Accessing gene expression at a single-cell level has unraveled often large heterogeneity among seemingly homogeneous cells, which remains obscured when using traditional population-based approaches. ...The computational analysis of single-cell transcriptomics data, however, still imposes unresolved challenges with respect to normalization, visualization and modeling the data. One such issue is differences in cell size, which introduce additional variability into the data and for which appropriate normalization techniques are needed. Otherwise, these differences in cell size may obscure genuine heterogeneities among cell populations and lead to overdispersed steady-state distributions of mRNA transcript numbers. We present cgCorrect, a statistical framework to correct for differences in cell size that are due to cell growth in single-cell transcriptomics data. We derive the probability for the cell-growth-corrected mRNA transcript number given the measured, cell size-dependent mRNA transcript number, based on the assumption that the average number of transcripts in a cell increases proportionally to the cell's volume during the cell cycle. cgCorrect can be used for both data normalization and to analyze the steady-state distributions used to infer the gene expression mechanism. We demonstrate its applicability on both simulated data and single-cell quantitative real-time polymerase chain reaction (PCR) data from mouse blood stem and progenitor cells (and to quantitative single-cell RNA-sequencing data obtained from mouse embryonic stem cells). We show that correcting for differences in cell size affects the interpretation of the data obtained by typically performed computational analysis.
The presence of circulating tumor cells (CTCs), detected as a form of liquid biopsy is associated with poor survival in both early and metastatic breast cancer. Monitoring tumor biology based on ...intrinsic subtypes delivers treatment-relevant information on the heterogeneity or biomarker conversion between primary and metastatic tumors. This study aimed to correlate the change of the apoptotic and intact CTC counts with mRNA-assessed intrinsic subtype change. Thirty-four breast cancer patients with available triplets of primary tumors, distant metastasis biopsies and data on intact and apoptotic CTC dynamics were included in the analysis. The intrinsic subtype was determined per RT-qPCR quantification of the gene expression ESR1, PGR, ERBB2 and MKI67. Both luminal (
= 0.038) and triple negative (
= 0.035) patients showed a significant downregulation of apoptotic CTCs. Repeated biopsies of distant metastatic sites, as well as determining a potential shift of the intrinsic subtype, combined with data on intact and apoptotic CTC dynamics from liquid biopsies might help personalize systemic therapy and generate additional surrogate markers for successful systemic therapy.
The treatment of haemorrhagic shock is a challenging task. Colloids have been regarded as standard treatment, but their safety and benefit have been the subject of controversial debates. Negative ...effects, including renal failure and increased mortality, have resulted in restrictions on their administration. The cerebral effects of different infusion regimens are largely unknown.
The current study investigated the impact of gelatine-polysuccinate, hydroxyethyl starch (HES) and balanced electrolyte solution (BES) on cerebral integrity, focusing on cerebral inflammation, apoptosis and blood flow in pigs.
Randomised experimental study.
University-affiliated large animal research unit.
Twenty-four juvenile pigs aged 8 to 12 weeks.
Haemorrhagic shock was induced by controlled arterial blood withdrawal to achieve a combination of relevant blood loss (30 to 40 ml kg-1) and haemodynamic deterioration. After 30 min of shock, fluid resuscitation was started with either gelatine-polysuccinate, HES or BES. The animals were then monitored for 4 h.
Cerebral perfusion and diffusion were measured via arterial-spin-labelling MRI. Peripheral tissue perfusion was evaluated via white light spectroscopy. Cortical and hippocampal samples were collected at the end of the experiment. The numbers of cerebral cell nuclei were counted and mRNA expression of markers for cerebral apoptosis glucose transporter protein type 1 (SLC2A), lipocalin 2 (LCN-2), aquaporin-4 (AQP4) and inflammation IL-6, TNF-α, glial fibrillary acidic protein (GFAP) were determined.
