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PubMed2002

Characterisation of a resource population of pigs screened for resistance to salmonellosis.

The degree of resistance to Salmonella choleraesuis infection in a reference family purposely bred to map resistance genes was assessed. Aspects of the innate and specific immune system were studied to find a parameter that might predict the resistance of pigs to salmonellosis. The family was bred from commercial full-sister pairs of F1-gilts and four boars. One boar (G398) was identified as breeding susceptible offspring, and one boar (G402) as breeding resistant offspring on the basis of pyrexial responses and numbers of Salmonella in liver and spleen post mortem. The other two boars were classified as 'possible resistant' (Y2008) and 'unknown' (Y6101) respectively. Functional differences in immune cells (neutrophils and lymphocytes) between the offspring of G398 and G402 were detected. The most resistant piglets had a higher number of circulating neutrophils and better polymorphonuclear neutrophils (PMNs) function, but a lower mitogenic response of lymphocytes both pre- and post-infection and a lower antibody response. Between the offspring groups of Y2008 and Y6101 no differences were found in the number of viable Salmonella in liver and spleen at post mortem or in immune cell function, however, the survival rate of these offspring groups was clearly different. Twenty three percent of the Y2008-offspring and 33% of the Y6101-offspring reached the predetermined humane clinical endpoint before the end of the experiment. Our findings suggest a role for several inherited immunological traits, including PMN function and lecithin-induced mitogenic proliferation, which appear to influence resistance to salmonellosis.

Animals↗

PubMed1981

Reconstruction of imperfectly ordered zinc-induced tubulin sheets using cross-correlation and real space averaging.

Large negatively-stained two-dimensional tubulin arrays induced by incubation with zinc were examined using electron microscopy. When Fourier methods are applied for the reconstruction, the resolution depends critically on the order of these arrays. The real space cross-correlation method as described in this paper, however, can be satisfactorily applied to disordered arrays. The method involves selection of a small area which is used as a reference to locate correlation peaks in other regions. In this way the locations of various unit cells are determined, often at points which deviate from the exact lattice. The unit cells at their determined locations are averaged, and the average is used as an improved reference in another search for correlation peaks. The process can be iterated to refine the reference and improve the correlation mapping. If necessary, poorly correlating unit cells can be ignored in the averaging, and rotational as well as translational corrections can be considered; but neither of these steps were found to be necessary in the studies on the zinc-induced tubulin sheets reported here. When both correlation and Fourier methods were compared for the same areas of selected sheets, the two methods gave comparable results for relatively well ordered regions, but the correlation images were superior for the more poorly ordered regions. In addition, even for the relatively well ordered regions the correlation images revealed some details that were lacking in the simple Fourier reconstructions but did appear in more extensive studies involving three-dimensional reconstruction. A direct comparison of the efficacy of real space and Fourier space reconstruction methods is presented using disordered model data.

Fourier Analysis↗

PubMed2003

k-Space based summary motion detection for functional magnetic resonance imaging.

Functional MRI studies are very sensitive to motion; head movements of as little as 1-mm translations or 1 degrees rotations may cause spurious signals. An algorithm was developed that uses k-space MRI data to monitor subject motion during functional MRI time series. A k-space weighted average of squared difference between the initial scan and subsequent scans is calculated, which summarizes subject motion in a single quality parameter; however, the quality parameter cannot be used for motion correction. The evolution of this quality parameter throughout a time series indicates whether head motion is within a predetermined limit. Fifty functional MRI studies were used to calibrate the sensitivity of the algorithm, using the six rigid-body registration parameters (three translations and three rotations) from the statistical parametric mapping (SPM99) package as a reference. The average correlation coefficient between the new quality parameter and the reference value from SPM was 0.84. The simple algorithm correctly classified acceptable or excessive motion with 90% accuracy, with the remaining 10% being borderline cases. This method makes it possible to evaluate brain motion within seconds after a scan and to decide whether a study needs to be repeated.

Algorithms↗

PubMed2026

Mapping the regulatory architecture of circadian clock adaptation: A genome-wide eQTL analysis in Drosophila melanogaster.

