The photoreceptor sensory code for pattern identification during visual masking.
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Animals↗
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The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
The structure of the complex between ribosomal protein L25 and a 37 nucleotide RNA molecule, which contains the E-loop and helix IV regions of the E-domain of Escherichia coli 5S rRNA, has been determined to an overall r.m.s. displacement of 1.08 A (backbone heavy atoms) by heteronuclear NMR spectroscopy (Protein Databank code 1d6k). The interacting molecular surfaces are bipartite for both the RNA and the protein. One side of the six-stranded beta-barrel of L25 recognizes the minor groove of the E-loop with very little change in the conformations of either the protein or the RNA and with the RNA-protein interactions occurring mainly along one strand of the E-loop duplex. This minor groove recognition module includes two parallel beta-strands of L25, a hitherto unknown RNA binding topology. Binding of the RNA also induces conversion of a flexible loop to an alpha-helix in L25, the N-terminal tip of which interacts with the widened major groove at the E-loop/helix IV junction of the RNA. The structure of the complex reveals that the E-domain RNA serves as a preformed docking partner, while the L25 protein has one preformed and one induced recognition module.
Amino Acid Sequence↗
A novel cell adhesive protein engineered by insertion of the Arg-Gly-Asp-Ser tetrapeptide.
A tetrapeptide Arg-Gly-Asp-Ser (RGDS) has been shown to be a versatile cell recognition signal of extracellular matrix components for the interaction with cells. We introduced the RGDS tetrapeptide into a truncated form of protein A, a staphylococcal immunoglobulin-binding protein, by inserting an oligonucleotide cassette encoding the tetrapeptide into the coding region of the protein A expression vector pRIT2T. The mutagenized protein was capable of not only binding to immunoglobulin G but also mediating cell attachment and spreading onto an inert substrate. Cell adhesion mediated by the mutagenized protein was inhibitable by a synthetic peptide Gly-Arg-Gly-Asp-Ser but not by a related peptide Gly-Arg-Gly-Glu-Ser, confirming that the inserted RGDS tetrapeptide served as a recognition signal for cell adhesion. Furthermore, the RGDS-containing protein was capable of adhering cells onto an immunoglobulin-coated surface which could not by itself support cell adhesion. Thus, the cell adhesive and immunoglobulin binding activities of the mutagenized protein appear to function coordinately. The protocol described here is essentially applicable to any protein and, therefore, provides a general principle in tailoring novel multifunctional proteins having cell adhesive activity.
Amino Acid Sequence↗
tRNA's wobble decoding of the genome: 40 years of modification.
The genetic code is degenerate, in that 20 amino acids are encoded by 61 triplet codes. In 1966, Francis Crick hypothesized that the cell's limited number of tRNAs decoded the genome by recognizing more than one codon. The ambiguity of that recognition resided in the third base-pair, giving rise to the Wobble Hypothesis. Post-transcriptional modifications at tRNA's wobble position 34, especially modifications of uridine 34, enable wobble to occur. The Modified Wobble Hypothesis proposed in 1991 that specific modifications of a tRNA wobble nucleoside shape the anticodon architecture in such a manner that interactions were restricted to the complementary base plus a single wobble pairing for amino acids with twofold degenerate codons. However, chemically different modifications at position 34 would expand the ability of a tRNA to read three or even four of the fourfold degenerate codons. One foundation of Crick's Wobble Hypothesis was that a near-constant geometry of canonical base-pairing be maintained in forming all three base-pairs between the tRNA anticodon and mRNA codon on the ribosome. In accepting an aminoacyl-tRNA, the ribosome requires maintenance of a specific geometry for the anticodon-codon base-pairing. However, it is the post-transcriptional modifications at tRNA wobble position 34 and purine 37, 3'-adjacent to the anticodon, that pre-structure the anticodon domain to ensure the correct codon binding. The modifications create both the architecture and the stability needed for decoding through restraints on anticodon stereochemistry and conformational space, and through selective hydrogen bonding. A physicochemical understanding of modified nucleoside contributions to the tRNA anticodon domain architecture and its decoding of the genome has advanced RNA world evolutionary theory, the principles of RNA chemistry, and the application of this knowledge to the introduction of new amino acids to proteins.
Anticodon↗
On the detection of Gabor signals and discrimination of Gabor textures.
