158 research outputs found
Transient band structures in the ultrafast demagnetization of ferromagnetic gadolinium and terbium
We compare the laser-driven demagnetization dynamics of the rare earths
gadolinium and terbium by mapping their transient valance band structures with
time- and angle-resolved photoelectron spectroscopy. In both metals, the
minority and majority spin valence bands evolve independently with different
time constants after optical excitation. The ultrafast shift of the partially
unoccupied minority spin bulk band to higher binding energy and of the
majority spin surface state to lower binding energy suggests spin transport
between surface and bulk. The slower response of the fully occupied majority
spin band follows the lattice temperature and is attributed to Elliott-Yafet
type spin-flip scattering. Terbium shows a stronger and faster decay of the
exchange splitting, pointing to ultrafast magnon emission via 4f spin-to-
lattice coupling
Fluence-dependent dynamics of the 5d6s exchange splitting in Gd metal after femtosecond laser excitation
We investigate the fluence-dependent dynamics of the exchange-split 5d6s
valence bands of Gd metal after femtosecond, near-infrared (IR) laser
excitation. Time- and angle-resolved photoelectron spectroscopy (tr-ARPES)
with extreme ultraviolet (XUV) probe pulses is used to simultaneously map the
transient binding energies of the minority and majority spin valence bands.
The decay constant of the exchange splitting increases with fluence. This
reflects the slower response of the occupied majority-spin component, which we
attribute to Elliot–Yafet spin-flip scattering in accordance with the
microscopic three-temperature model (M3TM). In contrast, the time constant of
the partly unoccupied minority-spin band stays unaffected by a change in pump
fluence. Here, we introduce as an alternative to superdiffusive spin transport
exchange scattering, which is an ultrafast electronic mechanism explaining the
observed dynamics. Exchange scattering can reduce the spin polarization in the
partially unoccupied minority-spin band and thus its energetic position
without effective demagnetization
The Valence Band Structure of Gadolinium Studied with Time-Resolved Photoemission
We have studied the response of the exchange split valence bands of
ferromagnetic gadolinium tofemtosecond laser excitation. We observe a drop of
the exchange splitting with a time constant of 0.9 ps but different response
times of minority and majority spin bands. Furthermore, even above the Curie
temperature there is a finite exchange splitting, which also decreases with
laser excitation
CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data
Cell-cell communication is essential for tissue development, regeneration and
function, and its disruption can lead to diseases and developmental
abnormalities. The revolution of single-cell genomics technologies offers
unprecedented insights into cellular identities, opening new avenues to resolve
the intricate cellular interactions present in tissue niches. CellPhoneDB is a
bioinformatics toolkit designed to infer cell-cell communication by combining a
curated repository of bona fide ligand-receptor interactions with a set of
computational and statistical methods to integrate them with single-cell
genomics data. Importantly, CellPhoneDB captures the multimeric nature of
molecular complexes, thus representing cell-cell communication biology
faithfully. Here we present CellPhoneDB v5, an updated version of the tool,
which offers several new features. Firstly, the repository has been expanded by
one-third with the addition of new interactions. These encompass interactions
mediated by non-protein ligands such as endocrine hormones and GPCR ligands.
Secondly, it includes a differentially expression-based methodology for more
tailored interaction queries. Thirdly, it incorporates novel computational
methods to prioritise specific cell-cell interactions, leveraging other
single-cell modalities, such as spatial information or TF activities (i.e.
CellSign module). Finally, we provide CellPhoneDBViz, a module to interactively
visualise and share results amongst users. Altogether, CellPhoneDB v5 elevates
the precision of cell-cell communication inference, ushering in new
perspectives to comprehend tissue biology in both healthy and pathological
states.Comment: 30 pages, 3 figures and 2 tables. Added previously missing figures
and tables; Updated the reference for 'An integrated single-cell reference
atlas of the human endometrium' pape
Recommended from our members
Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.
Human gut development requires the orchestrated interaction of differentiating cell types. Here, we generate an in-depth single-cell map of the developing human intestine at 6-10 weeks post-conception. Our analysis reveals the transcriptional profile of cycling epithelial precursor cells; distinct from LGR5-expressing cells. We propose that these cells may contribute to differentiated cell subsets via the generation of LGR5-expressing stem cells and receive signals from surrounding mesenchymal cells. Furthermore, we draw parallels between the transcriptomes of ex vivo tissues and in vitro fetal organoids, revealing the maturation of organoid cultures in a dish. Lastly, we compare scRNA-seq profiles from pediatric Crohn's disease epithelium alongside matched healthy controls to reveal disease-associated changes in the epithelial composition. Contrasting these with the fetal profiles reveals the re-activation of fetal transcription factors in Crohn's disease. Our study provides a resource available at www.gutcellatlas.org, and underscores the importance of unraveling fetal development in understanding disease
Effects on prostate cancer cells of targeting RNA polymerase III
RNA polymerase (pol) III occurs in two forms, containing either the POLR3G subunit or the related paralogue POLR3GL. Whereas POLR3GL is ubiquitous, POLR3G is enriched in undifferentiated cells. Depletion of POLR3G selectively triggers proliferative arrest and differentiation of prostate cancer cells, responses not elicited when POLR3GL is depleted. A small molecule pol III inhibitor can cause POLR3G depletion, induce similar differentiation and suppress proliferation and viability of cancer cells. This response involves control of the fate-determining factor NANOG by small RNAs derived from Alu short interspersed nuclear elements. Tumour initiating activity in vivo can be reduced by transient exposure to the pol III inhibitor. Untransformed prostate cells appear less sensitive than cancer cells to pol III depletion or inhibition, raising the possibility of a therapeutic window
