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.

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).

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.

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.

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.

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.

Structural Elucidation, Aggregation, and Dynamic Behaviour of N,N,N,N-Copper(I) Schiff Base Complexes in Solid and in Solution: A Combined NMR, X-ray Spectroscopic and Crystallographic Investigation.

A series of Cu(I) complexes of bidentate or tetradentate Schiff base ligands bearing either 1-H-imidazole or pyridine moieties were synthesized. The complexes were studied by a combination of NMR and X-ray spectroscopic techniques. The differences between the imidazole- and pyridine-based ligands were examined by 1H, 13C and 15N NMR spectroscopy. The magnitude of the 15Nimine coordination shifts was found to be strongly affected by the nature of the heterocycle in the complexes. These trends showed good correlation with the obtained Cu-Nimine bond lengths from single-crystal X-ray diffraction measurements. Variable-temperature NMR experiments, in combination with diffusion ordered spectroscopy (DOSY) revealed that one of the complexes underwent a temperature-dependent interconversion between a monomer, a dimer and a higher aggregate. The complexes bearing tetradentate imidazole ligands were further studied using Cu K-edge XAS and VtC XES, where DFT-assisted assignment of spectral features suggested that these complexes may form polynuclear oligomers in solid state. Additionally, the Cu(II) analogue of one of the complexes was incorporated into a metal-organic framework (MOF) as a way to obtain discrete, mononuclear complexes in the solid state.

The wild species genome ancestry of domestic chickens.

BACKGROUND: Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes. RESULTS: In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system. CONCLUSIONS: Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.

Understanding the Deactivation Phenomena of Small-Pore Mo/H-SSZ-13 during Methane Dehydroaromatisation.

Small pore zeolites have shown great potential in a number of catalytic reactions. While Mo-containing medium pore zeolites have been widely studied for methane dehydroaromatisation (MDA), the use of small pore supports has drawn limited attention due to the fast deactivation of the catalyst. This work investigates the structure of the small pore Mo/H-SSZ-13 during catalyst preparation and reaction by operando X-ray absorption spectroscopy (XAS), in situ synchrotron powder diffraction (SPD), and electron microscopy; then, the results are compared with the medium pore Mo/H-ZSM-5. While SPD suggests that during catalyst preparation, part of the MoOx anchors inside the pores, Mo dispersion and subsequent ion exchange was less effective in the small pore catalyst, resulting in the formation of mesopores and Al2(MOO4)3 particles. Unlike Mo/H-ZSM-5, part of the Mo species in Mo/H-SSZ-13 undergoes full reduction to Mo0 during MDA, whereas characterisation of the spent catalyst indicates that differences also exist in the nature of the formed carbon deposits. Hence, the different Mo speciation and the low performance on small pore zeolites can be attributed to mesopores formation during calcination and the ineffective ion exchange into well dispersed Mo-oxo sites. The results open the scope for the optimisation of synthetic routes to explore the potential of small pore topologies.

Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis aries).

Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits included SPOCK1 (age at first oestrus), GPR173 (mediator of ovarian cyclicity), HB-EGF (signalling early pregnancy success) and SMARCAL1 and HMGN3a (regulate gene expression during embryogenesis). The genes involved in male reproduction were FOXJ1 (sperm function and successful fertilization) and NME5 (spermatogenesis). We also observed genes such as PKD2L2, MAGED1 and KDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control of BMP15 while other genes that enhance male and female fertility are essential for reproductive fitness.

In Situ Flow MAS NMR Spectroscopy and Synchrotron PDF Analyses of the Local Response of the Brønsted Acidic Site in SAPO-34 during Hydration at Elevated Temperatures.

In situ flow magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and synchrotron-based pair distribution function (PDF) analyses were applied to study water's interactions with the Brønsted acidic site and the surrounding framework in the SAPO-34 catalyst at temperatures up to 300 °C for NMR spectroscopy and 700 °C for PDF. 29 Si enrichment of the sample enabled detailed NMR spectroscopy investigations of the T-atom generating the Brønsted site. By NMR spectroscopy, we observed dehydration above 100 °C and a coalescence of Si peaks due to local framework adjustments. Towards 300 °C, the NMR spectroscopy data indicated highly mobile acidic protons. In situ total X-ray scattering measurements analyzed by PDF showed clear changes in the Al local environment in the 250-300 °C region, as the Al-O bond lengths showed a sudden change. This fell within the same temperature range as the increased Brønsted proton mobility. We suggest that the active site in this catalyst under industrial conditions comprises not only the Brønsted proton but also SiO4 . To the best of our knowledge, this is the first work proposing a structural model of a SAPO catalyst by atomic PDF analysis. The combination of synchrotron PDF analysis with in situ NMR spectroscopy is promising in revealing the dynamic features of a working catalyst.

Chemical Structures of Specific Sodium Ion Battery Components Determined by Operando Pair Distribution Function and X-ray Diffraction Computed Tomography.

To improve lithium and sodium ion battery technology, it is imperative to understand how the properties of the different components are controlled by their chemical structures. Operando structural studies give us some of the most useful information for understanding how batteries work, but it remains difficult to separate out the contributions of the various components of a battery stack (e.g., electrodes, current collectors, electrolyte, and binders) and examine specific materials. We have used operando X-ray diffraction computed tomography (XRD-CT) to study specific components of an essentially unmodified working cell and extract detailed, space-resolved structural information on both crystalline and amorphous phases that are present during cycling by Rietveld and pair distribution function (PDF) methods. We illustrate this method with the first detailed structural examination of the cycling of sodium in a phosphorus anode, revealing surprisingly different mechanisms for sodiation and desodiation in this promising, high-capacity anode system.

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken.

BACKGROUND: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data. RESULTS: An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05). CONCLUSIONS: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

4,4'-Dimeth-oxybi-phenyl-3,3'-di-car-box-ylic acid.

The title compound, C16H14O6, was recrystallized under solvothermal conditions. The mol-ecules are located on inversion centres, with one complete mol-ecule generated from the asymmetric unit by inversion. There are intra-molecular O-H⋯O hydrogen bonds involving the carb-oxy-lic acid group and the O atom of the adjacent meth-oxy group. In the crystal, mol-ecules are linked via O-H⋯O hydrogen bonds, forming chains propagating along [100]. The chains are linked via C-H⋯O hydrogen bonds, forming sheets parallel to (001).

Dimethyl 3,3'-di-meth-oxy-biphenyl-4,4'-di-carboxyl-ate.

In the title compound, C18H18O6, the biphenyl moiety is twisted with a dihedral angle of 29.11 (10)°. The carbometh-oxy groups form C-C-C-O torsion angles of -18.3 (3) and -27.7 (3)° with the attached rings, as a result of steric hindrances from the nearby meth-oxy groups. In the absence of stacking inter-actions and with no H⋯O contacts shorter than 2.7 Å, the packing is dominated by weaker van der Waals inter-actions.

Methyl 5-iodo-2-meth-oxy-benzoate.

In the title compound, C9H9IO3, the mol-ecules are close to planar [maximum deviation from benzene ring plane = 0.229 (5) Šfor the methyl carboxylate C atom] with the methyl groups oriented away from each other. In the crystal, mol-ecules form stacked layers parallel to the ab plane, where every layer has either the iodine or meth-oxy/methyl carboxyl-ate substituents pointing towards each other in an alternating fashion.

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.

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.