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PubMed1996

Peptide specificity of alloreactive CD4 positive T lymphocytes directed against a major histocompatibility complex class I disparity.

The mouse strains C57BL/6 (B6, H2b) and Kbm1 mutant bm1 have a defined difference of three amino acids at position 152, 155, and 156 in the MHC class I K molecule. This causes a change in the side and the bottom of the antigen presenting groove of the K molecule resulting in strong allogeneic responses in vitro and in vivo. Here we report on the peptide specificity of CD4+ T cells of B6 origin directed against the Kbm1 mutant and speculate on the peptide specificity of CD8+ bm1-specific T lymphocytes of B6 origin. Bm1-specific CD4+ T helper cells recognized a peptide derived from the Kbm1 molecule encompassing the three mutations, presented by MHC class II molecules on syngeneic cells. The ability of this peptide to bind to MHC class II resulted from amino acid mutations at positions 155 and 156. Furthermore, the recognition of the natural peptide derived from the Kbm1 molecule presented by MHC class II I-Ab molecules on cells of bml origin could be blocked by addition of an MHC class II I-Ab binding competitor peptide. Thus, due to the mutations in an MHC class I molecule, indirect presentation via MHC class II molecules and MHC class II-restricted recognition of a peptide derived from such a MHC class I molecule is demonstrable.

Animals↗

PubMed2000

Caspase-8 specificity probed at subsite S(4): crystal structure of the caspase-8-Z-DEVD-cho complex.

Caspase-8 is an initiator enzyme in the Fas-mediated pathway of which the downstream executioner caspase-3 is a physiological target. Caspases are cysteine proteases that are specific for substrates with an aspartic acid residue at the P(1) position and have an optimal recognition motif that incorporates four amino acid residues N-terminal to the cleavage site. Caspase-8 has been classified as a group III caspase member because it shows a preference for a small hydrophobic residue at the P(4) substrate position. We report the X-ray crystallographic structure of caspase-8 in complex with benzyloxycarbonyl-Asp-Glu-Val-Asp-aldehyde (Z-DEVD), a specific group II caspase inhibitor. The structure shows that the inhibitor interacts favourably with the enzyme in subsite S(4). Kinetic data reveal that Z-DEVD (K(i) 2 nM) is an almost equally potent inhibitor of caspase-8 as the specific group III inhibitor Boc-IETD-aldehyde (K(i) 1 nM). In view of this finding, the original classification of caspases into three specificity groups needs to be modified, at least for caspase-8, which tolerates small hydrophobic residues as well as the acidic residue Asp in subsite S(4). We propose that the subsite S(3) must be considered as an important specificity-determining factor.

Binding Sites↗

PubMed1990

Benign nodal lesions mimicking metastases from pediatric renal neoplasms: a report of the National Wilms' Tumor Study Pathology Center.

Regional lymph node status is a key factor in the staging of pediatric renal tumors on the National Wilms' Tumor Study (NWTS). A review of cases entered on the NWTS has uncovered a number of cases where benign lymph node findings were mistaken for metastases. Most frequently, this was due to the presence of complexes of epithelial cells and Tamm-Horsfall protein within nodal sinuses. The epithelial cells were derived from damaged nephrons, usually resulting from obstruction by tumor. Another epithelial pseudometastic lesion, intranodal squamous epithelial cells, was found to originate from metaplastic calyceal urothelium. Benign mesothelial or coelomic inclusions similar to those previously described in pelvic and periaortic lymph nodes of adult females were found in nodes of four patients, including two boys, who are, to our knowledge, the first to be described with this finding. Other sources of confusion included protrusion of lymphoid follicles or germinal centers into nodal sinuses, thick endothelial cells of postcapillary venules mimicking epithelial tubules, nodal megakaryocytes resembling anaplastic nuclear changes, and histiocytic granulomas. Immunocytochemical methods were useful in evaluating some of these phenomena. Recognition of these pseudometastatic lesions is essential in order to avoid unnecessary and potentially hazardous therapeutic intensification.

Child↗

PubMed1994

TL antigen as a transplantation antigen recognized by TL-restricted cytotoxic T cells.

