Indices of response bias in the same-different experiment.

The same-different experiment is popular for assessing perceptual performance, including the performance of people with neuropsychological deficits. Although the measurement of accuracy with this experiment is now well understood, the measurement of response bias remains problematic. Reformulating the decision space for the experiment can yield new bias indices that are analogous to, but numerically different from, those of the more familiar yes-no experiment. Isobias curves that show how hit rate covaries with false alarm rate for constant bias but varying accuracy are presented for eight indices, and best-fitting parameters of the isobias functions are determined for a set of experimental data. The theoretical status of the bias indices and their relation to other formulations are reviewed.

UV-enhanced expression of a reporter gene is induced at lower UV fluences in transcription-coupled repair deficient compared to normal human fibroblasts, and is absent in SV40-transformed counterparts.

UV irradiation enhances transcription of a number of cellular and viral genes. We have compared dose responses for alterations in expression from reporter constructs driven by the human and murine cytomegalovirus (CMV) immediate early (IE) promoters in cells from patients with deficiencies in nucleotide excision repair (complementation groups of xeroderma pigmentosum and Cockayne syndrome) following UV exposure, or infection with UV-damaged recombinant vectors. Results suggest that unrepaired damage in active genes triggers increased reporter activity from constructs driven by the CMV promoters in human fibroblasts. Similar to human fibroblasts, HeLa cells and cells from Li-Fraumeni syndrome patients (characterized by an inherited mutation in the p53 gene) also displayed an increase in reporter activity following UV exposure; however, this response was absent in all simian virus 40 (SV40)-transformed cell lines examined. This suggests that a pathway affected by SV40-transformation (other than p53) plays an essential role in UV-enhanced expression from the CMV IE promoter.

Partial complementation of the DNA repair defects in cells from xeroderma pigmentosum groups A, C, D and F but not G by the denV gene from bacteriophage T4.

Endonuclease V (denV) from bacteriophage T4 was examined for its ability to complement the DNA repair defect in xeroderma pigmentosum (XP) cells from complementation groups A, C, D, F and G. The denV gene was introduced into SV40-transformed normal and XP cells using a retroviral vector. Expression of denV resulted in partial correction of UV sensitivity and increased host cell reactivation (HCR) of a UV-damaged reporter gene for XP cells from groups A, C and D, but not those from group G. Expression of denV in XP-F cells resulted in enhanced HCR of a UV-damaged reporter but did not affect UV sensitivity. The observed partial complementation is thought to reflect denV-mediated repair of cyclobutane-pyrimidine dimers (CPD), and is incomplete as denV does not recognize other UV-induced lesions, and may not even efficiently remove all CPD. As XP-F cells are believed to retain near-normal levels of CPD repair in the bulk of the genome, we believe that the disparity in the ability of denV to complement the repair deficiency in these cells results from an increased rate, but not level, of CPD repair. Furthermore, we suggest that the lack of correction in the XP-G cells examined results from an inability to process denV-incised CPD by the base excision repair pathway, as has been suggested for cells from the related genetic disorder, Cockayne syndrome. Expression of denV in repair proficient normal cells also resulted in increased HCR of the UV-damaged reporter construct, possibly arising from an increased rate of CPD repair in these cells.

UV-enhanced reactivation of a UV-damaged reporter gene suggests transcription-coupled repair is UV-inducible in human cells.

The genetic disorders xeroderma pigmentosum (XP) and Cockayne syndrome (CS) exhibit deficiencies in the repair of UV-induced DNA damage. CS fibroblasts retain proficient nucleotide excision repair (NER) of inactive (or bulk) DNA, but are deficient in the transcription-coupled repair (TCR) of active genes. In contrast, XP complementation group C (XP-C) fibroblasts retain proficient TCR, but are deficient in bulk DNA repair. The remaining NER-deficient XP groups exhibit deficiencies in both repair pathways. Ad5HCMVsp1lacZ is a recombinant adenovirus vector that is unable to replicate in human fibroblasts, but can efficiently infect and express the beta-galactosidase reporter gene in these cells. We have examined the host cell reactivation (HCR) of beta-galactosidase activity for UV-irradiated Ad5HCMVsp1lacZ in non-irradiated and UV-irradiated normal, XP-B, XP-C, XP-D, XP-F, XP-G, CS-A and CS-B fibroblasts. HCR of beta-galactosidase activity for UV-irradiated Ad5HCMVsp1lacZ was reduced in non-irradiated cells from each of the repair-deficient groups examined (including XP-C) relative to that in non-irradiated normal cells. Prior irradiation of cells with low UV fluences resulted in an enhancement of HCR for normal and XP-C strains, but not for the remaining XP and CS strains. HCR of the UV-damaged reporter gene in UV-irradiated XP and CS strains was similar to measurements of TCR reported previously for these cells. These results suggest that UV treatment results in an induced repair of UV-damaged DNA in the transcribed strand of an active gene in XP-C and normal cells through an enhancement of TCR or a mechanism which involves the TCR pathway.

Stability of memory for colour in context.

