A computational model for cell differentiation.

In this paper, we present a word set generating mechanism, called cell-differentiation system, inspired by the tissue process formation in multicellular organisms, which might model some properties of evolving communities of living cells at the syntactical level. The tools utilized to model these biological phenomena belong to the formal language theory. In this context chromosomal mutations are defined as operations on strings and the differentiation according to the control of gene expression is represented by some random-context conditions in formal languages. In the presented formal framework we prove that in a simplified form of this formalism, with only one cell-type which is regular, one single cell and no mitosis involved, the problem of establishing whether or not the set of vectors of integers indicating the number of cells in each population, is finite, linear or semilinear, is recursively undecidable. However, one can algorithmically decide whether or not a cell-differentiation system of finite cell-type can produce a specific generation of cells.

Results of a collaborative study of the EDNAP group regarding the reproducibility and robustness of the Y-chromosome STRs DYS19, DYS389 I and II, DYS390 and DYS393 in a PCR pentaplex format.

A collaborative exercise was carried out by the European DNA Profiling Group (EDNAP) in the frame work of the STADNAP program, i.e. standardization of DNA profiling in Europe, in order to evaluate the performance of a Y-chromosome STR pentaplex, which includes the loci DYS19, DYS389 I and II, DYS390 and DYS393 and to determine whether uniformity of results could be achieved among different European laboratories. Laboratories were asked to analyze the five Y-STRs using singleplex and multiplex conditions in three bloodstains and one mixed stain (95% female and 5% male). All the laboratories reported the same results even for the mixed stain included in the exercise. This demonstrates the reproducibility and robustness of Y-chromosome STR typing even with multiplex formats and proves the usefulness of Y-STR systems for analyzing mixed stains with a male component.A total of 930 male samples from 10 different populations from Europe were also analysed for all the loci included in the pentaplex. Eight of these ten populations also included haplotype data. As for single gene analysis, haplotype diversity was higher in Germany and Italy and lower in Western European countries and Finland. Pairwise haplotype analysis shows the Finnish departure from the rest of the populations and a relatively homogeneity in the other European populations with F(ST) estimates lower than 0.05.UPGMA analysis shows an association of Western European population (Ireland, UK, Portugal and Galicia) on the one hand and central European populations on the other.

New computing paradigms suggested by DNA computing: computing by carving.

Inspired by the experiments in the emerging area of DNA computing, a somewhat unusual type of computation strategy was recently proposed by one of us: to generate a (large) set of candidate solutions of a problem, then remove the non-solutions such that what remains is the set of solutions. This has been called a computation by carving. This idea leads both to a speculation with possible important consequences--computing non-recursively enumerable languages--and to interesting theoretical computer science (formal language) questions.

Reproducibility of mtDNA analysis between laboratories: a report of the European DNA Profiling Group (EDNAP).

The aim of this collaborative exercise was to determine whether uniformity of mtDNA sequencing results could be achieved among different EDNAP laboratories. Laboratories were asked to sequence mtDNAHV1 region (16024-16365) from three bloodstains, proceeding in accordance with the protocol and strategies currently used in each individual laboratory. Cycle sequencing was used by 11 laboratories and solid phase single stranded sequencing was used by one laboratory. Different PCR strategies and PCR conditions were used by the different laboratories. Three laboratories used semi-nested PCR, two nested PCR, three direct amplification of HV1 and four amplification of overlapping fragments covering the HV1 region. Despite the diversity of methodologies used, all the laboratories reported the same results. The successful result of this exercise shows that PCR based mtDNA typing by automated sequencing is a valid, robust and reliable means of forensic identification despite the different strategies and methodologies used by the different laboratories.

Population data on the loci LDLR, GYPA, HBGG, D7S8, and GC in three southwest European populations.

Three Southwest European populations: Galicia (NW Spain), a mixed Spanish population from the rest of Spain (outside Galicia), and a population sample from the Coimbra area (Centre of Portugal) have been studied for the Low Density Lipoprotein Receptor (LDLR), Glycophorin A (GYPA), Hemoglobin G Gammaglobin (HBGG), D7S8 and Group Specific Component (GC). The allele and genotype frequencies found have been compared with other previously published data. All loci meet Hardy-Weinberg expectations in the three sampled populations. There was no evidence of association in any of the three population samples, between the five loci studied. No significant differences were found with Caucasian populations, nevertheless, significant differences were observed between our three population studies and the US SW Hispanic and African populations. The AmpliType PM DNA test greatly facilitates DNA testing in forensic laboratories, providing quick results and a good discrimination power from a single test.

The distribution of HLA DQA1 and D1S80 (pMCT118) alleles and genotypes in the populations of Galicia and central Portugal.

Two South-West European populations (Galicia and Central Portugal) have been studied for the HLA DQA1 and D1S80 systems. The allele and genotype frequencies found have been compared with other previously published data. The distribution of the observed genotypes is in Hardy-Weinberg equilibrium for both systems. In the D1S80 system, no significant differences were found between both populations, although in the HLA DQA1 system the allele DQA1*0301 is twice as frequent in the Galician population. Other populations that have been compared showed a certain degree of divergence for the HLA DQA1 system. The combined chance of exclusion for both systems is 0.84 in Galicia and 0.85 in Central Portugal, and the combined power of discrimination is 0.993 in the 2 populations studied.

Orosomucoid (ORM1 and ORM2) types in the Spanish Basque Country, Galicia and northern Portugal.

The genetic variation of orosomucoid (ORM1 and ORM2) in three south-western European populations (Galicia, Spanish Basque Country and northern Portugal) was investigated using hybrid isoelectric focusing. Three common ORM1 alleles were observed in these populations, the frequencies of ORM1 *S observed in Galicia and northern Portugal being the highest found among populations of European origin. Rare variants were observed for both the ORM1 and ORM2 loci.

Fast isoelectric focusing of some polymorphic proteins and enzymes in miniaturized gels using an automated system.

Optimal programs for the separation of polymorphic proteins and enzymes in miniaturized polyacrylamide gels using an automated system (PhastSystem) are described. The potential advantages and disadvantages of the method and its application to forensic science laboratories are discussed.