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MHC antigens in urine as olfactory recognition cues.

The classical class I antigens of the major histocompatibility complex (MHC) are cell-surface glycoproteins which were originally discovered because they cause rapid rejection of cells or tissues grafted between unrelated individuals. These molecules are encoded by the K, D and L loci of the mouse MHC (and analogous loci in other species) which show extreme species polymorphism and a large number of alleles. In an outbreeding population 3.6 X 10(9) unique MHC class I phenotypes can be encoded by the 100 alleles at each of the K and D loci and the 6 alleles at the L locus. This level of polymorphism ensures that the cells and tissues of each unrelated individual are uniquely identified by their class I membrane-bound antigens. Like other membrane bound proteins, these class I molecules are anchored in the lipid bilayer by a hydrophobic domain encoded by exon 5. However, there have been reports of the occurrence of classical class I molecules in true solution in the blood of humans, mice, and rats. We report here that classical polymorphic class I molecules in normal rats are constitutively excreted in the urine and that untrained rats can distinguish the smell of urine samples taken from normal donors that differ only at the class I MHC locus and therefore excrete different allelomorphs of class I molecules in their urine.

Alleles↗

Electroactive C(2) symmetry receptors based on the biphenyl scaffold and tetrathiafulvalene units.

The synthesis of a family of biphenyl-tetrathiafulvalene (TTF) derivatives incorporating a binding site has been carried out in good to moderate yields through functionalization of the biphenyl scaffold. X-ray structure of one derivative (compound 3) of the series is provided and shows a dihedral angle of 74 degrees around the central Ar-Ar bond of the biphenyl unit in a cisoid conformation. (1)H NMR and cyclic-voltammetry studies demonstrate the critical importance of the nature of the substitution on the conformational rigidity and on the electrochemical behavior of the resulting biphenyl-TTF assemblies. This feature is underlined by an original electrochemical recognition process upon binding of Pb(2+), correlated to conformational changes occurring upon metal cation complexation.

Biphenyl Compounds↗

The use of soluble synthetic peptide combinatorial libraries to determine antigen recognition of T cells.

T cells identify by their T-cell receptor (TCR) short peptides in the context of major histocompatibility complex (MHC) molecules. The interaction of the trimolecular complex composed of the TCR and MHC bound peptide was extensively studied using substitution analogs of the original peptide ligands to define those residues important for T-cell recognition in the peptide chain. This approach has led to the observation that T-cell recognition is highly flexible and that many different peptides can be recognized by an individual TCR. Others and we have recently introduced synthetic peptide combinatorial libraries (SCL) to investigate T-cell recognition. Here we review the SCL-based approaches and describe our current techniques for mapping TCR motifs for CD4+ T cells. The implications of our findings for the understanding of T-cell recognition, as well as for future applications to study T-cell responses in infectious diseases, autoimmune disorders and cancer are discussed.

Amino Acid Sequence↗

The 'Reading the Mind in the Voice' test-revised: a study of complex emotion recognition in adults with and without autism spectrum conditions.

This study reports a revised version of the 'Reading the Mind in the Voice' (RMV) task. The original task (Rutherford et al., (2002), Journal of Autism and Developmental Disorders, 32, 189-194) suffered from ceiling effects and limited sensitivity. To improve that, the task was shortened and two more foils were added to each of the remaining items. About 50 adults with Asperger Syndrome (AS) or High Functioning Autism (HFA) and 22 matched controls took the revised task. Results show the revised task has good reliability and validity, is harder, and more sensitive in distinguishing the AS/HFA group from controls. Verbal IQ was positively correlated with performance, and females performed worse than males in the AS/HFA group. Results are discussed with regard to multi modal empathizing deficits in autism spectrum conditions (ASC).

Adolescent↗

Models of reflexive recognition. Wallon's Origines du caractère and Lacan's "Mirror stage".