In contrast to broadly expressed classical class I antigens of the major histocompatibility complex, structurally closely related TL antigens are expressed in a highly restricted fashion. Unlike classical class I antigens, TL antigens are not known to be targets of cytotoxic T cells or to mediate graft rejection. Whereas classical class I antigens function as antigen-presenting molecules to T cell receptors (TCR), the role of TL is yet to be defined. To elucidate the function of TL, we have derived transgenic mice expressing TL in most tissues including skin by introducing a TL gene, T3b of C57BL/6 mouse origin, driven by the H-2Kb promoter. By grafting the skin of transgenic mice, we demonstrate that TL can serve as a transplantation antigen and mediate a TCR-alpha/beta+ CD8+ cytotoxic T cell response. This T cell recognition of TL does not require antigen presentation by H-2 molecules. Furthermore, we show that C57BL/6 F1 mice develop CD8+ T cells that are cytotoxic for C57BL/6 TL+ leukemia cells, providing further support for the concept that aberrantly expressed nonmutated proteins such as TL can be recognized as tumor antigens.

Animals↗

PubMed1989

Binding of the herpes simplex virus type 1 UL9 gene product to an origin of viral DNA replication.

The binding of a herpes simplex virus type 1 (HSV-1) encoded polypeptide to a viral origin of DNA replication has been studied by using a gel retardation assay. Incubation of nuclear extract from HSV-1 infected cells with a labelled origin-containing fragment resulted in the formation of a specific retarded complex, the migration of which was further reduced in the presence of an antibody reactive with the UL9 gene product. Introduction of an additional copy of the UL9 gene, under the control of an immediate early (IE) promoter, conferred the ability to express origin binding activity at the non-permissive temperature upon an HSV-1 ts mutant blocked at the IE stage of infection. Endogenous or exogenous proteolytic activity revealed the presence of a relatively protease-resistant domain which retained sequence-specific DNA binding activity. The C-terminal 317 amino acids of the UL9 gene expressed as a fusion protein in Escherichia coli also bound to the origin. Our results demonstrate that the UL9 gene product binds to a viral origin and that sequence specific recognition and binding are specified by the C-terminal 37% of the polypeptide.

Animals↗

PubMed1993

Clinical aspects of epilepsy including diagnosis, management, pharmacotherapy, and surgery.

This review emphasizes clinical manifestations, recognition of specific epileptic syndromes, use of antiepileptic drugs, and surgical evaluation and outcome. Juvenile myoclonic epilepsy is increasingly recognized but still underdiagnosed. Good evidence exists for a relationship between Landau-Kleffner syndrome (acquired epileptic aphasia) and electrical status epilepticus during sleep, which reflects the course of the aphasia. In focal onset seizures, the type of aura may be as valuable for determining the lobe of seizure onset as electroencephalographic and neuroimaging techniques. In temporal lobe seizures, postictal language assessment was used to determine the side of origin, and hippocampal and temporal volumetry using magnetic resonance imaging proved reliable indicators of the side of involvement. Valproate sodium and carbamazepine were equally effective for secondarily generalized tonic-clonic seizures, but carbamazepine was superior to valproate for complex partial seizures. One study suggests that in children, increased daytime sleep tendency persists 4 to 5 months after discontinuation of antiepileptic drugs and that neither drugs nor seizure activity are necessarily involved. Many recent publications were devoted to surgical treatment. The main issues reviewed concern patient selection and correlation between preoperative parameters and outcome after surgery.

Anticonvulsants↗

PubMed1994

Bipartite DNA recognition by the human Oct-2 POU domain: POUs-specific phosphate contacts are analogous to those of bacteriophage lambda repressor.

