An operational definition of the biome for global change research

CITATION: Conradi, T. et al. 2020. An operational definition of the biome for global change research. New Phytologist, 227:1294–1306, doi:10.1111/nph.16580.The original publication is available at https://nph.onlinelibrary.wiley.comBiomes are constructs for organising knowledge on the structure and functioning of the world’s ecosystems, and serve as useful units for monitoring how the biosphere responds to anthropogenic drivers, including climate change. The current practice of delimiting biomes relies on expert knowledge. Recent studies have questioned the value of such biome maps for comparative ecology and global-change research, partly due to their subjective origin. Here we propose a flexible method for developing biome maps objectively. The method uses range modelling of several thousands of plant species to reveal spatial attractors for different growth-form assemblages that define biomes. The workflow is illustrated using distribution data from 23 500 African plant species. In an example application, we create a biome map for Africa and use the fitted species models to project biome shifts. In a second example, we map gradients of growth-form suitability that can be used to identify sites for comparative ecology. This method provides a flexible framework that (1) allows a range of biome types to be defined according to user needs and (2) enables projections of biome changes that emerge purely from the individualistic responses of plant species to environmental changes.Publisher's versio

Structure of the Helicase Domain of DNA Polymerase Theta Reveals a Possible Role in the Microhomology-Mediated End-Joining Pathway

DNA polymerase theta (Polθ) has been identified as a crucial alternative non-homologous end-joining factor in mammalian cells. Polθ is upregulated in a range of cancer cell types defective in homologous recombination, and knockdown has been shown to inhibit cell survival in a subset of these, making it an attractive target for cancer treatment. We present crystal structures of the helicase domain of human Polθ in the presence and absence of bound nucleotides, and a characterization of its DNA-binding and DNA-stimulated ATPase activities. Comparisons with related helicases from the Hel308 family identify several unique features. Polθ exists as a tetramer both in the crystals and in solution. We propose a model for DNA binding to the Polθ helicase domain in the context of the Polθ tetramer, which suggests a role for the helicase domain in strand annealing of DNA templates for subsequent processing by the polymerase domain

PNT cyber resilience : a Lab2Live observer based approach, Report 2: specifications for cyber testing facilities. Technical report 2

The use of global navigation satellite systems (GNSS) such as GPS and Galileo are vital sources of positioning, navigation and timing (PNT) information for vehicles. This information is of critical importance for connected autonomous vehicles (CAVs) due to their dependence on this information for localisation, route planning and situational awareness. A downside to solely relying on GNSS for PNT is that the signal strength arriving from navigation satellites in space is weak and currently there is no authentication included in the civilian GNSS adopted in the automotive industry. This means that cyber-attacks against the GNSS signal via jamming or spoofing are attractive to adversaries due to the potentially high impact they can achieve. This report introduces specifications and recommendations for GNSS cyber-security test facilities for CAVs. These specifications are based on a survey of academic literature, interviews with a select group of experts, and experiences obtained performing laboratory and real-world testing (shown in Figure 1)

PNT cyber resilience : a Lab2Live observer based approach, Report 1 : GNSS resilience and identified vulnerabilities. Technical Report 1

The use of global navigation satellite systems (GNSS) such as GPS and Galileo are vital sources of positioning, navigation and timing (PNT) information for vehicles. This information is of critical importance for connected autonomous vehicles (CAVs) due to their dependence on this information for localisation, route planning and situational awareness. A downside to solely relying on GNSS for PNT is that the signal strength arriving from navigation satellites in space is weak and currently there is no authentication included in the civilian GNSS adopted in the automotive industry. This means that cyber-attacks against the GNSS signal via jamming or spoofing are attractive to adversaries due to the potentially high impact they can achieve. This report reviews the vulnerabilities of GNSS services for CAVs (a summary is shown in Figure 1), as well as detection and mitigating techniques, summarises the opinions on PNT cyber testing sourced from a select group of experts, and finishes with a description of the associated lab-based and real-world feasibility study and proposed research methodology

Practical sand transport formula for non-breaking waves and currents

Open Access funded by Engineering and Physical Sciences Research Council Under a Creative Commons license Acknowledgements This work is part of the SANTOSS project (‘SANd Transport in OScillatory flows in the Sheet-flow regime’) funded by the UK's EPSRC (GR/T28089/01) and STW in The Netherlands (TCB.6586). JW acknowledges Deltares strategic research funding under project number 1202359.09. Richard Soulsby is gratefully acknowledged for valuable discussions and feedback on the formula during the SANTOSS project.Peer reviewedPostprin

An operational definition of the biome for global change research

CITATION: Conradi, T. et al. 2020. An operational definition of the biome for global change research. New Phytologist, 227:1294–1306, doi:10.1111/nph.16580.The original publication is available at https://nph.onlinelibrary.wiley.comBiomes are constructs for organising knowledge on the structure and functioning of the world’s ecosystems, and serve as useful units for monitoring how the biosphere responds to anthropogenic drivers, including climate change. The current practice of delimiting biomes relies on expert knowledge. Recent studies have questioned the value of such biome maps for comparative ecology and global-change research, partly due to their subjective origin. Here we propose a flexible method for developing biome maps objectively. The method uses range modelling of several thousands of plant species to reveal spatial attractors for different growth-form assemblages that define biomes. The workflow is illustrated using distribution data from 23 500 African plant species. In an example application, we create a biome map for Africa and use the fitted species models to project biome shifts. In a second example, we map gradients of growth-form suitability that can be used to identify sites for comparative ecology. This method provides a flexible framework that (1) allows a range of biome types to be defined according to user needs and (2) enables projections of biome changes that emerge purely from the individualistic responses of plant species to environmental changes.Publisher's versio

