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Structural unbalanced chromosome rearrangements resolved by comparative genomic hybridization.

The identification of unbalanced structural chromosome rearrangements using conventional cytogenetic techniques depends on recognition of the unknown material from its banding pattern. Even with optimally banded chromosomes, when large chromosome segments are involved, cytogeneticists may not always be able to determine the origin of extrachromosomal material and supernumerary chromosomes. We report here on the application of comparative genomic hybridization (CGH), a new molecular-cytogenetic assay capable of detecting chromosomal gains and losses, to six clinical samples suspected of harboring unbalanced structural chromosome abnormalities. CGH provided essential information on the nature of the unbalanced aberration investigated in five of the six samples. This approach has proved its ability to resolve complex karyotypes and to provide information when metaphase chromosomes are not available. In cases where metaphase chromosome spreads were available, confirmation of CGH results was easily obtained by fluorescence in situ hybridization (FISH) using specific probes. Thus the combined use of CGH and FISH provided an efficient method for resolving the origin of aberrant chromosomal material unidentified by conventional cytogenetic analysis.

Abortion, Spontaneous↗

Quality classification of tandem mass spectrometry data.

UNLABELLED: Peptide identification by tandem mass spectrometry is an important tool in proteomic research. Powerful identification programs exist, such as SEQUEST, ProICAT and Mascot, which can relate experimental spectra to the theoretical ones derived from protein databases, thus removing much of the manual input needed in the identification process. However, the time-consuming validation of the peptide identifications is still the bottleneck of many proteomic studies. One way to further streamline this process is to remove those spectra that are unlikely to provide a confident or valid peptide identification, and in this way to reduce the labour from the validation phase. RESULTS: We propose a prefiltering scheme for evaluating the quality of spectra before the database search. The spectra are classified into two classes: spectra which contain valuable information for peptide identification and spectra that are not derived from peptides or contain insufficient information for interpretation. The different spectral features developed for the classification are tested on a real-life material originating from human lymphoblast samples and on a standard mixture of 9 proteins, both labelled with the ICAT-reagent. The results show that the prefiltering scheme efficiently separates the two spectra classes.

Algorithms↗

Falx and interhemispheric fissure on axial CT: II. Recognition and differentiation of interhemispheric subarachnoid and subdural hemorrhage.

Interhemispheric hyperdensity or unenhanced computed tomography was originally considered a sign of subarachnoid hemorrhage, the "falx sign." It has since been identified as a normal feature and has also been seen with interhemispheric subdural hemorrhage. To determine the differential features of interhemispheric hemorrhage, 50 patients with subarachnoid hemorrhage and 32 patients with interhemispheric subdural hematomas were reviewed. Subarachnoid hemorrhage produced anterior interhemispheric hyperdensity only, with a zigzag contour and extension from the calvarium to the rostrum of the corpus callosum. Interhemispheric subdural hematomas produce unilateral crescentic hyperdensities that are largest in the posterior superior part of the fissure, behind and above the splenium of the corpus callosum. Interhemispheric hyperdensity in children is more complex. Because the anterior part of the fissure is narrow in younger patients, subarachnoid hemorrhage may go undetected. Likewise, interhemispheric subdural hematomas in children are smaller and more difficult to recognize. They produce asymmetric thickening of the falx shadow with extension over the tentorium. They are, however, of great significance since they are generally seen in abused patients and carry a poor prognosis.

Adolescent↗

Flexible structural comparison allowing hinge-bending, swiveling motions.

We present an efficient method for flexible comparison of protein structures, allowing swiveling motions. In all currently available methodologies developed and applied to the comparisons of protein structures, the molecules are considered to be rigid objects. The method described here extends and generalizes current approaches to searches for structural similarity between molecules by viewing proteins as objects consisting of rigid parts connected by rotary joints. During the matching, the rigid subparts are allowed to be rotated with respect to each other around swiveling points in one of the molecules. This technique straightforwardly detects structural motifs having hinge(s) between their domains. Whereas other existing methods detect hinge-bent motifs by initially finding the matching rigid parts and subsequently merging these together, our method automatically detects recurring substructures, allowing full 3 dimensional rotations about their swiveling points. Yet the method is extremely fast, avoiding the time-consuming full conformational space search. Comparison of two protein structures, without a predefinition of the motif, takes only seconds to one minute on a workstation per hinge. Hence, the molecule can be scanned for many potential hinge sites, allowing practically all C(alpha) atoms to be tried as swiveling points. This algorithm provides a highly efficient, fully automated tool. Its complexity is only O(n2), where n is the number of C(alpha) atoms in the compared molecules. As in our previous methodologies, the matching is independent of the order of the amino acids in the polypeptide chain. Here we illustrate the performance of this highly powerful tool on a large number of proteins exhibiting hinge-bending domain movements. Despite the motions, known hinge-bent domains/motifs which have been assembled and classified, are correctly identified. Additional matches are detected as well. This approach has been motivated by a technique for model based recognition of articulated objects originating in computer vision and robotics.

