Abiotic formation of amorphous carbonaceous particles by a HMX (cyclotetramethylenetetranitramine) explosion experiment: implication from organic matter and the quench effect

Poster P03 abrtract, HAYABUSA 2014: 2nd symposium of solar system materials (4-5 December 2014, Sagamihara, Japan

Large-scale Discovery of Substrates of the Human Kinome

ヒトのタンパク質キナーゼ基質の大規模同定に成功 --細胞内情報伝達の全貌の解明に向けて--. 京都大学プレスリリース. 2019-07-19.Kinase networks are important for cellular signal transduction. Despite tremendous efforts to uncover these signaling pathways, huge numbers of uncharacterized phosphosites still remain in the human proteome. Because of the transient nature of kinase-substrate interactions in vivo, it is almost impossible to identify direct substrates. Here, we present a strategy for the rapid, accurate and high-throughput discovery of in vitro kinase substrates using quantitative proteomics. Using 385 purified kinases (354 wild-type protein kinases, 21 mutants and 10 lipid kinases), we identified a total of 175, 574 potential direct kinase substrates. In addition, we identified novel kinase groups, such as one group containing 30 threonine-directed kinases and another containing 15 serine/threonine/tyrosine kinases. Surprisingly, we observed that the diversity of substrates for tyrosine kinases was much higher than that for serine-threonine kinases

Application of next-generation sequencing to investigation of norovirus diversity in shellfish collected from two coastal sites in Japan from 2013 to 2014

A better understanding of the role played by shellfish regarding the manner of pathogen contamination, persistence, and selection may help considering epidemiology of noroviruses. Thus, norovirus genotype profiles in shellfish (Crassostrea gigas and Mitilus galloprovincialis) were investigated by using Next-generation sequencing (NGS) technology. In genogroup I (GI), 7 genotypes (abbreviated as GI.2 to GI.7, and GI.9) were detected from C. gigas, whereas 9 genotypes (GI.1 to GI.9) were detected from M. galloprovincialis. The genotype with the highest proportion found in both C. gigas and M. galloprovincialis was GI.4, and the second highest was GI.3. In genogroup II (GII), 17 genotypes (GII.1 to GII.9, GII.11 to GII.17, GII.21 and GI.22) were detected from C. gigas, whereas 16 genotypes (GII.1 to GII.8, GII.11 to GII.17, GII.21 and GI.22) were detected from M. galloprovincialis. The genotype with the highest proportion in both C. gigas and M. galloprovincialis was GII.4, the next highest differed between C. gigas and M. galloprovincialis. To our knowledge, this study may be the first trial to utilize the latest technology in this field, and reveal the diversity of norovirus genotypes present in shellfish

Flavor retention characteristics of amorphous solid dispersion of flavors, prepared by vacuum-foam- and spray-drying under different conditions

We investigated the powderization of flavoring substances, using an amorphous solid dispersion (ASD) technique, in which hydrophobic molecules are separately embedded in a water-soluble carrier matrix. Six flavors, five carrier forming materials (polyvinylpyrrolidone/disaccharides), two solvents (methanol/ethanol) and two drying methods (vacuum-foam-/spray-drying) were employed. The drying conditions for the two drying processes were first examined, and under the optimal drying conditions, various flavor-carrier combinations and compositions of ASD samples were prepared and their flavor retention after drying and during storage under a vacuum were compared. Results demonstrated that flavor loss during drying and storage was minimized when the material was vacuum-foam-dried with polyvinylpyrrolidone. Vacuum-foam-drying in the presence of α-maltose or palatinose also resulted in a greater retention of flavor during drying and storage than a typical O/W emulsification-based powderization. These findings suggest that the ASD-based powderization of flavoring materials is a feasible alternative to the currently used produces

Large-Scale Identification of Phosphorylation Sites for Profiling Protein Kinase Selectivity

