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1.
Comput Methods Programs Biomed ; 190: 105385, 2020 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-32062090

RESUMO

BACKGROUND AND OBJECTIVE: Hand gesture recognition systems in operating rooms (ORs) are crucial for browsing and controlling computer-aided devices, which have been developed to decrease the risk of contamination during surgical procedures. METHODS: We proposed the use of hand gesture recognition to enhance accuracies and recognition areas with the capsule network (CapsNet) of deep neural network and Leap Motionâ Our method includes the i) extraction and preprocessing of infrared (IR) images (60 frames per second) from Leap Motion™, ii) training of various types of networks, and iii) gesture recognition evaluation in the OR. We trained the images of training dataset (N=903) and tested images (N=100) using five types of surgical hand gestures including hovering, grab, click, one peak, and two peaks by 10 subjects with various types of augmentation methods including rotate (0∘, 90∘, 180∘), scale, translation, illumination, and resize. RESULTS: CapsNet achieved a classification accuracy of 86.46% (around 10% improvement) compared with 73.67% for the baseline convolutional neural network (CNN) and 76.4% for VGG16. CONCLUSIONS: In conclusion, the accuracy of hand gesture recognition with CapsNet was better than that of conventional CNNs, which could be used to navigate and manipulate various types of computer-aided devices and applications through contactless gesture interaction.

2.
Sci Rep ; 10(1): 297, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31941937

RESUMO

IL-17A is an important cytokine in intestinal inflammation. However, anti-IL-17A therapy does not improve clinical outcomes in patients with Crohn's disease. We aimed to evaluate the role of RORγt+ innate lymphoid cells (ILCs) in murine colitis models in the absence of IL-17A. An acute colitis model was induced with either dextran sulfate sodium (DSS) or trinitrobenzenesulfonic acid (TNBS) and a chronic colitis model was induced by CD4+CD45RBhi T cell transfer from either wild-type C57BL/6 or Il17a-/- mice. An anti-IL-17A antibody, secukinumab, was also used to inhibit IL-17A function in the colitis model. Flow cytometry was performed to analyze the population of RORγt+ ILCs in the colonic lamina propria of mice with chronic colitis. Acute intestinal inflammation due to DSS and TNBS was attenuated in IL-17A knockout mice, whereas chronic colitis was not relieved by T cell transfer from Il17a-/- mice (% of original body weight: wild-type mice vs. Il17a-/- mice, 81.9% vs. 82.2%; P = 0.922). However, the mean proportion of Lin-RORγt+ lymphocytes was higher after T cell transfer from Il17a-/- mice than that after T cell transfer from wild-type mice (28.8% vs. 18.5%). The proportion of Lin-RORγt+ was also increased in Rag2-/- mice that received T cell transfer from wild-type mice when anti-IL-17A antibody was administered (31.7%). Additionally, Il6 and Il22 tended to be highly expressed after T cell transfer from Il17a-/- mice. In conclusion, RORγt+ ILCs may have an important role in the pathogenesis of chronic colitis in the absence of IL-17A. Blocking the function of IL-17A may upregulate Il6 and recruit RORγt+ ILCs in chronic colitis, thereby upregulating IL-22 and worsening the clinical outcomes of patients with Crohn's disease.

3.
Plant J ; 2020 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-31925835

RESUMO

Sessile plants have evolved distinct mechanisms to respond and adapt to adverse environmental conditions through diverse mechanisms including RNA processing. While the role of RNA processing in the stress response is well understood for Arabidopsis thaliana, limited information is available for rice (Oryza sativa). Here, we show that OsFKBP20-1b, belonging to the immunophilin family, interacts with the splicing factor OsSR45 in both nuclear speckles and cytoplasmic foci, and plays an essential role in post-transcriptional regulation of abiotic stress response. The expression of OsFKBP20-1b was highly upregulated under various abiotic stresses. Moreover genetic analysis revealed that OsFKBP20-1b positively affected transcription and pre-mRNA splicing of stress-responsive genes under abiotic stress conditions. In osfkbp20-1b loss-of-function mutants, the expression of stress-responsive genes was downregulated, while that of their splicing variants was increased. Conversely, in plants overexpressing OsFKBP20-1b, the expression of the same stress-responsive genes was strikingly upregulated under abiotic stress. In vivo experiments demonstrated that OsFKBP20-1b directly maintains protein stability of OsSR45 splicing factor. Furthermore, we found that the plant-specific OsFKBP20-1b gene has uniquely evolved as a paralogue only in some Poaceae species. Together, our findings suggest that OsFKBP20-1b-mediated RNA processing contributes to stress adaptation in rice.