Jacques Lacan drew on the empirical research of the psychologist Henri Wallon both in his 1938 theory of the mirror stage ("the intrusion complex") and in subsequent formulations. Yet, like Lacan's famous "return" to Freud, his recourse to Wallon is revisionary and, at times, antithetical. This essay examines the disparities between Wallon's and Lacan's work on the mirror experience, focusing especially on the status of the mirror and the identity of the reflected image. An analysis of these differences helps to clarify the meaning of the child's specular activity--"an ontological structure of the human world"--in Lacan's later view and the implications of reflexive recognition for his conception of parental agency.

Ego↗

In vivo maintenance of T-lymphocyte unresponsiveness induced by thymic medullary epithelium requires antigen presentation by radioresistant cells.

The T-cell repertoire developing in the thymus is rid of autospecific cells by the process of thymic negative selection. Recognition of major histocompatibility complex (MHC)/self-peptide complexes expressed by thymic antigen-presenting cells (APC) of bone marrow origin leads to induction of apoptotic death of autospecific thymocytes. Induction of tolerance to self-antigens not presented by thymic APC is mediated by medullary thymic epithelial cells (mTEC) which express a very wide range of proteins, e.g. inducible and tissue-specific proteins. The main type of tolerance induced by mTEC is non-deletional and the issue of how it is maintained outside the thymus is therefore of crucial interest. We have previously shown that the non-T-cell receptor (TCR) -transgenic T-cell repertoire developing in conditions in which tolerance to self-MHC/peptide ligands is exclusively induced by mTEC is tolerant to syngeneic targets in vivo but lyses such targets in vitro. Here we report that this non-deletional in vivo self-tolerance is not due to active tolerance assured by known naturally occurring regulatory or immune-modulating T lymphocytes. Importantly, we show that in vivo maintenance of this therefore probably anergic state requires continued interaction of autospecific T cells with self-MHC/peptide ligands expressed by radioresistant cells while APC are incapable of maintaining the tolerant state. Therefore, maintenance of non-deletional T-lymphocyte tolerance to the wide range of self-antigens expressed by mTEC depends on continued interaction with radioresistant cells that very probably express a much more limited repertoire of antigens. Our data may therefore have important consequences for tolerance to tissue-specific and inducible self-antigens.

Animals↗

Toll-like receptor 4 imparts ligand-specific recognition of bacterial lipopolysaccharide.

Lipopolysaccharide (LPS) is the main inducer of shock and death in Gram-negative sepsis. Recent evidence suggests that LPS-induced signal transduction begins with CD14-mediated activation of 1 or more Toll-like receptors (TLRs). The lipid A analogues lipid IVa and Rhodobacter sphaeroides lipid A (RSLA) exhibit an uncommon species-specific pharmacology. Both compounds inhibit the effects of LPS in human cells but display LPS-mimetic activity in hamster cells. We transfected human TLR4 or human TLR2 into hamster fibroblasts to determine if either of these LPS signal transducers is responsible for the species-specific pharmacology. RSLA and lipid IVa strongly induced NF-kappaB activity and IL-6 release in Chinese hamster ovary fibroblasts expressing CD14 (CHO/CD14), but these compounds antagonized LPS antagonists in CHO/CD14 fibroblasts that overexpressed human TLR4. No such antagonism occurred in cells overexpressing human TLR2. We cloned TLR4 from hamster macrophages and found that human THP-1 cells expressing the hamster TLR4 responded to lipid IVa as an LPS mimetic, as if they were hamster in origin. Hence, cells heterologously overexpressing TLR4 from different species acquired a pharmacological phenotype with respect to recognition of lipid A substructures that corresponded to the species from which the TLR4 transgene originated. These data suggest that TLR4 is the central lipid A-recognition protein in the LPS receptor complex.

Animals↗

Pattern playback revisited: unvoiced stop consonant perception.

