Analysis of clonality in cytologic material using the polymerase chain reaction (PCR)

Analysis of clonality in cytologic material using the polymerase chain reaction (PCR) Immunoglobulin heavy chain (IgH) gene rearrangement analysis was performed on 27 fine needle aspiration (FNA) specimens (13 reactive hyperplasia, 11 B cell non-Hodgkin's lymphoma (B-NHL), one Hodgkin's disease and two suspicious of non-Hodgkin's lymphoma). Satisfactory amplification was achieved in 23/27 cases. A polyclonal pattern was seen in 14 cases (11 reactive hyperplasia, one B-NHL, one suspicious of lymphoma, one Hodgkin's disease). A monoclonal band was seen in nine cases (eight B-NHL, one reactive hyperplasia). Amplification was unsuccessful in four cases. Clonal analysis by PCR-based IgH gene rearrangement analysis can be successfully applied to FNA material and can be useful in diagnosis, but the results must be interpreted in conjunction with morphology and other ancillary information. Analyse de la clonalité en utilisant la PCR sur matériel cytologique L'analyse des réarrangements géniques des chaînes lourdes des immunoglobulines (IgH) a été réalisée sur 27 produits de ponction à l'aiguille fine (13 cas d'hyperplasie réactionnelle, 11 cas de lymphome non hodgkinien de type B (LNH-B), un cas de maladie de Hodgkin et deux cas suspects de lymphome malin non hodgkinien. Une amplification satisfaisante a été obtenue dans 23 cas sur 27. Un aspect polychonal a été observé dans 14 cas (11 hyperplasies réactionnelles, 1 lymphome malin non hodgkinien de type B, 1 cas suspect de lymphome, 1 cas de maladie de Hodgkin). Une bande monoclonale a été observée dans 9 cas (8 LNH-B, 1 hyperplasie réactionnelle). L'amplification n'a pas réussi dans quatre cas. L'analyse de la clonalité par analyse des réarrangements géniques par PCR peut être appliquée avec succès au matériel cytologique qui est obtenu par ponction à l'aiguille fine et elle peut être utile au plan diagnostique, mais les résultats doivent étre interprétés en intégrant les informations morphologiques et les autres données complémentaires. Polymerase Chain Reaction an zytologischem Material Die Analyse schwerer Immunglobulinketten (IgH) wurde an 27 FNP (13 reaktive Hyperplasien, 11 B-NHL, 1 Hodgkin und und zwie verdächtige Fälle) analysiert. Eine ausreichende Amplifikation wurde in 23/27 Fällen erzielt. Ein polyklonales Muster wurde in 14 Fällen beobachtet (11 reaktive Hyperplasien, 1 B-NHL, 1 Hodgkin sowie 1 verdächtiger Fall). Ein monoklonales Band wurde 9 mal gefunden (8 B-NHL, 1 reaktive Hyperplasie). Die Amplifikation war ungenügend in 4 Fällen. Die PCR-Analyse kann für die Diagnostik von Nutzen sein muss jedoch zusammen mit der Morphologie und anderen Informationen interpretiert werden.     

eScience and the need for data standards in the life sciences: in pursuit of objectivity rather than truth

Referring to European history of natural sciences as an example, I discuss the relation between development of standards and the emergence of new epistemic virtues. I distinguish standards relating to scientific argumentation from standards relating to data production. The former are based on truth-seeking epistemic virtues and use criteria of logical coherence and empirical grounding. They are important for the justification of an explanatory hypothesis. Data and metadata standards, on the other hand, concern the data record itself and all steps and actions taken during data production and are based on virtues of objectivity. In the second part I focus on data and metadata standards and argue that, in order to meet the requirements of eScience, the specification of the currently popular minimum information checklists should be complemented to cover four aspects: (i) content standards, which increase reproducibility and operational transparency of data production, (ii) concept standards, which increase the semantic transparency of the terms used in data records, (iii) nomenclatural standards, which provide stable and unambiguous links between the terms used and their underlying definitions or their real referents, and (iv) format standards, which increase compatibility and computer-parsability of data records. I discuss the role of scientific terminology for standardizing data and the need for using semantically standardized and formalized data-reporting languages in the form of controlled vocabularies and ontologies for establishing content standards for data in the life sciences. Finally I comment on the necessity of community participation in the development and application of standards and in making data openly available.     

A population ‘consensus’, partial linkage map of Picea abies Karst. based on RAPD markers

 We built a “consensus” partial linkage map based on RAPD markers using 48 sibships of eight megagametophytes each from a natural population of Norway spruce. A RAPD linkage map for a single individual from the same population had previously been constructed. Using 30 random decamers that had yielded 83 RAPD markers in the single-tree map, eight megagametophytes for each of the 48 sibships were screened. The linkage relationship among markers was estimated considering each family of eight megagametophytes as a progeny of a phase-unknown backcross mating between a heterozygous mother and a fictitious ‘recessive’ father. Markers were assigned to windows using LOD=2.0 and θ=0.4 as thresholds, and ordered using a criterion of interval support ≥2.0. For eight “windows” of recombination selected on the single-tree map, we investigated the consistency of marker order in the two maps. We adopted restrictive criteria for rejecting co-linearity between the two locus orders. For each window we imposed the most likely locus order obtained from one data set to the other (and vice versa), obtaining two symmetrical log-likelihood differences. We considered the hypothesis of co-linearity rejected when both symmetrical differences were significant (ΔLOD>3.0). By bootstrapping a subset of markers for each window (highly informative, ‘framework’ loci chosen on the previous single-tree map using a matrix correlation method) the sampling variability of the single-tree and population maps was estimated. As expected the population map was affected by a larger variability than the single-tree map. Heterogeneity in pairwise recombination fractions among groups of sibship revealed a (possible) alternative genomic arrangement detected within a single recombination window. Received : 4 January 1997 / Accepted : 24 January 1997     

Resolution of complex neuronal arrangements in the blowfly visual system using triple fluorescence staining

Summary Consecutive application of the fluorescent dyes, Texas Red and Lucifer Yellow, followed by nuclear staining with Bisbenzimide, reveals spatial relationships between individual neurons and relationships between their cell bodies and the perikaryal rind. The method is particularly useful for light-microscopical studies of complex interrelationships between identified neurons. The method has specific advantages over intraneuropil staining with cobalt or with HRP. These advantages are: simplicity, speed, information content, and aesthetic considerations.     

