Risk assessment of recent Egyptian H5N1 influenza viruses.

Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are enzootic in poultry populations in different parts of the world, and have caused numerous human infections in recent years, particularly in Egypt. However, no sustained human-to-human transmission of these viruses has yet been reported. We tested nine naturally occurring Egyptian H5N1 viruses (isolated in 2014-2015) in ferrets and found that three of them transmitted via respiratory droplets, causing a fatal infection in one of the exposed animals. All isolates were sensitive to neuraminidase inhibitors. However, these viruses were not transmitted via respiratory droplets in three additional transmission experiments in ferrets. Currently, we do not know if the efficiency of transmission is very low or if subtle differences in experimental parameters contributed to these inconsistent results. Nonetheless, our findings heighten concern regarding the pandemic potential of recent Egyptian H5N1 influenza viruses.

Brute force meets Bruno force in parameter optimisation: introduction of novel constraints for parameter accuracy improvement by symbolic computation.

Recent remarkable advances in computer performance have enabled us to estimate parameter values by the huge power of numerical computation, the so-called 'Brute force', resulting in the high-speed simultaneous estimation of a large number of parameter values. However, these advancements have not been fully utilised to improve the accuracy of parameter estimation. Here the authors review a novel method for parameter estimation using symbolic computation power, 'Bruno force', named after Bruno Buchberger, who found the Gröbner base. In the method, the objective functions combining the symbolic computation techniques are formulated. First, the authors utilise a symbolic computation technique, differential elimination, which symbolically reduces an equivalent system of differential equations to a system in a given model. Second, since its equivalent system is frequently composed of large equations, the system is further simplified by another symbolic computation. The performance of the authors' method for parameter accuracy improvement is illustrated by two representative models in biology, a simple cascade model and a negative feedback model in comparison with the previous numerical methods. Finally, the limits and extensions of the authors' method are discussed, in terms of the possible power of 'Bruno force' for the development of a new horizon in parameter estimation.

Period-phase map: two-dimensional selection of circadian rhythm-related genes.

Many genes related to the circadian rhythm, especially those involved in phase shifts induced by different environmental stimuli, still remain enigmatic. In this study, the authors monitored the expression of rat genes measured with multiple phase-resetting stimuli, and developed a technique to extract the candidate genes for the changes in circadian rhythm by the stimuli, from microarray data. First, the spectra for the time series of gene expression were estimated by fast Fourier transform, and then two fitting methods, the random period fitting method and the conditional curve fitting method, using the estimated periods as the initial values, were applied to the control and the stimulated expression data to estimate the periods and the phases. Finally, by comparing the two sets of periods and phases, the period change and the phase shift by stimuli were estimated to extract the candidate genes related to the master clock, by mapping the period change and the phase shift on a two-dimensional space, a period-phase map (PPM). As an indirect validation of the genes selected by our method, the significant enrichment of extracted gene clusters on the PPM was further evaluated, in terms of biological function. As a result, the gene clusters related to photoreceptors and neural regulation emerged on the PPM, thus implying the relationships in the stimulus response of the master clock that resides in the brain at the intersection of the optic nerves. Thus, the present approach is a feasible means to explore the oscillatory genes related to stimulus responses.

System for automatically inferring a genetic netwerk from expression profiles.

A system is constructed to automatically infer a genetic network byapplication of graphical Gaussian modeling to the expression profiledata. Our system is composed of two parts: one part is automaticdetermination of cluster boundaries of profiles in hierarchicalclustering, and another part is inference of a genetic network byapplication of graphical Gaussian modeling to the clustered profiles.Since thousands of or tens of thousands of gene expression profiles aremeasured under only one hundred conditions, the profiles naturally showsome similar patterns. Therefore, a preprocessing for systematicallyclustering the profiles is prerequisite to infer the relationship betweenthe genes. For this purpose, a method for automatic determination ofcluster boundaries is newly developed without any biological knowledgeand any additional analyses. Then, the profiles for each cluster areanalyzed by graphical Gaussian modeling to infer the relationship betweenthe clusters. Thus, our system automatically provides a graph betweenclusters only by input the profile data. The performance of the presentsystem is validated by 2467 profiles from yeast genes. The clusters andthe genetic network obtained by our system are discussed in terms of thegene function and the known regulatory relationship between genes.