4.
Anticancer Res ; 40(1): 109-119, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31892559

RESUMO

BACKGROUND/AIM: Although molecular targeting therapy is an attractive treatment for cancer, resistance eventually develops in most cases. Here, we evaluated chemotherapeutic efficacy on non-small cell lung cancer (NSCLC) with acquired resistance to epidermal growth factor receptor inhibitors mechanistically. MATERIALS AND METHODS: Antitumor effects of taxotere were evaluated using multiple models, including xenograft, and patient-derived models developed from adenocarcinoma cancer patients. Protein expressions were analyzed after drug treatment. RESULTS: Taxotere inhibited tumor growth of NSCLC cells harboring drug resistance, and reduced the expression of phosphorylated MET proto-oncogene, receptor tyrosine kinase (MET). A tumor-inhibitory effect of taxotere was also demonstrated in vivo in xenografts in mice, patient-derived primary lung tumor cells and patient-derived xenograft with concomitant repression of phosphorylated MET expression. Chemotherapeutic and MET-targeting drug exhibited a synergistic cell growth-inhibitory effect. CONCLUSION: These results suggest that the anticancer drug taxane may be an adjuvant for lung tumors exhibiting enhanced signaling of MET networks.


Assuntos
Antineoplásicos/farmacologia , Docetaxel/farmacologia , Neoplasias/metabolismo , Proteínas Proto-Oncogênicas c-met/metabolismo , Animais , Biomarcadores , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Modelos Animais de Doenças , Humanos , Camundongos , Neoplasias/tratamento farmacológico , Neoplasias/patologia , Fosforilação , Inibidores de Proteínas Quinases/farmacologia , Transdução de Sinais , Ensaios Antitumorais Modelo de Xenoenxerto
5.
Plant Mol Biol ; 102(1-2): 19-38, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31786704

RESUMO

KEY MESSAGE: Plant possesses particular Golgi-resident cyclophilin 21 proteins (CYP21s) and the catalytic isomerase activities have a negative effect on ABA signalling gene expression during early seedling development. Cyclophilins (CYPs) are essential for diverse cellular process, as these catalyse a rate-limiting step in protein folding. Although Golgi proteomics in Arabidopsis thaliana suggests the existence of several CYPs in the Golgi apparatus, only one putative Golgi-resident CYP protein has been reported in rice (Oryza sativa L.; OsCYP21-4). Here, we identified the Golgi-resident CYP21 family genes and analysed their molecular characteristics in Arabidopsis and rice. The CYP family genes (CYP21-1, CYP21-2, CYP21-3, and CYP21-4) are plant-specific, and their appearance and copy numbers differ among plant species. CYP21-1 and CYP21-4 are common to all angiosperms, whereas CYP21-2 and CYP21-3 evolved in the Malvidae subclass. Furthermore, all CYP21 proteins localize to cis-Golgi, trans-Golgi or both cis- and trans-Golgi membranes in plant cells. Additionally, based on the structure, enzymatic function, and topological orientation in Golgi membranes, CYP21 proteins are divided into two groups. Genetic analysis revealed that Group I proteins (CYP21-1 and CYP21-2) exhibit peptidyl prolyl cis-trans isomerase (PPIase) activity and regulate seed germination and seedling growth and development by affecting the expression levels of abscisic acid signalling genes. Thus, we identified the Golgi-resident CYPs and demonstrated that their PPIase activities are required for early seedling growth and development in higher plants.

