Multiplex amplification of STR loci with gender alleles using infrared fluorescence detection.

The analysis of short tandem repeat (STR) polymorphisms has proven extremely useful for gene mapping, paternity testing, and forensic analysis. Several commercial products are currently available for performing amplification and analysis of STRs. We have adapted Promega Geneprint Systems for use with a high sensitivity infrared (IR) fluorescent automated DNA sequencer. IR-labeled amplification products are generated by including a small quantity of IR-labeled dATP in the reaction. Several Geneprint STR loci can be multiplexed together with the amelogenin sex identification locus in a single amplification reaction. We have successfully amplified up to five Geneprint STR loci together with the amelogenin locus thus improving the throughput of analysis. Purified genomic DNA as well as simulated forensic samples have been utilized for these multiplex amplifications.

Producing STR locus patterns from bloodstains and other forensic samples using an infrared fluorescent automated DNA sequencer.

Short tandem repeat (STR) analysis is increasingly being used in forensic case analysis because of the large number of STR loci in the human genome and their highly polymorphic nature. An automated DNA sequencer using high sensitivity infrared (IR) fluorescence technology was used to detect STR allele patterns from simulated forensic samples. The amplification strategy used a 19 base pair extension on the 5' end of one of the PCR primers. This sequence is identical to the sequence of a universal M13 Forward sequencing primer which is included in the amplification reaction. Allelic bands were detected by incorporation of the M13 primer-fluorescent dye conjugate into PCR products thus eliminating the need for direct conjugation of fluorescent dye to individual STR primers. By using an IR-based automated DNA sequencer and Tth DNA polymerase, polymorphic STR alleles were detected on-line rapidly and efficiently from bloodstains using only a high temperature incubation to extract DNA from blood cells. Five STR loci were also amplified using Chelex extracted DNA from simulated forensic samples. Multiplexing of three primer pairs in a single PCR mixture for amplification was accomplished using Taq polymerase. This system combines IR fluorescence chemistry and laser technology thus eliminating the need for radioactivity and the gel handling required with silver staining and fluor detection systems. Real-time detection permits immediate visualization of the data and STR alleles are displayed as familiar autoradiogramlike images that can be analyzed by computer. By loading a 64 lane gel twice and multiplexing with three primer pairs, forensic scientists can type at least three loci from 120 samples in one day.

An infrared fluorescent dATP for labeling DNA.

Near-infrared fluorescence provides a nonradioactive method of detection with high sensitivity and low background. An infrared fluorophore has been attached covalently to the nucleotide deoxyadenosine triphosphate (dATP) to provide a reagent for enzymatic labeling of various types of DNA molecules and for facilitating their detection with an automated DNA sequencing and analysis system. DNA sequencing reaction products can be labeled internally by performing limited polymerization utilizing infrared-labeled dATP (IR-dATP) as the sole source of adenine deoxynucleotide prior to a dideoxy-specific termination reaction. PCR products can be labeled fluorescently by the addition of limited quantities of IR-dATP to the amplification reaction. This latter strategy has been utilized for detection of short tandem repeat polymorphisms (STRPs) which are useful for gene mapping, genetic diagnostics, forensic analysis, and paternity testing. Restriction fragments can be labeled also by fill-in reactions of appropriate 5' overhangs. Diminutive amounts of such fluorescently labeled DNA molecules can be visualized rapidly and conveniently using infrared detection technology.

Analysis of tyrosinase gene mutations using direct automated infrared fluorescence DNA sequencing of amplified exons.

The ability to correctly diagnose the molecular cause of genetic diseases is becoming increasingly important in medicine. This requires an efficient method for the analysis of the DNA sequence of specific genes and the detection of mutations in affected individuals. We report a method to determine the mutations responsible for tyrosinase related albinism (OCA1) using a combination of polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis and direct DNA cycle sequencing using fluorescently labeled oligonucleotides and an automated DNA sequencer based on infrared fluorescence technology. This method allows DNA from several individuals to be sequenced quickly and simultaneously so that the specific location of each mutation and the carrier status of family members can be determined.

