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Computed tomography (CT) was used to study the interaction of NMs with the plant cell tissue in vivo using Zeiss Xradia 510 system on Arabidopsis thaliana leaf. T

This work was supported by the National Research Facility for Lab X-ray CT (NXCT) at the µ-VIS X-ray Imaging Centre, University of Southampton, through EPSRC grant EP/T02593X.

DT-LEMBAS cell line specific models

This contains 33 ensembles of 50 DT-LEMBAS models each. The models were trained on 33 cell line transcriptomic data from the L1000 dataset.

Validation of urine p-cresol glucuronide as renal cell carcinoma non-invasive biomarker

Description of the study: Renal cell carcinoma (RCC) stands among the most lethal urological malignancies. Most RCCs are incidentally diagnosed as initial symptoms are unspecific. Novel, minimally-invasive diagnostic and prognostic methods for RCC are needed, ideally in urine. Using UPLC-Q-ToF MS untargeted metabolomic analysis in urine, we previously revealed p-cresol glucuronide as potential RCC diagnostic marker. Additionally, urine samples one-year post-nephrectomy revealed isobutyryl-L-carnitine and L-proline betaine as potential RCC prognostic markers. Our present aim was to validate these differences in an independent cohort of RCC patients and healthy controls to strengthen their value as non-invasive biomarkers. In an independent cohort of 69 RCC patients and 52 controls we validated an increase in p-cresol glucuronide in urine from patients at diagnosis compared to controls (P=0.0043). It remained increased one-year post-nephrectomy (P=0.0288). The value of p-cresol glucuronide for RCC diagnosis was assessed with ROC curves analysis (AUC=0.66, 95% Confidence Interval 0.56-0.76). The role of isobutyryl-L-carnitine and <a name="_Hlk172707445"></a>L-proline betaine as prognostic markers could not be validated and will require a larger cohort. Our findings confirm the value of p-cresol glucuronide in urine as diagnostic marker for RCC in an independent cohort. This non-invasive method holds promise for enhancing patient care by reducing the need for potentially risky diagnostic procedures. Further metaproteomics-oriented approaches towards the tyrosine oxidation pathway and microbiota metagenomics studies may promote a holistic management of RCC. Description of the data: We provided data in .d format adquired with Agilent.

Effects of Pleurotus ferulae water extract (PWE) or Pleurotus ferulae ethanol extract (PEE) on lipid accumulation in 3T3-L1 cells.

Lipid accumulation was measured in 3T3-L1 adipocytes following Oil Red O staining, both with and without PWE or PEE treatment. Results are expressed as the mean ± standard deviation (SD) (n = 3). Different letters indicate significant differences (p < 0.05), as determined by one-way analysis of variance (ANOVA) followed by Tukey’s post hoc test.

On the cell broadening of mesoscale cellular convection in a well-mixed boundary layer

Open the record for dataset details and reuse information.