Memory for colours presented in isolation was compared with that for colours presented as part of a clip-art image or as part of a non-meaningful, Mondrian-like image. The area under the Receiver Operating Characteristic for deciding that two colours, presented at different delay intervals, were the same or different provided an index of memory for colour. The provision of a context reduced the decay of memory, regardless of whether the context was meaningful (clip-art images) or non-meaningful (Mondrian-like images). The result was seen as a generalisation of the auditory phenomenon of profile analysis, in which memory for the amplitude of a single component of a complex sound is more stable than that for the component in isolation.

Incomplete complementation of the DNA repair defect in cockayne syndrome cells by the denV gene from bacteriophage T4 suggests a deficiency in base excision repair.

Endonuclease V (denV) from bacteriophage T4 has been examined for its ability to complement the repair defect in Cockayne syndrome (CS) cells of complementation groups A and B. CS is an autosomal recessive disorder characterized by hypersensitivity to UV light and a defect in the preferential repair of UV-induced lesions in transcriptionally active DNA by the nucleotide excision repair (NER) pathway. The denV gene was introduced into non-transformed normal and CS fibroblasts transiently via a recombinant adenovirus (Ad) vector and into SV40-transformed normal and CS cells via a retroviral vector. Expression of denV in CS-A cells resulted in partial correction of the UV-sensitive phenotype in assays of gene-specific repair and cell viability, while correction of CS-B cells by expression of denV in the same assays was minimal or non-existent. In contrast, denV expression led to enhanced host cell reactivation (HCR) of viral DNA synthesis in both CS complementation groups to near normal levels. DenV is a glycosylase which is specific for cyclobutane-pyrimidine dimers (CPDs) but does not recognize other UV-induced lesions. Previous work has indicated that CS cells can efficiently repair all non-CPD UV-induced transcription blocking lesions (S.F. Barrett et al.. Mutation Res. 255 (1991) 281-291 [1]) and that denV incised lesions are believed to be processed via the base excision repair (BER) pathway. The inability of denV to complement the NER defect in CS cells to normal levels implies an impaired ability to process denV incised lesions by the BER pathway, and suggests a role for the CS genes, particularly the CS-B gene, in BER.

Wildtype p53 is required for heat shock and ultraviolet light enhanced repair of a UV-damaged reporter gene.

We have previously reported the use of a recombinant nonreplicating adenovirus type 5, Ad5HCMVsp1 lacZ, expressing the lacZ gene under control of the human cytomegalovirus (HCMV) immediate early promoter to assess repair of a UV-damaged reporter gene in UV and heat shock (HS) treated cells. Heat shock and UV-enhanced reactivation (HSER and UVER) of beta-galactosidase (beta-gal) activity for UV-irradiated Ad5HCMVsp1 lacZ in normal human fibroblasts involved the transcription coupled repair (TCR) pathway. However, this inducible DNA repair response was absent in p53 deficient tumour cell lines. In order to examine further the requirement for p53 in HSER and UVER, we have examined host cell reactivation (HCR) of the reporter construct in HS treated, UV treated and mock treated Li-Fraumeni syndrome (LFS) fibroblasts, which are heterozygous for a p53 mutation, and immortalized LFS cell sublines, which express only mutant p53. HCR of beta-gal activity for UV-irradiated Ad5HCMVsp1 lacZ was normal in all LFS cells examined. However, HCR of beta-gal activity for UV-irradiated Ad5HCMVsp1 lacZ was elevated by pretreatment of cells with either UV or HS in normal diploid human fibroblasts, but not in LFS cells. LFS cells appear to be deficient in an inducible pathway which stimulates repair of the reporter gene. These results support a role for p53 in a HS and UV inducible DNA repair response in human cells which is dependent on TCR.

Decision strategies and visual-field asymmetries in same-different judgments of word meaning.

The accuracy with which observers judged whether two words belonged to the same semantic category was determined from a detection-theoretic analysis of same-different judgments. In Experiment 1, one word was presented centrally and the other word in either the left visual field (LVF) or the right visual field (RVF); in Experiment 2, both words were presented to either the LVF or the RVF. In order to obtain receiver-operating characteristics (ROCs) of performance, observers were asked to rate their confidence that the two words belonged to the same semantic category. Two models of the decision strategy were fitted to the obtained characteristics: a differencing model, in which the decision variable was the difference between the two observations; and an optimal model, in which each observation was judged in relation to a criterion. In both experiments, the optimal model provided a better fit than the differencing model to the obtained characteristics. Maximum-likelihood estimates of both the criterion-free parameter, d', and the area under the operating characteristic, p(A), were greater for words presented in the RVF than for those presented in the LVF.

Perception of simple and complex visual stimuli: decision strategies and hemispheric differences in same-different judgments.

The accuracy with which observers could judge whether two visual stimuli were the same or different was measured with the rating method of detection theory. For judgments of whether two pictures referred to natural or manufactured things, the shape of the obtained receiver operating characteristic (ROC) was consistent with the observers adopting an optimal decision strategy. A similar result was found for judgments of complex but meaningless visual patterns. For judgments of whether two colours that differed along a simple sensory dimension were the same or different, however, the resulting ROC was consistent with the observers adopting a suboptimal differencing strategy. The accuracy of the judgments did not depend on the visual field to which the stimuli were presented.

