Integrated portable genetic analysis microsystem for pathogen/infectious disease detection.

An integrated portable genetic analysis microsystem including PCR amplification and capillary electrophoretic (CE) analysis coupled with a compact instrument for electrical control and laser-excited fluorescence detection has been developed. The microdevice contains microfabricated heaters, temperature sensors, and membrane valves to provide controlled sample positioning and immobilization in 200-nL PCR chambers. The instrument incorporates a solid-state laser and confocal fluorescence detection optics, electronics for sensing and powering the PCR reactor, and high-voltage power supplies for conducting CE separations. The fluorescein-labeled PCR products are amplified and electrophoretically analyzed in a gel-filled microchannel in <10 min. We demonstrate the utility of this instrument by performing pathogen detection and genotyping directly from whole Escherichia coli and Staphylococcus aureus cells. The E. coli detection assay consists of a triplex PCR amplification targeting genes that encode 16S ribosomal RNA, the fliC flagellar antigen, and the sltI shigatoxin. Serial dilution demonstrates a limit of detection of 2-3 bacterial cells. The S. aureus assay uses a femA marker to identify cells as S. aureus and a mecA marker to probe for methicillin resistance. This integrated portable genomic analysis microsystem demonstrates the feasibility of performing rapid high-quality detection of pathogens and their antimicrobial drug resistance.

High-throughput genetic analysis using microfabricated 96-sample capillary array electrophoresis microplates.

Capillary array electrophoresis (CAE) microplates that can analyze 96 samples in less than 8 min have been produced by bonding 10-cm-diameter micromachined glass wafers to form a glass sandwich structure. The microplate has 96 sample wells and 48 separation channels with an injection unit that permits the serial analysis of two different samples on each capillary. An elastomer sheet with an 8 by 12 array of holes is placed on top of the glass sandwich structure to define the sample wells. Samples are addressed with an electrode array that makes up the third layer of the assembly. Detection of all lanes with high temporal resolution was achieved by using a laser-excited confocal fluorescence scanner. To demonstrate the functionality of these microplates, electrophoretic separation and fluorescence detection of a restriction fragment marker for the diagnosis of hereditary hemochromatosis were performed. CAE microplates will facilitate all types of high-throughput genetic analysis because their high assay speed provides a throughput that is 50 to 100 times greater than that of conventional slab gels.

High-speed DNA genotyping using microfabricated capillary array electrophoresis chips.

Capillary array electrophoresis (CAE) chips have been designed and fabricated with the capacity to rapidly (< 160 s) analyze 12 different samples in parallel. Detection of all lanes with 0.3 s temporal resolution was achieved using a laser-excited confocal-fluorescence scanner. The operation and capabilities of these CAE microdevices were first determined by performing electrophoretic separations of pBR322 MspI DNA samples. Genotyping of HLA-H, a candidate gene for the diagnosis of hereditary hemochromatosis, was then performed to demonstrate the rapid analysis of biologically relevant samples. Two-color multiplex fluorescence detection of HLA-H genotypes was accomplished by prelabeling the standard pBR322 MspI DNA ladder with a red emitting bis-intercalation dye (butyl TOTIN) and on-column labeling of the HLA-H DNA with thiazole orange. This work establishes the feasibility of using CAE chips for high speed, high-throughput genotyping.

Evaluation of new primers for CSF1PO.

We describe new primers for the detection of the STR polymorphism at the CSF1PO locus. These primers have been designed to produce shorter amplicons (150-182 bp) than the primers in standard use (295-327 bp). The reliability of the new primers for CSF1PO typing has been demonstrated by testing on known samples and by sequence analysis. These primers are superior to the original primers with regard to electrophoretic resolution and utility for typing of severely degraded DNA.

DNA sequencing using a four-color confocal fluorescence capillary array scanner.

The design, construction and operation of a four-color capillary array electrophoresis scanner are presented. The use of sensitive energy transfer primers facilitates four-color detection of the DNA sequencing fragments following excitation at a single laser wavelength (488 nm). This scanner collects fluorescence data from up to 25 capillaries in parallel. The resulting four-color image files are automatically reduced to four-color line plots, and a base-calling program (Sax) is used to call the sequence. The performance of this system for DNA sequencing is demonstrated by examining twelve different motifs of the hypervariable region I of human mitochondrial (mt) DNA obtained from a Sierra Leone population.