Algorithms↗

Pulmonary arteriography in congenital heart disease.

Pulmonary outflow tract obstruction may occur at subvalve, valve, or pulmonary artery level. Selective ventriculography will usually define the intracardiac obstruction (whether valve, subvalve, or both) and may define pulmonary arterial abnormalities. Increasing experience in the surgical management of patients with tetralogy of Fallot and other conotruncal abnormalities characterized by significant pulmonary outflow tract obstruction suggests that preoperative recognition of pulmonary arterial stenosis is essential to the successful operative management of these patients (1-4). Because of the anatomicospacial relationships of the pulmonary arteries in "simple" (tetralogy of Fallot) and complex conotruncal malformations, selective ventriculography may not invariably provide sufficient detail about the morphologic state of the pulmonary arteries. Similarly, even selective pulmonary arteriography in the standard anterioposterior, lateral, and oblique views may not always allow accurate anatomic assessment of these vessels. Therefore, we wish to document a maneuver that has proved valuable in the assessment of pulmonary arteries during selective pulmonary arteriography. This maneuver was originally suggested to Peter M. Olley by Dr. L. M. Bargeron, Jr., and the surgical valve obtained from this angiographic view was stressed by Dr. John Kirklin in his John Keith lecture at the Canadian Cardiovascular Society (5). Although it is being used at some cardiovascular centers, we feel its application warrants this report.

Child, Preschool↗

The binding and lysis of target cells by cytotoxic lymphocytes: molecular and cellular aspects.

The characteristics of cytotoxic T lymphocyte (CTL) and natural killer (NK) cell recognition of and binding to target cells (conjugate formation), and the precise mechanism(s) by which the target cells are triggered to undergo apoptotic cell lysis are now being deciphered at the cellular and molecular levels. Involvement of a multitude of cell surface molecules, in addition to T cell receptor (TCR)-major histocompatibility (MHC)-peptide complexes, in the binding and signalling for lymphocyte-mediated lysis has been demonstrated. Two proposed mechanisms of lymphotoxicity currently appear to be valid: (i) a membranolytic one initiated by the formation of pores in target cell membranes by secreted molecules of lymphocyte origin, such as perforin and granzymes, and (ii) a nonsecretory one initiated by receptor-mediated triggering of apoptosis-inducing target cell surface molecules, but not involving the secretion of pore-forming agents and granzymes. Perforin and granzymes are probably involved in lymphocyte activation and are likely mediators of the membranolytic pathway of lymphotoxicity. Existence of the nonsecretory and receptor-triggered lytic mechanism was indicated by (i) the prelytic fragmentation of the target cell's DNA, which precedes release of intracellular (51Cr-labeled) components, (ii) the demonstration of cytolytic effector cells that are either devoid of or express background levels of lytic granules and perforin, and (iii) the observation that some CTL lyse target cells under conditions at which perforin and granzymes are neither secreted nor lytic, e.g. [Ca2+]o < 1 micromolar. These two mechanisms are not mutually exclusive and are probably used by different types of effector cells or by the same effector cells at different stages of differentiation. In fact, recent perforin gene knock-out experiments support the existence of both.

Animals↗

Development of a high-throughput scintillation proximity assay for the identification of C-domain translational initiation factor 2 inhibitors.

