4,818 research outputs found
ATLAS Fast Physics Monitoring: TADA
No full textThe ATLAS Experiment at the LHC is recording data from proton-proton collisions with 13 TeV center-of-mass energy since spring 2015. The collaboration is using a fast physics monitoring framework (TADA) to automatically perform a broad range of fast searches for early signs of new physics and to monitor the data quality across the year with the full analysis level calibrations applied to the rapidly growing data. TADA is designed to provide fast feedback directly after the collected data has been fully calibrated and processed at the Tier-0. The system can monitor a large range of physics channels, offline data quality and physics performance quantities nearly final analysis level object calibrations. TADA output is available on a website accessible by the whole collaboration that gets updated twice a day with the data from newly processed runs. Hints of potentially interesting physics signals or performance issues identified in this way are reported to be followed up by physics or combined performance groups. The poster reports as well about the technical aspects of TADA: the software structure to obtain the input TAG files, the framework workflow and structure, the webpage and its implementation
TADA incorporation in the Rv0950 deletion mutant.
No full textTADA incorporation was compared in M. tuberculosis wild type (WT, black), ΔRv0950c (red) and ΔRv0950c::Rv0950c (grey). A) Schematic diagram showing the mechanism of TADA incorporation reporting on polar growth (red) and side wall metabolism (turquoise), D-Ala: D-Alanine, NAG: N-acetylglucosamine, NAM: N-acetylmuramic acid. B) Representative fluorescence micrographs of stained cells. Scale bar = 5 μm. C) Fluorescence intensity profiles of M. tuberculosis labelled with TADA. 0% represents the brightest pole. Graph shows average of fluorescence intensity measured at 10% intervals of the cell length. ****p = 0.0008 and 4.09E-6 for mutant compared to wild type or complement respectively across the cell length. *p = 0.03 for wild type compared to complement. D) Average fluorescence intensity for each cell. **p = 0.0029 and 0.0049 comparing mutant to wild type and complement respectively. p values obtained by single factor ANOVA in Excel for three biological replicates. E) Average distribution of fluorescence between the bright pole (sum of fluorescence across the first 15% of the cell length), the side wall (sum of fluorescence between 16–84% of the cell length) and dim pole (sum of fluorescence from 85–100% of the cell length).</p
PCR diagnosis for Neospora caninum infection in aborted bovine fetuses and for Toxoplasma gondii infection in hares and goats in Italy
No full textFunctional divergence of HBHA from Mycobacterium tuberculosis and its evolutionary relationship with TadA from Rhodococcus opacus
No full textRhodococcus opacus PD630 and Rhodococcus jostii RHA1 are oleaginous bacteria able to synthesize and accumulate triacylglycerols (TAG) in lipid bodies (LB). Highly relevant to the structure of LB is a protein homologous to heparin-binding hemagglutinin (HBHA) (called TadA in rhodococci), which is a virulence factor found in Mycobacterium tuberculosis. HBHA is an adhesin involved in binding to non-phagocytic cells and extrapulmonary dissemination. We observed a conserved synteny of three genes encoding a transcriptional regulator (TR), the HBHA protein and a membrane protein (MP) between TAG-accumulating actinobacteria belonging to Rhodococcus, Mycobacterium, Nocardia and Dietzia genera, among others. A 354 bp-intergenic spacing containing a SigF-binding site was found between hbha and the TR genes in M. tuberculosis, which was absent in genomes of other investigated actinobacteria. Analyses of available “omic” information revealed that TadA and TR were co-induced in rhodococci under TAG-accumulating conditions; whereas in M. tuberculosis and Mycobacterium smegmatis, HBHA and TR were regulated independently under stress conditions occurring during infection. We also found differences in protein lengths, domain content and distribution between HBHA and TadA proteins from mycobacteria and rhodococci, which may explain their different roles in cells. Based on the combination of results obtained in model actinobacteria, we hypothesize that HBHA and TadA proteins originated from a common ancestor, but later suffered a process of functional divergence during evolution. Thus, rhodococcal TadA probably has maintained its original role; whereas HBHA may have evolved as a virulence factor in pathogenic mycobacteria.Fil: Lanfranconi, Mariana Patricia. Universidad Nacional de la Patagonia ; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Alvarez, Hector Manuel. Universidad Nacional de la Patagonia ; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin
<em>Tada</em>, <em>kada</em>, <em>šiada</em>, <em>andai</em>, <em>idant</em>
