Multicenter integrated analysis of noncoding CRISPRi screens.

The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.

Genome-wide enhancer maps link risk variants to disease genes.

Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complex traits, each of which could reveal insights into the mechanisms of disease1. Many of the underlying causal variants may affect enhancers2,3, but we lack accurate maps of enhancers and their target genes to interpret such variants. We recently developed the activity-by-contact (ABC) model to predict which enhancers regulate which genes and validated the model using CRISPR perturbations in several cell types4. Here we apply this ABC model to create enhancer-gene maps in 131 human cell types and tissues, and use these maps to interpret the functions of GWAS variants. Across 72 diseases and complex traits, ABC links 5,036 GWAS signals to 2,249 unique genes, including a class of 577 genes that appear to influence multiple phenotypes through variants in enhancers that act in different cell types. In inflammatory bowel disease (IBD), causal variants are enriched in predicted enhancers by more than 20-fold in particular cell types such as dendritic cells, and ABC achieves higher precision than other regulatory methods at connecting noncoding variants to target genes. These variant-to-function maps reveal an enhancer that contains an IBD risk variant and that regulates the expression of PPIF to alter the membrane potential of mitochondria in macrophages. Our study reveals principles of genome regulation, identifies genes that affect IBD and provides a resource and generalizable strategy to connect risk variants of common diseases to their molecular and cellular functions.

Evidence for long-term potentiation in phospholipid membranes.

Biological supramolecular assemblies, such as phospholipid bilayer membranes, have been used to demonstrate signal processing via short-term synaptic plasticity (STP) in the form of paired pulse facilitation and depression, emulating the brain's efficiency and flexible cognitive capabilities. However, STP memory in lipid bilayers is volatile and cannot be stored or accessed over relevant periods of time, a key requirement for learning. Using droplet interface bilayers (DIBs) composed of lipids, water and hexadecane, and an electrical stimulation training protocol featuring repetitive sinusoidal voltage cycling, we show that DIBs displaying memcapacitive properties can also exhibit persistent synaptic plasticity in the form of long-term potentiation (LTP) associated with capacitive energy storage in the phospholipid bilayer. The time scales for the physical changes associated with the LTP range between minutes and hours, and are substantially longer than previous STP studies, where stored energy dissipated after only a few seconds. STP behavior is the result of reversible changes in bilayer area and thickness. On the other hand, LTP is the result of additional molecular and structural changes to the zwitterionic lipid headgroups and the dielectric properties of the lipid bilayer that result from the buildup of an increasingly asymmetric charge distribution at the bilayer interfaces.

Adsorption, Orientation, and Speciation of Amino Acids at Air-Aqueous Interfaces for the Direct Air Capture of CO2.

Amino acids make up a promising family of molecules capable of direct air capture (DAC) of CO2 from the atmosphere. Under alkaline conditions, CO2 reacts with the anionic form of an amino acid to produce carbamates and deactivated zwitterionic amino acids. The presence of the various species of amino acids and reactive intermediates can have a significant effect on DAC chemistry, the role of which is poorly understood. In this study, all-atom molecular dynamics (MD) based computational simulations and vibrational sum frequency generation (vSFG) spectroscopy studies were conducted to understand the role of competitive interactions at the air-aqueous interface in the context of DAC. We find that the presence of potassium bicarbonate ions, in combination with the anionic and zwitterionic forms of amino acids, induces concentration and charge gradients at the interface, generating a layered molecular arrangement that changes under pre- and post-DAC conditions. In parallel, an enhancement in the surface activity of both anionic and zwitterionic forms of amino acids is observed, which is attributed to enhanced interfacial stability and favorable intermolecular interactions between the adsorbed amino acids in their anionic and zwitterionic forms. The collective influence of these competitive interactions, along with the resulting interfacial heterogeneity, may in turn affect subsequent capture reactions and associated rates. These effects underscore the need to consider dynamic changes in interfacial chemical makeup to enhance DAC efficiency and to develop successful negative emission and storage technologies.

Unravelling photoisomerization dynamics in a metastable-state photoacid.