6.
PLoS One ; 14(12): e0225961, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31800638

RESUMO

BACKGROUND: Although the high-throughput sequencing technique is useful for evaluating gastric microbiome, it is difficult to use clinically. We aimed to develop a predictive model for gastric microbiome based on serologic testing. METHODS: This study was designed to analyze sequencing data obtained from the Hanyang University Gastric Microbiome Cohort, which was established initially to investigate gastric microbial composition according to the intragastric environment. We evaluated the relationship between the relative abundance of potential gastric cancer-associated bacteria (nitrosating/nitrate-reducing bacteria or type IV secretion system [T4SS] protein gene-contributing bacteria) and serologic markers (IgG anti-Helicobacter pylori [HP] antibody or pepsinogen [PG] levels). RESULTS: We included 57 and 26 participants without and with HP infection, respectively. The relative abundance of nitrosating/nitrate-reducing bacteria was 4.9% and 3.6% in the HP-negative and HP-positive groups, respectively, while that of T4SS protein gene-contributing bacteria was 20.5% and 6.5% in the HP-negative and HP-positive groups, respectively. The relative abundance of both nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria increased exponentially as PG levels decreased. Advanced age (only for nitrosating/nitrate-reducing bacteria), a negative result of IgG anti-HP antibody, low PG levels, and high Charlson comorbidity index were associated with a high relative abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria. The adjusted coefficient of determination (R2) was 53.7% and 70.0% in the model for nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria, respectively. CONCLUSION: Not only the negative results of IgG anti-HP antibody but also low PG levels were associated with a high abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria.

7.
PLoS One ; 14(12): e0226907, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31860645

RESUMO

It has been suggested that manipulation of gut microbiota using antibiotics can inhibit colitis-associated colorectal cancer (CAC) in a mouse model. We investigated whether timing of gut microbial manipulation using antibiotics affects colon tumorigenesis in the azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced CAC model. CAC was induced in C57BL/6 mice by injection of 12.5 mg/kg AOM followed by three rounds of 1.7% DSS exposure. There were six groups based on timing of antibiotic administration. Colonic inflammation, proliferation, and tumorigenesis were evaluated after animal sacrifice. High-throughput sequencing of the mice feces was performed to characterize changes in gut microbiota. Full-time antibiotic treatment significantly decreased the number and size of tumors, histological scores, and expression of pro-inflammatory cytokines compared to the AOM/DSS group without antibiotic treatment. The early and late antibiotic groups, antibiotic administration from the first and second rounds of DSS to the end of the study, showed significantly lower histological scores and tumor burden. In contrast, the pretreatment antibiotic group, antibiotic administration from 3 weeks prior to AOM to the first round of DSS, did not exhibit decreased tumorigenesis. Principal coordinate analysis showed similar gut microbial community structures among the full-time, early, and late antibiotic groups, whereas other groups showed distinct gut microbial profiles. There was a positive correlation between number of tumors and number of operational taxonomic units. Colonic tumorigenesis was attenuated by antibiotic administration, except for that only prior to DSS administration, suggesting that gut microbial changes should be maintained throughout the entire period of inflammation to suppress tumorigenesis.

8.
Sci Rep ; 9(1): 12444, 2019 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-31455798

RESUMO

In addition to Helicobacter pylori infection, nitrosating/nitrate-reducing bacteria and type IV secretion system (T4SS) protein gene-contributing bacteria have been proposed as potential causes of gastric cancer development. However, bacterial modules related with gastric carcinogenesis have not been clarified. In this study, we analyzed gastric microbiome using the gastric mucosal samples obtained from the Hanyang University Gastric Microbiome Cohort by 16S rRNA gene sequencing. Weighted correlation network analysis was performed to construct a microbiome network and to identify microbial modules associated with gastric carcinogenesis. At the family level, 420 bacterial taxa were identified in the gastric microbiome of 83 participants. Through network analysis, 18 microbial modules were organized. Among them, two modules-pink and brown-were positively correlated with a higher-risk of gastric cancer development such as intestinal metaplasia with no current H. pylori infection (correlation coefficient [γ]: pink module, 0.31 [P = 0.004], brown module, 0.26 [P = 0.02]). At the family level, twenty-two and thirty-two bacterial taxa belonged to the pink and brown modules, respectively. They included nitrosating/nitrate-reducing bacteria, T4SS protein gene-contributing bacteria, and various other bacteria, including Gordoniaceae, Tsukamurellaceae, Prevotellaceae, Cellulomonadaceae, Methylococcaceae, and Procabacteriaceae. The blue module, which included H. pylori, was correlated negatively with intestinal metaplasia (γ = -0.49 [P < 0.001]). In conclusion, intragastric bacterial taxa associated with gastric carcinogenesis can be classified by network analysis. Microbial modules may provide an integrative view of the microbial ecology relevant to precancerous lesions in the stomach.

