Debugging programs that use macro-oriented data abstractions

Enhanced C (EC) is a set-oriented, extensible, C-like language. EC uses data abstractions to define new types. These data abstractions, called clusters, are macro-like devices that perform substitution on the typed syntax tree. Debugging programs that use clusters raise problems that are not encountered in ordinary programming languages. At compile time there is a need to determine and report whether the macro expansion will result in a legal program before this expansion actually takes place. At run-time the problems are how to account for replaced statements and how to handle variables whose types have been established by the clusters, variables that disappear, or variables whose names have been changed. This article presents these problems and their solutions as implemented by the EC compiler and the EC symbolic debugger. Similar debugging problems appear in other languages: The need to handle variables at run time is common to all languages that support data abstraction even if the abstractions are procedure oriented; also, a mild form of the problem of the replaced statement appears in inline procedure substitution of Ada. The solutions developed for the EC debugger apply to these cases as well.     

Promiscuous binding of synthetic copolymer 1 to purified HLA-DR molecules

Copolymer 1 (Cop 1) is a random synthetic amino acid copolymer of L-alanine, L-glutamic acid, L-lysine, and L-tyrosine, effective both in suppression of experimental allergic encephalomyelitis and in the treatment of relapsing forms of multiple sclerosis. Cop 1 binds promiscuously and very efficiently to living APCs of various HLA haplotypes. In the present study, a substantial part of the whole mixture of random polypeptides that compose Cop 1 was shown to bind to purified human HLA-DR1, DR2, and DR4 with high affinity in a temperature- and time (and, in the case of DR4, pH)-dependent manner, and was competitively inhibited by DR-restricted peptides, but not by peptide derivatives that bind with low affinity. Bacterial superantigens inhibited Cop 1 binding only at very high concentrations. The formation of the Cop 1-DR1 complex was also shown by SDS-PAGE. These findings represent the first direct evidence for interactions of Cop 1 with purified DR molecules, and suggest that its effectiveness in experimental allergic encephalomyelitis and multiple sclerosis may be directly related to its binding in the groove of HLA-DR proteins.     

Molecular cloning of a phosphotyrosine-independent ligand of the p56lck SH2 domain

A novel human cDNA encoding a cytosolic 62-kDa protein (p62) that binds to the Src homology 2 (SH2) domain of p56lck in a phosphotyrosine-independent manner has been cloned. The cDNA is composed of 2074 nucleotides with an open reading frame encoding 440 amino acids. Northern analysis suggests that p62 is expressed ubiquitously in all tissues examined. p62 is not homologous to any known protein in the data base. However, it contains a cysteine-rich region resembling a zinc finger motif, a potential G-protein-binding region, a PEST motif, and several potential phosphorylation sites. Using T7-epitope tagged p62 expression in HeLa cells, the expressed protein was shown to bind to the lck SH2 domain. Deletion of the N-terminal 50 amino acids abolished binding, but mutagenesis of the single tyrosine residue in this region had no effect on binding. Thus, the cloned cDNA indeed encodes the p62 protein, which is a phosphotyrosine-independent ligand for the lck SH2 domain. Its binding mechanism is unique with respect to binding modes of other known ligands for SH2 domains.     

Natural killer activating receptors trigger interferon gamma secretion from T cells and natural killer cells

Proliferation of human CD4+ alphabeta T cells expressing a natural killer cell activating receptor (NKAR) has been shown to be enhanced, particularly in response to low doses of antigen, if the target cells present appropriate human class I major histocompatibility complex (MHC) molecules. Here, we show that NKAR also enhance proliferation and killing of target cells by subsets of CD8+ alphabeta and CD8+ gammadelta T cells, as well as by NK cells. Strikingly, interferon gamma secretion from all of these types of lymphocytes was markedly increased by interaction of the NKAR with their MHC class I ligands, independently of enhancement of proliferation. Thus, the recognition of class I MHC molecules by NKAR on both T cells and NK cells may provide a regulatory mechanism that affects immune responses through the secretion of interferon gamma and possibly other cytokines. It represents a signal for cytokine secretion alternative and/or augmentative to that through the T cell receptor.     