Direct access to trans-cis photoisomerization in a metastable state photoacid (mPAH) remains challenging owing to the presence of competing excited-state relaxation pathways and multiple transient isomers with overlapping spectra. Here, we reveal the photoisomerization dynamics in an indazole mPAH using time-resolved fluorescence (TRF) spectroscopy by exploiting a unique property of this mPAH having fluorescence only from the trans isomer. The combination of these experimental results with time-dependent density function theory (TDDFT) calculations enables us to gain mechanistic insight into this key dynamical process.

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes.

Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.

Photochemically-Driven CO2 Release Using a Metastable-State Photoacid for Energy Efficient Direct Air Capture.

One of the grand challenges underlying current direct air capture (DAC) technologies relates to the intensive energy cost for sorbent regeneration and CO2 release, making the massive scale (GtCO2 /year) deployment required to have a positive impact on climate change economically unfeasible. This challenge underscores the critical need to develop new DAC processes with substantially reduced regeneration energies. Here, we report a photochemically-driven approach for CO2 release by exploiting the unique properties of an indazole metastable-state photoacid (mPAH). Our measurements on simulated and amino acid-based DAC systems revealed the potential of mPAH to be used for CO2 release cycles by regulating pH changes and associated isomers driven by light. Upon irradiating with moderate intensity light, a ≈55 % and ≈68 % to ≈78 % conversion of total inorganic carbon to CO2 was found for the simulated and amino acid-based DAC systems, respectively. Our results confirm the feasibility of on-demand CO2 release under ambient conditions using light instead of heat, thereby providing an energy efficient pathway for the regeneration of DAC sorbents.

Improving Rare-Earth Mineral Separation with Insights from Molecular Recognition: Functionalized Hydroxamic Acid Adsorption onto Bastnäsite and Calcite.

Enhancing the separation of rare-earth elements (REEs) from gangue materials in mined ores requires an understanding of the fundamental interactions driving the adsorption of collector ligands onto mineral interfaces. In this work, we examine five functionalized hydroxamic acid ligands as potential collectors for the REE-containing bastnäsite mineral in froth flotation using density functional theory calculations and a suite of surface-sensitive analytical spectroscopies. These include vibrational sum frequency generation, attenuated total reflectance Fourier transform infrared, Raman, and X-ray photoelectron spectroscopies. Differences in the chemical makeup of these ligands on well-defined bastnäsite and calcite surfaces allow for a systematic relationship connecting the structure to adsorption activity to be framed in the context of interfacial molecular recognition. We show how the intramolecular hydrogen bonding of adsorbed ligands requires the inclusion of explicit water solvent molecules to correctly map energetic and structural trends measured by experiments. We anticipate that the results and insights from this work will motivate and inform the design of improved flotation collectors for REE ores.

Correction: Interfacial acidity on the strontium titanate surface: a scaling paradigm and the role of the hydrogen bond.

Correction for 'Interfacial acidity on the strontium titanate surface: a scaling paradigm and the role of the hydrogen bond' by Robert C. Chapleski, Jr. et al., Phys. Chem. Chem. Phys., 2021, 23, 23478-23485, DOI: 10.1039/D1CP03587H.

Mapping the Interfacial Chemistry and Structure of Partially Fluorinated Bottlebrush Polymers and Their Linear Analogues.

Polymer interfaces are key to a range of applications including membranes for chemical separations, hydrophobic coatings, and passivating layers for antifouling. While important, challenges remain in probing the interfacial monolayer where the molecular ordering and orientation can change depending on the chemical makeup or processing conditions. In this work, we leverage surface specific vibrational sum frequency generation (SFG) and the associated dependence on molecular symmetry to elucidate the ordering and orientations of key functional groups for poly(2,2,2-trifluoroethyl methacrylate) bottlebrush polymers and their linear polymer analogues. These measurements were framed by atomistic molecular dynamic simulations to provide a complementary physical picture of the gas-polymer interface. Simulations and SFG measurements show that methacrylate backbones are buried beneath a layer of trifluoroethyl containing side groups that result in structurally similar interfaces regardless of the polymer molecular weight or architecture. The average orientational angles of the trifluoroethyl containing side groups differ depending on polymer linear and bottlebrush architectures, suggesting that the surface groups can reorient via available rotational degrees of freedom. Results show that the surfaces of the bottlebrush and linear polymer samples do not strongly depend on molecular weight or architecture. As such, one cannot rely on increasing the molecular weight or altering the architecture to tune surface properties. This insight into the polymer interfacial structure is expected to advance the design of new material interfaces with tailored chemical/functional properties.

