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Sample records for company profile tissue

  1. Company profile

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ Datacon was founded in 1986 and, since the beginning of 2005, has been part of the Dutch Besi group (BE Semiconductor Industries N.V.), an international group of companies operating in the semiconductor industry. Besi is a leading manufacturer of semiconductor die sorting, die bonding, packaging and plating equipment and provides the most cost efficient solution for RFID inlay production.

  2. Global electricity company profiles

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

    Global Electricity Company Profiles examines the operations and strategies of 60 of the leading electricity companies in the world. Through its analysis of the key players, the report provides a comprehensive review of the current state of the global electricity industry. Using electricity sales as its criteria, the most successful companies are compared in terms of their national, regional and global importance. Global Electricity Company Profiles provides an outline of each company, its structure and operations, as well as key financial data. The detailed performance benchmarking and review of expectations for future development for each individual company provide a wealth of invaluable strategic information not available elsewhere. (author)

  3. Marketing company profile: Consumer-led company features

    Directory of Open Access Journals (Sweden)

    Kovačević Ivana

    2005-01-01

    Full Text Available Starting point in defining modern company profile is its absolute orientation to customers. So called Customer-led companies are those which all their activities put toward customers instead of product which is offered. These companies try to make all their sectors to be oriented toward customers.

  4. Natural gas annual 1992: Supplement: Company profiles

    Energy Technology Data Exchange (ETDEWEB)

    1994-01-01

    The data for the Natural Gas Annual 1991 Supplement : Company Profiles are taken from Form EIA-176, (open quotes) Annual Report of Natural and Supplemental Gas Supply and Disposition (close quotes). Other sources include industry literature and corporate annual reports to shareholders. The companies appearing in this report are major interstate natural gas pipeline companies, large distribution companies, or combination companies with both pipeline and distribution operations. The report contains profiles of 45 corporate families. The profiles describe briefly each company, where it operates, and any important issues that the company faces. The purpose of this report is to show the movement of natural gas through the various States served by the 45 large companies profiled.

  5. Natural gas annual 1993 supplement: Company profiles

    Energy Technology Data Exchange (ETDEWEB)

    1995-02-01

    The Natural Gas Annual provides information on the supply and disposition of natural gas to a wide audience including industry, consumers, Federal and State agencies, and educational institutions. This report, the Natural Gas Annual 1993 Supplement: Company Profiles, presents a detailed profile of 45 selected companies in the natural gas industry. The purpose of this report is to show the movement of natural gas through the various States served by the companies profiled. The companies in this report are interstate pipeline companies or local distribution companies (LDC`s). Interstate pipeline companies acquire gas supplies from company owned production, purchases from producers, and receipts for transportation for account of others. Pipeline systems, service area maps, company supply and disposition data are presented.

  6. Genre Analysis of Online Company Profiles from Sporting Goods Brands

    Institute of Scientific and Technical Information of China (English)

    WANG Fei

    2015-01-01

    With the development of globalization and information technology, online company profile has been an effective commu⁃nication channel between companies and their target customers or clients. Online company profile, as a specific genre, has the dis⁃tinct features and functions in commercial activities. This study aims to do linguistic study of the constitution and the role of these company profiles about sporting goods for communication on the Internet. To realize it, six company profiles have been selected from the official websites of each sports company. The genre analysis of these samples is conducted from the perspective of Hasan’s Contextual Configuration (CC) and Generic Structure Potential (GSP). This thesis attempts to give the suggestions on how to compose a company profile for readers and sporting companies and the reference for the related researches in the future.

  7. Bank Risk Profile, Good Corporate Governance And Company Values in Banking Companies Go Public in Indonesia

    Directory of Open Access Journals (Sweden)

    Susi Retna Cahyaningtyas

    2017-06-01

    Full Text Available The latest Bank Indonesia Regulation No.14/18/PBI/2012 requires bank to have minimum capital of 8%-14% depends on the risk profile of each bank. Therefore, the main objective of this research is to assess whether the total of inherent risk profile of each bank meets the terms of this regulation. In addition, this study aims to examine the impact of inherent risk profile and GCG on the banking company value. The sample in this study is determined by purposive sampling method and resulted in 24 banks or 72 observations during 2011-2013. The results showed that 23 banks had low risk and low to moderate risk, and only one bank had moderate risk. The results also showed that inherent risk profile rating is equivalent to capital adequacy. In other words, inherent risk profile of these banks have complied with Bank Indonesia Regulation No.14/18/PBI/2012. Furthermore, this study indicated that GCG has significant and positive influence on the company value, while the inherent risk has no influence on the company value. Overall, this study suggest that go public banks in Indonesia are one of good alternative means of investment for its soundness as reflected by the fulfillment of minimum capital ratio required by the regulator.

  8. The Chinese-English Translation of Company Profiles-A Case Study Based on Foreign Trade Companies in Ningbo

    Institute of Scientific and Technical Information of China (English)

    朱颖; 滕雅芸

    2015-01-01

    As Chinese enterprises are seeking various ways to develop foreign cooperation abroad, the Chinese-English transla⁃tion of company profiles plays an ever greater role in communication with the whole world. However, a number of the transla⁃tion versions fail to achieve a satisfactory effect, neglecting target readers' cultural background and their mode of thinking. This thesis intends to make an exploration of differences between Chinese and English company profiles and discuss the pragmatic, cul⁃tural and linguistic translation errors appeared in some company profiles of foreign trade enterprises in the city of Ningbo.

  9. Tissue microarray profiling in human heart failure.

    Science.gov (United States)

    Lal, Sean; Nguyen, Lisa; Tezone, Rhenan; Ponten, Fredrik; Odeberg, Jacob; Li, Amy; Dos Remedios, Cristobal

    2016-09-01

    Tissue MicroArrays (TMAs) are a versatile tool for high-throughput protein screening, allowing qualitative analysis of a large number of samples on a single slide. We have developed a customizable TMA system that uniquely utilizes cryopreserved human cardiac samples from both heart failure and donor patients to produce formalin-fixed paraffin-embedded sections. Confirmatory upstream or downstream molecular studies can then be performed on the same (biobanked) cryopreserved tissue. In a pilot study, we applied our TMAs to screen for the expression of four-and-a-half LIM-domain 2 (FHL2), a member of the four-and-a-half LIM family. This protein has been implicated in the pathogenesis of heart failure in a variety of animal models. While FHL2 is abundant in the heart, not much is known about its expression in human heart failure. For this purpose, we generated an affinity-purified rabbit polyclonal anti-human FHL2 antibody. Our TMAs allowed high-throughput profiling of FHL2 protein using qualitative and semiquantitative immunohistochemistry that proved complementary to Western blot analysis. We demonstrated a significant relative reduction in FHL2 protein expression across different forms of human heart failure. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. An overview of the management consulting firms of the Spanish company in China: company profile and success and failure factors

    Directory of Open Access Journals (Sweden)

    A. Niñerola

    2016-03-01

    Full Text Available This article explores the vision of Management Consulting Firms (MCF specialized in internationalization processes of Spanish companies in China. The main objective is to shed light on a process full of uncertainty as is international expansion into emerging markets on the point of view of the advisors of that process. First, it is analyzed whether there is a Spanish company profile that is internationalized toward China in terms of sector of activity, size and experience in international business. And second, with their client’s experiences, success and failure factors in the internationalization process are studied. To achieve those objectives in depth interviews were held with partners and managers of six Management Consulting Firms with Spanish clients in their portfolio. As a result it is concluded that the sectors where the Spanish company has invested are several, the size of the company is important to undertake an implementation process in China and its international experience as well. Eight key factors were found relevant to invest in China successfully.  Five factors are related with their resources (humans and financials and the other three are related with their strategy. The main reasons of failure are also discussed. The article provides an outside perspective on the reasons why an internationalization process is successful and other fails.

  11. Age Changes of Jaws and Soft Tissue Profile

    Directory of Open Access Journals (Sweden)

    Padmaja Sharma

    2014-01-01

    Full Text Available Age-related changes of jaws and soft tissue profile are important both for orthodontists and general dentists. Mouth profile is the area which is manipulated during dental treatment. These changes should be planned in accordance with other components of facial profile to achieve ultimate aim of structural balance, functional efficacy, and esthetic harmony. Through this paper, the authors wish to discuss age changes of the hard and soft tissues of human face which would help not only the orthodontists but also oral surgeons, prosthodontists, pedodontists, and general dentists.

  12. A preseason cardiorespiratory profile of dancers in nine professional ballet and modern companies.

    Science.gov (United States)

    Bronner, Shaw; Ojofeitimi, Sheyi; Lora, Jennifer Bailey; Southwick, Heather; Kulak, Michelina Cassella; Gamboa, Jennifer; Rooney, Megan; Gilman, Greg; Gibbs, Richard

    2014-01-01

    While studies have investigated the physical demands of dance in terms of cardiorespiratory fitness, there are no recent comparisons of cardiorespiratory response to exercise among professional dancers of different genres. Our purpose was to: 1. develop a cardiorespiratory profile of professional dancers; 2. investigate differences in peak and recovery heart rate (HR) between professional modern and ballet dancers using an accelerated 3-minute step test; 3. demonstrate the relationship between cardiorespiratory variables; and 4. investigate the effects of company and work variables on the dancers' cardiorespiratory profiles. We hypothesized greater cardiorespiratory fitness in modern dancers than in ballet dancers, due to the nature of their repertory. Furthermore, we hypothesized that company profiles would reflect differences in work variables. Two hundred and eleven dancers (mean age 24.6 ± 4.7) from nine companies (two modern and seven ballet) performed a 3-minute step test. Demographics, height, mass, blood pressure (BP), smoking history, and resting peak and recovery HR were recorded. Body mass index (BMI) and fitness category were calculated. Independent t-tests were used to compare differences in demographics and cardiorespiratory variables due to genre, MANOVA were conducted to compare differences due to company, and correlations were calculated to determine the relationships between cardiorespiratory variables (p ballet dancers (p < 0.03). There were differences between companies in age, experience, BMI, BP, resting, peak, and recovery HR, and fitness category (p < 0.001). The differences in cardiorespiratory fitness levels that may be related to rigor of repertory, rehearsal and performance seasons, or off-season exercise training are discussed. Results support the need for comprehensive physical fitness screening to identify dancers who could benefit from aerobic conditioning to enhance overall performance preparedness and to minimize fatigue effects.

  13. Protein Profiling of Preeclampsia Placental Tissues

    Science.gov (United States)

    Shu, Chang; Liu, Zitao; Cui, Lifeng; Wei, Chengguo; Wang, Shuwen; Tang, Jian Jenny; Cui, Miao; Lian, Guodong; Li, Wei; Liu, Xiufen; Xu, Hongmei; Jiang, Jing; Lee, Peng; Zhang, David Y.

    2014-01-01

    Preeclampsia is a multi-system disorder involved in pregnancy without an effective treatment except delivery. The precise pathogenesis of this complicated disorder is still not completely understood. The objective of this study is to evaluate the alterations of protein expression and phosphorylations that are important in regulating placental cell function in preterm and term preeclampsia. Using the Protein Pathway Array, 38 proteins in placental tissues were found to be differentially expressed between preterm preeclampsia and gestational age matched control, while 25 proteins were found to be expressed differentially between term preeclampsia and matched controls. Among these proteins, 16 proteins and their associated signaling pathways overlapped between preterm and term preeclampsia, suggesting the common pathogenesis of two subsets of disease. On the other hand, many proteins are uniquely altered in either preterm or term preeclampsia and correlated with severity of clinical symptoms and outcomes, therefore, providing molecular basis for these two subsets of preeclampsia. Furthermore, the expression levels of some of these proteins correlated with neonatal small for gestational age (PAI-1 and PAPP-A) and adverse outcomes (Flt-1) in women with preterm preeclampsia. These proteins could potentially be used as candidate biomarkers for predicting outcomes of preeclampsia. PMID:25392996

  14. Protein profiling of preeclampsia placental tissues.

    Science.gov (United States)

    Shu, Chang; Liu, Zitao; Cui, Lifeng; Wei, Chengguo; Wang, Shuwen; Tang, Jian Jenny; Cui, Miao; Lian, Guodong; Li, Wei; Liu, Xiufen; Xu, Hongmei; Jiang, Jing; Lee, Peng; Zhang, David Y; He, Jin; Ye, Fei

    2014-01-01

    Preeclampsia is a multi-system disorder involved in pregnancy without an effective treatment except delivery. The precise pathogenesis of this complicated disorder is still not completely understood. The objective of this study is to evaluate the alterations of protein expression and phosphorylations that are important in regulating placental cell function in preterm and term preeclampsia. Using the Protein Pathway Array, 38 proteins in placental tissues were found to be differentially expressed between preterm preeclampsia and gestational age matched control, while 25 proteins were found to be expressed differentially between term preeclampsia and matched controls. Among these proteins, 16 proteins and their associated signaling pathways overlapped between preterm and term preeclampsia, suggesting the common pathogenesis of two subsets of disease. On the other hand, many proteins are uniquely altered in either preterm or term preeclampsia and correlated with severity of clinical symptoms and outcomes, therefore, providing molecular basis for these two subsets of preeclampsia. Furthermore, the expression levels of some of these proteins correlated with neonatal small for gestational age (PAI-1 and PAPP-A) and adverse outcomes (Flt-1) in women with preterm preeclampsia. These proteins could potentially be used as candidate biomarkers for predicting outcomes of preeclampsia.

  15. Objective Diagnosis of Cervical Cancer by Tissue Protein Profile Analysis

    Science.gov (United States)

    Patil, Ajeetkumar; Bhat, Sujatha; Rai, Lavanya; Kartha, V. B.; Chidangil, Santhosh

    2011-07-01

    Protein profiles of homogenized normal cervical tissue samples from hysterectomy subjects and cancerous cervical tissues from biopsy samples collected from patients with different stages of cervical cancer were recorded using High Performance Liquid Chromatography coupled with Laser Induced Fluorescence (HPLC-LIF). The Protein profiles were subjected to Principle Component Analysis to derive statistically significant parameters. Diagnosis of sample types were carried out by matching three parameters—scores of factors, squared residuals, and Mahalanobis Distance. ROC and Youden's Index curves for calibration standards were used for objective estimation of the optimum threshold for decision making and performance.

  16. Porphyromonas gingivalis infection-induced tissue and bone transcriptional profiles.

    Science.gov (United States)

    Meka, A; Bakthavatchalu, V; Sathishkumar, S; Lopez, M C; Verma, R K; Wallet, S M; Bhattacharyya, I; Boyce, B F; Handfield, M; Lamont, R J; Baker, H V; Ebersole, J L; Kesavalu, L

    2010-02-01

    Porphyromonas gingivalis has been associated with subgingival biofilms in adult periodontitis. However, the molecular mechanisms of its contribution to chronic gingival inflammation and loss of periodontal structural integrity remain unclear. This investigation aimed to examine changes in the host transcriptional profiles during a P. gingivalis infection using a murine calvarial model of inflammation and bone resorption. P. gingivalis FDC 381 was injected into the subcutaneous soft tissue over the calvaria of BALB/c mice for 3 days, after which the soft tissues and calvarial bones were excised. RNA was isolated from infected soft tissues and calvarial bones and was analysed for transcript profiles using Murine GeneChip((R)) arrays to provide a molecular profile of the events that occur following infection of these tissues. After P. gingivalis infection, 6452 and 2341 probe sets in the infected soft tissues and calvarial bone, respectively, were differentially expressed (P tissues and calvarial bone included cell adhesion (immune system) molecules, Toll-like receptors, B-cell receptor signaling, transforming growth factor-beta cytokine family receptor signaling, and major histocompatibility complex class II antigen processing pathways resulting in proinflammatory, chemotactic effects, T-cell stimulation, and downregulation of antiviral and T-cell chemotactic effects. P. gingivalis-induced inflammation activated osteoclasts, leading to local bone resorption. This is the first in vivo evidence that localized P. gingivalis infection differentially induces transcription of a broad array of host genes, the profiles of which differed between inflamed soft tissues and calvarial bone.

  17. Direct-to-PCR tissue preservation for DNA profiling.

    Science.gov (United States)

    Sorensen, Amy; Berry, Clare; Bruce, David; Gahan, Michelle Elizabeth; Hughes-Stamm, Sheree; McNevin, Dennis

    2016-05-01

    Disaster victim identification (DVI) often occurs in remote locations with extremes of temperatures and humidities. Access to mortuary facilities and refrigeration are not always available. An effective and robust DNA sampling and preservation procedure would increase the probability of successful DNA profiling and allow faster repatriation of bodies and body parts. If the act of tissue preservation also released DNA into solution, ready for polymerase chain reaction (PCR), the DVI process could be further streamlined. In this study, we explored the possibility of obtaining DNA profiles without DNA extraction, by adding aliquots of preservative solutions surrounding fresh human muscle and decomposing human muscle and skin tissue samples directly to PCR. The preservatives consisted of two custom preparations and two proprietary solutions. The custom preparations were a salt-saturated solution of dimethyl sulfoxide (DMSO) with ethylenediaminetetraacetic (EDTA) and TENT buffer (Tris, EDTA, NaCl, Tween 20). The proprietary preservatives were DNAgard (Biomatrica(®)) and Tissue Stabilising Kit (DNA Genotek). We obtained full PowerPlex(®) 21 (Promega) and GlobalFiler(®) (Life Technologies) DNA profiles from fresh and decomposed tissue preserved at 35 °C for up to 28 days for all four preservatives. The preservative aliquots removed from the fresh muscle tissue samples had been stored at -80 °C for 4 years, indicating that long-term archival does not diminish the probability of successful DNA typing. Rather, storage at -80 °C seems to reduce PCR inhibition.

  18. DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns.

    Science.gov (United States)

    Lokk, Kaie; Modhukur, Vijayachitra; Rajashekar, Balaji; Märtens, Kaspar; Mägi, Reedik; Kolde, Raivo; Koltšina, Marina; Nilsson, Torbjörn K; Vilo, Jaak; Salumets, Andres; Tõnisson, Neeme

    2014-04-01

    DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites. Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases. This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms.

  19. Full scattering profile of circular optical phantoms mimicking biological tissue

    Science.gov (United States)

    Feder, Idit; Wróbel, Maciej S.; Duadi, Hamootal; Fixler, Dror; Jedrzejewska-Szczerska, Malgorzata

    2017-02-01

    Human tissue is one of the most complex optical media since it is turbid and nonhomogeneous. In our poster, we suggest a new type of skin phantom and an optical method for sensing physiological tissue condition, basing on the collection of the ejected light at all exit angles, to receive the full scattering profile. Conducted experiments were carried out on an unique set-up for noninvasive encircled measurement. Set-up consisted of a laser, a photodetector and new tissues-like phantoms made with a polyvinyl chloride-plastisol (PVCP), silicone elastomer polydimethylsiloxane (PDMS) and PDMS with glycerol mixture. Our method reveals an isobaric point, which is independent of the optical properties. Furthermore, we present the angular distribution of cylindrical phantoms, in order to sense physiological tissue state.

  20. Subgingival bacterial colonization profiles correlate with gingival tissue gene expression

    Directory of Open Access Journals (Sweden)

    Handfield Martin

    2009-10-01

    Full Text Available Abstract Background Periodontitis is a chronic inflammatory disease caused by the microbiota of the periodontal pocket. We investigated the association between subgingival bacterial profiles and gene expression patterns in gingival tissues of patients with periodontitis. A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4 from a maxillary posterior region. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each tissue sample. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total. Plaque samples were analyzed using checkerboard DNA-DNA hybridizations with respect to 11 bacterial species. Random effects linear regression models considered bacterial levels as exposure and expression profiles as outcome variables. Gene Ontology analyses summarized the expression patterns into biologically relevant categories. Results Wide inter-species variation was noted in the number of differentially expressed gingival tissue genes according to subgingival bacterial levels: Using a Bonferroni correction (p -7, 9,392 probe sets were differentially associated with levels of Tannerella forsythia, 8,537 with Porphyromonas gingivalis, 6,460 with Aggregatibacter actinomycetemcomitans, 506 with Eikenella corrodens and only 8 with Actinomyces naeslundii. Cluster analysis identified commonalities and differences among tissue gene expression patterns differentially regulated according to bacterial levels. Conclusion Our findings suggest that the microbial content of the periodontal pocket is a determinant of gene expression in the gingival tissues and provide new insights into the differential ability of periodontal species to elicit a local host response.

  1. Subgingival bacterial colonization profiles correlate with gingival tissue gene expression.

    Science.gov (United States)

    Papapanou, Panos N; Behle, Jan H; Kebschull, Moritz; Celenti, Romanita; Wolf, Dana L; Handfield, Martin; Pavlidis, Paul; Demmer, Ryan T

    2009-10-18

    Periodontitis is a chronic inflammatory disease caused by the microbiota of the periodontal pocket. We investigated the association between subgingival bacterial profiles and gene expression patterns in gingival tissues of patients with periodontitis. A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4) from a maxillary posterior region. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each tissue sample. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total). Plaque samples were analyzed using checkerboard DNA-DNA hybridizations with respect to 11 bacterial species. Random effects linear regression models considered bacterial levels as exposure and expression profiles as outcome variables. Gene Ontology analyses summarized the expression patterns into biologically relevant categories. Wide inter-species variation was noted in the number of differentially expressed gingival tissue genes according to subgingival bacterial levels: Using a Bonferroni correction (p < 9.15 x 10(-7)), 9,392 probe sets were differentially associated with levels of Tannerella forsythia, 8,537 with Porphyromonas gingivalis, 6,460 with Aggregatibacter actinomycetemcomitans, 506 with Eikenella corrodens and only 8 with Actinomyces naeslundii. Cluster analysis identified commonalities and differences among tissue gene expression patterns differentially regulated according to bacterial levels. Our findings suggest that the microbial content of the periodontal pocket is a determinant of gene expression in the gingival tissues and provide new insights into the differential ability of periodontal species to elicit a local host response.

  2. Gene expression profiles in liver cancer and normal liver tissues

    Institute of Scientific and Technical Information of China (English)

    Lian Xin Liu; Hong Chi Jiang; An Long Zhu; Jin Zhou; Xiu Qin Wang; Min Wu

    2000-01-01

    AIM To describe a liver cancer = specific gene expression profile and to identify genes that showed alteredexpression between liver cancer tissues and their adjacent nearly normal tissues.METHODS The cDNA probes which were labeled with a-32P dATP were synthesized from total RNA ofliver cancer and adjacent normal tissues and hybridized separately to two identical Atlas human cancer eDNAexpression array membranes containing 588 known genes.RESULTS Autoradiographic results were analyzed by specific Atlas ImageTM (version 1. 0) software.Among the 588 genes analyzed, 18 genes were found up-regulated in cancer, including TFDP2, Aktl, E2F-3etc, and 25 genes were down-regulated in cancer, including TDGF1, BAK, LAR, etc. Expression levels ofgenes that associated with the regulation of cell proliferation, apoptosis, differentiation, cell-cellinteraction, invasion regulators and eytokines altered mostly.CONCLUSION The result obtained from Atlas microarray provides a comprehensive liver cancer-specificexpression profile. The results can lead to the identification of liver cancer-specific biomarkers and may behelpful in early diagnosis and dentifiction of target genes for designing rational therapeutic strategies.

  3. Microarray expression profiling in adhesion and normal peritoneal tissues.

    Science.gov (United States)

    Ambler, Dana R; Golden, Alicia M; Gell, Jennifer S; Saed, Ghassan M; Carey, David J; Diamond, Michael P

    2012-05-01

    To identify molecular markers associated with adhesion and normal peritoneal tissue using microarray expression profiling. Comparative study. University hospital. Five premenopausal women. Adhesion and normal peritoneal tissue samples were obtained from premenopausal women. Ribonucleic acid was extracted using standard protocols and processed for hybridization to Affymetrix Whole Transcript Human Gene Expression Chips. Microarray data were obtained from five different patients, each with adhesion tissue and normal peritoneal samples. Real-time polymerase chain reaction was performed for confirmation using standard protocols. Gene expression in postoperative adhesion and normal peritoneal tissues. A total of 1,263 genes were differentially expressed between adhesion and normal tissues. One hundred seventy-three genes were found to be up-regulated and 56 genes were down-regulated in the adhesion tissues compared with normal peritoneal tissues. The genes were sorted into functional categories according to Gene Ontology annotations. Twenty-six up-regulated genes and 11 down-regulated genes were identified with functions potentially relevant to the pathophysiology of postoperative adhesions. We evaluated and confirmed expression of 12 of these specific genes via polymerase chain reaction. The pathogenesis, natural history, and optimal treatment of postoperative adhesive disease remains unanswered. Microarray analysis of adhesions identified specific genes with increased and decreased expression when compared with normal peritoneum. Knowledge of these genes and ontologic pathways with altered expression provide targets for new therapies to treat patients who have or are at risk for postoperative adhesions. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  4. Significant factors in the technological profile of innovative companies in the return of capital in technological innovation

    Directory of Open Access Journals (Sweden)

    Eloisa de Moura Lopes

    2013-12-01

    Full Text Available  Aim to analyze the significance of factors of technological profile in innovative companies that contribute to the return of capital in innovation (ROEI. The method used was design of experiments, by the structure of non-balanced factorial design. The field research was done with seventy companies. The main return of the capital applied in innovation, should support the open innovation system, and exclusively systematic studies of ideas for new products.  

  5. Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues

    Directory of Open Access Journals (Sweden)

    Waldron Levi

    2012-03-01

    Full Text Available Abstract Background With over 20 million formalin-fixed, paraffin-embedded (FFPE tissue samples archived each year in the United States alone, archival tissues remain a vast and under-utilized resource in the genomic study of cancer. Technologies have recently been introduced for whole-transcriptome amplification and microarray analysis of degraded mRNA fragments from FFPE samples, and studies of these platforms have only recently begun to enter the published literature. Results The Emerging Technologies for Translational Bioinformatics symposium on gene expression profiling for archival tissues featured presentations of two large-scale FFPE expression profiling studies (each involving over 1,000 samples, overviews of several smaller studies, and representatives from three leading companies in the field (Illumina, Affymetrix, and NuGEN. The meeting highlighted challenges in the analysis of expression data from archival tissues and strategies being developed to overcome them. In particular, speakers reported higher rates of clinical sample failure (from 10% to 70% than are typical for fresh-frozen tissues, as well as more frequent probe failure for individual samples. The symposium program is available at http://www.hsph.harvard.edu/ffpe. Conclusions Multiple solutions now exist for whole-genome expression profiling of FFPE tissues, including both microarray- and sequencing-based platforms. Several studies have reported their successful application, but substantial challenges and risks still exist. Symposium speakers presented novel methodology for analysis of FFPE expression data and suggestions for improving data recovery and quality assessment in pre-analytical stages. Research presentations emphasized the need for careful study design, including the use of pilot studies, replication, and randomization of samples among batches, as well as careful attention to data quality control. Regardless of any limitations in quantitave transcriptomics for

  6. 公司简介翻译中的文化顺应%Cultural Adaptation in Translation of Company Profiles

    Institute of Scientific and Technical Information of China (English)

    吴青茹

    2014-01-01

    公司简介用来宣传介绍公司情况以吸引潜在顾客。由于中西文化的差异,在翻译公司简介的过程中译者应充分考虑文化因素,从历史传统、风俗习惯、宗教信仰和价值观三个方面让译文顺应目的语的文化语境,更好地传递信息,达到宣传的目的。%A company profile is brief introduction to a company which provides information about the product range or services that a company offers, and states the corporate values to invite potential buyers to contact it. As there are differences between Chi⁃nese Culture and Western Culture, translator should consider the culture influence when do the translation of company profile, making adaptation to accord with the cultural context of target language from three aspects: historical traditions, customs and conventions, religions and values. Thus information can transmit to the target language reader smoothly and the goal of company file can be achieved.

  7. ENTREPRENEURIAL CULTURE, PROFILE OF THE LEADER AND ENTREPRENEURIAL ORIENTATION: EMPIRICAL APPLICATION IN THE CASE OF THE TUNISIAN COMPANIES

    Directory of Open Access Journals (Sweden)

    Mighri ZOUHAYER

    2013-10-01

    Full Text Available Today, no company is safe from forces and pressures, which are exerted on it, because of a significant number of the requirements in particular as regards competitiveness, the need for change, or the crises, the deregulations and the cost of energy. To face this news gives, the company must reconsider its behaviors and its practices to renew itself, to open out and reinforce its international position in the market. Some of these practices form what one calls the entrepreneurial orientation. For this reason, we will devote this paper for better encircling and apprehending the concept of entrepreneurial orientation and this, by focusing on its relation with the entrepreneurial culture and the profile of the leader in the specific case of the Tunisian companies.

  8. A profile of corporate social responsibility for mining companies present in the Santurban Moorland, Santander, Colombia

    Directory of Open Access Journals (Sweden)

    Jonathan David Morales Méndez

    2016-04-01

    The strengths found amongst the Mining Companies in the Santurban Moorland include that most of them do have a CSR policy or strategy and demonstrate a positive attitude towards implementing this kind of program. In addition, they have gender equity and anti-discrimination policies and agreements that go beyond they law.

  9. Biodynamic profiling of three-dimensional tissue growth techniques

    Science.gov (United States)

    Sun, Hao; Merrill, Dan; Turek, John; Nolte, David

    2016-03-01

    Three-dimensional tissue culture presents a more biologically relevant environment in which to perform drug development than conventional two-dimensional cell culture. However, obtaining high-content information from inside three dimensional tissue has presented an obstacle to rapid adoption of 3D tissue culture for pharmaceutical applications. Biodynamic imaging is a high-content three-dimensional optical imaging technology based on low-coherence interferometry and digital holography that uses intracellular dynamics as high-content image contrast. In this paper, we use biodynamic imaging to compare pharmaceutical responses to Taxol of three-dimensional multicellular spheroids grown by three different growth techniques: rotating bioreactor, hanging-drop and plate-grown spheroids. The three growth techniques have systematic variations among tissue cohesiveness and intracellular activity and consequently display different pharmacodynamics under identical drug dose conditions. The in vitro tissue cultures are also compared to ex vivo living biopsies. These results demonstrate that three-dimensional tissue cultures are not equivalent, and that drug-response studies must take into account the growth method.

  10. Dentoskeletal and Soft Tissue Profile Changes Associated with Mandibular Setback Osteotomy: A Cephalometric Study

    Directory of Open Access Journals (Sweden)

    Manish Goyal

    2011-01-01

    The conclusions indicated that the facial concavity, in regard to the relationship of the hard and soft tissue chin to the upper face, was decreased by this surgical procedure; facial esthetics was improved. The mandible assumed a more normal relationship to the upper denture base. The least amount of change of the soft tissue profile was exhibited by the upper lip and maxillary sulcus of the upper lip. The greatest amount of change of the soft tissue profile was exhibited by the lower lip, the mandibular sulcus of the lower lip and the soft tissue chin.

  11. Injury profile of employees at a specific beverage manufacturing company: a retrospective study

    Directory of Open Access Journals (Sweden)

    L. Chetty

    2007-02-01

    Full Text Available This article reports on important information pertaining tothe prevalence of occupational injuries. At present very little data existson the prevalence of occupational injuries in South Africa.  A retrospective study was undertaken to detail the occupational injuries sustained by employees at a specific beverage manufacturing company.The aim of this study was to determine the mechanisms, type, classification, anatomical site, frequency and time of injuries at this beverage company.The sample consisted of all employees that reported to the occupational health clinic with occupational injuries during the six-month review period i.e. July 2004-December 2004. Results of this review were computed in a self-complied injury data spreadsheet. The data was presented descriptively and the level of significance was set at 0.05.  Incorrect lifting of manual materials was reported as the most common mechanism of injury. Repetitive strain injuries were the most common type of injury. The spine/trunk was the site of 48 (66.7% of regions injuries with the most frequently injured regions being the back (43.1% and neck (22.2%. Most of the injuries were sustained during the month of December (27.8%. It is recommended that aggressive health promotion and injury prevention strategies be implemented to reduce the burden of occupational injuries at this specific beverage manufacturing company.

  12. Identification and signature profiles for pro-resolving and inflammatory lipid mediators in human tissue

    National Research Council Canada - National Science Library

    Colas, Romain A; Shinohara, Masakazu; Dalli, Jesmond; Chiang, Nan; Serhan, Charles N

    2014-01-01

    ...(s) to classic eicosanoids in mammalian tissues. Lipid mediator (LM)-SPM levels and signature profiles of their biosynthetic pathways were investigated using liquid chromatography-tandem mass spectrometry (LC-MS-MS...

  13. Transcriptional profiling of tissue plasticity: Role of shifts in gene expression and technical limitations

    NARCIS (Netherlands)

    Flück, Martin; Däpp, Christoph; Schmutz, Silvia; Wit, Ernst; Hoppeler, Hans

    2005-01-01

    Reprogramming of gene expression has been recognized as a main instructive modality for the adjustments of tissues to various kinds of stress. The recent application of gene expression profiling has provided a powerful tool to elucidate the molecular pathways underlying such tissue remodeling. Howev

  14. Metabolic profiling of alternative NAD biosynthetic routes in mouse tissues.

    Directory of Open Access Journals (Sweden)

    Valerio Mori

    Full Text Available NAD plays essential redox and non-redox roles in cell biology. In mammals, its de novo and recycling biosynthetic pathways encompass two independent branches, the "amidated" and "deamidated" routes. Here we focused on the indispensable enzymes gating these two routes, i.e. nicotinamide mononucleotide adenylyltransferase (NMNAT, which in mammals comprises three distinct isozymes, and NAD synthetase (NADS. First, we measured the in vitro activity of the enzymes, and the levels of all their substrates and products in a number of tissues from the C57BL/6 mouse. Second, from these data, we derived in vivo estimates of enzymes'rates and quantitative contributions to NAD homeostasis. The NMNAT activity, mainly represented by nuclear NMNAT1, appears to be high and nonrate-limiting in all examined tissues, except in blood. The NADS activity, however, appears rate-limiting in lung and skeletal muscle, where its undetectable levels parallel a relative accumulation of the enzyme's substrate NaAD (nicotinic acid adenine dinucleotide. In all tissues, the amidated NAD route was predominant, displaying highest rates in liver and kidney, and lowest in blood. In contrast, the minor deamidated route showed higher relative proportions in blood and small intestine, and higher absolute values in liver and small intestine. Such results provide the first comprehensive picture of the balance of the two alternative NAD biosynthetic routes in different mammalian tissues under physiological conditions. This fills a gap in the current knowledge of NAD biosynthesis, and provides a crucial information for the study of NAD metabolism and its role in disease.

  15. THE COMPETITIVE PROFILE OF THE NATIONAL RAILWAY COMPANY FROM THE PERSPECTIVE USE OF KNOWLEDGE MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Dragan George Bogdan

    2013-12-01

    Full Text Available In the context of the current business environment, characterized by an increasing degree of competitiveness which diminishes the possibilities for differentiation, it is necessary to implement a successful strategic knowledge management process and adapt it to the company’s needs. The purpose is that it can help the company to translate its strategic vision and mission into action. Regarding the organizational environment, organizational needs analysis - expressed in terms of the knowledge society - determine "competitiveness" as a necessary condition of survival of the company. Competitiveness has always been an organizational goal. Is born, so the question: why competitiveness became just today, the key to success of business processes? The answer, we believe that it is in dynamic markets (supply, demand - dynamic value by bringing in goods and services, the widespread use of knowledge. The importance of knowledge-based activities has greatly increased in recent years. Also, knowledge began to be regarded as the main source of wealth production, protecting it represents an important element in achieving and maintaining a competitive advantage.

  16. Expression profiling of peroxisome proliferator-activated receptor-delta (PPAR-delta) in mouse tissues using tissue microarray.

    Science.gov (United States)

    Higashiyama, Hiroyuki; Billin, Andrew N; Okamoto, Yuji; Kinoshita, Mine; Asano, Satoshi

    2007-05-01

    Peroxisome proliferator-activated receptor-delta (PPAR-delta) is known as a transcription factor involved in the regulation of fatty acid oxidation and mitochondrial biogenesis in several tissues, such as skeletal muscle, liver and adipose tissues. In this study, to elucidate systemic physiological functions of PPAR-delta, we examined the tissue distribution and localization of PPAR-delta in adult mouse tissues using tissue microarray (TMA)-based immunohistochemistry. PPAR-delta positive signals were observed on variety of tissues/cells in multiple systems including cardiovascular, urinary, respiratory, digestive, endocrine, nervous, hematopoietic, immune, musculoskeletal, sensory and reproductive organ systems. In these organs, PPAR-delta immunoreactivity was generally localized on the nucleus, although cytoplasmic localization was observed on several cell types including neurons in the nervous system and cells of the islet of Langerhans. These expression profiling data implicate various physiological roles of PPAR-delta in multiple organ systems. TMA-based immunohistochemistry enables to profile comprehensive protein localization and distribution in a high-throughput manner.

  17. Use of focused ultrasonication in activity-based profiling of deubiquitinating enzymes in tissue.

    Science.gov (United States)

    Nanduri, Bindu; Shack, Leslie A; Rai, Aswathy N; Epperson, William B; Baumgartner, Wes; Schmidt, Ty B; Edelmann, Mariola J

    2016-12-15

    To develop a reproducible tissue lysis method that retains enzyme function for activity-based protein profiling, we compared four different methods to obtain protein extracts from bovine lung tissue: focused ultrasonication, standard sonication, mortar & pestle method, and homogenization combined with standard sonication. Focused ultrasonication and mortar & pestle methods were sufficiently effective for activity-based profiling of deubiquitinases in tissue, and focused ultrasonication also had the fastest processing time. We used focused-ultrasonicator for subsequent activity-based proteomic analysis of deubiquitinases to test the compatibility of this method in sample preparation for activity-based chemical proteomics.

  18. TMD FRICTION - a company profile; TMD FRICTION - ein Unternehmen stellt sich vor

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, E.

    2000-07-01

    TMD FRICTION came into existence in August 2000 by separation of the friction material sector from BBA PLC. This transaction was supported by HSBC PE, the private equity branch of HSBC, the third largest bank world-wide. This report shall give some market background, the current position of the company and information about the strategic orientation of the new group regarding R and D and production - especially against the background of our customers' global activities. (orig.) [German] TMD FRICTION entstand im August 2000 durch Ausgliederung des Reibbelag-Bereichs aus der BBA PLC. Diese Transaktion wurde unterstuetzt durch HSBC, PE, dem Private Equity-Zweig von HSBC, der drittgroessten Bank weltweit. Der Bericht erlaeutert Markthintergruende, die aktuelle Positionierung des Unternehmens und gibt Hinweise auf die strategische Ausrichtung der neuen Gruppierung im Bereich Entwicklung und Produktion - insbesondere vor dem Hintergrund der globalen Ausrichtung unserer Kunden. (orig.)

  19. Soft tissue profile changes following mandibular advancement surgery: predictability and long-term outcome.

    Science.gov (United States)

    Mobarak, K A; Espeland, L; Krogstad, O; Lyberg, T

    2001-04-01

    The objectives of this cephalometric study were to assess long-term changes in the soft tissue profile following mandibular advancement surgery and to investigate the relationship between soft tissue and hard tissue movements. The sample consisted of 61 patients treated consecutively for mandibular retrognathism with orthodontic therapy combined with bilateral sagittal split osteotomy and rigid fixation. Lateral cephalograms were taken on 6 occasions: immediately before surgery, immediately after surgery, 2 and 6 months after surgery, and 1 and 3 years after surgery. Postsurgical changes in the upper and the lower lips and the mentolabial fold were more pronounced among low-angle cases compared with high-angle cases. In accordance with other studies, the soft tissue chin and the mentolabial fold were generally found to follow their underlying skeletal structures in a 1:1 ratio. Because of the strong influence skeletal relapse has on soft tissue profile changes, alternative ratios of soft tissue-to-hard tissue movement that accounted for mean relapse were also generated. It is suggested that if a more realistic long-term prediction of the postsurgical soft tissue profile is desirable, then ratios incorporating mean relapse should be used rather than estimates based on a 1:1 relationship.

  20. Gene Expression Profiling during Pregnancy in Rat Brain Tissue.

    Science.gov (United States)

    Mann, Phyllis E

    2014-03-04

    The neurophysiological changes that occur during pregnancy in the female mammal have led to the coining of the phrases "expectant brain" and "maternal brain". Although much is known of the hormonal changes during pregnancy, alterations in neurotransmitter gene expression have not been well-studied. We examined gene expression in the ventromedial nucleus of the hypothalamus (VMH) during pregnancy based on the fact that this nucleus not only modulates the physiological changes that occur during pregnancy but is also involved in the development of maternal behavior. This study was designed to identify genes that are differentially expressed between mid- and late-pregnancy in order to determine which genes may be associated with the onset and display of maternal behavior and the development of the maternal brain. A commercially available PCR array containing 84 neurotransmitter receptor and regulator genes (RT2 Profiler PCR array) was used. Brains were harvested from rats on days 12 and 21 of gestation, frozen, and micropunched to obtain the VMH. Total RNA was extracted, cDNA prepared, and SYBR Green qPCR was performed. In the VMH, expression of five genes were reduced on day 21 of gestation compared to day 12 (Chrna6, Drd5, Gabrr2, Prokr2, and Ppyr1) whereas Chat, Chrm5, Drd4, Gabra5, Gabrg2, LOC289606, Nmu5r2, and Npy5r expression was elevated. Five genes were chosen to be validated in an additional experiment based on their known involvement in maternal behavior onset. This experiment confirmed that gene expression for both the CCK-A receptor and the GABAAR γ2 receptor increases at the end of pregnancy. In general, these results identify genes possibly involved in the establishment of the maternal brain in rats and indicate possible new genes to be investigated.

  1. Gene Expression Profiling during Pregnancy in Rat Brain Tissue

    Directory of Open Access Journals (Sweden)

    Phyllis E. Mann

    2014-03-01

    Full Text Available The neurophysiological changes that occur during pregnancy in the female mammal have led to the coining of the phrases “expectant brain” and “maternal brain”. Although much is known of the hormonal changes during pregnancy, alterations in neurotransmitter gene expression have not been well-studied. We examined gene expression in the ventromedial nucleus of the hypothalamus (VMH during pregnancy based on the fact that this nucleus not only modulates the physiological changes that occur during pregnancy but is also involved in the development of maternal behavior. This study was designed to identify genes that are differentially expressed between mid- and late-pregnancy in order to determine which genes may be associated with the onset and display of maternal behavior and the development of the maternal brain. A commercially available PCR array containing 84 neurotransmitter receptor and regulator genes (RT2 Profiler PCR array was used. Brains were harvested from rats on days 12 and 21 of gestation, frozen, and micropunched to obtain the VMH. Total RNA was extracted, cDNA prepared, and SYBR Green qPCR was performed. In the VMH, expression of five genes were reduced on day 21 of gestation compared to day 12 (Chrna6, Drd5, Gabrr2, Prokr2, and Ppyr1 whereas Chat, Chrm5, Drd4, Gabra5, Gabrg2, LOC289606, Nmu5r2, and Npy5r expression was elevated. Five genes were chosen to be validated in an additional experiment based on their known involvement in maternal behavior onset. This experiment confirmed that gene expression for both the CCK-A receptor and the GABAAR γ2 receptor increases at the end of pregnancy. In general, these results identify genes possibly involved in the establishment of the maternal brain in rats and indicate possible new genes to be investigated.

  2. Protein profile study of breast cancer tissues using HPLC-LIF: a pilot study

    Science.gov (United States)

    Menon, Suraj; Sujatha; Kumar, K. Kalyan; Kurien, Jacob; Krishnanand, B. R.; Mahato, K. K.; George, Sajan D.; Kartha, V. B.; C, Santhosh

    2007-02-01

    Proteomics based techniques are rapidly emerging as alternative techniques to conventional histo-pathological methods for detection and diagnosis of cancers. Tumor markers are of considerable importance in the study of various cancers. A study of various changes in the protein profile associated with breast cancer will facilitate a better understanding of the various dynamic changes associated with the disease. In our study we have used High Performance Liquid Chromatography coupled with highly sensitive Laser Induced Fluorescence for recording the protein profiles of breast tissue homogenates. The protein profiles were recorded from pathologically certified normal as well as malignant breast tissue samples. The recorded protein profiles were studied by using Principal Component Analysis. Good discrimination of normal, benign and malignant samples was achieved in this pilot study.

  3. Changes in soft tissue profile following the treatment using a Herbst appliance: A photographic analysis

    Directory of Open Access Journals (Sweden)

    Nedeljković Nenad

    2014-01-01

    Full Text Available Background/Aim. Aesthetics is the reason for most of the class II malocclusion patients to opt for orthodontic treatment. In order to regulate retrognathic profile Herbst appliance for anterior movement of the mandible can be a treatment of choice. The aim of this study was to determine the soft tissue profile changes following Herbst appliance therapy on before and after treatment photos, using the computer program. Methods. This investigation was performed on profile photographs of 20 class II patients (12 females and 8 males aged 18-23 years. Analysis of the changes in soft tissue facial structure relationships evident on the photographs before and after the Herbst appliance therapy was performed using Bentley Micro Station program. The first contour of the soft tissue profile was marked. The following reference lines were subsequently traced: Ricketts aesthetic E line and Juanita line. The area enclosed by these two lines included the nose, upper and lower lip, chin and free space in front of the lips. Using the computer program, the surfaces of the soft tissue structures and free space defined by the reference lines and profile contours were measured. Calculation of the relative proportion of surfaces was done for each photograph. The data obtained were then compared for each patient before and after the treatment. Skeletal and dentoalveolar treatment effects that support soft tissue changes were presented by the profile cephalometric parameters of sagital occlusion (SO analysis. Results. A reduction in the relative surface of the upper lip in males (p < 0.01 and females (p < 0.05 was shown by the pictures. The space occupied by the chin was reduced after the treatment for females only (p < 0.05. The relative surface of the nasal soft tissues, that was included in the reference space was increased (p < 0.01 in both genders. The relationship between the soft tissue and empty surface was changed in favor of the empty surface (p < 0.05 in

  4. Protein Profiling Gastric Cancer and Neighboring Control Tissues Using High-Content Antibody Microarrays

    OpenAIRE

    2016-01-01

    In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative gastric adenocarcinomas and adjacent non-cancerous control tissues were analyzed on microarrays that contain 813 antibodies targeting 724 proteins. Only 17 proteins were found to be differentially regulated, with much ...

  5. Simulation of the dependence of spatial fluence profiles on tissue optical properties

    Science.gov (United States)

    Miller, S.; Mitra, K.

    2016-03-01

    Medical laser applications are promoted as safe, effective treatments for a multiplicity of concerns, ranging from hyperthermal skin rejuvenation to subcutaneous tumor ablation. Chromophore and structural protein concentration and distribution within a patient's tissue vary from patient to patient and dictate the interaction of incident radiative energy of a specific wavelength with the target tissue. Laser parameters must be matched to tissue optical and thermal properties in order to achieve the desired therapeutic results without inducing unnecessary tissue damage, although accurate tissue optical properties are not always measured prior to and during laser therapies. A weighted variable step size Monte Carlo simulation of laser irradiation of skin tissue was used to determine the effects of variations in absorption (μa) and scattering coefficients (μs) and the degree of anisotropy (g) on the radiant energy transport per mm2 in response to steady-state photon propagation. The three parameters were varied in a factorial experimental design for the ranges of 0.25/mm isolate their impacts on the overall fluence distribution. Box plots of the resulting fluence profiles were created and compared to identify ranges in which optical property variance could be considered to significantly impact the spatial variance of fluence within the simulation volume. Results indicated that accurate prediction of the fluence profiles that will be achieved by any given medical laser treatment is unlikely without pre-treatment assessment of the tissue optical properties of individual patients.

  6. Comparison of soft tissue profile changes in serial extraction and late premolar extraction.

    Science.gov (United States)

    Wilson, J R; Little, R M; Joondeph, D R; Doppel, D M

    1999-04-01

    To assess soft tissue profile changes through time, a comparison was made of patients treated by serial extraction without subsequent orthodontic treatment (n=28), patients treated with serial extraction and orthodontic treatment (n=30), and patients treated orthodontically with late extraction (n=30). Cephalometric radiographs were traced and digitized; linear and angular measurements were made with a custom computer program that allowed digitization of specific soft tissue points. Maxillary, mandibular, and overall cephalometric superimpositions and linear measurements of change from the superimpositions were done by hand. Statistical analyses were made to determine if significant differences existed within each group at each time period and between groups at each time period, as well as between males and females at each time period. Data were also analyzed to determine if significant correlations existed between any hard tissue variable and any soft tissue variable, or between any soft tissue variable and any other soft tissue variable. It was found that in those patients treated with late premolar extraction, the most labial point of the mandibular incisor was more posterior from pretreatment to posttreatment than in the serial extraction group. While a great number of associations existed between variables, no significant differences were found between the soft tissue profiles of these three groups of patients. The gender differences that were found to exist were most likely due to normal maturational changes, not the treatment itself.

  7. Lipid Profiling of In Vitro Cell Models of Adipogenic Differentiation: Relationships With Mouse Adipose Tissues.

    Science.gov (United States)

    Liaw, Lucy; Prudovsky, Igor; Koza, Robert A; Anunciado-Koza, Rea V; Siviski, Matthew E; Lindner, Volkhard; Friesel, Robert E; Rosen, Clifford J; Baker, Paul R S; Simons, Brigitte; Vary, Calvin P H

    2016-09-01

    Our objective was to characterize lipid profiles in cell models of adipocyte differentiation in comparison to mouse adipose tissues in vivo. A novel lipid extraction strategy was combined with global lipid profiling using direct infusion and sequential precursor ion fragmentation, termed MS/MS(ALL) . Perirenal and inguinal white adipose tissue and interscapular brown adipose tissues from adult C57BL/6J mice were analyzed. 3T3-L1 preadipocytes, ear mesenchymal progenitor cells, and brown adipose-derived BAT-C1 cells were also characterized. Over 3000 unique lipid species were quantified. Principal component analysis showed that perirenal versus inguinal white adipose tissues varied in lipid composition of triacyl- and diacylglycerols, sphingomyelins, glycerophospholipids and, notably, cardiolipin CL 72:3. In contrast, hexosylceramides and sphingomyelins distinguished brown from white adipose. Adipocyte differentiation models showed broad differences in lipid composition among themselves, upon adipogenic differentiation, and with adipose tissues. Palmitoyl triacylglycerides predominate in 3T3-L1 differentiation models, whereas cardiolipin CL 72:1 and SM 45:4 were abundant in brown adipose-derived cell differentiation models, respectively. MS/MS(ALL) data suggest new lipid biomarkers for tissue-specific lipid contributions to adipogenesis, thus providing a foundation for using in vitro models of adipogenesis to reflect potential changes in adipose tissues in vivo. J. Cell. Biochem. 117: 2182-2193, 2016. © 2016 Wiley Periodicals, Inc.

  8. Microarray Expression Profiles of 20.000 Genes across 23 Healthy Porcine Tissues

    DEFF Research Database (Denmark)

    Hornshøj, Henrik; Conley, Lene Nagstrup; Hedegaard, Jakob

    2007-01-01

    Gene expression microarrays have been intensively applied to screen for genes involved in specific biological processes of interest such as diseases or responses to environmental stimuli. For mammalian species, cataloging of the global gene expression profiles in large tissue collections under...

  9. A study to evaluate cephalometric hard tissue profile of Tamil population for orthognathic surgery.

    Science.gov (United States)

    Nachiappan, S; Tharanikumar, S; Chandran, Ajay; Anusudha, P; Nandini, G D; Balasubramaniam, Murali

    2015-08-01

    The primary aim of this study is to compare, the cephalometric hard tissue profile values and analysis between Tamil and Caucasian population. The study also aims to create a better understanding in the facial proportions of Tamil Nadu population and to have better diagnosis and treatment planning for orthognathic surgery for Tamil population in Tamil Nadu.

  10. Comparison of cellular and tissue transcriptional profiles in canine mammary tumor

    NARCIS (Netherlands)

    Pawlowski, K.M.; Krol, M.; Majewska, A.; Badowska-Kozakiewicz, A.; Mol, J.A.; Malicka, E.; Motyl, T.

    2009-01-01

    J Physiol Pharmacol. 2009 May;60 Suppl 1:85-94. Comparison of cellular and tissue transcriptional profiles in canine mammary tumor. Pawlowski KM, Krol M, Majewska A, Badowska-Kozakiewicz A, Mol JA, Malicka E, Motyl T. Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw

  11. Difference in volatile profile between pericarp tissue and locular gel in tomato fruit

    Science.gov (United States)

    Aroma, a complex mixture of volatile compounds, plays an important role in the perception and acceptability of tomato products by consumers. Numerous studies have reported volatile profiles in tomatoes based on measurement of the whole fruit or pericarp tissue, however, little is understood regardin...

  12. Effect of head position on cephalometric evaluation of the soft-tissue facial profile

    NARCIS (Netherlands)

    Hoogeveen, R.C.; Sanderink, G.C.H.; Berkhout, W.E.R.

    2013-01-01

    Objectives: During a cone beam CT scan, the patient is in an upright or supine position. This position depends on the brand and type of the scanner. The aims of this study are: (1) to investigate if the head position has an effect on cephalometric evaluation of the soft-tissue facial profile, compar

  13. Comparison of PCB congener profiles in tissues of PCB-treated rats

    Energy Technology Data Exchange (ETDEWEB)

    Kania-Korwel, I.; Ludewig, G.; Robertson, L.W.; Lehmler, H.J. [Dept. of Occupational and Environmental Health, Univ. of Iowa, Iowa City (United States); Hornbuckle, K.C.; Peck, A. [Dept. of Civil and Environmental Engineering, Univ. of Iowa, Iowa City (United States); Sulkowski, W.W. [Dept. of Environmental Chemistry and Technology, Univ. of Silesia, Katowice (Poland)

    2004-09-15

    Information on the congener-specific distribution of PCBs in tissues of laboratory animals after exposure to technical or environmental PCB mixtures is limited. Typically PCB levels and profiles from adipose tissue, liver, blood and occasionally brain are reported. In the work presented here 120 PCB congeners were extracted from 9 tissues of rats exposed to two different PCB mixtures. One mixture was Aroclor 1254, a well studied technical mixture. The second mixture was an environmental mixture obtained after extraction of soil contaminated with Chlorofen, a highly chlorinated Polish PCB mixture. The study was designed to investigate how different chlorination levels and the structure of PCB congeners affect their distribution and total concentration in selected tissues. Principal Component Analysis and Hierarchical Cluster Analysis were employed to compare tissues of Aroclor and soil extract-treated animals.

  14. A Breast Tissue Protein Expression Profile Contributing to Early Parity-Induced Protection Against Breast Cancer

    Directory of Open Access Journals (Sweden)

    Christina Marie Gutierrez

    2015-11-01

    Full Text Available Background/Aims: Early parity reduces breast cancer risk, whereas, late parity and nulliparity increase breast cancer risk. Despite substantial efforts to understand the protective effects of early parity, the precise molecular circuitry responsible for these changes is not yet fully defined. Methods: Here, we have conducted the first study assessing protein expression profiles in normal breast tissue of healthy early parous, late parous, and nulliparous women. Breast tissue biopsies were obtained from 132 healthy parous and nulliparous volunteers. These samples were subjected to global protein expression profiling and immunohistochemistry. GeneSpring and MetaCore bioinformatics analysis software were used to identify protein expression profiles associated with early parity (low risk versus late/nulliparity (high risk. Results: Early parity reduces expression of key proteins involved in mitogenic signaling pathways in breast tissue through down regulation of EGFR1/3, ESR1, AKT1, ATF, Fos, and SRC. Early parity is also characterized by greater genomic stability and reduced tissue inflammation based on differential expression of aurora kinases, p53, RAD52, BRCA1, MAPKAPK-2, ATF-1, ICAM1, and NF-kappaB compared to late and nulli parity. Conclusions: Early parity reduces basal cell proliferation in breast tissue, which translates to enhanced genomic stability, reduced cellular stress/inflammation, and thus reduced breast cancer risk.

  15. Tannerella forsythia infection-induced calvarial bone and soft tissue transcriptional profiles.

    Science.gov (United States)

    Bakthavatchalu, V; Meka, A; Sathishkumar, S; Lopez, M C; Bhattacharyya, I; Boyce, B F; Mans, J J; Lamont, R J; Baker, H V; Ebersole, J L; Kesavalu, L

    2010-10-01

    Tannerella forsythia is associated with subgingival biofilms in adult periodontitis, although the molecular mechanisms contributing to chronic inflammation and loss of periodontal bone remain unclear. We examined changes in the host transcriptional profiles during a T. forsythia infection using a murine calvarial model of inflammation and bone resorption. Tannerella forsythia was injected into the subcutaneous soft tissue over calvariae of BALB/c mice for 3 days, after which the soft tissues and calvarial bones were excised. RNA was isolated and Murine GeneChip (Affymetrix, Santa Clara, CA) array analysis of transcript profiles showed that 3226 genes were differentially expressed in the infected soft tissues (P < 0.05) and 2586 genes were differentially transcribed in calvarial bones after infection. Quantitative real-time reverse transcription-polymerase chain reaction analysis of transcription levels of selected genes corresponded well with the microarray results. Biological pathways significantly impacted by T. forsythia infection in calvarial bone and soft tissue included leukocyte transendothelial migration, cell adhesion molecules (immune system), extracellular matrix-receptor interaction, adherens junction, and antigen processing and presentation. Histologic examination revealed intense inflammation and increased osteoclasts in calvariae compared with controls. In conclusion, localized T. forsythia infection differentially induces transcription of a broad array of host genes, and the profiles differ between inflamed soft tissues and calvarial bone.

  16. HER1-4 protein concentrations in normal breast tissue from breast cancer patients are expressed by the same profile as in the malignant tissue

    DEFF Research Database (Denmark)

    Olsen, Dorte Aa; Ostergaard, Birthe; Bokmand, Susanne;

    2009-01-01

    and the proteins extracted. The tissue and serum concentrations of HER1-4 were determined quantitatively using a commercially available enzyme linked immunosorbent assay (ELISA) method. Results: HER1 was down regulated in cancer tissue when compared to autologous reference tissue (p=8x10(-6)), while HER2 (p...-4 system. We have mapped the protein concentrations of HER1-4 in breast cancer tissue, autologous reference tissue, normal breast tissue and serum samples, to see whether non-cancer cells from these patients express a protein profile indicating general activation. Methods: Tissue samples from malignant...

  17. Differential Gene Expression Profiles Reflecting Macrophage Polarization in Aging and Periodontitis Gingival Tissues.

    Science.gov (United States)

    Gonzalez, O A; Novak, M J; Kirakodu, S; Stromberg, A; Nagarajan, R; Huang, C B; Chen, K C; Orraca, L; Martinez-Gonzalez, J; Ebersole, J L

    2015-01-01

    Recent evidence has determined a phenotypic and functional heterogeneity for macrophage populations. This plasticity of macrophage function has been related to specific properties of subsets (M1 and M2) of these cells in inflammation, adaptive immune responses and resolution of tissue destructive processes. This investigation hypothesized that targeted alterations in the distribution of macrophage phenotypes in aged individuals, and with periodontitis would be skewed towards M1 inflammatory macrophages in gingival tissues. The study used a non-human primate model to evaluate gene expression profiles as footprints of macrophage variation in healthy and periodontitis gingival tissues from animals 3-23 years of age and in periodontitis tissues in adult and aged animals. Significant increases in multiple genes reflecting overall increases in macrophage activities were observed in healthy aged tissues, and were significantly increased in periodontitis tissues from both adults and aged animals. Generally, gene expression patterns for M2 macrophages were similar in healthy young, adolescent and adult tissues. However, modest increases were noted in healthy aged tissues, similar to those seen in periodontitis tissues from both age groups. M1 macrophage gene transcription patterns increased significantly over the age range in healthy tissues, with multiple genes (e.g. CCL13, CCL19, CCR7 and TLR4) significantly increased in aged animals. Additionally, gene expression patterns for M1 macrophages were significantly increased in adult health versus periodontitis and aged healthy versus periodontitis. The findings supported a significant increase in macrophages with aging and in periodontitis. The primary increases in both healthy aged tissues and, particularly periodontitis tissues appeared in the M1 phenotype.

  18. The Application of Thematic Theory in English Company Profile%从主述位理论看企业英文简介

    Institute of Scientific and Technical Information of China (English)

    贾志芳

    2012-01-01

    Thematic theory is one of the key components of systemic functional grammar.The goodness of a company profile is closely related to the development of the company.A good English company profile can activate the potential customers to take greater interests and desire to purchase and focus on the products and service.The paper tends to adopt thematic theory as theoretical framework and to see how the theme theory is applied into English company profile for the purpose of shedding some lights on future teaching,writing and reading.%主位述位理论是系统功能语法中一项极为重要的组成部分。企业简介的好坏直接关乎企业的发展,一份好的企业英文简介不仅能够为企业赢得更高的知名度,而且也能激发更多潜在消费者的兴趣和购买欲。文章具体分析了主述位理论在企业英文简介中的应用,意在为今后语篇教学、撰写和阅读类似英文语篇提出几点建议。

  19. Spectral filtering in pulsed photothermal temperature profiling of collagen tissue phantoms

    Science.gov (United States)

    Milanič, Matija; Majaron, Boris

    2009-11-01

    We present an experimental comparison of pulsed photothermal (PPT) profiling in collagen-based tissue phantoms utilizing different midinfrared spectral bands. Laser-induced temperature profiles are reconstructed using a custom optimization code within the customary monochromatic approximation. Both experimental results and a detailed numerical simulation of the procedure demonstrate that, despite the associated reduction of signal-to-noise ratio, appropriate spectral filtering reduces the broadening of temperature peaks and thus improves the accuracy of temperature profiling. For our experimental system, best performance is obtained when applying a long-pass filter with cut-on wavelength at 3.4-3.8 μm. Because our collagen gel mimics infrared and thermal properties of human skin, we believe that this conclusion is transferrable to PPT radiometric profiling of human skin in vivo.

  20. Spectral filtering in pulsed photothermal temperature profiling of collagen tissue phantoms.

    Science.gov (United States)

    Milanic, Matija; Majaron, Boris

    2009-01-01

    We present an experimental comparison of pulsed photothermal (PPT) profiling in collagen-based tissue phantoms utilizing different midinfrared spectral bands. Laser-induced temperature profiles are reconstructed using a custom optimization code within the customary monochromatic approximation. Both experimental results and a detailed numerical simulation of the procedure demonstrate that, despite the associated reduction of signal-to-noise ratio, appropriate spectral filtering reduces the broadening of temperature peaks and thus improves the accuracy of temperature profiling. For our experimental system, best performance is obtained when applying a long-pass filter with cut-on wavelength at 3.4-3.8 microm. Because our collagen gel mimics infrared and thermal properties of human skin, we believe that this conclusion is transferrable to PPT radiometric profiling of human skin in vivo.

  1. Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling.

    Directory of Open Access Journals (Sweden)

    Daniel P Riordan

    Full Text Available Characterization of the molecular attributes and spatial arrangements of cells and features within complex human tissues provides a critical basis for understanding processes involved in development and disease. Moreover, the ability to automate steps in the analysis and interpretation of histological images that currently require manual inspection by pathologists could revolutionize medical diagnostics. Toward this end, we developed a new imaging approach called multidimensional microscopic molecular profiling (MMMP that can measure several independent molecular properties in situ at subcellular resolution for the same tissue specimen. MMMP involves repeated cycles of antibody or histochemical staining, imaging, and signal removal, which ultimately can generate information analogous to a multidimensional flow cytometry analysis on intact tissue sections. We performed a MMMP analysis on a tissue microarray containing a diverse set of 102 human tissues using a panel of 15 informative antibody and 5 histochemical stains plus DAPI. Large-scale unsupervised analysis of MMMP data, and visualization of the resulting classifications, identified molecular profiles that were associated with functional tissue features. We then directly annotated H&E images from this MMMP series such that canonical histological features of interest (e.g. blood vessels, epithelium, red blood cells were individually labeled. By integrating image annotation data, we identified molecular signatures that were associated with specific histological annotations and we developed statistical models for automatically classifying these features. The classification accuracy for automated histology labeling was objectively evaluated using a cross-validation strategy, and significant accuracy (with a median per-pixel rate of 77% per feature from 15 annotated samples for de novo feature prediction was obtained. These results suggest that high-dimensional profiling may advance the

  2. Epigenome-wide profiling of DNA methylation in paired samples of adipose tissue and blood.

    Science.gov (United States)

    Huang, Yen-Tsung; Chu, Su; Loucks, Eric B; Lin, Chien-Ling; Eaton, Charles B; Buka, Stephen L; Kelsey, Karl T

    2016-03-03

    Many epigenetic association studies have attempted to identify DNA methylation markers in blood that are able to mirror those in target tissues. Although some have suggested potential utility of surrogate epigenetic markers in blood, few studies have collected data to directly compare DNA methylation across tissues from the same individuals. Here, epigenomic data were collected from adipose tissue and blood in 143 subjects using Illumina HumanMethylation450 BeadChip array. The top axis of epigenome-wide variation differentiates adipose tissue from blood, which is confirmed internally using cross-validation and externally with independent data from the two tissues. We identified 1,285 discordant genes and 1,961 concordant genes between blood and adipose tissue. RNA expression data of the two classes of genes show consistent patterns with those observed in DNA methylation. The discordant genes are enriched in biological functions related to immune response, leukocyte activation or differentiation, and blood coagulation. We distinguish the CpG-specific correlation from the within-subject correlation and emphasize that the magnitude of within-subject correlation does not guarantee the utility of surrogate epigenetic markers. The study reinforces the critical role of DNA methylation in regulating gene expression and cellular phenotypes across tissues, and highlights the caveats of using methylation markers in blood to mirror the corresponding profile in the target tissue.

  3. Factors influencing the predictability of soft tissue profile changes following mandibular setback surgery.

    Science.gov (United States)

    Mobarak, K A; Krogstad, O; Espeland, L; Lyberg, T

    2001-06-01

    The objective of this cephalometric study was to assess long-term changes in the soft tissue profile following mandibular setback surgery and investigate the presence of factors that may influence the soft tissue response to skeletal repositioning. The subjects enrolled were 80 consecutive mandibular prognathism patients operated with bilateral sagittal split osteotomy and rigid fixation. Lateral cephalograms were taken at 6 occasions: immediate presurgical, immediate postsurgical, 2 and 6 months postsurgical, and 1 and 3 years postsurgical. The subjects were grouped according to gender and magnitude of setback. Ratios of soft tissue to hard tissue movements were calculated for the subgroups. Females generally demonstrated greater ratios than males with a statistically significant difference for the upper lip and chin (P < .05). Postsurgical alterations in the profiles were more predictable in patients with larger setbacks compared to patients with smaller ones. Skeletal relapse had a profound influence on long-term profile changes. Based on these findings, it is proposed that the database used in prediction software be adjusted to account for such factors in an attempt to improve the accuracy of computerized treatment simulations.

  4. Soft tissue thickness of face profile conditioning by dento-skeletal anomalies

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    Tanić Tatjana

    2011-01-01

    Full Text Available Introduction. Orthodontic treatment of dento-skeletal anomalies is generally based on the correction of teeth and jaws relationship, while it is expected that soft facial tissue spontaneously adapts to therapeutically achieved relationship and to accompany hard tissue changes. Objective. To establish facial soft tissue thickness conditioning by the presence of dento-skeletal anomalies. Methods. The study was performed at the Dental Clinic of Niš, and involved the analysis of cephalometric rendgenograms in 121 patients, aged 12-18 years, with no previous orthodontical treatment. According to dento-skeletal relationship between teeth and jaws the patients were divided into four groups; class I (control group, class II of division 1, class II of division 2 and class III. The standard analysis of dento-skeletal profile was done according to Steiner and soft tissue profile according to Burstone was done in all. Results. The patients of class II/1 had a significantly thinner upper lip (t=2.650; p<0.05 and thinner upper lip sulcus (t=1.999; p<0.05. The patients of class II/2 had a significantly thicker upper lip (t=2.912; p<0.01, while those of class III had a significantly thinner lower lip (t=3.900; p<0.001. Conclusion. The thickness of facial soft tissue considerably influences facial profile appearance in persons with a dento-skeletal anomaly. Not only do soft tissues adapt to the existing jaws relationship, but can also camouflage present anomalies.

  5. Laser microdissection of tomato fruit cell and tissue types for transcriptome profiling.

    Science.gov (United States)

    Martin, Laetitia B B; Nicolas, Philippe; Matas, Antonio J; Shinozaki, Yoshihito; Catalá, Carmen; Rose, Jocelyn K C

    2016-12-01

    This protocol enables transcriptome profiling of specific cell or tissue types that are isolated from tomato using laser microdissection (LM). To prepare tissue for LM, fruit samples are first fixed in optimal cutting temperature (OCT) medium and frozen in molds. The tissue is then sectioned using a cryostat before being dissected using an LM instrument. The RNAs contained in the harvested cells are purified and subjected to two rounds of amplification to yield sufficient quantities of RNA to generate cDNA libraries. Unlike several other techniques that are used to isolate specific cell types, LM has the advantage of being readily applied to any plant species without having to generate transgenic plants. Using the protocols described here, LM-mediated cell-type transcriptomic analysis of two samples requires ∼8 d from tissue harvest to RNA sequencing (RNA-seq), whereas each additional sample, up to a total of 12 samples, requires ∼1 additional day for the LM step. RNA obtained using this method has been successfully used for deep-coverage transcriptome profiling, which is a particularly effective strategy for identifying genes that are differentially expressed between cell or tissue types.

  6. Foraging at wastewater treatment works affects brown adipose tissue fatty acid profiles in banana bats.

    Science.gov (United States)

    Hill, Kate; van Aswegen, Sunet; Schoeman, M Corrie; Claassens, Sarina; Jansen van Rensburg, Peet; Naidoo, Samantha; Vosloo, Dalene

    2016-01-06

    In this study we tested the hypothesis that the decrease in habitat quality at wastewater treatment works (WWTW), such as limited prey diversity and exposure to the toxic cocktail of pollutants, affect fatty acid profiles of interscapular brown adipose tissue (iBrAT) in bats. Further, the antioxidant capacity of oxidative tissues such as pectoral and cardiac muscle may not be adequate to protect those tissues against reactive molecules resulting from polyunsaturated fatty acid auto-oxidation in the WWTW bats. Bats were sampled at two urban WWTW, and two unpolluted reference sites in KwaZulu-Natal, South Africa. Brown adipose tissue (BrAT) mass was lower in WWTW bats than in reference site bats. We found lower levels of saturated phospholipid fatty acids and higher levels of mono- and polyunsaturated fatty acids in WWTW bats than in reference site bats, while C18 desaturation and n-6 to n-3 ratios were higher in the WWTW bats. This was not associated with high lipid peroxidation levels in pectoral and cardiac muscle. Combined, these results indicate that WWTW bats rely on iBrAT as an energy source, and opportunistic foraging on abundant, pollutant-tolerant prey may change fatty acid profiles in their tissue, with possible effects on mitochondrial functioning, torpor and energy usage.

  7. Foraging at wastewater treatment works affects brown adipose tissue fatty acid profiles in banana bats

    Directory of Open Access Journals (Sweden)

    Kate Hill

    2016-02-01

    Full Text Available In this study we tested the hypothesis that the decrease in habitat quality at wastewater treatment works (WWTW, such as limited prey diversity and exposure to the toxic cocktail of pollutants, affect fatty acid profiles of interscapular brown adipose tissue (iBrAT in bats. Further, the antioxidant capacity of oxidative tissues such as pectoral and cardiac muscle may not be adequate to protect those tissues against reactive molecules resulting from polyunsaturated fatty acid auto-oxidation in the WWTW bats. Bats were sampled at two urban WWTW, and two unpolluted reference sites in KwaZulu-Natal, South Africa. Brown adipose tissue (BrAT mass was lower in WWTW bats than in reference site bats. We found lower levels of saturated phospholipid fatty acids and higher levels of mono- and polyunsaturated fatty acids in WWTW bats than in reference site bats, while C18 desaturation and n-6 to n-3 ratios were higher in the WWTW bats. This was not associated with high lipid peroxidation levels in pectoral and cardiac muscle. Combined, these results indicate that WWTW bats rely on iBrAT as an energy source, and opportunistic foraging on abundant, pollutant-tolerant prey may change fatty acid profiles in their tissue, with possible effects on mitochondrial functioning, torpor and energy usage.

  8. MALDI Imaging Mass Spectrometry Profiling of N-Glycans in Formalin-Fixed Paraffin Embedded Clinical Tissue Blocks and Tissue Microarrays

    Science.gov (United States)

    Powers, Thomas W.; Neely, Benjamin A.; Shao, Yuan; Tang, Huiyuan; Troyer, Dean A.; Mehta, Anand S.; Haab, Brian B.; Drake, Richard R.

    2014-01-01

    A recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) method to spatially profile the location and distribution of multiple N-linked glycan species in frozen tissues has been extended and improved for the direct analysis of glycans in clinically derived formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed tissues from normal mouse kidney, human pancreatic and prostate cancers, and a human hepatocellular carcinoma tissue microarray were processed by antigen retrieval followed by on-tissue digestion with peptide N-glycosidase F. The released N-glycans were detected by MALDI-IMS analysis, and the structural composition of a subset of glycans could be verified directly by on-tissue collision-induced fragmentation. Other structural assignments were confirmed by off-tissue permethylation analysis combined with multiple database comparisons. Imaging of mouse kidney tissue sections demonstrates specific tissue distributions of major cellular N-linked glycoforms in the cortex and medulla. Differential tissue distribution of N-linked glycoforms was also observed in the other tissue types. The efficacy of using MALDI-IMS glycan profiling to distinguish tumor from non-tumor tissues in a tumor microarray format is also demonstrated. This MALDI-IMS workflow has the potential to be applied to any FFPE tissue block or tissue microarray to enable higher throughput analysis of the global changes in N-glycosylation associated with cancers. PMID:25184632

  9. MALDI imaging mass spectrometry profiling of N-glycans in formalin-fixed paraffin embedded clinical tissue blocks and tissue microarrays.

    Science.gov (United States)

    Powers, Thomas W; Neely, Benjamin A; Shao, Yuan; Tang, Huiyuan; Troyer, Dean A; Mehta, Anand S; Haab, Brian B; Drake, Richard R

    2014-01-01

    A recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) method to spatially profile the location and distribution of multiple N-linked glycan species in frozen tissues has been extended and improved for the direct analysis of glycans in clinically derived formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed tissues from normal mouse kidney, human pancreatic and prostate cancers, and a human hepatocellular carcinoma tissue microarray were processed by antigen retrieval followed by on-tissue digestion with peptide N-glycosidase F. The released N-glycans were detected by MALDI-IMS analysis, and the structural composition of a subset of glycans could be verified directly by on-tissue collision-induced fragmentation. Other structural assignments were confirmed by off-tissue permethylation analysis combined with multiple database comparisons. Imaging of mouse kidney tissue sections demonstrates specific tissue distributions of major cellular N-linked glycoforms in the cortex and medulla. Differential tissue distribution of N-linked glycoforms was also observed in the other tissue types. The efficacy of using MALDI-IMS glycan profiling to distinguish tumor from non-tumor tissues in a tumor microarray format is also demonstrated. This MALDI-IMS workflow has the potential to be applied to any FFPE tissue block or tissue microarray to enable higher throughput analysis of the global changes in N-glycosylation associated with cancers.

