• 제목/요약/키워드: Differential expression analysis

검색결과 388건 처리시간 0.024초

Transcriptome-wide analysis reveals gluten-induced suppression of small intestine development in young chickens

  • Darae, Kang;Donghyun, Shin;Hosung, Choe;Doyon, Hwang;Andrew Wange, Bugenyi;Chong-Sam, Na;Hak-Kyo, Lee;Jaeyoung, Heo;Kwanseob, Shim
    • Journal of Animal Science and Technology
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    • 제64권4호
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    • pp.752-769
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    • 2022
  • Wheat gluten is an increasingly common ingredient in poultry diets but its impact on the small intestine in chicken is not fully understood. This study aimed to identify effects of high-gluten diets on chicken small intestines and the variation of their associated transcriptional responses by age. A total of 120 broilers (Ross Strain) were used to perform two animal experiments consisting of two gluten inclusion levels (0% or 25%) by bird's age (1 week or 4 weeks). Transcriptomics and histochemical techniques were employed to study the effect of gluten on their duodenal mucosa using randomly selected 12 broilers (3 chicks per group). A reduction in feed intake and body weight gain was found in the broilers fed a high-gluten containing diet at both ages. Histochemical photomicrographs showed a reduced villus height to crypt depth ratio in the duodenum of gluten-fed broilers at 1 week. We found mainly a significant effect on the gene expression of duodenal mucosa in gluten-fed broilers at 1 week (289 differentially expressed genes [DEGs]). Pathway analyses revealed that the significant DEGs were mainly involved in ribosome, oxidative phosphorylation, and peroxisome proliferator-activated receptor (PPAR) signaling pathways. These pathways are involved in ribosome protein biogenesis, oxidative phosphorylation and fatty acid metabolism, respectively. Our results suggest a pattern of differential gene expression in these pathways that can be linked to chronic inflammation, suppression of cell proliferation, cell cycle arrest and apoptosis. And via such a mode of action, high-gluten inclusion levels in poultry diets could lead to the observed retardation of villi development in the duodenal mucosa of young broiler chicken.

Differentially expressed serum proteins associated with calcium regulation and hypocalcemia in dairy cows

  • Shu, Shi;Bai, Yunlong;Wang, Gang;Xiao, Xinhuan;Fan, Ziling;Zhang, Jiang;Zhao, Chang;Zhao, Yang;Xia, Cheng;Zhang, Hongyou
    • Asian-Australasian Journal of Animal Sciences
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    • 제30권6호
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    • pp.893-901
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    • 2017
  • Objective: Hypocalcemia is an important metabolic disease of dairy cows during the transition period, although the effect of hypocalcemia on biological function in dairy cows remains unknown. Methods: In this study, proteomic, mass spectrum, bioinformatics and western blotting were employed to identify differentially expressed proteins related to serum Ca concentration. Serum samples from dairy cows were collected at three time points: 3rd days before calving (day -3), the day of calving (day 0), and 3rd days after calving (day +3). According to the Ca concentration on day 0, a total of 27 dairy cows were assigned to one of three groups (clinical, subclinical, and healthy). Samples collected on day -3 were used for discovery of differentially expressed proteins, which were separated and identified via proteomic analysis and mass spectrometry. Bioinformatics analysis was performed to determine the function of the identified proteins (gene ontology and pathway analysis). The differentially expressed proteins were verified by western blot analysis. Results: There were 57 differential spots separated and eight different proteins were identified. Vitamin D-binding protein precursor (group-specific component, GC), alpha-2-macroglobulin (A2M) protein, and apolipoprotein A-IV were related to hypocalcemia by bioinformatics analysis. Due to its specific expression (up-regulated in clinical hypocalcemia and down-regulated in subclinical hypocalcemia), A2M was selected for validation. The results were consistent with those of proteomic analysis. Conclusion: A2M was as an early detection index for distinguishing clinical and subclinical hypocalcemia. The possible pathogenesis of clinical hypocalcemia caused by GC and apolipoprotein A-IV was speculated. The down-regulated expression of GC was a probable cause of the decrease in calcium concentration.

Proteomic Assessment of the Relevant Factors Affecting Pork Meat Quality Associated with Longissimus dorsi Muscles in Duroc Pigs

  • Cho, Jin Hyoung;Lee, Ra Ham;Jeon, Young-Joo;Park, Seon-Min;Shin, Jae-Cheon;Kim, Seok-Ho;Jeong, Jin Young;Kang, Hyun-sung;Choi, Nag-Jin;Seo, Kang Seok;Cho, Young Sik;Kim, MinSeok S.;Ko, Sungho;Seo, Jae-Min;Lee, Seung-Youp;Shim, Jung-Hyun;Chae, Jung-Il
    • Asian-Australasian Journal of Animal Sciences
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    • 제29권11호
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    • pp.1653-1663
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    • 2016
  • Meat quality is a complex trait influenced by many factors, including genetics, nutrition, feeding environment, animal handling, and their interactions. To elucidate relevant factors affecting pork quality associated with oxidative stress and muscle development, we analyzed protein expression in high quality longissimus dorsi muscles (HQLD) and low quality longissimus dorsi muscles (LQLD) from Duroc pigs by liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analysis. Between HQLD (n = 20) and LQLD (n = 20) Duroc pigs, 24 differentially expressed proteins were identified by LC-MS/MS. A total of 10 and 14 proteins were highly expressed in HQLD and LQLD, respectively. The 24 proteins have putative functions in the following seven categories: catalytic activity (31%), ATPase activity (19%), oxidoreductase activity (13%), cytoskeletal protein binding (13%), actin binding (12%), calcium ion binding (6%), and structural constituent of muscle (6%). Silver-stained image analysis revealed significant differential expression of lactate dehydrogenase A (LDHA) between HQLD and LQLD Duroc pigs. LDHA was subjected to in vitro study of myogenesis under oxidative stress conditions and LDH activity assay to verification its role in oxidative stress. No significant difference of mRNA expression level of LDHA was found between normal and oxidative stress condition. However, LDH activity was significantly higher under oxidative stress condition than at normal condition using in vitro model of myogenesis. The highly expressed LDHA was positively correlated with LQLD. Moreover, LDHA activity increased by oxidative stress was reduced by antioxidant resveratrol. This paper emphasizes the importance of differential expression patterns of proteins and their interaction for the development of meat quality traits. Our proteome data provides valuable information on important factors which might aid in the regulation of muscle development and the improvement of meat quality in longissimus dorsi muscles of Duroc pigs under oxidative stress conditions.

Identification of Differentially Expressed Proteins in Liver in Response to Subacute Ruminal Acidosis (SARA) Induced by High-concentrate Diet

  • Jiang, X.Y.;Ni, Y.D.;Zhang, S.K.;Zhang, Y.S.;Shen, X.Z.
    • Asian-Australasian Journal of Animal Sciences
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    • 제27권8호
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    • pp.1181-1188
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    • 2014
  • The aim of this study was to evaluate protein expression patterns of liver in response to subacute ruminal acidosis (SARA) induced by high-concentrate diet. Sixteen healthy mid-lactating goats were randomly divided into 2 groups and fed either a high-forage (HF) diet or a high-concentrate (HC) diet. The HC diet was expected to induce SARA. After ensuring the occurrence of SARA, liver samples were collected. Proteome analysis with differential in gel electrophoresis technology revealed that, 15 proteins were significantly modulated in liver in a comparison between HF and HC-fed goats. These proteins were found mainly associated with metabolism and energy transfer after identified by matrix-assisted laser desorption ionization/time of flight. The results indicated that glucose, lipid and protein catabolism could be enhanced when SARA occurred. It prompted that glucose, lipid and amine acid in the liver mainly participated in oxidation and energy supply when SARA occurred, which possibly consumed more precursors involved in milk protein and milk fat synthesis. These results suggest new candidate proteins that may contribute to a better understanding of the mechanisms that mediate liver adaptation to SARA.