Spatially co-registered wide-field nonlinear optical imaging of living and complex biosystems in a total internal reflection geometry.

Nonlinear optical microscopy that leverages an objective based total internal reflection (TIR) excitation scheme is an attractive means for rapid, wide-field imaging with enhanced surface sensitivity. Through select combinations of distinct modalities, one can, in principle, access complementary chemical and structural information for various chemical species near interfaces. Here, we report a successful implementation of such a wide-field nonlinear optical microscope system, which combines coherent anti-Stokes Raman scattering (CARS), two-photon fluorescence (TPF), second harmonic generation (SHG), and sum frequency generation (SFG) modalities on the same platform. The intense optical fields needed to drive these high order nonlinear optical processes are achieved through the use of femtosecond pulsed light in combination with the intrinsic field confinement induced by TIR over a large field of view. The performance of our multimodal microscope was first assessed through the experimental determination of its chemical fidelity, intensity and polarization dependences, and spatial resolution using a set of well-defined model systems. Subsequently, its unique capabilities were validated through imaging complex biological systems, including Hydrangea quercifolia pollen grains and Pantoea sp. YR343 bacterial cells. Specifically, the spatial distribution of different molecular groups in the former was visualized via vibrational contrast mechanisms of CARS, whereas co-registered TPF imaging allowed the identification of spatially localized intrinsic fluorophores. We further demonstrate the feasibility of our microscope for wide-field CARS imaging on live cells through independent characterization of cell viability using spatially co-registered TPF imaging. This approach to TIR enabled wide-field imaging is expected to provide new insights into bacterial strains and their interactions with other species in the rhizosphere in a time-resolved and chemically selective manner.

Interfacial acidity on the strontium titanate surface: a scaling paradigm and the role of the hydrogen bond.

A fundamental understanding of acidity at an interface, as mediated by structure and molecule-surface interactions, is essential to elucidate the mechanisms of a range of chemical transformations. While the strength of an acid in homogeneous gas and solution phases is conceptually well understood, acid-base chemistry at heterogeneous interfaces is notoriously more complicated. Using density functional theory and nonlinear vibrational spectroscopy, we present a method to determine the interfacial Brønsted-Lowry acidity of aliphatic alcohols adsorbed on the (100) surface of the model perovskite, strontium titanate. While shorter and less branched alkanols are known to be less acidic in the gas phase and more acidic in solution, here we show that shorter alcohols are less acidic whereas less substituted alkanols are more acidic at the gas-oxide interface. Hydrogen bonding plays a critical role in defining acidity, whereas structure-acidity relationships are dominated by van der Waals interactions between the alcohol and the surface.

Nonlinear Optical Microscopy with Ultralow Quantum Light.

Nonlinear optical (NLO) microscopy relies on multiple light-matter interactions to provide unique contrast mechanisms and imaging capabilities that are inaccessible to traditional linear optical imaging approaches, making them versatile tools to understand a wide range of complex systems. However, the strong excitation fields that are necessary to drive higher-order optical processes efficiently are often responsible for photobleaching, photodegradation, and interruption in many systems of interest. This is especially true for imaging living biological samples over prolonged periods of time or in accessing intrinsic dynamics of electronic excited-state processes in spatially heterogeneous materials. This perspective outlines some of the key limitations of two NLO imaging modalities implemented in our lab and highlights the unique potential afforded by the quantum properties of light, especially entangled two-photon absorption based NLO spectroscopy and microscopy. We further review some of the recent exciting advances in this emerging filed and highlight some major challenges facing the realization of quantum-light-enabled NLO imaging modalities.

