205 research outputs found
BamView: viewing mapped read alignment data in the context of the reference sequence
Summary: BamView is an interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence. It supports the BAM (Binary Alignment/Map) format. It can be used in a number of contexts including SNP calling and structural annotation. BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features
Meeting report: a workshop on Best Practices in Genome Annotation
Efforts to annotate the genomes of a wide variety of model organisms are currently carried out by sequencing centers, model organism databases and academic/institutional laboratories around the world. Different annotation methods and tools have been developed over time to meet the needs of biologists faced with the task of annotating biological data. While standardized methods are essential for consistent curation within each annotation group, methods and tools can differ between groups, especially when the groups are curating different organisms. Biocurators from several institutes met at the Third International Biocuration Conference in Berlin, Germany, April 2009 and hosted the ‘Best Practices in Genome Annotation: Inference from Evidence’ workshop to share their strategies, pipelines, standards and tools. This article documents the material presented in the workshop
Forward pi^0 Production and Associated Transverse Energy Flow in Deep-Inelastic Scattering at HERA
Deep-inelastic positron-proton interactions at low values of Bjorken-x down
to x \approx 4.10^-5 which give rise to high transverse momentum pi^0 mesons
are studied with the H1 experiment at HERA. The inclusive cross section for
pi^0 mesons produced at small angles with respect to the proton remnant (the
forward region) is presented as a function of the transverse momentum and
energy of the pi^0 and of the four-momentum transfer Q^2 and Bjorken-x.
Measurements are also presented of the transverse energy flow in events
containing a forward pi^0 meson. Hadronic final state calculations based on QCD
models implementing different parton evolution schemes are confronted with the
data.Comment: 27 pages, 8 figures and 3 table
Circadian Rhythms of Fetal Liver Transcription Persist in the Absence of Canonical Circadian Clock Gene Expression Rhythms In Vivo
The cellular circadian clock and systemic cues drive rhythmicity in the transcriptome of adult peripheral tissues. However, the oscillating status of the circadian clocks in fetal tissues, and their response to maternal cues, are less clear. Most clock genes do not cycle in fetal livers from mice and rats, although tissue level rhythms rapidly emerge when fetal mouse liver explants are cultured in vitro. Thus, in the fetal mouse liver, the circadian clock does not oscillate at the cellular level (but is induced to oscillate in culture). To gain a comprehensive overview of the clock status in the fetal liver during late gestation, we performed microarray analyses on fetal liver tissues. In the fetal liver we did not observe circadian rhythms of clock gene expression or many other transcripts known to be rhythmically expressed in the adult liver. Nevertheless, JTK_CYCLE analysis identified some transcripts in the fetal liver that were rhythmically expressed, albeit at low amplitudes. Upon data filtering by coefficient of variation, the expression levels for transcripts related to pancreatic exocrine enzymes and zymogen secretion were found to undergo synchronized daily fluctuations at high amplitudes. These results suggest that maternal cues influence the fetal liver, despite the fact that we did not detect circadian rhythms of canonical clock gene expression in the fetal liver. These results raise important questions on the role of the circadian clock, or lack thereof, during ontogeny
Brucella abortus Uses a Stealthy Strategy to Avoid Activation of the Innate Immune System during the Onset of Infection
To unravel the strategy by which Brucella abortus establishes chronic infections, we explored its early interaction with innate immunity.
Methodology/Principal Findings
Brucella did not induce proinflammatory responses as demonstrated by the absence of leukocyte recruitment, humoral or cellular blood changes in mice. Brucella hampered neutrophil (PMN) function and PMN depletion did not influence the course of infection. Brucella barely induced proinflammatory cytokines and consumed complement, and was strongly resistant to bactericidal peptides, PMN extracts and serum. Brucella LPS (BrLPS), NH-polysaccharides, cyclic glucans, outer membrane fragments or disrupted bacterial cells displayed low biological activity in mice and cells. The lack of proinflammatory responses was not due to conspicuous inhibitory mechanisms mediated by the invading Brucella or its products. When activated 24 h post-infection macrophages did not kill Brucella, indicating that the replication niche was not fusiogenic with lysosomes. Brucella intracellular replication did not interrupt the cell cycle or caused cytotoxicity in WT, TLR4 and TLR2 knockout cells. TNF-α-induction was TLR4- and TLR2-dependent for live but not for killed B. abortus. However, intracellular replication in TLR4, TLR2 and TLR4/2 knockout cells was not altered and the infection course and anti-Brucella immunity development upon BrLPS injection was unaffected in TLR4 mutant mice.
Conclusion/Significance
We propose that Brucella has developed a stealth strategy through PAMPs reduction, modification and hiding, ensuring by this manner low stimulatory activity and toxicity for cells. This strategy allows Brucella to reach its replication niche before activation of antimicrobial mechanisms by adaptive immunity. This model is consistent with clinical profiles observed in humans and natural hosts at the onset of infection and could be valid for those intracellular pathogens phylogenetically related to Brucella that also cause long lasting infections
Inelastic photoproduction of J/Psi mesons at HERA
An analysis of inelastic photoproduction of J/Psi mesons is presented using data collected at the ep collider HERA corresponding to an integrated luminosity of above 80pb-1. Differential and double differential cross sections are measured in a wide kinematic region: 6
Inelastic Photoproduction of J/Psi Mesons at HERA
An analysis of inelastic photoproduction of J/Psi mesons is presented using
data collected at the ep collider HERA corresponding to an integrated
luminosity of above 80pb-1. Differential and double differential cross sections
are measured in a wide kinematic region: 60<W_gammap<260 GeV, 1<p_t^2< 60 GeV^2
and 0.05<z<0.9, where z is the fraction of the energy of the exchanged photon
transferred to the J/Psi meson in the rest frame of the target proton. Cross
sections at z<0.3 are presented for the first time. Theoretical calculations
within the Colour Singlet Model at NLO for direct photon processes are shown to
give a good description of the data in the medium z region (0.3<z<0.9) up to
the highest p_t^2 values. A calculation using a k_t factorisation approach in
LO in the Colour Singlet Model is also able to describe these data. The data in
the full z range are also compared to LO calculations within a non-relativistic
QCD framework including color octet and colour singlet contributions for direct
and resolved photons. It seems possible to reconcile data and theory with
modest contributions from colour octet processes. The polarisation of the J/Psi
meson is measured as a function of z and p_t,psi and is reasonably described by
the theoretical predictions.Comment: 30 pages, 11 figures, 11 table
Fructan and its relationship to abiotic stress tolerance in plants
Numerous studies have been published that attempted to correlate fructan concentrations with freezing and drought tolerance. Studies investigating the effect of fructan on liposomes indicated that a direct interaction between membranes and fructan was possible. This new area of research began to move fructan and its association with stress beyond mere correlation by confirming that fructan has the capacity to stabilize membranes during drying by inserting at least part of the polysaccharide into the lipid headgroup region of the membrane. This helps prevent leakage when water is removed from the system either during freezing or drought. When plants were transformed with the ability to synthesize fructan, a concomitant increase in drought and/or freezing tolerance was confirmed. These experiments indicate that besides an indirect effect of supplying tissues with hexose sugars, fructan has a direct protective effect that can be demonstrated by both model systems and genetic transformation
Antibody–Drug Conjugates for Tumor Targeting—Novel Conjugation Chemistries and the Promise of non-IgG Binding Proteins
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