A multiplexed barcode approach to simultaneously evaluate gene delivery by adeno-associated virus capsid variants in nonhuman primates.

BACKGROUND AND AIMS: Adeno-associated virus (AAV) vectors are widely used to deliver therapeutic transgenes to distinct tissues, including the liver. Vectors based on naturally occurring AAV serotypes as well as vectors using engineered capsids have shown variations in tissue tropism and level of transduction between different mouse models. Moreover, results obtained in rodents frequently lack translatability into large animal studies. In light of the increasing interest in AAV vectors for human gene therapy, an increasing number of studies are being performed in nonhuman primates. To keep animal numbers to a minimum and thus optimize the process of AAV capsid selection, we developed a multiplex barcoding approach to simultaneously evaluate the in vivo vector performance for a set of serotypes and capsid-engineered AAV vectors across multiple organs. APPROACH AND RESULTS: Vector biodistribution and transgene expression were assessed by quantitative PCR, quantitative reverse transcription PCR, vector DNA amplicon Illumina sequencing and vRNAseq in male and female rhesus macaques simultaneously dosed with a mixture of barcoded naturally occurring or engineered AAV vectors encoding the same transgene. As expected, our findings show animal-to-animal variation in both the biodistribution and tissue transduction pattern, which was partly influenced by each animal's distinctive serological status. CONCLUSIONS: This method offers a robust approach to AAV vector optimization that can be used to identify and validate AAV vectors for gene delivery to potentially any anatomical site or cell type.

Implementing the donor-acceptor approach in electronically conducting copolymers via electropolymerization.

Electropolymerization has become a convenient method for synthesizing and characterizing complex organic copolymers having intrinsic electronic conductivity, including the donor (D)-acceptor (A) class of electronically conducting polymers (ECPs). This review begins with an introduction to the electrosynthesis of common second-generation ECPs. The information obtainable from electroanalytical studies, charge carriers such as polarons (positive and negative) and bipolarons (positive and negative) and doping will be discussed. The evolutionary chain of ECPs is then presented. ECPs comprising electron-rich D and electron-deficient A moieties have been shown to possess intrinsic electronic conductivity and unique optical and electronic properties. They are third generation ECPs and electropolymerization of mixtures of D and A leads to stoichiometrically controlled block copolymers. These D-A type ECPs are discussed on the basis of selected representative materials. Since the discovery of electropolymerization as a powerful tool to synthesize copolymers of conjugated monomers with a pre-determined ratio of D and A repeat units present in the polymer, the field of D-A type ECPs has grown considerably and the literature available since 2004 to 2021 is summarized and tabulated. Electronic and optical properties of the materials determined by computational chemistry are presented. The data obtained from electrochemical and optical methods are compared with those obtained from computational methods and reasons for discrepancies are given. The literature on the concept of electropolymerization extended to synthesizing triblock and many-block copolymers is reviewed. Finally, applications of D-A polymers in optoelectronic devices (organic solar cells and field-effect transistors) and in bio-imaging are explained quoting appropriate examples.

Electrocatalytic CO2 reduction on earth abundant 2D Mo2C and Ti3C2 MXenes.

Mo2C and Ti3C2 MXenes were investigated as earth-abundant electrocatalyts for the CO2 reduction reaction (CO2RR). Mo2C and Ti3C2 exhibited faradaic efficiencies of 90% (250 mV overpotential) and 65% (650 mV overpotential), respectively, for the reduction of CO2 to CO in acetonitrile using an ionic liquid electrolyte. The use of ionic liquid 1-ethyl-2-methylimidazolium tetrafluoroborate as an electrolyte in organic solvent suppressed the competing hydrogen evolution reaction. Density functional theory (DFT) calculations suggested that the catalytic active sites are oxygen vacancy sites on both MXene surfaces. Also, a spontaneous dissociation of adsorbed COOH species to a water molecule and adsorbed CO on Mo2C promote the CO2RR.

