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Results for “reference mapping”

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PubMed2003

Detection of egg drop syndrome virus antigen or genome by enzyme-linked immunosorbent assay or polymerase chain reaction.

Mouse monoclonal antibodies (mAbs) were produced against an Indian isolate of egg drop syndrome (EDS) virus and characterized. Four hybridoma clones were secreting mAbs that bound to a 100 kDa protein, presumably the hexon protein. These mAbs were found to cross-react with two other Indian isolates of EDS virus and to the reference UK 127 strain. Three of these mAbs were mapped to the same epitope compared with the other mAb (F8), which bound to a different epitope. An antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) was developed using the F8 mAbs as capture antibody and polyclonal chicken serum against EDS virus as detection antibody. A polymerase chain reaction (PCR) was used to detect the EDS viral genome. Following experimental infection of oestrogen-treated chickens with EDS virus, cloacal swabs, oviduct, uterus and spleen were collected at different days post-infection and used in both AC-ELISA and PCR, directly and after a single passage in embryonated duck eggs. The sensitivity and specificity of antigen detection by AC-ELISA or PCR was 95% and 98%, respectively. For diagnosis of EDS viral infections, PCR is recommended due to its ease and the lack of requirement of prepared reagents such as mAbs or conjugates. We recommend that PCR be performed directly on boiled tissue homogenates. Any negative samples may be passaged in embryonated duck eggs and the allantoic fluids tested by PCR before a conclusive negative diagnosis is given.

Adenoviridae Infections↗

PubMed2026

Maize Gametophytic factor loci Ga3 through Ga11 modify reproductive barriers.

Gametophytic factor (Ga) barriers are maize (Zea mays ssp. mays) reproductive barriers controlled by molecular incompatibilities between pollen and silks. Twelve distinct Ga loci have been identified in maize populations since the first genetic evidence of a Ga barrier was reported in 1901. Of the twelve, however, only three have been validated by modern molecular, functional and genomic studies: Ga1, Ga2, and Tcb1. The remaining "higher" Ga loci, spanning Ga3 to Ga11, were reported in the historical literature, but their associated phenotypes segregated in unexpected ways or disappeared over subsequent generations. Here we introduce and explore the hypothesis that the higher Ga loci represent modifiers of Ga1, Ga2, and Tcb1 barrier functions. By revisiting the historical literature, we found that barrier phenotypes fall into two phenotypic and functional categories. Phenotypically, the two categories represented healthy pollen with a silk-length effect and unhealthy pollen without a silk-length effect. These phenotypic categories were supported by genomic data; we identified candidate genes in each higher Ga locus by comparing historical linkage mapping data to the corresponding genomic sequence of maize reference line B73. We discovered candidate genes related to two broad pathways: pollen tube growth and RNA-directed DNA methylation. We conclude that the past century of evidence aligns with our hypothesis that maize loci Ga3 through Ga11 modify rather than directly control Ga barriers. This brief investigation provides a starting point for geneticists and evolutionary biologists to explore how strong reproductive barriers are shaped by epistatic interactions.

Epistasis↗

PubMed1985

The genes for yeast ribosomal proteins S24 and L46 are adjacent and divergently transcribed.

Unlike most yeast ribosomal protein genes studied so far the genes coding for S24 and L46 are adjacent on the genome. Sequence analysis showed that the two genes are transcribed divergently, their initiation codons being 630 bp apart. Taking the respective ATG translation start sites as reference points, the 5'- end of L46 mRNA was mapped at position -26, while the S24 mRNA showed two major 5'-ends mapping at positions -13 and -16 respectively. Unlike most other yeast ribosomal protein genes, the gene for S24 does not contain an intron. Its coding region encompasses 390 nucleotides encoding a protein of 14762 D. The gene for L46 on the other hand is split by an intron of 386 nucleotides starting after its second codon. This gene encodes a small, very basic protein having a molecular weight of 6334 D. Yeast ribosomal proteins S24 and L46 show striking homologies with ribosomal proteins from other organisms. In particular, yeast L46 is clearly the evolutionary counterpart of rat liver L39. A search of the intergenic region for sequence elements previously identified as common to most yeast ribosomal protein genes, revealed the presence of a single conserved box (RPG-box) roughly equidistant from the transcription initiation sites of both genes. We suggest that this box acts as a regulatory signal in either orientation and thus influences the expression of both genes simultaneously.

Amino Acid Sequence↗

PubMed2004

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria and to navigate to related databases exploiting different cross-references. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd. isb-sib.ch.

Animals↗

PubMed1995

Five regional localizations to the sheep genome: first assignments to chromosomes 5 and 12.

