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PubMed2005

In search of the nature of specific nucleic acid-protein interactions.

The theory of "codon-amino acid coevolution" was first proposed by Woese in 1967. It suggests that there is a stereochemical matching - that is, affinity - between amino acids and certain of the base triplet sequences that code for those amino acids. We have constructed a Common Periodic Table of Codons and Amino Acids, where the Nucleic Acid Table showed perfect axial symmetry for codons and the corresponding Amino Acid Table also displayed periodicity regarding the biochemical properties (charge and hydrophobicity) of the 20 amino acids and the position of the stop signals. The Table indicates that the middle (2nd) amino acid in the codon has a prominent role in determining some of the structural features of the amino acids. The possibility that physical contact between codons and amino acids might exist was tested on restriction enzymes. Many recognition site-like sequences were found in the coding sequences of these enzymes and as many as 73 examples of codon-amino acid co-location were observed in the 7 known 3D structures (December 2003) of endonuclease-nucleic acid complexes. These results indicate that the smallest possible units of specific nucleic acid-protein interaction are indeed the stereochemically compatible codons and amino acids.

Algorithms↗

PubMed1985

Expression and T cell recognition of hybrid antigens with amino-terminal domains encoded by Qa-2 region of major histocompatibility complex and carboxyl termini of transplantation antigens.

Coding potential of the Q6 gene from the Qa-2a region of BALB/c Crgl mice was analyzed by a combination of hybrid class I gene construction and DNA-mediated gene transfer. Recombinant genes were created by exon shuffling of the 5' coding region of the Q6 gene and the 3' coding region of a gene encoding a transplantation antigen (Kd, Dd, or Ld), or the inverse. Some of these hybrid class I genes were expressed in the transfected mouse fibroblasts (L cells). The hybrid class I molecules encoded by the 5' end of the Q6 gene and the 3' end of the Ld gene precipitated as 45,000 mol wt molecules associated with beta 2-microglobulin. The expression of the hybrid proteins indicates that 926 basepairs of the 5' flanking region upstream of the structural Q6 gene contain a promoter that functions as a transcription initiation site in L cells. The 3' portion of the Q6 gene appears to be responsible for the lack of cell surface expression of the intact Q6 and the hybrid Ld/Q6 genes in mouse fibroblasts. Accordingly, this portion of the Q6 class I gene may play a regulatory role in tissue-specific expression. Serological analyses of hybrid Q6 proteins suggested that Q6 may be a structural gene for CR (H-2 crossreactive) antigen found normally on subpopulations of lymphocytes. If this identification is correct, Q6 gene will define a new category of class I genes encoding approximately 40,000 mol wt molecules and carrying a characteristic truncated cytoplasmic tail. Analysis of L cells transfected with Q6 hybrid genes demonstrated also that the cytotoxic T cells specific for Qa-2a region-coded antigens recognize the amino-terminal alpha 1-alpha 2 domain of Q6 fusion products. This recognition can be blocked by anti-Qa-2a alloantiserum and monoclonal antibodies reactive with the alpha 3-beta 2-microglobulin portion of the Q6 hybrids. We propose that the structural requirements for the anti-Qa-2a cytotoxic T lymphocyte-specific epitopes on target molecules are the same as for anti-H-2-alloreactive cytotoxic T lymphocyte determinants on transplantation antigens and that the mechanism of target recognition is similar in both cases. This interpretation is consistent with the following structural similarities found in both categories of class I molecules: (a) Kd and Q6 alpha 1-alpha 2 domains share serologically defined epitopes.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1996

Hepatitis B virus core and e antigen: immune recognition and use as a vaccine carrier moiety.

