Instituto de Investigaciones Químicas

KEGG (https://www.kegg.jp/) is a database resource for representation and analysis of biological systems. Pathway maps are the primary dataset in KEGG representing systemic functions of the cell and the organism in terms of molecular interaction and reaction networks. The KEGG Orthology (KO) system is a mechanism for linking genes and proteins to pathway maps and other molecular networks. Each KO is a generic gene identifier and each pathway map is created as a network of KO nodes. This architecture enables KEGG pathway mapping to uncover systemic features from KO assigned genomes and metagenomes. Additional roles of KOs include characterization of conserved genes and conserved units of genes in organism groups, which can be done by taxonomy mapping. A new tool has been developed for identifying conserved gene orders in chromosomes, in which gene orders are treated as sequences of KOs. Furthermore, a new dataset called VOG (virus ortholog group) is computationally generated from virus proteins and expanded to proteins of cellular organisms, allowing gene orders to be compared as VOG sequences as well. Together with these datasets and analysis tools, new types of pathway maps are being developed to present a global view of biological processes involving multiple organism groups.

SUMMARY: KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction. AVAILABILITY AND IMPLEMENTATION: KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A basic peptide derived from human immunodeficiency virus (HIV)-1 Tat protein (positions 48-60) has been reported to have the ability to translocate through the cell membranes and accumulate in the nucleus, the characteristics of which are utilized for the delivery of exogenous proteins into cells. Based on the fluorescence microscopic observations of mouse macrophage RAW264.7 cells, we found that various arginine-rich peptides have a translocation activity very similar to Tat-(48-60). These included such peptides as the d-amino acid- and arginine-substituted Tat-(48-60), the RNA-binding peptides derived from virus proteins, such as HIV-1 Rev, and flock house virus coat proteins, and the DNA binding segments of leucine zipper proteins, such as cancer-related proteins c-Fos and c-Jun, and the yeast transcription factor GCN4. These segments have no specific primary and secondary structures in common except that they have several arginine residues in the sequences. Moreover, these peptides were able to be internalized even at 4 degrees C. These results strongly suggested the possible existence of a common internalization mechanism ubiquitous to arginine-rich peptides, which is not explained by a typical endocytosis. Using (Arg)(n) (n = 4-16) peptides, we also demonstrated that there would be an optimal number of arginine residues (n approximately 8) for the efficient translocation.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecent Developments in the Synthesis and Utilization of Chiral SulfoxidesInmaculada Fernández and Noureddine KhiarView Author Information Instituto de Investigaciones Químicas, C.S.I.C-Universidad de Sevilla, c/. Américo Vespucio, s/n., Isla de la Cartuja, 41092 Sevilla, Spain, and Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, 41012 Sevilla, Spain Cite this: Chem. Rev. 2003, 103, 9, 3651–3706Publication Date (Web):August 1, 2003Publication History Received8 April 2002Published online1 August 2003Published inissue 1 September 2003https://pubs.acs.org/doi/10.1021/cr990372uhttps://doi.org/10.1021/cr990372uresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views9882Altmetric-Citations1063LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Alkyls,Ligands,Oxidation,Oxides,Sulfides Get e-Alerts

Partial substitution of Pb for Bi in the Bi-Sr-Ca-Cu-O system has been found to sharply increase the volume fraction of the high-T c phase when both the starting material (coprecipitated oxalate being used in the present study) and the heating process are appropriate. The sharp powder X-ray diffraction pattern obtained from well-grown particles, 5∼10 µm wide and 0.5 µm thick typically, was assigned to an orthorhombic cell with a=0.537 nm, b=2.682 nm, and c=3.726 nm. The electrical resistance dropped to zero at 107 K within the experimental limit of 10-6 Ω. A large diamagnetic response in the ac susceptibility due to the Meissner effect was seen below 120 K. The dominance of the high-T c phase over the low-T c phase was roughly estimated at 9/1 in volume.

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.

Phthalocyanines exhibit superior photoproperties that make them a surely attractive class of photosensitisers for photodynamic therapy of cancer. Several derivatives are at various phases of clinical trials, and efforts have been put continuously to improve their photodynamic efficacy. To this end, various strategies have been applied to develop advanced phthalocyanines with optimised photoproperties, dual therapeutic actions, tumour-targeting properties and/or specific activation at tumour sites. The advantageous properties and potential of phthalocyanines as advanced photosensitisers for photodynamic therapy of cancer are highlighted in this tutorial review.

