3,007 research outputs found
Hypoxia activates IKK-NF-κB and the immune response in <em>Drosophila melanogaster</em>
No full textHypoxia, or low oxygen availability, is an important physiological and pathological stimulus for multicellular organisms. Molecularly, hypoxia activates a transcriptional programme directed at restoration of oxygen homoeostasis and cellular survival. In mammalian cells, hypoxia not only activates the HIF (hypoxia-inducible factor) family, but also additional transcription factors such as NF-?B (nuclear factor ?B). Here we show that hypoxia activates the IKK–NF-?B [I?B (inhibitor of nuclear factor ?B)–NF-?B] pathway and the immune response in Drosophila melanogaster. We show that NF-?B activation is required for organism survival in hypoxia. Finally, we identify a role for the tumour suppressor Cyld, as a negative regulator of NF-?B in response to hypoxia in Drosophila. The results indicate that hypoxia activation of the IKK–NF-?B pathway and the immune response is an important and evolutionary conserved response.</p
nf-core/rnafusion: 2.0.0 update
No full textThe usage of the pipeline has been updated. It is recommended to reads the usage.md document.
Added
Added qualimap/rnaseq v2.2.2d from nf-core modules
Added UCSC gtfToGenePred v377
Added picard CollectRnaSeqMetrics v2.26.10
Added picard MarkDuplicates v2.26.10 from nf-core modules
Added cat/fastqc from nf-core modules
Added possibility for manually feeding the results of fusions from different tools to speed-up reruns
STAR-Fusion references can be downloaded or built but downloaded references are NOT RECOMMENDED as not thoroughly tested (--starfusion_build parameter is true by default, use --starfusion_build false to use downloaded STAR-Fusion references).
Changed
Upgrade default ensembl version to 102
Upgrade to nf-core/tools v2.3.2
Upgrade Arriba v1.2.0 to Arriba v2.2.1
Upgrade FusionCatcher v1.20 to FusionCatcher v1.33
Upgrade STAR-fusion v1.8.1 to STAR-fusion v1.10.1
Upgrade STAR v2.7.1 to STAR v2.7.9
Upgrade fusion-report v2.1.3 to fusion-report v2.1.5
Upgrade kallisto v0.44.0 to kallisto v0.46.2
Upgrade fastqc v0.11.8 to fastqc v0.11.9
Upgrade samtools v1.9 to samtools v1.15.1
Upgrade arriba references from v1.2.0 to v2.1.0
Upgrade fusioncatcher references from v98 to v102
Use arriba (detect only), kallisto and STAR from nf-core modules
Instead of separate script to build the references, added --build_references argument in the main --fasta argument is not required with --build_references and set by default to the ensembl references built in the detection workflow
Removed
Ericscript tool
GRCh37 support. Subdirectory with params.genome are removed
Running with cond
nf-core/rnafusion: 3.0.2
No full text<p>Bug fixes.</p>
<h3>Changelog:</h3>
<p><strong>Changed</strong></p>
<ul>
<li>Update to nf-tools 2.11.1 [https://github.com/nf-core/rnafusion/pull/457] (#457)</li>
<li>Update picard collectrnaseqmetrics memory requirements to 0.8x what is provided https://github.com/nf-core/rnafusion/pull/474</li>
</ul>
<p><strong>Fixed</strong></p>
<ul>
<li>fix bug when using parameter "whitelist" https://github.com/nf-core/rnafusion/pull/466</li>
<li>fix VCF_COLLECT handling when a tool is absent from FUSIONREPORT report https://github.com/nf-core/rnafusion/pull/458</li>
<li>fix VCF_COLLECT when fusioninspector output is empty but fusionreport is not https://github.com/nf-core/rnafusion/pull/465</li>
<li>fix VCF_COLLECT bug https://github.com/nf-core/rnafusion/pull/481</li>
<li>fix conda package for starfusion/detecthttps://github.com/nf-core/rnafusion/pull/482</li>
<li>fix logical gate so when stringtie should run but not starfusion, starfusion will not runhttps://github.com/nf-core/rnafusion/pull/482</li>
</ul>
NF-κB translocation assay ImageJ macro
No full textThis is ImageJ macro used to determine the degree of NF-κB translocation in cells stained for NF-κB and nuclear signal. It is a part of publication entitled "Plasma extracellular vesicles signal spleen fibroblasts facilitating Plasmodium vivax adherence". Please see the publication for full author details.</p
nf-core/rnafusion: 2.2.0
No full text<p>Version 2.0.0 includes <code>stringtie</code> in <code>--all</code>, a <code>fastp</code> trimming option, fixed for <code>arriba</code> references among other (see details below).</p>
<p><strong>Important: the references need to be rebuilt. </strong></p>
<p>Check <code>usage.md</code> for how to use the new options.</p>
<p>Detailed CHANGELOG:</p>
Added
<ul>
<li>exitStatus 140 now part of the retry strategy</li>
<li>stubs to all local modules</li>
<li><code>--stringtie</code> option added with StringTie v2.2.1 to detect splicing events. Not included in <code>fusion-report</code> or <code>fusionInspector</code> summaries. Included in the <code>--all</code> workflow</li>
<li>Generation of ribosomal RNA interval list with build_references and use it in picard CollectRnaMetrics</li>