Statistical estimation of cluster boundaries in gene expression profile data.

MOTIVATION: Gene expression profile data are rapidly accumulating due to advances in microarray techniques. The abundant data are analyzed by clustering procedures to extract the useful information about the genes inherent in the data. In the clustering analyses, the systematic determination of the boundaries of gene clusters, instead of by visual inspection and biological knowledge, still remains challenging. RESULTS: We propose a statistical procedure to estimate the number of clusters in the hierarchical clustering of the expression profiles. Following the hierarchical clustering, the statistical property of the profiles at the node in the dendrogram is evaluated by a statistics-based value: the variance inflation factor in the multiple regression analysis. The evaluation leads to an automatic determination of the cluster boundaries without any additional analyses and any biological knowledge of the measured genes. The performance of the present procedure is demonstrated on the profiles of 2467 yeast genes, with very promising results. AVAILABILITY: A set of programs will be electronically sent upon request. CONTACT: horimoto@post.saga-med.ac.jp; toh@beri.co.jp

Capsid protein gene variation among feline calicivirus isolates.

We amplified the capsid protein gene fragments of 30 Japanese isolates of feline calicivirus (FCV), including the C, D, and E regions, by reverse transcription-polymerase chain reaction (RT-PCR), followed by direct sequencing. Alignment of the predicted amino acid sequences, together with other published sequences from the isolates obtained in other countries, demonstrated a marked heterogeneity among the isolates, confirming the current definition of hypervariable regions within the capsid protein: these regions give rise to the antigenic variations seen in FCV isolates. Phylogenetic analysis of the nucleotide sequences could not identify significant geographically or temporally separated clusters of FCV isolates, supporting the theory of a single genotype.

Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes.

MOTIVATION: Following an extensive search for orthologous genes between the complete genomes from archaea and bacteria, the spatial association of the orthologs has been investigated in terms of synteny, the conservation of the order of neighboring genes. However, the relationships between the relative locations of remote orthologs over entire genomes have not been shown. RESULTS: Comprehensive comparisons between the locations of orthologs on nineteen archaeal and bacterial genomes are presented by the location to location correspondence based on the gene-location distance. When the two genomes are rotated such that a pair of orthologs with the shortest distance is set in the same angle, a statistically significant number of orthologs maintain their relative locations between the genomes. Even by the short distances at the 5% significance level, the rotations are restricted within a narrow range, suggesting an intrinsic angle for realizing similar locations between the orthologs in each genome pair. Furthermore, the rotations in the restricted range agree with the replication origin and terminus sites for the analyzed genomes where such sites are known. The relationship between location-maintained orthologs and gene function is also discussed.

Identification of the porcine cytomegalovirus major capsid protein gene.

A major capsid protein (MCP) gene homologue of porcine cytomegalovirus (PCMV) was identified. Sequence analysis indicated that the PCMV MCP gene is 4,026 nucleotides in length encoding a protein of 1,341 amino acid residues. The predicted molecular weight of the PCMV MCP is 151,456 Da, equivalent to those of other herpesvirus MCP counterparts. Phylogenetic analysis using herpesviral MCP gene sequences confirmed that PCMV is a betaherpesvirus with higher homology with human herpesvirus-6 and -7 than human and mouse cytomegaloviruses. The serum of pig experimentally infected with PCMV did not react with bacterially expressed MCP, suggesting that the PCMV MCP may not be related to the humoral immune response in the course of PCMV infection. Also, we established polymerase chain reaction (PCR) protocols using primers corresponding to MCP gene sequences for detection of PCMV infection. The PCR protocol would be effective for the diagnosis of slow-growing PCMV infection, for which traditional methods involving virus-isolation are not useful.