9.
Psychiatry Investig ; 16(8): 625-628, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31446688

RESUMO

The purpose of the present study was to examine the severity of suicidal ideation of the older adults according to the amount of involvement in grandchild care. Data for this research were drawn from a cross-sectional study conducted on community-dwelling adults aged 65 years or older. The 922 participants were divided into three groups according to their involvement in grandchild care: 18.5% had provided daily care, 12.4% had provided occasional care, and 69.1% had never cared for their grandchildren. ANCOVA analysis showed that the scores for depression was significantly lower in the group which took care of their grandchildren occasionally compared to the other two groups. The scores for suicidal ideation was significantly higher in the group which had never taken care of their grandchildren compared to the other two groups. Current study suggests that grandparenting may have a positive effect on suicidal ideation of the older adults.

10.
Korean J Radiol ; 20(8): 1275-1284, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31339015

RESUMO

OBJECTIVE: To develop algorithms using convolutional neural networks (CNNs) for automatic segmentation of acute ischemic lesions on diffusion-weighted imaging (DWI) and compare them with conventional algorithms, including a thresholding-based segmentation. MATERIALS AND METHODS: Between September 2005 and August 2015, 429 patients presenting with acute cerebral ischemia (training:validation:test set = 246:89:94) were retrospectively enrolled in this study, which was performed under Institutional Review Board approval. Ground truth segmentations for acute ischemic lesions on DWI were manually drawn under the consensus of two expert radiologists. CNN algorithms were developed using two-dimensional U-Net with squeeze-and-excitation blocks (U-Net) and a DenseNet with squeeze-and-excitation blocks (DenseNet) with squeeze-and-excitation operations for automatic segmentation of acute ischemic lesions on DWI. The CNN algorithms were compared with conventional algorithms based on DWI and the apparent diffusion coefficient (ADC) signal intensity. The performances of the algorithms were assessed using the Dice index with 5-fold cross-validation. The Dice indices were analyzed according to infarct volumes (< 10 mL, ≥ 10 mL), number of infarcts (≤ 5, 6-10, ≥ 11), and b-value of 1000 (b1000) signal intensities (< 50, 50-100, > 100), time intervals to DWI, and DWI protocols. RESULTS: The CNN algorithms were significantly superior to conventional algorithms (p < 0.001). Dice indices for the CNN algorithms were 0.85 for U-Net and DenseNet and 0.86 for an ensemble of U-Net and DenseNet, while the indices were 0.58 for ADC-b1000 and b1000-ADC and 0.52 for the commercial ADC algorithm. The Dice indices for small and large lesions, respectively, were 0.81 and 0.88 with U-Net, 0.80 and 0.88 with DenseNet, and 0.82 and 0.89 with the ensemble of U-Net and DenseNet. The CNN algorithms showed significant differences in Dice indices according to infarct volumes (p < 0.001). CONCLUSION: The CNN algorithm for automatic segmentation of acute ischemic lesions on DWI achieved Dice indices greater than or equal to 0.85 and showed superior performance to conventional algorithms.

11.
Sci Rep ; 9(1): 5123, 2019 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-30914690

RESUMO

Pathologic diagnoses mainly depend on visual scoring by pathologists, a process that can be time-consuming, laborious, and susceptible to inter- and/or intra-observer variations. This study proposes a novel method to enhance pathologic scoring of renal allograft rejection. A fully automated system using a convolutional neural network (CNN) was developed to identify regions of interest (ROIs) and to detect C4d positive and negative peritubular capillaries (PTCs) in giga-pixel immunostained slides. The performance of faster R-CNN was evaluated using optimal parameters of the novel method to enlarge the size of labeled masks. Fifty and forty pixels of the enlarged size images showed the best performance in detecting C4d positive and negative PTCs, respectively. Additionally, the feasibility of deep-learning-assisted labeling as independent dataset to enhance detection in this model was evaluated. Based on these two CNN methods, a fully automated system for renal allograft rejection was developed. This system was highly reliable, efficient, and effective, making it applicable to real clinical workflow.

