439 research outputs found
Impacts of Protected Areas on Local Livelihoods in Cambodia
SummaryImpact evaluation methods (mixed effects models and matching) were used to investigate the effect of protected areas (PAs) on poverty and livelihoods in Cambodia, comparing households inside PAs with bordering villages and controls. There was no evidence that PAs exacerbated local poverty or reduce agricultural harvests in comparison with controls. Households bordering the PAs were significantly better off due to greater access to markets and services. Non-timber forest product (NTFP) collectors inside PAs were significantly better off than controls and had greater rice harvests, because they had more secure access to land and forest resources. The PAs in Cambodia therefore have some positive impacts on households that use forest and land resources for their livelihoods
Ancestral function and diversification of a horizontally acquired oomycete carboxylic acid transporter
This is the author accepted manuscript. The final version is available from OUP via the DOI in this recordHorizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonise new environments. However, few studies have characterised the functions of HGT genes experimentally or examined post-acquisition functional divergence. Here we report the use of ancestral sequence reconstruction and heterologous expression in Saccharomyces cerevisiae to examine the evolutionary history of an oomycete transporter gene family that was horizontally acquired from fungi. We demonstrate that the inferred ancestral oomycete HGT transporter proteins and their extant descendants are predominantly localised to the plasma membrane when expressed in yeast, and that they transport dicarboxylic acids which are intermediates of the tricarboxylic acid cycle. The substrate specificity profile of the most ancestral protein has largely been retained throughout the radiation of oomycetes, including in both plant and animal pathogens and in a free-living saprotroph, indicating that the ancestral HGT transporter function has been maintained by selection across a range of different lifestyles. No evidence of neofunctionalization in terms of substrate specificity was detected for different HGT transporter paralogues which have different patterns of temporal expression. However, a striking expansion of substrate range was observed for one plant pathogenic oomycete, with a HGT derived paralogue from Pythium aphanidermatum encoding a protein that enables tricarboxylic acid uptake in addition to dicarboxylic acid uptake. This demonstrates that HGT acquisitions can provide functional additions to the recipient proteome as well as the foundation material for the evolution of new protein functions.This
work was supported by a Philip Leverhulme Award to T. A. R. We acknowledge related project
funding from the Gordon and Betty Moore Foundation (GBMF5514). T.A.R. is supported by a
Royal Society University Research Fellowshi
Evolutionary diversification of the RomR protein of the invasive deltaproteobacterium, Bdellovibrio bacteriovorus
This is the final version. Available on open access from Nature Research via the DOI in this recordBdellovibrio bacteriovorus is a predatory deltaproteobacterium that encounters
individual Gram-negative prey bacteria with gliding or swimming motility, and then is
able to invade such prey cells via type IVa pilus-dependent mechanisms. Movement
control (pili or gliding) in other deltaproteobacteria, such as the pack hunting
Myxococcus xanthus, uses a response regulator protein, RomRMx (which
dynamically relocalises between the cell poles) and a GTPase, MglAMx, previously
postulated as an interface between the FrzMx chemosensory system and gliding or
pilus-motility apparatus, to produce regulated bidirectional motility.
