Characterization of the oral and faecal microbiota associated with atopic dermatitis in dogs selected from a purebred Shiba Inu colony.

Atopic dermatitis (AD) is a chronic and relapsing multifactorial inflammatory skin disease that also affects dogs. The oral and gut microbiota are associated with many disorders, including allergy. Few studies have addressed the oral and gut microbiota in dogs, although the skin microbiota has been studied relatively well in these animals. Here, we studied the AD-associated oral and gut microbiota in 16 healthy and 9 AD dogs from a purebred Shiba Inu colony. We found that the diversity of the oral microbiota was significantly different among the dogs, whereas no significant difference was observed in the gut microbiota. Moreover, a differential abundance analysis detected the Family_XIII_AD3011_group (Anaerovoracaceae) in the gut microbiota of AD dogs; however, no bacterial taxa were detected in the oral microbiota. Third, the comparison of the microbial co-occurrence patterns between AD and healthy dogs identified differential networks in which the bacteria in the oral microbiota that were most strongly associated with AD were related to human periodontitis, whereas those in the gut microbiota were related to dysbiosis and gut inflammation. These results suggest that AD can alter the oral and gut microbiota in dogs.

The development of Weinstein's noise sensitivity scale.

Many studies have shown the significant correlation between noise annoyance and noise sensitivity identified by Weinstein's noise sensitivity scale (WNS). However, the validity of the scale has not been sufficiently assessed. This study was designed to investigate the validity of each question in WNS and to develop a more valid noise sensitivity measurement scale. A questionnaire study was conducted in a residential area along trunk roads in Kusatsu, Japan, and 301 responses were collected. In this paper, noise sensitivity was defined as the factor that induced individual variability in reactions caused by noise exposure and that is not affected by the noise exposure. The relationship between noise exposure and answers to each question in WNS was investigated by multiple logistic regression analysis, and the influence of response bias on the score of WNS was examined. The results showed that WNS contained some questions that were inappropriately related to noise exposure level and that the score was affected by response bias. The reported correlation between annoyance and the score of WNS could be confounded by noise exposure and response bias. A noise sensitivity measurement scale named WNS-6B was newly developed, excluding the biased questions from the original WNS and applying binary coding to six-response options in order to reduce the response bias. WNS-6B seemed to be more appropriate to assess noise sensitivity than the original scale.

The flip side of perception-action coupling: locomotor experience and the ontogeny of visual-postural coupling.

The possible role of motor development on psychological function is once again a topic of great theoretical and practical importance. The revival of this issue has stemmed from a different approach to the topic, away from Gesell's interest in the long-term prediction of psychological functions from early motoric assessments, toward an attempt to understand how the acquisition of motor skills orchestrates psychological changes. This paper describes how the acquisition of one motor skill, prone locomotion, has been linked to developmental changes in an infant's ability to regulate posture based on information available in patterns of optic flow. It is argued that the onset of prone locomotion presses the infant to differentiate spatially delimited regions of optic flow to effectively and efficiently control the important subtasks nested within the larger task of locomotion, namely, steering, attending to the surface of support, and maintaining postural control. Following this argument, a research program is described that aims to determine if locomotor experience is causally linked to improvements in the ability to functionalize peripheral optic flow for postural control or whether locomotor experience is merely a maturational forecaster of such improvements. Finally, a hypothesis is put forward that links the emergence of wariness of heights to infants' ability to regulate posture on the basis of peripheral optic flow. The paper's overarching theoretical point is the principle of probabilistic epigenesis, which states that one developmental acquisition produces experiences that bring about a host of new developmental changes in the same and different domains.

Whole genome sequencing of meticillin-resistant Staphylococcus aureus.

