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At least 73 records · Page 4Linked to original sources
PubMed1998

Transmission of tuberculosis in the metropolitan area of Zurich: a 3 year survey based on DNA fingerprinting.

Between 1991 and 1993, 444 inhabitants of the metropolitan area of Zurich were reported as confirmed or suspected cases of tuberculosis (TB). Overall, isolates of Mycobacterium tuberculosis of 361 patients (90% of the bacteriologically confirmed cases) were available to study the frequency of transmission of the strains on a molecular level. Restriction fragment length polymorphism (RFLP) analysis was performed by using IS6110 and the polymorphic GC-rich sequence (PGRS) as genetic markers. Ninety nine isolates shared by 77 patients (21.3%) were associated with 28 IS6110-defined clusters. However, secondary typing of low copy number isolates decreased the number of clusters to 25, encompassing 81 isolates from 63 (17.5%) patients. By deoxyribonucleic acid (DNA) fingerprinting plus conventional contact tracing, definite transmission of TB was proven in only five patients (1.4%) and assumed in 20 patients (5.6%). In all other cluster-associated isolates, no epidemiological connections between the patients could be found using the clinical and sociodemographic data available. The present study demonstrates that in the time period studied only minor transmission occurred.

Adolescent↗
PubMedDate not supplied

[Research on DNA polymorphism in mixed biological traces].

The authors present the results of VNTR-PCR DNA polymorphism of three STR loci. Gene profiles were determined in experimental spots of blood from 2 or 3 unrelated individuals mixed in the ratios 1:1-1:100. Genotypes were successfully determined in mixed blood spot samples of ratios 1:1-1:60. A small amount of DNA in all those samples manifested a light electrophoretic staining. The electrophoretic band disappearance in the mixed blood spot samples of high dilution (<1:70) did not allow for determination of their genotypes. In the paper the results obtained while identifying biological traces from sexual offences in which mixed DNA occurred have been also presented.

Blood Stains↗
PubMed2026

The prevalence and persistence of DNA in vehicles from incidental drivers and other occupants, and their associates, including after reuse by regular drivers.

It is common knowledge that when driving a vehicle, people leave traces of DNA behind. However, in the context of vehicle crimes, it is helpful for the police and investigative personnel to know the vehicle locations in which a perpetrator most likely left DNA during the incident. By specifying the most informative locations to sample for incidental driver DNA, time and resources can be saved in criminal investigations. This study extends previous knowledge by focusing on the prevalence and persistence of incidental driver DNA in vehicles. Furthermore, the current study investigates the prevalence of DNA on vehicle locations from the regular driver and the close associates of the regular driver and incidental driver. The same experiment was conducted by two laboratories, allowing for inter-laboratory comparisons. The results confirm that DNA from the last driver of the vehicle is most likely recovered from high contact areas for operation of the vehicle like the steering wheel and gear shift. Most sampled sites within the vehicle contain DNA from the regular driver of that vehicle. DNA from an incidental driver is most likely to persist, even after resumed use of the vehicle by the regular driver, on locations with a higher retention capacity for biological materials like the car seats and seat belts. Overall, this paper highlights the patterns of DNA transfer, persistence and recovery that occur depending on an individual's relationship to a vehicle. This information can be used by crime scene investigators for targeting the most relevant sampling locations given different scenarios of vehicle use.

Humans↗
PubMed1994

Electrochemically active DNA probes: detection of target DNA sequences at femtomole level by high-performance liquid chromatography with electrochemical detection.

Electrochemically active DNA probes were prepared by linking a ferrocene unit with 5'-aminohexyl-terminated oligonucleotides. The DNA sequences of probes 5a, 5b, and 5c were 5'-T12-3', 5'-T20-3', and 5'-TGCAG TTCCG GTGGC TGATC-3', respectively. Probe 5a could form a complex selectively with a single-strand poly(A) and a double-strand DNA fragment containing an A13 sequence and these complexes could be detected at femtomole levels by an electrochemical detector (ECD) on HPLC. The observed ECD response was proportional to the amount of the complex over the range 20-100 fmol. Probe 5c was capable of detecting femtomole levels of a restriction DNA fragment having oncogene v-myc. Moreover, probe 5b was able to detect picogram levels of mRNA taken from rat brain or yeast total cellular RNA. This proves that the electrochemically active DNA probes are useful in analyzing traces of DNA and RNA carrying the complementary sequence.

