Extreme Gradient Boosting Combined with Conformal Predictors for Informative Solubility Estimation

We used the extreme gradient boosting (XGB) algorithm to predict the experimental solubility of chemical compounds in water and organic solvents and to select significant molecular descriptors. The accuracy of prediction of our forward stepwise top-importance XGB (FSTI-XGB) on curated solubility data sets in terms of RMSE was found to be 0.59-0.76 Log(S) for two water data sets, while for organic solvent data sets it was 0.69-0.79 Log(S) for the Methanol data set, 0.65-0.79 for the Ethanol data set, and 0.62-0.70 Log(S) for the Acetone data set. That was the first step. In the second step, we used uncurated and curated AquaSolDB data sets for applicability domain (AD) tests of Drugbank, PubChem, and COCONUT databases and determined that more than 95% of studied ca. 500,000 compounds were within the AD. In the third step, we applied conformal prediction to obtain narrow prediction intervals and we successfully validated them using test sets' true solubility values. With prediction intervals obtained in the last fourth step, we were able to estimate individual error margins and the accuracy class of the solubility prediction for molecules within the AD of three public databases. All that was possible without the knowledge of experimental database solubilities. We find these four steps novel because usually, solubility-related works only study the first step or the first two steps.

Photo-responsive functional gold nanocapsules for inactivation of community-acquired, highly virulent, multidrug-resistant MRSA

The indiscriminate and sporadic use of antibiotics has contributed to the emergence of drug resistance phenomenon in bacteria including but not limited to Staphylococcus aureus. These drug-resistant bacteria have been threatening safety in hospitals and adversely affecting human health. Here we report a strategy to design photo-stimulated theranostic nanoprobes against methicillin-resistant Staphylococcus aureus (MRSA) "superbug" USA300. The nanocapsule probe is based on gold nanorods (GNRs) coated with pegylated thiol, mPEG-SH, which has been further modified by adding successively a natural antibacterial compound such as curcumin, and a cell targeting deoxyribonucleic acid (DNA) aptamer. We have used this novel gold nanocapsules for near-infrared (NIR) photophysical stimulation against pathogenic bacteria. We have found that the novel nanocapsule blocks biofilm formation and kills bacteria by photothermal action that causes disruption of the bacterial cell wall and membrane. In this approach, multiple drug-resistant Staphylococcus aureus has been captured by these nanocapsules through DNA aptamer targeting. All of the trapped bacteria could be killed in 30 minutes during the NIR stimulation due to the combination of photothermal effect, the generation of reactive oxygen species (ROS) and a loss of transmembrane potential (Δψ). Importantly we did not notice any resistance developed against the photothermal treatment. This is remarkable from an anti-biofilm activity point of view. Importantly, these multifunctional nanocapsules have also shown a surface enhanced Raman spectroscopy (SERS) effect, which could be used to evaluate the success of the inactivation effect during treatment. These results indicate that nanocapsule-based photo treatment can be an alternative antibacterial strategy without contributing to antibiotic resistance, and thus can be used for both environmental and therapeutic applications.

APTES Duality and Nanopore Seed Regulation in Homogeneous and Nanoscale-Controlled Reduction of Ag Shell on SiO2 Microparticle for Quantifiable Single Particle SERS

Noble-metal nanoparticles size and packing density are critical for sensitive surface-enhanced Raman scattering (SERS) and controlled preparation of such films required to achieve reproducibility. Provided that they are made reliable, Ag shell on SiO₂ microscopic particles (Ag/SiO₂) are promising candidates for lab-on-a-bead analytical measurements of low analyte concentration in liquid specimen. Here, we selected nanoporous silica microparticles as a substrate for reduction of AgNO₃ with 3-aminopropyltriethoxysilane (APTES). In a single preparation step, homogeneous and continuous films of Ag nanoparticles are formed on SiO₂ surfaces with equimolar concentration of APTES and silver nitrate in ethanol. It is discussed that amine and silane moieties in APTES contribute first to an efficient reduction on the silica and second to capping the Ag nanoparticles. The high density and homogeneity of nanoparticle nucleation is further regulated by the nanoporosity of the silica. The Ag/SiO₂ microparticles were tested for SERS using self-assembled 4-aminothiophenol monolayers, and an enhancement factor of ca. 2 × 10⁶ is measured. Importantly, the SERS relative standard deviation is 36% when a single microparticle is considered and drops to 11% when sets of 10 microparticles are considered. As prepared, the microparticles are highly suitable for state-of-the-art quantitative lab-on-a-bead interrogation of specimens.

