Search

This study presents the first genome and transcriptome analyses for Fusarium oxysporum f. sp. lactucae (Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with other F. oxysporum ff. spp. following mimp-based bioinformatic analyses. Notably, homologues of Secreted in Xylem (SIX) genes, also present in many other F. oxysporum ff. spp, were identified in Fola, with both SIX9 and SIX14 (multiple copies with sequence variants) present in both Fola1 and Fola4. All Fola4 isolates also contained an additional single copy of SIX8. RNAseq of lettuce following infection with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in other F. oxysporum ff. spp. including several in F. oxysporum f. sp. apii. Although SIX8, SIX9 and SIX14 were all highly expressed in Fola4, of the two SIX genes present in Fola1, only SIX9 was expressed as further analysis revealed that SIX14 gene copies were disrupted by insertion of a transposable element. Two variants of Fola4 were also identified based on different genome and effector-based analyses. This included two different SIX8 sequence variants which were divergently transcribed from a shared promoter with either PSE1 or PSL1 respectively. In addition, there was evidence of two independent instances of HCT in the different Fola4 variants. The involvement of helitrons in Fola genome rearrangement and gene expression is discussed. [ABSTRACT FROM AUTHOR]

Biogenic magnetite crystals produced by magnetotactic bacteria (MTB) and associated magnetofossils in sediments are characterized by variable morphologies, grain sizes, and chain structures. Magnetofossils are widely used in paleomagnetic and paleoenvironmental studies, but the complex magnetofossil shapes and particle arrangements significantly affect magnetic properties, hampering their magnetic detection and proxy interpretation. Here we perform coupled experimental and micromagnetic modeling analyses of typical magnetofossil‐rich sediments, where the effects of magnetofossil crystal forms and microstructures on magnetic properties can be quantitatively separated. Since the in situ magnetofossil chain structures in sediments remain poorly known, we compare results from magnetic measurements and micromagnetic simulations based on realistic magnetofossil shapes and grain size distributions. Our results suggest that bullet‐shaped magnetofossils certainly contribute to the biogenic hard (BH) coercivity component with a minor contribution from elongated prismatic particles, and collapsed equidimensional grains to the biogenic soft (BS) component. Micromagnetic simulations with different collapse models of bullet‐shaped magnetofossils produce variable FORC (first‐order reversal curve) central‐ridge contributions with similar coercivity distributions. Sensitivity test suggests that samples containing different forms of magnetofossils can produce the BH coercivity component if the proportion of the bullet‐shaped particles is more than ∼2%. Magnetofossil assemblages with a higher proportion of bullet‐shaped particles have higher coercivities, squareness ratios, and larger BH contents. Our data shed new light on understanding the origin of magnetofossil coercivity components and the in situ magnetofossil microstructures in sediments, which is widely useful for interpreting magnetofossil proxy signals in geological records. Plain Language Summary: Magnetotactic bacteria (MTB) that produce magnetic nanoparticles are widespread in sediments and water columns. Magnetofossils preserved in sediments after MTB death record ancient biological, geological, and environmental processes on Earth. The diversity of magnetofossil shapes and crystal arrangements significantly affects the magnetic properties of natural samples, making it difficult to interpret ancient environmental conditions. Here we carry out coupled magnetic analyses and numerical modeling to investigate the link between magnetic properties and magnetofossil configurations. Our analyses suggest that bullet‐shaped magnetofossils contribute to the most stable magnetic signals in sediments and that magnetofossils are arranged in highly collapsed arrangements rather than straight chains. Additionally, different combinations of magnetofossil morphologies significantly affect the magnetic properties of magnetofossil‐bearing samples. This study makes major contributions to the interpretation of magnetofossil proxy signals in paleomagnetic and paleoclimatic records. Key Points: Coupled experimental data and simulated results reveal the linkage between bullet‐shaped magnetite crystal and biogenic hard componentDifferent collapse models of bullet magnetofossils produce variable FORC central‐ridge contributions with similar coercivity distributionsSensitivity test suggests that more than ∼2% bullet‐shaped magnetofossils can produce a biogenic hard component [ABSTRACT FROM AUTHOR]

