Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect.

The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts that adaptation is due to a few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and using RAD-seq genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that one to two large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling. One QTL locus was shared across all populations and another was shared across three populations. One QTL locus showed strong signatures of recent natural selection in the corresponding wild population but another QTL locus did not. Some candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.

Molecular Precursor Approach to Sulfur-Free CuInSe2: Replacing Thiol Coordination in Soluble Metal Complexes.

Solution-processed CuInSe2 films have generally relied on sulfide or sulfoselenide precursor films that, during the grain growth process, hamper the growth of thicker films and lead to the formation of a fine-grain layer. However, recent research has indicated that sulfur reduction in the precursor film modifies the grain growth mechanism and may enable the fabrication of thicker absorbers that are free of any fine-grain layer. In this work, we pursue direct solution deposition of sulfur-free CuInSe2 films from the molecular precursor approach. To this end, we tune the amine-thiol reactive solvent system and study the changes to the resulting soluble complexes through a combination of analytical techniques. We show that by reactively dissolving indium(III) selenide and selenium in solutions of n-butylamine and 1,2-ethanedithiol, a metal thiolate species is formed, and that this metal thiolate can be modified by isolation from the thiol-containing solvent via precipitation. As the quantity of selenium in the ink increases, the thiol content in the complex decreases, eventually producing soluble [InSex]- species. Extending this method to be used with copper selenide as a copper source, molecular precursor inks can be made for solution-processed, sulfur-free CuInSe2 films. We then show that these CuInSe2 precursor films can be fully coarsened without a fine-grain layer formation, even at the desired thicknesses of 2 µm and greater.

Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer.

Androgen receptor (AR) inhibition is standard of care for advanced prostate cancer (PC). However, efficacy is limited by progression to castration-resistant PC (CRPC), usually due to AR re-activation via mechanisms that include AR amplification and structural rearrangement. These two classes of AR alterations often co-occur in CRPC tumors, but it is unclear whether this reflects intercellular or intracellular heterogeneity of AR. Resolving this is important for developing new therapies and predictive biomarkers. Here, we analyzed 41 CRPC tumors and 6 patient-derived xenografts (PDXs) using linked-read DNA-sequencing, and identified 7 tumors that developed complex, multiply-rearranged AR gene structures in conjunction with very high AR copy number. Analysis of PDX models by optical genome mapping and fluorescence in situ hybridization showed that AR residing on extrachromosomal DNA (ecDNA) was an underlying mechanism, and was associated with elevated levels and diversity of AR expression. This study identifies co-evolution of AR gene copy number and structural complexity via ecDNA as a mechanism associated with endocrine therapy resistance.

Variable rates of hybridization among contact zones between a pair of topminnow species, Fundulus notatus and F. olivaceus.

Pairs of species that exhibit broadly overlapping distributions, and multiple geographically isolated contact zones, provide opportunities to investigate the mechanisms of reproductive isolation. Such naturally replicated systems have demonstrated that hybridization rates can vary substantially among populations, raising important questions about the genetic basis of reproductive isolation. The topminnows, Fundulus notatus and F. olivaceus, are reciprocally monophyletic, and co-occur in drainages throughout much of the central and southern United States. Hybridization rates vary substantially among populations in isolated drainage systems. We employed genome-wide sampling to investigate geographic variation in hybridization, and to assess the possible importance of chromosome fusions to reproductive isolation among nine separate contact zones. The species differ by chromosomal rearrangements resulting from Robertsonian (Rb) fusions, so we hypothesized that Rb fusion chromosomes would serve as reproductive barriers, exhibiting steeper genomic clines than the rest of the genome. We observed variation in hybridization dynamics among drainages that ranged from nearly random mating to complete absence of hybridization. Contrary to predictions, our use of genomic cline analyses on mapped species-diagnostic SNP markers did not indicate consistent patterns of variable introgression across linkage groups, or an association between Rb fusions and genomic clines that would be indicative of reproductive isolation. We did observe a relationship between hybridization rates and population phylogeography, with the lowest rates of hybridization tending to be found in populations inferred to have had the longest histories of drainage sympatry. Our results, combined with previous studies of contact zones between the species, support population history as an important factor in explaining variation in hybridization rates.