Label-free multimodal coherent anti-Stokes Raman scattering analysis of microparticles in unconstrained microfluidics

Fast, label-free optical identification and quantification of biomolecules and other relevant biological materials in microfluidic devices and the vascular system will play a major role in liquid biopsy and related diagnoses. An optical microscope probing simultaneously non-linear coherent anti-Stokes Raman scattering (CARS) and linear scattering (LS) was used to probe microparticles in aqueous solutions flowed unconstrained in microfluidic channels. Despite the optical complexity of these systems, where out-of-focus microparticles randomly impede CARS and LS, and where water CARS generates a substantial background, we demonstrate that in-focus microparticles can be individually and unambiguously detected when CARS and LS are co-analyzed. The ability to chemically discriminate microscale features in optically realistic flows supports the relevance of multimodal CARS platforms for liquid biopsy.

Image-Based Tracking of Anticancer Drug-Loaded Nanoengineered Polyelectrolyte Capsules in Cellular Environments Using a Fast Benchtop Mid-Infrared (MIR) Microscope

Drug delivery monitoring and tracking in the human body are two of the biggest challenges in targeted therapy to be addressed by nanomedicine. The ability of imaging drugs and micro-/nanoengineered drug carriers and of visualizing their interactions at the cellular interface in a label-free manner is crucial in providing the ability of tracking their cellular pathways and will help understand their biological impact, allowing thus to improve the therapeutic efficacy. We present a fast, label-free technique to achieve high-resolution imaging at the mid-infrared (MIR) spectrum that provides chemical information. Using our custom-made benchtop infrared microscope using a high-repetition-rate pulsed laser (80 MHz, 40 ps), we were able to acquire images with subwavelength resolution (0.8 × λ) at very high speeds. As a proof-of-concept, we embarked on the investigation of nanoengineered polyelectrolyte capsules (NPCs) containing the anticancer drug, docetaxel. These NPCs were synthesized using a layer-by-layer approach built upon a calcium carbonate (CaCO₃) core, which was then removed away with ethylenediaminetetraacetic acid. The obtained MIR images show that NPCs are attached to the cell membrane, which is a good step toward an efficient drug delivery. This has been confirmed by both three-dimensional confocal fluorescence and stimulated emission depletion microscopy. Coupled with additional instrumentation and data processing advancements, this setup is capable of video-rate imaging speeds and will be significantly complementing current super-resolution microscopy techniques while providing an unperturbed view into living cells.

Control of piezoelectricity in amino acids by supramolecular packing

Piezoelectricity, the linear relationship between stress and induced electrical charge, has attracted recent interest due to its manifestation in biological molecules such as synthetic polypeptides or amino acid crystals, including gamma (γ) glycine. It has also been demonstrated in bone, collagen, elastin and the synthetic bone mineral hydroxyapatite. Piezoelectric coefficients exhibited by these biological materials are generally low, typically in the range of 0.1-10 pm V^-1, limiting technological applications. Guided by quantum mechanical calculations we have measured a high shear piezoelectricity (178 pm V^-1) in the amino acid crystal beta (β) glycine, which is of similar magnitude to barium titanate or lead zirconate titanate. Our calculations show that the high piezoelectric coefficients originate from an efficient packing of the molecules along certain crystallographic planes and directions. The highest predicted piezoelectric voltage constant for β-glycine crystals is 8 V mN^-1, which is an order of magnitude larger than the voltage generated by any currently used ceramic or polymer.

ABCC1 confers tissue-specific sensitivity to cortisol versus corticosterone: A rationale for safer glucocorticoid replacement therapy

The aim of treatment in congenital adrenal hyperplasia is to suppress excess adrenal androgens while achieving physiological glucocorticoid replacement. However, current glucocorticoid replacement regimes are inadequate because doses sufficient to suppress excess androgens almost invariably induce adverse metabolic effects. Although both cortisol and corticosterone are glucocorticoids that circulate in human plasma, any physiological role for corticosterone has been neglected. In the brain, the adenosine 5'-triphosphate-binding cassette transporter ABCB1 exports cortisol but not corticosterone. Conversely, ABCC1 exports corticosterone but not cortisol. We show that ABCC1, but not ABCB1, is expressed in human adipose and that ABCC1 inhibition increases intracellular corticosterone, but not cortisol, and induces glucocorticoid-responsive gene transcription in human adipocytes. Both C57Bl/6 mice treated with the ABCC1 inhibitor probenecid and FVB mice with deletion of Abcc1 accumulated more corticosterone than cortisol in adipose after adrenalectomy and corticosteroid infusion. This accumulation was sufficient to increase glucocorticoid-responsive adipose transcript expression. In human adipose tissue, tissue corticosterone concentrations were consistently low, and ABCC1 mRNA was up-regulated in obesity. To test the hypothesis that corticosterone effectively suppresses adrenocorticotropic hormone (ACTH) without the metabolic adverse effects of cortisol, we infused cortisol or corticosterone in patients with Addison's disease. ACTH suppression was similar, but subcutaneous adipose transcripts of glucocorticoid-responsive genes were higher after infusion with cortisol rather than with corticosterone. These data indicate that corticosterone may be a metabolically favorable alternative to cortisol for glucocorticoid replacement therapy when ACTH suppression is desirable, as in congenital adrenal hyperplasia, and justify development of a pharmaceutical preparation.