The POU motif defines a family of eukaryotic transcription factors broadly involved in tissue-specific gene expression and developmental regulation. The motif contains two DNA-binding domains: an N-terminal POU-specific domain (POUs) and C-terminal homeodomain (POUHD). Surprisingly, POUs has recently been found to be similar in structure to helix-turn-helix (HTH) domains of phage repressor and Cro proteins [Assa-Munt, N., Mortishire-Smith, R., Aurora, R., Herr, W., & Wright, P.E. (1993) Cell 73, 193-205; Dekker, N., Cox, M., Boelens, R., Verrijzer, C.P., van der Vliet, P.C., & Kaptein, R. (1993) Nature 362, 852-855]. Because POUHD and POUs are expected to bind DNA differently, we have used "methylphosphonate interference" to investigate the alignment of their HTH elements in a specific DNA complex. This neutral phosphate analogue, originally developed for applications in antisense drug design [Miller, P. S., & Ts'o, P. O. P. (1987) Anti-Cancer Drug Des. 2, 117-128], is shown to provide a sensitive probe for sites of backbone-specific protein-DNA interaction. Inferred POUs-phosphate contacts are in striking accord with cocrystal structures of bacteriophage repressor and Cro proteins. Alignment of POUHD and POUs in successive major grooves in each case predicts unique HTH-adenine contacts. This prediction is verified using DNA base analogues to effect interchange of AT functional groups by the method of 2'-deoxyinosine/5-methyl-2'-deoxycytosine substitution [McLaughlin, L. W., Benseler, F., Graeser, E., Piel, N., & Scholtissek, S. (1987) Biochemistry 26, 7238-7245]. Our results strongly support the hypothesis that the DNA-binding properties of POUs are analogous to those of bacteriophage lambda repressor.

5-Methylcytosine↗

PubMed2005

Diastereomeric molecular recognition and binding behavior of bile acids by L/D-tryptophan-modified beta-cyclodextrins.

[reaction: see text] Binding behavior of L- and D-tryptophan-modified beta-cyclodextrins (L/D-Trp-beta-CD) (1 and 2) with four bile acids, i.e., cholate (CA), deoxycholate (DCA), glycocholate (GCA), and taurocholate (TCA), has been investigated by fluorescence, circular dichroism, and 2D-NMR spectroscopies and fluorescence lifetime measurement, as well as isothermal titration microcalorimetry. From the induced circular dichroism (ICD) and 2D NMR spectra, it is deduced that the D-Trp moiety of 2 attached to beta-CD is more deeply self-included in the cavity than that of the antipodal L-Trp moiety of 1, indicating appreciably enantioselective binding of the chiral sidearm by beta-CD. Interestingly, the original difference in conformation between 1 and 2 led to quite a large difference in affinity toward DCA, giving 3.3 times higher binding ability for 2 than for 1. Thermodynamically, the inclusion complexation of 1 and 2 with bile acids was entirely driven by favorable enthalpy change (DeltaH degrees) with accompanying negative entropy change (DeltaS degrees). The stronger binding of bile acids by L/D-Trp-beta-CD is attributable to higher enthalpic gains. The combined use of the calorimetric and NMR ROESY spectral examinations revealed the correlation between the thermodynamic parameters and the role of sidearm conformation in modified beta-cyclodextrins.

Bile Acids and Salts↗

PubMed1987

The use of visual landmarks by gerbils: reaching a goal when landmarks are displaced.

Gerbils (Meriones unguiculatus) can specify the location of a goal by means of visual landmarks and will return to such a goal from different starting positions in the vicinity of the landmarks. To discover whether landmark-cues are used continuously during an approach to the goal, gerbils were trained to forage for sunflower seeds close to a single illuminated light-bulb on the floor of an arena. As they approached the bulb, it was switched off and another bulb in a variable position with respect to the first turned on. On 52 out of 71 trials the gerbils changed their trajectory (latency ca. 240 ms) to aim for the newly lit bulb (Fig. 1 A, B). On the remaining trials, gerbils maintained their original course towards the first bulb as though it were still lit and then paused after a longer delay before eventually changing direction (Fig. 1 C). Thus, an approach to a beacon is usually under continuous visual control. This ensures that the gerbil will reach its goal correctly despite any inaccuracies in its initial computation of its approach. When switches were made between more complex arrays of landmarks, the gerbils' behaviour was less clear-cut. Possible reasons for this difference are suggested.

Animals↗

PubMed2005

Performance evaluation of local descriptors.

