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PubMed2002

Identification of the neoplastically transformed cells in Marek's disease herpesvirus-induced lymphomas: recognition by the monoclonal antibody AV37.

Understanding the interactions between herpesviruses and their host cells and also the interactions between neoplastically transformed cells and the host immune system is fundamental to understanding the mechanisms of herpesvirus oncology. However, this has been difficult as no animal models of herpesvirus-induced oncogenesis in the natural host exist in which neoplastically transformed cells are also definitively identified and may be studied in vivo. Marek's disease (MD) herpesvirus (MDV) of poultry, although a recognized natural oncogenic virus causing T-cell lymphomas, is no exception. In this work, we identify for the first time the neoplastically transformed cells in MD as the CD4(+) major histocompatibility complex (MHC) class I(hi), MHC class II(hi), interleukin-2 receptor alpha-chain-positive, CD28(lo/-), phosphoprotein 38-negative (pp38(-)), glycoprotein B-negative (gB(-)), alphabeta T-cell-receptor-positive (TCR(+)) cells which uniquely overexpress a novel host-encoded extracellular antigen that is also expressed by MDV-transformed cell lines and recognized by the monoclonal antibody (MAb) AV37. Normal uninfected leukocytes and MD lymphoma cells were isolated directly ex vivo and examined by flow cytometry with MAb recognizing AV37, known leukocyte antigens, and MDV antigens pp38 and gB. CD28 mRNA was examined by PCR. Cell cycle distribution and in vitro survival were compared for each lymphoma cell population. We demonstrate for the first time that the antigen recognized by AV37 is expressed at very low levels by small minorities of uninfected leukocytes, whereas particular MD lymphoma cells uniquely express extremely high levels of the AV37 antigen; the AV37(hi) MD lymphoma cells fulfill the accepted criteria for neoplastic transformation in vivo (protection from cell death despite hyperproliferation, presence in all MD lymphomas, and not supportive of MDV production); the lymphoma environment is essential for AV37(+) MD lymphoma cell survival; pp38 is an antigen expressed during MDV-productive infection and is not expressed by neoplastically transformed cells in vivo; AV37(+) MD lymphoma cells have the putative immune evasion mechanism of CD28 down-regulation; AV37(hi) peripheral blood leukocytes appear early after MDV infection in both MD-resistant and -susceptible chickens; and analysis of TCR variable beta chain gene family expression suggests that MD lymphomas have polyclonal origins. Identification of the neoplastically transformed cells in MD facilitates a detailed understanding of MD pathogenesis and also improves the utility of MD as a general model for herpesvirus oncology.

Animals↗
PubMed1988

Environmental concerns associated with the design of genetic engineering facilities.

Recombinant DNA technology is being used to produce a wide spectrum of products, such as vaccines, interferon, insulin, and growth hormones. In the design of facilities employing this technology, critical consideration must be given to the protection of the environment, both in the prevention of releases of recombinant DNA organisms into the environment and in the treatment of wastes originating from the production facilities. The design requirements for containment of large-scale systems are complex and require detailed analysis to insure that the containment system can handle both the normal and emergency releases of recombinant DNA organisms. This must include the prevention of releases through either liquid discharges or air emissions. The "killing" method used in the process for either the cells (extracellular product) or the broth (intracellular product) is an important step and can have significant implications in downstream treatment of wastewaters. Since fermentation is the primary process used in the production of recombinant DNA products, wastewater characteristics from this area of the process are basically similar to those of other fermentation processes. They differ, however, because of the "killing" step in the process, which can introduce compounds not normally found in fermentation wastewaters. This can complicate the treatment process by requiring additional treatment operations. Characteristics of wastewaters from other areas of the process can be very diverse, and no general characterization can be made. Techniques for recovery and purification can vary from product to product or even from plant to plant, making characterization difficult. It is important, therefore, that each process be examined in detail so that waste characterization is meaningful and useful in the design of treatment facilities. Because of the complex nature of the processes involved in the production of recombinant DNA products, wastewater treatment can also become a very complex problem. Systems to treat these wastewaters can include many diverse unit operations, from pretreatment of selected streams to tertiary treatment of the combined streams to meet stringent effluent criteria. While biological treatment is almost always applicable, waste loads are very high, and multiple-stage systems could be required. Early and ongoing interface between the process development scientists and engineers and the environmental disciplines allows for the early recognition of potential environmental problems. With early recognition, many of these problems can be economically and efficiently addressed in the design of the facility.(ABSTRACT TRUNCATED AT 400 WORDS)

Containment of Biohazards↗
PubMed1998

Discovery and structure--activity relationship studies of a novel and specific peptide motif, Pro-X-X-X-Asp-X, as a platelet fibrinogen receptor antagonist.