We have explored the detection and discrimination of Gabor signals in two different paradigms in order to determine the signals' relative importance for spatial vision. In the first experiment we determined the "detection efficiency" of five such signals presented in isolation, and our results support the conclusion that, for optimal detection, the Gaussian profile should only span (to 1/e decay values) approximately two cycles. In three subsequent experiments we have observed the discriminability of textures composed of such signals over a range of spatial frequencies, Gaussian windows and orientation differences. Our results are consistent with the detection data only insofar as the discrimination thresholds vary in a predictable way with the Gaussian window parameters. Finally, we have determined the degree to which texture discrimination, in terms of differences in both orientation and spatial frequency, can be predicted from the independent manipulations of both codes within a given Gaussian window size.
Discrimination, Psychological↗
Learning generative models of natural images.
This work proposes an unsupervised learning process for analysis of natural images. The derivation is based on a generative model, a stochastic coin-flip process directly operating on many disjoint multivariate Gaussian distributions. Following the maximal likelihood principle and using the Potts encoding, the goodness-of-fit of the generative model to tremendous patches randomly sampled from natural images is quantitatively expressed by an objective function subject to a set of constraints. By further combination of the objective function and the minimal wiring criterion, we achieve a mixed integer and linear programming. A hybrid of the mean field annealing and the gradient descent method is applied to the mathematical framework and produces three sets of interactive dynamics for the learning process. Numerical simulations show that the learning process is effective for extraction of orientation, localization and bandpass features and the generative model can make an ensemble of a sparse code for natural images.
Learning↗
The role of letter identity and letter position in orthographic priming.
Four experiments are reported investigating orthographic priming effects in French by varying the number and the position of letters shared by prime and target stimuli. Using both standard masked priming and the novel incremental priming technique (Jacobs, Grainger, & Ferrand, 1995), it is shown that net priming effects are affected not only by the number of letters shared by prime and target stimuli but also by the number of letters in the prime not present in the target. Several null results are thus explained as a tradeoff between the facilitation generated by common letters and the inhibition generated by different letters. Inhibition was significantly reduced when different letters were replaced by nonalphabetic symbols. Facilitation effects disappeared when the common letters did not have the same relative position in the prime and target strings, thus supporting a relative-position coding scheme for letters in words.
Adult↗
Semantic congruity effects in perceptual comparisons.
Semantic congruity effects occur when, as in Experiment 1, for example, the time to select the shorter of two relatively short lines is faster than the time to select the longer; conversely, selection of the longer of two relatively long lines is faster than selection of the shorter. Semantic congruity effects are also demonstrated in experiments requiring comparisons of the heaviness of weights (Experiment 2) and horizontal extent (Experiment 3). In Experiment 1, the magnitude of the semantic congruity effect was larger under conditions emphasizing accuracy rather than speed and when the comparison was difficult. In fact, when comparisons were errorless, the effect was minimal (20 msec), thereby replicating previous failures to obtain the effect with supraliminal perceptual comparisons (Banks, Mermelstein, & Yu, 1982; Marschark & Paivio, 1981; Petrusic & Baranski, 1988a). In confirmation of Henmon's (1911) introspective analyses of psychophysical comparisons, Experiments 2 and 3 extend the range of the semantic congruity effect to include judgments of confidence. However, in each of the three experiments, semantic congruity effects were not evident with the response-accuracy measure. Finally, using highly confusable stimuli, in Experiment 3 the magnitude of the semantic congruity effect was shown to be larger for error than for correct response times. The implications of these findings for a decisional locus of the effect and for the semantic coding theory are discussed.
Attention↗
Cloning and sequencing of the melB gene encoding the melibiose permease of Salmonella typhimurium LT2.
The nucleotide sequence of the melB gene coding for the Na+ (Li+)/melibiose symporter of Salmonella typhimurium LT2 was determined, and its amino acid sequence was deduced. It consists of 1428 bp, corresponding to a protein of 476 amino acid residues (calculated molecular weight 52,800). The amino acid sequence is homologous to that of the melibiose permease of Escherichia coli K12, with 85% identical residues. All, except one, of the amino acid residues that have been reported to be important for cation or substrate recognition in the melibiose permease of E. coli are conserved in the melibiose permease of S. typhimurium. In addition, part of the sequence resembles the lactose permease of Streptococcus thermophilus, the animal glucose transporter (GLUT1), the plasmid-coded raffinose permease (RafB), and the NADH-ubiquinone oxidoreductase chain 4 (Nuo4) of Aspergillus amstelodami.