The direct borylation of hydrocarbons via C-H activation has reached an impressive level of sophistication and efficiency, emerging as a fundamental tool in synthesis because of the versatility offered by organoboron compounds. As a remarkable particularity, the catalytic systems originally developed for these reactions are relatively insensitive to directing effects, and the regioselectivity of the borylations is typically governed by steric factors. Likely stimulated by the great synthetic potential of the expected functionalised organoboranes, however, many groups have recently focused on the development of complementary strategies for directed, site-selective borylation reactions where a directing group controls the course of the reaction. In this tutorial review, the different strategies and findings related to the development of these directed borylation reactions via C(sp(2))-H or C(sp(3))-H activation will be summarized and discussed.

Multivalency plays a major role in biological processes and particularly in the relationship between pathogenic microorganisms and their host that involves protein-glycan recognition. These interactions occur during the first steps of infection, for specific recognition between host and bacteria, but also at different stages of the immune response. The search for high-affinity ligands for studying such interactions involves the combination of carbohydrate head groups with different scaffolds and linkers generating multivalent glycocompounds with controlled spatial and topology parameters. By interfering with pathogen adhesion, such glycocompounds including glycopolymers, glycoclusters, glycodendrimers and glyconanoparticles have the potential to improve or replace antibiotic treatments that are now subverted by resistance. Multivalent glycoconjugates have also been used for stimulating the innate and adaptive immune systems, for example with carbohydrate-based vaccines. Bacteria present on their surfaces natural multivalent glycoconjugates such as lipopolysaccharides and S-layers that can also be exploited or targeted in anti-infectious strategies.

A study is made on the dispersions of resistivity and dielectric constant of α-Fe2O3, γ-Fe2O3, Fe3O4, Zn ferrite, Mn ferrite, and MnZn ferrite fine particles over the frequency range of 10 Hz to 1 MHz in the temperature range from 77°K to 300°K. The Maxwell-Wagner interfacial polarization arising from the heterogeneity of oxidation is observed in the fine particles of the oxides, except α-Fe3O3, which are prepared from aqueous solutions of divalent metal salts as well as in the powders of ferrites containing ferrous ions which are prepared by the calcination at high temperatures. The structures of heterogeneity in the fine particles are explained by the model that there are high resistivity shells with poor ferrous ions on the surfaces of the particles.

The folding types of 135 proteins, the three-dimensional structures of which are known, were analyzed in terms of the amino acid composition. The amino acid composition of a protein was expressed as a point in a multidimensional space spanned with 20 axes, on which the corresponding contents of 20 amino acids in the protein were represented. The distribution pattern of proteins in this composition space was examined in relation to five folding types, alpha, beta, alpha/beta, alpha + beta, and irregular type. The results show that amino acid compositions of the alpha, beta, and alpha/beta types are located in different regions in the composition space, thus allowing distinct separation of proteins depending on the folding types. The points representing proteins of the alpha + beta and irregular types, however, are widely scattered in the space, and the existing regions overlap with those of the other folding types. A simple method of utilizing the "distance" in the space was found to be convenient for classification of proteins into the five folding types. The assignment of the folding type with this method gave an accuracy of 70% in the coincidence with the experimental data.

This tutorial review provides a systematic overview of the available methodologies for the atroposelective transformation of (heterobiaryl)biaryl precursors toward the synthesis of enantiomerically enriched products and the conceptual aspects associated to each type of transformation. Depending on the presence or absence of symmetry in the starting material and the participation of racemization or dynamization events along the process, several strategies have been developed, including desymmetrization, classical kinetic resolution (KR), dynamic kinetic resolution (DKR) and dynamic kinetic asymmetric transformation (DYKAT). Seminal contributions and a handful of selected examples are discussed to illustrate the potential of these synthetic tools.

Cyclodextrin (CD) history has been largely dominated by their unique ability to form inclusion complexes with guests fitting in their hydrophobic cavity. Chemical funcionalization was soon recognized as a powerful mean for improving CD applications in a wide range of fields, including drug delivery, sensing or enzyme mimicking. However, 100 years after their discovery, CDs are still perceived as novel nanoobjects of undeveloped potential. This critical review provides an overview of different strategies to promote interactions between CD conjugates and genetic material by fully exploiting the inside-outside/upper-lower face anisotropy of the CD nanometric platform. Covalent modification, self-assembling and supramolecular ligation can be put forward with the ultimate goal to build artificial viruses for programmed and efficient gene therapy (222 references).

Glycosphingolipid clustering and interactions at the cell membrane can be modeled by gold glyconanoparticles prepared with biologically significant oligosaccharides. Such water-soluble gold glyconanoparticles with highly polyvalent carbohydrate displays (see picture, gray hemisphere: gold nanoparticle) have been obtained by a simple and versatile strategy.