When compared with other phylogroups (PGs) of the Pseudomonas syringae species complex, P. syringae pv. syringae (Pss) strains within PG2 have a reduced repertoire of type III effectors (T3Es) but produce several phytotoxins. Effectors within the cherry pathogen Pss 9644 were grouped based on their frequency in strains from Prunus as the conserved effector locus (CEL) common to most P. syringae pathogens; a core of effectors common to PG2; a set of PRUNUS effectors common to cherry pathogens; and a FLEXIBLE set of T3Es. Pss 9644 also contains gene clusters for biosynthesis of toxins syringomycin, syringopeptin and syringolin A. After confirmation of virulence gene expression, mutants with a sequential series of T3E and toxin deletions were pathogenicity tested on wood, leaves and fruits of sweet cherry (Prunus avium) and leaves of ornamental cherry (Prunus incisa). The toxins had a key role in disease development in fruits but were less important in leaves and wood. An effectorless mutant retained some pathogenicity to fruit but not wood or leaves. Striking redundancy was observed amongst effector groups. The CEL effectors have important roles during the early stages of leaf infection and possibly acted synergistically with toxins in all tissues. Deletion of separate groups of T3Es had more effect in P. incisa than in P. avium. Mixed inocula were used to complement the toxin mutations in trans and indicated that strain mixtures may be important in the field. Our results highlight the niche‐specific role of toxins in P. avium tissues and the complexity of effector redundancy in the pathogen Pss 9644. [ABSTRACT FROM AUTHOR]

Palaeomagnetic measurements of meteorites (1-5) suggest that, shortly after the birth of the Solar System, the molten metallic cores of many small planetary bodies converted vigorously and were capable of generating magnetic fields (6). Convection on these bodies is currently thought to have been thermally driven (7, 8), implying that magnetic activity would have been short-lived (9). Here we report a time-series palaeomagnetic record derived from nano magnetic imaging (10) of the Imilac and Esquel pallasite meteorites, a group of meteorites consisting of centimetre-sized metallic and silicate phases. We find a history of long-lived magnetic activity on the pallasite parent body, capturing the decay and eventual shutdown of the magnetic field as core solidification completed. We demonstrate that magnetic activity driven by progressive solidification of an inner core (11-13) is consistent with our measured magnetic field characteristics and cooling rates (14). Solidification-driven convection was probably common among small body cores (15), and, in contrast to thermally driven convection, will have led to a relatively late (hundreds of millions of years after accretion), long-lasting, intense and widespread epoch of magnetic activity among these bodies in the early Solar System., The pallasites are slowly cooled (2-9 K per million years, Myr; ref. 14) meteorites consisting of olivine crystals embedded in an Fe-Ni matrix (16), which have been suggested to originate [...]

Red raspberry (Rubus idaeus L.) is an economically valuable soft-fruit species with a relatively small (~300 Mb) but highly heterozygous diploid (2n = 2x = 14) genome. Chromosome-scale genome sequences are a vital tool in unravelling the genetic complexity controlling traits of interest in crop plants such as red raspberry, as well as for functional genomics, evolutionary studies, and pan-genomics diversity studies. In this study, we developed genome sequences of a primocane fruiting variety ('Autumn Bliss') and a floricane variety ('Malling Jewel'). The use of long-read Oxford Nanopore Technologies sequencing data yielded long read lengths that permitted well resolved genome sequences for the two cultivars to be assembled. The de novo assemblies of 'Malling Jewel' and 'Autumn Bliss' contained 79 and 136 contigs respectively, and 263.0 Mb of the 'Autumn Bliss' and 265.5 Mb of the 'Malling Jewel' assembly could be anchored unambiguously to a previously published red raspberry genome sequence of the cultivar 'Anitra'. Single copy ortholog analysis (BUSCO) revealed high levels of completeness in both genomes sequenced, with 97.4% of sequences identified in 'Autumn Bliss' and 97.7% in 'Malling Jewel'. The density of repetitive sequence contained in the 'Autumn Bliss' and 'Malling Jewel' assemblies was significantly higher than in the previously published assembly and centromeric and telomeric regions were identified in both assemblies. A total of 42,823 protein coding regions were identified in the 'Autumn Bliss' assembly, whilst 43,027 were identified in the 'Malling Jewel' assembly. These chromosome-scale genome sequences represent an excellent genomics resource for red raspberry, particularly around the highly repetitive centromeric and telomeric regions of the genome that are less complete in the previously published 'Anitra' genome sequence. [ABSTRACT FROM AUTHOR]

Summary: Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence.Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus.Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface.The phyllosphere provides a dynamic environment for prophage‐mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome‐based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases. [ABSTRACT FROM AUTHOR]

