Synthetic Par polarity induces cytoskeleton asymmetry in unpolarized mammalian cells.

Polarized cells rely on a polarized cytoskeleton to function. Yet, how cortical polarity cues induce cytoskeleton polarization remains elusive. Here, we capitalized on recently established designed 2D protein arrays to ectopically engineer cortical polarity of virtually any protein of interest during mitosis in various cell types. This enables direct manipulation of polarity signaling and the identification of the cortical cues sufficient for cytoskeleton polarization. Using this assay, we dissected the logic of the Par complex pathway, a key regulator of cytoskeleton polarity during asymmetric cell division. We show that cortical clustering of any Par complex subunit is sufficient to trigger complex assembly and that the primary kinetic barrier to complex assembly is the relief of Par6 autoinhibition. Further, we found that inducing cortical Par complex polarity induces two hallmarks of asymmetric cell division in unpolarized mammalian cells: spindle orientation, occurring via Par3, and central spindle asymmetry, depending on aPKC activity.

Protein Design Using Physics Informed Neural Networks.

The inverse protein folding problem, also known as protein sequence design, seeks to predict an amino acid sequence that folds into a specific structure and performs a specific function. Recent advancements in machine learning techniques have been successful in generating functional sequences, outperforming previous energy function-based methods. However, these machine learning methods are limited in their interoperability and robustness, especially when designing proteins that must function under non-ambient conditions, such as high temperature, extreme pH, or in various ionic solvents. To address this issue, we propose a new Physics-Informed Neural Networks (PINNs)-based protein sequence design approach. Our approach combines all-atom molecular dynamics simulations, a PINNs MD surrogate model, and a relaxation of binary programming to solve the protein design task while optimizing both energy and the structural stability of proteins. We demonstrate the effectiveness of our design framework in designing proteins that can function under non-ambient conditions.

Precision materials: Computational design methods of accurate protein materials.

Nature has evolved a vast repertoire of structures and functions based on an ordered, orchestrated, protein building-blocks assembly. For decades these sophisticated materials have been studied, mimicked, and repurposed, yet recently, computational protein engineering methods provided an alternative route: creating protein materials de-novo, surpassing evolutionary constraints and optimized for specific tasks. We highlight two areas of research that fundamentally accelerate design of structurally well-defined programmable protein materials. First, implementations of hierarchical assembly and geometric sampling (docking) strategies to create designable backbones under pre-specified symmetry constraints. Second, progress in protein-protein interfaces and sequence design methods, using Rosetta, that drive programmable supramolecular assemblies. These approaches have proven effective in generating diverse protein assemblies in 0-, 1-, 2-, and 3-dimensional architectures (constituting single or multiple components), and as part of a synthetic or a biological system. We expect these methods shall transform the toolbox of protein designers developing next generation synthetic and biological materials.

Design of biologically active binary protein 2D materials.

Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3-5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9-12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.

The pivotal role of heme Oxygenase-1 in reversing the pathophysiology and systemic complications of NAFLD.

The pathogenesis and molecular pathways involved in non-alcoholic fatty liver disease (NAFLD) are reviewed, as well as what is known about mitochondrial dysfunction that leads to heart disease and the progression to steatohepatitis and hepatic fibrosis. We focused our discussion on the role of the antioxidant gene heme oxygenase-1 (HO-1) and its nuclear coactivator, peroxisome proliferator-activated receptor-gamma coactivator (PGC1-α) in the regulation of mitochondrial biogenesis and function and potential therapeutic benefit for cardiac disease, NAFLD as well as the pharmacological effect they have on the chronic inflammatory state of obesity. The result is increased mitochondrial function and the conversion of white adipocyte tissue to beige adipose tissue ("browning of white adipose tissue") that leads to an improvement in signaling pathways and overall liver function. Improved mitochondrial biogenesis and function is essential to preventing the progression of hepatic steatosis to NASH and cirrhosis as well as preventing cardiovascular complications.

