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PubMed1976

Pictorial superiority effect.

Pictures generally show superior recognition relative to their verbal labels. This experiment was designed to link this pictorial superiority effect to sensory or meaning codes associated with the two types of symbols. Paired-associate stimuli consisted of simple pictures or of their labels, with list items selected either from the same conceptual category or from different conceptual categories. In addition, schematic or visual similarity among the pictures was either high or low. At two rates of presentation equal amounts of conceptual interference were produced for pictures and their labels. High schematic similarity eliminated the pictorial superiority effects at the slow rate and completely reversed it at the fast rate. These results suggest that the meaning representations for simple pictures and their labels may be identical, and that the pictorial superiority effect is related to the qualitative superiority of the sensory codes for pictures.

Concept Formation↗
PubMedDate not supplied

[Cell molecular computer. IX. Coding principles in intracellular information processing].

Methods of coding the number and search for molecular program in a molecular computer are considered. The limited length of the nucleotide code is (see formula) where Pi -- probability of request of the given program, N -- total number of programs. Energetic expenditures for the synthesis of the code with the length l (in an ideal case without noise) E approximately 10 kT X l. Protein-nucleic recognition allows the work of the cell with almost the same expenditures on the account of Brown search in the presence of noise.

Cells↗
PubMed1998

Inborn errors of metabolism: medical and administrative "orphans".

CONTEXT: Inborn errors of metabolism are genetic conditions that affect the normal biochemical functions of the body in any organ and at any age. More than 500 metabolic diseases are known; almost all are classified as orphan diseases under the US Food and Drug Administration guidelines (incidence < 200,000 persons) and each has its own requirements for diagnosis and treatment. Management of these complex, lifelong, multisystem disorders often requires a coordinated, multidisciplinary approach involving several subspecialists and which may include complex laboratory evaluations, genetic counseling, nutritional therapy, and unusual therapeutic approaches that have been used in only a small number of cases. RESULTS: Not infrequently, inborn errors of metabolism fall outside current standard diagnostic and treatment guidelines of managed care plans. This results in delays in diagnosis and appropriate management, with increased costs to patients and to society. CONCLUSIONS: Patients with inborn errors of metabolism should not be discriminated against and all health plans should specify that access to specialists and metabolic centers are a covered benefit of the plan. The acceptance of treatment guidelines, the development of international disease classification codes for the disorders, and the performance of cost-benefit analyses would all greatly facilitate this process. However, without recognition that these disorders require such services, and steps to provide them by the insurance industry, the care of children with metabolic disorders and other chronic diseases will continue to be a source of frustration and anger among the caregivers and the families they serve.

Cost-Benefit Analysis↗
PubMed2002

[Isolation and characterization of functional replication origin from Streptomyces avermitilis].

Most eubacteria contain highly conservative gene clusters in the adjacent regions of oriC. According to this principle, a 1.4 kb DNA fragment containing parts of dnaA and dnaN genes of Streptomyces avermitilis was cloned by degenerate PCR. Sequence analysis of this fragment indicated that it encoded two partial genes in the order dnaA (the putative initiator protein) and dnaN (the beta subunit of DNA polymerase III). The intergenic non-coding region between dnaA and dnaN was found to contain 19 putative DnaA boxes, i.e. 9 nt long DnaA protein recognition sequences. It was confirmed that the location, orientation and spacing of DnaA boxes in this intergenic region are conserved among Streptomyces. The consensus sequence of DnaA box identified is (T/C)(T/C)(G/A/C)TCCACA (preferred bases in italic). When this fragment was cloned into Escherichia coli plasmid pQC156, which is otherwise non-replicative in Streptomyces, it exhibited autonomous replication activity in Streptomyces lividans, a closely related Streptomyces strain. Different parts of the oriC contribute unequally to the stability and transformation efficiency. The 3' region of oriC may contain features that support stable autonomous replication. The implications of these results for the understanding of the S. avermitilis oriC replication initiation process and its future application are discussed.