  10. MALDI imaging mass spectrometry profiling of N-glycans in formalin-fixed paraffin embedded clinical tissue blocks and tissue microarrays.

    Directory of Open Access Journals (Sweden)

    Thomas W Powers

    Full Text Available A recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS method to spatially profile the location and distribution of multiple N-linked glycan species in frozen tissues has been extended and improved for the direct analysis of glycans in clinically derived formalin-fixed paraffin-embedded (FFPE tissues. Formalin-fixed tissues from normal mouse kidney, human pancreatic and prostate cancers, and a human hepatocellular carcinoma tissue microarray were processed by antigen retrieval followed by on-tissue digestion with peptide N-glycosidase F. The released N-glycans were detected by MALDI-IMS analysis, and the structural composition of a subset of glycans could be verified directly by on-tissue collision-induced fragmentation. Other structural assignments were confirmed by off-tissue permethylation analysis combined with multiple database comparisons. Imaging of mouse kidney tissue sections demonstrates specific tissue distributions of major cellular N-linked glycoforms in the cortex and medulla. Differential tissue distribution of N-linked glycoforms was also observed in the other tissue types. The efficacy of using MALDI-IMS glycan profiling to distinguish tumor from non-tumor tissues in a tumor microarray format is also demonstrated. This MALDI-IMS workflow has the potential to be applied to any FFPE tissue block or tissue microarray to enable higher throughput analysis of the global changes in N-glycosylation associated with cancers.

  11. Differential expression profile of miRNAs in porcine muscle and adipose tissue during development.

    Science.gov (United States)

    Wang, Qi; Qi, Renli; Wang, Jing; Huang, Wenming; Wu, Yongjiang; Huang, Xiaofeng; Yang, Feiyun; Huang, Jinxiu

    2017-06-30

    MicroRNAs (miRNAs) are a class of non-coding RNAs that play a crucial regulatory role in many biological processes. Previous studies have reported miRNAs that are associated with the growth, differentiation, and proliferation of myocytes and adipocytes in pigs. However, differences in the miRNA expression profiles between muscle and adipose tissues during porcine development are unknown. Muscle and adipose tissues are the two major organs that are crucial for dynamic energy balance in the development and metabolism. Identification of differential expression profile of miRNAs will be useful for understanding the regulatory role of miRNAs in growth, development and evolution of these two tissues, and the research results will provide theoretical basis to improve meat quality. Therefore, we applied Hiseq sequencing to profile miRNAs in muscle and adipose tissues during four development stage at 1, 30, 90 and 240-day-old to explore their regulatory patterns at critical growth stages of pigs. We slaughtered 6 pigs at each developmental stages (24 pigs in total), respectively, RNA of three individual pigs were pooled and duplicate samples at each time point were given to sequence. We obtained a total of 96 million clean reads, and identified 329 known miRNAs and 157 novel miRNAs from all the libraries. We detected 37 miRNAs that were differentially expressed between porcine muscle and adipose tissues; 17 miRNAs which differentially expressed at 30, 90 and 240-day-old were considered as core differentially expressed miRNAs, among them, three miRNAs (ssc-miR-128, -133a-5p, -489) were differentially expressed at all four stages. KEGG analysis revealed the target genes of 17 core differentially expressed miRNAs were involved in 27 significantly enriched pathways (Pmuscle and adipose tissues, respectively, of 30, 90, and 240-day-old pigs compared with the tissues of 1-day-old pigs. We selected five miRNAs from 17 core differentially expressed miRNAs to validate the mi

  12. Multivariate analysis of the scattering profiles of healthy and pathological human breast tissues

    Energy Technology Data Exchange (ETDEWEB)

    Conceicao, A.L.C.; Antoniassi, M. [Departamento de Fisica e Matematica, FFCLRP, Universidade de Sao Paulo, Ribeirao Preto 14040-901, Sao Paulo (Brazil); Cunha, D.M. [Instituto de Fisica, Universidade Federal de Uberlandia, 38400-902, Uberlandia, Minas Gerais (Brazil); Ribeiro-Silva, A. [Departamento de Patologia, HCFMRP, Universidade de Sao Paulo, Ribeirao Preto 14040-901, Sao Paulo (Brazil); Poletti, M.E., E-mail: poletti@ffclrp.usp.br [Departamento de Fisica e Matematica, FFCLRP, Universidade de Sao Paulo, Ribeirao Preto 14040-901, Sao Paulo (Brazil)

    2011-10-01

    Scattering profiles of 106 healthy and pathological human breast samples were obtained using the angular dispersive X-ray scattering technique (AD-XRD) and synchrotron radiation covering the momentum transfer interval of 0.7 nm{sup -1}{<=}q(=4{pi} sin({theta}/2)/{lambda}){<=}70.5 nm{sup -1}. Multivariate analysis in the form of discriminant analysis was applied over the whole scattering profile curve of each sample in order to build a model for breast tissue classification. The classification results were validated and compared with histological sample classification obtained by microscopy analysis. Finally, the model allows classifying correctly 91.5% of the samples and presented values of 98.5%, 89.7% and 0.90 for sensitivity, specificity and Cohen's {kappa}, respectively, in correctly differentiating between healthy and pathological tissues.

  13. Genetic Profiling Differentiates Second Primary Tumors from Metastases in Adult Metachronous Soft Tissue Sarcoma

    Directory of Open Access Journals (Sweden)

    Josefin Fernebro

    2008-01-01

    Full Text Available Purpose. Patients with soft tissue sarcomas (STS are at increased risk of second primary malignancies, including a second STS, but distinction between metastases and a second primary STS is difficult. Patients and Methods. Array-based comparative genomic hybridization (aCGH was applied to 30 multiple STS of the extremities and the trunk wall from 13 patients. Different histotypes were present with malignant fibrous histiocytomas/undifferentiated pleomorphic sarcomas being the predominant subtype. Results. aCGH profiling revealed genetic complexity with multiple gains and losses in all tumors. In an unsupervised hierarchical cluster analysis, similar genomic profiles and close clustering between the first and subsequent STS were identified in 5 cases, suggesting metastatic disease, whereas the tumors from the remaining 8 patients did not cluster and showed only weak pairwise correlation, suggesting development of second primary STS. Discussion. The similarities and dissimilarities identified in the first and second STS suggest that genetic profiles can be used to distinguish soft tissue metastases from second primary STS. The demonstration of genetically different soft tissue sarcomas in the same patient suggests independent tumor origin and serves as a reminder to consider development of second primary STS, which has prognostic and therapeutic implications.

  14. Determination of agar tissue phantoms depth profiles with pulsed photothermal radiometry

    Science.gov (United States)

    Milanič, Matija; Majaron, Boris; Nelson, J. Stuart

    2007-07-01

    Pulsed photothermal radiometry (PPTR) can be used for non-invasive depth profiling of skin vascular lesions (e.g., port wine stain birthmarks), aimed towards optimizing laser therapy on an individual patient basis. Optimal configuration of the experimental setup must be found and its performance characterized on samples with well defined structure, before introducing the technique into clinical practice. The aim of our study is to determine how sample structure and width of spectruml acquisition band affect the accuracy of measured depth profiles. We have constructed tissue phantoms composed of multiple layers of agar and of thin absorbing layers between the agar layers. Three phantoms had a single absorber layer at various depths between 100 and 500 μm, and one phantom had two absorber layers. In each sample we induced a non-homogeneous temperature profile with a 585 nm pulsed laser and acquired the resulting radiometric signal with a fast InSb infrared camera. We tested two configurations of the acquisition system, one using the customary 3-5 um spectruml band and one with a custom 4.5 μm cut-on filter. The laser-induced temperature depth profiles were reconstructed from measured PPTR signals using a custom algorithm and compared with sample structure as determined by histology and optical coherent tomography (OCT). PPTR determined temperature profiles correlate well with sample structure in all samples. Determination of the absorbing layer depth shows good repeatability with spatial resolution decreasing with depth. Spectruml filtering improved the accuracy of reconstructed profiles for shallow absorption layers (100-200 μm). PPTR technique enables reliable determination of structure in tissue phantoms with thin absorbing layers. Narrowing of the spectruml acquisition band (to 4.5 - 5.3 μm) improves reconstruction of objects near the surface.

  15. Age-related expression profile of the SLC27A1 gene in chicken tissues.

    Science.gov (United States)

    Wang, Yan; Zhu, Qing; Zhao, Xiao-Ling; Yao, Yong-Gang; Liu, Yi-Ping

    2011-11-01

    The solute carrier family 27 (SLC27, also known as fatty acid transport proteins [FATPs]) plays important biological roles in cells. However, there is no report about the expression profile of SLC27 member in chicken. In this study, we quantified the expression of SLC27A1 (FATP1) mRNA in a mountainous black-boned chicken breed (MB) and a commercial meat type chicken breed (S01), to discern the tissue and age-related specific expression pattern and their potential involvement in fat deposition and muscle fatty acid metabolism. Real-time quantitative PCR assays were developed for accurate measurement of SLC27A1 mRNA levels in different tissues from chicken with different ages (0-12 weeks). Expression of SLC27A1 mRNA was detected in all tissues examined. There was a significantly age-related change of the SLC27A1 mRNAs in heart, breast muscle (BMW), leg muscle (LMW), liver, and abdominal fat (AF) tissues (P chicken had a higher expression of the SLC27A1 mRNA in breast muscle, subcutaneous fat, and heart tissues than the MB chicken. Our results showed that the expression of SLC27A1 mRNA in chicken tissues exhibits specific developmental changes and age-related patterns.

  16. In vitro cytokeratin expression profiling of human oral mucosa substitutes developed by tissue engineering.

    Science.gov (United States)

    Garzon, Ingrid; Serrato, Deyanira; Roda, Olga; Del Carmen Sanchez-Quevedo, Maria; Gonzales-Jaranay, Maximino; Moreu, Gerardo; Nieto-Aguilar, Renato; Alaminos, Miguel; Campos, Antonio

    2009-10-01

    In this work we performed a study of cytokeratin (CK) expression profiling on human artificial oral mucosa developed in vitro by tissue engineering at different stages of maturation (from immature to well-developed stages) at the protein and mRNA levels. Human artificial oral mucosa was generated in the laboratory using fibrin-agarose biomaterials. As controls, we used human native normal oral mucosa and embryonic oral tissues. Our results demonstrated that human embryonic oral tissues tended to express CK8 and CK19. In contrast, monolayered bioengineered oral mucosa did not show any CK expression by immunohistochemistry, whereas bilayered and multilayered artificial oral mucosa showed several markers of stratified epithelia, but did not express CK10. These results suggest that the CK expression pattern is strongly dependent on the maturation state of the artificial tissues and that the CK expression profile of our model of artificial oral mucosa was partially similar to that of the non-keratinized human adult oral mucosa. However, the expression of CK8 by the artificial oral mucosa suggests that these samples correspond to an early stage of development while kept in vitro.

  17. Reflected light intensity profile of two-layer tissues: phantom experiments.

    Science.gov (United States)

    Ankri, Rinat; Taitelbaum, Haim; Fixler, Dror

    2011-08-01

    Experimental measurements of the reflected light intensity from two-layer phantoms are presented. We report, for the first time, an experimental observation of a typical reflected light intensity behavior for the two-layer structure characterized by two different slopes in the reflected light profile of the irradiated tissue. The point in which the first slope changes to the second slope, named as the crossover point, depends on the upper layer thickness as well as on the ratio between the absorption coefficients of the two layers. Since similar experiments from one-layer phantoms present a monotonic decay behavior, the existence and the location of the crossover point can be used as a diagnostic fingerprint for two-layer tissue structures. This pertains to two layers with greater absorptivity in the upper layer, which is the typical biological case in tissues like skin.

  18. Profiling gene expression patterns of nasopharyngeal carcinoma and normal nasopharynx tissues with cDNA microarray

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    5 μg of total RNAs from normal nasopharynx and nasopharyngeal carcinoma tissue have been labeled with α-32P-dCTP during reverse transcription. The synthesized cDNA probes have been hybridized to high-density cDNA microarray containing 5184 genes or expression sequence tags (ESTs). Then image analysis software has been applied to comparing their expression profiles. Results show that 187 ESTs were of density value above 200 in nasopharyngeal carcinoma tissue while there were 307 such ESTs in normal nasopharynx tissue; 38 ESTs were strongly expressed in nasopharynx, but weakly expressed in nasopharyngeal carcinoma; 48 ESTs were strongly expressed in nasopharyngeal carcinoma, but weakly expressed in normal nasopharynx. These results suggest that there may exist some new differentially expressed genes involved in nasopharyngeal carcinoma development. Furthermore, the results strongly indicate that high-density cDNA microarray is a powerful and efficient tool for large-scale screening differentially expressed genes.

  19. Cell and tissue microarray technologies for protein and nucleic acid expression profiling.

    Science.gov (United States)

    Cardano, Marina; Diaferia, Giuseppe R; Falavigna, Maurizio; Spinelli, Chiara C; Sessa, Fausto; DeBlasio, Pasquale; Biunno, Ida

    2013-02-01

    Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform.

  20. Lipidomic Profiling of Mastoid Bone and Tissue from Patients with Chronic Otomastoiditis

    Directory of Open Access Journals (Sweden)

    Fazlollahi, Farbod

    2015-01-01

    Full Text Available Introduction Chronic otomastoiditis causes pain, otorrhea, and hearing loss resulting from the growth of tissue within the normally hollow mastoid cavity. Objectives In this report, we used a lipidomics approach to profile major mastoid bone and tissue lipids from patients with and without otomastoiditis. Methods The bone dust created during mastoidectomy, as well as the mastoid tissue, was analyzed from seven patients. Bone dust was also collected and analyzed in an additional four otologic cases (parotidectomy requiring mastoidectomy. Samples were subjected to a modified Bligh/Dyer lipid extraction, then high-performance thin-layer chromatography (HPTLC, combined gas chromatography/electron impact-mass spectrometry (GC/EI-MS, and flow-injection/electrospray ionization-tandem mass spectrometry (FI/ESI-MSMS. Data were analyzed for identification and profiling of major lipid components. Results HPTLC revealed the presence of various lipid classes, including phosphatidylcholines, cholesterol, and triacylglycerols. GC/EI-MS analysis revealed the presence of cholesterol and several fatty acids. FI/ESI-MSMS analysis revealed a host of phosphatidylcholines, phosphatidylethanolamines, and cholesteryl esters. Conclusion We used a lipidomics approach to develop an efficient (both in time and tissue amount methodology for analysis of these tissues, identify the most abundant and common lipid species, and create a base of knowledge from which more focused endeavors in biomarker discovery can emerge. In an effort toward improved patient categorization and individualized intervention, the ultimate goal of this work is to correlate these lipid molecules to disease state and progression. This is the first reported study of its kind on these tissues.

  1. Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma

    Directory of Open Access Journals (Sweden)

    Kern Rei Chng

    2016-06-01

    Full Text Available Cholangiocarcinoma (CCA is the primary cancer of the bile duct system. The role of bile duct tissue microbiomes in CCA tumorigenesis is unestablished. To address this, sixty primary CCA tumors and matched normals, from both liver fluke (Opisthorchis viverrini associated (OVa, n = 28 and non-O. viverrini associated (non-OVa, n = 32 cancers, were profiled using high-throughput 16S rRNA sequencing. A distinct, tissue-specific microbiome dominated by the bacterial families Dietziaceae, Pseudomonadaceae and Oxalobacteraceae was observed in bile duct tissues. Systemic perturbation of the microbiome was noted in tumor and paired normal samples (vs non-cancer normals for several bacterial families with a significant increase in Stenotrophomonas species distinguishing tumors vs paired normals. Comparison of parasite associated (OVa vs non-associated (non-OVa groups identified enrichment for specific enteric bacteria (Bifidobacteriaceae, Enterobacteriaceae and Enterococcaceae. One of the enriched families, Bifidobacteriaceae, was found to be dominant in the O. viverrini microbiome, providing a mechanistic link to the parasite. Functional analysis and comparison of CCA microbiomes revealed higher potential for producing bile acids and ammonia in OVa tissues, linking the altered microbiota to carcinogenesis. These results define how the unique microbial communities resident in the bile duct, parasitic infections and the tissue microenvironment can influence each other, and contribute to cancer.

  2. Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma.

    Science.gov (United States)

    Chng, Kern Rei; Chan, Sock Hoai; Ng, Amanda Hui Qi; Li, Chenhao; Jusakul, Apinya; Bertrand, Denis; Wilm, Andreas; Choo, Su Pin; Tan, Damien Meng Yew; Lim, Kiat Hon; Soetinko, Roy; Ong, Choon Kiat; Duda, Dan G; Dima, Simona; Popescu, Irinel; Wongkham, Chaisiri; Feng, Zhu; Yeoh, Khay Guan; Teh, Bin Tean; Yongvanit, Puangrat; Wongkham, Sopit; Bhudhisawasdi, Vajaraphongsa; Khuntikeo, Narong; Tan, Patrick; Pairojkul, Chawalit; Ngeow, Joanne; Nagarajan, Niranjan

    2016-06-01

    Cholangiocarcinoma (CCA) is the primary cancer of the bile duct system. The role of bile duct tissue microbiomes in CCA tumorigenesis is unestablished. To address this, sixty primary CCA tumors and matched normals, from both liver fluke (Opisthorchis viverrini) associated (OVa, n=28) and non-O. viverrini associated (non-OVa, n=32) cancers, were profiled using high-throughput 16S rRNA sequencing. A distinct, tissue-specific microbiome dominated by the bacterial families Dietziaceae, Pseudomonadaceae and Oxalobacteraceae was observed in bile duct tissues. Systemic perturbation of the microbiome was noted in tumor and paired normal samples (vs non-cancer normals) for several bacterial families with a significant increase in Stenotrophomonas species distinguishing tumors vs paired normals. Comparison of parasite associated (OVa) vs non-associated (non-OVa) groups identified enrichment for specific enteric bacteria (Bifidobacteriaceae, Enterobacteriaceae and Enterococcaceae). One of the enriched families, Bifidobacteriaceae, was found to be dominant in the O. viverrini microbiome, providing a mechanistic link to the parasite. Functional analysis and comparison of CCA microbiomes revealed higher potential for producing bile acids and ammonia in OVa tissues, linking the altered microbiota to carcinogenesis. These results define how the unique microbial communities resident in the bile duct, parasitic infections and the tissue microenvironment can influence each other, and contribute to cancer.

  3. Long non-coding RNA expression profile in cervical cancer tissues.

    Science.gov (United States)

    Zhu, Hua; Chen, Xiangjian; Hu, Yan; Shi, Zhengzheng; Zhou, Qing; Zheng, Jingjie; Wang, Yifeng

    2017-08-01

    Cervical cancer (CC), one of the most common types of cancer of the female population, presents an enormous challenge in diagnosis and treatment. Long non-coding (lnc)RNAs, non-coding (nc)RNAs with length >200 nucleotides, have been identified to be associated with multiple types of cancer, including CC. This class of nc transcripts serves an important role in tumor suppression and oncogenic signaling pathways. In the present study, the microarray method was used to obtain the expression profile of lncRNAs and protein-coding mRNAs and to compare the expression of lncRNAs between CC tissues and corresponding adjacent non-cancerous tissues in order to screen potential lncRNAs for associations with CC. Overall, 3356 lncRNAs with significantly different expression pattern in CC tissues compared with adjacent non-cancerous tissues were identified, while 1,857 of them were upregulated. These differentially expressed lncRNAs were additionally classified into 5 subgroups. Reverse transcription quantitative polymerase chain reactions were performed to validate the expression pattern of 5 random selected lncRNAs, and 2lncRNAs were identified to have significantly different expression in CC samples compared with adjacent non-cancerous tissues. This finding suggests that those lncRNAs with different expression may serve important roles in the development of CC, and the expression data may provide information for additional study on the involvement of lncRNAs in CC.

  4. Gene expression profiling of muscle tissue in Brahman steers during nutritional restriction.

    Science.gov (United States)

    Byrne, K A; Wang, Y H; Lehnert, S A; Harper, G S; McWilliam, S M; Bruce, H L; Reverter, A

    2005-01-01

    Expression profiling using microarrays allows for the detailed characterization of the gene networks that regulate an animal's response to environmental stresses. During nutritional restriction, processes such as protein turnover, connective tissue remodeling, and muscle atrophy take place in the skeletal muscle of the animal. These processes and their regulation are of interest in the context of managing livestock for optimal production efficiency and product quality. Here we expand on recent research applying complementary DNA (cDNA) microarray technology to the study of the effect of nutritional restriction on bovine skeletal muscle. Using a custom cDNA microarray of 9,274 probes from cattle muscle and s.c. fat libraries, we examined the differential gene expression profile of the LM from 10 Brahman steers under three different dietary treatments. The statistical approach was based on mixed-model ANOVA and model-based clustering of the BLUP solutions for the gene x diet interaction effect. From the results, we defined a transcript profile of 156 differentially expressed array elements between the weight loss and weight gain diet substrates. After sequence and annotation analyses, the 57 upregulated elements represented 29 unique genes, and the 99 downregulated elements represented 28 unique genes. Most of these co-regulated genes cluster into groups with distinct biological function related to protein turnover and cytoskeletal metabolism and contribute to our mechanistic understanding of the processes associated with remodeling of muscle tissue in response to nutritional stress.

  5. Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo

    Directory of Open Access Journals (Sweden)

    Hyun Cheol Roh

    2017-01-01

    Full Text Available Epigenomic mechanisms direct distinct gene expression programs for different cell types. Various in vivo tissues have been subjected to epigenomic analysis; however, these studies have been limited by cellular heterogeneity, resulting in composite gene expression and epigenomic profiles. Here, we introduce “NuTRAP,” a transgenic mouse that allows simultaneous isolation of cell-type-specific translating mRNA and chromatin from complex tissues. Using NuTRAP, we successfully characterize gene expression and epigenomic states of various adipocyte populations in vivo, revealing significant differences compared to either whole adipose tissue or in vitro adipocyte cell lines. We find that chromatin immunoprecipitation sequencing (ChIP-seq using NuTRAP is highly efficient, scalable, and robust with even limited cell input. We further demonstrate the general utility of NuTRAP by analyzing hepatocyte-specific epigenomic states. The NuTRAP mouse is a resource that provides a powerful system for cell-type-specific gene expression and epigenomic profiling.

  6. Gene expression profiling of normal thyroid tissue from patients with thyroid carcinoma.

    Science.gov (United States)

    Ria, Roberto; Simeon, Vittorio; Melaccio, Assunta; Di Meo, Giovanna; Trino, Stefania; Mazzoccoli, Carmela; Saltarella, Ilaria; Lamanuzzi, Aurelia; Morano, Annalisa; Gurrado, Angela; Pasculli, Alessandro; Lastilla, Gaetano; Musto, Pellegrino; Reale, Antonia; Dammacco, Franco; Vacca, Angelo; Testini, Mario

    2016-05-17

    Gene expression profiling (GEP) of normal thyroid tissue from 43 patients with thyroid carcinoma, 6 with thyroid adenoma, 42 with multinodular goiter, and 6 with Graves-Basedow disease was carried out with the aim of achieving a better understanding of the genetic mechanisms underlying the role of normal cells surrounding the tumor in the thyroid cancer progression. Unsupervised and supervised analyses were performed to compare samples from neoplastic and non-neoplastic diseases. GEP and subsequent RT-PCR analysis identified 28 differentially expressed genes. Functional assessment revealed that they are involved in tumorigenesis and cancer progression. The distinct GEP is likely to reflect the onset and/or progression of thyroid cancer, its molecular classification, and the identification of new potential prognostic factors, thus allowing to pinpoint selective gene targets with the aim of realizing more precise preoperative diagnostic procedures and novel therapeutic approaches.This study is focused on the gene expression profiling analysis followed by RT-PCR of normal thyroid tissues from patients with neoplastic and non-neoplastic thyroid diseases. Twenty-eight genes were found to be differentially expressed in normal cells surrounding the tumor in the thyroid cancer. The genes dysregulated in normal tissue samples from patients with thyroid tumors may represent new molecular markers, useful for their diagnostic, prognostic and possibly therapeutic implications.

  7. Identification of neurotoxic cytokines by profiling Alzheimer's disease tissues and neuron culture viability screening.

    Science.gov (United States)

    Wood, Levi B; Winslow, Ashley R; Proctor, Elizabeth A; McGuone, Declan; Mordes, Daniel A; Frosch, Matthew P; Hyman, Bradley T; Lauffenburger, Douglas A; Haigis, Kevin M

    2015-11-13

    Alzheimer's disease (AD) therapeutics based on the amyloid hypothesis have shown minimal efficacy in patients, suggesting that the activity of amyloid beta (Aβ) represents only one aspect of AD pathogenesis. Since neuroinflammation is thought to play an important role in AD, we hypothesized that cytokines may play a direct role in promoting neuronal death. Here, we profiled cytokine expression in a small cohort of human AD and control brain tissues. We identified AD-associated cytokines using partial least squares regression to correlate cytokine expression with quantified pathologic disease state and then used neuron cultures to test whether cytokines up-regulated in AD tissues could affect neuronal viability. This analysis identified cytokines that were associated with the pathological severity. Of the top correlates, only TNF-α reduced viability in neuron culture when applied alone. VEGF also reduced viability when applied together with Aβ, which was surprising because VEGF has been viewed as a neuro-protective protein. We found that this synthetic pro-death effect of VEGF in the context of Aβ was commensurate with VEGFR-dependent changes in multiple signaling pathways that govern cell fate. Our findings suggest that profiling of tissues combined with a culture-based screening approach can successfully identify new mechanisms driving neuronal death.

  8. Transcriptional profiling differences for articular cartilage and repair tissue in equine joint surface lesions

    Directory of Open Access Journals (Sweden)

    Stromberg Arnold J

    2009-09-01

    Full Text Available Abstract Background Full-thickness articular cartilage lesions that reach to the subchondral bone yet are restricted to the chondral compartment usually fill with a fibrocartilage-like repair tissue which is structurally and biomechanically compromised relative to normal articular cartilage. The objective of this study was to evaluate transcriptional differences between chondrocytes of normal articular cartilage and repair tissue cells four months post-microfracture. Methods Bilateral one-cm2 full-thickness defects were made in the articular surface of both distal femurs of four adult horses followed by subchondral microfracture. Four months postoperatively, repair tissue from the lesion site and grossly normal articular cartilage from within the same femorotibial joint were collected. Total RNA was isolated from the tissue samples, linearly amplified, and applied to a 9,413-probe set equine-specific cDNA microarray. Eight paired comparisons matched by limb and horse were made with a dye-swap experimental design with validation by histological analyses and quantitative real-time polymerase chain reaction (RT-qPCR. Results Statistical analyses revealed 3,327 (35.3% differentially expressed probe sets. Expression of biomarkers typically associated with normal articular cartilage and fibrocartilage repair tissue corroborate earlier studies. Other changes in gene expression previously unassociated with cartilage repair were also revealed and validated by RT-qPCR. Conclusion The magnitude of divergence in transcriptional profiles between normal chondrocytes and the cells that populate repair tissue reveal substantial functional differences between these two cell populations. At the four-month postoperative time point, the relative deficiency within repair tissue of gene transcripts which typically define articular cartilage indicate that while cells occupying the lesion might be of mesenchymal origin, they have not recapitulated differentiation to

  9. 中美制药公司简介体裁对比分析%Contrastive genre analysis of China-America pharmaceutical company profile

    Institute of Scientific and Technical Information of China (English)

    刘婕

    2012-01-01

      In this paper, Swales genre analysis theory as the foundation, to give qualitative and quantitative analysis of selected well-known pharmaceutical company profile for 40 articles. Research results show that the China-America pharmaceutical company has a similar language structure, but the forms to achieve are different. This paper gives suggestions to the profile translation of Chinese pharmaceutical company through research results, helps to improve the quality of translation.%  本文以Swales的体裁分析理论为基础,对所选取的40篇(中、美各20篇)知名制药公司简介进行定性和定量分析。研究结果表明中美制药公司简介具有相似的语步结构,但二者的语步实现形式有所不同。本文就研究结果,给中国制药公司简介英译提出建议,有助于英译质量的提高。

  10. Genetic profiling differentiates second primary tumors from metastases in adult metachronous soft tissue sarcoma

    DEFF Research Database (Denmark)

    Fernebro, Josefin; Carneiro, Ana; Rydholm, Anders

    2008-01-01

    Purpose. Patients with soft tissue sarcomas (STS) are at increased risk of second primary malignancies, including a second STS, but distinction between metastases and a second primary STS is difficult. Patients and Methods. Array-based comparative genomic hybridization (aCGH) was applied to 30...... multiple STS of the extremities and the trunk wall from 13 patients. Different histotypes were present with malignant fibrous histiocytomas/undifferentiated pleomorphic sarcomas being the predominant subtype. Results. aCGH profiling revealed genetic complexity with multiple gains and losses in all tumors....... In an unsupervised hierarchical cluster analysis, similar genomic profiles and close clustering between the first and subsequent STS were identified in 5 cases, suggesting metastatic disease, whereas the tumors from the remaining 8 patients did not cluster and showed only weak pairwise correlation, suggesting...

  11. Salivary tissue inhibitor of metalloproteinases-1 localization and glycosylation profile analysis

    DEFF Research Database (Denmark)

    Holten-Andersen, Lars; Thaysen-Andersen, Morten; Jensen, Siri Beier;

    2011-01-01

    tissue samples (four parotid gland and four submandibular gland biopsies) were analysed for the presence of TIMP-1 mRNA and protein expression. To assess TIMP-1 glycosylation profiles in blood and saliva, the protein was isolated from plasma and unstimulated and stimulated whole saliva as well...... as stimulated parotid and submandibular saliva and analysed by MALDI-TOF mass spectrometry. TIMP-1 protein was demonstrated in mucous acinar cells of the submandibular gland and in ductal cells of both the parotid and submandibular gland. However, no TIMP-1 mRNA was detected in any of these cells...

  12. Developmental MicroRNA Expression Profiling of Murine Embryonic Orofacial Tissue

    Science.gov (United States)

    Mukhopadhyay, Partha; Brock, Guy; Pihur, Vasyl; Webb, Cynthia; Pisano, M. Michele; Greene, Robert M.

    2011-01-01

    BACKGROUND Orofacial development is a multifaceted process involving precise, spatio-temporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs involved in gene silencing, represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. METHODS To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) -12, -13 and -14 murine orofacial tissue were compared utilizing miRXplore microarrays from Miltenyi Biotech. Quantitative real-time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. RESULTS Expression of over 26% of the 588 murine miRNA genes examined was detected in murine orofacial tissues from GD-12–GD-14. Among these expressed genes, several clusters were seen to be developmentally regulated. Differential expression of miRNAs within such clusters were shown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial-mesenchymal transformation, all processes critical for normal orofacial development. CONCLUSIONS Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein-encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs. PMID:20589883

  13. Effect of head position on cephalometric evaluation of the soft-tissue facial profile

    Science.gov (United States)

    Hoogeveen, RC; Sanderink, GCH; Berkhout, WER

    2013-01-01

    Objectives: During a cone beam CT scan, the patient is in an upright or supine position. This position depends on the brand and type of the scanner. The aims of this study are: (1) to investigate if the head position has an effect on cephalometric evaluation of the soft-tissue facial profile, comparing the recordings in natural head position (NHP) and supine head position (SHP) and (2) to investigate if age, gender and body mass index (BMI) are contributing factors to the effect of the head position. Methods: 90 subjects were photographed in profile both in NHP and in SHP. 12 soft-tissue angular and linear cephalometric values were calculated. Two-way random intraclass correlation coefficients were calculated to determine observer reliability. Paired t-tests and linear regression analyses were performed to investigate the differences between the head positions and the influence of age, gender and BMI. Results: Intraobserver reliability was generally high. Paired t-tests showed significant changes as a result of head positioning (p < 0.0001) in 9 of the 12 measurements. These differences were small and clinically not relevant, except for the “lower face—throat angle”. Regression analysis revealed no relevant influence of age, gender and BMI. Conclusions: Cephalometric soft-tissue evaluation from a recording in SHP is generally reliable, except for the throat–chin area where a clinically relevant difference was found. The contour of the submandibular tissues in SHP causes the chin to appear more prominently. This can cause incorrect orthodontic diagnosis and treatment planning. PMID:23412462

  14. Validation of tissue microarray for molecular profiling of canine and feline mammary tumours.

    Science.gov (United States)

    Muscatello, L V; Sarli, G; Beha, G; Asproni, P; Millanta, F; Poli, A; De Tolla, L J; Benazzi, C; Brunetti, B

    2015-01-01

    Tissue microarray (TMA) is a high-throughput method adopted for simultaneous molecular profiling of tissue samples from large patient cohorts. The aim of this study was to validate the TMA method for the molecular classification of canine and feline mammary tumours. Twelve samples, five feline and five canine mammary tumours and two canine haemangiosarcomas, were collected. TMA construction was based on Kononen's method of extracting a cylindrical core of paraffin wax-embedded 'donor' tissue and inserting it into a 'recipient' wax block. Seven consecutive sections from each tissue array block were subjected to immunohistochemistry (IHC) using primary antibodies specific for oestrogen receptor (OR), progesterone receptor (PR), c-erbB-2, cytokeratin (CK) 5/6, CK14, CK19 and p63. The same panel of antibodies was applied to the full sections from all cases. Comparison between full sections and TMA scores revealed different results depending on the antibodies. Labelling for OR, PR, CK19 and p63 showed total concordance, c-erbB2 (score +2, +3) was concordant in nine out of ten cases, CK5/6 and CK14 in eight out of ten cases. The TMA platform preserves the molecular profile of canine and feline mammary tumour markers, representing a useful tool for rapid and cost-effective analysis for the first phenotypic screening using OR, PR and c-erbB2 antibodies. Basal cytokeratin, used for triple negative identification, shows a multifocal 'niche' expression pattern, for which IHC of the full section or multiple core array is recommended.

  15. Fatty acid profiles in tissues of mice fed conjugated linoleic acid

    DEFF Research Database (Denmark)

    Gøttsche, Jesper; Straarup, Ellen Marie

    2006-01-01

    The incorporation of vaccenic acid (VA, 0.5 and 1.2%), conjugated linoleic acid (CLA, mixture of primarily c9,t11- and t10,c12-CLA, 1.2%), linoleic acid (LA, 1.2%) and oleic acid (OA, 1.2%) into different tissues of mice was examined. The effects on the fatty acid composition of triacylglycerols...... (TAG) and phospholipids (PL) in kidney, spleen, liver and adipose tissue were investigated. VA and CLA (c9,t11- and t10,c12-CLA) were primarily found in TAG, especially in kidney and adipose tissue, respectively. Conversion of VA to c9,t11-CLA was indicated by our results, as both fatty acids were...... incorporated into all the analyzed tissues when a diet containing VA but not c9,t11-CLA was fed. Most of the observed effects on the fatty acid profiles were seen in the CLA group, whereas only minor effects were observed in the VA groups compared with the CA group. Thus, CLA increased n-3 polyunsaturated...

  16. Comparison of Glucosinolate Profiles in Different Tissues of Nine Brassica Crops

    Directory of Open Access Journals (Sweden)

    Shiva Ram Bhandari

    2015-08-01

    Full Text Available Glucosinolate (GSL profiles and concentrations in various tissues (seeds, sprouts, mature root, and shoot were determined and compared across nine Brassica species, including cauliflower, cabbage, broccoli, radish, baemuchae, pakchoi, Chinese cabbage, leaf mustard, and kale. The compositions and concentrations of individual GSLs varied among crops, tissues, and growth stages. Seeds had highest total GSL concentrations in most of crops, whereas shoots had the lowest GSL concentrations. Aliphatic GSL concentrations were the highest in seeds, followed by that in sprouts, shoots, and roots. Indole GSL concentration was the highest in the root or shoot tissues in most of the crops. In contrast, aromatic GSL concentrations were highest in roots. Of the nine crops examined, broccoli exhibited the highest total GSL concentration in seeds (110.76 µmol·g−1 and sprouts (162.19 µmol·g−1, whereas leaf mustard exhibited the highest total GSL concentration in shoots (61.76 µmol·g−1 and roots (73.61 µmol·g−1. The lowest GSL concentrations were observed in radish across all tissues examined.

  17. Studying Biological Tissue with Fluorescence Lifetime Imaging: Microscopy, Endoscopy, and Complex Decay Profiles

    Science.gov (United States)

    Siegel, Jan; Elson, Daniel S.; Webb, Stephen E. D.; Lee, K. C. Benny; Vlandas, Alexis; Gambaruto, Giovanni L.; Léveque-Fort, Sandrine; Lever, M. John; Tadrous, Paul J.; Stamp, Gordon W. H.; Wallace, Andrew L.; Sandison, Ann; Watson, Tim F.; Alvarez, Fernando; French, Paul M. W.

    2003-06-01

    We have applied fluorescence lifetime imaging (FLIM) to the autofluorescence of different kinds of biological tissue in vitro , including animal tissue sections and knee joints as well as human teeth, obtaining two-dimensional maps with functional contrast. We find that fluorescence decay profiles of biological tissue are well described by the stretched exponential function (StrEF), which can represent the complex nature of tissue. The StrEF yields a continuous distribution of fluorescence lifetimes, which can be extracted with an inverse Laplace transformation, and additional information is provided by the width of the distribution. Our experimental results from FLIM microscopy in combination with the StrEF analysis indicate that this technique is ready for clinical deployment, including portability that is through the use of a compact picosecond diode laser as the excitation source. The results obtained with our FLIM endoscope successfully demonstrated the viability of this modality, though they need further optimization. We expect a custom-designed endoscope with optimized illumination and detection efficiencies to provide significantly improved performance.

  18. Transcriptome Profile Analysis of Ovarian Tissues from Diploid and Tetraploid Loaches Misgurnus anguillicaudatus.

    Science.gov (United States)

    Luo, Weiwei; Liu, Chuanshu; Cao, Xiaojuan; Huang, Songqian; Wang, Weimin; Wang, Yeke

    2015-07-14

    RNA sequencing and short-read assembly was utilized to produce a transcriptome of ovarian tissues from three-year-old diploid and tetraploid loaches (Misgurnus anguillicaudatus). A total of 28,369 unigenes were obtained, comprising 10,546 unigenes with length longer than 1000 bp. More than 73% of the unigenes were annotated through sequence comparison with databases. The RNA-seq data revealed that 2253 genes were differentially expressed between diploid and tetraploid loaches, including 1263 up-regulated and 990 down-regulated genes in tetraploid loach. Some differentially expressed genes, such as vitellogenin (Vtg), gonadotropin releasing hormone receptor type A (GnRHRA), steroidogenic acute regulatory protein (StAR), mitogen-activated protein kinase 14a (MAPK14a), ATP synthase subunit alpha (atp5a), and synaptonemal complex protein 1 (Scp1), were involved in regulation of cell proliferation, division, gene transcription, ovarian development and energy metabolism, suggesting that these genes were related to egg diameter of the loach. Results of transcriptome profiling here were validated using real time quantitative PCR in ten selected genes. The present study provided insights into the transcriptome profile of ovarian tissues from diploid and tetraploid loaches Misgurnus anguillicaudatus, which was made available to the research community for functional genomics, comparative genomics, polyploidy evolution and molecular breeding of this loach and other related species.

  19. Transcriptome Profile Analysis of Ovarian Tissues from Diploid and Tetraploid Loaches Misgurnus anguillicaudatus

    Directory of Open Access Journals (Sweden)

    Weiwei Luo

    2015-07-01

    Full Text Available RNA sequencing and short-read assembly was utilized to produce a transcriptome of ovarian tissues from three-year-old diploid and tetraploid loaches (Misgurnus anguillicaudatus. A total of 28,369 unigenes were obtained, comprising 10,546 unigenes with length longer than 1000 bp. More than 73% of the unigenes were annotated through sequence comparison with databases. The RNA-seq data revealed that 2253 genes were differentially expressed between diploid and tetraploid loaches, including 1263 up-regulated and 990 down-regulated genes in tetraploid loach. Some differentially expressed genes, such as vitellogenin (Vtg, gonadotropin releasing hormone receptor type A (GnRHRA, steroidogenic acute regulatory protein (StAR, mitogen-activated protein kinase 14a (MAPK14a, ATP synthase subunit alpha (atp5a, and synaptonemal complex protein 1 (Scp1, were involved in regulation of cell proliferation, division, gene transcription, ovarian development and energy metabolism, suggesting that these genes were related to egg diameter of the loach. Results of transcriptome profiling here were validated using real time quantitative PCR in ten selected genes. The present study provided insights into the transcriptome profile of ovarian tissues from diploid and tetraploid loaches Misgurnus anguillicaudatus, which was made available to the research community for functional genomics, comparative genomics, polyploidy evolution and molecular breeding of this loach and other related species.

  20. Changes in soft tissue profile using functional appliances in the treatment of skeletal class II malocclusion

    Directory of Open Access Journals (Sweden)

    Stamenković Zorana

    2015-01-01

    Full Text Available Introduction. The effects of orthodontic treatment are considered to be successful if the facial harmony is achieved, while the structures of soft tissue profile are in harmony with skeletal structures of neurocranium and viscerocranium. In patients with skeletal distal bite caused by mandibular retrognathism, facial esthetics is disturbed often, in terms of pronounced convexity of the profile and change in the position and relationship of the lips. Objective. The aim of this study was to determine the extent of soft tissue profile changes in patients with skeletal Class II malocclusion treated with three different orthodontic appliances: Fränkel functional regulator type I (FR-I, Balters’ Bionator type I and Hotz appliance. Methods. The study included 60 patients diagnosed with skeletal Class II malocclusion caused by mandibular retrognathism, in the period of early mixed dentition. Each subgroup of 20 patients was treated with a variety of orthodontic appliances. On the lateral cephalogram, before and after treatment, the following parameters were analyzed: T angle, H angle, the height of the upper lip, the position of the upper and lower lip in relation to the esthetic line. Within the statistical analysis the mean, maximum, minimum, standard deviation, coefficient of variation, two-factor analysis of variance with repeated measures and the factor analysis of variance were calculated using ANOVA, Bonferroni test and Student’s t-test. Results. A significant decrease of angles T and H was noticed in the application of FR-I, from 21.60° to 17.15°, and from 16.45° to 13.40° (p<0.001. FR-I decreased the height of the upper lip from 26.15 mm to 25.85 mm, while Hotz appliance and Balters’ Bionator type I increased the height of the upper lip, thereby deteriorating esthetics of the patient. Conclusion. All used orthodontic appliances lead to changes in soft tissue profile in terms of improving facial esthetics, with the most distinctive

  1. Global Gene Expression Profiling in Lung Tissues of Rat Exposed to Lunar Dust Particles

    Science.gov (United States)

    Yeshitla, Samrawit A.; Lam, Chiu-Wing; Kidane, Yared H.; Feiveson, Alan H.; Ploutz-Snyder, Robert; Wu, Honglu; James, John T.; Meyers, Valerie E.; Zhang, Ye

    2014-01-01

    The Moon's surface is covered by a layer of fine, potential reactive dust. Lunar dust contain about 1-2% respirable very fine dust (less than 3 micrometers). The habitable area of any lunar landing vehicle and outpost would inevitably be contaminated with lunar dust that could pose a health risk. The purpose of the study is to analyze the dynamics of global gene expression changes in lung tissues of rats exposed to lunar dust particles. F344 rats were exposed for 4 weeks (6h/d; 5d/wk) in nose-only inhalation chambers to concentrations of 0 (control air), 2.1, 6.8, 21, and 61 mg/m3 of lunar dust. Animals were euthanized at 1 day and 13 weeks after the last inhalation exposure. After being lavaged, lung tissue from each animal was collected and total RNA was isolated. Four samples of each dose group were analyzed using Agilent Rat GE v3 microarray to profile global gene expression of 44K transcripts. After background subtraction, normalization, and log transformation, t tests were used to compare the mean expression levels of each exposed group to the control group. Correction for multiple testing was made using the method of Benjamini, Krieger, and Yekuteli (1) to control the false discovery rate. Genes with significant changes of at least 1.75 fold were identified as genes of interest. Both low and high doses of lunar dust caused dramatic, dose-dependent global gene expression changes in the lung tissues. However, the responses of lung tissue to low dose lunar dust are distinguished from those of high doses, especially those associated with 61mg/m3 dust exposure. The data were further integrated into the Ingenuity system to analyze the gene ontology (GO), pathway distribution and putative upstream regulators and gene targets. Multiple pathways, functions, and upstream regulators have been identified in response to lunar dust induced damage in the lung tissue.

  2. SERUM LIPID PROFILE AND TRANSAMINASES LEVELS IN HIV PATIENTS ON HAART WITH ADIPOSE TISSUE ALTERATIONS

    Directory of Open Access Journals (Sweden)

    Vijay

    2016-02-01

    Full Text Available BACKGROUND HIV patients receiving highly active Anti-Retroviral Therapy (HAART usually suffer from side effects like hepatitis, neurological problems, abnormal fat distribution etc. Among these, the most physical, mental and cosmetically disturbing side effect is adipose tissue alterations (ATA, also called as lipodystrophy, which is abnormal fat deposition (Lipohypertrophy and/or fat atrophy (Lipoatrophy. AIM Several studies have shown dyslipidemia in patients on HAART, but there are very few studies on the lipid profile changes in patients on ART with ATA. Hence a study was conducted to assess the serum lipid profile and transaminases activity in patients on ART with ATA and also to evaluate whether lipid profile parameters can predict ATA changes in HIV patients on HAART. METHOD Randomly selected HIV positive patients, who were attending ART centre, were included in the study. Twenty five of these patients in whom HAART was yet to be started were considered as Control group, 25 patients on HAART for more than 12 months but without ATA as ART group and 23 patients on HAART with ATA as ATA group. Lipid profile and serum transaminases in all the groups were assayed by standard methods. RESULTS Serum cholesterol and LDL were significantly increased in ART group and ATA group when compared to control group, but there was no significant difference in lipid profile parameters between ART group and ATA group. Serum AST and ALT levels were significantly increased (p<0.02 in ATA group when compared to ART group. Buffalo hump was seen only in females in our study. Lipoatrophy (facial and limbs and central obesity was seen in males. CONCLUSION There was no significant change in lipid profile parameters in ATA group when compared with ART group. Hence lipid profile parameters are not good predictors of ATA changes in HIV patients on HAART. Significant increase in transaminase levels suggests increased hepatotoxity in ATA patients due to HAART drugs. There

  3. Microarray analysis of adipose tissue gene expression profiles between two chicken breeds

    Indian Academy of Sciences (India)

    Hongbao Wang; Hui Li; Qigui Wang; Yuxiang Wang; Huabin Han; Hui Shi

    2006-12-01

    The chicken is an important model organism that bridges the evolutionary gap between mammals and other vertebrates and provides a major protein source from meat and eggs throughout the world. Excessive accumulation of lipids in the adipose tissue is one of the main problems faced by the broiler industry nowadays. In order to visualize the mechanisms involved in the gene expression and regulation of lipid metabolism in adipose tissue, cDNA microarray containing 9 024 cDNA was used to construct gene expression profile and screen differentially expressed genes in adipose tissue between broilers and layers of 10 wk of age. Sixty-seven differentially expressed sequences were screened out, and 42 genes were found when blasted with the GenBank database. These genes are mainly related to lipid metabolism, energy metabolism, transcription and splicing factor, protein synthesis and degradation. The remained 25 sequences had no annotation available in the GenBank database. Furthermore, Northern blot and semi-quantitative RT-PCR were developed to confirm 4 differentially expressed genes screened by cDNA microarray, and it showed great consistency between the microarray data and Northern blot results or semi-quantitative RT-PCR results. The present study will be helpful for clarifying the molecular mechanism of obesity in chickens.

  4. Transcriptome profile analysis of adipose tissues from fat and short-tailed sheep.

    Science.gov (United States)

    Wang, Xiaolong; Zhou, Guangxian; Xu, Xiaochun; Geng, Rongqing; Zhou, Jiping; Yang, Yuxin; Yang, Zhaoxia; Chen, Yulin

    2014-10-10

    Recent studies in domestic animals have used RNA-seq to explore the transcriptome of different tissues in a limited number of individuals. In the present study, de novo transcriptome sequencing was used to compare sheep adipose tissue transcriptome profiles between a fat-tailed breed (Kazak sheep; KS) and a short-tailed (Tibetan sheep; TS). The RNA-seq data from these two groups revealed that 646 genes were differentially expressed between the KS and TS groups, including 280 up-regulated and 366 down-regulated genes. We identified genes relevant to fat metabolism in adipose tissues, including two top genes with the largest fold change (NELL1 and FMO3). Pathway analysis revealed that the differentially expressed genes between the KS and TS breeds belong to fatty acid metabolism relevant pathways (e.g. fat digestion and absorption, glycine, serine, and threonine metabolism) and cell junction-related pathways (e.g. cell adhesion molecules) which contribute to fat deposition. This work highlighted potential genes and gene networks that affect fat deposition and meat quality in sheep.

  5. Depth profiling of cells and tissues by using C 60+ and SF 5+ as sputter ions

    Science.gov (United States)

    Malmberg, Per; Kriegeskotte, Christian; Arlinghaus, Heinrich F.; Hagenhoff, Birgit; Holmgren, Jan; Nilsson, Mikael; Nygren, Håkan

    2008-12-01

    In the present study, SF 5+ and C 60+ were used as primary ions for sputtering and Bi 3+ was used as primary ions for analysis. The depth profiling procedure was utilized to make 3D images of the chemistry of single cultured cells and tissue samples of intact intestinal epithelium. The results show sputtering of organic material from cells and tissue with both SF 5+ and C 60+ sources. Cholesterol fragments were found in the superficial layers when sputtering with C 60+. Spectra were collected revealing the change in yield along the z-axis of the sample. 3D images of the localization of Na, K, phosphocholine and cholesterol were constructed with both ion sources for single cell cultures and the mouse intestine. Cryostate sections of mouse intestine were analysed in 2D and the results were compared with the 3D image of the intestine. The localization of cholesterol and phosphocholine was found to be similar in cryostate sections analysed in two dimensions and the sputtered, freeze-dried intestine analysed in 3D. The comparison of 2D and 3D images suggest that the phosphocholine signal faded with C 60+ sputtering. In conclusion, both C 60+ and SF 5+ can be used as primary ion sources for sputtering of organic material from cells and tissues. Consecutive analysis with a Bi 3+ source can be used to obtain image stacks that could be used for reconstruction of 3D images.

  6. Tissue-specific mRNA expression profiles of human solute carrier 35 transporters.

    Science.gov (United States)

    Nishimura, Masuhiro; Suzuki, Satoshi; Satoh, Tetsuo; Naito, Shinsaku

    2009-01-01

    Pairs of forward and reverse primers and TaqMan probes specific to each of 23 human solute carrier 35 (SLC35) transporters were prepared. The mRNA expression level of each target transporter was analyzed in total RNA from single and pooled specimens of adult human tissues (adipose tissue, adrenal gland, bladder, bone marrow, brain, cerebellum, colon, heart, kidney, liver, lung, mammary gland, ovary, pancreas, peripheral leukocytes, placenta, prostate, retina, salivary gland, skeletal muscle, small intestine, smooth muscle, spinal cord, spleen, stomach, testis, thymus, thyroid gland, tonsil, trachea, and uterus), from pooled specimens of fetal human tissues (brain, heart, kidney, liver, spleen, and thymus), and from three human cell lines (HeLa cell line ATCC#: CCL-2, human cell line Hep G2, and human breast carcinoma cell line MDA-435) by real-time reverse transcription PCR using an Applied Biosystems 7500 Fast Real-Time PCR System. The mRNA expression of SLC35As, SLC35Bs, SLC35Cs, SLC35D1, SLC35D2, SLC35Es, and SLC35F5 was found to be ubiquitous in both adult and fetal tissues. SLC35D3 mRNA was expressed at the highest levels in the adult retina. SLC35F1 mRNA was expressed at high levels in the adult and fetal brain. SLC35F2 mRNA was expressed at the highest levels in the adult salivary gland. Both SLC35F3 and SLC35F4 mRNAs were expressed at the highest levels in the adult cerebellum. Further, individual differences in the mRNA expression levels of human SLC35 transporters in the liver were also evaluated. Our newly determined expression profiles were used to study the gene expression in 31 adult human tissues, 6 fetal human tissues, and 3 cell lines, and tissues with high transcriptional activity for human SLC35 transporters were identified. These results are expected to be valuable for research concerning the clinical diagnosis of disease.

  7. A targeted quantitative proteomics strategy for global kinome profiling of cancer cells and tissues.

    Science.gov (United States)

    Xiao, Yongsheng; Guo, Lei; Wang, Yinsheng

    2014-04-01

    Kinases are among the most intensively pursued enzyme superfamilies as targets for anti-cancer drugs. Large data sets on inhibitor potency and selectivity for more than 400 human kinases became available recently, offering the opportunity to design rationally novel kinase-based anti-cancer therapies. However, the expression levels and activities of kinases are highly heterogeneous among different types of cancer and even among different stages of the same cancer. The lack of effective strategy for profiling the global kinome hampers the development of kinase-targeted cancer chemotherapy. Here, we introduced a novel global kinome profiling method, based on our recently developed isotope-coded ATP-affinity probe and a targeted proteomic method using multiple-reaction monitoring (MRM), for assessing simultaneously the expression of more than 300 kinases in human cells and tissues. This MRM-based assay displayed much better sensitivity, reproducibility, and accuracy than the discovery-based shotgun proteomic method. Approximately 250 kinases could be routinely detected in the lysate of a single cell line. Additionally, the incorporation of iRT into MRM kinome library rendered our MRM kinome assay easily transferrable across different instrument platforms and laboratories. We further employed this approach for profiling kinase expression in two melanoma cell lines, which revealed substantial kinome reprogramming during cancer progression and demonstrated an excellent correlation between the anti-proliferative effects of kinase inhibitors and the expression levels of their target kinases. Therefore, this facile and accurate kinome profiling assay, together with the kinome-inhibitor interaction map, could provide invaluable knowledge to predict the effectiveness of kinase inhibitor drugs and offer the opportunity for individualized cancer chemotherapy.

  8. Factors influencing soft tissue profile changes following orthodontic treatment in patients with Class II Division 1 malocclusion

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    Suhatcha Maetevorakul

    2016-05-01

    Full Text Available Abstract Background Several studies have shown soft tissue profile changes after orthodontic treatment in Class II Division 1 patients. However, a few studies have described factors influencing the soft tissue changes. The purpose of this study was to investigate the factors influencing the soft tissue profile changes following orthodontic treatment in Class II Division 1 patients. Methods The subjects comprised 104 Thai patients age 8–16 years who presented Class II Division 1 malocclusions and were treated with different orthodontic modalities comprising cervical headgear, Class II traction and extraction of the four first premolars. The profile changes were evaluated from the lateral cephalograms before and after treatment by means of the X-Y coordinate system. Significant soft tissue profile changes were evaluated by paired t test at a 0.05 significance level. The correlations among significant soft tissue changes and independent variables comprising treatment modality, age, sex, pretreatment skeletal, dental and soft tissue morphology were evaluated by stepwise multiple regression analysis at a 0.05 significance level. Results The multiple regression analysis indicated that different treatment modalities, age, sex, pretreatment skeletal, dental and soft tissue morphology were related to the profile changes. The predictive power of these variables on the soft tissue profile changes ranged from 9.9 to 40.3 %. Conclusions Prediction of the soft tissue profile changes following treatment of Class II Division 1 malocclusion from initial patient morphology, age, sex and types of treatment was complicated and required several variables to explain their variations. Upper lip change in horizontal direction could be found only at the stomion superius and was less predictable than those of the lower lip. Variations in upper lip retraction at the stomion superius were explained by types of treatment (R 2 = 0.099, whereas protrusion of the lower

  9. Proteomic Profiles Reveal the Function of Different Vegetative Tissues of Moringa oleifera.

    Science.gov (United States)

    Wang, Lei; Zou, Qiong; Wang, Jinxing; Zhang, Junjie; Liu, Zeping; Chen, Xiaoyang

    2016-12-01

    Moringa oleifera is a rich source of bioactive compounds and is widely used in traditional medicine and food for its nutritional value; however, the protein and peptide components of different tissues are rarely discussed. Here, we describe the first investigation of M. oleifera proteomes using mass spectrometry and bioinformatics methods. We aimed to elucidate the protein profiles of M. oleifera leaves, stem, bark, and root. Totally 202 proteins were identified from four vegetative organs. We identified 101 proteins from leaves, 51 from stem, 94 from bark and 67 from root, finding that only five proteins existed in both four vegetative parts. The calculated pI of most of the proteins is distributed in 5-10 and the molecular weight distributed below 100 kDa. Functional classification analysis revealed that proteins which are involved in catalytic activities are the most abundant both in leaves, stem, bark and root. Identification of several heat shock proteins in four vegetative tissues might be adaptive for resistance to high temperature environmental stresses of tropical or subtropical areas. Some enzymes involved in antioxidant processes were also identified in M. oleifera leaves, stem, bark and root. Among the four tissues studies here, leaves protein content and molecular diversity were the highest. The identification of the flocculating protein MO2.1 and MO2.2 in the bark and root provides clue to clarify the antimicrobial molecular mechanisms of root and bark. This study provides information on the protein compositions of M. oleifera vegetative tissues that will be beneficial for potential drug and food supplement development and plant physiology research.

  10. Isolation, sequence identification and tissue expression profiles of 3 novel porcine genes: ASPA, NAGA, and HEXA.

    Science.gov (United States)

    Shu, Xianghua; Liu, Yonggang; Yang, Liangyu; Song, Chunlian; Hou, Jiafa

    2008-01-01

    The complete coding sequences of 3 porcine genes - ASPA, NAGA, and HEXA - were amplified by the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved sequence information of the mouse or other mammals and referenced pig ESTs. These 3 novel porcine genes were then deposited in the NCBI database and assigned GeneIDs: 100142661, 100142664 and 100142667. The phylogenetic tree analysis revealed that the porcine ASPA, NAGA, and HEXA all have closer genetic relationships with the ASPA, NAGA, and HEXA of cattle. Tissue expression profile analysis was also carried out and results revealed that swine ASPA, NAGA, and HEXA genes were differentially expressed in various organs, including skeletal muscle, the heart, liver, fat, kidney, lung, and small and large intestines. Our experiment is the first one to establish the foundation for further research on these 3 swine genes.

  11. Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Anthon, Christian; Bak, Mads

    2012-01-01

    Background: MicroRNAs (miRNAs) are a class of non-protein-coding genes that play a crucial regulatory role in mammalian development and disease. Whereas a large number of miRNAs have been annotated at the structural level during the latest years, functional annotation is sparse. Actinobacillus...... pleuropneumoniae (APP) causes serious lung infections in pigs. Severe damage to the lungs, in many cases deadly, is caused by toxins released by the bacterium and to some degree by host mediated tissue damage. However, understanding of the role of microRNAs in the course of this infectious disease in porcine......R-451 and miR-15a appear as very promising candidates for microRNAs involved in response to pathogen infection. Conclusions: This is the first study revealing significant differences in composition and expression profiles of miRNAs in lungs infected with a bacterial pathogen. Our results extend...

  12. Methylation profiling of 48 candidate genes in tumor and matched normal tissues from breast cancer patients.

    Science.gov (United States)

    Li, Zibo; Guo, Xinwu; Wu, Yepeng; Li, Shengyun; Yan, Jinhua; Peng, Limin; Xiao, Zhi; Wang, Shouman; Deng, Zhongping; Dai, Lizhong; Yi, Wenjun; Xia, Kun; Tang, Lili; Wang, Jun

    2015-02-01

    Gene-specific methylation alterations in breast cancer have been suggested to occur early in tumorigenesis and have the potential to be used for early detection and prevention. The continuous increase in worldwide breast cancer incidences emphasizes the urgent need for identification of methylation biomarkers for early cancer detection and patient stratification. Using microfluidic PCR-based target enrichment and next-generation bisulfite sequencing technology, we analyzed methylation status of 48 candidate genes in paired tumor and normal tissues from 180 Chinese breast cancer patients. Analysis of the sequencing results showed 37 genes differentially methylated between tumor and matched normal tissues. Breast cancer samples with different clinicopathologic characteristics demonstrated distinct profiles of gene methylation. The methylation levels were significantly different between breast cancer subtypes, with basal-like and luminal B tumors having the lowest and the highest methylation levels, respectively. Six genes (ACADL, ADAMTSL1, CAV1, NPY, PTGS2, and RUNX3) showed significant differential methylation among the 4 breast cancer subtypes and also between the ER +/ER- tumors. Using unsupervised hierarchical clustering analysis, we identified a panel of 13 hypermethylated genes as candidate biomarkers that performed a high level of efficiency for cancer prediction. These 13 genes included CST6, DBC1, EGFR, GREM1, GSTP1, IGFBP3, PDGFRB, PPM1E, SFRP1, SFRP2, SOX17, TNFRSF10D, and WRN. Our results provide evidence that well-defined DNA methylation profiles enable breast cancer prediction and patient stratification. The novel gene panel might be a valuable biomarker for early detection of breast cancer.

  13. Profiling of Phenolic Compounds of Somatic and Reproductive Tissues of Agave Durangensis Gentry (Agavaceae

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    Norma Almaraz-Abarca

    2009-01-01

    Full Text Available Problem statement: In Durango, Mexico, mescal is elaborated from wild plants of Agave durangensis. This species shows a high morphological variability within and among populations, what makes its taxonomic delimitation a hard task. Approach: In this study the pollen and foliar phenolic compositions of Agave durangensis were analyzed by HPLC/DAD with the aim of determining the significance of phenol profiles to delimit this taxon. Results: The foliar phenol compositions were evaluated within and among two populations and between juvenile and adult plants. Agave asperrima Jacobi, Dasylirion sp. and juvenile samples of A. shrevei Gentry subsp. shrevei, A. shrevei Gentry subsp. matapensis Gentry and A. wocomahi Gentry, were also analyzed to stand comparisons with. The results from this study indicated that pollen and foliar tissues of Agave durangneisis were rich in kaempferol glycoside derivatives (13 and 23 different compounds can be present, respectively. Principal coordinates analysis (PCO, based on foliar profiles of adults, indicated the presence of several chemotypes within the Type locality of Agave durangensis and revealed chemical differences between the both analyzed populations. Conclusion/Recommendations: Chemical and morphological differences and biogeographical evidence suggest the recognition of two different taxonomic entities in this morphological variable group.

  14. Transcriptional Profiling of Swine Lung Tissue after Experimental Infection with Actinobacillus pleuropneumoniae

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    Xuewei Li

    2013-05-01

    Full Text Available Porcine pleuropneumonia is a highly contagious respiratory disease that causes great economic losses worldwide. In this study, we aimed to explore the underlying relationship between infection and injury by investigation of the whole porcine genome expression profiles of swine lung tissues post-inoculated with experimentally Actinobacillus pleuropneumoniae. Expression profiling experiments of the control group and the treatment group were conducted using a commercially available Agilent Porcine Genechip including 43,603 probe sets. Microarray analysis was conducted on profiles of lung from challenged versus non-challenged swine. We found 11,929 transcripts, identified as differentially expressed at the p ≤0.01 level. There were 1188 genes annotated as swine genes in the GenBank Data Base. GO term analysis identified a total of 89 biological process categories, 82 cellular components and 182 molecular functions that were significantly affected, and at least 27 biological process categories that were related to the host immune response. Gene set enrichment analysis identified 13 pathways that were significantly associated with host response. Many proinflammatory-inflammatory cytokines were activated and involved in the regulation of the host defense response at the site of inflammation; while the cytokines involved in regulation of the host immune response were suppressed. All changes of genes and pathways of induced or repressed expression not only led to a decrease in antigenic peptides presented to T lymphocytes by APCs via the MHC and alleviated immune response injury induced by infection, but also stimulated stem cells to produce granulocytes (neutrophils, eosinophils, and basophils and monocyte, and promote neutrophils and macrophages to phagocytose bacterial and foreign antigen at the site of inflammation. The defense function of swine infection with Actinobacillus pleuropneumoniae was improved, while its immune function was decreased.

  15. Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues.

    Science.gov (United States)

    Ali Hassan, Nur Zarina; Mokhtar, Norfilza Mohd; Kok Sin, Teow; Mohamed Rose, Isa; Sagap, Ismail; Harun, Roslan; Jamal, Rahman

    2014-01-01

    Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validation was performed using multiplex ligation probe amplification method. Genome-wide expression profiling was performed on 15 paired samples from the same group of patients using the Affymetrix Human Gene 1.0 ST array. Significant genes obtained from both array results were then overlapped. To identify molecular pathways, the data were mapped to the KEGG database. Whole genome CNV analysis that compared primary tumor and non-cancerous epithelium revealed gains in 1638 genes and losses in 36 genes. Significant gains were mostly found in chromosome 20 at position 20q12 with a frequency of 45.31% in tumor samples. Examples of genes that were associated at this cytoband were PTPRT, EMILIN3 and CHD6. The highest number of losses was detected at chromosome 8, position 8p23.2 with 17.19% occurrence in all tumor samples. Among the genes found at this cytoband were CSMD1 and DLC1. Genome-wide expression profiling showed 709 genes to be up-regulated and 699 genes to be down-regulated in CRC compared to non-cancerous samples. Integration of these two datasets identified 56 overlapping genes, which were located in chromosomes 8, 20 and 22. MLPA confirmed that the CRC samples had the highest gains in chromosome 20 compared to the reference samples. Interpretation of the CNV data in the context of the transcriptome via integrative analyses may provide more in-depth knowledge of the genomic landscape of CRC.

  16. Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues.

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    Nur Zarina Ali Hassan

    Full Text Available Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV and gene expression in colorectal cancer (CRC samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validation was performed using multiplex ligation probe amplification method. Genome-wide expression profiling was performed on 15 paired samples from the same group of patients using the Affymetrix Human Gene 1.0 ST array. Significant genes obtained from both array results were then overlapped. To identify molecular pathways, the data were mapped to the KEGG database. Whole genome CNV analysis that compared primary tumor and non-cancerous epithelium revealed gains in 1638 genes and losses in 36 genes. Significant gains were mostly found in chromosome 20 at position 20q12 with a frequency of 45.31% in tumor samples. Examples of genes that were associated at this cytoband were PTPRT, EMILIN3 and CHD6. The highest number of losses was detected at chromosome 8, position 8p23.2 with 17.19% occurrence in all tumor samples. Among the genes found at this cytoband were CSMD1 and DLC1. Genome-wide expression profiling showed 709 genes to be up-regulated and 699 genes to be down-regulated in CRC compared to non-cancerous samples. Integration of these two datasets identified 56 overlapping genes, which were located in chromosomes 8, 20 and 22. MLPA confirmed that the CRC samples had the highest gains in chromosome 20 compared to the reference samples. Interpretation of the CNV data in the context of the transcriptome via integrative analyses may provide more in-depth knowledge of the genomic landscape of CRC.

  17. Gene methylation profile of gastric cancerous tissue according to tumor site in the stomach.

    Science.gov (United States)

    Kupcinskaite-Noreikiene, Rita; Ugenskiene, Rasa; Noreika, Alius; Rudzianskas, Viktoras; Gedminaite, Jurgita; Skieceviciene, Jurgita; Juozaityte, Elona

    2016-01-26

    There is considerable information on the methylation of the promoter regions of different genes involved in gastric carcinogenesis. However, there is a lack of information on how this epigenetic process differs in tumors originating at different sites in the stomach. The aim of this study is to assess the methylation profiles of the MLH1, MGMT, and DAPK-1 genes in cancerous tissues from different stomach sites. Samples were acquired from 81 patients suffering stomach adenocarcinoma who underwent surgery for gastric cancer in the Lithuanian University of Health Sciences Hospital Kaunas Clinics in 2009-2012. Gene methylation was investigated with methylation-specific PCR. The study was approved by the Lithuanian Biomedical Research Ethics Committee. The frequencies of methylation in cancerous tissues from the upper, middle, and lower thirds of the stomach were 11.1, 23.1, and 45.4%, respectively, for MLH1; 22.2, 30.8, and 57.6%, respectively, for MGMT; and 44.4, 48.7, and 51.5%, respectively, for DAPK-1. MLH1 and MGMT methylation was observed more often in the lower third of the stomach than in the upper third (p stomach (coefficient, -0.48; p = 0.01). DAPK-1 and MLH1 methylation correlated inversely in tumors in the middle-third of the stomach (coefficient, -0.41; p = 0.01). Gene promoter methylation depends on the gastric tumor location.

  18. Differential lncRNA expression profiles in brown and white adipose tissues.

    Science.gov (United States)

    Chen, Jiantao; Cui, Xianwei; Shi, Chunmei; Chen, Ling; Yang, Lei; Pang, Lingxia; Zhang, Jun; Guo, Xirong; Wang, Jiaqin; Ji, Chenbo

    2015-04-01

    Long non-coding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. It can serve as key co-activators of proteins involved in transcriptional regulation. Studies have found that white and brown adipocytes both originate from the mesoderm. However, it remains unclear whether lncRNAs function during adipogenesis or in energy metabolism in brown adipose tissue (BAT) and white adipose tissue (WAT). In this study, we used lncRNA microarray technology to evaluate differences in the lncRNA expression profiles of WAT and BAT. We observed 735 up-regulated and 877 down-regulated lncRNAs (fold change >4.0). To reveal the potential functions of these lncRNAs, we applied GO and pathway analyses to study the differentially expressed lncRNAs. We found that AK142386 and AK133540 may affect adipogenesis and metabolism. Our data indicate that AK142386 and AK133540 may be involved in BAT and WAT development through their target genes Hoxa3 and Acad10. Together, we have identified numerous lncRNAs and these lncRNAs can potentially serve as a required component for proper adipogenesis.

  19. Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows

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    Foley Cathriona

    2012-09-01

    Full Text Available Abstract Background All cows experience bacterial contamination and tissue injury in the uterus postpartum, instigating a local inflammatory immune response. However mechanisms that control inflammation and achieve a physiologically functioning endometrium, while avoiding disease in the postpartum cow are not succinctly defined. This study aimed to identify novel candidate genes indicative of inflammation resolution during involution in healthy beef cows. Previous histological analysis of the endometrium revealed elevated inflammation 15 days postpartum (DPP which was significantly decreased by 30 DPP. The current study generated a genome-wide transcriptomic profile of endometrial biopsies from these cows at both time points using mRNA-Seq. The pathway analysis tool GoSeq identified KEGG pathways enriched by significantly differentially expressed genes at both time points. Novel candidate genes associated with inflammatory resolution were subsequently validated in additional postpartum animals using quantitative real-time PCR (qRT-PCR. Results mRNA-Seq revealed 1,107 significantly differentially expressed genes, 73 of which were increased 15 DPP and 1,034 were increased 30 DPP. Early postpartum, enriched immune pathways (adjusted P P SAA1/2, GATA2, IGF1, SHC2, and SERPINA14 genes were significantly elevated 30 DPP and are functionally associated with tissue repair and the restoration of uterine homeostasis postpartum. Conclusions The results of this study reveal an early activation of the immune response which undergoes a temporal functional change toward tissue proliferation and regeneration during endometrial involution in healthy postpartum cows. These molecular changes mirror the activation and resolution of endometrial inflammation during involution previously classified by the degree of neutrophil infiltration. SAA1/2, GATA2, IGF1, SHC2, and SERPINA14 genes may become potential markers for resolution of endometrial inflammation in

  20. Gene expression profiles resulting from stable loss of p53 mirrors its role in tissue differentiation.

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    Oliver Couture

    Full Text Available The tumor suppressor gene p53 is involved in a variety of cellular activities such as cellular stress responses, cell cycle regulation and differentiation. In our previous studies we have shown p53's transcription activating role to be important in osteoblast differentiation. There is still a debate in the literature as to whether p53 inhibits or promotes differentiation. We have found p53 heterozygous mice to show a p53 dependency on some bone marker gene expression that is absent in knockout mice. Mice heterozygous for p53 also show a higher incidence of osteosarcomas than p53 knockout mice. This suggests that p53 is able to modify the environment within osteoblasts. In this study we compare changes in gene expression resulting after either a transient or stable reduction in p53. Accordingly we reduced p53 levels transiently and stably in C2C12 cells, which are capable of both myoblast and osteoblast differentiation, and compared the changes in gene expression of candidate genes regulated by the p53 pathway. Using a PCR array to assay for p53 target genes, we have found different expression profiles when comparing stable versus transient knockdown of p53. As expected, several genes with profound changes after transient p53 loss were related to apoptosis and cell cycle regulation. In contrast, stable p53 loss produced a greater change in MyoD and other transcription factors with tissue specific roles, suggesting that long term loss of p53 affects tissue homeostasis to a greater degree than changes resulting from acute loss of p53. These differences in gene expression were validated by measuring promoter activity of different pathway specific genes involved in differentiation. These studies suggest that an important role for p53 is context dependent, with a stable reduction in p53 expression affecting normal tissue physiology more than acute loss of p53.

  1. Dietary structured lipids for post-weaning piglets: fat digestibility, nitrogen retention and fatty acid profiles of tissues

    DEFF Research Database (Denmark)

    Straarup, Ellen Marie; Danielsen, V.; Høy, Carl-Erik

    2006-01-01

    In four groups of post-weaning piglets the effects of triacylglycerol structure and fatty acid profiles of four dietary fats on apparent faecal nutrient digestibility, nitrogen retention and fatty acid profiles of platelet and erythrocyte membranes, liver, adipose tissue and skeletal muscle were...... to the third week in the groups R1 and R2. Fatty acid profiles in platelet and erythrocyte membranes and in tissues reflected the fatty acid profile of the dietary fat, except for medium-chain fatty acids, which were only found in low proportions, indicating that 10:0 was mainly used as an energy source....... examined. Dietary fats included as 10% (w/w) of the diets were two structured fats of rapeseed oil interesterified with tridecanoin (R1) or coconut oil (R2), respectively, one mixture of rapeseed oil and coconut oil (R3) and rapeseed oil as control (R4). Faeces and urine from piglets weaned at 28 days...

  2. GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles.

    Science.gov (United States)

    Klein, Michael I; Stern, David F; Zhao, Hongyu

    2017-06-26

    Personalizing treatment regimes based on gene expression profiles of individual tumors will facilitate management of cancer. Although many methods have been developed to identify pathways perturbed in tumors, the results are often not generalizable across independent datasets due to the presence of platform/batch effects. There is a need to develop methods that are robust to platform/batch effects and able to identify perturbed pathways in individual samples. We present Gene-Ranking Analysis of Pathway Expression (GRAPE) as a novel method to identify abnormal pathways in individual samples that is robust to platform/batch effects in gene expression profiles generated by multiple platforms. GRAPE first defines a template consisting of an ordered set of pathway genes to characterize the normative state of a pathway based on the relative rankings of gene expression levels across a set of reference samples. This template can be used to assess whether a sample conforms to or deviates from the typical behavior of the reference samples for this pathway. We demonstrate that GRAPE performs well versus existing methods in classifying tissue types within a single dataset, and that GRAPE achieves superior robustness and generalizability across different datasets. A powerful feature of GRAPE is the ability to represent individual gene expression profiles as a vector of pathways scores. We present applications to the analyses of breast cancer subtypes and different colonic diseases. We perform survival analysis of several TCGA subtypes and find that GRAPE pathway scores perform well in comparison to other methods. GRAPE templates offer a novel approach for summarizing the behavior of gene-sets across a collection of gene expression profiles. These templates offer superior robustness across distinct experimental batches compared to existing methods. GRAPE pathway scores enable identification of abnormal gene-set behavior in individual samples using a non-competitive approach that

  3. Experimental verification of bioheat transfer theories: measurement of temperature profiles around large artificial vessels in perfused tissue.

