Decision support for extracting and dissolving consumers’ uneasiness over foods using stochastic DEMATEL, Journal of Telecommunications and Information Technology, 2006, nr 4

In this paper we try to extract consumers’ uneasy factors on foods such as carcinogenic substance, bovine spongiform encephalopathy (BSE) problem, genetic recombination, etc., and try to construct structural models among these uneasy factors using stochastic DEMATEL. Stochastic DEMATEL is developed as a revised DEMATEL (Decision Making Trial and Evaluation Laboratory) to extract structural models of a complex problematique composed of many factors under uncertainty. For structural modeling of uneasy factors on foods we look at the binary relation such that “How much would it help to dissolve uneasy factor j by dissolving uneasy factor i?” Finally, we try to find the priority of dissolving each factor among all the uneasy factors based on the information of stochastic composite importance. This would contribute for decision support to dissolve uneasy feeling and to get sense of security on foods

Acetylome of acinetobacter baumannii SK17 reveals a highly-conserved modification of histone-like protein HU

Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13. HU is a dimeric DNA-binding protein critical for maintaining chromosomal architecture and other DNA-dependent functions. To analyze the effects of site-specific acetylation, homogenously Lys13-acetylated HU protein, HU(K13ac) was prepared by genetic code expansion. Whilst not exerting an obvious effect on the oligomeric state, Lys13 acetylation alters both the thermal stability and DNA binding kinetics of HU. Accordingly, this modification likely destabilizes the chromosome structure and regulates bacterial gene transcription. This work indicates that acetyllysine plays an important role in bacterial epigenetics

The role of endoscopic ultrasound in the evaluation of rectal polypoid lesions in 25 dogs

We investigated the role of endoscopic ultrasound in the evaluation of rectal polypoid lesions in 25 dogs. Twenty-five cases of rectal polypoid lesions in dogs who underwent surgery after endoscopic and EUS assessment were studied. The invasion depth of the polypoid lesion was classified as M stage (lesions in the mucosa only), SM stage (lesions in the mucosa and submucosa), and MP stage (lesions extending to the muscularis propria). Transabdominal ultrasound was performed in nine cases, but not all were evaluated in detail. EUS provided detailed images for all cases and showed a significant correlation with surgical pathology in the T stage (accuracy, 92%; κ = 0.77). As per classification by invasion depth, inflammatory polyps were only M polypoid lesions, whereas SM and MP polypoid lesions were only adenocarcinomas (P < 0.05). The average survival time according to specific condition was as follows: 1,235 days for inflammatory polyps, and 804 days for M adenocarcinoma. The survival time of two SM adenocarcinoma cases was 756 and 2,114 days, respectively, and the survival time of two MP adenocarcinoma cases was 16 and 42 days, respectively. EUS were useful for the evaluation of rectal polypoid lesions in dogs, whereas transabdominal ultrasound was not. Determination of the invasion depth of polypoid lesions using EUS may be useful for the evaluation of malignancy and prognosis

The characteristics of short- and long-term surviving Shiba dogs with chronic enteropathies and the risk factors for poor outcome

Background: The objectives of this study were to investigate the differences in the characteristics of short- and long-term surviving dogs, and the factors that predict poor outcome in Shiba dogs with chronic enteropathies (CE). Methods: A total of 25 Shiba dogs were included in this study, and classified as either short-term (≤6 months) survivors (Ss; n=16) or long-term (>6 months) survivors (Ls; n=9). The clinical and clinicopathological variables, histopathology, response to therapy, and outcomes were investigated between groups. Furthermore, these factors were tested for their ability to predict poor outcome. Results: All CE dogs were diagnosed as having inflammatory bowel disease (IBD) with lymphocytic-plasmacytic enteritis (LPE). Age and canine inflammatory bowel disease activity index (CIBDAI) were significantly higher in the Ss group than in the Ls group (age: p = 0.035, CIBDAI: p = 0.018), as determined via univariate logistic regression analysis. According to receiver operator characteristic (ROC) curve analysis, the best predictors of poor outcome were age and CIBDAI, with the cutoffs determined as 7 years and 9 points, respectively. The majority of the cases (84%) responded to initial treatment; in particular, 75% of dogs in Ss group responded to therapy. The time to response (days) to the initial treatment in the Ss group (median 42.5 days, range: 20-91 days) was significantly shorter than that of the Ls group (median 285 days, range: 196-1026 days). Approximately half (55.5%) of the dogs in the Ls group died due to relapse of CE. Conclusions: This study suggested that there is a high risk of early mortality in Shiba dogs with CE, particularly if the dogs are older (>7 years) and have a high CIBDAI score (>9 points). There appears to be a possibility of early mortality even if the initial treatment was efficacious. Furthermore, Shiba dogs with CE that become less responsive to initial therapy in the short-term (approximately 3 months) are more likely to have an early mortality. Thus, it is necessary to follow-up Shiba dogs with CE in the long-term, as approximately half of the long-term survivors eventually died due to a relapse of the signs

