Displaying publications 1 - 20 of 44 in total

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  1. Trusch F, Loebach L, Wawra S, Durward E, Wuensch A, Iberahim NA, et al.
    Nat Commun, 2018 06 14;9(1):2347.
    PMID: 29904064 DOI: 10.1038/s41467-018-04796-3
    The animal-pathogenic oomycete Saprolegnia parasitica causes serious losses in aquaculture by infecting and killing freshwater fish. Like plant-pathogenic oomycetes, S. parasitica employs similar infection structures and secretes effector proteins that translocate into host cells to manipulate the host. Here, we show that the host-targeting protein SpHtp3 enters fish cells in a pathogen-independent manner. This uptake process is guided by a gp96-like receptor and can be inhibited by supramolecular tweezers. The C-terminus of SpHtp3 (containing the amino acid sequence YKARK), and not the N-terminal RxLR motif, is responsible for the uptake into host cells. Following translocation, SpHtp3 is released from vesicles into the cytoplasm by another host-targeting protein where it degrades nucleic acids. The effector translocation mechanism described here, is potentially also relevant for other pathogen-host interactions as gp96 is found in both animals and plants.
  2. Wang S, Loreau M, Arnoldi JF, Fang J, Rahman KA, Tao S, et al.
    Nat Commun, 2017 05 19;8:15211.
    PMID: 28524860 DOI: 10.1038/ncomms15211
    The spatial scaling of stability is key to understanding ecological sustainability across scales and the sensitivity of ecosystems to habitat destruction. Here we propose the invariability-area relationship (IAR) as a novel approach to investigate the spatial scaling of stability. The shape and slope of IAR are largely determined by patterns of spatial synchrony across scales. When synchrony decays exponentially with distance, IARs exhibit three phases, characterized by steeper increases in invariability at both small and large scales. Such triphasic IARs are observed for primary productivity from plot to continental scales. When synchrony decays as a power law with distance, IARs are quasilinear on a log-log scale. Such quasilinear IARs are observed for North American bird biomass at both species and community levels. The IAR provides a quantitative tool to predict the effects of habitat loss on population and ecosystem stability and to detect regime shifts in spatial ecological systems, which are goals of relevance to conservation and policy.
  3. Zhou H, Wu L, Wang HQ, Zheng JC, Zhang L, Kisslinger K, et al.
    Nat Commun, 2017 11 14;8(1):1474.
    PMID: 29133800 DOI: 10.1038/s41467-017-01655-5
    Multi-layer structure of functional materials often involves the integration of different crystalline phases. The film growth orientation thus frequently exhibits a transformation, owing to multiple possibilities caused by incompatible in-plane structural symmetry. Nevertheless, the detailed mechanism of the transformation has not yet been fully explored. Here we thoroughly probe the heteroepitaxially grown hexagonal zinc oxide (ZnO) films on cubic (001)-magnesium oxide (MgO) substrates using advanced scanning transition electron microscopy, X-ray diffraction and first principles calculations, revealing two distinct interface models of (001) ZnO/(001) MgO and (100) ZnO/(001) MgO. We have found that the structure alternatives are controlled thermodynamically by the nucleation, while kinetically by the enhanced Zn adsorption and O diffusion upon the phase transformation. This work not only provides a guideline for the interface fabrication with distinct crystalline phases but also shows how polar and non-polar hexagonal ZnO films might be manipulated on the same cubic substrate.
  4. Lin R, Hu E, Liu M, Wang Y, Cheng H, Wu J, et al.
    Nat Commun, 2019 04 09;10(1):1650.
    PMID: 30967531 DOI: 10.1038/s41467-019-09248-0
    Despite the importance of studying the instability of delithiated cathode materials, it remains difficult to underpin the degradation mechanism of lithium-rich cathode materials due to the complication of combined chemical and structural evolutions. Herein, we use state-of-the-art electron microscopy tools, in conjunction with synchrotron X-ray techniques and first-principle calculations to study a 4d-element-containing compound, Li2Ru0.5Mn0.5O3. We find surprisingly, after cycling, ruthenium segregates out as metallic nanoclusters on the reconstructed surface. Our calculations show that the unexpected ruthenium metal segregation is due to its thermodynamic insolubility in the oxygen deprived surface. This insolubility can disrupt the reconstructed surface, which explains the formation of a porous structure in this material. This work reveals the importance of studying the thermodynamic stability of the reconstructed film on the cathode materials and offers a theoretical guidance for choosing manganese substituting elements in lithium-rich as well as stoichiometric layer-layer compounds for stabilizing the cathode surface.
  5. Zhang XC, Wang J, Shao GG, Wang Q, Qu X, Wang B, et al.
    Nat Commun, 2019 04 16;10(1):1772.