High-resolution capillary array electrophoretic sizing of multiplexed short tandem repeat loci using energy-transfer fluorescent primers.

Short tandem repeat regions (STRs) from the polymorphic loci VWFA, THO1, TPO and CSF were amplified by the multiplex polymerase chain reaction (PCR) and analyzed by capillary array electrophoresis with fluorescence detection of energy transfer (ET) labels. The fluorescent ET primers are labeled with one fluorescein at the 5' end and a second fluorescein at the position of the 7th or 9th (modified) base to produce fragments that fluoresce in the green (lambda max = 525 nm). M13 A-track sequencing fragments, used as an internal sizing standard, were generated with a universal primer that has a donor fluorescein at the 5' end and a rhodamine acceptor at the position of the 11th (modified) base to produce fragments fluorescing in the red (> 590 nm). The labeled DNA fragments were excited at 488 nm, and the fluorescence was detected with a two-color confocal fluorescence scanner. Separations were performed on arrays of hollow fused silica capillaries filled with denaturing and replaceable hydroxyethyl cellulose sieving matrices. Separations were complete in less than 50 min, and single base resolution as well as reproducible STR sizing was achieved. The relative standard deviation in sizing was below 0.6%. This work establishes the feasibility of high-resolution, high-speed and high-throughput STR typing of single-stranded DNA fragments using capillary array electrophoresis.

Characterization of a recombinant that locates the hereditary hemochromatosis gene telomeric to HLA-F.

The gene responsible for hereditary hemochromatosis has been shown to be closely linked to the HLA-A and D6S105 loci on the short arm of chromosome 6. Efforts at mapping the disease gene have been hindered, however, by a lack of informative recombinant in this region. We have identified two recombinant individuals in a single affected family and have confirmed recombination by analysis of 16 polymorphic markers located near HLA-A and D6S105. One of the recombinants provides evidence for the location of the hemochromatosis gene telomeric to HLA-F.

Rapid sizing of short tandem repeat alleles using capillary array electrophoresis and energy-transfer fluorescent primers.

Genetic typing of the short tandem repeat (STR) polymorphism HUMTHO1 has been performed using capillary array electrophoresis and energy-transfer fluorescent dye-labeled polymerase chain reaction primers. Target alleles were amplified by use of primers labeled with one fluorescein at the 5' end and another fluorescein at the position of the 15th (modified) base to produce fragments that fluoresce in the green (lambda max = 525 nm). Unknown alleles were electrophoretically separated together with a standard ladder made up of alleles having 6, 7, 8, and 9 four-base pair repeats, each of which was amplified with an energy-transfer primer having a donor fluorescein at the 5' end and a rhodamine acceptor at the position of the 7th (modified) base to produce standard fragments fluorescing in the red (> 590 nm). Separations were performed on arrays of hollow fused-silica capillaries filled with a replaceable sieving matrix consisting of 0.8% hydroxyethyl cellulose plus 1 microM 9-aminoacridine to enhance the resolution. The labeled DNA fragments were excited at 488 nm, and the fluorescence was detected with a two-color confocal fluorescence scanner. Separations are complete in less than 20 min and allow sizing with an average absolute error or accuracy of less than 0.4 base pair and an average standard deviation of approximately 0.5 base pair with no correction for mobility shift and cross-talk between the fluorescence channels. This work establishes the feasibility of high-speed, high-throughput STR typing of double-stranded DNA fragments using capillary array electrophoresis.

Exon structure at the human ACP1 locus supports alternative splicing model for f and s isozyme generation.

The human ACP1 locus encodes a genetically polymorphic cytoplasmic low-molecular-weight acid phosphatase. Each of the common alleles encodes two isoforms, f and s. Both isozymes are of equal length (157 residues) but differ in sequence over an internal 34 residue segment. Substantial portions of the ACP1*A, *B and *C alleles common to Europeans have been sequenced. Six linearly positioned exons containing codons 14 to 157 were identified. Two exons of equal length (114bp) interspaced by a short (41bp), probably nonfunctional, intron encode the specific f and s segments, respectively. These findings strongly support an alternative RNA splicing hypothesis. In addition, three allele-specific base substitutions were encountered.