    Science.gov (United States)

    Crezee, J; Lagendijk, J J

    1990-07-01

    The verification of thermal models for use in hyperthermia treatment planning is essential. We investigated the heat transfer between a single vessel and the surrounding vascularised tissue, comparing the conventional bioheat transfer theory and the recently developed keff model using analytical and numerical methods. A plastic tube inserted into the tissue of an isolated perfused organ served as an artificial vessel. This enabled us to vary the blood flow in the vessel and in the tissue independently. The organ used was a bovine kidney, turned into a perfused tissue phantom using an alcohol fixation technique. The temperature profile within the tissue was mapped with constantan-manganin thermocouple wire sensors with a total diameter of 50 microns. The temperature profile relative to the temperature difference between the vessel and organ was measured; increased perfusion caused a reduction of the vessel wall temperature but did not affect the width of the profile. Studying the transient tissue temperature after a step-wise change of the blood temperature in the vessel revealed a faster diffusion of heat at higher perfusion rates. These facts are in accordance with the keff model, but not with the conventional heat-sink theory.

  4. MicroRNA Expression Profiling of the Porcine Developing Hypothalamus and Pituitary Tissue

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    Xiaoling Jiang

    2013-10-01

    Full Text Available MicroRNAs (miRNAs, a class of small non-coding RNA molecules, play important roles in gene expressions at transcriptional and post-transcriptional stages in mammalian brain. So far, a growing number of porcine miRNAs and their function have been identified, but little is known regarding the porcine developing hypothalamus and pituitary. In the present study, Solexa sequencing analysis showed 14,129,397 yielded reads, 6,680,678 of which were related to 674 unique miRNAs. After a microarray assay, we detected 175 unique miRNAs in the hypothalamus, including 136 previously known miRNAs and 39 novel candidates, while a total of 140 miRNAs, including 104 known and 36 new candidate miRNAs, were discovered in pituitary. More importantly, 37 and 30 differentially expressed miRNAs from several developmental stages of hypothalamus and pituitary were revealed, respectively. The 37 differentially expressed miRNAs in hypothalamus represented 6 different expression patterns, while the 30 differentially expressed miRNAs in pituitary represented 7 different expression patterns. To clarify potential target genes and specific functions of these differentially expressed miRNAs in hypothalamus and pituitary, TargetScan and Gorilla prediction tools were then applied. The current functional analysis showed that the differentially expressed miRNAs in hypothalamus and pituitary shared many biological processes, with the main differences being found in tissue-specific processes including: CDP-diacylglycerol biosynthetic/metabolic process; phosphatidic acid biosynthetic/metabolic process; energy reserve metabolic process for hypothalamus; adult behavior; sterol transport/homeostasis; and cholesterol/reverse cholesterol transport for pituitary. Overall, this study identified miRNA profiles and differentially expressed miRNAs among various developmental stages in hypothalamus and pituitary and indicated miRNA profiles change with age and brain location, enhancing our

  5. MicroRNA expression profiling of the porcine developing hypothalamus and pituitary tissue.

    Science.gov (United States)

    Zhang, Lifan; Cai, Zhaowei; Wei, Shengjuan; Zhou, Huiyun; Zhou, Hongmei; Jiang, Xiaoling; Xu, Ningying

    2013-10-14

    MicroRNAs (miRNAs), a class of small non-coding RNA molecules, play important roles in gene expressions at transcriptional and post-transcriptional stages in mammalian brain. So far, a growing number of porcine miRNAs and their function have been identified, but little is known regarding the porcine developing hypothalamus and pituitary. In the present study, Solexa sequencing analysis showed 14,129,397 yielded reads, 6,680,678 of which were related to 674 unique miRNAs. After a microarray assay, we detected 175 unique miRNAs in the hypothalamus, including 136 previously known miRNAs and 39 novel candidates, while a total of 140 miRNAs, including 104 known and 36 new candidate miRNAs, were discovered in pituitary. More importantly, 37 and 30 differentially expressed miRNAs from several developmental stages of hypothalamus and pituitary were revealed, respectively. The 37 differentially expressed miRNAs in hypothalamus represented 6 different expression patterns, while the 30 differentially expressed miRNAs in pituitary represented 7 different expression patterns. To clarify potential target genes and specific functions of these differentially expressed miRNAs in hypothalamus and pituitary, TargetScan and Gorilla prediction tools were then applied. The current functional analysis showed that the differentially expressed miRNAs in hypothalamus and pituitary shared many biological processes, with the main differences being found in tissue-specific processes including: CDP-diacylglycerol biosynthetic/metabolic process; phosphatidic acid biosynthetic/metabolic process; energy reserve metabolic process for hypothalamus; adult behavior; sterol transport/homeostasis; and cholesterol/reverse cholesterol transport for pituitary. Overall, this study identified miRNA profiles and differentially expressed miRNAs among various developmental stages in hypothalamus and pituitary and indicated miRNA profiles change with age and brain location, enhancing our knowledge about spatial

  6. Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae

    Directory of Open Access Journals (Sweden)

    Podolska Agnieszka

    2012-09-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a class of non-protein-coding genes that play a crucial regulatory role in mammalian development and disease. Whereas a large number of miRNAs have been annotated at the structural level during the latest years, functional annotation is sparse. Actinobacillus pleuropneumoniae (APP causes serious lung infections in pigs. Severe damage to the lungs, in many cases deadly, is caused by toxins released by the bacterium and to some degree by host mediated tissue damage. However, understanding of the role of microRNAs in the course of this infectious disease in porcine is still very limited. Results In this study, the RNA extracted from visually unaffected and necrotic tissue from pigs infected with Actinobacillus pleuropneumoniae was subjected to small RNA deep sequencing. We identified 169 conserved and 11 candidate novel microRNAs in the pig. Of these, 17 were significantly up-regulated in the necrotic sample and 12 were down-regulated. The expression analysis of a number of candidates revealed microRNAs of potential importance in the innate immune response. MiR-155, a known key player in inflammation, was found expressed in both samples. Moreover, miR-664-5p, miR-451 and miR-15a appear as very promising candidates for microRNAs involved in response to pathogen infection. Conclusions This is the first study revealing significant differences in composition and expression profiles of miRNAs in lungs infected with a bacterial pathogen. Our results extend annotation of microRNA in pig and provide insight into the role of a number of microRNAs in regulation of bacteria induced immune and inflammatory response in porcine lung.

  7. The Impact of Tissue Fixatives on Morphology and Antibody-based Protein Profiling in Tissues and Cells

    OpenAIRE

    Paavilainen, Linda; Edvinsson, Åsa; Asplund, Anna; Hober, Sophia; Kampf, Caroline; Pontén, Fredrik; Wester, Kenneth

    2010-01-01

    Pathology archives harbor large amounts of formalin-fixed, paraffin-embedded tissue samples, used mainly in clinical diagnostics but also for research purposes. Introduction of heat-induced antigen retrieval has enabled the use of tissue samples for extensive immunohistochemical analysis, despite the fact that antigen retrieval may not recover all epitopes, owing to alterations of the native protein structure induced by formalin. The aim of this study was to investigate how different fixative...

  8. The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells.

    Science.gov (United States)

    Paavilainen, Linda; Edvinsson, Asa; Asplund, Anna; Hober, Sophia; Kampf, Caroline; Pontén, Fredrik; Wester, Kenneth

    2010-03-01

    Pathology archives harbor large amounts of formalin-fixed, paraffin-embedded tissue samples, used mainly in clinical diagnostics but also for research purposes. Introduction of heat-induced antigen retrieval has enabled the use of tissue samples for extensive immunohistochemical analysis, despite the fact that antigen retrieval may not recover all epitopes, owing to alterations of the native protein structure induced by formalin. The aim of this study was to investigate how different fixatives influence protein recognition by immunodetection methods in tissues, cell preparations, and protein lysates, as compared with formalin. Seventy-two affinity-purified polyclonal antibodies were used to evaluate seven different fixatives. The aldehyde-based fixative Glyo-fixx proved to be excellent for preservation of proteins in tissue detected by immunohistochemistry (IHC), similar to formalin. A non-aldehyde-based fixative, NEO-FIX was superior for fixation of cultured cells, in regard to morphology, and thereby also advantageous for IHC. Large variability in the amount of protein extracted from the differently fixed tissues was observed, and the HOPE fixative provided the overall highest yield of protein. In conclusion, morphological resolution and immunoreactivity were superior in tissues fixed with aldehyde-based fixatives, whereas the use of non-aldehyde-based fixatives can be advantageous in obtaining high protein yield for Western blot analysis. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.

  9. Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles.

    Science.gov (United States)

    Mc Sherry, E A; Mc Goldrick, A; Kay, E W; Hopkins, A M; Gallagher, W M; Dervan, P A

    2007-11-01

    Formalin-fixed paraffin-embedded (FFPE) archival clinical specimens are invaluable in discovery of prognostic and therapeutic targets for diseases such as cancer. However, the suitability of FFPE-derived genetic material for array-based comparative genomic hybridization (array-CGH) studies is underexplored. In this study, genetic profiles of matched FFPE and fresh-frozen specimens were examined to investigate DNA integrity differences between these sample types and determine the impact this may have on genetic profiles. Genomic DNA was extracted from three patient-matched FFPE and fresh-frozen clinical tissue samples. T47D breast cancer control cells were also grown in culture and processed to yield a fresh T47D sample, a fresh-frozen T47D sample and a FFPE T47D sample. DNA was extracted from all the samples; array-CGH conducted and genetic profiles of matched samples were then compared. A loss of high molecular weight DNA was observed in the FFPE clinical tissues and FFPE T47D samples. A dramatic increase in absolute number of genetic alterations was observed in all FFPE tissues relative to matched fresh-frozen counterparts. In future, alternative fixation and tissue-processing procedures, and/or new DNA extraction and CGH profiling protocols, may be implemented, enabling identification of changes involved in disease progression using stored clinical specimens.

  10. Fluorescent characteristics and pharmacokinetic profiles of the fluorescent probe BCECF in various tissues: the role of blood content

    Science.gov (United States)

    Devoisselle, Jean-Marie; Soulie-Begu, Sylvie; Mordon, Serge R.; Maillols, H.

    1997-05-01

    Microspectrofluorometry and fluorescence imaging have been largely used to measure the intracellular pH of living cells. Such in vivo measurements require the knowledge of the optical properties of the tissue and the pharmacokinetic of the dye. The purpose of this study was to investigate in vitro and in vivo spectral characteristics of BCECF. In vitro, measurements in presence of blood show that blood content can greatly affect pH measurement by increasing the fluorescence ratio. In vivo, the presence of blood in high vascularized tissue leads to the modification of BCECF spectral characteristics. Fluorescence kinetic profiles provides information about tissue perfusion. Consequently, pH measurements using BCECF or fluorescein derivatives by the double excitation method may be performed taking in account the tissue blood content and the tissue pharmacokinetic of the dye.

  11. Volatile Profiling of Aromatic Traditional Medicinal Plant, Polygonum minus in Different Tissues and Its Biological Activities

    Directory of Open Access Journals (Sweden)

    Rafidah Ahmad

    2014-11-01

    Full Text Available The aim of this research was to identify the volatile metabolites produced in different organs (leaves, stem and roots of Polygonum minus, an important essential oil producing crop in Malaysia. Two methods of extraction have been applied: Solid Phase Microextraction (SPME and hydrodistillation coupled with Gas Chromatography-Mass Spectrometry (GC-MS. Approximately, 77 metabolites have been identified and aliphatic compounds contribute significantly towards the aroma and flavour of this plant. Two main aliphatic compounds: decanal and dodecanal were found to be the major contributor. Terpenoid metabolites were identified abundantly in leaves but not in the stem and root of this plant. Further studies on antioxidant, total phenolic content, anticholinesterase and antimicrobial activities were determined in the essential oil and five different extracts. The plant showed the highest DPPH radical scavenging activity in polar (ethanol extract for all the tissues tested. For anti-acetylcholinesterase activity, leaf in aqueous extract and methanol extract showed the best acetylcholinesterase inhibitory activities. However, in microbial activity, the non-polar extracts (n-hexane showed high antimicrobial activity against Methicillin-resistant Staphylococcus aureus (MRSA compared to polar extracts. This study could provide the first step in the phytochemical profiles of volatile compounds and explore the additional value of pharmacology properties of this essential oil producing crop Polygonum minus.

  12. Volatile profiling of aromatic traditional medicinal plant, Polygonum minus in different tissues and its biological activities.

    Science.gov (United States)

    Ahmad, Rafidah; Baharum, Syarul Nataqain; Bunawan, Hamidun; Lee, Minki; Mohd Noor, Normah; Rohani, Emelda Roseleena; Ilias, Norashikin; Zin, Noraziah Mohamad

    2014-11-20

    The aim of this research was to identify the volatile metabolites produced in different organs (leaves, stem and roots) of Polygonum minus, an important essential oil producing crop in Malaysia. Two methods of extraction have been applied: Solid Phase Microextraction (SPME) and hydrodistillation coupled with Gas Chromatography-Mass Spectrometry (GC-MS). Approximately, 77 metabolites have been identified and aliphatic compounds contribute significantly towards the aroma and flavour of this plant. Two main aliphatic compounds: decanal and dodecanal were found to be the major contributor. Terpenoid metabolites were identified abundantly in leaves but not in the stem and root of this plant. Further studies on antioxidant, total phenolic content, anticholinesterase and antimicrobial activities were determined in the essential oil and five different extracts. The plant showed the highest DPPH radical scavenging activity in polar (ethanol) extract for all the tissues tested. For anti-acetylcholinesterase activity, leaf in aqueous extract and methanol extract showed the best acetylcholinesterase inhibitory activities. However, in microbial activity, the non-polar extracts (n-hexane) showed high antimicrobial activity against Methicillin-resistant Staphylococcus aureus (MRSA) compared to polar extracts. This study could provide the first step in the phytochemical profiles of volatile compounds and explore the additional value of pharmacology properties of this essential oil producing crop Polygonum minus.

  13. MicroRNA expression profiling in neurogenesis of adipose tissue-derived stem cells

    Indian Academy of Sciences (India)

    Jung Ah Cho; Ho Park; Eun Hye Lim; Kyo Won Lee

    2011-04-01

    Adipose tissue-derived stem cells (ADSCs) are one population of adult stem cells that can self renew and differentiate into multiple lineages. Because of advantages in method and quantity of acquisition, ADSCs are gaining attention as an alternative source of bone marrow mesenchymal stem cells. In this study, we performed microRNA profiling of undifferentiated and of neurally-differentiated ADSCs to identify the responsible microRNAs in neurogenesis using this type of stem cell. MicroRNAs from four different donors were analysed by microarray. Compared to the undifferentiation control, we identified 39–101 microRNAs with more than two-fold higher expression and 3–9 microRNAs with two-fold lower expression. The identified microRNAs were further analysed in terms of gene ontology (GO) in relation with neurogenesis, based on their target mRNAs predicted by computational analysis. This study revealed the specific microRNAs involved in neurogenesis via microRNA microarray, and may provide the basic information for genetic induction of adult stem cell differentiation using microRNAs.

  14. Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.

    Science.gov (United States)

    Schechter, Matthew A; Hsieh, Michael K H; Njoroge, Linda W; Thompson, J Will; Soderblom, Erik J; Feger, Bryan J; Troupes, Constantine D; Hershberger, Kathleen A; Ilkayeva, Olga R; Nagel, Whitney L; Landinez, Gina P; Shah, Kishan M; Burns, Virginia A; Santacruz, Lucia; Hirschey, Matthew D; Foster, Matthew W; Milano, Carmelo A; Moseley, M Arthur; Piacentino, Valentino; Bowles, Dawn E

    2014-01-01

    The molecular differences between ischemic (IF) and non-ischemic (NIF) heart failure are poorly defined. A better understanding of the molecular differences between these two heart failure etiologies may lead to the development of more effective heart failure therapeutics. In this study extensive proteomic and phosphoproteomic profiles of myocardial tissue from patients diagnosed with IF or NIF were assembled and compared. Proteins extracted from left ventricular sections were proteolyzed and phosphopeptides were enriched using titanium dioxide resin. Gel- and label-free nanoscale capillary liquid chromatography coupled to high resolution accuracy mass tandem mass spectrometry allowed for the quantification of 4,436 peptides (corresponding to 450 proteins) and 823 phosphopeptides (corresponding to 400 proteins) from the unenriched and phospho-enriched fractions, respectively. Protein abundance did not distinguish NIF from IF. In contrast, 37 peptides (corresponding to 26 proteins) exhibited a ≥ 2-fold alteration in phosphorylation state (pfailure etiology examined. Proteins exhibiting phosphorylation alterations were grouped into functional categories: transcriptional activation/RNA processing; cytoskeleton structure/function; molecular chaperones; cell adhesion/signaling; apoptosis; and energetic/metabolism. Phosphoproteomic analysis demonstrated profound post-translational differences in proteins that are involved in multiple cellular processes between different heart failure phenotypes. Understanding the roles these phosphorylation alterations play in the development of NIF and IF has the potential to generate etiology-specific heart failure therapeutics, which could be more effective than current therapeutics in addressing the growing concern of heart failure.

  15. Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep.

    Science.gov (United States)

    Sun, Limin; Bai, Man; Xiang, Lujie; Zhang, Guishan; Ma, Wei; Jiang, Huaizhi

    2016-09-20

    The Qianhua Mutton Merino (QHMM) is a new sheep (Ovis aries) variety with better meat performance compared with the traditional local variety Small Tail Han (STH) sheep. We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the QHMM and STH. We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH. The results showed that 960 genes were differentially expressed (405 were up-regulated and 555 were down-regulated). Among these, 463 differently expressed genes (DEGs) were probably associated with muscle growth and development and were involved in biological processes such as skeletal muscle tissue development and muscle cell differentiation; molecular functions such as catalytic activity and oxidoreductase activity; cellular components such as mitochondrion and sarcoplasmic reticulum; and pathways such as metabolic pathways and citrate cycle. From the potential genes, a gene-act-network and co-expression-network closely related to muscle growth and development were identified and established. Finally, the expressions of nine genes were validated by real-time PCR. The results suggested that some DEGs, including MRFs, GXP1 and STAC3, play crucial roles in muscle growth and development processes. This genome-wide transcriptome analysis of QHMM and STH muscle is reported for the first time.

  16. Focus on RNA isolation: obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue

    Science.gov (United States)

    Wang, Wang-Xia; Rajeev, Bernard W.; Baldwin, Donald A.; Isett, R. Benjamin; Ren, Na; Stromberg, Arnold; Nelson, Peter T.

    2008-01-01

    MicroRNAs (miRNAs) are present in all known plant and animal tissues and appear to be somewhat concentrated in the mammalian nervous system. Many different miRNA expression profiling platforms have been described. However, relatively little research has been published to establish the importance of ‘upstream’ variables in RNA isolation for neural miRNA expression profiling. We tested whether apparent changes in miRNA expression profiles may be associated with tissue processing, RNA isolation techniques, or different cell types in the sample. RNA isolation was performed on a single brain sample using eight different RNA isolation methods, and results were correlated using a conventional miRNA microarray and then cross-referenced to Northern blots. Differing results were seen between samples obtained using different RNA isolation techniques and between microarray and Northern blot results. Another complication of miRNA microarrays is tissue-level heterogeneity of cellular composition. To investigate this phenomenon, miRNA expression profiles were determined and compared between highly-purified primary cerebral cortical cell preparations of rat primary E15–E18 neurons versus rat primary E15–E18 astrocytes. Finally, to assess the importance of dissecting human brain gray matter from subjacent white matter in cerebral cortical studies, miRNA expression profiles were compared between gray matter and immediately contiguous white matter. The results suggest that for microarray studies, cellular composition is important, and dissecting white matter from gray matter improves the specificity of the results. Based on these data, recommendations for miRNA expression profiling in neural tissues, and considerations worthy of further study, are discussed. PMID:18316046

  17. Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue.

    Directory of Open Access Journals (Sweden)

    Zhixiu Wang

    Full Text Available Transcriptome profiles established using high-throughput sequencing can be effectively used for screening genome-wide differentially expressed genes (DEGs. RNA sequences (from RNA-seq and microRNA sequences (from miRNA-seq from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small-ear pig [DSP] and Tibetan pig [TP] and two introduced pig breeds (Landrace [LL] and Yorkshire [YY] were examined using HiSeq 2000 to identify and compare the differential expression of functional genes related to muscle growth and lipid deposition. We obtained 27.18 G clean data through the RNA-seq and detected that 18,208 genes were positively expressed and 14,633 of them were co-expressed in the muscle tissues of the four samples. In all, 315 DEGs were found between the Chinese pig group and the introduced pig group, 240 of which were enriched with functional annotations from the David database and significantly enriched in 27 Gene Ontology (GO terms that were mainly associated with muscle fiber contraction, cadmium ion binding, response to organic substance and contractile fiber part. Based on functional annotation, we identified 85 DEGs related to growth traits that were mainly involved in muscle tissue development, muscle system process, regulation of cell development, and growth factor binding, and 27 DEGs related to lipid deposition that were mainly involved in lipid metabolic process and fatty acid biosynthetic process. With miRNA-seq, we obtained 23.78 M reads and 320 positively expressed miRNAs from muscle tissues, including 271 known pig miRNAs and 49 novel miRNAs. In those 271 known miRNAs, 20 were higher and 10 lower expressed in DSP-TP than in LL-YY. The target genes of the 30 miRNAs were mainly participated in MAPK, GnRH, insulin and Calcium signaling pathway and others involved cell development, growth and proliferation, etc. Combining the DEGs and the differentially expressed (DE miRNAs, we drafted a network of 46

  18. Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.

    Directory of Open Access Journals (Sweden)

    Matthew A Schechter

    Full Text Available The molecular differences between ischemic (IF and non-ischemic (NIF heart failure are poorly defined. A better understanding of the molecular differences between these two heart failure etiologies may lead to the development of more effective heart failure therapeutics. In this study extensive proteomic and phosphoproteomic profiles of myocardial tissue from patients diagnosed with IF or NIF were assembled and compared. Proteins extracted from left ventricular sections were proteolyzed and phosphopeptides were enriched using titanium dioxide resin. Gel- and label-free nanoscale capillary liquid chromatography coupled to high resolution accuracy mass tandem mass spectrometry allowed for the quantification of 4,436 peptides (corresponding to 450 proteins and 823 phosphopeptides (corresponding to 400 proteins from the unenriched and phospho-enriched fractions, respectively. Protein abundance did not distinguish NIF from IF. In contrast, 37 peptides (corresponding to 26 proteins exhibited a ≥ 2-fold alteration in phosphorylation state (p<0.05 when comparing IF and NIF. The degree of protein phosphorylation at these 37 sites was specifically dependent upon the heart failure etiology examined. Proteins exhibiting phosphorylation alterations were grouped into functional categories: transcriptional activation/RNA processing; cytoskeleton structure/function; molecular chaperones; cell adhesion/signaling; apoptosis; and energetic/metabolism. Phosphoproteomic analysis demonstrated profound post-translational differences in proteins that are involved in multiple cellular processes between different heart failure phenotypes. Understanding the roles these phosphorylation alterations play in the development of NIF and IF has the potential to generate etiology-specific heart failure therapeutics, which could be more effective than current therapeutics in addressing the growing concern of heart failure.

  19. Tissue microarray immunohistochemical profiles of p53 and pRB in hepatocellular carcinoma and hepatoblastoma.

    Science.gov (United States)

    Azlin, Abdul Hadi; Looi, Lai Meng; Cheah, Phaik Leng

    2014-01-01

    The tumour suppressor genes, p53 and pRb, are known to play important roles in neoplastic transformation. While molecular routes to the uncontrolled growth of hepatocytes, leading to primary liver cancer have generated considerable interest, the roles of p53 and pRb mutations in hepatocellular carcinoma (HCC) and hepatoblastoma (HB) remain to be clarified. We examined the immunohistochemical expression of p53 and pRb gene products in 26 HCC and 9 HB, sampled into tissue microarray blocks. 10 (38%) of 26 HCC showed > 10% tumour nuclear staining for p53 protein, 3 of these also being HbsAg positive. Conversely, none of 9 HB expressed nuclear p53 immunopositivity. Some 24 (92%) HCC and 8 (89%) HB showed loss of pRb nuclear expression. Two of the 26 HCC and one of the 9 HB showed >10% tumour nuclear staining for pRb protein. Our results suggest that p53 does not have an important role in the development of HB but may contribute in HCC. There is also loss of pRb expression in the majority of HCC and HB, supporting loss of pRb gene function in the hepatocarcinogenesis pathway. However, a comparison of the staining profiles of p53 and pRb proteins in HCC and HB did not reveal a consistent pattern to differentiate between the two types of tumours immunohistochemically. Hence the use of p53 and pRB protein expression has no contribution in the situation where there is a diagnostic difficulty in deciding between HCC and HB.

  20. The composition of hydrogels for cartilage tissue engineering can influence glycosaminoglycan profile

    Directory of Open Access Journals (Sweden)

    QG Wang

    2010-02-01

    Full Text Available The injectable and hydrophilic nature of hydrogels makes them suitable candidates for cartilage tissue engineering. To date, a wide range of hydrogels have been proposed for articular cartilage regeneration but few studies have quantitatively compared chondrocyte behaviour and extracellular matrix (ECM synthesis within the hydrogels. Herein we have examined the nature of ECM synthesis by chondrocytes seeded into four hydrogels formed by either temperature change, self-assembly or chemical cross-linking. Bovine articular cartilage chondrocytes were cultured for 14 days in Extracel®, Pluronic F127 blended with Type II collagen, Puramatrix® and Matrixhyal®. The discriminatory and sensitive technique of fluorophore-assisted carbohydrate electrophoresis (FACE was used to determine the fine detail of the glycosaminoglycans (GAG; hyaluronan and chondroitin sulphate. FACE analysis for chondroitin sulphate and hyaluronan profiles in Puramatrix® closely matched that of native cartilage. For each hydrogel, DNA content, viability and morphology were assessed. Total collagen and total sulphated GAG production were measured and normalised to DNA content. Significant differences were found in total collagen synthesis. By day 14, Extracel® and Puramatrix® had significantly more total collagen than Matrixhyal® (1.77±0.26 µg and 1.97±0.26 µg vs. 0.60±0.26 µg; p<0.05. sGAG synthesis occurred in all hydrogels but a significantly higher amount of sGAG was retained within Extracel® at days 7 and 14 (p<0.05. In summary, we have shown that the biochemical and biophysical characteristics of each hydrogel directly or indirectly influenced ECM formation. A detailed understanding of the ECM in the development of engineered constructs is an important step in monitoring the success of cartilage regeneration strategies.

  1. Chill-coma recovery time, age and sex determine lipid profiles in Ceratitis capitata tissues.

    Science.gov (United States)

    Pujol-Lereis, Luciana Mercedes; Fagali, Natalia Soledad; Rabossi, Alejandro; Catalá, Ángel; Quesada-Allué, Luis Alberto

    2016-04-01

    The remodeling of membrane composition by changes in phospholipid head groups and fatty acids (FA) degree of unsaturation has been associated with the maintenance of membrane homeostasis under stress conditions. Overall lipid levels and the composition of cuticle lipids also influence insect stress resistance and tissue protection. In a previous study, we demonstrated differences in survival, behavior and Cu/Zn superoxide dismutase gene expression between subgroups of Ceratitis capitata flies that had a reversible recovery from chill-coma and those that developed chilling-injury. Here, we analyzed lipid profiles from comparable subgroups of 15 and 30-day-old flies separated according to their recovery time after a chill-coma treatment. Neutral and polar lipid classes of chill-coma subgroups were separated by thin layer chromatography and quantified by densitometry. FA composition of polar lipids of chill-coma subgroups and non-stressed flies was evaluated using gas chromatography coupled to mass spectrometry. Higher amounts of neutral lipids such as triglycerides, diacylglycerol, wax esters, sterol esters and free esters were found in male flies that recovered faster from chill-coma compared to slower flies. A multivariate analysis revealed changes in patterns of storage and cuticle lipids among subgroups both in males and females. FA unsaturation increased after cold exposure, and was higher in thorax of slower subgroups compared to faster subgroups. The changes in neutral lipid patterns and FA composition depended on recovery time, sex, age and body-part, and were not specifically associated with the development of chilling-injury. An analysis of phospholipid classes showed that the phosphatidylcholine to lysophosphatidylcholine ratio (PC/LPC) was significantly higher, or showed a tendency, in subgroups that may have developed chilling-injury compared to those with a reversible recovery from coma. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Transcriptome profiling of white adipose tissue in a mouse model for 15q duplication syndrome

    Directory of Open Access Journals (Sweden)

    Xiaoxi Liu

    2015-09-01

    Full Text Available Obesity is not only associated with unhealthy lifestyles, but also linked to genetic predisposition. Previously, we generated an autism mouse model (patDp/+ that carries a 6.3 Mb paternal duplication homologous to the human 15q11–q13 locus. Chromosomal abnormalities in this region are known to cause autism spectrum disorder, Prader–Willi syndrome, and Angelman syndrome in humans. We found that, in addition to autistic-like behaviors, patDp/+ mice display late-onset obesity and hypersensitivity to a high-fat diet. These phenotypes are likely to be the results of genetic perturbations since the energy expenditures and food intakes of patDp/+ mice do not significantly differ from those of wild-type mice. Intriguingly, we found that an enlargement of adipose cells precedes the onset of obesity in patDp/+ mice. To understand the underlying molecular networks responsible for this pre-obese phenotype, we performed transcriptome profiling of white adipose tissue from patDp/+ and wild-type mice using microarray. We identified 230 genes as differentially expressed genes. Sfrp5 — a gene whose expression is positively correlated with adipocyte size, was found to be up-regulated, and Fndc5, a potent inducer of brown adipogenesis was identified to be the top down-regulated gene. Subsequent pathway analysis highlighted a set of 35 molecules involved in energy production, lipid metabolism, and small molecule biochemistry as the top candidate biological network responsible for the pre-obese phenotype of patDp/+. The microarray data were deposited in NCBI Gene Expression Omnibus database with accession number GSE58191. Ultimately, our dataset provides novel insights into the molecular mechanism of obesity and demonstrated that patDp/+ is a valuable mouse model for obesity research.

  3. Association between plasma metabolites and gene expression profiles in five porcine endocrine tissues

    Directory of Open Access Journals (Sweden)

    Bassols Anna

    2011-07-01

    Full Text Available Abstract Background Endocrine tissues play a fundamental role in maintaining homeostasis of plasma metabolites such as non-esterified fatty acids and glucose, the levels of which reflect the energy balance or the health status of animals. However, the relationship between the transcriptome of endocrine tissues and plasma metabolites has been poorly studied. Methods We determined the blood levels of 12 plasma metabolites in 27 pigs belonging to five breeds, each breed consisting of both females and males. The transcriptome of five endocrine tissues i.e. hypothalamus, adenohypophysis, thyroid gland, gonads and backfat tissues from 16 out of the 27 pigs was also determined. Sex and breed effects on the 12 plasma metabolites were investigated and associations between genes expressed in the five endocrine tissues and the 12 plasma metabolites measured were analyzed. A probeset was defined as a quantitative trait transcript (QTT when its association with a particular metabolic trait achieved a nominal P value Results A larger than expected number of QTT was found for non-esterified fatty acids and alanine aminotransferase in at least two tissues. The associations were highly tissue-specific. The QTT within the tissues were divided into co-expression network modules enriched for genes in Kyoto Encyclopedia of Genes and Genomes or gene ontology categories that are related to the physiological functions of the corresponding tissues. We also explored a multi-tissue co-expression network using QTT for non-esterified fatty acids from the five tissues and found that a module, enriched in hypothalamus QTT, was positioned at the centre of the entire multi-tissue network. Conclusions These results emphasize the relationships between endocrine tissues and plasma metabolites in terms of gene expression. Highly tissue-specific association patterns suggest that candidate genes or gene pathways should be investigated in the context of specific tissues.

  4. Prolonged niacin treatment leads to increased adipose tissue PUFA synthesis and anti-inflammatory lipid and oxylipin plasma profile.

    Science.gov (United States)

    Heemskerk, Mattijs M; Dharuri, Harish K; van den Berg, Sjoerd A A; Jónasdóttir, Hulda S; Kloos, Dick-Paul; Giera, Martin; van Dijk, Ko Willems; van Harmelen, Vanessa

    2014-12-01

    Prolonged niacin treatment elicits beneficial effects on the plasma lipid and lipoprotein profile that is associated with a protective CVD risk profile. Acute niacin treatment inhibits nonesterified fatty acid release from adipocytes and stimulates prostaglandin release from skin Langerhans cells, but the acute effects diminish upon prolonged treatment, while the beneficial effects remain. To gain insight in the prolonged effects of niacin on lipid metabolism in adipocytes, we used a mouse model with a human-like lipoprotein metabolism and drug response [female APOE*3-Leiden.CETP (apoE3 Leiden cholesteryl ester transfer protein) mice] treated with and without niacin for 15 weeks. The gene expression profile of gonadal white adipose tissue (gWAT) from niacin-treated mice showed an upregulation of the "biosynthesis of unsaturated fatty acids" pathway, which was corroborated by quantitative PCR and analysis of the FA ratios in gWAT. Also, adipocytes from niacin-treated mice secreted more of the PUFA DHA ex vivo. This resulted in an increased DHA/arachidonic acid (AA) ratio in the adipocyte FA secretion profile and in plasma of niacin-treated mice. Interestingly, the DHA metabolite 19,20-dihydroxy docosapentaenoic acid (19,20-diHDPA) was increased in plasma of niacin-treated mice. Both an increased DHA/AA ratio and increased 19,20-diHDPA are indicative for an anti-inflammatory profile and may indirectly contribute to the atheroprotective lipid and lipoprotein profile associated with prolonged niacin treatment.

  5. Application of HPLC Combined with Laser Induced Fluorescence for Protein Profile Analysis of Tissue Homogenates in Cervical Cancer

    OpenAIRE

    Sujatha Bhat; Ajeetkumar Patil; Lavanya Rai; Kartha, V. B.; Santhosh Chidangil

    2012-01-01

    A highly objective method, High Performance Liquid Chromatography with Laser Induced Fluorescence (HPLC-LIF) technique was used to study the protein profiles of normal and cervical cancer tissue homogenates. A total of 44 samples including normal cervical biopsy samples from the hysterectomy patients and the patients suffering from different stages of the cervical cancer were recorded by HPLC-LIF and analysed by Principle Component Analysis (PCA) to get statistical information on different t...

  6. Detection of Colorectal Cancer by Serum and Tissue Protein Profiling: A Prospective Study in a Population at Risk

    Directory of Open Access Journals (Sweden)

    Judith Y.M.N. Engwegen

    2008-01-01

    Full Text Available Colorectal cancer (CRC is the second most common cause of cancer-related death in Europe and its prognosis is largely dependent on stage at diagnosis. Currently, there are no suitable tumour markers for early detection of CRC. In a retrospective study we previously found discriminative CRC serum protein profiles with surface enhanced laser desorption ionisation—time of flight mass spectrometry (SELDI-TOF MS. We now aimed at prospective validation of these profiles. Additionally, we assessed their applicability for follow-up after surgery and investigated tissue protein profiles of patients with CRC and adenomatous polyps (AP. Serum and tissue samples were collected from patients without known malignancy with an indication for colonoscopy and patients with AP and CRC during colonoscopy. Serum samples of controls (CON; n = 359, patients with AP (n = 177 and CRC (n = 73, as well as tissue samples from AP (n = 52 and CRC (n = 47 were analysed as described previously. Peak intensities were compared by non-parametric testing. Discriminative power of differentially expressed proteins was assessed with support vector machines (SVM. We confirmed the decreased serum levels of apolipoprotein C-1 in CRC in the current population. No differences were observed between CON and AP. Apolipoprotein C-I levels did not change significantly within 1 month post-surgery, although a gradual return to normal levels was observed. Several proteins differed between AP and CRC tissue, among which a peak with similar mass as apolipoprotein C-1. This peak was increased in CRC compared to AP. Although we prospectively validated the serum decrease of apolipoprotein C-1 in CRC, serum protein profiles did not yield SVM classifiers with suitable sensitivity and specificity for classification of our patient groups.

  7. Comparison of molecular profiles of human mesenchymal stem cells derived from bone marrow, umbilical cord blood, placenta and adipose tissue.

    Science.gov (United States)

    Heo, June Seok; Choi, Youjeong; Kim, Han-Soo; Kim, Hyun Ok

    2016-01-01

    Mesenchymal stem cells (MSCs) are clinically useful due to their capacity for self-renewal, their immunomodulatory properties and tissue regenerative potential. These cells can be isolated from various tissues and exhibit different potential for clinical applications according to their origin, and thus comparative studies on MSCs from different tissues are essential. In this study, we investigated the immunophenotype, proliferative potential, multilineage differentiation and immunomodulatory capacity of MSCs derived from different tissue sources, namely bone marrow, adipose tissue, the placenta and umbilical cord blood. The gene expression profiles of stemness-related genes [octamer-binding transcription factor 4 (OCT4), sex determining region Y-box (SOX)2, MYC, Krüppel-like factor 4 (KLF4), NANOG, LIN28 and REX1] and lineage‑related and differentiation stage-related genes [B4GALNT1 (GM2/GS2 synthase), inhibin, beta A (INHBA), distal-less homeobox 5 (DLX5), runt-related transcription factor 2 (RUNX2), proliferator‑activated receptor gamma (PPARG), CCAAT/enhancer-binding protein alpha (C/EBPA), bone morphogenetic protein 7 (BMP7) and SOX9] were compared using RT-PCR. No significant differences in growth rate, colony-forming efficiency and immunophenotype were observed. Our results demonstrated that MSCs derived from bone marrow and adipose tissue shared not only in vitro tri-lineage differentiation potential, but also gene expression profiles. While there was considerable inter-donor variation in DLX5 expression between MSCs derived from different tissues, its expression appears to be associated with the osteogenic potential of MSCs. Bone marrow-derived MSCs (BM-MSCs) significantly inhibited allogeneic T cell proliferation possibly via the high levels of the immunosuppressive cytokines, IL10 and TGFB1. Although MSCs derived from different tissues and fibroblasts share many characteristics, some of the marker genes, such as B4GALNT1 and DLX5 may be useful for

  8. Probing the Relationship Between Detected Ion Intensity, Laser Fluence, and Beam Profile in Thin Film and Tissue in MALDI MSI

    Science.gov (United States)

    Steven, Rory T.; Race, Alan M.; Bunch, Josephine

    2016-08-01

    Matrix assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) is increasingly widely used to provide information regarding molecular location within tissue samples. The nature of the photon distribution within the irradiated region, the laser beam profile, and fluence, will significantly affect the form and abundance of the detected ions. Previous studies into these phenomena have focused on circular-core optic fibers or Gaussian beam profiles irradiating dried droplet preparations, where peptides were employed as the analyte of interest. Within this work, we use both round and novel square core optic fibers of 100 and 50 μm diameter to deliver the laser photons to the sample. The laser beam profiles were recorded and analyzed to quantify aspects of the photon distributions and their relation to the spectral data obtained with each optic fiber. Beam profiles with a relatively small number of large beam profile features were found to give rise to the lowest threshold fluence. The detected ion intensity versus fluence relationship was investigated, for the first time, in both thin films of α-cyano-4-hydroxycinnamic acid (CHCA) with phosphatidylcholine (PC) 34:1 lipid standard and in CHCA coated murine tissue sections for both the square and round optic fibers in continuous raster imaging mode. The fluence threshold of ion detection was found to occur at between ~14 and ~64 J/m2 higher in tissue compared with thin film for the same lipid, depending upon the optic fiber employed. The image quality is also observed to depend upon the fluence employed during image acquisition.

  9. High-throughput profiling of tissue and tissue model microarrays: Combined transmitted light and 3-color fluorescence digital pathology

    Directory of Open Access Journals (Sweden)

    Michel Nederlof

    2011-01-01

    Full Text Available For many years pathologists have used Hematoxylin and Eosin (H&E, single marker immunohistochemistry (IHC and in situ hybridization with manual analysis by microscopy or at best simple digital imaging. There is a growing trend to update pathology to a digital workflow to improve objectivity and productivity, as has been done in radiology. There is also a need for tissue-based multivariate biomarker assays to improve the accuracy of diagnostic, prognostic, and predictive testing. Multivariate tests are not compatible with the traditional single marker, manual analysis pathology methods but instead require a digital platform with brightfield and fluorescence imaging, quantitative image analysis, and informatics. Here we describe the use of the Hamamatsu NanoZoomer Digital Pathology slide scanner with HCImage software for combined brightfield and multiplexed fluorescence biomarker analysis and highlight its applications in biomarker research and pathology testing. This combined approach will be an important aid to pathologists in making critical diagnoses.

  10. The female soft tissue profile as presented in fashion magazines during the 1900s: a photographic analysis.

    Science.gov (United States)

    Auger, T A; Turley, P K

    1999-01-01

    Numerous studies have emphasized the importance of the facial profile in orthodontic treatment planning, with some arguing that the esthetic ideal has remained unchanged for thousands of years. To evaluate changes in the white female facial profile, we measured 14 soft tissue variables on profile photographs presented in fashion magazines during the 1900s. Five time frames were studied, with a sample of 25 photographs from each period corrected for size and orientation. Between-group differences were examined by use of analysis of variance, using a P value corrected for a multivariable analysis. Significant between-group differences (P < 0.0001) were found for anteroposterior lip position, amount of visible lip tissue, and interlabial angle, with the more recent groups displaying fuller and more anteriorly positioned lips. No significant differences were found for measurements calculated superior to subnasale (frontonasal angle, nasal tip angle, and nasolabial angle) or in the relationship of the chin to the upper face (total facial angle). The results of this study suggest that standards for the esthetic white female facial profile are not static and show a trend in this century toward fuller and more anteriorly positioned lips.

  11. Magnetic resonance metabolic profiling of breast cancer tissue obtained with core needle biopsy for predicting pathologic response to neoadjuvant chemotherapy.

    Directory of Open Access Journals (Sweden)

    Ji Soo Choi

    Full Text Available The purpose of this study was to determine whether metabolic profiling of core needle biopsy (CNB samples using high-resolution magic angle spinning (HR-MAS magnetic resonance spectroscopy (MRS could be used for predicting pathologic response to neoadjuvant chemotherapy (NAC in patients with locally advanced breast cancer. After institutional review board approval and informed consent were obtained, CNB tissue samples were collected from 37 malignant lesions in 37 patients before NAC treatment. The metabolic profiling of CNB samples were performed by HR-MAS MRS. Metabolic profiles were compared according to pathologic response to NAC using the Mann-Whitney test. Multivariate analysis was performed with orthogonal projections to latent structure-discriminant analysis (OPLS-DA. Various metabolites including choline-containing compounds were identified and quantified by HR-MAS MRS in all 37 breast cancer tissue samples obtained by CNB. In univariate analysis, the metabolite concentrations and metabolic ratios of CNB samples obtained with HR-MAS MRS were not significantly different between different pathologic response groups. However, there was a trend of lower levels of phosphocholine/creatine ratio and choline-containing metabolite concentrations in the pathologic complete response group compared to the non-pathologic complete response group. In multivariate analysis, the OPLS-DA models built with HR-MAS MR metabolic profiles showed visible discrimination between the pathologic response groups. This study showed OPLS-DA multivariate analysis using metabolic profiles of pretreatment CNB samples assessed by HR- MAS MRS may be used to predict pathologic response before NAC, although we did not identify the metabolite showing statistical significance in univariate analysis. Therefore, our preliminary results raise the necessity of further study on HR-MAS MR metabolic profiling of CNB samples for a large number of cancers.

  12. Cold-Induced Browning Dynamically Alters the Expression Profiles of Inflammatory Adipokines with Tissue Specificity in Mice

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    Xiao Luo

    2016-05-01

    Full Text Available Cold exposure or β3-adrenoceptor agonist treatment induces the adipose tissues remodeling, relevant for beige adipogenesis within white adipose tissue (WAT. It remains unclear whether this process influences inflammatory adipokines expression in adipose tissues. We determine the temporal profile of cold or β3-adrenoceptor agonist (CL316,243-induced changes in the expression of inflammatory adipokines in adipose tissues in mice or primary mice adipocytes. Male C57BL/6J mice at eight weeks old were exposed to 4 °C for 1–5 days. Interscapular brown adipose tissue (iBAT, inguinal subcutaneous WAT (sWAT and epididymal WAT (eWAT were harvested for gene and protein expression analysis. In addition, cultured primary mice brown adipocyte (BA and white adipocyte (WA treated with or without CL316,243 were harvested for gene expression analysis. The inflammatory adipokines expressed significantly higher in WAT than BAT at baseline. They were rapidly changed in iBAT, while down-regulated in sWAT and up-regulated in eWAT during the cold acclimation. Upon CL316,243 treatment, detected inflammatory adipokines except Leptin were transiently increased in both BA and WA. Our in vivo and in vitro data demonstrate that the browning process alters the inflammatory adipokines expression in adipose tissues, which is acutely responded to in iBAT, dynamically decreased in sWAT whilst increased in eWAT for compensation.

  13. Network analysis of mitonuclear GWAS reveals functional networks and tissue expression profiles of disease-associated genes.

    Science.gov (United States)

    Johnson, Simon C; Gonzalez, Brenda; Zhang, Quanwei; Milholland, Brandon; Zhang, Zhengdong; Suh, Yousin

    2017-01-01

    While mitochondria have been linked to many human diseases through genetic association and functional studies, the precise role of mitochondria in specific pathologies, such as cardiovascular, neurodegenerative, and metabolic diseases, is often unclear. Here, we take advantage of the catalog of human genome-wide associations, whole-genome tissue expression and expression quantitative trait loci datasets, and annotated mitochondrial proteome databases to examine the role of common genetic variation in mitonuclear genes in human disease. Through pathway-based analysis we identified distinct functional pathways and tissue expression profiles associated with each of the major human diseases. Among our most striking findings, we observe that mitonuclear genes associated with cancer are broadly expressed among human tissues and largely represent one functional process, intrinsic apoptosis, while mitonuclear genes associated with other diseases, such as neurodegenerative and metabolic diseases, show tissue-specific expression profiles and are associated with unique functional pathways. These results provide new insight into human diseases using unbiased genome-wide approaches.

  14. Gene Expression Profiles in Paired Gingival Biopsies from Periodontitis-Affected and Healthy Tissues Revealed by Massively Parallel Sequencing

    Science.gov (United States)

    Båge, Tove; Lagervall, Maria; Jansson, Leif; Lundeberg, Joakim; Yucel-Lindberg, Tülay

    2012-01-01

    Periodontitis is a chronic inflammatory disease affecting the soft tissue and bone that surrounds the teeth. Despite extensive research, distinctive genes responsible for the disease have not been identified. The objective of this study was to elucidate transcriptome changes in periodontitis, by investigating gene expression profiles in gingival tissue obtained from periodontitis-affected and healthy gingiva from the same patient, using RNA-sequencing. Gingival biopsies were obtained from a disease-affected and a healthy site from each of 10 individuals diagnosed with periodontitis. Enrichment analysis performed among uniquely expressed genes for the periodontitis-affected and healthy tissues revealed several regulated pathways indicative of inflammation for the periodontitis-affected condition. Hierarchical clustering of the sequenced biopsies demonstrated clustering according to the degree of inflammation, as observed histologically in the biopsies, rather than clustering at the individual level. Among the top 50 upregulated genes in periodontitis-affected tissues, we investigated two genes which have not previously been demonstrated to be involved in periodontitis. These included interferon regulatory factor 4 and chemokine (C-C motif) ligand 18, which were also expressed at the protein level in gingival biopsies from patients with periodontitis. In conclusion, this study provides a first step towards a quantitative comprehensive insight into the transcriptome changes in periodontitis. We demonstrate for the first time site-specific local variation in gene expression profiles of periodontitis-affected and healthy tissues obtained from patients with periodontitis, using RNA-seq. Further, we have identified novel genes expressed in periodontitis tissues, which may constitute potential therapeutic targets for future treatment strategies of periodontitis. PMID:23029519

  15. The enzyme profiles in the connective tissue attaching pin bones to the surrounding tissue is specific in farmed salmon (Salmo salar) and cod (Gadus morhua L.).

    Science.gov (United States)

    Vuong, Tram T; Rønning, Sissel B; Kolset, Svein O; Pedersen, Mona E

    2017-02-01

    Post mortem storage is a necessary process for removal of pin bones without destruction of fillets, thereby avoiding volume and economic loss. However, the enzymes involved in loosening pin bones during storage have not been studied to a great extent. In this study, the activities and localization of MMPs in the connective tissue (CT) of pin bones dissected from fillet of salmon and cod were investigated. Interestingly, the enzyme activity profile in these two species was different during post mortem storage of fish fillets. Adding MMP inhibitor (GM6001) and serine protease inhibitor (Pefabloc) revealed different effects in the two species, suggesting different regulations in salmon and cod. In situ zymography with the same inhibitors verified MMP and serine protease activity in CT close to pin bone at early post mortem (6 h) in salmon. However, MMP inhibition was not evident in cod in this area at that time point. Immunohistochemistry further revealed MMP9 and MMP13 were located more to the outer rim of CT, facing the pin bone and adipose tissue, while MMP7 was more randomly distributed within CT in salmon. In contrast, all these three MMPs were randomly distributed in CT in cod. In summary, our study reveals different MMP enzyme profiles in salmon and cod in the pin bone area, influenced by serine proteases, and suggests that MMPs and serine proteases must be taken in consideration when studying the conditions for early pin bone removal.

  16. Comparison of prenatal musle tissue expression profiles of two pigs breed differing in muscle characteristics

    NARCIS (Netherlands)

    Cagnazzo, M.; Pas, te M.F.W.; Priem, J.; Wit, de A.A.C.; Pool, M.H.; Davoli, R.; Russo, V.

    2006-01-01

    The objective of this study was to compare purebred Duroc and Pietrain prenatal muscle tissue transcriptome expression levels at different stages of prenatal development to gain insight into the differences in muscle tissue development in these pig breeds. Commercial western pig breeds have been sel

  17. HdhQ111 Mice Exhibit Tissue Specific Metabolite Profiles that Include Striatal Lipid Accumulation.

    Directory of Open Access Journals (Sweden)

    Jeffrey B Carroll

    Full Text Available The HTT CAG expansion mutation causes Huntington's Disease and is associated with a wide range of cellular consequences, including altered metabolism. The mutant allele is expressed widely, in all tissues, but the striatum and cortex are especially vulnerable to its effects. To more fully understand this tissue-specificity, early in the disease process, we asked whether the metabolic impact of the mutant CAG expanded allele in heterozygous B6.HdhQ111/+ mice would be common across tissues, or whether tissues would have tissue-specific responses and whether such changes may be affected by diet. Specifically, we cross-sectionally examined steady state metabolite concentrations from a range of tissues (plasma, brown adipose tissue, cerebellum, striatum, liver, white adipose tissue, using an established liquid chromatography-mass spectrometry pipeline, from cohorts of 8 month old mutant and wild-type littermate mice that were fed one of two different high-fat diets. The differential response to diet highlighted a proportion of metabolites in all tissues, ranging from 3% (7/219 in the striatum to 12% (25/212 in white adipose tissue. By contrast, the mutant CAG-expanded allele primarily affected brain metabolites, with 14% (30/219 of metabolites significantly altered, compared to wild-type, in striatum and 11% (25/224 in the cerebellum. In general, diet and the CAG-expanded allele both elicited metabolite changes that were predominantly tissue-specific and non-overlapping, with evidence for mutation-by-diet interaction in peripheral tissues most affected by diet. Machine-learning approaches highlighted the accumulation of diverse lipid species as the most genotype-predictive metabolite changes in the striatum. Validation experiments in cell culture demonstrated that lipid accumulation was also a defining feature of mutant HdhQ111 striatal progenitor cells. Thus, metabolite-level responses to the CAG expansion mutation in vivo were tissue specific and

  18. IHC Profiler: an open source plugin for the quantitative evaluation and automated scoring of immunohistochemistry images of human tissue samples.

    Directory of Open Access Journals (Sweden)

    Frency Varghese

    Full Text Available In anatomic pathology, immunohistochemistry (IHC serves as a diagnostic and prognostic method for identification of disease markers in tissue samples that directly influences classification and grading the disease, influencing patient management. However, till today over most of the world, pathological analysis of tissue samples remained a time-consuming and subjective procedure, wherein the intensity of antibody staining is manually judged and thus scoring decision is directly influenced by visual bias. This instigated us to design a simple method of automated digital IHC image analysis algorithm for an unbiased, quantitative assessment of antibody staining intensity in tissue sections. As a first step, we adopted the spectral deconvolution method of DAB/hematoxylin color spectra by using optimized optical density vectors of the color deconvolution plugin for proper separation of the DAB color spectra. Then the DAB stained image is displayed in a new window wherein it undergoes pixel-by-pixel analysis, and displays the full profile along with its scoring decision. Based on the mathematical formula conceptualized, the algorithm is thoroughly tested by analyzing scores assigned to thousands (n = 1703 of DAB stained IHC images including sample images taken from human protein atlas web resource. The IHC Profiler plugin developed is compatible with the open resource digital image analysis software, ImageJ, which creates a pixel-by-pixel analysis profile of a digital IHC image and further assigns a score in a four tier system. A comparison study between manual pathological analysis and IHC Profiler resolved in a match of 88.6% (P<0.0001, CI = 95%. This new tool developed for clinical histopathological sample analysis can be adopted globally for scoring most protein targets where the marker protein expression is of cytoplasmic and/or nuclear type. We foresee that this method will minimize the problem of inter-observer variations across labs and

  19. IHC Profiler: An Open Source Plugin for the Quantitative Evaluation and Automated Scoring of Immunohistochemistry Images of Human Tissue Samples

    Science.gov (United States)

    Malhotra, Renu; De, Abhijit

    2014-01-01

    In anatomic pathology, immunohistochemistry (IHC) serves as a diagnostic and prognostic method for identification of disease markers in tissue samples that directly influences classification and grading the disease, influencing patient management. However, till today over most of the world, pathological analysis of tissue samples remained a time-consuming and subjective procedure, wherein the intensity of antibody staining is manually judged and thus scoring decision is directly influenced by visual bias. This instigated us to design a simple method of automated digital IHC image analysis algorithm for an unbiased, quantitative assessment of antibody staining intensity in tissue sections. As a first step, we adopted the spectral deconvolution method of DAB/hematoxylin color spectra by using optimized optical density vectors of the color deconvolution plugin for proper separation of the DAB color spectra. Then the DAB stained image is displayed in a new window wherein it undergoes pixel-by-pixel analysis, and displays the full profile along with its scoring decision. Based on the mathematical formula conceptualized, the algorithm is thoroughly tested by analyzing scores assigned to thousands (n = 1703) of DAB stained IHC images including sample images taken from human protein atlas web resource. The IHC Profiler plugin developed is compatible with the open resource digital image analysis software, ImageJ, which creates a pixel-by-pixel analysis profile of a digital IHC image and further assigns a score in a four tier system. A comparison study between manual pathological analysis and IHC Profiler resolved in a match of 88.6% (P<0.0001, CI = 95%). This new tool developed for clinical histopathological sample analysis can be adopted globally for scoring most protein targets where the marker protein expression is of cytoplasmic and/or nuclear type. We foresee that this method will minimize the problem of inter-observer variations across labs and further help in

  20. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.

    Science.gov (United States)

    Cejas, Paloma; Li, Lewyn; O'Neill, Nicholas K; Duarte, Melissa; Rao, Prakash; Bowden, Michaela; Zhou, Chensheng W; Mendiola, Marta; Burgos, Emilio; Feliu, Jaime; Moreno-Rubio, Juan; Guadalajara, Héctor; Moreno, Víctor; García-Olmo, Damián; Bellmunt, Joaquim; Mullane, Stephanie; Hirsch, Michelle; Sweeney, Christopher J; Richardson, Andrea; Liu, X Shirley; Brown, Myles; Shivdasani, Ramesh A; Long, Henry W

    2016-06-01

    Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation.

  1. The gene expression profile of non-cultured, highly purified human adipose tissue pericytes: Transcriptomic evidence that pericytes are stem cells in human adipose tissue.

    Science.gov (United States)

    da Silva Meirelles, Lindolfo; de Deus Wagatsuma, Virgínia Mara; Malta, Tathiane Maistro; Bonini Palma, Patrícia Viana; Araújo, Amélia Goes; Panepucci, Rodrigo Alexandre; Silva, Wilson Araújo; Kashima, Simone; Covas, Dimas Tadeu

    2016-12-10

    Pericytes (PCs) are a subset of perivascular cells that can give rise to mesenchymal stromal cells (MSCs) when culture-expanded, and are postulated to give rise to MSC-like cells during tissue repair in vivo. PCs have been suggested to behave as stem cells (SCs) in situ in animal models, although evidence for this role in humans is lacking. Here, we analyzed the transcriptomes of highly purified, non-cultured adipose tissue (AT)-derived PCs (ATPCs) to detect gene expression changes that occur as they acquire MSC characteristics in vitro, and evaluated the hypothesis that human ATPCs exhibit a gene expression profile compatible with an AT SC phenotype. The results showed ATPCs are non-proliferative and express genes characteristic not only of PCs, but also of AT stem/progenitor cells. Additional analyses defined a gene expression signature for ATPCs, and revealed putative novel ATPC markers. Almost all AT stem/progenitor cell genes differentially expressed by ATPCs were not expressed by ATMSCs or culture-expanded ATPCs. Genes expressed by ATMSCs but not by ATPCs were also identified. These findings strengthen the hypothesis that PCs are SCs in vascularized tissues, highlight gene expression changes they undergo as they assume an MSC phenotype, and provide new insights into PC biology. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Evaluation of endogenous references for gene expression profiling in different tissues of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Wang Jin-Jun

    2010-10-01

    Full Text Available Abstract Background Quantitative real-time reverse transcriptase PCR (RT-qPCR has been widely used for quantification of mRNA as a way to determine key genes involved in different biological processes. For accurate gene quantification analysis, normalization of RT-qPCR data is absolutely essential. To date, normalization is most frequently achieved by the use of internal controls, often referred to as reference genes. However, several studies have shown that the reference genes used for the quantification of mRNA expression can be affected by the experimental set-up or cell type resulting in variation of the expression level of these key genes. Therefore, the evaluation of reference genes is critical for gene expression profiling, which is often neglected in gene expression studies of insects. For this purpose, ten candidate reference genes were investigated in three different tissues (midgut, Malpighian tubules, and fat body of the oriental fruit fly, Bactrocera dorsalis (Hendel. Results Two different programs, geNorm and Normfinder, were used to analyze the data. According to geNorm, α-TUB + ACT5 are the most appropriate reference genes for gene expression profiling across the three different tissues in the female flies, while ACT3 + α-TUB are considered as the best for males. Furthermore, we evaluated the stability of the candidate reference genes to determine the sexual differences in the same tissue. In the midgut and Malpighian tubules, ACT2 + α-TUB are the best choice for both males and females. However, α-TUB + ACT1 are the best pair for fat body. Meanwhile, the results calculated by Normfinder are quite the same as the results with geNorm; α-TUB is always one of the most stable genes in each sample validated by the two programs. Conclusions In this study, we validated the suitable reference genes for gene expression profiling in different tissues of B. dorsalis. Moreover, appropriate reference genes were selected out for gene

  3. Profile of the subjects with soft tissue injuries attended at an occupational health service and the RSI

    Directory of Open Access Journals (Sweden)

    Camila de Freitas

    2015-07-01

    Full Text Available Aim: To investigate the profile of subjects with soft tissue injuries attended at the Reference Center of Occupational Health – CEREST in the municipality of Santos, Sao Paulo state, in 2010, and the social insurance benefits granted.Materials and Methods: Analysis of medical records of the subjects assisted at CEREST in 2010, surveying data on gender, age, occupation, clinical diagnostics, clinical complaints, retirement, etc. The clinical diagnostics were categorized according to the International Classification of Diseases - ICD-10, subjects with soft tissue injuries were selected, and the diagnostics related to mental health disorders were registered. Data were recorded in Microsoft Excel spreadsheet and analyzed using statistical software R Development Core Team.Results: Of the 206 medical records analyzed, 18.0% (n=37 showed soft tissue injuries, 81.1% were female and 18.9% were male, and the subjects’ mean age was 43.24 years (SD=8.76. Subjects between 31 and 50 years old (70.2% were the most affected. The most affected occupations were cleaners, general service workers, and bank clerks. The most prevalent clinical diagnoses were synovitis and tenosynovitis, shoulder bursitis, and rotator cuff syndrome, with 62.2% of the subjects presenting more than one clinical diagnosis. 13.5% of the subjects also presented mental disorders. Association between retirement from work and the presence of soft tissue injury was observed (p=0.032. Only 13.5% of the diagnoses had some association with the work conditions.Conclusions: The general profile of the workers with soft tissue injuries was obtained: prevalence in women, diseases manifested in productive age, difficulty of association with work conditions, need for interdisciplinary interventions.

  4. Expression profiles of genes involved in xenobiotic metabolism and disposition in human renal tissues and renal cell models

    Energy Technology Data Exchange (ETDEWEB)

    Van der Hauwaert, Cynthia; Savary, Grégoire [EA4483, Université de Lille 2, Faculté de Médecine de Lille, Pôle Recherche, 59045 Lille (France); Buob, David [Institut de Pathologie, Centre de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille (France); Leroy, Xavier; Aubert, Sébastien [Institut de Pathologie, Centre de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille (France); Institut National de la Santé et de la Recherche Médicale, UMR837, Centre de Recherche Jean-Pierre Aubert, Equipe 5, 59045 Lille (France); Flamand, Vincent [Service d' Urologie, Hôpital Huriez, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille (France); Hennino, Marie-Flore [EA4483, Université de Lille 2, Faculté de Médecine de Lille, Pôle Recherche, 59045 Lille (France); Service de Néphrologie, Hôpital Huriez, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille (France); Perrais, Michaël [Institut National de la Santé et de la Recherche Médicale, UMR837, Centre de Recherche Jean-Pierre Aubert, Equipe 5, 59045 Lille (France); and others

    2014-09-15

    Numerous xenobiotics have been shown to be harmful for the kidney. Thus, to improve our knowledge of the cellular processing of these nephrotoxic compounds, we evaluated, by real-time PCR, the mRNA expression level of 377 genes encoding xenobiotic-metabolizing enzymes (XMEs), transporters, as well as nuclear receptors and transcription factors that coordinate their expression in eight normal human renal cortical tissues. Additionally, since several renal in vitro models are commonly used in pharmacological and toxicological studies, we investigated their metabolic capacities and compared them with those of renal tissues. The same set of genes was thus investigated in HEK293 and HK2 immortalized cell lines in commercial primary cultures of epithelial renal cells and in proximal tubular cell primary cultures. Altogether, our data offers a comprehensive description of kidney ability to process xenobiotics. Moreover, by hierarchical clustering, we observed large variations in gene expression profiles between renal cell lines and renal tissues. Primary cultures of proximal tubular epithelial cells exhibited the highest similarities with renal tissue in terms of transcript profiling. Moreover, compared to other renal cell models, Tacrolimus dose dependent toxic effects were lower in proximal tubular cell primary cultures that display the highest metabolism and disposition capacity. Therefore, primary cultures appear to be the most relevant in vitro model for investigating the metabolism and bioactivation of nephrotoxic compounds and for toxicological and pharmacological studies. - Highlights: • Renal proximal tubular (PT) cells are highly sensitive to xenobiotics. • Expression of genes involved in xenobiotic disposition was measured. • PT cells exhibited the highest similarities with renal tissue.

  5. Diosgenin reorganises hyperglycaemia and distorted tissue lipid profile in high-fat diet-streptozotocin-induced diabetic rats.

    Science.gov (United States)

    Naidu, Parim Brahma; Ponmurugan, Ponnusamy; Begum, Mustapha Sabana; Mohan, Karthick; Meriga, Balaji; RavindarNaik, Ramavat; Saravanan, Ganapathy

    2015-12-01

    Diabetes is often connected with significant morbidity, mortality and also has a pivotal role in the development of cardiovascular diseases. Diet intervention, particularly naturaceutical antioxidants have anti-diabetic potential and avert oxidative damage linked with diabetic pathogenesis. The present study investigated the effects of diosgenin, a saponin from fenugreek, on the changes in lipid profile in plasma, liver, heart and brain in high-fat diet-streptozotocin (HFD-STZ)-induced diabetic rats. Diosgenin was administered to HFD-STZ induced diabetic rats by orally at 60 mg kg(-1) body weight for 30 days to assess its effects on body weight gain, glucose, insulin, insulin resistance and cholesterol, triglycerides, free fatty acids and phospholipids in plasma, liver, heart and brain. The levels of body weight, glucose, insulin, insulin resistance, cholesterol, triglycerides, free fatty acids, phospholipids, VLDL-C and LDL-C were increased significantly (P lipid profile in plasma and tissues. The traditional plant fenugreek and its constituents mediate its anti-diabetic potential through mitigating hyperglycaemic status, altering insulin resistance by alleviating metabolic dysregulation of lipid profile in both plasma and tissues. © 2014 Society of Chemical Industry.

  6. Application of HPLC combined with laser induced fluorescence for protein profile analysis of tissue homogenates in cervical cancer.

    Science.gov (United States)

    Bhat, Sujatha; Patil, Ajeetkumar; Rai, Lavanya; Kartha, V B; Chidangil, Santhosh

    2012-01-01

    A highly objective method, High Performance Liquid Chromatography with Laser Induced Fluorescence (HPLC-LIF) technique was used to study the protein profiles of normal and cervical cancer tissue homogenates. A total of 44 samples including normal cervical biopsy samples from the hysterectomy patients and the patients suffering from different stages of the cervical cancer were recorded by HPLC-LIF and analysed by Principle Component Analysis (PCA) to get statistical information on different tissue components. Discrimination of different stages of the samples was carried out by considering three parameters--scores of factor, spectral residual, and Mahalanobis Distance. Diagnostic accuracy of the method was evaluated using Receiver Operating Characteristic (ROC) analysis, and Youden's index (J) plots. The PCA results showed high sensitivity and specificity (~100) for cervical cancer diagnosis. ROC and Youden's index curves for both normal and malignant standard sets show good diagnostic accuracy with high AUC values. The statistical analysis has shown that the differences in protein profiles can be used to diagnose biochemical changes in the tissue, and thus can be readily applied for the detection of cervical cancer, even in situations where a histopathology examination is not easy because of nonavailability of experienced pathologists.

  7. Application of HPLC Combined with Laser Induced Fluorescence for Protein Profile Analysis of Tissue Homogenates in Cervical Cancer

    Directory of Open Access Journals (Sweden)

    Sujatha Bhat

    2012-01-01

    Full Text Available A highly objective method, High Performance Liquid Chromatography with Laser Induced Fluorescence (HPLC-LIF technique was used to study the protein profiles of normal and cervical cancer tissue homogenates. A total of 44 samples including normal cervical biopsy samples from the hysterectomy patients and the patients suffering from different stages of the cervical cancer were recorded by HPLC-LIF and analysed by Principle Component Analysis (PCA to get statistical information on different tissue components. Discrimination of different stages of the samples was carried out by considering three parameters—scores of factor, spectral residual, and Mahalanobis Distance. Diagnostic accuracy of the method was evaluated using Receiver Operating Characteristic (ROC analysis, and Youden's index (J plots. The PCA results showed high sensitivity and specificity (∼100 for cervical cancer diagnosis. ROC and Youden's index curves for both normal and malignant standard sets show good diagnostic accuracy with high AUC values. The statistical analysis has shown that the differences in protein profiles can be used to diagnose biochemical changes in the tissue, and thus can be readily applied for the detection of cervical cancer, even in situations where a histopathology examination is not easy because of nonavailability of experienced pathologists.

  8. Transcriptome analysis of the medulla tissue from cattle in response to bovine spongiform encephalopathy using digital gene expression tag profiling.

    Science.gov (United States)

    Basu, Urmila; Almeida, Luciane; Olson, N Eric; Meng, Yan; Williams, John L; Moore, Stephen S; Guan, Le Luo

    2011-01-01

    Bovine spongiform encephalopathy (BSE) is a transmissible, fatal neurodegenerative disorder of cattle produced by prions. The use of excessive parallel sequencing for comparison of gene expression in bovine control and infected tissues may help to elucidate the molecular mechanisms associated with this disease. In this study, tag profiling Solexa sequencing was used for transcriptome analysis of bovine brain tissues. Replicate libraries were prepared from mRNA isolated from control and infected (challenged with 100 g of BSE-infected brain) medulla tissues 45 mo after infection. For each library, 5-6 million sequence reads were generated and approximately 67-70% of the reads were mapped against the Bovine Genome database to approximately 13,700-14,120 transcripts (each having at least one read). About 42-47% of the total reads mapped uniquely. Using the GeneSifter software package, 190 differentially expressed (DE) genes were identified (>2.0-fold change, p < .01): 73 upregulated and 117 downregulated. Seventy-nine DE genes had functions described in the Gene Ontology (GO) database and 16 DE genes were involved in 38 different pathways described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Digital analysis expression by tag profiling may be a powerful approach to comprehensive transcriptome analysis to identify changes associated with disease progression, leading to a better understanding of the underlying mechanism of pathogenesis of BSE.

  9. Distinct effects of calorie restriction on adipose tissue cytokine and angiogenesis profiles in obese and lean mice

    Directory of Open Access Journals (Sweden)

    Kurki Eveliina

    2012-06-01

    Full Text Available Abstract Background Obesity associates with low-grade inflammation and adipose tissue remodeling. Using sensitive high-throughput protein arrays we here investigated adipose tissue cytokine and angiogenesis-related protein profiles from obese and lean mice, and in particular, the influence of calorie restriction (CR. Methods Tissue samples from visceral fat were harvested from obese mice fed with a high-fat diet (60% of energy, lean controls receiving low-fat control diet as well as from obese and lean mice kept under CR (energy intake 70% of ad libitum intake for 50 days. Protein profiles were analyzed using mouse cytokine and angiogenesis protein array kits. Results In obese and lean mice, CR was associated with 11.3% and 15.6% reductions in body weight, as well as with 4.0% and 4.6% reductions in body fat percentage, respectively. Obesity induced adipose tissue cytokine expressions, the most highly upregulated cytokines being IL-1ra, IL-2, IL-16, MCP-1, MIG, RANTES, C5a, sICAM-1 and TIMP-1. CR increased sICAM-1 and TIMP-1 expression both in obese and lean mice. Overall, CR showed distinct effects on cytokine expressions; in obese mice CR largely decreased but in lean mice increased adipose tissue cytokine expressions. Obesity was also associated with increased expressions of angiogenesis-related proteins, in particular, angiogenin, endoglin, endostatin, endothelin-1, IGFBP-3, leptin, MMP-3, PAI-1, TIMP-4, CXCL16, platelet factor 4, DPPIV and coagulation factor III. CR increased endoglin, endostatin and platelet factor 4 expressions, and decreased IGFBP-3, NOV, MMP-9, CXCL16 and osteopontin expressions both in obese and lean mice. Interestingly, in obese mice, CR decreased leptin and TIMP-4 expressions, whereas in lean mice their expressions were increased. CR decreased MMP-3 and PAI-1 only in obese mice, whereas CR decreased FGF acidic, FGF basic and coagulation factor III, and increased angiogenin and DPPIV expression only in lean mice

  10. Effects of warm ischemic time on gene expression profiling in colorectal cancer tissues and normal mucosa.

    Directory of Open Access Journals (Sweden)

    Valeria Musella

    Full Text Available BACKGROUND: Genome-wide gene expression analyses of tumors are a powerful tool to identify gene signatures associated with biologically and clinically relevant characteristics and for several tumor types are under clinical validation by prospective trials. However, handling and processing of clinical specimens may significantly affect the molecular data obtained from their analysis. We studied the effects of tissue handling time on gene expression in human normal and tumor colon tissues undergoing routine surgical procedures. METHODS: RNA extracted from specimens of 15 patients at four time points (for a total of 180 samples after surgery was analyzed for gene expression on high-density oligonucleotide microarrays. A mixed-effects model was used to identify probes with different expression means across the four different time points. The p-values of the model were adjusted with the Bonferroni method. RESULTS: Thirty-two probe sets associated with tissue handling time in the tumor specimens, and thirty-one in the normal tissues, were identified. Most genes exhibited moderate changes in expression over the time points analyzed; however four of them were oncogenes, and two confirmed the effect of tissue handling by independent validation. CONCLUSIONS: Our results suggest that a critical time point for tissue handling in colon seems to be 60 minutes at room temperature. Although the number of time-dependent genes we identified was low, the three genes that already showed changes at this time point in tumor samples were all oncogenes, hence recommending standardization of tissue-handling protocols and effort to reduce the time from specimen removal to snap freezing accounting for warm ischemia in this tumor type.

  11. Dietary structured lipids for post-weaning piglets: fat digestibility, nitrogen retention and fatty acid profiles of tissues

    DEFF Research Database (Denmark)

    Straarup, Ellen Marie; Danielsen, V.; Høy, Carl-Erik

    2006-01-01

    In four groups of post-weaning piglets the effects of triacylglycerol structure and fatty acid profiles of four dietary fats on apparent faecal nutrient digestibility, nitrogen retention and fatty acid profiles of platelet and erythrocyte membranes, liver, adipose tissue and skeletal muscle were...... interesterified fats or the physical mixtures (R1, R2 and R3) compared with rapeseed oil (R4). Apparent faecal nitrogen digestibility and retention were similar in all four groups in the three periods, but increased with time. Apparent faecal fat digestibilities were significantly improved from the first...... examined. Dietary fats included as 10% (w/w) of the diets were two structured fats of rapeseed oil interesterified with tridecanoin (R1) or coconut oil (R2), respectively, one mixture of rapeseed oil and coconut oil (R3) and rapeseed oil as control (R4). Faeces and urine from piglets weaned at 28 days...

  12. Biodynamic imaging for phenotypic profiling of three-dimensional tissue culture

    Science.gov (United States)

    Sun, Hao; Merrill, Daniel; An, Ran; Turek, John; Matei, Daniela; Nolte, David D.

