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PubMed2026

Development and evaluation of a one-pot RPA-Cas12a assay based on a primer-driven reverse screening strategy for preliminary screening of megalocytivirus-related viruses.

A primer-driven reverse-screening strategy was used to identify an RPA-Cas12a target suitable for the rapid preliminary screening of megalocytivirus-related viruses. The ISKNV reference genome NC_003494.1 was used as the initial template, and candidate amplification units were designed according to RPA primer-design requirements, primer physicochemical properties, and the availability of Cas12a protospacer-adjacent motif (PAM) sites and crRNA target sequences. Following preliminary amplification assessment, the retained candidate primers were aligned individually against 75 complete genome sequences of megalocytivirus-related viruses. Of these, 67 sequences met the predefined criteria for target-region integrity, primer-binding-site compatibility, and Cas12a recognition. Retrospective mapping to the reference genome located the candidate amplification region within ORF057L. Based on the resulting candidate detection unit, a one-pot RPA-Cas12a assay incorporating a commercially available lyophilized RPA amplification module was developed. Optimization showed that 400 nM reporter and 80 nM crRNA-1 provided relatively stable fluorescence output. A cut-off value of 1281.6 relative fluorescence units (RFU) was established as the mean plus three standard deviations of the endpoint fluorescence values obtained from 20 qPCR-negative samples. In analytical sensitivity testing, the assay generated fluorescence signals above the negative control at low plasmid copy numbers. However, because only a limited number of replicates were tested at these low template concentrations, these findings were not used to define a formal limit of detection. ISKNV, RSIV, and TRBIV samples tested positive, whereas the MRV sample produced an endpoint fluorescence value below the cut-off. Repeatability analysis of the same sample in six independent reactions yielded a coefficient of variation of 8.03%. Among the 39 samples examined, no discordant qualitative results were observed between the RPA-Cas12a assay and qPCR. These findings support the use of the ORF057L-targeted one-pot RPA-Cas12a assay as a rapid preliminary screening tool for megalocytivirus-related viruses. Nevertheless, its formal limit of detection, inter-batch stability, cross-reactivity with additional non-target pathogens, and clinical diagnostic performance require further evaluation.

Lyophilized RPA↗
PubMed2006

Linkage mapping of gene-associated SNPs to pig chromosome 11.

Single nucleotide polymorphisms (SNPs) were discovered in porcine expressed sequence tags (ESTs) orthologous to genes from human chromosome 13 (HSA13) and predicted to be located on pig chromosome 11 (SSC11). The SNPs were identified as sequence variants in clusters of EST sequences from pig cDNA libraries constructed in the Sino-Danish pig genome project. In total, 312 human gene sequences from HSA13 were used for similarity searches in our pig EST database. Pig ESTs showing significant similarity with HSA13 genes were clustered and candidate SNPs were identified. Allele frequencies for 26 SNPs were estimated in a group of 80 unrelated pigs from Danish commercial pig breeds: Duroc, Hampshire, Landrace and Large White. Eighteen of the 26 SNPs genotyped in the PiGMaP Reference Families were mapped by linkage analysis to SSC11. The EST-based SNPs published here are new genetic markers useful for linkage and association studies in commercial and experimental pig populations. This study represents the first gene-associated SNP linkage map of pig chromosome 11 and adds new comparative mapping information between SSC11 and HSA13. Furthermore, our data facilitate future studies aimed at the identification of interesting regions on pig chromosome 11, positional cloning and fine mapping of quantitative trait loci in pig.

Animals↗
PubMed1992

Waardenburg syndrome (WS) type I is caused by defects at multiple loci, one of which is near ALPP on chromosome 2: first report of the WS consortium.

Previous studies have localized the gene for Waardenburg syndrome (WS) type I to the distal portion of chromosome 2q, near the ALPP locus. We pooled linkage data obtained from 41 WS type I and 3 WS type II families which were typed for six polymorphic loci on chromosome 2q in order to refine the location of the WS locus (WS1) and evaluate the extent of genetic heterogeneity. In the course of this work, we developed diagnostic criteria for genetic and phenotypic studies. Our findings, based on two-locus and multilocus analysis using a linkage map established from reference pedigrees, suggest that there are two or more mutations causing WS, one of which (i.e., WS1) is located on chromosome 2q, between the ALPP and FN1 loci, at distances of 7.8 cM and 11.2 cM for each marker, respectively. The results also indicate that WS1 is responsible for the illness in approximately 45% of all families in this sample. However, the odds favoring this position over a location between ALPP and SAG are only 2:1 when alternate assumptions about the proportion of linked families are considered. We conclude that a more saturated map of this region of chromosome 2q, including highly polymorphic markers, will be needed to accurately distinguish linked families and, ultimately, isolate the mutant gene.

