• 제목/요약/키워드: Profiling Methods

검색결과 282건 처리시간 0.045초

Metabolomic profiling of postmortem aged muscle in Japanese Brown beef cattle revealed an interbreed difference from Japanese Black beef

  • Susumu Muroya;Riko Nomura;Hirotaka Nagai;Koichi Ojima;Kazutsugu Matsukawa
    • Animal Bioscience
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    • 제36권3호
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    • pp.506-520
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    • 2023
  • Objective: Japanese Brown (JBR) cattle, especially the Kochi (Tosa) pedigree (JBRT), is a local breed of moderately marbled beef. Despite the increasing demand, the interbreed differences in muscle metabolites from the highly marbled Japanese Black (JBL) beef remain poorly understood. We aimed to determine flavor-related metabolites and postmortem metabolisms characteristic to JBRT beef in comparison with JBL beef. Methods: Lean portions of the longissimus thoracis (loin) muscle from four JBRT cattle were collected at 0, 1, and 14 d postmortem. The muscle metabolomic profiles were analyzed using capillary electrophoresis time-of-flight mass spectrometry. The difference in post-mortem metabolisms and aged muscle metabolites were analyzed by statistical and bioinformatic analyses between JBRT (n = 12) and JBL cattle (n = 6). Results: A total of 240 metabolite annotations were obtained from the detected signals of the JBRT muscle samples. Principal component analysis separated the beef samples into three different aging point groups. According to metabolite set enrichment analysis, post-mortem metabolic changes were associated with the metabolism of pyrimidine, nicotinate and nicotinamide, purine, pyruvate, thiamine, amino sugar, and fatty acid; citric acid cycle; and pentose phosphate pathway as well as various amino acids and mitochondrial fatty acid metabolism. The aged JBRT beef showed higher ultimate pH and lower lactate content than aged JBL beef, suggesting the lower glycolytic activity in postmortem JBRT muscle. JBRT beef was distinguished from JBL beef by significantly different compounds, including choline, amino acids, uridine monophosphate, inosine 5'-monophosphate, fructose 1,6-diphosphate, and betaine, suggesting interbreed differences in the accumulation of nucleotide monophosphate, glutathione metabolism, and phospholipid metabolism. Conclusion: Glycolysis, purine metabolism, fatty acid catabolism, and protein degradation were the most common pathways in beef during postmortem aging. The differentially expressed metabolites and the relevant metabolisms in JBRT beef may contribute to the development of a characteristic flavor.

Growth promotion effect of red ginseng dietary fiber to probiotics and transcriptome analysis of Lactiplantibacillus plantarum

  • Hye-Young Yu;Dong-Bin Rhim;Sang-Kyu Kim;O-Hyun Ban;Sang-Ki Oh;Jiho Seo;Soon-Ki Hong
    • Journal of Ginseng Research
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    • 제47권1호
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    • pp.159-165
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    • 2023
  • Background: Red ginseng marc, the residue of red ginseng left after water extraction, is rich in dietary fiber. Dietary fiber derived from fruits or vegetables can promote the proliferation of probiotics, and it is a key technology in the food industry to increase the productivity of probiotics by adding growth-enhancing substances such as dietary fiber. In this study, the effect of red ginseng dietary fiber (RGDF) on the growth of probiotic bacterial strains was investigated at the phenotypic and genetic levels. Methods: We performed transcriptome profiling of Lactiplantibacillus plantarum IDCC3501 in two phases of culture (logarithmic (L)-phase and stationary (S)-phase) in two culture conditions (with or without RGDF) using RNA-seq. Differentially expressed genes (DEGs) were identified and classified according to Gene Ontology terms. Results: The growth of L.plantarum IDCC3501 was enhanced in medium supplemented with RGDF up to 2%. As a result of DEG analysis, 29 genes were upregulated and 30 were downregulated in the RGDF-treated group in the L-phase. In the S-phase, 57 genes were upregulated and 126 were downregulated in the RGDF-treated group. Among the upregulated genes, 5 were upregulated only in the L-phase, 10 were upregulated only in the S-phase, and 3 were upregulated in both the L- and S-phases. Conclusions: Transcriptome analysis could be a valuable tool for elucidating the molecular mechanisms by which RGDF promotes the proliferation of L.plantarum IDCC3501. This growth-promoting effect of RGDF is important, since RGDF could be used as a prebiotic source without additional chemical or enzymatic processing.

