KEGG is a reference knowledge base for biological interpretation of large‐scale molecular datasets, such as genome and metagenome sequences. It accumulates experimental knowledge about high‐level ...functions of the cell and the organism represented in terms of KEGG molecular networks, including KEGG pathway maps, BRITE hierarchies, and KEGG modules. By the process called KEGG mapping, a set of protein coding genes in the genome, for example, can be converted to KEGG molecular networks enabling interpretation of cellular functions and other high‐level features. Here we report a new version of KEGG Mapper, a suite of KEGG mapping tools available at the KEGG website (https://www.kegg.jp/ or https://www.genome.jp/kegg/), together with the KOALA family tools for automatic assignment of KO (KEGG Orthology) identifiers used in the mapping.
In contrast to artificial intelligence and machine learning approaches, KEGG (https://www.kegg.jp) has relied on human intelligence to develop “models” of biological systems, especially in the form ...of KEGG pathway maps that are manually created by capturing knowledge from published literature. The KEGG models can then be used in biological big data analysis, for example, for uncovering systemic functions of an organism hidden in its genome sequence through the simple procedure of KEGG mapping. Here we present an updated version of KEGG Mapper, a suite of KEGG mapping tools reported previously (Kanehisa and Sato, Protein Sci 2020; 29:28–35), together with the new versions of the KEGG pathway map viewer and the BRITE hierarchy viewer. Significant enhancements have been made for BRITE mapping, where the mapping result can be examined by manipulation of hierarchical trees, such as pruning and zooming. The tree manipulation feature has also been implemented in the taxonomy mapping tool for linking KO (KEGG Orthology) groups and modules to phenotypes.
BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct ...KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG Web site (http://www.kegg.jp/blastkoala/). In BlastKOALA, the KO assignment is performed by a modified version of the internally used KOALA algorithm after the BLAST search against a non-redundant dataset of pangenome sequences at the species, genus or family level, which is generated from the KEGG GENES database by retaining the KO content of each taxonomic category. In GhostKOALA, which utilizes more rapid GHOSTX for database search and is suitable for metagenome annotation, the pangenome dataset is supplemented with Cd-hit clusters including those for viral genes. The result files may be downloaded and manipulated for further KEGG Mapper analysis, such as comparative pathway analysis using multiple BlastKOALA results.
Display omitted
•Advanced bioinformatics methods are required to make use of genome sequencing data.•KEGG is a knowledge base for linking genomes to high-level biological functions.•BlastKOALA is a KEGG Web service for annotating genomes and understanding organisms.•GhostKOALA is another service for annotating metagenomes and understanding ecosystems.•Both are based on the newly developed non-redundant dataset of pangenome sequences.
Abstract
KEGG (Kyoto Encyclopedia of Genes and Genomes; https://www.kegg.jp/ or https://www.genome.jp/kegg/) is a reference knowledge base for biological interpretation of genome sequences and other ...high-throughput data. It is an integrated database consisting of three generic categories of systems information, genomic information and chemical information, and an additional human-specific category of health information. KEGG pathway maps, BRITE hierarchies and KEGG modules have been developed as generic molecular networks with KEGG Orthology nodes of functional orthologs so that KEGG pathway mapping and other procedures can be applied to any cellular organism. Unfortunately, however, this generic approach was inadequate for knowledge representation in the health information category, where variations of human genomes, especially disease-related variations, had to be considered. Thus, we have introduced a new approach where human gene variants are explicitly incorporated into what we call ‘network variants’ in the recently released KEGG NETWORK database. This allows accumulation of knowledge about disease-related perturbed molecular networks caused not only by gene variants, but also by viruses and other pathogens, environmental factors and drugs. We expect that KEGG NETWORK will become another reference knowledge base for the basic understanding of disease mechanisms and practical use in clinical sequencing and drug development.
Abstract
KEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. It also provides KEGG mapping ...tools, which enable understanding of cellular and organism-level functions from genome sequences and other molecular datasets. KEGG mapping is a predictive method of reconstructing molecular network systems from molecular building blocks based on the concept of functional orthologs. Since the introduction of the KEGG NETWORK database, various diseases have been associated with network variants, which are perturbed molecular networks caused by human gene variants, viruses, other pathogens and environmental factors. The network variation maps are created as aligned sets of related networks showing, for example, how different viruses inhibit or activate specific cellular signaling pathways. The KEGG pathway maps are now integrated with network variation maps in the NETWORK database, as well as with conserved functional units of KEGG modules and reaction modules in the MODULE database. The KO database for functional orthologs continues to be improved and virus KOs are being expanded for better understanding of virus-cell interactions and for enabling prediction of viral perturbations.
KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database ...entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.