Electron microscope studies of conditional spore cortexless mutants of Bacillus sphaericus

Spore cortex of conditional cortexless mutants of Bacillus sphaericus 9602 was not detectable by electron microscopy unless the medium was supplemented with meso-alpha,epsilon-diaminopimelic acid during sporulation. Other spore structures appeared normal. Spore shape was quite irregular in the absence of meso-alpha,epsilon-diaminopimelic acid.     

The impact of visual layout factors on performance in Web pages: a cross-language study

Visual layout has a strong impact on performance and is a critical factor in the design of graphical user interfaces (GUIs) and Web pages. Many design guidelines employed in Web page design were inherited from human performance literature and GUI design studies and practices. However, few studies have investigated the more specific patterns of performance with Web pages that may reflect some differences between Web page and GUI design. We investigated interactions among four visual layout factors in Web page design (quantity of links, alignment, grouping indications, and density) in two experiments: one with pages in Hebrew, entailing right-to-left reading, and the other with English pages, entailing left-to-right reading. Some performance patterns (measured by search times and eye movements) were similar between languages. Performance was particularly poor in pages with many links and variable densities, but it improved with the presence of uniform density. Alignment was not shown to be a performance-enhancing factor. The findings are discussed in terms of the similarities and differences in the impact of layout factors between GUIs and Web pages. Actual or potential applications of this research include specific guidelines for Web page design.     

Differential binding to HLA-C of p50-activating and p58-inhibitory natural killer cell receptors

Natural killer (NK) cell cytotoxicity is regulated in large part by the expression of NK cell receptors able to bind class I major histocompatibility complex glycoproteins. The receptors associated with recognition of HLA-C allospecificities are the two-domain Ig-like molecules, p50 and p58 proteins, with highly homologous extracellular domains but differing in that they have either an activating or inhibitory function, respectively, depending on the transmembrane domain and cytoplasmic tails that they possess. We have compared the binding to HLA-Cw7 of an inhibitory p58 molecule, NKAT2, the highly homologous activating p50 molecule, clone 49, and a second activating p50 molecule, clone 39, which has homologies to both NKAT1 and NKAT2. NKAT2 binds to HLA-Cw7 with very rapid association and dissociation rates. However, the p50 receptors bind only very weakly, if at all, to HLA-C. The molecular basis of this difference is analyzed, and the functional significance of these observations is discussed.     

Altered penicillin-binding components in penicillin-resistant mutants of Bacillus subtilis

Penicillin- (cloxacillin-) resistant mutants of Bacillus subtilis were isolated in a stepwise fashion and the five penicillin-binding components (PBCs) in each were examined to determine which of the proteins, if any, corresponds to the penicillin killing site. PBCs II and V were previously eliminated as the likely penicillin targett. In the present work, PBC IV showed no change in sensitivity to cloxacillin in any of the resistant mutants isolated. PBC I did not change until the fifth-step mutant, in which it could not be detected by penicillin binding. Since PBC I did not bind penicillins that are lethal for this mutant, it also cannot be the lethal target. PBC II showed increased resistance to cloxacillin in three discrete steps, i.e., in mutants 1, 4, and 5, accompanied by changes in its electrophoretic mobility. However, the sensitivity of PBC II to penicillin G changed very little. Correspondingly, the cloxacillin-resistant mutants were unaltered in their sensitivity to penicillin G in vivo. Thus, of the five PBCs found in B. subtilis, PBC II is the most likely target for killing by penicillins.     

Relationship between cortex content and properties of Bacillus sphaericus spores

The muramic lactam content of spores of Bacillus sphaericus mutants defective in meso-diaminopimelic acid synthesis increases almost linearly with an increase of meso-diaminopimelic acid concentration in the medium. Since muramic lactam content is a measure of cortex content, the amount of cortex in spores of the mutants can be easily varied by changing the meso-diaminopimelic acid concentration in the medium. Characteristic properties were tested in spores containing different amounts of cortex. Critical amounts of cortex were associated with different spore properties. Refractility and dipicolinic acid accumulation in the spores both required about 20% of the maximum cortex content (although refractility is independent of dipicolinic acid content). For xylene octanol resistance, about 25% of the maximum cortex content was required.