<li>Add csv output to fusionreport</li>
<li>Trimming workflow using <code>fastp</code>: use trimmed reads for all tools</li>
<li><code>whitelist</code> parameter to add custom fusions to the detected ones and consider the whole for the <code>fusionInspector</code> analysis</li>
<li>Compression to CRAM files for arriba, squid and starfusion workflows (fusioncatcher and pizzly do not produce SAM/BAM files, fusioninspector BAM files are too small to benefit from compression)</li>
<li><code>--qiagen</code> option to download from QIAGEN instead of COSMIC (use QIAGEN user and password for <code>cosmic_username</code> and <code>cosmic_passwd</code>)</li>
<li>Bumped <code>STAR genomegenerate</code> time request for building as it was always crashing for most users</li>
<li>Fixed issue with arriba visualisation parameters <a href="https://github.com/nf-core/rnafusion/issues/326">#326</a></li>
</ul>
Changed
<ul>
<li>Test profiles unified under 'test' but if the references do not all need to be downloaded, run with <code>-stub</code></li>
<li>Update CUSTOM_DUMPSOFTWAREVERSIONS to use multiqc version 1.13</li>
<li>Updated to nf-core template 2.7.2, with all module updates</li>
<li><code>MultiQC</code> updated to 1.13a in process dumpsoftwareversion</li>
<li>Patch fusion-report version with fixed mittelman DB and DB extraction date written into software_version.yaml</li>
<li><code>Arriba</code> references back to downloading with <code>build_references</code> instead of taking from container</li>
<li><code>Arriba</code> visualisation now running with <code>Arriba</code> v2.3.0</li>
<li>Updated <code>STAR-Fusion</code> to 1.12.0</li>
</ul>
Fixed
<ul>
<li>AWS megatest to display on nf-core website</li>
<li><code>arriba</code> visualisation references updated to 2.3.0</li>
<li>Removed issue with multiple outputs in samtools view for squid</li>
</ul>
Removed
<ul>
<li>FUSIONINSPECTOR_DEV process as the option fusioninspector_limitSjdbInsertNsj is part of the main starfusion release</li>
</ul>
Deletion of vitamin D receptor leads to premature emphysema/COPD by increased matrix metalloproteinases and lymphoid aggregates formation
No full textDeficiency of vitamin D is associated with accelerated decline in lung function. Vitamin D is a ligand for nuclear hormone vitamin D receptor (VDR), and upon binding it modulates various cellular functions. The level of VDR is reduced in lungs of patients with chronic obstructive pulmonary disease (COPD) which led us to hypothesize that deficiency of VDR leads to significant alterations in lung phenotype that are characteristics of COPD/emphysema associated with increased inflammatory response. We found that VDR knock-out (VDR(-/-)) mice had increased influx of inflammatory cells, phospho-acetylation of nuclear factor-kappaB (NF-κB) associated with increased proinflammatory mediators, and up-regulation of matrix metalloproteinases (MMPs) MMP-2, MMP-9, and MMP-12 in the lung. This was associated with emphysema and decline in lung function associated with lymphoid aggregates formation compared to WT mice. These findings suggest that deficiency of VDR in mouse lung can lead to an early onset of emphysema/COPD because of chronic inflammation, immune dysregulation, and lung destruction
Current concepts on oxidative/carbonyl stress, inflammation and epigenetics in pathogenesis of chronic obstructive pulmonary disease
No full textChronic obstructive pulmonary disease (COPD) is a global health problem. The current therapies for COPD are poorly effective and the mainstays of pharmacotherapy are bronchodilators. A better understanding of the pathobiology of COPD is critical for the development of novel therapies. In the present review, we have discussed the roles of oxidative/aldehyde stress, inflammation/immunity, and chromatin remodeling in the pathogenesis of COPD. An imbalance of oxidants/antioxidants caused by cigarette smoke and other pollutants/biomass fuels plays an important role in the pathogenesis of COPD by regulating redox-sensitive transcription factors (e.g., NF-κB), autophagy and unfolded protein response leading to chronic lung inflammatory response. Cigarette smoke also activates canonical/alternative NF-κB pathways and their upstream kinases leading to sustained inflammatory response in lungs. Recently, epigenetic regulation has been shown to be critical for the development of COPD because the expression/activity of enzymes that regulate these epigenetic modifications have been reported to be abnormal in airways of COPD patients. Hence, the significant advances made in understanding the pathophysiology of COPD as described herein will identify novel therapeutic targets for intervention in COPD
nf-core/rnafusion: 2.1.0 - 2022/07/12
No full text<p><strong>IMPORTANT</strong>
Since STAR has been updated, a new STAR index needs to be built as reference.