    2017-01-01

    Three-dimensional (3-D) tissue culture represents a more biologically relevant environment for testing new drugs compared to conventional two-dimensional cancer cell culture models. Biodynamic imaging is a high-content 3-D optical imaging technology based on low-coherence interferometry and digital holography that uses dynamic speckle as high-content image contrast to probe deep inside 3-D tissue. Speckle contrast is shown to be a scaling function of the acquisition time relative to the persistence time of intracellular transport and hence provides a measure of cellular activity. Cellular responses of 3-D multicellular spheroids to paclitaxel are compared among three different growth techniques: rotating bioreactor (BR), hanging-drop (HD), and nonadherent (U-bottom, UB) plate spheroids, compared with ex vivo living tissues. HD spheroids have the most homogeneous tissue, whereas BR spheroids display large sample-to-sample variability as well as spatial heterogeneity. The responses of BR-grown tumor spheroids to paclitaxel are more similar to those of ex vivo biopsies than the responses of spheroids grown using HD or plate methods. The rate of mitosis inhibition by application of taxol is measured through tissue dynamics spectroscopic imaging, demonstrating the ability to monitor antimitotic chemotherapy. These results illustrate the potential use of low-coherence digital holography for 3-D pharmaceutical screening applications.

  13. Metabolic profiling of the tissue-specific responses in mussel Mytilus galloprovincialis towards Vibrio harveyi challenge.

    Science.gov (United States)

    Liu, Xiaoli; Ji, Chenglong; Zhao, Jianmin; Wang, Qing; Li, Fei; Wu, Huifeng

    2014-08-01

    Mussel Mytilus galloprovincialis is a marine aquaculture shellfish distributing widely along the coast in north China. In this work, we studied the differential metabolic responses induced by Vibrio harveyi in digestive gland and gill tissues from M. galloprovincialis using NMR-based metabolomics. The differential metabolic responses in the two tissue types were detected, except the similarly altered taurine and betaine. These metabolic responses suggested that V. harveyi mainly induced osmotic disruption and reduced energy demand via the metabolic pathways of glucose synthesis and ATP/AMP conversion in mussel digestive gland. In mussel gill tissues, V. harveyi basically caused osmotic stress and possible reduced energy demand as shown by the elevated phosphocholine that is involved in one of the metabolic pathways of ATP synthesis from ADP and phosphocholine. The altered mRNA expression levels of related genes (superoxide dismutase with copper and zinc, heat shock protein 90, defensin and lysozyme) suggested that V. harveyi induced clear oxidative and immune stresses in both digestive gland and gill tissues. However, the mRNA expression levels of both lysozyme and defensin in digestive gland were more significantly up-regulated than those in gill from V. harveyi-challenged mussel M. galloprovincialis, meaning that the immune organ, digestive gland, was more sensitive than gill. Overall, our results indicated that V. harveyi could induce tissue-specific metabolic responses in mussel M. galloprovincialis.

  14. Profile analysis of hepatic porcine and murine brain tissue slices obtained with a vibratome.

    Science.gov (United States)

    Mattei, G; Cristiani, I; Magliaro, C; Ahluwalia, A

    2015-01-01

    This study is aimed at characterizing soft tissue slices using a vibratome. In particular, the effect of two sectioning parameters (i.e., step size and sectioning speed) on resultant slice thickness was investigated for fresh porcine liver as well as for paraformaldehyde-fixed (PFA-fixed) and fresh murine brain. A simple framework for embedding, sectioning and imaging the slices was established to derive their thickness, which was evaluated through a purposely developed graphical user interface. Sectioning speed and step size had little effect on the thickness of fresh liver slices. Conversely, the thickness of PFA-fixed murine brain slices was found to be dependent on the step size, but not on the sectioning speed. In view of these results, fresh brain tissue was sliced varying the step size only, which was found to have a significant effect on resultant slice thickness. Although precision-cut slices (i.e., with regular thickness) were obtained for all the tissues, slice accuracy (defined as the match between the nominal step size chosen and the actual slice thickness obtained) was found to increase with tissue stiffness from fresh liver to PFA-fixed brain. This quantitative investigation can be very helpful for establishing the most suitable slicing setup for a given tissue.

  15. Fat digestibility, nitrogen retention, and fatty acid profiles in blood and tissues of post-weaning piglets fed interesterified fats

    DEFF Research Database (Denmark)

    Straarup, Ellen Marie; Danielsen, V.; Jakobsen, K.

    2003-01-01

    The effects of a designer fat as to changes in triacylglycerol structure in dietary fat on nutrient digestibility, nitrogen retention and fatty acid profile of plasma, erythrocyte membranes, liver, adipose tissue and skeletal muscle were examined in four groups of post-weaning piglets. The test...... fats added by 10% (w/w) to the diets were: R1 regiospecific structured fats with decanoic acid mainly located in the sn-1/3 positions and a long-chain fatty acid from rapeseed oil in the sn-2 position, R2 similar fat subjected to chemical randomization, R3 physical mixture of tridecanoin and rapeseed...

  16. Global Gene Expression Profiling of Telangiectasial Tissue from Patients with Hereditary Haemorrhagic Telangiectasia

    DEFF Research Database (Denmark)

    Tørring, Pernille M; Larsen, Martin Jakob; Kjeldsen, Anette D

    2015-01-01

    members, and the exact mechanism of how endoglin and ALK1 haploinsufficiency leads to HHT manifestations remains to be identified. The purpose of this study was to detect significantly differentially regulated genes in HHT, and try to elucidate the pathways and regulatory mechanisms occurring......-telangiectasial (n=40) tissue using a paired design. Comparing HHT telangiectasial and non-telangiectasial tissue, significantly differentially expressed genes were detected using a paired t-test. Gene set analysis was performed using GSA-SNP. In the group of ENG mutation carriers, we detected 67 differentially...... expressed mRNAs, of which 62 were down regulated in the telangiectasial tissue. Gene set analysis identified the gene ontology (GO) terms vasculogenesis, TGF-β signalling, and Wnt signalling as differentially expressed in HHT1. Altered Wnt signalling might be related to HHT pathogenesis and a greater...

  17. Temporal and topographic profiles of tissue hypoxia following transient focal cerebral ischemia in rats.

    Science.gov (United States)

    Noto, Takahisa; Furuichi, Yasuhisa; Ishiye, Masayuki; Matsuoka, Nobuya; Aramori, Ichiro; Mutoh, Seitaro; Yanagihara, Takehiko; Manabe, Noboru

    2006-08-01

    Intravascular accumulation of blood cells after brain ischemia-reperfusion can cause obstruction of cerebral blood flow and tissue hypoxia/ischemia as a consequence. In the present study, we examined temporal and topographic changes of tissue hypoxia/ischemia after occlusion of the middle cerebral artery (MCA) for 60 min in rats with immunohistochemical staining for hypoxia (2-nitroimidazole hypoxia marker: hypoxyprobe-1 adducts). Our results showed that tissue hypoxia expressed as positive staining for hypoxyprobe-1 adducts preceded neuronal degeneration. Platelets and granulocytes were detected close to the hypoxyprobe-1 adducts positive area. These results suggested that the hypoxic environment could persist even after reperfusion of MCA, because of vascular obstruction with accumulation of platelets and granulocytes.

  18. Profiling Osteogenic microRNAs For RNAi-Functionalization Of Scaffolds In Bone Tissue Engineering

    DEFF Research Database (Denmark)

    Chang, Chi-Chih (Clare); Chen, Li; Venø, Morten Trillingsgaard

    is limited and grafts are required to assist in bone repair. The use of allografts can cause immunological complications, whilst autografts subject the patient to two surgeries. Bone tissue engineering is a multidisciplinary field encompassing material science, medicine, chemistry and molecular biology aimed...... both miRNAs that have been reported previously and many novel miRNAs with potent osteogenic capabilities. For tissue engineering applications, we then functionalized scaffolds with the miRNAs we identified and observed an increase in osteogenic capabilities in our 3D cultures. Our findings depicted...... the miRNA expression landscape as mesenchymal stem cells underwent osteogenic differentiation. We also highlight the potency of miRNAs as biological therapeutics in bone tissue engineering....

  19. THE INFLUENCE OF AUTOLYSIS ON THE PROTEIN-PEPTIDE PROFILE OF Bos taurus AND Sus scrofa HEART AND AORTA TISSUES

    Directory of Open Access Journals (Sweden)

    I. M. Chernukha

    2016-01-01

    Full Text Available The article presents the results of autolytic processes impact on the protein-peptide profile of Bos taurus and Sus scrofa cardiac muscle and aorta. The results of tissue-specific protein identification are also presented as well as the effect of autolysis. Apolipoprotein A-1 involved in the formation of high-density lipoproteins, peroxiredoxin-1 involved in the suppression of oxidative stress, galectin-1 induced apoptosis of T-lymphocytes, as well as number of heat shock proteins with molecular weight less than 30 kDa were identified in Sus scrofa aorta tissue. It was discovered that functional proteins with molecular weight less than 30 kDa are retained during the freezing process, but destroyed under the action of autolytic enzymes. This work was supported by the Russian Science Foundation (project No. 16–16–10073.

  20. White adipose tissue genome wide-expression profiling and adipocyte metabolic functions after soy protein consumption in rats.

    Science.gov (United States)

    Frigolet, Maria E; Torres, Nimbe; Uribe-Figueroa, Laura; Rangel, Claudia; Jimenez-Sanchez, Gerardo; Tovar, Armando R

    2011-02-01

    Obesity is associated with an increase in adipose tissue mass due to an imbalance between high dietary energy intake and low physical activity; however, the type of dietary protein may contribute to its development. The aim of the present work was to study the effect of soy protein versus casein on white adipose tissue genome profiling, and the metabolic functions of adipocytes in rats with diet-induced obesity. The results showed that rats fed a Soy Protein High-Fat (Soy HF) diet gained less weight and had lower serum leptin concentration than rats fed a Casein High-Fat (Cas HF) diet, despite similar energy intake. Histological studies indicated that rats fed the Soy HF diet had significantly smaller adipocytes than those fed the Cas HF diet, and this was associated with a lower triglyceride/DNA content. Fatty acid synthesis in isolated adipocytes was reduced by the amount of fat consumed but not by the type of protein ingested. Expression of genes of fatty acid oxidation increased in adipose tissue of rats fed Soy diets; microarray analysis revealed that Soy protein consumption modified the expression of 90 genes involved in metabolic functions and inflammatory response in adipose tissue. Network analysis showed that the expression of leptin was regulated by the type of dietary protein and it was identified as a central regulator of the expression of lipid metabolism genes in adipose tissue. Thus, soy maintains the size and metabolic functions of adipose tissue through biochemical adaptations, adipokine secretion, and global changes in gene expression.

  1. Gene expression profiling of prostate tissue identifies chromatin regulation as a potential link between obesity and lethal prostate cancer.

    Science.gov (United States)

    Ebot, Ericka M; Gerke, Travis; Labbé, David P; Sinnott, Jennifer A; Zadra, Giorgia; Rider, Jennifer R; Tyekucheva, Svitlana; Wilson, Kathryn M; Kelly, Rachel S; Shui, Irene M; Loda, Massimo; Kantoff, Philip W; Finn, Stephen; Vander Heiden, Matthew G; Brown, Myles; Giovannucci, Edward L; Mucci, Lorelei A

    2017-07-12

    Obese men are at higher risk of advanced prostate cancer and cancer-specific mortality; however, the biology underlying this association remains unclear. This study examined gene expression profiles of prostate tissue to identify biological processes differentially expressed by obesity status and lethal prostate cancer. Gene expression profiling was performed on tumor (n = 402) and adjacent normal (n = 200) prostate tissue from participants in 2 prospective cohorts who had been diagnosed with prostate cancer from 1982 to 2005. Body mass index (BMI) was calculated from the questionnaire immediately preceding cancer diagnosis. Men were followed for metastases or prostate cancer-specific death (lethal disease) through 2011. Gene Ontology biological processes differentially expressed by BMI were identified using gene set enrichment analysis. Pathway scores were computed by averaging the signal intensities of member genes. Odds ratios (ORs) for lethal prostate cancer were estimated with logistic regression. Among 402 men, 48% were healthy weight, 31% were overweight, and 21% were very overweight/obese. Fifteen gene sets were enriched in tumor tissue, but not normal tissue, of very overweight/obese men versus healthy-weight men; 5 of these were related to chromatin modification and remodeling (false-discovery rate 7, 41% vs 17%; P = 2 × 10(-4) ) and an increased risk of lethal disease that was independent of grade and stage (OR, 5.26; 95% confidence interval, 2.37-12.25). This study improves our understanding of the biology of aggressive prostate cancer and identifies a potential mechanistic link between obesity and prostate cancer death that warrants further study. Cancer 2017. © 2017 American Cancer Society. © 2017 American Cancer Society.

  2. Company analysis

    DEFF Research Database (Denmark)

    Jenster, Per V.; Hussey, David

    This volume looks at the company appraisal as a whole, examining the continuing need to appraise companies as part of the continuing strategy process. Building from a sound basis of theory, the text aims to be practical and to give guidance to senior managers and others involved in the strategy p...

  3. Carotenoid profiling, in silico analysis and transcript profiling of miRNAs targeting carotenoid biosynthetic pathway genes in different developmental tissues of tomato.

    Science.gov (United States)

    Koul, Archana; Yogindran, Sneha; Sharma, Deepak; Kaul, Sanjana; Rajam, Manchikatla Venkat; Dhar, Manoj K

    2016-11-01

    Carotenoid biosynthetic pathway is one of the highly significant and very well elucidated secondary metabolic pathways in plants. microRNAs are the potential regulators, widely known for playing a pivotal role in the regulation of various biological as well as metabolic processes. miRNAs may assist in the metabolic engineering of the secondary metabolites for the production of elite genotypes with increased biomass and content of various metabolites. miRNA mediated regulation of carotenoid biosynthetic genes has not been elucidated so far. To illustrate the potential regulatory role of miRNAs in carotenoid biosynthesis, transcript profiling of the known miRNAs and their possible target carotenoid genes was undertaken at eight different developmental stages of tomato, using stem-loop PCR approach combined with quantitative RT-PCR. The inter-relationship amongst carotenoid content, biosynthetic genes and miRNAs was studied in depth. Comparative expression profiles of miRNA and target genes showed variable expression in different tissues studied. The expression level of miRNAs and their target carotenoid genes displayed similar pattern in the vegetative tissues as compared to the reproductive ones, viz. fruit (different stages), indicating the possibility of regulation of carotenoid biosynthesis at various stages of fruit development. This was later confirmed by the HPLC analysis of the carotenoids. The present study has further enhanced the understanding of regulation of carotenoid biosynthetic pathway in plants. The identified miRNAs can be employed to manipulate the biosynthesis of different carotenoids, through metabolic engineering for the production of lycopene rich tomatoes.

  4. Adipose tissue gene expression profiles in ob/ob mice treated with leptin.

    Science.gov (United States)

    Zhang, Wei; Della-Fera, Mary Anne; Hartzell, Diane L; Hausman, Dorothy; Baile, Clifton A

    2008-07-04

    Leptin plays a critical role in regulating body weight, lipid metabolism, apoptosis and microvasculature of adipose tissue. To explore multiple signaling pathways of leptin action on adipose tissue, real-time PCR utilizing TaqMan low-density arrays was performed to compare mRNA expression in adipose tissue of ob/ob mice treated with vehicle or leptin (2.5 microg/d or 10 microg/d) for 14 days via subcutaneous osmotic minipumps. Of the 24 target genes selected for characterization, many were differentially expressed between control ob/ob mice and leptin-treated ob/ob mice. Increases in mRNA expression were found for hormone sensitive lipase (HSL), uncoupling protein 2 (UCP2), adrenergic receptor 3 (ADR3), mitofusin 2 (Mfn2), sirtuin 3 (Sirt3), transcription factor sterol regulatory element binding factor 1 (SREBF1), Bcl-2, Bax, Caspase 3, tumor necrosis factor alpha (TNFalpha), adiponectin and angiopoietin 2 (Ang-2). Decreases in expression were found for stearoyl-coenzyme A desaturase 1 (SCD1), fatty acid synthase (FAS), and retinol binding protein 4 (RBP4). There were no changes in expression of transcription factors involved in adipocyte differentiation (C/EBPalpha, PPARalpha, and PPARgamma). These results confirm that alterations in the expression of specific adipose tissue genes including those associated with the promotion of lipid mobilization, energy dissipation, and apoptosis may mediate leptin-induced fat loss in ob/ob mice.

  5. Transcriptomic and metabolomic profiling of chicken adipose tissue in response to insulin neutralization and fasting.

    Science.gov (United States)

    Ji, Bo; Ernest, Ben; Gooding, Jessica R; Das, Suchita; Saxton, Arnold M; Simon, Jean; Dupont, Joelle; Métayer-Coustard, Sonia; Campagna, Shawn R; Voy, Brynn H

    2012-08-31

    Domestic broiler chickens rapidly accumulate adipose tissue due to intensive genetic selection for rapid growth and are naturally hyperglycemic and insulin resistant, making them an attractive addition to the suite of rodent models used for studies of obesity and type 2 diabetes in humans. Furthermore, chicken adipose tissue is considered as poorly sensitive to insulin and lipolysis is under glucagon control. Excessive fat accumulation is also an economic and environmental concern for the broiler industry due to the loss of feed efficiency and excessive nitrogen wasting, as well as a negative trait for consumers who are increasingly conscious of dietary fat intake. Understanding the control of avian adipose tissue metabolism would both enhance the utility of chicken as a model organism for human obesity and insulin resistance and highlight new approaches to reduce fat deposition in commercial chickens. We combined transcriptomics and metabolomics to characterize the response of chicken adipose tissue to two energy manipulations, fasting and insulin deprivation in the fed state. Sixteen to 17 day-old commercial broiler chickens (ISA915) were fed ad libitum, fasted for five hours, or fed but deprived of insulin by injections of anti-insulin serum. Pair-wise contrasts of expression data identified a total of 2016 genes that were differentially expressed after correction for multiple testing, with the vast majority of differences due to fasting (1780 genes). Gene Ontology and KEGG pathway analyses indicated that a short term fast impacted expression of genes in a broad selection of pathways related to metabolism, signaling and adipogenesis. The effects of insulin neutralization largely overlapped with the response to fasting, but with more modest effects on adipose tissue metabolism. Tissue metabolomics indicated unique effects of insulin on amino acid metabolism. Collectively, these data provide a foundation for further study into the molecular basis for adipose

  6. Transcriptomic and metabolomic profiling of chicken adipose tissue in response to insulin neutralization and fasting

    Directory of Open Access Journals (Sweden)

    Ji Bo

    2012-08-01

    Full Text Available Abstract Background Domestic broiler chickens rapidly accumulate adipose tissue due to intensive genetic selection for rapid growth and are naturally hyperglycemic and insulin resistant, making them an attractive addition to the suite of rodent models used for studies of obesity and type 2 diabetes in humans. Furthermore, chicken adipose tissue is considered as poorly sensitive to insulin and lipolysis is under glucagon control. Excessive fat accumulation is also an economic and environmental concern for the broiler industry due to the loss of feed efficiency and excessive nitrogen wasting, as well as a negative trait for consumers who are increasingly conscious of dietary fat intake. Understanding the control of avian adipose tissue metabolism would both enhance the utility of chicken as a model organism for human obesity and insulin resistance and highlight new approaches to reduce fat deposition in commercial chickens. Results We combined transcriptomics and metabolomics to characterize the response of chicken adipose tissue to two energy manipulations, fasting and insulin deprivation in the fed state. Sixteen to 17 day-old commercial broiler chickens (ISA915 were fed ad libitum, fasted for five hours, or fed but deprived of insulin by injections of anti-insulin serum. Pair-wise contrasts of expression data identified a total of 2016 genes that were differentially expressed after correction for multiple testing, with the vast majority of differences due to fasting (1780 genes. Gene Ontology and KEGG pathway analyses indicated that a short term fast impacted expression of genes in a broad selection of pathways related to metabolism, signaling and adipogenesis. The effects of insulin neutralization largely overlapped with the response to fasting, but with more modest effects on adipose tissue metabolism. Tissue metabolomics indicated unique effects of insulin on amino acid metabolism. Conclusions Collectively, these data provide a foundation

  7. Transcriptional profiling of degraded RNA in cryopreserved and fixed tissue samples obtained at autopsy

    Directory of Open Access Journals (Sweden)

    Alhasan Samir

    2006-12-01

    Full Text Available Abstract Background Traditional multiplexed gene expression methods require well preserved, intact RNA. Such specimens are difficult to acquire in clinical practice where formalin fixation is the standard procedure for processing tissue. Even when special handling methods are used to obtain frozen tissue, there may be RNA degradation; for example autopsy samples where degradation occurs both pre-mortem and during the interval between death and cryopreservation. Although specimens with partially degraded RNA can be analyzed by qRT-PCR, these analyses can only be done individually or at low levels of multiplexing and are laborious and expensive to run for large numbers of RNA targets. Methods We evaluated the ability of the cDNA-mediated Annealing, Selection, extension, and Ligation (DASL assay to provide highly multiplexed analyses of cryopreserved and formalin fixed, paraffin embedded (FFPE tissues obtained at autopsy. Each assay provides data on 1536 targets, and can be performed on specimens with RNA fragments as small as 60 bp. Results The DASL performed accurately and consistently with cryopreserved RNA obtained at autopsy as well as with RNA extracted from formalin-fixed paraffin embedded tissue that had a cryopreserved mirror image specimen with high quality RNA. In FFPE tissue where the cryopreserved mirror image specimen was of low quality the assay performed reproducibly on some but not all specimens. Conclusion The DASL assay provides reproducible results from cryopreserved specimens and many FFPE specimens obtained at autopsy. Gene expression analyses of these specimens may be especially valuable for the study of non-cancer endpoints, where surgical specimens are rarely available.

  8. Comparison of Gene Expression Profile Between Tumor Tissue and Adjacent Non-tumor Tissue in Patients with Gastric Gastrointestinal Stromal Tumor (GIST).

    Science.gov (United States)

    Kou, Youwei; Zhao, Ying; Bao, Chenhui; Wang, Qiang

    2015-06-01

    Gastrointestinal stromal tumors (GISTs) are defined as spindle cell and/or epithelioid tumors originated from interstitial Cajal cells or precursors in the digestive tract. This study was conducted to identify genes differing in expression between the gastric tumors and the adjacent non-cancerous mucosas in patients with primary gastric GIST. The gene expression profile was determined by using oligonucleotide-based DNA microarrays and further validated by quantitative real-time PCR. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis was performed to predict signaling pathways involved in gastric GIST. Our data showed that the expression levels of 957 genes (RAB39B, member RAS oncogene family; VCAN, versican; etc.) were higher and that of 526 genes (CXCL14, chemokine C-X-C motif ligand 14; MTUS1, microtubule-associated tumor suppressor 1; etc.) were lower in the gastric tumor tissues as compared with normal gastric tissues. Results from KEGG pathway analysis revealed that the differentially expressed genes were enriched into 16 signaling transduction pathways, including Hedeghog and Wnt signaling pathways. Our study may provide basis for identification of novel biomarkers associated with primary gastric GIST pathogenesis and for exploration of underlying mechanisms involved in this gastric sarcoma.

  9. Generalized stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors, and cultured cells

    OpenAIRE

    2013-01-01

    Single-cell variations in gene and protein expression are important during development and disease. Cell-to-cell heterogeneities can be directly inspected one cell at a time, but global methods are usually not sensitive enough to work with such a small amount of starting material. Here, we provide a detailed protocol for stochastic profiling, a method that infers single-cell regulatory heterogeneities by repeatedly sampling small collections of cells at random. Repeated stochastic sampling is...

  10. Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep

    OpenAIRE

    Limin Sun; Man Bai; Lujie Xiang; Guishan Zhang; Wei Ma; Huaizhi Jiang

    2016-01-01

    The Qianhua Mutton Merino (QHMM) is a new sheep (Ovis aries) variety with better meat performance compared with the traditional local variety Small Tail Han (STH) sheep. We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the QHMM and STH. We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH. The results showed that 960 genes were differentially expressed (405 were up-regulated and 555 were dow...

  11. Proteome analysis and tissue array for profiling protein markers associated with type B thymoma subclassification

    Institute of Scientific and Technical Information of China (English)

    SUN Qiang-ling; FANG Wen-tao; FENG Jian; ZHANG Jie; YANG Xiao-hua; GU Zhi-tao; ZHU Lei; SHA Hui-fang

    2012-01-01

    Background The prognostic relevance of World Health Organization (WHO) subtypes within type B thymomas is still controversial.Understanding of the molecular characteristics of the different histologic types of thymomas will provide meaningful information for diagnosis and therapeutic management in type B thymoma.Methods Proteins extracted from twelve type B thymoma tissue specimens (six type B1 and six type B2) were analyzed by two-dimensional electrophoresis (2-DE) coupled with MALDI-TOF-MS.Differentially expressed proteins were then assayed in sixty-nine type B thymoma tissues (including B1,B2 and B3) by tissue array analysis with immunohistochemistry staining.The relationship of their expression with clinicopathological parameters,such as tumor stage or WHO classification,was estimated by Spearman's Rank Correlation Test.Results Sixteen differentially expressed proteins between type B1 and B2 thymoma tissues were identified.The differential levels of ezrin and glutathione S-transferase pi (GSTP1) were validated using immunohistochemistry staining.A statistically significant difference was observed in the positive rate of ezrin expression between type B1 thymoma and type B3 thymoma (Z=-2.963,P <0.01).Ezrin showed a tendency to be expressed in higher classification tumors from type B1 to B3.A statistical analysis demonstrated that type B2 and B3 tumors had significantly higher positive expression of GSTP1 than the B1 group (type B2 vs.B1:Z=-2.582,P ≤0.01; type B3 vs.B1:Z=-4.012,P≤0.001).The results also showed a strong correlation between GSTP1 and WHO type staging of B1 to B3 tumors (Spearman's correlation coefficient:0.633,P≤0.001).Statistical analysis showed that there was close correlation between GSTP1 and ezrin expression with the clinical stage (Spearman's correlation coefficients,ezrin:0.481,P <0.05; GSTP1:0.484,P <0.01).Conclusions Differentially expressed proteins between type B1 and B2 thymoma tissues were analyzed by comparative proteomic

  12. Proteome profiling in murine models of multiple sclerosis: identification of stage specific markers and culprits for tissue damage.

    Directory of Open Access Journals (Sweden)

    Ralf A Linker

    Full Text Available The identification of new biomarkers is of high interest for the prediction of the disease course and also for the identification of pathomechanisms in multiple sclerosis (MS. To specify markers of the chronic disease phase, we performed proteome profiling during the later phase of myelin oligodendrocyte glycoprotein induced experimental autoimmune encephalomyelitis (MOG-EAE, day 35 after immunization as a model disease mimicking many aspects of secondary progressive MS. In comparison to healthy controls, high resolution 2 dimensional gel electrophoresis revealed a number of regulated proteins, among them glial fibrilary acidic protein (GFAP. Phase specific up-regulation of GFAP in chronic EAE was confirmed by western blotting and immunohistochemistry. Protein levels of GFAP were also increased in the cerebrospinal fluid of MS patients with specificity for the secondary progressive disease phase. In a next step, proteome profiling of an EAE model with enhanced degenerative mechanisms revealed regulation of alpha-internexin, syntaxin binding protein 1, annexin V and glutamate decarboxylase in the ciliary neurotrophic factor (CNTF knockout mouse. The identification of these proteins implicate an increased apoptosis and enhanced axonal disintegration and correlate well the described pattern of tissue injury in CNTF -/- mice which involve oligodendrocyte (OL apoptosis and axonal injury.In summary, our findings underscore the value of proteome analyses as screening method for stage specific biomarkers and for the identification of new culprits for tissue damage in chronic autoimmune demyelination.

  13. Predicting tenocyte expression profiles and average molecular concentrations in Achilles tendon ECM from tissue strain and fiber damage.

    Science.gov (United States)

    Mehdizadeh, Arash; Gardiner, Bruce S; Lavagnino, Michael; Smith, David W

    2017-03-13

    In this study, we propose a method for quantitative prediction of changes in concentrations of a number of key signaling, structural and effector molecules within the extracellular matrix of tendon. To achieve this, we introduce the notion of elementary cell responses (ECRs). An ECR defines a normal reference secretion profile of a molecule by a tenocyte in response to the tenocyte's local strain. ECRs are then coupled with a model for mechanical damage of tendon collagen fibers at different straining conditions of tendon and then scaled up to the tendon tissue level for comparison with experimental observations. Specifically, our model predicts relative changes in ECM concentrations of transforming growth factor beta, interleukin 1 beta, collagen type I, glycosaminoglycan, matrix metalloproteinase 1 and a disintegrin and metalloproteinase with thrombospondin motifs 5, with respect to tendon straining conditions that are consistent with the observations in the literature. In good agreement with a number of in vivo and in vitro observations, the model provides a logical and parsimonious explanation for how excessive mechanical loading of tendon can lead to under-stimulation of tenocytes and a degenerative tissue profile, which may well have bearing on a better understanding of tendon homeostasis and the origin of some tendinopathies.

  14. Integrative miRNA-mRNA profiling of adipose tissue unravels transcriptional circuits induced by sleep fragmentation.

    Directory of Open Access Journals (Sweden)

    Sina A Gharib

    Full Text Available Obstructive sleep apnea (OSA is a prevalent condition and strongly associated with metabolic disorders. Sleep fragmentation (SF is a major consequence of OSA, but its contribution to OSA-related morbidities is not known. We hypothesized that SF causes specific perturbations in transcriptional networks of visceral fat cells, leading to systemic metabolic disturbances. We simultaneously profiled visceral adipose tissue mRNA and miRNA expression in mice exposed to 6 hours of SF during sleep, and developed a new computational framework based on gene set enrichment and network analyses to merge these data. This approach leverages known gene product interactions and biologic pathways to interrogate large-scale gene expression profiling data. We found that SF induced the activation of several distinct pathways, including those involved in insulin regulation and diabetes. Our integrative methodology identified putative controllers and regulators of the metabolic response during SF. We functionally validated our findings by demonstrating altered glucose and lipid homeostasis in sleep-fragmented mice. This is the first study to link sleep fragmentation with widespread disruptions in visceral adipose tissue transcriptome, and presents a generalizable approach to integrate mRNA-miRNA information for systematic mapping of regulatory networks.

  15. Livers, guts and gills: mapping the decay profiles of soft tissues to understand authigenic mineral replacement.

    Science.gov (United States)

    Clements, Thomas; Purnell, Mark; Gabbott, Sarah

    2016-04-01

    The hard mineralised parts of organisms such as shells, teeth and bones dominate the fossil record. There are, however, sites around the world where soft-tissues are preserved often through rapid replacement of original tissue by rapidly-precipitating authigenic minerals. These exceptionally well-preserved soft-bodied fossils are much more informative about the anatomy, physiology, ecology and behaviour of ancient organisms as well as providing a more inclusive picture of ecosystems and evolution throughout geological time. However, despite the wealth of information that soft-bodied fossils can provide they must first be correctly interpreted as the processes of both decay and preservation act to modify the carcass from its in vivo condition. Decay leads to alteration of the appearance and topology of anatomy, and ultimately to loss. Preservation is selective with some anatomical features being more likely to be captured than others. These problems are especially germane to the interpretation of deep-time and/or enigmatic fossils where no modern analogue exist for comparative anatomical analysis. It is therefore of vital importance to understand the processes carcasses undergo during the fossilisation process, , in order to interpret the anatomical remains of fossils and thus extract true evolutionary presence or absence of anatomy from absence due to taphonomic biases. We have designed a series of novel experiments to investigate, in real time, how decay processes affect the fossilisation potential of soft-tissues - especially of internal anatomy. Our data allow us to unravel both the timing and sequence of anatomical decay of different organs. At the same time through measuring Eh and pH in selected organs we can predict when anatomical features will fall in to the window of authigenic mineralization and thus potentially become preserved. We can also place constraints on which minerals will operate to capture tissues. Our findings are applied to the fossil record

  16. MALDI Orbitrap Mass Spectrometry Profiling of Dysregulated Sulfoglycosphingolipids in Renal Cell Carcinoma Tissues

    Science.gov (United States)

    Jirásko, Robert; Holčapek, Michal; Khalikova, Maria; Vrána, David; Študent, Vladimír; Prouzová, Zuzana; Melichar, Bohuslav

    2017-08-01

    Matrix-assisted laser desorption/ionization coupled with Orbitrap mass spectrometry (MALDI-Orbitrap-MS) is used for the clinical study of patients with renal cell carcinoma (RCC), as the most common type of kidney cancer. Significant changes in sulfoglycosphingolipid abundances between tumor and autologous normal kidney tissues are observed. First, sulfoglycosphingolipid species in studied RCC samples are identified using high mass accuracy full scan and tandem mass spectra. Subsequently, optimization, method validation, and statistical evaluation of MALDI-MS data for 158 tissues of 80 patients are discussed. More than 120 sulfoglycosphingolipids containing one to five hexosyl units are identified in human RCC samples based on the systematic study of their fragmentation behavior. Many of them are recorded here for the first time. Multivariate data analysis (MDA) methods, i.e., unsupervised principal component analysis (PCA) and supervised orthogonal partial least square discriminant analysis (OPLS-DA), are used for the visualization of differences between normal and tumor samples to reveal the most up- and downregulated lipids in tumor tissues. Obtained results are closely correlated with MALDI mass spectrometry imaging (MSI) and histologic staining. Important steps of the present MALDI-Orbitrap-MS approach are also discussed, such as the selection of best matrix, correct normalization, validation for semiquantitative study, and problems with possible isobaric interferences on closed masses in full scan mass spectra.

  17. Growth changes in the soft tissue profile of Yemenis females: A cross-sectional study

    Directory of Open Access Journals (Sweden)

    Fatma A Elsayed

    2015-01-01

    Full Text Available Aim: To investigate the changes in soft tissue parameters of three age groups of untreated Yemenis females. Materials and Methods: The sample comprised 300 Yemeni females which were randomly selected and divided according to age into three equal groups (Group I: 7.34 ± 0.65 years [prepubertal], Group II: 11.11 ± 1.07 years [pubertal], and Group III: 22.17 ± 3.04 years [postpubertal]. Lateral cephalometric radiographs were taken for each subject, and soft tissue measurements were performed. Comparison between the three groups was done. One cephalogram representing the mean of its group was selected from the three groups; the selected three cephalograms (one from each group were superimposed for growth changes evaluation. Results: Linear, as well as angular soft tissue measurements were significant for all measurements between the different age groups except Ls-Sn Pog', Li-Sn Pog', GSn Pog' and nasolabial angle, respectively. Conclusion: The identified changes with growth in Yemeni females having Class I skeletal and dental relationship should be considered during planning for orthodontic and/or orthognathic treatments.

  18. Thermogenic profiling using magnetic resonance imaging of dermal and other adipose tissues.

    Science.gov (United States)

    Kasza, Ildiko; Hernando, Diego; Roldán-Alzate, Alejandro; Alexander, Caroline M; Reeder, Scott B

    2016-08-18

    Dermal white adipose tissue (dWAT) was recently recognized for its potential to modify whole body metabolism. Here, we show that dWAT can be quantified using a high-resolution, fat-specific magnetic resonance imaging (MRI) technique. Noninvasive MRI has been used to describe adipocyte depots for many years; the MRI technique we describe uses an advanced fat-specific method to measure the thickness of dWAT, together with the total volume of WAT and the relative activation/fat depletion of brown adipose tissues (BAT). Since skin-embedded adipocytes may provide natural insulation, they provide an important counterpoint to the activation of thermogenic brown and beige adipose tissues, whereby these distinct depots are functionally interrelated and require simultaneous assay. This method was validated using characterized mouse cohorts of a lipodystrophic, dWAT-deficient strain (syndecan-1 KO) and 2 obese models (diet-induced obese mice and genetically obese animals, ob/ob). Using a preliminary cohort of normal human subjects, we found the thickness of skin-associated fat varied 8-fold, from 0.13-1.10 cm; on average, this depot is calculated to weigh 8.8 kg.

  19. Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition.

    Science.gov (United States)

    Tao, Xuan; Liang, Yan; Yang, Xuemei; Pang, Jianhui; Zhong, Zhijun; Chen, Xiaohui; Yang, Yuekui; Zeng, Kai; Kang, Runming; Lei, Yunfeng; Ying, Sancheng; Gong, Jianjun; Gu, Yiren; Lv, Xuebin

    2017-01-01

    Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.

  20. Postpartal subclinical endometritis alters transcriptome profiles in liver and adipose tissue of dairy cows.

    Science.gov (United States)

    Akbar, Haji; Cardoso, Felipe C; Meier, Susanne; Burke, Christopher; McDougall, Scott; Mitchell, Murray; Walker, Caroline; Rodriguez-Zas, Sandra L; Everts, Robin E; Lewin, Harris A; Roche, John R; Loor, Juan J

    2014-01-01

    Transcriptome alterations in liver and adipose tissue of cows with subclinical endometritis (SCE) at 29 d postpartum were evaluated. Bioinformatics analysis was performed using the Dynamic Impact Approach by means of KEGG and DAVID databases. Milk production, blood metabolites (non-esterified fatty acids, magnesium), and disease biomarkers (albumin, aspartate aminotransferase) did not differ greatly between healthy and SCE cows. In liver tissue of cows with SCE, alterations in gene expression revealed an activation of complement and coagulation cascade, steroid hormone biosynthesis, apoptosis, inflammation, oxidative stress, MAPK signaling, and the formation of fibrinogen complex. Bioinformatics analysis also revealed an inhibition of vitamin B3 and B6 metabolism with SCE. In adipose, the most activated pathways by SCE were nicotinate and nicotinamide metabolism, long-chain fatty acid transport, oxidative phosphorylation, inflammation, T cell and B cell receptor signaling, and mTOR signaling. Results indicate that SCE in dairy cattle during early lactation induces molecular alterations in liver and adipose tissue indicative of immune activation and cellular stress.

  1. Gene expression profiling of white adipose tissue reveals paternal transmission of proneness to obesity.

    Science.gov (United States)

    Morita, Sumiyo; Nakabayashi, Kazuhiko; Kawai, Tomoko; Hayashi, Keiko; Horii, Takuro; Kimura, Mika; Kamei, Yasutomi; Ogawa, Yoshihiro; Hata, Kenichiro; Hatada, Izuho

    2016-02-12

    Previously, we found that C57BL/6J (B6) mice are more prone to develop obesity than PWK mice. In addition, we analyzed reciprocal crosses between these mice and found that (PWK × B6) F1 mice, which have B6 fathers, are more likely to develop dietary obesity than (B6 × PWK) F1 mice, which have B6 mothers. These results suggested that diet-induced obesity is paternally transmitted. In this study, we performed transcriptome analysis of adipose tissues of B6, PWK, (PWK × B6) F1, and (B6 × PWK) F1 mice using next-generation sequencing. We found that paternal transmission of diet-induced obesity was correlated with genes involved in adipose tissue inflammation, metal ion transport, and cilia. Furthermore, we analyzed the imprinted genes expressed in white adipose tissue (WAT) and obesity. Expression of paternally expressed imprinted genes (PEGs) was negatively correlated with body weight, whereas expression of maternally expressed imprinted genes (MEGs) was positively correlated. In the obesity-prone B6 mice, expression of PEGs was down-regulated by a high-fat diet, suggesting that abnormally low expression of PEGs contributes to high-fat diet-induced obesity in B6 mice. In addition, using single-nucleotide polymorphisms that differ between B6 and PWK, we identified candidate imprinted genes in WAT.

  2. Expression profiling and structural characterization of microRNAs in adipose tissues of hibernating ground squirrels.

    Science.gov (United States)

    Wu, Cheng-Wei; Biggar, Kyle K; Storey, Kenneth B

    2014-12-01

    MicroRNAs (miRNAs) are small non-coding RNAs that are important in regulating metabolic stress. In this study, we determined the expression and structural characteristics of 20 miRNAs in brown (BAT) and white adipose tissue (WAT) during torpor in thirteen-lined ground squirrels. Using a modified stem-loop technique, we found that during torpor, expression of six miRNAs including let-7a, let-7b, miR-107, miR-150, miR-222 and miR-31 was significantly downregulated in WAT (Pstructure-influenced changes in pre-miRNA processing efficiency in the squirrel. As well, the expression of miRNA processing enzyme Dicer remained unchanged in both tissues during torpor. Overall, our findings suggest that changes of miRNA expression in adipose tissues may be linked to distinct biological roles in WAT and BAT during hibernation and may involve the regulation of signaling cascades.

  3. Comparative phytohormone profiles, lipid kinase and lipid phosphatase activities in barley aleurone, coleoptile, and root tissues.

    Science.gov (United States)

    Meringer, Maria V; Villasuso, Ana L; Pasquaré, Susana J; Giusto, Norma M; Machado, Estela E; Racagni, Graciela E

    2012-09-01

    We analyzed lipid kinase and lipid phosphatase activities and determined endogenous phytohormone levels by liquid chromatography-tandem mass spectrometry in root and coleoptile tissues following germination of barley (Hordeum vulgare) seeds. The enzymes showing highest activity in aleurone cells were diacylglycerol kinase (DAG-k, EC 2.7.1.107) and phosphatidate kinase (PA-k). The ratio of gibberellins (GAs) to abscisic acid (ABA) was 2-fold higher in aleurone than in coleoptile or root tissues. In coleoptiles, phosphatidylinositol 4-kinase (PI4-k, EC 2.7.1.67) showed the highest enzyme activity, and jasmonic acid (JA) level was higher than in aleurone. In roots, activities of PI4-k, DAG-k, and PA-k were similar, and salicylic acid (SA) showed the highest concentration. In the assays to evaluate the hydrolysis of DGPP (diacylglycerol pyrophosphate) and PA (phosphatidic acid) we observed that PA hydrolysis by LPPs (lipid phosphate phosphatases) was not modified; however, the diacylglycerol pyrophosphate phosphatase (DGPPase) was strikingly higher in coleoptile and root tissues than to aleurone. Relevance of these findings in terms of signaling responses and seedling growth is discussed.

  4. Epicardial and Subcutaneous Adipose Tissue Fatty Acids Profiles in Diabetic and Non-Diabetic Patients Candidate for Coronary Artery Bypass Graft

    OpenAIRE

    Masoud Pezeshkian; Mohammad-Reza Mahtabipour

    2013-01-01

    Introduction: We have recently shown that in high cholesterol-fed rabbits, the sensitivity of epicardial adipose tissue to changes in dietary fat is higher than that of subcutaneous adipose tissue. Although the effects of diabetes on epicardial adipose tissue thickness have been studied, the influence of diabetes on profile of epicardial free fatty acids (FFAs) has not been studied. The aim of this study is to investigate the effect of diabetes on the FFAs composition in serum and in the subc...

  5. Identification of genes showing differential expression profile associated with growth rate in skeletal muscle tissue of Landrace weanling pig

    Indian Academy of Sciences (India)

    YUUTA KOMATSU; SHIN SUKEGAWA; MAIYAMA SHITA; NAOKI KATSUDA; BIN TONG; TAKESHI OHTA; HIROYUKI KOSE; TAKAHISA YAMADA

    2016-06-01

    Suppression subtractive hybridization was used to identify genes showing differential expression profile associated withgrowth rate in skeletal muscle tissue of Landrace weanling pig. Two subtracted cDNA populations were generated from mus-culus longissimus muscle tissues of selected pigs with extreme expected breeding values at the age of 100 kg. Three upregu-lated genes (EEF1A2 ,TSG101andTTN) and six downregulated genes (ATP5B ,ATP5C1 ,COQ3 ,HADHA ,MYH1andMYH7)in pig with genetic propensity for higher growth rate were identified by sequence analysis of 12 differentially expressed clonesselected by differential screening following the generation of the subtracted cDNA population. Real-time PCR analysis con-firmed difference in expression profiles of the identified genes in musculus longissimus muscle tissues between the two Lan-drace weanling pig groups with divergent genetic propensity for growth rate. Further, differential expression of the identifiedgenes except for theTTNwas validated by Western blot analysis. Additionally, the eight genes other than theATP5C1co-localized with the same chromosomal positions as QTLs that have been previously identified for growth rate traits. Finally,the changes of expression predicted from gene function suggested association of upregulation of expression of theEEF1A2 ,TSG101andTTNgenes and downregulation of theATP5B ,ATP5C1 ,COQ3 ,HADHA ,MYH1andMYH7gene expressionwith increased growth rate. The identified genes will provide an important insight in understanding the molecular mechanismunderlying growth rate in Landrace pig breed.

  6. Identification of genes showing differential expression profile associated with growth rate in skeletal muscle tissue of Landrace weanling pig.

    Science.gov (United States)

    Komatsu, Yuuta; Sukegawa, Shin; Yamashita, Mai; Katsuda, Naoki; Tong, Bin; Ohta, Takeshi; Kose, Hiroyuki; Yamada, Takahisa

    2016-06-01

    Suppression subtractive hybridization was used to identify genes showing differential expression profile associated with growth rate in skeletal muscle tissue of Landrace weanling pig. Two subtracted cDNA populations were generated from musculus longissimus muscle tissues of selected pigs with extreme expected breeding values at the age of 100 kg. Three upregulated genes (EEF1A2, TSG101 and TTN) and six downregulated genes (ATP5B, ATP5C1, COQ3, HADHA, MYH1 and MYH7) in pig with genetic propensity for higher growth rate were identified by sequence analysis of 12 differentially expressed clones selected by differential screening following the generation of the subtracted cDNA population. Real-time PCR analysis confirmed difference in expression profiles of the identified genes in musculus longissimus muscle tissues between the two Landrace weanling pig groups with divergent genetic propensity for growth rate. Further, differential expression of the identified genes except for the TTN was validated by Western blot analysis. Additionally, the eight genes other than the ATP5C1 colocalized with the same chromosomal positions as QTLs that have been previously identified for growth rate traits. Finally, the changes of expression predicted from gene function suggested association of upregulation of expression of the EEF1A2, TSG101 and TTN genes and downregulation of the ATP5B, ATP5C1, COQ3, HADHA, MYH1 and MYH7 gene expression with increased growth rate. The identified genes will provide an important insight in understanding the molecular mechanism underlying growth rate in Landrace pig breed.

  7. Tissue-specific transcriptional profiling of iron-deficient and cadmium-stressed rice using laser capture microdissection

    Science.gov (United States)

    Ogo, Yuko; Kakei, Yusuke; Itai, Reiko Nakanishi; Kobayashi, Takanori; Nakanishi, Hiromi; Nishizawa, Naoko K

    2014-01-01

    Several metals are essential nutrients for plants. However, they become toxic at high levels and deleteriously affect crop yield and quality. We recently reported the spatial gene expression profiles of iron (Fe)-deficient and cadmium (Cd)-stressed rice using laser microdissection and microarray analysis. The roots of Fe-deficient and Cd-stressed rice were separated into the vascular bundle (VB), cortex (Cor), and epidermis plus exodermis (EP). In addition, vascular bundles from new and old leaves at the lowest node, which are important for metal distribution, were analyzed separately (newDC and oldDC, respectively). Genes expressed in a tissue-specific manner in the VB, Cor, EP, newDC, and oldDC formed large clusters. The genes upregulated in all of the VB, Cor, and EP by Fe deficiency formed a substantial cluster that was smaller than the tissue-specific clusters. Significant numbers of genes expressed in newDC or oldDC were also expressed in VB in roots, suggesting that vascular bundles in the lowest nodes and roots have a partially common function. The expression patterns of transporter families involved in metal homeostasis were investigated, and members of each family were either expressed differentially in each tissue or showed different responses to Fe deficiency. One potassium transporter gene, OsHAK22, was upregulated by Fe deficiency in VB, Cor, and EP, suggesting that OsHAK22 is involved in potassium transport associated with mugineic acids secretion. PMID:25763624

  8. Flavanol-Enriched Cocoa Powder Alters the Intestinal Microbiota, Tissue and Fluid Metabolite Profiles, and Intestinal Gene Expression in Pigs.

    Science.gov (United States)

    Jang, Saebyeol; Sun, Jianghao; Chen, Pei; Lakshman, Sukla; Molokin, Aleksey; Harnly, James M; Vinyard, Bryan T; Urban, Joseph F; Davis, Cindy D; Solano-Aguilar, Gloria

    2016-04-01

    Consumption of cocoa-derived polyphenols has been associated with several health benefits; however, their effects on the intestinal microbiome and related features of host intestinal health are not adequately understood. The objective of this study was to determine the effects of eating flavanol-enriched cocoa powder on the composition of the gut microbiota, tissue metabolite profiles, and intestinal immune status. Male pigs (5 mo old, 28 kg mean body weight) were supplemented with 0, 2.5, 10, or 20 g flavanol-enriched cocoa powder/d for 27 d. Metabolites in serum, urine, the proximal colon contents, liver, and adipose tissue; bacterial abundance in the intestinal contents and feces; and intestinal tissue gene expression of inflammatory markers and Toll-like receptors (TLRs) were then determined. O-methyl-epicatechin-glucuronide conjugates dose-dependently increased (Pcocoa powder. The concentration of 3-hydroxyphenylpropionic acid isomers in urine decreased as the dose of cocoa powder fed to pigs increased (75-85%,Pcocoa powder/d, respectively. Moreover, consumption of cocoa powder reducedTLR9gene expression in ileal Peyer's patches (67-80%,Pcocoa powder/d compared with pigs not supplemented with cocoa powder. This study demonstrates that consumption of cocoa powder by pigs can contribute to gut health by enhancing the abundance ofLactobacillusandBifidobacteriumspecies and modulating markers of localized intestinal immunity. © 2016 American Society for Nutrition.

  9. L-Rhamnose-binding lectins (RBLs) in channel catfish, Ictalurus punctatus: Characterization and expression profiling in mucosal tissues.

    Science.gov (United States)

    Thongda, Wilawan; Li, Chao; Luo, Yupeng; Beck, Benjamin H; Peatman, Eric

    2014-06-01

    Rhamnose-binding lectins (RBLs) have recently emerged as important molecules in the context of innate immunity in teleost fishes. Previously, using RNA-seq technology, we observed marked up-regulation of a RBL in channel catfish (Ictalurus punctatus) gill following a challenge with the bacterial pathogen Flavobacterium columnare. Furthermore, the magnitude of RBL up-regulation positively correlated with disease susceptibility. Moving forward from these findings, we wished to more broadly understand RBL function, diversity, and expression kinetics in channel catfish. Therefore, in the present study we characterized the RBL gene family present in select channel catfish tissues and profiled family member expression after challenge with two different Gram-negative bacterial pathogens. Here, six RBLs were identified from channel catfish and were designated IpRBL1a, IpRBL1b, IpRBL1c, IpRBL3a, IpRBL3b, and IpRBL5a. These RBLs contained carbohydrate recognition domains (CRD) ranging from one to three domains and each CRD contained the conserved motifs of -YGR- and -DPC-. Despite a level of structural conservation, the catfish RBLs showed low full-length identity with RBLs from outside the order Siluriformes. IpRBL expression after bacterial infection varied depending on both pathogen and tissue type, suggesting that IpRBLs may exert disparate functions or exhibit distinct tissue-selective roles in the host immune response to bacterial pathogens.

  10. Age and diet affect gene expression profiles in canine liver tissue.

    Directory of Open Access Journals (Sweden)

    Dong Yong Kil

    Full Text Available BACKGROUND: The liver plays a central role in nutrient and xenobiotic metabolism, but its functionality declines with age. Senior dogs suffer from many of the chronic hepatic diseases as elderly humans, with age-related alterations in liver function influenced by diet. However, a large-scale molecular analysis of the liver tissue as affected by age and diet has not been reported in dogs. METHODOLOGY/PRINCIPAL FINDINGS: Liver tissue samples were collected from six senior (12-year old and six young adult (1-year old female beagles fed an animal protein-based diet (APB or a plant protein-based diet (PPB for 12 months. Total RNA in the liver tissue was extracted and hybridized to Affymetrix GeneChip® Canine Genome Arrays. Using a 2.0-fold cutoff and false discovery rate <0.10, our results indicated that expression of 234 genes was altered by age, while 137 genes were differentially expressed by diet. Based on functional classification, genes affected by age and/or diet were involved in cellular development, nutrient metabolism, and signal transduction. In general, gene expression suggested that senior dogs had an increased risk of the progression of liver disease and dysfunction, as observed in aged humans and rodents. In particular for aged liver, genes related to inflammation, oxidative stress, and glycolysis were up-regulated, whereas genes related to regeneration, xenobiotic metabolism, and cholesterol trafficking were down-regulated. Diet-associated changes in gene expression were more common in young adult dogs (33 genes as compared to senior dogs (3 genes. CONCLUSION: Our results provide molecular insight pertaining to the aged canine liver and its predisposition to disease and abnormalities. Therefore, our data may aid in future research pertaining to age-associated alterations in hepatic function or identification of potential targets for nutritional management as a means to decrease incidence of age-dependent liver dysfunction.

  11. Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar.

    Science.gov (United States)

    Cribbin, Kayla M; Quackenbush, Corey R; Taylor, Kyle; Arias-Rodriguez, Lenin; Kelley, Joanna L

    2017-04-07

    The tropical gar (Atractosteus tropicus) is the southernmost species of the seven extant species of gar fishes in the world. In Mexico and Central America, the species is an important food source due to its nutritional quality and low price. Despite its regional importance and increasing concerns about overexploitation and habitat degradation, basic genetic information on the tropical gar is lacking. Determining genetic information on the tropical gar is important for the sustainable management of wild populations, implementation of best practices in aquaculture settings, evolutionary studies of ancient lineages, and an understanding of sex-specific gene expression. In this study, the transcriptome of the tropical gar was sequenced and assembled de novo using tissues from three males and three females using Illumina sequencing technology. Sex-specific and highly differentially expressed transcripts in brain and muscle tissues between adult males and females were subsequently identified. The transcriptome was assembled de novo resulting in 80,611 transcripts with a contig N50 of 3,355 base pairs and over 168 kilobases in total length. Male muscle, brain, and gonad as well as female muscle and brain were included in the assembly. The assembled transcriptome was annotated to identify the putative function of expressed transcripts using Trinotate and SwissProt, a database of well-annotated proteins. The brain and muscle datasets were then aligned to the assembled transcriptome to identify transcripts that were differentially expressed between males and females. The contrast between male and female brain identified 109 transcripts from 106 genes that were significantly differentially expressed. In the muscle comparison, 82 transcripts from 80 genes were identified with evidence for significant differential expression. Almost all genes identified as differentially expressed were sex-specific. The differentially expressed transcripts were enriched for genes involved in

  12. Diagnostic and prognostic gene expression signatures in 177 soft tissue sarcomas: hypoxia-induced transcription profile signifies metastatic potential

    Directory of Open Access Journals (Sweden)

    Bendahl Pär-Ola

    2007-03-01

    Full Text Available Abstract Background Soft tissue sarcoma (STS diagnosis is challenging because of a multitude of histopathological subtypes, different genetic characteristics, and frequent intratumoral pleomorphism. One-third of STS metastasize and current risk-stratification is suboptimal, therefore, novel diagnostic and prognostic markers would be clinically valuable. We assessed the diagnostic and prognostic value of array-based gene expression profiles using 27 k cDNA microarrays in 177, mainly high-grade, STS of 13 histopathological subtypes. Results Unsupervised analysis resulted in two major clusters – one mainly containing STS characterized by type-specific genetic alterations and the other with a predominance of genetically complex and pleomorphic STS. Synovial sarcomas, myxoid/round-cell liposarcomas, and gastrointestinal stromal tumors clustered tightly within the former cluster and discriminatory signatures for these were characterized by developmental genes from the EGFR, FGFR, Wnt, Notch, Hedgehog, RAR and KIT signaling pathways. The more pleomorphic STS subtypes, e.g. leiomyosarcoma, malignant fibrous histiocytoma/undifferentiated pleomorphic sarcoma and dedifferentiated/pleomorphic liposarcoma, were part of the latter cluster and were characterized by relatively heterogeneous profiles, although subclusters herein were identified. A prognostic signature partly characterized by hypoxia-related genes was identified among 89 genetically complex pleomorphic primary STS and could, in a multivariate analysis including established prognostic markers, independently predict the risk of metastasis with a hazard ratio of 2.2 (P = 0.04. Conclusion Diagnostic gene expression profiles linking signaling pathways to the different STS subtypes were demonstrated and a hypoxia-induced metastatic profile was identified in the pleomorphic, high-grade STS. These findings verify diagnostic utility and application of expression data for improved selection of high

  13. Effects of activator and high-pull headgear combination therapy: skeletal, dentoalveolar, and soft tissue profile changes.

    Science.gov (United States)

    Marşan, Gülnaz

    2007-04-01

    The aim of this study was to evaluate skeletal, dentoalveolar, and soft tissue profile changes with activator and high-pull headgear combination therapy in patients with Class II malocclusions caused by maxillary prognathism and mandibular retrognathism. The subjects, all in the mixed dentition, were selected from a single centre and were divided into two groups: 28 patients were treated with an incisor double capping activator and a high-pull headgear combination appliance (13 girls, 15 boys mean chronological age 11.7 +/- 1.2 years, skeletal age 12.1 +/- 1.4 years) and an untreated group of 28 subjects (14 girls, 14 boys mean chronological mean age 11.9 +/- 1.1 years, skeletal age 12.3 +/- 1.3 years). The skeletal, dentoalveolar, and soft tissue profile changes that occurred were compared on lateral cephalograms taken before treatment (T0) and after 1.1 +/- 0.3 years when the combination appliance was removed (T1). In the control group, the radiographs were obtained at the start (T0) and after an observation period 1.2 +/- 0.4 years (T1). Statistical analysis was undertaken with Wilcoxon's ranked-sum test for intra-group comparisons and differences between groups with t-test and Bonferroni's test at a level of significance of P high-pull headgear combination treatment in these growing patients resulted in a correction of the skeletal Class II relationship (ANB -3.4 degrees), a restriction of maxillary growth (SNA -2.0 degrees, OLp-A -2.3 mm), an advancement of the mandibular structures (SNB +2.6 degrees, FH-NPg +2.3 degrees, OLp-B +2.7 mm, OLp-Pg +2.2 mm), an increase in lower face height (ANS-Me +3.9 mm), a correction of the overjet (-5.4 mm), an improvement in overbite (-2.2 mm), uprighting of the maxillary incisors (U1-FH -5.3 degrees, OLp-U1 -2.5 mm), protrusion of the mandibular incisors (IMPA +2.0 degrees, OLp-L1 +2.7 mm), and a correction of the dental Class II malocclusion (OLp-L6 +3.5 mm). The soft tissue profile changes were a correction of facial

  14. Molecular profiling of signalling pathways in formalin-fixed and paraffin-embedded cancer tissues.

    Science.gov (United States)

    Berg, Daniela; Hipp, Susanne; Malinowsky, Katharina; Böllner, Claudia; Becker, Karl-Friedrich

    2010-01-01

    In most hospitals word-wide, histopathological cancer diagnosis is currently based on formalin-fixed and paraffin-embedded (FFPE) tissues. In the last few years new approaches and developments in patient-tailored cancer therapy have raised the need to select more precisely those patients, who will respond to personalised treatments. The most efficient way for optimal therapy and patient selection is probably to provide a tumour-specific protein network portrait prior to treatment. The discovery and characterisation of deregulated signalling molecules (e.g. human epidermal growth factor receptor 2, mitogen-activated protein kinases) are very promising candidates for the identification of new suitable therapy targets and for the selection of those patients who will receive the greatest benefit from individualised treatments. The reverse phase protein array (RPPA) is a promising new technology that allows quick, precise and simultaneous analysis of many components of a network. Importantly it requires only limited amounts of routine clinical material (e.g. FFPE biopsies) and can be used for absolute protein measurements. We and other research groups have described successful protein extraction from routine FFPE tissues. In this manuscript we show how these recent developments might facilitate the implementation of RPPA in clinical trials and routine settings.

  15. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.

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    Craig April

    Full Text Available BACKGROUND: We have developed a gene expression assay (Whole-Genome DASL, capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE specimens. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrated a similar level of sensitivity in gene detection between matched fresh-frozen (FF and FFPE samples, with the number and overlap of probes detected in the FFPE samples being approximately 88% and 95% of that in the corresponding FF samples, respectively; 74% of the differentially expressed probes overlapped between the FF and FFPE pairs. The WG-DASL assay is also able to detect 1.3-1.5 and 1.5-2 -fold changes in intact and FFPE samples, respectively. The dynamic range for the assay is approximately 3 logs. Comparing the WG-DASL assay with an in vitro transcription-based labeling method yielded fold-change correlations of R(2 approximately 0.83, while fold-change comparisons with quantitative RT-PCR assays yielded R(2 approximately 0.86 and R(2 approximately 0.55 for intact and FFPE samples, respectively. Additionally, the WG-DASL assay yielded high self-correlations (R(2>0.98 with low intact RNA inputs ranging from 1 ng to 100 ng; reproducible expression profiles were also obtained with 250 pg total RNA (R(2 approximately 0.92, with approximately 71% of the probes detected in 100 ng total RNA also detected at the 250 pg level. When FFPE samples were assayed, 1 ng total RNA yielded self-correlations of R(2 approximately 0.80, while still maintaining a correlation of R(2 approximately 0.75 with standard FFPE inputs (200 ng. CONCLUSIONS/SIGNIFICANCE: Taken together, these results show that WG-DASL assay provides a reliable platform for genome-wide expression profiling in archived materials. It also possesses utility within clinical settings where only limited quantities of samples may be available (e.g. microdissected material or when minimally invasive procedures are performed (e

  16. Correction of Class II malocclusion and soft tissue profile in an adult patient

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    Aditi Gaur

    2016-01-01

    Full Text Available Treatment of Class II malocclusion in nongrowing individuals is a challenging situation for the clinician. Class II malocclusion with bialveolar protrusion often dictates premolar extractions with maximum anchorage. The present article describes the case of an adult female with skeletal Class II malocclusion, bimaxillary protrusion, increased overjet, deep bite, lip protrusion, everted lower lip, deep mentolabial sulcus, and lip incompetence. To correct the malocclusion, all four first premolars were extracted. Direct anchorage from miniscrews was used for retraction of the anterior segment. The mandibular buccal segment was protracted into the extraction space using Class II mechanics. Ideal Class I canine and molar relation were achieved in 24 months. There was a significant improvement in facial profile and smile esthetics of the patient.

  17. Metastatic Tissue Proteomic Profiling Predicts 5-Year Outcomes in Patients with Colorectal Liver Metastases

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    Santiago Marfà

    2016-10-01

    Full Text Available Colorectal cancer (CRC is one of the most common cancers in the developed countries, and nearly 70% of patients with CRC develop colorectal liver metastases (CRLMs. During the last decades, several scores have been proposed to predict recurrence after CRLM resection. However, these risk scoring systems do not accurately reflect the prognosis of these patients. Therefore, this investigation was designed to identify a proteomic profile in human hepatic tumor samples to classify patients with CRLM as “mild” or “severe” based on the 5-year survival. The study was performed on 85 CRLM tumor samples. Firstly, to evaluate any distinct tumor proteomic signatures between mild and severe CRLM patients, a training group of 57 CRLM tumor samples was characterized by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, and a classification and regression tree (CART analysis was subsequently performed. Finally, 28 CRLM tumor samples were used to confirm and validate the results obtained. Based on all the protein peaks detected in the training group, the CART analysis was generated, and four peaks were considered to be the most relevant to construct a diagnostic algorithm. Indeed, the multivariate model yielded a sensitivity of 85.7% and a specificity of 86.1%, respectively. In addition, the receiver operating characteristic (ROC curve showed an excellent diagnostic accuracy to discriminate mild from severe CRLM patients (area under the ROC: 0.903. Finally, the validation process yielded a sensitivity and specificity of 68.8% and 83.3%, respectively. We identified a proteomic profile potentially useful to determine the prognosis of CRLM patients based on the 5-year survival.

  18. Proteomic Comparison of Two—Dimensional Gel Electrophoresis Profiles from Human Lung Squamous Carcinoma and Normal Bronchial Epithelial Tissues

    Institute of Scientific and Technical Information of China (English)

    CuiLi; XianquanZhan; MaoyuLi; XiaoyingWu; FengLi; JianlingLi; ZhiqiangXiao; ZhuchuChen; XuepingFeng; PingChen; JingyunXie; SongpingLiang

    2003-01-01

    Differential proteome profiles of human lung squamous carcinoma tissue compared to paired tumor-adjacent normal bronchial epithelial tissue were established and analyzed by means of immobilized pH gradient-based two-dimensional polyacrylamide gel electrophoresis(2-D PAGE)and matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF-MS).The results showed that well-resolved,reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were obtained under the condition of 0.75-mg protein-load.The average deviation of spot position was 0.733±0.101 mm in IEF direction,and 0.925±0.207mm in SDS-PAGE direction.For tumor tissue,a total of 1241±88 spots were detected,987±65 spots were matched with an average matching rate of 79.5%.For control,a total of 1190±72 spots were detected,and 875±48 spots were matched with an average matching rate of 73.5%.A total of 864±34 spots were matched between tumors and controls.Forth-three differential proteins were characterized:some proteins were related to oncogenes,and others involved in the regulation of cell cycle and signal transduction.It is suggested that the differential proteomic approach is valuable for mass identification of differentially expressed proteins involved in lung carcinogenesis.These data will be used to establish human lung cancer proteome database to further study human lung squamous carcinoma.

  19. Expression Profiling and Structural Characterization of MicroRNAs in Adipose Tissues of Hibernating Ground Squirrels

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    Cheng-Wei Wu

    2014-12-01

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs that are important in regulating metabolic stress. In this study, we determined the expression and structural characteristics of 20 miRNAs in brown (BAT and white adipose tissue (WAT during torpor in thirteen-lined ground squirrels. Using a modified stem-loop technique, we found that during torpor, expression of six miRNAs including let-7a, let-7b, miR-107, miR-150, miR-222 and miR-31 was significantly downregulated in WAT (P < 0.05, which was 16%–54% of euthermic non-torpid control squirrels, whereas expression of three miRNAs including miR-143, miR-200a and miR-519d was found to be upregulated by 1.32–2.34-fold. Similarly, expression of more miRNAs was downregulated in BAT during torpor. We detected reduced expression of 6 miRNAs including miR-103a, miR-107, miR-125b, miR-21, miR-221 and miR-31 (48%–70% of control, while only expression of miR-138 was significantly upregulated (2.91 ± 0.8-fold of the control, P < 0.05. Interestingly, miRNAs found to be downregulated in WAT during torpor were similar to those dysregulated in obese humans for increased adipogenesis, whereas miRNAs with altered expression in BAT during torpor were linked to mitochondrial β-oxidation. miRPath target prediction analysis showed that miRNAs downregulated in both WAT and BAT were associated with the regulation of mitogen-activated protein kinase (MAPK signaling, while the miRNAs upregulated in WAT were linked to transforming growth factor β (TGFβ signaling. Compared to mouse sequences, no unique nucleotide substitutions within the stem-loop region were discovered for the associated pre-miRNAs for the miRNAs used in this study, suggesting no structure-influenced changes in pre-miRNA processing efficiency in the squirrel. As well, the expression of miRNA processing enzyme Dicer remained unchanged in both tissues during torpor. Overall, our findings suggest that changes of miRNA expression in adipose tissues may

  20. Expression Profiling and Structural Characterization of MicroRNAs in Adipose Tissues of Hibernating Ground Squirrels

    Institute of Scientific and Technical Information of China (English)

    Cheng-Wei Wu; Kyle K. Biggar; Kenneth B. Storey

    2014-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs that are important in regulating metabolic stress. In this study, we determined the expression and structural characteristics of 20 miRNAs in brown (BAT) and white adipose tissue (WAT) during torpor in thirteen-lined ground squirrels. Using a modified stem-loop technique, we found that during torpor, expression of six miRNAs including let-7a, let-7b, miR-107, miR-150, miR-222 and miR-31 was significantly downregulated in WAT (P < 0.05), which was 16%–54% of euthermic non-torpid control squirrels, whereas expression of three miRNAs including miR-143, miR-200a and miR-519d was found to be upregulated by 1.32–2.34-fold. Similarly, expression of more miRNAs was downregulated in BAT during torpor. We detected reduced expression of 6 miRNAs including miR-103a, miR- 107, miR-125b, miR-21, miR-221 and miR-31 (48%–70% of control), while only expression of miR-138 was significantly upregulated (2.91 ± 0.8-fold of the control, P <0.05). Interestingly, miRNAs found to be downregulated in WAT during torpor were similar to those dysregulated in obese humans for increased adipogenesis, whereas miRNAs with altered expression in BAT during torpor were linked to mitochondrial b-oxidation. miRPath target prediction analysis showed that miRNAs downregulated in both WAT and BAT were associated with the regulation of mitogen- activated protein kinase (MAPK) signaling, while the miRNAs upregulated in WAT were linked to transforming growth factor b (TGFb) signaling. Compared to mouse sequences, no unique nucleotide substitutions within the stem-loop region were discovered for the associated pre-miRNAs for the miRNAs used in this study, suggesting no structure-influenced changes in pre-miRNA processing efficiency in the squirrel. As well, the expression of miRNA processing enzyme Dicer remained unchanged in both tissues during torpor. Overall, our findings suggest that changes of miRNA expression in adipose tissues may be linked to

  1. Chemical profiling of Jatropha tissues under different torrefaction conditions: application to biomass waste recovery.

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    Taiji Watanabe

    Full Text Available Gradual depletion of the world petroleum reserves and the impact of environmental pollution highlight the importance of developing alternative energy resources such as plant biomass. To address these issues, intensive research has focused on the plant Jatropha curcas, which serves as a rich source of biodiesel because of its high seed oil content. However, producing biodiesel from Jatropha generates large amounts of biomass waste that are difficult to use. Therefore, the objective of our research was to analyze the effects of different conditions of torrefaction on Jatropha biomass. Six different types of Jatropha tissues (seed coat, kernel, stem, xylem, bark, and leaf were torrefied at four different temperature conditions (200°C, 250°C, 300°C, and 350°C, and changes in the metabolite composition of the torrefied products were determined by Fourier transform-infrared spectroscopy and nuclear magnetic resonance analyses. Cellulose was gradually converted to oligosaccharides in the temperature range of 200°C-300°C and completely degraded at 350°C. Hemicellulose residues showed different degradation patterns depending on the tissue, whereas glucuronoxylan efficiently decomposed between 300°C and 350°C. Heat-induced depolymerization of starch to maltodextrin started between 200°C and 250°C, and oligomer sugar structure degradation occurred at higher temperatures. Lignin degraded at each temperature, e.g., syringyl (S degraded at lower temperatures than guaiacyl (G. Finally, the toxic compound phorbol ester degraded gradually starting at 235°C and efficiently just below 300°C. These results suggest that torrefaction is a feasible treatment for further processing of residual biomass to biorefinery stock or fertilizer.

  2. Chemical profiling of Jatropha tissues under different torrefaction conditions: application to biomass waste recovery.

    Science.gov (United States)

    Watanabe, Taiji; Shino, Amiu; Akashi, Kinya; Kikuchi, Jun

    2014-01-01

    Gradual depletion of the world petroleum reserves and the impact of environmental pollution highlight the importance of developing alternative energy resources such as plant biomass. To address these issues, intensive research has focused on the plant Jatropha curcas, which serves as a rich source of biodiesel because of its high seed oil content. However, producing biodiesel from Jatropha generates large amounts of biomass waste that are difficult to use. Therefore, the objective of our research was to analyze the effects of different conditions of torrefaction on Jatropha biomass. Six different types of Jatropha tissues (seed coat, kernel, stem, xylem, bark, and leaf) were torrefied at four different temperature conditions (200°C, 250°C, 300°C, and 350°C), and changes in the metabolite composition of the torrefied products were determined by Fourier transform-infrared spectroscopy and nuclear magnetic resonance analyses. Cellulose was gradually converted to oligosaccharides in the temperature range of 200°C-300°C and completely degraded at 350°C. Hemicellulose residues showed different degradation patterns depending on the tissue, whereas glucuronoxylan efficiently decomposed between 300°C and 350°C. Heat-induced depolymerization of starch to maltodextrin started between 200°C and 250°C, and oligomer sugar structure degradation occurred at higher temperatures. Lignin degraded at each temperature, e.g., syringyl (S) degraded at lower temperatures than guaiacyl (G). Finally, the toxic compound phorbol ester degraded gradually starting at 235°C and efficiently just below 300°C. These results suggest that torrefaction is a feasible treatment for further processing of residual biomass to biorefinery stock or fertilizer.

  3. Tissue-Specific Transcriptome Profiling of Plutella Xylostella Third Instar Larval Midgut

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    Wen Xie, Yanyuan Lei, Wei Fu, Zhongxia Yang, Xun Zhu, Zhaojiang Guo, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xuguo Zhou, Youjun Zhang

    2012-01-01

    Full Text Available The larval midgut of diamondback moth, Plutella xylostella, is a dynamic tissue that interfaces with a diverse array of physiological and toxicological processes, including nutrient digestion and allocation, xenobiotic detoxification, innate and adaptive immune response, and pathogen defense. Despite its enormous agricultural importance, the genomic resources for P. xylostella are surprisingly scarce. In this study, a Bt resistant P. xylostella strain was subjected to the in-depth transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes in the P. xylostella larval midgut.Using Illumina deep sequencing, we obtained roughly 40 million reads containing approximately 3.6 gigabases of sequence data. De novo assembly generated 63,312 ESTs with an average read length of 416bp, and approximately half of the P. xylostella sequences (45.4%, 28,768 showed similarity to the non-redundant database in GenBank with a cut-off E-value below 10-5. Among them, 11,092 unigenes were assigned to one or multiple GO terms and 16,732 unigenes were assigned to 226 specific pathways. In-depth analysis indentified genes putatively involved in insecticide resistance, nutrient digestion, and innate immune defense. Besides conventional detoxification enzymes and insecticide targets, novel genes, including 28 chymotrypsins and 53 ABC transporters, have been uncovered in the P. xylostella larval midgut transcriptome; which are potentially linked to the Bt toxicity and resistance. Furthermore, an unexpectedly high number of ESTs, including 46 serpins and 7 lysozymes, were predicted to be involved in the immune defense.As the first tissue-specific transcriptome analysis of P. xylostella, this study sheds light on the molecular understanding of insecticide resistance, especially Bt resistance in an agriculturally important insect pest, and lays the foundation for future functional genomics research. In

  4. An Assessment of the Utility of Tissue Smears in Rapid Cancer Profiling with Desorption Electrospray Ionization Mass Spectrometry (DESI-MS)

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    Woolman, Michael; Tata, Alessandra; Bluemke, Emma; Dara, Delaram; Ginsberg, Howard J.; Zarrine-Afsar, Arash

    2017-01-01

    Mass spectrometry imaging with desorption electrospray ionization mass spectrometry (DESI-MS) is used to characterize cancer from ex vivo slices of tissues. The process is time-consuming. The use of tissue smears for DESI-MS analysis has been proposed as it eliminates the time required to snap-freeze and section the tissue. To assess the utility of tissue smears for rapid cancer characterization, principal component analysis (PCA) was performed to evaluate the concordance between DESI-MS profiles of breast cancer from tissue slices and smears prepared on various surfaces. PCA suggested no statistical discrimination between DESI-MS profiles of tissue sections and tissue smears prepared on glass, polytetrafluoroethylene (PTFE), and porous PTFE. However, the abundances of cancer biomarker ions varied between sections and smears, with DESI-MS analysis of tissue sections yielding higher ion abundances of cancer biomarkers compared with smears. Coefficient of variance (CV) analysis suggests DESI-MS profiles from tissue smears are as reproducible as the ones from tissue sections. The limit of detection with smear samples from single pixel analysis is comparable to tissue sections that average the signal from a tissue area of 0.01 mm2. The smears prepared on the PTFE surface possessed a higher degree of homogeneity compared with the smears prepared on the glass surface. This allowed single MS scans ( 1 s) from random positions across the surface of the smear to be used in rapid cancer typing with good reproducibility, providing pathologic information for cancer typing at speeds suitable for clinical utility.