BACKGROUND: Staphylococcus aureus is one of the major causes of community-acquired and hospital-acquired infections. It produces numerous toxins including superantigens that cause unique disease entities such as toxic-shock syndrome and staphylococcal scarlet fever, and has acquired resistance to practically all antibiotics. Whole genome analysis is a necessary step towards future development of countermeasures against this organism. METHODS: Whole genome sequences of two related S aureus strains (N315 and Mu50) were determined by shot-gun random sequencing. N315 is a meticillin-resistant S aureus (MRSA) strain isolated in 1982, and Mu50 is an MRSA strain with vancomycin resistance isolated in 1997. The open reading frames were identified by use of GAMBLER and GLIMMER programs, and annotation of each was done with a BLAST homology search, motif analysis, and protein localisation prediction. FINDINGS: The Staphylococcus genome was composed of a complex mixture of genes, many of which seem to have been acquired by lateral gene transfer. Most of the antibiotic resistance genes were carried either by plasmids or by mobile genetic elements including a unique resistance island. Three classes of new pathogenicity islands were identified in the genome: a toxic-shock-syndrome toxin island family, exotoxin islands, and enterotoxin islands. In the latter two pathogenicity islands, clusters of exotoxin and enterotoxin genes were found closely linked with other gene clusters encoding putative pathogenic factors. The analysis also identified 70 candidates for new virulence factors. INTERPRETATION: The remarkable ability of S aureus to acquire useful genes from various organisms was revealed through the observation of genome complexity and evidence of lateral gene transfer. Repeated duplication of genes encoding superantigens explains why S aureus is capable of infecting humans of diverse genetic backgrounds, eliciting severe immune reactions. Investigation of many newly identified gene products, including the 70 putative virulence factors, will greatly improve our understanding of the biology of staphylococci and the processes of infectious diseases caused by S aureus.

The role of p16-cyclin d/CDK-pRb pathway in the tumorigenesis of endometrioid-type endometrial carcinoma.

We analysed p16 gene alteration and p16, cyclin-dependent kinase 4 (CDK4), CDK6, cyclin D1, cyclin D2, cyclin D3 and retinoblastoma protein (pRb) expression in ten normal endometriums (PE), 18 endometrial hyperplasias (EH) and 35 endometrial cancers (EC). Two of ten PE (20%), nine of 18 EH (50.0%) and 29 of 35 EC (82.9%) exhibited p16 nuclear staining. p16 expression was significantly higher in EC than EH (P = 0.0119). In the six p16 (-) EC, one was considered to have reduced gene dosage consistent with possible homozygous deletion of the CDKN2 gene and three had methylation in 5'CpG island in the promoter region of the p16 gene, whereas none showed such reduced gene dosage and four had methylation in the nine p16 (-) EH. Strong CDK4 staining was observed in 12 of 35 EC (34.3%) and one of 18 EH (5.6%). The strong expression of CDK4 was higher in EC than in EH (P = 0.0399). The expression of CDK4 was higher in EH than PE (P = 0.0054). The abnormalities of p16-cyclin D/CDK-pRb pathway were detected in 18 of 35 EC (51.4%). In conclusion, the expression of p16 and CDK4 may be an early event in the neoplastic transformation of endometrial cancer.

Relations of empathy and social responsibility to guilt feelings among undergraduate students.

Empathy and social responsibility as related to guilt feelings were investigated among undergraduate students. Subjects (337 men and 353 women) were assessed for guilt feelings, empathy, and social responsibility. The Guilt Inventory was used to assess guilt feelings. Analysis indicated that scores on the two empathy subscales, Fantasy and Personal Distress, were related to rated Trait Guilt and State Guilt, whereas Social Responsibility scores were associated with those on Moral Stan dards of the Guilt Inventory.

Diversity of restriction-modification gene homologues in Helicobacter pylori.

The complete genome sequences of two Helicobacter pylori strains have recently become available. We have searched them for homologues of restriction-modification genes. One strain (26695) carried 52 such homologues, and the other (J99) carried 53. Their sequence alignments were arranged in the form of a phylogenetic tree and compared with the tree based on rRNA. The trees showed that the homologues are scattered among diverse groups of bacteria. They also revealed high polymorphism within the species--there are 42 pairs with high homology, 10 specific to 26695, and 11 specific to J99. Many of the restriction-modification homologues were characterized by a GC content lower than that of the average gene in the genome. Some of the restriction-modification homologues showed a different codon use bias from the average genes. These observations are interpreted in terms of horizontal transfer of the restriction-modification genes.

Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes.

The complete genome sequences of two closely related organisms--two Helicobacter pylori strains--have recently become available. Comparison of these genomes at single base pair level has suggested the presence of a mechanism for bacterial gene mobility--insertion with long target duplications. This mechanism is formally similar to classical transposon insertion, but the duplication is much longer, often in the range of 100bp. Restriction and/or modification enzyme genes are often within or adjacent to the insertion. A similar process may have mediated insertion of the cag(+) pathogenicity island in H. pylori. A similar structure was identified in comparisons between Neisseria meningitidis and Neisseria gonorrhoeae genomes. We hypothesize that this mechanism, as well as two other types of polymorphism linked with restriction-modification genes (insertion accompanied by target deletion and a tripartite structure composed of substitution/inversion/deletion), have resulted from attack by restriction enzymes on the chromosome.

Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms.

Recent work suggests that restriction-modification gene complexes are mobile genetic elements that insert themselves into the genome and cause various genome rearrangements. In the present work, the complete genome sequences of Pyrococcus horikoshii and Pyrococcus abyssi, two species in a genus of hyperthermophilic archaeon (archaebacterium), were compared to detect large genome polymorphisms linked with restriction-modification gene homologs. Sequence alignments, GC content analysis, and codon usage analysis demonstrated the diversity of these homologs and revealed a possible case of relatively recent acquisition (horizontal transfer). In two cases out of the six large polymorphisms identified, there was insertion of a DNA segment with a modification gene homolog, accompanied by target deletion (simple substitution). In two other cases, homologous DNA segments carrying a modification gene homolog were present at different locations in the two genomes (transposition). In both cases, substitution (insertion/deletion) in one of the two loci was accompanied by inversion of adjacent chromosomal segment. In the fifth case, substitution by a DNA segment carrying type I restriction, modification, and specificity gene homologs was likewise accompanied by adjacent inversion. In the last case, two homologous DNA segments, were found at different loci in the two genomes (transposition), but only one of them had insertion of a modification homolog and an unknown ORF. The possible relationship of these polymorphisms to attack by restriction enzymes on the chromosome will be discussed.

Shaping the genome--restriction-modification systems as mobile genetic elements.

A restriction enzyme gene is often linked to a modification methylase gene the role of which is to protect a recognition site on DNA from breakage by the former. Loss of some restriction-modification gene complexes leads to cell death through restriction breakage in the genome. Their behavior as genomic parasites/symbionts may explain the distribution of restriction sites and clarify certain aspects of bacterial recombination repair and mutagenesis. A comparison of bacterial genomes supports the hypothesis that restriction-modification gene complexes are mobile elements involved in various genome rearrangements and evolution.

Significant differences in the frequency of transcriptional units, types and numbers of repetitive elements, GC content, and the number of CpG islands between a 1010-kb G-band genomic segment on chromosome 9q31.3 and a 1200-kb R-band genomic segment on chromosome 3p21.3.

We determined the nucleotide sequence of the entire 1,010,525-bp insert contained in CEPH YAC clone 867e8. This human genomic segment was derived from chromosome 9q31.3 and corresponds to a G-band region. We compared this segment, in terms of structure, with a previously characterized 1,201,033-bp sequence in CEPH YAC936c1 that had come from a portion of human chromosome 3p21.3 corresponding to an R-band region. The two segments were significantly different with respect to the frequency of transcriptional units, the types and numbers of repetitive elements present, their GC content, and the number of CpG islands. Alu elements, GC content, and CpG islands all showed positive correlations with the abundance of exons, but the distribution of LINE1s did not. These observations might reflect an influence of the first three of these features on the functions or expression of genes in the respective regions. In addition to a novel gene (F36) lying at the centromeric end of the 9q segment, we found a cluster of placenta-specific genes within a small section (about 400 kb) on the telomeric side of YAC867e8. This cluster consisted of four apparently unrelated ESTs and two genes, pregnancy-associated plasma protein-A (PAPP-A) and a novel gene (tentatively named EST-YD1). Our characterization of the two chromosomal regions provided evidence that genes are not evenly distributed throughout the human genome, and that gene richness is correlated with the GC content and with the frequency of either Alu elements or CpG islands.

Characterization of a 1200-kb genomic segment of chromosome 3p22-p21.3.

We previously determined the nucleotide sequence and characterized the 685-kb proximal half of CEPH YAC936c1, which corresponds to a portion of human chromosome 3p21.3. In the study reported here, we characterized the remaining 515-kb of this YAC clone corresponding to the telomeric half of its human insert. The newly sequenced region contained a total of ten genes including six reported previously: phospholipase C delta 1 (PLCD1), human activin receptor type IIB (hActR-IIB), organic cation transporter-like 1 (OCTL1), organic cation transporter-like 2 (OCTL2), oxidative stress response 1 (OSR1), and human xylulokinase-like protein (XYLB). The remaining four genes present in the telomeric region included two known genes, MyD88 and ACAA, and two novel genes. One (designated ENGL) of the novel sequences was found to encode an amino-acid sequence homologous to the family of DNA/RNA endonucleases, especially endonuclease G. The other gene F56 revealed no significant homology to any known genes. These results disclosed complete physical and transcriptional maps of the 1200-kb region of 3p present in YAC 936c1.