Gene editing and elimination of latent herpes simplex virus in vivo.

We evaluate gene editing of HSV in a well-established mouse model, using adeno-associated virus (AAV)-delivered meganucleases, as a potentially curative approach to treat latent HSV infection. Here we show that AAV-delivered meganucleases, but not CRISPR/Cas9, mediate highly efficient gene editing of HSV, eliminating over 90% of latent virus from superior cervical ganglia. Single-cell RNA sequencing demonstrates that both HSV and individual AAV serotypes are non-randomly distributed among neuronal subsets in ganglia, implying that improved delivery to all neuronal subsets may lead to even more complete elimination of HSV. As predicted, delivery of meganucleases using a triple AAV serotype combination results in the greatest decrease in ganglionic HSV loads. The levels of HSV elimination observed in these studies, if translated to humans, would likely significantly reduce HSV reactivation, shedding, and lesions. Further optimization of meganuclease delivery and activity is likely possible, and may offer a pathway to a cure for HSV infection.

Biomimetic System for the Application of Nanomaterials in Fluid Purification: Removal of Arsenic with Ferrihydrite.

The use of nanomaterials has transformed fields such as medicine and electronics. However, aggregation of nanomaterials in aqueous solutions, difficult recovery of spent nano-adsorbents from reactors, and a tremendous pressure loss caused by nano-adsorbents in adsorption columns have prevented the wide-scale use of nano-adsorbents in industrial applications for water purification. An over-reliance on traditional adsorption media for fluid purification practices has slowed innovation in this field. This study serves as a proof of concept for a new approach in utilizing nano-adsorbents in water treatment. A system based on the concept of renal dialysis was used to treat a solution of arsenite using two-line ferrihydrite (Fh) under environmental conditions. The performance was compared to traditional batch studies, and environmental variables pH and Eh were monitored. The system removed 67 and 91% of arsenite at 1.22 and 2.61 g/L Fh loadings, respectively, in comparison to batch experiments that removed 82 and 94% for similar loadings. Operational conditions and the physical design of the vessel limited the extent of removal that could be obtained with the system. Design advantages, shortcomings, and required improvements are discussed.

Highly Dispersed RuOOH Nanoparticles on Silica Spheres: An Efficient Photothermal Catalyst for Selective Aerobic Oxidation of Benzyl Alcohol.

Photothermal catalysis represents a promising strategy to utilize the renewable energy source (e.g., solar energy) to drive chemical reactions more efficiently. Successful and efficient photothermal catalysis relies on the availability of ideal photothermal catalysts, which can provide both large areas of catalytically active surface and strong light absorption power simultaneously. Such duplex requirements of a photothermal catalyst exhibit opposing dependence on the size of the catalyst nanoparticles, i.e., smaller size is beneficial for achieving higher surface area and more active surface, whereas larger size favors the light absorption in the nanoparticles. In this article, we report the synthesis of ultrafine RuOOH nanoparticles with a size of 2-3 nm uniformly dispersed on the surfaces of silica (SiOx) nanospheres of hundreds of nanometers in size to tackle this challenge of forming an ideal photothermal catalyst. The ultrasmall RuOOH nanoparticles exhibit a large surface area as well as the ability to activate adsorbed molecular oxygen. The SiOx nanospheres exhibit strong surface light scattering resonances to enhance the light absorption power of the small RuOOH nanoparticles anchored on the SiOx surface. Therefore, the RuOOH/SiOx composite particles represent a new class of efficient photothermal catalysts with a photothermal energy conversion efficiency of 92.5% for selective aerobic oxidation of benzyl alcohol to benzylaldehyde under ambient conditions.

Traditional Colonial-type cheese from the south of Brazil: A case to support the new Brazilian laws for artisanal cheese production from raw milk.

