Short tandem repeat typing of bodies from a mass disaster: high success rate and characteristic amplification patterns in highly degraded samples.

We have used a PCR-based DNA-typing method, involving the coamplification of four tetrameric short tandem repeat loci, in the analysis of a large number of severely degraded tissue samples taken from the scene of a mass disaster in which bodies were exposed to extreme thermal, physical and chemical insult. Analysis of the amplified DNA in a number of the samples revealed uniquely sized artifact PCR products resulting from the amplification of degraded genomic DNA as well as characteristic patterns in the amounts of PCR products generated from differently sized loci. This system has proved to be very reliable and robust, and we were successful in typing all of the four loci in 66% of the samples tested and at least one locus in 83% of the cases. A PCR-based sex test also proved to be very effective when applied to the degraded samples.

Identification of bodies from the scene of a mass disaster using DNA amplification of short tandem repeat (STR) loci.

The accompanying paper in this issue describes work conducted during a collaborative effort to identify the victims of a mass disaster that occurred on the 19th of April 1993 near Waco, Texas. The DNA identification programme was also used partly as an exercise to further investigate the robustness and reliability of a recently developed STR quadruplex. The preceding paper provides details of the loci used and also deals with efforts to assess the applicability of STR profiling and its suitability for forensic investigations of this nature. In this paper, we present the results obtained from 61 Waco bodies. Using reference blood samples and family trees 26 positive identifications were made using a 'paternity style' analytical approach. Worked examples, representing a range of casework situations, are used to illustrate the kind of approach taken in interpretation of the data and highlight factors which affected its success. Additionally, we report on the successful application of a PCR-based gender test to 24 of the Waco bodies.

Analysis and interpretation of mixed forensic stains using DNA STR profiling.

The use of multiplex PCR and fluorescent dye technology in the automated detection and analysis of short tandem repeat loci provides not only qualitative information about the profile--i.e. which alleles are present--but can also provide quantitative information on the relative intensities of the bands, and is therefore a measure of the amount of amplified DNA. The availability of this quantitative information allows for the interpretation of mixtures in a detailed way which has not been previously possible with many other human identification systems. In this paper we present a simple approach to the resolution and analysis of mixed STR profiles resulting from the testing of mixed biological stains in forensic casework and highlight factors which can affect it. This approach requires a detailed knowledge--gained through a mixture of experiments and validation studies--of the behaviour of each locus within the multiplex systems described. We summarise the available data from previously published experimental work and validation studies to examine the general principles underlying this approach.

Primer binding site mutations affecting the typing of STR loci contained within the AMPFlSTR SGM Plus kit.

The Forensic Science Service carries out human identification and familial investigations using the AMPFlSTR SGM Plus kit (PE Biosystems, Warrington, England). We have studied approximately 42,000 parent/child allelic transfers (meioses) for deviations from expected Mendelian Inheritance patterns. Of 55 apparent mutations detected, 20 had patterns suggestive of the presence of a primer binding site mutation producing a silent/null allele. The presence of a silent allele was unequivocally demonstrated in 13 of the 20 suspected cases by using alternative primer sets. Of the 13 confirmed cases, 9 involved the D18S51 locus. As the individuals in these cases all originated from the same geographic region of the Middle East, this cluster suggests the presence of a relatively common variant D18S51 allele in that particular group. These data taken together with our previously published work, confirm that the primer binding sites utilised for amplification of the loci contained in the AMPFlSTR SGM Plus kit have highly conserved nucleotide sequences.

Further validation of a quadruplex STR DNA typing system: a collaborative effort to identify victims of a mass disaster.

The relatively new, PCR-based technique of Short Tandem Repeat (STR) profiling has been used in the identification of the victims of a mass disaster. The analysis relied upon a recently developed multiplex reaction and the use of automated fluorescence technology to simulataneously analyse four tetrameric STR loci. The performance of the 'quadruplex' test was assessed by use of a collaborative study incorporating a blind trial and was demonstrated to be accurate, reliable and robust. Furthermore, the system proved to be highly successful despite the fact that many of the samples from the mass disaster scene were extremely degraded. The high success rate coupled with the discrimination power of the system enabled many severely decomposed human remains to be positively identified.

Induction of a phi C31 prophage inhibits rRNA transcription in Streptomyces coelicolor A3(2).

