Explore the vast range of titles available.

Chemists charged with manufacturing pharmaceuticals have recently been exploring the efficiency advantages of continuous flow techniques. Perera et al. now show that a flow apparatus can also accelerate reaction optimization earlier in the drug discovery process. They modified a high-performance liquid chromatography system to screen a wide variety of solvent, ligand, and base combinations to optimize carbon-carbon bond formation. Injecting stock solution aliquots of the catalyst and reactants into a carrier solvent stream let the authors vary the main solvent efficiently and scale up the optimal conditions for product isolation. Science , this issue p. 429 Chromatographic, flow-based screening of reaction conditions is demonstrated for Suzuki coupling in pharmaceutical research. The scarcity of complex intermediates in pharmaceutical research motivates the pursuit of reaction optimization protocols on submilligram scales. We report here the development of an automated flow-based synthesis platform, designed from commercially available components, that integrates both rapid nanomole-scale reaction screening and micromole-scale synthesis into a single modular unit. This system was validated by exploring a diverse range of reaction variables in a Suzuki-Miyaura coupling on nanomole scale at elevated temperatures, generating liquid chromatography–mass spectrometry data points for 5760 reactions at a rate of >1500 reactions per 24 hours. Through multiple injections of the same segment, the system directly produced micromole quantities of desired material. The optimal conditions were also replicated in traditional flow and batch mode at 50- to 200-milligram scale to provide good to excellent yields.

Inappropriate DNA methylation is frequently associated with human tumour development, and in specific cases, is associated with clinical outcomes. Previous reports of DNA methylation in low/intermediate grade non-muscle invasive bladder cancer (NMIBC) have suggested that specific patterns of DNA methylation may have a role as diagnostic or prognostic biomarkers. In view of the aggressive and clinically unpredictable nature of high-grade (HG) NMIBC, and the current shortage of the preferred treatment option (Bacillus:Calmette-Guerin), novel methylation analyses may similarly reveal biomarkers of disease outcome that could risk-stratify patients and guide clinical management at initial diagnosis. Promoter-associated CpG island methylation was determined in primary tumour tissue of 36 initial presentation high-grade NMIBCs, 12 low/intermediate-grade NMIBCs and 3 normal bladder controls. The genes HOXA9, ISL1, NKX6-2, SPAG6, ZIC1 and ZNF154 were selected for investigation on the basis of previous reports and/or prognostic utility in low/intermediate-grade NMIBC. Methylation was determined by Pyrosequencing of sodium-bisulphite converted DNA, and then correlated with gene expression using RT-qPCR. Methylation was additionally correlated with tumour behaviour, including tumour recurrence and progression to muscle invasive bladder cancer or metastases. The ISL1 genes' promoter-associated island was more frequently methylated in recurrent and progressive high-grade tumours than their non-recurrent counterparts (60.0% vs. 18.2%, p = 0.008). ISL1 and HOXA9 showed significantly higher mean methylation in recurrent and progressive tumours compared to non-recurrent tumours (43.3% vs. 20.9%, p = 0.016 and 34.5% vs 17.6%, p = 0.017, respectively). Concurrent ISL1/HOXA9 methylation in HG-NMIBC reliably predicted tumour recurrence and progression within one year (Positive Predictive Value 91.7%), and was associated with disease-specific mortality (DSM). In this study we report methylation differences and similarities between clinical sub-types of high-grade NMIBC. We report the potential ability of methylation biomarkers, at initial diagnosis, to predict tumour recurrence and progression within one year of diagnosis. We found that specific biomarkers reliably predict disease outcome and therefore may help guide patient treatment despite the unpredictable clinical course and heterogeneity of high-grade NMIBC. Further investigation is required, including validation in a larger patient cohort, to confirm the clinical utility of methylation biomarkers in high-grade NMIBC.

