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PubMed2006

Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes.

The reassignment of stop codons is common among many ciliate species. For example, Tetrahymena species recognize only UGA as a stop codon, while Euplotes species recognize only UAA and UAG as stop codons. Recent studies have shown that domain 1 of the translation termination factor eRF1 mediates stop codon recognition. While it is commonly assumed that changes in domain 1 of ciliate eRF1s are responsible for altered stop codon recognition, this has never been demonstrated in vivo. To carry out such an analysis, we made hybrid proteins that contained eRF1 domain 1 from either Tetrahymena thermophila or Euplotes octocarinatus fused to eRF1 domains 2 and 3 from Saccharomyces cerevisiae. We found that the Tetrahymena hybrid eRF1 efficiently terminated at all three stop codons when expressed in yeast cells, indicating that domain 1 is not the sole determinant of stop codon recognition in Tetrahymena species. In contrast, the Euplotes hybrid facilitated efficient translation termination at UAA and UAG codons but not at the UGA codon. Together, these results indicate that while domain 1 facilitates stop codon recognition, other factors can influence this process. Our findings also indicate that these two ciliate species used distinct approaches to diverge from the universal genetic code.

Animals↗
PubMed1999

Neural correlates of visual form and visual spatial processing.

Cortico-cortical projections for visual processing that originate from the striate cortex are organized into two streams. The dorsal stream projects to the parietal region and the ventral stream to the inferior temporal region. One hypothesis is that the dorsal stream processes visual spatial information, and the ventral stream processes visual object information. Although recognition of human faces or common objects has been shown preferentially to activate the ventral stream, the issue of when such processing starts to engage the ventral or the dorsal stream is not clear. The question explored in this study is whether processing of visual form per se without evoking the brain mechanisms that are associated with recognition of human faces or common objects is sufficient to activate the ventral stream more significantly relative to the condition when only visual spatial processing is involved. Functional magnetic resonance images were acquired while subjects performed a delayed comparison task in which either visual spatial or visual form information was processed. Cortical areas that were preferentially activated in visual spatial or visual form processing showed not only ventral-dorsal segregation, but also hemispheric laterality. The results extended previous findings by showing that preferential activation in the ventral pathway is not contingent upon such powerful stimuli as faces and common objects. Processing of simple visual form information is cause enough for such activation to be observed. A strong left hemisphere dominance in visual form recognition was also revealed. The observed laterality may be a reflection that the left hemisphere is more important in symbolic and/or semantic coding of visual form information.

Adult↗
PubMed1996

Sequence of the highly conserved gene encoding the human 54kDa subunit of signal recognition particle.

The complete sequence of the human gene encoding the 54kDa subunit of the signal recognition particle has been isolated from a cDNA library. Degenerate oligonucleotides based on the 5' and 3' coding region of the canine gene and a mammalian codon usage table, were used to amplify the sequence using PCR. The nucleotide sequence of the human gene shows that the human sequence shares a 95.8% nucleotide sequence homology and 100% amino acid sequence homology to it's canine counterpart. The sequence has been given the accession number X86373 in the EMBL database.

Amino Acid Sequence↗
PubMed1999

Global GacA-steered control of cyanide and exoprotease production in Pseudomonas fluorescens involves specific ribosome binding sites.

The conserved two-component regulatory system GacS/GacA determines the expression of extracellular products and virulence factors in a variety of Gram-negative bacteria. In the biocontrol strain CHA0 of Pseudomonas fluorescens, the response regulator GacA is essential for the synthesis of extracellular protease (AprA) and secondary metabolites including hydrogen cyanide. GacA was found to exert its control on the hydrogen cyanide biosynthetic genes (hcnABC) and on the aprA gene indirectly via a posttranscriptional mechanism. Expression of a translational hcnA'-'lacZ fusion was GacA-dependent whereas a transcriptional hcnA-lacZ fusion was not. A distinct recognition site overlapping with the ribosome binding site appears to be primordial for GacA-steered regulation. GacA-dependence could be conferred to the Escherichia coli lacZ mRNA by a 3-bp substitution in the ribosome binding site. The gene coding for the global translational repressor RsmA of P. fluorescens was cloned. RsmA overexpression mimicked partial loss of GacA function and involved the same recognition site, suggesting that RsmA is a downstream regulatory element of the GacA control cascade. Mutational inactivation of the chromosomal rsmA gene partially suppressed a gacS defect. Thus, a central, GacA-dependent switch from primary to secondary metabolism may operate at the level of translation.

Amino Acid Sequence↗
PubMed2007

Antigens and autophagy: the path less travelled?