In contrast, B. bacteriovorus predation is a more singular encounter between a lone
predator and prey; contact is always via the piliated, non-flagellar pole of the
predator, involving MglABd, but no Frz system. In this new study, tracking fluorescent
RomRBd microscopically during predatory growth shows that it does not dynamically
relocalise, in contrast to the M. xanthus protein; instead having possible roles in
growth events. Furthermore, transcriptional start analysis, site-directed mutagenesis
and bacterial two-hybrid interaction studies, indicate an evolutionary loss of RomRBd
activation (via receiver domain phosphorylation) in this lone hunting bacterium,
demonstrating divergence from its bipolar role in motility in pack-hunting M. xanthus
and further evolution that may differentiate lone from pack predators.Leverhulme TrustMedical Research Council (MRC)Biotechnology and Biological Sciences Research Council (BBSRC
Electrocerebral Recovery During the Intracarotid Amobarbital Procedure: Influence of Interval Between Injections
Purpose and Methods : During the intracarotid amobarbital procedure (IAP) at the University of Michigan, continuous scalp EEG monitoring guides the timing for presentation of memory items and postinjection testing. Most of our patients have undergone bilateral injections. The interval between injections varied from 22 to 60 min, depending on the test and recovery time, as well as the time to catheterize the second side. After noting a trend toward prolonged electro-graphic recovery following the second injection, we tested our clinical impression that recovery of the second hemisphere may be influenced by (a) the time between injections and (b) which hemisphere is injected first (epileptogenic or nonepileptogenic). To study these questions, we analyzed EEG recovery data from 48 consecutive IAPs. Approximately half the patients had the epileptogenic side injected first. Results : We found that (a) electrographic recovery after the second injection is prolonged if the interval between bilateral injections is less than 40 minutes and (b) electrographic recovery is more rapid after injection of the epileptogenic hemisphere. Conclusions : We now recommend waiting at least 45 min between injections. The pathophysiology of more prolonged amobarbital effect on the nonepileptogenic hemisphere than on the epileptogenic hemisphere remains unclear.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65275/1/j.1528-1157.1997.tb00067.x.pd
Distributed Synthesis in Continuous Time
We introduce a formalism modelling communication of distributed agents
strictly in continuous-time. Within this framework, we study the problem of
synthesising local strategies for individual agents such that a specified set
of goal states is reached, or reached with at least a given probability. The
flow of time is modelled explicitly based on continuous-time randomness, with
two natural implications: First, the non-determinism stemming from interleaving
disappears. Second, when we restrict to a subclass of non-urgent models, the
quantitative value problem for two players can be solved in EXPTIME. Indeed,
the explicit continuous time enables players to communicate their states by
delaying synchronisation (which is unrestricted for non-urgent models). In
general, the problems are undecidable already for two players in the
quantitative case and three players in the qualitative case. The qualitative
undecidability is shown by a reduction to decentralized POMDPs for which we
provide the strongest (and rather surprising) undecidability result so far
Resonance optimization of polychromatic light in disordered structures
Disorder offers rich possibilities for manipulating the phase and intensity of light and designing photonic devices for various applications including random lasers, light storage, and speckle-free imaging. Disorder-based optical systems can be implemented in one-dimensional structures based on random or pseudo-random alternating layers with different refractive indices. Such structures can be treated as sequences of scatterers, in which spatial light localization is characterized by random sets of spectral transmission resonances, each accompanied by a relatively high-intensity concentration. The control and manipulation of resonances is the key element in designing disorder-based photonic systems. In this work, we introduce a method of controlling disorder-induced resonances by using the established non-trivial interconnection between the symmetry of bi-directional light propagation properties and the features of the resonant transmissions. Considering a fiber with resonant Bragg gratings as an example, the mechanism of enhancing or suppressing the resonant transmission of polychromatic light and the effectiveness of the method have been demonstrated both theoretically and experimentally. The proposed algorithm of controlling disorder-induced resonances is general and applicable to classical waves and quantum particles, for disordered systems both with and without gain
Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists
This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordData availability:
