Allele frequency distributions at several variable number of tandem repeat (VNTR) and short tandem repeat (STR) loci in a restricted Caucasian population from south Italy and their evaluation for paternity and forensic use

Allele frequencies at six VNTR loci, 11 STR loci, and at the HLA-DQA1 locus were evaluated in a well-defined population from Campania (South Italy). The allele frequencies of three VNTR loci, 11 STR loci, and the HLA-DQA1 locus were compared with data obtained from a general Caucasian reference population in the USA. The aim of this study was to determine the power of each single locus and group of loci for forensic and paternity testing purposes. Significant differences between the allele frequencies of the two populations were found in two VNTR loci, four STR loci and in the HLA-DQA1 locus. The two populations were in Hardy-Weinberg equilibrium for the STR loci, but as expected, not for some VNTR loci. It was also found that: (i) the discriminatory power of two STR systems (nine and 11 loci, respectively) is similar in the two populations analysed; and (ii) that the allele frequencies for the STR systems of a large reference population can always be applied to subjects of a small subpopulation. In conclusion, for forensic purposes and for paternity testing, most of the 11 STR loci examined can be analysed using allele frequencies from a general Caucasian reference population without typing subpopulations, whereas the VNTR loci must be subtyped.     

United States population data on the multiplex short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--and the variable number tandem repeat locus D1S80

Allele frequencies for three tetrameric short tandem repeat (STR) loci HUMTHO1, TPOX, and CSF1PO and a variable number tandem repeat locus D1S80 were determined in United States Caucasian, African American, and Hispanic sample populations. All loci, except the TPOX locus in the Caucasian sample population, meet Hardy-Weinberg expectations. There is no evidence for association of alleles among the four loci. The allelic frequency data are similar to other comparable data within the same major population group.     

Sequence variation of a variable short tandem repeat at the D18S535 locus

A short tandem repeat in the D18S535 locus was sequenced in 25 selected alleles. A total of 8 different alleles were found which can be designated according to the total number of repeats. This STR is a simple hypervariable STR consisting of blocks of (GATA) repeats with a basic sequence structure (GATA)1(GACA)1(GATA)1 (GAT)1(GATA)9-16. Population data showed that this is a highly polymorphic STR with a heterozygosity of more than 0.80, a simple structure and small size (130-158 bp) which makes this an interesting DNA polymorphism for forensic and genetic purposes.     

Short tandem repeat (STR) locus HUMD8S306 in a large population sample from Germany

Applied DNA typing in medico-legal investigations, in criminalistic practice, and in paternity cases often relies on high inclusion and exclusion probabilities. For that reason, the short autosomal tandem repeat locus D8D306 was validated for forensic use and incorporated into a nonoverlapping multiplex reaction with HUMDHFRP2 and HUMCD4: The allele frequencies of D8S306 in four different regions of Germany (n = 1220 alleles) were determined for use in a population database; the allele distributions did not significantly deviate from each other. The hererozygosity of D8S306 is 83%, expected exclusion chance in stain cases is 96% (paternity cases: 69%), the lowest amount of successfully amplified DNA was 30 pg. The alleles are in Hardy-Weinberg equilibrium.     

Band shift analysis of three base-pair repeat alleles in the short tandem repeat locus D12S391

