Cystic fibrosis locus defined by a genetically linked polymorphic DNA marker.

A polymorphic DNA marker has been found genetically linked, in a set of 39 human families, to an autosomal recessive gene that causes cystic fibrosis (CF), a disease affecting one in 2000 Caucasian children. The DNA marker (called D0CRI-917) is also linked to the PON locus, which by independent evidence is linked to the CF locus. The best estimates of the genetic distances are 5 centimorgans between the DNA marker and PON and 15 centimorgans between the DNA marker and the CF locus, meaning that the location of the disease gene has been narrowed to about 1 percent of the human genome (about 30 million base pairs). Although the data are consistent with the interpretation that a single locus causes cystic fibrosis, the possibility of genetic heterogeneity remains. The discovery of a linked DNA polymorphism is the first step in molecular analysis of the CF gene and its causative role in the disease.

Charon phages: safer derivatives of bacteriophage lambda for DNA cloning.

The Charon lambda bacteriophages have been developed as vectors for cloning. Their construction incorporates mutations that make them simple to use and also greatly increases their safety for the biological containment of cloned recombinant DNA. Three of the Charon vector phages, 3A, 4A, and 16A, have been certified for use as EK2 vector-host systems, when propagated in bulk in a special bacterial host, DP50SupF. We present here some of the data on which the safety of these systems was evaluated. DNA fragments ranging in size from 0 to 2.2 X 10(4) base pairs can be cloned in these EK2 Charon phages.

Effect of movements on the electrodermal response after a startle event.

OBJECTIVES: In this work the effect of quasi-stationary movements on the electrodermal activity (EDA) after a startle event has been investigated and evaluated. In previous EDA research there is a discrepancy between the use of controlled environment studies and daily life surveys. This paper aims to address this by expanding the knowledge about EDA in real life applications. METHODS: A minimally obtrusive body-worn measurement device was designed and produced that simultaneously records EDA and finger movements. During this study, five subjects walked at different speeds and listened to startling sound events. The EDA response to these startle events was analyzed for different walking speeds using crosscorrelograms and cumulative frequency plots. RESULTS: The measured response to the startle event is consistent with the signal characteristics described in the literature. The results show that the faster a person is walking the more the signal property of the phasic part of the EDA is approaching a uniform distribution. However, even at a walking speed of 6 km/h the effect of the startle event is statistically still visible in the EDA (p < 0.05). CONCLUSIONS: The presented work offers a good understanding of the EDA while walking at different speeds. Although the artefacts evoked by walking cannot be determined directly, information on the movement can be useful. Depending on the walking speed a measurement about the reliability of peak detection could be introduced.

Molecular cloning and characterization of double-stranded cDNA coding for bovine chymosin.

A full-length cDNA copy of the mRNA encoding calf chymosin (also known as rennin), a proteolytic enzyme with commercial importance in the manufacture of cheese, has been cloned in an f1 bacteriophage vector. The nucleotide sequence of the cDNA was determined, and translation of that sequence into amino acids predicts that the zymogen prochymosin is actually synthesized in vivo as preprochymosin with a 16 amino acid signal peptide. In vitro translation of total poly(A)-enriched RNA from the calf fourth stomach (abomasum) and immunoprecipitation with antichymosin antiserum revealed that a form of chymosin (probably preprochymosin judging from the Mr-value) is the major in vitro translation product of RNA from that tissue. Gel-transfer hybridization of restriction endonuclease-cleaved bovine chromosomal DNA with labeled cDNA probes indicated that the two known forms of chymosin, A and B, must be products of two different alleles of a single chymosin gene.

Reuse of denaturing polyacrylamide gels for short tandem repeat analysis.