Translational initiation factor 2 (IF2) is the largest of the 3 factors required for translation initiation in prokaryotes and has been shown to be essential in Escherichia coli. It stimulates the binding of fMet-tRNA(f)(Met) to the 30S ribosomal subunit in the presence of GTP. The selectivity is achieved through specific recognition of the tRNA(f)(Met) blocked alpha-amino group. IF2 is composed of 3 structural domains: N-domain, whose function is not known; G-domain, which contains the GTP/GDP binding site and the GTPase catalytic center; and C-domain, which recognizes and binds fMet-tRNA(f)(Met). Its activity is strictly bacteria specific and highly conserved among prokaryotes. So far, antibiotics targeting IF2 function are not known, and this makes it an ideal target for new drugs with mechanisms of resistance not yet developed. A few assays have been developed in the past, which allow the detection of IF2 activity either directly or indirectly. In both instances, the assays are based on radioactive detection and do not allow for high throughput because of the need for separation or solvent extraction steps. The authors describe a novel biochemical assay for IF2 that exploits the molecular recognition of fMet-tRNA(f)(Met) by the C-domain. The assay is based on the incubation of biotinyl-IF2 with fMet-tRNA(f)(Met) and the subsequent capture of the radiolabeled complex by streptavidin-coated beads, exploiting the scintillation proximity assay (SPA) technology. The assay has been designed in an automatable, homogeneous, miniaturized fashion suitable for high-throughput screening and is rapid, sensitive, and robust to dimethyl sulfoxide (DMSO) up to 10% v/v. The assay, used to screen a limited chemical collection of about 5000 compounds and a subset of compounds originated by a 2-D substructural search, has shown to be able to detect potential IF2 inhibitors.

Binding, Competitive↗

Anomalous origin and malposition of the pulmonary arteries (crisscross pulmonary arteries) associated with complex congenital heart disease.

Anomalous origin and malposition of the branch pulmonary arteries is an uncommon malformation that has previously been noted only at the time of pathologic examination. Two infants with complex congenital cardiac disease had malposition of the branch pulmonary arteries (crisscross pulmonary arteries) detected by angiography and confirmed during surgery and in one case, at autopsy. The presence of this clinically unsuspected lesion complicated the accurate interpretation of both the two-dimensional echocardiographic appearance of the great vessels, and the catheter course and location during cardiac catheterization. Angiography clearly defined the crisscrossing pattern of the branch pulmonary arteries. The recognition of this malformation was important in planning and executing the surgical palliation or repair for these infants.

Electrocardiography↗

Antibody specificity of human glomerular basement membrane type IV collagen NC1 subunits. Species variation in subunit composition.

NC1 subunits were purified from gel filtration pools of acid-extracted, collagenase-digested human glomerular basement membranes (hGBM). This methodology, which enriches 28-kDa monomers (M28) in the total digest, allowed purification of these monomers and 24-kDa (M24) and 26-kDa (M26) monomers free from dimers. Reactivity of these subunits with Goodpasture autoantibodies using immunoblotting of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and two-dimensional nonequilibrium pH gradient electrophoresis gels showed strong reactivity with the purified M28 subunits. Inhibition enzyme-linked immunosorbent assay, used to quantitate the reactivity of the purified NC1 subunits, indicated that M28 had a greater than 10-fold increase in ability to inhibit binding to NC1 than NC1 itself. Comparison of hGBM NC1 components were made with those obtained from collagenase digests of salt and acid-extracted bovine and sheep GBM and Englebreth-Holm-Swarm tumor similarly purified by gel filtration and reverse-phase high performance liquid chromatography. Two-dimensional gel analysis of these NC1 isolates revealed absence of the very cationic M28 monomers. Reactivity with antibodies eluted from diseased kidneys of sheep immunized with hGBM (Steblay nephritis) was compared with Goodpasture autoantibody reactivity by immunoblotting two-dimensional gels of hGBM NC1. We conclude that a very cationic M28 monomer (M28 ) found only in hGBM is the probable target in Goodpasture syndrome, that the epitope is present on most NC1 components from extracted and unextracted hGBM, and is exposed by urea denaturation which is enhanced by acid treatment. A weakly cationic M28 monomer (M28+) is present in GBM from other species and is the probable target in Steblay nephritis. Differential recognition of the two M28 components by these antibodies points to different genetic origins or possibly distinct post-translational modifications for these components. This is supported by their presence or absence in different species and tissues, as well as biochemical differences from the M24/26 monomers which presumably are derived from alpha 1(IV) and alpha 2(IV) collagen chains.