The hepatitis B virus (HBV) core gene codes for two partially colinear antigens: a secreted antigen (HBeAg) and the particulate core antigen (HBcAg), which assembles to form subviral particles and in virions contains the viral genome and polymerase. In this review we summarize data on the immune recognition of HBc/eA and recent progress in the use of HBcAg as a carrier moiety for heterologous epitopes. During HBV infection, HBcAg and HBeAg are important targets of antiviral immunity. HBcAg and HBeAg are serologically distinct but share all characterized T-cell epitopes. The particulate HBcAg can elicit T-cell-independent as well as T-cell-dependent antibody responses, HBeAg is a strictly T-cell-dependent antigen. Neonatal tolerance to maternally derived circulating HBeAg may facilitate chronic HBV infection after vertical transmission of HBV. In a murine transgenic model, HBc/eAg-specific Th1 cells were more readily anergized, whereas Th2 cells more easily escaped tolerization. In human HBV infection, acute adult HBV infection with subsequent virus elimination was characterized by Th1-like alpha-HBV serum IgG subtype distribution, whereas a Th2-like distribution of IgG subtypes was observed during chronic infection. During chronic infection, core gene mutants which abolish HBeAg synthesis were frequently observed. To exploit the unusual immunogenicity of particulate HBcAg as a vaccine carrier moiety, insertion sites for foreign epitopes were defined in recombinant expression systems. While fusion of epitopes to the N-terminus required a linker sequence for surface accessibility, both fusion to the N-terminus and to the C-terminus was compatible with particle assembly and preserved the native antigenicity and immunogenicity of HBcAg. Epitope insertion at an immunodominant internal site of HBcAg reduced the HBcAg immunogenicity and antigenicity and most drastically enhanced the immunogenicity of the inserted foreign epitopes. This internal site of HBcAg was used to express circumsporozoite antigen (CS) repeat epitopes of two rodent malaria parasites and of Plasmodium falciparum. Purified hybrid HBcAg-CS proteins were particulate and displayed CS antigenicity as well as reduced native HBc antigenicity. Immunization of several mouse strains with HBcAg-CS hybrid particles resulted in high-titered serum anti-CS antibodies representing all murine IgG isotypes and protected BALB/c mice against plasmodial challenge. Immunization of mice with HBcAg or HBcAg-CS particles formulated on alum, complete Freund's or incomplete Freund's adjuvant resulted in equivalent anti-CS and anti-HBc serum antibody titers. Preexisting immunity to HBcAg did not significantly alter the immunogenicity of hybrid HBcAg particles suggesting that carrier-specific immune suppression does not limit the use of hybrid HBcAg with internal insertions. Immunization with HBcAg-CS particles universally primed HBcAg-specific T cells and in addition CS-specific T cells were if the insert contained a CS-specific T-cell site for the corresponding murine MHC class II haplotype. The internal amino acid position in HBcAg is therefore permissive for the inclusion of heterologous T-helper as well as B-cell epitopes.

Animals↗

PubMed1994

The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.

Discriminant analysis is applied to the problem of recognition 5'-, internal and 3'-exons in human DNA sequences. Specific recognition functions were developed for revealing exons of particular types. The method based on a splice site prediction algorithm that uses the linear Fisher discriminant to combine the information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotides in protein coding and intron regions (Solovyev, Lawrence, 1994). The accuracy of our splice site recognition function is about 97%. A discriminant function for 5'-exon prediction includes hexanucleotide composition of upstream region, triplet composition around the ATG codon, ORF coding potential, donor splice site potential and composition of downstream intron region. For internal exon prediction, we combine in a discriminant function the characteristics describing the 5'-intron region, donor splice site, coding region, acceptor splice site and 3'-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79% and a level of pseudoexon ORF prediction of 99.96%. The recognition quality computed at the level of individual nucleotides is 89% for exon sequences and 98% for intron sequences. A discriminant function for 3'-exon prediction includes octanucleotide composition of upstream intron region, triplet composition around the stop codon, ORF coding potential, acceptor splice site potential and hexanucleotide composition of downstream region.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Simulation↗

PubMed1995

The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes.

