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Objective: Few studies have reported intakes of fermented foods with their clear definitions. This study aimed to identify fermented foods and beverages consumed in Japan based on international definitions and to estimate their intake and contribution to energy and nutrients., Design: Data from a 16-d (four non-consecutive days within each season at 3-month intervals) semi-weighted dietary records (DR) were used. To identify 'entirely fermented foods' and 'partially fermented foods', a literature search on food processing and ingredients was conducted for all foods that appeared in the DR. For 'partially fermented foods', only the weight of the fermented food component was included in the estimation of total fermented food intake., Setting: Four regions in Japan: Osaka, Nagano, Tottori and Okinawa., Participants: Two-hundred forty-two apparently healthy Japanese adults aged 31-81 years., Results: Of the 1396 kinds of unique foods that appeared in the DR, 101 were 'entirely fermented foods' and 104 were 'partially fermented foods'. The mean intake of fermented foods was 438 g/d per person (17 % of the total weight). They were mainly derived from beer, coffee, bread and yogurt. The mean contribution of fermented foods to the total energy intake was 18 %. For nutrients, the contribution to total intake was high to Na (46 %), Mg (22 %) and Ca (20 %)., Conclusions: Fermented foods account for approximately one-fifth of the total weight and energy of dietary intake and are important contributors to some nutrients in Japanese adults.

Enhancer activation is essential for cell-type specific gene expression during cellular differentiation, however, how enhancers transition from a hypoacetylated "primed" state to a hyperacetylated-active state is incompletely understood. Here, we show SET domain-containing 5 (SETD5) forms a complex with NCoR-HDAC3 co-repressor that prevents histone acetylation of enhancers for two master adipogenic regulatory genes Cebpa and Pparg early during adipogenesis. The loss of SETD5 from the complex is followed by enhancer hyperacetylation. SETD5 protein levels were transiently increased and rapidly degraded prior to enhancer activation providing a mechanism for the loss of SETD5 during the transition. We show that induction of the CDC20 co-activator of the ubiquitin ligase leads to APC/C mediated degradation of SETD5 during the transition and this operates as a molecular switch that facilitates adipogenesis., (© 2021. The Author(s).)

Principal component analysis (PCA) has been widely used in nutritional epidemiology to derive dietary patterns. However, although PCA-derived dietary patterns are population-dependent, their reproducibility in different populations is largely unexplored. We aimed to investigate whether major dietary patterns are consistently identified among different populations within a country and, if so, how similar these dietary patterns are. We conducted a systematic review of PCA-derived dietary patterns in Japanese adults using PubMed and Web of Science for English articles and Ichushi-Web and CiNii databases for Japanese articles. We assessed the reproducibility of major dietary patterns using congruence coefficients (CCs), with values ≥0.80 considered to represent fair similarity. From 65 articles (80 studies) included in this review, 285 different dietary patterns were identified. Based on the names of these patterns, major dietary patterns were Western (n = 34), Japanese (n = 12), traditional (n = 10), traditional Japanese (n = 9), healthy (n = 18), and prudent (n = 9) patterns. When assessment was limited to high-quality data (i.e., studies based on a sample size ≥200 and use of a validated dietary assessment questionnaire or multiple-day dietary record), the median CC was low for Western (0.44), traditional (0.59), and traditional Japanese (0.31) patterns. Conversely, the median CC was 0.89 for healthy, 0.86 for prudent, and 0.80 for Japanese patterns; and the proportion of pairs with a CC ≥0.80 was 87.3%, 64.3%, and 50.0%, respectively. Characteristics shared among these 3 dietary patterns included higher intakes of mushrooms, seaweeds, vegetables, potatoes, fruits, pulses, and pickles. In conclusion, this systematic review showed that some of the major dietary patterns are relatively reproducible in different populations within a country, whereas others are not. This highlights the importance of careful interpretation of PCA-derived dietary patterns. Our findings in Japan should be confirmed in different countries and globally. This study was registered at https://www.crd.york.ac.uk/prospero/ as CRD42018087669., (© 2019 American Society for Nutrition.)

The measurement of the spatial profile of root elongation needs to determine matching points between time-lapse images and calculate their displacement. These data have been obtained by laborious manual methods in the past. Some computer-based programs have been developed to improve the measurement, but they require many time-series digital images or sprinkling graphite particles on the root prior to image capture. Here, we have developed GrowthTracer, a new image-analysis program for the kinematic study of root elongation. GrowthTracer employs a multiresolution image matching method with a nonlinear filter called the critical point filter (CPF), which extracts critical points from images at each resolution and can determine precise matching points by analysis of only two intact images, without pre-marking by graphite particles. This program calculates the displacement of each matching point and determines the displacement velocity profile along the medial axis of the root. In addition, a manual input of distinct matching points increases the matching accuracy. We show a successful application of this novel program for the kinematic analysis of root growth in Arabidopsis thaliana.