The effect of Pseudomonas aeruginosa (PA) exotoxin A (P-ExA) on CD3-induced T-cell activation was studied on the level of T-cells (proliferation, synthesis of interleukin (IL)-2, expression of IL-2R complex, ICAM-1,2 and LFA-1 molecules), and on the level of monocytes (expression of ICAM-1,2, LFA-1 molecules, as well as FcRI and CD14 receptors). We found that: (1) P-ExA blocked T-cell proliferation and this effect was totally reversed by intact monocytes, and partially by IL-2 or TPA but not by costimulatory cytokines (IL-1alpha, IL-1beta, TNF-alpha or IL-6); (2) P-ExA transiently, in short-term cultures (48 h), inhibited synthesis of IL-2; (3) prolonged stimulation (96 h) of peripheral blood mononuclear cells (PBMC) or CD4 + T-cells with P-ExA in high or low doses (100 and 10 ng/ml, respectively), enhanced the level of IL-2 in the cultures; (4) P-ExA at low dose, combined with IL-1beta, TNF-alpha or IL-6, up-regulated synthesis of IL-2; and (5) stimulation of T-cells with anti-CD3 monoclonal antibody (mAb) and P-ExA at high dose diminished the expression of the p55 chain but not of the p75 chain of IL-2R complex and slightly affected the expression of CD3 complex, ICAM-1,2 and LFA-1 molecules. Hence, P-ExA can regulate the level of IL-2 in cultures of CD3-induced T-cells either by inhibition of IL-2 consumption (when P-ExA is applied in high dose), or by induction of IL-2 production (a costimulatory effect exerted by P-ExA in low dose in combination with monokines). Action of P-ExA on monocytes resulted in: (1) inhibition of the expression of ICAM-1,2 molecules and their ligand LFA-1 molecule; (2) low expression of FcRI receptor (a ligand for Fc part of CD3 mAb); and (3) inhibition (over 90%) of the expression of CD14 molecule. In conclusion, P-ExA-induced anergy of T-cells depends on: (a) decrease in the affinity of IL-2R complex on activated T-cells; and (b) inhibition of the accessory activities of monocytes.     

Typing of the short tandem repeat D8S347 locus with different fluorescence markers

The short tandem repeat (STR) locus D8S347 was analyzed by capillary electrophoresis. Sequencing data and a population study of 203 individuals from a southwestern German population are presented. We detected 12 different alleles, 340-388 bp in length, and found 40 different genotypes. The heterozygosity index was 85.7%. Futhermore, we investigated the consequences of different fluorescent dyes, namely 6-FAM, HEX, and ROX, on the ABI-calculated fragment sizes of defined (i.e., sequenced) alleles (348-376 bp in length). 6-FAM-labeled fragments appear to be smaller than the corresponding HEX- or ROX-labeled fragments. On average, 6-FAM-labeled fragments differ by 3.52 bp from the sequencing data, HEX-labeled ones by 2.04 bp, and ROX-labeled ones by 1.42 bp. Generally, small alleles differ less from the expected sequencing data than larger ones.     

Instability in the ATCT variable number tandem repeat locus VWF.VNTR I in intron 40 of von Willebrand factor gene

The von Willebrand factor gene intron 40 variable number tandem repeat VWF.VNTR I exhibits 10 alleles making it highly polymorphic and useful for parentage and forensic testing, 45 unrelated families (210 meiotic events) were tested for VWF.VNTR I alleles. One spontaneous mutation was observed in a family member. Haplotype analysis demonstrated that this mutation was due to a gain of one motif repeat by a paternal allele. Sequence analysis confirmed the difference in the number of motif repeats between the proband and the alleles expressed by the parents. This instability emphasizes the importance of demonstrating exclusion in at least two separate loci in parentage testing.     

Analysis of variable number of tandem repeats of human genome D1S80 locus using capillary electrophoresis with laser-induced fluorescence detector

The conventional method of identifying individuals by DNA in the field of forensic medicine is slab gel electrophoresis, which is time-consuming, labor-intensive, and nonquantitative. Accordingly, the use of capillary electrophoresis with a laser-induced fluorescence detector (CE-LIF), human genome D1S80 locus, a DNA marker which has a variable number of tandem repeats (VNTR) on chromosome 1, was examined to improve DNA analysis for identification. Using an internal standard, fragment size of VNTR was accurately and rapidly determined.     

Analysis of nine short tandem repeat (STR) loci in the Slovenian population

A polymerase chain reaction (PCR)-based short tandem repeat (STR) system consisting of nine loci has recently been introduced in Slovenia for use in routine forensic identity testing. Fluorescently labelled PCR products were analysed using an ABI PRISM 310 Genetic Analyzer. The STR loci analysed exhibit between 6 and 14 observed alleles per locus and have a combined matching probability of 2.3 x 10(-10).     