  5. Comparative analysis of the expression profile of Wnk1 and Wnk1/Hsn2 splice variants in developing and adult mouse tissues.

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    Masoud Shekarabi

    Full Text Available The With No lysine (K family of serine/threonine kinase (WNK defines a small family of kinases with significant roles in ion homeostasis. WNK1 has been shown to have different isoforms due to what seems to be largely tissue specific splicing. Here, we used two distinct in situ hybridization riboprobes on developing and adult mouse tissues to make a comparative analysis of Wnk1 and its sensory associated splice isoform, Wnk1/Hsn2. The hybridization signals in developing mouse tissues, which were prepared at embryonic day e10.5 and e12.5, revealed a homogenous expression profile with both probes. At e15.5 and in the newborn mouse, the two probes revealed different expression profiles with prominent signals in nervous system tissues and also other tissues such as kidney, thymus and testis. In adult mouse tissues, the two expression profiles appeared even more restricted to the nervous tissues, kidney, thymus and testis, with no detectable signal in the other tissues. Throughout the nervous system, sensory tissues, as well as in Cornu Ammonis 1 (CA1, CA2 and CA3 areas of the hippocampus, were strongly labeled with both probes. Hybridization signals were also strongly detected in Schwann and supporting satellite cells. Our results show that the expression profiles of Wnk1 isoforms change during the development, and that the expression of the Wnk1 splice variant containing the Hsn2 exon is prominent during developing and in adult mouse tissues, suggesting its important role in the development and maintenance of the nervous system.

  6. B-cell subpopulations from normal human secondary lymphoid tissues with specific gene expression profiles and phenotypes

    DEFF Research Database (Denmark)

    Johnsen, Hans Erik; Schmitz, Alexander; Perez Andres, Martin;

    In order to improve insights into the B-cell biology and thereby B-cell myelomagenesis we have established a MSCNET standard for multiparametric flow cytometry (MFC) and cell sorting (FACS) for subsequent genetic analysis. The material analysed was fresh tonsils, blood and bone marrow. The method...... included homogenization, isolation of mononuclear cells, MFC and FACS sorting using multicolour fluorescence single tube panels.of antibodies against surface molecules as CD10/20/27/38/45, supplemented with tissue related antibodies. Isolated B-cell subpopulations were evaluated by morphological inspection...... and single gene expression analysis (qRT-PCR) for transcription factors as well as global gene expression profiling (GEP; GeneChip Human Exon 1.0 ST Array). For example for tonsils, based on the immunophenotypic presentation (including CD3/44/CXCR4 in the panel), B-cell subsets were identified and sorted...

  7. Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling

    DEFF Research Database (Denmark)

    Basse, Astrid L.; Dixen, Karen; Yadav, Rachita

    2015-01-01

    Background: Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). Results: We analyzed the postnatal transformation of adipose in sheep....... Conclusions: Using global gene expression profiling of the postnatal BAT to WAT transformation in sheep, we provide novel insight into adipose tissue plasticity in a large mammal, including identification of novel transcriptional components linked to adipose tissue remodeling. Moreover, our data set provides...

  8. Discovery of porcine microRNAs and profiling from skeletal muscle tissues during development.

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    Ting-Hua Huang

    Full Text Available MiRNAs (microRNAs play critical roles in many important biological processes such as growth and development in mammals. In this study, we identified hundreds of porcine miRNA candidates through in silico prediction and analyzed their expression in developing skeletal muscle using microarray. Microarray screening using RNA samples prepared from a 33-day whole embryo and an extra embryo membrane validated 296 of the predicted candidates. Comparative expression profiling across samples of longissimus muscle collected from 33-day and 65-day post-gestation fetuses, as well as adult pigs, identified 140 differentially expressed miRNAs amongst the age groups investigated. The differentially expressed miRNAs showed seven distinctive types of expression patterns, suggesting possible involvement in certain biological processes. Five of the differentially expressed miRNAs were validated using real-time PCR. In silico analysis of the miRNA-mRNA interaction sites suggested that the potential mRNA targets of the differentially expressed miRNAs may play important roles in muscle growth and development.

  9. Human epicardial adipose tissue expresses a pathogenic profile of adipocytokines in patients with cardiovascular disease

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    Kumar Sudhesh

    2006-01-01

    Full Text Available Abstract Introduction Inflammation contributes to cardiovascular disease and is exacerbated with increased adiposity, particularly omental adiposity; however, the role of epicardial fat is poorly understood. Methods For these studies the expression of inflammatory markers was assessed in epicardial fat biopsies from coronary artery bypass grafting (CABG patients using quantitative RT-PCR. Further, the effects of chronic medications, including statins, as well as peri-operative glucose, insulin and potassium infusion, on gene expression were also assessed. Circulating resistin, CRP, adiponectin and leptin levels were determined to assess inflammation. Results The expression of adiponectin, resistin and other adipocytokine mRNAs were comparable to that in omental fat. Epicardial CD45 expression was significantly higher than control depots (p Conclusion Epicardial and omental fat exhibit a broadly comparable pathogenic mRNA profile, this may arise in part from macrophage infiltration into the epicardial fat. This study highlights that chronic inflammation occurs locally as well as systemically potentially contributing further to the pathogenesis of coronary artery disease.

  10. Profiling of Disease-Related Metabolites in Grapevine Internode Tissues Infected with Agrobacterium vitis

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    Sung-Min Jung

    2016-12-01

    Full Text Available Green shoot cuttings of 10 different grapevine species were inoculated with Agrobacterium vitis to find disease-related metabolites in the grapevine. Crown galls formed 60 days after inoculation varied in gall severity (GS evaluated by gall incidence (GI and gall diameter (GD, which were classified into three response types as RR (low GI and small GD, SR (high GI and small GD, and SS (high GI and large GD, corresponding to resistant, moderately resistant, and susceptible responses, respectively. In this, 4, 4, and 2 Vitis species were classified into RR, SR, and SS, respectively. Gas chromatography mass spectrometry (GC-MS analysis of the grapevine stem metabolites with A. vitis infection showed 134 metabolites in various compound classes critically occurred, which were differentially clustered with the response types by the principal component analysis. Multivariate analysis of the metabolite profile revealed that 11 metabolites increased significantly in relation to the response types, mostly at post-inoculation stages, more prevalently (8 metabolites at two days after inoculation than other stages, and more related to SS (7 metabolites than RR (3 metabolites or SR (one metabolite. This suggests most of the disease-related metabolites may be rarely pre-existing but mostly induced by pathogen infection largely for facilitating gall development except stilbene compound resveratrol, a phytoalexin that may be involved in the resistance response. All of these aspects may be used for the selection of resistant grapevine cultivars and their rootstocks for the control of the crown gall disease of the grapevine.

  11. Gene expression profiling of human breast tissue samples using SAGE-Seq.

    Science.gov (United States)

    Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

    2010-12-01

    We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

  12. The cloning, genomic organization and tissue expression profile of the human DLG5 gene

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    Gibbs Richard A

    2002-02-01

    Full Text Available Abstract Background Familial atrial fibrillation, an autosomal dominant disease, was previously mapped to chromosome 10q22. One of the genes mapped to the 10q22 region is DLG5, a member of the MAGUKs (Membrane Associated Gyanylate Kinase family which mediates intracellular signaling. Only a partial cDNA was available for DLG5. To exclude potential disease inducing mutations, it was necessary to obtain a complete cDNA and genomic sequence of the gene. Methods The Northern Blot analysis performed using 3' UTR of this gene indicated the transcript size to be about 7.2 KB. Using race technique and library screening the entire cDNA was cloned. This gene was evaluated by sequencing the coding region and splice functions in normal and affected family members with familial atrial fibrillation. Furthermore, haploid cell lines from affected patients were generated and analyzed for deletions that may have been missed by PCR. Results We identified two distinct alternately spliced transcripts of this gene. The genomic sequence of the DLG5 gene spanned 79 KB with 32 exons and was shown to have ubiquitous human tissue expression including placenta, heart, skeletal muscle, liver and pancreas. Conclusions The entire cDNA of DLG5 was identified, sequenced and its genomic organization determined.

  13. Gene expression profiling of RNA extracted from FFPE tissues: NuGEN technologies' whole-transcriptome amplification system.

    Science.gov (United States)

    Turner, Leah; Heath, Joe Don; Kurn, Nurith

    2011-01-01

    Gene expression profiling of RNA isolated from formalin fixed, paraffin-embedded (FFPE) tissue samples has been historically challenging. Yet FFPE samples are sought-after because of the in-depth retrospective records typically associated with them rendering these samples a valuable resource for translational medicine studies. Extensive degradation, chemical modifications, and cross-linking have made it difficult to isolate RNA of sufficient quality required for large-scale gene expression profiling studies. NuGEN Technologies' WT-Ovation™ FFPE System linearly amplifies RNA from FFPE samples through a robust and simple whole-transcriptome approach using as little as 50 ng total RNA isolated from FFPE samples. The amplified material may be labeled with validated kits and/or protocols from NuGEN for analysis on any of the major gene expression microarray platforms, including: Affymetrix, Agilent, and Illumina gene expression arrays. Results compare well with those obtained using RNA from fresh-frozen samples. RNA quality from FFPE samples varies significantly and neither sample age nor sample size analysis via gel electrophoresis or the Agilent Bioanalyzer system accurately predict materials suitable for amplification. Therefore, NuGEN has validated a correlative qPCR-based analytical method for the RNA derived from FFPE samples which effectively predicts array results. The NuGEN approach enables fast and successful analysis of samples previously thought to be too degraded for gene expression analysis.

  14. Differential expression profiling between the relative normal and dystrophic muscle tissues from the same LGMD patient

    Directory of Open Access Journals (Sweden)

    Yang Wei

    2006-12-01

    Full Text Available Abstract Background Limb-girdle muscular dystrophy (LGMD is a group of heterogeneous muscular disorders with autosomal dominant and recessive inheritance, in which the pelvic or shoulder girdle musculature is predominantly or primarily involved. Although analysis of the defective proteins has shed some light onto their functions implicated in the etiology of LGMD, our understanding of the molecular mechanisms underlying muscular dystrophy remains incomplete. Methods To give insight into the molecular mechanisms of AR-LGMD, we have examined the differentially expressed gene profiling between the relative normal and pathological skeletal muscles from the same AR-LGMD patient with the differential display RT-PCR approach. The research subjects came from a Chinese AR-LGMD family with three affected sisters. Results In this report, we have identified 31 known genes and 12 unknown ESTs, which were differentially expressed between the relative normal and dystrophic muscle from the same LGMD patient. The expression of many genes encoding structural proteins of skeletal muscle fibers (such as titin, myosin heavy and light chains, and nebulin were dramatically down-regulated in dystrophic muscles compared to the relative normal muscles. The genes, reticulocalbin 1, kinectin 1, fatty acid desaturase 1, insulin-like growth factor binding protein 5 (IGFBP5, Nedd4 family interacting protein 1 (NDFIP1, SMARCA2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2, encoding the proteins involved in signal transduction and gene expression regulation were up-regulated in the dystrophic muscles. Conclusion The functional analysis of these expression-altered genes in the pathogenesis of LGMD could provide additional information for understanding possible molecular mechanisms of LGMD development.

  15. Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection.

    Science.gov (United States)

    Pelle, Karell G; Oh, Keunyoung; Buchholz, Kathrin; Narasimhan, Vagheesh; Joice, Regina; Milner, Danny A; Brancucci, Nicolas Mb; Ma, Siyuan; Voss, Till S; Ketman, Ken; Seydel, Karl B; Taylor, Terrie E; Barteneva, Natasha S; Huttenhower, Curtis; Marti, Matthias

    2015-01-01

    During intra-erythrocytic development, late asexually replicating Plasmodium falciparum parasites sequester from peripheral circulation. This facilitates chronic infection and is linked to severe disease and organ-specific pathology including cerebral and placental malaria. Immature gametocytes - sexual stage precursor cells - likewise disappear from circulation. Recent work has demonstrated that these sexual stage parasites are located in the hematopoietic system of the bone marrow before mature gametocytes are released into the bloodstream to facilitate mosquito transmission. However, as sequestration occurs only in vivo and not during in vitro culture, the mechanisms by which it is regulated and enacted (particularly by the gametocyte stage) remain poorly understood. We generated the most comprehensive P. falciparum functional gene network to date by integrating global transcriptional data from a large set of asexual and sexual in vitro samples, patient-derived in vivo samples, and a new set of in vitro samples profiling sexual commitment. We defined more than 250 functional modules (clusters) of genes that are co-expressed primarily during the intra-erythrocytic parasite cycle, including 35 during sexual commitment and gametocyte development. Comparing the in vivo and in vitro datasets allowed us, for the first time, to map the time point of asexual parasite sequestration in patients to 22 hours post-invasion, confirming previous in vitro observations on the dynamics of host cell modification and cytoadherence. Moreover, we were able to define the properties of gametocyte sequestration, demonstrating the presence of two circulating gametocyte populations: gametocyte rings between 0 and approximately 30 hours post-invasion and mature gametocytes after around 7 days post-invasion. This study provides a bioinformatics resource for the functional elucidation of parasite life cycle dynamics and specifically demonstrates the presence of the gametocyte ring stages

  16. Gene expression profiles of adipose tissue of high-fat diet-induced obese rats by cDNA microarrays.

    Science.gov (United States)

    Qiu, Jie; Cheng, Rui; Zhou, Xiao-yu; Zhu, Jin-gai; Zhu, Chun; Qin, Da-ni; Kou, Chun-zhao; Guo, Xi-rong

    2010-12-01

    To better understand the molecular basis of dietary obesity, we examined adipose tissue genes differentially expressed in a well-characterized rat model of high-fat diet (HFD)-induced obesity using cDNA microarrays. Male Sprague-Dawley rats were fed either the HFD or the normal diet. Seven weeks later, the weights of obese models (362.92 ± 39.65 g) were significantly higher than those of normal control rats (315.22 ± 42.30 g, P obese models. cDNA microarrays containing 9 216 genes/Ests were used to investigate gene expression of adipose tissue. Autoradiographic analysis showed that 532, 154, and 22 genes were differently expressed over 2-, 3-, and 5-fold, respectively. The analysis of gene expression profiles indicated that 276 genes were up-regulated and 432 genes were down-regulated in response to HFD-induced obesity. Different clusters of genes associated with lipid metabolism, extracellular matrix, signal transduction, cytoskeleton, cell apoptosis, etc., such as VLCS-H2, DGAT, ACADVL, PHYH, SCD, ACACA, ACS, MMP-2, MMP-15, CD38, CAMK2D, CACNA1F, CAPZA2, TMOD3, ARPC2, KNS2, TPM1, MAPK8, GADD45B, DAXX, TOK-1, PRKACA, STAT6, were concerned.

  17. Assessment of the relationships among posture, maxillomandibular denture complex, and soft-tissue profile of aesthetic adult Korean women.

    Science.gov (United States)

    Choi, B; Baek, S H; Yang, W S; Kim, S

    2000-11-01

    The objective of this study was to assess the relationships among the posture, the maxillomandibular denture complex, and the soft-tissue profile of aesthetic adult Korean women. From an initial group of 346 women, the authors examined 28 beautiful adult Korean women who had normal vertical and sagittal skeletal relationships and normal occlusion. There were no differences in the inclinations of the incisors to the occlusal planes in the maxilla and the mandible in the data for Korean women vs. Arnett's data for white women. However, the overbite and overjet in Korean women were slightly smaller than in white women. AB to maxillary occlusal plane angle (MxOP) represented the anteroposterior denture base discrepancy to the occlusal plane. Angulation of the maxillary occlusal plane to the Frankfurt (FH) plane and the true vertical line at submasale (TVL) (Sn) was a little steeper in Korean women than in white women. The FH plane was almost parallel to the true horizontal line in Korean women who had normal vertical and sagittal skeletal relationships and normal occlusion. With regard to soft-tissue variables, the upper lip length (Sn-Stms), interlabial gap, upper incisor exposure, nasolabial angle, lip and nose tip projection value, and TVL (Sn)-to-upper lip line (UL) angle showed interracial differences. The results of this study can assist in the diagnosis and treatment planning of orthognathic surgery.

  18. Alternative exon usage creates novel transcript variants of tumor suppressor SHREW-1 gene with differential tissue expression profile

    Science.gov (United States)

    Klemmt, Petra A. B.; Resch, Eduard; Smyrek, Isabell; Engels, Knut; Stelzer, Ernst H. K.

    2016-01-01

    ABSTRACT Shrew-1, also called AJAP1, is a transmembrane protein associated with E-cadherin-mediated adherence junctions and a putative tumor suppressor. Apart from its interaction with β-catenin and involvement in E-cadherin internalization, little structure or function information exists. Here we explored shrew-1 expression during postnatal differentiation of mammary gland as a model system. Immunohistological analyses with antibodies against either the extracellular or the cytoplasmic domains of shrew-1 consistently revealed the expression of full-length shrew-1 in myoepithelial cells, but only part of it in luminal cells. While shrew-1 localization remained unaltered in myoepithelial cells, nuclear localization occurred in luminal cells during lactation. Based on these observations, we identified two unknown shrew-1 transcript variants encoding N-terminally truncated proteins. The smallest shrew-1 protein lacks the extracellular domain and is most likely the only variant present in luminal cells. RNA analyses of human tissues confirmed that the novel transcript variants of shrew-1 exist in vivo and exhibit a differential tissue expression profile. We conclude that our findings are essential for the understanding and interpretation of future functional and interactome analyses of shrew-1 variants. PMID:27870635

  19. An abundant tissue macrophage population in the adult murine heart with a distinct alternatively-activated macrophage profile.

    Directory of Open Access Journals (Sweden)

    Alexander R Pinto

    Full Text Available Cardiac tissue macrophages (cTMs are a previously uncharacterised cell type that we have identified and characterise here as an abundant GFP(+ population within the adult Cx(3cr1(GFP/+ knock-in mouse heart. They comprise the predominant myeloid cell population in the myocardium, and are found throughout myocardial interstitial spaces interacting directly with capillary endothelial cells and cardiomyocytes. Flow cytometry-based immunophenotyping shows that cTMs exhibit canonical macrophage markers. Gene expression analysis shows that cTMs (CD45(+CD11b(+GFP(+ are distinct from mononuclear CD45(+CD11b(+GFP(+ cells sorted from the spleen and brain of adult Cx(3cr1(GFP/+ mice. Gene expression profiling reveals that cTMs closely resemble alternatively-activated anti-inflammatory M2 macrophages, expressing a number of M2 markers, including Mrc1, CD163, and Lyve-1. While cTMs perform normal tissue macrophage homeostatic functions, they also exhibit a distinct phenotype, involving secretion of salutary factors (including IGF-1 and immune modulation. In summary, the characterisation of cTMs at the cellular and molecular level defines a potentially important role for these cells in cardiac homeostasis.

  20. Genome-wide mutant fitness profiling identifies nutritional requirements for optimal growth of Yersinia pestis in deep tissue.

    Science.gov (United States)

    Palace, Samantha G; Proulx, Megan K; Lu, Shan; Baker, Richard E; Goguen, Jon D

    2014-08-19

    knowledge of this aspect of bacterial biology is important as a potential pathway to the development of novel therapeutics. Yersinia pestis, the plague bacterium, is highly virulent due to its rapid dissemination and growth in deep tissues, making it a good model for discovering bacterial adaptations that promote rapid growth during infection. Using Tn-seq, a genome-wide fitness profiling technique, we identified several functions required for fitness of Y. pestis in vivo that were not previously known to be important. Most of these functions are needed to acquire or synthesize nutrients. Interference with these critical nutrient acquisition pathways may be an effective strategy for designing novel antibiotics and vaccines. Copyright © 2014 Palace et al.

  1. Company analysis

    DEFF Research Database (Denmark)

    Jenster, Per V.; Hussey, David

    This volume looks at the company appraisal as a whole, examining the continuing need to appraise companies as part of the continuing strategy process. Building from a sound basis of theory, the text aims to be practical and to give guidance to senior managers and others involved in the strategy...... process. It is thus a book primarily aimed at managers, but should also be useful for MBA students undertaking strategy assignments It provides helpful, practical guidance and identifies weaknesses of traditional methods. It also presents a variety of tools which may be used in the appraisal process...

  2. Photogrammetric Comparison of Facial Soft Tissue Profile before and after Protraction Facemask Therapy in Class III Children (6-11 Years Old)

    Science.gov (United States)

    Moshkelgosha, Vahid; Raoof, Arghavan; Sardarian, Ahmadreza; Salehi, Parisa

    2017-01-01

    Statement of the Problem: Achieving a normal soft tissue facial profile is considered to be the main concern of class III patients and the goal of most class III treatments. Purpose: The purpose of this study was to investigate the effects of facemask treatment on profile with photogrammetric method. Materials and Method: Before (T0) and after (T1) treatment photograms of 40 class III patients profiles (20 male and 20 female individuals) treated with protraction face mask that met the inclusion criteria were digitized and analyzed using Aesthetic Analyzer software. Selected linear and angular measurements were performed for each patient and the changes were noted. Results: An increase in inferior facial height (pface and consequent fullness in the soft-tissue profile can be achieved by using protraction face mask. The response to treatment is not different between males and females.

  3. The effects of high-fat diets composed of different animal and vegetable fat sources on the health status and tissue lipid profiles of male Japanese quail (

    Directory of Open Access Journals (Sweden)

    Janine Donaldson

    2017-05-01

    Full Text Available Objective The current study aimed to investigate the impact of high-fat diets composed of different animal and vegetable fat sources on serum metabolic health markers in Japanese quail, as well as the overall lipid content and fatty acid profiles of the edible bird tissues following significantly increased dietary lipid supplementation. Methods Fifty seven male quail were divided into six groups and fed either a standard diet or a diet enriched with one of five different fats (22% coconut oil, lard, palm oil, soybean oil, or sunflower oil for 12 weeks. The birds were subjected to an oral glucose tolerance test following the feeding period, after which they were euthanized and blood, liver, breast, and thigh muscle samples collected. Total fat content and fatty acid profiles of the tissue samples, as well as serum uric acid, triglyceride, cholesterol, total protein, albumin, aspartate transaminase, and total bilirubin concentrations were assessed. Results High-fat diet feeding had no significant effects on the glucose tolerance of the birds. Dietary fatty acid profiles of the added fats were reflected in the lipid profiles of both the liver and breast and thigh muscle tissues, indicating successful transfer of dietary fatty acids to the edible bird tissues. The significantly increased level of lipid inclusion in the diets of the quail used in the present study was unsuccessful in increasing the overall lipid content of the edible bird tissues. Serum metabolic health markers in birds on the high-fat diets were not significantly different from those observed in birds on the standard diet. Conclusion Thus, despite the various high-fat diets modifying the fatty acid profile of the birds’ tissues, unlike in most mammals, the birds maintained a normal health status following consumption of the various high-fat diets.

  4. Gene expression profile of cervical and skin tissues from human papillomavirus type 16 E6 transgenic mice

    Directory of Open Access Journals (Sweden)

    Lambert PF

    2008-11-01

    Full Text Available Abstract Background Although K14E6 transgenic mice develop spontaneous tumors of the skin epithelium, no spontaneous reproductive tract malignancies arise, unless the transgenic mice were treated chronically with 17β-estradiol. These findings suggest that E6 performs critical functions in normal adult cervix and skin, highlighting the need to define E6-controlled transcriptional programs in these tissues. Methods We evaluated the expression profile of 14,000 genes in skin or cervix from young K14E6 transgenic mice compared with nontransgenic. To identify differentially expressed genes a linear model was implemented using R and the LIMMA package. Two criteria were used to select the set of relevant genes. First a set of genes with a Log-odds ≥ 3 were selected. Then, a hierarchical search of genes was based on Log Fold Changes. Results Microarray analysis identified a total of 676 and 1154 genes that were significantly up and down-regulated, respectively, in skin from K14E6 transgenic mice. On the other hand, in the cervix from K14E6 transgenic mice we found that only 97 and 252 genes were significantly up and down-regulated, respectively. One of the most affected processes in the skin from K14E6 transgenic mice was the cell cycle. We also found that skin from transgenic mice showed down-regulation of pro-apoptotic genes and genes related to the immune response. In the cervix of K14E6 transgenic mice, we could not find affected any gene related to the cell cycle and apoptosis pathways but did observe alterations in the expression of immune response genes. Pathways such as angiogenesis, cell junction and epidermis development, also were altered in their gene expression profiles in both tissues. Conclusion Expression of the HPV16 E6 oncoprotein in our model alters expression of genes that fell into several functional groups providing insights into pathways by which E6 deregulate cell cycle progression, apoptosis, the host resistance to infection

  5. Alternations in genes expression of pathway signaling in esophageal tissue with atresia: results of expression microarray profiling.

    Science.gov (United States)

    Smigiel, R; Lebioda, A; Blaszczyński, M; Korecka, K; Czauderna, P; Korlacki, W; Jakubiak, A; Bednarczyk, D; Maciejewski, H; Wizinska, P; Sasiadek, M M; Patkowski, D

    2015-04-01

    Esophageal atresia (EA) is a congenital defect of the esophagus involving the interruption of the esophagus with or without connection to the trachea (tracheoesophageal fistula [TEF]). EA/TEF may occur as an isolated anomaly, may be part of a complex of congenital defects (syndromic), or may develop within the context of a known syndrome or association. The molecular mechanisms underlying the development of EA are poorly understood. It is supposed that a combination of multigenic factors and epigenetic modification of genes play a role in its etiology. The aim of our work was to assess the human gene expression microarray study in esophageal tissue samples. Total RNA was extracted from 26 lower pouches of esophageal tissue collected during thoracoscopic EA repair in neonates with the isolated (IEA) and the syndromic form (SEA). We identified 787 downregulated and 841 upregulated transcripts between SEA and controls, and about 817 downregulated and 765 upregulated probes between IEA and controls. Fifty percent of these genes showed differential expression specific for either IEA or SEA. Functional pathway analysis revealed substantial enrichment for Wnt and Sonic hedgehog, as well as cytokine and chemokine signaling pathways. Moreover, we performed reverse transcription polymerase chain reaction study in a group of SHH and Wnt pathways genes with differential expression in microarray profiling to confirm the microarray expression results. We verified the altered expression in SFRP2 gene from the Wnt pathway as well as SHH, GLI1, GLI2, and GLI3 from the Sonic hedgehog pathway. The results suggest an important role of these pathways and genes for EA/TEF etiology. © 2014 International Society for Diseases of the Esophagus.

  6. Molecular cloning, sequence identification and tissue expression profile of three novel sheep (Ovis aries) genes - BCKDHA, NAGA and HEXA.

    Science.gov (United States)

    Liu, G Y; Gao, S Z

    2009-01-01

    The complete coding sequences of three sheep genes- BCKDHA, NAGA and HEXA were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR), based on the conserved sequence information of the mouse or other mammals. The nucleotide sequences of these three genes revealed that the sheep BCKDHA gene encodes a protein of 313 amino acids which has high homology with the BCKDHA gene that encodes a protein of 447 amino acids that has high homology with the Branched chain keto acid dehydrogenase El, alpha polypeptide (BCKDHA) of five species chimpanzee (93%), human (96%), crab-eating macaque (93%), bovine (98%) and mouse (91%). The sheep NAGA gene encodes a protein of 411 amino acids that has high homology with the alpha-N-acetylgalactosaminidase (NAGA) of five species human (85%), bovine (94%), mouse (91%), rat (83%) and chicken (74%). The sheep HEXA gene encodes a protein of 529 amino acids that has high homology with the hexosaminidase A(HEXA) of five species bovine (98%), human (84%), Bornean orangután (84%), rat (80%) and mouse (81%). Finally these three novel sheep genes were assigned to GenelDs: 100145857, 100145858 and 100145856. The phylogenetic tree analysis revealed that the sheep BCKDHA, NAGA, and HEXA all have closer genetic relationships to the BCKDHA, NAGA, and HEXA of bovine. Tissue expression profile analysis was also carried out and results revealed that sheep BCKDHA, NAGA and HEXA genes were differentially expressed in tissues including muscle, heart, liver, fat, kidney, lung, small and large intestine. Our experiment is the first to establish the primary foundation for further research on these three sheep genes.

  7. Quantitative profiling of bile acids in biofluids and tissues based on accurate mass high resolution LC-FT-MS: Compound class targeting in a metabolomics workflow

    NARCIS (Netherlands)

    Bobeldijk, I.; Hekman, M.; Vries de- Weij, J.van der; Coulier, L.; Ramaker, R.; Kleemann, R.; Kooistra, T.; Rubingh, C.; Freidig, A.; Verheij, E.

    2008-01-01

    We report a sensitive, generic method for quantitative profiling of bile acids and other endogenous metabolites in small quantities of various biological fluids and tissues. The method is based on a straightforward sample preparation, separation by reversed-phase high performance liquid-chromatograp

  8. Development of a 3D Tissue Culture-Based High-Content Screening Platform That Uses Phenotypic Profiling to Discriminate Selective Inhibitors of Receptor Tyrosine Kinases.

    NARCIS (Netherlands)

    Booij, T.H.; Klop, M.J.; Yan, K.; Szántai-Kis, C.; Szokol, B.; Orfi, L .; Water, van de B.; Keri, G.; Price, L.S.

    2016-01-01

    3D tissue cultures provide a more physiologically relevant context for the screening of compounds, compared with 2D cell cultures. Cells cultured in 3D hydrogels also show complex phenotypes, increasing the scope for phenotypic profiling. Here we describe a high-content screening platform that uses

  9. Development of a 3D Tissue Culture-Based High-Content Screening Platform That Uses Phenotypic Profiling to Discriminate Selective Inhibitors of Receptor Tyrosine Kinases.

    NARCIS (Netherlands)

    Booij, T.H.; Klop, M.J.; Yan, K.; Szántai-Kis, C.; Szokol, B.; Orfi, L .; Water, van de B.; Keri, G.; Price, L.S.

    2016-01-01

    3D tissue cultures provide a more physiologically relevant context for the screening of compounds, compared with 2D cell cultures. Cells cultured in 3D hydrogels also show complex phenotypes, increasing the scope for phenotypic profiling. Here we describe a high-content screening platform that uses

  10. Soft tissue profile changes after mandibular vestibuloplasty. A two-year follow-up study comparing the Edlan flap, mucosal and skin graft methods.

    Science.gov (United States)

    Hillerup, S; Solow, B

    1990-02-01

    It is the aim of the present study to examine the pattern of postoperative changes in the soft tissue profile of 50 edentulous patients after 3 common types of mandibular vestibuloplasty, the Edlan flap operation (n = 15), the buccal mucosal graft (n = 19), and the skin graft vestibuloplasty (n = 16). The soft tissue profile changes were recorded on lateral cephalometric radiographs taken preoperatively, and after 1, 3, 6, 12, and 24 months post surgery. The 3 groups did not differ with respect to clinical features or presurgical cranio-facial morphology. Neither was any significant difference in postoperative profile changes found between the groups. The surgery gave rise, directly and indirectly, to a number of changes in the facial soft tissue profile many of which were interrelated. The chin thickness increased by 2.3 mm, and the lower lip height exhibited a reduction of 1.8 mm at 1 month after surgery as a direct consequence of the operation. After 3 months the profile changes were mostly associated with the reduction of the anterior face height (overclosure).

  11. Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue

    Directory of Open Access Journals (Sweden)

    Giobbie-Hurder Anita

    2010-02-01

    Full Text Available Abstract Background The purpose of the work reported here is to test reliable molecular profiles using routinely processed formalin-fixed paraffin-embedded (FFPE tissues from participants of the clinical trial BIG 1-98 with a median follow-up of 60 months. Methods RNA from fresh frozen (FF and FFPE tumor samples of 82 patients were used for quality control, and independent FFPE tissues of 342 postmenopausal participants of BIG 1-98 with ER-positive cancer were analyzed by measuring prospectively selected genes and computing scores representing the functions of the estrogen receptor (eight genes, ER_8, the progesterone receptor (five genes, PGR_5, Her2 (two genes, HER2_2, and proliferation (ten genes, PRO_10 by quantitative reverse transcription PCR (qRT-PCR on TaqMan Low Density Arrays. Molecular scores were computed for each category and ER_8, PGR_5, HER2_2, and PRO_10 scores were combined into a RISK_25 score. Results Pearson correlation coefficients between FF- and FFPE-derived scores were at least 0.94 and high concordance was observed between molecular scores and immunohistochemical data. The HER2_2, PGR_5, PRO_10 and RISK_25 scores were significant predictors of disease free-survival (DFS in univariate Cox proportional hazard regression. PRO_10 and RISK_25 scores predicted DFS in patients with histological grade II breast cancer and in lymph node positive disease. The PRO_10 and PGR_5 scores were independent predictors of DFS in multivariate Cox regression models incorporating clinical risk indicators; PRO_10 outperformed Ki-67 labeling index in multivariate Cox proportional hazard analyses. Conclusions Scores representing the endocrine responsiveness and proliferation status of breast cancers were developed from gene expression analyses based on RNA derived from FFPE tissues. The validation of the molecular scores with tumor samples of participants of the BIG 1-98 trial demonstrates that such scores can serve as independent prognostic

  12. Progression in cutaneous malignant melanoma is associated with distinct expression profiles: a tissue microarray-based study.

    Science.gov (United States)

    Alonso, Soledad R; Ortiz, Pablo; Pollán, Marina; Pérez-Gómez, Beatriz; Sánchez, Lydia; Acuña, Ma Jesús; Pajares, Raquel; Martínez-Tello, Francisco J; Hortelano, Carlos M; Piris, Miguel A; Rodríguez-Peralto, José L

    2004-01-01

    Cutaneous malignant melanoma remains the leading cause of skin cancer death in industrialized countries. Clinical and histological variables that predict survival, such as Breslow's index, tumor size, ulceration, or vascular invasion have been identified in malignant melanoma. Nevertheless, the potential relevance of biological variables still awaits an in-depth exploration. Using tissue microarrays (TMAs), we retrospectively analyzed 165 malignant melanoma samples from 88 patients corresponding to distinct histological progression phases, radial, vertical, and metastases. A panel of 39 different antibodies for cell cycle, apoptosis, melanoma antigens, transcription factors, DNA mismatch repair, and other proteins was used. Integrating the information, the study has identified expression profiles distinguishing specific melanoma progression stages. Most of the detected alterations were linked to the control of cell cycle G1/S transition; cyclin D1 was expressed in radial cases 48% (12 of 25) with significant lost of expression in vertical cases 14% (9 of 65), P = 0.002; whereas p16(INK4a) (89% in vertical versus 71% in metastatic cases, P = 0.009) and p27(KIP1) (76% in radial versus 45% in vertical cases, P = 0.010) were diminished in advanced stages. The study also defines a combination of biological markers associated with shorter overall survival in patients with vertical growth phase melanoma, that provided a predictor model with four antibodies (Ki67, p16(INK4a), p21(CIP1), and Bcl-6). This predictor model was validated using an independent series of 72 vertical growth phase melanoma patients.

  13. Microarray analysis of Long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori Infection.

    Science.gov (United States)

    Zhu, Hong; Wang, Qiang; Yao, Yizheng; Fang, Jian; Sun, Fengying; Ni, Ying; Shen, Yixin; Wang, Hua; Shao, Shihe

    2015-12-21

    Although Helicobacter pylori (H.pylori) is the dominant gastrointestinal pathogen, the genetic and molecular mechanisms underlying H.pylori-related diseases have not been fully elucidated. Long non-coding RNAs (lncRNAs) have been identified in eukaryotic cells, many of which play important roles in regulating biological processes and pathogenesis. However, the expression changes of lncRNAs in human infected by H.pylori have been rarely reported. This study aimed to identify the dysregulated lncRNAs in human gastric epithelial cells and tissues infected with H.pylori. The aberrant expression profiles of lncRNAs and mRNAs in GES-1 cells with or without H.pylori infection were explored by microarray analysis. LncRNA-mRNA co-expression network was constructed based on Pearson correlation analysis. Gene Ontology (GO) and KEGG Pathway analyses of aberrantly expressed mRNAs were performed to identify the related biological functions and pathologic pathways. The expression changes of target lncRNAs were validated by qRT-PCR to confirm the microarray data in both cells and clinical specimens. Three hundred three lncRNAs and 565 mRNAs were identified as aberrantly expressed transcripts (≥2 or ≤0.5-fold change, P microarray. These dysregulated lncRNAs might contribute to the pathological processes during H.pylori infection.

  14. Identification and tissue expression profile of genes from three chemoreceptor families in an urban pest, Periplaneta americana.

    Science.gov (United States)

    Chen, Yan; He, Ming; Li, Zhao-Qun; Zhang, Ya-Nan; He, Peng

    2016-06-09

    Periplaneta americana is a notorious urban pest prevalent in human habitats; very little is known about its chemosensory mechanism. Employing the advanced next-generation sequencing technique, in the present study, we conducted transcriptome sequencing and analysis of the antennae of the adult males and females as well as their mouthparts using an Illumina platform. This resulted in the discovery of a huge number of the members of all major known chemosensory receptor families in P. americana, including 96 odorant receptors (ORs), 53 ionotropic receptors (IRs), and 33 gustatory receptors (GRs). Tissue expression profiles showed most of them mainly expressed in antennae and phylogenetic analysis demonstrated the expansion in the clade distinguishing them from other functionally well-known Lepidoptera species. A high percentage of chemosensory receptor genes (ORs in particular) showing female antenna bias in mRNA expression was observed. Our results provide a basis for further investigations on how P. americana coordinates its chemosensory receptor genes in chemical communication with environments, and for development of novel pest management approaches.

  15. Hypothalamus metabolomic profiling to elucidate the tissue-targeted biochemical basis of febrile response in yeast-induced pyrexia rats.

    Science.gov (United States)

    Liu, Haiyu; Zhang, Li; Zhao, Baosheng; Zhang, Zhixin; Qin, Lingling; Zhang, Qingqing; Wang, Qing; Lu, Zhiwei; Gao, Xiaoyan

    2015-04-25

    In the previous reports regarding thermoregulation, the hypothalamus is thought to be the primary centre in the central nervous system for controlling the body temperature. However, to date, there has not been sufficient evidence to reveal its thermoregulatory mechanism. In the current study, we utilised a tissue-targeted metabolomics strategy to elucidate the underlying biochemical mechanisms of thermoregulation in the fever process by analysing the global metabolic profile of the hypothalamus in yeast-induced pyrexia rats. Data acquisition was completed using the HPLC-LTQ-Orbitrap/MS in both positive and negative ion mode. Principal component analysis was used to observe the cluster characteristics between the control group and the pyrexia group. Potential biomarkers were screened using orthogonal partial least-squares-discriminant analysis. Seventeen potential biomarkers were identified in the hypothalamus samples to discriminate the control and pyrexia groups, including amino acids, nucleic acids, vitamins, carbohydrates, and phospholipids. As a result, purine metabolism was enhanced pronouncedly, and perturbation of lipid metabolism was also observed. Meanwhile, amino acid metabolism and energy metabolism were also activated significantly. In conclusion, the study indicated that hypothalamus-targeted metabolomics could provide a powerful tool to further understand the pathogenesis of febrile response. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  16. SAFER - Company Snapshot - SAFER - Company Snapshot

    Data.gov (United States)

    Department of Transportation — The Company Snapshot is a concise electronic record of company identification, size, commodity information, and safety record, including the safety rating (if any),...

  17. Microscopic resolution imaging and proteomics correlation at histogeographically identical location: point by point correlation between ex vivo tissue imaging with high field MRI and multiplex tissue immunoblotting for proteomics profiling

    Science.gov (United States)

    Matsuda, Kant M.; Chung, Joon-Yong; Ylaya, Kris; Dodd, Stephen; Fukunaga, Masaki; Hewitt, Stephen M.

    2010-03-01

    Histopathologic correlation is an essential component for validation of the radiological findings. There has been significant advancement in medical imaging technologies, including molecular imaging, such that, it is essential to establish the system beyond histopathologic correlation, to protein profiling that can be correlated with imaging at anatomically identical manner for accurate examination. Recently, a novel technology for proteomic profiling has been established, called "multiplex tissue immunoblotting (MTIB)" which can offer studying multiple protein expression from a single histology slide. Therefore, we attempted to establish the system to obtain an identical plane between high resolution imaging and histopathology at microscopic level so that proteomic profiling can be readily performed using MTIB. A variety of tissues were obtained from autopsy materials and initially scanned with high field MRI (14T) ex vivo along with the marker for tissue orientation. The histology slides were prepared from post-scanned tissue under the marker-guidance in order to obtain an identical plane with high resolution imaging. Subsequently, MTIB was carried out to study expression of proteins of interest and point by point correlation with high resolution imaging was performed at histogeographically identical manner.

  18. The metabolic effects of di (2-ethyl hexyl phthalate medium dose on lipid profiles in serum and liver tissue

    Directory of Open Access Journals (Sweden)

    Buang Y

    2011-02-01

    Full Text Available Background: Di (2-ethyl hexyl phthalate is the most widely used  plasticizer in blood storage bag for transfusion. This substance can modify lipid metabolism. This study was aimed to elucidate the metabolic effects of di (2-ethyl hexyl phthalate medium dose on lipid profiles in serum and liver tissue.Methods: Sprague Dawley rats were fed 1.0 % di (2-ethyl hexyl phthalate diet (DEHP group, n=5 or a non-supplemented diet (control group, n=5 for 10 days. The rats were allowed to freely access each food. Serum lipid concentrations were measured using enzyme assay kits. Lipids of liver tissues were extracted and the lipid contents were determined. A peach of liver was prepared to determine the activities of malic enzyme and carnitine palmitoyl transferase-1 (CPT-1.Results: Serum lipid concentrations (mg/dL of DEHP group decreased compared to control (P<0.05. The serum triglyceride (TG concentrations of control and DEHP groups were respectively (100.5±16.5 and (31.2±1.7; phospholipid (PL, (143.3±7.8 and (88.9±3.2; total cholesterol, (88.7±4.6 and (51.9±2.3. The liver TG content of control and DEHP group (mg/g liver were respectively, (40.8±4.4 and (23.7±1.3; liver cholesterol were (3.36±0.29 and (2.33±0.23; and the liver PL were (36.5±1.0 and (41.7±0.6. Malic enzyme and CPT-1 activities (nmol/min/mg protein of DEHP group increased compared to control (P<0.05, in which their increases were approximately by 4.35- and 2.33-folds,  respectively.Conclusion: The di (2-ethyl hexyl phthalate medium dose attenuates lipids secretion from the liver cells into the bloodstream. The increase of liver PL level accompanied with the promotions of malic enzyme and the CPT-1 activities are the key factors of the dietary di (2-ethyl hexyl phthalate effects in rats to attenuate the lipid secretions from the livers. (Med J Indones 2011; 20:20-6Keywords: Di (2-ethyl hexyl phthalate, hyperphospholipids, lipolysis, liver lipids, serum lipids

  19. Transcript profiles in longissimus dorsi muscle and subcutaneous adipose tissue: a comparison of pigs with different postweaning growth rates.

    Science.gov (United States)

    Pilcher, C M; Jones, C K; Schroyen, M; Severin, A J; Patience, J F; Tuggle, C K; Koltes, J E

    2015-05-01

    Although most pigs recover rapidly from stresses associated with the transition of weaning, a portion of the population lags behind their contemporaries in growth performance. The underlying biological and molecular mechanisms involved in postweaning differences in growth performance are poorly understood. The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop a better understanding of the metabolic basis for poor weaned-pig transition. A total of 1,054 pigs was reared in commercial conditions and weighed at birth, weaning, and 3 wk postweaning. Transition ADG (tADG) was calculated as the ADG for the 3-wk period postweaning. Nine pigs from both the lowest 10th percentile (low tADG) and the 60th to 70th percentile (high tADG) were harvested at 3 wk postweaning. Differential expression analysis was conducted in longissimus dorsi muscle (LM) and subcutaneous adipose tissue using RNA-Seq methodology. In LM, 768 transcripts were differentially expressed (DE), 327 with higher expression in low tADG and 441 with higher expression in high tADG pigs (q muscle metabolism and physiology, functional annotation analysis of the DE transcripts was conducted using DAVID and Pathway Studio analytic tools. The group of DE genes with lower expression in LM of low tADG pigs was enriched in genes with functions related to muscle contraction, glucose metabolism, cytoskeleton organization, muscle development, and response to hormone stimulus (enrichment score > 1.3). The list of DE genes with higher expression in low tADG LM was enriched in genes with functions related to protein catabolism (enrichment score > 1.3). Analysis of known gene-gene interactions identified possible regulators of these differences in gene expression in LM of high and low tADG pigs; these include forkhead box O1 (FOXO1), growth hormone (GH1), and the glucocorticoid receptor (NR3C1). Differences in gene expression between poor transitioning pigs and

  20. Epicardial and Subcutaneous Adipose Tissue Fatty Acids Profiles in Diabetic and Non-Diabetic Patients Candidate for Coronary Artery Bypass Graft

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    Masoud Pezeshkian

    2013-01-01

    Full Text Available Introduction: We have recently shown that in high cholesterol-fed rabbits, the sensitivity of epicardial adipose tissue to changes in dietary fat is higher than that of subcutaneous adipose tissue. Although the effects of diabetes on epicardial adipose tissue thickness have been studied, the influence of diabetes on profile of epicardial free fatty acids (FFAs has not been studied. The aim of this study is to investigate the effect of diabetes on the FFAs composition in serum and in the subcutaneous and epicardial adipose tissues in patients undergoing coronary artery bypass graft (CABG. Methods: Forty non-diabetic and twenty eight diabetic patients candidate for CABG with > 75% stenosis participated in this study.Fasting blood sugar (FBS and lipid profiles were assayed by auto analyzer. Phospholipids and non-estrified FFA of serum and the fatty acids profile of epicardial and subcutaneous adipose tissues were determined using gas chromatography method. Results: In the phospholipid fraction of diabetic patients’ serum, the percentage of 16:0, 18:3n-9, 18:2n-6 and monounsaturated fatty acids (MUFAs was lower than the corresponding values of the non-diabetics; whereas, 18:0 value was higher. A 100% increase in the amount of 18:0 and 35% decrease in the level of 18:1n-11 was observed in the diabetic patients’ subcutaneous adipose tissue. In epicardial adipose tissue, the increase of 18:0 and conjugated linolenic acid (CLA and decrease of 18:1n-11, ω3 (20:5n-3 and 22:6n-3 were significant; but, the contents of arachidonic acid and its precursor linoleic acid were not affected by diabetes. Conclusion: The fatty acids’ profile of epicardial and subcutaneous adipose tissues is not equally affected by diabetes. The significant decrease of 16:0 and ω3 fatty acids and increase of trans and conjugated fatty acids in epicardial adipose tissue in the diabetic patients may worsen the formation of atheroma in the related arteries.

  1. Dynamic Metabolic Profiles and Tissue-Specific Source Effects on the Metabolome of Developing Seeds of Brassica napus.

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    Helin Tan

    Full Text Available Canola (Brassica napus is one of several important oil-producing crops, and the physiological processes, enzymes, and genes involved in oil synthesis in canola seeds have been well characterized. However, relatively little is known about the dynamic metabolic changes that occur during oil accumulation in seeds, as well as the mechanistic origins of metabolic changes. To explore the metabolic changes that occur during oil accumulation, we isolated metabolites from both seed and silique wall and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS. The results showed that a total of 443 metabolites were identified from four developmental stages. Dozens of these metabolites were differentially expressed during seed ripening, including 20 known to be involved in seed development. To investigate the contribution of tissue-specific carbon sources to the biosynthesis of these metabolites, we examined the metabolic changes of silique walls and seeds under three treatments: leaf-detachment (Ld, phloem-peeling (Pe, and selective silique darkening (Sd. Our study demonstrated that the oil content was independent of leaf photosynthesis and phloem transport during oil accumulation, but required the metabolic influx from the silique wall. Notably, Sd treatment resulted in seed senescence, which eventually led to a severe reduction of the oil content. Sd treatment also caused a significant accumulation of fatty acids (FA, organic acids and amino acids. Furthermore, an unexpected accumulation of sugar derivatives and organic acid was observed in the Pe- and Sd-treated seeds. Consistent with this, the expression of a subset of genes involved in FA metabolism, sugar and oil storage was significantly altered in Pe and Sd treated seeds. Taken together, our studies suggest the metabolite profiles of canola seeds dynamically varied during the course of oil accumulation, which may provide a new insight into the mechanisms

  2. Gene expression profiling in gill tissues of White spot syndrome virus infected black tiger shrimp Penaeus monodon by DNA microarray.

    Science.gov (United States)

    Shekhar, M S; Gomathi, A; Gopikrishna, G; Ponniah, A G

    2015-06-01

    White spot syndrome virus (WSSV) continues to be the most devastating viral pathogen infecting penaeid shrimp the world over. The genome of WSSV has been deciphered and characterized from three geographical isolates and significant progress has been made in developing various molecular diagnostic methods to detect the virus. However, the information on host immune gene response to WSSV pathogenesis is limited. Microarray analysis was carried out as an approach to analyse the gene expression in black tiger shrimp Penaeus monodon in response to WSSV infection. Gill tissues collected from the WSSV infected shrimp at 6, 24, 48 h and moribund stage were analysed for differential gene expression. Shrimp cDNAs of 40,059 unique sequences were considered for designing the microarray chip. The Cy3-labeled cRNA derived from healthy and WSSV-infected shrimp was subjected to hybridization with all the DNA spots in the microarray which revealed 8,633 and 11,147 as up- and down-regulated genes respectively at different time intervals post infection. The altered expression of these numerous genes represented diverse functions such as immune response, osmoregulation, apoptosis, nucleic acid binding, energy and metabolism, signal transduction, stress response and molting. The changes in gene expression profiles observed by microarray analysis provides molecular insights and framework of genes which are up- and down-regulated at different time intervals during WSSV infection in shrimp. The microarray data was validated by Real Time analysis of four differentially expressed genes involved in apoptosis (translationally controlled tumor protein, inhibitor of apoptosis protein, ubiquitin conjugated enzyme E2 and caspase) for gene expression levels. The role of apoptosis related genes in WSSV infected shrimp is discussed herein.

  3. Dynamic Metabolic Profiles and Tissue-Specific Source Effects on the Metabolome of Developing Seeds of Brassica napus.

    Science.gov (United States)

    Tan, Helin; Xie, Qingjun; Xiang, Xiaoe; Li, Jianqiao; Zheng, Suning; Xu, Xinying; Guo, Haolun; Ye, Wenxue

    2015-01-01

    Canola (Brassica napus) is one of several important oil-producing crops, and the physiological processes, enzymes, and genes involved in oil synthesis in canola seeds have been well characterized. However, relatively little is known about the dynamic metabolic changes that occur during oil accumulation in seeds, as well as the mechanistic origins of metabolic changes. To explore the metabolic changes that occur during oil accumulation, we isolated metabolites from both seed and silique wall and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS). The results showed that a total of 443 metabolites were identified from four developmental stages. Dozens of these metabolites were differentially expressed during seed ripening, including 20 known to be involved in seed development. To investigate the contribution of tissue-specific carbon sources to the biosynthesis of these metabolites, we examined the metabolic changes of silique walls and seeds under three treatments: leaf-detachment (Ld), phloem-peeling (Pe), and selective silique darkening (Sd). Our study demonstrated that the oil content was independent of leaf photosynthesis and phloem transport during oil accumulation, but required the metabolic influx from the silique wall. Notably, Sd treatment resulted in seed senescence, which eventually led to a severe reduction of the oil content. Sd treatment also caused a significant accumulation of fatty acids (FA), organic acids and amino acids. Furthermore, an unexpected accumulation of sugar derivatives and organic acid was observed in the Pe- and Sd-treated seeds. Consistent with this, the expression of a subset of genes involved in FA metabolism, sugar and oil storage was significantly altered in Pe and Sd treated seeds. Taken together, our studies suggest the metabolite profiles of canola seeds dynamically varied during the course of oil accumulation, which may provide a new insight into the mechanisms of the oil

  4. Distinct Blood and Visceral Adipose Tissue Regulatory T Cell and Innate Lymphocyte Profiles Characterize Obesity and Colorectal Cancer

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    Gloria Donninelli

    2017-06-01

    Full Text Available Visceral adipose tissue (VAT is a main site where metabolic and immunologic processes interplay to regulate, at local and systemic level, the inflammatory status and immune response. Obesity-associated inflammation and immune dysfunctions are inextricably linked to tumor but, in spite of intense efforts, the mechanisms underpinning this association remain elusive. In this report, we characterized the profile of VAT-associated and circulating innate lymphocyte and regulatory T (Treg cell subsets underlying inflammatory conditions, such as obesity and colorectal cancer (CRC. Analysis of NK, NKT-like, γδ T, and Treg cell populations in VAT and blood of healthy lean subjects revealed that CD56hi NK and OX40+ Treg cells are more abundant in VAT with respect to blood. Conversely, CD56dim NK and total Treg cells are most present in the circulation, while γδ T lymphocytes are uniformly distributed in the two compartments. Interestingly, a reduced frequency of circulating activated Treg cells, and a concomitant preferential enrichment of OX40-expressing Treg cells in VAT, were selectively observed in obese (Ob subjects, and directly correlated with body mass index. Likewise, CRC patients were characterized by a specific enrichment of VAT-associated NKT-like cells. In addition, Ob and CRC-affected individuals shared a significant reduction of the Vγ9Vδ2/γδ T cell ratio at systemic level. The alterations in the relative proportions of Treg and NKT-like cells in VAT were found to correlate with the content of pro- and anti-inflammatory polyunsaturated fatty acids (PUFA, respectively. Overall, these results provide evidence for distinct alterations of the immune cell repertoire in the periphery with respect to the VAT microenvironment that uniquely characterize or are shared by different inflammatory conditions, such as obesity and CRC, and suggest that VAT PUFA composition may represent one of the factors that contribute to shape the immune

  5. Tissue-specific, development-dependent phenolic compounds accumulation profile and gene expression pattern in tea plant [Camellia sinensis].

    Directory of Open Access Journals (Sweden)

    Xiaolan Jiang

    Full Text Available Phenolic compounds in tea plant [Camellia sinensis (L.] play a crucial role in dominating tea flavor and possess a number of key pharmacological benefits on human health. The present research aimed to study the profile of tissue-specific, development-dependent accumulation pattern of phenolic compounds in tea plant. A total of 50 phenolic compounds were identified qualitatively using liquid chromatography in tandem mass spectrometry technology. Of which 29 phenolic compounds were quantified based on their fragmentation behaviors. Most of the phenolic compounds were higher in the younger leaves than that in the stem and root, whereas the total amount of proanthocyanidins were unexpectedly higher in the root. The expression patterns of 63 structural and regulator genes involved in the shikimic acid, phenylpropanoid, and flavonoid pathways were analyzed by quantitative real-time polymerase chain reaction and cluster analysis. Based on the similarity of their expression patterns, the genes were classified into two main groups: C1 and C2; and the genes in group C1 had high relative expression level in the root or low in the bud and leaves. The expression patterns of genes in C2-2-1 and C2-2-2-1 groups were probably responsible for the development-dependent accumulation of phenolic compounds in the leaves. Enzymatic analysis suggested that the accumulation of catechins was influenced simultaneously by catabolism and anabolism. Further research is recommended to know the expression patterns of various genes and the reason for the variation in contents of different compounds in different growth stages and also in different organs.

  6. Dietary Docosahexaenoic Acid and trans-10, cis-12-Conjugated Linoleic Acid Differentially Alter Oxylipin Profiles in Mouse Periuterine Adipose Tissue.

    Science.gov (United States)

    Adkins, Yuriko; Belda, Benjamin J; Pedersen, Theresa L; Fedor, Dawn M; Mackey, Bruce E; Newman, John W; Kelley, Darshan S

    2017-05-01

    Diets containing high n-3 polyunsaturated fatty acids (PUFA) decrease inflammation and the incidence of chronic diseases including cardiovascular disease and nonalcoholic fatty liver disease while trans-fatty acids (TFA) intake increases the incidence of these conditions. Some health benefits of n-3 PUFA are mediated through the impact of their oxygenated metabolites, i.e. oxylipins. The TFA, trans-10, cis-12-conjugated linoleic acid (CLA; 18:2n-6) is associated with adipose tissue (AT) inflammation, oxidative stress, and wasting. We examined the impact of a 4-week feeding of 0, 0.5, and 1.5% docosahexaenoic acid (DHA; 22:6n-3) in the presence and absence of 0.5% CLA on AT oxylipin profiles in female C57BL/6N mice. Esterified oxylipins in AT derived from linoleic acid (LNA), alpha-linolenic acid (ALA), arachidonic acid (ARA), eicosapentaenoic acid (EPA), DHA, and putative from CLA were quantified. CLA containing diets reduced AT mass by ~62%. Compared with the control diet, the DHA diet elevated concentrations of EPA-and DHA-derived alcohols and epoxides and LNA-derived alcohols, reduced ARA-derived alcohols, ketones, epoxides, and 6-keto-prostaglandin (PG) F1α (P < 0.05), and had mixed effects on ALA-derived alcohols. Dietary CLA lowered EPA-, DHA-, and ALA-derived epoxides, ARA-derived ketones and epoxides, and ALA-derived alcohols. While dietary CLA induced variable effects in EPA-, DHA-, and LNA-derived alcohols and LNA-derived ketones, it elevated ARA-derived alcohols and PGF1α, PGF2α, and F2-isoprostanes. DHA counteracted CLA-induced effects in 67, 57, 43, and 29% of total DHA-, ARA-, EPA-, and ALA-derived oxylipins, respectively. Thus, CLA elevated proinflammatory oxylipins while DHA increased anti-inflammatory oxylipins and diminished concentration of CLA-induced pro-inflammatory oxylipins in AT.

  7. Transcriptional profiling of rat white adipose tissue response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin.

    Science.gov (United States)

    Houlahan, Kathleen E; Prokopec, Stephenie D; Sun, Ren X; Moffat, Ivy D; Lindén, Jere; Lensu, Sanna; Okey, Allan B; Pohjanvirta, Raimo; Boutros, Paul C

    2015-10-15

    Polychlorinated dibenzodioxins are environmental contaminants commonly produced as a by-product of industrial processes. The most potent of these, 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD), is highly lipophilic, leading to bioaccumulation. White adipose tissue (WAT) is a major site for energy storage, and is one of the organs in which TCDD accumulates. In laboratory animals, exposure to TCDD causes numerous metabolic abnormalities, including a wasting syndrome. We therefore investigated the molecular effects of TCDD exposure on WAT by profiling the transcriptomic response of WAT to 100μg/kg of TCDD at 1 or 4days in TCDD-sensitive Long-Evans (Turku/AB; L-E) rats. A comparative analysis was conducted simultaneously in identically treated TCDD-resistant Han/Wistar (Kuopio; H/W) rats one day after exposure to the same dose. We sought to identify transcriptomic changes coinciding with the onset of toxicity, while gaining additional insight into later responses. More transcriptional responses to TCDD were observed at 4days than at 1day post-exposure, suggesting WAT shows mostly secondary responses. Two classic AHR-regulated genes, Cyp1a1 and Nqo1, were significantly induced by TCDD in both strains, while several genes involved in the immune response, including Ms4a7 and F13a1 were altered in L-E rats alone. We compared genes affected by TCDD in rat WAT and human adipose cells, and observed little overlap. Interestingly, very few genes involved in lipid metabolism exhibited altered expression levels despite the pronounced lipid mobilization from peripheral fat pads by TCDD in L-E rats. Of these genes, the lipolysis-associated Lpin1 was induced slightly over 2-fold in L-E rat WAT on day 4.

  8. Tissue-specific, development-dependent phenolic compounds accumulation profile and gene expression pattern in tea plant [Camellia sinensis].

    Science.gov (United States)

    Jiang, Xiaolan; Liu, Yajun; Li, Weiwei; Zhao, Lei; Meng, Fei; Wang, Yunsheng; Tan, Huarong; Yang, Hua; Wei, Chaoling; Wan, Xiaochun; Gao, Liping; Xia, Tao

    2013-01-01

    Phenolic compounds in tea plant [Camellia sinensis (L.)] play a crucial role in dominating tea flavor and possess a number of key pharmacological benefits on human health. The present research aimed to study the profile of tissue-specific, development-dependent accumulation pattern of phenolic compounds in tea plant. A total of 50 phenolic compounds were identified qualitatively using liquid chromatography in tandem mass spectrometry technology. Of which 29 phenolic compounds were quantified based on their fragmentation behaviors. Most of the phenolic compounds were higher in the younger leaves than that in the stem and root, whereas the total amount of proanthocyanidins were unexpectedly higher in the root. The expression patterns of 63 structural and regulator genes involved in the shikimic acid, phenylpropanoid, and flavonoid pathways were analyzed by quantitative real-time polymerase chain reaction and cluster analysis. Based on the similarity of their expression patterns, the genes were classified into two main groups: C1 and C2; and the genes in group C1 had high relative expression level in the root or low in the bud and leaves. The expression patterns of genes in C2-2-1 and C2-2-2-1 groups were probably responsible for the development-dependent accumulation of phenolic compounds in the leaves. Enzymatic analysis suggested that the accumulation of catechins was influenced simultaneously by catabolism and anabolism. Further research is recommended to know the expression patterns of various genes and the reason for the variation in contents of different compounds in different growth stages and also in different organs.

  9. RNA-Seq gene expression profiling of HepG2 cells: the influence of experimental factors and comparison with liver tissue.

    Science.gov (United States)

    Tyakht, Alexander V; Ilina, Elena N; Alexeev, Dmitry G; Ischenko, Dmitry S; Gorbachev, Alexey Y; Semashko, Tatiana A; Larin, Andrei K; Selezneva, Oksana V; Kostryukova, Elena S; Karalkin, Pavel A; Vakhrushev, Igor V; Kurbatov, Leonid K; Archakov, Alexander I; Govorun, Vadim M

    2014-12-15

    Human hepatoma HepG2 cells are used as an in vitro model of the human liver. High-throughput transcriptomic sequencing is an advanced approach for assessing the functional state of a tissue or cell type. However, the influence of experimental factors, such as the sample preparation method and inter-laboratory variation, on the transcriptomic profile has not been evaluated. The whole-transcriptome sequencing of HepG2 cells was performed using the SOLiD platform and validated using droplet digital PCR. The gene expression profile was compared to the results obtained with the same sequencing method in another laboratory and using another sample preparation method. We also compared the transcriptomic profile HepG2 cells with that of liver tissue. Comparison of the gene expression profiles between the HepG2 cell line and liver tissue revealed the highest variation, followed by HepG2 cells submitted to two different sample preparation protocols. The lowest variation was observed between HepG2 cells prepared by two different laboratories using the same protocol. The enrichment analysis of the genes that were differentially expressed between HepG2 cells and liver tissue mainly revealed the cancer-associated gene signature of HepG2 cells and the activation of the response to chemical stimuli in the liver tissue. The HepG2 transcriptome obtained with the SOLiD platform was highly correlated with the published transcriptome obtained with the Illumina and Helicos platforms, with moderate correspondence to microarrays. In the present study, we assessed the influence of experimental factors on the HepG2 transcriptome and identified differences in gene expression between the HepG2 cell line and liver cells. These findings will facilitate robust experimental design in the fields of pharmacology and toxicology. Our results were supported by a comparative analysis with previous HepG2 gene expression studies.

  10. Nutrition modulates Fto and Irx3 gene transcript levels, but does not alter their DNA methylation profiles in rat white adipose tissues.

    Science.gov (United States)

    Nowacka-Woszuk, Joanna; Pruszynska-Oszmalek, Ewa; Szydlowski, Maciej; Szczerbal, Izabela

    2017-02-05

    The fat mass and obesity associated (Fto) and iroquois homeobox 3 (Irx3) genes have been recognised as important obesity-related genes. Studies on the expression of these genes in the fat tissue of human and mouse have produced inconsistent results, while similar data on rat are limited. Environmental factors such as diet, should be considered as potential modulators of gene transcript levels through epigenetic mechanisms including DNA methylation. The aim of this study was to evaluate transcription levels and DNA methylation profiles of rat Fto and Irx3 genes in two white adipose tissue depots in response to high-fat and high-protein diets. The relative transcript levels of Fto and Irx3 were shown to be tissue-specific with higher levels detected in subcutaneous fat tissue than in abdominal fat tissue. Moreover, negative correlations between the transcripts of both genes were observed for subcutaneous fat tissue. The identified interactions (e.g. diet×duration of diet regimen) indicated that the diet had an impact on the transcript level; however, this effect was dependent on the duration of the diet regimen. The high-fat diet led to upregulation of Fto and Irx3 linearly with time across the two tissues. DNA methylation of the regulatory regions of the studied genes was very low and not related with the tissue, diet, or duration of diet regimen. Our study revealed that diet was an important factor modulating transcription of Fto and Irx3, but its affect depended on its duration. In contrast, the DNA methylation profiles of Fto and Irx3 were not altered by nutrition, which may indicate that the feeding type, when applied postnatally, did not affect DNA methylation of these genes.

  11. Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling.

    Science.gov (United States)

    Basse, Astrid L; Dixen, Karen; Yadav, Rachita; Tygesen, Malin P; Qvortrup, Klaus; Kristiansen, Karsten; Quistorff, Bjørn; Gupta, Ramneek; Wang, Jun; Hansen, Jacob B

    2015-03-19

    Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). We analyzed the postnatal transformation of adipose in sheep with a time course study of the perirenal adipose depot. We observed changes in tissue morphology, gene expression and metabolism within the first two weeks of postnatal life consistent with the expected transition from BAT to WAT. The transformation was characterized by massively decreased mitochondrial abundance and down-regulation of gene expression related to mitochondrial function and oxidative phosphorylation. Global gene expression profiling demonstrated that the time points grouped into three phases: a brown adipose phase, a transition phase and a white adipose phase. Between the brown adipose and the transition phase 170 genes were differentially expressed, and 717 genes were differentially expressed between the transition and the white adipose phase. Thirty-eight genes were shared among the two sets of differentially expressed genes. We identified a number of regulated transcription factors, including NR1H3, MYC, KLF4, ESR1, RELA and BCL6, which were linked to the overall changes in gene expression during the adipose tissue remodeling. Finally, the perirenal adipose tissue expressed both brown and brite/beige adipocyte marker genes at birth, the expression of which changed substantially over time. Using global gene expression profiling of the postnatal BAT to WAT transformation in sheep, we provide novel insight into adipose tissue plasticity in a large mammal, including identification of novel transcriptional components linked to adipose tissue remodeling. Moreover, our data set provides a useful resource for further studies in adipose tissue plasticity.

  12. Olfactory cells via nasal biopsy reflect the developing brain in gene expression profiles: utility and limitation of the surrogate tissues in research for brain disorders.

    Science.gov (United States)

    Horiuchi, Yasue; Kano, Shin-Ichi; Ishizuka, Koko; Cascella, Nicola G; Ishii, Seiji; Talbot, C Conover; Jaffe, Andrew E; Okano, Hideyuki; Pevsner, Jonathan; Colantuoni, Carlo; Sawa, Akira

    2013-12-01

    Human olfactory cells obtained by rapid nasal biopsy have been suggested to be a good surrogate system to address brain disease-associated molecular changes. Nonetheless, whether use of this experimental strategy is justified remains unclear. Here we compared expression profiles of olfactory cells systematically with those from the brain tissues and other cells. Principal component analysis indicated that the expression profiles of olfactory cells are very different from those of blood cells, but are closer to those of stem cells, in particular mesenchymal stem cells, that can be differentiated into the cells of the central nervous system.

  13. Highway Companies Deny Windfall Profits

    Institute of Scientific and Technical Information of China (English)

    Securities Daily

    2011-01-01

    @@ There is no denying that the real estate industry sees huge profits, but it is hard to imag-ine that the gross profits of highway companies have reached a very high level, becoming another typical industry of huge profits.The sky-high road toll is attracting more and more public concerns about the seemingly low-profile and stable industry.

  14. Comparative pharmacokinetic and tissue distribution profiles of four major bioactive components in normal and hepatic fibrosis rats after oral administration of Fuzheng Huayu recipe.

    Science.gov (United States)

    Yang, Tao; Liu, Shan; Wang, Chang-Hong; Tao, Yan-Yan; Zhou, Hua; Liu, Cheng-Hai

    2015-10-10

    Fuzheng Huayu recipe (FZHY) is a herbal product for the treatment of liver fibrosis approved by the Chinese State Food and Drug Administration (SFDA), but its pharmacokinetics and tissue distribution had not been investigated. In this study, the liver fibrotic model was induced with intraperitoneal injection of dimethylnitrosamine (DMN), and FZHY was given orally to the model and normal rats. The plasma pharmacokinetics and tissue distribution profiles of four major bioactive components from FZHY were analyzed in the normal and fibrotic rat groups using an ultrahigh performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method. Results revealed that the bioavailabilities of danshensu (DSS), salvianolic acid B (SAB) and rosmarinic acid (ROS) in liver fibrotic rats increased 1.49, 3.31 and 2.37-fold, respectively, compared to normal rats. There was no obvious difference in the pharmacokinetics of amygdalin (AMY) between the normal and fibrotic rats. The tissue distribution of DSS, SAB, and AMY trended to be mostly in the kidney and lung. The distribution of DSS, SAB, and AMY in liver tissue of the model rats was significantly decreased compared to the normal rats. Significant differences in the pharmacokinetics and tissue distribution profiles of DSS, ROS, SAB and AMY were observed in rats with hepatic fibrosis after oral administration of FZHY. These results provide a meaningful basis for developing a clinical dosage regimen in the treatment of hepatic fibrosis by FZHY. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Tissue Classification

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, David Gerald [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-01-01

    The project began as a e ort to support InLight and Lumidigm. With the sale of the companies to a non-New Mexico entity, the project then focused on supporting a new company Medici Technologies. The Small Business (SB) is attempting to quantify glucose in tissue using a series of short interferometer scans of the nger. Each scan is produced from a novel presentation of the nger to the device. The intent of the project is to identify and, if possible, implement improved methods for classi cation, feature selection, and training to improve the performance of predictive algorithms used for tissue classi cation.

  16. Tissue-restricted expression of Nrf2 and its target genes in zebrafish with gene-specific variations in the induction profiles.

    Directory of Open Access Journals (Sweden)

    Hitomi Nakajima

    Full Text Available The Keap1-Nrf2 system serves as a defense mechanism against oxidative stress and electrophilic toxicants by inducing more than one hundred cytoprotective proteins, including antioxidants and phase 2 detoxifying enzymes. Since induction profiles of Nrf2 target genes have been studied exclusively in cultured cells, and not in animal models, their tissue-specificity has not been well characterized. In this paper, we examined and compared the tissue-specific expression of several Nrf2 target genes in zebrafish larvae by whole-mount in situ hybridization (WISH. Seven zebrafish genes (gstp1, mgst3b, prdx1, frrs1c, fthl, gclc and hmox1a suitable for WISH analysis were selected from candidates for Nrf2 targets identified by microarray analysis. Tissue-restricted induction was observed in the nose, gill, and/or liver for all seven genes in response to Nrf2-activating compounds, diethylmaleate (DEM and sulforaphane. The Nrf2 gene itself was dominantly expressed in these three tissues, implying that tissue-restricted induction of Nrf2 target genes is defined by tissue-specific expression of Nrf2. Interestingly, the induction of frrs1c and gclc in liver and nose, respectively, was quite low and that of hmox1a was restricted in the liver. These results indicate the existence of gene-specific variations in the tissue specificity, which can be controlled by factors other than Nrf2.

  17. Trans-10,cis-12-CLA-caused lipodystrophy is associated with profound changes of fatty acid profiles of liver, white adipose tissue and erythrocytes in mice: possible link to tissue-specific alterations of fatty acid desaturation.

    Science.gov (United States)

    Jaudszus, Anke; Moeckel, Peter; Hamelmann, Eckard; Jahreis, Gerhard

    2010-01-01

    Dietary supplementation with conjugated linoleic acid (CLA) has been shown to reduce body fat mass. To investigate the effects of individual CLA isomers on the fatty acid profiles of lipogenic (liver and white adipose) and lipid sensitive (erythrocyte) tissues, BALB/c mice were fed with 1 of 2 diets supplemented with either a c9,t11-CLA-enriched and t10,c12-CLA-free or a CLA-mixture containing both isomers in equal amounts (1% w/w of the diet) for 5 weeks. A control group was fed with a diet enriched in sunflower oil to energy balance the CLA. Compared to the t10,c12-CLA-free and the control diets, we observed a significant reduction of adipose tissue accompanied by fatty livers in the CLA-mix-fed group. These alterations in body fat distribution entailed a conspicuous shift of the fatty acid profiles of adipose tissue and livers. Liver enlargement was mainly caused by accumulation of C18 monoenes that accounted for 67 ± 1% of total fatty acid methyl esters. The significant reduction of the 18:0/18:1 desaturation index in the liver upon CLA-mix diet indicated high stearoyl-CoA desaturase activity. In contrast, reduction in white adipose tissue was largely driven by percental reduction of monounsaturated fatty acids (p ≤ 0.001). 16:0/ 16:1 and 18:0/18:1 desaturation indices for white adipose tissue significantly increased, suggesting an inhibition of stearoyl-CoA desaturase upon CLA-mix diet. The fatty acid profile of the erythrocytes widely reflected that of livers, depending on the supplemented diet. These profound changes in fatty acid composition of lipogenic organs due to t10,c12-CLA intake may be the consequence of functional alterations of lipid metabolism.

  18. Power System Security and Stability Control Company

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    Branch Company Profile Power System Security and Stability Control Company is called "NARI Stability" to externals. It has a scientific research team, led by Prof. Yusheng Xue, who is an international renowned expert on stability technology, and an academician of the Chinese Academy of Engineering. Based on support and service of security and stability control technology and equipment,

  19. Gene expression profile of the cartilage tissue spontaneously regenerated in vivo by using a novel double-network gel: Comparisons with the normal articular cartilage

    Directory of Open Access Journals (Sweden)

    Kurokawa Takayuki

    2011-09-01

    Full Text Available Abstract Background We have recently found a phenomenon that spontaneous regeneration of a hyaline cartilage-like tissue can be induced in a large osteochondral defect by implanting a double-network (DN hydrogel plug, which was composed of poly-(2-Acrylamido-2-methylpropanesulfonic acid and poly-(N, N'-Dimetyl acrylamide, at the bottom of the defect. The purpose of this study was to clarify gene expression profile of the regenerated tissue in comparison with that of the normal articular cartilage. Methods We created a cylindrical osteochondral defect in the rabbit femoral grooves. Then, we implanted the DN gel plug at the bottom of the defect. At 2 and 4 weeks after surgery, the regenerated tissue was analyzed using DNA microarray and immunohistochemical examinations. Results The gene expression profiles of the regenerated tissues were macroscopically similar to the normal cartilage, but showed some minor differences. The expression degree of COL2A1, COL1A2, COL10A1, DCN, FMOD, SPARC, FLOD2, CHAD, CTGF, and COMP genes was greater in the regenerated tissue than in the normal cartilage. The top 30 genes that expressed 5 times or more in the regenerated tissue as compared with the normal cartilage included type-2 collagen, type-10 collagen, FN, vimentin, COMP, EF1alpha, TFCP2, and GAPDH genes. Conclusions The tissue regenerated by using the DN gel was genetically similar but not completely identical to articular cartilage. The genetic data shown in this study are useful for future studies to identify specific genes involved in spontaneous cartilage regeneration.