The representation of protein structures as small-world networks facilitates the search for topological determinants, which may relate to functionally important residues. Here, we aimed to investigate the performance of residue centrality, viewed as a family fold characteristic, in identifying functionally important residues in protein families. Our study is based on 46 families, including 29 enzyme and 17 non-enzyme families. A total of 80% of these central positions corresponded to active site residues or residues in direct contact with these sites. For enzyme families, this percentage increased to 91%, while for non-enzyme families the percentage decreased substantially to 48%. A total of 70% of these central positions are located in catalytic sites in the enzyme families, 64% are in hetero-atom binding sites in those families binding hetero-atoms, and only 16% belong to protein-protein interfaces in families with protein-protein interaction data. These differences reflect the active site shape: enzyme active sites locate in surface clefts, hetero-atom binding residues are in deep cavities, while protein-protein interactions involve a more planar configuration. On the other hand, not all surface cavities or clefts are comprised of central residues. Thus, closeness centrality identifies functionally important residues in enzymes. While here we focus on binding sites, we expect to identify key residues for the integration and transmission of the information to the rest of the protein, reflecting the relationship between fold and function. Residue centrality is more conserved than the protein sequence, emphasizing the robustness of protein structures.

Here, we represent protein structures as residue interacting networks, which are assumed to involve a permanent flow of information between amino acids. By removal of nodes from the protein network, we identify fold centrally conserved residues, which are crucial for sustaining the shortest pathways and thus play key roles in long-range interactions. Analysis of seven protein families (myoglobins, G-protein-coupled receptors, the trypsin class of serine proteases, hemoglobins, oligosaccharide phosphorylases, nuclear receptor ligand-binding domains and retroviral proteases) confirms that experimentally many of these residues are important for allosteric communication. The agreement between the centrally conserved residues, which are key in preserving short path lengths, and residues experimentally suggested to mediate signaling further illustrates that topology plays an important role in network communication. Protein folds have evolved under constraints imposed by function. To maintain function, protein structures need to be robust to mutational events. On the other hand, robustness is accompanied by an extreme sensitivity at some crucial sites. Thus, here we propose that centrally conserved residues, whose removal increases the characteristic path length in protein networks, may relate to the system fragility.

Unlabelled: The majority of real examples of small-world networks exhibit a power law distribution of edges among the nodes, therefore not fitting into the wiring model proposed by Watts and Strogatz. However, protein structures can be modeled as small-world networks, with a distribution of the number of links decaying exponentially as in the case of this wiring model. We approach the protein-protein interaction mechanism by viewing it as a particular rewiring occurring in the system of two small-world networks represented by the monomers, where a re-arrangement of links takes place upon dimerization leaving the small-world character in the dimer network. Due to this rewiring, the most central residues at the complex interfaces tend to form clusters, which are not homogenously distributed. We show that these highly central residues are strongly correlated with the presence of hot spots of binding free energy., Contact: ao-mesa@fujirebio.co.jp, Supplementary Information: http://www.fujirebio.co.jp/support/index.php (under construction).

We examined the effects of dietary proso-millet protein on plasma levels of high-density lipoprotein (HDL) cholesterol in different rats from animals reported in our previous studies. The results showed also, in this animal, that the ingestion of the millet protein elevates plasma levels of HDL-cholesterol like our earlier works. Taking into account the anti-atherogenic function of HDL, therefore, the millet protein would be useful as a new food ingredient which has the function that regulates cholesterol metabolism.

As mononuclear phagocytes have been implicated as important cellular elements in the process of bone resorption, we decided to study the relevancy of macrophage (M phi) activities to bone resorption. In this study, we investigated the phagocytic activity and activities of lysosomal enzymes of peritoneal resident M phi from rats fed a high-sucrose diet (Diet 2000) to appreciate the effects of Diet 2000 on systemic and local factors. Minkin et al. have postulated that bone-derived chemotactic factors were released from foci undergoing resorption. And so, we examined the effects of the supernatant from alveolar bone cultures (Bone-sup) prepared from rats fed Diet 2000 on the activities of glycogen induced peritoneal M phi. As a result we observed mild alveolar bone resorption with slight inflammation when the rats were fed Diet 2000 for six months. In the periodontal tissue, we found inflammatory cell infiltration, destruction of the periodontal ligament, and lacunae in the alveolar bone due to resorption. The phagocytic activity of M phi treated with Bone-sups was suppressed before the periodontal tissue, which is inflammatory condition such as alveolar bone resorption. Furthermore the phagocytic activity of resident M phi taken from rats on the Diet 2000 was suppressed. After one month of the Diet 2000, the activity of acid phosphatase (AcP), a lysosomal enzyme of M phi, was suppressed, but by six months it was enhanced. The activity of beta-N-acetyl-D-glucosaminidase (NAG), another lysosomal enzyme of M phi, was suppressed over the total period of Diet 2000 before the periodontal tissue was destroyed. These findings suggest that the capacity for defense against infection by M phi is suppressed when periodontitis is initiated by Diet 2000 feeding and that M phi activities are influenced by some factors elaborated by cells in the alveolar bone.