Alkaline Phosphatase↗
PubMed1988

Partial linkage map of chromosome 13q in the region of the Wilson disease and retinoblastoma genes.

Genetic linkage maps are useful tools for defining the location of disease genes. Previously published maps of human chromosome 13 have been incomplete and have had ambiguities of order in the vicinity of the Wilson disease (WND) and retinoblastoma (RB1) genes. We have defined a six-locus map of this region using a large reference pedigree from Venezuela. Our map provides landmarks which will aid in the localization of WND, in determining the extent of deletions in retinoblastoma, and in the mapping of other marker loci.

Chromosome Mapping↗
PubMed2005

[Estimation of China soil organic carbon storage and density based on 1:1,000,000 soil database].

Based on 1:1,000,000 soil database, and employing the methods of spatial expression, this paper estimated the soil organic carbon storage (SOCS) and density (SOCD) of China. The database consists of 1:1,000,000 digital soil map, soil profile attribution database, and soil reference system. The digital soil map contained 926 soil mapping units, 690 soil families, and 94 000 or more polygons, while the soil profile attribution database collected 7292 soil profiles, including 81 attribution fields. The SOCDs of soil profiles were calculated and linked to the soil polygons in the digital soil map by the method of "GIS linkage based on soil type", resulting in a vector map of 1:1,000,000 China SOCD. The SOCS of the country or of a soil could be estimated by summing up the SOCS of all polygons or the polygons of a soil, and their SOCD were the SOCS of them derived by their areas. The estimated SOCS and SOCD of the country was 89. 14 Pg (1 Pg = 10(15) g) and 9.60 kg m(-2), respectively, covered all the soils with a total area of 928.10 x 10(4) km2, which might be considered closest to the real value.

Carbon↗
PubMed1988

Chromosomal location and structure of the operon encoding peptide-chain-release factor 2 of Escherichia coli.

The prfB gene encodes peptide-chain-release factor 2 of Escherichia coli, which catalyzes translation termination at UGA and UAA codons. The gene, identified by sequencing, is located at the 62-min region of the E. coli chromosome. The prfB gene is followed by an open reading frame encoding a 57,603-Da protein. This downstream open reading frame was identified as herC, a gene defined by a suppressor mutation that restores replication of a ColE1 plasmid mutant. RNA blot hybridization and S1 nuclease protection analyses of in vivo transcripts showed that prfB and herC are cotranscribed into a 2800-base transcript in the counterclockwise direction with respect to the E. coli genetic map. Thus, we refer to the two genes as the prfB-herC operon. Data are presented that suggest that supK, a mutation in Salmonella typhimurium that suppresses UGA termination, is the structural gene for Salmonella release factor 2. Translation control within the prfB-herC operon and the relationship of these genes to a tRNA methyltransferase are discussed.

Amino Acid Sequence↗
PubMed2002

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome.

Based on published information, we have identified 991 genes and gene-family clusters for cattle and 764 for pigs that have orthologues in the human genome. The relative linear locations of these genes on human sequence maps were used as "rulers" to annotate bovine and porcine genomes based on a CSAM (contiguous sets of autosomal markers) approach. A CSAM is an uninterrupted set of markers in one genome (primary genome; the human genome in this study) that is syntenic in the other genome (secondary genome; the bovine and porcine genomes in this study). The analysis revealed 81 conserved syntenies and 161 CSAMs between human and bovine autosomes and 50 conserved syntenies and 95 CSAMs between human and porcine autosomes. Using the human sequence map as a reference, these 991 and 764 markers could correlate 72 and 74% of the human genome with the bovine and porcine genomes, respectively. Based on the number of contiguous markers in each CSAM, we classified these CSAMs into five size groups as follows: singletons (one marker only), small (2-4 markers), medium (5-10 markers), large (11-20 markers), and very large (> 20 markers). Several bovine and porcine chromosomes appear to be represented as di-CSAM repeats in a tandem or dispersed way on human chromosomes. The number of potential CSAMs for which no markers are currently available were estimated to be 63 between human and bovine genomes and 18 between human and porcine genomes. These results provide basic guidelines for further gene and QTL mapping of the bovine and porcine genomes, as well as insight into the evolution of mammalian genomes.

Animals↗
PubMed1996

Isolation, characterization, and chromosomal mapping of the human insulin promoter factor 1 (IPF-1) gene.