Artisanal Colonial-type cheese is made from raw milk and is the main cheese produced by rural families of the southern region of Brazil. The aim of this study was to investigate, identify problems, and propose solutions for the current situation of small family farms producing and informally selling artisanal Colonial-type cheese located in the western part of Santa Catarina State in Southern Brazil. A semistructured questionnaire was employed in 12 rural properties to analyze the mode of production. Physical-chemical and microbiological analyses of water, raw milk, and cheese were performed, and it was found that 92, 50, and 100% of the samples, respectively, were outside of the current Brazilian regulatory parameters. None of the cheesemakers involved in this study met the requirements, as established by law, for artisanal cheese production from raw milk. This study concluded that technical support and changes in public policy are needed to ensure the preservation of this artisanal cheese, considering the historical importance and cultural traditions of these local communities and the socioeconomic importance of cheesemaking to family farming. Furthermore, more research on the safety of the cheese produced from raw milk is needed as well as the development of specific microbiological standards for artisanal Brazilian cheeses. Public policies aimed at guaranteeing food safety that formalize the commercialization of these cheeses will increase food security in those communities that currently produce artisanal cheese informally.

High Electron Mobility of Amorphous Red Phosphorus Thin Films.

Black phosphorus (BP) has been gathering great attention for its electronic and optoelectronic applications due to its high electron mobility and high ION/OFF current switching ratio. The limitations of this material include its low synthetic yield and high cost. One alternative to BP is another type of phosphorus allotrope, red phosphorus (RP), which is much more affordable and easier to process. Although RP has been widely used in industry for hundreds of years and considered as an insulating material, in this study, we demonstrate through field-effect transistors (FET) measurements that amorphous red phosphorus (a-RP) films are semiconductive with a high mobility of 387 cm2 V-1 s-1 and a current switching ratio of ≈103 , which is comparable to the electronic characteristics previously reported for BP. The films were produced via a thermal evaporation method or a facile drop-casting approach onto Si/SiO2 substrates. We also report a study of the oxidation process of the films over time and a method to stabilize the films via doping a-RP with metal oxides. The doped films retain stability for one thousand I-V cycles, with no signs of degradation.

Antimicrobial Properties of 2D MnO2 and MoS2 Nanomaterials Vertically Aligned on Graphene Materials and Ti3C2 MXene.

Two-dimensional (2D) nanomaterials have attracted considerable attention in biomedical and environmental applications due to their antimicrobial activity. In the interest of investigating the primary antimicrobial mode-of-action of 2D nanomaterials, we studied the antimicrobial properties of MnO2 and MoS2, toward Gram-positive and Gram-negative bacteria. Bacillus subtilis and Escherichia coli bacteria were treated individually with 100 µg/mL of randomly oriented and vertically aligned nanomaterials for ∼3 h in the dark. The vertically aligned 2D MnO2 and MoS2 were grown on 2D sheets of graphene oxide, reduced graphene oxide, and Ti3C2 MXene. Measurements to determine the viability of bacteria in the presence of the 2D nanomaterials performed by using two complementary techniques, flow cytometry, and fluorescence imaging showed that, while MnO2 and MoS2 nanosheets show different antibacterial activities, in both cases, Gram-positive bacteria show a higher loss in membrane integrity. Scanning electron microscopy images suggest that the 2D nanomaterials, which have a detrimental effect on bacteria viability, compromise the cell wall, leading to significant morphological changes. We propose that the peptidoglycan mesh (PM) in the bacterial wall is likely the primary target of the 2D nanomaterials. Vertically aligned 2D MnO2 nanosheets showed the highest antimicrobial activity, suggesting that the edges of the nanosheets were likely compromising the cell walls upon contact.

Systematic Doping of Cobalt into Layered Manganese Oxide Sheets Substantially Enhances Water Oxidation Catalysis.