opencc-zeroJun 2021View details →

Inferring whole-organism metabolic rate from red blood cells in birds

Metabolic rate is a key ecological variable that quantifies the energy expenditure needed to fuel almost all biological processes in an organism. Metabolic rates are typically measured at the whole-organism level (woMR) with protocols that can elicit stress responses due to handling and confinement, potentially biasing resulting data. Improved, non-stressful methodology would be especially valuable for measures of field metabolic rate, which quantifies the energy expenditure of free-living individuals. Recently, techniques to measure cellular metabolic rate (cMR) in mitochondria of blood cells have become available, suggesting that blood-based cMR can be a proxy of organismal aerobic performance. Aerobic metabolism actually takes place in the mitochondria. Quantifying cMR from blood samples offers several advantages such as direct estimates of metabolism and minimized disturbance of individuals. To our knowledge, the hypothesis that blood-based cMR correlates with woMR has not yet been directly tested. We measured cMR in red blood cells of captive great tits (Parus major), first during their morning activity period and second after subjecting them to a 2.5 h day-time respirometry protocol to quantify woMR. We predicted cMR to decrease as individuals transitioned from an active to a resting state. In the two blood samples we also assessed circulating corticosterone concentrations to determine the perceived disturbance of individuals. From respirometry traces we extracted initial and final woMR measures to test for a predicted positive correlation with cMR measures, while accounting for corticosterone concentrations. Indeed, cMR declined from the first to the second measurement. Furthermore, woMR and cMR were positively related in individuals that had relatively low corticosterone concentrations and displayed little locomotor activity throughout respirometry. By contrast, woMR and cMR covaried negatively in birds that increased corticosterone concentrations and activity levels substantially. Our results show that red blood cell cMR represents a proxy for woMR when birds do not display signs of stress, i.e. either before increases in hormonal or behavioral parameters have occurred or after they have abated. This method represents a valuable tool for obtaining metabolic data repeatedly and in free-living individuals. Our findings also highlight the importance of accounting for individual stress responses when measuring metabolic rate at any level. Metabolic rate is a key ecological variable that quantifies the energy expenditure needed to fuel almost all biological processes in an organism. Metabolic rates are typically measured at the whole-organism level (woMR) with protocols that can elicit stress responses due to handling and confinement, potentially biasing resulting data. Improved, non-stressful methodology would be especially valuable for measures of field metabolic rate, which quantifies the energy expenditure of free-living individuals. Recently, techniques to measure cellular metabolic rate (cMR) in mitochondria of blood cells have become available, suggesting that blood-based cMR can be a proxy of organismal aerobic performance. Aerobic metabolism actually takes place in the mitochondria. Quantifying cMR from blood samples offers several advantages such as direct estimates of metabolism and minimized disturbance of individuals. To our knowledge, the hypothesis that blood-based cMR correlates with woMR has not yet been directly tested. We measured cMR in red blood cells of captive great tits (Parus major), first during their morning activity period and second after subjecting them to a 2.5 h day-time respirometry protocol to quantify woMR. We predicted cMR to decrease as individuals transitioned from an active to a resting state. In the two blood samples we also assessed circulating corticosterone concentrations to determine the perceived disturbance of individuals. From respirometry traces we extracted initial and final woMR measures to test for a predicted positive correlation with cMR measures, while accounting for corticosterone concentrations. Indeed, cMR declined from the first to the second measurement. Furthermore, woMR and cMR were positively related in individuals that had relatively low corticosterone concentrations and displayed little locomotor activity throughout respirometry. By contrast, woMR and cMR covaried negatively in birds that increased corticosterone concentrations and activity levels substantially. Our results show that red blood cell cMR represents a proxy for woMR when birds do not display signs of stress, i.e. either before increases in hormonal or behavioral parameters have occurred or after they have abated. This method represents a valuable tool for obtaining metabolic data repeatedly and in free-living individuals. Our findings also highlight the importance of accounting for individual stress responses when measuring metabolic rate at any level.

openMar 2020View details →

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Modern proteomics approaches can explore whole proteomes within a single mass spectrometry (MS) run. However, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and expertise needed from a diverse array of fields. In particular, in the field of microbiology, efforts to combine large-scale proteomic datasets have so far largely been missing. Thus, despite their relatively small genomes, the proteomes of most archaea remain incompletely characterized. This in turn undermines our ability to gain a greater understanding of archaeal cell biology. Therefore, we have initiated the Archaeal Proteome Project (ArcPP), a community effort that works towards a comprehensive analysis of archaeal proteomes. Starting with the model archaeon Haloferax volcanii, using state-of-the-art bioinformatic tools, we have: <ul> <li>reanalyzed more than 26 Mio. spectra</li> <li>optimized the analysis using parameter sweeps, multiple search engines implemented in Ursgal, and the combination of results through the combined PEP approach</li> <li>thoroughly controlled false discovery rates for high confidence protein identifications using the picked protein FDR approach and limiting FDR to 0.5%</li> <li>identified more than 45k peptides, corresponding to 3069 proteins (>75% of the proteome) with a median sequence coverage of 55%.</li> <li>analyzed N-terminal protein processing, including N-terminal acetylation and signal peptide cleavage</li> <li>performed a detailed glycoproteomic analysis, identifying >230 glycopeptides corresponding to 45 glycoproteins</li> </ul> Benefiting from the established bioinformatic infrastructure, we will follow up on this analysis focusing on H. volcanii proteogenomics as well as the characterization of additional post-translational modifications. Furthermore, ArcPP will integrate quantitative results obtained from the individual datasets in order to identify common regulatory mechanisms. These studies on the H. volcanii proteome can serve as a blueprint for comprehensive proteomic analyses performed on a diverse range of archaea and bacteria.   For further details, please refer to the following publications. Please also cite this work if you use these results for further analyses: Schulze, S., Adams, Z., Cerletti, M. et al. The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nat Commun 11, 3145 (2020). <a href="https://doi.org/10.1038/s41467-020-16784-7">https://doi.org/10.1038/s41467-020-16784-7</a> Schulze, S.; Pfeiffer, F.; Garcia, B.A.; Pohlschroder, M. (2021). Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea. PLOS Biol.  https://doi.org/10.1371/journal.pbio.3001277   An interactive website to explore the combined results can be found at <a href="https://archaealproteomeproject.org/">https://archaealproteomeproject.org/</a> Scripts and metadata used for the analysis can be found at <a href="https://github.com/arcpp/ArcPP">https://github.com/arcpp/ArcPP</a>   Updates version 1.3.0: - includes dataset PXD021827 Updates version 1.2.0: - Includes dataset PXD021874 - Includes results from a comprehensive glycoproteomic analysis of ArcPP datasets Updates version 1.1.0: - Natrialba magadii results are included in PXD009116.zip

