TGF-ß family ligands exhibit distinct signalling dynamics that are driven by receptor localisation.

Growth factor-induced signal transduction pathways are tightly regulated at multiple points intracellularly, but how cells monitor levels of extracellular ligand and translate this information into appropriate downstream responses remains unclear. Understanding signalling dynamics is thus a key challenge in determining how cells respond to external cues. Here, we demonstrate that different TGF-ß family ligands, namely activin A and BMP4, signal with distinct dynamics, which differ profoundly from those of TGF-ß itself. The signalling dynamics are driven by differences in the localisation and internalisation of receptors for each ligand, which in turn determine the capability of cells to monitor levels of extracellular ligand. By using mathematical modelling, we demonstrate that the distinct receptor behaviours and signalling dynamics observed may be primarily driven by differences in ligand-receptor affinity. Furthermore, our results provide a clear rationale for the different mechanisms of pathway regulation found in vivo for each of these growth factors.

Glycoside hydrolase DisH from Desulfovibrio vulgaris degrades the N-acetylgalactosamine component of diverse biofilms.

Biofilms of sulfate-reducing bacteria (SRB) produce H2 S, which contributes to corrosion. Although bacterial cells in biofilms are cemented together, they often dissolve their own biofilm to allow the cells to disperse. Using Desulfovibrio vulgaris as a model SRB, we sought polysaccharide-degrading enzymes that disperse its biofilm. Using a whole-genome approach, we identified eight enzymes as putative extracellular glycoside hydrolases including DisH (DVU2239, dispersal hexosaminidase), an enzyme that we demonstrated here, by utilizing various p-nitrooligosaccharide substrates, to be an N-acetyl-ß-D-hexosaminidase. For N-acetyl-ß-D-galactosamine (GalNAc), Vmax was 3.6 µmol of p-nitrophenyl/min (mg protein)-1 and Km was 0.8 mM; the specific activity for N-acetyl ß-D-glucosamine (GlcNAc) was 7.8 µmol of p-nitrophenyl/min (mg protein)-1 . Since GalNAc is one of the three exopolysaccharide matrix components of D. vulgaris, purified DisH was found to disperse 63 ± 2% biofilm as well as inhibit biofilm formation up to 47 ± 4%. The temperature and pH optima are 60°C and pH 6, respectively; DisH is also inhibited by copper and is secreted. In addition, since polymers of GalNAc and GlcNAc are found in the matrix of diverse bacteria, DisH dispersed biofilms of Pseudomonas aeruginosa, Escherichia coli and Bacillus subtilis. Therefore, DisH has the potential to inhibit and disperse a wide-range of biofilms.

Topological defects in liquid crystals as templates for molecular self-assembly.

Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly.

Patterned surface anchoring of nematic droplets at miscible liquid-liquid interfaces.

We report on the internal configurations of droplets of nematic liquid crystals (LCs; 10-50 µm-in-diameter; comprised of 4-cyano-4'-pentylbiphenyl and 4-(3-acryloyloxypropyloxy)benzoic acid 2-methyl-1,4-phenylene ester) sedimented from aqueous solutions of sodium dodecyl sulfate (SDS) onto interfaces formed with pure glycerol. We observed a family of internal LC droplet configurations and topological defects consistent with a remarkably abrupt transition from homeotropic (perpendicular) to tangential anchoring on the surface of the LC droplets in the interfacial environment. Calculations of the interdiffusion of water and glycerol at the aqueous-glycerol interface revealed the thickness of the diffuse interfacial region of the two miscible liquids to be small (0.2-0.5 µm) compared to the diameters of the LC droplets on the experimental time-scale (15-120 minutes), leading us to hypothesize that the patterned surface anchoring was induced by gradients in concentration of SDS and glycerol across the diameter of the LC droplets in the interfacial region. This hypothesis received additional support from experiments in which the time of sedimentation of the LC droplets onto the interface was systematically increased and the droplets were photo-polymerized to preserve their configurations: the configurations of the LC droplets were consistent with a time-dependent decrease in the fraction of the surface area of each droplet exhibiting homeotropic anchoring. Specifically, LC droplets with <10% surface area with tangential anchoring exhibited a bulk point defect within the LC droplet, whereas droplets with >10% surface area with tangential anchoring exhibited a boojum defect within the tangential region and a disclination loop separated the regions with tangential and homeotropic anchoring. The topological charge of these LC droplet configurations was found to be consistent with the geometrical theorems of Poincaré and Gauss and also well-described by computer simulations performed by minimization of a Landau-de Gennes free energy. Additional experimental observations (e.g., formation of "Janus-like" particles with one hemisphere exhibiting tangential anchoring and the other perpendicular anchoring) and simulations (e.g., a size-dependent set of LC droplet configurations with <10% surface area exhibiting tangential anchoring) support our general conclusion that placement of LC droplets into miscible liquid-liquid interfacial environments with compositional gradients can lead to a rich set of LC droplet configurations with symmetries and optical characteristics that are not encountered in LC droplet systems in homogeneous, bulk environments. Our results also reveal that translocation of LC droplets across liquid-liquid interfaces can define new transition pathways that connect distinct configurations of LC droplets.

