Reconstructing the genetic history of late Neanderthals.

Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

Observation of Two-Step Spin Transition in Graphene Oxide-Based Hybrids with Iron(II) 4-amino-1,2,4-triazole Spin Crossover Nanoparticles.

A novel experimental protocol based on a reverse micellar method is presented for the synthesis of graphene oxide (GO)-based hybrids with spin crossover nanoparticles (SCO NPs) of the 1D iron(II) coordination polymer with the formula [Fe(NH2trz)3](Br2). By introducing different quantities of 0.5% and 1.0% of GO (according to iron(II)) into the aqueous phase, two hybrids, NP4 and NP5, were synthesized, respectively. The morphological homogeneity of the NPs on the surface of the GO flakes is greatly improved in comparison to the pristine [Fe(NH2trz)3](Br2) NPs. From the magnetic point of view and at a low magnetic sweep rate of 1 K/min, a two-step hysteretic behavior is observed for NP4 and NP5, where the onset of the low-temperature second step appeared at 40% and 30% of the HS fraction, respectively. For faster sweep rates of 5-10 K/min, the two steps from the cooling branch are progressively smeared out, and the critical temperatures observed are T1/2↑ = 343 K and T1/2↓ = 288 K, with a thermal width of 55 K for both NP4 and NP5. A Raman laser power-assisted protocol was used to monitor the thermal tolerance of the hybrids, while XPS analysis revealed electronic interactions between the SCO NPs and the GO flakes.

The genetic history of Ice Age Europe.

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.

Limits of long-term selection against Neandertal introgression.

Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.

Carbon Nitride-Based Ruthenium Single Atom Photocatalyst for CO2 Reduction to Methanol.

With increasing concerns for global warming, the solar-driven photocatalytic reduction of CO2 into chemical fuels like methanol is a propitious route to enrich energy supplies, with concomitant reduction of the abundant CO2  stockpiles. Herein, a novel single atom-confinement and a strategy are reported toward single ruthenium atoms dispersion over porous carbon nitride surface. Ruthenium single atom character is well confirmed by EXAFS absorption spectrometric analysis unveiling the cationic coordination environment for the single-atomic-site ruthenium center, that is formed by Ru-N/C intercalation in the first coordination shell, attaining synergism in N-Ru-N connection and interfacial carrier transfer. From time resolved fluorescence decay spectra, the average carrier lifetime of the RuSA-mC3 N4 system is found to be higher compared to m-C3 N4 ; the fact uncovering the crucial role of single Ru atoms in promoting photocatalytic reaction system. A high yield of methanol (1500 µmol g-1 cat. after 6 h of the reaction) using water as an electron donor and the reusability of the developed catalyst without any significant change in the efficiency represent the superior aspects for its potential application in real industrial technologies.

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.

admixr-R package for reproducible analyses using ADMIXTOOLS.

SUMMARY: We present a new R package admixr, which provides a convenient interface for performing reproducible population genetic analyses (f3, D, f4, f4-ratio, qpWave and qpAdm), as implemented by command-line programs in the ADMIXTOOLS software suite. In a traditional ADMIXTOOLS workflow, the user must first generate a set of text configuration files tailored to each individual analysis, often using a combination of shell scripting and manual text editing. The non-tabular output files then need to be parsed to extract values of interest prior to further analyses. Our package simplifies this process by automating all low-level configuration and parsing steps, making analyses as simple as running a single R command. Furthermore, we provide a set of R functions for processing, filtering and manipulating datasets in the EIGENSTRAT format. By unifying all steps of the workflow under a single R framework, this package enables the automation of analytic pipelines, significantly improving the reproducibility of population genetic studies. AVAILABILITY AND IMPLEMENTATION: The source code of the R package is available under the MIT license. Installation instructions, reference manual and a tutorial can be found on the package website at https://bioinf.eva.mpg.de/admixr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Surface termination of MgB2 unveiled by a combination of adsorption experiments and theoretical calculations.