  20. Development of a 3D Tissue Culture–Based High-Content Screening Platform That Uses Phenotypic Profiling to Discriminate Selective Inhibitors of Receptor Tyrosine Kinases

    OpenAIRE

    Booij, T.H.; Klop, M.J.; Yan, K.; Szántai-Kis, C.; Szokol, B.; L. Orfi; Water, de; Keri, G.; Price, L. S.

    2016-01-01

    3D tissue cultures provide a more physiologically relevant context for the screening of compounds, compared with 2D cell cultures. Cells cultured in 3D hydrogels also show complex phenotypes, increasing the scope for phenotypic profiling. Here we describe a high-content screening platform that uses invasive human prostate cancer cells cultured in 3D in standard 384-well assay plates to study the activity of potential therapeutic small molecules and antibody biologics. Image analysis tools wer...

  1. Epigenomic profiling in visceral white adipose tissue of offspring of mice exposed to late gestational sleep fragmentation.

    Science.gov (United States)

    Cortese, R; Khalyfa, A; Bao, R; Andrade, J; Gozal, D

    2015-07-01

    Sleep fragmentation during late gestation (LG-SF) is one of the major perturbations associated with sleep apnea and other sleep disorders during pregnancy. We have previously shown that LG-SF induces metabolic dysfunction in offspring mice during adulthood. To investigate the effects of late LG-SF on metabolic homeostasis in offspring and to determine the effects of LG-SF on the epigenome of visceral white adipose tissue (VWAT) in the offspring. Time-pregnant mice were exposed to LG-SF or sleep control during LG (LG-SC) conditions during the last 6 days of gestation. At 24 weeks of age, lipid profiles and metabolic parameters were assessed in the offspring. We performed large-scale DNA methylation analyses using methylated DNA immunoprecipitation (MeDIP) coupled with microarrays (MeDIP-chip) in VWAT of 24-week-old LG-SF and LG-SC offspring (n=8 mice per group). Univariate multiple-testing adjusted statistical analyses were applied to identify differentially methylated regions (DMRs) between the groups. DMRs were mapped to their corresponding genes, and tested for potential overlaps with biological pathways and gene networks. We detected significant increases in body weight (31.7 vs 28.8 g; P=0.001), visceral (642.1 vs 497.0 mg; P=0.002) and subcutaneous (293.1 vs 250.1 mg; P=0.001) fat mass, plasma cholesterol (110.6 vs 87.6 mg dl(-1); P=0.001), triglycerides (87.3 vs 84.1 mg dl(-1); P=0.003) and homeostatic model assessment-insulin resistance values (8.1 vs 6.1; P=0.007) in the LG-SF group. MeDIP analyses revealed that 2148 DMRs (LG-SF vs LG-SC; P<0.0001, model-based analysis of tilling-arrays algorithm). A large proportion of the DMR-associated genes have reported functions that are altered in obesity and metabolic syndrome, such as Cartpt, Akt2, Apoe, Insr1 and so on. Overrepresented pathways and gene networks were related to metabolic regulation and inflammatory response. Our findings show a major role for epigenomic regulation of pathways

  2. Photogrammetric Comparison of Facial Soft Tissue Profile before and after Protraction Facemask Therapy in Class III Children (6-11 Years Old

    Directory of Open Access Journals (Sweden)

    Vahid Moshkelgosha

    2017-03-01

    Full Text Available Statement of the Problem: Achieving a normal soft tissue facial profile is considered to be the main concern of class III patients and the goal of most class III treatments. Purpose: The purpose of this study was to investigate the effects of facemask treatment on profile with photogrammetric method. Materials and Method: Before (T0 and after (T1 treatment photograms of 40 class III patients profiles (20 male and 20 female individuals treated with protraction face mask that met the inclusion criteria were digitized and analyzed using Aesthetic Analyzer software. Selected linear and angular measurements were performed for each patient and the changes were noted. Results: An increase in inferior facial height (p< 0.001 and inferior facial angle (p< 0.001 was observed. Nasal prominence and upper lip prominence also increased significantly (p< 0.001. Advancement of sub nasal area was observed to be significant in females (p< 0.05 in contrast to males. Conclusion: Remarkable advancement in the middle face and consequent fullness in the soft-tissue profile can be achieved by using protraction face mask. The response to treatment is not different between males and females.

  3. Development of a 3D Tissue Culture-Based High-Content Screening Platform That Uses Phenotypic Profiling to Discriminate Selective Inhibitors of Receptor Tyrosine Kinases.

    Science.gov (United States)

    Booij, Tijmen H; Klop, Maarten J D; Yan, Kuan; Szántai-Kis, Csaba; Szokol, Balint; Orfi, Laszlo; van de Water, Bob; Keri, Gyorgy; Price, Leo S

    2016-10-01

    3D tissue cultures provide a more physiologically relevant context for the screening of compounds, compared with 2D cell cultures. Cells cultured in 3D hydrogels also show complex phenotypes, increasing the scope for phenotypic profiling. Here we describe a high-content screening platform that uses invasive human prostate cancer cells cultured in 3D in standard 384-well assay plates to study the activity of potential therapeutic small molecules and antibody biologics. Image analysis tools were developed to process 3D image data to measure over 800 phenotypic parameters. Multiparametric analysis was used to evaluate the effect of compounds on tissue morphology. We applied this screening platform to measure the activity and selectivity of inhibitors of the c-Met and epidermal growth factor (EGF) receptor (EGFR) tyrosine kinases in 3D cultured prostate carcinoma cells. c-Met and EGFR activity was quantified based on the phenotypic profiles induced by their respective ligands, hepatocyte growth factor and EGF. The screening method was applied to a novel collection of 80 putative inhibitors of c-Met and EGFR. Compounds were identified that induced phenotypic profiles indicative of selective inhibition of c-Met, EGFR, or bispecific inhibition of both targets. In conclusion, we describe a fully scalable high-content screening platform that uses phenotypic profiling to discriminate selective and nonselective (off-target) inhibitors in a physiologically relevant 3D cell culture setting.

  4. Distinctive Glycerophospholipid Profiles of Human Seminoma and Adjacent Normal Tissues by Desorption Electrospray Ionization Imaging Mass Spectrometry

    Science.gov (United States)

    Masterson, Timothy A.; Dill, Allison L.; Eberlin, Livia S.; Mattarozzi, Monica; Cheng, Liang; Beck, Stephen D. W.; Bianchi, Federica; Cooks, R. Graham

    2011-08-01

    Desorption electrospray ionization mass spectrometry (DESI-MS) has been successfully used to discriminate between normal and cancerous human tissue from different anatomical sites. On the basis of this, DESI-MS imaging was used to characterize human seminoma and adjacent normal tissue. Seminoma and adjacent normal paired human tissue sections (40 tissues) from 15 patients undergoing radical orchiectomy were flash frozen in liquid nitrogen and sectioned to 15 μm thickness and thaw mounted to glass slides. The entire sample was two-dimensionally analyzed by the charged solvent spray to form a molecular image of the biological tissue. DESI-MS images were compared with formalin-fixed, hematoxylin and eosin (H&E) stained slides of the same material. Increased signal intensity was detected for two seminolipids [seminolipid (16:0/16:0) and seminolipid (30:0)] in the normal tubule testis tissue; these compounds were undetectable in seminoma tissue, as well as from the surrounding fat, muscle, and blood vessels. A glycerophosphoinositol [PI(18:0/20:4)] was also found at increased intensity in the normal testes tubule tissue when compared with seminoma tissue. Ascorbic acid (i.e., vitamin C) was found at increased amounts in seminoma tissue when compared with normal tissue. DESI-MS analysis was successfully used to visualize the location of several types of molecules across human seminoma and normal tissues. Discrimination between seminoma and adjacent normal testes tubules was achieved on the basis of the spatial distributions and varying intensities of particular lipid species as well as ascorbic acid. The increased presence of ascorbic acid within seminoma compared with normal seminiferous tubules was previously unknown.

  5. Screening of tissue-specific genes and promoters in tomato by comparing genome wide expression profiles of Arabidopsis orthologues.

    Science.gov (United States)

    Lim, Chan Ju; Lee, Ha Yeon; Kim, Woong Bom; Lee, Bok-Sim; Kim, Jungeun; Ahmad, Raza; Kim, Hyun A; Yi, So Young; Hur, Cheol-Goo; Kwon, Suk-Yoon

    2012-07-01

    Constitutive overexpression of transgenes occasionally interferes with normal growth and developmental processes in plants. Thus, the development of tissue-specific promoters that drive transgene expression has become agriculturally important. To identify tomato tissue-specific promoters, tissue-specific genes were screened using a series of in silico-based and experimental procedures, including genome-wide orthologue searches of tomato and Arabidopsis databases, isolation of tissue-specific candidates using an Arabidopsis microarray database, and validation of tissue specificity by reverse transcription-polymerase chain reaction (RT-PCR) analysis and promoter assay. Using these procedures, we found 311 tissue-specific candidate genes and validated 10 tissue-specific genes by RT-PCR. Among these identified genes, histochemical analysis of five isolated promoter::GUS transgenic tomato and Arabidopsis plants revealed that their promoters have different but distinct tissue-specific activities in anther, fruit, and root, respectively. Therefore, it appears these in silico-based screening approaches in addition to the identification of new tissue-specific genes and promoters will be helpful for the further development of tailored crop development.

  6. A diet enriched with Mugil cephalus processed roes modulates the tissue lipid profile in healthy rats: a biochemical and chemometric assessment.

    Science.gov (United States)

    Rosa, A; Atzeri, A; Putzu, D; Scano, P

    2016-01-01

    The effect of a diet enriched with mullet bottarga on the lipid profile (total lipids, total cholesterol, unsaturated fatty acids, α-tocopherol, and hydroperoxides) of plasma, liver, kidney, brain, and perirenal adipose tissues of healthy rats was investigated. Rats fed a 10% bottarga enriched-diet for 5 days showed body weights and tissue total lipid and cholesterol levels similar to those of animals fed control diet. Univariate and multivariate results showed that bottarga enriched-diet modified the fatty acid profile in all tissues, except brain. Significant increases of n-3 PUFA, particularly EPA, were observed together with a 20:4 n-6 decrease in plasma, liver, and kidney. Perirenal adipose tissue showed a fat accumulation that reflected the diet composition. The overall data suggest that mullet bottarga may be considered as a natural bioavailable source of n-3 PUFA and qualify it as a traditional food product with functional properties and a potential functional ingredient for preparation of n-3 PUFA enriched foods.

  7. Differential transcript profiles of MHC class Ib(Qa-1, Qa-2, and Qa-10) and Aire genes during the ontogeny of thymus and other tissues.

    Science.gov (United States)

    Melo-Lima, Breno Luiz; Evangelista, Adriane Feijó; de Magalhães, Danielle Aparecida Rosa; Passos, Geraldo Aleixo; Moreau, Philippe; Donadi, Eduardo Antonio

    2014-01-01

    Qa-2 and Qa-1 are murine nonclassical MHC class I molecules involved in the modulation of immune responses by interacting with T CD8(+) and NK cell inhibitory receptors. During thymic education, the Aire gene imposes the expression of thousands of tissue-related antigens in the thymic medulla, permitting the negative selection events. Aiming to characterize the transcriptional profiles of nonclassical MHC class I genes in spatial-temporal association with the Aire expression, we evaluated the gene expression of H2-Q7(Qa-2), H2-T23(Qa-1), H2-Q10(Qa-10), and Aire during fetal and postnatal development of thymus and other tissues. In the thymus, H2-Q7(Qa-2) transcripts were detected at high levels throughout development and were positively correlated with Aire expression during fetal ages. H2-Q7(Qa-2) and H2-T23(Qa-1) showed distinct expression patterns with gradual increasing levels according to age in most tissues analyzed. H2-Q10(Qa-10) was preferentially expressed by the liver. The Aire transcriptional profile showed increased levels during the fetal period and was detectable in postnatal ages in the thymus. Overall, nonclassical MHC class I genes started to be expressed early during the ontogeny. Their levels varied according to age, tissue, and mouse strain analyzed. This differential expression may contribute to the distinct patterns of mouse susceptibility/resistance to infectious and noninfectious disorders.

  8. Gene expression profiling of subcutaneous adipose tissue in morbid obesity using a focused microarray: distinct expression of cell-cycle- and differentiation-related genes.

    Science.gov (United States)

    Rodríguez-Acebes, Sara; Palacios, Nuria; Botella-Carretero, José I; Olea, Nuria; Crespo, Lorena; Peromingo, Roberto; Gómez-Coronado, Diego; Lasunción, Miguel A; Vázquez, Clotilde; Martínez-Botas, Javier

    2010-12-23

    Obesity results from an imbalance between food intake and energy expenditure, which leads to an excess of adipose tissue. The excess of adipose tissue and adipocyte dysfunction associated with obesity are linked to the abnormal regulation of adipogenesis. The objective of this study was to analyze the expression profile of cell-cycle- and lipid-metabolism-related genes of adipose tissue in morbid obesity. We used a custom-made focused cDNA microarray to determine the adipose tissue mRNA expression profile. Gene expression of subcutaneous abdominal fat samples from 15 morbidly obese women was compared with subcutaneous fat samples from 10 nonobese control patients. The findings were validated in an independent population of 31 obese women and 9 obese men and in an animal model of obesity (Lepob/ob mice) by real-time RT-PCR. Microarray analysis revealed that transcription factors that regulate the first stages of adipocyte differentiation, such as CCAAT/enhancer binding protein beta (C/EBPβ) and JUN, were upregulated in the adipose tissues of morbidly obese patients. The expression of peroxisome proliferator-activated receptor gamma (PPARγ), a transcription factor which controls lipid metabolism and the final steps of preadipocyte conversion into mature adipocytes, was downregulated. The expression of three cyclin-dependent kinase inhibitors that regulate clonal expansion and postmitotic growth arrest during adipocyte differentiation was also altered in obese subjects: p18 and p27 were downregulated, and p21 was upregulated. Angiopoietin-like 4 (ANGPTL4), which regulates angiogenesis, lipid and glucose metabolism and it is know to increase dramatically in the early stages of adipocyte differentiation, was upregulated. The expression of C/EBPβ, p18, p21, JUN, and ANGPTL4 presented similar alterations in subcutaneous adipose tissue of Lepob/ob mice. Our microarray gene profiling study revealed that the expression of genes involved in adipogenesis is profoundly

  9. Gene expression profiling of subcutaneous adipose tissue in morbid obesity using a focused microarray: Distinct expression of cell-cycle- and differentiation-related genes

    Science.gov (United States)

    2010-01-01

    Background Obesity results from an imbalance between food intake and energy expenditure, which leads to an excess of adipose tissue. The excess of adipose tissue and adipocyte dysfunction associated with obesity are linked to the abnormal regulation of adipogenesis. The objective of this study was to analyze the expression profile of cell-cycle- and lipid-metabolism-related genes of adipose tissue in morbid obesity. Methods We used a custom-made focused cDNA microarray to determine the adipose tissue mRNA expression profile. Gene expression of subcutaneous abdominal fat samples from 15 morbidly obese women was compared with subcutaneous fat samples from 10 nonobese control patients. The findings were validated in an independent population of 31 obese women and 9 obese men and in an animal model of obesity (Lepob/ob mice) by real-time RT-PCR. Results Microarray analysis revealed that transcription factors that regulate the first stages of adipocyte differentiation, such as CCAAT/enhancer binding protein beta (C/EBPβ) and JUN, were upregulated in the adipose tissues of morbidly obese patients. The expression of peroxisome proliferator-activated receptor gamma (PPARγ), a transcription factor which controls lipid metabolism and the final steps of preadipocyte conversion into mature adipocytes, was downregulated. The expression of three cyclin-dependent kinase inhibitors that regulate clonal expansion and postmitotic growth arrest during adipocyte differentiation was also altered in obese subjects: p18 and p27 were downregulated, and p21 was upregulated. Angiopoietin-like 4 (ANGPTL4), which regulates angiogenesis, lipid and glucose metabolism and it is know to increase dramatically in the early stages of adipocyte differentiation, was upregulated. The expression of C/EBPβ, p18, p21, JUN, and ANGPTL4 presented similar alterations in subcutaneous adipose tissue of Lepob/ob mice. Conclusions Our microarray gene profiling study revealed that the expression of genes

  10. Gene expression profiling of subcutaneous adipose tissue in morbid obesity using a focused microarray: Distinct expression of cell-cycle- and differentiation-related genes

    Directory of Open Access Journals (Sweden)

    Gómez-Coronado Diego

    2010-12-01

    Full Text Available Abstract Background Obesity results from an imbalance between food intake and energy expenditure, which leads to an excess of adipose tissue. The excess of adipose tissue and adipocyte dysfunction associated with obesity are linked to the abnormal regulation of adipogenesis. The objective of this study was to analyze the expression profile of cell-cycle- and lipid-metabolism-related genes of adipose tissue in morbid obesity. Methods We used a custom-made focused cDNA microarray to determine the adipose tissue mRNA expression profile. Gene expression of subcutaneous abdominal fat samples from 15 morbidly obese women was compared with subcutaneous fat samples from 10 nonobese control patients. The findings were validated in an independent population of 31 obese women and 9 obese men and in an animal model of obesity (Lepob/ob mice by real-time RT-PCR. Results Microarray analysis revealed that transcription factors that regulate the first stages of adipocyte differentiation, such as CCAAT/enhancer binding protein beta (C/EBPβ and JUN, were upregulated in the adipose tissues of morbidly obese patients. The expression of peroxisome proliferator-activated receptor gamma (PPARγ, a transcription factor which controls lipid metabolism and the final steps of preadipocyte conversion into mature adipocytes, was downregulated. The expression of three cyclin-dependent kinase inhibitors that regulate clonal expansion and postmitotic growth arrest during adipocyte differentiation was also altered in obese subjects: p18 and p27 were downregulated, and p21 was upregulated. Angiopoietin-like 4 (ANGPTL4, which regulates angiogenesis, lipid and glucose metabolism and it is know to increase dramatically in the early stages of adipocyte differentiation, was upregulated. The expression of C/EBPβ, p18, p21, JUN, and ANGPTL4 presented similar alterations in subcutaneous adipose tissue of Lepob/ob mice. Conclusions Our microarray gene profiling study revealed that the

  11. Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling

    DEFF Research Database (Denmark)

    Basse, Astrid L.; Dixen, Karen; Yadav, Rachita;

    2015-01-01

    abundance and down-regulation of gene expression related to mitochondrial function and oxidative phosphorylation. Global gene expression profiling demonstrated that the time points grouped into three phases: a brown adipose phase, a transition phase and a white adipose phase. Between the brown adipose......Background: Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). Results: We analyzed the postnatal transformation of adipose in sheep...... with a time course study of the perirenal adipose depot. We observed changes in tissue morphology, gene expression and metabolism within the first two weeks of postnatal life consistent with the expected transition from BAT to WAT. The transformation was characterized by massively decreased mitochondrial...

  12. Gene expression profiles reveal effect of a high-fat diet on the development of white and brown adipose tissues.

    Science.gov (United States)

    Kim, Hyeng-Soo; Ryoo, Zae Young; Choi, Sang Un; Lee, Sanggyu

    2015-07-01

    Because of the recent discovery of brown adipose tissues tissue in adult humans, brown adipose tissues have garnered additional attention. Many studies have attempted to transform the precursor cells within the white adipocyte cultures to Brite (brown-in-white) cells by using genomic modification or pharmacological activation in order to determine the therapeutic effect of obesity. However, genome-scale analysis of the genetic factors governing the development of white and brown adipose tissues remains incomplete. In order to identify the key genes that regulate the development of white and brown adipose tissues in mice, a transcriptome analysis was performed on the adipose tissues. Network analysis of differentially expressed genes indicated that Trim30 and Ucp3 play pivotal roles in energy balance and glucose homeostasis. In addition, it was discovered that identical biological processes and pathways in the white and brown adipose tissues might be regulated by different genes. Trim30 and Ucp3 might be used as genetic markers to precisely represent the stage of obesity during the early and late stages of adipose tissue development, respectively. These results may provide a stepping-stone for future obesity-related studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues.

    Science.gov (United States)

    Chakraborty, Sandeep; Britton, Monica; Martínez-García, P J; Dandekar, Abhaya M

    2016-03-01

    Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a filter, we present a broad analysis of the RNA-Seq derived transcriptome profiles obtained from twenty different tissues to extract the biodiversity and possible plant-microbe interactions in the walnut ecosystem in California. Since the residual nature of the transcripts being analyzed does not provide sufficient information to identify the exact strain, inferences made are constrained to the genus level. The presence of the pathogenic oomycete Phytophthora was detected in the root through the presence of a glyceraldehyde-3-phosphate dehydrogenase. Cryptococcus, the causal agent of cryptococcosis, was found in the catkins and vegetative buds, corroborating previous work indicating that the plant surface supported the sexual cycle of this human pathogen. The RNA-Seq profile revealed several species of the endophytic nitrogen fixing Actinobacteria. Another bacterial species implicated in aerobic biodegradation of methyl tert-butyl ether (Methylibium petroleiphilum) is also found in the root. RNA encoding proteins from the pea aphid were found in the leaves and vegetative buds, while a serine protease from mosquito with significant homology to a female reproductive tract protease from Drosophila mojavensis in the vegetative bud suggests egg-laying activities. The comprehensive analysis of RNA-seq data present also unraveled detailed, tissue-specific information of ~400 transcripts encoded by the largest family of resistance (R) genes (NBS-LRR), which possibly rationalizes the resistance of the specific walnut plant to the pathogens detected. Thus, we elucidate the biodiversity and possible plant-microbe interactions in several walnut (Juglans regia) tissues in California using deep RNA-Seq profiling.

  14. Fatty acid profile of plasma, muscle and adipose tissues in Chilota lambs grazing on two different low quality pasture types in Chiloé Archipelago (Chile).

    Science.gov (United States)

    Gallardo, Maria A; Dannenberger, Dirk; Rivero, Jordana; Pulido, Ruben; Nuernberg, Karin

    2014-11-01

    There is no information about the effect of different pasture types on tissue fatty acid profiles of a native rustic lamb breed of the Chiloe Archipelago, the Chilota. Eight Chilota lambs were grazed on a 'Calafatal' pasture (CP), a typical secondary succession of Chiloé Archipelago (Chile) and eight Chilota lambs were located to graze on naturalized pasture (NP) of Chiloé. Botanical, chemical and lipid composition of the two types of pastures and of different lamb tissues (muscle, subcutaneous - and tail adipose tissues) and plasma were performed. Both pasture types induced high n-3 polyunsaturated fatty acids (PUFA) and CLAcis-9,trans-11 proportions in Chilota meat. Thus, in muscle, Chilota lambs grazing CP showed higher sum PUFA, sum n-6 PUFA proportion and n-6/n-3 PUFA ratio compared with Chilota lambs grazing NP. In tail fats of Chilota lambs grazing CP significantly higher proportions of 18:3n-3, sum saturated fatty acids, sum PUFA, n-3 and n-6 PUFA were detected compared with Chilota lambs grazing NP. Feeding of different pasture types (CP vs. NP) caused significant differences in fatty acid composition of muscle and the two fat depots in Chilota lambs, but also point to tissue-specific responses of de novo synthesized fatty acid deposition in the tissues. © 2014 Japanese Society of Animal Science.

  15. Characterization of the expression profiles of adipogenesis-related factors, ZNF423, KLFs and FGF10, during preadipocyte differentiation and abdominal adipose tissue development in chickens.

    Science.gov (United States)

    Matsubara, Yusuke; Aoki, Michiru; Endo, Tonami; Sato, Kan

    2013-07-01

    Adipogenesis is controlled by a complicated process involving certain transcriptional events. In chicken adipogenesis, peroxisome proliferator-activated receptor γ (PPARγ) is a key regulator of preadipocyte differentiation and abdominal fat accumulation. However, in a recent study in mammals, some novel factors related to regulation of adipogenesis, including preadipocyte differentiation, were identified in mammals. Therefore, in this study, we aimed to determine the expression profiles of these mammalian adipogenesis-related factors, such as zinc-finger protein 423 (ZNF423), Krüppel-like factor -2, -5, and -15 (KLF-2, -5, -15), and FGF10, in the chicken (Gallus gallus). Specifically, we analyzed their expression in primary preadipocyte differentiation in vitro and also analyzed their tissue distribution and their temporal expression in adipose tissue development in vivo. During chicken adipocyte differentiation, the gene expression of ZNF423, KLF-2, KLF-5 and FGF10 was found to rapidly decrease in the early stage of preadipocyte differentiation. Expression of ZNF423 then increased in the late stage of differentiation. KLF-15 expression increased in a time-dependent manner for 48 h. Protein expressions of these factors were reflected by Western blot analysis. High levels of aP2, PPARγ and FGF10 mRNA were found in adipose tissue. In addition, aP2, PPARγ and ZNF423 mRNA levels in the adipose tissue were elevated at days 10 and 20. These expression profiles of the adipogenesis-related factors in chicken are, in part, different from mammalian adipogenesis but this seems to reflect the differences in the regulation of adipogenesis and in adipose tissue functions between avians and mammals.

  16. Analysis of normal-tumour tissue interaction in tumours: prediction of prostate cancer features from the molecular profile of adjacent normal cells.

    Directory of Open Access Journals (Sweden)

    Victor Trevino

    Full Text Available Statistical modelling, in combination with genome-wide expression profiling techniques, has demonstrated that the molecular state of the tumour is sufficient to infer its pathological state. These studies have been extremely important in diagnostics and have contributed to improving our understanding of tumour biology. However, their importance in in-depth understanding of cancer patho-physiology may be limited since they do not explicitly take into consideration the fundamental role of the tissue microenvironment in specifying tumour physiology. Because of the importance of normal cells in shaping the tissue microenvironment we formulate the hypothesis that molecular components of the profile of normal epithelial cells adjacent the tumour are predictive of tumour physiology. We addressed this hypothesis by developing statistical models that link gene expression profiles representing the molecular state of adjacent normal epithelial cells to tumour features in prostate cancer. Furthermore, network analysis showed that predictive genes are linked to the activity of important secreted factors, which have the potential to influence tumor biology, such as IL1, IGF1, PDGF BB, AGT, and TGFβ.

  17. Perfil lipídico tecidual de ratos alimentados com diferentes fontes lipídicas Tissue lipid profile of rats fed with different lipid sources

    Directory of Open Access Journals (Sweden)

    Martha Elisa Ferreira de Almeida

    2009-02-01

    Full Text Available OBJETIVO:Determinar se fontes lipídicas com diferentes razões de ácidos graxos insaturados e saturados (PUFA+MUFA/SFA na dieta altera o perfil lipídico tecidual, a concentração de lipídios (mg/g dos tecidos hepáticos e mesentérico e a digestibilidade lipídica. MÉTODOS: Foi realizada cromatografia gasosa para determinar o perfil de ácidos graxos nos tecidos hepático e adiposo de ratos alimentados com diferentes fontes lipídicas. O coeficiente de digestibilidade foi determinado a partir da relação entre a quantidade de lipídios consumidos e a quantidade fecal excretada. RESULTADOS:Diferentes fontes lipídicas (óleo de soja, manteiga, margarina e gorduras de porco e de peixe não alteraram o coeficiente de digestibilidade e o peso hepático, mas alteraram a deposição de lipídios em todos os tecidos adiposos estudados. Não foi possível fazer a correlação direta entre o perfil dietário dos ácidos graxos não essenciais e sua deposição nos tecidos estudados, visto que a lipogênese de novo impede a identificação dos ácidos graxos dietários. CONCLUSÃO:Não foi constatada uma relação direta entre o perfil dietário dos ácidos graxos e sua deposição nos tecidos estudados, exceto para os ácidos graxos trans e linoléico (C18:2 que não são sintetizados no rato. Esses ácidos graxos apresentaram uma concentração tecidual diretamente proporcional àquela das fontes dietárias. Quanto à razão (PUFA+MUFA/SFA, encontrada no tecido hepático dos diferentes grupos, observa-se que esta foi diretamente proporcional aos valores apresentados pelas fontes lipídicas dietárias. Entretanto, essa associação não foi observada nos tecidos adiposos analisados.OBJECTIVE:To determine if lipid sources with different unsaturated to saturated fatty acid ratios, (PUFA+MUFA/SFA in the diet alter the lipid profile of tissues, the lipid concentration (mg/g of the hepatic and mesenteric tissues and the lipid digestibility. METHODS

  18. Comprehensive expression profiling of highly homologous 39 hox genes in 26 different human adult tissues by the modified systematic multiplex RT-pCR method reveals tissue-specific expression pattern that suggests an important role of chromosomal structure in the regulation of hox gene expression in adult tissues.

    Science.gov (United States)

    Yamamoto, Miyako; Takai, Daisaku; Yamamoto, Fumiya; Yamamoto, Fumiichiro

    2003-01-01

    Homeobox genes play a crucial role as molecular address labels in early embryogenesis by conferring cell fate and establishing regional identity in tissues. Homeobox gene expression is not restricted to the early development, but it is also observed in the differentiated cells in adult tissues. To have a better understanding of the functionality of homeobox gene expression in adult tissues in physiological and pathological phenomena, it is important to determine the expression profiles of Hox genes. We established a system to study the expression of 39 human Hox genes by the modified Systematic Multiplex RT-PCR method. Using this system, we have systematically examined their expression in 26 different adult tissues. The results showed tissue-specific differential expression. They also revealed that the posterior tissues generally express more Hox genes than the anterior tissues and that the genes located centrally in the Hox Gene Complexes are expressed in more tissues than the genes located at the 5' or 3' end of the complexes. Instead of similar expression patterns among paralogous genes, we found that several neighboring Hox genes on the same chromosomes exhibited similar tissue-specific expression pattern, which may suggest that the regulation of Hox gene expression may be more dependent on chromosomal structure in adult tissues.

  19. Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues.

    Science.gov (United States)

    Webster, A Francina; Zumbo, Paul; Fostel, Jennifer; Gandara, Jorge; Hester, Susan D; Recio, Leslie; Williams, Andrew; Wood, Charles E; Yauk, Carole L; Mason, Christopher E

    2015-12-01

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for transcriptomic research. However, use of FFPE samples in genomic studies has been limited by technical challenges resulting from nucleic acid degradation. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues preserved in formalin for different amounts of time using 2 DNA microarray protocols and 2 whole-transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other methods by having the highest correlations of differentially expressed genes (DEGs), and best overlap of pathways, between FRO and FFPE groups. The effect of sample time in formalin (18 h or 3 weeks) on gene expression profiles indicated that test article treatment, not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18 h and 3 week FFPE samples compared with FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of time in paraffin on genomic profiles. Ribo-depletion RNA-seq analysis of 8-, 19-, and 26-year-old control blocks resulted in comparable quality metrics, including expected distributions of mapped reads to exonic, untranslated region, intronic, and ribosomal fractions of the transcriptome. Overall, our results indicate that FFPE samples are appropriate for use in genomic studies in which frozen samples are not available, and that ribo-depletion RNA-seq is the preferred method for this type of analysis in archival and long-aged FFPE samples.

  20. Quantitative amino acid profiling and stable isotopically labeled amino acid tracer enrichment used for in vivo human systemic and tissue kinetics measurements

    DEFF Research Database (Denmark)

    Bornø, Andreas; van Hall, Gerrit

    2014-01-01

    /ion exchange, derivatized using a phenylisothiocyanate reagent and each amino acid was quantitated with its own stable isotopically labeled internal standard (uniformly labeled-(13)C/(15)N). The method was validated according to general recommendations for chromatographic analytical methods. The calibration...... and plasma were 4.4 and 0.8%, and the interday variability was 3.4% and the recovery was 90.5%, respectively. In conclusion, we have developed and validated a method for quantitative amino acid profiling that meets the requirements for systemic and tissue human in vivo amino acid and protein turnover...

  1. Impact of sample acquisition and linear amplification on gene expression profiling of lung adenocarcinoma: laser capture micro-dissection cell-sampling versus bulk tissue-sampling

    Directory of Open Access Journals (Sweden)

    Wigle Dennis A

    2009-03-01

    Full Text Available Abstract Background The methods used for sample selection and processing can have a strong influence on the expression values obtained through microarray profiling. Laser capture microdissection (LCM provides higher specificity in the selection of target cells compared to traditional bulk tissue selection methods, but at an increased processing cost. The benefit gained from the higher tissue specificity realized through LCM sampling is evaluated in this study through a comparison of microarray expression profiles obtained from same-samples using bulk and LCM processing. Methods Expression data from ten lung adenocarcinoma samples and six adjacent normal samples were acquired using LCM and bulk sampling methods. Expression values were evaluated for correlation between sample processing methods, as well as for bias introduced by the additional linear amplification required for LCM sample profiling. Results The direct comparison of expression values obtained from the bulk and LCM sampled datasets reveals a large number of probesets with significantly varied expression. Many of these variations were shown to be related to bias arising from the process of linear amplification, which is required for LCM sample preparation. A comparison of differentially expressed genes (cancer vs. normal selected in the bulk and LCM datasets also showed substantial differences. There were more than twice as many down-regulated probesets identified in the LCM data than identified in the bulk data. Controlling for the previously identified amplification bias did not have a substantial impact on the differences identified in the differentially expressed probesets found in the bulk and LCM samples. Conclusion LCM-coupled microarray expression profiling was shown to uniquely identify a large number of differentially expressed probesets not otherwise found using bulk tissue sampling. The information gain realized from the LCM sampling was limited to differential analysis

  2. Gene Expression Profile of Human Skeletal Muscle and Adipose Tissue of Chinese Han Patients with Type 2 Diabetes Mellitus

    Institute of Scientific and Technical Information of China (English)

    YAN-LI YANG; RUO-LAN XIANG; CHANG YANG; XIAO-JUN LIU; WEN-JUN SHEN; JIN ZUO; YONG-SHENG CHANG; FU-DE FANG

    2009-01-01

    Objective To study the differential patterns of gene expression in skeletal muscle and adipose tissue between type 2 diabetes mellitus (T2DM) patients and healthy subjects using DNA microarray analysis. Methods T2DM patiens were divided into female group, young male group and old male group. DNA microarray analysis and quantitative real-time PCR were carried out to analyze the relation between gene expressions and T2DM. Results The mRNA expression of 298, 578, and 350 genes was changed in the skeletal muscle of diabetes mellitus patients compared with control subjects. The 1320, 1143, and 2847 genes were modified in adipose tissue of the three groups. Among the genes surveyed, the change of 25 and 39 gene transcripts in skeletal muscle and adipose tissue was ≥2 folds. These differentially expressed genes were classified into 15 categories according to their functions. Conclusion New genes are found and T2DM can be prevented or cured.

  3. Flavonoid profiles of immature and mature fruit tissues of Citrus grandis Osbeck (Dangyuja) and overall contribution to the antioxidant effect.

    Science.gov (United States)

    Yu, Eun Ae; Kim, Gon-Sup; Lee, Ji Eun; Park, Semin; Yi, Song; Lee, Soo Jung; Kim, Jae Hoon; Jin, Jong Sung; Abd El-Aty, A M; Shim, Jae-Han; Shin, Sung Chul

    2015-04-01

    Citrus fruits are a valuable functional food and their peel is used in East Asian folk medicine. In this study, the polar components of the fruit tissues of Citrus grandis Osbeck were analyzed using high-performance liquid chromatography-tandem mass spectrometry and compared with reported data. Among the 13 characterized compounds, eight flavonoids and one coumarin were identified for the first time in fruit tissues. The total amount of the identified components was the largest for the immature fruit peel, followed by mature fruit peel, mature fruit flesh, and immature fruit flesh. Naringin (2) and neohesperidin (3) were particularly rich in all samples. The antioxidant activity of the flavonoids extracted from fruit tissues increased in a dose-dependent manner. The activity of the fruit peels was significantly higher than that of the fruit flesh. Copyright © 2014 John Wiley & Sons, Ltd.

  4. Liquidation of the company

    OpenAIRE

    Procházka, Michal

    2011-01-01

    This work deals with the liquidation of the company focusing on commercial companies. It describes whole process of liquidation from decision to liquidate to delete the company from the Commercial Register. The work also focuses on legal, accounting and tax site of liquidation. Accounting practices in the liquidation process are illustrated on the example of a fictive company.

  5. A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

    Energy Technology Data Exchange (ETDEWEB)

    Shakoor, N; Nair, R; Crasta, O; Morris, G; Feltus, A; Kresovich, S

    2014-01-23

    Background: Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement. Results: This study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e. g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes. Conclusions: Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community.

  6. Protein histochemistry using coronaviral spike proteins: studying binding profiles and sialic acid requirements for attachment to tissues

    NARCIS (Netherlands)

    Ambepitiya Wickramasinghe, I.N.; Verheije, M.H.

    2015-01-01

    Protein histochemistry is a tissue-based technique that enables the analysis of viral attachment patterns as well as the identification of specific viral and host determinants involved in the first step in the infection of a host cell by a virus. Applying recombinantly expressed spike proteins of in

  7. Comparative Profiling of Triple-Negative Breast Carcinomas Tissue Glycoproteome by Sequential Purification of Glycoproteins and Stable Isotope Labeling

    Directory of Open Access Journals (Sweden)

    Xiang Chen

    2016-01-01

    Full Text Available Background: Women with triple negative breast cancers (TNBCs have a poor prognosis due to lack of suitable targeted therapies. Changes in the protein glycosylation are increasingly being recognized as an important modification associated with cancer etiology. Methods: In an attempt to identify TNBC biomarkers with greater diagnostic and prognostic capabilities, hydrazide- based chemistry method combined with LC-MS/MS were used to purify and identify N-linked glycopeptides or glycoproteins of tissues from TNBC patients. Results: A total of 550 unique N-linked glycoproteins were identified, among these proteins, 72 unique N-linked glycoproteins were significantly regulated in tumor tissues, of which 56 proteins were upregulated and 16 proteins were downregulated. To assess the validity of the results, three selected proteins including Vascular endothelial growth factor receptor 1, Insulin receptor, Tissue factor pathway inhibitor were selected for western blot analysis, and these proteins were found as potential biomarkers of TNBC. The top three pathways of differentially expressed glycoproteins participated in were caveolar-mediated endocytosis signaling, agrin interactions at neuromuscular junction and LXR/RXR activation. Conclusion: This work provides potential glycoprotein markers to function as a novel tissue-based biomarker for TNBC.

  8. Comparative nontargeted profiling of metabolic changes in tissues and biofluids in high-fat diet-fed Ossabaw pig

    DEFF Research Database (Denmark)

    Hanhineva, Kati; Barri, Thaer; Kolehmainen, Marjukka

    2013-01-01

    Typical clinical biomarker analyses on urine and plasma samples from human dietary interventions do not provide adequate information about diet-induced metabolic changes taking place in tissues. The aim of this study was to show how a large-scale non-targeted metabolomic approach can be used to r...

  9. Identifying Candidate Genes for Type 2 Diabetes Mellitus and Obesity through Gene Expression Profiling in Multiple Tissues or Cells

    Science.gov (United States)

    Meng, Yuhuan; Zhou, Jinghui; Zhuo, Min; Ling, Fei; Zhang, Yu; Du, Hongli; Wang, Xiaoning

    2013-01-01

    Type 2 Diabetes Mellitus (T2DM) and obesity have become increasingly prevalent in recent years. Recent studies have focused on identifying causal variations or candidate genes for obesity and T2DM via analysis of expression quantitative trait loci (eQTL) within a single tissue. T2DM and obesity are affected by comprehensive sets of genes in multiple tissues. In the current study, gene expression levels in multiple human tissues from GEO datasets were analyzed, and 21 candidate genes displaying high percentages of differential expression were filtered out. Specifically, DENND1B, LYN, MRPL30, POC1B, PRKCB, RP4-655J12.3, HIBADH, and TMBIM4 were identified from the T2DM-control study, and BCAT1, BMP2K, CSRNP2, MYNN, NCKAP5L, SAP30BP, SLC35B4, SP1, BAP1, GRB14, HSP90AB1, ITGA5, and TOMM5 were identified from the obesity-control study. The majority of these genes are known to be involved in T2DM and obesity. Therefore, analysis of gene expression in various tissues using GEO datasets may be an effective and feasible method to determine novel or causal genes associated with T2DM and obesity. PMID:24455749

  10. Identifying Candidate Genes for Type 2 Diabetes Mellitus and Obesity through Gene Expression Profiling in Multiple Tissues or Cells

    Directory of Open Access Journals (Sweden)

    Junhui Chen

    2013-01-01

    Full Text Available Type 2 Diabetes Mellitus (T2DM and obesity have become increasingly prevalent in recent years. Recent studies have focused on identifying causal variations or candidate genes for obesity and T2DM via analysis of expression quantitative trait loci (eQTL within a single tissue. T2DM and obesity are affected by comprehensive sets of genes in multiple tissues. In the current study, gene expression levels in multiple human tissues from GEO datasets were analyzed, and 21 candidate genes displaying high percentages of differential expression were filtered out. Specifically, DENND1B, LYN, MRPL30, POC1B, PRKCB, RP4-655J12.3, HIBADH, and TMBIM4 were identified from the T2DM-control study, and BCAT1, BMP2K, CSRNP2, MYNN, NCKAP5L, SAP30BP, SLC35B4, SP1, BAP1, GRB14, HSP90AB1, ITGA5, and TOMM5 were identified from the obesity-control study. The majority of these genes are known to be involved in T2DM and obesity. Therefore, analysis of gene expression in various tissues using GEO datasets may be an effective and feasible method to determine novel or causal genes associated with T2DM and obesity.

  11. Identifying candidate genes for Type 2 Diabetes Mellitus and obesity through gene expression profiling in multiple tissues or cells.

    Science.gov (United States)

    Chen, Junhui; Meng, Yuhuan; Zhou, Jinghui; Zhuo, Min; Ling, Fei; Zhang, Yu; Du, Hongli; Wang, Xiaoning

    2013-01-01

    Type 2 Diabetes Mellitus (T2DM) and obesity have become increasingly prevalent in recent years. Recent studies have focused on identifying causal variations or candidate genes for obesity and T2DM via analysis of expression quantitative trait loci (eQTL) within a single tissue. T2DM and obesity are affected by comprehensive sets of genes in multiple tissues. In the current study, gene expression levels in multiple human tissues from GEO datasets were analyzed, and 21 candidate genes displaying high percentages of differential expression were filtered out. Specifically, DENND1B, LYN, MRPL30, POC1B, PRKCB, RP4-655J12.3, HIBADH, and TMBIM4 were identified from the T2DM-control study, and BCAT1, BMP2K, CSRNP2, MYNN, NCKAP5L, SAP30BP, SLC35B4, SP1, BAP1, GRB14, HSP90AB1, ITGA5, and TOMM5 were identified from the obesity-control study. The majority of these genes are known to be involved in T2DM and obesity. Therefore, analysis of gene expression in various tissues using GEO datasets may be an effective and feasible method to determine novel or causal genes associated with T2DM and obesity.

  12. Metabolomic profiling from formalin-fixed, paraffin-embedded tumor tissue using targeted LC/MS/MS: application in sarcoma.

    Directory of Open Access Journals (Sweden)

    Andrew D Kelly

    Full Text Available The relatively new field of onco-metabolomics attempts to identify relationships between various cancer phenotypes and global metabolite content. Previous metabolomics studies utilized either nuclear magnetic resonance spectroscopy or gas chromatography/mass spectrometry, and analyzed metabolites present in urine and serum. However, direct metabolomic assessment of tumor tissues is important for determining altered metabolism in cancers. In this respect, the ability to obtain reliable data from archival specimens is desirable and has not been reported to date. In this feasibility study, we demonstrate the analysis of polar metabolites extracted directly from ten formalin-fixed, paraffin-embedded (FFPE specimens, including five soft tissue sarcomas and five paired normal samples. Using targeted liquid chromatography-tandem mass spectrometry (LC/MS/MS via selected reaction monitoring (SRM, we detect an average of 106 metabolites across the samples with excellent reproducibility and correlation between different sections of the same specimen. Unsupervised hierarchical clustering and principal components analysis reliably recovers a priori known tumor and normal tissue phenotypes, and supervised analysis identifies candidate metabolic markers supported by the literature. In addition, we find that diverse biochemical processes are well-represented in the list of detected metabolites. Our study supports the notion that reliable and broadly informative metabolomic data may be acquired from FFPE soft tissue sarcoma specimens, a finding that is likely to be extended to other malignancies.

  13. Sebaceous lipid profiling of bat integumentary tissues: quantitative analysis of free Fatty acids, monoacylglycerides, squalene, and sterols.

    Science.gov (United States)

    Pannkuk, Evan L; Gilmore, David F; Fuller, Nathan W; Savary, Brett J; Risch, Thomas S

    2013-12-01

    White-nose syndrome (WNS) is a fungal disease caused by Pseudogymnoascus destructans and is devastating North American bat populations. Sebaceous lipids secreted from host integumentary tissues are implicated in the initial attachment and recognition of host tissues by pathogenic fungi. We are interested in determining if ratios of lipid classes in sebum can be used as biomarkers to diagnose severity of fungal infection in bats. To first establish lipid compositions in bats, we isolated secreted and integral lipid fractions from the hair and wing tissues of three species: big brown bats (Eptesicus fuscus), Eastern red bats (Lasiurus borealis), and evening bats (Nycticeius humeralis). Sterols, FFAs, MAGs, and squalene were derivatized as trimethylsilyl esters, separated by gas chromatography, and identified by mass spectrometry. Ratios of sterol to squalene in different tissues were determined, and cholesterol as a disease biomarker was assessed. Free sterol was the dominant lipid class of bat integument. Squalene/sterol ratio is highest in wing sebum. Secreted wing lipid contained higher proportions of saturated FFAs and MAGs than integral wing or secreted hair lipid. These compounds are targets for investigating responses of P. destructans to specific host lipid compounds and as biomarkers to diagnose WNS. Copyright © 2013 Verlag Helvetica Chimica Acta AG, Zürich.

  14. Adipose Tissue Promotes a Serum Cytokine Profile Related to Lower Insulin Sensitivity after Chronic Central Leptin Infusion

    Science.gov (United States)

    Burgos-Ramos, Emma; Canelles, Sandra; Perianes-Cachero, Arancha; Arilla-Ferreiro, Eduardo; Argente, Jesús; Barrios, Vicente

    2012-01-01

    Obesity is an inflammatory state characterized by an augment in circulating inflammatory factors. Leptin may modulate the synthesis of these factors by white adipose tissue decreasing insulin sensitivity. We have examined the effect of chronic central administration of leptin on circulating levels of cytokines and the possible relationship with cytokine expression and protein content as well as with leptin and insulin signaling in subcutaneous and visceral adipose tissues. In addition, we analyzed the possible correlation between circulating levels of cytokines and peripheral insulin resistance. We studied 18 male Wistar rats divided into controls (C), those treated icv for 14 days with a daily dose of 12 μg of leptin (L) and a pair-fed group (PF) that received the same food amount consumed by the leptin group. Serum leptin and insulin were measured by ELISA, mRNA levels of interferon-γ (IFN-γ), interleukin-2 (IL-2), IL-4, IL-6, IL-10 and tumor necrosis factor-α (TNF-α) by real time PCR and serum and adipose tissue levels of these cytokines by multiplexed bead immunoassay. Serum leptin, IL-2, IL-4, IFN-γ and HOMA-IR were increased in L and TNF-α was decreased in PF and L. Serum leptin and IL-2 levels correlate positively with HOMA-IR index and negatively with serum glucose levels during an ip insulin tolerance test. In L, an increase in mRNA levels of IL-2 was found in both adipose depots and IFN-γ only in visceral tissue. Activation of leptin signaling was increased and insulin signaling decreased in subcutaneous fat of L. In conclusion, leptin mediates the production of inflammatory cytokines by adipose tissue independent of its effects on food intake, decreasing insulin sensitivity. PMID:23056516

  15. Adipose tissue promotes a serum cytokine profile related to lower insulin sensitivity after chronic central leptin infusion.

    Science.gov (United States)

    Burgos-Ramos, Emma; Canelles, Sandra; Perianes-Cachero, Arancha; Arilla-Ferreiro, Eduardo; Argente, Jesús; Barrios, Vicente

    2012-01-01

    Obesity is an inflammatory state characterized by an augment in circulating inflammatory factors. Leptin may modulate the synthesis of these factors by white adipose tissue decreasing insulin sensitivity. We have examined the effect of chronic central administration of leptin on circulating levels of cytokines and the possible relationship with cytokine expression and protein content as well as with leptin and insulin signaling in subcutaneous and visceral adipose tissues. In addition, we analyzed the possible correlation between circulating levels of cytokines and peripheral insulin resistance. We studied 18 male Wistar rats divided into controls (C), those treated icv for 14 days with a daily dose of 12 μg of leptin (L) and a pair-fed group (PF) that received the same food amount consumed by the leptin group. Serum leptin and insulin were measured by ELISA, mRNA levels of interferon-γ (IFN-γ), interleukin-2 (IL-2), IL-4, IL-6, IL-10 and tumor necrosis factor-α (TNF-α) by real time PCR and serum and adipose tissue levels of these cytokines by multiplexed bead immunoassay. Serum leptin, IL-2, IL-4, IFN-γ and HOMA-IR were increased in L and TNF-α was decreased in PF and L. Serum leptin and IL-2 levels correlate positively with HOMA-IR index and negatively with serum glucose levels during an ip insulin tolerance test. In L, an increase in mRNA levels of IL-2 was found in both adipose depots and IFN-γ only in visceral tissue. Activation of leptin signaling was increased and insulin signaling decreased in subcutaneous fat of L. In conclusion, leptin mediates the production of inflammatory cytokines by adipose tissue independent of its effects on food intake, decreasing insulin sensitivity.

  16. Comparison of gene expression profiling by reverse transcription quantitative PCR between fresh frozen and formalin-fixed, paraffin-embedded breast cancer tissues.

    Science.gov (United States)

    Sánchez-Navarro, Iker; Gámez-Pozo, Angelo; González-Barón, Manuel; Pinto-Marín, Alvaro; Hardisson, David; López, Rocío; Madero, Rosario; Cejas, Paloma; Mendiola, Marta; Espinosa, Enrique; Vara, Juan Angel Fresno

    2010-05-01

    Recent reports demonstrate the feasibility of quantifying gene expression by using RNA isolated from blocks of formalin-fixed, paraffin-embedded (FFPE) tumor tissue. The development of molecular tests for clinical use based on archival materials would be of great utility in the search for and validation of important genes or gene expression profiles. In this study, we compared the performance of different normalization strategies in the correlation of quantitative data between fresh frozen (FF) and FFPE samples and analyzed the parameters that characterize such correlation for each gene. Total RNA extracted from FFPE samples presented a shift in raw cycle threshold (Cq) values that can be explained by its extensive degradation. Proper normalization can compensate for the effects of RNA degradation in gene expression measurements. We show that correlation between normalized expression values is better for moderately to highly expressed genes whose expression varies significantly between samples. Nevertheless, some genes had no correlation. These genes should not be included in molecular tests for clinical use based on FFPE samples. Our results could serve as a guide when developing clinical diagnostic tests based on RT-qPCR analyses of FFPE tissues in the coming era of treatment decision-making based on gene expression profiling.

  17. Effect of inulin extracts or inulin-containing plant supplement on blood lipid indices and fatty acid profile in fattener tissues.

    Science.gov (United States)

    Grela, E R; Sobolewska, S; Roziński, T

    2014-01-01

    The objective of the study was to evaluate the effect of inulin or dandelion, chicory and Jerusalem artichoke powder on lipid indices and fatty acid profile in fattener tissues. The experiment involved 120 crossbred pigs (PL x PLW) x Duroc with an initial body weight of 25.0 +/- 0.5 kg. Animals were assigned into 6 groups. A diet for group I (control) did not comprise an inulin additive, group II and III received 2% inulin (water or water-alcohol extraction of inulin from chicory root, respectively), while the mixtures for group IV, V and VI contained 4% root powder from Jerusalem artichoke (topinambur), chicory or dandelion, respectively. The animals were slaughtered at 115 kg body weight. The samples of blood, liver and the muscle longissimus dorsi tissues as well as whole hearts were collected for analysis. Fatty acid profile, some lipid indices and crude fat and cholesterol content were evaluated. Dietary supplement of 40 g dandelion powder resulted in preferable significant changes in the blood lipid indices and fatty acids composition (increased PUFA share and decreased n-6/n-3 ratio).

  18. Calculating the iodine value for Italian heavy pig subcutaneous adipose tissue from fatty acid methyl ester profiles.

    Science.gov (United States)

    Lo Fiego, Domenico Pietro; Minelli, Giovanna; Volpelli, Luisa Antonella; Ulrici, Alessandro; Macchioni, Paolo

    2016-12-01

    In this work, different equations were compared as for their effectiveness in predicting the iodine value (IV), based on fatty acid (FA) composition of subcutaneous adipose tissue of Italian heavy pigs. In particular, six equations were tested: AOCS (1); modified AOCS (2), including all unsaturated FA (UFA); regression models obtained using the stepwise regression procedure as variable selection method, calculated considering only UFA (3) or all the FA (4); regression models obtained using the backward elimination procedure, calculated considering only UFA (5) or all the FA (6). The comparison of the equations performance, estimated using an external test set, showed that the use of regression models led to significant enhancements of prediction accuracy with respect to the AOCS equations. Using both equations 4 and 6, the average paired differences between experimental and predicted IV values were not statistically significant. Therefore, it is possible to use these equations for IV estimation of the subcutaneous adipose tissue of Italian heavy pigs.

  19. Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq

    Directory of Open Access Journals (Sweden)

    Shannon Farris

    2017-06-01

    Full Text Available Obtaining high quality RNA from complex biological tissues, such as the brain, is needed for establishing high-fidelity cell-type specific transcriptomes. Although combining genetic labeling techniques with laser capture microdissection (LCM is generally sufficient, concerns over RNA degradation and limited yields call into question results of many sequencing studies. Here we set out to address both of these issues by: (1 developing a fluorescence-assisted LCM protocol that yields high quality RNA from fresh-frozen tissues; and (2 determining a suitable RNA-Seq library generation method for limited amounts of RNA (1–5 ng total RNA. The latter focused on comparing commercially available kits able to produce libraries of sufficient concentration and complexity while limiting PCR amplification biases. We find that high quality RNA (RNA integrity number, RIN, >9 of sufficient concentration can be isolated from laser-captured material from thinly-sectioned tissues when digestion time and temperature are minimized. Furthermore, we found that library generation approaches that retain ribosomal RNA (rRNA through cDNA library generation required fewer cycles of PCR, minimizing bias in the resulting libraries. Lastly, end stage depletion of rRNA prior to sequencing enriches for target RNAs, thereby increasing read depth and level of gene detection while decreasing sequencing costs. Here we describe our protocol for generating robust RNA-Seq libraries from laser-captured tissue and demonstrate that with this method, we obtain samples with RNA quality superior to the current standard in the LCM field, and show that low-input RNA-Seq kits that minimize PCR bias produce high fidelity sequencing metrics with less variability compared to current practices.

  20. Protein Profiling of Isolated Leukocytes, Myofibroblasts, Epithelial, Basal, and Endothelial Cells from Normal, Hyperplastic, Cancerous, and Inflammatory Human Prostate Tissues

    Directory of Open Access Journals (Sweden)

    Zahraa I. Khamis, Kenneth A. Iczkowski, Ziad J. Sahab, Qing-Xiang Amy Sang

    2010-01-01

    Full Text Available In situ neoplastic prostate cells are not lethal unless they become invasive and metastatic. For cells to become invasive, the prostate gland must undergo degradation of the basement membrane and disruption of the basal cell layer underneath the luminal epithelia. Although the roles of proteinases in breaking down the basement membrane have been well-studied, little is known about the factors that induce basal cell layer disruption, degeneration, and its eventual disappearance in invasive cancer. It is hypothesized that microenvironmental factors may affect the degradation of the basal cell layer, which if protected may prevent tumor progression and invasion. In this study, we have revealed differential protein expression patterns between epithelial and stromal cells isolated from different prostate pathologies and identified several important epithelial and stromal proteins that may contribute to inflammation and malignant transformation of human benign prostate tissues to cancerous tissues using matrix-assisted laser desorption ionization time-of-flight mass spectrometry and proteomics methods. Cellular retinoic acid-binding protein 2 was downregulated in basal cells of benign prsotate. Caspase-1 and interleukin-18 receptor 1 were highly expressed in leukocytes of prostate cancer. Proto-oncogene Wnt-3 was downregulated in endothelial cells of prostatitis tissue and tyrosine phosphatase non receptor type 1 was only found in normal and benign endothelial cells. Poly ADP-ribose polymerase 14 was downregulated in myofibroblasts of prostatitis tissue. Interestingly, integrin alpha-6 was upregulated in epithelial cells but not detected in myofibroblasts of prostate cancer. Further validation of these proteins may generate new strategies for the prevention of basal cell layer disruption and subsequent cancer invasion.

  1. Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface

    Science.gov (United States)

    Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

    2015-06-01

    Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

  2. High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues.

    Science.gov (United States)

    van Essen, Hendrik F; Ylstra, Bauke

    2012-01-01

    We describe protocols to acquire high-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissues for the use in array comparative genome hybridization (CGH). Formalin fixation combined with paraffin embedding is routine procedure for solid malignancies in the diagnostic practice of the pathologist. As a consequence, large archives of FFPE tissues are available in pathology institutes across the globe. This archival material is for many research questions an invaluable resource, with long-term clinical follow-up and survival data available. FFPE is, thus, highly attractive for large genomics studies, including experiments requiring samples for test/learning and validation. Most larger array CGH studies have, therefore, made use of FFPE material and show that CNAs have tumor- and tissue-specific traits (Chin et al. Cancer Cell 10: 529-541, 2006; Fridlyand et al. BMC Cancer 6: 96, 2006; Weiss et al. Oncogene 22: 1872-1879, 2003; Jong et al. Oncogene 26: 1499-1506, 2007). The protocols described are tailored to array CGH of FFPE solid malignancies: from sectioning FFPE blocks to specific cynosures for pathological revisions of sections, DNA isolation, quality testing, and amplification. The protocols are technical in character and elaborate up to the labeling of isolated DNA while further processes and interpretation and data analysis are beyond the scope.

  3. Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications.

    Science.gov (United States)

    Pinnick, Katherine E; Nicholson, George; Manolopoulos, Konstantinos N; McQuaid, Siobhán E; Valet, Philippe; Frayn, Keith N; Denton, Nathan; Min, Josine L; Zondervan, Krina T; Fleckner, Jan; McCarthy, Mark I; Holmes, Chris C; Karpe, Fredrik

    2014-11-01

    Upper- and lower-body fat depots exhibit opposing associations with obesity-related metabolic disease. We defined the relationship between DEXA-quantified fat depots and diabetes/cardiovascular risk factors in a healthy population-based cohort (n = 3,399). Gynoid fat mass correlated negatively with insulin resistance after total fat mass adjustment, whereas the opposite was seen for abdominal fat. Paired transcriptomic analysis of gluteal subcutaneous adipose tissue (GSAT) and abdominal subcutaneous adipose tissue (ASAT) was performed across the BMI spectrum (n = 49; 21.4-45.5 kg/m(2)). In both depots, energy-generating metabolic genes were negatively associated and inflammatory genes were positively associated with obesity. However, associations were significantly weaker in GSAT. At the systemic level, arteriovenous release of the proinflammatory cytokine interleukin-6 (n = 34) was lower from GSAT than ASAT. Isolated preadipocytes retained a depot-specific transcriptional "memory" of embryonic developmental genes and exhibited differential promoter DNA methylation of selected genes (HOTAIR, TBX5) between GSAT and ASAT. Short hairpin RNA-mediated silencing identified TBX5 as a regulator of preadipocyte proliferation and adipogenic differentiation in ASAT. In conclusion, intrinsic differences in the expression of developmental genes in regional adipocytes provide a mechanistic basis for diversity in adipose tissue (AT) function. The less inflammatory nature of lower-body AT offers insight into the opposing metabolic disease risk associations between upper- and lower-body obesity.

  4. Transcriptomic Profiling of Adipose Tissue in Obese Women in Response to Acupuncture Catgut Embedding Therapy with Moxibustion.

    Science.gov (United States)

    Garcia-Vivas, Jessica M; Galaviz-Hernandez, Carlos; Fernandez-Retana, Jorge; Pedroza-Torres, Abraham; Perez-Plasencia, Carlos; Lopez-Camarillo, Cesar; Marchat, Laurence A

    2016-08-01

    Complementary and alternative medicine, such as Traditional Chinese Medicine, represents an efficient therapeutic option for obesity control. It was previously reported that acupuncture catgut embedding therapy (ACET) with moxibustion reduces body weight and reverts insulin resistance in obese women. This study aimed to evidence changes in adipokines and gene expression in adipose tissue that could explain the effects of ACET with moxibustion. Overweight/obese women were treated with ACET with moxibustion or sham acupuncture as control. Peripheral blood samples and fat biopsies were taken before and after intervention. Circulating adipokines (leptin, adiponectin, tumor necrosis factor alpha, and resistin) were quantified by enzyme-linked immunosorbent assay. Gene expression in adipose tissue was determined by cDNA microarray assays and assessed by quantitative reverse transcription real-time polymerase chain reaction. ACET with moxibustion did not modify circulating adipokines levels. However, correlations with anthropometric and biochemical parameters were affected. Interestingly, transcriptional changes in adipose tissue revealed the modulation of genes participating in homeostasis control, lipid metabolism, olfactory transduction, and gamma-aminobutyric acid signaling pathway. The effects of ACET with moxibustion on body weight and insulin resistance were associated with the regulation of biochemical events that are altered in obesity.

  5. Profiling the secretion of soluble mediators by end stage osteoarthritis synovial tissue explants reveals a reduced responsiveness to an inflammatory trigger.

    Directory of Open Access Journals (Sweden)

    Lobke M Gierman

    Full Text Available OBJECTIVE: Evidence is accumulating that synovial tissue plays an active role in osteoarthritis (OA, however, exact understanding of its contribution is lacking. In order to further elucidate its role in the OA process, we aimed to identify the secretion pattern of soluble mediators by synovial tissue and to assess its ability to initiate cartilage degeneration. METHODS: Synovial tissue explants (STEs obtained from donors without history of OA (n = 8 or from end stage OA patients (n = 16 were cultured alone or together with bovine cartilage explants in the absence or presence of IL-1α. The secretion of 48 soluble mediators was measured and the effect on glycosaminoglycan (GAG release and matrix metalloproteinase (MMP activity was determined. RESULTS: Normal and OA STEs secreted comparable levels of almost all measured soluble mediators. However, in the presence of IL-1α these mediators were less secreted by OA than by normal STEs of which 15 differed significantly (p<0.01. No effect of normal or OA STEs on GAG release from the cartilage explants was observed, and no differences in MMP activity between OA and normal STEs were detected. CONCLUSIONS: Unexpectedly, a comparable secretion profile of soluble mediators was found for OA and normal STEs while the reduced responsiveness of OA STEs to an inflammatory trigger indicates a different state of this tissue in OA patients. The effects could be the result of prolonged exposure to an inflammatory environment in OA development. Further understanding of the pro-inflammatory and inflammation resolving mechanisms during disease progression in synovial tissue may provide valuable targets for therapy in the future.

  6. Comparative expression profiles of mRNAs and microRNAs among human mesenchymal stem cells derived from breast, face, and abdominal adipose tissues.

    Science.gov (United States)

    Wang, Kai-Hung; Kao, An-Pei; Singh, Sher; Yu, Sung-Liang; Kao, Li-Pin; Tsai, Zong Yun; Lin, Sin-Daw; Li, Steven Shoei-Lung

    2010-03-01

    We determined the expression of both mRNAs and microRNAs (miRNAs) from human mesenchymal stem cells BM19, FM30, and AM3, which is derived from breast, face, and abdominal adipose tissues, respectively. BM19, FM30, and AM3 cells exhibited considerably similar mRNA profiles, and their 1,038 abundantly common genes were involved in regulating six cell adhesion and three cytoskeleton remodeling processes among the top ten GeneGo canonical pathway maps. The 39 most abundant miRNAs in AM3 cells were expressed at very similar levels in BM19 cells. However, seven abundant miRNAs (miR-19b, miR-320, miR-186, miR-199a, miR-339, miR-99a, and miR-152) in AM3 cells were expressed at much lower levels than that in FM30 cells, and 38 genes targeted by these miRNAs were consequently upregulated more than 3-fold in FM30 cells compared with AM3 cells. Therefore, autologous abdominal adipose-derived mesenchymal stem cells are suitable for tissue engineering of breast reconstruction because of very similar expression profiles of mRNAs and miRNAs between AM3 and BM19 cells. Conversely, abdominal AM3 cells might not be suitable for facial rejuvenation, since the 38 highly expressed genes targeted by miRNAs in FM30 cells might play an important role(s) in the development of facial tissue.

  7. Effects of olive and fish oil Ca soaps in ewe diets on milk fat and muscle and subcutaneous tissue fatty-acid profiles of suckling lambs.

    Science.gov (United States)

    Gallardo, B; Gómez-Cortés, P; Mantecón, A R; Juárez, M; Manso, T; de la Fuente, M A

    2014-07-01

    Enhancing healthy fatty acids (FAs) in ewe milk fat and suckling lamb tissues is an important objective in terms of improving the nutritional value of these foods for the consumer. The present study examined the effects of feeding-protected lipid supplements rich in unsaturated FAs on the lipid composition of ewe milk, and subsequently in the muscle and subcutaneous adipose tissues of lambs suckling such milk. Thirty-six pregnant Churra ewes with their new-born lambs were assigned to one of three experimental diets (forage/concentrate ratio 50 : 50), each supplemented with either 3% Ca soap FAs of palm (Control), olive (OLI) or fish (FO) oil. The lambs were nourished exclusively by suckling for the whole experimental period. When the lambs reached 11 kg BW, they were slaughtered and samples were taken from the Longissimus dorsi and subcutaneous fat depots. Although milk production was not affected by lipid supplementation, the FO diet decreased fat content (P0.05) and other trans-FAs between Control and FO treatments would indicate that FO treatment does not alter rumen biohydrogenation pathways under the assayed conditions. Changes in dam milk FA composition induced differences in the FA profiles of meat and fat depots of lambs, preferentially incorporated polyunsaturated FAs into the muscle rather than storing them in the adipose tissue. In the intramuscular fat of the FO treatment, all the n-3 FAs reached their highest concentrations: 0.97 (18:3 n-3), 2.72 (20:5 n-3), 2.21 (22:5 n-3) and 1.53% (22:6 n-3). In addition, not only did FO intramuscular fat have the most cis-9, trans-11 18:2 (1.66%) and trans-11 18:1 (3.75%), but also the lowest n-6/n-3 ratio (1.80) and saturated FA content were not affected. Therefore, FO exhibited the best FA profile from a nutritional point of view.

  8. 中国青年女性软组织侧貌特征研究%Study on soft tissue profile of features in Chinese young females

    Institute of Scientific and Technical Information of China (English)

    孙兆霞; 梁丽

    2014-01-01

    Objective To study the facial profile of aesthetic features about soft tissue in the normal young fe-males,evaluation of the young females′soft tissue of angles in facial profile,establish the relationship of the facial profile angles.The aim of this study was to provide a reference basis for aesthetics and plastic surgery of field op-eration treatment.Methods Seventy-two females in Grade 2010-2012 were selected randomly.The facial profile of angles in normal young females was measured and analyzed in the FreeHand MX software.Results The fron-tonasal angle,nasolabial angle and nasal tip angle were no difference in NoESR and E,ES,ESR (P>0.05).Up-per lip inclination angle,mentolabial sulcus inclination angle and ∠Z were significant difference between NoESR and E,ES,ESR (P0.05).Facial convexity angle and total facial convexity angle of soft tissue were significant difference between NoESR and E,ES,ESR (P0.05).The mean values of soft tissue of angles in facial profile were obtained from the ESR sample u-sing FreeHand MX software.Conclusion Young women facial profile of soft tissue of angles with ESR standard was harmonious,and the positive correlation between facial convexity angle,full facial convexity angle and ∠Z;the relations of forehead,nose,lips and chin were in harmony.The distance between trichion,soft tissue of nasal tip point,soft tissue pogonion and the tragus center was to equal.On the other hand facial profile of soft tissue of angles with NoESR,E,ES,standard was no harmonious,the position was been varied in forehead,nose,upper lips and chin.%目的:探讨正常青年女性侧貌软组织特征,建立符合侧貌美的青年女性侧面角度均值及各角度之间关系。方法选择72例2010-2012级在校汉族女学生,采用 FreeHand MX 软件对青年女学生面侧貌外部软组织角度进行测量分析。结果鼻额角、鼻唇角及鼻尖角在 NoESR 与 E、ES、ESR 之间差异无统计学意义(P >0.05);上唇

  9. Dietary sunflower oil modulates milk fatty acid composition without major changes in adipose and mammary tissue fatty acid profile or related gene mRNA abundance in sheep.

    Science.gov (United States)

    Castro-Carrera, T; Frutos, P; Leroux, C; Chilliard, Y; Hervás, G; Belenguer, A; Bernard, L; Toral, P G

    2015-04-01

    There are very few studies in ruminants characterizing mammary and adipose tissue (AT) expression of genes and gene networks for diets causing variations in milk fatty acid (FA) composition without altering milk fat secretion, and even less complementing this information with data on tissue FA profiles. This work was conducted in sheep in order to investigate the response of the mammary gland and the subcutaneous and perirenal AT, in terms of FA profile and mRNA abundance of genes involved in lipid metabolism, to a diet known to modify milk FA composition. Ten lactating Assaf ewes were randomly assigned to two treatments consisting of a total mixed ration based on alfalfa hay and a concentrate (60 : 40) supplemented with 0 (control diet) or 25 (SO diet) g of sunflower oil/kg of diet dry matter for 7 weeks. Milk composition, including FA profile, was analysed after 48 days on treatments. On day 49, the animals were euthanized and tissue samples were collected to analyse FA and mRNA abundance of 16 candidate genes. Feeding SO did not affect animal performance but modified milk FA composition. Major changes included decreases in the concentration of FA derived from de novo synthesis (e.g. 12:0, 14:0 and 16:0) and increases in that of long-chain FA (e.g. 18:0, c9-18:1, trans-18:1 isomers and c9,t11-CLA); however, they were not accompanied by significant variations in the mRNA abundance of the studied lipogenic genes (i.e. ACACA, FASN, LPL, CD36, FABP3, SCD1 and SCD5) and transcription factors (SREBF1 and PPARG), or in the constituent FA of mammary tissue. Regarding the FA composition of AT, the little influence of SO did not appear to be linked to changes in gene mRNA abundance (decreases of GPAM and SREBF1 in both tissues, and of PPARG in the subcutaneous depot). Similarly, the great variation between AT (higher contents of saturated FA and trans-18:1 isomers in the perirenal, and of cis-18:1, c9,t11-CLA and n-3 PUFA in the subcutaneous AT) could not be related to

  10. Flavanol-Enriched Cocoa Powder Alters the Intestinal Microbiota, Tissue and Fluid Metabolite Profiles, and Intestinal Gene Expression in Pigs1234

    Science.gov (United States)

    Jang, Saebyeol; Sun, Jianghao; Chen, Pei; Lakshman, Sukla; Molokin, Aleksey; Harnly, James M; Vinyard, Bryan T; Urban, Joseph F; Davis, Cindy D; Solano-Aguilar, Gloria

    2016-01-01

    Background: Consumption of cocoa-derived polyphenols has been associated with several health benefits; however, their effects on the intestinal microbiome and related features of host intestinal health are not adequately understood. Objective: The objective of this study was to determine the effects of eating flavanol-enriched cocoa powder on the composition of the gut microbiota, tissue metabolite profiles, and intestinal immune status. Methods: Male pigs (5 mo old, 28 kg mean body weight) were supplemented with 0, 2.5, 10, or 20 g flavanol-enriched cocoa powder/d for 27 d. Metabolites in serum, urine, the proximal colon contents, liver, and adipose tissue; bacterial abundance in the intestinal contents and feces; and intestinal tissue gene expression of inflammatory markers and Toll-like receptors (TLRs) were then determined. Results: O-methyl-epicatechin-glucuronide conjugates dose-dependently increased (P cocoa powder. The concentration of 3-hydroxyphenylpropionic acid isomers in urine decreased as the dose of cocoa powder fed to pigs increased (75–85%, P cocoa powder/d, respectively. Moreover, consumption of cocoa powder reduced TLR9 gene expression in ileal Peyer’s patches (67–80%, P cocoa powder/d compared with pigs not supplemented with cocoa powder. Conclusion: This study demonstrates that consumption of cocoa powder by pigs can contribute to gut health by enhancing the abundance of Lactobacillus and Bifidobacterium species and modulating markers of localized intestinal immunity. PMID:26936136

  11. Company Profile Dengfeng Chunsheng Refractories Co., Ltd.

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Dengfeng Chunsheng Refractories Co., Ltd. is an industrial enterprise integrating refractories research, design, manufacturing and engineering service into one and was entitled as one of China's high-quality silica bricks production and export bases.

  12. Company Profile Shandong Luyang Share Co. Ltd

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ Shandong Luyang Share Co. Ltd, established in 1984, after more than double decades' struggle and effort, has been developed to be the biggest professional manufacturer of ceramic fiber products in Asia.

  13. Metformin Effect on Nontargeted Metabolite Profiles in Patients With Type 2 Diabetes and in Multiple Murine Tissues.

    Science.gov (United States)

    Adam, Jonathan; Brandmaier, Stefan; Leonhardt, Jörn; Scheerer, Markus F; Mohney, Robert P; Xu, Tao; Bi, Jie; Rotter, Markus; Troll, Martina; Chi, Shen; Heier, Margit; Herder, Christian; Rathmann, Wolfgang; Giani, Guido; Adamski, Jerzy; Illig, Thomas; Strauch, Konstantin; Li, Yixue; Gieger, Christian; Peters, Annette; Suhre, Karsten; Ankerst, Donna; Meitinger, Thomas; Hrabĕ de Angelis, Martin; Roden, Michael; Neschen, Susanne; Kastenmüller, Gabi; Wang-Sattler, Rui

    2016-12-01

    Metformin is the first-line oral medication to increase insulin sensitivity in patients with type 2 diabetes (T2D). Our aim was to investigate the pleiotropic effect of metformin using a nontargeted metabolomics approach. We analyzed 353 metabolites in fasting serum samples of the population-based human KORA (Cooperative Health Research in the Region of Augsburg) follow-up survey 4 cohort. To compare T2D patients treated with metformin (mt-T2D, n = 74) and those without antidiabetes medication (ndt-T2D, n = 115), we used multivariable linear regression models in a cross-sectional study. We applied a generalized estimating equation to confirm the initial findings in longitudinal samples of 683 KORA participants. In a translational approach, we used murine plasma, liver, skeletal muscle, and epididymal adipose tissue samples from metformin-treated db/db mice to further corroborate our findings from the human study. We identified two metabolites significantly (P < 1.42E-04) associated with metformin treatment. Citrulline showed lower relative concentrations and an unknown metabolite X-21365 showed higher relative concentrations in human serum when comparing mt-T2D with ndt-T2D. Citrulline was confirmed to be significantly (P < 2.96E-04) decreased at 7-year follow-up in patients who started metformin treatment. In mice, we validated significantly (P < 4.52E-07) lower citrulline values in plasma, skeletal muscle, and adipose tissue of metformin-treated animals but not in their liver. The lowered values of citrulline we observed by using a nontargeted approach most likely resulted from the pleiotropic effect of metformin on the interlocked urea and nitric oxide cycle. The translational data derived from multiple murine tissues corroborated and complemented the findings from the human cohort.

