Enabling a bioinspired N,N,N-copper coordination motif through spatial control in UiO-67: synthesis and reactivity.

Metal-organic frameworks (MOFs) featuring zirconium-based clusters are widely used for the development of functionalized materials due to their exceptional stability. In this study, we report the synthesis of a novel N,N,N-ligand compatible with a biphenyl dicarboxylic acid-based MOF. However, the resulting copper(I) complex exhibited unexpected coordination behaviour, lacking the intended trifold coordination motif. Herein, we demonstrate the successful immobilization of a bioinspired ligand within the MOF, which preserved its crystalline and porous nature while generating a well-defined copper site. Comprehensive spectroscopic analyses, including X-ray absorption, UV/Vis, and infrared spectroscopy, were conducted to investigate the copper site and its thermal behaviour. The immobilized ligand exhibited the desired tridentate coordination to copper, providing access to a coordination motif otherwise unattainable. Notably, water molecules were also found to coordinate to copper. Upon heating, the copper centre within the MOF exhibited reversible dehydration, suggesting facile creation of open coordination sites. Furthermore, the copper site displayed reduction at elevated temperatures and subsequent susceptibility to oxidation by molecular oxygen. Lastly, both the molecular complexes and the MOF were evaluated as catalysts for the oxidation of cyclohexane using hydrogen peroxide. This work highlights the successful immobilization of a bioinspired ligand in a zirconium-based MOF, shedding light on the structural features, thermal behaviour, and catalytic potential of the resulting copper sites.

Replica exchange molecular dynamics for Li-intercalation in graphite: a new solution for an old problem.

Li intercalation and graphite stacking have been extensively studied because of the importance of graphite in commercial Li-ion batteries. Despite this attention, there are still questions about the atomistic structures of the intermediate states that exist during lithiation, especially when phase dynamics cause a disordered Li distribution. The Li migration event (diffusion coefficient of 10-5 nm2 ns-1) makes it difficult to explore the various Li-intercalation configurations in conventional molecular dynamics (MD) simulations with an affordable simulation timescale. To overcome these limitations, we conducted a comprehensive study using replica-exchange molecular dynamics (REMD) in combination with the ReaxFF force field. This approach allowed us to study the behavior of Li-intercalated graphite from any starting arrangement of Li at any value of x in LixC6. Our focus was on analyzing the energetic favorability differences between the relaxed structures. We rationalized the trends in formation energy on the basis of observed structural features, identifying three main structural features that cooperatively control Li rearrangement in graphite: Li distribution, graphite stacking mode and gallery height (graphene layer spacing). We also observed a tendency for clustering of Li, which could lead to dynamic local structures that approximate the staging models used to explain intercalation into graphite.

Unraveling the (De)sodiation Mechanisms of BiFeO3 at a High Rate with Operando XRD.

Development of new anode materials for Na-ion batteries strongly depends on a detailed understanding of their cycling mechanism. Due to instrumental limitations, the majority of mechanistic studies focus on operando materials' characterization at low cycling rates. In this work, we evaluate and compare the (de)sodiation mechanisms of BiFeO3 in Na-ion batteries at different current densities using operando X-ray diffraction (XRD) and ex situ X-ray absorption spectroscopy (XAS). BiFeO3 is a conversion-alloying anode material with a high initial sodiation capacity of ∼600 mAh g-1, when cycled at 0.1 A g-1. It does not change its performance or cycling mechanism, except for minor losses in capacity, when the current density is increased to 1 A g-1. In addition, operando XRD characterization carried out over multiple cycles shows that the Bi ⇋ NaBi (de)alloying reaction and the oxidation of Bi at the interface with the Na-Fe-O matrix are detrimental for cycling stability. The isolated NaBi ⇋ Na3Bi reaction is less damaging to the cycling stability of the material.

A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy.