A novel hexapeptide, H-Pro-Ser-Nva-Gly-Asp-Trp-OH 6, a specific antagonist of platelet fibrinogen receptor (GpIIb/IIIa), was discovered in a structure-activity relationship (SAR) study where the role of the N-terminal Pro moiety of an RGD-containing peptide, H-Pro-Ser-Arg-Gly-Asp-Trp-OH 1, which is a potent but not specific antagonist toward GpIIb/IIIa integrin, was investigated. This novel peptide 6 exhibits very high activity as a human platelet aggregation inhibitor (IC50 0.59 microM, human PRP/collagen) as well as marked specificity for GpIIb/IIIa. A series of substitutions at the third position (Nva residue) in this hexapeptide, focused on the conformational rigidity, led to compounds which are superior to the original novel peptide 6 with regard to anti-platelet activity. The peptides, H-Pro-Ser-Hyp-Gly-Asp-Trp-OH 17 and H-Pro-Ser-delta Pro-Gly-Asp-Trp-OH 18 with the 5-membered ring structure, which restricted the conformation of the peptide backbone at the third position, inhibited the aggregation of human platelets at submicromolar concentrations (IC50 0.39 and 0.30 microM, respectively). Further structure-activity relationship studies at each position of the peptide sequence suggest a novel motif sequence, Pro-X1-X2-X3-Asp-X4, for specific GpIIb/IIIa integrin recognition, in which the N-terminal free Pro residue and the Asp residue at the fifth position are essential to the activity. This motif sequence is summarized as follows: (1) a small amino acid such as Ser, Ala or Gly is preferable at X1 position; (2) X2 may be any amino acid, preferably a bulky amino acid such as Tle or a cyclic amino acid such as Pro; (3) X3 must be a small amino acid such as Gly; and (4) X4 is preferably an amino acid with an aromatic side chain.

Amino Acid Sequence↗
PubMed1996

Release of fibrinopeptides by the slow and fast forms of thrombin.

The release of fibrinopeptides A and B by the slow and fast forms of thrombin was studied over the temperature range from 5 to 45 degrees C and the salt concentration range from 100 to 800 mM. The sequential mechanism for the release of fibrinopeptides originally proposed by Shafer was found to be obeyed under all conditions examined. The origin of preferential binding of fibrinogen and fibrin I to the fast form of thrombin in the transition state is in the second-order rate constant for association, k(l). In the case of fibrinogen, the values of k(l) for interaction with the fast and slow forms at 25 degrees C are 19 +/- 4 and 2.5 +/- 0.3 microM(-1) s(-1), with an activation energy of about 10 kcal/mol in both forms. In the case of fibrin I, the analogous values of k(l) are 9.1 +/- 0.7 and 2.5 +/- 0.2 microM(-1) s(-1), and the activation energy is about 4.5 kcal/mol in both forms. The mechanism of recognition of fibrinogen and fibrin I by thrombin entails a diffusion-controlled step with a small energy barrier. Analysis of the temperature dependence of the coupling free energy for allosteric switching indicates that the preferential interaction of fibrinogen and fibrin I with the fast form of thrombin in the transition state is entropy-driven, signaling a contribution of the hydrophobic effect to the slow-->fast transition. The salt dependence of the release of fibrinopeptides shows a constant coefficient Gamma(salt) = d ln(k(cat)/K(m))/d ln [salt] in the concentration range examined. Interestingly, the value of Gamma(salt) is independent of the salt used (NaCl, ChCl, or NaF) and is -1.5 +/- 0.1 for fibrinopeptide A and -2.5 +/- 0.1 for fibrinopeptide B. Hence, Gamma(salt) reflects predominantly the electrostatic contribution to the formation of the transition state, with a larger contribution seen in the interaction of thrombin with fibrin I. It is concluded that the interaction of thrombin with fibrinogen and fibrin I, leading to the release of fibrinopeptides A and B, is driven by electrostatic forces that presumably favor the correct preorientation of the enzyme and the substrate to form a productive complex in the transition state. This electrostatic-steering effect, also reported for thrombin-hirudin interaction, leads to a diffusion-controlled encounter with a very small energy barrier. Once the complex is formed, the enzyme switches to the fast form as a result of entropic factors presumably linked to water release from a more extended surface of recognition. While the release of fibrinopeptides as a function of salt concentration was being studied, an important observation was made on the role of Cl- in the formation of the fibrin clot. This anion drastically and specifically reduces the thickness of fibrin fibers, as judged by the 10-fold decrease in the equilibrium turbidity of clots developed in NaCl as compared to the turbidity of clots developed in NaF. Hence, the transition from a "coarse" to a "fine" clot induced by an increase in ionic strength as first described by Ferry is, instead, due to the specific binding of Cl- to intermediates in the ensuing polymerization. In fact, no change in the clotting curve is observed when the ionic strength is changed with NaF.