Molecular organization of the non-bilayer phospholipid arrangements that induce an autoimmune disease resembling human lupus in mice

Abstract

Non-bilayer phospholipid arrangements are three-dimensional structures that can form when anionic phospholipids with an intermediate form of the tubular hexagonal phase II (H_II), such as phosphatidic acid, phosphatidylserine or cardiolipin, are present in a bilayer of lipids. The drugs chlorpromazine and procainamide, which trigger a lupus-like disease in humans, can induce the formation of non-bilayer phospholipid arrangements, and we have previously shown that liposomes with non-bilayer arrangements induced by these drugs cause an autoimmune disease resembling human lupus in mice. Here we show that liposomes with non-bilayer phospholipid arrangements induced by Mn²⁺ cause a similar disease in mice. We extensively characterize the physical properties and immunological reactivity of liposomes made of the zwitterionic lipid phosphatidylcholine and a H_II-preferring lipid, in the absence or presence of Mn²⁺, chlorpromazine or procainamide. We use an hapten inhibition assay to define the epitope recognized by sera of mice with the disease, and by a monoclonal antibody that binds specifically to non-bilayer phospholipid arrangements, and we report that phosphorylcholine and glycerolphosphorylcholine, which form part of the polar region of phosphatidylcholine, are the only haptens that block the binding of the tested antibodies to non-bilayer arrangements. We propose a model in which the negatively charged H_II-preferring lipids form an inverted micelle by electrostatic interactions with the positive charge of Mn²⁺, chlorpromazine or procainamide; the inverted micelle is inserted into the bilayer of phosphatidylcholine, whose polar regions are exposed and become targets for antibody production. This model may be relevant in the pathogenesis of human lupus.     

Sleep quality,sleepiness and the influence of workplace breaks: A cross-sectional survey of health-care workers in two US hospitals

ABSTRACT

This study assessed sleep quality, sleepiness and use of workplace break opportunities in 1285 health-care workers via an online questionnaire. Two hospitals were surveyed – one with and one without a fatigue mitigation policy. Across all respondents, 68.9% reported generally taking breaks of at least 30 min and 21.7% had access to a quiet place to rest, with no significant differences between hospitals. The presence of a fatigue mitigation policy was not associated with reduced sleepiness. However, accounting for hospital and shift characteristics, employees with access to a quiet place to rest while on break had significantly lower self-reported sleepiness scores.     

Structural classification of αββ and ββα supersecondary structure units in proteins

We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded β strands, preceded or followed by an α helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the α helix and β hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the orientation, preferences in the left/right handedness of the α–β connection are observed. These preferences can be explained by favorable side by side packing of the α helix and the β hairpin, local interactions in the region of the α–β connection or stabilizing environments in the parent protein. Furthermore, fold recognition procedures and structure prediction algorithms coupled to database-derived potentials suggest that the preferable nature of these arrangements does not imply their intrinsic stability. They usually accommodate a large number of sequences, of which only a subset is predicted to stabilize the motif. The motifs predicted as stable could correspond to nuclei formed at the very beginning of the folding process. Proteins 30:193–212, 1998. © 1998 Wiley-Liss, Inc.     

Cytological analysis of complex-heterozygotes in populations ofOenothera grandiflora (Onagraceae) in Alabama

Genetic analysis of unusual complex-heterozygous genotypes in populations ofO. grandiflora from Alabama (USA) has shown that these strains are composed of a typicalgrandiflora (B) complex and an altered B complex (designated as B^A) which probably contains genetic elements derived from an A genotype such as the beta complex ofO. biennis group 1. Analysis of the meiotic configurations of artificial hybrids between the new strains and a series of complexes of known segmental arrangement allowed determination of the arrangements of the unknown complexes. These data are evidence for origin of the altered B complexes.     

Structure of theEscherichia coli ATP synthase and role of the γ and ε subunits in coupling catalytic site and proton channeling functions

The structure of theEscherichia coli ATP synthase has been studied by electron microscopy and a model developed in which the and subunits of the F₁ part are arranged hexagonally (in top view) alternating with one another and surrounding a central cavity of around 35 Å at its widest point. The and subunits are interdigitated in side view for around 60 Å of the 90 Å length of the molecule. The F₁ narrows and has three-fold symmetry at the end furthest from the F₀ part. The F₁ is linked to F₀ by a stalk approximately 45 Å long and 25–30 Å in diameter. The F₀ part is mostly buried in the lipid bilayer. The subunit provides a domain that extends into the central cavity of the F₁ part. The and subunits are in a different conformation when ATP+Mg²⁺ are present in catalytic sites than when ATP+EDTA are present. This is consistent with these two small subunits switching conformations as a function of whether or not phosphate is bound to the enzyme at the position of the phosphate of ATP. We suggest that this switching is the key to the coupling of catalytic site events with proton translocation in the F₀ part of the complex.