Identification of unknown micro- and nano-sized mineral phases is commonly achieved by analyzing chemical maps generated from hyperspectral imaging data sets, particularly scanning electron microscope-energy dispersive X-ray spectroscopy (SEM-EDS). However, the accuracy and reliability of mineral identification are often limited by subjective human interpretation, non-ideal sample preparation, and the presence of mixed chemical signals generated within the electron-beam interaction volume. Machine learning has emerged as a powerful tool to overcome these problems. Here, we propose a machine-learning approach to identify unknown phases and unmix their overlapped chemical signals. This approach leverages the guidance of Gaussian mixture modeling clustering fitted on an informative latent space of pixel-wise elemental data points modeled using a neural network autoencoder, and unmixes the overlapped chemical signals of phases using non-negative matrix factorization. We evaluate the reliability and the accuracy of the new approach using two SEM-EDS data sets: a synthetic mixture sample and a real-world particulate matter sample. In the former, the proposed approach successfully identifies all major phases and extracts background-subtracted single-phase chemical signals. The unmixed chemical spectra show an average similarity of 83.0% with the ground truth spectra. In the second case, the approach demonstrates the ability to identify potentially magnetic Fe-bearing particles and their background-subtracted chemical signals. We demonstrate a flexible and adaptable approach that brings a significant improvement to mineralogical and chemical analysis in a fully automated manner. The proposed analysis process has been built into a user-friendly Python code with a graphical user interface for ease of use by general users. [ABSTRACT FROM AUTHOR]

The orientation of spins in a natural sample of Ti-bearing hematite ([Fe.sub.2][O.sub.3]) has been measured from 2-300 K using time-of-flight neutron powder diffraction. It is shown that the antiferromagnetic alignment vector is tilted out of the basal plane by an average angle of 30[degrees], independent of temperature, contrary to the normal expectation that all spins lie in the basal plane due to the suppression of the Morin transition by Ti. This unusual result is related to the non-uniform spatial distribution of Ti in this sample, which takes the form of ~1 nm exsolution lamellae of ilmenite (FeTi[O.sub.3]), observed using transmission electron microscopy. It is suggested that the exsolution lamellae lead to a localization of [Fe.sup.2+] species within the lamellar interfaces, which cause tilting of some spins toward the crystallographic c axis. The presence of an out-of-plane component of spin at room temperature reconciles experimental and computational attempts to explain the phenomenon of 'giant exchange bias' that appears when this sample is zero-field cooled below the ilmenite Neel temperature. Keywords: Hematite, magnetic properties, spin orientation, Morin transition, exchange bias DOI: 10.2138/am.2010.3402

In this study, we examine the effects of reheating on finely exsolved hematite-i|menite intergrowths from the ~91 Ma Ecstall pluton using reflected light microscopy, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). As a result of the emplacement of the younger adjacent ~52 Ma Quottoon pluton, samples closer to a thermal boundary have experienced greater degrees of thermal alteration. Five main microstructural features characterize hematite-ilmenite intergrowths from the Ecstall: (I) exsolution lamellae of hematite and ilmenite; (II) oxidation of ilmenite to form hematite, rutile, and other Ti-rich phases; (III) 20-50 nm magnetite precipitates in hematite; (IV) futile blitz texture; and (V) exsolution of hematite in rutile. Based on spatial relationships, textures II through V appear to be related to reheating of the Ecstall by the Quottoon, and samples up to ~14 km from the thermal boundary intrusive contact have been affected. We propose a mechanism, similar to that of Kontny and Dietl (2001), in which reheating has driven [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] conditions across the hematite-magnetite buffer to lower [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] resulting in the reduction of hematite. Higher temperatures also enhanced oxidation in ilmenite. The formation of magnetite altered the bulk magnetic properties of these samples, increasing NRM intensity. This study underscores the need to consider a pluton's post-emplacement thermal history before making tectonic interpretations based on paleomagnetic data. Keywords: Electron microscopy, hematite-ilmenite, magnetite, mineral intergrowths, Ecstall pluton DOI: 10.2138/am.2010.3191

When suspended in solution, clay platelets coated with nanometer-scale magnetite particles behave as magnetorheologic fluids that are important to a variety of industrial applications. Such dual-phase assemblages are also similar to natural aggregates that record the direction and intensity of the Earth's magnetic field in lake and marine depositional environments. This study characterizes the mineralogical structure and magnetic behavior of montmorillonite platelets coated with aggregates of nanometer-scale magnetite crystals. The distribution of magnetite crystal sizes in three different clay-magnetite assemblages was directly measured using conventional transmission electron microscopy and agrees within error with estimates derived from magnetic hysteresis measurements. Magnetic hysteresis and low field susceptibility measurements combined with electron holography experiments indicate that all three samples behave superparamagnetically at room temperature, and show increasing levels of single domain behavior as the samples are cooled to liquid nitrogen temperatures. At such low temperatures, magnetostatic interactions are observed to partially stabilize otherwise superparamagnetic grains in flux closure structures. Keywords: Magnetite, clay, smectite, TEM, electron holography, electron tomography, granulometry, magnetic properties