opencc-by-4.0Jun 2021View details →

In vitro protein and starch digestion kinetics of individual chickpea cells: from static to more complex in vitro digestion approaches

Attention has been given to more (semi-)dynamic in vitro digestion approaches ascertaining the consequences of dynamic in vivo aspects on in vitro digestion kinetics. As these often come with time and economical constraints, evaluating the consequence of stepwise increasing the complexity of static in vitro approaches using easy-to-handle digestion set-ups has been the center of our interest. Starting from the INFOGEST static in vitro protocol, we studied the influence of static gastric pH versus gradual gastric pH change (pH 6.3 to pH 2.5 in 2 h) on macronutrient digestion in individual cotyledon cells derived from chickpeas. Little effect on small intestinal proteolysis was observed comparing the applied digestion conditions. Contrary, the implementation of a gradual gastric pH change, with and without the addition of salivary α-amylase, altered starch digestion kinetics rates, and extents by 25%. The evaluation of starch and protein digestion, being co-embedded in cotyledon cells, did not only confirm but accounted for the interdependent digestion behavior. The insights generated in this study demonstrate the possibility of using a hypothesis-based approach to introduce dynamic factors to in vitro models while sticking to simple and cost-efficient set-ups.   The data used for the graphs in the paper: K. Pälchen, D. Michels, D. Duijsens, S. T. Gwala, A. K. Pallares Pallares, M. Hendrickx, A. Van Loey and T. Grauwet, Food Funct., 2021, DOI: 10.1039/D1FO01123E

opencc-by-4.0Jan 2021View details →

Cellular crowd control: overriding endogenous cell coordination makes cell migration more susceptible to external programming

The uploaded files include 1) raw data used to generate plots and graphs included in the manuscript, 2) the total raw dataset from all experiments, 3) representative raw videos per experimental condition and data corresponding to each of the videos, and 4) Matlab scripts written by the researchers used for data analysis.

opencc-by-3.0-usJul 2021View details →

The role of TAp63g and p53 point mutations in regulating DNA repair, mutational susceptibility and invasion of bladder cancer cell

Raw data set for the manuscript submitted to e-Life (10-06-2021-RA-eLife-71184 ) for peer-review.

opencc-zeroJan 2020View details →

RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity

AbstractCell cultures are often used to study physiological processes in health and disease. It is well-known that cells change their gene expression in vitro compared to in vivo, but it is rarely experimentally addressed. High glucose is a known trigger of apoptosis in proximal tubular cells (PTC). Here we used RNA-seq to detect differentially expressed genes in cultures of primary rat PTC, 3 days old, compared to cells retrieved directly from rat outer renal cortex and between PTC exposed to 15 mM glucose and control for 8 h. The expression of 6,174 genes was significantly up- or downregulated in the cultures of PTC compared to the cells in the outer renal cortex. Most altered were mitochondrial and metabolism related genes. Gene expression of proapoptotic proteins were upregulated and gene expression of antiapoptotic proteins were downregulated in PTC. Expression of transporter related genes were generally downregulated. After 8 h, high glucose had not altered the gene expression in PTC. The current study provides evidence that cells alter their gene expression in vitro compared to in vivo and suggests that short-term high glucose exposure can trigger apoptosis in PTC without changing the gene expression levels of apoptotic proteins.

