Background Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automated and objective analysis of the resulting images is essential to effectively extract biological information from this data. CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Results Herein we describe CellProfiler 4, a new version of this software with expanded functionality. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimizations to reduce the time and cost associated with running common large-scale analysis pipelines. Conclusions CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to CellProfiler’s powerful computational tools in the coming years.

The glucocorticoid receptor (GR) is a major drug target in inflammatory disease. However, chronic glucocorticoid (GC) treatment leads to disordered energy metabolism, including increased weight gain, adiposity, and hepatosteatosis — all programs modulated by the circadian clock. We demonstrated that while antiinflammatory GC actions were maintained irrespective of dosing time, the liver was significantly more GC sensitive during the day. Temporal segregation of GC action was underpinned by a physical interaction of GR with the circadian transcription factor REVERBa and co-binding with liver-specific hepatocyte nuclear transcription factors (HNFs) on chromatin. REVERBa promoted efficient GR recruitment to chromatin during the day, acting in part by maintaining histone acetylation, with REVERBa-dependent GC responses providing segregation of carbohydrate and lipid metabolism. Importantly, deletion of Reverba inverted circadian liver GC sensitivity and protected mice from hepatosteatosis induced by chronic GC administration. Our results reveal a mechanism by which the circadian clock acts through REVERBa in liver on elements bound by HNF4A/HNF6 to direct GR action on energy metabolism.

Image-based experiments can yield many thousands of individual measurements describing each object of interest, such as cells in microscopy screens. CellProfiler Analyst is a free, open-source software package designed for the exploration of quantitative image-derived data and the training of machine learning classifiers with an intuitive user interface. We have now released CellProfiler Analyst 3.0, which in addition to enhanced performance adds support for neural network classifiers, identifying rare object subsets, and direct transfer of objects of interest from visualisation tools into the Classifier tool for use as training data. This release also increases interoperability with the recently released CellProfiler 4, making it easier for users to detect and measure particular classes of objects in their analyses. Availability CellProfiler Analyst binaries for Windows and MacOS are freely available for download at https://cellprofileranalyst.org/. Source code is implemented in Python 3 and is available at https://github.com/CellProfiler/CellProfiler-Analyst/. A sample data set is available at https://cellprofileranalyst.org/examples, based on images freely available from the Broad Bioimage Benchmark Collection (BBBC).

TCR-gene-transfer is an efficient strategy to produce therapeutic T cells of defined antigen specificity. However, there are substantial variations in the cell surface expression levels of human TCRs, which can impair the function of engineered T cells. Here we demonstrate that substitutions of 3 amino acid residues in the framework of the TCR variable domains consistently increase the expression of human TCRs on the surface of engineered T cells.The modified TCRs mediate enhanced T cell proliferation, cytokine production and cytotoxicity, while reducing the peptide concentration required for triggering effector function up to 3000-fold. Adoptive transfer experiments in mice show that modified TCRs control tumor growth more efficiently than wild-type TCRs. Our data indicate that simple variable domain modifications at a distance from the antigen-binding loops lead to increased TCR expression and improved effector function. This finding provides a generic platform to optimize the efficacy of TCR gene therapy in humans.

In 10 nonasthmatic subjects and 11 patients with asthma, we measured pulmonary resistance (RL), functional residual capacity (FRC), and specific conductance (sGaw) before, during, and after submaximal treadmill exercise. Nonasthmatic subjects did not change RL, FRC, or sGaw from base-line resting values during or after exercise. In patients with asthma, RL decreased significantly during exercise, both when exercise was begun from the control resting state and from conditions of elevated RL after a preceding period of exercise. When asthmatic patients inhaled a standardized dose of aerosolized histamine, the increase in RL during exercise was significantly less than the increase in RL when they breathed histamine at rest. When patients hyperventilated at rest with tidal volumes, breathing frequencies, and end-tidal CO2 tensions similar to those during exercise conditions, bronchodilatation also occurred, and the increase in RL following inhaled histamine during isocapnic hyperventilation was also less than at rest. Since bronchodilatation and inhibition of histamine-induced bronchoconstriction occur during both exercise and isocapnic hyperventilation, we suggest that the mechanism of bronchodilatation during exercise may not necessarily be related to metabolic factors associated with exercise.

In order to determine the influence of two artificially induced alkalotic states on the ability to perform maximal exercise, six male subjects (mean age, 22.0 years; mean height, 176.8 cm; mean weight, 69.1 kg; mean VO2 max, 3.83 l min-1) were studied during three experimental trials. The subjects performed six 60-s cycling bouts, at a work rate corresponding to 125% VO2 max, with 60 s recovery between work bouts; these regimens were performed 1 h after the ingestion of a solution containing either; I, placebo; II, NaHCO3 in a dosage of 0.15 g per kg body weight; or III, NaHCO3 0.30 g per kg body weight. The sixth work bout was continued until the pedal velocity dropped below 50 rev min-1. Total work done for the entire work period was calculated. Blood samples were taken from a forearm vein prior to the exercise bouts for analysis of pH and HCO3. The results showed a significant pre-exercise difference in pH and HCO3 for all conditions (P less than 0.01). In conditions where artificial alkalosis had been achieved prior to exercise there was significant increase in the work produced: I, 121.6 kJ; II, 133.1 kJ; III, 133.5 kJ (P less than 0.05). The time to fatigue in the six bout was also significantly increased; I, 74.7 s; II, 111.0 s; III, 106.0 p (P less than 0.05). There were no significant differences between conditions II and III. Thus augmentation of the bicarbonate reserves has a significant positive effect on the energy metabolism in interval-type exercise, leading to an increase in the work done and in the time to fatigue.(ABSTRACT TRUNCATED AT 250 WORDS)

HIV-1 must replicate in cells that are equipped to defend themselves from infection through intracellular innate immune systems. HIV-1 evades innate immune sensing through encapsidated DNA synthesis and encodes accessory genes that antagonize specific antiviral effectors. Here, we show that both particle associated, and expressed HIV-1 Vpr, antagonize the stimulatory effect of a variety of pathogen associated molecular patterns by inhibiting IRF3 and NF-κB nuclear transport. Phosphorylation of IRF3 at S396, but not S386, was also inhibited. We propose that, rather than promoting HIV-1 nuclear import, Vpr interacts with karyopherins to disturb their import of IRF3 and NF-κB to promote replication in macrophages. Concordantly, we demonstrate Vpr-dependent rescue of HIV-1 replication in human macrophages from inhibition by cGAMP, the product of activated cGAS. We propose a model that unifies Vpr manipulation of nuclear import and inhibition of innate immune activation to promote HIV-1 replication and transmission.

CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Here we describe CellProfiler 4, a new version of this software which has been ported to the Python 3 language. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimisations to reduce the time and cost associated with running common large-scale analysis pipelines. This release will ensure that researchers will have continued access to CellProfiler’s powerful computational tools in the coming years.