Bacterial Proteins↗
PubMed1994

Characterization of the human gene encoding LBR, an integral protein of the nuclear envelope inner membrane.

We have characterized the human gene encoding LBR, an integral protein of the nuclear envelope inner membrane. Restriction mapping shows that the transcription unit spans approximately 35 kilobases. A transcription start site is located approximately 4 kilobases 5' to the translation initiation codon, and an RNA splice of 3863 bases occurs in the 5'-untranslated region to generate mature HeLa cell mRNA. 5' to the identified transcription start site are two CCAAT sequences and potential recognition sites for several transcription factors including Sp1, AP-1, AP-2, and NF-kB. There are 13 protein coding exons in the LBR gene. LBR's nucleoplasmic domain is encoded by exons 1-4, and its hydrophobic domain, with eight putative transmembrane segments, is encoded by exons 5-13. The hydrophobic domain is homologous to three yeast polypeptides, suggesting that this higher eukaryotic gene could have evolved from recombination between a gene that encoded a soluble nuclear protein and a membrane protein gene similar to those in yeast. These results are the first to demonstrate the structural organization of a vertebrate gene encoding an integral membrane protein of the nuclear envelope that may be a member of a family of polypeptides conserved in evolution.

Amino Acid Sequence↗
PubMed2003

Changes in corticospinal motor excitability induced by non-motor linguistic tasks.

The excitability of the corticospinal motor pathways to transcranial magnetic stimulation (TMS) can be differentially modulated by a variety of motor tasks. However, there is emerging evidence that linguistic tasks may alter excitability of the corticospinal motor pathways also. In this study we evaluated the effect of several movement-free, low-level linguistic processes involved in reading and writing on the excitability of the bilateral corticospinal motor pathways in a group of right-handed subjects. The study included two series of tasks, visual searching/matching and imaginal writing/drawing. The tasks were designed to roughly correspond with elemental aspects of the reading and writing, grapheme recognition and grapheme generation, respectively. Each task series included separate blocks with different task targets: letters, digits, semantically easy-to-code (i.e. geometric) shapes, and semantically hard-to-code shapes, as well as control blocks with no task. During task performance, TMS was delivered randomly over the hand area of either the left or right motor cortex and the modulation of the excitability of the corticospinal motor pathways was measured bilaterally through changes of the size of the motor-evoked potential (MEP) induced in the relaxed right and left first dorsal interosseous (FDI) muscles. We found that the size of the MEP in hand muscles increased during visual searching/matching tasks, particularly when targets were letters or geometric shapes, and the increase was significant for the dominant hand (left hemisphere) only. No such consistent effects were seen across subjects during imaginal tasks. This study provides evidence that even the performance of certain low-level linguistic tasks can modulate the excitability of the corticospinal motor pathways, particularly those originating from the left (dominant) hemisphere, despite the absence of overt motor activity. Moreover, in the light of the recently increased awareness of the role of "mirror neurons" in perception, the results suggest that activation of motor circuits used in generation of the written output may be an essential part of the perception of the written material as well. Understanding the patterns of task-dependent changes in excitability of the corticospinal motor pathways will provide insights into the organisation of central nervous system functional networks involved in linguistic processes, and may also be useful for future development of novel approaches to rehabilitation therapy of linguistic and motor functions.

Adult↗
PubMed1996

RNA structure is a critical determinant of poly(A) site recognition by cleavage and polyadenylation specificity factor.

Sequence conservation among mammalian poly(A) sites is limited to the sequence AAUAAA, coupled with an amorphous downstream U- or GU-rich region. Since these sequences may also occur within the coding region of mRNAs, additional information must be required to define authentic poly(A) sites. Several poly(A) sites have been shown to contain sequences outside the core elements that enhance the efficiency of 3' processing in vivo and in vitro. The human immunodeficiency virus type 1, equine infectious anemia virus, and adenovirus L1 3' processing enhancers have been shown to promote the binding of cleavage and polyadenylation specificity factor (CPSF), the factor responsible for recognition of AAUAAA, to the pre-mRNA, thereby facilitating the assembly of a stable 3' processing complex. We have used in vitro selection to examine the mechanism by which the human immunodeficiency virus type 1 3' processing enhancer promotes the interaction of CPSF with the AAUAAA hexamer. Surprisingly, RNAs selected for efficient polyadenylation were related by structure rather than sequence. Therefore, in the absence of extensive sequence conservation, our results strongly suggest that RNA structure is a critical determinant of poly(A) site recognition by CPSF and may play a key role in poly(A) site definition.