    PMID: 30992440 DOI: 10.1038/s41467-019-09762-1
    Deep understanding of the genomic and immunological differences between Chinese and Western lung cancer patients is of great importance for target therapy selection and development for Chinese patients. Here we report an extensive molecular and immune profiling study of 245 Chinese patients with non-small cell lung cancer. Tumor-infiltrating lymphocyte estimated using immune cell signatures is found to be significantly higher in adenocarcinoma (ADC, 72.5%) compared with squamous cell carcinoma (SQCC, 54.4%). The correlation of genomic alterations with immune signatures reveals that low immune infiltration was associated with EGFR mutations in ADC samples, PI3K and/or WNT pathway activation in SQCC. While KRAS mutations are found to be significantly associated with T cell infiltration in ADC samples. The SQCC patients with high antigen presentation machinery and cytotoxic T cell signature scores are found to have a prolonged overall survival time.
  6. Runting RK, Meijaard E, Abram NK, Wells JA, Gaveau DL, Ancrenaz M, et al.
    Nat Commun, 2015 04 14;6:6819.
    PMID: 25871635 DOI: 10.1038/ncomms7819
    Balancing economic development with international commitments to protect biodiversity is a global challenge. Achieving this balance requires an understanding of the possible consequences of alternative future scenarios for a range of stakeholders. We employ an integrated economic and environmental planning approach to evaluate four alternative futures for the mega-diverse island of Borneo. We show what could be achieved if the three national jurisdictions of Borneo coordinate efforts to achieve their public policy targets and allow a partial reallocation of planned land uses. We reveal the potential for Borneo to simultaneously retain ∼50% of its land as forests, protect adequate habitat for the Bornean orangutan (Pongo pygmaeus) and Bornean elephant (Elephas maximus borneensis), and achieve an opportunity cost saving of over US$43 billion. Such coordination would depend on enhanced information sharing and reforms to land-use planning, which could be supported by the increasingly international nature of economies and conservation efforts.
  7. Syafruddin SE, Rodrigues P, Vojtasova E, Patel SA, Zaini MN, Burge J, et al.
    Nat Commun, 2019 03 11;10(1):1152.
    PMID: 30858363 DOI: 10.1038/s41467-019-09116-x
    Transcriptional networks are critical for the establishment of tissue-specific cellular states in health and disease, including cancer. Yet, the transcriptional circuits that control carcinogenesis remain poorly understood. Here we report that Kruppel like factor 6 (KLF6), a transcription factor of the zinc finger family, regulates lipid homeostasis in clear cell renal cell carcinoma (ccRCC). We show that KLF6 supports the expression of lipid metabolism genes and promotes the expression of PDGFB, which activates mTOR signalling and the downstream lipid metabolism regulators SREBF1 and SREBF2. KLF6 expression is driven by a robust super enhancer that integrates signals from multiple pathways, including the ccRCC-initiating VHL-HIF2A pathway. These results suggest an underlying mechanism for high mTOR activity in ccRCC cells. More generally, the link between super enhancer-driven transcriptional networks and essential metabolic pathways may provide clues to the mechanisms that maintain the stability of cell identity-defining transcriptional programmes in cancer.
  8. Ewers RM, Boyle MJ, Gleave RA, Plowman NS, Benedick S, Bernard H, et al.
    Nat Commun, 2015 Apr 13;6:6836.
    PMID: 25865801 DOI: 10.1038/ncomms7836
    Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests.
  9. Luskin MS, Albert WR, Tobler MW
    Nat Commun, 2017 12 05;8(1):1783.
    PMID: 29208916 DOI: 10.1038/s41467-017-01656-4
    The continuing development of improved capture-recapture (CR) modeling techniques used to study apex predators has also limited robust temporal and cross-site analyses due to different methods employed. We develop an approach to standardize older non-spatial CR and newer spatial CR density estimates and examine trends for critically endangered Sumatran tigers (Panthera tigris sumatrae) using a meta-regression of 17 existing densities and new estimates from our own fieldwork. We find that tiger densities were 47% higher in primary versus degraded forests and, unexpectedly, increased 4.9% per yr from 1996 to 2014, likely indicating a recovery from earlier poaching. However, while tiger numbers may have temporarily risen, the total potential island-wide population declined by 16.6% from 2000 to 2012 due to forest loss and degradation and subpopulations are significantly more fragmented. Thus, despite increasing densities in smaller parks, we conclude that there are only two robust populations left with >30 breeding females, indicating Sumatran tigers still face a high risk of extinction unless deforestation can be controlled.
  10. Jeofry H, Ross N, Le Brocq A, Graham AGC, Li J, Gogineni P, et al.
    Nat Commun, 2018 Nov 01;9(1):4576.