A lysogen of Streptomyces coelicolor A3(2) containing a thermoinducible mutant of the temperate phage phi C31 (phi C31 cts1) was used to obtain synchronous phage development. Filter hybridization experiments indicated a marked reduction in rRNA synthesis after prophage induction. S1 nuclease mapping showed that transcription from each of the four promoters of one rRNA gene set (rrnD) was reduced to approximately the same extent, and that inhibition required protein synthesis. Crude preparations of RNA polymerase from induced lysogens had enhanced transcribing activity for phi C31 DNA which was lost upon further purification. The purified preparations were unimpaired in their ability to transcribe from the rrnD promoters in vitro and apparently unchanged in polypeptide composition. The factor(s) responsible for stimulating phage transcription, and possibly for inhibiting rRNA synthesis, may have been separated from the enzyme during purification.

Global transcription pattern of phi C31 after induction of a Streptomyces coelicolor lysogen at different growth stages.

Using two complementary strategies for low-resolution S1 mapping, the global pattern of phi C31 transcription was studied after induction of thermoinducible phi C31 lysogens of Streptomyces coelicolor A3(2). A complex pattern of early transcripts was seen, with a peak of abundance at about 10 min post-induction. Nearly all of these transcripts were from DNA located to the right of the c (repressor) gene and to the left of the attP site: a region of about 14 kb. Early transcription was also observed immediately to the left of the c gene. The c gene itself was also induced, with an earlier expression peak (about 5 min post-induction). Primary late transcripts were generally relatively long, but degraded. They apparently corresponded to most of the 18 kb region to the left of the c gene. Some shorter and more persistent late transcripts corresponded to DNA close to or overlapping the cos site. Large late transcripts from a region close to the left-hand end of the phi C31 genome showed evidence of processing to more stable, smaller RNA species. A failure of older cultures (more than 12 h old) to be induced productively was correlated with a much longer period of early transcription, reduced late transcription, failure to synthesize a major virion protein, and failure to package phi C31 DNA. Moreover, heat treatment of the older lysogenic cultures did not result in the phi C31-dependent shut-down of host rRNA transcription previously observed for young cultures (Rodríguez et al., Journal of General Microbiology (1986) 132, 1695-1701; Clayton & Bibb, Molecular Microbiology (1990) 4, 2179-2185).

Homogenisation and oxygen transfer rates in large agitated and sparged animal cell bioreactors: Some implications for growth and production.

Because of concern for cell damage, very low agitation energy inputs have been used in industrial animal cell bioreactors, typical values being two orders of magnitude less than those found in bacterial fermentations. Aeration rates are also very small. As a result, such bioreactors might be both poorly mixed and also unable to provide the higher oxygen up-take rates demanded by more intensive operation. This paper reports experimental studies both of K( L ) a and of mixing (via pH measurements) in bioreactors up to 8 m(3) at Wellcome and of scaled down models of such reactors at Birmingham. Alongside these physical measurements, sensitivity of certain cell lines to continuously controlled dO(2) has been studied and the oxygen up-take rates measured in representative growth conditions. An analysis of characteristic times and mixing theory, together with other recent work showing that more vigorous agitation and aeration can be used especially in the presence of Pluronic F-68, indicates ways of improving their performance. pH gradients offer a special challenge.

The validation of short tandem repeat (STR) loci for use in forensic casework.

A quadruplex reaction has been developed which amplifies the short tandem repeat (STR) loci HUM-VWA31/A, HUMTHO1, HUMF13A1 and HUMFES/FPS. Detection of the PCR products employs denaturing polyacrylamide gels coupled with fluorescent-based technology. This system has been evaluated for use in routine forensic casework and has been shown to be both robust and reproducible. The quadruplex reaction is as sensitive as the commercially available HLA DQ alpha Amplitype typing system and can be used on both degraded and aged material. The problems of environmental contamination have been shown to be limited provided strict procedural practices are followed-i.e. physical separation of sample extraction and amplified products; the use of dedicated equipment such as pipettes; the separation of amplification preparation area. The ability of the system to detect mixtures and the successful analysis of case stains has shown that this system is well suited as a tool for forensic investigation.

Hepatic intra-arterial delivery of a retroviral vector expressing the cytosine deaminase gene, controlled by the CEA promoter and intraperitoneal treatment with 5-fluorocytosine suppresses growth of colorectal liver metastases.

Targeting of colorectal liver metastases by regional gene therapy was tested in a clinically relevant syngeneic model. First, the CEA-CD-113 retroviral vector containing the cytosine deaminase gene controlled by the CEA specific tumour cell promoter, was shown in vitro to convert 5-fluorocytosine to 5-fluorouracil, resulting in cancer cell killing with a large bystander effect. Second, 10 days after the establishment of liver metastases, retroviral vectors were delivered to the liver by hepatic artery injection. After 5-fluorocytosine administration for 7 days, most surface metastases disappeared and tumour volumes were suppressed up to 8.2-fold. The results support the development of this approach for patient treatment.