Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this article, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study, we demonstrate our improvements to numerical stability and computational complexity.     

Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease

The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.     

Electrochemical Detection of Artemisinin Using Cobalt Sulphide/Reduced Graphene Oxide Nanocomposite

Solvothermally synthesized cobalt sulphide/reduced graphene oxide (CoS/rGO) was used to fabricate an electrochemical sensor for detection of artemisinin. Microscopic techniques were used to characterize CoS/rGO nanocomposite. The electrochemical sensor was fabricated by modifying the surface of glassy carbon electrode with CoS/rGO nanocomposite. [Fe(CN)6]^3−/4− was used as a mediator to aid oxidation of artemisinin. Differential pulse voltammetric technique was used for the detection of artemisinin. A linear range of 30–100 μM was used. Experimentally, a detection limit of 0.5 μM was obtained. Therefore, the developed sensor can be used for quality control of artemisinin.     

Design and Development of a Non-Enzymatic Electrochemical Biosensor for the Detection of Glutathione

Glutathione (GSH-reduced form) is a tripeptide that plays a vital role as an antioxidant to remove xenobiotics in the human body and changes in GSH levels are a marker for the progression of various diseases. In this context, a highly sensitive non-enzymatic electrochemical biosensor for the detection of GSH has been developed using reduced graphene oxide Manganese oxide (rGMnO) nanocomposite as the nano-interface. Initially, graphene oxide was synthesized by Hummer's method and then thermally reduced in the presence of MnO₂ in a blast furnace to obtain rGMnO nanocomposite. The nanocomposite was characterized to validate its structure and morphological properties via Scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman, and X-ray photoelectron spectroscopy (XPS). Cyclic voltammetry and amperometry studies showed that upon the addition of GSH, the Pt/rGMnO modified working electrode exhibited a linear response in the range of 1–100 μM at an input voltage of −0.62 V. The developed sensor was found to have a sensitivity of 0.3256 μA μM⁻¹ and LOD of 970 nM with a recovery of 92–104 % in real blood serum samples.     

Influence of Potassium Metal-Support Interactions on Dendrite Growth

Combined synchrotron X-ray nanotomography imaging, cryogenic electron microscopy (cryo-EM) and modeling elucidate how potassium (K) metal-support energetics influence electrodeposit microstructure. Three model supports are employed: O-functionalized carbon cloth (potassiophilic, fully-wetted), non-functionalized cloth and Cu foil (potassiophobic, nonwetted). Nanotomography and focused ion beam (cryo-FIB) cross-sections yield complementary three-dimensional (3D) maps of cycled electrodeposits. Electrodeposit on potassiophobic support is a triphasic sponge, with fibrous dendrites covered by solid electrolyte interphase (SEI) and interspersed with nanopores (sub-10 nm to 100 nm scale). Lage cracks and voids are also a key feature. On potassiophilic support, the deposit is dense and pore-free, with uniform surface and SEI morphology. Mesoscale modeling captures the critical role of substrate-metal interaction on K metal film nucleation and growth, as well as the associated stress state.     

Ethene-1,1-disulfonyl Difluoride (EDSF) for SuFEx Click Chemistry: Synthesis of SuFExable 1,1-Bissulfonylfluoride Substituted Cyclobutene Hubs

We present the synthesis of 1,1-bis(fluorosulfonyl)-2-(pyridin-1-ium-1-yl)ethan-1-ide, a bench-stable precursor to ethene-1,1-disulfonyl difluoride (EDSF). The novel SuFEx reagent, EDSF, is demonstrated in the preparation of 26 unique 1,1-bissulfonylfluoride substituted cyclobutenes via a cycloaddition reaction. The regioselective click cycloaddition reaction is rapid, straightforward, and highly efficient, enabling the generation of highly functionalized 4-membered ring (4MR) carbocycles. These carbocycles are valuable structural motifs found in numerous bioactive natural products and pharmaceutically relevant small molecules. Additionally, we showcase diversification of the novel cyclobutene cores through selective Cs₂CO₃-activated SuFEx click chemistry between a single S−F group and an aryl alcohol, yielding the corresponding sulfonate ester products with high efficiency. Finally, density functional theory calculations offer mechanistic insights about the reaction pathway.     

Experimental Confirmation of a Predicted Porous Hydrogen-Bonded Organic Framework

Hydrogen-bonded organic frameworks (HOFs) with low densities and high porosities are rare and challenging to design because most molecules have a strong energetic preference for close packing. Crystal structure prediction (CSP) can rank the crystal packings available to an organic molecule based on their relative lattice energies. This has become a powerful tool for the a priori design of porous molecular crystals. Previously, we combined CSP with structure-property predictions to generate energy-structure-function (ESF) maps for a series of triptycene-based molecules with quinoxaline groups. From these ESF maps, triptycene trisquinoxalinedione (TH5) was predicted to form a previously unknown low-energy HOF (TH5-A) with a remarkably low density of 0.374 g cm⁻³ and three-dimensional (3D) pores. Here, we demonstrate the reliability of those ESF maps by discovering this TH5-A polymorph experimentally. This material has a high accessible surface area of 3,284 m² g⁻¹, as measured by nitrogen adsorption, making it one of the most porous HOFs reported to date.     

Mechanically Activated Solid-State Radical Polymerization and Cross-Linking via Piezocatalysis

Piezocatalysis offers a means to transduce mechanical energy into chemical potential, harnessing physical force to drive redox reactions. Working in the solid state, we show here that piezoelectric BaTiO₃ nanoparticles can transduce mechanical load into a flux of reactive radical species capable of initiating solid state free radical polymerization. Activation of a BaTiO₃ powder by ball milling, striking with a hammer, or repeated compressive loading generates highly reactive hydroxyl radicals (⋅OH), which readily initiate radical chain growth and crosslinking of solid acrylamide, acrylate, methacrylate and styrenic monomers. Control experiments indicate a critical role for chemisorbed water on the BaTiO₃ nanoparticle surface, which is oxidized to ⋅OH via mechanoredox catalysis. The force-induced production of radicals by compressing dry piezoelectric materials represents a promising new route to harness mechanical energy for solid state radical synthesis.     

A Hemilabile NHC-Gold Complex and its Application to the Redox Neutral 1,2-Oxyarylation of Feedstock Alkenes

We describe a Au^I complex of a hemi-labile (C^N) N-heterocyclic carbene ligand that is able to mediate oxidative addition of aryl iodides. Detailed computational and experimental investigations have been undertaken to verify and rationalize the oxidative addition process. Application of this initiation mode has resulted in the first examples of “exogenous oxidant-free” Au^I/Au^III catalyzed 1,2-oxyarylations of ethylene and propylene. These demanding yet powerful processes establish these commodity chemicals as nucleophilic-electrophilic building blocks in catalytic reaction design.     

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7**

The sirtuins are NAD⁺-dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.