12.
Helicobacter ; 24(1): e12547, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30440093

RESUMO

BACKGROUND: Despite recent advances in studies on the gastric microbiome, the role of the non-Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM. METHODS: Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori- infection status (H. pylori-positive and H. pylori-negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium. RESULTS: Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori-negative CSG, H. pylori-negative IM, H. pylori-negative cancer, H. pylori-positive CSG, H. pylori-positive IM, and H. pylori-positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori-negative CSG group compared to in the H. pylori-negative IM and H. pylori-negative cancer groups (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori-negative IM group (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori-infected stomachs progressed from gastritis to IM. In the H. pylori-negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-. CONCLUSIONS: The relative abundance of Rhizobiales was higher in patients with H. pylori-negative IM than in those with H. pylori-negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.


Assuntos
Microbioma Gastrointestinal/genética , Infecções por Helicobacter/microbiologia , Infecções por Helicobacter/patologia , Intestinos/microbiologia , Intestinos/patologia , Metaplasia/microbiologia , Adulto , Idoso , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Progressão da Doença , Feminino , Gastrite/microbiologia , Gastrite/patologia , Gastrite Atrófica/tratamento farmacológico , Gastrite Atrófica/microbiologia , Gastrite Atrófica/patologia , Microbioma Gastrointestinal/efeitos dos fármacos , Infecções por Helicobacter/tratamento farmacológico , Helicobacter pylori/efeitos dos fármacos , Helicobacter pylori/genética , Helicobacter pylori/isolamento & purificação , Humanos , Masculino , Metagenômica , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Neoplasias Gástricas/microbiologia , Neoplasias Gástricas/patologia , Sistemas de Secreção Tipo IV/genética , Adulto Jovem
13.
Molecules ; 23(12)2018 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-30501110

RESUMO

Protein kinases are deeply involved in immune-related diseases and various cancers. They are a potential target for structure-based drug discovery, since the general structure and characteristics of kinase domains are relatively well-known. However, the ATP binding sites in protein kinases, which serve as target sites, are highly conserved, and thus it is difficult to develop selective kinase inhibitors. To resolve this problem, we performed molecular dynamics simulations on 26 kinases in the aqueous solution, and analyzed topological water networks (TWNs) in their ATP binding sites. Repositioning of a known kinase inhibitor in the ATP binding sites of kinases that exhibited a TWN similar to interleukin-1 receptor-associated kinase 4 (IRAK4) allowed us to identify a hit molecule. Another hit molecule was obtained from a commercial chemical library using pharmacophore-based virtual screening and molecular docking approaches. Pharmacophoric features of the hit molecules were hybridized to design a novel compound that inhibited IRAK4 at low nanomolar levels in the in vitro assay.


Assuntos
Desenho de Drogas , Quinases Associadas a Receptores de Interleucina-1/antagonistas & inibidores , Inibidores de Proteínas Quinases/farmacologia , Água/química , Sítios de Ligação , Avaliação Pré-Clínica de Medicamentos , Reposicionamento de Medicamentos , Simulação de Acoplamento Molecular , Inibidores de Proteínas Quinases/química , Estaurosporina/química , Estaurosporina/farmacologia
14.
J Korean Med Sci ; 33(52): e347, 2018 Dec 24.
Artigo em Inglês | MEDLINE | ID: mdl-30584419