Continuous, on-line DNA sequencing using a versatile infrared laser scanner/electrophoresis apparatus.

A new apparatus for continuously detecting fluorescently labeled DNA fragments is based on infrared fluorescence technology. This technology combines state-of-the-art developments in chemistry, laser technology, and detection, while achieving improved reliability, sensitivity, and flexibility for applications including DNA sequencing. DNA molecules labeled with a novel infrared fluorophore are detected during electrophoresis using a scanning infrared fluorescence microscope. The microscope consists of a laser diode for exciting the fluorophore and a silicon avalanche photodiode for detecting the infrared emission. Optimum conditions for detection and throughput are obtained by adjusting electrophoresis, scanning and imaging parameters. Typical DNA sequencing runs (test templates) allow identification of over 500 bases per sample with greater than 99% accuracy.

Expression of virally-transduced mouse tyrosinase in cultured chick embryo cells.

A cDNA encoding mouse tyrosinase was inserted into a plasmid containing the provirus of a replication competent Avian Leukosis Virus (ALV). A viral stock produced from the plasmid was used to infect cultured tyrosinase-negative (ca/ca) unpigmented chick embryo pigment cells. Five days after infection many cells were producing very dark discrete pigment granules. Cultures of tyrosinase positive, sex linked albino (sal) pigment cells produced no additional pigmentation. White Leghorn pigment cells responded to viral infection like the sal pigment cells.

Expression of virally transduced mouse tyrosinase in tyrosinase-negative chick embryo melanocytes in culture.

A cDNA encoding mouse tyrosinase was inserted into a plasmid containing the provirus of a replication competent avian leukosis virus (ALV). A viral stock produced from the plasmid was used to infect cultured tyrosinase-negative (ca/ca) unpigmented chick embryo melanocytes. Five days after infection many cells were producing very dark discrete melanosomes.

Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores.

A method for sequencing DNA by using a difluoresceinated primer and laser excitation is described. Dideoxy protocols have been determined that provide sequences for 600 bases starting with base 1 with less than 1% error in a single load. Electrophoresis is at 20 W and the bands are detected 24 cm from the bottom of the loading well with a scanning fluorescence detector. Bands are imaged on a TV screen in two dimensions. The sequences can be read from the TV screen manually or semiautomatically by using a simple software program. The system allows more bases to be read with a lower error rate than any other reported automated sequencing method.

C pigment locus mutants of the fowl produce enzymatically inactive tyrosinase-like molecules.

Three albino mutants of the fowl were tested for tyrosinase activity. Two of these mutants (c and ca) are alleles at the autosomal C locus, while the third mutant (sal) is sex-linked. Both the standard type, E, and sal are tyrosinase positive whereas the two C mutants are tyrosinase negative. Anti-chicken tyrosinase mouse serum was produced and all four genotypes were found to have cross-reacting material to this antiserum. Tyrosinase from the standard type was isolated and its location on denaturing two-dimensional gels determined. A co-migrating series of spots was found within the protein pattern of both the standard type and the tyrosinase positive albino, sal. The same pattern of spots was also observed for c and ca with no apparent change in either the pI or the molecular weight. Transmembrane blots also showed spots that reacted with anti-tyrosinase serum in all four genotypes and that migrated to the same location as that of standard tyrosinase. It is proposed that both c and ca are CRM+ mutants which produce tyrosinase-like molecules that are inactive due to a change that is electrophoretically and antigenically "silent".

Detection of melanogenic proteins in cultured chick-embryo melanocytes.