Glycosphingolipid clustering and interactions at the cell membrane can be modeled by gold glyconanoparticles prepared with biologically significant oligosaccharides. Such water-soluble gold glyconanoparticles with highly polyvalent carbohydrate displays (see picture, gray hemisphere: gold nanoparticle) have been obtained by a simple and versatile strategy.

By means of the activated reactive evaporation, YBa2Cu3O7-x single-crystal thin films with the c axis perpendicular to the substrate plane have been directly and epitaxially grown on the (100) surface of SrTiO3. The substrate temperature was kept below 600°C and the oxidation treatment was performed at below 500°C. The ac-resistive measurement for a film with 2000 Å thickness gave a sharp superconducting transition, where the endpoint was 90.2 K and Δ T c(10–90%)=1.7 K. From the complex susceptibility measurement we confirmed the Meissner effect as well as the structural uniformity of the specimen.

The imidazo[1,5-a]pyridine skeleton provides a versatile platform for the generation of new types of stable N-heterocyclic carbenes. Rh(I) mono- (6) and biscarbenes (7) from imidazo[1,5-a]pyridin-3-ylidenes (ImPy) and derivatives such as 13 from a mesoionic carbene were synthesized and characterized.

Abstract Approximately 8% to 19% of patients with acute myeloid leukemia (AML) have isocitrate dehydrogenase-2 (IDH2) mutations, which occur at active site arginine residues R140 and R172. IDH2 mutations produce an oncometabolite, 2-hydroxyglutarate (2-HG), which leads to DNA and histone hypermethylation and impaired hematopoietic differentiation. Enasidenib is an oral inhibitor of mutant-IDH2 proteins. This first-in-human phase 1/2 study evaluated enasidenib doses of 50 to 650 mg/d, administered in continuous 28-day cycles, in patients with mutant-IDH2 hematologic malignancies. Overall, 214 of 345 patients (62%) with relapsed or refractory (R/R) AML received enasidenib, 100 mg/d. Median age was 68 years. Forty-two patients (19.6%) attained complete remission (CR), 19 patients (10.3%) proceeded to an allogeneic bone marrow transplant, and the overall response rate was 38.8% (95% confidence interval [CI], 32.2-45.7). Median overall survival was 8.8 months (95% CI, 7.7-9.6). Response and survival were comparable among patients with IDH2-R140 or IDH2-R172 mutations. Response rates were similar among patients who, at study entry, were in relapse (37.7%) or were refractory to intensive (37.5%) or nonintensive (43.2%) therapies. Sixty-six (43.1%) red blood cell transfusion–dependent and 53 (40.2%) platelet transfusion–dependent patients achieved transfusion independence. The magnitude of 2-HG reduction on study was associated with CR in IDH2-R172 patients. Clearance of mutant-IDH2 clones was also associated with achievement of CR. Among all 345 patients, the most common grade 3 or 4 treatment-related adverse events were hyperbilirubinemia (10%), thrombocytopenia (7%), and IDH differentiation syndrome (6%). Enasidenib was well tolerated and induced molecular remissions and hematologic responses in patients with AML for whom prior treatments had failed. The study is registered at www.clinicaltrials.gov as #NCT01915498.

Carboxylesterases hydrolyze numerous endogenous and exogenous ester-containing compounds. They play a role in the detoxification of many agrochemicals including pyrethroids, organophosphates, and carbamates. Research on these enzymes is still developing and there are several topics that should be addressed to further investigations in this area. This paper focuses on a number of these issues including enzyme nomenclature, catalytic mechanism, substrate specificity, agrochemical metabolism, role in insecticide resistance and environmental significance. It is expected that carboxylesterase research will increase with specific emphasis on isozyme and substrate identification. Future research directions are discussed and the current state of the field is evaluated. © Pesticide Science Society of Japan

Dense and uniform layers of a biologically active carbonate‐containing hydroxyapatite can be formed on various kinds of organic polymers by the following biomimetic method. First, a substrate is set in contact with particles of CaO–SiO 2 ‐based glass soaked in a simulated body fluid (SBF) with ion concentrations nearly equal to those of human blood plasma for forming the apatite nuclei on the substrate. Second, the substrate is soaked in another solution highly supersaturated with respect to the apatite, e.g, with ion concentrations 1.5 times those of SBF (1.5SBF) for making the apatite nuclei grow on the substrate in situ. The induction period for the apatite nucleation, which is defined as the time of the first treatment required for forming enough of the apatite nuclei to make the continuous layer after the second treatment, was almost 24 h for most of the examined polymers. The adhesive strength of the formed apatite layer to the polymers was as high as 3 to 4 M Pa for poly(ethylene terephthalate), poly‐ether sulfone, and poly (vinyl alcohol) hydrogel. This type of apatite–organic polymer composite is expected to be useful for repairing not only living hard tissues but also soft ones.