Experimental Insights into the Nanostructure of the Cores of Topological Defects in Liquid Crystals.

The nanoscopic structure of the cores of topological defects in anisotropic condensed matter is an unresolved issue, although a number of theoretical predictions have been reported. In the experimental study reported in this Letter, we template the assembly of amphiphilic molecules from the cores of defects in liquid crystals and thereby provide the first experimental evidence that the cores of singular defects that appear optically to be points (with strength m=+1) are nanometer-sized closed-loop, disclination lines. We also analyze this result in the context of a model that describes the influence of amphiphilic assemblies on the free energy and stability of the defects. Overall, our experimental results and theoretical predictions reveal that the cores of defects with opposite strengths (e.g., m=+1 vs m=-1) differ in ways that profoundly influence processes of molecular self-assembly.

Lineage tracing reveals multipotent stem cells maintain human adenomas and the pattern of clonal expansion in tumor evolution.

The genetic and morphological development of colorectal cancer is a paradigm for tumorigenesis. However, the dynamics of clonal evolution underpinning carcinogenesis remain poorly understood. Here we identify multipotential stem cells within human colorectal adenomas and use methylation patterns of nonexpressed genes to characterize clonal evolution. Numerous individual crypts from six colonic adenomas and a hyperplastic polyp were microdissected and characterized for genetic lesions. Clones deficient in cytochrome c oxidase (CCO(-)) were identified by histochemical staining followed by mtDNA sequencing. Topographical maps of clone locations were constructed using a combination of these data. Multilineage differentiation within clones was demonstrated by immunofluorescence. Methylation patterns of adenomatous crypts were determined by clonal bisulphite sequencing; methylation pattern diversity was compared with a mathematical model to infer to clonal dynamics. Individual adenomatous crypts were clonal for mtDNA mutations and contained both mucin-secreting and neuroendocrine cells, demonstrating that the crypt contained a multipotent stem cell. The intracrypt methylation pattern was consistent with the crypts containing multiple competing stem cells. Adenomas were epigenetically diverse populations, suggesting that they were relatively mitotically old populations. Intratumor clones typically showed less diversity in methylation pattern than the tumor as a whole. Mathematical modeling suggested that recent clonal sweeps encompassing the whole adenoma had not occurred. Adenomatous crypts within human tumors contain actively dividing stem cells. Adenomas appeared to be relatively mitotically old populations, pocketed with occasional newly generated subclones that were the result of recent rapid clonal expansion. Relative stasis and occasional rapid subclone growth may characterize colorectal tumorigenesis.

Liquid Crystal Interfaces Programmed with Enzyme-Responsive Polymers and Surfactants.

Synthesis of biologically active peptide-polymer amphiphiles (PPAs), and characterization of assemblies formed by PPAs at the interfaces of liquid crystal (LC) microdroplets, is shown to permit the use of PPAs in strategies that can trigger ordering transitions in LC microdroplets in response to targeted biomolecular events.

Synthetic Mimics of Bacterial Lipid A Trigger Optical Transitions in Liquid Crystal Microdroplets at Ultralow Picogram-per-Milliliter Concentrations.

We report synthetic six-tailed mimics of the bacterial glycolipid Lipid A that trigger changes in the internal ordering of water-dispersed liquid crystal (LC) microdroplets at ultralow (picogram-per-milliliter) concentrations. These molecules represent the first class of synthetic amphiphiles to mimic the ability of Lipid A and bacterial endotoxins to trigger optical responses in LC droplets at these ultralow concentrations. This behavior stands in contrast to all previously reported synthetic surfactants and lipids, which require near-complete monolayer coverage at the LC droplet surface to trigger ordering transitions. Surface-pressure measurements and SAXS experiments reveal these six-tailed synthetic amphiphiles to mimic key aspects of the self-assembly of Lipid A at aqueous interfaces and in solution. These and other results suggest that these amphiphiles trigger orientational transitions at ultralow concentrations through a unique mechanism that is similar to that of Lipid A and involves formation of inverted self-associated nanostructures at topological defects in the LC droplets.

Reversible Switching of Liquid Crystalline Order Permits Synthesis of Homogeneous Populations of Dipolar Patchy Microparticles.

The spontaneous positioning of colloids on the surfaces of micrometer-sized liquid crystalline droplets and their subsequent polymerization offers the basis of a general and facile method for the synthesis of patchy microparticles. The existence of multiple local energetic minima, however, can generate kinetic traps for colloids on the surfaces of the liquid crystal (LC) droplets and result in heterogeneous populations of patchy microparticles. To address this issue, here we demonstrate that adsorbate-driven switching of the internal configurations of LC droplets can be used to sweep colloids to a single location on the LC droplet surfaces, thus resulting in the synthesis of homogeneous populations of patchy microparticles. The surface-driven switching of the LC can be triggered by addition of surfactant or salts, and permits the synthesis of dipolar microparticles as well as "Janus-like" microparticles. By using magnetic colloids, we illustrate the utility of the approach by synthesizing magnetically-responsive patchy microdroplets of LC with either dipolar or quadrupolar symmetry that exhibit distinct optical responses upon application of an external magnetic field.

Organized assemblies of colloids formed at the poles of micrometer-sized droplets of liquid crystal.

We report on the formation of organized assemblies of 1 µm-in-diameter colloids (polystyrene (PS)) at the poles of water-dispersed droplets (diameters 7-20 µm) of nematic liquid crystal (LC). For 4-cyano-4'-pentylbiphenyl droplets decorated with two to five PS colloids, we found 32 distinct arrangements of the colloids to form at the boojums of bipolar droplet configurations. Significantly, all but one of these configurations (a ring comprised of five PS colloids) could be mapped onto a local (non-close packed) hexagonal lattice. To provide insight into the origin of the hexagonal lattice, we investigated planar aqueous-LC interfaces, and found that organized assemblies of PS colloids did not form at these interfaces. Experiments involving the addition of salts revealed that a repulsive interaction of electrostatic origin prevented formation of assemblies at planar interfaces, and that regions of high splay near the poles of the LC droplets generated cohesive interactions between colloids that could overcome the repulsion. Support for this interpretation was obtained from a model that included (i) a long-range attraction between adsorbed colloids and the boojum due to the increasing rate of strain (splay) of LC near the boojum (splay attraction), (ii) an attractive inter-colloid interaction that reflects the quadrupolar symmetry of the strain in the LC around the colloids, and (iii) electrostatic repulsion between colloids. The model predicts that electrostatic repulsion between colloids can lead to a ∼1000kBT energy barrier at planar interfaces of LC films, and that the repulsive interaction can be overcome by splay attraction of the colloids to the boojums of the LC droplets. Overall, the results reported in this paper advance our understanding of the directed assembly of colloids at interfaces of LC droplets.

Liquid crystal droplet-based amplification of microvesicles that are shed by mammalian cells.

Membrane-derived microvesicles (MVs) shed by cells are being investigated for their role in intercellular communication and as potential biomarkers of disease, but facile and sensitive methods for their analysis do not exist. Here we demonstrate new principles for analysis of MVs that use micrometer-sized droplets of liquid crystals (LCs) to amplify MVs that are selectively captured via antibody-mediated interactions. The influence of the MVs on the micrometer-sized LC droplets is shown to be readily quantified via use of flow cytometry. The methodology was developed using MVs shed by epidermoid carcinoma A431 cells that contain epidermal growth factor receptor (EGFR) as an important and representative example of MVs containing signaling proteins that play a central role in cancer. The LC droplets were found to be sensitive to 10(6) MVs containing EGFR (relative to controls using isotype control antibody) and to possess a dynamic range of response across several orders of magnitude. Because the 100 nm-sized MVs captured via EGFR generate an optical response in the micrometer-sized LC droplets that can be readily detected by flow cytometry in light scattering mode, the approach possesses significant advantages over direct detection of MVs by flow cytometry. The LC droplets are also substantially more sensitive than techniques such as immunoblotting because the lipid-component of the MVs serves to amplify the antibody-mediated capture of the target proteins in the MVs. Other merits of the approach are defined and discussed in the paper.

Inhibitory CCK+ basket synapse defects in mouse models of dystroglycanopathy.

Dystroglycan (Dag1) is a transmembrane glycoprotein that links the extracellular matrix to the actin cytoskeleton. Mutations in Dag1 or the genes required for its glycosylation result in dystroglycanopathy, a type of congenital muscular dystrophy characterized by a wide range of phenotypes including muscle weakness, brain defects, and cognitive impairment. We investigated interneuron (IN) development, synaptic function, and associated seizure susceptibility in multiple mouse models that reflect the wide phenotypic range of dystroglycanopathy neuropathology. Mice that model severe dystroglycanopathy due to forebrain deletion of Dag1 or Pomt2, which is required for Dystroglycan glycosylation, show significant impairment of CCK+/CB1R+ IN development. CCK+/CB1R+ IN axons failed to properly target the somatodendritic compartment of pyramidal neurons in the hippocampus, resulting in synaptic defects and increased seizure susceptibility. Mice lacking the intracellular domain of Dystroglycan have milder defects in CCK+/CB1R+ IN axon targeting, but exhibit dramatic changes in inhibitory synaptic function, indicating a critical postsynaptic role of this domain. In contrast, CCK+/CB1R+ IN synaptic function and seizure susceptibility was normal in mice that model mild dystroglycanopathy due to partially reduced Dystroglycan glycosylation. Collectively, these data show that inhibitory synaptic defects and elevated seizure susceptibility are hallmarks of severe dystroglycanopathy, and show that Dystroglycan plays an important role in organizing functional inhibitory synapse assembly.

Degradation by Design: New Cyclin K Degraders from Old CDK Inhibitors.

Small molecules that induce protein degradation hold the potential to overcome several limitations of the currently available inhibitors. Monovalent or molecular glue degraders, in particular, enable the benefits of protein degradation without the disadvantages of high molecular weight and the resulting challenge in drug development that are associated with bivalent molecules like Proteolysis Targeting Chimeras. One key challenge in designing monovalent degraders is how to build in the degrader activity─how can we convert an inhibitor into a degrader? If degradation activity requires very specific molecular features, it will be difficult to find new degraders and challenging to optimize those degraders toward drugs. Herein, we demonstrate that an unexpectedly wide range of modifications to the degradation-inducing group of the cyclin K degrader CR8 are tolerated, including both aromatic and nonaromatic groups. We used these findings to convert the pan-CDK inhibitors dinaciclib and AT-7519 to Cyclin K degraders, leading to a novel dinaciclib-based compound with improved degradation activity compared to CR8 and confirm the mechanism of degradation. These results suggest that general design principles can be generated for the development and optimization of monovalent degraders.

