Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions

<p>Abstract</p> <p>Background</p> <p>It is essential in modern biology to understand how transcriptional regulatory regions are composed of <it>cis</it>-elements, yet we have limited knowledge of, for example, the combinational uses of these elements and their positional distribution.</p> <p>Results</p> <p>We predicted the positions of 228 known binding motifs for transcription factors in phylogenetically conserved regions within -2000 and +1000 bp of transcriptional start sites (TSSs) of human genes and visualized their correlated non-overlapping occurrences. In the 8,454 significantly correlated motif pairs, two major classes were observed: 248 pairs in Class 1 were mainly found around TSSs, whereas 4,020 Class 2 pairs appear at rather arbitrary distances from TSSs. These classes are distinct in a number of aspects. First, the positional distribution of the Class 1 constituent motifs shows a single peak near the TSSs, whereas Class 2 motifs show a relatively broad distribution. Second, genes that harbor the Class 1 pairs are more likely to be CpG-rich and to be expressed ubiquitously than those that harbor Class 2 pairs. Third, the 'hub' motifs, which are used in many different motif pairs, are different between the two classes. In addition, many of the transcription factors that correspond to the Class 2 hub motifs contain domains rich in specific amino acids; these domains may form disordered regions important for protein-protein interaction.</p> <p>Conclusion</p> <p>There exist at least two classes of motif pairs with respect to TSSs in human promoters, possibly reflecting compositional differences between promoters and enhancers. We anticipate that our visualization method may be useful for the further characterisation of promoters.</p

Cross-cultural validity of a dietary questionnaire for studies of dental caries risk in Japanese

Background: Diet is a major modifiable contributing factor in the etiology of dental caries. The purpose of this paper is to examine the reliability and cross-cultural validity of the Japanese version of the Food Frequency Questionnaire to assess dietary intake in relation to dental caries risk in Japanese. Methods: The 38-item Food Frequency Questionnaire, in which Japanese food items were added to increase content validity, was translated into Japanese, and administered to two samples. The first sample comprised 355 pregnant women with mean age of 29.2 +/- 4.2 years for the internal consistency and criterion validity analyses. Factor analysis (principal components with Varimax rotation) was used to determine dimensionality. The dietary cariogenicity score was calculated from the Food Frequency Questionnaire and used for the analyses. Salivary mutans streptococci level was used as a semi-quantitative assessment of dental caries risk and measured by Dentocult SM. Dentocult SM scores were compared with the dietary cariogenicity score computed from the Food Frequency Questionnaire to examine criterion validity, and assessed by Spearman's correlation coefficient (r(s)) and Kruskal-Wallis test. Test-retest reliability of the Food Frequency Questionnaire was assessed with a second sample of 25 adults with mean age of 34.0 +/- 3.0 years by using the intraclass correlation coefficient analysis. Results: The Japanese language version of the Food Frequency Questionnaire showed high test-retest reliability (ICC = 0.70) and good criterion validity assessed by relationship with salivary mutans streptococci levels (r(s) = 0.22; p < 0.001). Factor analysis revealed four subscales that construct the questionnaire (solid sugars, solid and starchy sugars, liquid and semisolid sugars, sticky and slowly dissolving sugars). Internal consistency were low to acceptable (Cronbach's alpha = 0.67 for the total scale, 0.46-0.61 for each subscale). Mean dietary cariogenicity scores were 50.8 +/- 19.5 in the first sample, 47.4 +/- 14.1, and 40.6 +/- 11.3 for the first and second administrations in the second sample. The distribution of Dentocult SM score was 6.8% (score = 0), 34.4% (score = 1), 39.4% (score = 2), and 19.4% (score = 3). Participants with higher scores were more likely to have higher dietary cariogenicity scores (p < 0.001; Kruskal-Wallis test). Conclusions: These results provide the preliminary evidence for the reliability and validity of the Japanese language Food Frequency Questionnaire

Deep palmar arteries of monkeys, with special reference to the palmar metacarpal arteries.

The palmar metacarpal arteries in monkey hands were studied. The palmar metacarpal arteries arose from the deep palmar arch or catella palmaris proximalis and descended in the deep palm, forming the catella palmaris distalis at the distal end of the metacarpus. The palmar metacarpal arteries could be classified into four kinds in relation to the interosseous muscles and metacarpal bones: (i) the superficial palmar metacarpal (sM) arteries descending on the palmar surfaces of the interosseous muscles along the metacarpal bones, (ii) the superficial palmar intermetacarpal (sI) arteries descending on the palmar surfaces of the interosseous muscles along the intermetacarpal spaces, (iii) the deep palmar metacarpal (dM) arteries descending deep in the interosseous muscles along the metacarpal bones, and (iv) the deep palmar intermetacarpal (dI) arteries descending deep in the interosseous muscles along the intermetacarpal spaces. These findings largely coincide with those obtained from studies of the human hand by Murakami (1969).</p