The Epstein-Barr virus (EBV)-coded nuclear antigen (EBNA) 1, a latent cycle protein endogenously expressed in EBV-transformed B lymphoblastoid cell lines (LCLs), is reported to be processed for CD4(+) T cell recognition by an intracellular route involving antigen delivery to the endosome/lyosome (MHC class II loading) compartment via macroautophagy. In contrast we find that, in the same cell type, two other virus-coded nuclear proteins of the latent cycle, EBNA2 and EBNA3C, are processed by a different route that is unaffected by autophagy inhibition. This involves the intercellular transfer of an antigenic moiety, detectable in cell-free culture supernatants, and its uptake and processing as exogenous antigen by neighboring cells. The process is cumulative and leads over several days of LCL culture to high levels of CD4+ T cell epitope display. The presentation of certain EBV lytic cycle proteins to CD4+ T cells has also recently been found to involve a similar intercellular antigen transfer. It becomes important to know why, even in the same cell type, some antigens but not others appear to access the MHC class II presentation pathway by autophagy.

Antigen Presentation↗
PubMed1999

Neural mechanisms subserving the perception of human actions.

Our ability to generate actions and to recognize actions performed by others is the bedrock of our social life. Behavioral evidence suggests that the processes underlying perception and action might share a common representational framework. That is, observers might understand the actions of another individual in terms of the same neural code that they use to produce the same actions themselves. What neurophysiological evidence, if any, supports such a hypothesis? In this article, brain imaging studies addressing this question are reviewed and examined in the light of the functional segregation of the perceptual mechanisms subtending visual recognition and those used for action. We suggest that there are not yet conclusive arguments for a clear neurophysiological substrate supporting a common coding between perception and action.

Journal Article↗
PubMedDate not supplied

Plasma-membrane-bound macromolecules are dynamically aggregated to form non-random codistribution patterns of selected functional elements. Do pattern recognition processes govern antigen presentation and intercellular interactions?

Molecular recognition processes between cell surface elements are discussed with special reference to cell surface pattern formation of membrane-bound integral proteins. The existence, as detected by flow cytometric resonance energy transfer (Appendix), and significance of cell surface patterns involving the interleukin-2 receptor, the T-cell receptor-CD3 system, the intercellular adhesion molecule ICAM-1, and the major histocompatibility complex class I and class II molecules in the plasma membrane of lymphocytes are described. The modulation of antigen presentation by transmembrane potential changes is discussed, and a general role of transmembrane potential changes, and therefore of ion channel activities, adduced as one of the major regulatory mechanisms of cell-cell communication. A general role in the mediation and regulation of intercellular interactions is suggested for cell-surface macromolecular patterns. The dynamic pattern of protein and lipid molecules in the plasma membrane is generated by the genetic code, but has a remarkable flexibility and may be one of the major instruments of accommodation and recognition processes at the cellular level.

Animals↗
PubMed1992

A two-component regulatory system for self/non-self recognition in Ustilago maydis.

In U. maydis the multiallelic b locus controls sexual and pathogenic development. In the b locus a gene coding for a regulatory protein had been identified, and it was suggested that the interaction of two b polypeptides specified by different alleles programs sexual development in this fungus. We now demonstrate the existence of a second regulatory gene in the b locus. We term this gene bW and refer to the former as the bE gene. Both genes exist in many alleles. Although unrelated in primary sequence, both genes are similar in their overall organization. The gene products display allele-specific variability in their N-terminal domains, show a high degree of sequence conservation in the C-terminal domains, and contain a homeodomain-related motif. Genetic evidence is provided to show that the pair of bE and bW polypeptides encoded by different b alleles is the key regulatory species.

Alleles↗
PubMed1988

Lymphoid V(D)J recombination: nucleotide insertion at signal joints as well as coding joints.

The coding regions of antigen receptor genes assembled by variable-diversity-joining region [V(D)J] recombination are known in many cases to have undergone deletions of several nucleotides and also to contain insertions of noncoded nucleotides at the recombined junction (the coding joint). By using extrachromosomal recombination substrates to transfect lymphoid cell lines, we show that the signal joint (the fusion of the corresponding recognition signal sequences) can also contain insertions; however, nucleotide loss from the signals is very rare. The frequency of nucleotide addition varies among pre-B-cell lines in a manner proportional to their content of terminal deoxynucleotidyltransferase. We also find frequent nucleotide additions (and deletions) at coding joints, but in this case there is no strong correlation with the level of terminal deoxynucleotidyltransferase activity. Inserts at both signal and coding joints are rich in G + C, consistent with the base utilization preference of this enzyme.

Animals↗
PubMed1966

Privileged communications. The effect of California's new evidence code as it concerns physicians and psychotherapists.