수중에서 적용가능한 대구경 현장타설말뚝의 굴착공 벽면거칠기 측정장치의 보정에 관한 연구 (Calibration of Borehole Roughness Measurement System for Large Diameter Drilled Shafts in Water)

  • 박봉근;남문석;최용규
    • 한국지반공학회논문집
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    • 제25권8호
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    • pp.5-21
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    • 2009
  • 암반에 근입된 현장타설말뚝의 주면마찰력에 대한 최근의 연구결과에 따르면 주면마찰력은 암석의 일축압축강도 외에 굴착면의 거칠기, 암반의 재료특성, 초기 수직음력, 말뚝의 직경, 암반의 절리 및 풍화도 등에 크게 영향을 받는 것으로 보고되어 있다. 지금까지 개발된 굴착면 거칠기 시스템들은 공기 중에서만 측정가능하므로 현장의 굴착공내에서 직접 측정하는 것은 불가능하였다. 따라서, 본 연구에서는 수중에서 사용가능한 굴착공 벽면거칠기 측정 시스템(BKS-LRPS)을 개발하였으며, 특수 제작된 보정장치를 통하여 여러 가지 경우에 대한 검증을 수행하였다. 연구결과에 의하면, 개발된 BKS-LRPS는 장치제작조건 및 현장조건을 반영하도록 계획된 검증조건들에 대하여 유효측정영역을 제시할 수 있었다.

Microbial profiling of peri-implantitis compared to the periodontal microbiota in health and disease using 16S rRNA sequencing

  • Hyun-Joo Kim;Dae-Hee Ahn;Yeuni Yu;Hyejung Han;Si Yeong Kim;Ji-Young Joo;Jin Chung;Hee Sam Na;Ju-Youn Lee
    • Journal of Periodontal and Implant Science
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    • 제53권1호
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    • pp.69-84
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    • 2023
  • Purpose: The objective of this study was to analyze the microbial profile of individuals with peri-implantitis (PI) compared to those of periodontally healthy (PH) subjects and periodontitis (PT) subjects using Illumina sequencing. Methods: Buccal, supragingival, and subgingival plaque samples were collected from 109 subjects (PH: 30, PT: 49, and PI: 30). The V3-V4 region of 16S rRNA was sequenced and analyzed to profile the plaque microbiota. Results: Microbial community diversity in the PI group was higher than in the other groups, and the 3 groups showed significantly separated clusters in the buccal samples. The PI group showed different patterns of relative abundance from those in the PH and PT groups depending on the sampling site at both genus and phylum levels. In all samples, some bacterial species presented considerably higher relative abundances in the PI group than in the PH and PT groups, including Anaerotignum lactatifermentans, Bacteroides vulgatus, Faecalibacterium prausnitzii, Olsenella uli, Parasutterella excrementihominis, Prevotella buccae, Pseudoramibacter alactolyticus, Treponema parvum, and Slackia exigua. Network analysis identified that several well-known periodontal pathogens and newly recognized bacteria were closely correlated with each other. Conclusions: The composition of the microbiota was considerably different in PI subjects compared to PH and PT subjects, and these results could shed light on the mechanisms involved in the development of PI.

뉴로모픽 환경에서 QoS를 고려한 최적의 SNN 모델 파라미터 생성 기법 (QoS-Aware Optimal SNN Model Parameter Generation Method in Neuromorphic Environment)

  • 김서연;김봉재;정진만
    • 스마트미디어저널
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    • 제12권4호
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    • pp.19-26
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    • 2023
  • 뉴로모픽 아키텍처 기반 하드웨어를 이용한 IoT 엣지 서비스는 단말 장치에서 지능형 처리를 수행할 수 있기 때문에 자율형 IoT 응용 지원에 적합하다. 그러나 IoT 개발자가 뉴로모픽 하드웨어에서 사용되는 SNN을 이해하기에는 어려움이 있다. 본 논문에서는 뉴로모픽 하드웨어의 제약조건을 고려하며 사용자의 요구 성능을 만족하는 SNN 모델 생성 기법을 제안한다. 제안 기법은 프로파일링된 데이터에서 최적의 SNN 모델 파라미터를 찾도록 전처리된 데이터로 사전 학습한 모델을 활용한다. 전체 탐색 기법과 비교 결과, 두 기법 모두 사용자 요구사항을 모두 만족하였지만, 제안 기법이 수행 시간 측면에서 더 좋은 성능을 보였다. 또한, 신규 하드웨어의 제약조건을 명확히 알지 못하더라도 새로운 하드웨어의 프로파일링된 데이터를 활용할 수 있으므로 높은 확장성을 제공할 수 있다.