BACKGROUND: Low-pass whole-genome sequencing and imputation offer significant cost savings, enabling substantial increases in sample size and statistical power. This approach is particularly promising in livestock breeding, providing an affordable means of screening individuals for deleterious alleles or calculating genomic breeding values. Consequently, it may also be of value in companion animal genomics to support pedigree breeding. We sought to evaluate in dogs the impact of low coverage sequencing and reference-guided imputation on genotype concordance and association analyses. RESULTS: DNA isolated from saliva of 30 Labrador retrievers was sequenced at low (0.9X and 3.8X) and high (43.5X) coverage, and down-sampled from 43.5X to 9.6X and 17.4X. Genotype imputation was performed using a diverse reference panel (1021 dogs), and two subsets of the former panel (256 dogs each) where one had an excess of Labrador retrievers relative to other breeds. We observed little difference in imputed genotype concordance between reference panels. Association analyses for a locus acting as a disease proxy were performed using single-marker (GEMMA) and haplotype-based (XP-EHH) tests. GEMMA results were highly correlated (r ≥ 0.97) between 43.5X and ≥ 3.8X depths of coverage, while for 0.9X the correlation was lower (r ≤ 0.8). XP-EHH results were less well correlated, with r ranging from 0.58 (0.9X) to 0.88 (17.4X). Across a random sample of 10,000 genomic regions averaging 17 kb in size, we observed a median of three haplotypes per dog across the sequencing depths, with 5% of the regions returning more than eight haplotypes. Inspection of one such region revealed genotype and phasing inconsistencies across sequencing depths. CONCLUSIONS: We demonstrate that saliva-derived canine DNA is suitable for whole-genome sequencing, highlighting the feasibility of client-based sampling. Low-pass sequencing and imputation require caution as incorrect allele assignments result when the subject possesses alleles that are absent in the reference panel. Larger panels have the capacity for greater allelic diversity, which should reduce the potential for imputation error. Although low-pass sequencing can accurately impute allele dosage, we highlight issues with phasing accuracy that impact haplotype-based analyses. Consequently, if accurately phased genotypes are required for analyses, we advocate sequencing at high depth (> 20X).

When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera.

The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates.

Sunlight-Driven Photocatalytic Degradation of Methylene Blue with Facile One-Step Synthesized Cu-Cu2O-Cu3N Nanoparticle Mixtures.

Sunlight-driven photocatalytic degradation is an effective and eco-friendly technology for the removal of organic pollutants from contaminated water. Herein, we describe the one-step synthesis of Cu-Cu2O-Cu3N nanoparticle mixtures using a novel non-aqueous, sol-gel route and their application in the solar-driven photocatalytic degradation of methylene blue. The crystalline structure and morphology were investigated with XRD, SEM and TEM. The optical properties of the as-prepared photocatalysts were investigated with Raman, FTIR, UV-Vis and photoluminescence spectroscopies. The influence of the phase proportions of Cu, Cu2O and Cu3N in the nanoparticle mixtures on the photocatalytic activity was also investigated. Overall, the sample containing the highest quantity of Cu3N exhibits the highest photocatalytic degradation efficiency (95%). This enhancement is attributed to factors such as absorption range broadening, increased specific surface of the photocatalysts and the downward band bending in the p-type semiconductors, i.e., Cu3N and Cu2O. Two different catalytic dosages were studied, i.e., 5 mg and 10 mg. The higher catalytic dosage exhibited lower photocatalytic degradation efficiency owing to the increase in the turbidity of the solution.

Correction: 5D total scattering computed tomography reveals the full reaction mechanism of a bismuth vanadate lithium ion battery anode.

Correction for '5D total scattering computed tomography reveals the full reaction mechanism of a bismuth vanadate lithium ion battery anode' by Jonas Sottmann et al., Phys. Chem. Chem. Phys., 2022, 24, 27075-27085, https://doi.org/10.1039/D2CP03892G.

Signatures of purifying selection and site-specific positive selection on the mitochondrial DNA of dromedary camels (Camelus dromedarius).