A physician has an ethical duty to hold in confidence communications made to him by his patient. A legal recognition of this ethical duty is found in the concept of privilege, which is the subject of this article. January 1967 will bring to California physicians a new protection for patients' communications. The physician-patient privilege has been redefined to include confidential communications made during diagnostic evaluation, those made to non-licensed physicians, interns and medical aides, and those overheard by eavesdroppers. There has been added a psychotherapist-patient privilege designed to facilitate communications required in psychotherapy as well as in behavioral research. This paper first presents a brief historical background and discusses the protections and limitations afforded by the new California Evidence Code. There follows a section on the psychotherapist-patient privilege with the recommendation that in the context of psychotherapy, patients of physicians who are not psychiatrists should be afforded the additional benefits of the psychotherapist-patient privilege. Lastly, advice is given concerning the physician's conduct in relation to his duty to claim privilege under the new code.

Ethics, Medical↗
PubMedDate not supplied

Construction of phosphorylatable monoclonal antibody CC49 with a casein kinase II recognition site.

A phosphorylation site for casein kinase II was introduced into chimeric monoclonal antibody CC49 (MAb-chCC49) by site-specific mutation of the coding sequence. The phosphorylation site for the casein kinase II was positioned at the carboxyl terminus of the heavy chain constant region of the MAb-chCC49. The resultant modified MAb-chCC49CKII was expressed in NS0 cells and purified. The MAb-chCC49CKII protein was phosphorylated by casein kinase II with [gamma-32P]ATP to high radiospecific activity. The 32P-labeled MAb-chCC49CKII binds to cells expressing TAG-72 antigens. The introduction of the phosphorylation sites for casein kinase II into monoclonal antibodies (MAb) provides a new reagent for the diagnosis and treatment of cancers. This demonstrates that the casein kinase II recognition site can also be used to introduce phosphorylation sites into proteins.

Amino Acid Sequence↗
PubMed1996

Effects of visual and verbal interference tasks on olfactory memory: the role of task complexity.

Recent studies have demonstrated that visual and verbal suppression tasks interfere with olfactory memory in a manner which is partially consistent with a dual coding interpretation. However, it has been suggested that total task complexity rather than modality specificity of the suppression tasks might account for the observed pattern of results. This study addressed the issue of whether or not the level of difficulty and complexity of suppression tasks could explain the apparent modality effects noted in earlier experiments. A total of 608 participants were each allocated to one of 19 experimental conditions involving interference tasks which varied suppression type (visual or verbal), nature of complexity (single, double or mixed) and level of difficulty (easy, optimal or difficult) and presented with 13 target odours. Either recognition of the odours or free recall of the odour names was tested on one occasion, either within 15 minutes of presentation or one week later. Both recognition and recall performance showed an overall effect for suppression nature, suppression level and time of testing with no effect for suppression type. The results lend only limited support to Paivio's (1986) dual coding theory, but have a number of characteristics which suggest that an adequate account of olfactory memory may be broadly similar to current theories of face and object recognition. All of these phenomena might be dealt with by an appropriately modified version of dual coding theory.

Acoustic Stimulation↗
PubMed1983

Recognition patterns for exon-intron junctions in higher organisms as revealed by a computer search.

Most genes of higher eukaryotes are discontinuous. The DNA which codes for a protein is interrupted by introns. In the nucleus, certain machinery is supposed to recognize the exon-intron and intron-exon junctions. Applying computer searching to eighteen genes from various biological species, we examined what kinds of patterns or nucleotide sequences are necessary and sufficient to recognize the splice junctions. We propose that four common patterns of AG/GTA, /GTAAGT, RG/GTGAG and AG/GTXXGT, where R = A or G and X = A, T, G, or C, are often used as signals for exon-intron junctions. This proposal is based on the facts that they are not found in the exons of the genes examined and on the assumption that the recognition machinery scans the mRNA precursor from the 5'-end to the 3'-end.

Animals↗
PubMed1993

Recognition of the Qa-2k tumor antigen by T cell receptor gamma/delta of an immunopotentiator-induced tumoricidal T cell of mice.