Amino Acid Sequence↗
Exceptional codon recognition by the glutamine tRNAs in Saccharomyces cerevisiae.
Recently, it was shown that wild-type glutamine tRNAs in yeast cause low-level nonsense suppression that can be enhanced by increasing glutamine tRNA gene copy number. In order to investigate glutamine tRNA behavior further, anticodon mutations that confer nonsense suppression were identified in yeast sup70 gene, which codes for glutamine tRNA(CAG). In this study we show that suppressors derived by mutation severely limit growth such that suppressor-bearing spores germinate but arrest cell division at approximately the 50 cell stage. Analysis of a sup70 deletion was used to establish that growth limitation results from loss of wild-type glutamine tRNA(CAG) function. By exploiting the growth inhibition of sup70 alleles, some exceptional codon recognition properties of glutamine tRNAs were revealed. Our results indicate that amber suppressor glutamine tRNA(UAG) can translate 5'-CAG-3' glutamine codons with low efficiency in the presence of an A/C mismatch at the first position of the codon, suggesting that reading may occur at a low level by a two-out-of-three reading mechanism. In addition, when glutamine tRNA(CAA) is over-expressed in vivo, it translates 5'-CAG-3' codons using a mechanism that resembles prokaryotic-like U/G wobble, which normally does not occur in yeast. Our studies also suggest that the yeast glutamine tRNA suppressors could potentially be exploited to express ciliated protozoan genes that normally contain internal 5'-UAG-3' and 5'-UAA-3' codons.
Base Sequence↗
Cell-mediated lympholytic responses against autologous cells modified with haptenic sulfhydryl reagents. I. Effector cells can recognize two distinct classes of hapten-reactive self sites on cell surface proteins.
Mouse spleen cells were modified with a sulfhydryl-reactive reagent, N-iodoacetyl-N'-(5-sulfonic-1-naphthyl) ethylene diamine (I-AED) and used as stimulator cells in primary in vitro cultures with unmodified spleen cells of the same strain. CTL could be readily demonstrated when tested on hapten-modified syngeneic target cells. These CML responses were hapten specific and H-2 restricted. In the H-2b strain, effector cell populations were identified that recognized AED in association with K-end and D-end coded self MHC products. Functional modification of the target cells by I-AED can be effectively blocked by prereacting the cells with other SH-reagents, which is consistent with CTL recognition of the hapten on cysteine residues. Since these premodifications of the cell surface do not block the functional modification by trinitrobenzene sulfonate (TNBS), the sulfhydryl-reactive compounds and TNBS modify distinct classes of cell surface groups as determined by CTL function. The results of antibody inhibition experiments are also consistent with this interpretation. Using fluorescent labeled anti-hapten antibodies, FACS II analysis showed that there are approximately 20-fold fewer AED than TNP groups on the approximately 20-fold fewer AED than TNP groups on the cell surface when equivalent concentrations of I-AED and TNBS are compared. The possibility is discussed that these sulfhydryl-reactive compounds can be used together with the H-2Kb mutants for the localization of H-2 coded self determinants recognized in association with foreign antigens.
Animals↗
Specificity of origin recognition by replication initiator protein in plasmids of the pT181 family is determined by a six amino acid residue element.
We have investigated the specificity of replication origin recognition by the initiator proteins of a set of six closely related Staphylococcus aureus plasmids, the pT181 family. These plasmids replicate by an asymmetric rolling-circle mechanism using plasmid-coded initiators that nick the replication origins and form a phosphotyrosine bond at the 5' nick terminus. Five of the plasmids are in different incompatibility groups and their initiator proteins do not cross-complement the cloned origins of any but their own plasmid. One pair is weakly incompatible and their initiator proteins and origins do cross-complement for replication in vivo. This pattern of cross-reactivity led to the prediction that the determinant of specificity would correspond to a homologously positioned set of six residues in the C-terminal domain of the protein, some 80 residues away from the active site tyrosine, that are divergent for all of the compatible plasmids and identical for the incompatible pair. Site-directed mutagenesis was used to exchange these six residues among three pairs of plasmids and these exchanges brought about the predicted switching of origin recognition specificity. Single substitution within this six residue set reduced or eliminated the activity of the protein but did not alter the origin recognition specificity. These six and flanking residues cannot form an amphipathic alpha-helix nor do they conform to the classical helix-turn-helix or other known DNA binding motifs. A novel type of interaction is suggested in which the protein binds to its recognition site, bends and melts the DNA, and causes or enhances the extrusion of an adjacent cruciform containing the nick site. This configuration would juxtapose the nicking target and the active site tyrosine residue and would unwind the highly G + C-rich replication origin.