On the Food Habits of the Dragonets, Genus Callionymus : I. Food Habits of Callionymus punctatus LANGSDORFF

ネズミゴチの食性を明らかにするために,瀬戸内海中部の小型底曳網漁獲物の中から採集したネズミゴチ46個体の消化管内容物を調査し,さらに瀬戸内海中部の仙酔島の砂場および藻場のベントスとそこで採集した23個体のネズミゴチの消化管内容物をそれぞれ調査して次のような結果を得た。 1) ネズミゴチの餌生物は甲殻類のCumacea, Ostracoda, カニ類, Amphipoda, Copepoda,エビ類, Anomura, オキアミ類, Branchiopoda, Mycidaceaと巻貝,二枚貝および多毛類であるが,調査したネズミゴチの半数以上の個体に捕食されていたCumacea, Ostracodaおよび巻貝が重要な餌生物である。 2) ネズミゴチの成魚の餌生物組成は雌雄の間で差異がなく,また体長110～129mmと130～164mmとの間についても差異がない。 3) 仙酔島の砂場のベントスの組成と藻場のベントスの組成とは著しく相違しているのに対し,砂場と藻場の両者において,それぞれのベントスとそこで採集したネズミゴチの消化管内容物の組成は極めてよく類似していた。すなわち個体数において,砂場ではウミホタルが卓越してベントスの53%を占め,ネズミゴチの消化管内容物の中では79%を占めた。次いで砂場では貝類が多数出現して,それはベントスの28%を占めたのに対し,消化管内容物では8%を占めた。藻場ではホトトギスガイが卓越してベントスの87%を占め,消化管内容物の中では59%を占めた。 4) 藻場に生息していたネズミゴチの消化管内容物の59%を占め,ネズミゴチの最も重要な餌生物の一つであるホトトギスガイは仙酔島の藻場に比較的多く出現したアサヒアナハゼ,クジメおよびアイナメには殆んど捕食されていなかった。しかし藻場のネズミゴチに殆んど捕食されていないGammarideaはこれら3種の魚類によってしばしば捕食されており,それらの最も重要な餌生物であることがわかった。したがってネズミゴチは藻場ではアサヒアナハゼ,クジメおよびアイナメと食物について競合関係がない。The dragonets, genus Callionymus, is very common and found frequently with other demersal fish in the catch of a small trawl in the Seto Inland Sea. In this study, the food habits of "Nezumigochi", Callionymus punctatus LANGSDORFF, have been investigated through analysis of their gut contents and benthos of their habitat, Sensui-shima in the central region of the Seto Inland Sea (Fig. 1). The material of 46 individuals were caught by a small trawl net. They ranged from 110 mm to 163 mm in standard length (Fig. 2). To compair the diet of this fish with the benthos of their habitat, 14 individuals in the sand area and 9 individuals in the Zostra zone were sampled by spear, the benthos of the area were also sampled by quardrat method (Fig. 4 ). The general conclusions reached in this study are as follows: 1) The food organisms occurred in the guts were crustacea, bivalvia, gastropod a, and poly-chaeta. The crustacea contained the following organisms: branchiopoda, ostracoda, copepoda, mysidacea, cumacea, amphipoda, euphausiacea, macurura, anomura, brachyuran and stomatopoda. The main food organisms were cumacea for 72 % of the 46 stomachs, gastropoda for 65 %and ostracoda for 61 %. On the contrary, euphausiacea, macurura and anomura seemed to be preied on only occasionally, and branchiopoda, mysidacea and stomatopoda still more rarely (Table 1). 2) The difference between the diet of the male and female adult could not be statistically determined (Fig. 3). The diets of the specimens of 110-129mm and those of 130-164 mm were very similar. 3) The benthos of the sand area and that of the Zostera zone were clearly different in composition. Namely, in the benthos of the sand area Cypridina hilgendorfii (ostracoda) occupied 53%, but in the benthos of the Zostera zone Musculus (Musculista) senhousia (bivalvia) 87%. The composition of the food organisms and benthos sampled in each habitat were very similar to each other (Table 3). In the sand area, Cypridina hilgendorfii occupied 53% of the benthos but 79% in the food organisms. In the Zostera zone, Musculus (Musculista) senhousia occupied 87% of the benthos, but 59% in the food organisms (Table 2). 4) Musculus (Musculista) senhousia, the main food organisms of C. punctatus in the Zostera zone, were rarely taken in by the common inhabitant of the Zostera zone around Sensui-shima: Pseudoblennius cottoides, Agrammus agrammus and Hexagrammos otakii. But gammaridae that occupied only 6% in the food organisms of C. punctatus in the Zostera zone were often eaten by these 3 species mentioned above (Fig. 5). Accordingly, it is considered that C. punctatus is not in competition with these 3 species for prey