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The proto-oncogene c-ros codes for a transmembrane tyrosine protein kinase sharing sequence and structural homology with sevenless protein of Drosophila melanogaster.

Our earlier study predicted that proto-oncogene c-ros codes for a receptor-like tyrosine protein kinase (TPK). To further understand its protein structure and physiological function, we have analysed its expression in various tissues of chicken and have isolated and sequenced cDNA clones containing the entire coding region of the gene. Confirming our earlier study, we found that kidney is the organ that expresses the highest level of c-ros mRNA, in addition, we found a lower level of expression in gonad, thymus, bursa and brain. A distinctive 8.3 kb c-ros mRNA is present in kidney. No detectable amount of c-ros mRNA was found in the rest of tissues examined. Nucleotide sequence of the c-ros cDNA predicts that it codes for a transmembrane (TM) TPK molecule of 2311 amino acids (aa). The extracellular domain consists of 1873 amino acids which share 20 to 43% homology with that of the Drosophila sevenless protein and TPK domains of the two genes have 58 to 74% homology. The extracellular domain containing 37 potential N-linked glycosylation sites is preceded by a 5' hydrophobic sequence resembling a typical signal peptide. An internal hydrophobic domain of 26 amino acids, the presumed transmembrane domain, is followed by a spacer sequence of 58 amino acids, a TPK domain of 270 amino acids and a carboxyl tail of 84 amino acids. Overall, our result indicates that c-ros codes for a glycosylated transmembrane TPK molecule which shares a remarkable sequence and structural homology with that of Drosophila sevenless protein.

Amino Acid Sequence↗

Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system.

Homologs of the eukaryotic DNA-end-binding protein Ku were identified in several bacterial and one archeal genome using iterative database searches with sequence profiles. Identification of prokaryotic Ku homologs allowed the dissection of the Ku protein sequences into three distinct domains, the Ku core that is conserved in eukaryotes and prokaryotes, a derived von Willebrand A domain that is fused to the amino terminus of the core in eukaryotic Ku proteins, and the newly recognized helix-extension-helix (HEH) domain that is fused to the carboxyl terminus of the core in eukaryotes and in one of the Ku homologs from the Actinomycete Streptomyces coelicolor. The version of the HEH domain present in eukaryotic Ku proteins represents the previously described DNA-binding domain called SAP. The Ku homolog from S. coelicolor contains a distinct version of the HEH domain that belongs to a previously unnoticed family of nucleic-acid-binding domains, which also includes HEH domains from the bacterial transcription termination factor Rho, bacterial and eukaryotic lysyl-tRNA synthetases, bacteriophage T4 endonuclease VII, and several uncharacterized proteins. The distribution of the Ku homologs in bacteria coincides with that of the archeal-eukaryotic-type DNA primase and genes for prokaryotic Ku homologs form predicted operons with genes coding for an ATP-dependent DNA ligase and/or archeal-eukaryotic-type DNA primase. Some of these operons additionally encode an uncharacterized protein that may function as nuclease or an Slx1p-like predicted nuclease containing a URI domain. A hypothesis is proposed that the Ku homolog, together with the associated gene products, comprise a previously unrecognized prokaryotic system for repair of double-strand breaks in DNA.

Amino Acid Motifs↗

[A code governing specific binding of regulatory proteins to DNA and structure of stereospecific sites of regulatory proteins].