Spatial-domain filter enhanced subtraction microscopy and application to mid-IR imaging

We have experimentally investigated the enhancement in spatial resolution by image subtraction in mid-infrared central solid-immersion lens (c-SIL) microscopy. The subtraction exploits a first image measured with the c-SIL point-spread function (PSF) realized with a Gaussian beam and a second image measured with the beam optically patterned by a silicon π-step phase plate, to realize a centrally hollow PSF. The intense sides lobes in both PSFs that are intrinsic to the SIL make the conventional weighted subtraction methods inadequate. A spatial-domain filter with a kernel optimized to match both experimental PSFs in their periphery was thus developed to modify the first image prior to subtraction, and this resulted in greatly improved performance, with polystyrene beads 1.4 ± 0.1 µm apart optically resolved with a mid-IR wavelength of 3.4 µm in water. Spatial-domain filtering is applicable to other PSF pairs, and simulations show that it also outperforms conventional subtraction methods for the Gaussian and doughnut beams widely used in visible and near-IR microscopy.

Biosynthesis of magnetic nanoparticles by human mesenchymal stem cells following transfection with the magnetotactic bacterial gene mms6

The use of stem cells to support tissue repair is facilitated by loading of the therapeutic cells with magnetic nanoparticles (MNPs) enabling magnetic tracking and targeting. Current methods for magnetizing cells use artificial MNPs and have disadvantages of variable uptake, cellular cytotoxicity and loss of nanoparticles on cell division. Here we demonstrate a transgenic approach to magnetize human mesenchymal stem cells (MSCs). MSCs are genetically modified by transfection with the mms6 gene derived from Magnetospirillum magneticum AMB-1, a magnetotactic bacterium that synthesises single-magnetic domain crystals which are incorporated into magnetosomes. Following transfection of MSCs with the mms6 gene there is bio-assimilated synthesis of intracytoplasmic magnetic nanoparticles which can be imaged by MR and which have no deleterious effects on cell proliferation, migration or differentiation. The assimilation of magnetic nanoparticle synthesis into mammalian cells creates a real and compelling, cytocompatible, alternative to exogenous administration of MNPs.

Doubling the far-field resolution in mid-infrared microscopy

The spatial resolution in far-field mid-infrared (λ>2.5 µm) microscopy and micro-spectroscopy remains limited with the full-width at half maximum of the point-spread function ca. λ/1.3; a value that is very poor in comparison to that commonly accessible with visible and near-infrared optics. Hereafter, it is demonstrated however that polymer beads that are centre-to-centre spaced by λ/2.6 can be resolved in the mid-infrared. The more than 2-fold improvement in resolution in the far-field is achieved by exploiting a newly constructed scanning microscope built around a mid-infrared optical parametric oscillator and a central solid-immersion lens, and by enforcing the linear polarization unidirectional resolution enhancement with a novel and robust specimen error minimization based on a particle swarm optimization. The method is demonstrated with specimens immersed in air and in water, and its robustness shown by the analysis of dense and complex self-assembled bead islands.

Exploring the cellular and tissue uptake of nanomaterials in a range of biological samples using multimodal nonlinear optical microscopy

The uptake of nanomaterials (NMs) by cells is critical in determining their potential biological impact, whether beneficial or detrimental. Thus, investigation of NM internalization by cells is a common consideration in hazard and efficacy studies. There are currently a number of approaches that are routinely used to investigate NM-cell interactions, each of which have their own advantages and limitations. Ideally, imaging modalities used to investigate NM uptake by cells should not require the NM to be labelled (e.g. with fluorophores) to facilitate its detection. We present a multimodal imaging approach employing a combination of label-free microscopies that can be used to investigate NM-cell interactions. Coherent anti-Stokes Raman scattering microscopy was used in combination with either two-photon photoluminescence or four-wave mixing (FWM) to visualize the uptake of gold or titanium dioxide NMs respectively. Live and fixed cell imaging revealed that NMs were internalized by J774 macrophage and C3A hepatocyte cell lines (15-31 μg ml(-1)). Sprague Dawley rats were exposed to NMs (intratracheal instillation, 62 μg) and NMs were detected in blood and lung leucocytes, lung and liver tissue, demonstrating that NMs could translocate from the exposure site. Obtained data illustrate that multimodal nonlinear optical microscopy may help overcome current challenges in the assessment of NM cellular uptake and biodistribution. It is therefore a powerful tool that can be used to investigate unlabelled NM cellular and tissue uptake in three dimensions, requires minimal sample preparation, and is applicable to live and fixed cells.