Electrochemistry↗
PubMed2005

Regularized Least Squares Cancer classifiers from DNA microarray data.

BACKGROUND: The advent of the technology of DNA microarrays constitutes an epochal change in the classification and discovery of different types of cancer because the information provided by DNA microarrays allows an approach to the problem of cancer analysis from a quantitative rather than qualitative point of view. Cancer classification requires well founded mathematical methods which are able to predict the status of new specimens with high significance levels starting from a limited number of data. In this paper we assess the performances of Regularized Least Squares (RLS) classifiers, originally proposed in regularization theory, by comparing them with Support Vector Machines (SVM), the state-of-the-art supervised learning technique for cancer classification by DNA microarray data. The performances of both approaches have been also investigated with respect to the number of selected genes and different gene selection strategies. RESULTS: We show that RLS classifiers have performances comparable to those of SVM classifiers as the Leave-One-Out (LOO) error evaluated on three different data sets shows. The main advantage of RLS machines is that for solving a classification problem they use a linear system of order equal to either the number of features or the number of training examples. Moreover, RLS machines allow to get an exact measure of the LOO error with just one training. CONCLUSION: RLS classifiers are a valuable alternative to SVM classifiers for the problem of cancer classification by gene expression data, due to their simplicity and low computational complexity. Moreover, RLS classifiers show generalization ability comparable to the ones of SVM classifiers also in the case the classification of new specimens involves very few gene expression levels.

Algorithms↗
PubMed1994

Bioactive Arg-Gly-Asp conformations in anti-integrin GPIIb-IIIa antibodies.

Antibodies can mimic the biological function of physiological ligands, yet few examples indicate the structural similarity between antibodies and the ligands that they mimic. Originally, the competition of antibodies for ligand binding sites was conjectured to be through similar three-dimensional conformations, which represent the "internal image" of the given ligand. Here we show that residues in a complementary determining region (CDR) can adopt the same bioactive structures observed in ligands. Structure-function studies of three anti-GPIIb-IIIa murine monoclonal antibodies, PAC-1, LJ-CP3, and OP-G2, indicate that the RYD sequence in their H-CDR3 domain occupies the same conformational space as RGD in conformationally constrained, bioactive, GPIIb-IIIa cell-surface adhesion ligands. The relative location of the guanidinium and carboxylate groups in the RXD regions is identified as an important recognition feature, and the conformational space occupied by this region in the antibodies is only slightly larger than that in the most bioactive peptides. Additionally, we show that antibodies can unveil other potential bioactive sequences, which may impart specificity. Thus antibodies are an exquisite probe for identifying motifs of short adhesion stretches, thereby revealing amino acid sequences and restricted geometries that might be used as lead compounds in drug design.

Amino Acid Sequence↗
PubMed1990

Recognition of tRNA(Tyr) by tyrosyl-tRNA synthetase.

In this review, I have brought together and compared the available data on the interaction between tRNA(Tyr) and tyrosyl-tRNA synthetases (TyrTS) of prokaryotic origins. The amino acid sequences of the heterologous TyrTS that can charge Escherichia coli tRNA(Tyr), show that the residues involved in the binding and recognition of tyrosine are strictly conserved whereas those involved in the interaction with tRNA(Tyr) are only weakly similar. The results of in vivo genetic complementation experiments indicate that the identity elements of tRNAs and the recognition mechanisms of such elements by the synthetases have been conserved during evolution. Heterologous or mutant tRNA(Tyr) are quantitatively charged by E coli TyrTS; the set of their common residues contains less than 10 elements if one excludes the invariant and semi-invariant residues of tRNAs. The residues of this set are candidates for a specific recognition by TyrTS. So far, adenosine-73 is the only residue for which a specific recognition of the base has been demonstrated. The residues that might serve as identity elements for E coli tRNA(Tyr) [McClain WH, Nicholas Jr HB (1987) J Mol Biol 194, 635-642] do not belong to the above set of conserved residues and therefore probably play negative roles, enabling tRNA(Tyr) to avoid non-cognate synthetases. Comparison of the charging and stability properties of mutant tRNA(Tyr) su +3 shows that bases 1 and 72 must pair (either by Watson-Crick or non-canonical hydrogen bonds) and adopt a geometry which is compatible with the helical structure of the acceptor stem in order for the mutant tRNA(Tyr) to be charged with tyrosine. If bases 1 and 72 or bases 2 and 71 cannot form such pairings, the suppressor phenotype of the mutant tRNA(Tyr)su +3 becomes thermosensitive. The weakening of base pair 1/72 by mutation or the change of adenosine-73 into guanosine results in the charging of tRNA(Tyr)su +3 with glutamine. Comparison of the structural model of the TyrTS/tRNA(Tyr) complex with the crystallographic structure of the GlnTS/tRNA(Gln) complex indicates that the mechanisms for the recognition of the acceptor arm are different in the 2 cases. Chemical attack and molecular modeling experiments have indicated that the acceptor end of tRNA(Tyr) ... CCCA3'-OH, remains mobile after the initial binding of tRNA(Tyr) to TyrTS.