Studies on phage T3 and T7 have shown that these viruses avoid restriction not only by the phage-coded Ocr (and S-adenosylmethionine hydrolase) protein functions or by the complete loss of specific recognition sites for certain restriction endonucleases from their genomes, but also that there are two additional modes: resistance towards EcoP15 (which recognizes a non-symmetrical sequence) is achieved by an identical orientation of all the recognition sites in the virus genome (strand bias) and in the case of EcoRII by the extreme reduction in number and thereby greater distance between recognition sites in the genome. These observations led to the discovery that certain restriction endonucleases require the simultaneous cooperation with two DNA sites for their function, as well as to the ongoing elucidation of the molecular modes of action of these enzymes. Type II and type III enzymes display fundamentally different mechanisms of protein-DNA interaction. For EcoRII we favor a model of simultaneous binding of two DNA sites to a dimeric enzyme molecule (neighbouring sites of the same, looping, DNA molecule or sites located on different DNA molecules), while the action of EcoP15 seems to conform with a tracking-collision model of two enzyme molecules bound to inversely oriented recognition sites. In addition to podoviruses T3 and T7, strand bias of recognition sequences for different type III DNA modification-restriction enzymes is also observed in the inoviruses M13, IKE and PF3.

Bacteriophage T3↗

PubMed2003

Learning optimized features for hierarchical models of invariant object recognition.

There is an ongoing debate over the capabilities of hierarchical neural feedforward architectures for performing real-world invariant object recognition. Although a variety of hierarchical models exists, appropriate supervised and unsupervised learning methods are still an issue of intense research. We propose a feedforward model for recognition that shares components like weight sharing, pooling stages, and competitive nonlinearities with earlier approaches but focuses on new methods for learning optimal feature-detecting cells in intermediate stages of the hierarchical network. We show that principles of sparse coding, which were previously mostly applied to the initial feature detection stages, can also be employed to obtain optimized intermediate complex features. We suggest a new approach to optimize the learning of sparse features under the constraints of a weight-sharing or convolutional architecture that uses pooling operations to achieve gradual invariance in the feature hierarchy. The approach explicitly enforces symmetry constraints like translation invariance on the feature set. This leads to a dimension reduction in the search space of optimal features and allows determining more efficiently the basis representatives, which achieve a sparse decomposition of the input. We analyze the quality of the learned feature representation by investigating the recognition performance of the resulting hierarchical network on object and face databases. We show that a hierarchy with features learned on a single object data set can also be applied to face recognition without parameter changes and is competitive with other recent machine learning recognition approaches. To investigate the effect of the interplay between sparse coding and processing nonlinearities, we also consider alternative feedforward pooling nonlinearities such as presynaptic maximum selection and sum-of-squares integration. The comparison shows that a combination of strong competitive nonlinearities with sparse coding offers the best recognition performance in the difficult scenario of segmentation-free recognition in cluttered surround. We demonstrate that for both learning and recognition, a precise segmentation of the objects is not necessary.

Learning↗

PubMed1994

Early recognition of children with autism: a study of first birthday home videotapes.

Coded home videotapes of 11 autistic and 11 normally developing children's first year birthday parties for social, affective, joint attention, and communicative behaviors and for specific autistic symptoms. Autistic children displayed significantly fewer social and joint attention behaviors and significantly more autistic symptoms. In combination, four behaviors correctly classified 10 of 11 autistic children and 10 of 11 normal children. These behaviors consisted of pointing, showing objects, looking at others, and orienting to name.

Anniversaries and Special Events↗

PubMed1997

Molecular cloning and analysis of Schizosaccharomyces pombe Reb1p: sequence-specific recognition of two sites in the far upstream rDNA intergenic spacer.

The coding sequences for a Schizosaccharomyces pombe sequence-specific DNA binding protein, Reb1p, have been cloned. The predicted S. pombe Reb1p is 24-29% identical to mouse TTF-1 (transcription termination factor-1) and Saccharomyces cerevisiae REB1 protein, both of which direct termination of RNA polymerase I catalyzed transcripts. The S.pombe Reb1 cDNA encodes a predicted polypeptide of 504 amino acids with a predicted molecular weight of 58.4 kDa. The S. pombe Reb1p is unusual in that the bipartite DNA binding motif identified originally in S.cerevisiae and Klyveromyces lactis REB1 proteins is uninterrupted and thus S.pombe Reb1p may contain the smallest natural REB1 homologous DNA binding domain. Its genomic coding sequences were shown to be interrupted by two introns. A recombinant histidine-tagged Reb1 protein bearing the rDNA binding domain has two homologous, sequence-specific binding sites in the S. pomber DNA intergenic spacer, located between 289 and 480 nt downstream of the end of the approximately 25S rRNA coding sequences. Each binding site is 13-14 bp downstream of two of the three proposed in vivo termination sites. The core of this 17 bp site, AGGTAAGGGTAATGCAC, is specifically protected by Reb1p in footprinting analysis.