Superconductivity in polycrystalline and thin-film MgB2 is strongly affected by the termination of its surface, but a reliable determination of the surface termination is still a challenging task of surface chemistry. Here, the surface properties of superconducting MgB2 were investigated using a combination of inverse gas chromatography and van der Waals corrected density functional theory calculations. The dispersive surface energy was measured as a function of the surface coverage and its value (58 mJ m-2 to 48 mJ m-2) was verified by high-level non-local EXX + RPA calculations, which predicted that the dispersive contribution to the cleavage energy was 56 mJ m-2. The isosteric adsorption enthalpies of cyclohexane, dioxane, acetone and acetonitrile molecules were measured on an MgB2 sample and compared to the DFT calculated enthalpies for the Mg-terminated MgB2, B-terminated MgB2 and MgO(001) surfaces. The close agreement between theory and experiment for the Mg-terminated surface suggested that the magnesium termination is the dominant surface phase of MgB2. Thus, combining inverse gas chromatography experiments with theoretical calculations may provide information about the surface termination.

Transformations of ferrates(iv,v,vi) in liquids: Mössbauer spectroscopy of frozen solutions.

The kinetics and mechanism of ferrate(iv), (v) and (vi) transformations in water and in polar organic solvents (namely ethanol and tetrahydrofuran) have been investigated by the method of 57Fe Mössbauer spectroscopy of frozen solutions. Ethanol with a very limited amount of water under an inert atmosphere, significantly slows down the transformation reactions of ferrates(iv and v) and provides direct proof of the existence of intermediate states. Simultaneously, ethanol is oxidized to caboxylates in the close vicinity of the surface of ferrate crystallites as proven by X-ray photoelectron spectroscopy. On the contrary, any transformation of ferrate(vi) in pure ethanol (with a very limited amount of water) was not observed. Mössbauer spectroscopy of frozen solutions enabled us to experimentally identify and quantify intermediates of ferrate(iv) and ferrate(v) transformations for the first time. Sodium ferrate(iv) in its tetrahedral form, Na4FeO4, undergoes a two-step charge disproportionation to Fe(iii) and Fe(vi) via a Fe(v) intermediate without any evolution of oxygen in polar protic and aprotic solvents, specifically 2Fe(iv) → Fe(iii) + Fe(v), and Fe(iv) + Fe(v) → Fe(iii) + Fe(vi), i.e. in sum 3Fe(iv) → 2Fe(iii) + Fe(vi). Ferrate(v) (K3FeO4) transforms to Fe(iii) and Fe(vi) without any indication of the Fe(iv) intermediate within the detection limit of the method. In addition to a charge disproportionation reaction proceeding in polar liquids, 3Fe(v) → Fe(iii) + 2Fe(vi), a competitive reduction of Fe(v) directly to Fe(iii) accompanied by oxygen evolution takes place in water. Oxygen evolution was also measured for ferrate(iv and vi) transformations in water, but to a higher and a smaller extent compared to ferrate(v), respectively. The thermodynamics of the suggested ferrate(iv) and ferrate(v) transformation pathways was examined by DFT calculations.

Doping with Graphitic Nitrogen Triggers Ferromagnetism in Graphene.

Nitrogen doping opens possibilities for tailoring the electronic properties and band gap of graphene toward its applications, e.g., in spintronics and optoelectronics. One major obstacle is development of magnetically active N-doped graphene with spin-polarized conductive behavior. However, the effect of nitrogen on the magnetic properties of graphene has so far only been addressed theoretically, and triggering of magnetism through N-doping has not yet been proved experimentally, except for systems containing a high amount of oxygen and thus decreased conductivity. Here, we report the first example of ferromagnetic graphene achieved by controlled doping with graphitic, pyridinic, and chemisorbed nitrogen. The magnetic properties were found to depend strongly on both the nitrogen concentration and type of structural N-motifs generated in the host lattice. Graphenes doped below 5 at. % of nitrogen were nonmagnetic; however, once doped at 5.1 at. % of nitrogen, N-doped graphene exhibited transition to a ferromagnetic state at ∼69 K and displayed a saturation magnetization reaching 1.09 emu/g. Theoretical calculations were used to elucidate the effects of individual chemical forms of nitrogen on magnetic properties. Results showed that magnetic effects were triggered by graphitic nitrogen, whereas pyridinic and chemisorbed nitrogen contributed much less to the overall ferromagnetic ground state. Calculations further proved the existence of exchange coupling among the paramagnetic centers mediated by the conduction electrons.