Adenoviridae↗
PubMed2005

Psychophysical investigations of cetylpyridinium chloride in rats: its inherent taste and modifying effects on salt taste.

Salts are transduced by at least 2 mechanisms: (a) antagonized by amiloride and (b) antagonized by cetylpyridinium chloride (CPC). The authors report on 4 behavioral experiments in rats that characterize the orosensory properties of CPC itself as well as its effect in suppressing the intensity of NaCl and KCl taste. Experiments 1 and 2 indicated that CPC has a quinine-like taste quality. Experiments 3 and 4 demonstrated that the recognition of KCl, but not NaCl, is modestly reduced by mixture with CPC. However, control experiments call into question the mechanism of the salt suppression of CPC, because both CPC-salt and quinine-salt mixtures had similar effects. The relevance of these studies for understanding salt and bitter taste coding is discussed.

Animals↗
PubMed1995

Structure, function and evolution of seryl-tRNA synthetases: implications for the evolution of aminoacyl-tRNA synthetases and the genetic code.

Two aspects of the evolution of aminoacyl-tRNA synthetases are discussed. Firstly, using recent crystal structure information on seryl-tRNA synthetase and its substrate complexes, the coevolution of the mode of recognition between seryl-tRNA synthetase and tRNA(ser) in different organisms is reviewed. Secondly, using sequence alignments and phylogenetic trees, the early evolution of class 2 aminoacyl-tRNA synthetases is traced. Arguments are presented to suggest that synthetases are not the oldest of protein enzymes, but survived as RNA enzymes during the early period of the evolution of protein catalysts. In this view, the relatedness of the current synthetases, as evidenced by the division into two classes with their associated subclasses, reflects the replacement of RNA synthetases by protein synthetases. This process would have been triggered by the acquisition of tRNA 3' end charging activity by early proteins capable of activating small molecules (e.g., amino acids) with ATP. If these arguments are correct, the genetic code was essentially frozen before the protein synthetases that we know today came into existence.

Acylation↗
PubMed1998

Coding spatial variations in faces and simple shapes: a test of two models.

Faces all have the same basic elements in the same overall arrangement, and must be discriminated using variations in this shared configuration. An efficient way to represent these variations would be to code how each configuration differs from an average face (norm-based coding model). Alternatively, configurations could be represented simply by coding their absolute values in some coordinate system (absolute coding model). The two models differ in the variables they predict will influence an image's recognizability. Absolute coding predicts that recognizability will depend on an image's distinctiveness and degree of distortion from its veridical target. Norm-based coding predicts that recognizability will also depend on the way the image differs from a norm or average face, namely its distance from the norm and/or its degree of displacement from the norm-deviation vector for the target. We determined the effects of these four critical variables on recognition of undistorted (veridical) images, caricatures, anticaricatures and 'lateral' distortions of famous faces (Experiment 1), newly learned faces (Experiment 2), and simple shapes that also share a configuration (Experiment 2). The results favored absolute coding of both faces and shapes, and indicate that caricatures derive their power from their distinctiveness.

Adult↗
PubMed2002

Targeted transposition by the V(D)J recombinase.