The regional localization of five reference loci to sheep chromosomes is reported. The newly mapped loci are the T-cell receptor, beta (TCRB), coagulation factor X (F10), laminin gamma 1 (LAMC1), cyclic GMP rod phosphodiesterase, alpha (PDEA) and fibroblast growth factor 2 (FGF2). The assignments of PDEA and LAMC1 to chromosomes 5q23-q31 and 12q22-q24 respectively provide the first markers physically assigned to these chromosomes. They also allow the provisional assignment of sheep syntenic group U19 to chromosome 5 and U1 to chromosome 12. The mapping of FGF2 to chromosome 17q23-q25 anchors the unassigned linkage group 'A' to chromosome 17, and the assignment of TCRB to chromosome 4q32-qter facilitates the orientation of a linkage group on sheep chromosome 4. The mapping of F10 to sheep chromosome 10q23-qter supports the recent assignment of bovine syntenic group U27 to cattle chromosome 12, as sheep chromosome 10 and cattle chromosome 12 are banded homologues.

Animals↗

PubMed1985

A photogrammetric method for monitoring changes in the residual alveolar ridge form.

Resorption of the residual alveolar ridge calls for regular attention to the fitting surface of a denture. In the case of distal extension partial dentures, changes which occur in less than a year may require attention. These changes are apparent, though difficult to measure using radiographic techniques. Stereophotogrammetry is a means of recording and measuring contours of land masses. A short focus non-metric camera was used in this study to produce stereoscopic paired pictures of four casts of the same partial dentition. Additional casts were made 2 and 12 months after a partial denture had been made. A stereophotogrammetric plotting instrument was used to map the alveolar ridge area of each cast. A prescribed area for each map was traced out and the volume above a reference height was calculated. The percentage error between the four columns for the pre-treatment casts was +/- 2%. A 10% loss of ridge volume was observed after wearing a partial denture for 2 months. The same area observed 12 months later revealed an 18% volume reduction. Short range stereophotogrammetry may be applied to study changes in alveolar ridge morphology which may result from wearing a partial denture.

Alveolar Process↗

PubMed2005

Characteristics of slow waves on EEG associated with epileptic spasms.

PURPOSE: The high-voltage slow waves (HVSs) on EEG associated with epileptic spasms were investigated to clarify their characteristics and their relation to the pathophysiology of spasms in West syndrome and related disorders. METHODS: In 14 patients, digitally recorded EEG segments showing the ictal HVSs were extracted and their traces were overlaid by using an average reference. The ictal HVSs were also averaged to build maps for investigation of the pattern of potential distribution over the scalp. RESULTS: In a total of 685 recorded spasms, 346 (50.5%) with minimal artifacts were selected to demonstrate that the ictal HVSs had a largely consistent waveform and distribution in each patient. The ictal HVSs were symmetrical in 10 patients and asymmetrical in the other four, and were relatively negative over the posterior region and positive over the frontal or temporal regions in 11 patients. Two symptomatic patients showed a marked deviation of the distribution of HVSs to the pathologically more involved hemisphere. An infant with Aicardi syndrome had two different types of spasms, each type showing a consistent pattern of HVSs with a lateralized distribution. CONCLUSIONS: The patterns of distribution of the ictal HVS may be related to the abnormal activation of the brain in the generation of spasms.

Brain↗

PubMedDate not supplied

Attributes of the oral cavity as a site for basal body temperature measurements.

The thermal topography of the oral cavity of 11 women was mapped with thermocouples in early morning waking conditions. A reference thermocouple was placed in the vagina. No significant difference was found in the time required to reach a steady-state oral temperature and in the achieved steady-state temperature difference (Tv-To) in the preovulatory and postovulatory phases of the menstrual cycle. Location of the thermocouple in the oral cavity had a significant effect on steady-state temperature differences. After equilibration of oral thermometers, women breathed through their mouths for exactly five minutes. Mouths were closed and a second temperature equilibration phase was recorded. Mouth breathing had a significantly greater effect on the temperature of the anterior sublingual and dorsum of the tongue sites than on the posterior sublingual and buccal trough sites.

Adult↗

PubMed1999

Electrical bioimpedance related to structural differences and reactions in skin and oral mucosa.

Electrical bioimpedance can reflect structural and chemical changes of the skin and the oral mucosa in the beta-dispersion frequency range. From our measured multifrequency data set, four physically distinct indices have been formulated to distinguish the electrical properties for different anatomical locations and to detect different reactions and conditions of the skin and the oral mucosa. In comparison with the skin, the differences for various anatomical regions were greater in the oral cavity, which showed as well a different impedance pattern after irritant responses. We conclude that the impedance technique is able to classify and quantify different responses and conditions, preferably by using contralateral reference sites, or following a site in time; however, mapping of baseline properties facilitates the use of the method even if a large part of the skin or the oral mucosa is involved. The method has the potential of becoming a diagnostic decision support tool.