In this paper, we compare the performance of descriptors computed for local interest regions, as, for example, extracted by the Harris-Affine detector. Many different descriptors have been proposed in the literature. It is unclear which descriptors are more appropriate and how their performance depends on the interest region detector. The descriptors should be distinctive and at the same time robust to changes in viewing conditions as well as to errors of the detector. Our evaluation uses as criterion recall with respect to precision and is carried out for different image transformations. We compare shape context, steerable filters, PCA-SIFT, differential invariants, spin images, SIFT, complex filters, moment invariants, and cross-correlation for different types of interest regions. We also propose an extension of the SIFT descriptor and show that it outperforms the original method. Furthermore, we observe that the ranking of the descriptors is mostly independent of the interest region detector and that the SIFT-based descriptors perform best. Moments and steerable filters show the best performance among the low dimensional descriptors.

Algorithms↗

PubMedDate not supplied

A 60x computer-based Holter tape processing system.

Since its introduction in 1968, the basic algorithm for automatic recognition of ventricular ectopic depolarizations, developed at Worcester Polytechnic Institute, has been implemented and modified by a number of investigators. The modified multi-template algorithm is conceptually similar to the original algorithm except that there are eight templates stored for each patient. A new template is stored whenever the match with each of the old templates yields a correlation coefficient less than 0.79. The system reads a Holter tape at 60 x real time for heart rates of 80 beats per minute, with relatively few false positives.

Arrhythmias, Cardiac↗

PubMed1983

Topography of simian virus 40 A protein-DNA complexes: arrangement of pentanucleotide interaction sites at the origin of replication.

Investigation of the DNA binding properties of the simian virus 40 (SV40) A protein (large T antigen) and the hybrid adenovirus-SV40 D2 protein revealed that both viral proteins protect similar regions of SV40 DNA from digestion by DNase I or methylation by dimethyl sulfate. However, the interaction of D2 protein with DNA was more sensitive to increases of NaCl concentration than was the interaction of wild-type SV40 A protein. Dimethylsulfate footprinting identified 13 DNA pentanucleotide contact sites at the viral origin of replication. The sequences of these sites corresponded to the consensus family 5'-(G greater than T) (A greater than G)GGC-3'. The pentanucleotides were distributed in three regions of origin DNA. Region I contained three pentanucleotide contact sites arranged as direct repetitions encompassing a span of 23 base pairs. In region II, four pentanucleotides were oriented as inverted repetitions that also spanned a total of 23 base pairs. Region III had six recognition pentanucleotides arranged as direct repetitions in a space of 59 base pairs. These fundamental variations in DNA arrangement are likely to determine different patterns of protein binding in each region.

Antigens, Viral↗

PubMed2000

Twenty-four-color spectral karyotyping reveals chromosome aberrations in cytogenetically normal acute myeloid leukemia.

Multicolor spectral karyotyping allows simultaneous visualization of all human chromosomes and screening for chromosomal rearrangements without a priori knowledge of any abnormalities involved. Based on this potentially increased sensitivity, we investigated, in a preliminary manner, whether spectral karyotyping could detect cytogenetic aberrations in karyotypically normal leukemia. The test population was comprised of 28 cryopreserved, cytogenetically normal acute myeloid leukemia (AML) samples from patients registered to a randomized trial for previously untreated AML (SWOG 9031). Two normal and 12 samples with known cytogenetic aberrations were used to validate and establish the diagnostic accuracy of the spectral karyotyping assay and instrumentation in a clinical setting. Enumeration and region-specific DNA fluorescence in situ hybridization (FISH) probes verified discrepant results. In the validation data set, spectral karyotyping refined complex karyotypic rearrangements in six cases and defined the chromosomal origin of a "jumping" homogeneously staining region; however, the technology was less sensitive in the detection of subtelomeric rearrangements and double minute chromosomes. In the test population, spectral karyotyping identified previously undetected cytogenetic aberrations in two cases (7%) of karyotypically normal AML: a cryptic 11q23 translocation in 20/20 cells and a minor monosomy 7 clone in 3/21 cells (FISH, 10.5%). Both of these abnormalities are considered to confer a poor prognosis when based on classical cytogenetic prognostic criteria. As an adjunct to classical cytogenetics and standard FISH analyses, the additive resolution of spectral karyotyping, in particular, with chromosome paints spiked with subtelomeric and/or locus-specific probes, may allow significant gains to be made in diagnostic accuracy and recognition of genotype/phenotype prognostic relationships, and in defining underlying biologic mechanisms in cancer. Genes Chromosomes Cancer 28:318-328, 2000.