DBGET/LinkDB: an integrated database retrieval system.

The integrated database retrieval system DBGET/LinkDB is the backbone of the Japanese GenomeNet service. DBGET is used to search and extract entries from a wide range of molecular biology databases, while LinkDB is used to search and compute links between entries in different databases. DBGET/LinkDB is designed to be a network distributed database system with an open architecture, which is suitable for incorporating local databases or establishing a specialized server environment. It also has an advantage of simple architecture allowing rapid daily updates of all the major databases. The WWW version of DBGET/LinkDB at GenomeNet is integrated with other search tools, such as BLAST, FASTA and MOTIF, and with local helper applications, such as RasMol. In addition to factual links between database entries, LinkDB is being extended to included similarity links and biological links toward computerization of logical reasoning processes.

A study for prevention of chronic fatigue. part 2. effects of strenuous physical exercise performed in a training camp on serum enzyme activity levels and subjective fatigue.

The principal objective of this paper is to develop a simple and rapid method of estimating levels of fatigue so that chronic fatigue can be prevented. Long-distance runners belonging to a successful corporate team (Group A; 25 males) and representative runners at the prefectural level (Group B; 14 males) participated in this study. We examined the effects of strenuous physical exercise on serum enzyme activity and the fatigue level felt by the runners (subjective fatigue).The following parameters were measured on two consecutive mornings during a training period: physical characteristics, serum-biochemistry using the dry-chemistry method, and subjective fatigue determined using the questionnaire regarding subjective symptoms authorized by the Japan Association of Industrial Health and the Profile of Mood State (POMS). Group A was divided into A-Senior (17 males; highest performance level) and A-Freshman (8 males) subgroups according to the length of employment within the corporation (one year or more and less than one year, respectively).The levels of serum aspartate aminotransferase (AST) and creatine kinase (CK) were significantly lower in the A-Senior group than the other groups and this group displayed the "iceberg" POMS profile at both examinations. Some significant correlations between the elements of POMS and serum enzyme activity levels were observed among all three groups during both examinations. The decline of serum CK levels tended to accompany a decrease in "Fatigue" according to POMS among 9 of 17 members of the A-Senior group. This tendency between the A-Senior and the A-Freshman groups statistically differed according to theX - square analysis.Our results suggest that the effects of physical stress on serum enzyme activity levels and subjective fatigue are affected by performance levels. Physical fatigue seemed to be reflected by serum CK levels. Monitoring subjective fatigue while measuring serum enzyme activity levels using the dry-chemistry method immediately provides clinical value to players and coaches on site, and should therefore help to prevent a shift from "overreaching" to "overtraining".

Age-related changes in ventilatory and heart rate responses to acute ozone exposure in the conscious rat.

To evaluate the effect of age on toxicant-induced pulmonary and extrapulmonary changes, we examined the effect of inhalation exposure to oxone (O3) on the ventilatory and heart rate (HR) responses in 4-6 and 20-22-month-old male rats. The rats, chronically implanted with an electrocardiographic (ECG) electrodes, were placed in a head-out plethysmograph for continuous ventilatory measurements of tidal volume and breathing frequency. Simultaneous measurements of HR were also obtained. A 6-hr exposure of each rat to filtered air was followed 2 days later by a 5-hr exposure to 0.1 ppm O3, 5 days later by a 5-hr exposure to 0.3 ppm O3 and 10 days later by a 5-hr exposure to 0.5 ppm O3. Each of the O3 exposures was preceded by a 1-hr exposure to filtered air. Transient rapid shallow breathing with slightly increased HR appeared 1-2 min after the start of O3 exposure. It was suggested on the basis of the electroencephalographic (EEG) activity of the olfactory bulb that this transient response was mediated through olfactory sensation. Persistent rapid shallow breathing with a progressive decrease in HR occurred with a latent period of 1-2 hr. The last 90-min averaged values for relative minute ventilation tended to decrease with the increase in the level of exposure to O3 and these values for young rats were significantly lower than those for old rats. An exposure of young rats to 0.1 ppm O3 for shorter than 5 hr significantly decreased the tidal volume and HR and increased breathing frequency, but no significant changes were observed in old rats. There were no differences between young and old rats in non-observable-adverse-effect-levels (NOAELs) for the O3-induced persistent ventilatory and HR responses, when the NOAELs were determined by exposure to 0.3 and 0.5 ppm O3. The present results, as well as the reported decrease in body temperature and blood pressure, suggested that the age-related changes in patterns and magnitude of the persistent rapid shallow breathing with a progressive decrease in HR are mediated through some age-related defense mechanism acting against O3 inhalation. The validity of the occupational exposure limit for O3 in workplaces was discussed in the light of the present findings.