Lorentz transmission electron microscopy has been used to study fine-scale exsolution microstructures in ilmenite-hematite, as part of a wider investigation of the lamellar magnetism hypothesis. Pronounced asymmetric contrast is visible in out-of-focus Lorentz images of ilmenite lamellae in hematite. The likelihood that lamellar magnetism may be responsible for this contrast is assessed using simulations that incorporate interfacial magnetic moments on the (001) basal planes of hematite and ilmenite. The simulations suggest qualitatively that the asymmetric contrast is magnetic in origin. However, the magnitude of the experimental contrast is higher than that in the simulations, suggesting that an alternative origin for the observed asymmetry cannot be ruled out. Electron tomography was used to show that the lamellae have lens-like shapes and that (001) planes make up a significant proportion of the interfacial surface that they share with their host. Keywords: Hematite, ilmenite, lamellar magnetism, Lorentz electron microscopy, electron tomography, transmission electron microscopy

Morphometry (i.e., the quantitative determination of grain size and shape information) is an essential component of all rock and environmental magnetic studies. Electron microscopy is often used to image magnetic mineral grains, but the current lack of systematic image processing tools makes it challenging to quantify key morphological features of magnetic minerals in natural samples. Here, we present an easy‐to‐use machine learning framework MagNet for automated morphological recognition of magnetic mineral grains in microscopic images. This framework, based on a convolutional neural network, performs well in the recognition and classification of magnetofossil nanoparticles in transmission electron microscopy images after training and testing. MagNet is open‐source and can easily be extended to process different types of mineral images. This tool has the potential, therefore, to extract key quantitative information of magnetic mineral populations within heterogeneous terrestrial and meteoritic samples for the interpretations of Earth and planetary processes. Plain Language Summary: Morphological characteristics of magnetic mineral grains, such as size and shape, in natural materials are linked to a wide range of environmental, geological, and biological processes during mineral formation. These morphological features also determine the magnetic properties of natural samples that are often measured in the laboratory for the interpretations of Earth and environmental science problems. To analyze the morphological features of magnetic mineral grains, researchers often visually identify magnetic mineral grains in microscopic images and then determine their size and shape manually. The procedure is time‐consuming and prone to artificial errors. It is also not practical to apply such manual analyses to large datasets. In this study, we have developed a machine‐learning‐based analytical tool—MagNet. This open‐source computer tool can perform automatic processing of large image datasets to extract key morphological information of magnetic mineral particles in natural samples with high accuracy. Moreover, the MagNet framework has high portability, and researchers can apply it to diverse categories of magnetic minerals by training their own image datasets. Key Points: A convolutional neural network framework (MagNet) provides automatic and rapid morphological recognition of magnetic mineral grains within microscopic imagesMagNet performs well in the recognition and classification of magnetofossil nanoparticles in transmission electron microscopy imagesMagNet is open‐source and can easily be extended to process diverse mineral populations within highly heterogeneous natural samples [ABSTRACT FROM AUTHOR]

We have used a combination of classical and quantum-mechanical atomistic calculations, together with Monte Carlo simulations, to study order-disorder phenomena in the spinel mineral qandilite, [Mg.sub.2]Ti[O.sub.4]. Using an interatomic potential model akin to those previously used for 2-3 spinels yielded a general increase in energy E as a function of inversion parameter x, and thus incorrectly predicted a normal-spinel ground state, whereas the E(x) behavior as modeled by density-functional theory exhibited a maximum at an intermediate degree of inversion and correctly predicted an inverse-spinel ground state. We therefore used the quantum-mechanical simulations to derive pair interaction parameters (for nearest-neighbor tetrahedral-tetrahedral, octahedral-octahedral, and tetrahedral-octahedral interactions) and chemical potential to use in Monte Carlo simulations of order-disorder in qandilite. The simulated cation distributions compared favorably with those obtained experimentally, although the long-range ordering transition to the tetragonal P[4.sub.1]22 phase was not observed when using only nearest-neighbor interactions. However, this transition could be observed following the addition of two extra parameters to the model. The simulations were used to calculate the effect of short- and long-range cation order on the configurational entropy of qandilite as a function of temperature. The calculated entropy of the high-temperature cubic phase was in very good agreement with the experimental value recently determined, supporting the suggestion that there is considerable short-range order in qandilite. Keywords: Qandilite, [Mg.sub.2]Ti[O.sub.4], spinel, thermodynamics, Monte Carlo simulation, density-functional theory calculations