Base Sequence↗
PubMed1999

The RRM domain of MINT, a novel Msx2 binding protein, recognizes and regulates the rat osteocalcin promoter.

Msx2 is a homeodomain transcriptional repressor that exerts tissue-specific actions during craniofacial skeletal and neural development. To identify coregulatory molecules that participate in transcriptional repression by Msx2, we applied a Farwestern expression cloning strategy to identify transcripts encoding proteins that bind Msx2. A lambdagt11 expression library from mouse brain was screened with radiolabeled GST-Msx2 fusion protein encompassing the core suppressor domain of Msx2. A cDNA was isolated that encodes a novel protein fragment that binds radiolabeled Msx2. Homeoprotein binding activity was confirmed by Farwestern analysis of the T7-epitope-tagged recombinant protein fragment, and interactions in vitro require Msx2 residues necessary for transcriptional suppression in vivo. On the basis of biochemical analyses, this novel protein was named MINT, an acronym for Msx2-interacting nuclear target protein. The original clone is part of a 12.6 kb transcript expressed at high levels in testis and at lower levels in calvarial osteoblasts and brain. Multiple clones isolated from a mouse testis library were sequenced to construct a MINT cDNA contig of 11 kb. Starting from an initiator Met in good Kozak context, a large nascent polypeptide of 3576 amino acids is predicted, in contiguous open reading frame with the Msx2 interaction domain residues 2070-2394. Protein sequence analysis reveals that MINT has three N-terminal RNA recognition motifs (RRMs) and four nuclear localization signals. Western blot analysis of fractionated cell extracts reveals that mature approximately 110 kDa (N-terminal) and approximately 250 kDa (C-terminal) MINT protein fragments accumulate in chromatin and nuclear matrix fractions, cosegregating with Msx2 and topoisomerase II. In gel shift assays, the MINT RRM domain selectively binds T- and G-rich DNA sequences; this includes a large G/T-rich inverted repeat element present in the proximal rat osteocalcin (OC) promoter, overlapping three cognates that support OC expression in osteoblasts. MINT and OC mRNAs are reciprocally regulated during differentiation of MC3T3E1 calvarial osteoblasts. Consistent with its proposed role as a nuclear transcriptional factor, transient expression of MINT(1-812) suppresses the FGF/forskolin-activated OC promoter, does not significantly regulate CMV promoter activity, but markedly upregulates the HSV thymidine kinase promoter in MC3T3E1 cells. In toto, these data indicate that the novel nuclear protein MINT binds the homeoprotein Msx2 and coregulates OC during craniofacial development. Msx2 and MINT both target an information-dense, osteoblast-specific regulatory region of the OC proximal promoter, nucleotides -141 to -111. The N-terminal MINT RRM domain represents an authentic dsDNA binding module for this novel vertebrate nuclear matrix protein. Acting as a scaffold protein, MINT potentially exerts both positive and negative regulatory actions by organizing transcriptional complexes in the nuclear matrix.

Amino Acid Sequence↗
PubMed1990

Anti idiotypic recognition of auto and allo antibodies to factor VIII by immunoglobulin preparations from single blood donors and large plasma pool.

