Global Assessment of Grassland Carrying Capacities and Relative Stocking Densities of Livestock

Although many suggest that future diets should include more plant-based proteins, animal-sourced foods are unlikely to completely disappear from our diet. Grasslands yield a notable part of the world’s animal protein production, but thus far, there is no global insight into the relationship between current livestock stocking densities and the availability of grassland forage resources. This inhibits acting upon concerns over the negative effects of overgrazing in some areas and utilising the potential for increasing production in others. Previous research has examined the potential of sustainable grazing but lacks generic and observation-based methods needed to fully understand the opportunities and threats of grazing. Here we provide a novel framework and method to estimate global livestock carrying capacity and relative stocking density, i.e. the reported livestock distribution relative to the estimated carrying capacity. We first estimate the aboveground biomass that is available for grazers on grasslands and savannas based on the MODIS Net Primary Production (NPP) approach on a global scale. This information is then used to calculate reasonable livestock carrying capacities, using slopes, forest cover and animal forage requirements as restrictions. With this approach, we found that stocking rates exceed the forage provided by grasslands in northwestern Europe, midwestern United States, southern China and the African Sahel. In this study, we provide the highest resolution global datasets to date. Our results have implications for prospective global food system modelling as well as national agricultural and environmental policies. These maps and findings can assist with conservation efforts to reduce land degradation associated with overgrazing and help identify undergrazed areas for targeted sustainable intensification efforts

All-optical formation of coherent dark states of silicon-vacancy spins in diamond

Spin impurities in diamond can be versatile tools for a wide range of solid-state-based quantum technologies, but finding spin impurities which offer sufficient quality in both photonic and spin properties remains a challenge for this pursuit. The silicon-vacancy center has recently attracted a lot of interest due to its spin-accessible optical transitions and the quality of its optical spectrum. Complementing these properties, spin coherence is essential for the suitability of this center as a spin-photon quantum interface. Here, we report all-optical generation of coherent superpositions of spin states in the ground state of a negatively charged silicon-vacancy center using coherent population trapping. Our measurements reveal a characteristic spin coherence time, T2*, exceeding 250 nanoseconds at 4 K. We further investigate the role of phonon-mediated coupling between orbital states as a source of irreversible decoherence. Our results indicate the feasibility of all-optical coherent control of silicon-vacancy spins using ultrafast laser pulses.Comment: Additional data and analysis is available for download in PDF format at the publications section of http://www.amop.phy.cam.ac.uk/amop-m

Risk of Climate-Related Impacts on Global Rangelands – A Review and Modelling Study

Climate change threatens the ability of global rangelands to provide food, support livelihoods and deliver important ecosystems services. The extent and magnitude of potential impacts are however poorly understood. In this study, we review the risk of climate impacts along the rangeland systems food supply chain. We also present results from biophysical modelling simulations and spatial data analyses to identify where and to what extent rangelands may be at climatic risk. Although a quantification of the net impacts of climate change on rangeland production systems is beyond the reach of our current understanding, there is strong evidence that there will be impacts throughout the supply chain, from feed and animal production to processing, storage, transport, retailing and human consumption. Regarding grazing biomass production, this study finds that mean herbaceous biomass is projected to decrease across global rangelands between 2000 and 2050 under RCP 8.5 (-4.7%), while inter- (year-to-year) and intra- (month-to-month) annual variabilities are projected to increase (+21.3% and +8.2%, respectively). These averaged global estimates mask large spatial heterogeneities, with 74% of global rangeland area projected to experience a decline in mean biomass, 64% an increase in inter-annual variability and 54% an increase in intra-annual variability. The potentially most damaging vegetation trends for livestock production (i.e., simultaneous decreases in mean biomass and increases in inter-annual variability) are projected to occur in rangeland communities that are currently the most vulnerable (here, with the lowest livestock productivities and economic development levels and with the highest projected increases in human population densities). Large uncertainties remain as to climate futures and the exposure and responses of the interlinked human and natural systems to climatic changes over time. Consequently, adaptation choices will need to build on robust methods of designing, implementing and evaluating detailed development pathways, and account for a wide range of possible futures

Scribble modulates the MAPK/Fra1 pathway to disrupt luminal and ductal integrity and suppress tumour formation in the mammary gland