Local multiple alignment of numerical sequences: detection of subtle motifs from protein sequences and structures.

This paper presents a new method to find motifs from multiple protein sequences and multiple protein structures. The method consists of two parts: quantification and local multiple alignment. In the former part, protein sequences and protein structures are transformed into sequences of real numbers and real vectors respectively. In the latter part, fixed length regions having similar shapes are located. A Gibbs sampling algorithm for sequences of real numbers/vectors is newly developed for finding common regions. The results of the comparison with a standard Gibbs sampling program show that the method is particularly useful when structural information is available.

Analysis of porcine cytomegalovirus DNA polymerase by consensus primer PCR.

We used a consensus primer PCR method to amplify a region of herpesviral DNA-directed DNA polymerase gene using degenerate primers for initial characterization of the porcine cytomegalovirus (PCMV) genome. The sequence of the PCR product from PCMV DNA template and its alignment with other herpesvirus DNA polymerase counterparts showed that both conserved amino acid residues and conservative amino acid substitutions are in parallel. Phylogenetic analysis revealed that PCMV should be included in the clade comprising human herpesvirus 6 and 7, rather than human and mouse cytomegaloviruses, in Betaherpesvirus subfamily.

[Observation of physiological change in the human ciliary body using an ultrasound biomicroscope during accommodation].

PURPOSE: To evaluate changes in the ciliary body during accommodation using an ultrasound biomicroscope (UBM). SUBJECTS AND METHODS: Eleven healthy persons, aged from 24 to 33 years, served as subjects. They were asked to lie in the supine position and to fixate a target placed on the ceiling 2 m above with the left eye. A concave lens with the power of -6 to -8 diopters was then placed before the fixating left eye. The thickness of the ciliary body in the right eye was measured by UBM in the nonaccommodative and accommodative states. FINDINGS: The anterior chamber in the right eye became significantly shallow during accommodation. The thickness of the ciliary body significantly increased during accommodation at 0.5 mm and 1.0 mm posterior to the scleral spur. It significantly decreased at 2.0 mm, 2.5 mm and 3.0 mm posterior to the scleral spur. CONCLUSION: During induced accommodation in the left eye, the anterior portion of the ciliary body in the right eye increased and the posterior portion decreased in thickness. The findings imply that the circular ciliary muscles are mainly involved in accommodation and not the longitudinal muscles.

A method for comparing circular genomes from gene locations: application to mitochondrial genomes.

MOTIVATION: Data on the entire structures of organelle and bacterial genomes, most of which are known to be circular, have accumulated at a rapid pace. This information enables us to utilize the locations of homologous gene pairs for measuring the dissimilarity between complete genomic structures. RESULTS: A macroscopic distance is presented for comparing circular genomes from their overall structures, on the basis of the locations of two pairs of homologous genes on the compared genomes. The novel aspect of our method is that the comparison between the genomes automatically reveals a relationship based on the information on all gene locations, by incorporating the mobility of each gene, which includes not only the gene order, but also the relative location between gene pairs. The plausibility of the newly defined distances is evaluated by means of 44 mitochondrial genomes. The genome distance shows high performance for quantitatively describing the differences between the gene organizations of the genomes. AVAILABILITY: Since the programs implementing these calculations require well-arranged gene organization data, they have not been released yet. However, one of the authors will analyze circular genomes upon request. Data on the gene organizations may be submitted electronically to the address below.

Sodium hyaluronate eyedrops enhance tear film stability.