Amino Acid Sequence↗
A human performance evaluation of graphic symbol-design features.
16 subjects learned each of two tactical display symbol sets (conventional symbols and iconic symbols) in turn and were then shown a series of graphic displays containing various symbol configurations. For each display, the subject was asked questions corresponding to different behavioral processes relating to symbol use (identification, search, comparison, pattern recognition). The results indicated that: (a) conventional symbols yielded faster pattern-recognition performance than iconic symbols, and iconic symbols did not yield faster identification than conventional symbols, and (b) the portrayal of additional feature information (through the use of perimeter density or vector projection coding) slowed processing of the core symbol information in four tasks, but certain symbol-design features created less perceptual interference and had greater correspondence with the portrayal of specific tactical concepts than others. The results were discussed in terms of the complexities involved in the selection of symbol design features for use in graphic tactical displays.
Attention↗
Intact priming of patterns despite impaired memory.
The priming of patterns was examined in normal control subjects (NCS) and in the amnesic patient H.M., whose anterograde amnesia followed bilateral medial temporal-lobe excision 33 years earlier. Despite H.M.'s impaired recognition of the patterns, he demonstrated a pattern priming effect equivalent in magnitude to that of the NCS. The results demonstrated that intact priming with novel, nonverbal material can occur despite severe amnesia. Pattern priming may reflect adaptive visual processes involved in learning novel perceptual organizations of known visual codes, such as letters, words, shapes, and objects.
Amnesia↗
Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code.
Insertion of lysine during protein synthesis depends on the enzyme lysyl-tRNA synthetase (LysRS), which exists in two unrelated forms, LysRS1 and LysRS2. LysRS1 has been found in most archaea and some bacteria, and LysRS2 has been found in eukarya, most bacteria, and a few archaea, but the two proteins are almost never found together in a single organism. Comparison of structures of LysRS1 and LysRS2 complexed with lysine suggested significant differences in their potential to bind lysine analogues with backbone replacements. One such naturally occurring compound, the metabolic intermediate S-(2-aminoethyl)-L-cysteine, is a bactericidal agent incorporated during protein synthesis via LysRS2. In vitro tests showed that S-(2-aminoethyl)-L-cysteine is a poor substrate for LysRS1, and that it inhibits LysRS1 200-fold less effectively than it inhibits LysRS2. In vivo inhibition by S-(2-aminoethyl)-L-cysteine was investigated by replacing the endogenous LysRS2 of Bacillus subtilis with LysRS1 from the Lyme disease pathogen Borrelia burgdorferi. B. subtilis strains producing LysRS1 alone were relatively insensitive to growth inhibition by S-(2-aminoethyl)-L-cysteine, whereas a WT strain or merodiploid strains producing both LysRS1 and LysRS2 showed significant growth inhibition under the same conditions. These growth effects arising from differences in amino acid recognition could contribute to the distribution of LysRS1 and LysRS2 in different organisms. More broadly, these data demonstrate how diversity of the aminoacyl-tRNA synthetases prevents infiltration of the genetic code by noncanonical amino acids, thereby providing a natural reservoir of potential antibiotic resistance.
Bacillus subtilis↗
Nonlinear and higher-order approaches to the encoding of natural scenes.
Linear operations can only partially exploit the statistical redundancies of natural scenes, and nonlinear operations are ubiquitous in visual cortex. However, neither the detailed function of the nonlinearities nor the higher-order image statistics are yet fully understood. We suggest that these complicated issues can not be tackled by one single approach, but require a range of methods, and the understanding of the crosslinks between the results. We consider three basic approaches: (i) State space descriptions can theoretically provide complete information about statistical properties and nonlinear operations, but their practical usage is confined to very low-dimensional settings. We discuss the use of representation-related state-space coordinates (multivariate wavelet statistics) and of basic nonlinear coordinate transformations of the state space (e.g., a polar transform). (ii) Indirect methods, like unsupervised learning in multi-layer networks, provide complete optimization results, but no direct information on the statistical properties, and no simple model structures. (iii) Approximation by lower-order terms of power-series expansions is a classical strategy that has not yet received broad attention. On the statistical side, this approximation amounts to cumulant functions and higher-order spectra (polyspectra), on the processing side to Volterra Wiener systems. In this context we suggest that an important concept for the understanding of natural scene statistics, of nonlinear neurons, and of biological pattern recognition can be found in AND-like combinations of frequency components. We investigate how the different approaches can be related to each other, how they can contribute to the understanding of cortical nonlinearities such as complex cells, cortical gain control, end-stopping and other extraclassical receptive field properties, and how we can obtain a nonlinear perspective on overcomplete representations and invariant coding in visual cortex.