RESUMO

Background: Smartphone addiction has recently been highlighted as a major health issue among adolescents. In this study, we assessed the degree of agreement between adolescents' and parents' ratings of adolescents' smartphone addiction. Additionally, we evaluated the psychosocial factors associated with adolescents' and parents' ratings of adolescents' smartphone addiction. Methods: In total, 158 adolescents aged 12-19 years and their parents participated in this study. The adolescents completed the Smartphone Addiction Scale (SAS) and the Isolated Peer Relationship Inventory (IPRI). Their parents also completed the SAS (about their adolescents), SAS-Short Version (SAS-SV; about themselves), Generalized Anxiety Disorder-7 (GAD-7), and Patient Health Questionnaire-9 (PHQ-9). We used the paired t-test, McNemar test, and Pearson's correlation analyses. Results: Percentage of risk users was higher in parents' ratings of adolescents' smartphone addiction than ratings of adolescents themselves. There was disagreement between the SAS and SAS-parent report total scores and subscale scores on positive anticipation, withdrawal, and cyberspace-oriented relationship. SAS scores were positively associated with average minutes of weekday/holiday smartphone use and scores on the IPRI and father's GAD-7 and PHQ-9 scores. Additionally, SAS-parent report scores showed positive associations with average minutes of weekday/holiday smartphone use and each parent's SAS-SV, GAD-7, and PHQ-9 scores. Conclusion: The results suggest that clinicians need to consider both adolescents' and parents' reports when assessing adolescents' smartphone addiction, and be aware of the possibility of under- or overestimation. Our results cannot only be a reference in assessing adolescents' smartphone addiction, but also provide inspiration for future studies.


Assuntos
Comportamento Aditivo/patologia , Pais/psicologia , Smartphone , Adolescente , Criança , Feminino , Humanos , Internet , Masculino , Psicologia do Adolescente , Inquéritos e Questionários , Adulto Jovem
15.
Genes Genomics ; 40(11): 1157-1167, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30315522

RESUMO

Sulfolobus species can grow on a variety of organic compounds as carbon and energy sources. These species degrade glucose to pyruvate by the modified branched Entner-Doudoroff pathway. We attempted to determine the differentially expressed genes (DEGs) under sugar-limited and sugar-rich conditions. RNA sequencing (RNA-seq) was used to quantify the expression of the genes and identify those DEGs between the S. acidocaldarius cells grown under sugar-rich (YT with glucose) and sugar-limited (YT only) conditions. The functions and pathways of the DEGs were examined using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Quantitative real-time PCR (qRT-PCR) was performed to validate the DEGs. Transcriptome analysis of the DSM 639 strain grown on sugar-limited and sugar-rich media revealed that 853 genes were differentially expressed, among which 481 were upregulated and 372 were downregulated under the glucose-supplemented condition. In particular, 70 genes showed significant changes in expression levels of ≥ twofold. GO and KEGG enrichment analyses revealed that the genes encoding components of central carbon metabolism, the respiratory chain, and protein and amino acid biosynthetic machinery were upregulated under the glucose condition. RNA-seq and qRT-PCR analyses indicated that the sulfur assimilation genes (Saci_2197-2204) including phosphoadenosine phosphosulfate reductase and sulfite reductase were significantly upregulated in the presence of glucose. The present study revealed metabolic networks in S. acidocaldarius that are induced in a glucose-dependent manner, improving our understanding of biomass production under sugar-rich conditions.


Assuntos
Glucose/metabolismo , Sulfolobus acidocaldarius/genética , Aminoácidos/metabolismo , Carbono/metabolismo , Perfilação da Expressão Gênica , Análise de Sequência de RNA , Sulfolobus acidocaldarius/crescimento & desenvolvimento , Sulfolobus acidocaldarius/metabolismo , Enxofre/metabolismo , Regulação para Cima
16.
Comput Methods Programs Biomed ; 161: 39-44, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29852966

RESUMO

BACKGROUND AND OBJECTIVE: Contactless operating room (OR) interfaces are important for computer-aided surgery, and have been developed to decrease the risk of contamination during surgical procedures. METHODS: In this study, we used Leap Motion™, with a personalized automated classifier, to enhance the accuracy of gesture recognition for contactless interfaces. This software was trained and tested on a personal basis that means the training of gesture per a user. We used 30 features including finger and hand data, which were computed, selected, and fed into a multiclass support vector machine (SVM), and Naïve Bayes classifiers and to predict and train five types of gestures including hover, grab, click, one peak, and two peaks. RESULTS: Overall accuracy of the five gestures was 99.58% ±â€¯0.06, and 98.74% ±â€¯3.64 on a personal basis using SVM and Naïve Bayes classifiers, respectively. We compared gesture accuracy across the entire dataset and used SVM and Naïve Bayes classifiers to examine the strength of personal basis training. CONCLUSIONS: We developed and enhanced non-contact interfaces with gesture recognition to enhance OR control systems.