A model is proposed for the structure of stereospecific sites in regulatory proteins. On its basis a possible code is suggested that governs the binding of regulatory proteins at specific control sites on DNA. Stereospecific sites of regulatory proteins are assumed to contain pairs of antiparallel polypeptide chain segments which form a right-hand twisted antiparallel beta-sheet, with single-stranded regions at the ends of the beta-structure. The model predicts that binding reaction between a regulatory protein and double-helical DNA is a cooperative phenomenon and is accompanied by significant structural alteration at the stereospecific site of the protein. Half of hydrogen bonds normally existing in beta-structure are broken upon complex formation with DNA and a new set of hydrogen bonds is formed between polypeptide amide groups and DNA base pairs. In a stereospecific site, one chain (t-chain) is attached through hydrogen bonds to the carbonyl oxygens of pyramides and N3 adenines lying in one DNA strand, while the second polypeptide chain (g chain) is hydrogen bonded to the 2-amino groups of guanine residues lying in the opposite DNA strand. The amide groups serve as specific reaction sites being hydrogen bond acceptors in g-chain and hydrogen bond donors in t-chain. The single-stranded portions of t- and g-chains lying in neighbouring subunits of regulatory protein interact with each other forming deformed beta-sheets. The recognition of regulatory sequences by proteins is based on the structural complementarity between stereospecific sites of regulatory proteins and base pairs sequences at the control sites. An essential feature of these sequences is the asymmetrical distribution of guanine residues between the two DNA strands. The code predicts that there are six fundamental amino acid residues (serine, threonine, asparagine, histidine, glutamine and cysteine) whose sequence in stereospecific site determines the base pair sequence to which a given regulatory protein would bind preferentially. The code states a correspondence between four amino acid residues at the stereospecific site of regulatory protein with the two residues being in t- and g-segments, respectively, and AT(GC) base pair at the control site. It is thus possible to determine which amino acid residues in the repressor and which base pairs in the operator DNA are involved in specific interactions with each other, as exemplified by lac repressor binding to lac operator.

Amino Acid Sequence↗

The 24 kDa outer envelope membrane protein from spinach chloroplasts: molecular cloning, in vivo expression and import pathway of a protein with unusual properties.

The 24 kDa outer envelope membrane protein of spinach chloroplasts (omp24) represents a major constituent of this membrane. Sequences of tryptic and endoprotease Glu-C peptides derived from omp24 allowed the design of oligonucleotides which were used to generate a DNA fragment by polymerase chain reaction using spinach cDNA as template. This fragment served as a probe to screen a cDNA library for a full-length clone of the omp24 coding sequence. The protein predicted from the complete sequence only has 148 amino acids and a molecular mass of 16294 Da. It is an acidic protein (calculated isoelectric point 4.8) with a high content of proline residues. Expression of the coding sequence in Escherichia coli and characterization of the purified recombinant protein produced revealed that the overestimation of its molecular mass by SDS-PAGE (ca. 25 kDa) is due to its abnormal amino acid composition. Despite its rather low hydrophobicity (polarity index 49%), omp24 appears to be deeply embedded in the outer membrane. Insertion of omp24 into the membrane proceeds almost independently of surface receptors or targeting sequence but, in contrast to other known outer envelope membrane proteins, is stimulated by ATP.

Amino Acid Sequence↗

Identification and recombinant expression of glyceraldehyde-3-phosphate dehydrogenase of Plasmodium falciparum.

The gene coding for the cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12) was isolated from Plasmodium falciparum. The gene contains 1 intron and the A+T content is characteristic for the codon usage of P. falciparum. The predicted open reading frame codes for 337 amino acids (36651Da) and is 63.5% identical to the human erythrocytic GAPDH. GAPDH sequences from several field isolates of P. falciparum displayed 100% conservation. Phylogenetic analysis supports the hypothesis that dinoflagellates and Plasmodium are closely related. The protein encoded by the pfGAPDH was expressed recombinantly in Escherichia coli and exhibited enzymatic activity with NAD(+) but not with NADP(+) as cofactor. Antiserum raised against the recombinantly expressed enzyme detected specifically all developmental stages of cultured P. falciparum blood-stage parasites.

Amino Acid Sequence↗

Reaction-based model describing competitive sorption and transport of Cd, Zn, and Ni in an acidic soil.

Predicting the mobility of heavy metals in soils requires models that accurately describe metal adsorption in the presence of competing cations. They should also be easily adjustable to specific soil materials and applicable in reactive transport codes. In this study, Cd adsorption to an acidic soil material was investigated over a wide concentration range (10(-8) to 10(-2) M CdCl2) in the presence of different background electrolytes (10(-4) to 10(-2) M CaCl2 or MgCl2 or 0.05 to 0.5 M NaCl). The adsorption experiments were conducted at pH values between 4.6 and 6.5 A reaction-based sorption model was developed using a combination of nonspecific cation exchange reactions and competitive sorption reactions to sites with high affinity for heavy metals. This combined cation exchange/specific sorption (CESS) model accurately described the entire Cd sorption data set. Coupled to a solute transport code, the model accurately predicted Cd breakthrough curves obtained in column transport experiments. The model was further extended to describe competitive sorption and transport of Cd, Zn, and Ni. At pH 4.6, both Zn and Ni exhibited similar sorption and transport behavior as observed for Cd. In all transport experiments conducted under acidic conditions, heavy metal adsorption was shown to be reversible and kinetic effects were negligible within time periods ranging from hours up to four weeks.