    PMID: 30385741 DOI: 10.1038/s41467-018-06679-z
    Satellite imagery reveals flowstripes on Foundation Ice Stream parallel to ice flow, and meandering features on the ice-shelf that cross-cut ice flow and are thought to be formed by water exiting a well-organised subglacial system. Here, ice-penetrating radar data show flow-parallel hard-bed landforms beneath the grounded ice, and channels incised upwards into the ice shelf beneath meandering surface channels. As the ice transitions to flotation, the ice shelf incorporates a corrugation resulting from the landforms. Radar reveals the presence of subglacial water alongside the landforms, indicating a well-organised drainage system in which water exits the ice sheet as a point source, mixes with cavity water and incises upwards into a corrugation peak, accentuating the corrugation downstream. Hard-bedded landforms influence both subglacial hydrology and ice-shelf structure and, as they are known to be widespread on formerly glaciated terrain, their influence on the ice-sheet-shelf transition could be more widespread than thought previously.
  11. Osuri AM, Ratnam J, Varma V, Alvarez-Loayza P, Hurtado Astaiza J, Bradford M, et al.
    Nat Commun, 2016 04 25;7:11351.
    PMID: 27108957 DOI: 10.1038/ncomms11351
    Defaunation is causing declines of large-seeded animal-dispersed trees in tropical forests worldwide, but whether and how these declines will affect carbon storage across this biome is unclear. Here we show, using a pan-tropical data set, that simulated declines of large-seeded animal-dispersed trees have contrasting effects on aboveground carbon stocks across Earth's tropical forests. In our simulations, African, American and South Asian forests, which have high proportions of animal-dispersed species, consistently show carbon losses (2-12%), but Southeast Asian and Australian forests, where there are more abiotically dispersed species, show little to no carbon losses or marginal gains (±1%). These patterns result primarily from changes in wood volume, and are underlain by consistent relationships in our empirical data (∼2,100 species), wherein, large-seeded animal-dispersed species are larger as adults than small-seeded animal-dispersed species, but are smaller than abiotically dispersed species. Thus, floristic differences and distinct dispersal mode-seed size-adult size combinations can drive contrasting regional responses to defaunation.
  12. Singh R, Low ET, Ooi LC, Ong-Abdullah M, Nookiah R, Ting NC, et al.
    Nat Commun, 2014 Jun 30;5:4106.
    PMID: 24978855 DOI: 10.1038/ncomms5106
    Oil palm, a plantation crop of major economic importance in Southeast Asia, is the predominant source of edible oil worldwide. We report the identification of the virescens (VIR) gene, which controls fruit exocarp colour and is an indicator of ripeness. VIR is a R2R3-MYB transcription factor with homology to Lilium LhMYB12 and similarity to Arabidopsis production of anthocyanin pigment1 (PAP1). We identify five independent mutant alleles of VIR in over 400 accessions from sub-Saharan Africa that account for the dominant-negative virescens phenotype. Each mutation results in premature termination of the carboxy-terminal domain of VIR, resembling McClintock's C1-I allele in maize. The abundance of alleles likely reflects cultural practices, by which fruits were venerated for magical and medicinal properties. The identification of VIR will allow selection of the trait at the seed or early-nursery stage, 3-6 years before fruits are produced, greatly advancing introgression into elite breeding material.
  13. 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.
  14. Wit F, Müller D, Baum A, Warneke T, Pranowo WS, Müller M, et al.
    Nat Commun, 2015;6:10155.
    PMID: 26670925 DOI: 10.1038/ncomms10155
    River outgassing has proven to be an integral part of the carbon cycle. In Southeast Asia, river outgassing quantities are uncertain due to lack of measured data. Here we investigate six rivers in Indonesia and Malaysia, during five expeditions. CO2 fluxes from Southeast Asian rivers amount to 66.9 ± 15.7 Tg C per year, of which Indonesia releases 53.9 ± 12.4 Tg C per year. Malaysian rivers emit 6.2 ± 1.6 Tg C per year. These moderate values show that Southeast Asia is not the river outgassing hotspot as would be expected from the carbon-enriched peat soils. This is due to the relatively short residence time of dissolved organic carbon (DOC) in the river, as the peatlands, being the primary source of DOC, are located near the coast. Limitation of bacterial production, due to low pH, oxygen depletion or the refractory nature of DOC, potentially also contributes to moderate CO2 fluxes as this decelerates decomposition.
  15. Auburn S, Benavente ED, Miotto O, Pearson RD, Amato R, Grigg MJ, et al.
    Nat Commun, 2018 07 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.
  16. Luskin MS, Brashares JS, Ickes K, Sun IF, Fletcher C, Wright SJ, et al.
    Nat Commun, 2017 12 20;8(1):2231.