Among the most influential publications in speech perception is Liberman, Delattre, and Cooper's [Am. J. Phys. 65, 497-516 (1952)] report on the identification of synthetic, voiceless stops generated by the Pattern Playback. Their map of stop consonant identification shows a highly complex relationship between acoustics and perception. This complex mapping poses a challenge to many classes of relatively simple pattern recognition models which are unable to capture the original finding of Liberman et al. that identification of /k/ was bimodal for bursts preceding front vowels but otherwise unimodal. A replication of this experiment was conducted in an attempt to reproduce these identification patterns using a simulation of the Pattern Playback device. Examination of spectrographic data from stimuli generated by the Pattern Playback revealed additional spectral peaks that are consistent with harmonic distortion characteristic of tube amplifiers of that era. Only when harmonic distortion was introduced did bimodal /k/ responses in front-vowel context emerge. The acoustic consequence of this distortion is to add, e.g., a high-frequency peak to midfrequency bursts or a midfrequency peak to a low-frequency burst. This likely resulted in additional /k/ responses when the second peak approximated the second formant of front vowels. Although these results do not challenge the main observations made by Liberman et al. that perception of stop bursts is context dependent, they do show that the mapping from acoustics to perception is much less complex without these additional distortion products.

Acoustic Stimulation↗

Structural basis of replication origin recognition by the DnaA protein.

Escherichia coli DnaA binds to 9 bp sequences (DnaA boxes) in the replication origin, oriC, to form a complex initiating chromosomal DNA replication. In the present study, we determined the crystal structure of its DNA-binding domain (domain IV) complexed with a DnaA box at 2.1 A resolution. DnaA domain IV contains a helix-turn-helix motif for DNA binding. One helix and a loop of the helix- turn-helix motif are inserted into the major groove and 5 bp (3' two-thirds of the DnaA box sequence) are recognized through base-specific hydrogen bonds and van der Waals contacts with the C5-methyl groups of thymines. In the minor groove, Arg399, located in the loop adjacent to the motif, recognizes three more base pairs (5' one-third of the DnaA box sequence) by base-specific hydrogen bonds. DNA bending by approximately 28 degrees was also observed in the complex. These base-specific interactions explain how DnaA exhibits higher affinity for the strong DnaA boxes (R1, R2 and R4) than the weak DnaA boxes (R3 and M) in the replication origin.

Amino Acid Sequence↗

The initiator protein E1 binds to the bovine papillomavirus origin of replication as a trimeric ring-like structure.

The replication initiator protein E1 binds to the origin of replication of bovine papillomavirus in several forms. E1 can bind to its recognition sequence as a monomer together with the viral transcription factor E2, or as a trimeric E1 complex. The trimerization of E1 is mediated by the sequence-specific binding of E1 to DNA, and results in an E1 complex that is linked topologically to the DNA because the three molecules of E1 form a ring-like structure that encircles the DNA. These results demonstrate that E1 utilizes unusual mechanisms for sequence-specific binding to DNA and for the generation of a structure that encircles the DNA. We believe that these forms of E1 bound to the origin of replication represent intermediates in a transition in the function of E1, from a sequence-specific origin of replication recognition protein to a form of E1 that is competent for the initiation of viral DNA replication.

Base Sequence↗

Toxoplasma gondii and MHC-restricted antigen presentation: on degradation, transport and modulation.