The three fluid protocols all stabilised the macrocirculation. Fluid resuscitation significantly increased the cerebral perfusion. Gelatine-polysuccinate and HES initially led to a higher cardiac output but caused haemodilution. Cerebral cell counts (as cells μm-2) were lower after colloid administration in the cortex (gelatine-polysuccinate, 1.8 ± 0.3; HES, 1.9 ± 0.4; each P < 0.05 vs. BES, 2.3 ± 0.2) and the hippocampus (gelatine-polysuccinate, 0.8 ± 0.2; HES, 0.9 ± 0.2; each P < 0.05 vs. BES, 1.1 ± 0.1). After gelatine-polysuccinate, the hippocampal SLC2A and GFAP were lower. After gelatine-polysuccinate, the cortical LCN-2 and TNF-α expression levels were increased (each P < 0.05 vs. BES).
In a porcine model, fluid resuscitation by colloids, particularly gelatine-polysuccinate, was associated with the occurrence of cerebral injury.
23 177-07/G 15-1-092; 01/2016.
ABSTRACT
We study the highly magnified arc SGAS J122651.3+215220 caused by a star-forming galaxy at zs = 2.93 crossing the lensing caustic cast by the galaxy cluster SDSS J1226+2152 (zl = 0.43), ...using Hubble Space Telescope observations. We report in the arc several asymmetric surface brightness features whose angular separations are a fraction of an arcsecond from the lensing critical curve and appear to be highly but unequally magnified image pairs of underlying compact sources, with one brightest pair having clear asymmetry consistently across four filters. One explanation of unequal magnification is microlensing by intracluster stars, which induces independent flux variations in the images of individual or groups of source stars in the lensed galaxy. For a second possibility, intracluster dark matter subhaloes invisible to telescopes effectively perturb lensing magnifications near the critical curve and give rise to persistently unequal image pairs. Our modelling suggests, at least for the most prominent identified image pair, that the microlensing hypothesis is in tension with the absence of notable asymmetry variation over a six-year baseline, while subhaloes of ∼106–$10^8\, \mathrm{ M}_\odot$ anticipated from structure formation with cold dark matter typically produce stationary and sizable asymmetries. We judge that observations at additional times and more precise lens models are necessary to stringently constrain temporal variability and robustly distinguish between the two explanations. The arc under this study is a scheduled target of a Director’s Discretionary Early Release Science program of the James Webb Space Telescope, which will provide deep images and a high-resolution view with integral field spectroscopy.
The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members
. Here we investigate how chromatinized E-boxes are engaged ...by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs.
). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch
, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes
at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
As a lightweight metal with mechanical properties similar to natural bone, Mg and its alloys are great prospects for biodegradable, load bearing implants. However, rapid degradation and H
gas ...production in physiological media has prevented widespread use of Mg alloys. Surface heterogeneities in the form of intermetallic particles dominate the corrosion response. This research shows that surface homogenization significantly improved the biological corrosion response observed during immersion in simulated body fluid (SBF). The laser processed Mg alloy exhibited a 50% reduction in mass loss and H
evolution after 24 h of immersion in SBF when compared to the wrought, cast alloy. The laser processed samples exhibited increased wettability as evident from wetting angle studies, further suggesting improved biocompatibility. Electrochemical analysis by potentiodynamic polarization measurements showed that the anodic and cathodic kinetics were reduced following laser processing and are attributed to the surface chemical homogeneity.
Tumour-specific splicing is known to contribute to cancer progression. In the case of the L1 cell adhesion molecule (L1CAM), which is expressed in many human tumours and often linked to bad ...prognosis, alternative splicing results in a full-length form (FL-L1CAM) and a splice variant lacking exons 2 and 27 (SV-L1CAM). It has not been elucidated so far whether SV-L1CAM, classically considered as tumour-associated, or whether FL-L1CAM is the metastasis-promoting isoform. Here, we show that both variants were expressed in human ovarian carcinoma and that exposure of tumour cells to pro-metastatic factors led to an exclusive increase of FL-L1CAM expression. Selective overexpression of one isoform in different tumour cells revealed that only FL-L1CAM promoted experimental lung and/or liver metastasis in mice. In addition, metastasis formation upon up-regulation of FL-L1CAM correlated with increased invasive potential and elevated Matrix metalloproteinase (MMP)-2 and -9 expression and activity in vitro as well as enhanced gelatinolytic activity in vivo. In conclusion, we identified FL-L1CAM as the metastasis-promoting isoform, thereby exemplifying that high expression of a so-called tumour-associated variant, here SV-L1CAM, is not per se equivalent to a decisive role of this isoform in tumour progression.
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