Amino Acid Sequence↗

PubMed1990

Transcription of the promoter of the rat NF-1 gene depends on the integrity of an Sp1 recognition site.

The transcription start site and promoter of the rat gene coding for the transcription factor NF-1 have been identified. The NF-1 promoter was fused to the chloramphenicol acetyltransferase-coding sequence, and the resulting plasmid was transcriptionally active in the HepG2 cell line. Footprinting and gel retardation analysis indicated that the transcription factor Sp1 binds to the NF-1 promoter. Mutants in the Sp1-binding site displayed a strong reduction in transcriptional activity.

Animals↗

PubMed2001

Human cortical processing of colour and pattern.

The present study investigates human visual processing of simple two-colour patterns using a delayed match to sample paradigm with positron emission tomography (PET). This study is unique in that we specifically designed the visual stimuli to be the same for both pattern and colour recognition with all patterns being abstract shapes not easily verbally coded composed of two-colour combinations. We did this to explore those brain regions required for both colour and pattern processing and to separate those areas of activation required for one or the other. We found that both tasks activated similar occipital regions, the major difference being more extensive activation in pattern recognition. A right-sided network that involved the inferior parietal lobule, the head of the caudate nucleus, and the pulvinar nucleus of the thalamus was common to both paradigms. Pattern recognition also activated the left temporal pole and right lateral orbital gyrus, whereas colour recognition activated the left fusiform gyrus and several right frontal regions.

Adult↗

PubMed2000

Sensory and cognitive contributions of color to the recognition of natural scenes.

Although color plays a prominent part in our subjective experience of the visual world, the evolutionary advantage of color vision is still unclear [1] [2], with most current answers pointing towards specialized uses, for example to detect ripe fruit amongst foliage [3] [4] [5] [6]. We investigated whether color has a more general role in visual recognition by looking at the contribution of color to the encoding and retrieval processes involved in pattern recognition [7] [8] [9]. Recognition accuracy was higher for color images of natural scenes than for luminance-matched black and white images, and color information contributed to both components of the recognition process. Initially, color leads to an image-coding advantage at the very early stages of sensory processing, most probably by easing the image-segmentation task. Later, color leads to an advantage in retrieval, presumably as the result of an enhanced image representation in memory due to the additional attribute. Our results ascribe color vision a general role in the processing of visual form, starting at the very earliest stages of analysis: color helps us to recognize things faster and to remember them better.

Cognition↗

PubMed1994

Structure and localization on the X chromosome of the gene coding for the human filopodial protein moesin (MSN).

Moesin is a member of a recently discovered family of closely related proteins that includes ezrin, radixin, and merlin. It is widely expressed in different tissues and cells and has been localized to filopodia and other membranous protrusions that are important for cell-cell recognition and signaling and cell movement. Here, we have localized the coding gene (MSN) to Xq11.2-q12 by Southern and Western blot analyses of Chinese hamster x human somatic cell hybrids and by fluorescence chromosomal in situ hybridization. Moesin-like sequences were identified on chromosomes 5 and 6. The murine Msn locus was mapped to the X chromosome as well by studying a rodent x mouse hybrid panel. The structure of the human moesin gene has been determined. The 12 exons are distributed over > 30 kb, and the exon/intron junctions demarcate individual highly conserved domains. Primer extension analysis revealed two major start transcription sites, 184 and 133 bp upstream of the initiation codon. The 5'-flanking region is GC-rich, lacks a TATA box, and contains four SP1 and one AP1 binding sites.

Animals↗

PubMed2006

The TREC 2004 genomics track categorization task: classifying full text biomedical documents.