The circadian clock enables organisms to align internal daily rhythms with environmental cues, with major consequences for survival and fitness. Although the molecular framework of this system in Drosophila melanogaster is well characterized through transcription translation feedback loops involving ten core clock genes, the genetic basis of natural variation in their expression remains poorly understood. Here, we used natural expression variation to identify expression quantitative trait loci (eQTLs) through genome-wide association mapping. Using the Drosophila Genetic Reference Panel, we measured relative expression of all core clock genes at a single time point two hours after light onset. We identified 109 significant SNPs and 28 indels associated with expression variation across the clock network. Expression levels varied widely, with Pdp1ε showing the greatest variation (an 86-fold difference between extreme lines) and cyc the least (11.3-fold). Only three significant SNPs were located within clock genes themselves, all in Clk, whereas most associations represented trans-eQTLs in genes with diverse molecular functions. Candidate regulators included transcription factors such as Abd-B, tai, and E5; RNA binding proteins including Pum, Bru-3, and Mbl; and several long noncoding and antisense RNAs. Variants were also detected in gbb and the BMP pathway transcription factor Mad. Consistent with this, Mad knockdown reduced vri expression. Together, these results reveal a complex regulatory architecture underlying natural variation in circadian gene expression.

Journal Article↗

PubMed1998

Mapping of porcine genes belonging to two different cytochrome P450 subfamilies.

Three cDNA clones from a porcine small intestine cDNA library, tentatively identified as transcripts of two different cytochrome P450 (CYP) gene subfamilies, were sequenced and mapped. One of the clones was found to comprise an open reading frame of 503 amino acids and showed up to an 80% similarity to genes from the CYP3A subfamily. Translation of the other two cDNA clones revealed high similarity to genes from the CYP2C subfamily. One of these clones was truncated, lacking a part of the 5' end of the coding region, whereas the other encodes a putative pseudogene. The CYP3A gene was mapped cytogenetically by means of a pig/rodent somatic hybrid cell panel to pig chromosome 3, in the region p16-p17 or p11. The CYP2C pseudogene was mapped genetically to pig chromosome 14, using the PiGMaP shared reference pedigrees. The localisations provide information for the human/pig comparative map.

Amino Acid Sequence↗

PubMed2004

Identification and ablation of three types of ventricular tachycardia involving the his-purkinje system in patients with heart disease.

INTRODUCTION: Ventricular tachycardia (VT) with involvement of the His-Purkinje system (HPS) can be difficult to recognize in patients with heart disease, but it may be particularly susceptible to ablation targeting the HPS. This study defines the incidence and types of HPS involvement in VT. METHODS AND RESULTS: Involvement of the HPS was sought during electrophysiologic study with catheter mapping in 234 consecutive patients referred for catheter ablation of recurrent VT associated with heart disease. HPS VT was observed in 20 (8.5%) patients (mean ejection fraction 29%+/- 17%); in 9 (11%) of 81 patients with nonischemic heart disease and 11 (7.1%) of 153 patients with coronary artery disease (P = NS). Three types of HPS VT were observed: 16 patients (group 1) had typical bundle branch reentry, 2 patients (group 2) had bundle branch reentry and interfascicular reentry, and 2 patients (group 3) had VT consistent with a focal origin in the distal HPS. In all three groups, the VT QRS had morphologic similarity to the sinus rhythm QRS. Ablation of HPS VT was successful in all patients in whom it was attempted but produced high-degree AV block in 6 (30%). In 12 patients (60%), other VTs due to reentry through scar also were inducible. CONCLUSION: Involvement of the HPS in VT associated with heart disease has three distinct clinical forms, all of which are susceptible to ablation. Ablation often is not sufficient as the sole therapy due to other induced VT's and conduction abnormalities, requiring pacemaker and/or defibrillator implantation.

Adult↗

PubMed1997

Place cells and place navigation.