Obatoclax belongs to a class of compounds known as BH3 mimetics which function as antagonists of Bcl-2 family apoptosis regulators. It has undergone extensive preclinical and clinical evaluation as a cancer therapeutic. Despite this, it is clear that obatoclax has additional pharmacological effects that contribute to its cytotoxic activity. It has been claimed that obatoclax, either alone or in combination with other molecularly targeted therapeutics, induces an autophagic form of cell death. In addition, obatoclax has been shown to inhibit lysosomal function, but the mechanism of this has not been elucidated. We have evaluated the mechanism of action of obatoclax in eight ovarian cancer cell lines. Consistent with its function as a BH3 mimetic, obatoclax induced apoptosis in three cell lines. However, in the remaining cell lines another form of cell death was evident because caspase activation and PARP cleavage were not observed. Obatoclax also failed to show synergy with carboplatin and paclitaxel, chemotherapeutic agents which we have previously shown to be synergistic with authentic Bcl-2 family antagonists. Obatoclax induced a profound accumulation of LC-3 but knockdown of Atg-5 or beclin had only minor effects on the activity of obatoclax in cell growth assays suggesting that the inhibition of lysosomal function rather than stimulation of autophagy may play a more prominent role in these cells. To evaluate how obatoclax inhibits lysosomal function, confocal microscopy studies were conducted which demonstrated that obatoclax, which contains two basic pyrrole groups, accumulates in lysosomes. Studies using pH sensitive dyes demonstrated that obatoclax induced lysosomal alkalinization. Furthermore, obatoclax was synergistic in cell growth/survival assays with bafilomycin and chloroquine, two other drugs which cause lysosomal alkalinization. These studies explain, for the first time, how obatoclax inhibits lysosomal function and suggest that lysosomal alkalinization contributes to the cytotoxic activity of obatoclax.

The efficient separation of chiral molecules is a fundamental challenge in the manufacture of pharmaceuticals and light-polarising materials. We developed an approach that combines machine learning with a physics-based representation to predict resolving agents for chiral molecules, using a transformer-based neural network. In retrospective tests, our approach reaches a four to six-fold improvement over the historical - trial and error based - hit rate. We further validate the model in a prospective experiment, where we use the model to design a resolution screen for six unseen racemates. We successfully resolved three of the six mixtures in a single round of experiments and obtained an overall 8-to-1 true positive to false negative ratio. Together with this study, we release a previously proprietary dataset of over 6000 resolution experiments, the largest diastereomeric salt crystallisation dataset to date. More broadly, our approach and open crystallisation data lay the foundation for accelerating and reducing the costs of chiral resolutions. The efficient separation of chiral molecules is a fundamental challenge in the manufacture of pharmaceuticals and light-polarising materials. Here, the authors develop an approach that combines machine learning with a physics-based representation to predict resolving agents for chiral molecules, using a transformer-based neural network.

Candidiasis is a major fungal infection by Candida species, causing life-threatening invasive disease in immunocompromised patients. C. albicans , which is adapted to commensalism of human mucosae, is the most common cause. While several other species cause infection, most are less prevalent or less virulent. Candida species are a leading cause of opportunistic, hospital-associated bloodstream infections with high mortality rates, typically in immunocompromised patients. Several species, including Candida albicans , the most prevalent cause of infection, belong to the monophyletic CUG clade of yeasts. Innate immune cells such as macrophages are crucial for controlling infection, and C. albicans responds to phagocytosis by a coordinated induction of pathways involved in catabolism of nonglucose carbon sources, termed alternative carbon metabolism, which together are essential for virulence. However, the interactions of other CUG clade species with macrophages have not been characterized. Here, we analyzed transcriptional responses to macrophage phagocytosis by six Candida species across a range of virulence and clinical importance. We define a core induced response common to pathogenic and nonpathogenic species alike, heavily weighted to alternative carbon metabolism. One prominent pathogen, Candida parapsilosis , showed species-specific expansion of phagocytosis-responsive genes, particularly metabolite transporters. C. albicans and Candida tropicalis , the other prominent pathogens, also had species-specific responses, but these were largely comprised of functionally uncharacterized genes. Transcriptional analysis of macrophages also demonstrated highly correlated proinflammatory transcriptional responses to different Candida species that were largely independent of fungal viability, suggesting that this response is driven by recognition of conserved cell wall components. This study significantly broadens our understanding of host interactions in CUG clade species, demonstrating that although metabolic plasticity is crucial for virulence in Candida , it alone is not sufficient to confer pathogenicity. Instead, we identify sets of mostly uncharacterized genes that may explain the evolution of pathogenicity. IMPORTANCE Candidiasis is a major fungal infection by Candida species, causing life-threatening invasive disease in immunocompromised patients. C. albicans , which is adapted to commensalism of human mucosae, is the most common cause. While several other species cause infection, most are less prevalent or less virulent. As innate immune cells are the primary defense against Candida infection, we compared the transcriptional responses of C. albicans and related species to phagocytosis by macrophages, to understand the basis of variation in pathogenesis. This response, including the metabolic remodeling required for virulence in C. albicans , was strikingly conserved across the virulence spectrum. Macrophage responses to different species were also highly similar. This study indicates that important elements of host-pathogen interactions in C. albicans are not driven by adaptation to the mammalian host and improves our understanding of pathogenicity in opportunistic fungal species that are understudied but collectively impose a significant threat of their own.