Assuntos
Gestos , Informática Médica/métodos , Salas Cirúrgicas , Reconhecimento Automatizado de Padrão , Algoritmos , Teorema de Bayes , Registros Eletrônicos de Saúde , Mãos , Humanos , Modelos Estatísticos , Reprodutibilidade dos Testes , Software , Máquina de Vetores de Suporte , Interface Usuário-Computador
17.
J Microbiol Biotechnol ; 28(6): 909-916, 2018 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-29642287

RESUMO

Previously, a cytosolic trehalase (TreH) from the hyperthermophilic archaeon Sulfolobus acidocaldarius was reported; however, the gene responsible for the trehalase activity was not identified. Two genes, saci_1816 and saci_1250, that encode the glycoside hydrolase family 15 type glucoamylase-like proteins in S. acidocaldarius were targeted and expressed in Escherichia coli, and their abilities to hydrolyze trehalose were examined. Recombinant Saci_1816 hydrolyzed trehalose exclusively without any help from a cofactor. The mass spectrometric analysis of partially purified native TreH also confirmed that Saci_1816 was involved in proteins exhibiting trehalase activity. Optimal trehalose hydrolysis activity of the recombinant Saci_1816 was observed at pH 4.0 and 60°C. The pH dependence of the recombinant enzyme was similar to that of the native enzyme, but its optimal temperature was 20-25°C lower, and its thermostability was also slightly reduced. From the biochemical and structural results, Saci_1816 was identified as a trehalase responsible for trehalose degradation in S. acidocaldarius. Identification of the treH gene confirms that the degradation of trehalose in Sulfolobus species occurs via the TreH pathway.


Assuntos
Sulfolobus acidocaldarius/enzimologia , Trealase/metabolismo , Trealose/metabolismo , Clonagem Molecular , Estabilidade Enzimática , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Concentração de Íons de Hidrogênio , Hidrólise , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Temperatura Ambiente , Trealase/química , Trealase/genética
18.
Front Plant Sci ; 8: 1250, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28775727

RESUMO

CYP21-4 is a novel Golgi-localized cyclophilin protein involved in oxidative stress tolerance. Here, we generated transgenic plants overexpressing AtCYP21-4 and OsCYP21-4 in potato and rice, respectively. The stems and roots of AtCYP21-4-overexpressing potato plants were longer than those of wild-type (WT) plants, which resulted in heavier tubers. In vitro tuberization in the transgenic potato also resulted in significantly greater tuber number and weight, as well as a shorter time to microtuber formation. Similarly, OsCYP21-4-overexpressing transgenic rice plants had higher biomass and productivity with longer early-stage internodes than the WT and higher seed weight. Immunoblot analysis with CYP21-4 antibody showed that these productivity-enhancing phenotypes were associated with high CYP21-4s protein expression. Anatomically, transgenic potato stems exhibited higher lignin content in xylem cells and thicker leaves. In addition, relative content of mannosidic glycoproteins per unit of total protein was above 20% in transgenic potato tubers and rice grains. Based on these findings, we propose that CYP21-4s are involved in the growth and development of plant vegetative and storage tissues via their effects on glycoprotein abundance or glycan processing in the Golgi apparatus. Thus, increasing CYP21-4s expression in crops could represent an alternative way to increase crop productivity and yield.

19.
J Biosci Bioeng ; 124(3): 289-295, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28479043

RESUMO

The putative gene cluster involved in the degradation of the raffinose family oligosaccharides (RFO) was identified in Caldicellulosiruptor bescii. Within the cluster, the gene encoding a putative α-galactosidase (CbAga36) was cloned and expressed in Escherichia coli. Size exclusion chromatography of the purified rCbAga36 indicated that the native form was a tetramer. Its primary sequence was similar to the family of glycoside hydrolase 36. The purified recombinant CbAga36 (rCbAga36) was optimally active at pH 5.0 and 70°C and had a half-life of 15 h and 10 h at 70°C and 80°C, respectively. rCbAga36 showed high activity with the artificial substrate (p-nitrophenyl α-d-galactopyranoside, pNPαGal) exhibiting lower Km and higher kcat than natural substrates such as melibiose and raffinose. Although rCbAga36 demonstrated preferential activity toward the hydrolysis of RFO such as raffinose and stachyose, it did not degrade the polymeric galactomannans. Our results imply that CbAga36 may play a role in the degradation of RFO, transported into the cytoplasm via a transporter into galactose, which is further utilized as an energy source in C. bescii. Furthermore, its ability to synthesize novel oligosaccharides by transglycosylation renders this enzyme potentially useful for the production of dietary oligosaccharides with novel function.