Insulin promoter factor 1 (IPF-1) is a homeodomain-containing protein that is thought to be a key regulator of pancreatic islet development and insulin gene transcription in beta-cells. This report describes the isolation and characterization of the human IPF-1 gene. The coding region, which showed 83% nucleotide identity with the mouse IPF-1 gene, was encoded by two exons that extended over a 5-kb region of human genome. The deduced human IPF-1 protein contained 283 amino acids, 1 amino acid less than the mouse IPF-1 protein. The homeodomain region of IPF-1 was encoded by the second exon, and it was highly conserved among species. The human IPF-1 gene was mapped to chromosome 13q12(12.1) by fluorescent in situ hybridization (FISH) analysis. A simple sequence repeat polymorphism (ipf1CA2) was identified in the genomic clone. Polymerase chain reaction (PCR) amplification of this repeat region revealed two alleles (heterozygosity = 0.32). This simple sequence repeat polymorphism, and thus the IPF-1 gene, was incorporated into the human linkage map by genotyping reference Human Polymorphism Study Center (CEPH) pedigrees. Multipoint analysis with the CEPH genotype database placed the gene with equal likelihood between two marker intervals: D13S292-cdx3GA1 and cdx3GA1-D13S289 on chromosome 13, consistent with the results of FISH analysis. Two-point linkage analysis inferred that the most likely location for ipf1CA2 was at theta = 0 from cdx3GA1 locus. The exon-intron boundaries of the IPF-1 gene were sequenced, and primers were synthesized to search the homeodomain region for potential variants in patients with NIDDM. By single-strand conformational polymorphism analysis, no variants were found within this region in 61 Japanese patients, which could contribute to the pathogenesis of NIDDM. The isolation of the human IPF-1 gene, along with characterization of its genomic structure and chromosomal mapping, will now permit the assessment of the role of this gene in the pathogenesis of NIDDM in various populations.

Amino Acid Sequence↗
PubMed2005

Applying hybrid algorithms for text matching to automated biomedical vocabulary mapping.

Several biomedical vocabularies are often used by clinical applications due to their different domain(s) of coverage, intended use, etc. Mapping them to a reference terminology is essential for inter-systems interoperability. Manual vocabulary mapping is labor-intensive and allows room for inconsistencies. It requires manual searching for synonyms, abbreviation expansions, variations, etc., placing additional burden on the mappers. Furthermore, local vocabularies may use non-standard words and abbreviations, posing additional problems. However, much of this process can be automated to provide decision-support, allowing mappers to focus on steps that absolutely need their expertise. We developed hybrid algorithms comprising of rules, permutations, sequence alignment and cost algorithms that utilize the UMLS SPECIALIST Lexicon, a custom knowledgebase and a search engine to automatically find probable matches, allowing mappers to select the best match from this list. We discuss the techniques, results from assisting to map a local codeset, and scope for generalizability.

Algorithms↗
PubMed2004

Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat.

Expressed sequence tags (ESTs) are a valuable source of molecular markers. To enhance the resolution of an existing linkage map and to identify putative functional polymorphic gene loci in hexaploid wheat (Triticum aestivum L.), over 260,000 ESTs from 5 different grass species were analyzed and 5418 SSR-containing sequences were identified. Using sequence similarity analysis, 156 cross-species superclusters and 138 singletons were used to develop primer pairs, which were then tested on the genomic DNA of barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and wheat. Three-hundred sixty-eight primer pairs produced PCR amplicons from at least one species and 227 primer pairs amplified DNA from two or more species. EST-SSR sequences containing dinucleotide motifs were significantly more polymorphic (74%) than those containing trinucleotides (56%), and polymorphism was similar for markers in both coding and 5' untranslated (UTR) regions. Out of 112 EST-SSR markers, 90 identified 149 loci that were integrated into a reference wheat genetic map. These loci were distributed on 19 of the 21 wheat chromosomes and were clustered in the distal chromosomal regions. Multiple-loci were detected by 39% of the primer pairs. Of the 90 mapped ESTs, putative functions for 22 were identified using BLASTX queries. In addition, 80 EST-SSR markers (104 loci) were located to chromosomes using nullisomic-tetrasomic lines. The enhanced map from this study provides a basis for comparative mapping using orthologous and PCR-based markers and for identification of expressed genes possibly affecting important traits in wheat.

Chromosome Mapping↗
PubMed1999

An experimental pain model based on electric stimulations of the colon mucosa.