  14. Distinct microRNA expression profiles in mouse renal cortical tissue after 177Lu-octreotate administration.

    Directory of Open Access Journals (Sweden)

    Emil Schüler

    Full Text Available The aim of this study was to investigate the variation of the miRNA expression levels in normal renal cortical tissue after 177Lu-octreotate administration, a radiopharmaceutical used for treatment of neuroendocrine cancers.Female BALB/c nude mice were i.v. injected with 1.3, 3.6, 14, 45, or 140 MBq 177Lu-octreotate, while control animals received saline. The animals were killed at 24 h after injection and total RNA, including miRNA, was extracted from the renal cortical tissue and hybridized to the Mouse miRNA Oligo chip 4plex to identify differentially regulated miRNAs between exposed and control samples.In total, 57 specific miRNAs were differentially regulated in the exposed renal cortical tissues with 1, 29, 21, 27, and 31 miRNAs identified per dose-level (0.13, 0.34, 1.3, 4.3, and 13 Gy, respectively. No miRNAs were commonly regulated at all dose levels. miR-194, miR-107, miR-3090, and miR-3077 were commonly regulated at 0.34, 1.3, 4.3, and 13 Gy. Strong effects on cellular mechanisms ranging from immune response to p53 signaling and cancer-related pathways were observed at the highest absorbed dose. Thirty-nine of the 57 differentially regulated miRNAs identified in the present study have previously been associated with response to ionizing radiation, indicating common radiation responsive pathways.In conclusion, the 177Lu-octreotate associated miRNA signatures were generally dose-specific, thereby illustrating transcriptional regulation of radiation responsive miRNAs. Taken together, these results imply the importance of miRNAs in early immunological responses in the kidneys following 177Lu-octreotate administration.

  15. B-cell subpopulations from normal human secondary lymphoid tissues with specific gene expression profiles and phenotypes

    DEFF Research Database (Denmark)

    Johnsen, Hans Erik; Schmitz, Alexander; Perez Andres, Martin

    included homogenization, isolation of mononuclear cells, MFC and FACS sorting using multicolour fluorescence single tube panels.of antibodies against surface molecules as CD10/20/27/38/45, supplemented with tissue related antibodies. Isolated B-cell subpopulations were evaluated by morphological inspection......, naïve, centroblast, centrocyte, memory, and plasmablasts. The identity of the tonsillar subpopulations was verified using qRT-PCR and exon microarray GEP based on the used discriminative phenotypic markers as well as transcriptions factors BACH2, BCL6, PAX5, IRF4, P27, PRDM1 and XBP1. Globally, the B...

  16. Growth factor and proteinase profile of Vivostat® platelet-rich fibrin linked to tissue repair

    DEFF Research Database (Denmark)

    Ågren, Sven Per Magnus; Rasmussen, Karina; Pakkenberg, Bente

    2014-01-01

    . Leucocyte, erythrocyte and platelet counts in whole blood and fibrin-I were determined by automated haematology analyser. Platelet concentration in PRF was quantified manually by stereologic analysis of Giemsa-stained tissue sections, and the total content of five growth factors and MMP-9 by enzyme...... and matrix metalloproteinase (MMP)-9 were quantified using novel analytical methods. MATERIALS AND METHODS: Ten healthy non-thrombocytopenic volunteers donated blood for generation of intermediate fibrin-I and final PRF. Anticoagulated whole blood and serum procured in parallel served as baseline controls......·001]. MMP-9 was reduced 139-fold (P applications....

  17. Proteoglycan and proteome profiling of central human pulmonary fibrotic tissue utilizing miniaturized sample preparation: a feasibility study

    DEFF Research Database (Denmark)

    Malmström, Johan; Larsen, Kristoffer; Hansson, Lennart;

    2002-01-01

    The objective of this study was to isolate fibrotic cells from human lung biopsies taken from different central pulmonary locations. A comparison was made of cell morphology, proteoglycan- and protein-expression in mesenchymal cell cultures obtained from human bronchial biopsies from patients...... tissue; one of contractile type with lamellipodia that facilitate migration and a second cell type with an increased cell size, which most likely is of a synthetic phenotype. This is the first evidence of alterations in the proteoglycan expression pattern of versican, perlecan, biglycan and decorin which...

  18. The expression profiles of circRNAs in lung tissues from rats with lipopolysaccharide-induced acute respiratory distress syndrome: A microarray study.

    Science.gov (United States)

    Wan, Qi-Quan; Wu, Di; Ye, Qi-Fa

    2017-08-31

    The development of circular RNA (circRNA) microarray has facilitated the study of the role of circRNAs in regulating gene expression through a circRNA-miRNA-mRNA network. In our study, microarray was performed to detect the expression profiles of circRNAs during lipopolysaccharide (LPS)-induced acute respiratory distress syndrome (ARDS). Twenty rats were randomly divided into 2 groups, the control group and the LPS group, 10 rats in each group. Three rats each from both groups were randomly selected. Using circRNA microarray data, we compared the circRNA expression profiles in lung tissues between these 6 rats. The most differentially expressed circRNA species from these profiles were validated and optimized as ARDS biomarkers and potential therapeutic targets. Overall, 395 and 562 circRNAs were significantly up- and down-regulated in LPS group vs. control group, respectively. Six up-regulated and 4 down-regulated circRNAs from the top 10 candidates were eventually selected to be validated. Among them, only 4 up-regulated circRNAs (mmu_circRNA_19423, rno_circRNA_010489, rno_circRNA_011426, mmu_circRNA_30664) and 1 down-regulated circRNA (rno_circRNA_005564) exhibited significant validation. The 5 highest ranking target miRNAs of these 5 validated circRNAs were predicted according to the miRNA support vector regression method. This is the first study to investigate circRNA expression profile and a large number of aberrantly expressed circRNAs were revealed during ARDS. The significantly over- or under-expressed circRNA may represent a novel biomarker and be developed as a novel therapeutic target for the clinical management of ARDS. The results are preliminary and need to be confirmed in further well-designed studies with larger sample size. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Transcriptional profiling of peripheral lymphoid tissue reveals genes and networks linked to SSBP/1 scrapie pathology in sheep.

    Science.gov (United States)

    Gossner, Anton; Roupaka, Sofia; Foster, Jim; Hunter, Nora; Hopkins, John

    2011-12-15

    Transmissible spongiform encephalopathies (TSEs) are slow and progressive neurodegenerative diseases of humans and animals. The major target organ for all TSEs is the brain but some TSE agents are associated with prior accumulation within the peripheral lymphoid system. Many studies have examined the effects of scrapie infection on the expression of central nervous system (CNS) genes, but this study examines the progression of scrapie pathology in the peripheral lymphoid system and how scrapie infection affects the transcriptome of the lymph nodes and spleen. Infection of sheep with SSBP/1 scrapie resulted in PrP(Sc) deposition in the draining prescapular lymph node (PSLN) by 25 days post infection (dpi) in VRQ/VRQ genotype sheep and 75 dpi in tonsils and spleen. Progression of PrP(Sc) deposition in VRQ/ARR animals was 25 dpi later in the PSLN and 250 dpi later in spleen. Microarray analysis of 75 dpi tissues from VRQ/VRQ sheep identified 52 genes in PSLN and 37 genes in spleen cells that showed significant difference (P ≤ 0.05) between scrapie-infected and mock-infected animals. Transcriptional pathway analysis highlighted immunological disease, cell death and neurological disease as the biological pathways associated with scrapie pathogenesis in the peripheral lymphoid system. PrP(Sc) accumulation of lymphoid tissue resulted in the repression of genes linked to inflammation and oxidative stress, and the up-regulation of genes related to apoptosis.

  20. Tissue specific transcript profiling of wheat phosphate transporter genes and its association with phosphate allocation in grains

    Science.gov (United States)

    Shukla, Vishnu; Kaur, Mandeep; Aggarwal, Sipla; Bhati, Kaushal Kumar; Kaur, Jaspreet; Mantri, Shrikant; Pandey, Ajay K.

    2016-01-01

    Approaches enabling efficient phosphorus utilization in crops are of great importance. In cereal crop like wheat, utilization of inorganic phosphate (Pi) is high and mature grains are the major sink for Pi utilization and storage. Research that addresses the importance of the Pi homeostasis in developing grains is limited. In an attempt to understand the Pi homeostasis in developing wheat grains, we identified twelve new phosphate transporters (PHT), these are phyologentically well distributed along with the members reported from Arabidopsis and rice. Enhanced expression of PHT1-subfamily genes was observed in roots subjected to the Pi starvation suggesting their active role in Pi homeostasis. Differential expression patterns of all the PHT genes during grain filling stages suggested their importance in the filial tissues. Additionally, high accumulation of Pi and total P in aleurone correlates well with the expression of TaPHTs and other phosphate starvation related genes. Tissue specific transcript accumulation of TaPHT1.1, TaPHT1.2, TaPHT1.4 in aleurone; TaPHT3.1 in embryo and TaPHT4.2 in the endosperm was observed. Furthermore, their transcript abundance was affected in low phytate wheat grains. Altogether, this study helps in expanding the knowledge and prioritize the candidate wheat Pi-transporters to modulate the Pi homeostasis in cereal grains. PMID:27995999

  1. Transcriptome profiling reveals divergent expression shifts in brown and white adipose tissue from long-lived GHRKO mice.

    Science.gov (United States)

    Stout, Michael B; Swindell, William R; Zhi, Xu; Rohde, Kyle; List, Edward O; Berryman, Darlene E; Kopchick, John J; Gesing, Adam; Fang, Yimin; Masternak, Michal M

    2015-09-29

    Mice lacking the growth hormone receptor (GHRKO) exhibit improved lifespan and healthspan due to loss of growth hormone signaling. Both the distribution and activity of brown and white adipose tissue (BAT and WAT) are altered in GHRKO mice, but the contribution of each tissue to age-related phenotypes has remained unclear. We therefore used whole-genome microarrays to evaluate transcriptional differences in BAT and WAT depots between GHRKO and normal littermates at six months of age. Our findings reveal a unique BAT transcriptome as well as distinctive responses of BAT to Ghr ablation. BAT from GHRKO mice exhibited elevated expression of genes associated with mitochondria and metabolism, along with reduced expression of genes expressed by monocyte-derived cells (dendritic cells [DC] and macrophages). Largely the opposite was observed in WAT, with increased expression of DC-expressed genes and reduced expression of genes associated with metabolism, cellular respiration and the mitochondrial inner envelope. These findings demonstrate divergent response patterns of BAT and WAT to loss of GH signaling in GHRKO mice. These patterns suggest both BAT and WAT contribute in different ways to phenotypes in GHRKO mice, with Ghr ablation blunting inflammation in BAT as well as cellular metabolism and mitochondrial biogenesis in WAT.

  2. High-fat diet feeding induces sex-dependent changes in inflammatory and insulin sensitivity profiles of rat adipose tissue.

    Science.gov (United States)

    Estrany, Maria E; Proenza, Ana M; Gianotti, Magdalena; Lladó, Isabel

    2013-08-01

    The aim of the study was to determine, in rats of both sexes, the effect of HF diet feeding on the expression of adipokines involved in inflammatory status and insulin sensitivity and on the levels of proteins involved in lipid handling of retroperitoneal adipose tissue. Eight-week-old Wistar rats of both sexes were fed a control diet (2.9% w/w fat) or an HF diet (30% w/w fat) for 14 weeks. Adiponectin, peroxisome proliferator-activated receptor γ and inflammatory marker mRNA levels were analyzed by real-time polymerase chain reaction. Levels of insulin receptor, glucose transporter 4, carnitine palmitoyltransferase 1, fatty acid synthase, hormone-sensitive lipase and lipoprotein lipase were determined by Western blot. HF diet feeding did not induce hyperphagia or body weight gain but did promote an increase in adiposity although only in male rats. HF diet impaired glucose tolerance and the expression of inflammatory and insulin sensitivity markers in adipose tissue of male rats, but not in female rats. Male rats seem to be more prone to disorders associated with an unbalanced composition of the diet, even in the absence of hyperphagia. In contrast, female rats counteract excessive fat intake by improving their ability to use lipid fuels, which limits adiposity and maintains insulin sensitivity. Copyright © 2012 John Wiley & Sons, Ltd.

  3. Effects of birth weight and maternal dietary fat source on the fatty acid profile of piglet tissue.

    Science.gov (United States)

    Tanghe, S; Millet, S; Missotten, J; Vlaeminck, B; De Smet, S

    2014-11-01

    This study aimed to investigate the effects and possible interactions of birth weight and n-3 polyunsaturated fatty acid (PUFA) supplementation of the maternal diet on the fatty acid status of different tissues of newborn piglets. These effects are of interest as both parameters have been associated with pre-weaning mortality. Sows were fed a palm oil diet or a diet containing 1% linseed, echium or fish oil from day 73 of gestation. As fish oil becomes a scarce resource, linseed and echium oil were supplemented as sustainable alternatives, adding precursor fatty acids for DHA to the diet. At birth, the lightest and heaviest male piglet per litter were killed and samples from liver, brain and muscle were taken for fatty acid analysis. Piglets that died pre-weaning had lower birth weights than piglets surviving lactation (1.27±0.04 v. 1.55±0.02 kg; Poil was included in the sow diet. Independent of birth weight, echium or linseed oil in the sow diet increased the DHA concentration of the piglet tissues to the same extent, but the concentrations were not as high as when fish oil was fed.

  4. Transcriptome-wide N⁶-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification.

    Science.gov (United States)

    Li, Yuli; Wang, Xiliang; Li, Cuiping; Hu, Songnian; Yu, Jun; Song, Shuhui

    2014-01-01

    N(6)-methyladenosine (m(6)A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m(6)A modification becomes feasible. Here we present a transcriptome-wide m(6)A modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m(6)A-modified genes, respectively. The m(6)A peak (m(6)A-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m(6)A peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m(6)A-modified genes between the 2 samples, we define 1,792 and 6,508 tissue-specific m(6)A-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are selectively m(6)A-modified (SMGs) only in one of the 2 tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further enlarge our knowledge on the function of RNA m(6)A modification.

  5. Quantitative multiplex quantum dot in-situ hybridisation based gene expression profiling in tissue microarrays identifies prognostic genes in acute myeloid leukaemia

    Energy Technology Data Exchange (ETDEWEB)

    Tholouli, Eleni [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom); MacDermott, Sarah [The Medical School, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom); Hoyland, Judith [School of Biomedicine, Faculty of Medical and Human Sciences, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom); Yin, John Liu [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom); Byers, Richard, E-mail: richard.byers@cmft.nhs.uk [School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, The University of Manchester, Stopford Building, Oxford Road, M13 9PT Manchester (United Kingdom)

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer Development of a quantitative high throughput in situ expression profiling method. Black-Right-Pointing-Pointer Application to a tissue microarray of 242 AML bone marrow samples. Black-Right-Pointing-Pointer Identification of HOXA4, HOXA9, Meis1 and DNMT3A as prognostic markers in AML. -- Abstract: Measurement and validation of microarray gene signatures in routine clinical samples is problematic and a rate limiting step in translational research. In order to facilitate measurement of microarray identified gene signatures in routine clinical tissue a novel method combining quantum dot based oligonucleotide in situ hybridisation (QD-ISH) and post-hybridisation spectral image analysis was used for multiplex in-situ transcript detection in archival bone marrow trephine samples from patients with acute myeloid leukaemia (AML). Tissue-microarrays were prepared into which white cell pellets were spiked as a standard. Tissue microarrays were made using routinely processed bone marrow trephines from 242 patients with AML. QD-ISH was performed for six candidate prognostic genes using triplex QD-ISH for DNMT1, DNMT3A, DNMT3B, and for HOXA4, HOXA9, Meis1. Scrambled oligonucleotides were used to correct for background staining followed by normalisation of expression against the expression values for the white cell pellet standard. Survival analysis demonstrated that low expression of HOXA4 was associated with poorer overall survival (p = 0.009), whilst high expression of HOXA9 (p < 0.0001), Meis1 (p = 0.005) and DNMT3A (p = 0.04) were associated with early treatment failure. These results demonstrate application of a standardised, quantitative multiplex QD-ISH method for identification of prognostic markers in formalin-fixed paraffin-embedded clinical samples, facilitating measurement of gene expression signatures in routine clinical samples.

  6. Longitudinal profiling of the tissue-specific expression of genes related with insulin sensitivity in dairy cows during lactation focusing on different fat depots.

    Directory of Open Access Journals (Sweden)

    Behnam Saremi

    Full Text Available In dairy cows the milk associated energy output in early lactation exceeds the input via voluntary feed intake. To spare glucose for mammary lactose synthesis, peripheral insulin sensitivity (IS is reduced and fat mobilization is stimulated. For these processes a link between IS and the endocrine functions of adipose tissue (AT is likely; we thus aimed to characterise the mRNA expression from bovine AT derived proteins and receptors that are related to IS according to the literature in metabolically active tissues plus systemic IS throughout lactation. Conjugated linoleic acids (CLA reduce milk fat thus decreasing the milk drain of energy and potentially dampening lipolysis, but may also affect IS. Subcutaneous (s.c. AT and liver from pluriparous cows receiving either control fat or CLA supplement (100 g/day from 1 to 182 days in milk each were biopsied covering week -3 to 36 relative to parturition. In an additional trial with primiparous cows treated analogously and slaughtered on days in milk 1, 42 or 105, samples from liver, udder, skeletal muscle and 3 visceral and 3 s.c. AT were obtained and assayed for mRNA abundance of adiponectin, its receptors, leptin, leptin receptor, PPARγ, PPARγ2, IL-6, and TNF-α. In pluriparous animals, the mRNA abundance of most of the target genes decreased after parturition in s.c. AT but increased in liver. In primiparous cows, AT depot specific differences were mostly related to retroperitoneal AT; adiponectin receptor 1 and TNF-α were affected predominantly. CLA effects in primiparous cows were largely limited to decreased PPARγ2 mRNA abundance in udder tissue. In pluriparous cows, insulin secretion was increased by CLA resulting in decreased systemic IS but without consistent changes in tissue target mRNA abundance. The temporal gene expression profiles from the adipokines and related receptors support their coactive function in adapting to the needs of lactation.

  7. Physiological performance and differential expression profiling of genes associated with drought tolerance in root tissue of four contrasting varieties of two Gossypium species.

    Science.gov (United States)

    Singh, Ruchi; Pandey, Neha; Kumar, Anil; Shirke, Pramod A

    2016-01-01

    Root growth in drying soil is generally limited by a combination of mechanical impedance and water stress. As the major function of root tissue is water and nutrient uptake, so it imparts an important role in plant growth and stress management. Previously, we have studied physiological performance and expression profiling of gene associated with drought tolerance in leaf tissue of four cotton varieties. Here, we have further continued our studies with the root tissue of these varieties. The Gossypium hirsutum species JKC-770 is drought-tolerant and KC-2 is drought-sensitive, while Gossypium herbaceum species JKC-717 is drought-tolerant and RAHS-187 is drought-sensitive. JKC-770 and JKC-717 the drought-tolerant varieties showed a comparatively high glutathione-S-transferase, superoxide dismutase, proline along with their gene expression, and low malondialdehyde content indicating low membrane damage and better antioxidative defense under drought condition. The expression levels of cellulose synthase, xyloglucan:xyloglucosyl transferase, and glycosyl hydrolases suggest modulation in cell wall structure and partitioning of sugars towards osmoprotectants instead of cell wall biosynthesis in tolerant varieties. Heat shock proteins and serine/threonine protein phosphotases show upregulation under drought condition, which are responsible for temperature tolerance and protein phosphorylation, respectively. These effects many metabolic processes and may be playing a key role in drought tolerance and adaptability of JKC-770 towards drought tolerance. The long-term water use efficiency (WUE) estimated in terms of carbon isotope discrimination (∆(13)C) in the root tissues showed maximum depletion in the ∆(13)C values in JKC-770 variety, while minimum in RAHS-187 under drought stress with reference to their respective control, suggesting a high WUE in JKC-770 variety.

  8. Profile summary.

    Science.gov (United States)

    2003-01-01

    All drugs appearing in the Adis Profile Summary table have been selected based on information contained in R&D Insight trade mark, a proprietary product of Adis International. The information in the profiles is gathered from the world's medical and scientific literature, at international conferences and symposia, and directly from the developing companies themselves. The emphasis of Drugs in R&D is on the clinical potential of new drugs, and selection of agents for inclusion is based on products in late-phase clinical development that have recently had a significant change in status.

  9. Microarray Expression Profile of Circular RNAs in Heart Tissue of Mice with Myocardial Infarction-Induced Heart Failure

    Directory of Open Access Journals (Sweden)

    Hong-Jin Wu

    2016-06-01

    Full Text Available Background/Aims: Myocardial infarction (MI is a serious complication of atherosclerosis associated with increasing mortality attributable to heart failure. This study is aimed to assess the global changes in and characteristics of the transcriptome of circular RNAs (circRNAs in heart tissue during MI induced heart failure (HF. Methods: Using a post-myocardial infarction (MI model of HF in mice, we applied microarray assay to examine the transcriptome of circRNAs deregulated in the heart during HF. We confirmed the changes in circRNAs by quantitative PCR. Results: We revealed and confirmed a number of circRNAs that were deregulated during HF, which suggests a potential role of circRNAs in HF. Conclusions: The distinct expression patterns of circulatory circRNAs during HF indicate that circRNAs may actively respond to stress and thus serve as biomarkers of HF diagnosis and treatment.

  10. Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python

    Directory of Open Access Journals (Sweden)

    Nicolas eRey-Villamizar

    2014-04-01

    Full Text Available In this article, we describe use of Python for large-scale automated server-based bio-image analysis in FARSIGHT, a free and open-source toolkit of image analysis methods for quantitative studies of complex and dynamic tissue microenvironments imaged by modern optical microscopes including confocal, multi-spectral, multi-photon, and time-lapse systems. The core FARSIGHT modules for image segmentation, feature extraction, tracking, and machine learning are written in C++, leveraging widely used libraries including ITK, VTK, Boost, and Qt. For solving complex image analysis task, these modules must be combined into scripts using Python. As a concrete example, we consider the problem of analyzing 3-D multi-spectral brain tissue images surrounding implanted neuroprosthetic devices, acquired using high-throughput multi-spectral spinning disk step-and-repeat confocal microscopy. The resulting images typically contain 5 fluorescent channels, 6,000$times$10,000$times$500 voxels with 16 bits/voxel, implying image sizes exceeding 250GB. These images must be mosaicked, pre-processed to overcome imaging artifacts, and segmented to enable cellular-scale feature extraction. The features are used to identify cell types, and perform large-scale analytics for identifying spatial distributions of specific cell types relative to the device. Python was used to build a server-based script (Dell 910 PowerEdge servers with 4 sockets/server with 10 cores each, 2 threads per core and 1TB of RAM running on Red Hat Enterprise Linux linked to a RAID 5 SAN capable of routinely handling image datasets at this scale and performing all these processing steps in a collaborative multi-user multi-platform environment consisting. Our Python script enables efficient data storage and movement between compute and storage servers, logging all processing steps, and performs full multi-threaded execution of all codes, including open and closed-source third party libraries.

  11. Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python.

    Science.gov (United States)

    Rey-Villamizar, Nicolas; Somasundar, Vinay; Megjhani, Murad; Xu, Yan; Lu, Yanbin; Padmanabhan, Raghav; Trett, Kristen; Shain, William; Roysam, Badri

    2014-01-01

    In this article, we describe the use of Python for large-scale automated server-based bio-image analysis in FARSIGHT, a free and open-source toolkit of image analysis methods for quantitative studies of complex and dynamic tissue microenvironments imaged by modern optical microscopes, including confocal, multi-spectral, multi-photon, and time-lapse systems. The core FARSIGHT modules for image segmentation, feature extraction, tracking, and machine learning are written in C++, leveraging widely used libraries including ITK, VTK, Boost, and Qt. For solving complex image analysis tasks, these modules must be combined into scripts using Python. As a concrete example, we consider the problem of analyzing 3-D multi-spectral images of brain tissue surrounding implanted neuroprosthetic devices, acquired using high-throughput multi-spectral spinning disk step-and-repeat confocal microscopy. The resulting images typically contain 5 fluorescent channels. Each channel consists of 6000 × 10,000 × 500 voxels with 16 bits/voxel, implying image sizes exceeding 250 GB. These images must be mosaicked, pre-processed to overcome imaging artifacts, and segmented to enable cellular-scale feature extraction. The features are used to identify cell types, and perform large-scale analysis for identifying spatial distributions of specific cell types relative to the device. Python was used to build a server-based script (Dell 910 PowerEdge servers with 4 sockets/server with 10 cores each, 2 threads per core and 1TB of RAM running on Red Hat Enterprise Linux linked to a RAID 5 SAN) capable of routinely handling image datasets at this scale and performing all these processing steps in a collaborative multi-user multi-platform environment. Our Python script enables efficient data storage and movement between computers and storage servers, logs all the processing steps, and performs full multi-threaded execution of all codes, including open and closed-source third party libraries.

  12. Ergosterol profiles, fatty acid composition, and antioxidant activities of button mushrooms as affected by tissue part and developmental stage.

    Science.gov (United States)

    Shao, Suqin; Hernandez, Marta; Kramer, John K G; Rinker, Danny L; Tsao, Rong

    2010-11-24

    This article investigated the mycochemical profiles and the antioxidant activities of the lipophilic extracts of the white and brown button mushrooms. We found that only free ergosterols were present in both mushrooms at 2.04-4.82 mg/g dry matter (DM). Ergosterol concentration was higher in early growth stages but decreased as the mushrooms grew, and it distributed evenly between the caps and stems during early developmental stages but accumulated more in the caps after maturation. The photochemiluminescence (PCL) values of the two mushrooms were 5.49-10.48 nmol trolox equivalent/mg DM, and the EC50 values of 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay ranged 20.19-41.49 mg DM/μg DPPH. The ergosterol content positively correlated with the antioxidant activities (r2>0.89). The total fatty acid content was 8.7 mg/g DM in the white and 5.1 mg/g DM in the brown button mushroom and contained mainly linoleic, palmitic, and stearic acids. Our data provide guidance for optimized harvesting time of mushrooms and maximized health benefits.

  13. Macaques with Rapid Disease Progression and Simian Immunodeficiency Virus Encephalitis Have a Unique Cytokine Profile in Peripheral Lymphoid Tissues

    Science.gov (United States)

    Orandle, Marlene S.; Williams, Kenneth C.; MacLean, Andrew G.; Westmoreland, Susan V.; Lackner, Andrew A.

    2001-01-01

    The influence of host cytokine response on viral load, disease progression, and neurologic lesions was investigated in the simian immunodeficiency virus (SIV)-infected macaque model of AIDS. Cytokine gene expression (interleukin-1β [IL-1β], IL-2, IL-6, IL-10, gamma interferon [IFN-γ], and tumor necrosis factor alpha [TNF-α]) and viral loads were evaluated by semiquantitative reverse transcription-PCR in lymph nodes of 5 control animals and 28 animals infected with SIVmac251 at the terminal stages of AIDS. Infected animals showed higher expression of IFN-γ, IL-6, and IL-10 mRNAs compared with controls. Levels of all cytokines were comparable between animals with rapid (survival, 200 days) disease progression. However, among rapid progressors, the eight animals with SIV encephalitis had a unique cytokine profile (increased IL-2, IL-6, and IFN-γ) that was associated with higher viral loads. These observations provide evidence that host cytokine responses may influence SIV neuropathogenesis independent of disease progression. PMID:11287599

  14. Molecular and phenotypic profiling from the base to the crown in maritime pine wood-forming tissue.

    Science.gov (United States)

    Paiva, Jorge A P; Garcés, Marcelo; Alves, Ana; Garnier-Géré, Pauline; Rodrigues, José Carlos; Lalanne, Céline; Porcon, Stéphane; Le Provost, Grégoire; Perez, Denilson da Silva; Brach, Jean; Frigerio, Jean-Marc; Claverol, Stéphane; Barré, Aurélien; Fevereiro, Pedro; Plomion, Christophe

    2008-01-01

    Environmental, developmental and genetic factors affect variation in wood properties at the chemical, anatomical and physical levels. Here, the phenotypic variation observed along the tree stem was explored and the hypothesis tested that this variation could be the result of the differential expression of genes/proteins during wood formation. Differentiating xylem samples of maritime pine (Pinus pinaster) were collected from the top (crown wood, CW) to the bottom (base wood, BW) of adult trees. These samples were characterized by Fourier transform infrared spectroscopy (FTIR) and analytical pyrolysis. Two main groups of samples, corresponding to CW and BW, could be distinguished from cell wall chemical composition. A genomic approach, combining large-scale production of expressed sequence tags (ESTs), gene expression profiling and quantitative proteomics analysis, allowed identification of 262 unigenes (out of 3512) and 231 proteins (out of 1372 spots) that were differentially expressed along the stem. A good relationship was found between functional categories from transcriptomic and proteomic data. A good fit between the molecular mechanisms involved in CW-BW formation and these two types of wood phenotypic differences was also observed. This work provides a list of candidate genes for wood properties that will be tested in forward genetics.

  15. Digital gene expression profiling of flax (Linum usitatissimum L.) stem peel identifies genes enriched in fiber-bearing phloem tissue.

    Science.gov (United States)

    Guo, Yuan; Qiu, Caisheng; Long, Songhua; Chen, Ping; Hao, Dongmei; Preisner, Marta; Wang, Hui; Wang, Yufu

    2017-08-30

    To better understand the molecular mechanisms and gene expression characteristics associated with development of bast fiber cell within flax stem phloem, the gene expression profiling of flax stem peels and leaves were screened, using Illumina's Digital Gene Expression (DGE) analysis. Four DGE libraries (2 for stem peel and 2 for leaf), ranging from 6.7 to 9.2 million clean reads were obtained, which produced 7.0 million and 6.8 million mapped reads for flax stem peel and leave, respectively. By differential gene expression analysis, a total of 975 genes, of which 708 (73%) genes have protein-coding annotation, were identified as phloem enriched genes putatively involved in the processes of polysaccharide and cell wall metabolism. Differential expression genes (DEGs) was validated using quantitative RT-PCR, the expression pattern of all nine genes determined by qRT-PCR fitted in well with that obtained by sequencing analysis. Cluster and Gene Ontology (GO) analysis revealed that a large number of genes related to metabolic process, catalytic activity and binding category were expressed predominantly in the stem peels. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the phloem enriched genes suggested approximately 111 biological pathways. The large number of genes and pathways produced from DGE sequencing will expand our understanding of the complex molecular and cellular events in flax bast fiber development and provide a foundation for future studies on fiber development in other bast fiber crops. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Influence of the Laser Spot Size, Focal Beam Profile, and Tissue Type on the Lipid Signals Obtained by MALDI-MS Imaging in Oversampling Mode

    Science.gov (United States)

    Wiegelmann, Marcel; Dreisewerd, Klaus; Soltwisch, Jens

    2016-12-01

    To improve the lateral resolution in matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) beyond the dimensions of the focal laser spot oversampling techniques are employed. However, few data are available on the effect of the laser spot size and its focal beam profile on the ion signals recorded in oversampling mode. To investigate these dependencies, we produced 2 times six spots with dimensions between 30 and 200 μm. By optional use of a fundamental beam shaper, square flat-top and Gaussian beam profiles were compared. MALDI-MSI data were collected using a fixed pixel size of 20 μm and both pixel-by-pixel and continuous raster oversampling modes on a QSTAR mass spectrometer. Coronal mouse brain sections coated with 2,5-dihydroxybenzoic acid matrix were used as primary test systems. Sizably higher phospholipid ion signals were produced with laser spots exceeding a dimension of 100 μm, although the same amount of material was essentially ablated from the 20 μm-wide oversampling pixel at all spot size settings. Only on white matter areas of the brain these effects were less apparent to absent. Scanning electron microscopy images showed that these findings can presumably be attributed to different matrix morphologies depending on tissue type. We propose that a transition in the material ejection mechanisms from a molecular desorption at large to ablation at smaller spot sizes and a concomitant reduction in ion yields may be responsible for the observed spot size effects. The combined results indicate a complex interplay between tissue type, matrix crystallization, and laser-derived desorption/ablation and finally analyte ionization.

  17. Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria

    Directory of Open Access Journals (Sweden)

    Liles W Conrad

    2006-11-01

    Full Text Available Abstract Background The development and outcome of cerebral malaria (CM reflects a complex interplay between parasite-expressed virulence factors and host response to infection. The murine CM model, Plasmodium berghei ANKA (PbA, which simulates many of the features of human CM, provides an excellent system to study this host/parasite interface. We designed "combination" microarrays that concurrently detect genome-wide transcripts of both PbA and mouse, and examined parasite and host transcriptional programs during infection of CM-susceptible (C57BL/6 and CM-resistant (BALB/c mice. Results Analysis of expression data from brain, lung, liver, and spleen of PbA infected mice showed that both host and parasite gene expression can be examined using a single microarray, and parasite transcripts can be detected within whole organs at a time when peripheral blood parasitemia is low. Parasites display a unique transcriptional signature in each tissue, and lung appears to be a large reservoir for metabolically active parasites. In comparisons of susceptible versus resistant animals, both host and parasite display distinct, organ-specific transcriptional profiles. Differentially expressed mouse genes were related to humoral immune response, complement activation, or cell-cell interactions. PbA displayed differential expression of genes related to biosynthetic activities. Conclusion These data show that host and parasite gene expression profiles can be simultaneously analysed using a single "combination" microarray, and that both the mouse and malaria parasite display distinct tissue- and strain-specific responses during infection. This technology facilitates the dissection of host-pathogen interactions in experimental cerebral malaria and could be extended to other disease models.

  18. How companies fare through deregulation

    Energy Technology Data Exchange (ETDEWEB)

    Chwalowski, M.

    1977-01-01

    The electric utility industry must learn from past deregulation mistakes in order to develop successful corporate structures, services, and technologies that will succeed in a competitive environment. Failure to act will leave the average utility with less than a 50-50 chance of survival five years after deregulation commences. Most examinations of deregulation focus on its political aspects as well as its impacts on consumers, labor relations and safety. There are very few, if any, discussions about how companies themselves change. This article examines trends in the airline industry before and after deregulation. It concentrates on key indicators (e.g., internal structure, management team, employee profile, strategy, products and businesses, profitability) at discrete points in time. The conclusions point to general trends that characterized those transitions including the traits of successful companies.

  19. Tissue-associated bacterial alterations in rectal carcinoma patients revealed by 16S rRNA community profiling

    Directory of Open Access Journals (Sweden)

    Andrew Maltez Thomas

    2016-12-01

    Full Text Available Sporadic and inflammatory forms of colorectal cancer (CRC account for more than 80% of cases. Recent publications have shown mechanistic evidence for the involvement of gut bacteria in the development of both CRC-forms. Whereas colon and rectal cancer have been routinely studied together as CRC, increasing evidence show these to be distinct diseases. Also, the common use of fecal samples to study microbial communities may reflect disease state but possibly not the tumor microenvironment. We performed this study to evaluate differences in bacterial communities found in tissue samples of 18 rectal-cancer subjects when compared to 18 non-cancer controls. Samples were collected during exploratory colonoscopy (non-cancer group or during surgery for tumor excision (rectal-cancer group. High throughput 16S rRNA amplicon sequencing of the V4-V5 region was conducted on the Ion PGM platform, reads were filtered using Qiime and clustered using UPARSE. We observed significant increases in species richness and diversity in rectal cancer samples, evidenced by the total number of OTUs and the Shannon and Simpson indexes. Enterotyping analysis divided our cohort into two groups, with the majority of rectal cancer samples clustering into one enterotype, characterized by a greater abundance of Bacteroides and Dorea. At the phylum level, rectal-cancer samples had increased abundance of candidate phylum OD1 (also known as Parcubacteria whilst non-cancer samples had increased abundance of Planctomycetes. At the genera level, rectal-cancer samples had higher abundances of Bacteroides, Phascolarctobacterium, Parabacteroides, Desulfovibrio and Odoribacter whereas non-cancer samples had higher abundances of Pseudomonas, Escherichia, Acinetobacter, Lactobacillus and Bacillus. Two Bacteroides fragilis OTUs were more abundant among rectal-cancer patients seen through 16S rRNA amplicon sequencing, whose presence was confirmed by immunohistochemistry and enrichment verified

  20. Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling

    Science.gov (United States)

    Thomas, Andrew M.; Jesus, Eliane C.; Lopes, Ademar; Aguiar, Samuel; Begnami, Maria D.; Rocha, Rafael M.; Carpinetti, Paola Avelar; Camargo, Anamaria A.; Hoffmann, Christian; Freitas, Helano C.; Silva, Israel T.; Nunes, Diana N.; Setubal, João C.; Dias-Neto, Emmanuel

    2016-01-01

    Sporadic and inflammatory forms of colorectal cancer (CRC) account for more than 80% of cases. Recent publications have shown mechanistic evidence for the involvement of gut bacteria in the development of both CRC-forms. Whereas, colon and rectal cancer have been routinely studied together as CRC, increasing evidence show these to be distinct diseases. Also, the common use of fecal samples to study microbial communities may reflect disease state but possibly not the tumor microenvironment. We performed this study to evaluate differences in bacterial communities found in tissue samples of 18 rectal-cancer subjects when compared to 18 non-cancer controls. Samples were collected during exploratory colonoscopy (non-cancer group) or during surgery for tumor excision (rectal-cancer group). High throughput 16S rRNA amplicon sequencing of the V4–V5 region was conducted on the Ion PGM platform, reads were filtered using Qiime and clustered using UPARSE. We observed significant increases in species richness and diversity in rectal cancer samples, evidenced by the total number of OTUs and the Shannon and Simpson indexes. Enterotyping analysis divided our cohort into two groups, with the majority of rectal cancer samples clustering into one enterotype, characterized by a greater abundance of Bacteroides and Dorea. At the phylum level, rectal-cancer samples had increased abundance of candidate phylum OD1 (also known as Parcubacteria) whilst non-cancer samples had increased abundance of Planctomycetes. At the genera level, rectal-cancer samples had higher abundances of Bacteroides, Phascolarctobacterium, Parabacteroides, Desulfovibrio, and Odoribacter whereas non-cancer samples had higher abundances of Pseudomonas, Escherichia, Acinetobacter, Lactobacillus, and Bacillus. Two Bacteroides fragilis OTUs were more abundant among rectal-cancer patients seen through 16S rRNA amplicon sequencing, whose presence was confirmed by immunohistochemistry and enrichment verified by digital

  1. MERGER ACCOUTING FOR COMPANIES

    Directory of Open Access Journals (Sweden)

    SUCIU GHEORGHE

    2014-05-01

    Full Text Available Companies, especially nowadays, are characterized through great mobility, fast circulation of capital, occurring in their chase for profit. In this context, companies look for alliances, economical and political assistance. These objectives can materialize through merging of companies. The merger can be internal (between Romanian companies or transboundary, which includes foreign companies. In order to correctly reflect these events, the merger operations must be regulated and must respect national and international regulations. One important request concerning the merger operations is that the accounting values of the assets, debts and ownership equity must be brought to the present financial value.

  2. Effects of Arginine Supplementation on Amino Acid Profiles in Blood and Tissues in Fed and Overnight-Fasted Rats

    Directory of Open Access Journals (Sweden)

    Milan Holecek

    2016-04-01

    Full Text Available Chronic arginine intake is believed to have favorable effects on the body. However, it might be hypothesized that excessive consumption of an individual amino acid exerts adverse effects on distribution and metabolism of other amino acids. We evaluated the effect of chronic intake of arginine on amino acid concentrations in blood plasma, liver, kidneys, and soleus and extensor digitorum longus muscles. Rats were fed a standard diet or a high-arginine diet (HAD for two months. Half of the animals in each group were sacrificed in the fed state, and the other half after fasting overnight. HAD increased blood plasma concentrations of urea, creatinine, arginine, and ornithine and decreased most other amino acids. Arginine and ornithine also increased in muscles and kidneys; an increase of lysine was observed in both muscle types. Methionine, phenylalanine, threonine, asparagine, glycine, serine, and taurine decreased in most tissues of HAD fed animals. Most of the effects of HAD disappeared after overnight fasting. It is concluded that (i enhanced dietary arginine intake alters distribution of almost all amino acids; and (ii to attain a better assessment of the effects of various nutritional interventions, an appropriate number of biochemical measurements must be performed in both postprandial and postabsorptive states.

  3. Integrative proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer.

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    Yansheng Liu

    Full Text Available Lung cancer is the leading cause of cancer deaths worldwide. Clinically, the treatment of non-small cell lung cancer (NSCLC can be improved by the early detection and risk screening among population. To meet this need, here we describe the application of extensive peptide level fractionation coupled with label free quantitative proteomics for the discovery of potential serum biomarkers for lung cancer, and the usage of Tissue microarray analysis (TMA and Multiple reaction monitoring (MRM assays for the following up validations in the verification phase. Using these state-of-art, currently available clinical proteomic approaches, in the discovery phase we confidently identified 647 serum proteins, and 101 proteins showed a statistically significant association with NSCLC in our 18 discovery samples. This serum proteomic dataset allowed us to discern the differential patterns and abnormal biological processes in the lung cancer blood. Of these proteins, Alpha-1B-glycoprotein (A1BG and Leucine-rich alpha-2-glycoprotein (LRG1, two plasma glycoproteins with previously unknown function were selected as examples for which TMA and MRM verification were performed in a large sample set consisting about 100 patients. We revealed that A1BG and LRG1 were overexpressed in both the blood level and tumor sections, which can be referred to separate lung cancer patients from healthy cases.

  4. Relationship between the Balance of Hypertrophic/Hyperplastic Adipose Tissue Expansion and the Metabolic Profile in a High Glucocorticoids Model

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    María Guillermina Zubiría

    2016-07-01

    Full Text Available Adipose tissue (AT expansion is the result of two processes: hyperplasia and hypertrophy; and both, directly or indirectly, depend on the adipogenic potential of adipocyte precursor cells (APCs. Glucocorticoids (GCs have a potent stimulatory effect on terminal adipogenesis; while their effects on early stages of adipogenesis are largely unknown. In the present work, we study, in a model of high GC levels, the adipogenic potential of APCs from retroperitoneal AT (RPAT and its relationship with RPAT mass expansion. We employed a model of hyper-adiposity (30- and 60-day-old rats due to high endogenous GC levels induced by neonatal treatment with l-monosodium glutamate (MSG. We found that the RPAT APCs from 30-day-old MSG rats showed an increased adipogenic capacity, depending on the APCs’ competency, but not in their number. Analyses of RPAT adipocyte diameter revealed an increase in cell size, regardless of the rat age, indicating the prevalence of a hypertrophic process. Moreover, functional RPAT alterations worsened in 60-day-old rats, suggesting that the hyperplastic AT expansion found in 30-day-old animals might have a protective role. We conclude that GCs chronic excess affects APCs’ adipogenic capacity, modifying their competency. This change would modulate the hyperplastic/hypertrophic balance determining healthy or unhealthy RPAT expansion and, therefore, its functionality.

  5. Effect of sample volume size and sampling method on feline longitudinal myocardial velocity profiles from color tissue Doppler imaging.

    Science.gov (United States)

    Granström, Sara; Pipper, Christian Bressen; Møgelvang, Rasmus; Sogaard, Peter; Willesen, Jakob Lundgren; Koch, Jørgen

    2012-12-01

    The aims of this study were to compare the effect of sample volume (SV) size settings and sampling method on measurement variability and peak systolic (s'), and early (e') and late (a') diastolic longitudinal myocardial velocities using color tissue Doppler imaging (cTDI) in cats. Twenty cats with normal echocardiograms and 20 cats with hypertrophic cardiomyopathy. We quantified and compared empirical variance and average absolute values of s', e' and a' for three cardiac cycles using eight different SV settings (length 1,2,3 and 5 mm; width 1 and 2 mm) and three methods of sampling (end-diastolic sampling with manual tracking of the SV, end-systolic sampling without tracking, and random-frame sampling without tracking). No significant difference in empirical variance could be demonstrated between most of the tested SVs. However, the two settings with a length of 1 mm resulted in a significantly higher variance compared with all settings where the SV length exceeded 2 mm (p sampling method on the variability of measurements (p = 0.003) and manual tracking obtained the lowest variance. No difference in average values of s', e' or a' could be found between any of the SV settings or sampling methods. Within the tested range of SV settings, an SV length of 1 mm resulted in higher measurement variability compared with an SV length of 3 and 5 mm, and should therefore be avoided. Manual tracking of the sample volume is recommended. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Influence of Phenobarbital and Carbon tetrachloride on the Modulation of Tissue Retention Profile of Hexachlorocyclohexane in Rats

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The study was designed to investigate the role of hepatic metabolic activity on body burden of HCH residue. Male albino rats were orally administered 0, 5, and 10 mg/kg HCH for 90 days, followed by either sodium phenobarbital or carbon tetrachloride treatment for 0, 15 and 30 days after withdrawal of their respective HCH administration. The liver weight was significantly increased at 30 days after the administration of phenobarbital and carbon tetrachloride in both 5 mg and 10 mg/kg HCH withdrawal groups when compared to control. HCH residue was maximun in fat followed by adrenal>thymus>liver>kidney>spleen>testes>brain>plasma. Carbon tetrachloride caused an accumul-ation of HCH residues in the liver 15 and 30 days after administration of both doses of HCH. Phenobarbital did not show significant variation in HCH residues in hepatic tissue. Phenobarbital treatment caused significant induction of hepatic RED, APD, AHH, GST and QR activities. Significant decreases in activities were observed by carbon tetrachloride when compared to animals treated with HCH alone. The overall results clearly suggest the role of P450 protein on the body burden of HCH residues.

  7. Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and In Silico Mapping in Relation to Resistance Markers

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    Bernarda Calla

    2009-07-01

    Full Text Available White mold, caused by (Lib. de Bary, can be a serious disease of crops grown under cool, moist environments. In many plants, such as soybean [ (L. Merr.], complete genetic resistance does not exist. To identify possible genes involved in defense against this pathogen, and to determine possible physiological changes that occur during infection, a microarray screen was conducted using stem tissue to evaluate changes in gene expression between partially resistant and susceptible soybean genotypes at 8 and 14 hours post inoculation. RNA from 15 day-old inoculated plants was labeled and hybridized to soybean cDNA microarrays. ANOVA identified 1270 significant genes from the comparison between time points and 105 genes from the comparison between genotypes. Selected genes were classified into functional categories. The analyses identified changes in cell-wall composition and signaling pathways, as well as suggesting a role for anthocyanin and anthocyanidin synthesis in the defense against . In-silico mapping of both the differentially expressed transcripts and of public markers associated with partial resistance to white mold, provided evidence of several differentially expressed genes being closely positioned to white mold resistance markers, with the two most promising genes encoding a PR-5 and anthocyanidin synthase.

  8. Effect of maturation degree on fatty acid profile of different tissues in wild and farmed rohu (Labeo rohita

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    Nadeem, Shahid

    2011-06-01

    Full Text Available During the breeding season, lots of physiological changes occur in the bodies of fish which lead to other phenotypical, anatomical and behavioral changes. To evaluate the impact of breeding on the bodily composition of fish, tests were conducted to determine the fatty acid profile of the brooder and Non-brooder wild and farmed fish. Samples were analyzed by gas liquid chromatography using a flame ionization detector.There are non significant differences in the amount of saturated and unsaturated fatty acids in wild and farmed nonbrooder fish whereas in case of brooder there are significant differences. Brooder farmed fish contained more saturates in gonads approximately twice that of wild fish with C16:0 as the dominating fatty acid. C18:2n-6 and C20:5n-6 were the dominating unsaturated fatty acids in the gonads. Non-brooder fish contained more unsaturated fatty acids in the meat as compared to the brooder fish and farmed fish contained higher amounts of saturated fatty acids as compared to wild fish. C18:1n-9 and C20:4n-6 fatty acids were found in higher quantities and among the saturated acids, C16:0 is the dominating one. More or less similar results were found in the case of the liver fatty acid profile of breeding and nonbreeding fish. Fish of lower weight categories contained more unsaturated fatty acids and so better for consumption to leave the brooders of higher weight categories for the breeding of future generation.Durante la época de reproducción numerosos cambios fisiológicos ocurren en el cuerpo de los peces que guían a cambios anatómicos y de comportamiento. Para evaluar el impacto de la etapa de reproducción en la composición de los peces, ensayos para determinar el perfil de ácidos grasos fueron conducidos en peces salvajes y criados, en dos categorías de peso, maduro (booder o inmaduro (non-brooder. Las muestras fueron analizadas por cromatografía de gases usando un detector de ionización de llama. No hubo

  9. Gene expression profile of normal and cancer-associated fibroblasts according to intratumoral inflammatory cells phenotype from breast cancer tissue.

    Science.gov (United States)

    González, Lucía; Eiro, Noemi; Fernandez-Garcia, Belen; González, Luis O; Dominguez, Francisco; Vizoso, Francisco J

    2016-11-01

    The biological heterogeneity of breast cancer leads to the need for finding new approaches to understand the mechanisms implicated in breast cancer progression. The tumor stroma appears as a key in the progression of solid tumors towards a malignant phenotype. Cancer associated fibroblasts (CAFs) may orchestrate a functional "corrupted" stroma which in turn helps metastatic spread. In this study, we investigated by real-time PCR, the expression of 19 factors by normal breast-associated fibroblasts (NAFs) and CAFs, which were implicated in several actions promoting tumor growth, such as extracellular matrix remodeling, inflammation and invasion. Also, we explored the influence of inflammatory cells phenotypes (MMP11 status) and breast cancer cell lines (MCF-7 and MDA-MB-231) on the molecular profile of CAFs. If we consider that one of the major sources of CAFs are resident NAFs, the transition of NAFs into CAFs is associated with molecular changes involving the overexpression of some molecular factors of biological importance in tumor progression. In addition, the characterization of the tumor stroma regarding to the MMP11 status by MICs reflects a type of fibroblasts which contribute even more to tumor progression. Moreover, different patterns in the induction of the expression of factors by CAFs were observed, depending on the tumor cell line which they were co-cultured with. Furthermore, CAFs influence TGFβ expression in both cancer cell lines. Therefore, this study can help to a better characterization of tumor stroma in order to improve the prognostic evaluation, as well as to define the different populations of CAFs as potential therapeutic targets in breast cancer. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  10. Profile of muscle tissue gene expression specific to water buffalo: Comparison with domestic cattle by genome array.

    Science.gov (United States)

    Zhang, Yingying; Wang, Hongbao; Gui, Linsheng; Wang, Hongcheng; Mei, Chugang; Zhang, Yaran; Xu, Huaichao; Jia, Cunlin; Zan, Linsen

    2016-02-10

    In contrast with the past, the water buffalo is now not only a draft animal, but also an important food source of milk and meat. It is increasingly apparent that the water buffalo have huge potential for meat production, but its breeding needs to be investigated. Regarding the molecular mechanisms involved in the meat quality difference between the buffalo (Bubalus bulabis) and yellow cattle (Bos taurus), 12 chemical-physical characteristics related to the meat quality of longissimus thoracis muscles (LTM) have been compared at the age of 36 months. Intramuscular lipid and b* (yellowness) were greater in cattle than the buffalo, whereas a* (redness) was greater in the buffalo. Gene expression profiles were constructed by bovine genome array. A total of 8884 and 10,960 probes were detected in buffalo and cattle, respectively, with 1580 genes being differentially expressed. Over 400 probes were upregulated and nearly 1200 were downregulated in LTM of the buffalo, most being involved in ribosomal RNA (rRNA) processing, cholesterol homeostasis, regulation of transcription, response to hypoxia, and glycolysis. Quantitative real-time PCR was used to validate the microarray data. Enriched GO analyses of highly expressed genes in LTM showed that protein biosynthesis, striated muscle contraction, iron homeostasis, iron transport, glycolysis and glucose metabolism were similar between the buffalo and cattle. High protein content, low fat content and deep meat color of buffalo LTM may be closely associated with the increased expression of genes involved in cholesterol and iron homeostasis, while also reducing the expression of genes involved in ubiquitin-mediated proteolysis and protein oxidative phosphorylation. These results establish the groundwork for further studies on buffalo meat quality and will be beneficial in improving water buffalo breeding by molecular biotechnology.

  11. Cell Type-dependent Gene Transcription Profile in Three Dimensional Human Skin Tissue Model Exposed to Low Doses of Ionizing Radiation: Implications for Medical Exposures

    Energy Technology Data Exchange (ETDEWEB)

    Freiin von Neubeck, Claere H.; Shankaran, Harish; Karin, Norman J.; Kauer, Paula M.; Chrisler, William B.; Wang, Xihai; Robinson, Robert J.; Waters, Katrina M.; Tilton, Susan C.; Sowa, Marianne B.

    2012-04-17

    The concern over possible health risks from exposures to low doses of ionizing radiation has been driven largely by the increase in medical exposures, the routine implementation of X-ray backscatter devices for airport security screening, and, most recently, the nuclear incident in Japan. Due to a paucity of direct epidemiological data at very low doses, cancer risk must be estimated from high dose exposure scenarios. However, there is increasing evidence that low and high dose exposures result in different signaling events and may have different mechanisms of cancer induction. We have examined the radiation induced temporal response of an in vitro three dimensional (3D) human skin tissue model using microarray-based transcriptional profiling. Our data shows that exposure to 100 mGy of X-rays is sufficient to affect gene transcription. Cell type specific analysis showed significant changes in gene expression with the levels of > 1400 genes altered in the dermis and > 400 genes regulated in the epidermis. The two cell types rarely exhibited overlapping responses at the mRNA level. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) measurements validated the microarray data in both regulation direction and value. Key pathways identified relate to cell cycle regulation, immune responses, hypoxia, reactive oxygen signaling, and DNA damage repair. We discuss in particular the role of proliferation and emphasizing how the disregulation of cellular signaling in normal tissue may impact progression towards radiation induced secondary diseases.

  12. Microarray expression profiles of genes in lung tissues of rats subjected to focal cerebral ischemia-induced lung injury following bone marrow-derived mesenchymal stem cell transplantation.

    Science.gov (United States)

    Hu, Yue; Xiong, Liu-Lin; Zhang, Piao; Wang, Ting-Hua

    2017-01-01

    Ischemia-induced stroke is the most common disease of the nervous system and is associated with a high mortality rate worldwide. Cerebral ischemia may lead to remote organ dysfunction, particular in the lungs, resulting in lung injury. Nowadays, bone marrow-derived mesenchymal stem cells (BMSCs) are widely studied in clinical trials as they may provide an effective solution to the treatment of neurological and cardiac diseases; however, the underlying molecular mechanisms remain unknown. In this study, a model of permanent focal cerebral ischemia-induced lung injury was successfully established and confirmed by neurological evaluation and lung injury scores. We demonstrated that the transplantation of BMSCs (passage 3) via the tail vein into the lung tissues attenuated lung injury. In order to elucidate the underlying molecular mechanisms, we analyzed the gene expression profiles in lung tissues from the rats with focal cerebral ischemia and transplanted with BMSCs using a Gene microarray. Moreover, the Gene Ontology database was employed to determine gene function. We found that the phosphoinositide 3-kinase (PI3K)-AKT signaling pathway, transforming growth factor-β (TGF-β) and platelet-derived growth factor (PDGF) were downregulated in the BMSC transplantation groups, compared with the control group. These results suggested that BMSC transplantation may attenuate lung injury following focal cerebral ischemia and that this effect is associated with the downregulation of TGF-β, PDGF and the PI3K-AKT pathway.

  13. Differential adipose tissue gene expression profiles in abacavir treated patients that may contribute to the understanding of cardiovascular risk: a microarray study.

    Science.gov (United States)

    Shahmanesh, Mohsen; Phillips, Kenneth; Boothby, Meg; Tomlinson, Jeremy W

    2015-01-01

    To compare changes in gene expression by microarray from subcutaneous adipose tissue from HIV treatment naïve patients treated with efavirenz based regimens containing abacavir (ABC), tenofovir (TDF) or zidovidine (AZT). Subcutaneous fat biopsies were obtained before, at 6- and 18-24-months after treatment, and from HIV negative controls. Groups were age, ethnicity, weight, biochemical profile, and pre-treatment CD4 count matched. Microarray data was generated using the Agilent Whole Human Genome Microarray. Identification of differentially expressed genes and genomic response pathways was performed using limma and gene set enrichment analysis. There were significant divergences between ABC and the other two groups 6 months after treatment in genes controlling cell adhesion and environmental information processing, with some convergence at 18-24 months. Compared to controls the ABC group, but not AZT or TDF showed enrichment of genes controlling adherence junction, at 6 months and 18-24 months (adjusted ptissue. If similar changes are also taking place in other tissues including the coronary vasculature they may contribute to the increased risk of cardiovascular events reported in patients recently started on abacavir-containing regimens.

  14. Effect of dietary sunflower oil and coconut oil on adipose tissue gene expression, fatty acid composition and serum lipid profile of grower pigs.

    Science.gov (United States)

    Iyer, Mohan N Harihara; Sarmah, Babul C; Tamuli, Madan K; Das, Anubrata; Kalita, Dhireswar

    2012-08-01

    The present study was conducted to assess whether the partial replacement of feed energy by vegetable oils containing high medium-chain saturated fatty acids (MCFA) and n-6 polyunsaturated fatty acids (PUFA) would modify lipogenic gene expression and other parameter of fat metabolism in pigs. Eighteen pigs (17-19 kg body weight) received one of three experimental diets for 60 days (six animals per group): (i) Control diet; (ii) a diet with sunflower oil (SO) or (iii) a diet with coconut oil (CO). In diets SO and CO, 10% of the feed energy was replaced by the respective oils. The experimental treatment did not influence the performance of the pigs. In blood serum, an increased content of total cholesterol was observed for SO and CO fed animals, whereas no significant changes for total triglycerides and different lipoprotein fractions were detected. The fatty acid composition of adipose tissue was significantly modified, with an increased content of MCFA and n-6 PUFA in CO and SO fed pigs, respectively. The gene expression for fatty acid synthase was decreased for SO and CO fed pigs; for stearoyl CoA desaturase and sterol regulatory element binding protein, a depression was observed in SO but not in CO fed pigs. The results of present study suggest that the type of dietary fat can modulate the adipose tissue gene expression and fatty acid composition differentially, with minimal effect on serum lipid profile.

  15. Genome-wide mRNA-seq profiling reveals predominant down-regulation of lipid metabolic processes in adipose tissues of Small Tail Han than Dorset sheep.

    Science.gov (United States)

    Miao, Xiangyang; Luo, Qingmiao; Qin, Xiaoyu; Guo, Yuntao; Zhao, Huijing

    2015-11-13

    Small Tail Han and Dorset sheep are two different sheep with distinguished morphologies in fat depositions. In order to characterize their gene expression profiles, our present study took the advantages of RNA sequencing technology with the aims to identify important genes regulating the metabolisms in adipose tissues of two different sheep. In obtained high quality sequencing reads, 85.9 (Han) and 86.1% (Dorset) were uniquely aligned to Oar v3.1 sheep reference genome, and over 76% of bases in mapped reads corresponded to mRNA. Using R package EBSeq, we identified 602 differentially expressed genes. Using the 602 genes, GO analysis showed that 30 out of 56 significantly enriched biological processes were metabolism related, of which the most significant one was triglyceride biosynthetic process. The KEGG pathway analysis indicated the down-regulation of several fat metabolic pathways. The predominant down-regulation of massive metabolic processes, particularly the lipid metabolism, in adipose tissues of Han sheep could explain, at least in part, the distinguished fat deposition between two different sheep, and our data constitute a basic picture of transcriptomes in these sheep for better understanding of underline biological mechanism in their lipid metabolisms.

  16. Glutathione S-transferases in human renal cortex and neoplastic tissue: enzymatic activity, isoenzyme profile and immunohistochemical localization.

    Science.gov (United States)

    Rodilla, V; Benzie, A A; Veitch, J M; Murray, G I; Rowe, J D; Hawksworth, G M

    1998-05-01

    1. Glutathione S-transferase (GST) activity in the cytosol of renal cortex and tumours from eight men and eight women was measured using 1-chloro-2,4-dinitrobenzene (CDNB) as a substrate. GST activities ranged from 685 to 2192 nmol/min/mg protein in cortex (median 1213) and from non-detectable (minimum 45) to 2424 nmol/min/mg protein in tumours (median 469). The activities in the tumours were lower than those in the normal cortices (p 0.05). 3. The age of the patients ranged from 42 to 81 years (median 62) and was not found to play a role in the levels of GST activity observed in cortex or in renal tumours from either sex. 4. Immunoblotting and immunohistochemical studies confirmed that GST-alpha was the predominant form expressed both in normal cortex and tumour and probably accounted for most of the GST activity present in these samples. GST-mu and GST-phi were expressed in both tumours and normal cortex and, while in some cases the level of expression in the cortices was higher than that found in the tumours, the reverse was also observed. Within the GST-mu class, GST M1/M2 was only detected in one sample (tumour), which showed the highest overall expression of GST-mu. GSTM3 was the predominant isoenzyme of the mu class in normal and tumour tissue, whereas GTM4 and GSTM5 were not detected. 5. These differences could have functional significance where xenobiotics or cytotoxic drugs are specific substrates for the different classes of GSTs.

  17. Effect of a long-chain n-3 polyunsaturated fatty acid-enriched diet on adipose tissue lipid profiles and gene expression in Holstein dairy cows.

    Science.gov (United States)

    Elis, Sebastien; Desmarchais, Alice; Freret, Sandrine; Maillard, Virginie; Labas, Valérie; Cognié, Juliette; Briant, Eric; Hivelin, Celine; Dupont, Joëlle; Uzbekova, Svetlana

    2016-12-01

    The objective of this study was to determine whether fish oil supplement has an effect on adipose tissue lipid profiles and gene expression in postpartum dairy cows. Holstein cows were supplemented with either long-chain n-3 polyunsaturated fatty acid (PUFA; protected fish oil) or control PUFA (n-6; toasted soybeans) for 2mo after calving (n=23 per diet). These cows showed no difference in milk production or metabolic parameters, but exhibited a tendency toward a decrease in early embryo mortality rate after artificial insemination. We hypothesized that, in addition to this effect, modifications in adipose tissue (AT) gene expression and lipid profiles would occur in response to diet. Subcutaneous AT samples were thus collected from the dewlaps of n-3 and n-6 dairy cows at 1mo antepartum, and 1wk, 2mo, and 5mo postpartum for the analysis of lipids and gene expression. Lipid profiles were obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in both positive and negative modes. We found 37 lipid species in the 200 to 1,200 m/z range, which differed between the n-3 and control groups, suggesting that the n-3 supplement affected the lipid composition through the enrichment of lipids integrating long-chain PUFA from fish oil sources: eicosapentaenoic and docosahexaenoic acid. Moreover, a decrease in triacylglycerolipids was observed in AT of n-3 supplemented cows. The expression of 44 genes involved in fatty acid metabolism and the adipokine system was assessed by real-time reverse-transcription PCR. Hierarchical clustering, according to either postpartum stage or diet, enabled us to group genes exhibiting similar kinetic properties during lactation or by those that varied in similar ways after n-3 supplementation, respectively. Among the genes exhibiting a dietary effect, FABP4, LIPE, CD36, and PLIN1 were overexpressed in n-3 AT samples compared with the control, suggesting an increase in lipolysis due to n-3 supplementation, which

  18. Differential adipose tissue gene expression profiles in abacavir treated patients that may contribute to the understanding of cardiovascular risk: a microarray study.

    Directory of Open Access Journals (Sweden)

    Mohsen Shahmanesh

    Full Text Available To compare changes in gene expression by microarray from subcutaneous adipose tissue from HIV treatment naïve patients treated with efavirenz based regimens containing abacavir (ABC, tenofovir (TDF or zidovidine (AZT.Subcutaneous fat biopsies were obtained before, at 6- and 18-24-months after treatment, and from HIV negative controls. Groups were age, ethnicity, weight, biochemical profile, and pre-treatment CD4 count matched. Microarray data was generated using the Agilent Whole Human Genome Microarray. Identification of differentially expressed genes and genomic response pathways was performed using limma and gene set enrichment analysis.There were significant divergences between ABC and the other two groups 6 months after treatment in genes controlling cell adhesion and environmental information processing, with some convergence at 18-24 months. Compared to controls the ABC group, but not AZT or TDF showed enrichment of genes controlling adherence junction, at 6 months and 18-24 months (adjusted p<0.05 and focal adhesions and tight junction at 6 months (p<0.5. Genes controlling leukocyte transendothelial migration (p<0.05 and ECM-receptor interactions (p = 0.04 were over-expressed in ABC compared to TDF and AZT at 6 months but not at 18-24 months. Enrichment of pathways and individual genes controlling cell adhesion and environmental information processing were specifically dysregulated in the ABC group in comparison with other treatments. There was little difference between AZT and TDF.After initiating treatment, there is divergence in the expression of genes controlling cell adhesion and environmental information processing between ABC and both TDF and AZT in subcutaneous adipose tissue. If similar changes are also taking place in other tissues including the coronary vasculature they may contribute to the increased risk of cardiovascular events reported in patients recently started on abacavir-containing regimens.

  19. The efficacy of flapless implant surgery on soft-tissue profile comparing immediate loading implants to delayed loading implants: A comparative clinical study

    Directory of Open Access Journals (Sweden)

    Ravindran Deepak

    2010-01-01

    Full Text Available Aims and Objectives : To assess the efficacy of flapless implant surgery on soft-tissue profile and to compare the clinical outcomes of flapless implant therapy on immediate loading (IL implants to delayed loading (DL implants. Materials and Methods : The study sample consisted of 20 patients who were partially edentulous in the anterior maxillary region. They were divided into two groups. In group I (IL 10 implants were placed and immediately provisionalized and restored with a metal ceramic crown on the 14th day. In group II (DL 10 implants were placed and loaded after 4 months. Single-piece implants were used for the IL group and two-piece implants were used for the DL group. All soft tissue parameters i.e., modified plaque index (mPI, modified bleeding index (mBI, papillary index (PPI, marginal level of soft tissue (ML and width of keratinized mucosa (WKM were recorded at baseline, Day 60, Day 120 and Day 180. Results: The success rate in group I was found to be 80%, which was lower than the success rate in group II which was found to be 90%. On comparison, there is no statistically significant difference in success rate between the two study groups. There was no statistically significant difference between the groups over time in parameters like mPI, mBI, ML and WKM. The mean PPI score in group II showed a significant increase from when compared to group I. Conclusion: The results of this study indicated that flapless implant surgery using either immediately loading implants or DL implants, demonstrate enhancement of implant esthetics.

  20. Comparative pharmacokinetics and tissue distribution profiles of lignan components in normal and hepatic fibrosis rats after oral administration of Fuzheng Huayu recipe.

    Science.gov (United States)

    Yang, Tao; Liu, Shan; Zheng, Tian-Hui; Tao, Yan-Yan; Liu, Cheng-Hai

    2015-05-26

    Fuzheng Huayu recipe (FZHY) is formulated on the basis of Chinese medicine theory in treating liver fibrosis. To illuminate the influence of the pathological state of liver fibrosis on the pharmacokinetics and tissue distribution profiles of lignan components from FZHY. Male Wistar rats were randomly divided into normal group and Hepatic fibrosis group (induced by dimethylnitrosamine). Six lignan components were detected and quantified by ultrahigh performance liquid chromatography-tandem mass spectrometry(UHPLC-MS/MS)in the plasma and tissue of normal and hepatic fibrosis rats. A rapid, sensitive and convenient UHPLC-MS/MS method has been developed for the simultaneous determination of six lignan components in different rat biological samples successfully. After oral administration of FZHY at a dose of 15g/kg, the pharmacokinetic behaviors of schizandrin A (SIA), schizandrin B (SIB), schizandrin C (SIC), schisandrol A (SOA), Schisandrol B (SOB) and schisantherin A (STA) have been significantly changed in hepatic fibrosis rats compared with the normal rats, and their AUC(0-t) values were increased by 235.09%, 388.44%, 223.30%, 669.30%, 295.08% and 267.63% orderly (Pdistribution results showed the amount of SIA, SIB, SOA and SOB were significant increased in heart, lung, spleen and kidney of hepatic fibrosis rats compared with normal rats at most of the time point (Pdistribution of lignan components in normal and hepatic fibrosis rats. The hepatic fibrosis could alter the pharmacokinetics and tissue distribution properties of lignan components in rats after administration of FZHY. The results might be helpful for guide the clinical application of this medicine. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  1. Spectra from 2.5-15 {mu}m of tissue phantom materials, optical clearing agents and ex vivo human skin: implications for depth profiling of human skin

    Energy Technology Data Exchange (ETDEWEB)

    Viator, John A [Beckman Laser Institute, University of California, 1002 Health Sciences Road East, Irvine, CA (United States); Choi, Bernard [Beckman Laser Institute, University of California, 1002 Health Sciences Road East, Irvine, CA (United States); Peavy, George M [Beckman Laser Institute, University of California, 1002 Health Sciences Road East, Irvine, CA (United States); Kimel, Sol [Beckman Laser Institute, University of California, 1002 Health Sciences Road East, Irvine, CA (United States); Nelson, J Stuart [Beckman Laser Institute, University of California, 1002 Health Sciences Road East, Irvine, CA (United States)

    2003-01-21

    Infrared measurements have been used to profile or image biological tissue, including human skin. Usually, analysis of such measurements has assumed that infrared absorption is due to water and collagen. Such an assumption may be reasonable for soft tissue, but introduction of exogenous agents into skin or the measurement of tissue phantoms has raised the question of their infrared absorption spectrum. We used Fourier transform infrared spectroscopy in attenuated total reflection mode to measure the infrared absorption spectra, in the range of 2-15 {mu}m, of water, polyacrylamide, Intralipid, collagen gels, four hyperosmotic clearing agents (glycerol, 1,3-butylene glycol, trimethylolpropane, Topicare{sup TM}), and ex vivo human stratum corneum and dermis. The absorption spectra of the phantom materials were similar to that of water, although additional structure was noted in the range of 6-10 {mu}m. The absorption spectra of the clearing agents were more complex, with molecular absorption bands dominating between 6 and 12 {mu}m. Dermis was similar to water, with collagen structure evident in the 6-10 {mu}m range. Stratum corneum had a significantly lower absorption than dermis due to a lower content of water. These results suggest that the assumption of water-dominated absorption in the 2.5-6 {mu}m range is valid. At longer wavelengths, clearing agent absorption spectra differ significantly from the water spectrum. This spectral information can be used in pulsed photothermal radiometry or utilized in the interpretation of reconstructions in which a constant {mu}{sub ir} is used. In such cases, overestimating {mu}{sub ir} will underestimate chromophore depth and vice versa, although the effect is dependent on actual chromophore depth. (note)

  2. Quantitative amino acid profiling and stable isotopically labeled amino acid tracer enrichment used for in vivo human systemic and tissue kinetics measurements.

    Science.gov (United States)

    Bornø, Andreas; van Hall, Gerrit

    2014-03-01

    An important area within clinical functional metabolomics is in vivo amino acid metabolism and protein turnover measurements for which accurate amino acid concentrations and stable isotopically labeled amino acid enrichments are mandatory not the least when tissue metabolomics is determined. The present study describes a new sensitive liquid chromatography tandem mass-spectrometry method quantifying 20 amino acids and their tracer(s) ([ring-(13)C6]/D5Phenylalanine) in human plasma and skeletal muscle specimens. Before analysis amino acids were extracted and purified via deprotonization/ion exchange, derivatized using a phenylisothiocyanate reagent and each amino acid was quantitated with its own stable isotopically labeled internal standard (uniformly labeled-(13)C/(15)N). The method was validated according to general recommendations for chromatographic analytical methods. The calibration curve correlations for amino acids were on average; r(2)=0.998. Interday accuracy for amino acids determined in spiked plasma was on average 97.3% and the coefficient of variation (CV) was 2.6%. The ([ring-(13)C6]/D5Phenylalanine) enrichment CV's for machine reproducibility in muscle tissue fluid and plasma were 4.4 and 0.8%, and the interday variability was 3.4% and the recovery was 90.5%, respectively. In conclusion, we have developed and validated a method for quantitative amino acid profiling that meets the requirements for systemic and tissue human in vivo amino acid and protein turnover kinetics measurements. Moreover, citrulline, ornithine, π-methyl-histidine, τ-methyl-l-histidine, hydroxy-proline and carnitine were analysed but when similar precision and accuray are required an additional stable istopically labeled internal standard for these meatablites should be be added.

  3. Quail FMO3 gene cloning, tissue expression profiling, polymorphism detection and association analysis with fishy taint in eggs.

    Directory of Open Access Journals (Sweden)

    Fengtao Mo

    Full Text Available Quail eggs comprise a significant and favourable part of table eggs in certain countries. Some quail eggs, however, present fishy off-flavor which directly influences their quality. It is reported that flavin-containing monooxygenase 3 (FMO3 is associated with fish-odour trait in human and animal products. FMO3 is responsible for the degradation of trimethylamine (TMA in vivo. Loss-of-function mutations in FMO3 gene can result in defective TMA N-oxygenation, giving rise to disorder known as "fish-odour syndrome" in human, as well as the fishy off-flavor in cow milk and chicken eggs. In order to reveal the genetic factor of fishy taint in quail eggs, we cloned the cDNA sequence of quail FMO3 gene, investigated FMO3 mRNA expression level in various tissues, detected SNPs in the coding region of the gene and conducted association analysis between a mutation and the TMA content in quail egg yolks. The 1888 bp cDNA sequence of quail FMO3 gene encoding 532 amino acids was obtained and characterized. The phylogenetic analysis revealed quail FMO3 had a closer relationship with chicken FMO3. The FMO3 mRNA was highly expressed in liver and kidney of quail. Nine SNPs were detected in the coding sequence of quail FMO3 gene, including a nonsense mutation (Q319X which was significantly associated with the elevated TMA content in quail egg yolks. Genotype TT at Q319X mutation loci was sensitive to choline. With addition of choline in the feed, the quails with homozygote TT at the Q319X mutation loci laid fish-odour eggs, indicating an interaction between genotype and diet. The results indicated that Q319X mutation was associated with the fishy off-flavor in quail eggs. Identification of the unfavorable allele T of quail FMO3 gene can be applied in future quail breeding to eliminate fishy off-flavor trait in quail eggs.