Call for a Computer-Aided Cancer Detection and Classification Research Initiative in Oman

  • Mirzal, Andri;Chaudhry, Shafique Ahmad
    • Asian Pacific Journal of Cancer Prevention
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    • 제17권5호
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    • pp.2375-2382
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    • 2016
  • Cancer is a major health problem in Oman. It is reported that cancer incidence in Oman is the second highest after Saudi Arabia among Gulf Cooperation Council countries. Based on GLOBOCAN estimates, Oman is predicted to face an almost two-fold increase in cancer incidence in the period 2008-2020. However, cancer research in Oman is still in its infancy. This is due to the fact that medical institutions and infrastructure that play central roles in data collection and analysis are relatively new developments in Oman. We believe the country requires an organized plan and efforts to promote local cancer research. In this paper, we discuss current research progress in cancer diagnosis using machine learning techniques to optimize computer aided cancer detection and classification (CAD). We specifically discuss CAD using two major medical data, i.e., medical imaging and microarray gene expression profiling, because medical imaging like mammography, MRI, and PET have been widely used in Oman for assisting radiologists in early cancer diagnosis and microarray data have been proven to be a reliable source for differential diagnosis. We also discuss future cancer research directions and benefits to Oman economy for entering the cancer research and treatment business as it is a multi-billion dollar industry worldwide.

Differential Behaviour of Selenium Analogs against Anticancer Drug Induced Apoptosis of Lymphocytes in Human Peripheral Blood

  • Elango, Sonaa;Subbiah, Usha;Jain, Jeong
    • Asian Pacific Journal of Cancer Prevention
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    • 제17권5호
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    • pp.2527-2533
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    • 2016
  • Sensitising cancer cells and at the same time desensitizing normal cells is a double task in cancer management. Agents which can combat the debilitating side effects of cancer therapeutics and simultaneously synergize with anticancer agents in specifically targeting cancer cells are needed. Selenium, a proven anticarcinogen, gains due importance in terms of its efficacy to combat the side effects of cancer therapy. This study is a comparative analysis of the chemoprotective effects of selenium compounds, methyl selenol (generated from organic selenomethionine (5mmol/L ; METase 40U/L)) and sodium selenite (inorganic form)($30{\mu}M$) in peripheral blood human lymphocytes exposed to cisplatin and mitomycin. Biochemical alterations occurring in many cells during apoptosis include loss of plasma membrane phospholipid asymmetry, DNA fragmentation, and activation of caspase-3. The present study demonstrated that the selenium metabolite and selenite are efficient in protecting lymphocytes undergoing DNA damage and exerted their activity by reducing caspase 3 expression. Interestingly organic methylselenol (MeSe) was found to offer more protective effects compared to inorganic selenite (SeL), by reducing the induction of apoptosis by the cytotoxic agents. This suggests that MeSe and to a lesser extent selenite might have potential for assessment in clinical trials and could be considered as strong candidates in pharmacogenomics or in the nutriprotective arena.

철근콘크리트 부재의 균열 후 강성 이론 (Theoretical Stiffness of Cracked Reinforced Concrete Elements)

  • 김장훈
    • 콘크리트학회논문집
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    • 제11권5호
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    • pp.79-88
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    • 1999
  • The purpose of this paper is to develop a mathematical expression for computing crack angles based on reinforcement volumes in the longitudinal and transverse directions, member end-fixity and length-to-width aspect ratio. For this a reinforced concrete beam-column element is assumed to possess a series of potential crack planes represented by a number of differential truss elements. Depending on the boundary condition, a constant angle truss or a variable angle truss is employed to model the cracked structural concrete member. The truss models are then analyzed using the virtual work method of analysis to relate forces and deformations. Rigorous and simplified solution schemes are presented. An equation to estimate the theoretical crack angle is derived by considering the energy minimization on the virtual work done over both the shear and flexural components the energy minimization on the virtual work done over both the shear and flexural components of truss models. The crack angle in this study is defined as the steepest one among fan-shaped angles measured from the longitudinal axis of the member to the diagonal crack. The theoretical crack angle predictions are validated against experimentally observed crack angle reported by previous researchers in the literature. Good agreement between theory and experiment is obtained.