Cold-Pressed Nigella Sativa Oil Standardized to 3% Thymoquinone Potentiates Omega-3 Protection against Obesity-Induced Oxidative Stress, Inflammation, and Markers of Insulin Resistance Accompanied with Conversion of White to Beige Fat in Mice.

Excessive lipid accumulation in white adipose tissue (WAT) results in adipocyte hypertrophy and chronic low-grade inflammation, which is the major cause of obesity-associated insulin resistance and consequent metabolic disease. The development of beige adipocytes in WAT (browning of WAT) increases energy expenditure and has been considered as a novel strategy to counteract obesity. Thymoquinone (TQ) is the main bioactive quinone derived from the plant Nigella Sativa and has antioxidative and anti-inflammatory capacities. Fish oil omega 3 (ω3) enhances both insulin sensitivity and glucose homeostasis in obesity, but the involved mechanisms remain unclear. The aim of this study is to explore the effects of TQ and ω3 PUFAs (polyunsaturated fatty acids) on obesity-associated inflammation, markers of insulin resistance, and the metabolic effects of adipose tissue browning. 3T3-L1 cells were cultured to investigate the effects of TQ and ω3 on the browning of WAT. C57BL/6J mice were fed a high-fat diet (HFD), supplemented with 0.75% TQ, and 2% ω3 in combination for eight weeks. In 3T3-L1 cells, TQ and ω3 reduced lipid droplet size and increased hallmarks of beige adipocytes such as uncoupling protein-1 (UCP1), PR domain containing 16 (PRDM16), fibroblast growth factor 21 (FGF21), Sirtuin 1 (Sirt1), Mitofusion 2 (Mfn2), and heme oxygenase 1 (HO-1) protein expression, as well as increased the phosphorylation of Protein Kinase B (AKT) and insulin receptors. In the adipose tissue of HFD mice, TQ and ω3 treatment attenuated levels of inflammatory adipokines, Nephroblastoma Overexpressed (NOV/CCN3) and Twist related protein 2 (TWIST2), and diminished adipocyte hypoxia by decreasing HIF1α expression and hallmarks of beige adipocytes such as UCP1, PRDM16, FGF21, and mitochondrial biogenesis markers Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α), Sirt1, and Mfn2. Increased 5' adenosine monophosphate-activated protein kinase (AMPK) and acetyl-CoA carboxylase (ACC) phosphorylation and HO-1 expression were observed in adipose with TQ and ω3 treatment, which led to increased pAKT and pIRS1 Ser307 expression. In addition to the adipose, TQ and ω3 also increased inflammation and markers of insulin sensitivity in the liver, as demonstrated by increased phosphorylated insulin receptor (pIR tyr972), insulin receptor beta (IRß), UCP1, and pIRS1 Ser307 and reduced NOV/CCN3 expression. Our data demonstrate the enhanced browning of WAT from TQ treatment in combination with ω3, which may play an important role in decreasing obesity-associated insulin resistance and in reducing the chronic inflammatory state of obesity.

Feasibility of a Dual Evaluation/Intervention Program for Morbidly Obese Adolescents.

BACKGROUND: In the absence of evidence-based guidelines for screening adolescent candidates for bariatric surgery, or improving their adherence to preoperative recommendations, we designed a dual-phase multidisciplinary program aiming for observation-based preoperative assessment/ intervention, as well as for post-operative/ conservative follow up. METHODS: This study focused on the preoperative 3-month phase. Fifteen morbidly obese adolescents attending the eating disorders unit of a pediatric hospital underwent the program protocol consisting of medical examinations/ tests, psychological measures, self-monitoring, tailored diet, physical activity schedule, individual and group cognitive behavior-oriented therapy, and psycho educational parent training. RESULTS: All patients completed the preoperative phase. Most of them (70%) followed the structured diet with a significant reduction in BMI. The patients complied with self-monitoring, and body dissatisfaction score improved. Parental participation in therapy was poor. Four patients with low adherence were found ineligible for surgery. CONCLUSIONS: The findings support the feasibility of our dual screening/intervention protocol. Measures to improve parental participation are warranted.

