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PubMed2001

Spin-column isolation of DNA-protein interactions from complex protein mixtures for AFM imaging.

Applications of atomic force microscopy (AFM) to investigate structural-functional interactions between DNA and proteins, at the molecular level, should prove valuable for gaining a better understanding of gene expression. Specific genomic DNA-protein interactions occur within a sea of intracellular proteins. Successful AFM imaging requires isolating the specific DNA-protein complex free of background protein contamination. Using spin-column chromatography, we report the successful isolation and AFM imaging of transcription factor DNA complexes from DNA molecules incubated with crude cell lysates. This method should be applicable for the isolation and imaging of other specific DNA-protein complexes pertinent to functional genomic research.

Chromatography, Gel↗
PubMed2006

Carcinogenic Cr(VI) and the nutritional supplement Cr(III) induce DNA deletions in yeast and mice.

Industrial Cr(VI) emissions contaminate drinking water sources across the U.S., and many people take Cr(III) nutritional supplements. Cr(VI) is a human pulmonary carcinogen, but whether it is carcinogenic in the drinking water is not known. Due to widespread human exposure, it is imperative to determine the carcinogenic potential of Cr(VI) and Cr(III). DNA deletions and other genome rearrangements are involved in carcinogenesis. We determined the effects of Cr(VI) as potassium dichromate and Cr(III) as chromium(III) chloride on the frequencies of DNA deletions measured with the deletion assay in Saccharomyces cerevisiae and the in vivo p(un) reversion assay in C57BL/6J p(un)/p(un) mice. Exposing yeast and mice via drinking water to Cr(VI) and Cr(III) significantly increased the frequency of DNA deletions. We quantified intracellular chromium concentrations in yeast and tissue chromium concentrations in mice after exposure. Surprisingly, this revealed that Cr(III) is a more potent inducer of DNA deletions than Cr(VI) once Cr(III) is absorbed. This study concludes that both the environmental contaminant Cr(VI) and the nutritional supplement Cr(III) increase DNA deletions in vitro and in vivo, when ingested via drinking water.

Animals↗
PubMed2001

Forensic mitochondrial DNA analysis: two years of commercial casework experience in the United States.

AIM: To describe mitochondrial DNA (mtDNA) forensic casework experience in a commercial laboratory in the United States. METHODS: Frequency statistics were kept for two years on all aspects of mtDNA forensic cases, including types of clientele, types of samples, levels of sample success and failure, site heteroplasmy, length heteroplasmy, contamination, rates of failures to exclude, and match statistics using a mtDNA sequence database. RESULTS: Low sample failure rate was observed, especially since an "ancient DNA" approach was used for samples with degraded DNA. Levels of contamination were low, and the observed site and length heteroplasmy did not confound the interpretation of results. The data collected from mtDNA haplotypes developed in casework showed extremely high diversity of haplotypes consistent with other formally developed databases. CONCLUSIONS: MtDNA forensic analysis in the private sector was successfully applied to many different types of samples overall, with minimal rates of complication due to sample handling challenges (degraded DNA, minimal samples, contamination) and sequence-specific phenomena (site and length heteroplasmy).

Blood Chemical Analysis↗
PubMed2001

Responses of chub (Leuciscus cephalus) populations to chemical stress, assessed by genetic markers, DNA damage and cytochrome P4501A induction.

Indicators of effects at the population level (genetic variation using allozymes) and early indicators of pollution (EROD activity and DNA strand break formation) were analysed in chub (Leuciscus cephalus) living in weakly and heavily contaminated stations of the Rhône River watershed. The genetic erosion was mainly detected in a fish population living in a contaminated small river system, through modifications in allelic and genotypic frequencies for PGM-2 locus and could be linked to a genetic bottleneck and to the reduced gene flow from upstream unable to maintain or restore the genetic diversity. In a contaminated large river system, the genetic diversity for PGM-2 and other loci was maintained and was probably the consequence of a high gene flow from upstream, linked to a sustained drift of larvae and juveniles in the system. A convergent increase of the frequency of the 90 allele at PGM-2 was observed in two contaminated stations compared with the reference station, this trend being confirmed on a more extensive geographic scale over the Rhône River basin. A high level of EROD activity was detected in both contaminated sites but only the fish in the large river system showed a significant DNA damage level compared to the reference population. The low DNA damage level and high hepato-somatic ratio characterized the impacted population of the small river system and could be associated to a chronic high-level exposure of fish to pollutants which selected individuals exhibiting a high level of DNA damage repair. In the two contaminated systems, some genotypes at the PGM-2 and EST-2 loci showed a low level of DNA damage and/or a high EROD activity and may be considered as being tolerant to pollutants. A higher tolerance of the most heterozygous fish was also detected in the contaminated large system and confirmed that a high level of heterozygosity may be necessary for survival in such a system.