Analysis of the internal configurations of droplets of liquid crystal using flow cytometry.

We report the use of flow cytometry to identify the internal ordering (director configurations) of micrometer-sized droplets of thermotropic liquid crystals (LCs) dispersed in aqueous solutions of adsorbates (surfactants and phospholipids). We reveal that changes in the configurations of the LC droplets induced by the adsorbates generate distinct changes in light scattering plots (side versus forward scattering). Specifically, when compared to bipolar droplets, radial droplets generate a narrower distribution of side scattering intensities (SSC, large angle light scattering) for a given intensity of forward scattering (FSC, small angle light scattering). This difference is shown to arise from the rotational symmetry of a radial LC droplet which is absent for the bipolar configuration of the LC droplet. In addition, the scatter plots for radial droplets possess a characteristic "S-shape", with two or more SSC intensities observed for each intensity of FSC. The origin of the experimentally observed S-shape is investigated via calculation of form factors and established to be due to size-dependent interference effects that differ for the forward and side scattered light. Finally, by analyzing emulsions composed of mixtures of bipolar and radial droplets at rates of up to 10,000 droplets per second, we demonstrate that flow cytometry permits precise determination of the percentage of radial droplets within the mixture with a coefficient of determination of 0.98 (as validated by optical microscopy). Overall, the results presented in this paper demonstrate that flow cytometry provides a promising approach for high throughput quantification of the internal configurations of LC emulsion microdroplets. Because large numbers of droplets can be characterized, it enables statistically robust analyses of LC droplets. The methodology also appears promising for quantification of chemical and biological assays based on adsorbate-induced ordering transitions within LC droplets.

Nematic-field-driven positioning of particles in liquid crystal droplets.

Common nematic oils, such as 5CB, experience planar anchoring at aqueous interfaces. When these oils are emulsified, this anchoring preference and the resulting topological constraints lead to the formation of droplets that exhibit one or two point defects within the nematic phase. Here, we explore the interactions of adsorbed particles at the aqueous interface through a combination of experiments and coarse-grained modeling, and demonstrate that surface-active particles, driven by elastic forces in the droplet, readily localize to these defect regions in a programmable manner. When droplets include two nanoparticles, these preferentially segregate to the two poles, thereby forming highly regular dipolar structures that could serve for hierarchical assembly of functional structures. Addition of sufficient concentrations of surfactant changes the interior morphology of the droplet, but pins defects to the interface, resulting in aggregation of the two particles.

Introduction to optical methods for characterizing liquid crystals at interfaces.

This Instructional Review describes methods and underlying principles that can be used to characterize both the orientations assumed spontaneously by liquid crystals (LCs) at interfaces and the strength with which the LCs are held in those orientations (so-called anchoring energies). The application of these methods to several different classes of LC interfaces is described, including solid and aqueous interfaces as well as planar and nonplanar interfaces (such as those that define a LC-in-water emulsion droplet). These methods, which enable fundamental studies of the ordering of LCs at polymeric, chemically functionalized, and biomolecular interfaces, are described in this Instructional Review on a level that can be easily understood by a nonexpert reader such as an undergraduate or graduate student. We focus on optical methods because they are based on instrumentation that is found widely in research and teaching laboratories.

Influence of droplet size, pH and ionic strength on endotoxin-triggered ordering transitions in liquid crystalline droplets.