Insight into the Mechanisms Driving the Self-Assembly of Functional Interfaces: Moving from Lipids to Charged Amphiphilic Oligomers.

Polymer-stabilized liquid/liquid interfaces are an important and growing class of bioinspired materials that combine the structural and functional capabilities of advanced synthetic materials with naturally evolved biophysical systems. These platforms have the potential to serve as selective membranes for chemical separations and molecular sequencers and to even mimic neuromorphic computing elements. Despite the diversity in function, basic insight into the assembly of well-defined amphiphilic polymers to form functional structures remains elusive, which hinders the continued development of these technologies. In this work, we provide new mechanistic insight into the assembly of an amphiphilic polymer-stabilized oil/aqueous interface, in which the headgroups consist of positively charged methylimidazolium ionic liquids, and the tails are short, monodisperse oligodimethylsiloxanes covalently attached to the headgroups. We demonstrate using vibrational sum frequency generation spectroscopy and pendant drop tensiometery that the composition of the bulk aqueous phase, particularly the ionic strength, dictates the kinetics and structures of the amphiphiles in the organic phase as they decorate the interface. These results show that H-bonding and electrostatic interactions taking place in the aqueous phase bias the grafted oligomer conformations that are adopted in the neighboring oil phase. The kinetics of self-assembly were ionic strength dependent and found to be surprisingly slow, being composed of distinct regimes where molecules adsorb and reorient on relatively fast time scales, but where conformational sampling and frustrated packing takes place over longer time scales. These results set the stage for understanding related chemical phenomena of bioinspired materials in diverse technological and fundamental scientific fields and provide a solid physical foundation on which to design new functional interfaces.

Publisher Correction: Reply to: On the ferroelectricity of CH3NH3PbI3 perovskites.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Total internal reflection enabled wide-field coherent anti-Stokes Raman scattering microscopy.

Wide-field coherent anti-Stokes Raman scattering (CARS) microscopy offers an attractive means for the rapid and simultaneous acquisition of vibrationally resolved images across a large field of view. A major challenge in the implementation lies in how to achieve sufficiently strong excitation fields necessary to drive the third-order optical responses over the large focal region. Here, we report a new wide-field CARS microscope enabled by a total internal reflection excitation scheme using a femtosecond Ti:Sapphire oscillator to generate pump and broadband near-infrared Stokes pulses. The spectrally broad Stokes pulse, in combination with its inherent chirp, offers not only access to a wide range of Raman modes spanning ∼1000 to ∼3500cm-1 but also a straightforward means to select vibrational transitions within this range by simply varying the time delay between the pulses. The unique capabilities of this wide-field CARS microscope were validated by acquiring high-quality CARS images from the model and complex biological samples on conventional microscope coverslips.

Connecting Femtosecond Transient Absorption Microscopy with Spatially Coregistered Time Averaged Optical Imaging Modalities.

Multimodal all-optical imaging involving coregistered femtosecond transient absorption microscopy (TAM), time-integrated photoluminescence (PL), and steady-state modalities such as confocal reflectance and transmission offers an appealing approach to gain a comprehensive understanding of complex electronic excited-state phenomena in spatially heterogeneous systems. A unique combination of these modalities allows us to unravel not only the competing electronic excited-state dynamical processes but also the underlying morphological information with simultaneous high temporal and spatial resolution. However, correlating the various images obtained from time-resolved and time-independent modalities is generally nontrivial and particularly challenging when the electronic dynamics under study evolve in both time and space. Here, we demonstrate a new approach for rationally correlating time-resolved microscopy with coregistered time-integrated or steady-state modalities. Specifically, our approach involves an extended global lifetime analysis of the time-resolved microscopic data set to separate distinct dynamical processes taking place on commensurate time scales, and the resulting decay-associated amplitude maps (DAAMs) were applied to explore correlations with the images acquired using time-independent modalities. The feasibility of our approach was validated through analyzing a multimodal data set acquired from a thin film of chloride-containing mixed lead halide perovskites (CH3NH3PbI3-xClx) using femtosecond transient absorption, time-integrated PL, and confocal reflectance microscopies. Analysis of the results obtained enable us to gain new insight into the complex ultrafast relaxation dynamics in this highly heterogeneous system.