Enhancing Tumor Cell Response to Chemotherapy through the Targeted Delivery of Platinum Drugs Mediated by Highly Stable, Multifunctional Carboxymethylcellulose-Coated Magnetic Nanoparticles.

The fabrication of nanoparticles using different formulations, and which can be used for the delivery of chemotherapeutics, has recently attracted considerable attention. We describe herein an innovative approach that may ultimately allow for the selective delivery of anticancer drugs to tumor cells by using an external magnet. A conventional antitumor drug, cisplatin, has been incorporated into new carboxymethylcellulose-stabilized magnetite nanoparticles conjugated with the fluorescent marker Alexa Fluor 488 or folic acid as targeting agent. The magnetic nanocarriers possess exceptionally high biocompatibility and colloidal stability. These cisplatin-loaded nanoparticles overcome the resistance mechanisms typical of free cisplatin. Moreover, experiments aimed at the localization of the nanoparticles driven by an external magnet in a medium that mimics physiological conditions confirmed that this localization can inhibit tumor cell growth site-specifically.

Drop coating deposition of a liposome suspension on surfaces with different wettabilities: "coffee ring" formation and suspension preconcentration.

Evaporation of a drop of biomolecular solution on a solid surface typically creates a ring-shaped drying pattern, formed by the so-called "coffee ring" effect. The size and shape of the "coffee ring" pattern is strongly dependent on the properties of the surface as well as on the deposited molecular solution or suspension. In this paper, we tested six types of surfaces differing in their physico-chemical surface characteristics (contact angles, wettability and roughness) as well as in the presence or absence of a base metal layer. The tested surfaces include two fluorocarbon coated metallic surfaces (commercial SpectRIM™ from Tienta Sciences, Inc. based on a smoothed stainless steel and non-commercial aluminium surface), three silanized glass surfaces and polished CaF2. The results showed that the formation of a "coffee ring" was influenced by surface wettability as well as by lipid concentration in the drop. Drop coating deposition Raman (DCDR) spectroscopy was used to compare the ability of the tested surfaces to preconcentrate molecules in the ring and therefore improve detection sensitivity. It was shown that surfaces with a contact angle of 90° and higher produce smaller drying patterns than more hydrophilic surfaces. In these drying patterns, the model liposomes were more efficiently preconcentrated, which resulted in a higher Raman signal of the liposomes. The applicability of surfaces with static contact angles less than 90°, high water contact angle hysteresis and no metal layer (silanized glass, CaF2) is limited to samples with high liposome concentrations.

Biomimetic Superhydrophobic/Superoleophilic Highly Fluorinated Graphene Oxide and ZIF-8 Composites for Oil-Water Separation.

Superhydrophobic/superoleophilic composites HFGO@ZIF-8 have been prepared from highly fluorinated graphene oxide (HFGO) and the nanocrystalline zeolite imidazole framework ZIF-8. The structure-directing and coordination-modulating properties of HFGO allow for the selective nucleation of ZIF-8 nanoparticles at the graphene surface oxygen functionalities. This results in localized nucleation and size-controlled ZIF-8 nanocrystals intercalated in between HFGO layers. The composite microstructure features fluoride groups bonded at the graphene. Self-assembly of a unique micro-mesoporous architecture is achieved, where the micropores originate from ZIF-8 nanocrystals, while the functionalized mesopores arise from randomly organized HFGO layers separated by ZIF-8 nanopillars. The hybrid material displays an exceptional high water contact angle of 162° and low oil contact angle of 0° and thus reveals very high sorption selectivity, fast kinetics, and good absorbencies for nonpolar/polar organic solvents and oils from water. Accordingly, Sponge@HFGO@ZIF-8 composites are successfully utilized for oil-water separation.

