induced undercondensations are localized not only in most of the distamycin A/DAPI-bright heterochromatic regions but also in many telomeric C-bands of the chromosomes. Furthermore, 5-azacytidine preserves the somatic pairing between heterochromatic regions from the interphase nuclei into the metaphase stage. The homeologies and differences in the chromosomal localization of the various classes of heterochromatin, 5-azacytidine-sensitive regions, 5-methylcytosine-rich DNA sequences, and satellite DNAs in the gorilla, chimpanzee, orangutan, and man are discussed.     

The use of pH indicators to identify suitable environments for freezing samples in aqueous and mixed aqueous/nonaqueous solutions

The colours of frozen solutions containing pH indicators are shown to provide a test for changes in pH in the solvent environment which occur on freezing. Yeast alcohol dehydrogenase loses activity on freezing in phosphate buffer (a buffer in which pH indicator colour changes shows a marked decrease in pH on freezing) but when frozen in bis-tris, Hepes, or N-glycylglycine buffers (all of which show little change in the colour of universal pH indicator and hence of pH on freezing) is stable on freezing. The effects of freezing in different buffer systems on the rate of decomposition of NADPH, and on the rate hydrolysis of 4-nitrophenyl acetate, are rationalised in terms of the pH shifts in these buffers which were determined using universal pH indicator. It is proposed that a major reason for the instability of samples on freezing is the pH changes which occur when some systems are frozen. From the results a general scheme for selecting the best environment for safely freezing samples is proposed which is based on the use of pH indicators.     

The use of LC-MS to identify differentially expressed proteins in docetaxel-resistant prostate cancer cell lines

Docetaxel is a taxane-derived chemotherapy drug that has been approved for treatment of prostate cancer. While docetaxel is frequently used as a treatment for hormone-refractory prostate cancer, a subset of patients either do not respond to this treatment or those that do respond eventually become resistant to the drug over time. Resistance to docetaxel is complex and multi-factoral and further understanding of the cellular biochemistry underlying resistance is vital to improve treatment efficacy. To identify proteins altered in the resistant phenotype, three parental cell lines DU145, 22RV1 and PC-3, as well as their docetaxel resistant sub-lines, were subjected to quantitative label-free LC-MS proteomic profiling. A total of 189 significant (p < 0.05) protein abundance changes were identified in the DU145 resistant sub-lines, 254 in the 22RV1 sub-lines, and 51 and 72 in the 8 and 12 nM resistant PC-3 sub-lines, respectively. From these, 29 proteins demonstrated a significant (p < 0.05) fold change across two or more resistant variants. These included proteins indicative of an epithelial-to-mesenchemyl transition as well as altered heat shock response elements.     

The use of a fuel containing Chlorella vulgaris in a diesel engine

There is a need for sustainable fuels for diesel engines and fuels containing particles will function as a fuel in diesel engines. Some microalgae such as Chlorella vulgaris are unicellular and 5–10 μm in size, which is suitable for combining in an emulsion fuel. An emulsion consisting of transesterified rapeseed oil, a surfactant and a slurry of C. vulgaris was used as a fuel in an unmodified single cylinder diesel engine. The fuel consumption and emissions of this fuel was determined and although the carbon monoxide levels were higher the NO_x emission was lower than that of diesel.     

The use of bulk segregant analysis to identify a RAPD marker linked to leaf rust resistance in barley

An F₂ population from a cross between barley accession Q21861 and the Australian barley variety Galleon was used to develop RAPD markers for resistance to barley leaf rust (Puccinia hordei). Resistant and susceptible DNA bulks were constructed following the classification of F₂ plants by leaf rust infection type. Bulked segregant analysis was then used to identify a 2.7-kb marker, designated OU02₂₇₀₀ and located approximately 12cM from RphQ, a leaf rust resistance gene in Q21861. The marker was generated by PCR with the oligonucleotide primer OPU-02 (Operon). Infection types of F₃ progeny were used to confirm assignment of F₂ genotypes. OU02₂₇₀₀ was shown, retrospectively, to be useful in the identification of individual F₂ plants that had been originally misclassified as having susceptible infection types. Both the RAPD marker and RphQ will be potentially useful in the development of new barley cultivars.     

The use of cysteine proteinase inhibitors to engineer resistance against potyviruses in transgenic tobacco plants

As the processing mechanism of all known potyviruses involves the activity of cysteine proteinases, we asked whether constitutive expression of a rice cysteine proteinase inhibitor gene could induce resistance against two important potyviruses, tobacco etch virus (TEV) and potato virus Y (PVY), in transgenic tobacco plants. Tobacco lines expressing the foreign gene at varying levels were examined for resistance against TEV and PVY infection. There was a clear, direct correlation between the level of oryzacystatin message, inhibition of papain (a cysteine proteinase), and resistance to TEV and PVY in all lines tested. The inhibitor was ineffective against tobacco mosaic virus (TMV) infection because processing of this virus does not involve cysteine proteinases. These results show that plant cystatins can be used against different potyviruses and potentially also against other viruses, whose replication involves cysteine proteinase activity.     

The use of direct cDNA selection to rapidly and effectively identify genes in the fungus Aspergillus fumigatus

Aspergillus fumigatus is one of the causes of invasive lung disease in immunocompromised individuals. To rapidly identify genes in this fungus, including potential targets for chemotherapy, diagnostics, and vaccine development, we constructed cDNA libraries. We began with non-normalized libraries, then to improve this approach we constructed a normalized cDNA library using direct cDNA selection. Normalization resulted in a reduction of the frequency of clones with highly expressed genes and an enrichment of underrepresented cDNAs. Expressed sequence tags generated from both the original and the normalized libraries were compared with the genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans, indicating that a large proportion of A. fumigatus genes do not have orthologs in these fungal species. This method allowed the expeditious identification of genes in a fungal pathogen. The same approach can be applied to other human or plant pathogens to rapidly identify genes without the need for genomic sequence information.