Silver is easily available and is known to have microbicidal effect; moreover, it does not impose any adverse effects on the human body. The microbicidal effect is mainly due to silver ions, which ...have a wide antibacterial spectrum. Furthermore, the development of multidrug-resistant bacteria, as in the case of antibiotics, is less likely. Silver ions bind to halide ions, such as chloride, and precipitate; therefore, when used directly, their microbicidal activity is shortened. To overcome this issue, silver nanoparticles (Ag NPs) have been recently synthesized and frequently used as microbicidal agents that release silver ions from particle surface. Depending on the specific surface area of the nanoparticles, silver ions are released with high efficiency. In addition to their bactericidal activity, small Ag NPs (<10 nm in diameter) affect viruses although the microbicidal effect of silver mass is weak. Because of their characteristics, Ag NPs are useful countermeasures against infectious diseases, which constitute a major issue in the medical field. Thus, medical tools coated with Ag NPs are being developed. This review outlines the synthesis and utilization of Ag NPs in the medical field, focusing on environment-friendly synthesis and the suppression of infections in healthcare workers (HCWs).
Multiple‐site optical recordings with NK2761, a voltage‐sensitive absorption dye, were applied to the embryonic chick olfactory system, and the functional development of olfactory nerve (N.I)‐related ...neural circuits was examined in the forebrain. The stimulation of the N. I elicited neural responses in N.I‐olfactory bulb (OB)‐forebrain preparations at the embryonic 8–12 day (E8‐E12) stages. At the E11 stage, we functionally identified two circuits projecting from the OB to the forebrain. The first circuit passed through the ventral side of the forebrain and spread in the dorso‐caudal direction, whereas the second circuit passed through the dorsal side to the first circuit. Pharmacological experiments showed that N‐methyl‐D‐aspartate (NMDA) receptor function was more significant for the transfer of sensory information in these circuits. The functional development of N.I‐related circuits was investigated, and the results obtained revealed that the ventral circuit was generated earlier than the dorsal circuit. Neural responses in the ventral circuit were detected from the E9 stage in normal physiological solution and the E8 stage in Mg2+‐free solution, which activated NMDA receptor function. At the E10 stage, neural responses in the dorsal circuit were clearly recognised in addition to ventral responses. We attempted to identify possible candidates for relay nuclei in the forebrain by comparing contour line maps of the optical signal amplitude with previously reported neuroanatomical data. The results suggest that N.I‐related neural circuits from the periphery to the subpallium functionally mature earlier than those to the pallium during ontogenesis.
We applied voltage‐sensitive dye recording to the embryonic chick olfactory system and examined functional development of olfactory nerve‐related neural circuits in the forebrain. We functionally identified two neural circuits projecting from the olfactory bulb to the forebrain—the ventral circuit that spread in the dorso‐caudal direction, and the dorsal circuit that passed dorsally to the ventral circuit—and found that the ventral circuit was generated earlier than the dorsal circuit. In comparison with previously reported anatomical data, we suggest that the olfactory nerve‐related neural circuit from the periphery to the subpallium functionally matures earlier than that to the pallium during ontogenesis.
Background: Analyzing real-world data, including health insurance claims, may help provide insights into preventing and treating various diseases. We developed a database covering Shizuoka Prefecture ...(Shizuoka Kokuho Database SKDB) in Japan, which included individual-level linked data on health- and care-insurance claims and health checkup results.Methods: Anonymized claims data on health insurance (National Health Insurance age <75 years and Latter-Stage Elderly Medical Care System age ≥75 years), care insurance, subscriber lists, annual health checkups, and all dates of death were collected from 35 municipalities in Shizuoka Prefecture. To efficiently link claims and health checkups, unique individual IDs were assigned using a novel procedure.Results: From April 2012 to September 2018, the SKDB included 2,230,848 individuals (men, 1,019,687; 45.7%). The median age (min–max) of men and women was 60 (0–106) and 62 (0–111) years, respectively. During the study period, the median subscription time was 4.4 years; 40.8% of individuals continuously subscribed for the 6.5 years; 213,566 individuals died. Health checkup data were available for 654,035 individuals, amounting to 2,469,648 records. Care-service recipient data were available for 283,537 individuals; they used care insurance to pay for care costs.Conclusion: SKDB, a population-based longitudinal cohort, provides a comprehensive dataset covering health checkups, disorders, medication, and care service. This database may provide a robust platform to identify epidemiological problems and generate hypotheses for preventing and treating disorders in the elderly.
Pregnancy and postpartum are periods in which women develop psychosocially. However, becoming a mother is stressful, and mood disorders related to anxiety and depression often develop. In recent ...years, research on interoception-sensations related to the body's internal physiological state-has attracted attention. Interoception has multifaceted characteristics. It involves directly perceiving information in the body while also inferring and evaluating it. In this study, we examined interoception, anxiety, and depression in Japanese pregnant women. Empirical examinations and questionnaire surveys were used to measure interoception in 32 pregnant women not at high risk of pregnancy. A Japanese adaption of the Multidimensional Assessment of Interoceptive Awareness was used to measure interoceptive sensibility, and a heartbeat counting task performance was used to measure interoceptive accuracy. Anxiety and depression were measured using the Japanese versions of the State-Trait Anxiety Inventory and the Edinburgh Postnatal Depression Scale, respectively. A correlation analysis was performed between interoception, anxiety and depression and between differences between sensibility and accuracy of interoception, anxiety and depression. We revealed that interoceptive sensibility and differences between sensibility and accuracy of interoception were associated with anxiety. Based on results of this pilot study, it is necessary to investigate using longitudinal studies whether interoception might be an effective predictor tool for early detection of anxiety during pregnancy and postpartum.
PDF