Alleles↗
PubMed1996

DNA recovery and PCR quantification of catechol 2,3-dioxygenase genes from different soil types.

With the objective of monitoring xenobiotic degrading bacteria in soil, a method for rapid extraction of DNA from soil, amenable to amplification by PCR, was developed. The method was based on lysis by freeze-thawing and subsequent addition of sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide and proteinase K. The extraction method required 2 h and was tested on six different soils differing in organic content, water holding capacity and pH, including ones from which DNA extraction is difficult. DNA yields from the soils ranged from 6.1 to 54.0 micrograms of DNA per g soil. The efficiency and reproducibility of the DNA extraction method were evaluated by competitive PCR. The organic content in the soils was a major factor affecting the amount of obtained DNA amenable for amplification by PCR. A PCR primer-pair was designed on the basis of the known nucleotide sequences of several catechol 2,3-dioxygenase genes. The specificity of the primer-pair was demonstrated on different sequenced catechol 2,3-dioxygenase genes and on site-specific bacterial isolates from polycyclic aromatic hydrocarbon (PAH)-contaminated soil. The concentration of catechol 2,3-dioxygenase DNA in PAH-contaminated sediment undergoing an ex situ compost process was quantified by competitive PCR over a period of 16 weeks. The concentration of PAHs and catechol 2,3-dioxygenase DNA in the soil samples, was found to correlate.

Catechol 2,3-Dioxygenase↗
PubMed1988

Beta-adrenergic receptors and enzymes in rat myocardial membranes: implications of fractionation procedures and beta-adrenoceptor antagonists.

1. We performed an enzymatic characterization of two different fractionation procedures of ventricles from rat hearts. The enzymatic assays covered succinic dehydrogenase as a marker for inner mitochondrial membranes, monoamine oxidase as a marker for outer mitochondrial membranes, NADPH-cytochrome c reductase and RNA as endoplasmatic reticular markers, acid phosphatase as a lysosomal marker, and lactic dehydrogenase as a marker for the "soluble" compartment; DNA was estimated for nuclear contamination. 2. The plasma membrane markers 5'-nucleotidase, Ca2+-ATPase, Mg2+-ATPase, Na+-K+-ATPase, and adenylate cyclase were determined. 3. The roughly prepared membrane fractions showed increased yields of the membrane markers; the number of beta receptors, determined with (-)-[3H] dihydroalprenolol and DL-propranolol, amounted to 68 +/- 6 fmol/mg protein (KD = 3390 +/- 450 pmol, Hill coefficient = 1.5). 4. The membrane fraction prepared with a linear sucrose gradient showed an increased inner mitochondrial membrane marker; presumably the outer mitochondrial membrane was stripped off. The beta-receptor number was 39 +/- 3 fmol/mg protein (KD = 6250 +/- 300 pmol; Hill coefficient = 1.2).

Animals↗
PubMed2003

Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing.

Rice is an important crop and a model system for monocot genomics, and is a target for whole genome sequencing by the International Rice Genome Sequencing Project (IRGSP). The IRGSP is using a clone by clone approach to sequence rice based on minimum tiles of BAC or PAC clones. For chromosomes 10 and 3 we are using an integrated physical map based on two fingerprinted and end-sequenced BAC libraries to identifying a minimum tiling path of clones. In this study we constructed and tested two rice genomic libraries with an average insert size of 10 kb (10-kb library) to support the gap closure and finishing phases of the rice genome sequencing project. The HaeIII library contains 166,752 clones covering approximately 4.6x rice genome equivalents with an average insert size of 10.5 kb. The Sau3AI library contains 138,960 clones covering 4.2x genome equivalents with an average insert size of 11.6 kb. Both libraries were gridded in duplicate onto 11 high-density filters in a 5 x 5 pattern to facilitate screening by hybridization. The libraries contain an unbiased coverage of the rice genome with less than 5% contamination by clones containing organelle DNA or no insert. An efficient method was developed, consisting of pooled overgo hybridization, the selection of 10-kb gap spanning clones using end sequences, transposon sequencing and utilization of in silico draft sequence, to close relatively small gaps between sequenced BAC clones. Using this method we were able to close a majority of the gaps (up to approximately 50 kb) identified during the finishing phase of chromosome-10 sequencing. This method represents a useful way to close clone gaps and thus to complete the entire rice genome.