BACKGROUND: Pain intensity and distribution related to diseases of the gut are important diagnostic indicators in gastroenterology. Experimental pain models provide a unique possibility for standardized activation of the nociceptive system, but only few human models exist. METHODS: An experimental pain model based on electric stimuli in the human colon was developed and applied. Eleven patients who were referred for surveillance colonoscopy due to earlier polyps in the colon were included. None had any abdominal pain complaints. The following areas were stimulated with 'single', 'repeated', or 'continuous' electric current: the cecum, the hepatic and splenic flexures, and the rectosigmoid junction. RESULTS: All subjects felt deep, diffuse pain during the stimulation, with referral to localized somatic structures. The pain detection thresholds after repeated stimuli were similar in the four areas. The threshold for single stimulation was higher than the threshold for repeated stimulation. Most reported pain in the lower and left site of the abdominal wall during stimuli at the splenic flexure and rectosigmoid junction. Stimuli at the right colon, however, resulted mostly in pain at the contralateral site of the abdomen. CONCLUSIONS: The presented model was robust and suitable for eliciting pain in different regions of the large intestine. The importance of temporal summation in visceral pain was shown. Mapping of the referred pain areas mimics clinical observations and has ontogenetic and anatomic consistency. The model may therefore improve the evaluation of pain in patients with diseases of the colon.

Abdominal Pain↗
PubMed1997

Genome structure and phylogeny in the genus Brucella.

PacI and SpeI restriction maps were obtained for the two chromosomes of each of the six species of the genus Brucella: B. melitensis, B. abortus, B. suis, B. canis, B. ovis, and B. neotomae. Three complementary techniques were used: hybridization with the two replicons as probes, cross-hybridization of restriction fragments, and a new mapping method. For each type strain, a unique I-SceI site was introduced in each of the two replicons, and the location of SpeI sites was determined by linearization at the unique site, partial digestion, and end labeling of the fragments. The restriction and genetic maps of the six species were highly conserved. However, numerous small insertions or deletions, ranging from 1 to 34 kb, were observed by comparison with the map of the reference strain of the genus, B. melitensis 16M. A 21-kb Spel fragment specific to B. ovis was found in the small chromosome of this species. A 640-kb inversion was demonstrated in the B. abortus small chromosome. All of these data allowed the construction of a phylogenetic tree, which reflects the traditional phenetic classification of the genus.

Brucella↗
PubMedDate not supplied

Inter- and intra-individual probability maps in EEG cartography by use of nonparametric Fisher tests.

The three types of non-parametric permutation Fisher tests have been applied to inter-individual group studies and further to intra-individual multiple EEG recording sequences, providing computations of EEG probability maps testing two ordinal hypotheses. Two examples of previous group studies with "EEG local cerebral activation" are given: mental computation in a group of 20 controls and caffeine effects versus placebo in a group of 10 controls. For the intra-individual study, two successive recordings of 2.3 min eyes closed (EC1 and EC2), obtained at 50 min intervals, were compared by paired exact permutation Fisher tests (over 15 or 42 synchronous EEG sequences). These tests were applied to descriptive spectral parameters: RMS and % amplitudes, mean frequencies, resonance coefficient, for raw unfiltered EEG and delta, theta, alpha, alpha 1, alpha 2, beta 1, beta 2 frequency bands. Two hypotheses were tested for each of the computed 31 parameters, providing two probability maps indicating if the parameter was greater or lower in the first EEG recording or in the second. The second EEG sequence, EC2, was "EEG activated" compared to the first sequence EC1 if the following were present: decreased amplitudes mainly in raw EEG, low activity and alpha bands; increased frequencies mainly, in raw EEG, delta and beta 1 fast activities; increased fast activity percentages; decreased coefficient of resonance. The effect of choice of reference was also evaluated: probability maps for a frontal reference were different than other probability maps obtained after computation of average reference or source derivation.(ABSTRACT TRUNCATED AT 250 WORDS)

Brain Mapping↗
PubMed1999

Automatic 3-D segmentation of internal structures of the head in MR images using a combination of similarity and free-form transformations: Part I, Methodology and validation on normal subjects.

The study presented in this paper tests the hypothesis that the combination of a global similarity transformation and local free-form deformations can be used for the accurate segmentation of internal structures in MR images of the brain. To quantitatively evaluate our approach, the entire brain, the cerebellum, and the head of the caudate have been segmented manually by two raters on one of the volumes (the reference volume) and mapped back onto all the other volumes, using the computed transformations. The contours so obtained have been compared to contours drawn manually around the structures of interest in each individual brain. Manual delineation was performed twice by the same two raters to test inter- and intrarater variability. For the brain and the cerebellum, results indicate that for each rater, contours obtained manually and contours obtained automatically by deforming his own atlas are virtually indistinguishable. Furthermore, contours obtained manually by one rater and contours obtained automatically by deforming this rater's own atlas are more similar than contours obtained manually by two raters. For the caudate, manual intra- and interrater similarity indexes remain slightly better than manual versus automatic indexes, mainly because of the spatial resolution of the images used in this study. Qualitative results also suggest that this method can be used for the segmentation of more complex structures, such as the hippocampus.