Amino Acids↗

Urban zoonoses caused by Bartonella, Coxiella, Ehrlichia, and Rickettsia species.

The last half of the 20th Century witnessed an increase in the occurrence and recognition of urban zoonoses caused by members of the genera Bartonella, Coxiella, Ehrlichia, and Rickettsia, all traditionally considered to be members of the family Rickettsiaceae. In recent years, new human pathogens (Bartonella elizabethae, Bartonella henselae, and Rickettsia felis) have been recognized in urban environments. Other newly recognized pathogens (Ehrlichia chaffeensis and Ehrlichia phagocytophila in the United States) have sylvan zoonotic cycles but are present in urban areas because their vertebrate hosts and associated ectoparasitic arthropod vectors are able to survive in cities. Still other agents, which were primarily of historical importance (Bartonella quintana) or have not traditionally been associated with urban environments (Rickettsia rickettsii), have been recognized as causes of human disease in urban areas. Some diseases that have traditionally been associated with urban environments, such as rickettsialpox (caused by Rickettsia akari) and murine typhus (caused by Rickettsia typhi), still occur in large cities at low or undetermined frequencies and often go undetected, despite the availability of effective measures to diagnose and control them. In addition, alternate transmission cycles have been discovered for Coxiella burnetii, Rickettsia prowazekii, and R. typhi that differ substantially from their established, classic cycles, indicating that the epidemiology of these agents is more complex than originally thought and may be changing. Factors leading to an increase in the incidence of illnesses caused by these bacteria in urban areas include societal changes as well as intrinsic components of the natural history of these organisms that favor their survival in cities. Transovarial and transstadial transmission of many of the agents in their arthropod hosts contributes to the highly focal nature of many of the diseases they cause by allowing the pathogens to persist in areas during adverse times when vertebrate amplifying hosts may be scarce or absent. Domesticated animals (primarily cats, dogs, and livestock) or commensal rodents [primarily Norway rats (Rattus norvegicus) and house mice (Mus musculus)] can serve as vertebrate amplifying hosts and bring these agents and their ectoparasitic arthropod vectors into direct association with humans and help maintain transmission cycles in densely populated urban areas. The reasons for the increase in these urban zoonoses are complex. Increasing population density worldwide, shifts in populations from rural areas to cities, increased domestic and international mobility, an increase in homelessness, the decline of inner-city neighborhoods, and an increase in the population of immunosuppressed individuals all contribute to the emergence and recognition of human diseases caused by these groups of agents. Due to the focal nature of infections in urban areas, control or prevention of these diseases is possible. Increased physician awareness and public health surveillance support will be required to detect and treat existing urban infections caused by these agents, to determine the disease burden caused by them, to design and implement control programs to combat and prevent their spread, and to recognize emerging or resurging infections caused by members of these genera as they occur.

Animals↗

Evolution of the major histocompatibility complex: independent origin of nonclassical class I genes in different groups of mammals.

The class I major histocompatibility complex genes are composed of classical and nonclassical genes, the latter being largely nonfunctional. To understand the evolutionary relationships of the two groups of class I genes, a phylogenetic analysis of DNA sequences was conducted using 45 genes from six mammalian and one avian species. The results indicate that nonclassical genes in one species are more closely related to classical genes from the same species than to nonclassical genes from a species belonging to a different order or family. This indicates that the differentiation of classical and nonclassical genes occurs rather rapidly in the genome. Classical genes are apparently duplicated with a high frequency in the evolutionary process, and many of the duplicated genes seem to degenerate into nonclassical genes as a result of deleterious mutation. The nonclassical Qa genes in the mouse have sequences homologous to regulatory sequences involved in the universal expression of classical class I genes, but they have accumulated numerous nucleotide substitutions in these sequences. The pattern of nucleotide substitution in nonclassical genes is different from that in classical genes. In nonclassical genes, the rate of nonsynonymous substitution is higher in the antigen recognition site than in other gene regions, as is true of classical genes. However, unlike the case of classical genes, the nonsynonymous rate does not always exceed the synonymous rate in the antigen recognition site. Nonclassical proteins further differ from classical proteins in having amino acid replacements in conserved antigen recognition site positions. These observations are consistent with the hypothesis that nonclassical genes have originated from classical genes but have lost classical class I function because of deleterious mutation.

