Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity.

During 25 surveys of global Phytophthora diversity, conducted between 1998 and 2020, 43 new species were detected in natural ecosystems and, occasionally, in nurseries and outplantings in Europe, Southeast and East Asia and the Americas. Based on a multigene phylogeny of nine nuclear and four mitochondrial gene regions they were assigned to five of the six known subclades, 2a-c, e and f, of Phytophthora major Clade 2 and the new subclade 2g. The evolutionary history of the Clade appears to have involved the pre-Gondwanan divergence of three extant subclades, 2c, 2e and 2f, all having disjunct natural distributions on separate continents and comprising species with a soilborne and aquatic lifestyle and, in addition, a few partially aerial species in Clade 2c; and the post-Gondwanan evolution of subclades 2a and 2g in Southeast/East Asia and 2b in South America, respectively, from their common ancestor. Species in Clade 2g are soilborne whereas Clade 2b comprises both soil-inhabiting and aerial species. Clade 2a has evolved further towards an aerial lifestyle comprising only species which are predominantly or partially airborne. Based on high nuclear heterozygosity levels ca. 38 % of the taxa in Clades 2a and 2b could be some form of hybrid, and the hybridity may be favoured by an A1/A2 breeding system and an aerial life style. Circumstantial evidence suggests the now 93 described species and informally designated taxa in Clade 2 result from both allopatric non-adaptive and sympatric adaptive radiations. They represent most morphological and physiological characters, breeding systems, lifestyles and forms of host specialism found across the Phytophthora clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single Phytophthora clade highlight a critical lack of information on the scale of the unknown pathogen threats to forests and natural ecosystems, underlining the risk of basing plant biosecurity protocols mainly on lists of named organisms. More surveys in natural ecosystems of yet unsurveyed regions in Africa, Asia, Central and South America are needed to unveil the full diversity of the clade and the factors driving diversity, speciation and adaptation in Phytophthora. Taxonomic novelties: New species: Phytophthora amamensis T. Jung, K. Kageyama, H. Masuya & S. Uematsu, Phytophthora angustata T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, Phytophthora balkanensis I. Milenkovic, Z. Tomic, T. Jung & M. Horta Jung, Phytophthora borneensis T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora calidophila T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora catenulata T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, Phytophthora celeris T. Jung, L. Oliveira, M. Tarigan & I. Milenkovic, Phytophthora curvata T. Jung, A. Hieno, H. Masuya & M. Horta Jung, Phytophthora distorta T. Jung, A. Durán, E. Sanfuentes von Stowasser & M. Horta Jung, Phytophthora excentrica T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora falcata T. Jung, K. Kageyama, S. Uematsu & M. Horta Jung, Phytophthora fansipanensis T. Jung, N.M. Chi, T. Corcobado & C.M. Brasier, Phytophthora frigidophila T. Jung, Y. Balci, K. Broders & I. Milenkovic, Phytophthora furcata T. Jung, N.M. Chi, I. Milenkovic & M. Horta Jung, Phytophthora inclinata N.M. Chi, T. Jung, M. Horta Jung & I. Milenkovic, Phytophthora indonesiensis T. Jung, M. Tarigan, L. Oliveira & I. Milenkovic, Phytophthora japonensis T. Jung, A. Hieno, H. Masuya & J.F. Webber, Phytophthora limosa T. Corcobado, T. Majek, M. Ferreira & T. Jung, Phytophthora macroglobulosa H.-C. Zeng, H.-H. Ho, F.-C. Zheng & T. Jung, Phytophthora montana T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora multipapillata T. Jung, M. Tarigan, I. Milenkovic & M. Horta Jung, Phytophthora multiplex T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora nimia T. Jung, H. Masuya, A. Hieno & C.M. Brasier, Phytophthora oblonga T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora obovoidea T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora obturata T. Jung, N.M. Chi, I. Milenkovic & M. Horta Jung, Phytophthora penetrans T. Jung, Y. Balci, K. Broders & I. Milenkovic, Phytophthora platani T. Jung, A. Pérez-Sierra, S.O. Cacciola & M. Horta Jung, Phytophthora proliferata T. Jung, N.M. Chi, I. Milenkovic & M. Horta Jung, Phytophthora pseudocapensis T. Jung, T.-T. Chang, I. Milenkovic & M. Horta Jung, Phytophthora pseudocitrophthora T. Jung, S.O. Cacciola, J. Bakonyi & M. Horta Jung, Phytophthora pseudofrigida T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora pseudoccultans T. Jung, T.-T. Chang, I. Milenkovic & M. Horta Jung, Phytophthora pyriformis T. Jung, Y. Balci, K.D. Boders & M. Horta Jung, Phytophthora sumatera T. Jung, M. Tarigan, M. Junaid & A. Durán, Phytophthora transposita T. Jung, K. Kageyama, C.M. Brasier & H. Masuya, Phytophthora vacuola T. Jung, H. Masuya, K. Kageyama & J.F. Webber, Phytophthora valdiviana T. Jung, E. Sanfuentes von Stowasser, A. Durán & M. Horta Jung, Phytophthora variepedicellata T. Jung, Y. Balci, K. Broders & I. Milenkovic, Phytophthora vietnamensis T. Jung, N.M. Chi, I. Milenkovic & M. Horta Jung, Phytophthora ×australasiatica T. Jung, N.M. Chi, M. Tarigan & M. Horta Jung, Phytophthora ×lusitanica T. Jung, M. Horta Jung, C. Maia & I. Milenkovic, Phytophthora ×taiwanensis T. Jung, T.-T. Chang, H.-S. Fu & M. Horta Jung. Citation: Jung T, Milenkovic I, Balci Y, Janousek J, Kudlácek T, Nagy ZÁ, Baharuddin B, Bakonyi J, Broders KD, Cacciola SO, Chang T-T, Chi NM, Corcobado T, Cravador A, Dordevic B, Durán A, Ferreira M, Fu C-H, Garcia L, Hieno A, Ho H-H, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira LSS, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivukovic Z, Tarigan M, Thu PQ, Tomic Z, Tomsovský M, Uematsu S, Webber JF, Zeng H-C, Zheng F-C, Brasier CM, Horta Jung M (2024). Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Studies in Mycology 107: 251-388. doi: 10.3114/sim.2024.107.04.