We have developed, for the first time, an advanced modeling infrastructure in space simulations (AMITIS) with an embedded three-dimensional self-consistent grid-based hybrid model of plasma (kinetic ions and fluid electrons) that runs entirely on graphics processing units (GPUs). The model uses NVIDIA GPUs and their associated parallel computing platform, CUDA, developed for general purpose processing on GPUs. The model uses a single CPU-GPU pair, where the CPU transfers data between the system and GPU memory, executes CUDA kernels, and writes simulation outputs on the disk. All computations, including moving particles, calculating macroscopic properties of particles on a grid, and solving hybrid model equations are processed on a single GPU. We explain various computing kernels within AMITIS and compare their performance with an already existing well-tested hybrid model of plasma that runs in parallel using multi-CPU platforms. We show that AMITIS runs ∼10 times faster than the parallel CPU-based hybrid model. We also introduce an implicit solver for computation of Faraday's Equation, resulting in an explicit-implicit scheme for the hybrid model equation. We show that the proposed scheme is stable and accurate. We examine the AMITIS energy conservation and show that the energy is conserved with an error < 0.2% after 500,000 timesteps, even when a very low number of particles per cell is used.

The ice-rich south polar layered deposits of Mars were probed with the Mars Advanced Radar for Subsurface and Ionospheric Sounding on the Mars Express orbiter. The radar signals penetrate deep into the deposits (more than 3.7 kilometers). For most of the area, a reflection is detected at a time delay that is consistent with an interface between the deposits and the substrate. The reflected power from this interface indicates minimal attenuation of the signal, suggesting a composition of nearly pure water ice. Maps were generated of the topography of the basal interface and the thickness of the layered deposits. A set of buried depressions is seen within 300 kilometers of the pole. The thickness map shows an asymmetric distribution of the deposits and regions of anomalous thickness. The total volume is estimated to be 1.6 x 10⁶ cubic kilometers, which is equivalent to a global water layer approximately 11 meters thick.

The equatorial Medusae Fossae Formation (MFF) is enigmatic and perhaps among the youngest geologic deposits on Mars. They are thought to be composed of volcanic ash, eolian sediments, or an ice-rich material analogous to polar layered deposits. The Mars Advanced Radar for Subsurface and Ionospheric Sounding (MARSIS) instrument aboard the Mars Express Spacecraft has detected nadir echoes offset in time-delay from the surface return in orbits over MFF material. These echoes are interpreted to be from the subsurface interface between the MFF material and the underlying terrain. The delay time between the MFF surface and subsurface echoes is consistent with massive deposits emplaced on generally planar lowlands materials with a real dielectric constant of ~2.9 ± 0.4. The real dielectric constant and the estimated dielectric losses are consistent with a substantial component of water ice. However, an anomalously low-density, ice-poor material cannot be ruled out. If ice-rich, the MFF must have a higher percentage of dust and sand than polar layered deposits. The volume of water in an ice-rich MFF deposit would be comparable to that of the south polar layered deposits.

The problem of plasma expansion into a vacuum is revisited with the addition of a finite boundary condition; an electrically insulated surface. As plasma expands towards a charge-accumulating surface, the leading electron cloud charges the surface negatively, which in turn repels electrons and attracts ions. This plasma–surface interaction is shown to result in a feedback process which accelerates the plasma expansion. In addition, we examine the decrease in (negative) surface potential and associated near-surface electron density. To investigate this plasma coupling with an electrically floating surface, we develop an analytic model including four neighbouring plasma regions: (i) undisturbed plasma, (ii) quasi-neutral self-similar expansion, (iii) ion front boundary layer and (iv) electron cloud. A key innovation in our approach is a self-contained analytic approximation of the ion front boundary layer, providing a spatially continuous electric field model for the early phase of bounded plasma expansion.

Although aberrant DNA methylation has been described in rheumatoid arthritis (RA), no studies have interrogated this epigenetic modification in early disease. Following recent investigations of T and B lymphocytes in established disease, we now characterize in these cell populations genome-wide DNA methylation in treatment-naive patients with early RA. HumanMethylation450 BeadChips were used to examine genome-wide DNA methylation in lymphocyte populations from 23 early RA patients and 11 healthy individuals. Approximately 2000 CpGs in each cell type were differentially methylated in early RA. Clustering analysis identified a novel methylation signature in each cell type (150 sites in T lymphocytes, 113 sites in B lymphocytes) that clustered all patients separately from controls. A subset of sites differentially methylated in early RA displayed similar changes in established disease. Treatment-naive early RA patients display novel disease-specific DNA methylation aberrations, supporting a potential role for these changes in the development of RA.