Numerical Model for Cerebrovascular Hemodynamics with Indocyanine Green Fluorescence Videoangiography

  • Hwayeong Cheon;Young-Je Son;Sung Bae Park;Pyoung-Seop Shim;Joo-Hiuk Son;Hee-Jin Yang
    • Journal of Korean Neurosurgical Society
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    • 제66권4호
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    • pp.382-392
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    • 2023
  • Objective : The use of indocyanine green videoangiography (ICG-VA) to assess blood flow in the brain during cerebrovascular surgery has been increasing. Clinical studies on ICG-VA have predominantly focused on qualitative analysis. However, quantitative analysis numerical modelling for time profiling enables a more accurate evaluation of blood flow kinetics. In this study, we established a multiple exponential modified Gaussian (multi-EMG) model for quantitative ICG-VA to understand accurately the status of cerebral hemodynamics. Methods : We obtained clinical data of cerebral blood flow acquired the quantitative analysis ICG-VA during cerebrovascular surgery. Varied asymmetric peak functions were compared to find the most matching function form with clinical data by using a nonlinear regression algorithm. To verify the result of the nonlinear regression, the mode function was applied to various types of data. Results : The proposed multi-EMG model is well fitted to the clinical data. Because the primary parameters-growth and decay rates, and peak center and heights-of the model are characteristics of model function, they provide accurate reference values for assessing cerebral hemodynamics in various conditions. In addition, the primary parameters can be estimated on the curves with partially missed data. The accuracy of the model estimation was verified by a repeated curve fitting method using manipulation of missing data. Conclusion : The multi-EMG model can possibly serve as a universal model for cerebral hemodynamics in a comparison with other asymmetric peak functions. According to the results, the model can be helpful for clinical research assessment of cerebrovascular hemodynamics in a clinical setting.

유전 요인과 생활환경 요인의 상호작용이 제2형 당뇨병 발생에 미치는 영향: 한국인유전체역학 조사사업(KoGES) 자료를 이용하여 (Effects of gene-lifestyle environment interactions on type 2 diabetes mellitus development: an analysis using the Korean Genome and Epidemiology Study data)

  • 현수진;전상은
    • Journal of Korean Biological Nursing Science
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    • 제25권1호
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    • pp.73-85
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    • 2023
  • Purpose: This study focused on identifying the interaction effects of genetic and lifestyle-environmental factors on the development of type 2 diabetes mellitus (T2D). Methods: Study subjects were selected from the Korean Genome and Epidemiology Study (KoGES) from 2001 to 2014. Data on genetic variations, anthropometric measurements, biochemical data, and seven lifestyle factors (diet, physical activity, alcohol drinking, smoking, sleep, depression, and stress) were obtained from 4,836 Koreans aged between 40 and 59 years, including those with T2D at baseline (n = 1,209), newly developed T2D (n= 1,298) and verified controls (n = 3,538). The genetic risk score (GRS) was calculated by using 11 single-nucleotide polymorphisms (SNPs) related to T2D development and the second quartile was used as the reference category. A Cox proportional hazards regression model was used to evaluate the associations of GRS and lifestyle factors with T2D risk, controlling for covariates. Results: Multivariate regression analysis revealed that GRS was the strongest risk factor for T2D, and body mass index (BMI), smoking, drinking, and spicy food preference also increased the risk. Lifestyle/environmental factors that showed significant interactions with GRS were BMI, current smoking, current drinking, fatty food preference, and spicy food preference. Conclusions: Interactions between genetic factors and lifestyle/environmental factors were associated with an increased risk of T2D. The results will be useful to provide a new perspective on genetic profiling for the earlier detection of T2D risk and clues for personalized interventions, which might be more effective prevention strategies or therapies in individuals with a genetic predisposition to T2D.

CRYSTALS-Dilithium 대상 비프로파일링 기반 전력 분석 공격 성능 개선 연구 (A Study on Performance Improvement of Non-Profiling Based Power Analysis Attack against CRYSTALS-Dilithium)

  • 장세창;이민종;강효주;하재철
    • 정보보호학회논문지
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    • 제33권1호
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    • pp.33-43
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    • 2023
  • 최근 미국의 국립표준기술연구소(NIST: National Institute of Standards and Technology)는 양자 내성 암호(PQC: Post-Quantum Cryptography, 이하 PQC) 표준화 사업을 진행하여 4개의 표준 암호 알고리즘을 발표하였다. 본 논문에서는 전자서명 분야에서 표준화가 확정된 CRYSTALS-Dilithium 알고리즘을 이용하여 서명을 생성하는 과정에서 동작하는 다항식 계수별 곱셈 알고리즘을 대상으로 비프로파일링 기반 전력 분석 공격인 CPA(Correlation Power Analysis)나 DDLA(Differential Deep Learning Analysis) 공격에 의해 개인 키가 노출될 수 있음을 실험을 통해 증명한다. ARM-Cortex-M4 코어에 알고리즘을 탑재하여 실험결과, CPA 공격과 DDLA 공격에서 개인 키 계수를 복구할 수 있음을 확인하였다. 특히 DDLA 공격에서 StandardScaler 전처리 및 연속 웨이블릿 변환을 적용한 전력 파형을 이용하였을 때 공격에 필요한 최소 전력 파형의 개수가 줄어들고 NMM(Normalized Maximum Margin) 값이 약 3배 증가하여 공격 성능이 크게 향상됨을 확인하였다.