Complete mtDNA sequences assembled from this study are available at GenBank under the accession numbers MK188935 to MK188947, MN082144 and MN082145. Sequencing data are available under NCBI BioProject PRJNA379597. Reads have been deposited at NCBI Sequence Read Archive with accession number SRP102236. Partial mtDNA contigs and other important contigs mentioned in the text are available from Figshare at https://doi.org/10.6084/m9.figshare.7314728. Nuclear SAG assemblies are available from Figshare at https://doi.org/10.6084/m9.figshare.7352966. A protocol is available from protocols.io at: https://doi.org/10.17504/protocols.io.ywpfxdn.Code availability:
The bioinformatic workflow is available at https://doi.org/10.5281/zenodo.192677; additional statistical analysis code is available at https://doi.org/10.6084/m9.figshare.9884309.Most eukaryotic microbial diversity is uncultivated, under-studied and lacks nuclear genome data. Mitochondrial genome sampling is more comprehensive, but many phylogenetically important groups remain unsampled. Here, using a single-cell sorting approach combining tubulin-specific labelling with photopigment exclusion, we sorted flagellated heterotrophic unicellular eukaryotes from Pacific Ocean samples. We recovered 206 single amplified genomes, predominantly from underrepresented branches on the tree of life. Seventy single amplified genomes contained unique mitochondrial contigs, including 21 complete or near-complete mitochondrial genomes from formerly under-sampled phylogenetic branches, including telonemids, katablepharids, cercozoans and marine stramenopiles, effectively doubling the number of available samples of heterotrophic flagellate mitochondrial genomes. Collectively, these data identify a dynamic history of mitochondrial genome evolution including intron gain and loss, extensive patterns of genetic code variation and complex patterns of gene loss. Surprisingly, we found that stramenopile mitochondrial content is highly plastic, resembling patterns of variation previously observed only in plants.Gordon and Betty Moore FoundationLeverhulme TrustDavid and Lucile Packard FoundationRoyal SocietyEuropean Molecular Biology OrganizationCONICYT FONDECYTGenome Canad
Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, Paramecium bursaria
This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility
The raw reads generated during transcriptome and sRNA sequencing are available on the NCBI Sequence Read Archive (accessions: SAMN14932981, SAMN14932982). All other datasets are available on Figshare (https://doi.org/10.6084/m9.figshare.c.5241983.v1), under the relevant headings. Custom scripts for host and endosymbiont transcript binning [80] (https://github.com/fmaguire/dendrogenous, https://doi.org/10.5281/zenodo.4639294) and sRNA read processing [81] (https://github.com/guyleonard/paramecium, https://doi.org/10.5281/zenodo.4638888) are available on GitHub and archived within the Zenodo repository.Endosymbiosis was fundamental for the evolution of eukaryotic complexity. Endosymbiotic interactions can be dissected through forward- and reverse-genetic experiments, such as RNA-interference (RNAi). However, distinguishing small (s)RNA pathways in a eukaryote-eukaryote endosymbiotic interaction is challenging. Here, we investigate the repertoire of RNAi pathway protein-encoding genes in the model nascent endosymbiotic system, Paramecium bursaria-Chlorella spp. Using comparative genomics and transcriptomics supported by phylogenetics, we identify essential proteome components of the small interfering (si)RNA, scan (scn)RNA and internal eliminated sequence (ies)RNA pathways. Our analyses reveal that copies of these components have been retained throughout successive whole genome duplication (WGD) events in the Paramecium clade. We validate feeding-induced siRNA-based RNAi in P. bursaria via knock-down of the splicing factor, u2af1, which we show to be crucial to host growth. Finally, using simultaneous knock-down 'paradox' controls to rescue the effect of u2af1 knock-down, we demonstrate that feeding-induced RNAi in P. bursaria is dependent upon a core pathway of host-encoded Dcr1, Piwi and Pds1 components. Our experiments confirm the presence of a functional, host-derived RNAi pathway in P. bursaria that generates 23-nt siRNA, validating the use of the P. bursaria-Chlorella spp. system to investigate the genetic basis of a nascent endosymbiosis.EMBORoyal SocietyEuropean Research Council (ERC)Wellcome TrustLister institut
Emergent RNAâRNA interactions can promote stability in a facultative phototrophic endosymbiosis