Sexual abuse of children. The detection of semen on skin.

OBJECTIVE: The detection of semen on the skin of children who present within 72 hours of an episode of sexual assault is critical to medical, forensic, and legal personnel. The Wood's Lamp, a UV light that causes semen to fluoresce, and four forensic laboratory techniques were compared to determine their sensitivity and decline in sensitivity over time. DESIGN: A descriptive study. PARTICIPANTS: Eleven adult female volunteers. MEASUREMENTS/MAIN RESULTS: Semen was placed on the skin of the volunteers. Samples of the dried semen were assessed during a 28-hour period with the Wood's Lamp, microscopy, the acid phosphatase assay, and two assays for the prostatic protein p30 (counterimmunoelectrophoresis and enzyme-linked immunosorbent assay). The intensity of the Wood's Lamp fluorescence of semen diminished dramatically by 28 hours; in contrast, the fluorescence of urine persisted up to 80 hours. Over time, the p30-enzyme-linked immunosorbent assay technique was more sensitive than microscopy, the acid phosphatase assay, and p30-counterimmunoelectrophoresis in detecting semen on skin. CONCLUSIONS: The Wood's Lamp is not a sensitive screening tool and should be used with caution. To improve the detection of sexual abuse in children, we recommend that the p30-enzyme-linked immunosorbent assay be used because of its potential as a more sensitive assay than those in current clinical use.

Human red cell acid phosphatase (ACP1). The amino acid sequence of the two isozymes Bf and Bs encoded by the ACP1*B allele.

The pair of isozymes, Bf and Bs, encoded by the human red cell acid phosphatase ACP1*B allele has been sequenced. Similar but not identical primary structures were observed. Both isozymes consist of a single peptide chain of 157 amino acid residues, which is acetylated at the amino-terminal alanine residue. The Bf and Bs isozymes are not glycosylated, and the calculated molecular masses are 17,932 and 17,867 Da, respectively. They are identical except for the sequence segment 40-73, which is peculiar to the respective isozyme. This is consistent with our hypothesis that the two isozymes are generated as the result of alternative splicing of the primary RNA transcript. The finding of a signature sequence offers the basis for the characteristic differences in catalytic and molecular properties of the Bf and Bs isozymes. A high degree of homology was found between the Bs isozyme and the 18-kDa cytosolic acid phosphatase from bovine liver. No homology was observed with other sequenced proteins, and this establishes these low molecular weight acid phosphatases as products of a distinct gene family.

Seminal plasma protein p30: simplified purification and evidence for identity with prostate specific antigen.

A rapid high yield purification scheme is described for the major 30,000 molecular weight glycoprotein (p30) in human seminal plasma. Immunological and protein sequence evidence demonstrates the identity of this protein with prostate specific antigen (PSA) and gamma-seminoprotein (gamma SM).

DNA typing from single hairs.

The characterization of genetic variation at the DNA level has generated significant advances in gene and disease mapping, and in the forensic identification of individuals. The most common method of DNA analysis, that of restriction fragment length polymorphism (RFLP), requires microgram amounts of relatively undegraded DNA for multi-locus typing, and hundreds of nanograms for single-locus comparisons. Such DNA frequently cannot be obtained from forensic samples such as single hairs and blood stains, or from anthropological, genetic or zoological samples collected in the field. To detect polymorphic DNA sequences from single human hairs, we have used the polymerase chain reaction (PCR), in which specific short regions of a gene can be greatly amplified in vitro from as little as a single molecule of DNA. We have detected genetically variable mitochondrial and nuclear DNA sequences from the root region of shed, as well as freshly-plucked, single hairs; mitochondrial DNA (mtDNA) sequences have been detected in a sample from a single hair shaft. We have used three different means of DNA typing on these samples: the determination of amplified DNA fragment length differences, hybridization with allele-specific oligonucleotide probes, and direct DNA sequencing.

