Displaying publications 1 - 20 of 112 in total

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  1. Andrighetto G, Szekely A, Guido A, Gelfand M, Abernathy J, Arikan G, et al.
    Nat Commun, 2024 Feb 16;15(1):1436.
    PMID: 38365869 DOI: 10.1038/s41467-024-44999-5
    The emergence of COVID-19 dramatically changed social behavior across societies and contexts. Here we study whether social norms also changed. Specifically, we study this question for cultural tightness (the degree to which societies generally have strong norms), specific social norms (e.g. stealing, hand washing), and norms about enforcement, using survey data from 30,431 respondents in 43 countries recorded before and in the early stages following the emergence of COVID-19. Using variation in disease intensity, we shed light on the mechanisms predicting changes in social norm measures. We find evidence that, after the emergence of the COVID-19 pandemic, hand washing norms increased while tightness and punishing frequency slightly decreased but observe no evidence for a robust change in most other norms. Thus, at least in the short term, our findings suggest that cultures are largely stable to pandemic threats except in those norms, hand washing in this case, that are perceived to be directly relevant to dealing with the collective threat.
  2. Arunkumar GA, Bhavsar D, Li T, Strohmeier S, Chromikova V, Amanat F, et al.
    Nat Commun, 2021 10 25;12(1):6161.
    PMID: 34697321 DOI: 10.1038/s41467-021-26409-2
    A panel of influenza virus-like sequences were recently documented in fish and amphibians. Of these, the Wuhan spiny eel influenza virus (WSEIV) was found to phylogenetically cluster with influenza B viruses as a sister clade. Influenza B viruses have been documented to circulate only in humans, with certain virus isolates found in harbor seals. It is therefore interesting that a similar virus was potentially found in fish. Here we characterize the putative hemagglutinin (HA) and neuraminidase (NA) surface glycoproteins of the WSEIV. Functionally, we show that the WSEIV NA-like protein has sialidase activity comparable to B/Malaysia/2506/2004 influenza B virus NA, making it a bona fide neuraminidase that is sensitive to NA inhibitors. We tested the functionality of the HA by addressing the receptor specificity, stability, preferential airway protease cleavage, and fusogenicity. We show highly specific binding to monosialic ganglioside 2 (GM2) and fusogenicity at a range of different pH conditions. In addition, we found limited antigenic conservation of the WSEIV HA and NA relative to the B/Malaysia/2506/2004 virus HA and NA. In summary, we perform a functional and antigenic characterization of the glycoproteins of WSEIV to assess if it is indeed a bona fide influenza virus potentially circulating in ray-finned fish.
  3. Auburn S, Benavente ED, Miotto O, Pearson RD, Amato R, Grigg MJ, et al.
    Nat Commun, 2018 Jul 03;9(1):2585.
    PMID: 29968722 DOI: 10.1038/s41467-018-04965-4
    The incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination.
  4. Battlay P, Wilson J, Bieker VC, Lee C, Prapas D, Petersen B, et al.
    Nat Commun, 2023 Mar 27;14(1):1717.
    PMID: 36973251 DOI: 10.1038/s41467-023-37303-4
    Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. Here, we leverage extensive contemporary and historical collections of Ambrosia artemisiifolia-an aggressively invasive weed and primary cause of pollen-induced hayfever-to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-indicative of chromosomal inversions-contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolia's global spread across vast climatic gradients.
  5. Beck MW, Losada IJ, Menéndez P, Reguero BG, Díaz-Simal P, Fernández F
    Nat Commun, 2018 06 12;9(1):2186.
    PMID: 29895942 DOI: 10.1038/s41467-018-04568-z
    Coral reefs can provide significant coastal protection benefits to people and property. Here we show that the annual expected damages from flooding would double, and costs from frequent storms would triple without reefs. For 100-year storm events, flood damages would increase by 91% to $US 272 billion without reefs. The countries with the most to gain from reef management are Indonesia, Philippines, Malaysia, Mexico, and Cuba; annual expected flood savings exceed $400 M for each of these nations. Sea-level rise will increase flood risk, but substantial impacts could happen from reef loss alone without better near-term management. We provide a global, process-based valuation of an ecosystem service across an entire marine biome at (sub)national levels. These spatially explicit benefits inform critical risk and environmental management decisions, and the expected benefits can be directly considered by governments (e.g., national accounts, recovery plans) and businesses (e.g., insurance).
  6. Belton B, Little DC, Zhang W, Edwards P, Skladany M, Thilsted SH
    Nat Commun, 2020 11 16;11(1):5804.
