Oxidative Stress Responses and Nutrient Starvation in MCHM Treated Saccharomyces cerevisiae

In 2014, the coal cleaning chemical 4-methylcyclohexane methanol (MCHM) spilled into the water supply for 300,000 West Virginians. Initial toxicology tests showed relatively mild results, but the underlying effects on cellular biology were underexplored. Treated wildtype yeast cells grew poorly, but there was only a small decrease in cell viability. Cell cycle analysis revealed an absence of cells in S phase within thirty minutes of treatment. Cells accumulated in G1 over a six-hour time course, indicating arrest instead of death. A genetic screen of the haploid knockout collection revealed 329 high confidence genes required for optimal growth in MCHM. These genes encode three major cell processes: mitochondrial gene expression/translation, the vacuolar ATPase, and aromatic amino acid biosynthesis. The transcriptome showed an upregulation of pleiotropic drug response genes and amino acid biosynthetic genes and downregulation in ribosome biosynthesis. Analysis of these datasets pointed to environmental stress response activation upon treatment. Overlap in datasets included the aromatic amino acid genes ARO1, ARO3, and four of the five TRP genes. This implicated nutrient deprivation as the signal for stress response. Excess supplementation of nutrients and amino acids did not improve growth on MCHM, so the source of nutrient deprivation signal is still unclear. Reactive oxygen species and DNA damage were directly detected with MCHM treatment, but timepoints showed these accumulated slower than cells arrested. We propose that wildtype cells arrest from nutrient deprivation and survive, accumulating oxidative damage through the implementation of robust environmental stress responses

Effects of linker flexibility on phase behavior and structure of linked colloidal gels

Colloidal nanocrystal gels can be assembled using a difunctional "linker" molecule to mediate bonding between nanocrystals. The conditions for gelation and the structure of the gel are controlled macroscopically by the linker concentration and microscopically by the linker's molecular characteristics. Here, we demonstrate using a toy model for a colloid-linker mixture that linker flexibility plays a key role in determining both phase behavior and structure of the mixture. We fix the linker length and systematically vary its bending stiffness to span the flexible, semiflexible, and rigid regimes. At fixed linker concentration, flexible-linker and rigid-linker mixtures phase separate at low colloid volume fractions in agreement with predictions of first-order thermodynamic perturbation theory, but the semiflexible-linker mixtures do not. We correlate and attribute this qualitatively different behavior to undesirable "loop" linking motifs that are predicted to be more prevalent for linkers with end-to-end distances commensurate with the locations of chemical bonding sites on the colloids. Linker flexibility also influences the spacing between linked colloids, suggesting strategies to design gels with desired phase behavior, structure, and by extension, structure-dependent properties.Comment: 11 pages, 8 figures, supplementary materia

Universal Gelation of Metal Oxide Nanocrystals via Depletion Attractions

Nanocrystal gelation provides a powerful framework to translate nanoscale properties into bulk materials and to engineer emergent properties through the assembled microstructure. However, many established gelation strategies rely on chemical reactions and specific interactions, e.g., stabilizing ligands or ions on the surface of the nanocrystals, and are therefore not easily transferrable. Here, we report a general gelation strategy via non-specific and purely entropic depletion attractions applied to three types of metal oxide nanocrystals. The gelation thresholds of two compositionally distinct spherical nanocrystals agree quantitatively, demonstrating the adaptability of the approach for different chemistries. Consistent with theoretical phase behavior predictions, nanocrystal cubes form gels at a lower polymer concentration than nanocrystal spheres, allowing shape to serve as a handle to control gelation. These results suggest that the fundamental underpinnings of depletion-driven assembly, traditionally associated with larger colloidal particles, are also applicable at the nanoscale

Colorimetric quantification of linking in thermoreversible nanocrystal gel assemblies

Nanocrystal gels can be responsive, tunable materials, but designing their structure and properties is challenging. By using reversibly bonded molecular linkers, gelation can be realized under conditions predicted by thermody- namics. However, simulations have offered the only microscopic insights, with no experimental means to monitor linking leading to gelation. We introduce a metal coordination linkage with a distinct optical signature allowing us to quantify linking in situ and establish structural and thermodynamic bases for assembly. Because of coupling between linked indium tin oxide nanocrystals, their infrared absorption shifts abruptly at a chemically tunable gelation temperature. We quantify bonding spectroscopically and use molecular simulation to understand temperature-dependent bonding motifs, revealing that gel formation is governed by reaching a critical number of effective links that extend the nanocrystal network. Microscopic insights from our colorimetric linking chemistry enable switchable gels based on thermodynamic principles, opening the door to rational design of programmable nanocrystal networks.We would like to thank the University of Texas at Austin Mass Spectrometry and NMR Facility for the use of the Bruker AVANCE III 500: NIH grant number 1 S10 OD021508-01 and the Texas Materials Institute for the use of the SAXSLAB Ganesha, acquired using an NSF MRI grant CBET-1624659. We thank the Texas Advanced Computing Center (TACC) at the University of Texas at Austin for HPC resources. Funding: This research was primarily supported by the National Science Foundation through the Center for Dynamics and Control of Materials: an NSF Materials Research Science and Engineering Center (NSF MRSEC) under Cooperative Agreement DMR-1720595. E.V.A. acknowledges support from the Welch Regents Chair (F-0046). D.J.M. and T.M.T. also acknowledge support by the Welch Foundation (F-1696 and F-1848). This work was also supported by an NSF Graduate Research Fellowships (DGE-1610403) to S.A.V. and Arnold O. Beckman Postdoctoral Fellowship to Z.M.S.Center for Dynamics and Control of Material