Probiotic supplementation has sex-dependent effects on immune responses in association with the gut microbiota in community-dwelling older adults: a randomized, double-blind, placebo-controlled, multicenter trial

  • Chong-Su Kim;Min Ho Jung;Eun Young Choi;Dong-Mi Shin
    • Nutrition Research and Practice
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    • 제17권5호
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    • pp.883-898
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    • 2023
  • BACKGROUND/OBJECTIVES: Probiotics have been suggested as potent modulators of age-related disorders in immunological functions, yet little is known about sex-dependent effects of probiotic supplements. Therefore, we aimed to investigate sex-dependent effects of probiotics on profiles of the gut microbiota and peripheral immune cells in healthy older adults. SUBJECTS/METHODS: In a randomized, double-blind, placebo-controlled, multicenter trial, healthy elderly individuals ≥ 65 yrs old were administered probiotic capsules (or placebo) for 12 wk. Gut microbiota was analyzed using 16S rRNA gene sequencing and bioinformatic analyses. Peripheral immune cells were profiled using flow cytometry for lymphocytes (natural killer, B, CD4+ T, and CD8+ T cells), dendritic cells, monocytes, and their subpopulations. RESULTS: Compared with placebo, phylum Firmicutes was significantly reduced in the probiotic group in women, but not in men. At the genus level, sex-specific responses included reductions in the relative abundances of pro-inflammatory gut microbes, including Catabacter and unclassified_Coriobacteriales, and Burkholderia and unclassified Enterobacteriaceae, in men and women, respectively. Peripheral immune cell profiling analysis revealed that in men, probiotics significantly reduced the proportions of dendritic cells and CD14+ CD16- monocytes; however, these effects were not observed in women. In contrast, the proportion of total CD4+ T cells was significantly reduced in women in the probiotic group. Additionally, serum lipopolysaccharide-binding protein levels showed a decreasing tendency that were positively associated with changes in gut bacteria, including Catabacter (ρ = 0.678, P < 0.05) and Burkholderia (ρ = 0.673, P < 0.05) in men and women, respectively. CONCLUSIONS: These results suggest that probiotic supplementation may reduce the incidence of inflammation-related diseases by regulating the profiles of the gut microbiota and peripheral immune cells in healthy elders in a sex-specific manner.

The effects of dietary self-monitoring intervention on anthropometric and metabolic changes via a mobile application or paper-based diary: a randomized trial

  • Taiyue Jin;Gyumin Kang;Sihan Song;Heejin Lee;Yang Chen;Sung-Eun Kim;Mal-Soon Shin;Youngja H Park;Jung Eun Lee
    • Nutrition Research and Practice
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    • 제17권6호
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    • pp.1238-1254
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    • 2023
  • BACKGROUND/OBJECTIVES: Weight loss via a mobile application (App) or a paper-based diary (Paper) may confer favorable metabolic and anthropometric changes. SUBJECTS/METHODS: A randomized parallel trial was conducted among 57 adults whose body mass indices (BMIs) were 25 kg/m2 or greater. Participants randomly assigned to either the App group (n = 30) or the Paper group (n = 27) were advised to record their foods and supplements through App or Paper during the 12-week intervention period. Relative changes of anthropometries and biomarker levels were compared between the 2 intervention groups. Untargeted metabolic profiling was identified to discriminate metabolic profiles. RESULTS: Out of the 57 participants, 54 participants completed the trial. Changes in body weight and BMI were not significantly different between the 2 groups (P = 0.11). However, body fat and low-density lipoprotein (LDL)-cholesterol levels increased in the App group but decreased in the Paper group, and the difference was statistically significant (P = 0.03 for body fat and 0.02 for LDL-cholesterol). In the metabolomics analysis, decreases in methylglyoxal and (S)-malate in pyruvate metabolism and phosphatidylcholine (lecithin) in linoleic acid metabolism from pre- to post-intervention were observed in the Paper group. CONCLUSIONS: In the 12-week randomized parallel trial of weight loss through a App or a Paper, we found no significant difference in change in BMI or weight between the App and Paper groups, but improvement in body fatness and LDL-cholesterol levels only in the Paper group under the circumstances with minimal contact by dietitians or health care providers.