    PMID: 33199697 DOI: 10.1038/s41467-020-19679-9
    Recent literature on marine fish farming brands it as potentially compatible with sustainable resource use, conservation, and human nutrition goals, and aligns with the emerging policy discourse of 'blue growth'. We advance a two-pronged critique. First, contemporary narratives tend to overstate marine finfish aquaculture's potential to deliver food security and environmental sustainability. Second, they often align with efforts to enclose maritime space that could facilitate its allocation to extractive industries and conservation interests and exclude fishers. Policies and investments that seek to increase the availability and accessibility of affordable and sustainable farmed aquatic foods should focus on freshwater aquaculture.
  7. Besser K, Malyon GP, Eborall WS, Paro da Cunha G, Filgueiras JG, Dowle A, et al.
    Nat Commun, 2018 12 03;9(1):5125.
    PMID: 30510200 DOI: 10.1038/s41467-018-07575-2
    Woody (lignocellulosic) plant biomass is an abundant renewable feedstock, rich in polysaccharides that are bound into an insoluble fiber composite with lignin. Marine crustacean woodborers of the genus Limnoria are among the few animals that can survive on a diet of this recalcitrant material without relying on gut resident microbiota. Analysis of fecal pellets revealed that Limnoria targets hexose-containing polysaccharides (mainly cellulose, and also glucomannans), corresponding with the abundance of cellulases in their digestive system, but xylans and lignin are largely unconsumed. We show that the limnoriid respiratory protein, hemocyanin, is abundant in the hindgut where wood is digested, that incubation of wood with hemocyanin markedly enhances its digestibility by cellulases, and that it modifies lignin. We propose that this activity of hemocyanins is instrumental to the ability of Limnoria to feed on wood in the absence of gut symbionts. These findings may hold potential for innovations in lignocellulose biorefining.
  8. Biria M, Banca P, Healy MP, Keser E, Sawiak SJ, Rodgers CT, et al.
    Nat Commun, 2023 Jun 27;14(1):3324.
    PMID: 37369695 DOI: 10.1038/s41467-023-38695-z
    There has been little analysis of neurochemical correlates of compulsive behaviour to illuminate its underlying neural mechanisms. We use 7-Tesla proton magnetic resonance spectroscopy (1H-MRS) to assess the balance of excitatory and inhibitory neurotransmission by measuring glutamate and GABA levels in anterior cingulate cortex (ACC) and supplementary motor area (SMA) of healthy volunteers and participants with Obsessive-Compulsive Disorder (OCD). Within the SMA, trait and clinical measures of compulsive behaviour are related to glutamate levels, whereas a behavioural index of habitual control correlates with the glutamate:GABA ratio. Participants with OCD also show the latter relationship in the ACC while exhibiting elevated glutamate and lower GABA levels in that region. This study highlights SMA mechanisms of habitual control relevant to compulsive behaviour, common to the healthy sub-clinical and OCD populations. The results also demonstrate additional involvement of anterior cingulate in the balance between goal-directed and habitual responding in OCD.
  9. Brodie Rudolph T, Ruckelshaus M, Swilling M, Allison EH, Österblom H, Gelcich S, et al.
    Nat Commun, 2020 07 17;11(1):3600.
    PMID: 32681109 DOI: 10.1038/s41467-020-17410-2
    Human wellbeing relies on the Biosphere, including natural resources provided by ocean ecosystems. As multiple demands and stressors threaten the ocean, transformative change in ocean governance is required to maintain the contributions of the ocean to people. Here we illustrate how transition theory can be applied to ocean governance. We demonstrate how current economic and social systems can adapt to existing pressures and shift towards ocean stewardship through incorporation of niche innovations within and across economic sectors and stakeholder communities. These novel approaches support an emergent but purposeful transition and suggest a clear path to a thriving and vibrant relationship between humans and the ocean. Oceans provide important natural resources, but the management and governance of the ocean is complex and the ecosystem is suffering as a result. The authors discuss current barriers to sustainable ocean governance and suggest pathways forward.
  10. Bruce JP, To KF, Lui VWY, Chung GTY, Chan YY, Tsang CM, et al.
    Nat Commun, 2021 07 07;12(1):4193.
    PMID: 34234122 DOI: 10.1038/s41467-021-24348-6
    Interplay between EBV infection and acquired genetic alterations during nasopharyngeal carcinoma (NPC) development remains vague. Here we report a comprehensive genomic analysis of 70 NPCs, combining whole-genome sequencing (WGS) of microdissected tumor cells with EBV oncogene expression to reveal multiple aspects of cellular-viral co-operation in tumorigenesis. Genomic aberrations along with EBV-encoded LMP1 expression underpin constitutive NF-κB activation in 90% of NPCs. A similar spectrum of somatic aberrations and viral gene expression undermine innate immunity in 79% of cases and adaptive immunity in 47% of cases; mechanisms by which NPC may evade immune surveillance despite its pro-inflammatory phenotype. Additionally, genomic changes impairing TGFBR2 promote oncogenesis and stabilize EBV infection in tumor cells. Fine-mapping of CDKN2A/CDKN2B deletion breakpoints reveals homozygous MTAP deletions in 32-34% of NPCs that confer marked sensitivity to MAT2A inhibition. Our work concludes that NPC is a homogeneously NF-κB-driven and immune-protected, yet potentially druggable, cancer.