Resistance against Toxoplasma gondii, an obligate intracellular protozoan parasite surrounded by a parasitophorous vacuolar membrane, is mediated by the cellular arm of the immune system, namely CD8+ and CD4+ T cells. Thus, priming and activation of these cells by presentation of antigenic peptides in the context of major histocompatibility complex class I and class II molecules have to take place. This is despite the fact that the vacuolar membrane avoids fusion with the endocytic compartment and acts like a molecular sieve, restricting passive diffusion of larger molecules. This raises several cell biological and immunological questions which will be discussed in this review in the context of our current knowledge about major histocompatibility complex-restricted antigen presentation in other systems: (1) By which pathways are parasite-derived antigens presented to T cells? (2) Has the parasite evolved mechanisms to interfere with major histocompatibility complex-restricted antigen presentation in order to avoid immune recognition? (3) To what extent and by which mechanism is antigenic material, originating from the parasite, able to pass through the vacuolar membrane into the cytosol of the infected cell and is it then accessible to the antigen presentation machinery of the infected cell? (4) What are the actual antigen-presenting cells which prime specific T cells in lymphoid organs? An understanding of these mechanisms will not only provide new insights into the pathogenesis of Toxoplasma gondii and possibly other intravacuolar parasites, but will also improve vaccination strategies.

Animals↗

Were RNA replication and translation directly coupled in the RNA (+protein?) World?

The ribosome is proposed to have evolved from an ancestor that simultaneously replicated and translated template RNA. At its decoding site, this ancestor to the ribosome carried a ribozyme that assembled product RNA by sequentially ligating anticodon triplets excised from tRNAs. This ribozyme was the ancestor of the Group I introns, which are still present on some ribosomal RNA precursors. Coupling of reversible RNA replication by transesterification with the thermodynamically favourable process of transpeptidation provides a rationale for the evolution of the complete ribosome as a replicase for large RNAs in the RNA (+protein?) world. A detailed and experimentally verifiable mechanism can be proposed for simultaneous replication and translation. Sequence requirements for recognition of the decoding complex as a substrate helix by these ribozymes are consistent with earlier models for the origin of the genetic code, but require an indirect mode for ribosomal self-replication. This proposal has the potential to explain the location of Group I introns in the anticodon loops of some tRNAs.

Animals↗

Oriented coupling of major histocompatibility complex (MHC) to sensor surfaces using light assisted immobilisation technology.

Controlled and oriented immobilisation of proteins for biosensor purposes is of extreme interest since this provides more efficient sensors with a larger density of active binding sites per area compared to sensors produced by conventional immobilisation. In this paper oriented coupling of a major histocompatibility complex (MHC class I) to a sensor surface is presented. The coupling was performed using light assisted immobilisation--a novel immobilisation technology which allows specific opening of particular disulphide bridges in proteins which then is used for covalent bonding to thiol-derivatised surfaces via a new disulphide bond. Light assisted immobilisation specifically targets the disulphide bridge in the MHC-I molecule alpha(3)-domain which ensures oriented linking of the complex with the peptide binding site exposed away from the sensor surface. Structural analysis reveals that a similar procedure can be used for covalent immobilisation of MHC class II complexes. The results open for the development of efficient T cell sensors, sensors for recognition of peptides of pathogenic origin, as well as other applications that may benefit from oriented immobilisation of MHC proteins.

Adsorption↗

Directed forgetting deficits in patients with temporal lobe epilepsy: an information processing perspective.

Although mesial temporal lobe brain damage is frequently associated with memory loss, it is unclear whether the deficit results entirely from a disruption in the processing of relevant information or whether it also reflects interference from irrelevant information. Directed forgetting is one procedure that can be used, along with standard tests of memory, to investigate this distinction. Seventeen patients with a diagnosis of complex-partial seizures of temporal lobe origin and 17 healthy volunteers were compared on lexical decision, free recall, and recognition tests in a directed-forgetting paradigm. These tests created a memory profile to measure the influence of task relevant and irrelevant information in implicit and explicit memory. Compared with healthy volunteers, the patients were significantly impaired on the memory tasks overall [F(5,25) = 5.01, p < .01]. Specifically, directed forgetting in lexical decision and recognition both discriminated between the groups [stepdown F(1,26) = 6.84, eta 2 = .26, p < .05 and stepdown F(1,25) = 5.36, eta 2 = .13, p < .05, respectively]. The results suggest that interictal memory performance in temporal lobe epilepsy may be disrupted in part because of a deficit in the differential processing of task relevant and task irrelevant information, particularly at retrieval.