Therapeutic immunoglobulins from commercial origin were administered to patients with allo and auto antibodies to factor VIII. The protocol used was similar to the prescription suggested for ITP, 0.4 g/kg body weight for five consecutive days. In patients with auto antibodies two kinds of effects were observed: A direct interaction between IVIg and the factor VIII inhibitor and long term interaction on antibody synthesis. The direct interaction observed in vivo was demonstrated to be mediated through Fab'2 fragments of both idiotypic interaction. This was also demonstrated using binding experiments and affinity chromatography experiments: Fab'2 fragments of IVIg were coupled to sepharose and Fab'2 fragments of patients IgG with allo and auto antibodies to Factor VIII were circulated through the column. The recovery of anti Factor VIII antibodies after elution was possible in 2 cases of allo antibodies out of 3 tested and 3 cases of auto antibodies out of 4. The question of anti idiotypes against factor VIII inhibitors in single individuals was investigated. IgG and Fab'2 fragments from single blood donors were isolated and tested for their inhibitory capacity against Fab'2 fragments of three different auto antibodies. The results did not show statistical differences between males and females however in the group of male blood donors, aging was a positive parameter for the presence of anti idiotypic antibodies against factor VIII inhibitors. Anti idiotypic antibodies against factor VIII inhibitors were present in 17.2% of the blood donor tested.

Antibodies, Anti-Idiotypic↗
PubMed2004

Supramolecular recognition of heteropairs of lanthanide ions: a step toward self-assembled bifunctional probes.

Three unsymmetrical ditopic hexadentate ligands coded for the recognition of trivalent lanthanide ions have been synthesized, L(AB), L(AC), and L(BC), where A represents a benzimidazole-pyridine-benzimidazole coordination unit, B a benzimidazole-pyridine-carboxamide one, and C a benzimidazole-pyridine-carboxylic acid moiety. Under stoichiometric 2:3 (Ln:L) conditions, these ligands self-assemble with lanthanide ions to yield triple-stranded bimetallic helicates having a sizable stability in acetonitrile: log beta(23) values for Eu are equal to 23.9 +/- 0.5 (L(AB)), 23.3 +/- 0.7 (deprotonated L(AC)), and 29.8 +/- 0.5 (deprotonated L(BC)). The crystal structure of the EuEu helicate with L(AB) shows 9-coordinate metal ions and an HHH (H stands for head) configuration of the helically wrapped ligand strands. In the presence of equimolar quantities of Ln and Ln' ions, L(AB) displays a remarkable predisposition to form HHH-heterobimetallic edifices, as proved both in the solid state by the crystal structures of the LaEu, LaTb, PrEr, and PrLu helicates and in solution by NMR spectroscopy. In all cases, the benzimidazole-pyridine-carboxamide units of the three ligands are bound to the smaller lanthanide ion, a fact further ascertained by high-resolution luminescence data on LaEu and by (1)H NMR. Analysis of the lanthanide-induced (1)H NMR shifts and of the spin-lattice relaxation times of the [LnLu(L(AB))(3)](6+) series (Ln = Ce, Pr, Nd, Sm, Eu) demonstrates the isostructural nature of the complexes in solution and that the crystal structure of LaTb is a good model for the solution structure. The selectivity of L(AB) for heteropairs of Ln(III) ions increases with increasing difference in ionic radius, resulting in 70% of the heterobimetallic species for deltar(i) = 0.1 A and up to 90% for LaLu (deltar(i) = 0.18 A), and corresponding to delta(deltaG) in the range 3-10 kJ.mol(-)(1). The origins of this stabilization are discussed in terms of the donor properties of the coordinating units and of the preferential formation of HHH isomers.

Journal Article↗
PubMed1978

Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox.

The 40,000-fold variation in eukaryote haploid DNA content is unrelated to organismic complexity or to the numbers of protein-coding genes. In eukaryote microorganisms, as well as in animals and plants, DNA content is strongly correlated with cell volume and nuclear volume, and with cell cycle length and minimum generation time. These correlations are simply explained by postulating that DNA has 2 major functions unrelated to its protein-coding capacity: (1) the control of cell volume by the number of replicon origins, and (2) the determination of nuclear volume by the overall bulk of the DNA: cell growth rates are determined by the cell volume and by the area of the nuclear envelope available for nucleocytoplasmic transport of RNA, which in turn depends on the nuclear volume and therefore on the DNA content. During evolution nuclear volume, and therefore DNA content, has to be adjusted to the cell volume to allow reasonable growth rates. The great diversity of cell volumes and growth rates, and therefore of DNA contents, among eukaryotes results from a varying balance in different species between r-selection, which favours small cells and rapid growth rates and therefore low DNA C-values, and K-selection which favours large cells and slow growth rates and therefore high DNA C-values. In multicellular organisms cell size needs to vary in different tissues: size differences between somatic cells result from polyteny, endopolyploidy, or the synthesis of nucleoskeletal RNA. Conflict between the need for large ova and small somatic cells explains why lampbrush chromosomes, nurse cells, chromatin diminution and chromosome elimination evolved. Similar evolutionary considerations clarify the nature of polygenes, the significance of the distribution of haploidy, diploidy and dikaryosis in life cycles and of double fertilization in angiosperms, and of heteroploidy despite DNA constancy in cultured cells, and other puzzles in eukaryote chromosome biology. Eukaryote DNA can be divided into genic DNA (G-DNA), which codes for proteins (or serves as recognition sites for proteins involved in transcription, replication and recombination), and nucleoskeletal DNA (S-DNA) which exists only because of its nucleoskeletal role in determining the nuclear volume (which it shares with G-DNA, and performs not only directly, but also indirectly by coding for nucleoskeletal RNA). Mechanistic and evolutionary implications of this are discussed.