Animals↗
Functional role for the angiotensin II receptor (AT1A) 3'-untranslated region in determining cellular responses to agonist: evidence for recognition by RNA binding proteins.
We demonstrate a functional role for the 3'-untranslated region (3'-UTR) of the angiotensin II (Ang II) receptor subtype AT1A mRNA in Chinese hamster ovary (CHO-K1) cells by stably transfecting the coding region of the receptor gene with or without the 845 bp 3'-UTR. Two cell lines expressing similar levels of cell-surface receptors (with 3'-UTR, Bmax=571 fmol/mg protein; without 3'-UTR, Bmax=663 fmol/mg protein) were used in the present study. Both cell lines expressed high-affinity receptors (with 3'-UTR, Kd=0.83 nM; without 3'-UTR, Kd=0.82 nM), and binding studies with 125I-labelled Ang II in the presence of GTP[S] demonstrated that both coupled to heterotrimeric G-proteins. Despite these similarities, significant differences were observed for receptor-mediated cell signalling pathways. In cells without the 3'-UTR, Ang II stimulated an increase in cAMP accumulation (11-fold above control) and in cells with the 3'-UTR no stimulation was observed, which was consistent with previous observations in most endogenous Ang II receptor (AT1)-expressing cells. Activation of cAMP by Ang II in cells without the 3'-UTR correlated with an inhibition of DNA synthesis, determined by [3H]thymidine incorporation. Ang II-mediated responses were blocked by EXP3174, a selective non-peptide receptor antagonist. We also observed differences in the transient profiles of intracellular calcium between cells with and without the 3'-UTR in response to Ang II. In cells with the 3'-UTR, a sustained level of intracellular calcium was observed after Ang II stimulation, whereas cells without the 3'-UTR displayed a full return to basal level within 50 s of Ang II treatment. Even though the expressed exogenous gene is under the control of a constitutively expressing promoter (cytomegalovirus promoter), Northern-blot analysis revealed a considerably greater accumulation of AT1A mRNA in cells without the 3'-UTR compared with cells with the 3'-UTR. Analysis of the decay rate of the AT1A mRNA in cells with and without the 3'-UTR revealed that the normally unstable AT1A receptor mRNA became highly stable by removing its 3'-UTR, identifying a role for the 3'-UTR in mRNA destabilization. Interestingly, both cells express similar levels of receptors at the cell surface, suggesting that the 3'-UTR is also involved in the efficient translation and/or translocation of the receptor protein to the plasma membrane. We hypothesized that these 3'-UTR-mediated functions of the receptor are regulated by RNA-binding proteins. To identify possible RNA-binding proteins for the AT1A 3'-UTR, cellular extracts were prepared from parental CHO-K1 cells and 3'-UTR-binding assays, electrophoretic mobility-shift assays and UV crosslinking studies were performed. A major cellular protein of 55 kDa was identified, which specifically interacted with the 3'-UTR. Our data suggest that the 3'-UTR of the AT1A can control specific receptor functions, perhaps via selective recognition of the 3'-UTR by RNA-binding proteins.
Angiotensin II↗
The transcript coding for an RNA-binding protein is localized in the anterior side of the ascidian 2-cell stage embryo.
We have cloned a putative ascidian RNA-binding protein gene, CiRGG1, which has three RNA-recognition motifs and two arginine-glycine-glycine domains. Its deduced amino acid sequence has a weak similarity to nucleolin, which is one of the known components of messenger ribonucleoproteins. Its maternal transcript is transiently accumulated into the anterior side of 2-cell stage embryos. Zygotic expression of CiRGG1 is strongest in the brain, mesenchyme and endoderm of the trunk region of the tailbud stage embryo. This mRNA is the first example of an anterior-localized molecule in the ascidian 2-cell stage embryo.
Amino Acid Sequence↗