Cleavage by the V(D)J recombinase at a pair of recombination signal sequences creates two coding ends and two signal ends. The RAG proteins can integrate these signal ends, without sequence specificity, into an unrelated target DNA molecule. Here we demonstrate that such transposition events are greatly stimulated by--and specifically targeted to--hairpins and other distorted DNA structures. The mechanism of target selection by the RAG proteins thus appears to involve recognition of distorted DNA. These data also suggest a novel mechanism for the formation of alternative recombination products termed hybrid joints, in which a signal end is joined to a hairpin coding end. We suggest that hybrid joints may arise by transposition in vivo and propose a new model to account for some recurrent chromosome translocations found in human lymphomas. According to this model, transposition can join antigen receptor loci to partner sites that lack recombination signal sequence elements but bear particular structural features. The RAG proteins are capable of mediating all necessary breakage and joining events on both partner chromosomes; thus, the V(D)J recombinase may be far more culpable for oncogenic translocations than has been suspected.

Animals↗
PubMed1997

Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase.

Oligonucleotides that recapitulate the acceptor stems of tRNAs are substrates for aminoacylation by many tRNA synthetases in vitro, even though these substrates are missing the anticodon trinucleotides of the genetic code. In the case of tRNAAla a single acceptor stem G.U base pair at position 3.70 is essential, based on experiments where the wobble pair has been replaced by alternatives such as I.U, G.C, and A.U, among others. These experiments led to the conclusion that the minor-groove free 2-amino group (of guanosine) of the G.U wobble pair is essential for charging. Moreover, alanine-inserting tRNAs (amber suppressors) that replace G. U with mismatches such as G.A and C.A are partially active in vivo and can support growth of an Escherichia coli tRNAAla knockout strain, leading to the hypothesis that a helix irregularity and nucleotide functionalities are important for recognition. Herein we investigate the charging in vitro of oligonucleotide and full-length tRNA substrates that contain mismatches at the position of the G.U pair. Although most of these substrates have undetectable activity, G.A and C.A variants retain some activity, which is, nevertheless, reduced by at least 100-fold. Thus, the in vivo assays are much less sensitive to large changes in aminoacylation kinetic efficiency of 3.70 variants than is the in vitro assay system. Although these functional data do not clarify all of the details, it is now clear that specific atomic groups are substantially more important in determining kinetic efficiency than is a helical distortion. By implication, the activity of mutant tRNAs measured in the in vivo assays appears to be more dependent on factors other than aminoacylation kinetic efficiency.

Alanine-tRNA Ligase↗
PubMed1990

Repertoires of antibodies to culture filtrate antigens in different mouse strains infected with Mycobacterium bovis BCG.

Two susceptible (Bcgs) mouse strains, BALB/c and C57BL/6, were compared by Western blot (immunoblot) analysis for their immunoglobulin G response to 14-day-old BCG culture filtrate (CF) following intravenous infection with live Mycobacterium bovis BCG. The two strains demonstrated a completely different antibody repertoire. BALB/c antibodies were directed against a wide range of CF antigens between 20 and about 100 kilodaltons (kDa), with a preferential recognition of the 65-kDa heat shock protein and the 32-kDa fibronectin-binding protein. C57BL/6 sera, on the other hand, showed a much more restricted antibody pattern, almost exclusively directed against three antigens with estimated molecular sizes of 37, 38, and 40 kDa. Whereas the 37- and 38-kDa antigens were also recognized by BALB/c mice, the 40-kDa antigen was very intensely stained by C57BL/6 sera only. F1 mice had the restricted antibody pattern of C57BL/6 after one injection of BCG and had a hybrid BALB/c-C57BL/6 phenotype following a boost injection of BCG 2 months after the initial infection. Analysis of seven recombinant inbred strains derived from the BALB/c x C57BL/6 cross and of congenic mice differing in major histocompatibility complex-coding chromosome 17 fragments suggests that a gene in the K-IA region of the H-2 locus is associated with the preferential recognition of certain CF antigens. Inoculation with the same dose of killed BCG failed to elicit an antibody response to these filtrate antigens.

Animals↗
PubMed1998

Regulation of alternative polyadenylation by U1 snRNPs and SRp20.