Human red cell acid phosphatase (ACP1): evidence for differences in the primary structure of the two isozymes encoded by the ACP1*B allele.

Molecular properties of the two isozymes expressed by the B allele at the red cell acid phosphatase locus (ACP1) have been studied to distinguish between possible mechanisms for their production. The difference in electric charge exhibited by the native isozymes was retained under denaturing conditions; the unfolded peptide chains renatured without conversion of one form to the other. Chromatographic analysis [thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC)] of tryptic digests showed 12 peptides common to both isozymes but also revealed 5 peptides unique to one isozyme and 3 (possibly 4) peptides unique to the other. These findings argue against both conformational isomerization and simple posttranslational modification as the mechanism of generation of the two isozymes. We suggest that the two isozymes are synthesized as discrete molecular entities.

Phenotypic variation in the phosphotransferase activity of human red cell acid phosphatase (ACP1).

Red cell acid phosphatase (ACP1) catalyses the transfer of phosphate from phosphate ester substrates to suitable acceptor alcohols such as methanol and glycerol. The rate of substrate turnover in the presence of acceptors is increased by the increment of the phosphotransferase reaction, thus allowing this activity to be measured. There is specificity with regard to acceptors: (a) polyols (e.g., glycerol) are better acceptors than the corresponding n-alcohols, and (b) polyol configuration and chain length determine acceptor activity. Ribitol was the most efficient acceptor found. Each of the three common ACP1 alleles is represented electrophoretically by two isozyme bands; the phosphotransferase activity of the anodal isozyme was found to be more than twice that of the cathodal isozyme. The extent of phosphotransferase activity is also genotype dependent. In the presence of 2 M glycerol, the relative phosphotransferase efficiencies for the three homozygote types were: ACP1 B = 3.7, ACP1 A = 3.4, and ACP1 C = 2.5. This pattern of B greater than A greater than C is the same as found for the modulation of ACP1 by purines and folates.

Genetic relationships among Neisseria species assessed by comparative enzyme electrophoresis.

The electrophoretic mobilities of 12 enzymes from 19 Neisseria species (including 6 strains of N. perflava), Gemella haemolysans, Escherichia coli and Branhamella catarrhalis were characterized by polyacrylamide slab gel electrophoresis. All strains and species tested exhibited qualitatively different zymogram patterns. Species and strain relationships were quantified by pairwise comparisons of all 12 enzyme systems to obtain similarity indices; these data were subjected to numerical clustering methods to obtain groups and a phenogram. The electrophoretic classification compared favourably with those obtained by other criteria. In addition, the quantitative clustering data indicated that N. ovis and N. caviae are sufficiently different from the other Neisseria species to warrant their separation into a distinct group. These two species also lacked the characteristic NADPH-diaphorase zymogram pattern found in all the other Neisseria species. Intra-species similarity indices were generally greater than the inter-species index values. However, certain species such as N. meningitidis and N. gonorrhoeae had similarity index values in the range of inter-strain index values.

Postcoital detection of a male-specific semen protein. Application to the investigation of rape.

Identification of semen in vaginal fluid may provide documentation of sexual contact in alleged victims of rape. We describe an enzyme-linked immunosorbent assay for a semen glycoprotein of prostatic origin, designated p30. This test detects as little as 3 ng of the p30 antigen per milliliter in various body fluids. Semen from normal and vasectomized men contains high levels of p30 (mean, 1.55 mg per milliliter of seminal plasma), and urine from men contains low levels (mean, 260 ng per milliliter). However, the antigen cannot be detected in body fluids from women, including vaginal fluid and urine, suggesting that p30 may be a male-specific antigen. The p30 antigen was detectable in vaginal fluid for a mean period of 27 hours after coitus, as compared with 14 hours for prostatic acid phosphatase. Of 27 vaginal fluid samples from women who were allegedly raped in which the acid phosphatase test was negative, 7 (26 per cent) were unequivocally positive for p30 by our assay. We conclude that the assay for p30 offers a more sensitive and specific method of semen detection in rape investigation than the enzyme assay for prostatic acid phosphatase.