Animals↗

Computer recognition of skin structures using discriminant and cluster analysis.

BACKGROUND/AIMS: Automated image analysis of complex tissues is usually limited by the difficulty of recognizing special structures by computer. The aim of this study was to test the applicability of discriminant and cluster analysis to the interpretation of skin images. METHODS: Digital images from microscopic, dermatoscopic and clinical views of skin specimens were electronically dissected into elements of equal size and shape, and a set of grey level, colour and texture features was assessed for each element. Elements were classified interactively and submitted to discriminant analysis. Furthermore, hierarchical cluster analysis was used to enable the system to classify the tissue elements automatically, based on the available digital information. The classification results were relocated to the original image in order to evaluate the performance of the procedure. RESULTS: The system performs well in reproducibly detecting different skin structures in digital images. Discriminant analysis of interactively classified elements yielded a correct reclassification in 98 to 100% of tissue elements. Among the cluster analysis procedures, the conservative Ward method after removal of all highly correlated features produced the best results. The method turned out to be applicable irrespective of the image source used. CONCLUSIONS: Discriminant and cluster analysis may be helpful techniques for a user-independent, subjectively unbiased measurement system of skin structures.

Journal Article↗

Induced fit on sugar binding activates ribokinase.

The enzyme ribokinase phosphorylates ribose at O5* as the first step in its metabolism. The original X-ray structure of Escherichia coli ribokinase represented the ternary complex including ribose and ADP. Structures are presented here for the apo enzyme, as well as the ribose-bound state and four new ternary complex forms. Combined, the structures suggest that large and small conformational changes play critical roles in the function of this kinase. An initially open apo form can allow entry of the ribose substrate. After ribose binding, the active site lid is observed in a closed conformation, with the sugar trapped underneath. This closure and associated changes in the protein appear to assist ribokinase in recognition of the co-substrate ATP as the next step. Binding of the nucleotide brings about further, less dramatic adjustments in the enzyme structure. Additional small movements are almost certainly required during the phosphoryltransfer reaction. Evidence is presented that some types of movements of the lid are allowed in the ternary complex, which may be critical to the creation and breakdown of the transition state. Similar events are likely to take place during catalysis by other related carbohydrate kinases, including adenosine kinase.

Adenosine Diphosphate↗

Pathogenesis of ankylosing spondylitis: current concepts.

More than three decades after the discovery of HLA-B27 as a major genetic clue to the origins of ankylosing spondylitis, much has been learned about pathogenesis. However, the role of this major histocompatibility complex class I allele remains undefined. Studies from animal models have demonstrated that HLA-B27 overexpression can cause inflammatory disease with spondyloarthritis features, and together with investigations of patient-derived material, both innate adaptive and immune responses have been implicated. The gastrointestinal immune response to pathogens and even normal flora, with subclinical or overt inflammation, may play a role as an environmental component of these diseases. Although there has been a large conceptual emphasis on mechanisms involving autoreactive T-cell recognition of HLA-B27 complexes displaying arthritogenic peptides, and more recently non-canonical recognition of abnormal forms of HLA-B27 free of beta(2)m (heavy-chain dimers or monomers), it remains unclear whether immunological recognition plays a role in pathogenesis. The recognition that the HLA-B27 heavy chain misfolds during assembly, and causes endoplasmic reticulum 'stress', has led to the observation that this activates the unfolded protein response. This has opened additional areas of investigation into the response of immune system cells to protein misfolding, and suggested novel alternative concepts that may explain the role of HLA-B27 in pathogenesis. This chapter will discuss available data and current concepts regarding the pathogenesis of ankylosing spondylitis.

Animals↗

Care of the potential pediatric organ donor.