Characterization and mapping of retr04, retr05 and retr06 broad-spectrum resistances to Turnip mosaic virus in Brassica juncea, and the development of robust methods for utilizing recalcitrant genotyping data

Turnip mosaic virus (TuMV) induces disease in susceptible hosts, notably impacting cultivation of important crop species of the Brassica genus. Few effective plant viral disease management strategies exist with the majority of current approaches aiming to mitigate the virus indirectly through control of aphid vector species. Multiple sources of genetic resistance to TuMV have been identified previously, although the majority are strain-specific and have not been exploited commercially. Here, two Brassica juncea lines (TWBJ14 and TWBJ20) with resistance against important TuMV isolates (UK 1, vVIR24, CDN 1, and GBR 6) representing the most prevalent pathotypes of TuMV (1, 3, 4, and 4, respectively) and known to overcome other sources of resistance, have been identified and characterized. Genetic inheritance of both resistances was determined to be based on a recessive two-gene model. Using both single nucleotide polymorphism (SNP) array and genotyping by sequencing (GBS) methods, quantitative trait loci (QTL) analyses were performed using first backcross (BC1) genetic mapping populations segregating for TuMV resistance. Pairs of statistically significant TuMV resistance-associated QTLs with additive interactive effects were identified on chromosomes A03 and A06 for both TWBJ14 and TWBJ20 material. Complementation testing between these B. juncea lines indicated that one resistance-linked locus was shared. Following established resistance gene nomenclature for recessive TuMV resistance genes, these new resistance-associated loci have been termed retr04 (chromosome A06, TWBJ14, and TWBJ20), retr05 (A03, TWBJ14), and retr06 (A03, TWBJ20). Genotyping by sequencing data investigated in parallel to robust SNP array data was highly suboptimal, with informative data not established for key BC1 parental samples. This necessitated careful consideration and the development of new methods for processing compromised data. Using reductive screening of potential markers according to allelic variation and the recombination observed across BC1 samples genotyped, compromised GBS data was rendered functional with near-equivalent QTL outputs to the SNP array data. The reductive screening strategy employed here offers an alternative to methods relying upon imputation or artificial correction of genotypic data and may prove effective for similar biparental QTL mapping studies

Getting It on Record: Issues and Strategies for Ethnographic Practice in Recording Studios

The recording studio has been somewhat neglected as a site for ethnographic fieldwork in the field of ethno-musicology and, moreover, the majority of published studies tend to overlook the specific concerns faced by the researcher within these contexts. Music recording studios can be places of creativity, artistry, and collaboration, but they often also involve challenging, intimidating, and fractious relations. Given that recording studios are, first and foremost, concerned with documenting musicians’ performances, we discuss the concerns of getting studio interactions “on record” in terms of access, social relations, and methods of data collection. This article reflects on some of the issues we faced when conducting our fieldwork within British music recording facilities and makes suggestions based on strategies that we employed to address these issues

Levofloxacin prophylaxis in patients with newly diagnosed myeloma (TEAMM): a multicentre, double-blind, placebo-controlled, randomised, phase 3 trial.

BACKGROUND: Myeloma causes profound immunodeficiency and recurrent, serious infections. Around 5500 new cases of myeloma are diagnosed per year in the UK, and a quarter of patients will have a serious infection within 3 months of diagnosis. We aimed to assess whether patients newly diagnosed with myeloma benefit from antibiotic prophylaxis to prevent infection, and to investigate the effect on antibiotic-resistant organism carriage and health care-associated infections in patients with newly diagnosed myeloma. METHODS: TEAMM was a prospective, multicentre, double-blind, placebo-controlled randomised trial in patients aged 21 years and older with newly diagnosed myeloma in 93 UK hospitals. All enrolled patients were within 14 days of starting active myeloma treatment. We randomly assigned patients (1:1) to levofloxacin or placebo with a computerised minimisation algorithm. Allocation was stratified by centre, estimated glomerular filtration rate, and intention to proceed to high-dose chemotherapy with autologous stem cell transplantation. All investigators, patients, laboratory, and trial co-ordination staff were masked to the treatment allocation. Patients were given 500 mg of levofloxacin (two 250 mg tablets), orally once daily for 12 weeks, or placebo tablets (two tablets, orally once daily for 12 weeks), with dose reduction according to estimated glomerular filtration rate every 4 weeks. Follow-up visits occurred every 4 weeks up to week 16, and at 1 year. The primary outcome was time to first febrile episode or death from all causes within the first 12 weeks of trial treatment. All randomised patients were included in an intention-to-treat analysis of the primary endpoint. This study is registered with the ISRCTN registry, number ISRCTN51731976, and the EU Clinical Trials Register, number 2011-000366-35. FINDINGS: Between Aug 15, 2012, and April 29, 2016, we enrolled and randomly assigned 977 patients to receive levofloxacin prophylaxis (489 patients) or placebo (488 patients). Median follow-up was 12 months (IQR 8-13). 95 (19%) first febrile episodes or deaths occurred in 489 patients in the levofloxacin group versus 134 (27%) in 488 patients in the placebo group (hazard ratio 0·66, 95% CI 0·51-0·86; p=0·0018. 597 serious adverse events were reported up to 16 weeks from the start of trial treatment (308 [52%] of which were in the levofloxacin group and 289 [48%] of which were in the placebo group). Serious adverse events were similar between the two groups except for five episodes (1%) of mostly reversible tendonitis in the levofloxacin group. INTERPRETATION: Addition of prophylactic levofloxacin to active myeloma treatment during the first 12 weeks of therapy significantly reduced febrile episodes and deaths compared with placebo without increasing health care-associated infections. These results suggest that prophylactic levofloxacin could be used for patients with newly diagnosed myeloma undergoing anti-myeloma therapy. FUNDING: UK National Institute for Health Research