Graphene derivative-based ink advances inkjet printing technology for fabrication of electrochemical sensors and biosensors.

The field of biosensing would significantly benefit from a disruptive technology enabling flexible manufacturing of uniform electrodes. Inkjet printing holds promise for this, although realizing full electrode manufacturing with this technology remains challenging. We introduce a nitrogen-doped carboxylated graphene ink (NGA-ink) compatible with commercially available printing technologies. The water-based and additive-free NGA-ink was utilized to produce fully inkjet-printed electrodes (IPEs), which demonstrated successful electrochemical detection of the important neurotransmitter dopamine. The cost-effectiveness of NGA-ink combined with a total cost per electrode of $0.10 renders it a practical solution for customized electrode manufacturing. Furthermore, the high carboxyl group content of NGA-ink (13 wt%) presents opportunities for biomolecule immobilization, paving the way for the development of advanced state-of-the-art biosensors. This study highlights the potential of NGA inkjet-printed electrodes in revolutionizing sensor technology, offering an affordable, scalable alternative to conventional electrochemical systems.

Correction: α-Fe2O3/TiO2 3D hierarchical nanostructures for enhanced photoelectrochemical water splitting.

Correction for 'α-Fe2O3/TiO2 3D hierarchical nanostructures for enhanced photoelectrochemical water splitting' by Hyungkyu Han et al., Nanoscale, 2017, 9, 134-142, https://doi.org/10.1039/C6NR06908H.

Modeling the spatiotemporal spread of beneficial alleles using ancient genomes.

Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.

Analyzing the genomes of our ancient ancestors can reveal how certain traits spread through the human population over the course of evolution. Mutations that make individuals better equipped to survive their environment are more likely to be passed on to the next generation and become more common. For example, a genetic variant that enables adult people to digest sugars in dairy products has become more common in humans over time. Yet evolution does not only happen across time: it transverses space as well. Modeling the geographic spread of such genetic mutations is challenging using existing methods. To overcome this, Muktupavela et al. developed a new computational method that uses modern and ancient human genomes to study the evolution of specific genetic variants across space and time. The tool can determine where certain variants first emerged, how quickly they spread across geographic areas, and how rapidly they became prevalent in human populations. Muktupavela et al. applied their new method, which was based on a previously published framework, to track the spread of two common genetic variations that have previously been reported to be subject to natural selection: one that allows adult humans to digest dairy products, and another associated with skin pigmentation. They found that the mutation that enabled dairy consumption originated around what is now southwestern Russia or eastern Ukraine. The variation then spread westward, becoming increasingly more common over the course of the Holocene. The mutation related to skin pigmentation emerged further south than the dairy-related variation, and then also spread westward. Massive human migrations during the Neolithic and Bronze Age eras may have helped disperse both variants. The model developed by Muktupavela et al. could help scientists track the geographic spread of other genetic variants in human populations, as well as provide new insights into how humans adapt to changing environmental conditions. Incorporating major events into the model, like mass migrations or glacial retreats, may lead to even more insights.

Reusable Co-nanoparticles for general and selective N-alkylation of amines and ammonia with alcohols.

A general cobalt-catalyzed N-alkylation of amines with alcohols by borrowing hydrogen methodology to prepare different kinds of amines is reported. The optimal catalyst for this transformation is prepared by pyrolysis of a specific templated material, which is generated in situ by mixing cobalt salts, nitrogen ligands and colloidal silica, and subsequent removal of silica. Applying this novel Co-nanoparticle-based material, >100 primary, secondary, and tertiary amines including N-methylamines and selected drug molecules were conveniently prepared starting from inexpensive and easily accessible alcohols and amines or ammonia.

Sulfidated nano-scale zerovalent iron is able to effectively reduce in situ hexavalent chromium in a contaminated aquifer.