The two species of the Old World Camelini tribe, dromedary and Bactrian camels, show superior adaptability to the different environmental conditions they populate, e.g. desert, mountains and coastal areas, which might be associated with adaptive variations on their mitochondrial DNA. Here, we investigate signatures of natural selection in the 13-mitochondrial protein-coding genes of different dromedary camel populations from the Arabian Peninsula, Africa and southwest Asia. The full mitogenome sequences of 42 dromedaries, 38 domestic Bactrian, 29 wild Bactrian camels and 31 samples representing the New World Lamini tribe reveal species-wise genetic distinction among Camelidae family species, with no evidence of geographic distinction among dromedary camels. We observe gene-wide signals of adaptive divergence between the Old World and New World camels, with evidence of purifying selection among Old World camel species. Upon comparing the different Camelidae tribes, 27 amino acid substitutions across ten mtDNA protein-coding genes were found to be under positive selection, in which, 24 codons were defined to be under positive adaptive divergence between Old World and New World camels. Seven codons belonging to three genes demonstrated positive selection in dromedary lineage. A total of 89 codons were found to be under positive selection in Camelidae family based on investigating the impact of amino acid replacement on the physiochemical properties of proteins, including equilibrium constant and surrounding hydrophobicity. These mtDNA variants under positive selection in the Camelidae family might be associated with their adaptation to their contrasting environments.

Structural properties of mixed conductor Ba1-xGd1-yLax+yCo2O6-δ.

Ba1-xGd1-yLax+yCo2O6-δ (BGLC) compositions with large compositional ranges of Ba, Gd, and La have been characterised with respect to phase compositions, structure, and thermal and chemical expansion. The results show a system with large compositional flexibility, enabling tuning of functional properties and thermal and chemical expansion. We show anisotropic chemical expansion and detailed refinements of emerging phases as La is substituted for Ba and Gd. The dominating phase is the double perovskite structure Pmmm, which is A-site ordered along the c-axes and with O vacancy ordering along the b-axis in the Ln-layer. Phases emerging when substituting La for Ba are orthorhombic Ba-deficient Pbnm and cubic LaCoO3-based R3̄c. When La is almost completely substituted for Gd, the material can be stabilised in Pmmm, or cubic Pm3̄m, depending on thermal and atmospheric history. We list thermal expansion coefficients for x = 0-0.3, y = 0.2.

5D total scattering computed tomography reveals the full reaction mechanism of a bismuth vanadate lithium ion battery anode.

We have used operando 5D synchrotron total scattering computed tomography (TSCT) to understand the cycling and possible long term deactivation mechanisms of the lithium-ion battery anode bismuth vanadate. This anode material functions via a combined conversion/alloying mechanism in which nanocrystals of lithium-bismuth alloy are protected by an amorphous matrix of lithium vanadate. This composite is formed in situ during the first lithiation of the anode. The operando TSCT data were analyzed and mapped using both pair distribution function and Rietveld methods. We can follow the lithium-bismuth alloying reaction at all stages, gaining real structural insight including variations in nanoparticle sizes, lattice parameters and bond lengths, even when the material is completely amorphous. We also observe for the first time structural changes related to the cycling of lithium ions in the lithium vanadate matrix, which displays no interactions beyond the first shell of V-O bonds. The first 3D operando mapping of the distribution of different materials in an amorphous anode reveals a decline in coverage caused by either agglomeration or partial dissolution of the active material, hinting at the mechanism of long term deactivation. The observations from the operando experiment are backed up by post mortem transmission electron microscope (TEM) studies and theoretical calculations to provide a complete picture of an exceptionally complex cycling mechanism across a range of length scales.

Real-time regeneration of a working zeolite monitored via operando X-ray diffraction and crystallographic imaging: how coke flees the MFI framework.

We have monitored the regeneration of H-ZSM-5 via operando time-resolved powder X-Ray diffraction (PXRD) coupled with mass spectroscopy (MS). Parametric Rietveld refinements and calculation of the extra-framework electronic density by differential Fourier maps analysis provide details on the mode of coke removal combined with the corresponding sub-unit cell changes of the zeolite structure. It is clear that the coke removal is a complex process that occurs in at least two steps; a thermal decomposition followed by oxidation. In a coked zeolite, the straight 10-ring channel circumference is warped to an oval shape due to structural distortion induced by rigid aromatic coke species. The data presented explain why the difference in length between the a-vector and the b-vector of the MFI unit cell is a robust descriptor for bulky coke, as opposed to the unit cell volume, which is affected also by adsorbed species and thermal effects. Our approach holds the promise to quantify and identify coke removal (and formation) in structurally distinct locations within the zeolite framework.

Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.

BACKGROUND: In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. RESULTS: We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS. CONCLUSIONS: Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.

Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones.

Honey bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environment and mate naturally with queens from the local subspecies. The resulting admixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to subspecies, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP-chip or by low-pass sequencing, or (iii) selecting SNPs compatible with the requirements of genotyping chips.

A locus conferring tolerance to Theileria infection in African cattle.

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Bos indicus (Boran) cattle demonstrating heritable tolerance to infection with T. parva (h2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on bovine chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained variant in a paralogue of the FAF1 gene in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa's most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva.

Synthesis of substituted (N,C) and (N,C,C) Au(III) complexes: the influence of sterics and electronics on cyclometalation reactions.

Cyclometalated Au(III) complexes are of interest due to their catalytic, medicinal, and photophysical properties. Herein, we describe the synthesis of derivatives of the type (N,C)Au(OAcF)2 (OAcF = trifluoroacetate) and (N,C,C)AuOAcF by a cyclometalation route, where (N,C) and (N,C,C) are chelating 2-arylpyridine ligands. The scope of the synthesis is explored by substituting the 2-arylpyridine core with electron donor or acceptor substituents at one or both rings. Notably, a variety of functionalized Au(III) complexes can be obtained in one step from the corresponding ligand and Au(OAc)3, eliminating the need for organomercury intermediates, which is commonly reported for similar syntheses. The influence of substituents in the ligand backbone on the resulting complexes was assessed using DFT calculations, 15N NMR spectroscopy and single-crystal X-ray diffraction analysis. A correlation between the electronic properties of the (N,C) ligands and their ability to undergo cyclometalation was found from experimental studies combined with natural charge analysis, suggesting the cyclometalation at Au(III) to take place via an electrophilic aromatic substitution-type mechanism. The formation of Au(III) pincer complexes from tridentate (N,C,C) ligands was investigated by synthesis and DFT calculations, in order to assess the feasibility of C(sp3)-H bond activation as a synthetic pathway to (N,C,C) cyclometalated Au(III) complexes. It was found that C(sp3)-H bond activation is feasible for ligands containing different alkyl groups (isopropyl and ethyl), although the C-H activation is less energetically favored compared to a ligand containing tert-butyl groups.

Operando XRD studies on Bi2MoO6as anode material for Na-ion batteries.

Based on the same rocking-chair principle as rechargeable Li-ion batteries, Na-ion batteries are promising solutions for energy storage benefiting from low-cost materials comprised of abundant elements. However, despite the mechanistic similarities, Na-ion batteries require a different set of active materials than Li-ion batteries. Bismuth molybdate (Bi2MoO6) is a promising NIB anode material operating through a combined conversion/alloying mechanism. We report anoperandox-ray diffraction (XRD) investigation of Bi2MoO6-based anodes over 34 (de)sodiation cycles revealing both basic operating mechanisms and potential pathways for capacity degradation. Irreversible conversion of Bi2MoO6to Bi nanoparticles occurs through the first sodiation, allowing Bi to reversibly alloy with Na forming the cubic Na3Bi phase. Preliminary electrochemical evaluation in half-cellsversusNa metal demonstrated specific capacities for Bi2MoO6to be close to 300 mAh g-1during the initial 10 cycles, followed by a rapid capacity decay.OperandoXRD characterisation revealed that the increased irreversibility of the sodiation reactions and the formation of hexagonal Na3Bi are the main causes of the capacity loss. This is initiated by an increase in crystallite sizes of the Bi particles accompanied by structural changes in the electronically insulating Na-Mo-O matrix leading to poor conductivity in the electrode. The poor electronic conductivity of the matrix deactivates the NaxBi particles and prevents the formation of the solid electrolyte interface layer as shown by post-mortem scanning electron microscopy studies.

Inherited Tolerance in Cattle to the Apicomplexan Protozoan Theileria parva is Associated with Decreased Proliferation of Parasite-Infected Lymphocytes.