Adsorption↗

Better prediction of sub-cellular localization by combining evolutionary and structural information.

The native sub-cellular compartment of a protein is one aspect of its function. Thus, predicting localization is an important step toward predicting function. Short zip code-like sequence fragments regulate some of the shuttling between compartments. Cataloguing and predicting such motifs is the most accurate means of determining localization in silico. However, only few motifs are currently known, and not all the trafficking appears regulated in this way. The amino acid composition of a protein correlates with its localization. All general prediction methods employed this observation. Here, we explored the evolutionary information contained in multiple alignments and aspects of protein structure to predict localization in absence of homology and targeting motifs. Our final system combined statistical rules and a variety of neural networks to achieve an overall four-state accuracy above 65%, a significant improvement over systems using only composition. The system was at its best for extra-cellular and nuclear proteins; it was significantly less accurate than TargetP for mitochondrial proteins. Interestingly, all methods that were developed on SWISS-PROT sequences failed grossly when fed with sequences from proteins of known structures taken from PDB. We therefore developed two separate systems: one for proteins of known structure and one for proteins of unknown structure. Finally, we applied the PDB-based system along with homology-based inferences and automatic text analysis to annotate all eukaryotic proteins in the PDB (http://cubic.bioc.columbia.edu/db/LOC3D). We imagine that this pilot method-certainly in combination with similar tools-may be valuable target selection in structural genomics.

Algorithms↗

The complete sequence of a 9000 bp fragment of the right arm of Saccharomyces cerevisiae chromosome VII contains four previously unknown open reading frames.

We report the sequence of a 9000 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of the sequence revealed four complete previously unknown open reading frames, which were named G7587, G7589, G7591 and G7594 following standard rules for provisional nomenclature. Outstanding features of some of these proteins were the homology of the putative protein coded by G7589 with proteins involved in transcription regulation and the transmembrane domains predicted in the putative protein coded by G7591.

Amino Acid Sequence↗

Mutation analysis of the BRCA2 gene in 49 site-specific breast cancer families.

The hereditary breast cancer gene BRCA2 was recently cloned and is believed to account for almost half of site-specific breast cancer families and the majority of male breast cancer families. We screened 49 site-specific breast cancer families for mutations in the BRCA2 gene using single strand conformation analysis (SSCA) followed by direct sequencing. We found mutations in eight families, including all four families with male breast cancer. The eight mutations were small deletions with the exception of a single nonsense mutation, an all were predicted to interrupt the BRCA2 coding sequence and to lead to a truncated protein product. Other factors which predicted the presence of a BRCA2 mutation included a case of breast cancer diagnosed at age 35 or below (P = 0.01) and a family history of pancreatic cancer (P = 0.03). Two mutations were seen twice, including a 8535delAG, which was detected in two French Canadian families. Our results suggest the possibility that the proportion of site-specific breast cancer families attributable to BRCA2 may be overestimated.

Adult↗

Standardized color-coded scales for anterior and posterior elevation maps of scanning slit corneal topography.

PURPOSE: To find the most appropriate color-coded scales for the anterior and posterior elevation maps of scanning slit topography in the screening of abnormal corneas such as keratoconus. DESIGN: Retrospective case-control study. PARTICIPANTS: Eighty eyes of 40 normal subjects and 175 eyes of 95 patients with keratoconus. INTERVENTION: Anterior and posterior corneal elevations were assessed using Orbscan 2. Best-fit sphere maps were drawn with several color-coded scales: 2-, 5-, 10-, and 20-microm height per each color interval. MAIN OUTCOME MEASURES: The maps were judged to be abnormal when more than three colors (discriminant number) were found within the central 3-mm area. For each color-coded scale, sensitivity, specificity, positive predictive value, negative predictive value, and sensitivity + specificity were calculated. After determining the most appropriate color-coded scales for the anterior and posterior elevation maps, validity of the discriminant number was assessed. By varying the discriminant number from two to eight, receiver operator characteristic (ROC) curves were created using the sensitivity and specificity for each threshold number. RESULTS: The highest sensitivity + specificity values and highly balanced predictive values were obtained with the 10- and 20-microm scales for the anterior and posterior elevation maps, respectively. The ROC curve analyses showed that the best discriminant color number is three, indicating that maps with four or more colors within the central 3-mm area are judged abnormal in screening. CONCLUSIONS: The 10- and 20-microm interval color scales are most appropriate for the anterior and posterior elevation maps of the scanning slit topography, respectively.