Chromosomes, Artificial, Bacterial↗
PubMed2005

Origin of (-)-geosmin on grapes: on the complementary action of two fungi, botrytis cinerea and penicillium expansum.

One of the consequences of rot on grapes is the development of volatile compounds giving fungal, mouldy or earthy odours. Among these compounds, (-)-geosmin (trans-1,10-dimethyl-trans-9-decalol), a powerful aromatic compound with an earthy smell is a persistent defect in grape juice and wines made with at least partially rotten grapes. A microbiota analysis of rotten grapes containing (-)-geosmin was carried out on sites from four French regions from 1999 to 2002, to clarify the involvement in geosmin appearance of Streptomyces spp. and Penicillium spp., two types of microorganisms present on grape, that are known for their ability to produce geosmin. In earthy grapes, Botrytis cinerea was largely present. Different species of Streptomyces were also isolated, but their pH sensitivity was an extremely limiting parameter for their development on grape juice, grapes or stem, and consequently for their potentiality to generate geosmin in the vineyard. Penicillium expansum, producing geosmin on a model medium, was omnipresent. Penicillium carneum, which is also a geosmin producer, was represented by a single colony during the 4 years of this study. P. expansum alone was able to produce geosmin on a model medium but not on grapes. However, after 7 days' pre-culture of some B. cinerea strains on grape juice, this juice became favourable to geosmin production by P. expansum. We demonstrated the necessary and complementary action of B. cinerea and P. expansum in geosmin production in grape juice and in crushed grape berries.

Beverages↗
PubMed1976

The similarities of ribosomal and basic chromosomal proteins from fungi.

We have compared the physical and chemical properties of yeast and fungal ribosomal proteins with those of higher eukaryotic histones. We have found that acidic urea gel electrophoresis, sodium dodecyl sulfate gel electrophoresis or chromatography on carboxymethylcellulose columns failed to distinguish ribosomal proteins from histones. The majority of the ribosomal proteins did not adsorb to an amberlite CG-50 column in the presence of 8% guanidine hydrochloride. Histones quantitatively adsorbed to an amberlite CG-50 column in the presence of 8% guanidine hydrochloride. A small number of fungal acid-soluble nuclear proteins, which coelectrophoresed with histones, were identified in a presumed nucleolar and nuclear membrane fraction. This fraction contained large amounts of RNA and small amounts of DNA. It is suggested that contamination of yeast and fungal chromosome preparations by a small number of ribosomal proteins can occur. Furthermore, several commonly employed criteria did not distinguish contaminating ribosomal proteins from authentic histones.

Binding Sites↗
PubMedDate not supplied

Free nonimmobilized ligands as a tool for purification of proteins.

Purification of proteins on a large scale is a complex multistep process, and alternative economic strategies are required. This study presents a novel approach (Affinity Sinking, AS) for purification of native proteins utilizing nonimmobilized modified ligands. The nonimmobilized state of the ligand circumvents the need for immobilizing ligands to polymeric supports. Therefore, purification from large volumes can be accomplished without the use of industrial-scale affinity columns. The mechanism of product capture is formation and precipitation of a specific [target-protein/modified-ligand] complex by using a soluble interconnecting entity that generates an insoluble [target-protein/modified-ligand/interconnecting entity] sediment containing the target protein. Rabbit IgG and two glycoproteins were purified accordingly, utilizing free avidin (as the interconnecting entity) and either desthiobiotinylated-protein A (DB-ProA) or desthiobiotinylated-concanavalin A (DB-ConA) as the modified ligand. The recovery yields for the IgG and the two glycoproteins were 80-86% and 70-75%, respectively. Target proteins are eluted from the generated pellet nearly without disrupting the [modified-ligand/interconnecting entity] macro-complex, thus enabling a practical procedure of recovering target proteins. Leaching of the DB-ProA ligand under eluting conditions (pH 3) was found to be lower than 1%. The two modified ligands, DB-ProA and DB-ConA, were regenerated without any chromatographic procedure in 80% and 85%-89% yield, respectively. The advantage of excluding the polymeric component from the purification process and obtaining highly purified proteins has been demonstrated, and it implies that other contaminants (e.g. endotoxins, prions, host DNA) could be excluded as well, thereby reducing the number of purification steps in a typical downstream process.

Animals↗
PubMed1982

Distribution of tightly bound proteins in the chicken ovalbumin gene region.

A method for investigating the distribution of the DNA-tightly bound proteins (TBP) in the chicken ovalbumin gene regions is described. The TBP are operationally defined as the proteins that remain bound to the DNA in the presence of 2 M NaCl. Nuclei from chicken erythrocytes, livers, and oviducts were lysed in 2 M NaCl and sheared, the lysed chromatin was chromatographed through a Sepharose 4B column to separate protein and DNA which contains the TBP. The DNA fraction, after digestion with restriction endonuclease EcoRI, was passed through a GF/C glass fiber filter. The filter retains the DNA-TBP but not the protein-free DNA. In all cases, only about 0.5% of the total genomic DNA was retained on the filter. The ovalbumin gene sequences in the DNA-TBP were analyzed by the Southern blot. It was found that the copy number of the ovalbumin gene in the DNA-TBP isolated from erythrocyte or liver nuclei is not significantly different from that in the total unfractionated nuclear DNA. Liquid hybridization of nick-translation-labeled DNA-TBP with a large excess of total chicken nuclear DNA also demonstrated that the DNA is not a specific subset of the genome. In the nuclei from laying hen oviducts in which the ovalbumin gene but not the globin is actively expressed, approximately 3-fold enrichment of the ovalbumin gene was found in the DNA-TBP. The enrichment could have been due to a contamination of transcriptional complexes during the purification of the DNA-TBP, since no depletion in the globin gene sequences was found in the same sample. These results suggest a random distribution of the TBP in that genome, due possibly to a transient interaction between DNA and TBP. Precautions for evaluation of the results dealing with the TBP published in the literature are also discussed.

Animals↗
PubMed1999

Variability of polymerase chain reaction detection of the bcl-2-IgH translocation in an international multicentre study.

BACKGROUND: The capacity of the polymerase chain reaction (PCR) to detect very low numbers of cells bearing a t(14;18) translocation has led to its application in assessment of the results of treatment for follicular lymphoma, and suggestions that therapy might be guided by molecular studies. To test the reliability of PCR a collaborative study was undertaken to compare results from different laboratories in Europe and North America. METHODS: Twenty laboratories with records of publication in molecular diagnostics were sent blood from normal donors with varying numbers of t(14;18)-bearing cells added from a cell line with a translocation in the major breakpoint region (MBR) of the bcl-2 gene. Samples contained 1000, 100, 10, 1 or 0 cells per ml of whole blood and were sent blinded in duplicate. PCR methodology varied widely, with the total number of amplification cycles between 30 and 70, and 13 different primers used for the MBR region. Twelve laboratories used nested PCR and eight single round amplification. RESULTS: The sensitivity of nested and single round PCR was similar at 100 cells/ml but below this the nested method proved significantly more sensitive. The false positive rate was 28%, with 11 samples from 9 laboratories reported as positive when no t(14;18) cells were added. PCR product size and sequence analysis showed that false positives were due to contamination from cell-line DNA rather than background translocations in the donors. There was no significant difference in false positive rates between nested and single round techniques. CONCLUSION: The polymerase chain reaction to detect bcl-2-IgH rearrangements is presently carried out with widely disparate results. Further effort is required to bring forward a standard PCR protocol which can be re-tested in different laboratories to improve accuracy and reproducibility. The application of quantitative techniques such as real-time PCR may resolve many of the problems presently encountered.

Adult↗
PubMed2002

Inactivation of parvovirus B19 during pasteurization of human serum albumin.

BACKGROUND: It has been shown that HSA may be contaminated with parvovirus B19 (B19) DNA. However, the presence of B19 DNA does not necessarily indicate infectious virus. HSA is pasteurized at 60 degrees C for 10 hours and it remains unclear whether this procedure inactivates B19. Studies with animal parvoviruses indicate considerable heat resistance at 60 degrees C. However, due to the lack of a suitable cell culture system, the pasteurization process has not been investigated in the past. STUDY DESIGN AND METHODS: The recently described cell clone KU812Ep6 was used to establish a system for investigation of B19 inactivation during pasteurization. Virus-infected cells were detected by immunofluorescent staining of viral capsid antigen and by RT-PCR assay of virus-specific capsid mRNA. RESULTS: B19 was inactivated after 10 minutes at 60 degrees C for > or = 4 log. In contrast, porcine parvovirus was widely resistant at 60 degrees C. Inactivation of B19 was independent of the analyzed albumin products (5, 20, and 25% albumin from three manufacturers) and from the specific virus source used for the inactivation experiments. Degradation of B19 DNA by deoxyribonuclease I treatment after pasteurization indicated that the virus capsid is destroyed during heat treatment. CONCLUSION: Heat resistance of B19 markedly differs from heat resistance of animal parvoviruses. While animal parvoviruses widely withstand pasteurization of albumin, B19 was rapidly inactivated. These results confirm the safety of pasteurized albumin and are in line with its good clinical safety record with respect to B19 infection. However, conclusions regarding the safety of other blood-derived medicinal products should not be derived from B19 inactivation in albumin, because different processes or different composition of product intermediates may significantly influence B19 stability during heat treatment.

Hot Temperature↗
PubMed1994

Characterization of a replication-competent retrovirus resulting from recombination of packaging and vector sequences.

A replication-competent retrovirus (RCR) was detected by S+/L- assays in three lots of retroviral vector G1Na that were harvested on consecutive days from a single culture of PA317/G1Na producer cells. Using a number of retrovirus-specific primer pairs, it was shown that this RCR was a novel recombinant created by exchanges between G1Na and helper sequence pPAM3 and was not an existing RCR introduced by cross-contamination. Sequencing of clones of DNA amplified in six independent PCR reactions confirmed that the 3' portion of this RCR was composed of retroviral envelope sequences unique to pPAM3 joined to a 3' long terminal repeat (LTR) unique to G1Na. Comparison of pPAM3 and G1Na sequences at the site corresponding to this junction revealed a short segment of patchy nucleotide identity (8 out of 10 bp), suggesting that these helper and vector sequences were joined by homologous recombination. Generation of RCR by exchanges between helper and vector sequences underscores the necessity of testing by efficient methods all retroviral vectors for the presence of RCR before their use. Production of 171 lots (855 liters) of various retroviral vectors that were free of RCR, including 42 lots of G1Na, however, indicates that the combination of exchanges required to generate an RCR are infrequent in this system.

Animals↗
PubMed1998

A closed culture system for the ex vivo transduction and expansion of human T lymphocytes.

A phase I clinical trial is currently being performed at our institution, with the aim of evaluating the feasibility and toxicity related to the administration of herpes simplex thymidine kinase gene-expressing human primary T lymphocytes following allogeneic hematopoietic stem cell transplantation. The need for safe and standardized preparation conditions for gene-modified cells is crucial. We describe the closed culture system used in the current trial for ex vivo retroviral-mediated gene transfer and transduced cell selection. Cell handling is performed in closed systems using a sterile connection device that avoids opening the culture system. Cell numbers during the production process increased from 93 +/- 16 on day 0 to 440 +/- 92 x 10(6) on day 12 (7.2 +/- 1.4-fold increase) (n = 11). Transduction efficiency before and after G418 resistance-based selection was 13.5 +/- 3.8% and 90.0 +/- 1.4%, respectively. Safety and efficacy testing included a search for replication-competent retrovirus, endotoxins, Mycoplasma, and bacterial contamination (n = 0/9), PCR-DNA, % CD3+ cells (91 +/- 2%), and viability after thawing (82 +/- 3%). Effective working time from day 0 to day 12 is approximately 20 h. The closed system we developed allows for safe and reproducible ex vivo preparation of gene-modified primary T lymphocytes for clinical use.

Cell Culture Techniques↗
PubMed1983

Purification and molecular weight determination of measles virus genomic RNA.

A purification procedure for genomic measles virus RNA, free of contaminating smaller RNA and of DNA, is described. Viral nucleocapsids were prepared from MA160 cells infected in spinner cultures with measles virus (Edmonston strain). Nucleic acid was extracted, treated with DNase and RNA sedimenting at about 50S in sucrose gradients was isolated. This method yielded 0.5 to 1.5 micrograms of genomic RNA per litre of culture. A molecular weight of 4.5 X 10(6) was determined by gel electrophoresis under fully denaturing conditions.

Animals↗