Tumor-specific expression of Qa-2k antigen coded by the Q5k gene on various mouse tumor cells and immunological response of the host mice to the antigen have been demonstrated [Seo et al. (1992) J Exp Med 175: 547; Tanino et al. (1992) Cancer Immunol Immunother 35: 230]. The possibility was examined that Qa-2 antigen is one of the recognition target molecules of immunopotentiator-induced, H-2-nonrestricted tumoricidal lymphocytes of Qa-2-mice. Lymphocytes stimulated in vivo with P. acnes or culture-induced anomalous killers of B6.K1 mice did not exhibit significant in vitro cytotoxicity against B6.K1 lymphoblasts but lysed their Qa-2,3-congenic counterpart B6 lymphoblasts. To demonstrate the Qa-2 specificity of such cytotoxic cells more precisely, an L cell transformant clone (LQ7b/Kb), which expressed the alpha 1 and alpha 2 domains of the Qa-2 antigen (Q7b gene product), was generated by transfecting a cloned plasmid DNA containing a hybrid gene constructed from the 5' half of the Q7b gene and the 3' half of the H-2Kb gene (pQ7b/Kb). Using LQ7b/Kb cells as the target cells and the nylon-wool-nonadherent fraction of lymphocytes from P. acnes-stimulated (C3H/He x B6.K1)F1 mice (H-2k, Qa-2-) as the effector cells of the in vitro cytotoxicity reaction, the presence of cytotoxic cells that recognize the alpha 1/alpha 2 region of the Q7b gene product was demonstrated. The cytotoxic activity was dependent on T cells bearing T cell receptors of the gamma/delta type (TCR gamma/delta). The (C3H/He x B6.K1)F1 effector cells, as well as the B6.K1 effector cells also lysed BW5147 lymphoma cells (Qa-2k+) derived from AKR mice (Qa-2-, H-2k). By target-competition experiments it was shown that some of the effector cells lytic to BW5147 were identical to those that lysed LQ7b/Kb. Therefore some of the tumoricidal cells induced by the immunopotentiator interact with the target tumor cells through recognition of the alpha 1/alpha 2 region of the Qa-2k tumor antigen by TCR gamma/delta.

Adjuvants, Immunologic↗
PubMed2004

Recognizing cognates and interlingual homographs: effects of code similarity in language-specific and generalized lexical decision.

In four experiments, we investigated how cross-linguistic overlap in semantics, orthography, and phonology affects bilingual word recognition in different variants of the lexical decision task. Dutch-English bilinguals performed a language-specific or a generalized lexical decision task including words that are spelled and/or pronounced the same in English and in Dutch and that matched one-language control words from both languages. In Experiments 1 and 3, "false friends" with different meanings in the two languages (e.g., spot) were presented, whereas in Experiments 2 and 4 cognates with the same meanings across languages (e.g., film) were presented. The language-specific Experiments 1 and 2 replicated and qualified an earlier study (Dijkstra, Grainger, & Van Heuven, 1999). In the generalized Experiment 3, participants reacted equally quickly on Dutch-English homographs and Dutch control words, indicating that their response was based primarily on the fastest available orthographic code (i.e., Dutch). In Experiment 4, cognates were recognized faster than English and Dutch controls, suggesting coactivation of the cognates' semantics. The nonword results indicate that the bilingual rejection procedure can, to some extent, be language specific. All results are discussed within the BIA+ (bilingual interactive activation) model for bilingual word recognition.

Adolescent↗
PubMed2006

Disruption of order information by irrelevant items: a serial recognition paradigm.

Irrelevant speech effect (ISE) is defined as a decrement in visually presented digit-list short-term memory performance due to exposure to irrelevant auditory material. Perhaps the most successful theoretical explanation of the effect is the changing state hypothesis. This hypothesis explains the effect in terms of confusion between amodal serial order cues, and represents a view based on the interference caused by the processing of similar order information of the visual and auditory materials. An alternative view suggests that the interference occurs as a consequence of the similarity between the visual and auditory contents of the stimuli. An important argument for the former view is the observation that ISE is almost exclusively observed in tasks that require memory for serial order. However, most short-term memory tasks require that both item and order information be retained in memory. An ideal task to investigate the sensitivity of maintenance of serial order to irrelevant speech would be one that calls upon order information but not item information. One task that is particularly suited to address this issue is serial recognition. In a typical serial recognition task, a list of items is presented and then probed by the same list in which the order of two adjacent items has been transposed. Due to the re-presentation of the encoding string, serial recognition requires primarily the serial order to be maintained while the content of the presented items is deemphasized. In demonstrating a highly significant ISE of changing versus steady-state auditory items in a serial recognition task, the present finding lends support for and extends previous empirical findings suggesting that irrelevant speech has the potential to interfere with the coding of the order of the items to be memorized.

Adolescent↗
PubMed2004

Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition.

Early work on aminoacylation of alanine-specific tRNA (tRNA(Ala)) by alanyl-tRNA synthetase (AlaRS) gave rise to the concept of an early "second genetic code" imbedded in the acceptor stems of tRNAs. A single conserved and position-specific G:U base pair in the tRNA acceptor stem is the key identity determinant. Further understanding has been limited due to lack of a crystal structure of the enzyme. We determined a 2.14 A crystal structure of the 453 amino acid catalytic fragment of Aquifex aeolicus AlaRS. It contains the catalytic domain characteristic of class II synthetases, a helical domain with a hairpin motif critical for acceptor-stem recognition, and a C-terminal domain of a mixed alpha/beta fold. Docking of tRNA(Ala) on AlaRS shows critical contacts with the three domains, consistent with previous mutagenesis and functional data. It also suggests conformational flexibility within the C domain, which might allow for the positional variation of the key G:U base pair seen in some tRNA(Ala)s.

Alanine-tRNA Ligase↗