Acute Disease↗

PubMed2006

Interaction of mannan binding lectin with alpha2 macroglobulin via exposed oligomannose glycans: a conserved feature of the thiol ester protein family?

The serum collectin mannan-binding lectin (MBL) binds to oligomannose and GlcNAc-terminating glycans present on microorganisms. Using a commercial affinity chromatography resin containing immobilized MBL we screened human and mouse serum for endogenous MBL-binding targets. We isolated the serum protease inhibitor alpha(2) macroglobulin (alpha2M), a heavily glycosylated thiol ester protein (TEP) composed of four identical 180-kDa subunits, each of which has eight N-linked glycosylation sites. alpha2M has previously been reported to interact with MBL; however, the interaction was not characterized. We investigated the mechanism of formation of complexes between alpha2M and MBL and concluded that they form by the direct binding of oligomannose glycans Man(5-7) occupying Asn-846 on alpha2M to the lectin domains (carbohydrate recognition domains) of MBL. The oligomannose glycans are accessible for lectin binding on both active alpha2M (thiol ester intact) and protease-cleaved alpha2M (thiol ester cleaved). We demonstrate that MBL is able to interact with alpha2M in the fluid phase, but the interaction does not inhibit the binding of MBL to mannan-coated surfaces. In addition to alpha2M, two other members of the TEP family, C3 and C4, which also contain oligomannose glycans, were captured from human serum using the MBL resin. MBL binding may be a conserved feature of the TEPs, dating from their ancestral origins. We suggest that the inhibition of proteases on the surface of microorganisms by an ancestral alpha2M-like TEP may generate "arrays" of oligomannose glycans to which MBL or other lectins can bind. Binding would lead to opsonization or activation of enzyme systems such as complement.

Animals↗

PubMed2005

Diagnosis of lyme borreliosis.

A large amount of knowledge has been acquired since the original descriptions of Lyme borreliosis (LB) and of its causative agent, Borrelia burgdorferi sensu stricto. The complexity of the organism and the variations in the clinical manifestations of LB caused by the different B. burgdorferi sensu lato species were not then anticipated. Considerable improvement has been achieved in detection of B. burgdorferi sensu lato by culture, particularly of blood specimens during early stages of disease. Culturing plasma and increasing the volume of material cultured have accomplished this. Further improvements might be obtained if molecular methods are used for detection of growth in culture and if culture methods are automated. Unfortunately, culture is insensitive in extracutaneous manifestations of LB. PCR and culture have high sensitivity on skin samples of patients with EM whose diagnosis is based mostly on clinical recognition of the lesion. PCR on material obtained from extracutaneous sites is in general of low sensitivity, with the exception of synovial fluid. PCR on synovial fluid has shown a sensitivity of up to >90% (when using four different primer sets) in patients with untreated or partially treated Lyme arthritis, making it a helpful confirmatory test in these patients. Currently, the best use of PCR is for confirmation of the clinical diagnosis of suspected Lyme arthritis in patients who are IgG immunoblot positive. PCR should not be used as the sole laboratory modality to support a clinical diagnosis of extracutaneous LB. PCR positivity in seronegative patients suspected of having late manifestations of LB most likely represents a false-positive result. Because of difficulties in direct methods of detection, laboratory tests currently in use are mainly those detecting antibodies to B. burgdorferi sensu lato. Tests used to detect antibodies to B. burgdorferi sensu lato have evolved from the initial formats as more knowledge on the immunodominant antigens has been collected. The recommendation for two-tier testing was an attempt to standardize testing and improve specificity in the United States. First-tier assays using whole-cell sonicates of B. burgdorferi sensu lato need to be standardized in terms of antigen composition and detection threshold of specific immunoglobulin classes. The search for improved serologic tests has stimulated the development of recombinant protein antigens and the synthesis of specific peptides from immunodominant antigens. The use of these materials alone or in combination as the source of antigen in a single-tier immunoassay may someday replace the currently recommended two-tier testing strategy. Evaluation of these assays is currently being done, and there is evidence that certain of these antigens may be broadly cross-reactive with the B. burgdorferi sensu lato species causing LB in Europe.