Although all of this information may create the impression that caring for a potential organ donor is an exceedingly complex task, in the authors' experience, this often is not true, and much energy can--and should--be devoted to the care of the bereaved family. Of crucial importance are the early recognition of brain death and the consequent radical switch of the treatment goal from preservation of the patient's brain and life to preservation of organs for the lives of others. Care for the donor is the natural extension of care for a critically ill or injured patient. During the foregoing discussion, the authors had to stress the absence of sound evidence on many points. Because many reports originate from transplant centers dedicated to a specific organ, gaining a comprehensive view on management options in the ICU further is hampered. Thus, this situation leaves another field in which investigations originating from pediatric intensivists could provide evidence urgently needed to make optimal choices. The next decade should see the thyroid hormone controversy solved by at least one controlled prospective study and the differential applicability of inotropic, vasoactive, or fluid-centered strategies. It seems self-evident that only graft survival and related parameters can form adequate endpoints for future studies.

Brain Death↗

Histiocyte-rich B-cell lymphoma.

This is the second report of histiocyte-rich B-cell lymphoma and the first case analyzed by flow cytometry and cytogenetic study. The immunophenotype determined by flow cytometry was that of a B-cell antigen-positive, surface immunoglobulin-negative B-cell lymphoma with 79% CD11c positive histiocytes. The lymphoid cells were composed of 76% neoplastic B-cells and 24% reactive T-cells. Immunohistochemical staining showed large numbers of histiocytes positive for CD68 and lysozyme in the lymph node and the bone marrow. Neoplastic lymphoid cells were positive for CD20, CD45, CD74 and CDw75. The monoclonality of the tumor cells was established by the evidence of rearrangements of the heavy chain and kappa light chain genes and a complex clonal cytogenetic abnormalities including t(8;14)(q11;q32). The tumor cells were large, pleomorphic lymphoid cells and showed no features resembling those of the L/H cells of Hodgkin's disease as previously reported. The rapidly progressive clinical course in the present case is consistent with the clinical features shown in the original study. The histiocytic component in this tumor is presumably recruited by a lymphokine with the nature of a growth factor from the tumor cells that may also be responsible for the rapid proliferation of the tumor cells and the aggressive clinical course. This entity merits special recognition because it leads to a predictable poor prognosis and because of its potential of being misdiagnosed as true histiocytic lymphoma.

Aged↗

Specific, major histocompatibility complex-unrestricted recognition of tumor-associated mucins by human cytotoxic T cells.

We have previously reported the establishment of cytotoxic T-cell lines from pancreatic cancer patients, by continuously stimulating tumor-draining lymph node cells with allogeneic pancreatic tumor cell lines. After the preliminary characterization of their phenotype and tumor specificity, detailed studies performed with one of the cell lines, W.D., show that it recognizes a specific antigen, a large and heavily glycosylated mucin molecule, expressed on pancreatic and breast tumors and tumor cell lines. Although this recognition appears major histocompatibility complex (MHC)-unrestricted, the antigen receptor used by the cytotoxic T cell is the alpha/beta heterodimer, typically found on MHC-restricted T cells. The target antigen is atypical, however, in its ability to directly bind and activate the T cells in the absence of self MHC, presumably by abundant and regularly repeated antigenic epitopes. These findings are important because they demonstrate a specific T-cell response against a human tumor-associated antigen. In addition to pancreatic and breast tumors, various mucin molecules are known to be produced by other tumors of epithelial cell origin and could be expected to stimulate similar T-cell-mediated immune responses.

Adenocarcinoma↗

High-titer interferon-alpha antibodies in a patient with pemphigus foliaceus.

Among 13 patients with pemphigus or bullous pemphigoid, high titers of anti-interferon-alpha (IFN-alpha) antibodies were present in all serum samples of one patient suffering from pemphigus foliaceus. This patient was characterized by a relatively benign course of the disease. The IFN antibodies were of oligoclonal or polyclonal origin, predominantly of the IgG subtype, and displayed a broad spectrum of specificity including various natural and recombinant IFN-alpha subtypes as well as recombinant IFN-omega 1. In vitro, these antibodies neutralized both the antiviral and antiproliferative activities of the respective IFN types. Recognition of the patient's endogenous IFN-alpha demonstrated their autoantibody nature. The IFN antibodies were present at diagnosis and resistant to continued immunosuppressive treatment. Despite clinical remission, the IFN antibodies persisted, suggesting that they were not pathogenically related to the skin manifestations of the pemphigus. There were no sings of immune complex-mediated organ damage. IFN antibodies constitute a new class of autoantibodies that may occur in conjunction with pemphigus and likely interfere with the endogenous IFN system.

Adult↗