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51.
52.
Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays 总被引:1,自引:0,他引:1
Background
Reproducibility of results can have a significant impact on the acceptance of new technologies in gene expression analysis. With the recent introduction of the so-called next-generation sequencing (NGS) technology and established microarrays, one is able to choose between two completely different platforms for gene expression measurements. This study introduces a novel methodology for gene-ranking stability analysis that is applied to the evaluation of gene-ranking reproducibility on NGS and microarray data. 相似文献53.
Tanja Višnjar Mateja Erdani Kreft 《In vitro cellular & developmental biology. Animal》2013,49(3):196-204
Optimizing culture conditions is known to be crucial for the differentiation of urothelial cell cultures and the formation of the permeability barrier. However, so far, no data exist to confirm if air–liquid (AL) and liquid–liquid (LL) interfaces are physiologically relevant during urothelial differentiation and barrier formation. To reveal the influence of interfaces on the proliferation, differentiation, and barrier formation of the urothelial cells (UCs) in vitro, we cultured UCs under four different conditions, i.e., at the AL or LL interfaces with physiological calcium concentration and without serum or without physiological calcium concentration and with serum. For each of the four models, the urothelial integrity was tested by measuring the transepithelial resistance (TER), and the differentiation stage was examined by immunolabeling of differentiation-related markers and ultrastructural analysis. We found that the UCs at a LL interface, regardless of the presence or absence of calcium or serum, form the urothelium with more cell layers and achieve a higher TER than UCs at an AL interface. However, UCs grown at an AL interface with physiological concentration of calcium in medium form only one- to two-layered urothelium of UCs, which are larger and express more differentiation-related proteins uroplakins than UCs in other models. These results demonstrate that the interface itself can play a major, although so-far neglected, role in urothelial physiology, particularly in the formation of the urothelial permeability barrier in vitro and the regulatory mechanisms related with urothelial differentiation. In the study, the culturing of UCs in three successive steps is proposed. 相似文献
54.
Globular domain of the prion protein needs to be unlocked by domain swapping to support prion protein conversion 总被引:1,自引:0,他引:1
Hafner-Bratkovic I Bester R Pristovsek P Gaedtke L Veranic P Gaspersic J Mancek-Keber M Avbelj M Polymenidou M Julius C Aguzzi A Vorberg I Jerala R 《The Journal of biological chemistry》2011,286(14):12149-12156
Prion diseases are fatal transmissible neurodegenerative diseases affecting many mammalian species. The normal prion protein (PrP) converts into a pathological aggregated form, PrPSc, which is enriched in the β-sheet structure. Although the high resolution structure of the normal PrP was determined, the structure of the converted form of PrP remains inaccessible to high resolution techniques. To map the PrP conversion process we introduced disulfide bridges into different positions within the globular domain of PrP, tethering selected secondary structure elements. The majority of tethered PrP mutants exhibited increased thermodynamic stability, nevertheless, they converted efficiently. Only the disulfides that tether subdomain B1-H1-B2 to subdomain H2-H3 prevented PrP conversion in vitro and in prion-infected cell cultures. Reduction of disulfides recovered the ability of these mutants to convert, demonstrating that the separation of subdomains is an essential step in conversion. Formation of disulfide-linked proteinase K-resistant dimers in fibrils composed of a pair of single cysteine mutants supports the model based on domain-swapped dimers as the building blocks of prion fibrils. In contrast to previously proposed structural models of PrPSc suggesting conversion of large secondary structural segments, we provide evidence for the conservation of secondary structural elements of the globular domain upon PrP conversion. Previous studies already showed that dimerization is the rate-limiting step in PrP conversion. We show that separation and swapping of subdomains of the globular domain is necessary for conversion. Therefore, we propose that the domain-swapped dimer of PrP precedes amyloid formation and represents a potential target for therapeutic intervention. 相似文献
55.
Majerle A Pristovsek P Mancek-Keber M Jerala R 《The Journal of biological chemistry》2011,286(29):26228-26237
HIV-1 represents an elusive target for therapeutic compounds due to its high rate of mutation. Targeting structural patterns instead of a constantly changing specific three-dimensional structure may represent an approach that is less sensitive to viral mutations. The V3 loop of gp120 of HIV-1, which is responsible for binding of viral gp120 to CCR5 or CXCR4 coreceptors, has already been identified as an effective target for the inhibition of viral entry. The peptide derived from the V3 loop of gp120 specifically interacts with the lipid A moiety of LPS, as does the full gp120 protein. NMR analysis of V3 in complex with LPS shows formation of an amphipathic turn. The interaction between LPS and V3 relies on the structural pattern, comprising a combination of hydrophobic and charge interactions, similar to the interaction between antimicrobial peptides and LPS. LPS inhibited binding of gp120 to the surface of target T cells. Nonendotoxic LPS antagonists inhibited viral infection, demonstrating the possibility for the development of an inhibitor of HIV-1 attachment to T cells based on the recognition of a conserved structural pattern. 相似文献
56.