Denaturing polyacrylamide gel electrophoretic analysis of amplified polymorphic short tandem repeat (STR) loci using fluorescent markers is a mainstay of forensic and paternity testing. To reduce the drawback of preparing gels or using expensive precast gels, we have developed a simple and rapid method to reuse gels between 2 and 8 times over a period of several days. Following the initial electrophoresis and scan, the original samples are removed from the gel by a 1-1.5-h reverse-electrophoresis step. This step heats the gel for the next set of samples and can be performed several days after the initial electrophoresis. Sample bands remain sharp on subsequent runs, but edge effects (frowning of the outside lanes) become progressively worse and ultimately limit gel reuse. Well distortions and separation of the gel from the plates become problems if the gel is used more than twice. However, degassing the gel solution and bonding the gel to both plates eliminate these problems. Precast gels also can be used multiple times. Using this technique, we have successfully analyzed samples amplified with a nine-locus multiplex system and characterized the separated products using a fluorescent scanner and software.

The GenePrint Light method for Southern transfer and chemiluminescent detection of human genomic DNA.

A simple, fast and sensitive method to perform Southern transfer and hybridization with nonradioactive detection of genetic loci is described. With a 10-ng sample of human genomic DNA, alleles of the D2S44 locus can be detected within 7 h of completing gel electrophoresis.

General approach to analysis of polymorphic short tandem repeat loci.

Polymerase chain reaction amplification products of 22 known polymorphic short tandem repeat (STR) loci were subjected to denaturing polyacrylamide gel electrophoresis and detected using a silver staining method. Loci that amplified efficiently and revealed the fewest amplification-related artifacts with this detection method were selected for development of allelic ladders. The combination of allelic ladders and silver stain detection provides an inexpensive and general non-isotopic analytical method for DNA identification. This approach has immediate application in forensic analysis, paternity determination, human cell line identification and monitoring of bone marrow transplants. It can also be adapted to more general applications of genetic analysis in human and other species including detection of genetic disorders and cancers.

Multiplex sets for the amplification of polymorphic short tandem repeat loci--silver stain and fluorescence detection.

Multiplex PCR amplification systems were developed using well-characterized, polymorphic short tandem repeat (STR) loci. Eight loci utilized in the multiplex amplifications included HUMCSF1PO, HUMTPOX, HUMTH01, HUMVWFA31, HUMF13A01, HUMFESFPS, HUMBFXIII and HUMLIPOL. From this list, three or four non-overlapping loci were simultaneously amplified, separated by denaturing polyacrylamide gel electrophoresis and visualized using silver stain or fluorescence detection. The multiplex PCR amplification systems offer a non-isotopic method for rapid, simple and accurate analysis of STR loci. This high-throughput method for DNA identification has immediate and valuable application in forensic analysis, paternity determination, tissue culture strain identification and bone marrow transplantation studies.

Multiplex systems for the amplification of short tandem repeat loci: evaluation of laser fluorescence detection.

Short tandem repeat (STR) loci are ideal markers for personal identification and for genomic mapping. Two fluorescent multiplex systems, each designed for simultaneous PCR amplification of four polymorphic STR loci (HUMCSF1PO, HUMTPOX, HUMTH01 and HUMVWFA31, and HUMF13A01, HUMFESFPS, HUMBFXIII and HUMLIPOL), were evaluated on three laser fluorescence detection instruments. Concordant DNA typing results were obtained with all three detection methods. These fluorescent multiplex STR systems offer an accurate, reproducible and versatile method of DNA profiling that is well-suited for forensic identity testing and other genetic analyses.

Model-based detection of spiculated lesions in mammograms.

Computer-aided mammographic prompting systems require the reliable detection of a variety of signs of cancer. In this paper we concentrate on the detection of spiculated lesions in mammograms. A spiculated lesion is typically characterized by an abnormal pattern of linear structures and a central mass. Statistical models have been developed to describe and detect both these aspects of spiculated lesions. We describe a generic method of representing patterns of linear structures, which relies on the use of factor analysis to separate the systematic and random aspects of a class of patterns. We model the appearance of central masses using local scale-orientation signatures based on recursive median filtering, approximated using principal-component analysis. For lesions of 16 mm and larger the pattern detection technique results in a sensitivity of 80% at 0.014 false positives per image, whilst the mass detection approach results in a sensitivity 80% at 0.23 false positives per image. Simple combination techniques result in an improved sensitivity and specificity close to that required to improve the performance of a radiologist in a prompting environment.

Chinese population data on three tetrameric short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--derived using multiplex PCR and manual typing.

Allele and genotype frequencies for three tetrameric short tandem repeat (STR) loci were determined in a Chinese sample population using multiplex polymerase chain reaction (PCR), electrophoresis of the PCR products in DNA sequencing gels and subsequent detection by silver staining. The loci are HUMTHO1, TPOX, and CSF1PO. All loci meet Hardy-Weinberg expectations. In addition, there is no evidence for association of alleles among the three loci. The allelic frequency data can be used in human identity testing to estimate the frequency of a multiple STR locus DNA profile in the Chinese population.

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.

Investigation of species specificity using nine PCR-based human STR systems.

Several eukaryotic genomes contain polymorphic markers consisting of trimeric and tetrameric short tandem repeats (STR). Recent reports have demonstrated the variability of short tandem repeat (STR) polymorphisms at a variety of loci among several human population groups. Currently, there are nine commercially available STR PCR systems from Promega Corporation that may be utilized for human identification. We report here the analysis of 23 different species DNA's using these nine STR primer systems to assess their specificity for human euchromatin. The STR systems tested include, CSF1PO, TPOX, THO1, HPRTB, FESFPS, vWF and F13A01 as single systems and as triplex systems (CSF1PO/TPOX/THO1 and HPRTB/FESFPS/vWF). There were no STR PCR products observed for seventeen of the twenty-three species regardless of the STR system. Amplified STR fragments were detected in rhesus DNA for CSF1PO, TPOX and HPRTB systems. STR PCR products were detected for human, gorilla, chimpanzee, and orangutan DNAs using eight of the nine systems. FESFPS primers did not amplify DNA fragments from any of the species tested. Most of the STR PCR products detected from primate DNAs electrophoretically migrated outside of the human allelic ladder fragments and as a result, allele designations were not possible.

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.

Validation of multiplex polymorphic STR amplification sets developed for personal identification applications.

Polymorphic short tandem repeat (STR) loci, which typically consist of variations in the number of 3-7 base pair repeats present at a site, provide an effective means of personal identification. Typing can be accomplished by amplification of genomic DNA using the polymerase chain reaction (PCR) and locus-specific primers, separation of amplified alleles using gel electrophoresis and their display using silver staining or fluorescent detection. Primers for several STR loci can be combined in a single multiplex reaction so typing of multiple loci can be accomplished rapidly and with less DNA than required if each locus were analyzed separately. Before such muliplex systems are used in forensic or paternity applications, it is desirable that they undergo testing for their reliability. This study evaluates the performance of two STR triplex systems, one containing the loci HUMCSF1PO, HUMTPOX, and HUMTH01, and the other containing HUMHPRTB, HUMFESFPS, and HUMVWFA31. Protocols for amplification of these two triplexes, and their corresponding monoplexes, were evaluated for sensitivity of detection, resistance to changes in the annealing temperature of the amplification protocol, and the ability to identify the minority contributor in amplification of mixed samples. In addition, five laboratories determined the alleles of twenty DNA samples, each extracted by one of four different extraction methods. The results illustrate that the two STR triplex systems and the monoplex systems contained within them can be used with as little as 0.25 ng of DNA template. Both triplexes amplified with 100% success using the Perkin Elmer Model 480 thermal cycler. With the GeneAmp 9600 System, the CTT triplex amplified with 100% success and the HFv triplex in 95.6% of attempts. These experiments meet many requirements for use in validation of DNA typing systems for forensic cases and paternity identification.

TWGDAM validation of a nine-locus and a four-locus fluorescent STR multiplex system.

The Gene Print PowerPlex 1.1/Amelogenin and FFFL Fluorescent STR Systems have been validated following the recommendations presented by the Technical Working Group on DNA Analysis Methods (TWGDAM). The PowerPlex 1.1/Amelogenin System supports simultaneous amplification of eight short tandem repeat loci and the Amelogenin gender identification marker. The loci D16S539, D7S820, D13S317, and D5S818 are labeled with fluorescein (FL) while the loci CSF1PO, TP0X, TH01, vWA and Amelogenin are labeled with carboxy-tetramethylrhodamine (TMR). The FFFL Multiplex System is composed of the loci F13A01, FESFPS, F13B, and LPL, each labeled with fluorescein. We have observed no overlap of alleles across loci labeled with an individual fluorescent dye. Samples of each system were amplified and labeled in a single reaction, separated by electrophoresis through a denaturing polyacrylamide gel, and amplified alleles detected using a Hitachi FMBIO Fluorescent Scanner. Alterations from the standard amplification protocols in cycle number and annealing temperature generally produced excellent results. In experiments testing sensitivity as little as 0.2 ng of DNA template could be detected. As expected, different body fluids from the same individuals generated identical DNA profile results. Template DNA derived from blood-strains deposited on a variety of matrix supports displayed robust amplification except for material derived from deposits on wood and Japanese orchid leaves. Mixtures of DNA templates could be interpreted with the minor component present in as little as ten percent of the total sample. Monoplex and multiplex amplifications produced identical amplified allele patterns, indicating that STR multiplex systems save template and increase efficiency in the amplification procedure without loss of quality. Analyses of genotype frequencies in African-American, Caucasian-American and Hispanic-American populations using all twelve loci were used to determine matching probabilities smaller than 1 in 1.14 x 10(8) and 1 in 2658 for the PowerPlex 1.1 and the FFFL Multiplex Systems, respectively. The matching probability achieved with the two systems combined is smaller than 1 in 3.03 x 10(11). The independence of alleles within loci was generally demonstrated by applying the exact test to demonstrate Hardy-Weinberg Equilibrium. All of the studies performed indicate that the PowerPlex 1.1/Amelogenin and FFFL Multiplex Systems are powerful, robust, and reliable investigative tools that can be used in the analysis of forensic samples.

Responsible inclusion for students with learning disabilities.

The purpose of this article is to contrast responsible with irresponsible inclusion practices for students with learning disabilities. Guidelines for responsible inclusion are that the student and family are considered first, teachers choose to participate in inclusion classrooms, adequate resources are provided for inclusion classrooms, models are developed and implemented at the school-based level, a continuum of services is maintained, the service delivery model is evaluated continuously, and ongoing professional development is provided.

Grouping for reading instruction: does one size fit all?

Twenty-nine third-grade teachers and selected students from their classes participated. Study 1 used teacher interviews and classroom observations to examine teachers' perceptions and practices for grouping for reading instruction; Study 2 examined the impact of these grouping practices on the academic progress, social progress, and attitudes about reading of students representing a range of achievement levels, including students with learning disabilities. Results indicated that, overall, teachers used whole class instruction for reading and the same materials for all students, including students with learning disabilities. Students with learning disabilities made little academic progress and their attitudes about reading did not improve over time.

Which motoric condition is most effective for teaching spelling to students with and without learning disabilities?

The purpose of this study was to determine the efficacy of three motoric conditions (writing, tracing, and computer keyboarding) on the spelling performance of 24 third- and fourth-grade students without learning disabilities (NLD) (15 males, 9 females) and 24 third- and fourth-grade students with learning disabilities (LD) (16 males, 8 females). This study applied empirically based procedures for teaching spelling, examined student performance over time, and incorporated student interviews concerning their preference for motoric condition. For number of words spelled and proportion of bi-grams (correct letter sequences) used correctly, significant differences were found between the LD and NLD groups, both at posttest and follow-up, with the NLD students learning to spell more words and apply more correct bi-grams than the students with LD. There was no significant effect for condition for either words spelled or bi-grams, indicating that students did not learn significantly more words in the writing, tracing, or computer condition. There was also a significant time effect indicating that the accuracy of both groups decreased over time from posttest to follow-up for both words and bi-grams. Interviews revealed that students in both groups preferred the computer condition; however, they believed that they learned best in the writing and tracing conditions.