Polarity coordinates cell movement, differentiation, proliferation and apoptosis to build and maintain complex epithelial tissues such as the mammary gland. Loss of polarity and the deregulation of these processes are critical events in malignant progression but precisely how and at which stage polarity loss impacts on mammary development and tumourigenesis is unclear. Scrib is a core polarity regulator and tumour suppressor gene however to date our understanding of Scrib function in the mammary gland has been limited to cell culture and transplantation studies of cell lines. Utilizing a conditional mouse model of Scrib loss we report for the first time that Scrib is essential for mammary duct morphogenesis, mammary progenitor cell fate and maintenance, and we demonstrate a critical and specific role for Scribble in the control of the early steps of breast cancer progression. In particular, Scrib-deficiency significantly induced Fra1 expression and basal progenitor clonogenicity, which resulted in fully penetrant ductal hyperplasia characterized by high cell turnover, MAPK hyperactivity, frank polarity loss with mixing of apical and basolateral membrane constituents and expansion of atypical luminal cells. We also show for the first time a role for Scribble in mammalian spindle orientation with the onset of mammary hyperplasia being associated with aberrant luminal cell spindle orientation and a failure to apoptose during the final stage of duct tubulogenesis. Restoring MAPK/Fra1 to baseline levels prevented Scrib-hyperplasia, whereas persistent Scrib deficiency induced alveolar hyperplasia and increased the incidence, onset and grade of mammary tumours. These findings, based on a definitive genetic mouse model provide fundamental insights into mammary duct maturation and homeostasis and reveal that Scrib loss activates a MAPK/Fra1 pathway that alters mammary progenitor activity to drive premalignancy and accelerate tumour progression

PILER-CR: Fast and accurate identification of CRISPR repeats

BACKGROUND: Sequencing of prokaryotic genomes has recently revealed the presence of CRISPR elements: short, highly conserved repeats separated by unique sequences of similar length. The distinctive sequence signature of CRISPR repeats can be found using general-purpose repeat- or pattern-finding software tools. However, the output of such tools is not always ideal for studying these repeats, and significant effort is sometimes needed to build additional tools and perform manual analysis of the output. RESULTS: We present PILER-CR, a program specifically designed for the identification and analysis of CRISPR repeats. The program executes rapidly, completing a 5 Mb genome in around 5 seconds on a current desktop computer. We validate the algorithm by manual curation and by comparison with published surveys of these repeats, finding that PILER-CR has both high sensitivity and high specificity. We also present a catalogue of putative CRISPR repeats identified in a comprehensive analysis of 346 prokaryotic genomes. CONCLUSION: PILER-CR is a useful tool for rapid identification and classification of CRISPR repeats. The software is donated to the public domain. Source code and a Linux binary are freely available at

Single-Pair FRET Microscopy Reveals Mononucleosome Dynamics

We applied spFRET microscopy for direct observation of intranucleosomal DNA dynamics. Mononucleosomes, reconstituted with DNA containing a FRET pair at the dyad axis and exit of the nucleosome core particle, were immobilized through a 30 bp DNA tether on a polyethyleneglycol functionalized slide and visualized using Total Internal Reflection Fluorescence microscopy. FRET efficiency time-traces revealed two types of dynamics: acceptor blinking and intramolecular rearrangements. Both Cy5 and ATTO647N acceptor dyes showed severe blinking in a deoxygenated buffer in the presence of 2% βME. Replacing the triplet quencher βME with 1 mM Trolox eliminated most blinking effects. After suppression of blinking three subpopulations were observed: 90% appeared as dissociated complexes; the remaining 10% featured an average FRET efficiency in agreement with intact nucleosomes. In 97% of these intact nucleosomes no significant changes in FRET efficiency were observed in the experimentally accessible time window ranging from 10 ms to 10’s of seconds. However, 3% of the intact nucleosomes showed intervals with reduced FRET efficiency, clearly distinct from blinking, with a lifetime of 120 ms. These fluctuations can unambiguously be attributed to DNA breathing. Our findings illustrate not only the merits but also typical caveats encountered in single-molecule FRET studies on complex biological systems

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats

<p>Abstract</p> <p>Background</p> <p>Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes.</p> <p>Results</p> <p>CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT proved to be a huge improvement over Patscan. Both CRT and Pilercr were comparable in speed, however CRT was faster for genomes containing large numbers of repeats.</p> <p>Conclusion</p> <p>In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, showed some important improvements over current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(<it>n</it>) in space and O(<it>nm</it>/<it>l</it>) in time.</p