  11. Chaibun T, Puenpa J, Ngamdee T, Boonapatcharoen N, Athamanolap P, O'Mullane AP, et al.
    Nat Commun, 2021 02 05;12(1):802.
    PMID: 33547323 DOI: 10.1038/s41467-021-21121-7
    Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-consuming and requires expensive instrumentation. Here, we report an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification (RCA) for rapid detection of SARS-CoV-2. The assay involves the hybridization of the RCA amplicons with probes that were functionalized with redox active labels that are detectable by an electrochemical biosensor. The one-step sandwich hybridization assay could detect as low as 1 copy/μL of N and S genes, in less than 2 h. Sensor evaluation with 106 clinical samples, including 41 SARS-CoV-2 positive and 9 samples positive for other respiratory viruses, gave a 100% concordance result with qRT-PCR, with complete correlation between the biosensor current signals and quantitation cycle (Cq) values. In summary, this biosensor could be used as an on-site, real-time diagnostic test for COVID-19.
  12. Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, et al.
    Nat Commun, 2019 04 16;10(1):1784.
    PMID: 30992455 DOI: 10.1038/s41467-018-08148-z
    The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.
  13. Chang KY, Riley WJ, Knox SH, Jackson RB, McNicol G, Poulter B, et al.
    Nat Commun, 2021 04 15;12(1):2266.
    PMID: 33859182 DOI: 10.1038/s41467-021-22452-1
    Wetland methane (CH4) emissions ([Formula: see text]) are important in global carbon budgets and climate change assessments. Currently, [Formula: see text] projections rely on prescribed static temperature sensitivity that varies among biogeochemical models. Meta-analyses have proposed a consistent [Formula: see text] temperature dependence across spatial scales for use in models; however, site-level studies demonstrate that [Formula: see text] are often controlled by factors beyond temperature. Here, we evaluate the relationship between [Formula: see text] and temperature using observations from the FLUXNET-CH4 database. Measurements collected across the globe show substantial seasonal hysteresis between [Formula: see text] and temperature, suggesting larger [Formula: see text] sensitivity to temperature later in the frost-free season (about 77% of site-years). Results derived from a machine-learning model and several regression models highlight the importance of representing the large spatial and temporal variability within site-years and ecosystem types. Mechanistic advancements in biogeochemical model parameterization and detailed measurements in factors modulating CH4 production are thus needed to improve global CH4 budget assessments.
  14. Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, et al.
    Nat Commun, 2014;5:3233.
    PMID: 24481126 DOI: 10.1038/ncomms4233
    Comparative whole-genome sequencing enables the identification of specific mutations during adaptation of bacteria to new environments and allelic replacement can establish their causality. However, the mechanisms of action are hard to decipher and little has been achieved for epistatic mutations, especially at the metabolic level. Here we show that a strain of Escherichia coli carrying mutations in the rpoC and glpK genes, derived from adaptation in glycerol, uses two distinct metabolic strategies to gain growth advantage. A 27-bp deletion in the rpoC gene first increases metabolic efficiency. Then, a point mutation in the glpK gene promotes growth by improving glycerol utilization but results in increased carbon wasting as overflow metabolism. In a strain carrying both mutations, these contrasting carbon/energy saving and wasting mechanisms work together to give an 89% increase in growth rate. This study provides insight into metabolic reprogramming during adaptive laboratory evolution for fast cellular growth.
  15. Chong CT, Ng JH
    Nat Commun, 2023 Dec 09;14(1):8156.
    PMID: 38071199 DOI: 10.1038/s41467-023-44049-6
    Renewable jet fuel (RJF) is often touted as the only viable sustainable energy source for the aviation sector, given the difficulties faced by other low-carbon energy sources in overcoming technological barriers. Despite that, the sustainability of RJF is still in dispute due to the conflicting requirements in natural resource for producing the fuels. We introduce a holistic 25-indicator sustainability index encompassing the four domains of energy-water-food nexus and governance, that measures the potential impact of RJF production on 154 countries (and territories) through the oil-to-jet, alcohol-to-jet and gas-to-jet conversion methods. Countries and territories are ranked according to the composite index scores of the four domains. The sustainability index model provides insights on how RJF affords the aviation sector a clean slate in determining the manner of development in a sustainably and equitable way, while also marching towards the long-term goal of carbon neutrality, in alignment with the Sustainable Development Goals.
  16. Chong WK, Ng BJ, Lee YJ, Tan LL, Putri LK, Low J, et al.
    Nat Commun, 2023 Nov 24;14(1):7676.