Base Sequence↗
PubMed1983

DNA methylation patterns in the 5S DNAs of Xenopus laevis.

The frequency of cytosine methylation at specific sites in the somatic 5S DNA (X1s) and trace oocyte 5S DNA (X1t) of X. laevis has been determined using restriction enzymes that are inhibited by the presence of 5-methylcytosine (5mC) within their cleavage sequences. 5S DNA methylation patterns were determined in genomic DNA from mature red blood cells, which express neither type of 5S gene, and from liver, which expresses only X1s. All the sites examined in X1t are greater than 95% methylated in red cells and liver. In the X1s of red cells all the sites examined are methylated in greater than 95% of repeats, while in liver some sites are modified in only 90% of repeats. Repeats containing unmethylated sites are randomly distributed throughout the tandem arrays in both red cells and liver. The high levels of methylation for X1s are in marked contrast to the situation with other Xenopus genes which do have sites of significant undermethylation in tissues where they are active. Thus, undermethylation in active genetic regions may not be a general feature for all classes of eukaryotic genes.

5-Methylcytosine↗
PubMed1990

Electrophoretic karyotyping of typical and atypical Candida albicans.

Electrophoretic karyotypes of atypical isolates of Candida albicans, e.g., strains that were germ tube negative, failed to express proteinase activity, demonstrated low virulence for mice, formed hyperchlamydoconidia, produced hyperhyphae, or were sucrose negative (including the type strain of Candida stellatoidea), were compared with those of typical C. albicans. Karyotypes of whole-cell DNA of classical C. albicans examined with transverse alternating-field electrophoresis under specific conditions were composed of seven DNA bands with a specific migration pattern. Certain atypical strains and representatives of the three serotypes of C. stellatoidea produced discrete karyotypes with 5 to 10 bands. All isolates demonstrated a significant degree of DNA relatedness, suggesting their conspecificity. Densitometric tracings of DNA bands provided an objective and standardized method for comparing bands within the gels.

Candida albicans↗
PubMed2004

Permanent neonatal diabetes due to paternal germline mosaicism for an activating mutation of the KCNJ11 Gene encoding the Kir6.2 subunit of the beta-cell potassium adenosine triphosphate channel.

Activating mutations in the KCNJ11 gene encoding for the Kir6.2 subunit of the beta-cell ATP-sensitive potassium channel have recently been shown to be a common cause of permanent neonatal diabetes. In 80% of probands, these are isolated cases resulting from de novo mutations. We describe a family in which two affected paternal half-siblings were found to be heterozygous for the previously reported R201C mutation. Direct sequencing of leukocyte DNA showed that their clinically unaffected mothers and father were genotypically normal. Quantitative real-time PCR analysis of the father's leukocyte DNA detected no trace of mutant DNA. These results are consistent with the father being a mosaic for the mutation, which is restricted to his germline. This is the first report of germline mosaicism in any form of monogenic diabetes. The high percentage of permanent neonatal diabetes cases due to de novo KCNJ11 mutations suggests that germline mosaicism may be common. The possibility of germline mosaicism should be considered when counseling recurrence risks for the parents of a child with an apparently de novo KCNJ11 activating mutation.

Adenosine Triphosphate↗
PubMed1998

Trace alignment and some of its applications.

MOTIVATION: Extra useful information can be extracted from a DNA chromatogram trace, over that contained in the base-called DNA sequence. Many sequencing applications can benefit from examination of these traces. RESULTS: An algorithm, based on dynamic programming, for aligning a DNA chromatogram to a DNA sequence is described and implemented. Its applications to vector clipping, EST alignment and mutation detection are discussed.

Algorithms↗
PubMed2007

A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices.

Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace. The resulting ambiguity sequence is aligned to the genome, identifying one template sequence. A second template sequence is then inferred from this alignment. This technique makes possible many exciting biological applications. Here we present two such applications, alternate splice finding and elucidation of multiple insertion sites in a random insertional mutagenesis library. Our results demonstrate that RT-PCR followed by Trace Recalling is a more efficient and cost effective way to find alternate splices than traditional methods. We also present a method for mapping double-insertion events in a random insertional-mutagenesis library.

Algorithms↗
PubMed1989

Trace detection of modified DNA bases via moving-belt liquid chromatography-mass spectrometry using electrophoric derivatization and negative chemical ionization.

Electrophoric derivatives of 5-methylcytosine and 5-hydroxymethyluracil nucleobases are determined using high-performance liquid chromatography-mass spectrometry coupled via a moving-belt interface. Standards as well as samples derived from DNA are analysed. As little as 9.9 pg (signal-to-noise ratio 5) and 180 fg (signal-to-noise ratio 10) of the respective nucleobases are detected in the electron-capture negative chemical ionization mode, and linear responses are observed over a moderate dynamic range. In a comparison study, liquid chromatography-electron-capture negative chemical ionization mass spectrometry is found to have a sensitivity comparable to gas chromatography-electron-capture negative chemical ionization mass spectrometry for 5-hydroxymethyluracil. A detection limit of 60 fg (signal-to-noise ratio 5) by gas chromatography-mass spectrometry is only three-fold better than the amount detected by liquid chromatography-mass spectrometry using the same mass spectrometer.

5-Methylcytosine↗
PubMedDate not supplied

Probabilistic reasoning in the law. Part 2: Assessment of probabilities and explanation of the value of trace evidence other than DNA.

Problems associated with the interpretation of scientific evidence (fibres and glass) in forensic science are investigated with reference to measures of uncertainty associated with the presentation of such evidence in an adversarial context. The investigation includes the use of probabilistic arguments associated with expert scientific testimony in the courts. Cases where scientific evidence has been presented in court are studied. A series of problems were developed for, and given to, forensic medicine students' forensic science students and practitioners (advocates and forensic scientists) in Scotland to investigate their understanding of uncertainty.

Bayes Theorem↗
PubMed2006

DNA pooling: a comprehensive, multi-stage association analysis of ACSL6 and SIRT5 polymorphisms in schizophrenia.

Many candidate gene association studies have evaluated incomplete, unrepresentative sets of single nucleotide polymorphisms (SNPs), producing non-significant results that are difficult to interpret. Using a rapid, efficient strategy designed to investigate all common SNPs, we tested associations between schizophrenia and two positional candidate genes: ACSL6 (Acyl-Coenzyme A synthetase long-chain family member 6) and SIRT5 (silent mating type information regulation 2 homologue 5). We initially evaluated the utility of DNA sequencing traces to estimate SNP allele frequencies in pooled DNA samples. The mean variances for the DNA sequencing estimates were acceptable and were comparable to other published methods (mean variance: 0.0008, range 0-0.0119). Using pooled DNA samples from cases with schizophrenia/schizoaffective disorder (Diagnostic and Statistical Manual of Mental Disorders edition IV criteria) and controls (n=200, each group), we next sequenced all exons, introns and flanking upstream/downstream sequences for ACSL6 and SIRT5. Among 69 identified SNPs, case-control allele frequency comparisons revealed nine suggestive associations (P<0.2). Each of these SNPs was next genotyped in the individual samples composing the pools. A suggestive association with rs 11743803 at ACSL6 remained (allele-wise P=0.02), with diminished evidence in an extended sample (448 cases, 554 controls, P=0.062). In conclusion, we propose a multi-stage method for comprehensive, rapid, efficient and economical genetic association analysis that enables simultaneous SNP detection and allele frequency estimation in large samples. This strategy may be particularly useful for research groups lacking access to high throughput genotyping facilities. Our analyses did not yield convincing evidence for associations of schizophrenia with ACSL6 or SIRT5.

Case-Control Studies↗
PubMed1999

DNA sequence chromatogram browsing using JAVA and CORBA.

DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence. [The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.]

Animals↗
PubMed1990

Hydrogen peroxide-induced base damage in deoxyribonucleic acid.

Aqueous solutions of calf thymus deoxyribonucleic acid (DNA) were exposed to hydrogen peroxide in the presence of air. Base products formed in DNA were identified and quantitated following acid hydrolysis and trimethylsilylation using gas chromatography-mass spectrometry. The yields of these products were dependent upon the hydrogen peroxide concentration, and increased in the following order: 8-hydroxyadenine, cytosine glycol, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, 8-hydroxyguanine, thymine glycol, and 4,6-diamino-5-formamidopyrimidine. Previous studies have shown that these compounds are typically formed in DNA in aqueous solution by hydroxyl radicals generated by ionizing radiation. Hydrogen peroxide is thought to participate in a Fenton-like reaction with transition metals, which are readily bound to DNA in trace quantities, resulting in the production of hydroxyl radicals close to the DNA. This proposed mechanism was examined by exposing DNA to hydrogen peroxide either in the presence of a hydroxyl radical scavenger or following pretreatment of DNA with metal-ion chelators. The results indicate that trace quantities of transition metal ions can react readily with hydrogen peroxide to produce radical species. The production of radical species was monitored by determining the altered bases that resulted from the reaction between radicals and DNA. The yields of the base products were reduced by 40 to 60% with 10 mmol dm-3 of dimethyl sulfoxide. A 100-fold increase in the concentration of dimethyl sulfoxide did not result in a further reduction in hydrogen peroxide-induced base damage. DNA which was freed from bound metal ions by pretreatment with metal ion chelators followed by exhaustive dialysis was found to be an ineffective substrate for hydrogen peroxide. The yields of base products measured in this DNA were at background levels. These results support the role of metal ions bound to DNA in the site-specific formation of highly reactive radical species, most likely hydroxyl radicals, in hydrogen peroxide-induced damage to the bases in DNA.

Base Sequence↗
PubMed1994

DNA sequencing using ultra small amounts of reagents and template.

One of the key points in the genome project is finding ways to reduce the running cost in DNA sequencing. One way is to use a highly-sensitive fluorescent DNA sequencer, where only trace amounts of template DNA and reagents are needed. An experimental protocol optimized for the trace amounts of DNA analysis was established by using the hybridization reaction rate coefficient of primers on template DNA, which was estimated to be 7.5 x 10(5) M-1sec-1 at 37 degrees C. One femtomole of template DNA with 0.001 unit of modified T7 DNA polymerase (Sequenase Ver. 2.0) and also 0.45 fmol of M13 template DNA with 0.01 unit of Taq DNA polymerase were enough to sequence DNA of up to 400 bases.

Bacteriophage M13↗
PubMed2006

[Characteristics and Influencing factors of Sperm Interaction with Exogenous DNA].

Exogenous DNA localization and the frequency of spermatozoa carrying exogenous DNA after sperm/DNA co-culture are key to a successful sperm mediated-gene transfer (SMGT). In the study, the characteristics and influencing factors of exogenous DNA uptake by spermatozoa were tested using digoxigenin (DIG) labeled DNA as trace. Results showed that goat spermatozoa could spontaneously take up exogenous DNA. The exogenous DNA was initially bound to the outer sperm membrane at postacrosomal region; subsequently party of the bound DNA was internalized into nucleus. There were considerable differences in the capability of spermatozoa from different donors to bind and internalize exogenous DNA. In 35 samples, binding rates (before DNase I digestion) and internalization rates (the positive rate after DNase I digestion) varied between 4.6%-62.4% and 2.1%-53.8%, respectively. For the spermatozoa from the same goat, the binding and internalization capacities were mostly inhibited by the seminal fluid. Compared to ejaculate sperm, the binding rate and internalization rate were increased three and five times in washed sperm cells, respectively. At the same time, capacitated spermatozoa also had lower exogenous DNA uptake (P<0.01). Dead spermatozoa did not complete the internalization process. The highest positive rate (before DNase I digestion) was found in membrane-broken spermatozoa as a result of freeze-thawing and this was independent of the sperm donors. These results suggest that selection of appropriate sperm donors and optimization of sperm processing procedures are the key steps for successful SMGT.

Animals↗