Adolescent↗

Large T-antigen mutants define multiple steps in the initiation of simian virus 40 DNA replication.

The biochemical activities of a series of transformation-competent, replication-defective large T-antigen point mutants were examined. The assays employed reflect partial reactions required for the in vitro replication of simian virus 40 (SV40) DNA. Mutants which failed to bind specifically to SV40 origin sequences bound efficiently to single-stranded DNA and exhibited nearly wild-type levels of helicase activity. A mutation at proline 522, however, markedly reduced ATPase, helicase, and origin-specific unwinding activities. This mutant bound specifically to the SV40 origin of replication, but under certain conditions it was defective in binding to both single-stranded DNA and the partial duplex helicase substrate. This suggests that additional determinants outside the amino-terminal-specific DNA-binding domain may be involved in nonspecific binding of T antigen to single-stranded DNA and demonstrates that origin-specific DNA binding can be separated from binding to single-stranded DNA. A mutant containing a lesion at residue 224 retained nearly wild-type levels of helicase activity and recognized SV40 origin sequences, yet it failed to function in an origin-specific unwinding assay. This provides evidence that origin recognition and helicase activities are not sufficient for unwinding to occur. The distribution of mutant phenotypes reflects the complex nature of the initiation reaction and the multiplicity of functions provided by large T antigen.

Antigens, Polyomavirus Transforming↗

Rotated drawing: the range of performance and anatomical correlates in a series of 16 patients.

Recently there has been interest in an unusual neuropsychological disorder in which the patient copies a complex drawing in a position which is grossly rotated relative to the original. This disorder is of interest partly because of its relationship to current theories of the process of object recognition, but the range of performances typically seen, as well as its anatomical correlates, remain obscure. We report 16 cases who produced grossly rotated drawings of the Rey and Taylor Complex Figures. These patients were drawn from an unselected series of 240 cases, with a wide variety of lesion types and sites. The performances of the 16 patients displayed striking similarities. We describe the formal features of these drawings and plot their anatomical correlates.

Adolescent↗

Diversity in protein recognition by PTB domains.

Phosphotyrosine-binding (PTB) domains were originally identified as modular domains that recognize phosphorylated Asn-Pro-Xxx-p Tyr-containing proteins. Recent binding and structural studies of PTB domain complexes with target peptides have revealed a number of deviations from the previously described mode of interaction, with respect to both the sequences of possible targets and their structures within the complexes. This diversity of recognition by PTB domains extends and strengthens our general understanding of modular binding domain recognition.

Phosphorylation↗

Recognition of the adenovirus type 2 origin of DNA replication by the virally encoded DNA polymerase and preterminal proteins.

Initiation of adenovirus DNA synthesis is preceded by the assembly of a nucleoprotein complex at the origin of DNA replication containing three viral proteins, preterminal protein, DNA polymerase and DNA binding protein, and two cellular proteins, nuclear factors I and III. While sequence specific interactions of the cellular proteins with their cognate sites in the origin of DNA replication are well characterized, the question of how the viral replication proteins recognize the origin has remained unanswered. Preterminal protein and DNA polymerase were therefore purified to homogeneity from recombinant baculovirus infected insect cells. Gel filtration demonstrated that while DNA polymerase existed in monomeric and dimeric forms, preterminal protein was predominantly monomeric and when combined the proteins formed a stable heterodimer. In a gel electrophoresis DNA binding assay each of the protein species recognized DNA within the origin of DNA replication with unique specificity. Competition analysis and DNase I protection experiments revealed that although each protein could recognize the origin, the heterodimer did so with enhanced specificity, protecting bases 8-17 from cleavage with the nuclease. Thus the highly conserved 'core' of the origin of DNA replication, present in all human adenoviruses, is recognized by the preterminal protein--DNA polymerase heterodimer.

Adenoviruses, Human↗