Animals↗
PubMed1985

Clonal analysis of cytolytic T lymphocyte-mediated lysis of target cells with inducible antigen expression: correlation between antigen density and requirement for Lyt-2/3 function.

The lysis by allospecific cytolytic T lymphocytes (CTL) of the BALB/c lymphoma ST-4.5, a cell line that can be induced by interferon-gamma (IFN-gamma) to express increased amounts of major histocompatibility complex (MHC) class I antigens, was investigated. Culture of ST-4.5 in IFN-gamma increased the surface expression of Kd molecules from originally low levels and Dd from undetectable amounts by approximately fivefold as determined by fluorescence-activated cell sorter (FACS) analysis, whereas the levels of several other antigens (Ld, I-Ad, Thy-1, Lyt-2, L3T4, and LFA-1) were not affected. The lysis of ST-4.5 by Dd- and Ld-specific CTL clones correlated with the expression of those antigens on target cells as determined by both FACS and biochemical analysis. Lysis of ST-4.5 by CTL clones specific for Kd antigen fell into two distinct groups: those that could lyse targets cultured either normally or in IFN-gamma, and those that could only lyse targets that had been precultured in IFN-gamma. The apparent sensitivity to antigen exhibited by the Kd-specific CTL clones predicted their sensitivity to inhibition of target lysis by anti-Lyt-2/3 antibody. Those CTL clones that were only active against ST-4.5 expressing higher amounts of surface antigen (resulting from IFN-gamma preculture) were readily inhibited by anti-Lyt-2/3 antibody, whereas those CTL capable of lysing normally cultured targets having lower amounts of surface antigen were heterogeneous in their sensitivity to anti-Lyt-2/3; some were inhibitable, whereas others were resistant. In addition, another CTL clone that was resistant to inhibition by anti-Lyt-2/3 alone was readily inhibited by a synergistic combination of anti-Lyt-2/3 plus anti-Kd (but not anti-Dd or Ld) antibodies. These results indicate that CTL antigen receptor sensitivity to (or affinity for) antigen and the level of specific antigen expression by the target cell may both be important criteria in assessing Lyt-2/3 molecule function in CTL-mediated cytolysis. The function of recognition-associated molecules such as Lyt-2/3 may be to strengthen and increase the number of receptor-ligand binding events that facilitate CTL-target membrane interactions that lead to the lysis of the target cell.

Animals↗
PubMed1982

Responses to coloured patterns in the macaque lateral geniculate nucleus: analysis of receptive field properties.

Response patterns to complex visual stimuli were further analysed. Patterns were correlated with linear or non-linear components of the stimulus pattern at various wavelengths. Resulting correlograms revealed the spatial and spectral structure of receptive fields; they showed peaks or troughs according to whether that wavelength was associated with an increase or decrease in cell firing. Spectral response curves as derived from linear correlograms were similar to those reported for monochromatic stimuli. Variability in responsiveness and crossover wavelengths was high between parvocellular layer (PCL) cells even of the same class. Spatial differences between excitatory and suppressive receptive field components, i.e. a centre-surround organisation, are not apparent in linear correlograms from PCL cells. In this respect, spectral response curves do not qualitatively change with stimulus size. Correlation in time and the derivation of impulse functions showed that, even in magnocellular layer (MCL) cells, responses to luminance steps are of mainly temporal origin and due to a transient component in the response. A description of cell responses based on linear processing accounted well for the response patterns obtained in our experiments. Of various non-linear interactions investigated, only some kind of non-linear spectral differentiation provided an improvement in the description of cell responses. This improvement, however, was only minor and not present in all cells.

Animals↗
PubMed1991

Growth hormone heterogeneity: genes, isohormones, variants, and binding proteins.