Assuntos
Bactérias Gram-Positivas/enzimologia , alfa-Galactosidase/metabolismo , Estabilidade Enzimática , Escherichia coli/genética , Galactose/metabolismo , Glicólise , Glicosídeos/metabolismo , Bactérias Gram-Positivas/genética , Meia-Vida , Concentração de Íons de Hidrogênio , Hidrólise , Cinética , Melibiose/metabolismo , Oligossacarídeos/metabolismo , Rafinose/metabolismo , Especificidade por Substrato , alfa-Galactosidase/genética , alfa-Galactosidase/isolamento & purificação
20.
J Ethnopharmacol ; 196: 75-83, 2017 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-27965051

RESUMO

ETHNOPHARMACOLOGICAL EVIDENCE: Peucedani Radix (PR), the root of Peucedanum praeruptorum Dunn (PPD) or Peucedanum decursivum (Miq.) Maxim. (PDM), has long been used in Korea to eliminate sputum, relieve cough, and reduce bronchus contraction. Furthermore, these therapeutic strategies are recognized as general and effective methods in western medicine as well as traditional Korean medicine. AIM OF THE STUDY: To determine and compare the anti-inflammatory effects of PPD extracts (PPDE) and PDM extracts (PDME) on allergic lung inflammation, using in vivo OVA-induced airway inflammation in mice and in vitro primary cell culture systems. MATERIALS AND METHODS: Eight-week-old female C57BL/6 mice were placed into four groups (n=4 per group): saline control, OVA-induced allergic lung inflammation with vehicle, or PPDE (200mg/kg) or PDME (200mg/kg) treatment. PR extracts (PRE) were administered from 1 week before 1st OVA sensitization to the day before sacrifice. Mice were sacrificed 18h after last OVA intra-nasal challenge followed by histological and biochemical analyses. RESULTS: Inflammatory phenotypes were alleviated with oral administration of PRE. PRE treatment decreased mucus production in airway epithelium, inflammatory cell number, eosinophilia, type 2 cytokines, and histamine in bronchoalveolar lavage fluid (BALF). Mice with PRE administration showed diminished activated CD4 T cell (CD4+CD25+ cell) and GATA-3 level in the lung. In addition, PRE treatment reduced Th2 cell activation in vitro, using Th2 polarization system. CONCLUSION: Our findings indicate that the anti-inflammatory effects of PRE arise from reduced Th2 cell activation and validate the clinical use of PR in traditional Korean medicine.


Assuntos
Antiasmáticos/uso terapêutico , Apiaceae , Asma/tratamento farmacológico , Extratos Vegetais/uso terapêutico , Alérgenos/imunologia , Animais , Antiasmáticos/farmacologia , Asma/imunologia , Asma/patologia , Líquido da Lavagem Broncoalveolar/química , Líquido da Lavagem Broncoalveolar/citologia , Líquido da Lavagem Broncoalveolar/imunologia , Linfócitos T CD4-Positivos/efeitos dos fármacos , Linfócitos T CD4-Positivos/imunologia , Contagem de Células , Citocinas/imunologia , Eosinofilia/tratamento farmacológico , Eosinofilia/imunologia , Eosinofilia/patologia , Feminino , Fator de Transcrição GATA3/imunologia , Histamina/imunologia , Imunoglobulina E/sangue , Pulmão/efeitos dos fármacos , Pulmão/imunologia , Pulmão/patologia , Camundongos Endogâmicos C57BL , Muco/metabolismo , Ovalbumina/imunologia , Extratos Vegetais/farmacologia , Raízes de Plantas
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