Use of viability PCR for detection of live Chlamydia trachomatis in clinical specimens
BackgroundThe current testing approach to diagnose Chlamydia trachomatis (CT) infection relies on nucleic acid amplification tests (NAATs). These tests are highly sensitive, but do not distinguish between active infection and residual bacterial nucleic acid which may remain after resolution of infection, or via cross-contamination. Better methods to assess the viability of CT detected in clinical samples would be useful in determining the relevance of CT detection in a variety of clinical settings. The goal of this study was to test viability PCR (vPCR) as a method to distinguish viable bacteria from non-viable CT.MethodsThe vPCR relies on a propidium monoazide dye (PMAxx), which intercalates into accessible DNA from dead organisms and prevents their detection in a PCR assay for the CT ompA gene. We used digital PCR to quantify absolute genome copy numbers from samples. We validated the vPCR approach using laboratory stocks of CT with known viability. Then, we tested total DNA, viable CT DNA, and culture results from 18 clinical vaginal specimens and 25 rectal clinical specimens, all of which had tested positive by NAAT.ResultsIn laboratory stocks of CT, vPCR using defined ratios of heat-killed to live bacteria tracked closely with expected results. In vaginal clinical specimens, vPCR and total DNA results were correlated, though total DNA genomes outnumbered viable genomes by 2.2–52.6-fold more copies. As expected, vPCR detected more total genomes than culture results. Both vPCR and total DNA correlated with culture results (Spearman correlation R = 0.8425 for total DNA and 0.8056 for vPCR). Ten rectal NAAT positive specimens were negative by total DNA PCR, vPCR, and were negative or inconclusive by culture. Of the 6 rectal specimens that were culture positive, all were total DNA and vPCR positive. vPCR additionally detected viable bacterial DNA in 8 specimens which were NAAT + and culture negative, though levels were very low (mean 1,357 copies/ml)ConclusionsvPCR is a fast and easy method to assess viability in clinical specimens and is more correlated with culture results than total DNA PCR. Inconsistent ratios between total DNA and vPCR results suggest that the amount of dead bacteria varies considerably in clinical specimens. Results from rectal specimens suggest that many NAAT positive specimens do not in fact represent live replicating bacteria, and likely result in significant overuse of unnecessary antibiotics
Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung
Cellular diversity of the lung endothelium has not been systematically characterized in humans. We provide a reference atlas of human lung endothelial cells (ECs) to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium. METHODS: We reprocessed human control single-cell RNA sequencing (scRNAseq) data from 6 datasets. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by fluorescent microscopy and in situ hybridization. scRNAseq of primary lung ECs cultured in vitro was performed. The signaling network between different lung cell types was studied. For cross-species analysis or disease relevance, we applied the same methods to scRNAseq data obtained from mouse lungs or from human lungs with pulmonary hypertension. RESULTS: Six lung scRNAseq datasets were reanalyzed and annotated to identify >15 000 vascular EC cells from 73 individuals. Differential expression analysis of EC revealed signatures corresponding to endothelial lineage, including panendothelial, panvascular, and subpopulation-specific marker gene sets. Beyond the broad cellular categories of lymphatic, capillary, arterial, and venous ECs, we found previously indistinguishable subpopulations; among venous EC, we identified 2 previously indistinguishable populations: pulmonary–venous ECs (COL15A1(neg)) localized to the lung parenchyma and systemic–venous ECs (COL15A1(pos)) localized to the airways and the visceral pleura; among capillary ECs, we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1, and TBX2 and general capillary EC. We confirmed that all 6 endothelial cell types, including the systemic–venous ECs and aerocytes, are present in mice and identified endothelial marker genes conserved in humans and mice. Ligand-receptor connectome analysis revealed important homeostatic crosstalk of EC with other lung resident cell types. scRNAseq of commercially available primary lung ECs demonstrated a loss of their native lung phenotype in culture. scRNAseq revealed that endothelial diversity is maintained in pulmonary hypertension. Our article is accompanied by an online data mining tool (www.LungEndothelialCellAtlas.com). CONCLUSIONS: Our integrated analysis provides a comprehensive and well-crafted reference atlas of ECs in the normal lung and confirms and describes in detail previously unrecognized endothelial populations across a large number of humans and mice
Recommended from our members
Real-time spatial characterization of micrometer-sized X-ray free-electron laser beams focused by bendable mirrors
A real-time and accurate characterization of the X-ray beam size is essential to enable a large variety of different experiments at free-electron laser facilities. Typically, ablative imprints are employed to determine shape and size of μm-focused X-ray beams. The high accuracy of this state-of-the-art method comes at the expense of the time required to perform an ex-situ image analysis. In contrast, diffraction at a curved grating with suitably varying period and orientation forms a magnified image of the X-ray beam, which can be recorded by a 2D pixelated detector providing beam size and pointing jitter in real time. In this manuscript, we compare results obtained with both techniques, address their advantages and limitations, and demonstrate their excellent agreement. We present an extensive characterization of the FEL beam focused to ≈1 μm by two Kirkpatrick-Baez (KB) mirrors, along with optical metrology slope profiles demonstrating their exceptionally high quality. This work provides a systematic and comprehensive study of the accuracy provided by curved gratings in real-time imaging of X-ray beams at a free-electron laser facility. It is applied here to soft X-rays and can be extended to the hard X-ray range. Furthermore, curved gratings, in combination with a suitable detector, can provide spatial properties of μm-focused X-ray beams at MHz repetition rate
- …