The Monte Carlo (MC) simulation technique is a powerful tool for the investigation of thermodynamic and kinetic phenomena in minerals, and is especially well suited to the study of cation ordering. We have performed MC simulations of eight end-member 2-3 spinels ([X.sup.2+] = Mg, Fe, Zn, Ni; [X.sup.3+] = Al, Fe) using pair interaction parameters, [J.sub.i], and chemical potentials, [mu], derived from atomistic simulations. The [J.sub.i] values for all but one of these spinels are remarkably similar, despite their different character (normal vs. inverse). The sign of [mu], and hence the tendency to form a normal of inverse spinel, was correctly predicted in all cases. Agreement between the simulated and observed cation distributions as a function of temperature is good for the normal spinels and poor for the inverse spinels. Agreement could be greatly improved for the inverse spinels through relatively modest adjustments to the simulation parameters (usually increasing the strength of the tetrahedral-octahedral, T-O, interactions, and decreasing the magnitude of [mu]). We have developed an atomistic random-mixing model for cation ordering in spinels and compared it with the macroscopic O'Neill-Navrotsky model. In so doing, we have determined the relative contributions of [mu], tetrahedral-tetrahedral (T-T), octahedral-octahedral (O-O), and T-O interactions to the O'Neill-Navrotsky coefficients [alpha] and [beta]. We found that the value of [beta] depends on the relative enthalpy contributions of (T-T + O-O) vs. T-O interactions, a useful insight considering the large spread of values found experimentally to be taken by [beta]. We used the thermodynamic integration technique to quantify the entropy, and hence the amount of short-range order, present in the spinels studied. We found that there is virtually no short-range order in the normal spinels. There is significant short-range order in the inverse spinels, though in the experimentally accessible temperature range, the contribution of this short-range order to the entropy is comparatively small. At very low temperatures, we find that the octahedral cations in the inverse spinels become ordered, reducing the symmetry to P[4.sub.1]22, in agreement with other simulated findings for 2-3 spinels and experimental findings for 4-2 spinels. Keywords: Spinel, thermodynamics, Monte Carlo simulation, O'Neill-Navrotsky model, short-range order

The energetics of magnetic and cation ordering have been modeled using an atomistic approach based on empirical exchange interaction parameters. The model has been applied to the study of magnetic and cation ordering in the ilmenite-hematite solid solution via Monte Carlo simulations, providing new insight into the effect of nanoscale microstrnctures on the magnetic properties of this system. The lowest energy state for intermediate compositions is an intergrowth of cation-disordered antiferromagnetic (AF) hematite and cation-ordered paramagnetic (PM) ilmenite, separated by mixed [Fe.sup.2+]/[Fe.sup.3+] 'contact layers.' The intergrowth carries a stable defect moment ('lamellar magnetism') due to the presence of uncompensated spins. The net magnetization is parallel to the spin alignment direction, i.e., perpendicular to the spin-canted magnetization of the AF hematite. Contact-layer spins are coordinated to fewer magnetic neighbors than bulk spins and thus disorder more rapidly on heating. This leads to a decrease of net moment with increasing temperature. A small net moment is present, however, up to the Neel temperature of the AF hematite phase. The maximum temperature for acquisition of a chemical remanent magnetization due to lamellar magnetism is 800 [+ or -] 25 K, corresponding to the temperature for the eutectoid reaction PM hematite [right arrow] AF hematite + PM ilmenite. If only cation interactions are considered, [Fe.sup.3+] and [Fe.sup.2+] in the contact layers become ordered so that [Fe.sup.3+] shares an octahedral face with [Fe.sup.3+] in the neighboring hematite layer and [Fe.sup.2+] shares an octahedral face with [Ti.sup.4+] in the neighboring ilmenite layer. If both cation and magnetic interactions are considered, however, an alternative ordering scheme is stabilized, whereby [Fe.sup.3+] shares an octahedral face with [Ti.sup.4+] in the neighboring ilmenite layer and [Fe.sup.2+] shares an octahedral face with [Fe.sup.3+] in the neighboring hematite layer. The model has been used to investigate the nature of exchange coupling between ordered/anti-ordered domains and disordered antiphase boundaries, with a view to elucidating the mechanism of self-reversed thermoremanent magnetization. Antiphase boundaries are enriched in Fe relative to the ordered/antiordered domains, with enhanced enrichment observed in simulations performed within the PM hematite + PM ilmenite miscibility gap. Monte Carlo simulations of magnetic ordering show no evidence of self-reversal in systems containing two equally well-ordered ferrimagnetic (FM) domains separated by Fe-enriched AF boundaries. Systems displaying partial long-range order, however, do display self-reversed magnetization. Partial long-range order is characterized by a mixture of highly ordered Ti-rich FM domains and poorly ordered Fe-rich domains with a weak FM moment. The magnetic ordering temperature of the poorly ordered Fe-rich domains is significantly higher than that of the highly ordered Ti-rich domains, and act as the 'x-phase.' Evidence in support of the proposed mechanism from neutron diffraction and transmission electron microscopy is presented. Keywords: Magnetism, microstructure, ilmenite, hematite