<code>nextflow run nf-core/rnafusion --genomes_base /PATH/TO/REFERENCES --starindex --build_references --outdir OUTDIR -profile singularity or docker</code></p>
Added
<ul>
<li><code>FusionCatcher</code> single_end support for single reads ABOVE 130 bp</li>
<li><code>--fusioninspector_only</code> parameter to run FusionInspector standalone feeding gene list manually with parameter <code>--fusioninspector_fusions PATH</code></li>
<li><code>--fusioncatcher_limitSjdbInsertNsj</code> parameter to feed --limitSjdbInsertNsj to FusionCatcher</li>
<li><code>--fusioninspector_limitSjdbInsertNsj</code> parameter to feed --limitSjdbInsertNsj to FusionInspector !!Any other value than default will use the dev version of FusionInspector!!</li>
<li>OPTIONAL trimming option <code>--trim</code> for hard trimming to 75 bp in case of high read-through. Only fusioncatcher uses trimmed reads as STAR-based fusion detection tools are less sensitive to read-through</li>
<li><code>picard</code> metrics, STAR final log, and QualiMap output included in <code>MultiQC</code> report</li>
</ul>
Changed
<ul>
<li><code>seq_platform</code> and <code>seq_center</code> changed from boolean to string</li>
<li><code>seq_platform</code> set to an empty string and <code>seq_center</code> set to an empty string if not existing</li>
<li>Arriba use ensembl references-built starindex independently of <code>starfusion_build</code> parameter</li>
<li>ftp to http protocol for STARFUSION_BUILD process <code>Pfam-A.hmm.gz</code> download as ftp causes issues on some servers</li>
<li>Updated README and usage documentation with more detailed information and metro map</li>
<li>Arriba use ensembl references-built starindex independently of starfusion_build parameter</li>
<li>Update of the single-end reads support table in README, added recommendation to use single-end reads only in last resort</li>
<li>STAR updated to 2.7.10a</li>
<li>Arriba updated to 2.3.0, references for blacklist and protein domains changed to 2.3.0 from singularity/docker container -> arriba download of references not necessary any more</li>
<li>multiQC updated to 1.13a</li>
<li>picard updated to 2.27.4</li>
<li>dumpsoftwareversions module updated to use multiqc=1.12 containers</li>
</ul>
Fixed
<ul>
<li>FusionInspector does not mix sample reads with fusion lists and meta information from other samples anymore</li>
<li>Arriba visualisation does not mix sample reads with fusion lists and meta information from other samples anymore</li>
<li>logging of STAR-fusion and fusionreport version</li>
</ul>
nf-core/rnafusion: 2.3.0
No full textAdded
Shell specification to bash
COSMIC password put into quotes
Trimmed reads QC in MultiQC
Add ARRIBA_VISUALISATION to processed affected by --skip_vis
Option fusionreport_filter to in/activate fusionreport displaying of fusions detected by 2 or more tools
Changed
Arriba visualisation now runs for FusionInspector (combined tools) results, not only Arriba results
Updated metro map with trimming options and placed Arriba visualisation after FusionInspector
Exit with error when using squid in combination with any ensembl version different from 102
Fixed
Channel issue with indexing of files with using --cram squid
Arriba references published in the correct folde
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