Adolescent↗

Pattern separation and synchronization in spiking associative memories and visual areas.

Scene analysis in the mammalian visual system, conceived as a distributed and parallel process, faces the so-called binding problem. As a possible solution, the temporal correlation hypothesis has been suggested and implemented in phase-coding models. We propose an alternative model that reproduces experimental findings of synchronized and desynchronized fast oscillations more closely. This model is based on technical considerations concerning improved pattern separation in associative memories on the one hand, and on known properties of the visual cortex on the other. It consists of two reciprocally connected areas, one corresponding to a peripheral visual area (P), the other a central association area (C). P implements the orientation-selective subsystem of the primary visual cortex, while C was modeled as an associative memory with connections formed by Hebbian learning of all assemblies corresponding to stimulus objects. Spiking neurons including habituation and correlated noise were incorporated as well as realistic synaptic delays. Three learned stimuli were presented simultaneously and correlation analysis was performed on spike recordings. Generally, we found two states of activity: (i) relatively slow and unordered oscillations at about 20-25 Hz, synchronized only within small regions; and (ii) faster and more precise oscillations around 50-60 Hz, synchronized over the whole simulated area. The neuron groups representing one stimulus tended to be simultaneously in either the slow or the fast state. At each particular time, only one assembly was found to be in the fast state. Activation of the three assemblies switched on a time scale of 100 ms. This can be interpreted as self-generated attention switching. On the time scale corresponding to gamma oscillations, cross correlations between local neuron groups were either modulated or flat. Modulated correlograms resulted if the groups coded features corresponding to a common object. Otherwise, the correlograms remained flat. This behavior is in agreement with experimental results, while phase-code models would generally predict modulated correlations also in the case of different objects. Furthermore, we derive a technical version from our biological associative memory model that accomplishes fast pattern separation parallel in O(log2 n) steps for n neurons and sparse coding.

Action Potentials↗

Computer simulation for prediction of performance and thermodynamic parameters of high energy materials.

A new code viz., Linear Output Thermodynamic User-friendly Software for Energetic Systems (LOTUSES) developed during this work predicts the theoretical performance parameters such as density, detonation factor, velocity of detonation, detonation pressure and thermodynamic properties such as heat of detonation, heat of explosion, volume of explosion gaseous products. The same code also assists in the prediction of possible explosive decomposition products after explosion and power index. The developed code has been validated by calculating the parameters of standard explosives such as TNT, PETN, RDX, and HMX. Theoretically predicated parameters are accurate to the order of +/-5% deviation. To the best of our knowledge, no such code is reported in literature which can predict a wide range of characteristics of known/unknown explosives with minimum input parameters. The code can be used to obtain thermochemical and performance parameters of high energy materials (HEMs) with reasonable accuracy. The code has been developed in Visual Basic having enhanced windows environment, and thereby advantages over the conventional codes, written in Fortran. The theoretically predicted HEMs performance can be directly printed as well as stored in text (.txt) or HTML (.htm) or Microsoft Word (.doc) or Adobe Acrobat (.pdf) format in the hard disk. The output can also be copied into the Random Access Memory as clipboard text which can be imported/pasted in other software as in the case of other codes.

Chemistry, Physical↗

Development and verification of a "virtual" cohort using the National VA Health Information System.