[Fe.sup.2]/[Fe.sup.3+] charge ordering in the contact layers of lamellar magnetism in the hematite-ilmenite series is not a postulate of the lamellar magnetism hypothesis. Such ordering is possible, however, and a model was suggested earlier in which contact layer [Fe.sup.3+] octahedra share faces with ilmenite layer [Ti.sup.4+] octahedra, and contact layer [Fe.sup.3+] octahedra share faces with hematite layer [Fe.sup.3+] octahedra, thus copying the shared-face configurations of ilmenite and hematite, respectively. This model and related charge-balance matters could be explored using bond-valence theory, a simplified picture of complex bonding which takes into account the relationship between bond strength and bond distance, but ignores magnetism. This has now been done, and shows that local oxygen charge satisfaction is strongly favored by a different charge-ordering scheme, in which contact layer [Fe.sup.3+] octahedra share faces with ilmenite layer [Ti.sup.4+] octahedra, and contact layer [Fe.sup.3+] octahedra share faces with hematite layer [Fe.sup.3+] octahedra. A new, more sophisticated, Monte Carlo simulation of the interface, including electrostatic and magnetic interaction parameters of cations, reported in detail elsewhere, independently shows the same charge-ordering scheme. For the cation ordered metastable ilmenite 50 composition, bond-valence theory indicates that, unlike the contact layers, the favored charge ordering scheme in Fe layers would have the same shared-face configurations as ilmenite and hematite. Keywords: Crystal chemistry, bond valence, hematite, ilmenite, magnetic properties, lamellar magnetism, order-disorder, Fe charge ordering

Grains consisting of finely exsolved members of the hematite-ilmenite solid-solution series, such as are present in some slowly cooled middle Proterozoic igneous and metamorphic rocks, impart unusually strong and stable remanent magnetization. TEM analysis shows multiple generations of ilmenite and hematite exsolution lamellae, with lamellar widths ranging from millimeters to nanometers. Rock-magnetic experiments suggest remanence is thermally locked to the antiferromagnetism of the hematite component of the intergrowths, yet is stronger than can be explained by canted antiferromagnetic (CAF) hematite or coexisting paramagnetic (PM) Fe-Ti-ordered (R[bar.3]) ilmenite alone. In alternating field demagnetization to 100 mT, many samples lose little remanence, indicating that the NRM is stable over billions of years. This feature has implications for understanding magnetism of deep rocks on Earth, or on planets like Mars that no longer have a magnetic field. Atomic-scale simulations of an R[bar.3] ilmenite lamella in a CAF hematite host, based on empirical cation-cation and spin-spin pair interaction parameters, show that contacts of the lamella are occupied by 'contact layers' with a hybrid composition of Fe ions intermediate between [Fe.sup.2+]-rich layers in ilmenite and [Fe.sup.3+]-rich layers in hematite. Structural configurations dictate that each lamella has two contact layers magnetically in phase with each other, and out of phase with the magnetic moment of an odd non-self-canceling [Fe.sup.3+]-rich layer in the hematite host. The two contact layers and the odd hematite layer form a magnetic substructure with opposite but unequal magnetic moments: a lamellar 'ferrimagnetism' made possible by the exsolution. Because it is confined to magnetic interaction involving the moments of just three ionic layers associated with each individual exsolution lamella, lamellar magnetism is unique and quite distinct from conventional ferrimagnetism. Simulation cells indicate that the magnetic moments of contact layers are locked to the magnetic moments of adjacent AF hematite layers and are parallel to the basal plane (001). Thus, lamellar magnetism is created at the temperature of chemical exsolution, and is a chemical remanent, rather than thermal remanent, magnetization. However, in thermal demagnetization experiments, too short for lamellar resorption, demagnetization temperatures are those of the CAF hematite, considerably higher than temperatures of original lamellae formation. Internal crystal structure cannot dictate that the contact layers of different lamellae will form magnetically in phase with each other to give the highest net magnetic moment, but magnetic moments of lamellae can be made to form in phase by the external force of the magnetizing field at the time of exsolution. A thesis of this paper is that an external magnetic field can dictate the magnetic moments and hence the chemical location of ilmenite lamellae in a hematite host, and that once in place, neither the location nor the magnetic moment will be easily disturbed. In an ilmenite host, the external magnetic field cannot control the chemical location of a hematite lamella, which is dictated by the enclosing ilmenite, but once lamellae have formed, the field can dictate their magnetic moments. These moments, however, are not locked chemically to the host, resulting in lower coercivity. The effectiveness of the external force in single crystals is dictated by their orientation with respect to the magnetizing field. In grains with (001) oriented parallel to the field, it would be effective in producing in-phase magnetic moments and very strong remanence. In grains with (001) normal to the field, the field would be less effective in producing in-phase magnetic moments, hence producing weak remanence. The most intense lamellar magnetism per formula unit occurs with in-phase magnetization, high lamellar yields, and the largest number of lamellae per unit volume (i.e., smallest lamellar size). Compared to the magnetic moment per formula unit ([M.sub.pfu]) and magnetic moment per unit volume ([M.sub.v]) of end-member magnetite ([M.sub.pfu] = 4 [[micro].sub.B], [M.sub.v] = 480 kA/m) and hematite ([M.sub.pfu] = 0.0115 [[micro].sub.B], [M.sub.v] = 2.1 kA/m), results for some atomic models reasonably tied to natural conditions are [M.sub.pfu] = 0.46-I .36 [[micro].sub.B] and [M.sub.v] = 84-250 kA/m.