The assumption that hippocampal place cells (PCs) form the neural substrate of cognitive maps can be experimentally tested by comparing the effect of experimental interventions on PC activity and place navigation. Conditions that interfere with place navigation (darkness, cholinergic blockade) but leave PC activity unaffected obviously disrupt spatial memory at a post-PC level. Situations creating a conflict between egocentric and allocentric orientation (place navigation in the Morris water maze filled with slowly rotating water) slow down spatial learning. PC recording in rats searching food pellets in a rotating arena makes it possible to determine which firing fields are stable relative to the room (allocentrically dependent on sighted extramaze landmarks), to the surface of the arena (dependent on egocentric path integration mechanisms and intra-arena cues), or disappear during rotation. Such comparison is made possible by the computerized tracking system simultaneously displaying a rat's locomotion and the respective firing rate maps both in the room reference and arena reference frames. More severe conflict between allocentric and egocentric inputs is produced in the field clamp situation when the rat searching food in a ring-shaped arena is always returned by rotation of the arena to the same allocentric position. Ten-minute exposure to this condition caused subsequent disintegration or remapping of 70% PCs (n = 100). Simultaneous examination of PC activity and navigation is possible in the place avoidance task. A rat searching food in a stationary or rotating arena learns to avoid an allocentrically or egocentrically defined location where it receives mild electric footshock. In the place preference task the rat releases pellet delivery by entering an unmarked goal area and staying in it for a criterion time. Both tasks allow direct comparison of the spatial reference frames used by the PCs and by the behaving animal.

Animals↗

PubMed1984

Cyclic AMP-dependent phosphorylation of the precursor to beta subunit of mitochondrial F1-ATPase: a physiological mistake?

By using the purified rat liver protein for reference in electrophoresis and peptide mapping experiments, I have identified the beta subunit of mitochondrial F1-ATPase and its cytoplasmic precursor in two-dimensional gel patterns of proteins from S49 mouse lymphoma cells. The beta subunit precursor is a substrate for cAMP-dependent phosphorylation during its synthesis. Normally, both nonphosphorylated and phosphorylated forms of beta subunit precursor are processed rapidly to the smaller, more acidic forms of mature beta subunit. When processing is inhibited with valinomycin, both nonphosphorylated and phosphorylated forms of beta subunit precursor are stabilized. Nonphosphorylated beta subunit is one of the most stable of cellular proteins, but the phosphorylated form is eliminated within minutes of processing. This suggests that phosphorylated beta subunit is recognized as aberrant and excluded from assembly into the ATPase complex. These results argue that cAMP-dependent phosphorylation of the beta subunit precursor is a physiological mistake that is remedied after mitochondrial import and processing.

Animals↗

PubMed2005

Establishing scales of perceived severity for clinical situations during anaesthesia.

BACKGROUND: In many clinical, teaching, and research situations it would be useful to have graded scales of the urgency or other subjective properties for clinical situations that can arise during anaesthesia. Such a scale could serve as a reference point for the appropriate mapping of the urgency in audible alarms or visual warnings, provide a basis for training of graduated difficulty during anaesthesia simulation, provide a benchmark in risk assessment exercises, guide prioritization of decisions in computerized decision support systems for anaesthesia and help in assessing anaesthetist occupational stress. METHODS: A questionnaire-based instrument was developed to assess the perceived severity of a range of anaesthetic clinical situations. Four scales were tested: the severity of the situation for the patient, the urgency of response required by the anaesthetist, attention required by the anaesthetist, and anxiety experienced. Over 300 anaesthetists in three cohorts of 100 were consulted in the selection of the situations to be studied. The final version of the questionnaire, which included 25 situations, was circulated to a further 229 anaesthetists for validation. The pair-wise relationships of the four properties and hence their independence, was examined using Kendall's tau and correlation analysis. RESULTS: The subjective assessments of urgency and attention were closely related, as were severity and anxiety. Comparing the mean rank for the severity scale with the subjective risk scores revealed a statistically significant correlation of tau=0.647 (P<0.01). CONCLUSION: Subjective assessment of severity by anaesthetists was found to be consistent across the clinical situations studied.

Anesthesia↗

PubMed1988

Lethal and amanitin-resistance mutations in the Caenorhabditis elegans ama-1 and ama-2 genes.