The Role of Lewis Acid Sites in γ-Al2 O3 Oligomerization.

Olefin oligomerization by γ-Al2 O3 has recently been reported, and it was suggested that Lewis acid sites are catalytic. The goal of this study is to determine the number of active sites per gram of alumina to confirm that Lewis acid sites are indeed catalytic. Addition of an inorganic Sr oxide base resulted in a linear decrease in the propylene oligomerization conversion at loadings up to 0.3 wt %; while, there is a >95 % loss in conversion above 1 wt % Sr. Additionally, there was a linear decrease in the intensity of the Lewis acid peaks of absorbed pyridine in the IR spectra with an increase in Sr loading, which correlates with the loss in propylene conversion, suggesting that Lewis acid sites are catalytic. Characterization of the Sr structure by XAS and STEM indicates that single Sr2+ ions are bound to the γ-Al2 O3 surface and poison one catalytic site per Sr ion. The maximum loading needed to poison all catalytic sites, assuming uniform surface coverage, was ∼0.4 wt % Sr, giving an acid site density of ∼0.2 sites per nm2 of γ-Al2 O3 , or approximately 3 % of the alumina surface.

Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect.

The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts the influence of few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that a few large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling, where some (but not all) of these QTL loci were shared across all populations, and some (but not all) of these loci showed signatures of recent natural selection in the corresponding wild population. Some strong candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.

Intermetallic alloy structure-activity descriptors derived from inelastic X-ray scattering.

Synchrotron spectroscopy and Density Functional Theory (DFT) are combined to develop a new descriptor for the stability of adsorbed chemical intermediates on metal alloy surfaces. This descriptor probes the separation of occupied and unoccupied d electron density in platinum and is related to shifts in Resonant Inelastic X-ray Scattering (RIXS) signals. Simulated and experimental spectroscopy are directly compared to show that the promoter metal identity controls the orbital shifts in platinum electronic structure. The associated RIXS features are correlated with the differences in the band centers of the occupied and unoccupied d bands, providing chemical intuition for the alloy ligand effect and providing a connection to traditional descriptions of chemisorption. The ready accessibility of this descriptor to both DFT calculations and experimental spectroscopy, and its connection to chemisorption, allow for deeper connections between theory and characterization in the discovery of new catalysts.

Highly stable, antiviral, antibacterial cotton textiles via molecular engineering.

Cotton textiles are ubiquitous in daily life and are also one of the primary mediums for transmitting viruses and bacteria. Conventional approaches to fabricating antiviral and antibacterial textiles generally load functional additives onto the surface of the fabric and/or their microfibres. However, such modifications are susceptible to deterioration after long-term use due to leaching of the additives. Here we show a different method to impregnate copper ions into the cellulose matrix to form a copper ion-textile (Cu-IT), in which the copper ions strongly coordinate with the oxygen-containing polar functional groups (for example, hydroxyl) of the cellulose chains. The Cu-IT displays high antiviral and antibacterial performance against tobacco mosaic virus and influenza A virus, and Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa and Bacillus subtilis bacteria due to the antimicrobial properties of copper. Furthermore, the strong coordination bonding of copper ions with the hydroxyl functionalities endows the Cu-IT with excellent air/water retainability and superior mechanical stability, which can meet daily use and resist repeated washing. This method to fabricate Cu-IT is cost-effective, ecofriendly and highly scalable, and this textile appears very promising for use in household products, public facilities and medical settings.

Nuclear corepressors NCOR1/NCOR2 regulate B cell development, maintain genomic integrity and prevent transformation.

The nuclear corepressors NCOR1 and NCOR2 interact with transcription factors involved in B cell development and potentially link these factors to alterations in chromatin structure and gene expression. Herein, we demonstrate that Ncor1/2 deletion limits B cell differentiation via impaired recombination, attenuates pre-BCR signaling and enhances STAT5-dependent transcription. Furthermore, NCOR1/2-deficient B cells exhibited derepression of EZH2-repressed gene modules, including the p53 pathway. These alterations resulted in aberrant Rag1 and Rag2 expression and accessibility. Whole-genome sequencing of Ncor1/2 DKO B cells identified increased number of structural variants with cryptic recombination signal sequences. Finally, deletion of Ncor1 alleles in mice facilitated leukemic transformation, whereas human leukemias with less NCOR1 correlated with worse survival. NCOR1/2 mutations in human leukemia correlated with increased RAG expression and number of structural variants. These studies illuminate how the corepressors NCOR1/2 regulate B cell differentiation and provide insights into how NCOR1/2 mutations may promote B cell transformation.