TMEM120A and B: Nuclear Envelope Transmembrane Proteins Important for Adipocyte Differentiation

Recent work indicates that the nuclear envelope is a major signaling node for the cell that can influence tissue differentiation processes. Here we present two nuclear envelope trans-membrane proteins TMEM120A and TMEM120B that are paralogs encoded by the Tmem120A and Tmem120B genes. The TMEM120 proteins are expressed preferentially in fat and both are induced during 3T3-L1 adipocyte differentiation. Knockdown of one or the other protein altered expression of several genes required for adipocyte differentiation, Gata3, Fasn, Glut4, while knockdown of both together additionally affected Pparg and Adipoq. The double knockdown also increased the strength of effects, reducing for example Glut4 levels by 95% compared to control 3T3-L1 cells upon pharmacologically induced differentiation. Accordingly, TMEM120A and B knockdown individually and together impacted on adipocyte differentiation/metabolism as measured by lipid accumulation through binding of Oil Red O and coherent anti-Stokes Raman scattering microscopy (CARS). The nuclear envelope is linked to several lipodystrophies through mutations in lamin A; however, lamin A is widely expressed. Thus it is possible that the TMEM120A and B fat-specific nuclear envelope transmembrane proteins may play a contributory role in the tissue-specific pathology of this disorder or in the wider problem of obesity.

Label-free assessment of adipose-derived stem cell differentiation using coherent anti-Stokes Raman scattering and multiphoton microscopy

Adult stem cells (SCs) hold great potential as likely candidates for disease therapy but also as sources of differentiated human cells in vitro models of disease. In both cases, the label-free assessment of SC differentiation state is highly desirable, either as a quality-control technology ensuring cells to be used clinically are of the desired lineage or to facilitate in vitro time-course studies of cell differentiation. We investigate the potential of nonlinear optical microscopy as a minimally invasive technology to monitor the differentiation of adipose-derived stem cells (ADSCs) into adipocytes and osteoblasts. The induction of ADSCs toward these two different cell lineages was monitored simultaneously using coherent anti-Stokes Raman scattering, two photon excitation fluorescence (TPEF), and second harmonic generation at different time points. Changes in the cell's morphology, together with the appearance of biochemical markers of cell maturity were observed, such as lipid droplet accumulation for adipo-induced cells and the formation of extra-cellular matrix for osteo-induced cells. In addition, TPEF of flavoproteins was identified as a proxy for changes in cell metabolism that occurred throughout ADSC differentiation toward both osteoblasts and adipocytes. These results indicate that multimodal microscopy has significant potential as an enabling technology for the label-free investigation of SC differentiation.

Raman spectroscopy and CARS microscopy of stem cells and their derivatives

The characterisation of stem cells is of vital importance to regenerative medicine. Failure to separate out all stem cells from differentiated cells before therapies can result in teratomas - tumours of multiple cell types. Typically, characterisation is performed in a destructive manner with fluorescent assays. A truly non-invasive method of characterisation would be a major breakthrough in stem cell-based therapies. Raman spectroscopy has revealed that DNA and RNA levels drop when a stem cell differentiates into other cell types, which we link to a change in the relative sizes of the nucleus and cytoplasm. We also used Raman spectroscopy to investigate the biochemistry within an early embryo, or blastocyst, which differs greatly from colonies of embryonic stem cells. Certain cell types that differentiate from stem cells can be identified by directly imaging the biochemistry with CARS microscopy; examples presented are hydroxyapatite - a precursor to bone, and lipids in adipocytes.

Non linear optical microscopy of adipose-derived stem cells induced towards osteoblasts and adipocytes

Adipose-derived stem cells (ADSCs) are adult stem cells isolated from lipoaspirates. They are a good candidate for autologuous cell therapy and tissue engineering. For these applications, label-free imaging could be critical to assess noninvasively the efficiency of stem cell (SC) differentiation. We report on the development and application of a multimodal microscope to monitor and quantify ADSC differentiation into osteoblasts and adipocytes.