Nature Communications
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Multi-indicator sustainability assessment of global food systems Abstract Food systems are at the heart of at least 12 of the 17 Sustainable Development Goals (SDGs). The wide scope of the SDGs call for holistic approaches that integrate previously “siloed” food sustainability assessments. Here we present a first global-scale analysis quantifying the status of national food system performance of 156 countries, employing 25 sustainability indicators across 7 domains as follows: nutrition, environment, food affordability and availability, sociocultural well-being, resilience, food safety, and waste. The results show that different countries have widely varying patterns of performance with unique priorities for improvement. High-income nations score well on most indicators, but poorly on environmental, food waste, and health-sensitive nutrient-intake indicators. Transitioning from animal foods toward plant-based foods would improve indicator scores for most countries. Our nation-specific quantitative results can help policy-makers to set improvement targets on specific areas and adopt new practices, while keeping track of the other aspects of sustainability.
Nature Communications - Tập 9 Số 1
AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex Abstract Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of anti-CRISPRs that suppress these immune systems. Here we report structures of anti-CRISPR protein IF9 (AcrIF9) in complex with the type I-F CRISPR RNA-guided surveillance complex (Csy). In addition to sterically blocking the hybridization of complementary dsDNA to the CRISPR RNA, our results show that AcrIF9 binding also promotes non-sequence-specific engagement with dsDNA, potentially sequestering the complex from target DNA. These findings highlight the versatility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems.
Nature Communications - Tập 11 Số 1
Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD+ degradation Abstract The intense arms race between bacteria and phages has led to the development of diverse antiphage defense systems in bacteria. Unlike well-known restriction-modification and CRISPR-Cas systems, recently discovered systems are poorly characterized. One such system is the Thoeris defense system, which consists of two genes, thsA and thsB . Here, we report structural and functional analyses of ThsA and ThsB. ThsA exhibits robust NAD+ cleavage activity and a two-domain architecture containing sirtuin-like and SLOG-like domains. Mutation analysis suggests that NAD+ cleavage is linked to the antiphage function of Thoeris. ThsB exhibits a structural resemblance to TIR domain proteins such as nucleotide hydrolases and Toll-like receptors, but no enzymatic activity is detected in our in vitro assays. These results further our understanding of the molecular mechanism underlying the Thoeris defense system, highlighting a unique strategy for bacterial antiphage resistance via NAD+ degradation.
Nature Communications - Tập 11 Số 1
Mucin induces CRISPR-Cas defense in an opportunistic pathogen Abstract Parasitism by bacteriophages has led to the evolution of a variety of defense mechanisms in their host bacteria. However, it is unclear what factors lead to specific defenses being deployed upon phage infection. To explore this question, we co-evolved the bacterial fish pathogen Flavobacterium columnare and its virulent phage V156 in presence and absence of a eukaryotic host signal (mucin) for sixteen weeks. The presence of mucin leads to a dramatic increase in CRISPR spacer acquisition, especially in low nutrient conditions where over 60% of colonies obtain at least one new spacer. Additionally, we show that the presence of a competitor bacterium further increases CRISPR spacer acquisition in F. columnare . These results suggest that ecological factors are important in determining defense strategies against phages, and that the phage-bacterium interactions on mucosal surfaces may select for the diversification of bacterial immune systems.
Nature Communications - Tập 13 Số 1
Repeated growth and bubbling transfer of graphene with millimetre-size single-crystal grains using platinum
Nature Communications - Tập 3 Số 1
Basal body multipotency and axonemal remodelling are two pathways to a 9+0 flagellum Abstract Eukaryotic cilia/flagella exhibit two characteristic ultrastructures reflecting two main functions; a 9+2 axoneme for motility and a 9+0 axoneme for sensation and signalling. Whether, and if so how, they interconvert is unclear. Here we analyse flagellum length, structure and molecular composition changes in the unicellular eukaryotic parasite Leishmania during the transformation of a life cycle stage with a 9+2 axoneme (the promastigote) to one with a 9+0 axoneme (the amastigote). We show 9+0 axonemes can be generated by two pathways: by de novo formation and by restructuring of existing 9+2 axonemes associated with decreased intraflagellar transport. Furthermore, pro-basal bodies formed under conditions conducive for 9+2 axoneme formation can form a 9+0 axoneme de novo . We conclude that pro-centrioles/pro-basal bodies are multipotent and not committed to form either a 9+2 or 9+0 axoneme. In an alternative pathway structures can also be removed from existing 9+2 axonemes to convert them to 9+0.
Nature Communications - Tập 6 Số 1
Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity Abstract Cas9-based RNA-guided nuclease (RGN) has emerged to be a versatile method for genome editing due to the ease of construction of RGN reagents to target specific genomic sequences. The ability to control the activity of Cas9 with a high temporal resolution will facilitate tight regulation of genome editing processes for studying the dynamics of transcriptional regulation or epigenetic modifications in complex biological systems. Here we show that fusing ligand-binding domains of nuclear receptors to split Cas9 protein fragments can provide chemical control over split Cas9 activity. The method has allowed us to control Cas9 activity in a tunable manner with no significant background, which has been challenging for other inducible Cas9 constructs. We anticipate that our design will provide opportunities through the use of different ligand-binding domains to enable multiplexed genome regulation of endogenous genes in distinct loci through simultaneous chemical regulation of orthogonal Cas9 variants.
Nature Communications - Tập 7 Số 1
Social networks predict the life and death of honey bees Abstract In complex societies, individuals’ roles are reflected by interactions with other conspecifics. Honey bees (Apis mellifera ) generally change tasks as they age, but developmental trajectories of individuals can vary drastically due to physiological and environmental factors. We introduce a succinct descriptor of an individual’s social network that can be obtained without interfering with the colony. This ‘network age’ accurately predicts task allocation, survival, activity patterns, and future behavior. We analyze developmental trajectories of multiple cohorts of individuals in a natural setting and identify distinct developmental pathways and critical life changes. Our findings suggest a high stability in task allocation on an individual level. We show that our method is versatile and can extract different properties from social networks, opening up a broad range of future studies. Our approach highlights the relationship of social interactions and individual traits, and provides a scalable technique for understanding how complex social systems function.
Nature Communications - Tập 12 Số 1
Ionic field effect and memristive phenomena in single-point ferroelectric domain switching
Nature Communications - Tập 5 Số 1
Revealing the role of defects in ferroelectric switching with atomic resolution
Nature Communications - Tập 2 Số 1
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