Human GH represents a family of proteins rather than a single hormone. The circulation contains a bewildering array of GH forms, including several monomeric variants, their homo- and heteropolymers, fragments, and complexes with at least two BPs. The net biological activity of this mixture is difficult to predict, as the various molecular forms interact as partial agonists and/or antagonists at the receptor level. The number of GH forms that can be counted in plasma exceeds 100. Table 5 attempts to illustrate what is known and provide estimates for circulating variants. It does not include GH-V and its variants, which have to be added in pregnancy. Of note, what is commonly understood as "plasma GH," i.e. free monomeric 22K, represents only 21% of total immunoreactivity in plasma. In view of this complicated picture, it should be no surprise that different assays of plasma GH yield different results (107, 108, 290). While immunoassays are relatively unaffected by the BPs (291), receptor assays are seriously affected by the high affinity BP (261). Immunoassays, particularly of the monoclonal variety, are vulnerable to differential recognition of molecular variants depending on the unique epitope specificity of the antibody used. Polyclonal assays are more robust in this regard because of "epitope averaging" among the wide spectrum of epitope specificities present in the antibody population. Future work should aim at developing antibodies that are specific for individual GH variants. Such molecular probes will be helpful not only in standardizing immunoassays, but also in delineating the biological role of the various GH forms. The physiological significance of the numerous GH forms (or of the BPs) is still largely unknown. Progress in this area has been hampered, on the one hand, by the unavailability of pure GH variants in quantities sufficient for biological studies, and, on the other, by a certain lack of interest stemming from suspicions about artifacts. The recent resurgence of interest in GH and in its receptor and BPs should also refocus attention on the various molecular forms. Thus far, this interest has been largely confined to monomeric 22K, which is certainly effective for its original intended purpose, namely growth promotion. Whether 22K is sufficient for optimal growth and development, or whether it can fulfill all the functions of the GH family is unknown. It can be argued that evolutionarily conserved GH variants probably have biological importance.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1993

A rule-based neural controller for inverted pendulum system.

This paper tries to demonstrate how a heuristic neural control approach can be used to solve a complex nonlinear control problem. The control task is to swing up a pendulum mounted on a cart from its stable position (vertically down) to the zero state (up right) and keep it there by applying a sequence of two opposing constant forces of equal magnitude to the mass center of the cart. In addition, the displacement of the cart itself is confined to within a preset limit during the swinging up action and it will eventually be brought to the origin of the track. This is truly a nontrivial nonlinear regulation problem and is considerably difficult compared to the pendulum balancing problem (and its variations) widely adopted as a benchmarking test system for neural controllers. Through the solution of this specific control problem, we try to illustrate a heuristic neural control approach with task decomposition, control rule extraction and neural net rule implementation as its basic elements. Specializing to the pendulum problem, the global control task is decomposed into subtasks namely pendulum positioning and cart positioning. Accordingly, three separate neural subcontrollers are designed to cater to the subtasks and their coordination, i.e., pendulum subcontroller (PSC), cart subcontroller (CSC) and the switching subcontroller (SSC). Each of the subcontrollers is designed based on the rules and guidelines obtained from the experiences of a human operator. The simulation result is included to show the actual performance of the controller.

Algorithms↗
PubMed2003

Modified magnetic resonance image based parcellation method for cerebral cortex using successive fuzzy clustering and boundary detection.

Development of the accurate and reproducible parcellation of the human brain can be used to resolve the complex structure-functional relationships in the brain. We propose a modified parcellation method that provides the reliable and reproducible regions of interest using successive fuzzy c-means (sFCM) and boundary-detection algorithm. This method displays simultaneously both original brain image for identifying the sulcal landmarks and its tissue-classified image for referring to patterns of sulci. The whole cerebral region is extracted by the semiautomated region growing method and then classified to gray matter, white matter, and cerebrospinal fluid by sFCM. Referred to the other previous researches, the volume ratio of gray matter to white matter was shown to find that the efficiency of classification was improved (conventional FCM: 0.80 +/- 0.12 vs. sFCM: 1.57 +/- 0.18). Inter-rater reliability, estimated by the regression analysis, demonstrated that the proposed method was more reliable and reproducible than conventional methods [ANALYZE: correlation coefficient (CC)=0.341, Sig.=0.335 vs. proposed method: CC=0.816, Sig.=0.004]. The volume ratio of the whole cerebrum to the parceled object can be used to investigate structural abnormalities for the pathological detection of the various mental diseases such as schizophrenia, obsessive-compulsive disorder.

Algorithms↗
PubMed2004

[Identification of Langerhans cells in dermatology].