The phorbol ester, 12-0-tetradecanoylphorbol-13-acetate (TPA), was used as a reversible inhibitor of melanogenesis. Chick-melanocyte cultures of the black genotype, E/E, were grown in conditioned medium plus TPA. After growth in TPA and after its removal, the cells were pulse labeled with 3H-leucine. The membrane fraction, which included all tyrosinase activity as well as both mature and immature melanosomes, was solubilized with Triton X-100. The proteins were separated using two-dimensional electrophoresis and visualized by fluorography. One defined melanogenic protein, tyrosinase, was isolated, and its location was determined in the two-dimensional protein pattern. The protein patterns for both the TPA-inhibited cells and the cells in which the TPA effects were reversed after removal were compared. In addition to tyrosinase, at least nine TPA-sensitive proteins were found. These were designated as being putative melanogenic proteins which, along with tyrosinase, may be responsible for melanin-granule synthesis.

Purification and isoelectric heterogeneity of chicken tyrosinase.

Tyrosinase (EC 1.14.18.1) was purified from regenerating chicken feathers. Most of the enzyme activity was in the insoluble fraction, which was solubilized with 0.5% sodium cholate. Solubilized tyrosinase showed multiple forms on isoelectric focusing. The isoelectric points had the following pI values: 5.06, 4.83, 4.68, 4.56, 4.44, 4.32, 4.24, 4.14, 4.06 and 3.97. This tyrosinase fraction was subjected to trypsin (EC 3.4.21.4) cleavage, Sephacryl S-200, hydroxylapatite and DEAE-cellulose chromatography. Purified enzymatically active tyrosinase also showed multiple forms. Their isoelectric points were: 4.23, 4.14, 4.06, 3.99 and 3.91. Each active form had almost the same molecular weight, estimated at 66 000. Staining for 1,2-diol groups of glycoproteins and neuraminidase (EC 3.2.1.18) treatment suggested that chicken tyrosinase is a glycoprotein. The enzyme showed both dopa(L-3,4-dihydroxylphenylalanine) oxidase activity and tyrosine hydroxylase activity.

Heterokaryon analysis of the genetic control of pigment synthesis in chick embryo melanocytes.

The genetic control of pigmentation was analyzed using five unlinked mutants, namely, c, pk, Bl, ev and l. Each mutant blocks or reduces pigmentation. Chick melanocyte cultures of each mutant type were fused to produce all ten possible pair combinations of nondividing heterokaryons. Heterokaryons were identified autoradiographically (One partner in each pair was labeled with 3H-thymidine.) Crosses produced comparable pairs of double heterozygotes that were analyzed in vivo and in vitro. Heterokaryon pairs were compared to their corresponding double heterozygotes.--Some combinations showed complementation and produced wild-type pigment. Others showed noncomplementation having little or no pigment. Double heterozygotes complemented each other except in the cases involving the dominant mutant, l. Four heterokaryon pairs gave different results from their corresponding double heterozygotes. The pk-Bl and pk-ev combinations failed to complement as heterokaryons but did complement as double heterozygotes. On the other hand the l-c and I-Bl combinations complemented as heterokaryons but not as double heterozygotes. Based on these differences it is hypothesized that the pk and I loci are nuclearly restricted regulatory elements. Examples in the literature from other systems are cited to support such a hypothesis.

Dopa oxidase expression in fibroblast x melanoma fusions. Extinction in heterokaryons and maintenance in non-dividing cybrids.

Pigmented B-16 mouse melanoma cells were fused with chick embryo fibroblasts or fibroblast cytoplasts and maintained as heterokaryons or non-dividing cybrids, respectively. These single cells were examined ultrastructurally for evidence or pigment gene expression using a cytochemical test for dopa oxidase, the initial enzyme in the conversion of dopa to melanin. Heterokaryons showed significantly less enzyme activity than control cells, whereas non-dividing cybrids showed no significant difference. Therefore, the presence of the intact nuclear membranes in the heterokaryons did not serve as a barrier to the interactions resulting in extinction of differentiated function(s). However, the presence of the fibroblast nucleus was necessary to elicit continued response.

Lavender, a chick melanocyte mutant with defective melanosome translocation: a possible role for 10 nm filaments and microfilaments but not microtubules.