The complex polyploid genome architecture of sugarcane.

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Date fruit melanin is primarily based on (-)-epicatechin proanthocyanidin oligomers.

Plant-based melanin seems to be abundant, but it did not receive scientific attention despite its importance in plant biology and medicinal applications, e.g. photoprotection, radical scavenging, antimicrobial properties, etc. Date fruit melanin (DM) has complex, graphene-like, polymeric structure that needs characterization to understand its molecular properties and potential applications. This study provides the first investigation of the possible molecular composition of DM. High performance size-exclusion chromatography (HPSEC) suggested that DM contains oligomeric structures (569-3236 Da) and transmission electron microscopy (TEM) showed agglomeration of these structures in granules of low total porosity (10-1000 Å). Nuclear magnetic resonance (NMR) spectroscopy provided evidence for the presence of oligomeric proanthocyanidins and electron paramagnetic resonance (EPR) spectroscopy revealed a g-factor in the range 2.0034-2.005. Density functional theory (DFT) calculations suggested that the EPR signals can be associated with oligomeric proanthocyanidin structures having 4 and above molecular units of (-)-epicatechin. The discovery of edible melanin in date fruits and its characterization are expected to open a new area of research on its significance to nutritional and sensory characteristics of plant-based foods.

The implementation of an easy-to-apply NMR cryoporometric instrument for porous materials.

Time-domain NMR has been extensively utilised to study various characteristics of fluid-saturated porous,materials for instance their mobility, dynamics, stiffness, viscosity and rigidity features, particularly for solid hydrocarbons, rubbers and other polymers. As a unique time-domain technique available for over 30 years, NMR cryoporometry (NMRC) may be used to obtain pore-size distributions of the measured samples. To accurately control the sample temperature, a Peltier thermo-electrically cooled variable temperature probe has been developed and integrated with a highly compact precision NMR time-domain relaxation spectrometer, therefore providing the community with a high-performance instrument for NMR Cryoporometry. To extend the application of aforementioned high-performance NMRC instrument into more senarios, we designed a series of light-weight, compact and integral models with optional NMR frequencies from 12 MHz up to 23 MHz. The measured sample temperature can be precisely controlled from about -60 °C to +80 °C, with an excellent temperature resolution of 10 mK or better near the probe liquid bulk melting point. Therefore, it offers a fairly wide NMRC pore-size distribution ranging from about 1 nm to 2 µm by using water as the probe liquid in the pores, significantly wider than is possible when applying generic NMR Spectrometers for NMRC. A preliminary example of NMR Cryoporometric measurements on two special cement samples is shown in the paper in which the measured pore scales as well as their repeatability are demonstrated. Furthermore, various nano-materials, such as MOF, zeolite and shale kerogen would be potential materials to study by using these new available NMRC instrument models. We aim to offer this technique as a quantitative and easy-to-apply unitary benck-top tool for an even wider range of porous material.

Buried graphene heterostructures for electrostatic doping of low-dimensional materials.

The fabrication and characterization of steep slope transistor devices based on low-dimensional materials requires precise electrostatic doping profiles with steep spatial gradients in order to maintain maximum control over the channel. In this proof-of-concept study we present a versatile graphene heterostructure platform with three buried individually addressable gate electrodes. The platform is based on a vertical stack of embedded titanium and graphene separated by an intermediate oxide to provide an almost planar surface. We demonstrate the functionality and advantages of the platform by exploring transfer and output characteristics at different temperatures of carbon nanotube field-effect transistors with different electrostatic doping configurations. Furthermore, we back up the concept with finite element simulations to investigate the surface potential. The presented heterostructure is an ideal platform for analysis of electrostatic doping of low-dimensional materials for novel low-power transistor devices.

Concordance of three point of care testing devices with clinical chemistry laboratory standard assays and patient-reported outcomes of blood sampling methods.

BACKGROUND: Point of care testing (POCT) devices have been developed to facilitate immediate results with the potential to aid screening for new disease and enable patients to self-monitor their disease. Non-communicable diseases (NCDs) are the major cause of mortality globally and are increasing in prevalence as the population ages. Allied health care professionals (AHPs) are skilled in undertaking risk assessment and delivering preventative advice, providing opportunities to access large proportions of the population who may not visit their doctor, within non-traditional community settings. There is evidence of high levels of support from public, patients and health professionals for engaging AHPs in risk-targeted early case detection of certain NCDs. Thus, POCT devices offer a potential alternative to traditional venous blood collection, as novel care pathways for increasing early case detection and access to preventative care. The objectives of this study were to: (i) determine the concordance of the specific POCT devices with laboratory-based standard assays employed within clinical biochemistry laboratories. (ii) compare the sampling experience of both methods via patient-reported experiences. METHODS: A prospective, two-centre study was undertaken involving 158 participants who provided informed consent. Venous blood was collected for traditional assays of HbA1c, creatinine/ estimated Glomerular-Filtration-Rate (eGFR) and vitamin-D. Capillary blood was collected by finger prick test and also assayed for the same biochemical indices (Nova StatSensor (creatinine/eGFR); Siemens DCA-Vantage (HbA1C); CityAssays (vitamin-D)). All users were provided with device training. Participants reported any discomfort experienced by each simultaneously applied method (randomised in order) via a 100 mm Visual-Analogue-Scale. RESULTS: Results for each POCT device and the laboratory standard were analysed by Bland-Altman plots to determine assay concordance. POCT devices demonstrated good concordance with laboratory testing, with at least 95% of all samples being within two standard deviations, for each of the devices tested. The majority of participants reported less discomfort with POCT than venepuncture, with the average reported discomfort being 17/100 mm less for POCT compared to venous blood sample collection on the visual analogue scale. CONCLUSIONS: The POCT devices demonstrated acceptable concordance with laboratory-based assays, and patients reported lower levels of discomfort compared to traditional means of blood collection. This study demonstrates the potential of using these devices as acceptable methods for opportunistic testing of "at-risk" individuals within non-traditional community care settings.

A comparison between the characteristics of a biochar-NPK granule and a commercial NPK granule for application in the soil.

Continual application of nitrogen (N), phosphorous (P) and potassium (K) fertilizer may not return a profit to farmers due to the costs of application and the loss of NPK from soil in various ways. Thus, a combination of NPK granule with a porous biochar (termed here as BNPK) appears to offer multiple benefits resulting from the excellent properties of biochar. Given the lack of information on the properties of NPK and BNPK fertilizers, it is necessary to investigate the characteristics of both to achieve a good understanding of why BNPK granule is superior to NPK granule. Therefore, this study aims to investigate the characteristics of a maize straw biochar mixed with NPK granule, before and after application to soil, and compare them to those for a commercial NPK granule. The BNPK granule, with a greater surface area and porosity, showed a higher capacity to store and donate electrons than the NPK granule. Relatively lower concentrations of Ca, P, K, Si and Mg were dissolved from the BNPK, indicating the ability of the BNPK granule to maintain these mineral elements and reduce dissolution rate. To study the nutrient storage mechanism of the BNPK granule in the soil, short- and long-term leaching experiments were conducted. During the experiments, organo-mineral clusters, comprising C, P, K, Si, Al and Fe, were formed on the surface and inside the biochar pores. However, BNPK was not effective in reducing N leaching, in the absence of plants, in a red chromosol soil.

Extensive morphological and behavioural diversity among fourteen new and seven described species in Phytophthora Clade 10 and its evolutionary implications.

During extensive surveys of global Phytophthora diversity 14 new species detected in natural ecosystems in Chile, Indonesia, USA (Louisiana), Sweden, Ukraine and Vietnam were assigned to Phytophthora major Clade 10 based on a multigene phylogeny of nine nuclear and three mitochondrial gene regions. Clade 10 now comprises three subclades. Subclades 10a and 10b contain species with nonpapillate sporangia, a range of breeding systems and a mainly soil- and waterborne lifestyle. These include the previously described P. afrocarpa, P. gallica and P. intercalaris and eight of the new species: P. ludoviciana, P. procera, P. pseudogallica, P. scandinavica, P. subarctica, P. tenuimura, P. tonkinensis and P. ukrainensis. In contrast, all species in Subclade 10c have papillate sporangia and are self-fertile (or homothallic) with an aerial lifestyle including the known P. boehmeriae, P. gondwanensis, P. kernoviae and P. morindae and the new species P. celebensis, P. chilensis, P. javanensis, P. multiglobulosa, P. pseudochilensis and P. pseudokernoviae. All new Phytophthora species differed from each other and from related species by their unique combinations of morphological characters, breeding systems, cardinal temperatures and growth rates. The biogeography and evolutionary history of Clade 10 are discussed. We propose that the three subclades originated via the early divergence of pre-Gondwanan ancestors > 175 Mya into water- and soilborne and aerially dispersed lineages and subsequently underwent multiple allopatric and sympatric radiations during their global spread. Citation: Jung T, Milenkovic I, Corcobado T, et al. 2022. Extensive morphological and behavioural diversity among fourteen new and seven described species in Phytophthora Clade 10 and its evolutionary implications. Persoonia 49: 1-57. https://doi.org/10.3767/persoonia.2022.49.01.

Resuscitation and emergency care in drowning: A scoping review.

BACKGROUND: The ILCOR Basic Life Support Task Force and the international drowning research community considered it timely to undertake a scoping review of the literature to identify evidence relating to the initial resuscitation, hospital-based interventions and criteria for safe discharge related to drowning. METHODS: Medline, PreMedline, Embase, Cochrane Reviews and Cochrane CENTRAL were searched from 2000 to June 2020 to identify relevant literature. Titles and abstracts and if necessary full text were reviewed in duplicate. Studies were eligible for inclusion if they reported on the population (adults and children who are submerged in water), interventions (resuscitation in water/boats, airway management, oxygen administration, AED use, bystander CPR, ventilation strategies, ECMO, protocols for hospital discharge (I), comparator (standard care) and outcomes (O) survival, survival with a favourable neurological outcome, CPR quality, physiological end-points). RESULTS: The database search yielded 3242 references (Medline 1104, Pre-Medline 202, Embase 1722, Cochrane reviews 12, Cochrane CENTRAL 202). After removal of duplicates 2377 papers were left for screening titles and abstracts. In total 65 unique papers were included. The evidence identified was from predominantly high-income countries and lacked consistency in the populations, interventions and outcomes reported. Clinical studies were exclusively observational in nature. CONCLUSION: This scoping review found that there is very limited evidence from observational studies to inform evidence based clinical practice guidelines for drowning. The review highlights an urgent need for high quality research in drowning.

Microbial pathogen removal from domestic effluent using coral sand in Kiribati.

AIM: Infiltration experiments aimed to show the effectivity of coral sand to remove micro-organisms in septic tank wastewater treatment system, in South Tarawa, Kiribati. METHODS AND RESULTS: Laboratory experiments evaluated effective microbial removal properties of a packed bed of coral beach sand conditioned with domestic effluent. Bacterial and viral indicators Escherichia coli J6-2, Enterococci faecalis and f-RNA (MS2) bacteriophage, along with viral pathogens adenovirus, echovirus, norovirus and rotavirus, were dosed (at 106 -107  CFU, PFU or genome copies per ml concentration) with effluent to unsaturated coral sand-packed columns. For the conditions simulated, all organisms showed removal efficiencies of >4-Log Removal Values (LRVs) (i.e. >99·99% effective reduction in number). Results revealed that the conditioned coral sand had a higher affinity for attenuating viruses than the bacteria tested. MS2 phage, adenovirus, echovirus, norovirus and rotavirus were absent in leachate from the base of the sand columns. E. coli J6-2 and E. faecalis were recovered at 100 -101  CFU (colony forming units) per ml in the column effluent, following a dosage of 106  CFU per ml. Destructive sampling of the columns after experiments revealed that a high proportion of viral pathogens were retained in the top 30 mm of the sand. CONCLUSIONS: On the basis of the relative spatial distribution of trace organisms in the sand, we speculate that adsorption processes likely dominated attenuation of the viral pathogens, more so than physical straining effects. Further study is required to fully elucidate the removal mechanisms. SIGNIFICANCE AND IMPACT OF THE STUDY: To the best of our knowledge this is the first study of the effective microbial removal capacity of coral sand under unsaturated conditions. The work represents an initial exploratory step of developing some standardized design practice of on-site wastewater treatment systems in Kiribati, to offer enhanced protection of groundwater resources and reduce diarrhoeal disease.

Credit-card sized field and benchtop NMR relaxometers using field programmable gate arrays.

The tools for developing systems for NMR improve each year. Some firmware based designs based on Field Programmable Gate Arrays (FPGAs) have been developed to implement both the core and peripheral apparatus for NMR Relaxometers and NMR Cryoporometers. Hand held in size they are particularly suitable for desktop, mobile and field use. Software tools now enable the writing of firmware that enable the rapid design of digital and digitised R.F. data and control systems. This firmware can then be loaded into and run on hardware that often is only the size of a credit-card. These devices can include a single-chip Linux computer with an FPGA capable of processing digital RF on the same chip. These can generate RF signals digitally, process RF signals for up- and down-conversion, and can provide an on chip NMR pulse sequencer. An extremely well tested NMR digital transmitter has been upgraded to use the latest surface-mount Bipolar and Field Effect Transistors. The circuitry is now the size of a book of matches, and interfaces to credit-card sized FPGA modules for RF generation, phase shifting and drive signals. This NMR transmitter design uses digital logic principles rather than conventional tuned R.F. techniques Offering both active-damping and active-quench, a very square R.F. Pulse with fast turn off is achieved, with Mark 1 giving 2.6 µs π/2 and 4.8 µs π pulses into a 5 mm diameter NMR sample (2.7 mT B1) at 20 MHz for Protons. T1ρ pulses are stable and consistent.

Utility of HbA1c assessment in people with diabetes awaiting liver transplantation.

AIMS: To investigate the relationship between HbA1c and glucose in people with co-existing liver disease and diabetes awaiting transplant, and in those with diabetes but no liver disease. METHODS: HbA1c and random plasma glucose data were collected for 125 people with diabetes without liver disease and for 29 people awaiting liver transplant with diabetes and cirrhosis. Cirrhosis was caused by non-alcoholic fatty liver disease, hepatitis C, alcoholic liver disease, hereditary haemochromatosis, polycystic liver/kidneys, cryptogenic/non-cirrhotic portal hypertension and α-1-antitrypsin-related disease. RESULTS: The median (interquartile range) age of the diabetes with cirrhosis group was 55 (49-63) years compared to 60 (50-71) years (P=0.13) in the group without cirrhosis. In the diabetes with cirrhosis group there were 21 men (72%) compared with 86 men (69%) in the group with diabetes and no cirrhosis (P=0.82). Of the group with diabetes and cirrhosis, 27 people (93%) were of white European ethnicity, two (7%) were South Asian and none was of Afro-Caribbean/other ethnicity compared with 94 (75%), 16 (13%), 10 (8%)/5 (4%), respectively, in the group with diabetes and no cirrhosis (P=0.20). Median (interquartile range) HbA1c was 41 (32-56) mmol/mol [5.9 (5.1-7.3)%] vs 61 (52-70) mmol/mol [7.7 (6.9-8.6)%] (P<0.001), respectively, in the diabetes with cirrhosis group vs the diabetes without cirrhosis group. The glucose concentrations were 8.4 (7.0-11.2) mmol/l vs 7.3 (5.2-11.5) mmol/l (P=0.17). HbA1c was depressed by 20 mmol/mol (1.8%; P<0.001) in 28 participants with cirrhosis but elevated by 28 mmol/mol (2.6%) in the participant with α-1-antitrypsin disorder. Those with cirrhosis and depressed HbA1c had fewer larger erythrocytes, and higher red cell distribution width and reticulocyte count. This was reflected in the positive association of glucose with mean cell volume (r=0.39) and haemoglobin level (r=0.49) and the negative association for HbA1c (r=-0.28 and r=-0.26, respectively) in the diabetes group with cirrhosis. CONCLUSION: HbA1c is not an appropriate test for blood glucose in people with cirrhosis and diabetes awaiting transplant as it reflects altered erythrocyte presentation.

Rab35-dependent extracellular nanovesicles are required for induction of tumour supporting stroma.

Communication between diseased cells and the microenvironment is a complex yet crucial element in progression of varied pathological processes. Recent studies in cancer highlight an important role for small extracellular nanovesicles secreted by cancer cells as modulators of cancer-associated stroma, leading to enhanced angiogenesis and metastatic priming. The intrinsic factors regulating extracellular nanovesicle biogenesis and secretion are therefore relevant in studies of nano-communication in the cancer milieu. We generated prostate cancer cells bearing stable knockdown of several candidate vesicle regulating factors and examined the impact on cell health, vesicle secretion and on communication with fibroblastic stromal cells. We highlight that RAB11B and RAB35 regulate phenotypically distinct nanovesicle populations, each accounting for only around 20% of the total. Depleting RAB35, but not RAB11B leaves a remaining population of vesicles whose phenotype is insufficient for driving fibroblast to myofibroblast differentiation, leading to attenuated motile behaviours in 3D in vitro models. Co-implantation of tumour cells with stromal fibroblasts in xenografts similarly showed that RAB11B knockdown had little effect on growth rates in vivo. In contrast, significant attenuation in growth, and attenuation of myofibroblasts at the tumour site was evident when using RAB35-knockdown cells. The study concludes that a RAB35 regulated nanovesicle sub-population is particularly important for communication between cancer and stromal cells, and is required for generating a tumour-supportive microenvironment.

Population structure of the ash dieback pathogen, Hymenoscyphus fraxineus, in relation to its mode of arrival in the UK.

The ash dieback fungus, Hymenoscyphus fraxineus, a destructive, alien pathogen of common ash (Fraxinus excelsior), has spread across Europe over the past 25 years and was first observed in the UK in 2012. To investigate the relationship of the pathogen's population structure to its mode of arrival, isolates were obtained from locations in England and Wales, either where established natural populations of ash had been infected by wind-dispersed ascospores or where the fungus had been introduced on imported planting stock. Population structure was determined by tests for vegetative compatibility (VC), mating type and single-nucleotide polymorphisms (SNPs). VC heterogeneity was high at all locations, with 96% of isolate pairings being incompatible. Frequencies of the MAT1-1-1 and MAT1-2-1 idiomorphs were approximately equal, consistent with H. fraxineus being an obligate outbreeder. Most SNP variation occurred within study location and there was little genetic differentiation between the two types of location in the UK, or between pathogen populations in the UK and continental Europe. There was modest differentiation between UK subpopulations, consistent with genetic variation between source populations in continental Europe. However, there was no evidence of strong founder effects, indicating that numerous individuals of H. fraxineus initiated infection at each location, regardless of the route of pathogen transmission. The ssRNA virus HfMV1 was present at moderate to high frequencies in all UK subpopulations. The results imply that management of an introduced plant pathogen requires action against its spread at the continental level involving coordinated efforts by European countries.

Multi-band magnetotransport in exfoliated thin films of Cu x Bi2Se3.

We report magnetotransport studies in thin (<100 nm) exfoliated films of Cu x Bi2Se3 and we detect an unusual electronic transition at low temperatures. Bulk crystals show weak superconductivity with [Formula: see text] K and a possible electronic phase transition around 200 K. Following exfoliation, superconductivity is supressed and a strongly temperature dependent multi-band conductivity is observed for T < 30 K. This transition between competing conducting channels may be enhanced due to the presence of electronic ordering, and could be affected by the presence of an effective internal stress due to Cu intercalation. By fitting to the weak antilocalisation conductivity correction at low magnetic fields we confirm that the low temperature regime maintains a quantum phase coherence length [Formula: see text] nm indicating the presence of topologically protected surface states.

Atomic layer deposited oxide films as protective interface layers for integrated graphene transfer.

The transfer of chemical vapour deposited graphene from its parent growth catalyst has become a bottleneck for many of its emerging applications. The sacrificial polymer layers that are typically deposited onto graphene for mechanical support during transfer are challenging to remove completely and hence leave graphene and subsequent device interfaces contaminated. Here, we report on the use of atomic layer deposited (ALD) oxide films as protective interface and support layers during graphene transfer. The method avoids any direct contact of the graphene with polymers and through the use of thicker ALD layers (≥100 nm), polymers can be eliminated from the transfer-process altogether. The ALD film can be kept as a functional device layer, facilitating integrated device manufacturing. We demonstrate back-gated field effect devices based on single-layer graphene transferred with a protective Al2O3 film onto SiO2 that show significantly reduced charge trap and residual carrier densities. We critically discuss the advantages and challenges of processing graphene/ALD bilayer structures.

Fluorescence labelling of extracellular vesicles using a novel thiol-based strategy for quantitative analysis of cellular delivery and intracellular traffic.

Extracellular vesicles, including exosomes, are naturally derived nanovesicles generated in and released by numerous cell types. As extracellular entities they have the capacity to interact with neighbouring cells and distant tissues and affect physiological processes as well as being implicated in numerous diseases including tumorigenesis and neurodegeneration. They are also under intense investigation as delivery vectors for biotherapeutics. The ways in which EVs interact with recipient cells to influence cell physiology and deliver a macromolecular payload are at the early stages of exploration. A significant challenge within these studies is the ability to label EVs directly or indirectly with fluorescent probes to allow visualization without compromising functionality. Here, we present a thiol-based fluorescence labelling method allowing comprehensive analysis of the cellular uptake of prostate cancer derived EVs in live cells using confocal microscopy. Labelling of the EVs in this way did not influence their size and had no effect on their ability to induce differentiation of lung fibroblasts to myofibroblasts. For endocytosis analyses, depletion of key endocytic proteins and the use of chemical inhibitors (Dynasore, EIPA, Rottlerin and IPA-3) indicated that fluid-phase endocytosis and/or macropinocytosis was involved in EV internalisation. Over a period of six hours EVs were observed to increasingly co-localise with lysosomes, indicating a possible termination point following internalisation. Overall this method provides new opportunities for analysing the cellular dynamics of EVs as biological entities affecting cell and whole body physiology as well as investigating their potential as drug delivery vectors.

Giant quantum Hall plateaus generated by charge transfer in epitaxial graphene.

Epitaxial graphene has proven itself to be the best candidate for quantum electrical resistance standards due to its wide quantum Hall plateaus with exceptionally high breakdown currents. However one key underlying mechanism, a magnetic field dependent charge transfer process, is yet to be fully understood. Here we report measurements of the quantum Hall effect in epitaxial graphene showing the widest quantum Hall plateau observed to date extending over 50 T, attributed to an almost linear increase in carrier density with magnetic field. This behaviour is strong evidence for field dependent charge transfer from charge reservoirs with exceptionally high densities of states in close proximity to the graphene. Using a realistic framework of broadened Landau levels we model the densities of donor states and predict the field dependence of charge transfer in excellent agreement with experimental results, thus providing a guide towards engineering epitaxial graphene for applications such as quantum metrology.