BACKGROUND: The VA's integrated electronic medical record makes it possible to create a "virtual" cohort of veterans with and without HIV infection to monitor trends in utilization, toxicity, and outcomes. OBJECTIVES: We sought to develop a virtual cohort of HIV-infected veterans by adapting an existing algorithm, verifying this algorithm against independent clinical data, and finally identifying demographically-similar HIV-uninfected comparators. RESEARCH DESIGN: Subjects were identified from VA administrative data in fiscal years 1998-2003 using a modified existing algorithm, then linked with Immunology Case Registry (ICR, the VA's HIV registry) and Pharmacy Benefits Management (centralized database of outpatient prescriptions) to verify accuracy of identification. The algorithm was modified to maximize positive predictive value (PPV) against ICR. Finally, 2 HIV-uninfected comparators were matched to each HIV-infected subject. RESULTS: Using a single HIV code, 30,564 subjects were identified (positive predictive value 69%). Modification to require >1 outpatient or 1 inpatient code improved the positive predictive value to 88%. The lack of confirmatory laboratory and pharmacy data for the majority of subjects with a single outpatient code also supported this change. Of subjects identified with the modified algorithm, 89% had confirmatory evidence. When the modified algorithm was applied to fiscal years 1997-2004, 33,420 HIV-infected subjects were identified. Two HIV-uninfected comparators were matched to each subject for an overall cohort sample of 100,260. CONCLUSIONS: In the HAART era, HIV-related codes are sufficient for identifying HIV-infected subjects from administrative data when patients with a single outpatient code are excluded. A large cohort of HIV-infected subjects and matched comparators can be identified from existing VA administrative datasets.

Adult↗

Accuracy of hospital discharge abstracts for identifying stroke.

BACKGROUND AND PURPOSE: Much of the available data on stroke occurrence, service use, and cost of care originated with hospital discharge abstracts. This article uses the unique resources of the Rochester Epidemiology Project to estimate the sensitivity and positive predictive value of hospital discharge abstracts for incident stroke. METHODS: The Rochester Stroke Registry was used to identify all confirmed first strokes (hospitalized and nonhospitalized) among Rochester residents for 1970, 1980, 1984, and 1989 (n = 364). The sensitivity of discharge abstracts was estimated by following these individuals for 12 months after stroke to determine the proportion assigned a discharge diagnosis of cerebrovascular disease (International Classification of Diseases [ICD] codes 430 through 438.9). The positive predictive value of discharge abstracts was assessed by identifying all hospitalizations of Rochester residents with an ICD code of 430-438.9 in 1970, 1980, and 1989 (n = 377). Events were categorized as incident stroke, recurrent stroke, stroke sequelae, or nonstroke after review of the complete community-based medical record by a neurologist. RESULTS: Only 86% (n = 313) of all first-stroke patients in 1970, 1980, 1984, and 1989 were hospitalized. Of hospitalized patients, only 76% were assigned a principal discharge diagnosis code of 430-438.9. Fatal strokes and those occurring during a hospitalization were less likely to be identified. Among all hospitalizations of Rochester residents in 1970, 1980, and 1989, there were 377 with a principal diagnosis code of 430-438.9. Less than half (n = 177) were determined by the neurologist to be incident stroke; only 60% (n = 225) were either incident or recurrent stroke. Comparison of alternative approaches showed the validity of discharge abstracts was enhanced by increasing the number of diagnoses and excluding codes with poor positive predictive value. CONCLUSIONS: This study provides previously unavailable estimates of the sensitivity of stroke-coded hospitalizations for a US community. A model for improving the sensitivity and positive predictive value of discharge abstracts is presented.

Aged↗

Stimulus and response representations underlying orthogonal stimulus-response compatibility effects.

One of the most important findings in recent years regarding response selection is that stimulus-response compatibility (SRC) effects occur for situations in which stimulus and response sets vary along orthogonal dimensions. For two-choice tasks, two types of orthogonal SRC effects are found: an overall advantage for the up-right/down-left mapping, and mapping preferences that vary as a function of position of the response apparatus and responding hand. We review evidence regarding the nature of both types of orthogonal SRC effects. Only asymmetric coding accounts have been proposed for the up-right/down-left advantage, and the evidence indicates that this asymmetry is a property of both verbal and spatial codes. Motoric and coding accounts, as well as a hybrid account based on end-state comfort, have been proposed for the second type of orthogonal SRC effect. In this case, the effects of response-apparatus position, hand, and hand posture conform more closely to predictions of the asymmetric coding accounts than to those of the motoric accounts. We also evaluate the mechanisms proposed by the alternative accounts in terms of related literature on the properties of spatial and verbal codes. Evidence indicates that spatial information is represented in categorical and coordinate codes, and both categorical spatial codes and verbal codes are asymmetric. Experiments on mental rotation suggest that it is unlikely that the direction of rotation is determined automatically by movement constraints, as the end-state comfort hypothesis suggests. An explanation in terms of salient features and referential coding can accommodate the range of orthogonal SRC effects.