    PMID: 37996415 DOI: 10.1038/s41467-023-43331-x
    Engineering an efficient semiconductor to sustainably produce green hydrogen via solar-driven water splitting is one of the cutting-edge strategies for carbon-neutral energy ecosystem. Herein, a superhydrophilic green hollow ZnIn2S4 (gZIS) was fabricated to realize unassisted photocatalytic overall water splitting. The hollow hierarchical framework benefits exposure of intrinsically active facets and activates inert basal planes. The superhydrophilic nature of gZIS promotes intense surface water molecule interactions. The presence of vacancies within gZIS facilitates photon energy utilization and charge transfer. Systematic theoretical computations signify the defect-induced charge redistribution of gZIS enhancing water activation and reducing surface kinetic barriers. Ultimately, the gZIS could drive photocatalytic pure water splitting by retaining close-to-unity stability for a full daytime reaction with performance comparable to other complex sulfide-based materials. This work reports a self-activated, single-component cocatalyst-free gZIS with great exploration value, potentially providing a state-of-the-art design and innovative aperture for efficient solar-driven hydrogen production to achieve carbon-neutrality.
  17. Collins DS, Avdis A, Allison PA, Johnson HD, Hill J, Piggott MD, et al.
    Nat Commun, 2017 06 15;8:15698.
    PMID: 28643789 DOI: 10.1038/ncomms15698
    Modern mangroves are among the most carbon-rich biomes on Earth, but their long-term (≥106 years) impact on the global carbon cycle is unknown. The extent, productivity and preservation of mangroves are controlled by the interplay of tectonics, global sea level and sedimentation, including tide, wave and fluvial processes. The impact of these processes on mangrove-bearing successions in the Oligo-Miocene of the South China Sea (SCS) is evaluated herein. Palaeogeographic reconstructions, palaeotidal modelling and facies analysis suggest that elevated tidal range and bed shear stress optimized mangrove development along tide-influenced tropical coastlines. Preservation of mangrove organic carbon (OC) was promoted by high tectonic subsidence and fluvial sediment supply. Lithospheric storage of OC in peripheral SCS basins potentially exceeded 4,000 Gt (equivalent to 2,000 p.p.m. of atmospheric CO2). These results highlight the crucial impact of tectonic and oceanographic processes on mangrove OC sequestration within the global carbon cycle on geological timescales.
  18. Contreras E, Masuyer G, Qureshi N, Chawla S, Dhillon HS, Lee HL, et al.
    Nat Commun, 2019 06 28;10(1):2869.
    PMID: 31253776 DOI: 10.1038/s41467-019-10732-w
    Clostridial neurotoxins, including tetanus and botulinum neurotoxins, generally target vertebrates. We show here that this family of toxins has a much broader host spectrum, by identifying PMP1, a clostridial-like neurotoxin that selectively targets anopheline mosquitoes. Isolation of PMP1 from Paraclostridium bifermentans strains collected in anopheline endemic areas on two continents indicates it is widely distributed. The toxin likely evolved from an ancestral form that targets the nervous system of similar organisms, using a common mechanism that disrupts SNARE-mediated exocytosis. It cleaves the mosquito syntaxin and employs a unique receptor recognition strategy. Our research has an important impact on the study of the evolution of clostridial neurotoxins and provides the basis for the use of P. bifermentans strains and PMP1 as innovative, environmentally friendly approaches to reduce malaria through anopheline control.
  19. Cooper HV, Evers S, Aplin P, Crout N, Dahalan MPB, Sjogersten S
    Nat Commun, 2020 01 21;11(1):407.
    PMID: 31964892 DOI: 10.1038/s41467-020-14298-w
    Conversion of tropical peat swamp forest to drainage-based agriculture alters greenhouse gas (GHG) production, but the magnitude of these changes remains highly uncertain. Current emissions factors for oil palm grown on drained peat do not account for temporal variation over the plantation cycle and only consider CO2 emissions. Here, we present direct measurements of GHGs emitted during the conversion from peat swamp forest to oil palm plantation, accounting for CH4 and N2O as well as CO2. Our results demonstrate that emissions factors for converted peat swamp forest is in the range 70-117 t CO2 eq ha-1 yr-1 (95% confidence interval, CI), with CO2 and N2O responsible for ca. 60 and ca. 40% of this value, respectively. These GHG emissions suggest that conversion of Southeast Asian peat swamp forest is contributing between 16.6 and 27.9% (95% CI) of combined total national GHG emissions from Malaysia and Indonesia or 0.44 and 0.74% (95% CI) of annual global emissions.
  20. Cooper HV, Evers S, Aplin P, Crout N, Bin Dahalan MP, Sjogersten S
    Nat Commun, 2020 Apr 01;11(1):1717.
    PMID: 32238813 DOI: 10.1038/s41467-020-15178-z
    An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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