Sodium hyaluronate eyedrops can relieve various dry eye symptoms by prolonging the stability of the precorneal tear film. To determine the most effective concentration of sodium hyaluronate, we studied the concentration-dependent effects of sodium hyaluronate eyedrops on the precorneal tear film breakup time (BUT) in 12 volunteers. These subjects had a BUT of 10 seconds or less and a low tear volume determined with the phenol red thread test. They received four different concentrations of sodium hyaluronate eyedrops (0, 0.05, 0.1 and 0.3%). BUT was measured noninvasively using a non-contact specular microscope before the sodium hyaluronate eyedrop instillation and again after 5, 15, 30, 60, 120 and 180 minutes. The tear film stability period was prolonged significantly with 0.1% and 0.3% eyedrops at all measurement times (P < 0.05), while the eyes treated with 0% and 0.05% eyedrops showed no significant prolongation of tear film stability at any measurement times. The findings of this study confirm that sodium hyaluronate at a concentration of at least 0.1% is required to delay the breakup of the precorneal tear film.

Resolution of Fusarium sporotrichioides Proteins by Two-Dimensional Polyacrylamide Gel Electrophoresis and Identification by Sequence Homology Comparison in Protein Data Base.

Proteins from Fusarium sporotrichioides M-1-1, a T2-toxin-producing strain, were separated by two-dimensional polyacrylamide gel electrophoresis. One thousand two hundred and forty-four protein spots were resolved and 103 protein spots were subjected to N-terminal sequencing. Fifty-eight protein spots were sequenced and 48 proteins were observed to have blocked N termini. Forty out of 58 sequenced proteins were identified by homology search against the PIR protein sequence data base and protein superfamily data base, while the residual 18 sequences were not identified. Twenty-seven of the N-terminal-blocked proteins were subjected to mild anhydrous hydrazine vapor deblocking. Twenty-four spots were not deblocked indicating the presence of acyl groups at the N termini, while 3 proteins were deblocked showing the blocked group to be pyrroglutamyl carboxylic acid residues. The results can provide a more global view of cellular genetic expression than any other technique. The created data may offer a unique opportunity to link information with DNA sequence data. Copyright 1995 S. Karger AG, Basel

Prevalence of dry eye in Japanese eye centers.

BACKGROUND: The purpose of the investigation was to ascertain the prevalence of dry eye in new outpatients. METHODS: A total of 2127 consecutive new outpatients seen in eight Japanese centers from April 1992 to January 1993 underwent comprehensive examinations, including double vital staining and measurement of tear film break-up time, basal tear secretion, and tear clearance. Dry eye was diagnosed if patients had abnormalities of both the tear film and the ocular surface. RESULTS: Three hundred fifty-nine patients (17%) had dry eye. There was no seasonal pattern for dry eye. The condition was significantly more common in Tokyo than in suburban areas (P < 0.01). The prevalence of dry eye in visual display terminal (VDT) users and contact lens (CL) wearers was significantly higher than in non-VDT users and non-CL wearers (P < 0.05 and P < 0.02, respectively). CONCLUSION: Our findings suggest that dry eye is one of the most common ocular disorders encountered by physicians. Furthermore, if patients use VDTs or wear CLs, the likelihood of dry eye occurring is higher.

A simple procedure for assigning a sequence motif with an obscure pattern: application to the basic/helix-loop-helix motif.

We have developed a simple method to assign a sequence motif with an obscure pattern. Given a multiple sequence alignment for a region of protein that is known or strongly believed to have the same secondary and tertiary structures, the quantification method by principal component analysis is designed to find the regions most likely to have the same structure in a protein outside of the original set. The potential of this newly developed method was evaluated with reference to the known basic/helix-loop-helix (bHLH) motifs, and its characteristics were discussed with four obscure but well-defined motifs and compared with the other methods for searching sequence motifs. The method was also applied to assign the bHLH motif in Epstein-Barr virus nuclear antigen 1 (EBNA-1). This application revealed one candidate for the basic/helix 1 region and two candidates for the helix 2 region in the bHLH motif, within the region from amino acid residues 460 to 600, which is in good agreement with our previous experimental studies on the DNA binding region of EBNA-1. The basic/helix-loop-helix-loop-helix structure thus assigned suggests a function of EBNA-1 which is associated with both replication and transcription.