This paper describes our own findings on the role of Langerhans' cells in dermatology and discusses literature data on their detection in seven different dermatoses. The skin is an integral part of immune system. During the past 30 years, increasing evidence has been accumulated that the skin contains cellular elements which are needed for the initiation and expression of immune response. Langerhans' cells (LCs) are dendritic cells originating in the bone marrow. They reside mainly within stratified squamous epithelia and constitute approximately 2-4% of epithelial cells. LCs are epidermal antigen presenting cells which play a crucial role in allergic contact hypersensitivity, viral diseases, graft versus host disease and elimination of neo-plastic cell clones. They express antigens conjugated with major histocompatibility complex (MHC) class II positive molecules on their surfaces for presentation to T-helper lymphocytes. LCs cannot be identified in routinely prepared histologic testing but can be visualised at the light microscope level by histochemical and immunologic techniques. Appropriate methods for the detection of Langerhans' cells in dermatology (also shown by our own experience) are histoenzymatic methods of adenosintriphosphatase (ATP-ase), acid phosphatase (AP), alpha-naphthylacetatesterase (ANAE and peroxidase-antiperoxidase immunohistochemistry method with polyclonal S-100 protein antibody (PAP). LCs are the only cells in normal skin with ATP-ase activity. Histoenzymatic methods used in patients with atopic dermatitis, vitiligo, mycosis fungoides, Behcet's disease, lichen ruber planus, psoriasis vulgaris, irritant dermatitis and allergic contact dermatitis demonstrated LSs in epidermis and dermis. ANAE and AP showed concordance and were suitable histochemical markers for LC distribution and macrophages in the dermis in mycosis fungoides, atopic dermatitis, psoriasis vulgaris, irritant chronic dermatitis and Bechet's disease. Our experience of the human skin showed a strong activity of calcium-activated adenosine triphosphatase in LCs. LCs in the guinea pig skin can be demonstrated by Mg++ and Ca++ activated adenosine triphosphatase, but a stronger activity of Ca++ activated adenosine triphosphatase in LCs after irritation. Ca++ ATP-ase as an indicator of energy-dependent pump is the reflection of intracellular calcium level, which is a significant factor for regulating the growth and metabolism of the cells. LCs are found as target cells during the efferent phase of contact allergic reaction. Immunohistochemical methods, define the role of LCs in dermatology more precisely and allow complete immunologic recognition within the epidermis.

Dermatitis, Allergic Contact↗
PubMed2001

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.

Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to incorporate artificial amino acid residues into proteins in vivo. In a previous paper, the binding to aspartyl-tRNA synthetase of the substrate Asp and the analogue Asn were compared by molecular dynamics free energy simulations. Molecular dynamics combined with Poisson-Boltzmann free energy calculations represent a less expensive approach, suitable for examining multiple active site mutations in an engineering effort. Here, Poisson-Boltzmann free energy calculations for aspartyl-tRNA synthetase are first validated by their ability to reproduce selected molecular dynamics binding free energy differences, then used to examine the possibility of Asn binding to native and mutant aspartyl-tRNA synthetase. A component analysis of the Poisson-Boltzmann free energies is employed to identify specific interactions that determine the binding affinities. The combined use of molecular dynamics free energy simulations to study one binding process thoroughly, followed by molecular dynamics and Poisson-Boltzmann free energy calculations to study a series of related ligands or mutations is proposed as a paradigm for protein or ligand design. The binding of Asn in an alternate, "head-to-tail" orientation observed in the homologous asparagine synthetase is analyzed, and found to be more stable than the "Asp-like" orientation studied earlier. The new orientation is probably unsuitable for catalysis. A conserved active site lysine (Lys198 in Escherichia coli) that recognizes the Asp side-chain is changed to a leucine residue, found at the corresponding position in asparaginyl-tRNA synthetase. It is interesting that the binding of Asp is calculated to increase slightly (rather than to decrease), while that of Asn is calculated, as expected, to increase strongly, to the same level as Asp binding. Insight into the origin of these changes is provided by the component analyses. The double mutation (K198L,D233E) has a similar effect, while the triple mutation (K198L,Q199E,D233E) reduces Asp binding strongly. No binding measurements are available, but the three mutants are known to have no ability to adenylate Asn, despite the "Asp-like" binding affinities calculated here. In molecular dynamics simulations of all three mutants, the Asn ligand backbone shifts by 1-2 A compared to the experimental Asp:AspRS complex, and significant side-chain rearrangements occur around the pocket. These could reduce the ATP binding constant and/or the adenylation reaction rate, explaining the lack of catalytic activity in these complexes. Finally, Asn binding to AspRS with neutral K198 or charged H449 is considered, and shown to be less favorable than with the charged K198 and neutral H449 used in the analysis.

Amino Acid Substitution↗