opencc-by-4.0May 2021View details →

Physical phenotype of blood cells is altered in COVID-19

Clinical syndrome coronavirus disease 2019 (COVID-19) induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by rapid spreading and high mortality worldwide. While the pathology is not yet fully understood, hyper-inflammatory response and coagulation disorders leading to congestions of microvessels are considered to be key drivers of the still increasing death toll. Until now, physical changes of blood cells have not been considered to play a role in COVID-19 related vascular occlusion and organ damage. Here we report an evaluation of multiple physical parameters including the mechanical features of five frequent blood cell types, namely erythrocytes, lymphocytes, monocytes, neutrophils, and eosinophils. More than 4 million blood cells of 17 COVID-19 patients at different levels of severity, 24 volunteers free from infectious or inflammatory diseases, and 14 recovered COVID-19 patients were analyzed. We found significant changes in lymphocyte stiffness, monocyte size, neutrophil size and deformability, and heterogeneity of erythrocyte deformation and size. While some of these changes recovered to normal values after hospitalization, others persisted for months after hospital discharge, evidencing the long-term imprint of COVID-19 on the body.

opencc-by-4.0Jul 2021View details →

Machine readable code lists for an algorithm to identify incident non-small cell lung cancer (NSCLC) in United States healthcare claims data

Machine readable code lists for an algorithm to identify incident non-small cell lung cancer (NSCLC) in United States healthcare claims data

opencc-zeroJul 2021View details →

Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density

During growth, cells must expand their cell volumes in coordination with biomass to control the level of cytoplasmic macromolecular crowding. Dry-mass density, the average ratio of dry mass to volume, is roughly constant between different nutrient conditions in bacteria, but it remains unknown whether cells maintain dry-mass density constant at the single-cell level and during non-steady conditions. Furthermore, the regulation of dry-mass density is fundamentally not understood in any organism. Using quantitative phase microscopy and a new image-analysis pipeline, we measured absolute single-cell mass and shape of the model organisms Escherichia coli and Caulobacter crescentus with improved precision and accuracy. We found that cells control dry-mass density indirectly, by expanding their surface, rather than volume, in direct proportion to biomass growth – according to a new surface growth law. At the same time, cell width is controlled independently. Therefore, cellular dry-mass density varies systematically with cell shape, both during the cell cycle or after nutrient shifts, while the surface-to-mass ratio remains nearly constant on the generation time scale. Transient deviations from constancy during nutrient shifts can be reconciled with turgor-pressure variations and the resulting elastic changes in surface area. Finally, we find that plastic changes of cell width after nutrient shifts are likely driven by turgor variations, demonstrating an important regulatory role of mechanical forces for width regulation. In conclusion, turgor-dependent cell width and a new, slowly varying surface-to-mass coupling constant are the independent variables that determine dry-mass density.

opencc-zeroJul 2021View details →

HINC dataset from: Homeopathic treatment as an add-on therapy may improve quality of life and prolong survival in patients with non-small cell lung cancer: A prospective, randomized, placebo-controlled, double-blind, three-arm, multicenter study

Background: Patients with advanced non-small cell lung cancer (NSCLC) have limited treatment options. Alongside conventional anticancer treatment, additive homeopathy might help to alleviate side effects of conventional therapy. The aim of the present study was to investigate whether additive homeopathy might influence quality of life (QoL) and survival in NSCLC patients. Methods: In this prospective, randomized, placebo-controlled, double-blind, three-arm, multicenter, phase III study, we evaluated the possible effects of additive homeopathic treatment compared with placebo in NSCLC stage IV patients with respect to QoL in the two randomized groups and survival time in all three groups. Treated patients visited the outpatients' centers every 9 weeks. 150 Patients with stage IV NSCLC were included in the study. 98 received either individualized homeopathic remedies (n=51) or placebo (n=47) in a double-blinded fashion. 52 control patients without any homeopathic treatment were observed for survival only. The constituents of the different homeopathic remedies were mainly of plant, mineral or animal origin. The remedies were manufactured by stepwise dilution and succussion, thereby preparing stable Good Manufacturing Practice grade formulations. Results: QoL as well as functional and symptom scales showed significant improvement in the homeopathy group when compared with placebo after 9 and 18 weeks of homeopathic treatment (p<0.001). Median survival time was significantly longer in the homeopathy group (435 days) vs placebo (257 days; p=0.010) as well as vs control (228 days; p<0.001). Survival rate in the homeopathy group differed significantly from placebo (p=0.020) and from control (p<0.001). Conclusion: QoL improved significantly in the homeopathy group compared with placebo. In addition, survival was significantly longer in the homeopathy group versus placebo and control. A higher QoL might have contributed to the prolonged survival. The study suggests that homeopathy positively influences not only QoL but also survival. Further studies including other tumor entities are warranted.