The effect on the electrocatalytic oxygen evolution reaction (OER) of cobalt incorporation into the metal oxide sheets of the layered manganese oxide birnessite was investigated. Birnessite and cobalt-doped birnessite were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and conductivity measurements. A cobalt:manganese ratio of 1:2 resulted in the most active catalyst for the OER. In particular, the overpotential (η) for the OER was 420 mV, significantly lower than the η = 780 mV associated with birnessite in the absence of Co. Furthermore, the Tafel slope for Co/birnessite was 81 mV/dec, in comparison to a Tafel slope of greater than 200 mV/dec for birnessite. For chemical water oxidation catalysis, an 8-fold turnover number (TON) was achieved (h = 70 mmol of O2/mol of metal). Density functional theory (DFT) calculations predict that cobalt modification of birnessite resulted in a raising of the valence band edge and occupation of that edge by holes with enhanced mobility during catalysis. Inclusion of extra cobalt beyond the ideal 1:2 ratio was detrimental to catalysis due to disruption of the layered structure of the birnessite phase.

Cobalt Intercalated Layered NiFe Double Hydroxides for the Oxygen Evolution Reaction.

We present a combined experimental and theoretical study to demonstrate that the electrocatalytic activity of NiFe layered double hydroxides (NiFe LDHs) for the oxygen evolution reaction (OER) can be significantly enhanced by systematic cobalt incorporation using coprecipitation and/or intercalation. Electrochemical measurements show that cobalt modified NiFe LDH possesses an enhanced activity for the OER relative to pristine NiFe LDH. The Co-modified NiFe LDH exhibits overpotentials in the range of 290-322 mV (at 10 mA cm-2), depending on the degree of cobalt content. The best catalyst, cobalt intercalated NiFe LDH achieved a current density of 10 mA cm-2 at an overpotential of ∼265 mV (compared to 310 mV for NiFe LDH), with a near unity (99%) faradaic efficiency and long-term stability. Density functional theory calculations revealed that enhanced activity of Co-modified NiFe LDH could be attributed to the ability of Co to tune the electronic structure of the NiFe LDH so that optimal binding of OER reaction intermediates could be achieved.

Redox properties of birnessite from a defect perspective.

Birnessite, a layered-structure MnO2, is an earth-abundant functional material with potential for various energy and environmental applications, such as water oxidation. An important feature of birnessite is the existence of Mn(III) within the MnO2 layers, accompanied by interlayer charge-neutralizing cations. Using first-principles calculations, we reveal the nature of Mn(III) in birnessite with the concept of the small polaron, a special kind of point defect. Further taking into account the effect of the spatial distribution of Mn(III), we propose a theoretical model to explain the structure-performance dependence of birnessite as an oxygen evolution catalyst. We find an internal potential step which leads to the easy switching of the oxidation state between Mn(III) and Mn(IV) that is critical for enhancing the catalytic activity of birnessite. Finally, we conduct a series of comparative experiments which support our model.

Effect of Interlayer Spacing on the Activity of Layered Manganese Oxide Bilayer Catalysts for the Oxygen Evolution Reaction.

We investigated the dependence of the electrocatalytic activity for the oxygen evolution reaction (OER) on the interlayer distance of five compositionally distinct layered manganese oxide nanostructures. Each individual electrocatalyst was assembled with a different alkali metal intercalated between two nanosheets (NS) of manganese oxide to form a bilayer structure. Manganese oxide NS were synthesized via the exfoliation of a layered material, birnessite. Atomic force microscopy was used to determine the heights of the bilayer catalysts. The interlayer spacing of the supported bilayers positively correlates with the size of the alkali cation: NS/Cs+/NS > NS/Rb+/NS > NS/K+/NS > NS/Na+/NS > NS/Li+/NS. The thermodynamic origins of these bilayer heights were investigated using molecular dynamics simulations. The overpotential (η) for the OER correlates with the interlayer spacing; NS/Cs+/NS has the lowest η (0.45 V), while NS/Li+/NS exhibits the highest η (0.68 V) for OER at a current density of 1 mA/cm2. Kinetic parameters (η and Tafel slope) associated with NS/Cs+/NS for the OER were superior to that of the bulk birnessite phase, highlighting the structural uniqueness of these nanoscale assemblies.