Modular mixing in plasmonic metal oxide nanocrystal gels with thermoreversible links

Gelation offers a powerful strategy to assemble plasmonic nanocrystal networks incorporating both the distinctive optical properties of con- stituent building blocks and customizable collective properties. Beyond what a single-component assembly can offer, the characteristics of nanocrystal networks can be tuned in a broader range when two or more components are intimately combined. Here, we demonstrate mixed nanocrystal gel networks using thermoresponsive metal–terpyridine links that enable rapid gel assembly and disassembly with ther- mal cycling. Plasmonic indium oxide nanocrystals with different sizes, doping concentrations, and shapes are reliably intermixed in linked gel assemblies, exhibiting collective infrared absorption that reflects the contributions of each component while also deviating systematically from a linear combination of the spectra for single-component gels. We extend a many-bodied, mutual polarization method to simulate the optical response of mixed nanocrystal gels, reproducing the experimental trends with no free parameters and revealing that spectral devia- tions originate from cross-coupling between nanocrystals with distinct plasmonic properties. Our thermoreversible linking strategy directs the assembly of mixed nanocrystal gels with continuously tunable far- and near-field optical properties that are distinct from those of the building blocks or mixed close-packed structures.This research was primarily supported by the National Science Foundation through the Center for Dynamics and Control of Mate- rials: an NSF MRSEC under Cooperative Agreement No. DMR- 1720595, with additional support from an Arnold O. Beckman Postdoctoral Fellowship (Z.M.S.) and the Welch Foundation (Grant Nos. F-1696 and F-1848). E.V.A. acknowledges support from the Welch Regents Chair (No. F-0046). We acknowledge the Texas Advanced Computing Center (TACC) at the University of Texas at Austin for providing HPC resources.Center for Dynamics and Control of Material

Plasmonic response of complex nanoparticle assemblies

Optical properties of nanoparticle assemblies reflect distinctive characteristics of their building blocks and spatial organization, giving rise to emergent phenomena. Integrated experimental and computational studies have established design principles connecting the structure to properties for assembled clusters and superlattices. However, conventional electromagnetic simulations are too computationally expensive to treat more complex assemblies. Here we establish a fast, materials agnostic method to simulate the optical response of large nanoparticle assemblies incorporating both structural and compositional complexity. This many-bodied, mutual polarization method resolves limitations of established approaches, achieving rapid, accurate convergence for configurations including thousands of nanoparticles, with some overlapping. We demonstrate these capabilities by reproducing experimental trends and uncovering far- and near-field mechanisms governing the optical response of plasmonic semiconductor nanocrystal assemblies including structurally complex gel networks and compositionally complex mixed binary superlattices. This broadly applicable framework will facilitate the design of complex, hierarchically structured, and dynamic assemblies for desired optical characteristics.This research was primarily supported by the National Science Foundation through the Center for Dynamics and Control of Materials: an NSF Materials Research Science and Engineering Center (NSF MRSEC) under Cooperative Agreement DMR-1720595. E.V.A. acknowledges support from the Welch Regents Chair (F-0046). D.J.M. and T.M.T. acknowledge support from the Welch Foundation (F-1696 and F-1848) and NSF (CHE-1905263). This work was supported by an NSF Graduate Research Fellowship (DGE-1610403) to S.A.V. and Arnold O. Beckman Postdoctoral Fellowship to Z.M.S. We acknowledge the Texas Materials Institute for use of the SAXSLAB Ganesha, acquired using an NSF MRI grant CBET-1624659.Center for Dynamics and Control of Material

Assembly of Linked Nanocrystal Colloids by Reversible Covalent Bonds

The use of dynamically bonding molecules designed to reversibly link solvent-dispersed nanocrystals (NCs) is a promising strategy to form colloidal assemblies with controlled structure and macroscopic properties. In this work, tin-doped indium oxide NCs are functionalized with ligands that form reversible covalent bonds with linking molecules to drive assembly of NC gels. We monitor gelation using small angle X-ray scattering and characterize how changes in the gel structure affect infrared optical properties arising from the localized surface plasmon resonance of the NCs. The assembly is reversible because of the designed linking chemistry, and we disassemble the gels using two strategies: addition of excess NCs to change the ratio of linking molecules to NCs and addition of a capping molecule that displaces the linking molecules. The assembly behavior is rationalized using a thermodynamic perturbation theory to compute the phase diagram of the NC–linking molecule mixture. Coarse-grained molecular dynamics simulations reveal the competition between loop and bridge linking motifs essential for understanding NC gelation. This combined experimental, computational, and theoretical work provides a platform for controlling and designing the properties of reversible colloidal assemblies that incorporate NC and solvent compositions beyond those compatible with other contemporary (e.g, DNA-based) linking strategies.We would like to acknowledge the UT Mass Spectrometry Facility for their instrumental help and the UT NMR facilities for equipment use and assistance: NIH Grant Number 1 S10 OD021508-01. This work was primarily supported by the National Science Foundation through the Center for Dynamics and Control of Materials: an NSF Materials Research Science and Engineering Center (NSF MRSEC) under Cooperative Agreement DMR-1720595. This work was also supported by NSF Graduate Research Fellowships DGE-1610403 (M.N.D. and S.V.), an Arnold O. Beckman Postdoctoral Fellowship (Z.M.S.), NSF (CHE- 1905263), and the Welch Foundation (F-1848 and F-1696). E.V.A. acknowledges support from the Welch Regents Chair (F-0046). We acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing HPC resources.Center for Dynamics and Control of Material

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts