The magnetisation data presented in the main text were acquired in a Quantum Design MPMS3 magnetometer. The magnetometer returns measurements of the total magnetic moment of the sample in emu. The total magnetic moment of the sample contains the contributions due to the substrate, thin film, and any spurious signal such as those described by Garcia et al. [1] . Careful sample handing was used to minimise spurious contributions to the total moment. The linear diamagnetic background due to the substrate was subtracted from the total measured moment. We report the data after substrate subtraction as the area normalised magnetic moment (moment/area) in emu/cm by measuring the area of the sample. For a uniform slab of ferromagnetic material, the volume magnetisation (M) can be determined by dividing the saturation moment/area by the thickness of the ferromagnetic layer. M can also be reliably determined by measuring several samples of varying thickness. If one plots moment/area versus thickness (d), as per Figure S1, then the fitted gradient will be M , moment/area = Md. (S1)

We report on the electrical transport properties of Nb based Josephson junctions with Pt/Co[Formula: see text]B[Formula: see text]/Pt ferromagnetic barriers. The barriers exhibit perpendicular magnetic anisotropy, which has the main advantage for potential applications over magnetisation in-plane systems of not affecting the Fraunhofer response of the junction. In addition, we report that there is no magnetic dead layer at the Pt/Co[Formula: see text]B[Formula: see text] interfaces, allowing us to study barriers with ultra-thin Co[Formula: see text]B[Formula: see text]. In the junctions, we observe that the magnitude of the critical current oscillates with increasing thickness of the Co[Formula: see text]B[Formula: see text] strong ferromagnetic alloy layer. The oscillations are attributed to the ground state phase difference across the junctions being modified from zero to [Formula: see text]. The multiple oscillations in the thickness range [Formula: see text] nm suggests that we have access to the first zero-[Formula: see text] and [Formula: see text]-zero phase transitions. Our results fuel the development of low-temperature memory devices based on ferromagnetic Josephson junctions.

Abstract We report on the electrical transport properties of Nb based Josephson junctions with Pt/Co $$_{68}$$ 68 B $$_{32}$$ 32 /Pt ferromagnetic barriers. The barriers exhibit perpendicular magnetic anisotropy, which has the main advantage for potential applications over magnetisation in-plane systems of not affecting the Fraunhofer response of the junction. In addition, we report that there is no magnetic dead layer at the Pt/Co $$_{68}$$ 68 B $$_{32}$$ 32 interfaces, allowing us to study barriers with ultra-thin Co $$_{68}$$ 68 B $$_{32}$$ 32 . In the junctions, we observe that the magnitude of the critical current oscillates with increasing thickness of the Co $$_{68}$$ 68 B $$_{32}$$ 32 strong ferromagnetic alloy layer. The oscillations are attributed to the ground state phase difference across the junctions being modified from zero to $$\pi $$ π . The multiple oscillations in the thickness range $$0.2~\leqslant ~d_\text {CoB}~\leqslant ~1.4$$ 0.2 ⩽ d CoB ⩽ 1.4 nm suggests that we have access to the first zero- $$\pi $$ π and $$\pi $$ π -zero phase transitions. Our results fuel the development of low-temperature memory devices based on ferromagnetic Josephson junctions.

Many artisanal meat professionals believe that the microbial populations on the outer crust of dry-aged beef contribute to variation in sensory profiles; however, to date there is minimal information about the microbes themselves that grow on commercially produced dry-aged beef. The microbiome of dry-aged beef bone-in strip loins (Institutional Meat Purchase Specifications #175) from 5 commercial dry aging facilities, including one utilizing ultraviolet light treatment, were surveyed to assess the microbial populations residing on and within each subprimal. Each strip loin was sampled at multiple spatial locations and depths, and the microbial sequences present in the samples were identified using a nextgeneration sequencing approach. Insufficient microbial DNA was isolated from ultraviolet-light-treated strip loins, indicating that this treatment eliminates all or most microbial growth on the meat. Sequencing results indicated that each establishment was producing meat with different microbial communities, based on Permutational Multivariate Analysis of Variance (P < 0.01) and clustering in the Principal Coordinates Analysis plot of Jaccard distances. The position on strip loins from which samples were taken had negligible influence on microbial community structure. Aging facility, and the relative unique environmental conditions within, was determined to be the only observed driver of community structure. Notable operational taxonomic units (OTUs) detected included the spoilage-associated bacterium Pseudomonas fragi and the fungal species Debaryomyces udenii and Penicillium polonicum. An OTU identified as Mucor sp. PG272 was found to be present in over 75% of all samples. This OTU may represent a species similar to Thamnidium, a mold that has been associated with product quality. This study established a general core microbiome for dry-aged beef observed in commercial facilities, variations of which may—as future research could indicate—contribute to distinct sensory properties.

ObjectivesDespite the high cost and significant attention to detail in the processing of dry aged beef, there is very little information about how quality attributes are incorporated into the meat. Consequently, there are many different dry-aging techniques that are thought to impart unique flavors into the finished product. Many artisanal meat professionals believe the microbial populations present on the outer crust contribute to these flavor profiles; however, to-date there is very little information about the microbial species that grow on dry-aged beef. The fungal and bacterial communities of 9 dry aged beef loins from 5 aging facilities were compared to assess differences in the types of microbes present and relative ratios of detection.Materials and MethodsThe loins were aged for 49 d in refrigerated conditions. The average temperatures for the aging facilities ranged from 35.0 to 39.4°F, and average relative humidity ranged from 75.9 to 91.0%. Of these 5 facilities, 1 facility aged the meat under Ultraviolet light. Each loin was sampled in multiple spatial locations for DNA extraction and the fungal and bacterial sequences present in the samples were identified using a next-generation sequencing approach and subsequent bioinformatic computational pipeline.ResultsInsufficient microbial DNA was isolated from UV-treated loins, indicating that this treatment eliminates all or most microbial growth on the meat. The results indicated that each aging establishment, with the UV-treated facility removed from the dataset, was producing meat with different microbial communities, based on PERMANOVA (p < 0.01) and visual analysis of clustering in the principal coordinates analysis plot of Bray-Curtis dissimilarity. The position on the loins from which samples were taken had negligible influence on microbial community structure. Aging facility was determined to be the only observed driver of community structure. Notable operational taxonomic units (OTUs) that were detected in a majority of samples included the bacterial spoilage-associated species Pseudomonas fragi, and the fungal species Debaryomyces udenii and Penicillium polonicum. Additionally, an OTU identified as Mucor sp. PG272 was found to be present in over 75% of all samples. While this specific species is not known to be associated with dry aged beef or related products, we believe this OTU may represent a species similar to Thamnidium, a mold to which industry insiders often associate with product quality.ConclusionThe proportions of these populations were variable depending on the meat’s location of origin, and may have significant consequences in the resulting sensory properties of the edible, cooked meat produced from their host loins. This study established a general core microbiome for dry aged beef, as well as confirmed that there can be significant differences in the microbial communities on dry aged beef from different aging facilities, which may be contributing to distinct flavors and improved tenderness of dry aged beef.

Avirulence (AVR) genes in Magnaporthe oryzae, the fungal pathogen that causes the devastating rice blast disease, have been documented to be major targets subject to mutations to avoid recognition by resistance (R) genes. In this study, an AVR-gene-based diagnosis tool for determining the virulence spectrum of a rice blast pathogen population was developed and validated. A set of 77 single-spore field isolates was subjected to pathotype analysis using differential lines, each containing a single R gene, and classified into 20 virulent pathotypes, except for 4 isolates that lost pathogenicity. In all, 10 differential lines showed low frequency (<24%) of resistance whereas 8 lines showed a high frequency (>95%), inferring the effectiveness of R genes present in the respective differential lines. In addition, the haplotypes of seven AVR genes were determined by polymerase chain reaction amplification and sequencing, if applicable. The calculated frequency of different AVR genes displayed significant variations in the population. AVRPiz-t and AVR-Pii were detected in 100 and 84.9% of the isolates, respectively. Five AVR genes such as AVR-Pik-D (20.5%) and AVR-Pik-E (1.4%), AVRPiz-t (2.7%), AVR-Pita (0%), AVR-Pia (0%), and AVR1-CO39 (0%) displayed low or even zero frequency. The frequency of AVR genes correlated almost perfectly with the resistance frequency of the cognate R genes in differential lines, except for International Rice Research Institute-bred blast-resistant lines IRBLzt-T, IRBLta-K1, and IRBLkp-K60. Both genetic analysis and molecular marker validation revealed an additional R gene, most likely Pi19 or its allele, in these three differential lines. This can explain the spuriously higher resistance frequency of each target R gene based on conventional pathotyping. This study demonstrates that AVR-gene-based diagnosis provides a precise, R-gene-specific, and differential line-free assessment method that can be used for determining the virulence spectrum of a rice blast pathogen population and for predicting the effectiveness of target R genes in rice varieties.

A collection of 122 isolates of Magnaporthe oryzae, from nine sub-Saharan African countries, was assessed for virulence diversity and genetic relatedness. The virulence spectrum was assessed by pathotype analysis with a panel of 43 rice genotypes consisting of differential lines carrying 24 blast resistance genes (R-genes), contemporary African rice cultivars, and susceptible checks. The virulence spectrum among isolates ranged from 5 to 80%. Five isolates were avirulent to the entire rice panel, while two isolates were virulent to ∼75% of the panel. Overall, cultivar 75-1-127, the Pi9 R-gene donor, was resistant to all isolates (100%), followed by four African rice cultivars (AR105, NERICA 15, 96%; NERICA 4, 91%; and F6-36, 90%). Genetic relatedness of isolates was assessed by single nucleotide polymorphisms derived from genotyping-by-sequencing and by vegetative compatibility tests. Phylogenetic analysis of SNPs of a subset of isolates (n = 78) revealed seven distinct clades that differed in virulence. Principal component analysis showed isolates from East Africa were genetically distinct from those from West Africa. Vegetative compatibility tests of a subset of isolates (n = 65) showed no common groups among countries. This study shows that blast disease could be controlled by pyramiding of Pi9 together with other promising R-genes into rice cultivars that are adapted to East and West African regions.

Three fungi in the genus Ophiosphaerella,—O. herpotricha, O. korrae, and O. narmari—are the causal agents of spring dead spot of bermudagrass. The extent to which Ophiosphaerella spp. can colonize and infect other plant hosts and the mechanism by which they render host cells necrotic remain unknown. In other plant–pathogen interactions, it has been shown that the hypersensitive response (HR), initiated by the formation of reactive oxygen species (ROS) in the host, can promote the infection of necrotrophic fungi. The objectives of these studies were to investigate the formation of ROS during infection of plant cells and to characterize the host range of Ophiosphaerella spp. To assess ROS production, roots of three bermudagrass cultivars—Tifway 419, Midlawn, and U3—were each inoculated with an isolate of either O. herpotricha or O. korrae. The roots were stained with 2′,7′‐dichlorofluorescein diacetate at 4 to 74 h after inoculation. Staining of root cells indicated formation of ROS in response to fungal infection. The cultivar U3, which is tolerant to spring dead spot, is more likely to form high levels of ROS than the interspecific hybrid cultivars Midlawn and Tifway 419. To determine the potential host range of O. herpotricha and O. korrae, several warm‐season grasses, cool‐season grasses, and dicotyledonous plants were evaluated for colonization at 2 to 14 d after inoculation. The colonization process was similar for O. herpotricha and O. korrae on most plant species tested. Grass plant roots were readily colonized, and some showed symptoms of necrosis. The dicot plants evaluated were nonhosts. Significantly higher ROS production by the tolerant bermudagrass cultivar U3 suggests that root necrosis caused by Ophiosphaerella spp. is independent of HR associated with plant‐generated ROS. Colonization studies show that these fungi have a broad monocotyledonous host range.

Bermudagrass (Cynodon dactylon, C. transvaalensis and C. dactylon x C. transvaalensis) is a widely used sports turfgrass worldwide. One of the most damaging diseases of bermudagrass is spring dead spot (SDS), caused by Ophiosphaerella herpotricha, O. korrae, and O. narmari. These fungi are characterized as necrotrophic, but the mechanism by which they render host cells necrotic remains unknown. Necrotrophs can produce toxins and are able to exploit the host hypersensitive response (HR) to colonize and infect host cells. The objective of these studies was to investigate the formation of reactive oxygen species (ROS) during fungal infection of plant cells, which is a common feature of the HR. Roots of three bermudagrass cultivars, 'Tifway', 'Midlawn' and 'U3', were each inoculated with tdTOM-transformed isolate (red fluorescence) of O. herpotricha or O. korrae. The roots were stained with 2', 7'-dichlorofluorescein diacetate at 4 to 72 h after inoculation. Roots were examined using bright-field and fluorescence microscopy. Based on positive staining, root cells were considered to have formed ROS in response to fungal infection. In C. dactylon cultivar U3, which is tolerant of SDS, higher levels of ROS were more likely to have been produced than in the interspecific hybrid cultivars Midlawn and Tifway. Formation of ROS was observed consistently at the hyphal tips of colonizing fungi in all cultivar/fungi combinations tested, with O. herpotricha producing ROS more frequently than O. korrae. These studies suggest that root necrosis caused by SDS fungi is independent of HR associated with plant-generated ROS. In addition, the increased production of ROS by SDS fungi at the time of root penetration suggests a role of fungal-produced ROS during SDS-fungal attack of bermudagrass.

Bermudagrass (Cynodon spp.) is the most commonly used turfgrass in the southern United States where it is severely affected by spring dead spot (SDS) caused by Ophiosphaerella herpotricha, O. korrae, and O. narmari. In this study, infection of bermudagrass roots and stolons by O. korrae was characterized using a transformant that expressed the red fluorescent protein tdTomato. Roots of interspecific hybrid cultivars Midlawn and Tifway 419, C. transvaalensis accessions Uganda and 3200, and C. dactylon cultivar U3 were inoculated and observed from 2 to 14 days postinoculation (DPI) while stolons were observed from 2 to 22 DPI. For all five cultivars tested, a similar level of root colonization was observed; however, differences were observed in the rate of necrosis development. Necrosis of Tifway 419 and Midlawn tissues was evident at 2 DPI, in Uganda and 3200 at 8 DPI, and in U3 necrosis was often absent as late as 14 DPI. The fungus rapidly penetrated the root epidermis and colonized the cortex of all cultivars by 4 DPI. Colonization of stele tissues by O. korrae was rare in hybrid cultivars but common in C. transvaalensis and C. dactylon accessions. On intact stolons, the fungus did not penetrate the epidermis 22 DPI though epidermal necrosis was evident on the surface of only the hybrid bermudagrasses. Wounded stolons became necrotic in all cultivars. Infection and colonization of various bermudagrasses by O. korrae was found to be similar to that by O. herpotricha, suggesting that host genetic resistance may be used for effective management of SDS caused by both species.

Rice blast, caused by Magnaporthe oryzae, is a disease that can cause severe losses in rice yields. Recent studies showed that demand for rice is increasing faster than the increase in production in Africa, and there is a need to mitigate production challenges such as rice blast. Breeding for resistance to rice blast in Africa requires knowledge of M. oryzae diversity and the history of resistance in the pathosystem. A core collection isolates of M. oryzae (n=100) from nine African countries (Benin, Burkina Faso, Ghana, Kenya, Mali, Nigeria, Tanzania, Togo, and Uganda) were assessed for vegetative compatibility groups (VCG) and for disease reactions based on an International Rice Research Institute set of differential lines and African interspecific cultivars. Preliminary analysis showed that VCGs were unique for each country, but the virulence phenotypes of isolates were not associated with the country of origin. Avirulence was observed in a range 25%-75% of the subset (n=49) of the isolates that were pathotyped using the 31 differential lines. The Pi9 resistance gene was most effective against the core set of isolates, conferring resistance against 75% of the isolates, followed by unknown resistances in two African interspecific cultivars, which conferred resistance against 56% of the isolates. Findings of this study will facilitate resistance breeding efforts to enhance effective control of rice blast in Africa.