Mutants of Caenorhabditis elegans resistant to alpha-amanitin have been isolated at a frequency of about 1.6 x 10(-6) after EMS mutagenesis of the wild-type strain, N2. Four new dominant resistance mutations have been studied genetically. Three are alleles of a previously identified gene, ama-1 IV, encoding the largest subunit of RNA polymerase II. The fourth mutation defines a new gene, ama-2 V. Unlike the ama-1 alleles, the ama-2 mutation exhibits a recessive-lethal phenotype. Growth and reproduction of N2 was inhibited at a concentration of 10 micrograms/ml amanitin, whereas ama-2/+ animals were inhibited at 100 micrograms/ml, and 800 micrograms/ml was required to inhibit growth of ama-1/+ larvae. We have also determined that two reference strains used for genetic mapping, dpy-11(e224)V and sma-1(e30)V, are at least four-fold more sensitive to amanitin that the wild-type strain. Using an amanitin-resistant ama-1(m118) or ama-1(m322) strain as a parent, we have isolated amanitin-sensitive mutants that carry recessive-lethal ama-1 alleles. The frequency of EMS-induced lethal ama-1 mutations is approximately 1.7 x 10(-3), 1000-fold higher than the frequency of amanitin-resistance alleles. Nine of the lethal alleles are apparent null mutations, and they exhibit L1-lethal phenotypes at both 20 degrees and 25 degrees. Six alleles result in partial loss of RNA polymerase II function as determined by their sterile phenotypes at 20 degrees. All but one of these latter mutations exhibit a more severe phenotype at 25 degrees C. We have also selected seven EMS-induced revertants of three different ama-1 lethals. These revertants restore dominant resistance to amanitin. The selection for revertants also produced eight new dominant amanitin resistance alleles on the balancer chromosome, nT1.

Alleles↗

PubMed2000

The eukaryotic promoter database (EPD).

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. WWW-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. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch

Database Management Systems↗

PubMed2002

The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.

The Eukaryotic Promoter Database (EPD) is an annotated, non-redundant collection of eukaryotic Pol II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. World Wide Web-based interfaces have been developed which 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. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch.

Animals↗

PubMed1981

Sequences homologous to retrovirus-like genes of the mouse are present in multiple copies in the Syrian hamster genome.

The genome of M. musculus contains many copies of DNA sequences homologous to the 35S RNA of intracisternal type-A particles (IAP) (1,2). A major class of IAP genes has been identified and isolated from a mouse library in Charon 4A (3). Cloned mouse IAP genes were used as probes to study homologous sequences in the DNA of other species. Sequences related to mouse IAP genes were detected in the DNAs from a variety of animal cells. DNAs from rat, gerbil, and hamster cells all gave strong reactions which could be localized to discrete restriction fragments on genomic blots. The reaction of Syrian hamster DNA was particularly strong. Fragments derived from different parts of the IAP gene all reacted with Syrian hamster DNA, and the reactive restriction fragments in the Syrian hamster DNA could be ordered with reference to the known restriction map of the IAP genes. The data suggest that sequences related to mouse IAP genes make up a 7 Kb unit in the Syrian hamster genome. Since the majority of the hamster sequences are quite divergent from those in the mouse, the ease with which they are detected suggests that they must be reiterated in the hamster genome.

Animals↗

PubMedDate not supplied

Genetic analysis of Père David's x red deer interspecies hybrids.

Interspecies hybrids provide unique opportunities for fundamental genetic analyses and for genetic improvement of farmed deer. We have bred F1 hybrids by artificial insemination of red deer hinds (Cervus elaphus) with semen from Père David's deer (Elaphurus davidianus). The male and female F1 Père David deer x red deer hybrids were fertile and in matings with red deer have produced over 300 viable backcross hybrids. DNA was collected from the backcross progeny as an international reference panel for gene linkage mapping and to investigate associations between segregating species-specific genetic markers and phenotypic traits. We have measured a range of phenotypic traits in the backcross hybrids and red deer. Several traits appear suitable for genetic analysis using mapped genetic markers, including gestation length, growth rate, live weight, head morphometrics, and tail length. Typically these traits show a large difference between Père David's deer and red deer and a high variance in the backcross so that many individuals have a phenotype outside the range observed in red deer.