Although considerable information is currently available about the factors involved in constitutive vertebrate polyadenylation, the factors and mechanisms involved in facilitating communication between polyadenylation and splicing are largely unknown. Even less is known about the regulation of polyadenylation in genes in which 3'-terminal exons are alternatively recognized. Here we demonstrate that an SR protein, SRp20, affects recognition of an alternative 3'-terminal exon via an effect on the efficiency of binding of a polyadenylation factor to an alternative polyadenylation site. The gene under study codes for the peptides calcitonin and calcitonin gene-related peptide. Its pre-mRNA is alternatively processed by the tissue-specific inclusion or exclusion of an embedded 3'-terminal exon, exon 4, via factors binding to an intronic enhancer element that contains both 3' and 5' splice site consensus sequence elements. In cell types that preferentially exclude exon 4, addition of wild-type SRp20 enhances exon 4 inclusion via recognition of the intronic enhancer. In contrast, in cell types that preferentially include exon 4, addition of a mutant form of SRp20 containing the RNA-binding domain but missing the SR domain inhibits exon 4 inclusion. Inhibition is likely at the level of polyadenylation, because the mutant SRp20 inhibits binding of CstF to the exon 4 poly(A) site. This is the first demonstration that an SR protein can influence alternative polyadenylation and suggests that this family of proteins may play a role in recognition of 3'-terminal exons and perhaps in the communication between polyadenylation and splicing.

Animals↗
PubMed2004

Comparative evaluation of word composition distances for the recognition of SCOP relationships.

MOTIVATION: Alignment-free metrics were recently reviewed by the authors, but have not until now been object of a comparative study. This paper compares the classification accuracy of word composition metrics therein reviewed. It also presents a new distance definition between protein sequences, the W-metric, which bridges between alignment metrics, such as scores produced by the Smith-Waterman algorithm, and methods based solely in L-tuple composition, such as Euclidean distance and Information content. RESULTS: The comparative study reported here used the SCOP/ASTRAL protein structure hierarchical database and accessed the discriminant value of alternative sequence dissimilarity measures by calculating areas under the Receiver Operating Characteristic curves. Although alignment methods resulted in very good classification accuracy at family and superfamily levels, alignment-free distances, in particular Standard Euclidean Distance, are as good as alignment algorithms when sequence similarity is smaller, such as for recognition of fold or class relationships. This observation justifies its advantageous use to pre-filter homologous proteins since word statistics techniques are computed much faster than the alignment methods. AVAILABILITY: All MATLAB code used to generate the data is available upon request to the authors. Additional material available at http://bioinformatics.musc.edu/wmetric

Algorithms↗
PubMed1999

Cloning of mnuA, a membrane nuclease gene of Mycoplasma pulmonis, and analysis of its expression in Escherichia coli.

Membrane nucleases of mycoplasmas are believed to play important roles in growth and pathogenesis, although no clear evidence for their importance has yet been obtained. As a first step in defining the function of this unusual membrane activity, studies were undertaken to clone and analyze one of the membrane nuclease genes from Mycoplasma pulmonis. A novel screening strategy was used to identify a recombinant lambda phage expressing nuclease activity, and its cloned fragment was analyzed. Transposon mutagenesis was used to identify an open reading frame of 1,410 bp, which coded for nuclease activity in Escherichia coli. This gene coded for a 470-amino-acid polypeptide of 53,739 Da and was designated mnuA (for "membrane nuclease"). The MnuA protein contained a prolipoprotein signal peptidase II recognition sequence along with an extensive hydrophobic region near the amino terminus, suggesting that the protein may be lipid modified or that it is anchored in the membrane by this membrane-spanning region. Antisera raised against two MnuA peptide sequences identified an M. pulmonis membrane protein of approximately 42 kDa by immunoblotting, which corresponded to a trypsin-sensitive nucleolytic band of the same size. Maxicell experiments with E. coli confirmed that mnuA coded for a nuclease of unknown specificity. Hybridization studies showed that mnuA sequences are found in few Mycoplasma species, suggesting that mycoplasma membrane nucleases display significant sequence variation within the genus Mycoplasma.

Amino Acid Sequence↗