Nickel Confined in the Interlayer Region of Birnessite: an Active Electrocatalyst for Water Oxidation.

We report a synthetic method to enhance the electrocatalytic activity of birnessite for the oxygen evolution reaction (OER) by intercalating Ni(2+) ions into the interlayer region. Electrocatalytic studies showed that nickel (7.7 atomic %)-intercalated birnessite exhibits an overpotential (η) of 400 mV for OER at an anodic current of 10 mA cm(-2) . This η is significantly lower than the η values for birnessite (η≈700 mV) and the active OER catalyst ß-Ni(OH)2 (η≈550 mV). Molecular dynamics simulations suggest that a competition among the interactions between the nickel cation, water, and birnessite promote redox chemistry in the spatially confined interlayer region.

Oxidation of arsenite to arsenate on birnessite in the presence of light.

The effect of simulated solar radiation on the oxidation of arsenite [As(III)] to arsenate [As(V)] on the layered manganese oxide, birnessite, was investigated. Experiments were conducted where birnessite suspensions, under both anoxic and oxic conditions, were irradiated with simulated solar radiation in the presence of As(III) at pH 5, 7, and 9. X-ray absorption spectroscopy (XAS) was used to determine the nature of the adsorbed product on the surface of the birnessite. The oxidation of As(III) in the presence of birnessite under simulated solar light irradiation occurred at a rate that was faster than in the absence of light at pH 5. At pH 7 and 9, As(V) production was significantly less than at pH 5 and the amount of As(V) production for a given reaction time was the same under dark and light conditions. The first order rate constant (kobs) for As(III) oxidation in the presence of light and in the dark at pH 5 were determined to be 0.07 and 0.04 h-1, respectively. The As(V) product was released into solution along with Mn(II), with the latter product resulting from the reduction of Mn(IV) and/or Mn(III) during the As(III) oxidation process. Post-reaction XAS analysis of As(III) exposed birnessite showed that arsenic was present on the surface as As(V). Experimental results also showed no evidence that reactive oxygen species played a role in the As(III) oxidation process.

Frustrated Solvation Structures Can Enhance Electron Transfer Rates.

Polar surfaces can interact strongly with nearby water molecules, leading to the formation of highly ordered interfacial hydration structures. This ordering can lead to frustration in the hydrogen bond network, and, in the presence of solutes, frustrated hydration structures. We study frustration in the hydration of cations when confined between sheets of the water oxidation catalyst manganese dioxide. Frustrated hydration structures are shown to have profound effects on ion-surface electron transfer through the enhancement of energy gap fluctuations beyond those expected from Marcus theory. These fluctuations are accompanied by a concomitant increase in the electron transfer rate in Marcus's normal regime. We demonstrate the generality of this phenomenon-enhancement of energy gap fluctuations due to frustration-by introducing a charge frustrated XY model, likening the hydration structure of confined cations to topological defects. Our findings shed light on recent experiments suggesting that water oxidation rates depend on the cation charge and Mn-oxidation state in these layered transition metal oxide materials.

Copper-Intercalated Birnessite as a Water Oxidation Catalyst.