Animals↗

PubMed1999

Conformational attractors on the Ramachandran map.

Frequency distributions of protein backbone dihedral angles phi and psi have been analyzed systematically for their apparent correlation with various crystallographic parameters, including the resolution at which the protein structures had been determined, the R factor and the free R factor, and the results have been displayed in novel differential Ramachandran maps. With improved sensitivity compared with conventionally derived heuristic Ramachandran maps, such differential maps automatically reveal conformational 'attractors' to which phi/psi distributions converge as the crystallographic resolution improves, as well as conformations tied specifically to low-resolution structures. In particular, backbone angular combinations associated with residues in alpha--helical conformation show a pronounced consolidation with substantially narrowed phi/psi distributions at higher (better) resolution. Convergence to distinct conformational attractors was also observed for all other secondary-structural types and random-coil conformations. Similar resolution-dependent phi/psi evolutions were obtained for different crystallographic refinement packages, documenting the absence of any significant artificial biases in the refinement programs investigated here. A comparison of differential Ramachandran maps derived for the R factor and the free R factor as independent parameters proved the better suitability of the free R factor for structure-quality assessment. The resolution-based differential Ramachandran map is available as a reference for comparison with actual protein structural data under WebMol, a Java-based structure viewing and analysis program (http://www. cmpharm.ucsf.edu/cgi-bin/webmol.pl).

Crystallography↗

PubMed1998

Digital imaging colposcopy: corrected area measurements using shape-from-shading.

The quantitative measurement of areas on the cervix is of interest to researchers studying the natural history of human papilloma viral lesions. Measurement of areas from images obtained through a colposcope are, however, inherently in error due to the image being a two-dimensional projection of a three-dimensional object. The ability to correct for these errors through use of digital imaging colposcopy and a practical application of a shape from shading algorithm was developed in this study. The shape from shading technique requires empirical measurement of the relationship between observed light intensity and the viewing angle (referred to as a reflection map). It was found that a population mean reflection map provided a correction that was about as accurate as using an individual's own reflection map (making it unnecessary to measure a map for each exam). Digital red filtering of the images increased accuracy and precision of measurement.

Adolescent↗

PubMed2006

Pose and motion recovery from feature correspondences and a digital terrain map.

A novel algorithm for pose and motion estimation using corresponding features and a Digital Terrain Map is proposed. Using a Digital Terrain (or Digital Elevation) Map (DTM/DEM) as a global reference enables the elimination of the ambiguity present in vision-based algorithms for motion recovery. As a consequence, the absolute position and orientation of a camera can be recovered with respect to the external reference frame. In order to do this, the DTM is used to formulate a constraint between corresponding features in two consecutive frames. Explicit reconstruction of the 3D world is not required. When considering a number of feature points, the resulting constraints can be solved using nonlinear optimization in terms of position, orientation, and motion. Such a procedure requires an initial guess of these parameters, which can be obtained from dead-reckoning or any other source. The feasibility of the algorithm is established through extensive experimentation. Performance is compared with a state-of-the-art alternative algorithm, which intermediately reconstructs the 3D structure and then registers it to the DTM. A clear advantage for the novel algorithm is demonstrated in variety of scenarios.

Algorithms↗

PubMed1986

Global control in Salmonella typhimurium: two-dimensional electrophoretic analysis of starvation-, anaerobiosis-, and heat shock-inducible proteins.

The response of Salmonella typhimurium to various forms of environmental stress was examined by using O'Farrell two-dimensional gel electrophoresis. Polypeptides (a total of 110) which quantitatively increased during various starvations, anaerobiosis, or heat shock were identified and cataloged in reference to a standard polypeptide map. Although significant overlap was noted during comparison of proteins induced by different starvations, only a few proteins produced during heat shock or anaerobiosis were also identified as starvation inducible.

Anaerobiosis↗