Adult↗

PubMed1982

Serology of Neisseria gonorrhoeae: coagglutination serogroups WI and WII/III correspond to different outer membrane protein I molecules.

The 125I-labeled tryptic peptides of the outer membrane protein I of 33 previously characterized serological reference strains of Neisseria gonorrhoeae were investigated by peptide maps in relation to their coagglutination W serogroup. Serogroup WI strains tended to have lower-molecular-weight protein I molecules than did WII strains, and WIII strains had the highest-molecular-weight protein I molecules, although the serogroup could not be predicted from the molecular weights of the protein I molecules for a given strain. All 13 strains belonging to serogroup WI were found to have 11 peptides in common, as judged by their migration with respect to one another and to the internal marker valine in the peptide maps. Common peptides isolated from a given strain were found to comigrate with the corresponding common peptides from other strains in the same serogroup under various electrophoretic conditions. The 20 strains belonging to serogroups WII and WIII were all found to have 10 common peptides by the same criteria. When common peptides from serogroup WI were compared with the common peptides of serogroups WII and WIII, only three of these peptides appeared to be similar. Thus, two different outer membrane protein I molecules seem to exist which are mutually exclusive. Protein IA molecules contain the antigens recognized as serogroup WI, and protein IB molecules contain the antigens that characterize serogroups WII and WIII.

Agglutination Tests↗

PubMed2005

Spikernels: predicting arm movements by embedding population spike rate patterns in inner-product spaces.

Inner-product operators, often referred to as kernels in statistical learning, define a mapping from some input space into a feature space. The focus of this letter is the construction of biologically motivated kernels for cortical activities. The kernels we derive, termed Spikernels, map spike count sequences into an abstract vector space in which we can perform various prediction tasks. We discuss in detail the derivation of Spikernels and describe an efficient algorithm for computing their value on any two sequences of neural population spike counts. We demonstrate the merits of our modeling approach by comparing the Spikernel to various standard kernels in the task of predicting hand movement velocities from cortical recordings. All of the kernels that we tested in our experiments outperform the standard scalar product used in linear regression, with the Spikernel consistently achieving the best performance.

Action Potentials↗

PubMed2004

Reference structure tomography.

Reference structure tomography (RST) uses multidimensional modulations to encode mappings between radiating objects and measurements. RST may be used to image source-density distributions, estimate source parameters, or classify sources. The RST paradigm permits scan-free multidimensional imaging, data-efficient and computation-efficient source analysis, and direct abstraction of physical features. We introduce the basic concepts of RST and illustrate the use of RST for multidimensional imaging based on a geometric radiation model.

Journal Article↗

PubMed2026

Genome-Resolved Functional Profiling of Osteoporosis-Associated Gut Bacteria Highlights Putative Metabolic and Immunogenic Signatures of the Gut-Bone Axis.

The gut microbiota has emerged as a potential regulator of bone metabolism, but the genome-encoded functional repertoire of osteoporosis-associated gut bacteria remains insufficiently characterized. This study performed in silico functional profiling of gut bacterial taxa associated with osteoporosis, low bone mineral density, or comparator bone-related phenotypes. Twenty candidate taxa were selected from evidence in the human microbiome and represented by 26 curated bacterial reference genomes. Genome-wide annotations were used to map predicted gut-bone axis signatures, carbohydrate-active enzyme (CAZyme) repertoires, selected Kyoto Encyclopedia of Genes and Genomes pathways, and gutSMASH-predicted metabolic gene clusters. Functional burdens were normalized as hits per 1000 annotated proteins and integrated into metabolic, immunogenic, CAZyme, KEGG, and metabolic gene cluster profiles. Twelve predicted gut-bone axis signatures were identified, comprising 3337 primary candidate protein hits and a strict high-confidence subset of 2497 hits. Dominant signatures included vitamin B12/cobalamin metabolism, folate/one-carbon metabolism, peptidoglycan/cell-wall biosynthesis, and short-chain fatty acid-related functions. Dialister invisus, Dialister succinatiphilus, Megamonas funiformis, and Megamonas hypermegale showed the strongest normalized predicted gut-bone axis signal. These hypothesis-generating findings prioritize microbial metabolic and immunogenic features for future metagenomic, metabolomic, and experimental validation studies.

Osteoporosis↗

PubMed2002

[The sentinal node: the Dijon experience].

OBJECTIVES: The goal of this study was to evaluate the technical feasibility of sentinel node biopsy in breast cancer and its capacity to predict axillary node status. MATERIAL AND METHODS: Between February 2000 and June 2001, 70 patients with invasive breast carcinomas referred to the cancer center of Dijon, underwent lymphatic mapping (patent blue dye and lymphoscintigraphy with a gamma probe) and sentinel node biopsy followed by axillary clearance (Berg's level 1 and 2). RESULTS: A sentinel node was identified in 94.26% of the patients. We noted 2 false negative sentinel lymph nodes. The sentinel lymph node was involved in 32.8% of the patients and was the only node involved in 14.2% of the patients. CONCLUSION: This study confirms the feasibility of sentinal node mapping, emphasizing the advantage of using two methods (patent blue dye and gamma probe). A learning curve is required. This procedure is not adapted for tumors larger than 3 cm because of a greater risk of sentinel node involvement and the need for a complete procedure with an axillary clearance.

Adult↗

PubMed2002

Minimalist approach: functional mapping.

The ability to accurately map functional cortex both preoperatively and intraoperatively is an important neurosurgical challenge for the next decade. The central concept of preoperative mapping is to superimpose blood flow and electrical activation data on a three-dimensional matrix created by MR imaging and image processing. The gold standard, at present, is direct cortical stimulation, which can identify primary motor, sensory, speech, and visual cortices. Cortical mapping can be performed intraoperatively or through implanted subdural electrodes at the bedside. The tasks for the next decade include the validation of these preoperative techniques (fMRI, MEG, TMS, EP): 1. Correlation of direct cortical stimulation with advanced perioperative stimulation/monitoring systems, in a wide variety of cases. In addition, extension of these applications into intraoperative imaging systems like the GE Signa unit should also be envisaged. 2. Evaluation of how various pathologies such as AVMs, well-circumscribed tumors, and infiltrative tumors affect the data obtained by these techniques. 3. Expansion of mapping to areas outside the primary motor and sensory cortices, including those referred to as "associative" and to higher functions collectively termed as "cognition."

Brain↗

PubMed1991

Biomedical database inter-connectivity: an experiment linking MIM, GENBANK, and META-1 via MEDLINE.

The linkage of disparate biomedical databases is an important goal of the Unified Medical Language (UMLS) Project. We conducted an experiment to investigate the feasibility of using UMLS resources to link databases in clinical genetics and molecular biology. References from MIM ("Mendelian Inheritance in Man") were lexically mapped to the equivalent citations in MEDLINE. The MeSH major subject headings by which the citations in a particular MIM entry had been indexed were used to develop a "genetic-disorder-centered view of the world" in Meta-1 (the first official version of the UMLS Metathesaurus). Our hypothesis was that these MeSH subject headings could provide access to a "semantic neighborhood" in Meta-1 that would be relevant to a particular genetic disorder. By browsing in this "semantic neighborhood," a user could select various combinations of terms with which to search MEDLINE through an interface between Meta-1 and Grateful Med. Such searches might retrieve citations that were more recent than those in MIM or that provided useful supplementary information. Since some MEDLINE records contain pointers to entries in GENBANK, information about genetic sequences related to a particular clinical genetic disorder could also be retrieved. This scenario was implemented for a small number of MIM entries, providing a concrete demonstration that linking disparate electronic databases in an important subdomain of biomedicine is relatively straightforward.

Databases, Factual↗

PubMed1978

[Genetics of influenza viruses].

An account is given of important fundamentals, working methods, and recent results in the context of influenza virus genetics. Reference is made to the potentials implied in gene mapping and to the possibility of elucidating the correlations between the single gene and all biological properties of the influenza virus. Discussed against that background are the polyacrylamide electrophoresis of virus RNA, hybridisation with complementary RNA, immunological and chemical differentiation of gene products, as well as the use of defect mutants and of recombinant formation. It is shown that successful elucidation of the genesis of new virus strains is possible by means of those methods which also enable the preparation of virus strains with desired properties. This is likely to open up new horizons for more progress in the context of immunoprophylaxis against virus influenza.

Genes, Viral↗

PubMed1998

A neural network approach to the analysis and classification of human craniofacial growth.

Planning of treatment in the field of orthodontics and maxillo-facial surgery is largely dependent on the individual growth of a patient. In the present work, the growth of 43 orthodontically untreated children was analysed by means of lateral cephalograms taken at the ages of 7 and 15. For the description of craniofacial skeletal changes, the concept of tensor analysis and related methods have been applied. Thus the geometric and analytical shortcomings of conventional cephalometric methods have been avoided. Through the use of an artificial neural network, namely self-organizing neural maps, the resultant growth data were classified and the relationships of the various growth patterns were monitored. As a result of self-organization, the 43 children were topologically ordered on the emerging map according to their craniofacial size and shape changes during growth. As a new patient can be allocated on the map, this type of network provides a frame of reference for classifying and analysing previously unknown cases with respect to their growth pattern. If landmarks are used for the determination of growth, the morphometric methods applied as well as the subsequent visualization of the growth data by means of neural networks can be employed for the analysis and classification of growth-related skeletal changes in general.

Adolescent↗