We report a synthetic method to increase the catalytic activity of birnessite toward water oxidation by intercalating copper in the interlayer region of the layered manganese oxide. Intercalation of copper, verified by XRD, XPS, ICP, and Raman spectroscopy, was accomplished by exposing a suspension of birnessite to a Cu(+)-bearing precursor molecule that underwent disproportionation in solution to yield Cu(0) and Cu(2+). Electrocatalytic studies showed that the Cu-modified birnessite exhibited an overpotential for water oxidation of ∼490 mV (at 10 mA/cm(2)) and a Tafel slope of 126 mV/decade compared to ∼700 mV (at 10 mA/cm(2)) and 240 mV/decade, respectively, for birnessite without copper. Impedance spectroscopy results suggested that the charge transfer resistivity of the Cu-modified sample was significantly lower than Cu-free birnessite, suggesting that Cu in the interlayer increased the conductivity of birnessite leading to an enhancement of water oxidation kinetics. Density functional theory calculations show that the intercalation of Cu(0) into a layered MnO2 model structure led to a change of the electronic properties of the material from a semiconductor to a metallic-like structure. This conclusion from computation is in general agreement with the aforementioned impedance spectroscopy results. X-ray photoelectron spectroscopy (XPS) showed that Cu(0) coexisted with Cu(2+) in the prepared Cu-modified birnessite. Control experiments using birnessite that was decorated with only Cu(2+) showed a reduction in water oxidation kinetics, further emphasizing the importance of Cu(0) for the increased activity of birnessite. The introduction of Cu(0) into the birnessite structure also increased the stability of the electrocatalyst. At a working current of 2 mA, the Cu-modified birnessite took ∼3 times longer for the overpotential for water oxdiation to increase by 100 mV compared to when Cu was not present in the birnessite.

Molecular Insights into Inhibition of the Methylated Histone-Plant Homeodomain Complexes by Calixarenes.

Plant homeodomain (PHD) finger-containing proteins are implicated in fundamental biological processes, including transcriptional activation and repression, DNA damage repair, cell differentiation, and survival. The PHD finger functions as an epigenetic reader that binds to posttranslationally modified or unmodified histone H3 tails, recruiting catalytic writers and erasers and other components of the epigenetic machinery to chromatin. Despite the critical role of the histone-PHD interaction in normal and pathological processes, selective inhibitors of this association have not been well developed. Here we demonstrate that macrocyclic calixarenes can disrupt binding of PHD fingers to methylated lysine 4 of histone H3 in vitro and in vivo. The inhibitory activity relies on differences in binding affinities of the PHD fingers for H3K4me and the methylation state of the histone ligand, whereas the composition of the aromatic H3K4me-binding site of the PHD fingers appears to have no effect. Our approach provides a novel tool for studying the biological roles of methyllysine readers in epigenetic signaling.

Decoration of the layered manganese oxide birnessite with Mn(II/III) gives a new water oxidation catalyst with fifty-fold turnover number enhancement.

The role of the manganese average oxidation state (AOS) in water oxidation catalysis by birnessite was investigated. Low AOS samples were most active, generating O2 immediately. Samples with a relatively high AOS showed an initial induction period and decreased turnover. Mn(ii- and iii)-enriched samples gave a 10-50 fold enhancement in turnover number.

Effect of Phospholipid on Pyrite Oxidation and Microbial Communities under Simulated Acid Mine Drainage (AMD) Conditions.

The effect of phospholipid on the biogeochemistry of pyrite oxidation, which leads to acid mine drainage (AMD) chemistry in the environment, was investigated. Metagenomic analyses were carried out to understand how the microbial community structure, which developed during the oxidation of pyrite-containing coal mining overburden/waste rock (OWR), was affected by the presence of adsorbed phospholipid. Using columns packed with OWR (with and without lipid adsorption), the release of sulfate (SO4(2-)) and soluble iron (FeTot) was investigated. Exposure of lipid-free OWR to flowing pH-neutral water resulted in an acidic effluent with a pH range of 2-4.5 over a 3-year period. The average concentration of FeTot and SO4(2-) in the effluent was ≥20 and ≥30 mg/L, respectively. In contrast, in packed-column experiments where OWR was first treated with phospholipid, the effluent pH remained at ∼6.5 and the average concentrations of FeTot and SO4(2-) were ≤2 and l.6 mg/L, respectively. 16S rDNA metagenomic pyrosequencing analysis of the microbial communities associated with OWR samples revealed the development of AMD-like communities dominated by acidophilic sulfide-oxidizing bacteria on untreated OWR samples, but not on refuse pretreated with phospholipid.