openother-openJul 2021View details →

zaplotnik/Hadley-cell-strength: Hadley cell strength

Timeseries of Hadley cell strength in the period 1979-2018 in ERA5 and ERA-Interim reanalyses. The timeseries and their trends are derived from different measures of HC strength.

opencc-by-4.0Dec 2020View details →

BRG1 shRNA knockdown in ALCL cell lines

To determine the consequences of Brg1 expression in ALCL, cells were transfected with shRNA to Brg1 leading to a decrease in Brg1 transcript and protein levels. RNA was isolated 72 hours later from the shRNA5 (TRCN0000015551) expressing cells and sequencing conducted to examine changes to the transcriptome mediated by Brg1. Following differential gene expression analysis of the scrambled shRNA versus shRNA5, the transcriptome was identified as being dramatically altered showing both downregulation (2,527 mRNA transcripts: of a cumulative 26,833 genes, adj. p ≤ 0.05) and upregulation (2,900 mRNA transcripts, of a cumulative 26,833 genes, adj. p ≤ 0.05) of genes. When analysing the the 15,285 protein-coding genes alone, 1,934 (13%) were downregulated while 2,797 (18%) were upregulated (adj. p ≤ 0.05). To establish which physiological processes are most affected by the activity of BRG1, pathway enrichment analyses were undertaken. The input comprised of the significant (adj. p ≤ 0.05) protein-coding targets, where the absolute log2 fold change of expression was ± 1.5. Transcripts whose expression was either induced (n=33) or repressed (n=243) by BRG1 were investigated. Reactome analysis suggests that BRG1 plays roles in upregulating genes associated with the cell cycle, while suppressing genes associated with epigenetic regulation.

opencc-byJul 2021View details →

PKHhigh/CD133+/CD24− Renal Stem-Like Cells Isolated from Human Nephrospheres Exhibit In Vitro Multipotency.

The mechanism upon which human kidneys undergo regeneration is debated, though different lineage-tracing mouse models have tried to explain the cellular types and the mechanisms involved. Different sources of human renal progenitors have been proposed, but it is difficult to argue whether these populations have the same capacities that have been described in mice. Using the nephrosphere (NS) model, we isolated the quiescent population of adult human renal stem-like PKHhigh/CD133+/CD24− cells (RSC). The aim of this study was to deepen the RSC in vitro multipotency capacity. RSC, not expressing endothelial markers, generated secondary nephrospheres containing CD31+/vWf+ cells and cytokeratin positive cells, indicating the coexistence of endothelial and epithelial commitment. RSC cultured on decellularized human renal scaffolds generated endothelial structures together with the proximal and distal tubular structures. CD31+ endothelial committed progenitors sorted from nephrospheres generated spheroids with endothelial-like sprouts in Matrigel. We also demonstrated the double commitment toward endothelial and epithelial lineages of single RSC. The ability of the plastic RSC population to recapitulate the development of tubular epithelial and endothelial renal lineages makes these cells a good tool for the creation of organoids with translational relevance for studying the parenchymal and endothelial cell interactions and developing new therapeutic strategies.

opencc-zeroJul 2021View details →

Extraordinarily rapid proliferation of cultured muscle satellite cells from migratory birds

Migratory birds experience bouts of muscle growth and depletion as they prepare for, and undertake prolonged flight. Our studies of migratory bird muscle physiology in vitro led to the discovery that sanderling (Calidris alba) muscle satellite cells proliferate more rapidly than other normal cell lines. Here we determined the proliferation rate of muscle satellite cells isolated from five migratory species (sanderling; ruff, Calidris pugnax; western sandpiper, Calidris mauri; yellow-rumped warbler, Setophaga coronata; Swainson's thrush, Catharus ustulatus) from two families (shorebirds and songbirds) and with different migratory strategies. Ruff and sanderling satellite cells exhibited rapid proliferation, with population doubling times of 9.3±1.3 and 11.4±2.0 hrs whereas the remaining species' cell doubling times were ≥24 hrs. The results indicate that the rapid proliferation of satellite cells is not associated with total migration distance but may be related to flight bout duration and interact with lifespan.