N-glycosylation is required for human CD2 immunoadhesion functions.

The T-lymphocyte glycoprotein receptor, CD2, mediates cell-cell adhesion by binding to the surface molecule CD58 (LFA-3) on many cell types including antigen presenting cells. Two domains comprise the CD2 extracellular segment, with all adhesion functions localized to the amino-terminal domain that contains a single N-glycosylation site at Asn65. We have defined an important role for the N-linked glycans attached to Asn65 of this domain in mediating CD2-CD58 interactions and also characterize its N-glycotype structure. Analysis of deglycosylated soluble recombinant CD2 as well as a mutant transmembrane CD2 molecule containing a single Asn65-Gln65 substitution demonstrates that neither deglycosylated CD2 nor the mutant CD2 transmembrane receptor binds CD58 or monoclonal antibodies directed at native CD2 adhesion domain epitopes. Electrospray ionization-mass spectrometry demonstrates that high mannose oligosaccharides ((Man)nGlcNAc2, n = 5-9) are the only N-glycotypes occupying Asn65 when soluble CD2 is expressed in Chinese hamster ovary cells. Based on a model of human CD2 secondary structure, we propose that N-glycosylation is required for stabilizing domain 1 in the human receptor. Thus, N-glycosylation is essential for human CD2 adhesion functions.

Expression and function of a human initiator tRNA gene in the yeast Saccharomyces cerevisiae.

We showed previously that the human initiator tRNA gene, in the context of its own 5'- and 3'-flanking sequences, was not expressed in Saccharomyces cerevisiae. Here we show that switching its 5'-flanking sequence with that of a yeast arginine tRNA gene allows its functional expression in yeast cells. The human initiator tRNA coding sequence was either cloned downstream of the yeast arginine tRNA gene, with various lengths of intergenic spacer separating them, or linked directly to the 5'-flanking sequence of the yeast arginine tRNA coding sequence. The human initiator tRNA made in yeast cells can be aminoacylated with methionine, and it was clearly separated from the yeast initiator and elongator methionine tRNAs by RPC-5 column chromatography. It was also functional in yeast cells. Expression of the human initiator tRNA in transformants of a slow-growing mutant yeast strain, in which three of the four endogenous initiator tRNA genes had been inactivated by gene disruption, resulted in enhancement of the growth rate. The degree of growth rate enhancement correlated with the steady-state levels of human tRNA in the transformants. Besides providing a possible assay for in vivo function of mutant human initiator tRNAs, this work represents the only example of the functional expression of a vertebrate RNA polymerase III-transcribed gene in yeast cells.

The nucleotide sequence and characterization of four chloroplast tRNAs from the alga codium fragile.

The nucleotide sequences of four chloroplast tRNAs (methionine elongator, lysine, glycine, and arginine) from the siphonaceous green alga Codium fragile have been determined. These tRNAs have an unusually high A-U content compared to other chloroplast tRNAs and show varied, but in general only limited, sequence homology to the corresponding tRNAs of other chloroplasts. The locations of the genes for these four tRNAs have been determined and they show no similarity to the location of the corresponding tRNA genes in other chloroplasts. The Codium chloroplast glycine tRNA has an unmodified uridine in the wobble position of the anticodon, a characteristic rarely found in tRNA but present in mitochondrial tRNAs which read the genetic code by extended wobble.

A novel variety of 4.5 S RNA from Codium fragile chloroplasts.

An unusual new chloroplast RNA has been isolated and sequenced in the siphonous green alga, Codium fragile. This RNA is 94 nucleotides in length, has an unusually high A + U content (73%), contains no modified residues, and is as abundant as a single chloroplast tRNA species. Although this RNA is 4.5 S in size, it bears little sequence homology to the widely found and highly conserved 4.5 S RNAs present in the chloroplasts of higher plants. Nevertheless, this RNA may indeed by analogous to the higher plant 4.5 S RNAs, since the Codium 4.5 S RNA has the potential to form a secondary structure which in many respects is remarkably similar to that of known chloroplast 4.5 S RNAs, and hybridization data strongly suggests that the 4.5 S RNA is part of the ribosomal RNA operon, as is the case in higher plant chloroplasts.

Nucleotide sequence of a spinach chloroplast isoleucine tRNA.

The nucleotide sequence of a spinach chloroplast isoleucine tRNA (spinach chloroplast tRNAIle1) has been determined. This tRNA has an unusual structural feature in that it contains an extra non-base paired nucleotide within the double-stranded anticodon stem. Spinach chloroplast tRNAIle1 shows surprisingly little homology to other isoleucine tRNAs. Moreover, the homology it does show is essentially equal for the isoleucine tRNAs from prokaryotes, eukaryotes, and chloroplasts. In addition, this tRNA is as homologous to the methionine elongator tRNAs of Escherichia coli and spinach chloroplasts as it is to other isoleucine tRNAs. Spinach chloroplast tRNA1Ile contains the modified residue N2,N2-dimethylguanosine which is characteristically found in eukaryotic but not in prokaryotic tRNAs.