A high-performance hydroxide exchange membrane enabled by Cu2+-crosslinked chitosan.

Ion exchange membranes are widely used to selectively transport ions in various electrochemical devices. Hydroxide exchange membranes (HEMs) are promising to couple with lower cost platinum-free electrocatalysts used in alkaline conditions, but are not stable enough in strong alkaline solutions. Herein, we present a Cu2+-crosslinked chitosan (chitosan-Cu) material as a stable and high-performance HEM. The Cu2+ ions are coordinated with the amino and hydroxyl groups of chitosan to crosslink the chitosan chains, forming hexagonal nanochannels (~1 nm in diameter) that can accommodate water diffusion and facilitate fast ion transport, with a high hydroxide conductivity of 67 mS cm-1 at room temperature. The Cu2+ coordination also enhances the mechanical strength of the membrane, reduces its permeability and, most importantly, improves its stability in alkaline solution (only 5% conductivity loss at 80 °C after 1,000 h). These advantages make chitosan-Cu an outstanding HEM, which we demonstrate in a direct methanol fuel cell that exhibits a high power density of 305 mW cm-2. The design principle of the chitosan-Cu HEM, in which ion transport channels are generated in the polymer through metal-crosslinking of polar functional groups, could inspire the synthesis of many ion exchange membranes for ion transport, ion sieving, ion filtration and more.

Low-pH seawater alters indirect interactions in rocky-shore tidepools.

Ocean acidification is expected to degrade marine ecosystems, yet most studies focus on organismal-level impacts rather than ecological perturbations. Field studies are especially sparse, particularly ones examining shifts in direct and indirect consumer interactions. Here we address such connections within tidepool communities of rocky shores, focusing on a three-level food web involving the keystone sea star predator, Pisaster ochraceus, a common herbivorous snail, Tegula funebralis, and a macroalgal basal resource, Macrocystis pyrifera. We demonstrate that during nighttime low tides, experimentally manipulated declines in seawater pH suppress the anti-predator behavior of snails, bolstering their grazing, and diminishing the top-down influence of predators on basal resources. This attenuation of top-down control is absent in pools maintained experimentally at higher pH. These findings suggest that as ocean acidification proceeds, shifts of behaviorally mediated links in food webs could change how cascading effects of predators manifest within marine communities.

MXene-Supported, Atomic-Layered Iridium Catalysts Created by Nanoparticle Re-Dispersion for Efficient Alkaline Hydrogen Evolution.

Tailoring the structure of metal components and interaction with their anchored substrates is essential for improving the catalytic performance of supported metal catalysts; the ideal catalytic configuration, especially down to the range of atomic layers, clusters, and even single atoms, remains a subject under intensive study. Here, an Ir-on-MXene (Mo2 TiC2 Tx ) catalyst with controlled morphology changing from nanoparticles down to flattened atomic layers, and finally ultrathin layers and single atoms dispersed on MXene nanosheets at elevated temperature, is presented. The intermediate structure, consisting of mostly Ir atomic layers, shows the highest activity toward the hydrogen evolution reaction (HER) under industry-compatible alkaline conditions. In addition, the better HER activity of Ir atomic layers than that of single atoms suggests that the former serves as the main active sites. Detailed mechanism analysis reveals that the nanoparticle re-dispersion process and Ir atomic layers with a moderate interaction to the substrate associate with unconventional electron transfer from MXene to Ir, leading to suitable H* adsorption. The results indicate that the structural design is important for the development of highly efficient catalysts.

Onset of High Methane Combustion Rates over Supported Palladium Catalysts: From Isolated Pd Cations to PdO Nanoparticles.

