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At least 1,045 records · Page 58

Molecular pathways for learning in the single-cell Stentor coeruleus

The single-cell Stentor coeruleus contracts in response to mechanical taps but habituates and learns to ignore the taps after repeated stimulation. Here, we explored the molecular changes that occur during the formation of this cellular memory in order to improve our understanding of non-synaptic learning. We impaired cellular protein synthesis with cycloheximide and puromycin and found that, contrary to the effects of such treatments on metazoa, these drugs accelerate habituation and prolong memory retention in Stentor . Exploratory proteomic and transcriptomic analyses identified candidate proteins and genes that changed over the course of habituation and response recovery, pointing toward the regulation of Stentor learning by calcium signaling and protein phosphorylation. Building on these results, we found that using RNA interference to knock down the calcium-binding, EF-hand domain-containing protein SteCoe_6763 accelerated habituation. Furthermore, increased extracellular calcium improved Stentor learning, while treatment with kinase and phosphatase inhibitors impaired learning. In particular, KN-93, a drug known to inhibit calcium/calmodulin-dependent kinase II and voltage-gated calcium channels, decreased both the rate and extent of habituation in Stentor , similar to its effects on learning in metazoa. We also discovered that habituation memory can be maintained in progeny following cell division. Taken together, these results suggest that response recovery in Stentor requires new protein synthesis and that memory formation involves the modification of delocalized mechanoreceptors by phosphorylation and calcium signaling. This is consistent with our previous model of Stentor learning, in which habituation occurs through the inactivation of cell-surface receptors.

CaMKII↗

Enhancing microsegregation during rapid directional solidification through ternary microalloying

The nano-cellular dendritic microstructure formed during rapid directional solidification in powder bed fusion additive manufacturing creates unique properties such as simultaneous improvement in strength and ductility. However, process control of microsegregation features remains challenging due to low sensitivity of critical solidification mechanisms to process parameters. This study leverages microalloying to achieve large changes in dendrite composition, microstructure, and interdendritic zone width during laser powder bed fusion without modifying process parameters. CALPHAD simulations predict that the addition of Zr significantly steepens the solidus line of the dilute Cu-Cr alloy system, leading to enhanced Cr rejection into the melt and greater than 95% reduction in solubility of Cr in the solidified Cu matrix. Experimental validation using time-of-flight secondary ion mass spectrometry and Kelvin probe force microscopy reveals that the ternary alloy containing 0.01 wt% Zr exhibited wider interdendritic regions compared to the binary, a significantly higher number of Cr-rich particles within interdendritic regions, near-complete ejection of oxygen impurities from the matrix, and greater nanoscale work function contrast. These features indicate more aggressive Cr segregation in the presence of Zr and a purer Cu matrix and provide a potentially robust method for engineering the nano-cellular dendritic solidification microstructure.

CALPHAD↗

Small-world complex network generation on a digital quantum processor

Abstract Quantum cellular automata (QCA) evolve qubits in a quantum circuit depending only on the states of their neighborhoods and model how rich physical complexity can emerge from a simple set of underlying dynamical rules. The inability of classical computers to simulate large quantum systems hinders the elucidation of quantum cellular automata, but quantum computers offer an ideal simulation platform. Here, we experimentally realize QCA on a digital quantum processor, simulating a one-dimensional Goldilocks rule on chains of up to 23 superconducting qubits. We calculate calibrated and error-mitigated population dynamics and complex network measures, which indicate the formation of small-world mutual information networks. These networks decohere at fixed circuit depth independent of system size, the largest of which corresponding to 1,056 two-qubit gates. Such computations may enable the employment of QCA in applications like the simulation of strongly-correlated matter or beyond-classical computational demonstrations.