BACKGROUND: The TREC 2004 Genomics Track focused on applying information retrieval and text mining techniques to improve the use of genomic information in biomedicine. The Genomics Track consisted of two main tasks, ad hoc retrieval and document categorization. In this paper, we describe the categorization task, which focused on the classification of full-text documents, simulating the task of curators of the Mouse Genome Informatics (MGI) system and consisting of three subtasks. One subtask of the categorization task required the triage of articles likely to have experimental evidence warranting the assignment of GO terms, while the other two subtasks were concerned with the assignment of the three top-level GO categories to each paper containing evidence for these categories. RESULTS: The track had 33 participating groups. The mean and maximum utility measure for the triage subtask was 0.3303, with a top score of 0.6512. No system was able to substantially improve results over simply using the MeSH term Mice. Analysis of significant feature overlap between the training and test sets was found to be less than expected. Sample coverage of GO terms assigned to papers in the collection was very sparse. Determining papers containing GO term evidence will likely need to be treated as separate tasks for each concept represented in GO, and therefore require much denser sampling than was available in the data sets. The annotation subtask had a mean F-measure of 0.3824, with a top score of 0.5611. The mean F-measure for the annotation plus evidence codes subtask was 0.3676, with a top score of 0.4224. Gene name recognition was found to be of benefit for this task. CONCLUSION: Automated classification of documents for GO annotation is a challenging task, as was the automated extraction of GO code hierarchies and evidence codes. However, automating these tasks would provide substantial benefit to biomedical curation, and therefore work in this area must continue. Additional experience will allow comparison and further analysis about which algorithmic features are most useful in biomedical document classification, and better understanding of the task characteristics that make automated classification feasible and useful for biomedical document curation. The TREC Genomics Track will be continuing in 2005 focusing on a wider range of triage tasks and improving results from 2004.

Journal Article↗

PubMed2005

Low rates of testing and diagnostic codes usage in a commercial clinical laboratory: evidence for lack of physician awareness of chronic kidney disease.

Improving outcomes for chronic kidney disease (CKD) requires early identification and recognition by physicians. There are few data on rates of testing or use of diagnostic codes for CKD. A cross-sectional analysis was performed of patients who were older than 40 yr and had one or more laboratory tests between April 1, 2002, and March 31, 2003, at a Laboratory Corporation of America regional laboratory. Objectives were to determine the frequency of testing for serum creatinine; prevalence of CKD, defined as estimated GFR <60 ml/min per 1.73 m2; and sensitivity of diagnostic codes for CKD for patients with and without risk factors for CKD and with or without cardiovascular disease (CVD). Of the 277,111 patients, 19% had serum creatinine measured, compared with 33 and 71% who had measurements of serum glucose and lipids, respectively. Patients with hypertension, diabetes, and age >60 yr were more likely to be tested for serum creatinine with odds ratio (OR; 95% confidence interval) of 2.09 (2.05 to 2.14), 1.22 (1.19 to 1.25), and 1.24 (1.22 to 1.27) respectively. Among patients tested, 30% had CKD. Sensitivity and specificity of kidney disease diagnostic codes compared with CKD defined by estimated GFR <60 ml/min per 1.73 m2 were 11 and 96%, respectively. In patients with hypertension, diabetes, age >60 years, and CVD, rates of testing and sensitivity of diagnostic codes were 53 and 14%, respectively. Low rates of testing for serum creatinine and insensitivity of diagnostic codes for CKD, even in high-risk patients, suggests inadequate physician awareness of CKD and limited utility of administrative databases for identification of patients with CKD.

Adult↗

PubMed1988

Cloning and analysis of the HaeIII and HaeII methyltransferase genes.

The HaeIII methyltransferase (MTase) gene from Haemophilus aegyptius (recognition sequence: 5'-GGCC-3') was cloned into Escherichia coli in the plasmid vector pBR322. The gene was isolated on a single EcoRI fragment and on a single HindIII fragment. Clones carrying additional adjacent fragments were found to code also for the HaeII restriction endonuclease and HaeII modification MTase (recognition sequence: 5'-PuGCGCPy-3'). The sequence of the HaeIII modification gene was determined. The inferred amino acid sequence of the protein was found to share extensive similarity with other sequenced m5C-MTases. The central 'non-conserved' region of the M.HaeIII MTase, thought to form the nucleotide sequence-specificity domain, is almost identical to that of the M.BsuRI, M.BspRI and M.NgoPII MTases, which also recognize the sequence 5'-GGCC-3'.