Industrial low-temperature methane combustion catalyst Pd/Al2O3 suffers from H2O-induced deactivation. It is imperative to design Pd catalysts free from this deactivation and with high atomic efficiency. Using a small-pore zeolite SSZ-13 as support, herein we report well-defined Pd catalysts with dominant active species as finely dispersed Pd cations, uniform PdO particles embedded inside the zeolite framework, or PdO particles decorating the zeolite external surface. Through detailed reaction kinetics and spectroscopic and microscopic studies, we show that finely dispersed sites are much less active than PdO nanoparticles. We further demonstrate that H2O-induced deactivation can be readily circumvented by using zeolite supports with high Si/Al ratios. Finally, we provide a few rational catalyst design suggestions for methane oxidation based on the new knowledge learned in this study.

Structural Evolution of MOF-Derived RuCo, A General Catalyst for the Guerbet Reaction.

Guerbet alcohols, a class of ß-branched terminal alcohols, find widespread application because of their low melting points and excellent fluidity. Because of the limitations in the activity and selectivity of existing Guerbet catalysts, Guerbet alcohols are not currently produced via the Guerbet reaction but via hydroformylation of oil-derived alkenes followed by aldol condensation. In pursuit of a one-step synthesis of Guerbet alcohols from simple linear alcohol precursors, we show that MOF-derived RuCo alloys achieve over a million turnovers in the Guerbet reaction of 1-propanol, 1-butanol, and 1-pentanol. The active catalyst is formed in situ from ruthenium-impregnated metal-organic framework MFU-1. XPS and XAS studies indicate that the precatalyst is composed of Ru precursor trapped inside the MOF pores with no change in the oxidation state or coordination environment of Ru upon MOF incorporation. The significantly higher reactivity of Ru-impregnated MOF versus a physical mixture of Ru precursor and MOF suggests that the MOF plays an important role in templating the formation of the active catalyst and/or its stabilization. XPS reveals partial reduction of both ruthenium and MOF-derived cobalt under the Guerbet reaction conditions, and TEM/EDX imaging shows that Ru is decorated on the edges of dense nanoparticles, as well as thin nanoplates of CoOx. The use of ethanol rather than higher alcohols as a substrate results in lower turnover frequencies, and RuCo recovered from ethanol upgrading lacks nanostructures with plate-like morphology and does not exhibit Ru-enrichment on the surface and edge sites. Notably, 1H and 31P NMR studies show that through use of K3PO4 as a base promoter in the RuCo-catalyzed alcohol upgrading, the formation of carboxylate salts, a common side product in the Guerbet reaction, was effectively eliminated.

Reactivity of (bi-Oxazoline)organonickel Complexes and Revision of a Catalytic Mechanism.

Bi-Oxazoline (biOx) has emerged as an effective ligand framework for promoting nickel-catalyzed cross-coupling, cross-electrophile coupling, and photoredox-nickel dual catalytic reactions. This report fills the knowledge gap of the organometallic reactivity of (biOx)Ni complexes, including catalyst reduction, oxidative electrophile activation, radical capture, and reductive elimination. The biOx ligand displays no redox activity in (biOx)Ni(I) complexes, in contrast to other chelating imine and oxazoline ligands. The lack of ligand redox activity results in more negative reduction potentials of (biOx)Ni(II) complexes and accounts for the inability of zinc and manganese to reduce (biOx)Ni(II) species. On the basis of these results, we revise the formerly proposed "sequential reduction" mechanism of a (biOx)Ni-catalyzed cross-electrophile coupling reaction by excluding catalyst reduction steps.

Structural and Chemical Transformations of Zinc Oxide Ultrathin Films on Pd(111) Surfaces.