Polymerase chain reaction typing of D21S11 short tandem repeat polymorphism by capillary electrophoresis. Allele frequencies and sequencing data in a population sample from central Italy

One component of the mechanism by which imidazoline compounds promote insulin secretion involves closure of ATP-sensitive K+ channels in the beta-cell plasma membrane. Recently, however, it has also been proposed that these compounds may exert important effects on more distal effector systems. In the present work, we have investigated the contribution played by protein kinases A and C to the insulin secretory responses of isolated rat islets of Langerhans treated with efaroxan and RX871024 (1-phenyl-2-(imidazolin-2-yl) benzimidazole). Removal of extracellular Ca2+ or blockade of voltage-sensitive Ca2+ channels prevented stimulation of insulin secretion by efaroxan, confirming a critical role for increased Ca2+ influx in the secretory response. By contrast, inhibition of protein kinases A or C failed to alter efaroxan-induced insulin secretion. RX871024 dose-dependently increased insulin secretion from cultured islets incubated with 20 mM glucose. This effect was unaffected by modulation of protein kinase C, but was significantly attenuated by a selective inhibitor of protein kinase A (Rp-cAMPs). Measurements of cAMP revealed that RX871024 increased the islet cAMP content by more than 3-fold; reaching values similar in magnitude to those elicited by 50 microM 3-isobutyl-1-methyl xanthine. The results reveal that neither protein kinase A nor protein kinase C is obligatory for stimulation of insulin secretion by imidazolines. However, they suggest that a rise in cAMP may contribute to the amplified secretory response observed when cultured islets are incubated with RX871024 in the presence of a stimulatory glucose concentration.     

Analysis of allele distribution for six short tandem repeat loci in the French Canadian population of Québec

Short tandem repeat (STR) loci represent a rich source of highly polymorphic markers in the human genome which are useful for the purposes of forensic identification and determination of biological relatedness of individuals. Here, as a part of an ongoing extensive study, we report the analysis of a multilocus genotype survey of 642 to 870 chromosomes in the French Canadian Caucasian population of Québec at six STR loci. The loci HUMCSF1PO, HUMTPOX, HUMTH01, HUMF13A01, HUMFESFPS, and HUMvWA were typed using two multiplex polymerase chain reactions (PCR). Amplified DNA samples were subsequently analyzed by polyacrylamide gel electrophoresis followed by silver staining. The heterozygote frequencies of the loci range from 0.614 to 0.820 (0.661 to 0.818 expected) and the number of alleles from 7 to 12 per locus. Although statistically significant deviation from Hardy-Weinberg expectations of genotype frequencies was noted at some loci by one or more tests, in general, the genotype frequencies are well estimated from the product of allele frequencies at all loci. The most frequent six-locus genotype is expected to occur in the French Canadian population with a frequency of 3.50 by 10(-5) and together, these six loci have an average probability of discrimination of 0.9999985. The study presented here indicates that these six STR loci are informative genetic markers for identity testing purposes in the French Canadian Caucasian population of Québec.     

Development and population study of an eight-locus short tandem repeat (STR) multiplex system

Amplification of short tandem repeat (STR) loci has become a useful tool for human identification applications. To improve throughput and efficiency for such uses, the polymorphic STR loci CSF1PO, TPOX, TH01, vWA, D16S539, D7S820, D13S317, D5S818, F13A01, FESFPS, F13B, and LPL have been evaluated, developed, and configured into fluorescently labeled multiplex systems. Eight of these STR loci were combined to generate the PowerPlex System, a two-color multiplex system that supports rapid, accurate, reliable analysis and designation of alleles. The remaining four loci comprise the FFFL System, a one-color multiplex system. The PowerPlex System may be evaluated alternatively as two one-color, four-locus multiplex systems, CTTv Multiplex and GammaSTR Multiplex. The products of multiplex amplification may be analyzed with a variety of fluorescence detection instruments. Determination of genotypes of over 200 individuals from each of three different population/ethnic groups revealed independence of inheritance of the loci and allowed calculation of matching probability, typical paternity index, and power of exclusion for each multiplex.     

Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology

Analysis of mitochondrial (mt)DNA size polymorphism in the form of variable number tandem repeats (mtVNTRs) has become an increasingly popular methodology for addressing questions in molecular ecology. When detected by PCR, mtVNTR analysis can provide a sensitive, rapid, and cost-effective measure of genetic variability that may be exploited in studies of population differentiation and biogeography. Despite the emergence of this approach, there has been little critical evaluation of its success or utility as a practical tool. In this review, we identify problematic methodological, theoretical and interpretive factors that can influence the utility of mtVNTR analysis. The reliability of the procedure is considered in terms of both detection of alleles and scoring of intra-individual allele frequencies. While many of the potential technical problems of the technique do not raise serious practical concerns, this rapid and sensitive methodology is seriously compromised by the difficulty of reliably assessing allele frequencies, of assaying only germline tissue, and in our ignorance of the mechanisms generating mtVNTR diversity. Thus, although there is a considerable potential for mtVNTR pilot studies to assess genetic diversity, the utility of the technique to resolve broader questions in molecular ecology should be treated cautiously until such a time as the system is better understood.     

A comparison of a 30-cluster survey method used in India and a purposive method in the estimation of immunization coverages in Tamil Nadu

The reaction mechanisms of p-nitrophenyl phosphate hydrolysis catalyzed by two rat liver isoenzymes of the low M(r) phosphotyrosine protein phosphatase (AcP1 and AcP2) were compared. Furthermore, the effect of some heterocyclic compounds on their activities were tested. Cyclic GMP and guanosine causes a particularly high activation of the isoenzyme AcP2, whereas its effect on AcP1 is very poor. A study on the mechanism of cyclic GMP activation was carried out. The results suggest that cyclic GMP activates the AcP2 isoenzyme by increasing the rate of the step that leads to the hydrolysis of the covalent enzyme-substrate phosphorylated complex formed during the catalytic process. The physiological significance of cyclic GMP activation of only one of the two isoenzymes (AcP2) remains uncertain.     

Minisatellite variant repeat (MVR) analysis of the HRAS1 minisatellite locus

Two alternative electrophoretic strategies were used to study the internal variation of the HRAS1 minisatellite after minisatellite variant repeat mapping (MVR-PCR) was carried out. While the use of automated sequencers with fluorescent based technology is ideal for analyzing fragment size, and therefore, for analyzing the repeat number, the use of polyacrylamide gels and silver staining is more appropriate for the analysis of internal variation. Thirteen different fragments ranging from 27 to 80 repeats were found in a sample from 80 healthy Caucasian individuals. By using MVR mapping we were able to detect heterozygotes which appear as homozygotes when fragment length analysis was used. As a result of this, the 13 alleles, which we had detected, increased to 16 alleles when MVR sequences were analyzed. The extremely conservative arrays of repeats allow us to infer the theoretical origin of rare alleles from a major group of specific alleles. The HRAS1 minisatellite has been extensively studied due to its association with cancer. However, the methodology used up to now has limited the scope of previous research. Our approach permits the identification of alleles in a fast and reliable way using their MVR codes, thus allowing association studies with cancer.     

D4S43 locus DNA typing in the Japanese population and application to teeth with degraded DNA

The purpose of this research was to determine the incidence and intensity of infection in experimental host of minute intestinal trematode, Stellantchasmus falcatus (family Heterophyidae). Experimental hosts consisting of uninfected mice (Mus musculus) and one-day-old chicks (Gallus gallus domesticus) were orally force fed with a hundred metacercariae of S. falcatus obtained from the body cavity of the freshwater fish Dermogenys pusillus. The worms, then, were checked from 24 hours to 30 days post-infection. The heterophyid flukes were distributed in the ileum and jejunum of the chicks and small intestine of mice with 70% (21/30) and 80% (24/30) of incidence and intensity of infection range from 1-44 (24.6) and 1-67 (7.8), respectively. The body size of S. falcatus at 24 hours; was 0.1-0.15 (0.13) x 0.29-0.39 (0.33) mm in chicks and 0.14-0.17 (0.15) x 0.29-0.32 (0.3) mm in mice. The maximum length and width of the worms were found within 5 days post-infection, of 0.2-0.25 (0.22) x 0.49-0.62 (0.55) in chicks and 0.19-0.22 (0.2) x 0.38-0.52 (0.44) mm in mice. Developing egg was found in the second day after infection and the number of egg increase with the age of the parasite. Embryonated eggs were recovered in the feces of mice 9 day post-infection. S. falcatus infection in the other experimental host was done in rat (Rattus norvegicus), but rats were fed with whole number of metacercariae which found in a body cavity of fish, D. pusillus. The results appear to be the same as in the chicks and mice.     