Amino Acid Sequence↗

PubMed2004

Orientation-contingent face aftereffects and implications for face-coding mechanisms.

Humans have an impressive ability to discriminate between faces despite their similarity as visual patterns. This expertise relies on configural coding of spatial relations between face features and/or holistic coding of overall facial structure. These expert face-coding mechanisms appear to be engaged most effectively by upright faces, with inverted faces engaging primarily feature-coding mechanisms. We show that opposite figural aftereffects can be induced simultaneously for upright and inverted faces, demonstrating that distinct neural populations code upright and inverted faces. This result also suggests that expert (upright) face-coding mechanisms can be selectively adapted. These aftereffects occur for judgments of face normality and face gender and are robust to changes in face size, ruling out adaptation of low-level, retinotopically organized coding mechanisms. Our results suggest a resolution of a paradox in the face recognition literature. Neuroimaging studies have found surprisingly little orientation selectivity in the fusiform face area (FFA) despite evidence that this region plays a role in expert face coding and that expert face-coding mechanisms are selectively engaged by upright faces. Our results, demonstrating orientation-contingent adaptation of face-coding mechanisms, suggest that the FFA's apparent lack of orientation selectivity may be an artifact of averaging across distinct populations within the FFA that respond to upright and inverted faces.

Adult↗

PubMed1983

Use of a cDNA clone for the fourth component of human complement (C4) for analysis of a genetic deficiency of C4 in guinea pig.

A cDNA clone for the fourth complement component (C4), pC4AL1, has been isolated from a human adult liver cDNA library by using a synthetic oligonucleotide mixture containing all 384 possible sequences coding for residues 14-21 of the C4 gamma-chain amino acid sequence. This clone spans the entire C4 gamma-chain coding sequence and includes a short 3' untranslated region, a poly(A) recognition site, and 16 nucleotides of the poly(A) tail. The 5' end of the clone begins 18 nucleotides upstream from the amino terminus of the C4 gamma chain and codes for Arg-Asn-Arg-Arg-Arg-Arg, a highly charged proteolytic cleavage site involved in the processing of pro-C4 to native C4. Liver mRNA preparations from C4-deficient guinea pigs were incapable of directing synthesis of pro-C4 or C4 peptides in cell-free translation experiments. Southern blot analysis using pC4AL1 as a hybridization probe of C4-deficient guinea pig DNA established that the deficiency is not the result of deletion of the entire C4 gene. RNA blot analysis using pC4AL1 as a hybridization probe of normal guinea pig liver mRNA revealed a C4 mRNA of 5.0 kilobases (kb). No such mRNA species was observed in C4-deficient guinea pig liver mRNA; however, a 7.0-kb RNA was detected, indicating the presence of a C4 precursor RNA. These results suggest that the basis of C4 deficiency in the guinea pig is a post-transcriptional defect in the processing of C4 precursor RNA to mature C4 mRNA.

Amino Acid Sequence↗

PubMed1981

Computer-assisted structure-activity studies of chemical carcinogens. Aromatic amines.

Studies of molecular structure-carcinogenicity relations for a set of 157 aromatic amines are reported. A computer-assisted approach using pattern-recognition methods was used to develop a series of discriminants for aromatic amino carcinogenic potential. The 157 compounds were divided into subsets according to tumor site, route of administration, and activity. Sets of calculated molecular structure descriptors were generated that could support linear discriminant functions able to separate sets of active carcinogens from inactive compounds. Prominent among the important structural descriptors were those coding sizes and shapes of the amines. The pattern-recognition results were not strongly affected by differences in active site, and the study showed that mixed data sets could be used in computer-assisted structure-carcinogenicity studies.

Amines↗