97 MATHEMATICS AND COMPUTING↗

Mechanism of tethered agonist-mediated signaling by polycystin-1

Mutations of polycystin-1 (PC1) are the major cause (85% of cases) of autosomal dominant polycystic kidney disease (ADPKD), which is the fourth leading cause of kidney failure. PC1 is thought to function as an atypical G protein-coupled receptor, yet the mechanism by which PC1 regulates G-protein signaling remains poorly understood. A significant portion of ADPKD mutations of PC1 encode a protein with defects in maturation or reduced function that may be amenable to functional rescue. In this work, we have combined complementary biochemical and cellular assay experiments and accelerated molecular simulations, which revealed an allosteric transduction pathway in activation of the PC1 C-terminal fragment. Our findings will facilitate future rational drug design efforts targeting the PC1 signaling function. Polycystin-1 (PC1) is an important unusual G protein-coupled receptor (GPCR) with 11 transmembrane domains, and its mutations account for 85% of cases of autosomal dominant polycystic kidney disease (ADPKD). PC1 shares multiple characteristics with Adhesion GPCRs. These include a GPCR proteolysis site that autocatalytically divides these proteins into extracellular, N-terminal, and membrane-embedded, C-terminal fragments (CTF), and a tethered agonist (TA) within the N-terminal stalk of the CTF that is suggested to activate signaling. However, the mechanism by which a TA can activate PC1 is not known. Here, we have combined functional cellular signaling experiments of PC1 CTF expression constructs encoding wild type, stalkless, and three different ADPKD stalk variants with all-atom Gaussian accelerated molecular dynamics (GaMD) simulations to investigate TA-mediated signaling activation. Correlations of residue motions and free-energy profiles calculated from the GaMD simulations correlated with the differential signaling abilities of wild type and stalk variants of PC1 CTF. They suggested an allosteric mechanism involving residue interactions connecting the stalk, Tetragonal Opening for Polycystins (TOP) domain, and putative pore loop in TA-mediated activation of PC1 CTF. Key interacting residues such as N3074–S3585 and R3848–E4078 predicted from the GaMD simulations were validated by mutagenesis experiments. Together, these complementary analyses have provided insights into a TA-mediated activation mechanism of PC1 CTF signaling, which will be important for future rational drug design targeting PC1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tritium Transport Modeling at the Pore Scale in Ceramic Breeder Materials Using TMAP8

Fusion reactors depend on the blanket material to breed and release tritium at the same rate or faster than it is consumed by the fusion reaction. Cellular ceramic breeders (CCBs) are dense materials that can maintain a high tritium breeding ratio while promoting tritium release because of highly connected pores. Assessing the tritium breeding capabilities of these materials requires a combination of extensive experimental and modeling efforts. In this work, we develop and calibrate a multiphysics model of tritium transport. This novel model accounts for ceramic and pore diffusion, trapping and detrapping, and several surface reactions at the pore surface. We perform a sensitivity analysis and calibrate the model by comparing its predictions against experimental measurements of deuterium absorption. The calibrated model is then used to model tritium absorption in samples with different pore microstructures to investigate the effect of pore interconnectivity on tritium absorption. The model is part of the development of the multiscale, multiphysics framework for tritium transport [i.e., the Tritium Migration Analysis Program (TMAP8)], which is itself built on top of the finite-element multiphysics framework multiphysics object-oriented simulation environment (MOOSE). This study demonstrates some of TMAP8’s capabilities and is the first step toward assessing the tritium breeding capabilities of ceramic breeder material designs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Rutin is a potent senomorphic agent to target senescent cells and can improve chemotherapeutic efficacy

Aging is a major risk factor for most chronic disorders, for which cellular senescence is one of the central hallmarks. Senescent cells develop the pro-inflammatory senescence-associated secretory phenotype (SASP), which significantly contributes to organismal aging and age-related disorders. Development of senotherapeutics, an emerging class of therapeutic agents to target senescent cells, allows to effectively delay aging and alleviate chronic pathologies. Here we report preliminary outputs from screening of a natural medicinal agent (NMA) library for senotherapeutic candidates and validated several agents with prominent potential as senomorphics. Rutin, a phytochemical constituent found in a number of plants, showed remarkable capacity in targeting senescent cells by dampening expression of the full spectrum SASP. Further analysis indicated that rutin restrains the acute stress-associated phenotype (ASAP) by specifically interfering with the interactions of ATM with HIF1α, a master regulator of cellular and systemic homeostasis activated during senescence, and of ATM with TRAF6, part of a key signaling axis supporting the ASAP development toward the SASP. Conditioned media produced by senescent stromal cells enhanced the malignant phenotypes of prostate cancer cells, including in vitro proliferation, migration, invasion, and more importantly, chemoresistance, while rutin remarkably downregulated these gain-of-functions. Although classic chemotherapy reduced tumor progression, the treatment outcome was substantially improved upon combination of a chemotherapeutic agent with rutin. Our study provides a proof of concept for rutin as an emerging natural senomorphic agent, and presents an effective therapeutic avenue for alleviating age-related pathologies including cancer.

60 APPLIED LIFE SCIENCES↗

A robust approach to 3D neuron shape representation for quantification and classification

We consider the problem of finding an accurate representation of neuron shapes, extracting sub-cellular features, and classifying neurons based on neuron shapes. In neuroscience research, the skeleton representation is often used as a compact and abstract representation of neuron shapes. However, existing methods are limited to getting and analyzing “curve” skeletons which can only be applied for tubular shapes. This paper presents a 3D neuron morphology analysis method for more general and complex neuron shapes. First, we introduce the concept of skeleton mesh to represent general neuron shapes and propose a novel method for computing mesh representations from 3D surface point clouds. A skeleton graph is then obtained from skeleton mesh and is used to extract sub-cellular features. Finally, an unsupervised learning method is used to embed the skeleton graph for neuron classification. Extensive experiment results are provided and demonstrate the robustness of our method to analyze neuron morphology.

3D neuron morphology↗

Nanoscale mapping of the three-dimensional deformation field within commercial nanodiamonds

Here, the unique properties of nanodiamonds make them suitable for use in a wide range of applications, including as biomarkers for cellular tracking in vivo at the molecular level. The sustained fluorescence of nanodiamonds containing nitrogen-vacancy (N-V) centres is related to their internal structure and strain state. Theoretical studies predict that the location of the N-V centre and the nanodiamonds' residual elastic strain state have a major influence on their photoluminescence properties. However, to date there have been no direct measurements made of their spatially resolved deformation fields owing to the challenges that such measurements present. Here we apply the recently developed technique of Bragg coherent diffractive imaging (BCDI) to map the three-dimensional deformation field within a single nanodiamond of approximately 0.5 µm diameter. The results indicate that there are high levels of residual elastic strain present in the nanodiamond which could have a critical influence on its optical and electronic properties.

36 MATERIALS SCIENCE↗

Completing the Connected Home with Smart Window Shades

Heat transfer through windows accounts for a significant percentage of a building’s energy use and adds substantially to the peak cooling load of a home. Window attachment manufacturers currently offer motorized shading devices for certain product lines, but this automation is typically marketed as a convenience and security feature for the homeowner and often does not include energy optimized control algorithms or dynamic and responsive features. This paper describes the experimental results of testing the energy performance of high-efficiency, dynamically operated, cellular shades in Pacific Northwest National Laboratory’s (PNNL) Lab Homes. The results of both heating and cooling season experiments will be presented, where testing is designed to assess the whole home energy savings resulting from both the thermal insulating properties as well as the automated and dynamic control strategies of shading devices. Control schemes tested include common “connected home” strategies where controls are integrated and coordinated between the window shading device, building thermostats, and external sensors. The presentation will also include results from testing designed to examine the benefits (in terms of comfort, energy savings, and responsiveness) of coordinating the operation of cellular shades with HVAC as a demand-response measure. These experiments demonstrate that highly insulating, dynamic window coverings that are reliably controlled can dramatically reduce the heating and cooling energy associated with windows and should be considered an important component of any “smart” home design.

energy savings, cellular shades, honeycomb shades,↗

Assessment of the Biological Impact of Engineered Nanomaterials Using Mass Spectrometry-based MultiOmics Approaches

The widespread use of engineered nanomaterials (ENMs) has expanded further than our understanding of their toxicity, prompting research into the biological responses against exposure to such materials. Genomics and transcriptomics have been extensively used to evaluate the biological effects of exposure to various ENMs. By determining gene activities, these studies provided valuable information to infer how cells respond to the toxicological effects of many ENMs. The application of mass spectrometry (MS)-based omics tools, such as proteomics, lipidomics, and metabolomics, offer post-genomic perspectives of what cellular processes are altered. Individually, these technologies have revealed the proteome, lipidome, and metabolome landscape upon exposure to ENMs. Together, these approaches demonstrate the ENM-induced adaptation in a broad range of cellular processes at multiple levels and the complexity of ENM-cell interactions. As a result, integrating multiple layers of MS-based omics data is trending to complement genomics data. In this review chapter, we discuss the applications of these tools for a comprehensive systems-level characterization of the biological responses induced by engineered nanomaterials.

Engineered nanomaterials, Proteomics, Metabolomics↗

Shape-Preserved Transformation of Biological Cells into Synthetic Hydrogel Microparticles

The synthesis of materials that can mimic the mechanical, and ultimately functional, properties of biological cells can broadly impact the development of biomimetic materials, as well as engineered tissues and therapeutics. Yet, it is challenging to synthesize, for example, microparticles that share both the anisotropic shapes and the elastic properties of living cells. Here in paper, a cell-directed route to replicate cellular structures into synthetic hydrogels such as polyethylene glycol (PEG) is described. First, the internal and external surfaces of chemically fixed cells are replicated in a conformal layer of silica using a sol–gel process. The template is subsequently removed to render shape-preserved, mesoporous silica replicas. Infiltration and cross-linking of PEG precursors and dissolution of the silica result in a soft hydrogel replica of the cellular template as demonstrated using erythrocytes, HeLa, and neuronal cultured cells. The elastic modulus can be tuned over an order of magnitude (≈10–100 kPa) though with a high degree of variability. Furthermore, synthesis without removing the biotemplate results in stimuli-responsive particles that swell/deswell in response to environmental cues. Overall, this work provides a foundation to develop soft particles with nearly limitless architectural complexity derived from dynamic biological templates.

59 BASIC BIOLOGICAL SCIENCES↗

Head on Comparison of Self- and Nano-Assemblies of Gamma Peptide Nucleic Acid Amphiphiles

Peptide nucleic acids (PNAs) are nucleic acid analogs with hybridization properties and enzymatic stability superior to that of DNA. In addition to gene targeting applications, PNAs have garnered significant attention as bio-polymers due to the Watson–Crick-based molecular recognition and flexibility of synthesis. Here, in this work, PNA amphiphiles are engineered using chemically modified gamma PNA (8 mer in length) containing hydrophilic diethylene glycol units at the gamma position and covalently conjugated lauric acid (C12) as a hydrophobic moiety. Gamma PNA ($\gamma$PNA) amphiphiles self-assemble into spherical vesicles. Further, nano-assemblies (NA) are formulated using the amphiphilic $\gamma$PNA as a polymer via ethanol injection-based protocols. Comprehensive head-on comparison of the physicochemical and cellular uptake properties of PNA derived self- and NA is performed. Small-angle neutron and X-ray scattering analysis reveal ellipsoidal morphology of $\gamma$PNA NA that results in superior cellular delivery compate to the spherical self-assembly. Next, the functional activities of $\gamma$PNA self-and NA in lymphoma cells via multiple endpoints, including gene expression, cell viability, and apoptosis-based assays are compared. Overall, it is established that $\gamma$PNA amphiphile is a functionally active bio-polymer to formulate NA for a wide range of biomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗

Design of the First‐in‐Class, Highly Potent Irreversible Inhibitor Targeting the Menin‐MLL Protein–Protein Interaction

Abstract The structure‐based design of M‐525 as the first‐in‐class, highly potent, irreversible small‐molecule inhibitor of the menin‐MLL interaction is presented. M‐525 targets cellular menin protein at sub‐nanomolar concentrations and achieves low nanomolar potencies in cell growth inhibition and in the suppression of MLL‐regulated gene expression in MLL leukemia cells. M‐525 demonstrates high cellular specificity over non‐MLL leukemia cells and is more than 30 times more potent than its corresponding reversible inhibitors. Mass spectrometric analysis and co‐crystal structure of M‐525 in complex with menin firmly establish its mode of action. A single administration of M‐525 effectively suppresses MLL‐regulated gene expression in tumor tissue. An efficient procedure was developed to synthesize M‐525. This study demonstrates that irreversible inhibition of menin may be a promising therapeutic strategy for MLL leukemia.

Xu, Shilin↗

Design of the First-in-Class, Highly Potent Irreversible Inhibitor Targeting the Menin-MLL Protein–Protein Interaction

The structure-based design of M-525 as the first-in-class, highly potent, irreversible small-molecule inhibitor of the menin-MLL interaction is presented. M-525 targets cellular menin protein at sub-nanomolar concentrations and achieves low nanomolar potencies in cell growth inhibition and in the suppression of MLL-regulated gene expression in MLL leukemia cells. M-525 demonstrates high cellular specificity over non-MLL leukemia cells and is more than 30 times more potent than its corresponding reversible inhibitors. Mass spectrometric analysis and co-crystal structure of M-525 in complex with menin firmly establish its mode of action. A single administration of M-525 effectively suppresses MLL-regulated gene expression in tumor tissue. An efficient procedure was developed to synthesize M-525. This study demonstrates that irreversible inhibition of menin may be a promising therapeutic strategy for MLL leukemia.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Improved two–stage protein expression and purification via autoinduction of both autolysis and auto DNA/RNA hydrolysis conferred by phage lysozyme and DNA/RNA endonuclease

We report improved release of recombinant proteins in Escherichia coli, which relies on combined cellular autolysis and DNA/RNA autohydrolysis, conferred by the tightly controlled autoinduction of both phage lysozyme and the nonspecific DNA/RNA endonuclease from Serratia marcescens. Autoinduction occurs in a two–stage process wherein heterologous protein expression and autolysis enzymes are induced upon entry into stationary phase by phosphate depletion. Cytoplasmic lysozyme and periplasmic endonuclease are kept from inducing lysis until membrane integrity is disrupted. After cell harvest, the addition of detergent (0.1% Triton X–100) and a single 30 min freeze–thaw cycle results in >90% release of protein, green fluorescent protein. Here, this cellular lysis is accompanied by complete oligonucleotide hydrolysis. The approach has been validated for shake flask cultures, high–throughput cultivation in microtiter plates, and larger scale stirred–tank bioreactors. This tightly controlled system enables robust growth and resistance to lysis in routine media when cells are propagated and autolysis/hydrolysis genes are only induced upon phosphate depletion

59 BASIC BIOLOGICAL SCIENCES↗

Impact of media and antifoam selection on monoclonal antibody production and quality using a high throughput micro-bioreactor system