Differential Activation of T Cells by T-Cell Receptor Ligand Analogs

  • Choi, Yun-Hi;Suh, Yu-Jin;Kim, Kil-Hyoun
    • BMB Reports
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    • 제30권6호
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    • pp.415-420
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    • 1997
  • Although $CD4^+$ T cell responses to protein-derived antigen have well been understood, the epitopes recognized by hapten-specific $CD4^+$ T cells have not been fully defined. In this study, we characterized the response of a T cell hybridoma (5Di0.1B8) which is specific for a hapten. N-hydroxysuccinimidyl-4-azidobenzoate (HSAB) restricted by MHC class II $I-A^d$. Using three different antigen presenting cells (APCs) expressing $I-A^d$, the role of class II MHC proteins in haptenic antigen presentation and subsequent activation of 5D10.1B8 has been examined. Activation of 5D10.1B8 T cells by HSAB analogs was also performed. Our results show that each APC activated T cells differentially and that interleukin-2 (IL-2) augmented antigen-presenting ability of all the APCs, suggesting that increased expression of class II MHC protein by IL-2 played an important role in HSAB presentation and T cell activation. Finally, early T cell receptor-dependent signals induced by HSAB or its analogs were examined by phosphotyrosine immunoblot analysis, and showed that tyrosine phosphorylation level of a 18-20 kD protein increased upon stimulation.

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Elasto-plastic stability of circular cylindrical shells subjected to axial load, varying as a power function of time

  • Sofiyev, A.H.;Schnack, E.;Demir, F.
    • Structural Engineering and Mechanics
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    • 제24권5호
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    • pp.621-639
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    • 2006
  • Stability of a cylindrical shell subject to a uniform axial compression, which is a power function of time, is examined within the framework of small strain elasto-plasticity. The material of the shell is incompressible and the effect of the elastic unloading is considered. Initially, employing the infinitesimal elastic-plastic deformation theory, the fundamental relations and Donnell type stability equations for a cylindrical shell have been obtained. Then, employing Galerkin's method, those equations have been reduced to a time dependent differential equation with variable coefficient. Finally, for two initial conditions applying a Ritz type variational method, the critical static and dynamic axial loads, the corresponding wave numbers and dynamic factor have been found. Using those results, the effects of the variations of loading parameters and the variations of power of time in the axial load expression as well as the variations of the radius to thickness ratio on the critical parameters of the shells for two initial conditions are also elucidated. Comparing results with those in the literature validates the present analysis.

보증 클레임 시계열 데이터를 위한 퍼지 PID 제어 (Fuzzy PID Control of Warranty Claims Time Series)

  • 이상현;이상준;문경일;조성의
    • 한국IT서비스학회지
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    • 제8권4호
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    • pp.175-185
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    • 2009
  • Objectifying claims filed during the warranty period, analyzing the current circumstances and improving on the problem in question is an activity worth doing that could reduce the likelihood of claims to occur, cut down on the costs, and enhance the corporate image of the manufacturer. Existing analyses of claims are confronted with two problems. First, you can't precisely assess the risks of claims involved by means of the value of claims per 100 products alone. Second, even in a normal state, the existing approach fails to capture the probabilistic conflicts that escape the upper control limit of claims, thus leading to wrong control activities. To solve the first problem, this paper proposed that a time series detection concept where the claim rate is monitored based on the date when problems are processed and a hazard function for expression of the claim rate be utilized. For the second problem, this paper designed a model whereby to define a normal state by making use of PID (Proportion, Integral, Differential) and infer by way of a fuzzy concept. This paper confirmed the validity and applicability of the proposed approach by applying methods suggested in the actual past data of warranty claims of a large-scaled automotive firm, unlike hypothetical simulation data, in order to apply them directly in industrial job sites, as well as making theoretical suggestions for analysis of claims.