This is the final version. Available on open access from the National Academy of Sciences via the DOI in this recordData Availability: The sequence data, code, and datasets have been deposited in NCBI Sequence Read Archive, GitHub, Figshare, and Zenodo. The raw reads generated during sRNA sequencing are available on the NCBI Sequence Read Archive (accession numbers SAMN14932981 and SAMN14932982). All other datasets are available on Figshare (https://doi.org/10.6084/m9.figshare.c.4978160.v3) under the relevant headings (77). Custom scripts for sRNA read processing (https://github.com/guyleonard/paramecium, https://doi.org/10.5281/zenodo.4638888) and eDicer comparative analysis (https://github.com/fmaguire/eDicer, https://doi.org/10.5281/zenodo.4659378) are available on GitHub and archived within the Zenodo repository.Eukaryoteâeukaryote endosymbiosis was responsible for the spread of chloroplast (plastid) organelles. Stability is required for the metabolic and genetic integration that drives the establishment of new organelles, yet the mechanisms that act to stabilize emergent endosymbiosesâbetween two fundamentally selfish biological organismsâare unclear. Theory suggests that enforcement mechanisms, which punish misbehavior, may act to stabilize such interactions by resolving conflict. However, how such mechanisms can emerge in a facultative endosymbiosis has yet to be explored. Here, we propose that endosymbiontâhost RNAâRNA interactions, arising from digestion of the endosymbiont population, can result in a cost to host growth for breakdown of the endosymbiosis. Using the model facultative endosymbiosis between Paramecium bursaria and Chlorella spp., we demonstrate that this mechanism is dependent on the host RNA-interference (RNAi) system. We reveal through small RNA (sRNA) sequencing that endosymbiont-derived messenger RNA (mRNA) released upon endosymbiont digestion can be processed by the host RNAi system into 23-nt sRNA. We predict multiple regions of shared sequence identity between endosymbiont and host mRNA, and demonstrate through delivery of synthetic endosymbiont sRNA that exposure to these regions can knock down expression of complementary host genes, resulting in a cost to host growth. This process of host gene knockdown in response to endosymbiont-derived RNA processing by host RNAi factors, which we term âRNAi collisions,â represents a mechanism that can promote stability in a facultative eukaryoteâeukaryote endosymbiosis. Specifically, by imposing a cost for breakdown of the endosymbiosis, endosymbiontâhost RNAâRNA interactions may drive maintenance of the symbiosis across fluctuating ecological conditions.European Molecular Biology OrganizationRoyal SocietyEuropean Research Council (ERC)Wellcome TrustLister InstituteDonald Hill Family Fellowshi
Systematic comparison of unilamellar vesicles reveals that archaeal core lipid membranes are more permeable than bacterial membranes
This is the final version. Available on open access from the Public Library of Science via the DOI in this recordData Availability: All relevant data are within the paper's Supporting Information files. Numerical values for Fig 4 can be found at https://doi.org/10.6084/m9.figshare.22086647One of the deepest branches in the tree of life separates the Archaea from the Bacteria. These prokaryotic groups have distinct cellular systems including fundamentally different phospholipid membrane bilayers. This dichotomy has been termed the lipid divide and possibly bestows different biophysical and biochemical characteristics on each cell type. Classic experiments suggest that bacterial membranes (formed from lipids extracted from Escherichia coli, for example) show permeability to key metabolites comparable to archaeal membranes (formed from lipids extracted from Halobacterium salinarum), yet systematic analyses based on direct measurements of membrane permeability are absent. Here, we develop a new approach for assessing the membrane permeability of approximately 10 ÎŒm unilamellar vesicles, consisting of an aqueous medium enclosed by a single lipid bilayer. Comparing the permeability of 18 metabolites demonstrates that diether glycerol-1-phosphate lipids with methyl branches, often the most abundant membrane lipids of sampled archaea, are permeable to a wide range of compounds useful for core metabolic networks, including amino acids, sugars, and nucleobases. Permeability is significantly lower in diester glycerol-3-phosphate lipids without methyl branches, the common building block of bacterial membranes. To identify the membrane characteristics that determine permeability, we use this experimental platform to test a variety of lipid forms bearing a diversity of intermediate characteristics. We found that increased membrane permeability is dependent on both the methyl branches on the lipid tails and the ether bond between the tails and the head group, both of which are present on the archaeal phospholipids. These permeability differences must have had profound effects on the cell physiology and proteome evolution of early prokaryotic forms. To explore this further, we compare the abundance and distribution of transmembrane transporter-encoding protein families present on genomes sampled from across the prokaryotic tree of life. These data demonstrate that archaea tend to have a reduced repertoire of transporter gene families, consistent with increased membrane permeation. These results demonstrate that the lipid divide demarcates a clear difference in permeability function with implications for understanding some of the earliest transitions in cell origins and evolution.Gordon and Betty and Gordon Moore FoundationBiotechnology and Biological Sciences Research Council (BBSRC)European Union Horizon 2020Volkswagen FoundationMerton College, University of Oxford (NATI
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