Challenges, solutions and research priorities for sustainable rangelands

Australia’s rangeland communities, industries, and environment are under increasing pressures from anthropogenic activities and global changes more broadly. We conducted a horizon scan to identify and prioritise key challenges facing Australian rangelands and their communities, and outline possible avenues to address these challenges, with a particular focus on research priorities. We surveyed participants of the Australian Rangeland Society 20th Biennial Conference, held in Canberra in September 2019, before the conference and in interactive workshops during the conference, in order to identify key challenges, potential solutions, and research priorities. The feedback was broadly grouped into six themes associated with supporting local communities, managing natural capital, climate variability and change, traditional knowledge, governance, and research and development. Each theme had several sub-themes and potential solutions to ensure positive, long-term outcomes for the rangelands. The survey responses made it clear that supporting ‘resilient and sustainable rangelands that provide cultural, societal, environmental and economic outcomes simultaneously’ is of great value to stakeholders. The synthesis of survey responses combined with expert knowledge highlighted that sustaining local communities in the long term will require that the inherent social, cultural and natural capital of rangelands are managed sustainably, particularly in light of current and projected variability in climate. Establishment of guidelines and approaches to address these challenges will benefit from: (i) an increased recognition of the value and contributions of traditional knowledge and practices; (ii) development of better governance that is guided by and benefits local stakeholders; and (iii) more funding to conduct and implement strong research and development activities, with research focused on addressing critical knowledge gaps as identified by the local stakeholders. This requires strong governance with legislation and policies that work for the rangelands. We provide a framework that indicates the key knowledge gaps and how innovations may be implemented and scaled out, up and deep to achieve the resilience of Australia’s rangelands. The same principles could be adapted to address challenges in rangelands on other continents, with similar beneficial outcomes

Articulating the effect of food systems innovation on the Sustainable Development Goals

Food system innovations will be instrumental to achieving multiple Sustainable Development Goals (SDGs). However, major innovation breakthroughs can trigger profound and disruptive changes, leading to simultaneous and interlinked reconfigurations of multiple parts of the global food system. The emergence of new technologies or social solutions, therefore, have very different impact profiles, with favourable consequences for some SDGs and unintended adverse side-effects for others. Stand-alone innovations seldom achieve positive outcomes over multiple sustainability dimensions. Instead, they should be embedded as part of systemic changes that facilitate the implementation of the SDGs. Emerging trade-offs need to be intentionally addressed to achieve true sustainability, particularly those involving social aspects like inequality in its many forms, social justice, and strong institutions, which remain challenging. Trade-offs with undesirable consequences are manageable through the development of well planned transition pathways, careful monitoring of key indicators, and through the implementation of transparent science targets at the local level

Livestock and sustainable food systems: Status, trends, and priority actions

Livestock are a critically important component of the food system, although the sector needs a profound transformation to ensure that it contributes to a rapid transition towards sustainable food systems. This chapter reviews and synthesises the evidence available on changes in demand for livestock products in the last few decades, and the multiple socio-economic roles that livestock have around the world. We also describe the nutrition, health, and environmental impacts for which the sector is responsible. We propose eight critical actions for transitioning towards a more sustainable operating space for livestock. (1) Facilitate shifts in the consumption of animal source foods (ASF), recognising that global reductions will be required, especially in communities with high consumption levels, while promoting increased levels in vulnerable groups, including the undernourished, pregnant women and the elderly. (2) Continue work towards the sustainable intensification of livestock systems, paying particular attention to animal welfare, food-feed competition, blue water use, disease transmission and perverse economic incentives. (3) Embrace the potential of circularity in livestock systems as a way of partially decoupling livestock from land. (4) Adopt practices that lead to the direct or indirect mitigation of greenhouse gases. (5) Adopt some of the vast array of novel technologies at scale and design incentive mechanisms for their rapid deployment. (6) Diversify the protein sources available for human consumption and feed, focusing on the high-quality alternative protein sources that have lower environmental impacts. (7) Tackle antimicrobial resistance effectively through a combination of technology and new regulations, particularly for the fast-growing poultry and pork sectors and for feedlot operations. (8) Implement true cost of food and true-pricing approaches to ASF consumption