In a number of laboratory studies, sulfidated nanoscale zero-valent iron (S-nZVI) particles showed increased reactivity, reducing capacity, and electron selectivity for Cr(VI) removal from contaminated waters. In our study, core-shell S-nZVI particles were successfully injected into an aquifer contaminated with Cr(VI) at a former chrome plating facility. S-nZVI migrated towards monitoring wells, resulting in a rapid decrease in Cr(VI) and Crtot concentrations and a long-term decrease in groundwater redox potential observed even 35 m downstream the nearest injection well. Characterization of materials recovered from the injection and monitoring wells confirmed the presence of nZVI particles, together with iron corrosion products. Chromium was identified on the surface of the recovered iron particles as Cr(III), and its occurrence was linked to the formation of insoluble chromium-iron (oxyhydr)oxides such as CrxFe(1-x)(OH)3(s). Injected S-nZVI particles formed aggregates, which were slowly transformed into iron (oxyhydr)oxides and carbonate green rust. Elevated contents of Fe0 were detected even several months after injection, indicating good S-nZVI longevity. The sulfide shell was gradually disintegrated and/or dissolved. Geochemical modelling confirmed the overall stability of the resulting Cr(III) phase at field conditions. This study demonstrates the applicability of S-nZVI for the remediation of a Cr(VI)-contaminated aquifer.

Carboxylated Graphene for Radical-Assisted Ultra-Trace-Level Water Treatment and Noble Metal Recovery.

Sorption technologies, enabling removal of heavy metals, play a pivotal role in meeting the global demands for unrestricted access to drinking water. Standard sorption technologies suffer from limited efficiency related to the weak sorbent-metal interaction. Further challenges include the development of technologies enabling smart metal recovery and sorbent regeneration. To this end, a densely functionalized graphene, with 33% by mass content of carboxyl groups, linked through direct C-C bonds (graphene acid, GA) represents a previously unexplored solution to this challenge. GA revealed excellent efficiency for removal of highly toxic metals, such as Cd2+ and Pb2+. Due to its selective chemistry, GA can bind heavy metals with high affinity, even at concentrations of 1 mg L-1 and in the presence of competing ions of natural drinking water, and reduce them down to drinking water allowance levels of a few µg L-1. This is not only due to carboxyl groups but also due to the stable radical centers of the GA structure, enabling metal ion-radical interactions, as proved by EPR, XPS, and density functional theory calculations. GA offers full structural integrity during the highly acidic and basic treatment, which is exploited for noble metal recovery (Ga3+, In3+, Pd2+) and sorbent regeneration. Owing to these attributes, GA represents a fully reusable metal sorbent, applicable also in electrochemical energy technologies, as illustrated with a GA/Pt catalyst derived from Pt4+-contaminated water.

Covalent Graphene-MOF Hybrids for High-Performance Asymmetric Supercapacitors.

In this work, the covalent attachment of an amine functionalized metal-organic framework (UiO-66-NH2  = Zr6 O4 (OH)4 (bdc-NH2 )6 ; bdc-NH2  = 2-amino-1,4-benzenedicarboxylate) (UiO-Universitetet i Oslo) to the basal-plane of carboxylate functionalized graphene (graphene acid = GA) via amide bonds is reported. The resultant GA@UiO-66-NH2 hybrid displayed a large specific surface area, hierarchical pores and an interconnected conductive network. The electrochemical characterizations demonstrated that the hybrid GA@UiO-66-NH2 acts as an effective charge storing material with a capacitance of up to 651 F g-1 , significantly higher than traditional graphene-based materials. The results suggest that the amide linkage plays a key role in the formation of a π-conjugated structure, which facilitates charge transfer and consequently offers good capacitance and cycling stability. Furthermore, to realize the practical feasibility, an asymmetric supercapacitor using a GA@UiO-66-NH2 positive electrode with Ti3 C2 TX MXene as the opposing electrode has been constructed. The cell is able to deliver a power density of up to 16 kW kg-1 and an energy density of up to 73 Wh kg-1 , which are comparable to several commercial devices such as Pb-acid and Ni/MH batteries. Under an intermediate level of loading, the device retained 88% of its initial capacitance after 10 000 cycles.