Functional Laterality↗

Genotyping of the arylamine N-acetyltransferase polymorphism in the prediction of idiosyncratic reactions to trimethoprim-sulfamethoxazole in infants.

The pathogenesis of hypersensitivity to trimethoprim-sulfamethoxazole (TMP-SMX) is supposed to be associated with the slow acetylation phenotype. This pharmacogenetic defect is associated with the mutations of the arylamine N-acetyltransferase (NAT2) encoding gene. The aim of the study was to compare the usefulness of the acetylation phenotype and NAT2 coding genotype in the prediction of idiosyncratic reaction to Cotrimoxazole in infants. The study was carried out in the group of 20 infants, aged 2-12 months (mean age 6.3 months) treated with Cotrimoxazole, administered at 100 mg/kg b.w./24 h doses. In seven children (35%) no adverse effects of the treatment have been observed, whereas in 13 (65%) children various adverse effects occurred as a result of the therapy, such as rash (4 children), granulocytopenia with anemization (5 children) or liver impairment (4 children). The acetylation phenotype of each child was determined on the basis of urine of N-acetyl isoniazid/isoniazid ratio, after ingestion of isoniazid as a model drug. Furthermore we used polymerase chain reaction (PCR) followed by the analysis of restriction fragments length polymorphism (RFLP) technique to identify the known mutant alleles of the NAT2 gene. It has been presumed that the genotype determining fast acetylation contains at least one of wild-type allele. No correlation has been found between the observed adverse effects of Cotrimoxazole and age, gender and acetylation phenotype. However, it has been demonstrated that the risk of adverse effects of Cotrimoxazole is considerably higher in children with mutations of the NAT2 encoding gene. The comparison of the results from PCR-RFLP genotyping with phenotyping suggested that in infants, the NAT2 genotype rather than phenotype provides the basis for the detection of hypersensitivity to TMP-SMX.

Acetylation↗

Frequency code: orofacial correlates of fundamental frequency.

In the human voice, lip retraction as in smiling can be associated with high fundamental (Fo) and formant frequencies. The aim of this study was to investigate under naturalistic conditions the cross-species generality of the frequency code hypothesis and related orofacial correlates in Fo. Digital spectral, spectrographic, and cinegraphic measurements were made of spontaneous chimpanzee vocalizations and orofacial movements produced and recorded in the field. A significant decline in Fo was found in submissive-scream-to-aggressive-waahbark transitions as predicted by the frequency code. Teeth and lip opening distances during sounds were positively correlated with their duration, Fo, frequency rise and tempo. These positive correlates and a trivariate regression between orofacial opening and Fo give support to the coordination of these appeasing facial and vocal features proposed in the frequency code hypothesis.

Acoustics↗

Sparse basis selection: new results and application to adaptive prediction of video source traffic.

Real-time prediction of video source traffic is an important step in many network management tasks such as dynamic bandwidth allocation and end-to-end quality-of-service (QoS) control strategies. In this paper, an adaptive prediction model for MPEG-coded traffic is developed. A novel technology is used, first developed in the signal processing community, called sparse basis selection. It is based on selecting a small subset of inputs (basis) from among a large dictionary of possible inputs. A new sparse basis selection algorithm is developed that is based on efficiently updating the input selection adaptively. When a new measurement is received, the proposed algorithm updates the selected inputs in a recursive manner. Thus, adaptability is not only in the weight adjustment, but also in the dynamic update of the inputs. The algorithm is applied to the problem of single-step-ahead prediction of MPEG-coded video source traffic, and the developed method achieves improved results, as compared to the published results in the literature. The present analysis indicates that the adaptive feature of the developed algorithm seems to add significant overall value.

Algorithms↗