Lavender is a mutation of chick neural-crest-derived melanocytes showing dilute feather pigmentation. This defect, previously attributed to a lack of attenuation of dendrites, was found to be due to a defect in melanosome translocation. The mutant phenotype, of melanincongested perikarya and pigmentless dendrites is expressed both in vivo and in vitro. Studies with colcemid and cytochalasin B suggest that the avian melanocyte resembles a dispersing amphibian melanophore in its requirement for microfilaments but not microtubules. Ultrastructural analysis revealed a normal complement of intracellular filaments. Microtubules, however, are scarce. Intermediate (10 nm) filaments surround and are closely associated with intracellular organelles, while microfilaments interconnect all filaments and organelles. While-cell centrifugation at 300 g showed that 10 nm filaments stream behind and appear to attach to mobile membrane-bound organelles including the nucleus, lipid granules and mitochondria, as well as melanosomes. It is suggested that all intracellular filaments, especially microfilaments and intermediate filaments, interconnect forming a network responsible for organelle motility.

Complementation and noncomplementation in heterokaryons of three unlinked pigment mutants of the fowl.

This study shows that melanocyte heterokaryons formed between cells of the blue and recessive white genotypes complement one another to produce normal pigmentation, while heterokaryons of the blue and pinkeye genotypes fail to complement. The simplest interpretation of these findings is that the blue and recessive white mutations affect different aspects of pigment synthesis so that when both kinds of nuclei exist in the same cytoplasm, they can correct (complement) each other's defect. On the other hand, the blue and pinkeye mutations, although unlinked, apparently affect the same aspect of pigment synthesis so that when both kinds of nuclei are in a common cytoplasm, they cannot correct each other's defect. This suggests that one of these two loci exerts some kind of control, or "regulation," over the other. It has previously been shown that recessive white--pinkeye heterokaryons can complement. Thus, only two heterokaryon complementation groups are evident within the three mutants examined.

Effects of chronic exercise on the ultrastructure of the adrenocortical cells in the rat.

Four groups of male rats were exercised for periods of 2, 4, 6, and 8 weeks with controls in each group. As a result of chronic exercise there was an increase in the width of the zona fasciculata of the adrenal cortex. Also, there was an increase in the number and size of the mitochondria, and an increase in the quantity of smooth endoplasmic reticulum, and during the first 4 weeks of exercise an increase in the number of lipid droplets in the zona fasciculata. The close relationship between the smooth endoplasmic reticulum and the mitochondria, and the relationship between the smooth endoplasmic reticulum and the lipid droplets suggests a possible means for a transport mechanism for movement of precursors between these organelles.

The gene action and function of two dopa oxidase positive melanocyte mutants of the fowl.

Ultrastructural and autoradiographic analysis revealed the developmental genetic differences between the dopa oxidase positive pk and I mutations of the fowl. The differences were revealed by the results of five measurements involving homozygous mutant melanocytes, heterozygous melanocytes, and standard melanocytes at each of the loci. The measurements were: ultrastructural comparisons of melanosomes in pigmented epithelial (PE) and neural crest derived (NC) melanocytes, the number of 3H-dopa and 3H-leucine grains/mu2 of melanosome, the 3H-dopa/3H-leucine ratio, and the percentage of cytoplasmic 3H-leucine grains that were melanosomal. The pk mutation altered both PE and NC melanosomes. +/pk melanocytes were characterized by suppressed 3H-dopa/mu2 and 3H-dopa/3H-leucine values. +/pk cells, however, had the same percentage of melanosomal 3H-leucine grains as the "pk" standard. The I mutation altered only NC melanosomes. +/I melanocytes were characterized by 3H-dopa/mu2 and 3H-dopa/3H-leucine values similar to the "I" standard. +/I cells had a lower percentage of melanosomal 3H-leucine grains that the "I" standard, however. These data suggest that pk is a structural mutation affecting melanin binding to the premelanosome, while I seems to be a control gene mutation partially suppressing the production of premelanosomal components in NC melanocytes.