Greigite magnetosomes produced by magnetotactic bacteria (MTB) are widely distributed in natural environments, but large uncertainties remain regarding their magnetic biosignatures. Here, we have constructed micromagnetic models with realistic biogenic greigite particles to quantify the magnetic properties and magnetotaxis efficiency of greigite‐producing MTB cells. Our calculations suggest coercivity (Bc) of ∼15–21 mT for intact greigite‐producing rod‐shaped MTB and many‐celled magnetotactic prokaryotes, with Bc decreasing to ∼11 mT for greigite magnetofossils with clumped particles. These magnetic signatures make biogenic greigite distinguishable from typical biogenic magnetite and inorganic greigite, providing reliable magnetic criteria to detect biogenic greigite in a wide range of environmental and geological settings. Our numerical calculations suggest that rod‐shaped greigite‐producing MTB have a similar magnetotaxis efficiency to magnetite MTB, likely by biomineralizing more greigite crystals to compensate for the lower saturation magnetization of greigite and less ordered chains in greigite MTB cells, demonstrating biological‐controlled optimization of their magnetic nanostructure. Plain Language Summary: Magnetic bacteria can produce greigite (Fe3S4) or magnetite (Fe3O4) nanoparticles arranged in chains and use them as nano‐compass for navigating along the geomagnetic field lines. Dead magnetic bacteria can be fossilized in the geological records that retain important signals of past geomagnetic field, environmental conditions, and biochemical processes in the Earth surface. Until now magnetic biosignatures of bacterial greigite are unclear because it is difficult to obtain pure greigite magnetotactic bacteria samples to measure their magnetic properties. Here, we constructed computer models that mimic those found in living greigite‐producing magnetic bacteria. Model calculations determined robust magnetic fingerprints of biogenic greigite that can be used to search for fossilized biogenic greigite nanoparticles in natural environments. Moreover, according to our calculations, greigite‐producing magnetic bacteria have similar navigational ability to bacterial magnetite counterparts by producing more biogenic greigite crystals in the bacterial cells, suggesting that magnetic nanostructures are optimized by those magnetic microorganisms. Key Points: Micromagnetic calculations reveal robust magnetic biosignatures of biogenic greigite that have been difficult to determine experimentallyModeled hysteresis properties of biogenic greigite provide magnetic criteria for their identification in a wide range of environmentsGreigite‐producing magnetotactic microorganisms likely have optimized their magnetic nanostructure for navigational and other purposes [ABSTRACT FROM AUTHOR]