Energetics at the Surface: Direct Optical Mapping of Core and Surface Electronic Structure in CdSe Quantum Dots Using Broadband Electronic Sum Frequency Generation Microspectroscopy.

Understanding and controlling the electronic structure of nanomaterials is the key to tailoring their use in a wide range of practical applications. Despite this need, many important electronic states are invisible to conventional optical measurements and are typically identified indirectly based on their inferred impact on luminescence properties. This is especially common and important in the study of nanomaterial surfaces and their associated defects. Surface trap states play a crucial role in photophysical processes yet remain remarkably poorly understood. Here we demonstrate for the first time that broadband electronic sum frequency generation (eSFG) microspectroscopy can directly map the optically bright and dark states of nanoparticles, including the elusive below gap states. This new approach is applied to model cadmium selenide (CdSe) quantum dots (QDs), where the energies of surface trap states have eluded direct optical characterization for decades. Our eSFG measurements show clear signatures of electronic transitions both above the band gap, which we assign to previously reported one- and two-photon transitions associated with the CdSe core, as well as broad spectral signatures below the band gap that are attributed to surface states. In addition to the core states, this analysis reveals two distinct distributions of below gap states, providing the first direct optical measurement of both shallow and deep surface states on this system. Finally, chemical modification of the surfaces via oxidation results in the relative increase in the signals originating from the surface states. Overall, our eSFG experiments provide an avenue to directly map the entirety of the QD core and surface electronic structure, which is expected to open up opportunities to study how these materials are grown in situ and how surface states can be controlled to tune functionality.

Chemical nature of ferroelastic twin domains in CH3NH3PbI3 perovskite.

The extraordinary optoelectronic performance of hybrid organic-inorganic perovskites has resulted in extensive efforts to unravel their properties. Recently, observations of ferroic twin domains in methylammonium lead triiodide drew significant attention as a possible explanation for the current-voltage hysteretic behaviour in these materials. However, the properties of the twin domains, their local chemistry and the chemical impact on optoelectronic performance remain unclear. Here, using multimodal chemical and functional imaging methods, we unveil the mechanical origin of the twin domain contrast observed with piezoresponse force microscopy in methylammonium lead triiodide. By combining experimental results with first principles simulations we reveal an inherent coupling between ferroelastic twin domains and chemical segregation. These results reveal an interplay of ferroic properties and chemical segregation on the optoelectronic performance of hybrid organic-inorganic perovskites, and offer an exploratory path to improving functional devices.

Structural correlations tailor conductive properties in polymerized ionic liquids.

Polymerized ionic liquids (PolyILs) are promising materials for applications in electrochemical devices spanning from fuel cells to capacitors and batteries. In principle, PolyILs have a competitive advantage over traditional electrolytes in being single ion conductors and thus enabling a transference number close to unity. Despite this perceived advantage, surprisingly low room temperature ionic conductivities measured in the lab raise an important fundamental question: how does the molecular structure mediate conductivity? In this work, wide-angle X-ray scattering (WAXS), vibrational sum frequency generation (vSFG), and density functional theory (DFT) calculations were used to study the bulk and interfacial structure of PolyILs, while broad band dielectric spectroscopy (BDS) was used to probe corresponding dynamics and conductive properties for a series of the PolyIL samples with tunable chemistries and structures. Our results reveal that the size of the mobile anions has a tremendous impact on chain packing in PolyILs that wasn't addressed previously. Larger mobile ions tend to create a well-packed structure, while smaller ions frustrate chain packing. The magnitude of these changes and level of structural heterogeneity are shown to depend on the chemical functionality and flexibility of studied PolyILs. Furthermore, these experimental and computational results provide new insight into the correlation between conductivity and structure in PolyILs, suggesting that structural heterogeneity helps to reduce the activation energy for ionic conductivity in the glassy state.