1,135 research outputs found
Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome
Transposable elements (TEs) have no longer been totally considered as âjunk DNAâ for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE
playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2Ă1016; IMR90 fibroblasts: r = 0.94, P < 2.2 Ă 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3Ă10â4; IMR90: r=0.934, P=2Ă10â2; Promoter: hESC: r = 0.995, P = 3.8 Ă 10â4; IMR90: r = 0.996, P = 3.2 Ă 10â4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes
In vivo and in vitro studies of Th17 response to specific immunotherapy in house dust mite-induced allergic rhinitis patients
10.1371/journal.pone.0091950PLoS ONE93-POLN
Immunoprophylaxis of respiratory syncytial virus: global experience
Respiratory syncytial virus (RSV) infects nearly all children by age 2 years, and it causes considerable illness and death in certain high-risk pediatric populations. Historically, treatment for RSV has been symptomatic, and developing a safe and effective vaccine has been a challenge. Therefore, research efforts have turned to passive immunization as the best option to control RSV. Palivizumab, a genetically engineered humanized monoclonal antibody, has been shown to reduce RSV-related hospitalizations significantly, with few adverse effects. It was approved for use in high-risk children in the USA in 1998 and in Europe in 1999; it is now approved for use in more than 45 countries. The efficacy and safety of palivizumab continue to be supported by both clinical trial and outcomes data
Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9âMb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core. RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta
Optimization of insect cell based protein production processes - online monitoring, expression systems, scale-up
Due to the increasing use of insect cell based expression systems in research and industrial recombinant protein production, the development of efficient and reproducible production processes remains a challenging task. In this context, the application of online monitoring techniques is intended to ensure high and reproducible product qualities already during the early phases of process development. In the following chapter, the most common transient and stable insect cell based expression systems are briefly introduced. Novel applications of insect cell based expression systems for the production of insect derived antimicrobial peptides/proteins (AMPs) are discussed using the example of G. mellonella derived gloverin. Suitable in situ sensor techniques for insect cell culture monitoring in disposable and common bioreactor systems are outlined with respect to optical and capacitive sensor concepts. Since scale-up of production processes is one of the most critical steps in process development, a conclusive overview is given about scale up aspects for industrial insect cell culture processes
Expansion of CD4+CD25+ and CD25- T-Bet, GATA-3, Foxp3 and RORÎłt Cells in Allergic Inflammation, Local Lung Distribution and Chemokine Gene Expression
Allergic asthma is associated with airway eosinophilia, which is regulated by
different T-effector cells. T cells express transcription factors T-bet, GATA-3,
RORÎłt and Foxp3, representing Th1, Th2, Th17 and Treg cells respectively. No
study has directly determined the relative presence of each of these T cell
subsets concomitantly in a model of allergic airway inflammation. In this study
we determined the degree of expansion of these T cell subsets, in the lungs of
allergen challenged mice. Cell proliferation was determined by incorporation of
5-bromo-2âČ-deoxyuridine (BrdU) together with 7-aminoactnomycin (7-AAD).
The immunohistochemical localisation of T cells in the lung microenvironments
was also quantified. Local expression of cytokines, chemokines and receptor
genes was measured using real-time RT-PCR array analysis in tissue sections
isolated by laser microdissection and pressure catapulting technology. Allergen
exposure increased the numbers of T-bet+,
GATA-3+, RORÎłt+ and
Foxp3+ cells in CD4+CD25+
and CD4+CD25- T cells, with the greatest expansion of
GATA-3+ cells. The majority of
CD4+CD25+ T-bet+,
GATA-3+, RORÎłt+ and
Foxp3+ cells had incorporated BrdU and underwent
proliferation during allergen exposure. Allergen exposure led to the
accumulation of T-bet+, GATA-3+ and
Foxp3+ cells in peribronchial and alveolar tissue,
GATA-3+ and Foxp3+ cells in perivascular
tissue, and RORÎłt+ cells in alveolar tissue. A total of 28
cytokines, chemokines and receptor genes were altered more than 3 fold upon
allergen exposure, with expression of half of the genes claimed in all three
microenvironments. Our study shows that allergen exposure affects all T effector
cells in lung, with a dominant of Th2 cells, but with different local cell
distribution, probably due to a distinguished local inflammatory milieu
Performance of the CMS Cathode Strip Chambers with Cosmic Rays
The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device
in the CMS endcaps. Their performance has been evaluated using data taken
during a cosmic ray run in fall 2008. Measured noise levels are low, with the
number of noisy channels well below 1%. Coordinate resolution was measured for
all types of chambers, and fall in the range 47 microns to 243 microns. The
efficiencies for local charged track triggers, for hit and for segments
reconstruction were measured, and are above 99%. The timing resolution per
layer is approximately 5 ns
Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector
The inclusive and dijet production cross-sections have been measured for jets
containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass
energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The
measurements use data corresponding to an integrated luminosity of 34 pb^-1.
The b-jets are identified using either a lifetime-based method, where secondary
decay vertices of b-hadrons in jets are reconstructed using information from
the tracking detectors, or a muon-based method where the presence of a muon is
used to identify semileptonic decays of b-hadrons inside jets. The inclusive
b-jet cross-section is measured as a function of transverse momentum in the
range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet
cross-section is measured as a function of the dijet invariant mass in the
range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets
and the angular variable chi in two dijet mass regions. The results are
compared with next-to-leading-order QCD predictions. Good agreement is observed
between the measured cross-sections and the predictions obtained using POWHEG +
Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet
cross-section. However, it does not reproduce the measured inclusive
cross-section well, particularly for central b-jets with large transverse
momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final
version published in European Physical Journal
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