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Supplemental carnitine affects the microRNA expression profile in skeletal muscle of obese Zucker rats

Supplemental carnitine affects the microRNA expression profile in skeletal muscle of obese Zucker rats

The large number of target genes (about 1,500) pre- dicted from the most strongly regulated miRNAs and the other not explicitly mentioned data from gene-term en- richment analysis for the targets identified shows that car- nitine supplementation may cause several other biological effects than up-regulation of IGF-1 or inhibition of ubiquitin-mediated proteolysis via miRNA-mRNA inter- actions. However, the biological implications of most of the observed carnitine-mediated changes in the miRNA expression profile and its impact on specific metabolic and signalling pathways and whole metabolism cannot be resolved with certainty using biostatistics tools alone, be- cause the prediction of target genes from differentially expressed miRNAs is only an in silico-approach and, thus, has clear limitations. Therefore, time-consuming experi- mental studies with cultured muscle cells, in which the effect of carnitine in the presence of miRNA-specific in- hibitors or during over-expression or knockdown of spe- cific miRNAs on target gene expression is studied, are necessary in the future to validate at least some of the carnitine-mediated miRNA-mRNA interactions. Given that most of the detectable miRNAs (152 out of 259) were regulated by carnitine, it would be interesting to investi- gate in a future time-course experiment whether there are early and late responding miRNAs which behave differ- ently to carnitine supplementation.
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Expression profile of components of the acetylcholine-system in rat testicular tissue and function in non-germ cell populations

Expression profile of components of the acetylcholine-system in rat testicular tissue and function in non-germ cell populations

111 An interesting observation is the presence of both, subunits α4 and α7, in TM. Until now, most studies reported the presence of α4 and the absence of α7 in macrophage subpopulations such as mouse alveolar macrophage (AM) cell line MH-S, AM of FVB mice, rat AM, macrophages from the gut and peritoneal macrophages [122, 308- 310]. However, Wang et al. [56] demonstrated the mRNA expression of α7 in human monocyte-derived macrophages. These previous data and the finding in this study might lead to the proposal of species-specific differences and even tissue specific differences within the same species for the nAChR-mRNA expression profile in macrophages [308]. Variations in the expression-level of other molecules such as cytokines (IL-1 and TNFα) or cell surface proteins (receptors, CD) have been described for macrophages in liver, lung and peritoneum [305, 306, 311]. TM and peritoneal macrophages (PM) feature differences in the mRNA expression level of TLRs [304]. Similar results could be observed for AM, PM and intestinal macrophages (IM). CD14, TLR4, MD2, iNOS, TNFa and iNOS displayed cell- specific mRNA expression profils in absence or presence of LPS [302, 303]. Differentiation of adipose tissue macrophages (ATM) in adipose (F4/80 + CD11c + ) and normal mice (F4/80 + CD11c - ) results in modified subsequent gene expression of IL-6, iNOS and ApoE [307].
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Global gene expression profile mining in stem cells and their progeny

Global gene expression profile mining in stem cells and their progeny

DNA microarrays are now being used in scientific research and medical diagnosis to address a wide range of very diverse questions. In addition, novel applications of DNA microarrays emerged with genome sequencing projects that provided the complete sequence information of a given or- ganism. This genome-wide sequence information now allows measure- ments that are more than just comparing gene expression levels. For ex- ample, DNA microarrays are being designed for determining single nu- cleotide polymorphisms (SNPs) in order to map and relate individual genuine variations with a particular disease or phenotype. Another newly developed form of DNA microarrays is the tiling array. Such tiling arrays cover the organisms’ entire genomic sequence to systematically interrogate genomic regions. For example, the seven Affymetrix human tiling arrays contain 45 million oligonucleotide probes tiling the entire human genome at an average resolution of 35 base pairs. Such tiling arrays are most suitable to precisely map novel RNA transcripts and therefore extend the information that is obtained by conventional gene expression arrays. Ad- ditionally, tiling arrays are now being used in chromatin immunoprecipi- tation (ChIP) studies to map the positions of transcription factors and other DNA binding molecules on a global scale. Epigenetics represents an very active field of research where tiling arrays are used; allowing to posi- tion the histone modifications using immunoprecipitation (Mockler et al., 2005).
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Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation

Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation

Public microarray repository annotation Gene Expression Omnibus (GEO) [1] is the largest public web repository of microarray experiments. GEO, like ArrayExpress and Stanford MicroArray Database, provides descriptions of microarray experiments in free text making it difficult to search and comprehensively link those data to other knowledge resources. Text mining techniques applied to microarray experiment annotation are chal- lenged by poor and/or ambiguous free text description and consequently leave some objects unlabelled. Previous work organized GEO entries at the level of series (GSE) and data sets (GDS) [2] using the Unified Medical Lan- guage System (UMLS) [3]. GSE and GDS description are often too broad and a better quality of annotation can be achieved if the GEO samples (GSM) are considered directly. Here we report on a novel approach for annotat- ing GSM objects by employing a combination of text min- ing and global gene expression similarity. We hypothesize that the biological material analyzed on microarrays is related if unlabeled and labeled objects are highly similar in expression values and hence the class/annotation of one object can help annotate an unlabeled object. Our new method allows us to achieve a higher percentage of semantic annotation by combining both types of infor- mation stored in microarray databases.
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A Novel Binding Protein for Fibroblast Growth Factors (FGF-BP2):Cloning, Expression Profile, Tumorigenic Activity and Regulation of Gene Expression by Fetal Bovine Serum and Retinoic Acid.

A Novel Binding Protein for Fibroblast Growth Factors (FGF-BP2):Cloning, Expression Profile, Tumorigenic Activity and Regulation of Gene Expression by Fetal Bovine Serum and Retinoic Acid.

Some of the most effective and best-studied angiogenic factors are members of the Fibroblast Growth Factor (FGF) family of polypeptides (Baird and Klagesbrun, 1991; Gospodarowicz et al., 1987). The FGFs are a family of at least 21 distinct growth factors which can interact with their membrane receptors coded for by four separate receptor genes and numerous protein products due to alternative splicing (reviewed in Schreiber et al., 1986; Powers C.J. et al., 2000). Members of the FGF family regulate various developmental processes and are potent stimulators of new blood vessel growth during wound healing and during tumor growth (Folkman and Klagsbrun, 1987; Burgess et al., 1989; Baird et al., 1990). FGF-1 (aFGF), FGF-2 (bFGF) and FGF-4 (K-FGF) have all been shown to be angiogenic activators (Burgess et al., 1989) and have therefore been a major focus of research in tumor vascularisation. aFGF and bFGF are widely expressed in normal tissues and in tumors of different origin, although not at elevated levels (Burgess et al., 1989; Moscatelli et al. 1986). The observation that aFGF and bFGF are expressed in normal tissues, which are not undergoing proliferation or angiogenesis, suggests that mechanisms other than their expression exist which regulate FGF activation. Unlike other members of the FGF- family, aFGF and bFGF do not contain a signal sequence and are not secreted into the media in a classical way (Burgess et al., 1989; Mason, 1994). In fact, these growth factors are deposited into the extracellular matrix (ECM) where they are found tightly bound to membrane-attached heparansulfate proteoglycans. The immobilization of FGFs in the ECM quenches their biological activities by preventing them from reaching their high affinity receptors in the endothelial cell membrane (Vlodavsky et al., 1987; Rogelj et al., 1989; Saksela et al., 1988; Kiefer et al., 1990).
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Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation

Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation

7. Chen R, Li L, Butte AJ: AILUN: reannotating gene expression data automatically. Nature Methods 2007, 4:879. Table 1: GSM object annotation coverage. Platform GSM object number (a) Labeled objects by ProMiner (b) Raw data available/ProMiner labeled (c)

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Spatio-temporal expression profile of sirtuins during aging of the annual fish Nothobranchius furzeri

Spatio-temporal expression profile of sirtuins during aging of the annual fish Nothobranchius furzeri

The founding member of the sirtuin family, yeast Sir2, was the first evolutionarily conserved gene to be iden- tified as a regulator of longevity. Sirtuins constitute a protein family of metabolic sensors, translating changes in NAD + levels into adaptive responses, thereby acting as crucial regulators of the network that controls energy homeostasis and as such determines healthspan. In mammals the sirtuin family comprises seven proteins, SIRT1- SIRT7, which vary in tissue speci ficity, subcellular localization, enzymatic activity and targets. Here, we report the identi fication and a detailed spatio-temporal expression profile of sirtuin genes in the short-lived fish Nothobranchius furzeri, from embryogenesis to late adulthood, mapping its entire life cycle. Database exploration of the recently published N. furzeri genome revealed eight orthologues corresponding to the seven known mammalian sirtuins, including two copies of the sirt5 gene. Phylogenetic analysis showed high cross species similarity of individual sirtuins in both their overall amino acid sequence and catalytic domain, suggesting a high degree of functional conservation. Moreover, we show that N. furzeri sirtuins exhibit ubiquitous and wide tissue distribution with a unique spatial expression pattern for each individual member of this enzyme family. Specifically, we observed a transcriptional down-regulation of several sirtuin genes with age, most significantly sirt1, sirt5a, sirt6 and sirt7 in a wide range of functionally distinct tissues. Overall, this spatio-temporal expression analysis provides the foundation for future research, both into genetic and pharmacological manipulation of this important group of enzymes in Nothobranchius furzeri, an emerging model organism for aging research.
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Common Criteria Protection Profile

Common Criteria Protection Profile

Biometric products, which are conformant to this Protection Profile, provide a verification process to verify the claimed identity of a human being using a unique characteristic of his body. This PP should cover the biometric verification process on a generic level and should be applicable to any biometric verification system. Therefore the descriptions of the requirements for the TOE are kept on a very general level so that the manufacturing of conformant products is possible for various IT environments. Where a relation to a certain biometric characteristic was necessary, fingerprint recognition is used in this PP. In these cases other technologies are addressed via application notes. The basic processes of a biometric verification system are described in chapter 2.1.
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Low Assurance Protection Profile

Low Assurance Protection Profile

A PP defines an implementation-independent set of IT security requirements for a category of TOEs which are intended to meet common consumer needs for IT security. The development and certification of a PP or the reference to an existent one gives consumers the possibility to express their IT security needs without referring to a special product. Product or system certifications can be based on Protection Profiles. For products which have been certified based on a Protection Profile an individual certificate will be issued.

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Common Criteria Protection Profile

Common Criteria Protection Profile

Application Note 5: Since the SyS is being operated in a well-controlled environment of the company intranet, the focus of the security requirements on the SyS lies upon (i) the[r]

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Standards und Profile für Öffentliche Bibliotheken

Standards und Profile für Öffentliche Bibliotheken

ISSN 14 38-76 62 Abstract: Was sind Standards? Klassische bibliothekarische Standards, Grenzen Input-orien- tierter Standards, Qualitätsstandards, Verfahrensstandards im Sinn der Qualitäts- norm, Standards für Bibliotheksdienstleistungen (Leseförderung, Informationskom- petenz, Informations- und Benutzungsdienst, Qualitätsstandards im Bibliothekskon- zept Südtirol, Public Library Service Standards, IFLA/UNESCO Guidelines for Deve- lopment), Profile und Standards, Gewinnung und In-Kraft-Setzung von Standards. Die klassischen, fast nur Input-orientierten Standards (2 Medien pro Einwohner usw.) werden nicht bedeutungslos, verlieren aber an Bedeutung, weil sie auf dem Hinter- grund der knappen Kassen ins Leere laufen und weil sie keineswegs automatisch „gute“ Dienstleistungen bewirken. Auch mit geringeren Ressourcen sind exzellente Leistungen möglich, teilweise allerdings auf begrenzten Feldern. Fast völlig ver- nachlässigt wurden in der bisherigen Fachdebatte Qualitätsstandards, die verbindlich beschreiben, welche Merkmale „gute“ Dienstleistungen von Bibliotheken aufweisen. Ausgangspunkt für derartige Qualitätsstandards ist das Leitbild der Bibliothek. Dieses muss auf Ziele des Unterhaltsträgers ebenso Bezug nehmen wie auf Interessen des Personals und die Sicht der Kunden (Stakeholder-Ansatz). Die Standards können überbetrieblich oder innerbetrieblich gewonnen werden. Durch eine entsprechende Auswahl aus einem überbetrieblichen Set an Standards können betriebsindividuelle Profile gebildet werden. Die gewählten Standards müssen in jedem Fall seitens der einzelnen Bibliothek, die sich zu diesen Standards bekennt, öffentlich propagiert werden, innerbetrieblich durch Fortbildungsveranstaltungen (z. B. Inhouse Seminar) an alle Mitarbeiter vermittelt und in Zielvereinbarungen mit den Mitarbeitern fest- gehalten werden, darüber hinaus, wenn sie Entscheidungen des Unterhaltsträgers tangieren (z. B. hinsichtlich Erwerbungsetat oder Schwerpunktsetzungen), mit dem Unterhaltsträger abgestimmt oder von diesem in Kraft gesetzt werden.
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Usage-Driven Unified Model for User Profile and Data Source Profile Extraction

Usage-Driven Unified Model for User Profile and Data Source Profile Extraction

Usage Analysis in IR systems 4.1. Introduction Nowadays, the world of computer science is overwhelmed by applications intended to be used by always connected end-users. In this kind of applications, the quality of service is directly related to the user satisfaction. This implies that the design process should integrate the user model. Depending on the role given to the model, we can distinguish two different levels of application: individual and group levels. At the individual level, the user model, which is also the user profile, is mostly used for adaptation and personalization, i.e., basically, to improve the human-machine interaction (the interface) [Fis01] or to adapt the information content with respect to the user interests and characteristics [JCECWtC00]. As examples of individual user profile we can cite: web page personalization and recommender system. At the group level, the user profile is extended to groups of users sharing similar character- istics. In addition to the advantages related to a single user profile, the profile of a group allows the users to exchange easily their content within the group, especially in some specific network applications, like: sharing data over P2P networks, data propagation on mobile networks or extracting documents in a distributed informa- tion retrieval system.
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Common Criteria Protection Profile

Common Criteria Protection Profile

• The TOE does not disclose any TOE data as a result of an archive request. • All rules specified by the organization using the TOE shall be performed by the TOE in ac- cordance with t[r]

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Common Criteria Protection Profile

Common Criteria Protection Profile

o Archive Evidence Request means, the Client Software Application requests evidence data to the fact that ar- chival information packages does exist unmodified within the stora[r]

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Bildungswissenschaften - Begriff - Profile - Perspektiven

Bildungswissenschaften - Begriff - Profile - Perspektiven

Dabei sind (a) inhaltliche Wissensbe- stände zu den Kompetenzbereichen aus den verschiedenen Bildungswissen- schaften (Pädagogik, Psychologie, Soziologie, Philosophie, Politikwissen- [r]

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Protection Profile IoT Secure Element Protection Profile (IoT-SE-PP) Version 1.0.0

Protection Profile IoT Secure Element Protection Profile (IoT-SE-PP) Version 1.0.0

FTP_PRO.3 Defines the requirement for well-defined key derivation mechanisms in the trusted channel protocol, which may be used to derive further data authentication keys (e.g., sess[r]

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Protection Profile IoT Secure Communications Module Protection Profile (IoT-SCM-PP), Version 1.0.0

Protection Profile IoT Secure Communications Module Protection Profile (IoT-SCM-PP), Version 1.0.0

A TOE evaluated and certified according to this PP shall make use of an evaluated and certified IoT Secure Element (IoT SE) as specified by the separate Protection Profile IoT-SE-PP. One of the main goals of the IoT-SE-PP is to define requirements how an IoT SE protects all data, which are stored and processed internally, from unauthorized disclosure or modification. To do so, the IoT-SE-PP also defines requirements concerning physical protection and side- channel resistance of the IoT SE. The hardware of the IoT SE may be shared by the IoT SCM (and even the IoT application) for a higher level of integration, e.g. in terms of a system on chip (SoC).
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Changing profile of education in Afghanistan

Changing profile of education in Afghanistan

While in quantitative terms and variety of initiatives the developments are significant, the quality and efficiency of education continue to be a challenge for national auth[r]

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D6.2.1 – AEROMACS PROFILE RECOMMENDATION DOCUMENT

D6.2.1 – AEROMACS PROFILE RECOMMENDATION DOCUMENT

The WiMAX standard 802.16e [WiM02] [WiM03] includes many profiles defined by the PHY layer, the MAC layer and the RF profiles. The PHY profiles define bandwidths (BWs), access schemes, frame structures, coding, modulation techniques and other characteristics. They are mainly divided in single-carrier and multi-carrier transmissions. The multi-carrier technique OFDM is designed to avoid Inter Symbol Interference (ISI) and is thus suitable to multipath propagation channels, such as the airport propagation channel. Hence, only the multi-carrier option is considered for AeroMACS profile. The WiMAX standard distinguishes furthermore between Orthogonal Frequency-Division Multiplexing (OFDM) profile and Orthogonal Frequency-Division Multiple Access (OFDMA) profile. Both profiles are considered in the preliminary WP6.2 considerations for AeroMACS suitability given in this section. Then, considering the analysis provided in this section, but also in the course of the parallel SESAR activities, the relevant set of profiles and parameters is reduced. Hence, later in Section 4, a detailed analysis is done regarding the airport propagation conditions and performing simulations to evaluate particular options and parameters. The 802.16e standard contains a wide range of techniques and parameters set. WiMAX Forum proposes to obtain this scope defining a limited number of system profiles and certification profiles. A system profile defines the subset of mandatory and optional physical and MAC layer features selected by WiMAX Forum from the IEEE 802.16-2004 or IEEE 802.16e-2005 standard. The mandatory and optional status of a particular feature within a WiMAX system profile may be different from what it is in the original IEEE standard.
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Pixel und Profile - Fernerkundung in den Bodenwissenschaften

Pixel und Profile - Fernerkundung in den Bodenwissenschaften

Böden sind sowohl in räumlicher, als auch zeitliche Hinsicht heterogen, so dass eine einheitliche Bewirtschaftung, wie zum Beispiel eine konstante Düngemenge für de[r]

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