Monoclonal antibody production in commercial scale cell culture bioprocessing requires a thorough understanding of the engineering process and components used throughout manufacturing. It is important to identify high impact components early on during the lifecycle of a biotechnology-derived product. While cell culture media selection is of obvious importance to the health and productivity of mammalian bioreactor operations, other components such as antifoam selection can also play an important role in bioreactor cell culture. Silicone polymer-based antifoams were known to have negative impacts on cell health, production, and downstream filtration and purification operations. High throughput screening in micro-scale bioreactors provides an efficient strategy to identify initial operating parameters. Here, we utilized a micro-scale parallel bioreactor system to study an IgG1 producing CHO cell line, to screen Dynamis, ProCHO5, PowerCHO2, EX-Cell Advanced, and OptiCHO media, and 204, C, EX-Cell, SE-15, and Y-30 antifoams and their impacts on IgG1 production, cell growth, aggregation, and process control. This study found ProCHO5, EX-Cell Advanced, and PowerCHO2 media supported strong cellular growth profiles, with an IVCD of 25-35 3 106 cells-d/ mL, while maintaining specific antibody production (Qp> 2 pg/cell-d) for our model cell line and a monomer percentage above 94%. Antifoams C, EX-Cell, and SE-15 were capable of providing adequate control of foaming while antifoam 204 and Y-30 noticeably stunted cellular growth. This work highlights the utility of high throughput micro bioreactors and the importance of identifying both positive and negative impacts of media and antifoam selection on a model IgG1 producing CHO cell line.

59 BASIC BIOLOGICAL SCIENCES↗

Compensatory grazing by Daphnia generates a trade‐off between top‐down and bottom‐up effects across phytoplankton taxa

Abstract Trade‐offs among traits that shape different components of fitness determine the potential for species to coexist in communities and the regulation of ecosystem productivity by consumers vs. resources. We compared functional and structural traits of 14 species of freshwater phytoplankton to test the influence of life history (exponential growth rate, r, and asymptotic density, K), cell volume, cellular fatty acid ( FA ) biochemistry, and stoichiometry (cellular C:N and C:P ratios) on grazing and growth rate of Daphnia consumers. Grazers exerted the strongest top‐down effects on algae with the highest C:N and C:P, and lower levels of FA unsaturation. In contrast, the grazer's growth rate was most associated with phytoplankton species’ FA unsaturation and chain length. Different traits were related to grazing rate and trophic transfer efficiency, and as a result, the grazing rate on a particular phytoplankton taxon was unrelated to the grazers’ growth rate. The best nutrient competitors (those with high C:N, C:P, and K, which previous experiments showed had lower minimum requirements for nutrients) were most heavily affected by grazing, but did not contribute the most to grazer growth. Our results indicate that Daphnia increase their food consumption rate in order to compensate for low stoichiometric food quality. Strong competitors with low nutrient demands may therefore be subject to the most intense grazing by individual consumers but not support greater production of higher trophic levels.

Mandal, Shovon↗

A deep learning-guided automated workflow in LipidOz for detailed characterization of fungal fatty acid unsaturation by ozonolysis

Understanding fungal lipid biology and metabolism is critical for antifungal target discovery as lipids play central roles in cellular processes. Nuances in lipid structural differences can significantly impact their functions, making it necessary to characterize lipids in detail to enable and understanding of their roles in these complex systems. In particular, lipid double bond (DB) locations are an important component of lipid structure that can only be determined using a few specialized analytical techniques. Ozone-induced dissociation mass spectrometry (OzID-MS) is one such technique that uses ozone to break lipid DBs, producing pairs of characteristic fragments that allow the determination of DB positions. In this work we apply OzID-MS and LipidOz software to analyze the complex lipids of Saccharomyces cerevisiae yeast strains transfected with different fatty acid desaturases from Histoplasma capsulatum to determine the specific unsaturated lipids produce. The automated data analysis in LipidOz made the determination of DB positions from this large dataset more practical, but manual verification for all targets was still time-consuming. The DL model reduces manual involvement in data analysis, but since it was trained using mammalian lipid extracts, the prediction accuracy on yeast-derived data was reduced. We addressed both shortcomings by retraining the DL model to act as a pre-filter to prioritize targets for automated analysis, providing confident manually verified results but requiring less computational time and manual effort. Our workflow resulted in the determination of novel DB positions and enzymatic specificity.

mass spectrometry, deep learning, Lipidomics, doub↗