Theileria parva is the causative agent of East Coast fever and Corridor disease, which are fatal, economically important diseases of cattle in eastern, central and southern Africa. Improved methods of control of the diseases are urgently required. The parasite transforms host lymphocytes, resulting in a rapid, clonal expansion of infected cells. Resistance to the disease has long been reported in cattle from T. parva-endemic areas. We reveal here that first- and second-generation descendants of a single Bos indicus bull survived severe challenge with T. parva, (overall survival rate 57.3% compared to 8.7% for unrelated animals) in a series of five field studies. Tolerant cattle displayed a delayed and less severe parasitosis and febrile response than unrelated animals. The in vitro proliferation of cells from surviving cattle was much reduced compared to those from animals that succumbed to infection. Additionally, some pro-inflammatory cytokines such as IL1ß, IL6, TNFα or TGFß which are usually strongly expressed in susceptible animals and are known to regulate cell growth or motility, remain low in tolerant animals. This correlates with the reduced proliferation and less severe clinical reactions observed in tolerant cattle. The results show for the first time that the inherited tolerance to T. parva is associated with decreased proliferation of infected lymphocytes. The results are discussed in terms of whether the reduced proliferation is the result of a perturbation of the transformation mechanism induced in infected cells or is due to an innate immune response present in the tolerant cattle.

Clinical Evaluation of Corridor Disease in Bos indicus (Boran) Cattle Naturally Infected With Buffalo-Derived Theileria parva.

Corridor disease (CD) is a fatal condition of cattle caused by buffalo-derived Theileria parva. Unlike the related condition, East Coast fever, which results from infection with cattle-derived T. parva, CD has not been extensively studied. We describe in detail the clinical and laboratory findings in cattle naturally infected with buffalo-derived T. parva. Forty-six cattle were exposed to buffalo-derived T. parva under field conditions at the Ol Pejeta Conservancy, Kenya, between 2013 and 2018. The first signs of disease observed in all animals were nasal discharge (mean day of onset was 9 days post-exposure), enlarged lymph nodes (10 days post-exposure), and pyrexia (13.7 days post-exposure). Coughing and labored breathing were observed in more than 50% of animals (14 days post-exposure). Less commonly observed signs, corneal edema (22%) and diarrhea (11%), were observed later in the disease progression (19 days post-exposure). All infections were considered clinically severe, and 42 animals succumbed to infection. The mean time to death across all studies was 18.4 days. The mean time from onset of clinical signs to death was 9 days and from pyrexia to death was 4.8 days, indicating a relatively short duration of clinical illness. There were significant relationships between days to death and the days to first temperature (chi2 = 4.00, p = 0.046), and days to peak temperature (chi2 = 25.81, p = 0.001), animals with earlier onset pyrexia died sooner. These clinical indicators may be useful for assessing the severity of disease in the future. All infections were confirmed by the presence of macroschizonts in lymph node biopsies (mean time to parasitosis was 11 days). Piroplasms were detected in the blood of two animals (4%) and 20 (43%) animals seroconverted. In this study, we demonstrate the successful approach to an experimental field study for CD in cattle. We also describe the clinical progression of CD in naturally infected cattle, including the onset and severity of clinical signs and pathology. Laboratory diagnoses based on examination of blood samples are unreliable, and alternatives may not be available to cattle keepers. The rapid development of CD requires recognition of the clinical signs, which may be useful for early diagnosis of the disease and effective intervention for affected animals.

Cu-catalyzed C(sp2)-N-bond coupling of boronic acids and cyclic imides.

A general Cu-catalyzed strategy for coupling cyclic imides and alkenylboronic acids by forming C(sp2)-N-bonds is reported. The method enables the practical and mild preparation of (E)-enimides. A large range of cyclic imides are allowed, and di- and tri-substituted alkenylboronic acids can be used. Full retention was observed in the configuration of the alkene double bond in the coupled products. The method is also applicable for preparing N-arylimides, using arylboronic acids as coupling partners. The usefulness of this strategy is exemplified by the convenient derivatization of the chemotherapy medication 5-flurouracil, the nucleoside uridine and the anti-epileptic drug phenytoin.