No full textLITH. TADA, KADA, ŠIADA, ANDAI, IDANTSummaryThe author discusses the origin of the Lithuanian forms tada, kada, šiada; kadai, kadaise kadan, kadangi; andai; idant etc. and concludes the following:The Lithuanian compounds of this type are related to the corresponding Slavic and Indo-Iranian compounds. The element -d- in the Lithuanian compounds belongs to the stems of the demonstrative pronoun *do/*de (OP din, dīgi) as the same element in OInd. tadā́, kadā́, yadā́. The element -g- in the Slavic and Baltic compounds (OCS togda, Russ. тогда, OPol. tegdy, Czech, tehda etc., Lith. tagačiaus, tagatės, Latv. tagad) could be reconstructed from the particle *go (i. e. the one related to Slavic же, OInd. gh, ha, Gk. γε, γα, Goth, -k in mi-k "me")
{TADA}: {T}axonomy Adaptive Domain Adaptation
No full textTraditional domain adaptation addresses the task of adapting a model to a novel target domain under limited or no additional supervision. While tackling the input domain gap, the standard domain adaptation settings assume no domain change in the output space. In semantic prediction tasks, different datasets are often labeled according to different semantic taxonomies. In many real-world settings, the target domain task requires a different taxonomy than the one imposed by the source domain. We therefore introduce the more general taxonomy adaptive domain adaptation (TADA) problem, allowing for inconsistent taxonomies between the two domains. We further propose an approach that jointly addresses the image-level and label-level domain adaptation. On the label-level, we employ a bilateral mixed sampling strategy to augment the target domain, and a relabelling method to unify and align the label spaces. We address the image-level domain gap by proposing an uncertainty-rectified contrastive learning method, leading to more domain-invariant and class discriminative features. We extensively evaluate the effectiveness of our framework under different TADA settings: open taxonomy, coarse-to-fine taxonomy, and partially-overlapping taxonomy. Our framework outperforms previous state-of-the-art by a large margin, while capable of adapting to target taxonomies
The <i>Rhodococcus opacus</i> PD630 Heparin-Binding Hemagglutinin Homolog TadA Mediates Lipid Body Formation
No full textABSTRACT
Generally, prokaryotes store carbon as polyhydroxyalkanoate, starch, or glycogen. The Gram-positive actinomycete
Rhodococcus opacus
strain PD630 is noteworthy in that it stores carbon in the form of triacylglycerol (TAG). Several studies have demonstrated that
R. opacus
PD630 can accumulate up to 76% of its cell dry weight as TAG when grown under nitrogen-limiting conditions. While this process is well studied, the underlying molecular and biochemical mechanisms leading to TAG biosynthesis and subsequent storage are poorly understood. We designed a high-throughput genetic screening to identify genes and their products required for TAG biosynthesis and storage in
R. opacus
PD630. We identified a gene predicted to encode a putative heparin-binding hemagglutinin homolog, which we have termed
tadA
(
t
riacylglycerol
a
ccumulation
d
eficient), as being important for TAG accumulation. Kinetic studies of TAG accumulation in both the wild-type (WT) and mutant strains demonstrated that the
tadA
mutant accumulates 30 to 40% less TAG than the parental strain (WT). We observed that lipid bodies formed by the mutant strain were of a different size and shape than those of the WT. Characterization of TadA demonstrated that the protein is capable of binding heparin and of agglutinating purified lipid bodies. Finally, we observed that the TadA protein localizes to lipid bodies in
R. opacus
PD630 both
in vivo
and
in vitro
. Based on these data, we hypothesize that the TadA protein acts to aggregate small lipid bodies, found in cells during early stages of lipid storage, into larger lipid bodies and thus plays a key role in lipid body maturation in
R. opacus
PD630.
</jats:p
Improved cytosine base editors generated from TadA variants
No full textCytosine base editors (CBEs) enable programmable genomic C·G-to-T·A transition mutations and typically comprise a modified CRISPR–Cas enzyme, a naturally occurring cytidine deaminase, and an inhibitor of uracil repair. Previous studies have shown that CBEs utilizing naturally occurring cytidine deaminases may cause unguided, genome-wide cytosine deamination. While improved CBEs that decrease stochastic genome-wide off-targets have subsequently been reported, these editors can suffer from suboptimal on-target performance. Here, we report the generation and characterization of CBEs that use engineered variants of TadA (CBE-T) that enable high on-target C·G to T·A across a sequence-diverse set of genomic loci, demonstrate robust activity in primary cells and cause no detectable elevation in genome-wide mutation. Additionally, we report cytosine and adenine base editors (CABEs) catalyzing both A-to-I and C-to-U editing (CABE-Ts). Together with ABEs, CBE-Ts and CABE-Ts enable the programmable installation of all transition mutations using laboratory-evolved TadA variants with improved properties relative to previously reported CBEs
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