Self-assembled metallic nanowire-based vertical organic field-effect transistor.

We report on in situ, self-assembly, solution-processing of metallic (Au/Ag) nanowire-based transparent electrodes integrated to vertical organic field-effect transistors (VOFETs). In the VOFET architecture, the nanowires' microstructure facilitates current modulation by the gate across the otherwise shielding sandwiched source electrode. We show N-type VOFETs operation with on/off ratio ∼1 × 10(5) and high current density (>1 mA cm(-2) at VDS = 5 V). The integration of the device design and the transparent electrode deposition methods offers a potential route for all-solution processing-based, large-area, high-efficiency organic electronics.

Low-temperature molecular vapor deposition of ultrathin metal oxide dielectric for low-voltage vertical organic field effect transistors.

We demonstrate a low-temperature layer-by-layer formation of a metal-oxide-only (AlOx) gate dielectric to attain low-voltage operation of a self-assembly based vertical organic field effect transistor (VOFET). The AlOx deposition method results in uniform films characterized by high quality dielectric properties. Pin-hole free ultrathin layers with thicknesses ranging between 1.2 and 24 nm feature bulk dielectric permittivity, εAlOx, of 8.2, high breakdownfield (>8 MV cm(-1)), low leakage currents (<10(-7) A cm(-2) at 3MV cm(-1)), and high capacitance (up to 1 µF cm(-2)). We show the benefits of the tunable surface properties of the oxide-only dielectric utilized here, in facilitating the subsequent nanostructuring steps required to realize the VOFET patterned source electrode. Optimal wetting properties enable the directional block-copolymer based self-assembly patterning, as well as the formation of robust and continuous ultrathin metallic films. Supported by computer modeling, the vertical architecture and the methods demonstrated here offer a simple, low-cost, and free of expensive lithography route for the realization of low-voltage (VGS/DS≤3 V), low-power, and potentially high-frequency large-area electronics.

Unraveling the physics of vertical organic field effect transistors through nanoscale engineering of a self-assembled transparent electrode.

While organic transistors' performances are continually pushed to achieve lower power consumption, higher working frequencies, and higher current densities, a new type of organic transistors characterized by a vertical architecture offers a radically different design approach to outperform its traditional counterparts. Naturally, the distinct vertical architecture gives way to different governing physical ground rules and structural key features such as the need for an embedded transparent electrode. In this paper, we make use of a zero-frequency electric field-transparent patterned electrode produced through block-copolymer self-assembly based lithography to control the performances of the vertical organic field effect transistor (VOFET) and to study its governing physical mechanisms. Unlike other VOFET structures, this design, involving well-defined electrode architecture, is fully tractable, allowing for detailed modeling, analysis, and optimization. We provide for the first time a complete account of the physics underpinning the VOFET operation, considering two complementary mechanisms: the virtual contact formation (Schottky barrier lowering) and the induced potential barrier (solid-state triode-like shielding). We demonstrate how each mechanism, separately, accounts for the link between controllable nanoscale structural modifications in the patterned electrode and the VOFET performances. For example, the ON/OFF current ratio increases by up to 2 orders of magnitude when the perforations aspect ratio (height/width) decreases from ∼0.2 to ∼0.1. The patterned electrode is demonstrated to be not only penetrable to zero-frequency electric fields but also transparent in the visible spectrum, featuring uniformity, spike-free structure, material diversity, amenability with flexible surfaces, low sheet resistance (20-2000 Ω sq(-1)) and high transparency (60-90%). The excellent layer transparency of the patterned electrode and the VOFET's exceptional electrical performances make them both promising elements for future transparent and/or efficient organic electronics.