We report an investigation of ordering transitions that are induced in water-dispersed, micrometer-sized droplets of a thermotropic liquid crystal (LC) by the bacterial lipopolysaccharide endotoxin. We reveal that the ordering transitions induced by endotoxin - from a bipolar state of the droplets to a radial state - are strongly dependent on the size of the LC droplets. Specifically, as the diameters of the LC droplets increase from 2 µm to above 10 µm (in phosphate buffered saline with an ionic strength of 90 mM and a pH of 7.2), we measured the percentage of droplets exhibiting a radial configuration in the presence of 100 pg/mL endotoxin to decrease from 98 ± 1 % to 3 ± 2 %. In addition, we measured a decrease in either the ionic strength or pH of the aqueous phase to reduce the percentage of droplets exhibiting a radial configuration in the presence of endotoxin. These results, when interpreted within the context of a simple thermodynamic model that incorporates the contributions of elasticity and surface anchoring to the free energies of the LC droplets, lead us to conclude that (i) the elastic constant K24 plays a central role in determining the size-dependent response of the LC droplets to endotoxin, and (ii) endotoxin-triggered ordering transitions occur only under solution conditions (pH, ionic strength) where the combined contributions of elasticity and surface anchoring to the free energies of the bipolar and radial configurations of the LC droplets are similar in magnitude. Our analysis also suggests that the presence of endotoxin perturbs the free energies of the LC droplets by ~10-17 J/droplet, which is comparable to the standard free energy of self-association of ~103 endotoxin molecules. These results, when combined with prior reports of localization of endotoxin at the center of LC droplets, are consistent with the hypothesis that self-assembly of endotoxin within micrometer-sized LC droplets provides the driving force for the ordering transitions. Overall, these results advance our understanding of ordering transitions triggered by the interactions of analytes with LC droplets and, more broadly, provide guidance to the design of LC droplet systems as the basis of stimuli-responsive soft materials.

Discovery of an In Vivo Chemical Probe for BCL6 Inhibition by Optimization of Tricyclic Quinolinones.

B-cell lymphoma 6 (BCL6) is a transcriptional repressor and oncogenic driver of diffuse large B-cell lymphoma (DLBCL). Here, we report the optimization of our previously reported tricyclic quinolinone series for the inhibition of BCL6. We sought to improve the cellular potency and in vivo exposure of the non-degrading isomer, CCT373567, of our recently published degrader, CCT373566. The major limitation of our inhibitors was their high topological polar surface areas (TPSA), leading to increased efflux ratios. Reducing the molecular weight allowed us to remove polarity and decrease TPSA without considerably reducing solubility. Careful optimization of these properties, as guided by pharmacokinetic studies, led to the discovery of CCT374705, a potent inhibitor of BCL6 with a good in vivo profile. Modest in vivo efficacy was achieved in a lymphoma xenograft mouse model after oral dosing.

New neurons generated from running are broadly recruited into neuronal activation associated with three different hippocampus-involved tasks.

Running increases the formation of new neurons in the adult rodent hippocampus. However, the function of new neurons generated from running is currently unknown. One hypothesis is that new neurons from running contribute to enhanced cognitive function by increasing plasticity in the adult hippocampus. An alternative hypothesis is that new neurons generated from running incorporate into experience-specific hippocampal networks that only become active during running. The purpose of this experiment was to determine if new neurons generated from running are selectively activated by running, or can become recruited into granule cell activity occurring during performance on other behavioral tasks that engage the hippocampus. Therefore, the activation of new 5-6 week neurons was detected using BrdU, NeuN, and Zif268 triple-label immunohistochemistry in cohorts of female running and sedentary adult C57BL/6J mice following participation in one of three different tasks: the Morris water maze, novel environment exploration, or wheel running. Results showed that running and sedentary mice displayed a nearly equivalent proportion of new neurons that expressed Zif268 following each task. Since running approximately doubled the number of new neurons, the results demonstrated that running mice had a greater number of new neurons recruited into the Zif268 induction in the granule cell layer following each task than sedentary mice. The results suggest that new neurons incorporated into hippocampal circuitry from running are not just activated by wheel running itself, but rather become broadly recruited into granule cell layer activity during distinct behavioral experiences.

Encoding BRAF inhibitor functions in protein degraders.

Various BRAF kinase inhibitors were developed to treat cancers carrying the BRAFV600E mutation. First-generation BRAF inhibitors could lead to paradoxical activation of the MAPK pathway, limiting their clinical usefulness. Here, we show the development of two series of BRAFV600E-targeting PROTACs and demonstrate that the exchange of the inhibitor scaffold from vemurafenib to paradox-breaker ligands resulted in BRAFV600E degraders that did not cause paradoxical ERK activation.