Protein kinase selectivity is largely governed by direct binding to the target site(s) on the substrate. Thus, substrate determinants identified from sequences around phosphorylation sites are desirable resources for matching kinases to their substrates. In this study, we tried to identify kinase-selective substrate determinants, including motif sequences, based on large-scale discovery of kinase/substrate pairs. For this purpose, we employed a combination strategy of <i>in vitro</i> kinase reaction followed by LC–MS/MS analysis and applied it to three well-studied kinases: c-AMP regulated protein kinase A (PKA), extracellular signal-regulated kinase 1 (ERK1), and RAC-alpha serine/threonine-protein kinase (AKT1). Cellular proteins were fractionated, dephosphorylated with thermosensitive alkaline phosphatase, phosphorylated with the target kinase, and digested with Lys-C/trypsin, and then phosphopeptides were enriched using TiO₂-based hydroxy acid-modified metal oxide chromatography (HAMMOC) and subjected to LC–MS/MS. As a result, 3585, 4347, and 1778 <i>in vitro</i> phosphorylation sites were identified for PKA, ERK1, and AKT1, respectively. As expected, these extensive identifications of phosphorylation sites enabled extraction of both known and novel motif sequences, and this in turn permitted fine discrimination of the specificities of PKA and AKT1, which both belong to the AGC kinase family. Other unique features of the kinases were also characterized, including phospho-acceptor preference (Ser or Thr) and bias ratio of singly/multiply phosphorylated peptides. More motifs were found with this methodology as compared with target kinase phosphorylation of peptides obtained by predigestion of proteins with Lys-C/trypsin. Thus, this approach to characterization of kinase substrate determinants is effective for identification of kinases associated with particular phosphorylation sites

Relationship between tongue pressure and dysphagia diet in patients with acute stroke.

A dysphagia diet is important for patients with stroke to help manage their nutritional state and prevent aspiration pneumonia. Tongue pressure measurement is a simple, non-invasive, and objective method for diagnosing dysphagia. We hypothesized that tongue pressure may be useful in making a choice of diet for patients with acute stroke. Using balloon-type equipment, tongue pressure was measured in 80 patients with acute stroke. On admission, a multidisciplinary swallowing team including doctors, nurses, speech therapists, and management dietitians evaluated and decided on the possibility of oral intake and diet form; the tongue pressure was unknown to the team. Diet form was defined and classified as dysphagia diet Codes 0 to 4 and normal form (Code 5 in this study) according to the 2013 Japanese Dysphagia Diet Criteria. In multivariate analysis, only tongue pressure was significantly associated with the dysphagia diet form (p<0.001). Receiver operating characteristic analyses revealed that the optimal cutoff tongue pressure for predicting diet Codes 1, 2, 3, 4, and 5 was 3.6 (p<0.001, area under the curve [AUC] = 0.997), 9.6 (p<0.001, AUC = 0.973), 12.8 (p<0.001, AUC = 0.963), 16.5 (p<0.001, AUC = 0.979), and 17.3 kPa (p<0.001, AUC = 0.982), respectively. Tongue pressure is one of the sensitive indicators for choosing dysphagia diet forms in patients with acute stroke. A combination of simple modalities will increase the accuracy of the swallowing assessment and choice of the diet form

Flavor retention characteristics of amorphous solid dispersion of flavors, prepared by vacuum-foam- and spray-drying under different conditions

We investigated the powderization of flavoring substances, using an amorphous solid dispersion (ASD) technique, in which hydrophobic molecules are separately embedded in a water-soluble carrier matrix. Six flavors, five carrier forming materials (polyvinylpyrrolidone/disaccharides), two solvents (methanol/ethanol) and two drying methods (vacuum-foam-/spray-drying) were employed. The drying conditions for the two drying processes were first examined, and under the optimal drying conditions, various flavor-carrier combinations and compositions of ASD samples were prepared and their flavor retention after drying and during storage under a vacuum were compared. Results demonstrated that flavor loss during drying and storage was minimized when the material was vacuum-foam-dried with polyvinylpyrrolidone. Vacuum-foam-drying in the presence of α-maltose or palatinose also resulted in a greater retention of flavor during drying and storage than a typical O/W emulsification-based powderization. These findings suggest that the ASD-based powderization of flavoring materials is a feasible alternative to the currently used produces.</p