Antibodies, Bacterial↗

PubMed1977

Structural and functional heterogeneity of mammalian nephrons.

Since the anatomical descriptions of Bowman showing differences between nephrons originating in the superficial and deep cortex, the concept of heterogeneity has been extended from identification of dissimilarities between nephrons to recognition of inhomogeneity within major portions of individual nephrons. We are now aware of functional correlates for the anatomical differences between nephrons, between analogous parts of different nephrons, and between the three portions of the proximal tubule and the three or more parts of the distal tubule. The implications of all of these differences for major renal processes, such as isosmotic fluid transport, salt balance, hypertension, urinary acidification, and the concentration or urine are now being defined. It seems likely that new conceptual and technical approaches, especially electron probe microanalysis, will add appreciably to defining the role of heterogeneity in these and other processes. Despite the increasing complexity of nephron heterogeneity, it is recommended that our basic nomenclature be retained and that new findings be incorporated into the schema set forth by Karl Peter. It would be very helpful if reports of investigations on single nephrons or segments of nephrons were to include diagrams delineating the structures on which the work was performed.

Animals↗

PubMed2004

Idiopathic fascicular ventricular tachycardia.

Idiopathic fascicular ventricular tachycardia is an important cardiac arrhythmia with specific electrocardiographic features and therapeutic options. It is characterized by relatively narrow QRS complex and right bundle branch block pattern. The QRS axis depends on which fascicle is involved in the re-entry. Left axis deviation is noted with left posterior fascicular tachycardia and right axis deviation with left anterior fascicular tachycardia. A left septal fascicular tachycardia with normal axis has also been described. Fascicular tachycardia is usually seen in individuals without structural heart disease. Response to verapamil is an important feature of fascicular tachycardia. Rare instances of termination with intravenous adenosine have also been noted. A presystolic or diastolic potential preceding the QRS, presumed to originate from the Purkinje fibers can be recorded during sinus rhythm and ventricular tachycardia in many patients with fascicular tachycardia. This potential (P potential) has been used as a guide to catheter ablation. Prompt recognition of fascicular tachycardia especially in the emergency department is very important. It is one of the eminently ablatable ventricular tachycardias. Primary ablation has been reported to have a higher success, lesser procedure time and fluoroscopy time.

Editorial↗

PubMed2007

Predicting tissue-specific enhancers in the human genome.

Determining how transcriptional regulatory signals are encoded in vertebrate genomes is essential for understanding the origins of multicellular complexity; yet the genetic code of vertebrate gene regulation remains poorly understood. In an attempt to elucidate this code, we synergistically combined genome-wide gene-expression profiling, vertebrate genome comparisons, and transcription factor binding-site analysis to define sequence signatures characteristic of candidate tissue-specific enhancers in the human genome. We applied this strategy to microarray-based gene expression profiles from 79 human tissues and identified 7187 candidate enhancers that defined their flanking gene expression, the majority of which were located outside of known promoters. We cross-validated this method for its ability to de novo predict tissue-specific gene expression and confirmed its reliability in 57 of the 79 available human tissues, with an average precision in enhancer recognition ranging from 32% to 63% and a sensitivity of 47%. We used the sequence signatures identified by this approach to successfully assign tissue-specific predictions to approximately 328,000 human-mouse conserved noncoding elements in the human genome. By overlapping these genome-wide predictions with a data set of enhancers validated in vivo, in transgenic mice, we were able to confirm our results with a 28% sensitivity and 50% precision. These results indicate the power of combining complementary genomic data sets as an initial computational foray into a global view of tissue-specific gene regulation in vertebrates.

Animals↗