  4. Quail FMO3 gene cloning, tissue expression profiling, polymorphism detection and association analysis with fishy taint in eggs.

    Science.gov (United States)

    Mo, Fengtao; Zheng, Jiangxia; Wang, Peng; Lian, Ling; Yi, Guoqiang; Xu, Guiyun; Yang, Ning

    2013-01-01

    Quail eggs comprise a significant and favourable part of table eggs in certain countries. Some quail eggs, however, present fishy off-flavor which directly influences their quality. It is reported that flavin-containing monooxygenase 3 (FMO3) is associated with fish-odour trait in human and animal products. FMO3 is responsible for the degradation of trimethylamine (TMA) in vivo. Loss-of-function mutations in FMO3 gene can result in defective TMA N-oxygenation, giving rise to disorder known as "fish-odour syndrome" in human, as well as the fishy off-flavor in cow milk and chicken eggs. In order to reveal the genetic factor of fishy taint in quail eggs, we cloned the cDNA sequence of quail FMO3 gene, investigated FMO3 mRNA expression level in various tissues, detected SNPs in the coding region of the gene and conducted association analysis between a mutation and the TMA content in quail egg yolks. The 1888 bp cDNA sequence of quail FMO3 gene encoding 532 amino acids was obtained and characterized. The phylogenetic analysis revealed quail FMO3 had a closer relationship with chicken FMO3. The FMO3 mRNA was highly expressed in liver and kidney of quail. Nine SNPs were detected in the coding sequence of quail FMO3 gene, including a nonsense mutation (Q319X) which was significantly associated with the elevated TMA content in quail egg yolks. Genotype TT at Q319X mutation loci was sensitive to choline. With addition of choline in the feed, the quails with homozygote TT at the Q319X mutation loci laid fish-odour eggs, indicating an interaction between genotype and diet. The results indicated that Q319X mutation was associated with the fishy off-flavor in quail eggs. Identification of the unfavorable allele T of quail FMO3 gene can be applied in future quail breeding to eliminate fishy off-flavor trait in quail eggs.

  5. Open Source Telecommunication Companies

    Directory of Open Access Journals (Sweden)

    Peter Liu

    2007-08-01

    Full Text Available Little is known about companies whose core business is selling telecommunications products that lever open source projects. Open source telecommunications (OST companies operate in markets that are very different from typical software product markets. The telecommunications market is regulated, vertically integrated, and proprietary designs and special chips are widely used. For a telecommunications product to be useful, it must interact with both access network products and core network products. Due to specifications in Service Agreements Levels, penalties for failures of telecommunications products are very high. This article shares information that is not widely known, including a list of OST companies and the open source projects on which they depend, the size and diversity of venture capital investment in OST companies, the nature of the commercial product-open source software and company-project relationships, ways in which OST companies make money, benefits and risks of OST companies, and competition between OST companies. Analysis of this information provides insights into the ways in which companies can build business models around open source software. These findings will be of interest to entrepreneurs, top management teams of incumbent companies that sell telecommunications products, and those who care about Ontario's ability to compete globally.

  6. The Danish East India Company

    DEFF Research Database (Denmark)

    Sørensen, Karsten Engsig

    2005-01-01

    The article analysis the first Danish East India Company incorporated in 1616, which was the first Danish Stock Company and which has impacts even on modern Danish company la......The article analysis the first Danish East India Company incorporated in 1616, which was the first Danish Stock Company and which has impacts even on modern Danish company la...

  7. Overview of transcriptomic analysis of all human proteases, non-proteolytic homologs and inhibitors: Organ, tissue and ovarian cancer cell line expression profiling of the human protease degradome by the CLIP-CHIP™ DNA microarray.

    Science.gov (United States)

    Kappelhoff, Reinhild; Puente, Xose S; Wilson, Claire H; Seth, Arun; López-Otín, Carlos; Overall, Christopher M

    2017-08-07

    The protease degradome is defined as the complete repertoire of proteases and inhibitors, and their nonfunctional homologs present in a cell, tissue or organism at any given time. We review the tissue distribution of virtually the entire degradome in 23 different human tissues and 6 ovarian cancer cell lines. To do so, we developed the CLIP-CHIP™, a custom microarray based on a 70-mer oligonucleotide platform, to specifically profile the transcripts of the entire repertoire of 473 active human proteases, 156 protease inhibitors and 92 non-proteolytically active homologs known at the design date using one specific 70-mer oligonucleotide per transcript. Using the CLIP-CHIP™ we mapped the expression profile of proteases and their inhibitors in 23 different human tissues and 6 ovarian cancer cell lines in 104 sample datasets. Hierarchical cluster analysis showed that expression profiles clustered according to their anatomic locations, cellular composition, physiologic functions, and the germ layer from which they are derived. The human ovarian cancer cell lines cluster according to malignant grade. 110 proteases and 42 inhibitors were tissue specific (1 to 3 tissues). Of these 110 proteases 69% (74) are mainly extracellular, 30% (34) intracellular and 1% intramembrane. Notably, 35% (197/565) of human proteases and 30% (47/156) of inhibitors were ubiquitously expressed in all 23 tissues; 27% (155) of proteases and 21% (32) of inhibitors were broadly expressed in 4-20 tissues. Our datasets provide a valuable resource for the community of baseline protease and inhibitor relative expression in normal human tissues and can be used for comparison with diseased tissue, e.g. ovarian cancer, to decipher pathogenesis, and to aid drug development. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  8. Comparative MiRNA Expressional Profiles and Molecular Networks in Human Small Bowel Tissues of Necrotizing Enterocolitis and Spontaneous Intestinal Perforation.

    Directory of Open Access Journals (Sweden)

    Pak Cheung Ng

    Full Text Available Necrotizing enterocolitis (NEC and spontaneous intestinal perforation (SIP are acute intestinal conditions which could result in mortality and severe morbidity in preterm infants. Our objective was to identify dysregulated micro-RNAs (miRNAs in small bowel tissues of NEC and SIP, and their possible roles in disease pathophysiology.We performed differential miRNA arrays on tissues of NEC (n = 4, SIP (n = 4 and surgical-control (Surg-CTL; n = 4, and validated target miRNAs by qPCR (n = 10 each group. The association of target miRNAs with 52 dysregulated mRNAs was investigated by bioinformatics on functional and base-pair sequence algorithms, and correlation in same tissue samples.We presented the first miRNA profiles of NEC, SIP and Surg-CTL intestinal tissues in preterm infants. Of 28 validated miRNAs, 21 were significantly different between NEC or SIP and Surg-CTL. Limited overlapping in the aberrant expression of miRNAs between NEC and SIP indicated their distinct molecular mechanisms. A proposed network of dysregulated miRNA/mRNA pairs in NEC suggested interaction at bacterial receptor TLR4 (miR-31, miR-451, miR-203, miR-4793-3p, mediated via key transcription factors NFKB2 (miR-203, AP-1/FOSL1 (miR-194-3p, FOXA1 (miR-21-3p, miR-431 and miR-1290 and HIF1A (miR-31, and extended downstream to pathways of angiogenesis, arginine metabolism, cell adhesion and chemotaxis, extracellular matrix remodeling, hypoxia/oxidative stress, inflammation and muscle contraction. In contrast, upregulation of miR-451 and miR-223 in SIP suggested modulation of G-protein-mediated muscle contraction.The robust response of miRNA dysregulation in NEC and SIP, and concerted involvement of specific miRNAs in the molecular networks indicated their crucial roles in mucosa integrity and disease pathophysiology.

  9. Profil jaringan lunak wajah kasus borderline maloklusi klas I pada perawatan ortodonti dengan dan tanpa pencabutan gigi (Facial soft tissue profile on borderline class I malocclusion in orthodontic treatment with or without teeth extraction

    Directory of Open Access Journals (Sweden)

    Pinandi Sri Pudyani

    2013-12-01

    Full Text Available Background: Determination of orthodontic treatment plan with or without teeth extraction remains controversial, especially in borderline cases, so it requires more data and information to establish appropriate treatment plans in order to obtain optimal treatment results. Purpose: The study was aimed to determine the facial soft tissue changes in the borderline class I cases treated with and without tooth extraction on post-orthodontic treatment. Methods: The study was conducted on 28 lateral cephalograms, divided into two groups; 13 cases with tooth extraction, and 15 cases without tooth extraction. The subject criterias were as follows; class I malocclusion treated with straightwire technique, skeletal class I, in range of age between 18 to 30 years old, normal overjet 2-4 mm, arch length discrepancy between 2.5 to 5 mm, Index of Fossa Canine (IFC between 37% to 44%, did not using extraoral devices, and treated with teeth extraction of 4 second premolars or without tooth extraction. The measurement of nasolabial angle, labiomental angle, and linear position of the upper and lower lip to E-Ricketts line were done on each cephalogram before and after orthodontic treatment. Results: In teeth extraction cases, there was a change on upper and lower lips positions (p<0.05, but there were no changes on nasolabial angle and labiomental angle (p>0.05. In non teeth extraction cases, there were no changes in nasolabial angle, labiomental angle, and lips positions (p>0.05. Both of groups also have indicated that there were no changes on linear position of the upper and lower lip (p>0.05. Post-orthodontic treatment indicated a significant differences between extraction and nonextraction cases on nasolabial and labiomental angle, and lips position (p<0.05. Conclusion: The facial soft tissue profile changes on teeth extraction case was more retruded than non- teeth extraction case.Latar belakang: Penentuan rencana perawatan ortodonti dengan pencabutan atau

  10. Investigation of the biochemical state of paramagnetic ions in vivo using the magnetic field dependence of 1T/sub 1/ of tissue protons (NMRD profile): applications to contrast agents for magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Koenig, S.H.; Brown, R.D. III; Spiller, M.; Wolf, G.L.

    1988-01-01

    Nuclear magnetic relaxation dispersion (NMRD) profiles of protons are obtained in homogenous aqueous solutions of the paramagnetic ions, Mn/sup 2 +/ and Gd/sup 3 +/ and their chelate and macromolecular complexes in vitro, giving information regarding the biochemical state of these ions. Similarly NMRD profiles of protons of excised rabbit tissues containing Mn/sup 2 +/ and Gd/sup 3 +/ complexes are obtained. These NMRD profiles are shown to be very useful for determining the fate of potentially useful paramagnetic NMR imaging contrast agents in vivo. (U.K.).

  11. Tissue-specific human beta-defensins (HBD-1, HBD-2 and HBD-3 secretion profile from human amniochorionic membranes stimulated with Candida albicans in a two-compartment tissue culture system

    Directory of Open Access Journals (Sweden)

    Zaga-Clavellina Veronica

    2012-09-01

    Full Text Available Abstract Background During intrauterine infection, amniochorionic membranes represent a mechanical and immunological barrier against dissemination of infection. Human beta defensins (HBD-1, HBD-2, and HBD-3 are key elements of innate immunity that represent the first line of defense against different pathogen microorganisms associated with preterm labor. The aim of this work was to characterize the individual contribution of the amnion (AMN and choriodecidua (CHD regions to the secretion of HBD-1, HBD-2 and HBD-3, after stimulation with Candida albicans. Methods Full-thickness human amniochorionic membranes were obtained after delivery by elective cesarean section from women at 37-40 wk of gestation with no evidence of active labor. The membranes were cultured in a two-compartment experimental model in which the upper compartment is delimited by the amnion and the lower chamber by the choriodecidual membrane. One million of Candida albicans were added to either the AMN or the CHD face or to both and compartmentalized secretion profiles of HBD-1, HBD-2, and HBD-3 were quantified by ELISA. Tissue immunolocalization was performed to detect the presence of HBD-1, -2, -3 in tissue sections stimulated with Candida albicans. Results HBD-1 secretion level by the CHD compartment increased 2.6 times (27.30 [20.9-38.25] pg/micrograms protein when the stimulus with Candida albicans was applied only on this side of the membrane and 2.4 times (26.55 [19.4-42.5] pg/micrograms protein when applied to both compartments simultaneously. HBD-1 in the amniotic compartment remained without significant changes. HBD-2 secretion level increased significantly in the CHD when the stimulus was applied only to this region (2.49 [1.49-2.95] pg/micrograms protein and simultaneously to both compartments (2.14 [1.67- 2.91] pg/micrograms protein. When the stimulus was done in the amniotic compartment HBD-2 remained without significant changes in both compartments. HBD-3 remained

  12. Qualitative Value Profiling

    DEFF Research Database (Denmark)

    Duus, Henrik Johannsen; Bjerre, Mogens

    2015-01-01

    Qualitative value profiling (QVP) is a relatively unknown method of strategic analysis for companies in international business-to-business settings. The purpose of QVP is to reduce the information complexity that is faced by international companies in dealing with business partners. The QVP method...... allows the development of 1) profiles of the target country in which operations are to take place, 2) profiles of the buying center (i.e. the group of decision makers) in the partner company, and 3) profiles of the product/service offering. It also allows the development of a semantic scaling method...... for deeper analysis of all involved factors. This paper presents the method and compares and contrasts it with other similar methods like the PESTELE method known from corporate strategy, the STEEPAL method known from scenario analysis, and the Politics-Institutions-Economy (PIE) framework known from...

  13. MicroRNA profiling of the intestinal tissue of Kazakh sheep after experimental Echinococcus granulosus infection, using a high-throughput approach

    Science.gov (United States)

    Jiang, Song; Li, Xin; Wang, Xuhai; Ban, Qian; Hui, Wenqiao; Jia, Bin

    2016-01-01

    Cystic echinococcosis (CE), caused by infection with the larval stage of the cestode Echinococcus granulosus, is a chronic zoonosis, to which sheep are highly susceptible. Previously, we found that Kazakh sheep with different MHC haplotypes differed in CE infection. Sheep with haplotype MHCMvaIbc-SacIIab-Hin1Iab were resistant to CE infection, while their counterparts without this haplotype were not. MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at the post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. To identify microRNA controlling resistance to CE in the early stage of infection, microRNA profiling was conducted in the intestinal tissue of sheep with resistant and non-resistant MHC haplotypes after peroral infection with E. granulosus eggs. A total of 351 known and 186 novel miRNAs were detected in the resistant group, against 353 known and 129 novel miRNAs in the non-resistant group. Among these miRNAs, 83 known miRNAs were significantly differentially expressed, including 75 up-regulated and 8 down-regulated miRNAs. Among these known microRNAs, miR-21-3p, miR-542-5p, miR-671, miR-134-5p, miR-26b, and miR-27a showed a significantly higher expression in CE-resistant sheep compared to the CE-non-resistant library, with the FC > 3. Functional analysis showed that they were NF-kB pathway-responsive miRNAs, which are involved in the inflammation process. The results suggest that these microRNAs may play important roles in the response of intestinal tissue to E. granulosus. PMID:27235195

  14. Antimicrobial resistance profile of Staphylococcus aureus isolates obtained from skin and soft tissue infections of outpatients from a university hospital in Recife - PE, Brazil*

    Science.gov (United States)

    Caraciolo, Fabiana Beserra; Maciel, Maria Amélia Vieira; dos Santos, Josemir Belo; Rabelo, Marcelle Aquino; Magalhães, Vera

    2012-01-01

    BACKGROUND Staphylococcus aureus has a notable ability to acquire resistance to antibiotics, and methicillin resistance represents a growing public health problem. Methicillin-resistant S. aureus (MRSA) has also become important outside the hospital environment, particularly in the United States. In Brazil, since 2005, cases of community skin infections caused by MRSA have been reported, but resistance studies involving outpatients are scarce. OBJECTIVE To know the resistance profile of S. aureus involved in skin and soft tissue infections of patients seen at the Dermatology outpatient clinic of a university hospital in Recife, Pernambuco State, northeastern Brazil. METHODS Prospective study involving 30 patients with skin and soft tissue infections, seen at the Dermatology outpatient clinic from May until November 2011. To evaluate the susceptibility of S. aureus to antibiotics, the disk diffusion method and oxacillin screening agar were used. RESULTS From a total of 30 samples of skin lesions, 19 (63%) had positive culture for S. aureus. The following resistance patterns of S. aureus were observed: penicillin, 95%; tetracycline, 32%; erythromycin, 21%; gentamicin, 16%; cefoxitin, 11%; oxacillin, 11%; trimethoprim-sulfamethoxazole, 11%; chloramphenicol, 11%; clindamycin, 5% ; and ciprofloxacin, 0%. One of the identified MRSA was obtained from a patient without risk factors for its acquisition, and was resistant, beyond to the beta-lactams, only to tetracycline. CONCLUSIONS With regard to the resistance patterns of S. aureus, resistances to tetracycline, erythromycin and gentamicin were the highest. It was documented, for the first time in Pernambuco, a case of skin infection caused by community-associated MRSA. PMID:23197204

  15. MicroRNA profiling of the intestinal tissue of Kazakh sheep after experimental Echinococcus granulosus infection, using a high-throughput approach

    Directory of Open Access Journals (Sweden)

    Jiang Song

    2016-01-01

    Full Text Available Cystic echinococcosis (CE, caused by infection with the larval stage of the cestode Echinococcus granulosus, is a chronic zoonosis, to which sheep are highly susceptible. Previously, we found that Kazakh sheep with different MHC haplotypes differed in CE infection. Sheep with haplotype MHCMvaIbc-SacIIab-Hin1Iab were resistant to CE infection, while their counterparts without this haplotype were not. MicroRNAs (miRNAs, a class of small non-coding RNAs, are key regulators of gene expression at the post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. To identify microRNA controlling resistance to CE in the early stage of infection, microRNA profiling was conducted in the intestinal tissue of sheep with resistant and non-resistant MHC haplotypes after peroral infection with E. granulosus eggs. A total of 351 known and 186 novel miRNAs were detected in the resistant group, against 353 known and 129 novel miRNAs in the non-resistant group. Among these miRNAs, 83 known miRNAs were significantly differentially expressed, including 75 up-regulated and 8 down-regulated miRNAs. Among these known microRNAs, miR-21-3p, miR-542-5p, miR-671, miR-134-5p, miR-26b, and miR-27a showed a significantly higher expression in CE-resistant sheep compared to the CE-non-resistant library, with the FC > 3. Functional analysis showed that they were NF-kB pathway-responsive miRNAs, which are involved in the inflammation process. The results suggest that these microRNAs may play important roles in the response of intestinal tissue to E. granulosus.

  16. EFFECTS OF RAISING CAPITAL ON FINANCIAL INDICATORS OF THE COMPANY

    OpenAIRE

    Gheorghe NEGOESCU

    2014-01-01

    The financial consequences of growth capital are different depending of accomplishing technical. In these circumstances the General Meeting of Shareholders decide to increase capital. The decision depends on the effect of increasing the potential financial capital, financial stability and financial structure of the company. Next, I will present the financial consequences of growth capital to a company profile in the petrochemical industry.

  17. Tissue-specific methylation profile in obese patients with type 2 diabetes before and after Roux-en-Y gastric bypass.

    Science.gov (United States)

    Sala, Priscila; de Miranda Torrinhas, Raquel Susana Matos; Fonseca, Danielle Cristina; Ravacci, Graziela Rosa; Waitzberg, Dan Linetzky; Giannella-Neto, Daniel

    2017-01-01

    Eating habits, lifestyles, and exposure to specific environmental factors can greatly impact the risk of developing type 2 diabetes (T2D), influence the genome epigenetically, and affect the expression of genes, including genes related to glycemic control, at any stage of life. The epigenetic mechanism underlying obesity and T2D pathogenesis remains poorly understood. Conventional strategies for the treatment of obesity and its comorbidities often have poor long-term adherence, and pharmacological interventions are limited. Bariatric surgery is the most effective current option to treat severe obesity, and Roux-en-Y gastric bypass (RYGB) is the most applied technique worldwide. Epigenetic changes differ depending on the approach used to treat obesity and its associated comorbidities (clinical or surgical). Compared to primary clinical care, bariatric surgery leads to much greater loss of body weight and higher remission rates of T2D and metabolic syndrome, with methylation profiles in promoter regions of genes in obese individuals becoming similar to those of normal-weight individuals. Bariatric surgery can influence DNA methylation in parallel with changes in gene expression pattern. Changes in clinical biomarkers that reflect improvements in glucose and lipid metabolism after RYGB often occur before major weight loss and are coordinated by surgery-induced changes in intestinal hormones. Therefore, the intestine methylation profile would assist in understanding the mechanisms involved in improved glycemic control after bariatric surgery. The main objectives in this area for the future are to identify epigenetic marks that could be used as early indicators of metabolic risk, and to develop treatments able to delay or even reverse these epigenetic changes. Studies that provide the "human epigenetic profile" will be of considerable value to identify tissue-specific epigenetic signatures and their role in the development of chronic diseases. Further studies should

  18. Submission to NCBI Sequence Read Archive (SRA): Raw read files from manuscript “RNA-seq transcriptome profiling of upland cotton (Gossypium hirsutum) root tissue under water deficit stress” NCBI SRA Accession No. PRJNA210770

    Science.gov (United States)

    Gossypium hirsutum L. cultivar Siokra L-23 was grown under rainfed and irrigated treatments in a field with very sandy soil. Root samples were collected for each treatment during the reproductive growth period. The RNA of all root tissues was used in an RNA-seq transcriptome profiling study with an ...

  19. Conclusion: The balanced company

    DEFF Research Database (Denmark)

    2013-01-01

    This concluding chapter brings together the various research findings of the book "The balanced company - organizing for the 21st Century" and develops a general overview of their implications for our understanding of the balancing processes unfolding in companies and organizations....

  20. Virtual Company and Modelbank

    DEFF Research Database (Denmark)

    Thorsteinsson, Uffe

    1996-01-01

    Ansøgning til Socrates programmet vedr. Tematisk netværk inden for området Virtual Company and Modelbank......Ansøgning til Socrates programmet vedr. Tematisk netværk inden for området Virtual Company and Modelbank...

  1. Allocation for manufacturing companies

    Directory of Open Access Journals (Sweden)

    2010-06-01

    Full Text Available Assuring a high material availability for production is while reducing sourcing costs remains a major logistical challenge for producing companies. Lean economic processes, flexibility and responsiveness - beneficial both for the customer and for the supplier - are characteristics of an excellent customer-supplier relationship. Standard sourcing models offer a field-tested approach for setting up across company boarders processes.

  2. The mortality of companies

    Science.gov (United States)

    Daepp, Madeleine I. G.; Hamilton, Marcus J.; West, Geoffrey B.; Bettencourt, Luís M. A.

    2015-01-01

    The firm is a fundamental economic unit of contemporary human societies. Studies on the general quantitative and statistical character of firms have produced mixed results regarding their lifespans and mortality. We examine a comprehensive database of more than 25 000 publicly traded North American companies, from 1950 to 2009, to derive the statistics of firm lifespans. Based on detailed survival analysis, we show that the mortality of publicly traded companies manifests an approximately constant hazard rate over long periods of observation. This regularity indicates that mortality rates are independent of a company's age. We show that the typical half-life of a publicly traded company is about a decade, regardless of business sector. Our results shed new light on the dynamics of births and deaths of publicly traded companies and identify some of the necessary ingredients of a general theory of firms. PMID:25833247

  3. Molecular cloning and in silico analysis of the duck (Anas platyrhynchos MEF2A gene cDNA and its expression profile in muscle tissues during fetal development

    Directory of Open Access Journals (Sweden)

    Hehe Liu

    2012-01-01

    Full Text Available The role of myogenic enhancer transcription factor 2a (MEF2A in avian muscle during fetal development is unknown. In this work, we cloned the duck MEF2A cDNA sequence (GenBank accession no. HM460752 and examined its developmental expression profiles in cardiac muscle, non-vascular smooth muscle and skeletal muscle. Duck MEF2A cDNA comprised 1479 bp encoding 492 amino acid residues. In silico analysis showed that MEF2A contained MADS (MCM1, AGAMOUS, DEFICIENS and SRF -serum response factor, MEF2 and mitogen-activated protein kinase (MAPK transcription domains with high homology to related proteins in other species. Modified sites in these domains were conserved among species and several variants were found. Quantitative PCR showed that MEF2A was expressed in all three muscles at each developmental stage examined, with the expression in smooth muscle being higher than in the other muscles. These results indicate that the conserved domains of duck MEF2A, including the MADS and MEF2 domains, are important for MEF2A transcription factor function. The expression of MEF2A in duck smooth muscle and cardiac muscle suggests that MEF2A plays a role in these two tissues.

  4. Defensive Armor of Potato Tubers: Nonpolar Metabolite Profiling, Antioxidant Assessment, and Solid-State NMR Compositional Analysis of Suberin-Enriched Wound-Healing Tissues.

    Science.gov (United States)

    Dastmalchi, Keyvan; Kallash, Linda; Wang, Isabel; Phan, Van C; Huang, Wenlin; Serra, Olga; Stark, Ruth E

    2015-08-05

    The cultivation, storage, and distribution of potato tubers are compromised by mechanical damage and suboptimal healing. To investigate wound-healing progress in cultivars with contrasting russeting patterns, metabolite profiles reported previously for polar tissue extracts were complemented by GC/MS measurements for nonpolar extracts and quantitative (13)C NMR of interfacial solid suspensions. Potential marker compounds that distinguish cultivar type and wound-healing time point included fatty acids, fatty alcohols, alkanes, glyceryl esters, α,ω-fatty diacids, and hydroxyfatty acids. The abundant long-chain fatty acids in nonpolar extracts and solids from the smooth-skinned Yukon Gold cultivar suggested extensive suberin biopolymer formation; this hypothesis was supported by high proportions of arenes, alkenes, and carbonyl groups in the solid and among the polar markers. The absence of many potential marker classes in nonpolar Atlantic extracts and interfacial solids suggested a limited extent of suberization. Modest scavenging activities of all nonpolar extracts indicate that the majority of antioxidants produced in response to wounding are polar.

  5. SICHUAN GEOPHYSICAL COMPANY

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    Sichuan Geophysical Company (abbreviated as SCGC below), originally named Sichuan Geophysical Company of CNPC Sichuan Petroleum, was founded in 1956 and is a subsidiary of CNPC Chuanqing Drilling Engineering Company Limited. With more than 50 years' development, SCGC now owns almost 3800 employees and has become a big oil & gas seismic exploration engineering service enterprise with the characteristic mountain seismic exploration techniques, and its annual business turnover reaches nearly 2 billion RMB. It can provide the integrated seismic exploration engineering service including seismic data acquisition, processing, interpretation, and geological comprehensive evaluation in various complex regions for clients at home and abroad.

  6. Valuation of Companies

    Directory of Open Access Journals (Sweden)

    J. Lisník

    2007-01-01

    Full Text Available This paper deals with valuating telecommunications companies. Six groups operating mainly in the European countries are compared. The comparison is based on financial and techno-economic indicators.These indicators are used to value the company by the DCF method. However, many companies have only a very short history. To value these, classical methods like DCF or real options are not suitable. In this case, methods based on market confrontation seem to be efficient. A further exploration of these methods is also the topic of my graduate studies 

  7. Qualitative Value Profiling

    DEFF Research Database (Denmark)

    Duus, Henrik Johannsen; Bjerre, Mogens

    2015-01-01

    Qualitative value profiling (QVP) is a relatively unknown method of strategic analysis for companies in international business-to-business settings. The purpose of QVP is to reduce the information complexity that is faced by international companies in dealing with business partners. The QVP method...... and consequently, for the advancement of international development. Further use of QVP is recommended and suggestions for future research are provided....

  8. 78 FR 11638 - Michigan Consolidated Gas Company, DTE Gas Company, DTE Gas Company; Notice of Petition

    Science.gov (United States)

    2013-02-19

    ... Energy Regulatory Commission Michigan Consolidated Gas Company, DTE Gas Company, DTE Gas Company; Notice... Docket Nos. PR13-29-000, and PR13-30-000 (not consolidated), Michigan Consolidated Gas Company (MichCon) and DTE Gas Company (DTE Gas) filed to institute a name change to both itself from MichCon to DTE...

  9. 75 FR 13524 - Northern Natural Gas Company, Southern Natural Gas Company, Florida Gas Transmission Company, LLC...

    Science.gov (United States)

    2010-03-22

    ... Energy Regulatory Commission Northern Natural Gas Company, Southern Natural Gas Company, Florida Gas... of Application March 16, 2010. Take notice that on March 5, 2010, Northern Natural Gas Company... other owners, Southern Natural Gas Company, Florida Gas Transmission Company, LLC, Transcontinental...

  10. Genome-wide gene expression profiles in lung tissues of pig breeds differing in resistance to porcine reproductive and respiratory syndrome virus.

    Directory of Open Access Journals (Sweden)

    Jinyi Xing

    Full Text Available Porcine reproductive and respiratory syndrome (PRRS caused by PRRS virus (PRRSV is an infectious disease characterized by severe reproductive deficiency in pregnant sows, typical respiratory symptoms in piglets, and high mortality rate of piglets. In this study, we employed an Affymetrix microarray chip to compare the gene expression profiles of lung tissue samples from Dapulian (DPL pigs (a Chinese indigenous pig breed and Duroc×Landrace×Yorkshire (DLY pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited a range of clinical features that typify the disease, whereas the DPL pigs showed only mild signs of the disease. Overall, the DPL group had a lower percentage of CD4(+ cells and lower CD4(+/CD8(+ratios than the DLY group (p<0.05. For both IL-10 and TNF-α, the DLY pigs had significantly higher levels than the DPL pigs (p<0.01. The DLY pigs have lower serum IFN-γ levels than the DPL pigs (p<0.01. The serum IgG levels increased slightly from 0 dpi to 7 dpi, and peaked at 14 dpi (p<0.0001. Microarray data analysis revealed 16 differentially expressed (DE genes in the lung tissue samples from the DLY and DPL pigs (q≤5%, of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The mRNA expression levels of 10 out of the 16 DE genes were validated by real-time quantitative RT-PCR and their fold change was consistent with the result of microarray data analysis. We further analyzed the mRNA expression level of 8 differentially expressed genes between the DPL and DLY pigs for both uninfected and infected groups, and found that TF and USP18 genes were important in underlying porcine resistance or susceptibility to PRRSV.

  11. Effects of Addition of Linseed and Marine Algae to the Diet on Adipose Tissue Development, Fatty Acid Profile, Lipogenic Gene Expression, and Meat Quality in Lambs.

    Science.gov (United States)

    Urrutia, Olaia; Mendizabal, José Antonio; Insausti, Kizkitza; Soret, Beatriz; Purroy, Antonio; Arana, Ana

    2016-01-01

    This study examined the effect of linseed and algae on growth and carcass parameters, adipocyte cellularity, fatty acid profile and meat quality and gene expression in subcutaneous and intramuscular adipose tissues (AT) in lambs. After weaning, 33 lambs were fed three diets up to 26.7 ± 0.3 kg: Control diet (barley and soybean); L diet (barley, soybean and 10% linseed) and L-A diet (barley, soybean, 5% linseed and 3.89% algae). Lambs fed L-A diet showed lower average daily gain and greater slaughter age compared to Control and L (P algae increased α-linolenic acid and eicosapentaenoic acid contents in both AT (P Algae had adverse effects on meat quality, with greater lipid oxidation and reduced ratings for odor and flavor. The expression of lipogenic genes was downregulated in the subcutaneous AT (P < 0.05): acetyl-CoA carboxylase 1 (ACACA) in L and L-A and lipoprotein lipase (LPL) and stearoyl-CoA desaturase (SCD) in L-A. Fatty acid desaturase 1 (FADS1), fatty acid desaturase 2 (FADS2) and fatty acid elongase 5 (ELOVL5) were unaffected. In the subcutaneous AT, supplementing either L or L-A increased peroxisome proliferator-activated receptor gamma (PPARG) and CAAT-enhancer binding protein alpha (CEBPA) (P < 0.05), although it had no effect on sterol regulatory element-binding factor 1 (SREBF1). In the intramuscular AT, expression of ACACA, SCD, FADS1 and FADS2 decreased in L and L-A (P < 0.001) and LPL in L (P < 0.01), but PPARG, CEBPA and SREBF1 were unaffected.

  12. Expression profile of peripheral tissue antigen genes in medullary thymic epithelial cells (mTECs) is dependent on mRNA levels of autoimmune regulator (Aire).

    Science.gov (United States)

    Oliveira, Ernna H; Macedo, Claudia; Donate, Paula B; Almeida, Renata S; Pezzi, Nicole; Nguyen, Catherine; Rossi, Marcos A; Sakamoto-Hojo, Elza T; Donadi, Eduardo A; Passos, Geraldo A

    2013-01-01

    In the thymus of non-obese diabetic (NOD) mice, the expression of the autoimmune regulator (Aire) gene varies with age, and its down-regulation in young mice precedes the later emergence of type 1 diabetes mellitus (T1D). In addition, the insulin (Ins2) peripheral tissue antigen (PTA) gene, which is Aire-dependent, is also deregulated in these mice. Based in these findings, we hypothesized that the imbalance in PTA gene expression in the thymus can be associated with slight variations in Aire transcript levels. To test this, we used siRNA to knockdown Aire by in vivo electro-transfection of the thymus of BALB/c mice. The efficiency of the electro-transfection was monitored by assessing the presence of irrelevant Cy3-labeled siRNA in the thymic stroma. Importantly, Aire-siRNA reached medullary thymic epithelial cells (mTECs) down-regulating Aire. As expected, the in vivo Aire knockdown was partial and transient; the maximum 59% inhibition occurred in 48 h. The Aire knockdown was sufficient to down-regulate PTA genes; however, surprisingly, several others, including Ins2, were up-regulated. The modulation of these genes after in vivo Aire knockdown was comparable to that observed in NOD mice before the emergence of T1D. The in vitro transfections of 3.10 mTEC cells with Aire siRNA resulted in samples featuring partial (69%) and complete (100%) Aire knockdown. In these Aire siRNA-transfected 3.10 mTECs, the expression of PTA genes, including Ins2, was down-regulated. This suggests that the expression profile of PTA genes in mTECs is affected by fine changes in the transcription level of Aire. Copyright © 2012 Elsevier GmbH. All rights reserved.

  13. Oil Companies Climb Global List

    Institute of Scientific and Technical Information of China (English)

    JESSY ZHANG

    2006-01-01

    @@ Backed by the huge market size,China's energy companies have been ranked in the group of the world's largest industry players. On September 6th,eight companies from the Chinese mainland and six companies from Hong Kong SAR were included in this year's Platts Top 250 Energy Companies List.

  14. Captive insurance companies.

    Science.gov (United States)

    Strauss, Peter

    2014-01-01

    The landscape of the business world is changing; and now, more than ever, business owners are recognizing that life is filled with risks: known risk, calculated risk, and unexpected risk. Every day, businesses thrive or fail based on understanding the risk of owning and operating their business, and business owners are recognizing that there are alternative risk financing mechanisms other than simply taking out a basket of standard coverage as recommended by your friendly neighborhood agent. A captive insurance company is an insurance company established to provide a broad range of risk management capabilities to affiliated companies. The captive is owned by the business owner and can provide insurance to the business for potential future losses, whether or not the losses are already covered by a commercial carrier or are "self-insured." The premiums paid by your business are tax deductible. Meanwhile, the premiums that your captive collects are tax-free up to $1.2 million annually.

  15. Companies as "Cyborgs"?

    DEFF Research Database (Denmark)

    Thompson, Grahame

    This paper investigates the legal and commercial consequences of companies being considered as both an entity and a person in law – hence the notion of ‘cyborg’ in its title. It concentrates upon legal personhood and relates this particular feature to the issue of corporate citizenship. In turn...... corporate citizenship provides a link to considering the political role of companies, since in claiming citizenship they are implicitly at least claiming a particular set of political rights consequent upon that status, and announcing a particular politically constrained context associated...... with their operational characteristics. But what would be involved in granting companies full citizenship rights in the image of natural person citizenship? The paper explores this issue in connection to the differences between corporate social responsibility and an earlier idea of the socially responsible corporation...

  16. Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - potential regulatory sequences in monolignol biosynthetic pathway.

    Science.gov (United States)

    Ong, Seong Siang; Wickneswari, Ratnam

    2011-11-30

    Lignin, after cellulose, is the second most abundant biopolymer accounting for approximately 15-35% of the dry weight of wood. As an important component during wood formation, lignin is indispensable for plant structure and defense. However, it is an undesirable component in the pulp and paper industry. Removal of lignin from cellulose is costly and environmentally hazardous process. Tremendous efforts have been devoted to understand the role of enzymes and genes in controlling the amount and composition of lignin to be deposited in the cell wall. However, studies on the impact of downregulation and overexpression of monolignol biosynthesis genes in model species on lignin content, plant fitness and viability have been inconsistent. Recently, non-coding RNAs have been discovered to play an important role in regulating the entire monolignol biosynthesis pathway. As small RNAs have critical functions in various biological process during wood formation, small RNA profiling is an important tool for the identification of complete set of differentially expressed small RNAs between low lignin and high lignin secondary xylem. In line with this, we have generated two small RNAs libraries from samples with contrasting lignin content using Illumina GAII sequencer. About 10 million sequence reads were obtained in secondary xylem of Am48 with high lignin content (41%) and a corresponding 14 million sequence reads were obtained in secondary xylem of Am54 with low lignin content (21%). Our results suggested that A. mangium small RNAs are composed of a set of 12 highly conserved miRNAs families found in plant miRNAs database, 82 novel miRNAs and a large proportion of non-conserved small RNAs with low expression levels. The predicted target genes of those differentially expressed conserved and non-conserved miRNAs include transcription factors associated with regulation of the lignin biosynthetic pathway genes. Some of these small RNAs play an important role in epigenetic silencing

  17. RESTRUCTURING COMPANIES UNDER CRISIS

    Directory of Open Access Journals (Sweden)

    Hezi Aviram SHAYB

    2016-12-01

    Full Text Available Nobody is planning to fail, but many companies are failing because of lack of planning. Real business experience showed during the years that crisis can be prevented, avoided or limited. If detected in time, the risks associated with the crisis can be mitigated and the effects can be diminished, with the condition that the actions required are done fast, in a sharp and accurate manner. When it comes, a crisis brings an intense level of pressure and under these conditions there is no time or room for mistakes. Delays, losing focus and lack of planning will bring a company one step away from failure. The right way to deal with crisis, if required measures are not done in time, is to minimize the losses and reposition in the best way possible. Analysing the success stories of some of the biggest and strongest companies in the world, led to an important conclusion: the majority of these companies were in the situation to face huge crises which threatened their ability to survive in certain moments, on their way to success. With the right planning and by setting a proper organisational structure, the negative aspects of the crisis can be turned into benefits and opportunities for the company. The most critical challenge for management is to assess the level of exposure to risk of the company and identify the key points to focus on in order to overcome the crisis and create value. In order to set up a strong plan in dealing with crisis, a business organisation needs reliable, efficient and effective tools and this is what this article is all about.

  18. RESTRUCTURING COMPANIES UNDER CRISIS

    Directory of Open Access Journals (Sweden)

    Hezi Aviram SHAYB

    2016-12-01

    Full Text Available Nobody is planning to fail, but many companies are failing because of lack of planning. Real business experience showed during the years that crisis can be prevented, avoided or limited. If detected in time, the risks associated with the crisis can be mitigated and the effects can be diminished, with the condition that the actions required are done fast, in a sharp and accurate manner. When it comes, a crisis brings an intense level of pressure and under these conditions there is no time or room for mistakes. Delays, losing focus and lack of planning will bring a company one step away from failure. The right way to deal with crisis, if required measures are not done in time, is to minimize the losses and reposition in the best way possible. Analysing the success stories of some of the biggest and strongest companies in the world, led to an important conclusion: the majority of these companies were in the situation to face huge crises which threatened their ability to survive in certain moments, on their way to success. With the right planning and by setting a proper organisational structure, the negative aspects of the crisis can be turned into benefits and opportunities for the company. The most critical challenge for management is to assess the level of exposure to risk of the company and identify the key points to focus on in order to overcome the crisis and create value. In order to set up a strong plan in dealing with crisis, a business organisation needs reliable, efficient and effective tools and this is what this article is all about.

  19. PREVENTION OF COMPANY RISKS

    Directory of Open Access Journals (Sweden)

    SUCI U GHEORGHE

    2014-10-01

    Full Text Available A company’s manager has to create and maintain a healthy internal control system. An efficient internal control system implies the implementation in the company of risk management. Each company, but also each individual, who tries to attain certain objectives, establishes the activities which lead to the achievement of goals and, at the same time, tries to identify as many “threats” as possible, in order to take the necessary measures to eliminate them. Thus, even if one is not familiar with the concepts of risk and risk management, one acts, consciously or not, for that purpose.

  20. Competitor Analysis : Company X

    OpenAIRE

    Valkama, Suvi

    2014-01-01

    The purpose of the thesis was to create a competitor analysis of the market of stainless steel swimming pools for the commissioner Company X, a company that will be set up in the near future. The thesis aimed at finding out the commissioner’s assets in producing stainless steel swimming pools as well as defining its competitive advantage. This was done by identifying the relative strengths and weaknesses of the main competitors named by the commissioner. Moreover, the purpose of the thesis wa...

  1. COMPANY ACTIVITY FINANCIAL RISK

    Directory of Open Access Journals (Sweden)

    Caruntu Genu Alexandru

    2012-12-01

    Full Text Available In economic and financial activity, risk is an inherent financial decisions, encountered in daily agenda of managers of companies. Unexpected changes in the price of a product development not only affect the financial results of a company, but can cause even bankruptcy. In fact, the nature of financial decisions involve uncertainty. Financial decisions are made based on cash flows under future contracts, which are par excellence incerte.Activitatea an enterprise that holds any weight in the industry is subject to risks, since it can not predict with certainty different components of its outcome (cost, quantity, price and operating cycle (purchase, processing, sales.

  2. Risk profile of microbiological and chemical contamination in the production chain of nine horticultural products for fresh consumption of a group of agricultural companies in the Costa Rican Central Valley

    Directory of Open Access Journals (Sweden)

    Guillermo Vargas Hernández

    2015-11-01

    Full Text Available The risk of microbiological or chemical contamination was determined in each of the processes of the production system of produce for fresh consumption, in a population of 164 agricultural companies in the central valley of Costa Rica. The risk quantification was calculated using the responses to a 46-item survey conducted with the managers of the companies included in the study. The responses to the 46 items were grouped according to the production process; the risk contamination calculation formula validated by the authors in another study was used to obtain the risk value per process. The microbiological or chemical contamination risk results were calculated for the land preparation and planting process, cultural management of the crop, human factor performing the cultural management of the crop, phytosanitary control, harvesting, packaging, and the human factor involved in packaging. The risk analysis results indicate that the human factor participating in the packaging obtains the highest risk rating, followed by the cultural management of the crop and, in third place, by the harvesting process. In all processes where the risk was quantified, the results showed values close to or greater than 50 in a 0 to 100 risk scale. These results should alert producers and consumers of produce for fresh consumption in the analyzed population. The effect of the buyer on the packaging risk values was also observed; when the producers are supermarket chain suppliers the risk values are lower as compared to those of producers who are not supermarket chain suppliers.

  3. The integration of GC-MS and LC-MS to assay the metabolomics profiling in Panax ginseng and Panax quinquefolius reveals a tissue- and species-specific connectivity of primary metabolites and ginsenosides accumulation.

    Science.gov (United States)

    Liu, Jia; Liu, Yang; Wang, Yu; Abozeid, Ann; Zu, Yuan-Gang; Tang, Zhong-Hua

    2017-02-20

    The traditional medicine Ginseng mainly including Panax ginseng and Panax quinquefolius is the most widely consumed herbal product in the world. Despite the extensive investigation of biosynthetic pathway of the active compounds ginsenosides, our current understanding of the metabolic interlink between ginsenosides synthesis and primary metabolism at the whole-plant level. In this study, the tissue-specific profiling of primary and the secondary metabolites in two different species of ginseng were investigated by gas chromatography- and liquid chromatography coupled to mass spectrometry. A complex continuous coordination of primary- and secondary-metabolic network was modulated by tissues and species factors during growth. The results showed that altogether 149 primary compounds and 10 ginsenosides were identified from main roots, lateral roots, stems, petioles and leaves in P. ginseng and P. quinquefolius. The partial least squares-discriminate analysis (PLS-DA) revealed obvious compounds distinction among tissue-specific districts relative to species. To survey the dedication of carbon and nitrogen metabolism in different tissues to the accumulation of ginsenosides, we inspected the tissue-specific metabolic changes. Our study testified that the ginsenosides content was dependent on main roots and lateral roots energy metabolism, whereas independent of leaves and petiole photosynthesis during ginsenosides accumulation. When tow species were compared, the results indicated that high rates of C assimilation to C accumulation are closely associated with ginsenosides accumulation in P. ginseng main roots and P. quinquefolius lateral roots, respectively. Taken together, our results suggest that tissue-specific metabolites profiling dynamically changed in process of ginsenosides biosynthesis, which may offer a new train of thoughts to the mechanisms of the ginsenosides biosynthesis at the metabolite level. Copyright © 2016 The Author(s). Published by Elsevier B.V. All

  4. Smart customers, dumb companies.

    Science.gov (United States)

    Locke, C

    2000-01-01

    Customers today are being bombarded with an overwhelming array of choices. To alleviate customer frustration, say Steven Cristol and Peter Sealey in Simplicity Marketing, companies should stop creating new brands and product extensions. Better to consolidate product and service functions by following a four R approach: replace, repackage, reposition, and replenish. That's an outmoded, dictatorial view of markets, says Christopher Locke. Far from being stymied by choices, customers are rapidly becoming smarter than the companies that pretend to serve them. In this networked economy, people are talking among themselves, and that changes everything. Locke predicts we'll see a growing number of well-defined micromarkets--groups of customers converging in real time around entertaining and knowledgeable voices--such as NPR's car guys and the Motley Fool investment site. "Micromedia" Web sites will replace traditional advertising because they'll provide credible user-supplied news about products and services. Locke contends that an open exchange of information solves the "problem" of choice much better than manipulative strategies like simplicity or even permission marketing. Companies can participate in micromarkets through what Locke dubs "gonzo marketing." If Ford, for example, discovers that a subset of its employees are organic gardeners, it may offer support to a big independent organic-gardening Web site with donations and employee volunteers. This marketing effort would be driven not by advertising managers but by people with genuine interest in each micromarket, so it would have credibility with customers. With gonzo marketing, both companies and their markets will benefit.

  5. Pork in good company?

    DEFF Research Database (Denmark)

    Verbeke, Wim; Perez-Cueto, Federico J.; de Barcellos, Marcia D.

    2013-01-01

    (odds ratio=1.30) as side dishes to pork meat. Substantial cross-cultural differences were revealed in line with typical pork consumption and meal composition habits in the respective countries. Finally, this study found that the company of family plays a significant role when choosing side dishes...

  6. Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling

    DEFF Research Database (Denmark)

    Basse, Astrid L.; Dixen, Karen; Yadav, Rachita;

    2015-01-01

    NR1H3, MYC, KLF4, ESR1, RELA and BCL6, which were linked to the overall changes in gene expression during the adipose tissue remodeling. Finally, the perirenal adipose tissue expressed both brown and brite/beige adipocyte marker genes at birth, the expression of which changed substantially over time...

  7. A saturated fatty acid-rich diet induces an obesity-linked proinflammatory gene expression profile in adipose tissue of subjects at risk of metabolic syndrome

    NARCIS (Netherlands)

    Dijk, van S.J.; Feskens, E.J.M.; Bos, M.B.; Hoelen, D.W.; Heijligenberg, R.; Bromhaar, M.G.; Groot, de C.P.G.M.; Vries, de J.H.M.; Müller, M.R.; Afman, L.A.

    2009-01-01

    Background: Changes in dietary fat composition could lower the risk of developing metabolic syndrome. Adipose tissue is an interesting tissue in this respect because of its role in lipid metabolism and inflammation. Objective: Our objective was to investigate the effect of a saturated fatty acid (SF

  8. Orosomucoid expression profiles in liver, adipose tissues and serum of lean and obese domestic pigs, Göttingen minipigs and Ossabaw minipigs

    DEFF Research Database (Denmark)

    Højbøge, Tina Rødgaard; Stagsted, Jan; Christoffersen, Berit Ø.;

    2013-01-01

    , the expression of ORM has not yet been characterized in such pig models. The objective of this study was to investigate the expression of ORM1 mRNA in liver, visceral adipose tissue, subcutaneous adipose tissue (SAT) from the abdomen or retroperitoneal abdominal adipose tissue (RPAT) and SAT from the neck......, as well as the serum concentration of ORM protein in three porcine obesity models; the domestic pig, Göttingen minipigs and Ossabaw minipigs.No changes in ORM1 mRNA expression were observed in obese pigs compared to lean pigs in the four types of tissues. However, obese Ossabaw minipigs, but none...... of the other breeds, showed significantly elevated ORM serum concentrations compared to their lean counterparts. Studies in humans have shown that the expression of ORM was unchanged in adipose tissue depots in obese humans with an increased serum concentration of ORM. Thus in this respect, obese Ossabaw...

  9. Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source--sink tissues in a segregating potato population

    Directory of Open Access Journals (Sweden)

    Kloosterman Bjorn

    2012-02-01

    Full Text Available Abstract Background With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs in two different potato tissues of a segregating potato population and query the potato genome sequence to differentiate between cis- and trans-acting eQTLs in relation to gene subfunctionalization. Results Leaf and tuber samples were analysed and screened for the presence of conserved and tissue dependent eQTLs. Expression QTLs present in both tissues are predominantly cis-acting whilst for tissue specific QTLs, the percentage of trans-acting QTLs increases. Tissue dependent eQTLs were assigned to functional classes and visualized in metabolic pathways. We identified a potential regulatory network on chromosome 10 involving genes crucial for maintaining circadian rhythms and controlling clock output genes. In addition, we show that the type of genetic material screened and sampling strategy applied, can have a high impact on the output of genetical genomics studies. Conclusions Identification of tissue dependent regulatory networks based on mapped differential expression not only gives us insight in tissue dependent gene subfunctionalization but brings new insights into key biological processes and delivers targets for future haplotyping and genetic marker development.

  10. EFFECTS OF RAISING CAPITAL ON FINANCIAL INDICATORS OF THE COMPANY

    Directory of Open Access Journals (Sweden)

    Gheorghe NEGOESCU

    2014-06-01

    Full Text Available The financial consequences of growth capital are different depending of accomplishing technical. In these circumstances the General Meeting of Shareholders decide to increase capital. The decision depends on the effect of increasing the potential financial capital, financial stability and financial structure of the company. Next, I will present the financial consequences of growth capital to a company profile in the petrochemical industry.

  11. Temperature measurement methods during direct heat arterial tissue fusion.

    Science.gov (United States)

    Cezo, James D; Kramer, Eric; Taylor, Kenneth D; Ferguson, Virginia; Rentschler, Mark E

    2013-09-01

    Fusion of biological tissues through direct and indirect heating is a growing area of medical research, yet there are still major gaps in understanding this procedure. Several companies have developed devices which fuse blood vessels, but little is known about the tissue's response to the stimuli. The need for accurate measurements of tissue behavior during tissue fusion is essential for the continued development and improvement of energy delivery devices. An experimental study was performed to measure the temperatures experienced during tissue fusion and the resulting burst pressure of the fused arteries. An array of thermocouples was placed in the lumen of a porcine splenic artery segment and sealed using a ConMed Altrus thermal fusion device. The temperatures within the tissue, in the device, and at the tissue-device interface were recorded. These measurements were then analyzed to calculate the temperature profile in the lumen of the artery. The temperature in the artery at the site of tissue fusion was measured to range from 142 to 163 °C using the ConMed Altrus. The corresponding burst pressure for arteries fused at this temperature was measured as 416 ± 79 mmHg. This study represents the first known experimental measurement of temperature at the site of vessel sealing found in the literature.

  12. Protein profiles of Taenia solium cysts obtained from skeletal muscles and the central nervous system of pigs: Search for tissue-specific proteins.

    Science.gov (United States)

    Navarrete-Perea, José; Moguel, Bárbara; Bobes, Raúl José; Villalobos, Nelly; Carrero, Julio César; Sciutto, Edda; Soberón, Xavier; Laclette, Juan Pedro

    2017-01-01

    Taeniasis/cysticercosis caused by the tapeworm Taenia solium is a parasite disease transmitted among humans and pigs, the main intermediate host. The larvae/cysts can lodge in several tissues of the pig, i.e. skeletal muscles and different locations of the central nervous system. The molecular mechanisms associated to tissue preferences of the cysts remain poorly understood. The major public health concern about this zoonosis is due to the human infections by the larval form in the central nervous system, causing a highly pleomorphic and debilitating disease known as neurocysticercosis. This study was aimed to explore the 2DE protein maps of T. solium cysts obtained from skeletal muscles and central nervous system of naturally infected pigs. The gel images were analyzed through a combination of PDQuest™ and multivariate analysis. Results showed that differences in the protein patterns of cysts obtained from both tissues were remarkably discrete. Only 7 protein spots were found specifically associated to the skeletal muscle localization of the cysts; none was found significantly associated to the central nervous system. The use of distinct protein fractions of cysts allowed preliminary identification of several tissue-specific antigenic bands. The implications of these findings are discussed, as well as several strategies directed to achieve the complete characterization of this parasite's proteome, in order to extend our understanding of the molecular mechanisms underlying tissue localization of the cysts and to open avenues for the development of immunological tissue-specific diagnosis of the disease.

  13. Building Company Loyalty System

    OpenAIRE

    Haniková, Alžběta

    2010-01-01

    The thesis discusses the importance of loyal customers, and loyalty system as a tool for building loyalty. It defines loyalty and customer satisfaction, it deals with the issue of customer retention. It describes the history and types of loyalty programs, important factors for deciding on their implementation and problems associated with them. The practical part is concerned with the clothing market, Orsay company and its Orsay Club loyalty systeme. The work also includes a survey of the loya...

  14. Building Company Loyalty System

    OpenAIRE

    Haniková, Alžběta

    2010-01-01

    The thesis discusses the importance of loyal customers, and loyalty system as a tool for building loyalty. It defines loyalty and customer satisfaction, it deals with the issue of customer retention. It describes the history and types of loyalty programs, important factors for deciding on their implementation and problems associated with them. The practical part is concerned with the clothing market, Orsay company and its Orsay Club loyalty systeme. The work also includes a survey of the loya...

  15. enjoy the company of

    Institute of Scientific and Technical Information of China (English)

    柳延延

    2004-01-01

    @@ 请先读一段文字: John is a clean-cut, great-looking guy who likes his father and mother, who frowns on drugs, who takes his profession seriously, who likes to have a good time, who enjoys the company of the opposite sex, and who has his own goals and values. He's a boy with no surprise up in his sleeve.

  16. 12 CFR 583.15 - Parent company.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Parent company. 583.15 Section 583.15 Banks and... SAVINGS AND LOAN HOLDING COMPANIES § 583.15 Parent company. The term parent company means any company which directly or indirectly controls any other company or companies....

  17. Factors Affecting Internationalization of Indonesia Franchise Companies

    Directory of Open Access Journals (Sweden)

    Erwin Halim

    2013-05-01

    Full Text Available Franchise is one of successful business strategies in business expansion. Franchise format has been already adopted in all countries. The success is proven in the world and also in Indonesia. Franchise system can be implemented not only in franchisor country but also in other countries. The spirit of internalization is not only because of market saturated, but also to increase reputation of franchise companies and to follow competitors or customers. Important thing discussed in this research is the franchise life-cycle, franchise growth model, and franchise companies’ profile.  It is found that the Indonesia franchise companies are in the introduction stage. The stage in life-cycle shows its reputation. This study used literature review as methodology, and the purpose of this study is to give a big picture for Indonesia franchise companies to make internationalization. There are some Indonesia franchise business profiles in the discussion part. The factors affecting franchise internationalization were analyzed by PESTEL analysis. Some strategies should be prepared in making decision to go international.  At the end, there are some recommendations and future research relating to internationalize franchise business.

  18. Organizational architecture of multinational companies

    OpenAIRE

    Sikorová, Lenka

    2017-01-01

    The main goal of the bachelor thesis Organizational Architecture of Multinational Companies is to elaborate the overview of organizational structures that are used by modern global companies. The thesis contains an analysis of such companies development, principles of functioning, pros and cons and the opportunities which these brings. It also contains a description of the basic concepts associated with organizational architecture such as globalization, multinational companies and organizatio...

  19. IMPLEMENTATION OF QUALITATIVE RULES IN COMPANY`S INFORMATION MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Anna WOLNOWSKA

    2012-07-01

    Full Text Available In the article there were presented chosen issues of quality management. Important role of information and work processes in companies were emphasized . Based on eight rules of quality management, TQM standards and ideas of discipline pioneers like Deming, Juran, Crosby and Shewart, author has constructed way of using chosen rules and assumptions to company`s information circulation. Analogy, suggested by author, has not only emphasized importance of information as a company`s resource, but also has pointed to possibility of improving ways of managing this information.

  20. Organizational architecture of multinational company

    OpenAIRE

    Vrbová, Tereza

    2012-01-01

    The Bachelor's Thesis ,,Organizational architecture of multinational company" sets the target to analyse organizational structures used in multinational companies at present. In the teoretical section is briefly described development of this subject, basic concepts associated with organizational architecture such as globalization, multinational companies and organizational architecture. I also generalized main characteristics of organizational forms and describe their pros and cons. The pract...

  1. Orosomucoid expression profiles in liver, adipose tissues and serum of lean and obese domestic pigs, Göttingen minipigs and Ossabaw minipigs.

    Science.gov (United States)

    Rødgaard, Tina; Stagsted, Jan; Christoffersen, Berit Ø; Cirera, Susanna; Moesgaard, Sophia G; Sturek, Michael; Alloosh, Mouhamad; Heegaard, Peter M H

    2013-02-15

    The acute phase protein orosomucoid (ORM) has anti-inflammatory and immunomodulatory effects, and may play an important role in the maintenance of metabolic homeostasis in obesity-induced low-grade inflammation. Even though the pig is a widely used model for obesity related metabolic symptoms, the expression of ORM has not yet been characterized in such pig models. The objective of this study was to investigate the expression of ORM1 mRNA in liver, visceral adipose tissue, subcutaneous adipose tissue (SAT) from the abdomen or retroperitoneal abdominal adipose tissue (RPAT) and SAT from the neck, as well as the serum concentration of ORM protein in three porcine obesity models; the domestic pig, Göttingen minipigs and Ossabaw minipigs. No changes in ORM1 mRNA expression were observed in obese pigs compared to lean pigs in the four types of tissues. However, obese Ossabaw minipigs, but none of the other breeds, showed significantly elevated ORM serum concentrations compared to their lean counterparts. Studies in humans have shown that the expression of ORM was unchanged in adipose tissue depots in obese humans with an increased serum concentration of ORM. Thus in this respect, obese Ossabaw minipigs behave more similarly to obese humans than the other two pig breeds investigated.

  2. Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency

    Science.gov (United States)

    Residual feed intake (RFI) is a measure of feed efficiency, where low RFI denotes high feed efficiency. Caloric restriction (CR) is associated with feed efficiency in livestock species and relevant to human health benefits such as longevity and cancer prevention. We generated transcript profiles of ...

  3. Angular Photogrammetric Analysis of the Soft tissue Facial Profile of Attractive Uygur Females in Xinjiang%新疆维吾尔族美貌女性侧貌软组织形态角度测量分析

    Institute of Scientific and Technical Information of China (English)

    姬晓炜; 梁学萍; 葛菲

    2012-01-01

    Objective; To obtain objective angular measurements of the soft tissue facial profile of the attractive Uygur female in Xinjiang to use them as a guide for aesthetic clinicians and explore the relationship between angular analysis and facial profile. Methods: Thirty one attractive Uygur women were selected. Standardized facial photographic records were taken in the natural head position(NHP) and 13 standard anthropometric marks were determined, then 15 measurements were performed by photoshopCS software. The reliability of the method was analysed using Dahlberg's formula. Result: The objective average measurements of the soft tissue facial profile of the attractive Uygur female in Xinjiang were obtained. Wide individual variations existed in nasolabial. mentolabial and ethnic pyramid angles. Conclusion: Angular analysis plays a significant role in the measurement of the soft tissue facial profile. Aesthetic triangles could be used as standard screening values for profile analysis and that ethnic pyramid could be used to consider ethnicity.%目的:建立新疆维吾尔族美貌女性侧貌软组织角度参考值并分析角度与侧貌特征的关系,为口腔颌面相关学科医生提供临床参考数据.方法:按标准选取31名新疆维吾尔族美貌女性,在自然头位摄取其侧面数码照片,在计算机上用photoshopCS软件选择13个软组织标志点,测量15个角度值,应用SPSS13.0统计软件包对数据进行处理,使用Dahlberg's公式计算测量方法误差.结果:新疆维吾尔族美貌女性侧貌软组织角度测量值范围.方法误差显示了测量方法的可靠性和可重复性.结论:所测角度在侧貌软组织特征分析中具有重要作用,“美学三角”可以作为侧貌美学分析的参考平面,“种族金字塔”中的3个角度可用于分析种族的差异性.

  4. The dissection profile and mechanism of tissue-selective dissection of the piezo actuator-driven pulsed water jet as a surgical instrument: laboratory investigation using Swine liver.

    Science.gov (United States)

    Yamada, Masato; Nakano, Toru; Sato, Chiaki; Nakagawa, Atsuhiro; Fujishima, Fumiyoshi; Kawagishi, Naoki; Nakanishi, Chikashi; Sakurai, Tadashi; Miyata, Go; Tominaga, Teiji; Ohuchi, Noriaki

    2014-01-01

    The water jet technique dissects tissue while sparing cord-like structures such as blood vessels. The mechanism of such tissue-selective dissection has been unknown. The novel piezo actuator-driven pulsed water jet (ADPJ) system can achieve dissection with remarkably reduced water consumption compared to the conventional water jet; however, the system's characteristics and dissection capabilities on any organ have not been clarified. The purposes of this study were to characterize the physical properties of the novel ADPJ system, evaluate the dissection ability in swine organs, and reveal the mechanism of tissue-selective dissection. The pulsed water jet system comprised a pump chamber driven by a piezo actuator, a stainless steel tube, and a nozzle. The peak pressure of the pulsed water jet was measured through a sensing hole using a pressure sensor. The pulsed water jet technique was applied on swine liver in order to dissect tissue on a moving table using one-way linear ejection at a constant speed. The dissection depth was measured with light microscopy and evaluated histologically. The physical properties of swine liver were evaluated by breaking strength tests using tabletop universal testing instruments. The liver parenchyma was also cut with three currently available surgical devices to compare the histological findings. The peak pressure of the pulsed water jet positively correlated with the input voltage (R(2) = 0.9982, p dissection depth. The dissection depth negatively correlated with the breaking strength of the liver parenchyma (R(2) = 0.6694, p dissected, preserving the hepatic veins and Glisson's sheaths in contrast to what is commonly observed with electrocautery or ultrasonic instruments. The dissection depth of liver tissue is well controlled by input voltage and is influenced by the moving velocity and the physical properties of the organ. We showed that the device can be used to assure liver resection with tissue selectivity due to tissue

  5. Profiling of adrenocorticotropic hormone and arginine vasopressin in human pituitary gland and tumor thin tissue sections using droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS.

    Science.gov (United States)

    Kertesz, Vilmos; Calligaris, David; Feldman, Daniel R; Changelian, Armen; Laws, Edward R; Santagata, Sandro; Agar, Nathalie Y R; Van Berkel, Gary J

    2015-08-01

    Described here are the results from the profiling of the proteins arginine vasopressin (AVP) and adrenocorticotropic hormone (ACTH) from normal human pituitary gland and pituitary adenoma tissue sections, using a fully automated droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS system for spatially resolved sampling, HPLC separation, and mass spectrometric detection. Excellent correlation was found between the protein distribution data obtained with this method and data obtained with matrix-assisted laser desorption/ionization (MALDI) chemical imaging analyses of serial sections of the same tissue. The protein distributions correlated with the visible anatomic pattern of the pituitary gland. AVP was most abundant in the posterior pituitary gland region (neurohypophysis), and ATCH was dominant in the anterior pituitary gland region (adenohypophysis). The relative amounts of AVP and ACTH sampled from a series of ACTH-secreting and non-secreting pituitary adenomas correlated with histopathological evaluation. ACTH was readily detected at significantly higher levels in regions of ACTH-secreting adenomas and in normal anterior adenohypophysis compared with non-secreting adenoma and neurohypophysis. AVP was mostly detected in normal neurohypophysis, as expected. This work reveals that a fully automated droplet-based liquid-microjunction surface-sampling system coupled to HPLC-ESI-MS-MS can be readily used for spatially resolved sampling, separation, detection, and semi-quantitation of physiologically-relevant peptide and protein hormones, including AVP and ACTH, directly from human tissue. In addition, the relative simplicity, rapidity, and specificity of this method support the potential of this basic technology, with further advancement, for assisting surgical decision-making. Graphical Abstract Mass spectrometry based profiling of hormones in human pituitary gland and tumor thin tissue sections.

  6. The European Model Company Act

    DEFF Research Database (Denmark)

    Cleff, Evelyne Beatrix

    2011-01-01

    European Company Law regulation is currently undergoing a reform. These reforms raise a number of regulatory questions, such as what should be the aims of companies' legislation, and how these aims should best be met by regulation. Many of the reforms and discussions (both on EU and national level......) on the organisation of company laws reflect an interesting paradigm shift. Whereas, previously company law was primarily focused on preventing abuse, there is now a trend towards legislation that promote commerce and satisfy the needs of business. This means that the goal of economic efficiency is having...... an increasing influence on the framing of company legislation, such as the choice between mandatory or default rules. This article introduces the project 'European Company Law and the choice of Regulatory Method' which is carried out in collaboration with the 'European Model Company Act Group'. The project aims...

  7. CSR in TSL companies

    Directory of Open Access Journals (Sweden)

    Joanna DYCZKOWSKA

    2015-03-01

    Full Text Available TSL companies are characterized by high dynamics of an increase of incomes, and hence increased shipping. Owing to a rational policy in the area of the consolidation of production and distribution, they may boast of a better use of the means of transport. The purpose of this article is to present the activities in the area of the eco-friendly CSR aspect in the activities of TSL companies taking into consideration particularly logistic operators. The research methods used in the study include an analysis of secondary data, observations and comparative analyses. Road transport in the shipping structure comes first and it constitutes 84% of freights. In the year 2009, in Poland greenhouse gas emissions from road transport amounted to 42.5 million tons (4.84% of the EU member states and CO emissions were 41.9 million tons (analogically, 4.83% of environment pollutions in the European Union. This causes an emission of fumes into the atmosphere. The policy of sustainable development pursued by logistic operators under corporate social responsibility is a response to the abovementioned data. They take decisions concerning social and environmental aspects. The activities of TSL companies under CSR need to provide an answer to customer expectations and needs, and they have to cause an increase of competitiveness on the market. The selected four largest logistic operators conduct the following eco-friendly activities on the highest level: fume emission reports and the control of these emissions, transport of hazardous goods (ADR, voluntary services in the scope of environmental protection and cooperation with eco-friendly organizations. There are those activities which call for improvement: a limitation of the emission of fumes, waste management and sewage treatment policy.

  8. Transcriptome profiling from adipose tissue during a low-calorie diet reveals predictors of weight and glycemic outcomes in obese, nondiabetic subjects

    DEFF Research Database (Denmark)

    Armenise, Claudia; Lefebvre, Gregory C; Carayol, Jérôme

    2017-01-01

    Background: A low-calorie diet (LCD) reduces fat mass excess, improves insulin sensitivity, and alters adipose tissue (AT) gene expression, yet the relation with clinical outcomes remains unclear.Objective: We evaluated AT transcriptome alterations during an LCD and the association with weight...

  9. Profiling signalling pathways in formalin-fixed and paraffin-embedded breast cancer tissues reveals cross-talk between EGFR, HER2, HER3 and uPAR.

    Science.gov (United States)

    Berg, Daniela; Wolff, Claudia; Malinowsky, Katharina; Tran, Kai; Walch, Axel; Bronger, Holger; Schuster, Tibor; Höfler, Heinz; Becker, Karl-Friedrich

    2012-01-01

    In the last few years, new approaches and developments in patient-tailored cancer therapies have raised the need to select, more precisely, those patients who will respond to personalized treatments. Therefore, the most efficient way for optimal therapy and patient selection is to provide a tumour-specific protein network portrait prior to treatment. The aim of our study was to monitor protein networks in formalin-fixed and paraffin-embedded (FFPE) breast cancer tissues, with special emphasis on epidermal growth factor receptor 2 (HER2)-mediated signalling pathways, to identify and validate new disease markers. For this purpose we used a recently developed technology to extract full-length proteins from FFPE tissues and analysed 23 molecules involved in HER2-related signalling by reverse phase protein microarray (RPPA) in a series of 106 FFPE breast cancer tissue samples. We found a significant correlation of HER2 with human epidermal growth factor receptor 3 (HER3/erbB3), epidermal growth factor receptor 1 (EGFR/HER1/erbB1) and urokinase plasminogen receptor (uPAR) in routinely used FFPE breast cancer tissues. Thus, targeting HER2, EGFR, HER3 and uPAR together may offer a more efficient treatment option for patients with breast cancer.

  10. Effect of aqueous extract of Ajuga iva supplementation on plasma lipid profile and tissue antioxidant status in rats fed a high-cholesterol diet.

    Science.gov (United States)

    Chenni, A; Yahia, D Ait; Boukortt, F O; Prost, J; Lacaille-Dubois, M A; Bouchenak, M

    2007-01-19

    The present study was designed to explore the possible antioxidant and hypolipidemic effects of the aqueous extract of Ajuga iva (0.5% in the diet) in rats fed a high-cholesterol (1%) diet (HCD). The results indicated that the HCD-Ai versus HCD treatment led to many changes in biochemical parameters. They showed a decrease of plasma total cholesterol (TC) and VLDL-cholesterol but an increase of HDL(2)-cholesterol. The triacylglycerol contents were reduced in plasma and in VLDL. The lipid peroxidation determined by TBARS was decreased by 75% in plasma. TBARS in liver, heart and kidneys were highly reduced excepted in the adipose tissue. Ajuga iva treatment enhanced superoxide dismutase activity in liver and kidney. Glutathione reductase activity was lowered in adipose tissue but increased in liver and in kidney. A significant increase was noted in glutathione peroxidase activity in liver, heart and kidney but a low value in adipose tissue was observed. In conclusion, the present study demonstrates that in addition to its potent TG and TC-lowering effects, Ajuga iva is effective in improving the antioxidant status by reducing lipid peroxidation in plasma and tissues and enhancing the antioxidant enzymes in rats fed high-cholesterol diet. Furthermore, Ajuga iva may reduce intestinal cholesterol absorption.

  11. Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue.

    Science.gov (United States)

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation...

  12. Ultra-performance liquid chromatography-tandem mass spectrometry determination and depletion profile of flunixin residues in tissues after single oral administration in rabbits.

    Science.gov (United States)

    Zhu, Ai-Ling; Peng, Tao; Liu, Liang; Xia, Xi; Hu, Ting; Tao, Xiao-Qi; Wen, Kai; Cheng, Lin-Li; Li, Jian-Cheng; Ding, Shuang-Yang; Cao, Xing-Yuan; Jiang, Hai-Yang

    2013-09-01

    An ultra-performance liquid chromatography with tandem mass spectrometric detection (UPLC-MS/MS) method was developed for the detection of flunixin residues in rabbit tissues. The samples were extracted with acidic acetonitrile, defatted with n-hexane, and then purified by HLB solid-phase extraction cartridge. Analysis was carried out on UPLC-ESI-MS/MS working with multiple reaction monitoring (MRM) mode. The limits of detection (LODs) of the method were 0.3-0.8μgkg(-1) and limits of quantification (LOQs) were 1.0-3.0μgkg(-1) in rabbit tissues, respectively. In all fortified samples at a concentration range of 1.0-300.0μgkg(-1), mean recoveries were 61.7-115.7% with relative standard deviations (RSDs) below 16%. Residue depletion of flunixin in rabbit was conducted after oral administration at a dose of 5mgkg(-1) of body weight. The average concentrations for flunixin measured 2h post-administration in kidney and intestine were significantly higher than in liver, heart and muscle. The concentrations for flunixin in all rabbit tissues were below the LOD or not detected in all tissues after 96h administration of drug. A minimum withdrawal time of 21h was indicated for residue levels in heart, liver, kidney, intestine and muscle below the maximum residue limits (MRLs).

  13. Genome-wide DNA methylation profiles and their replationship with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos Taurine)

    Science.gov (United States)

    DNA methylation is a key epigenetic modification in mammals, having essential and important roles in muscle development. We sample longissimus thoracis tissues from a well-known elite native breed of Chinese Qinchuan cattle living within comparable environments at fetal and adult stages, using methy...

  14. Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue.

    Science.gov (United States)

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation...

  15. A Comprehensive MicroRNA Expression Profile of Liver and Lung Metastases of Colorectal Cancer with Their Corresponding Host Tissue and Its Prognostic Impact on Survival

    Science.gov (United States)

    Pecqueux, Mathieu; Liebetrau, Isabell; Werft, Wiebke; Dienemann, Hendrik; Muley, Thomas; Pfannschmidt, Joachim; Müssle, Benjamin; Rahbari, Nuh; Schölch, Sebastian; Büchler, Markus W.; Weitz, Jürgen; Reissfelder, Christoph; Kahlert, Christoph

    2016-01-01

    MicroRNAs are small non-coding RNAs with a length of 18–25 nucleotides. They can regulate tumor invasion and metastasis by changing the expression and translation of their target mRNAs. Their expression is substantially altered in colorectal cancer cells as well as in the adjacent tumor-associated stroma. Both of these compartments have a mutual influence on tumor progression. In the development of metastases, cancer cells initially interact with the host tissue. Therefore, compartment-specific expression signatures of these three locations—tumor, associated stroma, and host tissue—can provide new insights into the complex tumor biology of colorectal cancer. Frozen tissue samples of colorectal liver (n = 25) and lung metastases (n = 24) were laser microdissected to separate tumor cells and the adjacent tumor-associated stroma cells. Additionally, normal lung and liver tissue was collected from the same patients. We performed a microarray analysis in four randomly selected liver metastases and four randomly selected lung metastases, analyzing a total of 939 human miRNAs. miRNAs with a significant change >2-fold between the tumor, tumor stroma, and host tissue were analyzed in all samples using RT-qPCR (11 miRNAs) and correlated with the clinical data. We found a differential expression of several miRNAs between the tumor, the tumor-associated stroma, and the host tissue compartment. When comparing liver and lung metastases, miR-194 showed a 1.5-fold; miR-125, miR-127, and miR-192 showed a 2.5-fold; miR-19 and miR-215 a 3-fold; miR-145, miR-199-3, and miR-429 a 5-fold; miR-21 a 7-fold; and, finally, miR-199-5 a 12.5-fold downregulation in liver metastases compared to lung metastases. Furthermore miR-19, miR-125, miR-127, miR-192, miR-194, miR-199-5, and miR-215 showed a significant upregulation in the normal liver tissue compared to the normal lung tissue. Univariate analysis identified an association of poor survival with the expression of miR-125 (p = 0