Automatic construction of knowledge base from biological papers.

We designed a system that acquires domain specific knowledge from human written biological papers, and we call this system IFBP (Information Finding from Biological Papers). IFBP is divided into three phases, Information Retrieval (IR), Information Extraction (IE) and Dictionary Construction (DC). We propose a query modification method using automatically constructed thesaurus for IR and a statistical keyword prediction method for IE. A dictionary of domain specific terms, which is one of the central knowledge sources for the task of knowledge acquisition, is also constructed automatically in the DC phase. IFBP is currently used for constructing the Transcription Factor DataBase (TFDB) and shows good performance. Since the model of knowledge base construction that is adopted into IFBP is carried out entirely automatically, this system can be easily ported across domains.

A study for prevention of chronic fatigue Part 1. Effects of endurance running during one month on blood properties and subjective fatigue.

The principal objective of this paper is basic research on the development of methods for the prevention of chronic fatigue. Overtraining was paid special attention to as one of the types of chronic fatigue condition. Six healthy male participants in a distance-running competition were recruited and used as subjects for this study with informed consent for all examinations. Subjects, that is, participants in the competition, tried to achieve their objective maximum running distance designated before the competition during one month, while in the same period performing their routine work duties. It was reported that the competition caused participants to exhibit an overtrained condition. In this paper, effects of endurance running during one month on blood properties and the fatigue level felt by the subject (subjective fatigue) were studied.Examinations carried out in this research were as follows; 1) physical examination was conducted 3 times during the study; 1 week before the competition, immediately before and 3 weeks after the end of the competition, 2) blood sampling was conducted 4 times; prior to the competition, 1 week after the beginning of and immediately before the end of the competition, and about 3 weeks after the competition, 3) subjective fatigue levels were monitored 8 times; 1 week before and one time in every week during the competition, and 1 week and again 3 weeks after the competition.Immediately before the end of the competition, when subjects might be expected to exhibit the overtrained condition, minor influences on fatigue levels were found. However, effects of the endurance run seemed to remain more than 3 weeks after the competition as indicated by changes of the population of white blood cells and blood hormone levels.The above mentioned results suggest that it is important to determine signs of overtraining at an early stage. To determine overtraining at an early stage, norepinephrine, testosterone and the ratio of testosterone to cortisol may be the most useful indices. These, as well as the element of "drowsiness and dullness" in the questionnaire on subjective symptoms of fatigue authorized by the Japan Association of Industrial Health and the elements of "anger", "fatigue", and "confusion" in the Profile of Mood State (POMS) questionnaire are thought to be the most important subjective indices.

Construction and analysis of a profile library characterizing groups of structurally known proteins.

A new sequence motif library StrProf was constructed characterizing the groups of related proteins in the PDB three-dimensional structure database. For a representative member of each protein family, which was identified by cross-referencing the PDB with the PIR superfamily classification, a group of related sequences was collected by the BLAST search against the nonredundant protein sequence database. For every group, the motifs were identified automatically according to the criteria of conservation and uniqueness of pentapeptide patterns and with a dual dynamic programming algorithm. In the StrProf library, motifs are represented by profile matrices rather than consensus patterns to allow more flexible search capabilities. Another dynamic programming algorithm was then developed to search this motif library. When the computationally derived StrProf was compared with PROSITE, which is a manually derived motif library in the best consensus pattern representation, the numbers of identified patterns were comparable. StrProf missed about one third of the PROSITE motifs, but there were also new motifs lacking in PROSITE. The new library was incorporated in SMART (Sequence Motif Analysis and Retrieval Tool), a computer tool designed to help search and annotate biologically important sites in an unknown protein sequence. The client program is available free of charge through the Internet.