    PMID: 29263381 DOI: 10.1038/s41467-017-01920-7
    Native species that forage in farmland may increase their local abundances thereby affecting adjacent ecosystems within their landscape. We used two decades of ecological data from a protected primary rainforest in Malaysia to illutrate how subsidies from neighboring oil palm plantations triggered powerful secondary 'cascading' effects on natural habitats located >1.3 km away. We found (i) oil palm fruit drove 100-fold increases in crop-raiding native wild boar (Sus scrofa), (ii) wild boar used thousands of understory plants to construct birthing nests in the pristine forest interior, and (iii) nest building caused a 62% decline in forest tree sapling density over the 24-year study period. The long-term, landscape-scale indirect effects from agriculture suggest its full ecological footprint may be larger in extent than is currently recognized. Cross-boundary subsidy cascades may be widespread in both terrestrial and marine ecosystems and present significant conservation challenges.
  17. Qie L, Lewis SL, Sullivan MJP, Lopez-Gonzalez G, Pickavance GC, Sunderland T, et al.
    Nat Commun, 2017 12 19;8(1):1966.
    PMID: 29259276 DOI: 10.1038/s41467-017-01997-0
    Less than half of anthropogenic carbon dioxide emissions remain in the atmosphere. While carbon balance models imply large carbon uptake in tropical forests, direct on-the-ground observations are still lacking in Southeast Asia. Here, using long-term plot monitoring records of up to half a century, we find that intact forests in Borneo gained 0.43 Mg C ha-1 per year (95% CI 0.14-0.72, mean period 1988-2010) above-ground live biomass. These results closely match those from African and Amazonian plot networks, suggesting that the world's remaining intact tropical forests are now en masse out-of-equilibrium. Although both pan-tropical and long-term, the sink in remaining intact forests appears vulnerable to climate and land use changes. Across Borneo the 1997-1998 El Niño drought temporarily halted the carbon sink by increasing tree mortality, while fragmentation persistently offset the sink and turned many edge-affected forests into a carbon source to the atmosphere.
  18. Qie L, Lewis SL, Sullivan MJP, Lopez-Gonzalez G, Pickavance GC, Sunderland T, et al.
    Nat Commun, 2018 01 19;9(1):342.
    PMID: 29352254 DOI: 10.1038/s41467-018-02920-x
    The original version of this Article contained an error in the third sentence of the abstract and incorrectly read "Here, using long-term plot monitoring records of up to half a century, we find that intact forests in Borneo gained 0.43 Mg C ha-1 year-1 (95% CI 0.14-0.72, mean period 1988-2010) above-ground live biomass", rather than the correct "Here, using long-term plot monitoring records of up to half a century, we find that intact forests in Borneo gained 0.43 Mg C ha-1 year-1 (95% CI 0.14-0.72, mean period 1988-2010) in above-ground live biomass carbon". This has now been corrected in both the PDF and HTML versions of the Article.
  19. Wiedenmann J, Bocquillon E, Deacon RS, Hartinger S, Herrmann O, Klapwijk TM, et al.
    Nat Commun, 2016;7:10303.
    PMID: 26792013 DOI: 10.1038/ncomms10303
    The Josephson effect describes the generic appearance of a supercurrent in a weak link between two superconductors. Its exact physical nature deeply influences the properties of the supercurrent. In recent years, considerable efforts have focused on the coupling of superconductors to the surface states of a three-dimensional topological insulator. In such a material, an unconventional induced p-wave superconductivity should occur, with a doublet of topologically protected gapless Andreev bound states, whose energies vary 4π-periodically with the superconducting phase difference across the junction. In this article, we report the observation of an anomalous response to rf irradiation in a Josephson junction made of a HgTe weak link. The response is understood as due to a 4π-periodic contribution to the supercurrent, and its amplitude is compatible with the expected contribution of a gapless Andreev doublet. Our work opens the way to more elaborate experiments to investigate the induced superconductivity in a three-dimensional insulator.
  20. Neagu D, Papaioannou EI, Ramli WKW, Miller DN, Murdoch BJ, Ménard H, et al.
    Nat Commun, 2017 11 30;8(1):1855.
    PMID: 29187751 DOI: 10.1038/s41467-017-01880-y
    Metal nanoparticles prepared by exsolution at the surface of perovskite oxides have been recently shown to enable new dimensions in catalysis and energy conversion and storage technologies owing to their socketed, well-anchored structure. Here we show that contrary to general belief, exsolved particles do not necessarily re-dissolve back into the underlying perovskite upon oxidation. Instead, they may remain pinned to their initial locations, allowing one to subject them to further chemical transformations to alter their composition, structure and functionality dramatically, while preserving their initial spatial arrangement. We refer to this concept as chemistry at a point and illustrate it by tracking individual nanoparticles throughout various chemical transformations. We demonstrate its remarkable practical utility by preparing a nanostructured earth abundant metal catalyst which rivals platinum on a weight basis over hundreds of hours of operation. Our concept enables the design of compositionally diverse confined oxide particles with superior stability and catalytic reactivity.
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