Structure–activity characteristics of phenylalanine analogs selectively transported by L-type amino acid transporter 1 (LAT1)

Abstract L-type amino acid transporter 1 (LAT1) is a transmembrane protein responsible for transporting large neutral amino acids. While numerous LAT1-targeted compound delivery for the brain and tumors have been investigated, their LAT1 selectivity often remains ambiguous despite high LAT1 affinity. This study assessed the LAT1 selectivity of phenylalanine (Phe) analogs, focusing on their structure–activity characteristics. We discovered that 2-iodo-l-phenylalanine (2-I-Phe), with an iodine substituent at position 2 in the benzene ring, markedly improves LAT1 affinity and selectivity compared to parent amino acid Phe, albeit at the cost of reduced transport velocity. l-Phenylglycine (Phg), one carbon shorter than Phe, was found to be a substrate for LAT1 with a lower affinity, exhibiting a low level of selectivity for LAT1 equivalent to Phe. Notably, (R)-2-amino-1,2,3,4-tetrahydro-2-naphthoic acid (bicyclic-Phe), with an α-methylene moiety akin to the α-methyl group in α-methyl-l-phenylalanine (α-methyl-Phe), a known LAT1-selective compound, showed similar LAT1 transport maximal velocity to α-methyl-Phe, but with higher LAT1 affinity and selectivity. In vivo studies revealed tumor-specific accumulation of bicyclic-Phe, underscoring the importance of LAT1-selectivity in targeted delivery. These findings emphasize the potential of bicyclic-Phe as a promising LAT1-selective component, providing a basis for the development of LAT1-targeting compounds based on its structural framework

Acetylome with Structural Mapping Reveals the Significance of Lysine Acetylation in <i>Thermus thermophilus</i>

Lysine acetylation in proteins has recently been globally identified in bacteria and eukaryotes. Even though acetylproteins are known to be involved in various cellular processes, its physiological significance has not yet been resolved. Using a proteomics approach in combination with immunoprecipitation, we identified 197 lysine acetylation sites and 4 N-terminal acetylation sites from 128 proteins in <i>Thermus thermophilus</i> HB8, an extremely thermophilic eubacterium. Our analyses revealed that identified acetylproteins are well conserved across all three domains of life and are mainly involved in central metabolism and translation. To characterize the functional significance further, we successfully mapped 172 acetylation sites on their 59 authentic and 54 homologous protein structures. Although the percentage of acetylation on ordered structures was higher than that of the disordered structure, no tendency of acetylation in <i>T. thermophilus</i> was detected in secondary structures. However, the acetylated lysine was situated near the negatively charged glutamic acid residues. In tertiary structure analyses, 58 sites of 103 acetylations mapped on 59 authentic structures of <i>T. thermophilus</i> were located within a considerable distance that can disrupt electrostatic interactions and hydrogen bonding networks on protein surfaces, demonstrating the physiological significance of the acetylation that can directly alter the protein structure. In addition, we found 16 acetylation sites related to Schiff base formation, ligand binding, and protein–RNA and protein–protein interactions that involve the potential function of the proteins. The structural mapping of acetylation sites provides new molecular insight into the role of lysine acetylation in the proteins

Acetylome with Structural Mapping Reveals the Significance of Lysine Acetylation in <i>Thermus thermophilus</i>

Lysine acetylation in proteins has recently been globally identified in bacteria and eukaryotes. Even though acetylproteins are known to be involved in various cellular processes, its physiological significance has not yet been resolved. Using a proteomics approach in combination with immunoprecipitation, we identified 197 lysine acetylation sites and 4 N-terminal acetylation sites from 128 proteins in <i>Thermus thermophilus</i> HB8, an extremely thermophilic eubacterium. Our analyses revealed that identified acetylproteins are well conserved across all three domains of life and are mainly involved in central metabolism and translation. To characterize the functional significance further, we successfully mapped 172 acetylation sites on their 59 authentic and 54 homologous protein structures. Although the percentage of acetylation on ordered structures was higher than that of the disordered structure, no tendency of acetylation in <i>T. thermophilus</i> was detected in secondary structures. However, the acetylated lysine was situated near the negatively charged glutamic acid residues. In tertiary structure analyses, 58 sites of 103 acetylations mapped on 59 authentic structures of <i>T. thermophilus</i> were located within a considerable distance that can disrupt electrostatic interactions and hydrogen bonding networks on protein surfaces, demonstrating the physiological significance of the acetylation that can directly alter the protein structure. In addition, we found 16 acetylation sites related to Schiff base formation, ligand binding, and protein–RNA and protein–protein interactions that involve the potential function of the proteins. The structural mapping of acetylation sites provides new molecular insight into the role of lysine acetylation in the proteins