Structural and chemical transformations of ultrathin oxide films on transition metals lie at the heart of many complex phenomena in heterogeneous catalysis, such as the strong metal-support interaction (SMSI). However, there is limited atomic-scale understanding of these transformations, especially for irreducible oxides such as ZnO. Here, by combining density functional theory calculations and surface science techniques, including scanning tunneling microscopy, X-ray photoelectron spectroscopy, high-resolution electron energy loss spectroscopy, and low-energy electron diffraction, we investigated the interfacial interaction of well-defined ultrathin ZnOxHy films on Pd(111) under varying gas-phase conditions [ultrahigh vacuum (UHV), 5 × 10-7 mbar of O2, and a D2/O2 mixture] to shed light on the SMSI effect of irreducible oxides. Sequential treatment of submonolayer zinc oxide films in a D2/O2 mixture (1:4) at 550 K evoked reversible structural transformations from a bilayer to a monolayer and further to a Pd-Zn near-surface alloy, demonstrating that zinc oxide, as an irreducible oxide, can spread on metal surfaces and show an SMSI-like behavior in the presence of hydrogen. A mixed canonical-grand canonical phase diagram was developed to bridge the gap between UHV conditions and true SMSI environments, revealing that, in addition to surface alloy formation, certain ZnOxHy films with stoichiometries that do not exist in bulk are stabilized by Pd in the presence of hydrogen. Based on the combined theoretical and experimental observations, we propose that SMSI metal nanoparticle encapsulation for irreducible oxide supports such as ZnO involves both surface (hydroxy)oxide and surface alloy formation, depending on the environmental conditions.

Engineering single-atomic ruthenium catalytic sites on defective nickel-iron layered double hydroxide for overall water splitting.

Rational design of single atom catalyst is critical for efficient sustainable energy conversion. However, the atomic-level control of active sites is essential for electrocatalytic materials in alkaline electrolyte. Moreover, well-defined surface structures lead to in-depth understanding of catalytic mechanisms. Herein, we report a single-atomic-site ruthenium stabilized on defective nickel-iron layered double hydroxide nanosheets (Ru1/D-NiFe LDH). Under precise regulation of local coordination environments of catalytically active sites and the existence of the defects, Ru1/D-NiFe LDH delivers an ultralow overpotential of 18 mV at 10 mA cm-2 for hydrogen evolution reaction, surpassing the commercial Pt/C catalyst. Density functional theory calculations reveal that Ru1/D-NiFe LDH optimizes the adsorption energies of intermediates for hydrogen evolution reaction and promotes the O-O coupling at a Ru-O active site for oxygen evolution reaction. The Ru1/D-NiFe LDH as an ideal model reveals superior water splitting performance with potential for the development of promising water-alkali electrocatalysts.

Olefin oligomerization by main group Ga3+ and Zn2+ single site catalysts on SiO2.

In heterogeneous catalysis, olefin oligomerization is typically performed on immobilized transition metal ions, such as Ni2+ and Cr3+. Here we report that silica-supported, single site catalysts containing immobilized, main group Zn2+ and Ga3+ ion sites catalyze ethylene and propylene oligomerization to an equilibrium distribution of linear olefins with rates similar to that of Ni2+. The molecular weight distribution of products formed on Zn2+ is similar to Ni2+, while Ga3+ forms higher molecular weight olefins. In situ spectroscopic and computational studies suggest that oligomerization unexpectedly occurs by the Cossee-Arlman mechanism via metal hydride and metal alkyl intermediates formed during olefin insertion and ß-hydride elimination elementary steps. Initiation of the catalytic cycle is proposed to occur by heterolytic C-H dissociation of ethylene, which occurs at about 250 °C where oligomerization is catalytically relevant. This work illuminates new chemistry for main group metal catalysts with potential for development of new oligomerization processes.

A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.

Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability across cavefish populations to gain insight into this potential source of cave adaptation. The surface fish genome reference now provides a more complete resource for comparative, functional and genetic studies of drastic trait differences within a species.

Single Co-Atoms as Electrocatalysts for Efficient Hydrazine Oxidation Reaction.

Single-atom catalysts (SACs) have aroused great attention due to their high atom efficiency and unprecedented catalytic properties. A remaining challenge is to anchor the single atoms individually on support materials via strong interactions. Herein, single atom Co sites have been developed on functionalized graphene by taking advantage of the strong interaction between Co2+ ions and the nitrile group of cyanographene. The potential of the material, which is named G(CN)Co, as a SAC is demonstrated using the electrocatalytic hydrazine oxidation reaction (HzOR). The material exhibits excellent catalytic activity for HzOR, driving the reaction with low overpotential and high current density while remaining stable during long reaction times. Thus, this material can be a promising alternative to conventional noble metal-based catalysts that are currently widely used in HzOR-based fuel cells. Density functional theory calculations of the reaction mechanism over the material reveal that the Co(II) sites on G(CN)Co can efficiently interact with hydrazine molecules and promote the NH bond-dissociation steps involved in the HzOR.