Algorithms↗
PubMed1991

Predictive testing for Wilson's disease using tightly linked and flanking DNA markers.

We studied DNA polymorphisms for five new chromosome 13 markers in 52 Wilson's disease (WD) families from Europe, North America, and the Middle East. There was significant evidence for linkage between the Wilson's disease locus (WND) and all the marker loci. Multilocus linkage analysis, using a genetic linkage map established from reference pedigrees, suggested that WND is most likely between D13S31 and D13S59, at distances of 0.4 and 1.2 centimorgans, respectively. Our results suggest that the chromosomal location of the Wilson's disease gene is the same in all families from the populations studied. This evidence and the availability of many close, flanking, and polymorphic DNA markers make possible accurate and informative testing of potential carriers and WD homozygotes in families with at least one previously affected child. An advantage of a genetic linkage test over other laboratory methods for prediction of genotype in WD is that a reliable diagnosis can be made at a much earlier stage in life, including prenatally. In addition, DNA testing can be used in place of an invasive liver biopsy procedure to confirm a diagnosis in patients with borderline serum ceruloplasmin levels. Presymptomatic identification will also allow therapeutic intervention to prevent symptoms before irreparable liver or neurologic damage occurs. We describe the implementation of prenatal and preclinical diagnosis for two families with WD.

Chromosome Mapping↗
PubMed2002

Radiofrequency ablation of cardiac arrhythmias using a three-dimensional real-time position management and mapping system.

A recently developed three-dimensional real-time position management system (RPM) uses an ultrasound ranging technique that enables multiple distance measurements between two reference catheters and a mapping catheter each equipped with ultrasound transducers. In addition to three-dimensional representation of the catheters and ablation sites it displays real-time movements of catheters (including the tip and shaft). A recently released version of the system enables additional geometry reconstruction of the heart chamber and activation mapping. This study included 21 patients (mean age 59 +/- 14.5 years) referred for radiofrequency catheter ablation of various arrhythmias. Geometry was reconstructed by tracing the endocardial contour of the respective heart chambers. Global and local color coded activation maps were constructed to confirm the nature of arrhythmia and to guide ablation. Spontaneous or induced arrhythmias were typical atrial flutter (n = 8), atypical atrial flutter (n = 3), atrioventricular nodal reentrant tachycardia (n = 3), atrial tachycardia (n = 2), atrial fibrillation (n = 2), ventricular tachycardia (n = 2), and Wolff-Parkinson-White syndrome (n = 1). Geometry reconstruction and mapping of arrhythmias were possible in 20 of 21 patients. RPM-guided radiofrequency ablation was successful in 19 (95%) of 20 patients. Due to difficulties in steering the RPM mapping/ablation catheter, in 6 (28%) successfully mapped patients, radiofrequency ablation was performed using another catheter. In one patient, the RPM-guided map was inconclusive and in another patient, ablation failed due to multiple reentrant circuits. No complications were observed. In conclusion, the new RPM system enables geometry reconstruction and three-dimensional positioning of the ablation catheters, reconstruction of the activation maps, marking of anatomic structures and reproducible tracking of multiple ablation sites. The system could be used to guide radiofrequency ablation of atrial and ventricular arrhythmias.

Arrhythmias, Cardiac↗
PubMed2005

The rich stereochemistry of eight-vertex polyhedra: a continuous shape measures study.

A stereochemical study of polyhedral eight-vertex structures is presented, based on continuous shape measures (CShM). Reference polyhedra, shape maps, and minimal-distortion interconversion paths are presented for eight-vertex polyhedral and polygonal structures within the CShM framework. The application of these stereochemical tools is analyzed for several families of experimental structures: 1) coordination polyhedra of molecular transition-metal coordination compounds, classified by electron configuration and ligands; 2) edge-bonded polyhedra, including cubane structures, realgar, and metal clusters; 3) octanuclear transition-metal supramolecular architectures; and 4) coordination polyhedra in extended structures in inorganic solids. Structural classification is shown to be greatly facilitated by these tools, and the detection of less common structures, such as the gyrobifastigium, is straightforward.

Journal Article↗