Bacterial canker is a major disease of stone fruits and is a critical limiting factor to sweet cherry (Prunus avium) production worldwide. One important strategy for disease control is the development of resistant varieties. Partial varietal resistance in sweet cherry is discernible using shoot or whole tree inoculations; however, these quantitative differences in resistance are not evident in detached leaf assays. To identify novel sources of resistance to canker, we used a rapid leaf pathogenicity test to screen a range of wild cherry, ornamental Prunus species and sweet cherry × ornamental cherry hybrids with the canker pathogens, Pseudomonas syringae pvs syringae, morsprunorum races 1 and 2, and avii. Several Prunus accessions exhibited limited symptom development following inoculation with each of the pathogens, and this resistance extended to 16 P. syringae strains pathogenic on sweet cherry and plum. Resistance was associated with reduced bacterial multiplication after inoculation, a phenotype similar to that of commercial sweet cherry towards nonhost strains of P. syringae. Progeny resulting from a cross of a resistant ornamental species Prunusincisa with susceptible sweet cherry (P. avium) exhibited resistance indicating it is an inherited trait. Identification of accessions with resistance to the major bacterial canker pathogens is the first step towards characterizing the underlying genetic mechanisms of resistance and introducing these traits into commercial germplasm. [ABSTRACT FROM AUTHOR]

Author(s): Peter Robinson (corresponding author) [1, 2]; Richard J. Harrison [3]; Suzanne A. McEnroe [1, 2]; Robert B. Hargraves [4] Magnetic anomalies associated with slowly cooled igneous and metamorphic rocks [...]

Hematite carries magnetic signals of interest in tectonic, paleoclimatic, paleomagnetic, and planetary studies. First‐order reversal curve (FORC) diagrams have become an important tool for assessing the domain state of, and magnetostatic interactions among, magnetic particles in such studies. We present here FORC diagrams for diverse hematite samples, which provide a catalog for comparison with other studies and explain key features observed for hematite. Ridge‐type signatures typical of uniaxial single‐domain particle assemblages and "kidney‐shaped" FORC signatures, and combinations of these responses, occur commonly in natural and synthetic hematite. Asymmetric features that arise from the triaxial basal plane anisotropy of hematite contribute to vertical spreading in kidney‐shaped FORC distributions and are intrinsic responses even for magnetostatically noninteracting particles. The dominant FORC distribution type in a sample (ridge, kidney‐shaped, or mixture) depends on the balance between uniaxial/triaxial switching. The identified signals explain magnetization switching and anisotropy features that are intrinsic to the magnetic properties of hematite and other materials with multiaxial magnetic anisotropy. Plain Language Summary: First‐order reversal curve (FORC) diagrams have become a standard method for identifying the domain state of magnetic materials. It has recently been demonstrated that the magnetic anisotropy type can also be identified using FORC diagrams. The magnetic domain state and anisotropy type of a magnetic mineral control the fidelity of recording of magnetic information, so identifying these features is fundamental to paleomagnetic, rock magnetic, and environmental magnetic studies. Hematite is a naturally abundant magnetic mineral that is encountered commonly in such studies, so it is important to have extensive FORC reference data for this mineral. We present the most comprehensive available FORC study of diverse natural and synthetic hematite samples, including numerical simulation results, to seek to explain key domain state and anisotropy signals for hematite. Key Points: FORC diagrams are presented for diverse natural and synthetic hematite samples to demonstrate domain state and anisotropy signaturesKidney‐shaped FORC distributions are indicative of multiaxial anisotropy and central ridge‐type distributions reflect uniaxial anisotropyThe dominant FORC distribution type depends on the balance between uniaxial and triaxial switching mechanisms [ABSTRACT FROM AUTHOR]

Over the last two centuries, breeders have drastically modified the fruit quality of strawberries through artificial selection. However, there remains significant variation in quality across germplasm with scope for further improvements to be made. We reported extensive phenotyping of fruit quality and yield traits in a multi-parental strawberry population to allow genomic prediction and quantitative trait nucleotide (QTN) identification, thereby enabling the description of genetic architecture to inform the efficacy of implementing advanced breeding strategies. A negative relationship (r = −0.21) between total soluble sugar content and class one yield was identified, indicating a trade-off between these two essential traits. This result highlighted an established dilemma for strawberry breeders and a need to uncouple the relationship, particularly under June-bearing, protected production systems comparable to this study. A large effect of quantitative trait nucleotide was associated with perceived acidity and pH whereas multiple loci were associated with firmness. Therefore, we recommended the implementation of both marker assisted selection (MAS) and genomic prediction to capture the observed variation respectively. Furthermore, we identified a large effect locus associated with a 10% increase in the number of class one fruit and a further 10 QTN which, when combined, are associated with a 27% increase in the number of marketable strawberries. Ultimately, our results suggested that the best method to improve strawberry yield is through selecting parental lines based upon the number of marketable fruits produced per plant. Not only were strawberry number metrics less influenced by environmental fluctuations, but they had a larger additive genetic component when compared with mass traits. As such, selecting using "number" traits should lead to faster genetic gain. [ABSTRACT FROM AUTHOR]