Grego E Bertolotti L Peletto S Amore G Tomassone L Mannelli A 《Journal of molecular evolution》2007,65(5):512-518
In this study, Borrelia lusitaniae DNA extracted from ticks and lizards was used to amplify the outer surface protein A (OspA) gene in order to increase knowledge
about sequence variability in the Mediterranean basin area, to better understand how Borrelia lusitaniae has evolved and how its distribution has expanded. Phylogenetic trees including Italian and reference sequences showed a
clear separation of B. lusitaniae OspA strains in two different major clades. North African isolates form a clade with Portuguese POTIB strains, whereas Italian
samples are grouped with German strains and a human Portuguese strain. This subdivision was supported by very high posterior
probability values in the trees, by both analysis of molecular variance and selective pressure. These results, based on phylogenetic
information contained in the OspA gene sequences, show the presence of two different B. lusitaniae strains circulating in the Mediterranean basin area, suggesting two different evolution paths. 相似文献
57.
Mateja Štefančič Dominik Vodnik Franci Štampar Gregor Osterc 《Trees - Structure and Function》2007,21(4):497-496
The early responses of leafy stem cuttings of Prunus and Castanea species with differing rooting abilities were assessed in a fog system using fluorescence measurements. Different types of
cuttings of each species were used: cherry Prunus (‘GiSelA 5’, Prunus cerasus × Prunus canescens—148/2) and chestnut Castanea (‘Marsol’ and ‘Maraval’, Castanea crenata × Castanea sativa). The physiological status of cuttings in the early initiation phase was compared to the rooting results. For all cuttings,
fluorescence measurements revealed a close-to-optimum photochemical efficiency, indicating that physiological stress (severance,
water, etc.) was minimal. In cherry, the potential photochemical efficiency (Fv/Fm) differed slightly between terminal and
basal cherry cuttings, being lower in the basal ones at the time of severance. Later in the propagation process, the differences
were smaller. The photochemical efficiency did not differ between two ‘difficult-to-root’ Castanea clones, nor was it dependent on the length of the cuttings. The high rooting capacity of long Castanea cuttings (50 cm) indicated that physiological stress could be minimized under a fogging system.
An erratum to this article can be found at 相似文献
58.
Katarina Maher Barbara Jeri? Kokelj Miha Butinar Georgy Mikhaylov Mateja Man?ek-Keber Veronika Stoka Olga Vasiljeva Boris Turk Sergei A. Grigoryev Nata?a Kopitar-Jerala 《The Journal of biological chemistry》2014,289(46):31736-31750
Stefin B (cystatin B) is an endogenous cysteine cathepsin inhibitor, and the loss-of-function mutations in the stefin B gene were reported in patients with Unverricht-Lundborg disease (EPM1). In this study we demonstrated that stefin B-deficient (StB KO) mice were significantly more sensitive to the lethal LPS-induced sepsis and secreted higher amounts of pro-inflammatory cytokines IL-1β and IL-18 in the serum. We further showed that increased caspase-11 gene expression and better pro-inflammatory caspase-1 and -11 activation determined in StB KO bone marrow-derived macrophages resulted in enhanced IL-1β processing. Pretreatment of macrophages with the cathepsin inhibitor E-64d did not affect secretion of IL-1β, suggesting that the increased cathepsin activity determined in StB KO bone marrow-derived macrophages is not essential for inflammasome activation. Upon LPS stimulation, stefin B was targeted into the mitochondria, and the lack of stefin B resulted in the increased destabilization of mitochondrial membrane potential and mitochondrial superoxide generation. Collectively, our study demonstrates that the LPS-induced sepsis in StB KO mice is dependent on caspase-11 and mitochondrial reactive oxygen species but is not associated with the lysosomal destabilization and increased cathepsin activity in the cytosol. 相似文献
59.
Tina Cirman Matej Beltram Petra Schollmayer Primož Rožman Mateja Erdani Kreft 《Cell and tissue banking》2014,15(2):177-192
Amniotic membrane (AM) is the innermost, multilayered part of the placenta. When harvested, processed and stored properly, its properties, stemming from AM biological composition, make it a useful tissue for ophthalmic surgery. AM was shown to have several beneficial effects: it promotes epithelization, has antimicrobial effects, decreases inflammation, fibrosis and neovascularization. Many case reports and case series as well as practical experience (e.g. reconstruction of conjunctival and corneal defects, treatment of corneal ulcers) demonstrated the beneficial effect of AM for different ophthalmological indications. The combination of the above mentioned beneficial effects and reasonable mechanical properties are also the reason why AM is used as a substrate for ex vivo expansion of epithelial progenitor cells. Recently, amnion-derived cells, which also have stem cell characteristics, have been proposed as potential contributors to cell-based treatment of ocular surface disease. However, the use of AM remains one of the least standardized methods in ophthalmic surgery. In this review, the various properties of AM and its current clinical use in ophthalmology in Slovenia are discussed. 相似文献
60.
Mirjana Liovic Mateja Ozir Apolonija Bedina Zavec Spela Peternel Radovan Komel Tina Zupancic 《Microbial cell factories》2012,11(1):1-5