Allele distribution at nine STR loci--D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820--in the Japanese population by multiplex PCR and capillary electrophoresis

Nine tetranucleotide short tandem repeat (STR) loci, D3S1358, vWA, FGA TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820, were analyzed in the Japanese population with a newly released kit for personal identification using multiplex PCR with fluorescent-labeled primers following capillary electrophoresis. The observed heterozygosities were 0.67, 0.77, 0.82, 0.61, 0.62, 0.73, 0.78, 0.81 and 0.74, respectively, and the combined discrimination power of the nineplex was 0.9999999991. None of the nine loci deviated from Hardy-Weinberg equilibrium expectations using the chi-square test, homozygosity test, likelihood ratio test and exact test after the grouping of the alleles. The nine STR loci allele frequencies were significantly different from those of other ethnic populations.     

The variable number of tandem repeats in the renin gene of rats and possible significance in hypertension

The variable number of tandem repeats (VNTR) in the first intron of renin gene for the spontaneously hypertensive rat (SHR), its controls Wistar-Kyoto (WKY), renal hypertensive rat, and Sprague-Dawley rat (SD) were compared by polymerase chain reaction (PCR) method. An analysis of VNTR from WKY, Wistar and SD showed that there are two different renin gene alleles and three genetypes 2.0kb/2.0kb, 2.0kb/1.8kb, 1.8kb/1.8kb. The genetype from renal hypertensive rats is same as those seen in the normal controls. However, compared with the WKY, Wistar and SD genes, a "deletion" of approximately 1.0kb was found in the first intron of the SHR renin gene. Our results strongly suggest that the cause and mechanism of elevated blood pressure is complex, and the molecular basis of the genetic-prone hypertension is existed.     

Report of the European DNA profiling group (EDNAP)--towards standardisation of short tandem repeat (STR) loci

BACKGROUND AND PURPOSE: We sought to examine risk factors for all strokes and for ischemic stroke and primary intracerebral hemorrhage separately. METHODS: This was a population-based case-control study. Each case subject meeting World Health Organization criteria for stroke (n = 536) from a population-based register of acute cerebrovascular events compiled in Perth, Western Australia, in 1989 to 1990 was matched for age and sex with up to five control subjects drawn from the same geographical area. Objective confirmation of the type of stroke was available from computed tomography, magnetic resonance imaging, or necropsy for 86% of the case subjects. Data on medical history and lifestyle factors were collected from case and control subjects by interview of the subject or a proxy informant. RESULTS: Current smoking, consumption of meat more than four times weekly, and a history of hypertension or intermittent claudication were each associated with increased risk in multivariate models for all strokes and for all first-ever strokes. Consumption of 1 to 20 g/d alcohol in the preceding week was associated with a significant reduction in the risk of all strokes, all ischemic strokes, and of primary intracerebral hemorrhage, while eating fish more than two times per month appeared to protect against first-ever stroke and against primary intracerebral hemorrhage. Diabetes mellitus was associated with a significantly increased risk of ischemic stroke but a decreased risk of hemorrhagic stroke. CONCLUSIONS: Risk factors for ischemic and hemorrhagic stroke are not exactly the same. Changes in lifestyle relating to tobacco and diet might make important contributions to further reductions in the incidence of stroke.     

Cellular distribution of calbindin D28K mRNAs in the adult mouse brain

Catching a moving object requires the ability to predict the future trajectory of the object. To test whether infants can use visual information predictively, reaching for a toy moving at different speeds was investigated in six infants around 11 months of age. The toy was occluded from view by a screen during the last part of its approach. Gaze arrived at the exit side of the screen and the hand started to move forward before the toy had disappeared behind the occluder; these actions were prospectively geared to certain times before the toy would reappear. In addition, hand-movement duration was found to be related to the time of reappearance of the toy--the information used to regulate duration of hand movement being picked up before the toy disappeared behind the occluder. In a longitudinal experiment, the development of predictive reaching was investigated in two infants between the ages of 20 and 48 weeks. At all ages studied, gaze anticipated the reappearance of the moving toy. However, anticipation with hand movement of the disappearance of the toy and the ability to gear actions prospectively to the time (instead of distance) the toy was away from certain points on the track developed relatively late and marked the transition to successfully catching faster-moving toys.