95 research outputs found
Chlorovirus and myovirus diversity in permafrost thaw ponds
Permafrost thaw ponds occur in high abundance across the northern landscape of Canada and are sites of intense microbial activity, resulting
in carbon dioxide and methane emissions to the atmosphere. In this study, we focused on viruses as largely unstudied agents of top-down control in
these high-latitude microbial ecosystems. Specifically, we compared the diversity of myovirus, chlorovirus and host microbial communities in an
organic soil palsa valley pond and a mineral soil lithalsa valley pond. These 2 subarctic permafrost landscapes are both common in northern Québec,
Canada. Sequence analysis of ribosomal small subunit RNA genes showed that the community structure of bacteria and microbial eukaryotes
differed significantly between the 2 ponds, which both differed from microbial communities in a rock-basin lake (whose formation was not related
to permafrost thawing and which we used as a reference pond) in the same region. The viral assemblages included 439 OTUs in the uncultured
Myoviridae category and 41 OTUs in the family Phycodnaviridae. Phylogenetic analysis of the latter based on an amino acid sequence alignment
revealed a single large clade related to chloroviruses, consistent with the abundant presence of chlorophytes in these waters. As there was for the
bacterial and eukaryotic communi-ties, there were also significant differences in the community structure of these viral groups among the 3 ponds.
These results suggest that host community composition is influenced by environmental filtering, which in turn contributes to driving viral diversity
across landscape types
Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem
Background: The sulfur cycle encompasses a series of complex aerobic and anaerobic transformations of S-containing
molecules and plays a fundamental role in cellular and ecosystem-level processes, influencing biological carbon transfers and
other biogeochemical cycles. Despite their importance, the microbial communities and metabolic pathways involved in
these transformations remain poorly understood, especially for inorganic sulfur compounds of intermediate oxidation states
(thiosulfate, tetrathionate, sulfite, polysulfides). Isolated and highly stratified, the extreme geochemical and environmental
features of meromictic ice-capped Lake A, in the Canadian High Arctic, provided an ideal model ecosystem to resolve the
distribution and metabolism of aquatic sulfur cycling microorganisms along redox and salinity gradients.
Results: Applying complementary molecular approaches, we identified sharply contrasting microbial communities and
metabolic potentials among the markedly distinct water layers of Lake A, with similarities to diverse fresh, brackish and saline
water microbiomes. Sulfur cycling genes were abundant at all depths and covaried with bacterial abundance. Genes for
oxidative processes occurred in samples from the oxic freshwater layers, reductive reactions in the anoxic and sulfidic
bottom waters and genes for both transformations at the chemocline. Up to 154 different genomic bins with potential for
sulfur transformation were recovered, revealing a panoply of taxonomically diverse microorganisms with complex metabolic
pathways for biogeochemical sulfur reactions. Genes for the utilization of sulfur cycle intermediates were widespread
throughout the water column, co-occurring with sulfate reduction or sulfide oxidation pathways. The genomic bin
composition suggested that in addition to chemical oxidation, these intermediate sulfur compounds were likely produced
by the predominant sulfur chemo- and photo-oxidisers at the chemocline and by diverse microbial degraders of organic
sulfur molecules.
Conclusions: The Lake A microbial ecosystem provided an ideal opportunity to identify new features of the biogeochemical
sulfur cycle. Our detailed metagenomic analyses across the broad physico-chemical gradients of this permanently stratified
lake extend the known diversity of microorganisms involved in sulfur transformations over a wide range of environmental
conditions. The results indicate that sulfur cycle intermediates and organic sulfur molecules are major sources of electron
donors and acceptors for aquatic and sedimentary microbial communities in association with the classical sulfur cycl
Eukaryotic richness in the abyss: insights from pyrotag sequencing
Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes.French ANR Aquaparadox; ANR DeepOases; Swiss National Science Foundation [31003A-125372]; WM Keck foundationinfo:eu-repo/semantics/publishedVersio
Coordinated Activation of Candidate Proto-Oncogenes and Cancer Testes Antigens via Promoter Demethylation in Head and Neck Cancer and Lung Cancer
Background: Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported. We used an integrative method to analyze expression in primary head and neck squamous cell carcinoma (HNSCC) and pharmacologically demethylated cell lines to identify aberrantly demethylated and expressed candidate proto-oncogenes and cancer testes antigens in HNSCC. Methodology/Principal Findings: We noted coordinated promoter demethylation and simultaneous transcriptional upregulation of proto-oncogene candidates with promoter homology, and phylogenetic footprinting of these promoters demonstrated potential recognition sites for the transcription factor BORIS. Aberrant BORIS expression correlated with upregulation of candidate proto-oncogenes in multiple human malignancies including primary non-small cell lung cancers and HNSCC, induced coordinated proto-oncogene specific promoter demethylation and expression in non-tumorigenic cells, and transformed NIH3T3 cells. Conclusions/Significance: Coordinated, epigenetic unmasking of multiple genes with growth promoting activity occurs i
Metacarpal trabecular bone varies with distinct hand-positions used in hominid locomotion
Trabecular bone remodels during life in response to loading and thus should, at least in part, reflect potential variation in the magnitude, frequency and direction of joint loading across different hominid species. Here we analyse the trabecular structure across all non-pollical metacarpal distal heads (Mc2-5) in extant great apes, expanding on previous volume of interest and whole-epiphysis analyses that have largely focussed on only the first or third metacarpal. Specifically, we employ both a univariate statistical mapping and a multivariate approach to test for both inter-ray and interspecific differences in relative trabecular bone volume fraction (RBV/TV) and degree of anisotropy (DA) in Mc2-5 subchondral trabecular bone. Results demonstrate that while DA values only separate Pongo from African apes (Pan troglodytes, Pan paniscus, Gorilla gorilla), RBV/TV distribution varies with the predicted loading of the metacarpophalangeal (McP) joints during locomotor behaviours in each species. Gorilla exhibits a relatively dorsal distribution of RBV/TV consistent with habitual hyper-extension of the McP joints during knuckle-walking, whereas Pongo has a palmar distribution consistent with flexed McP joints used to grasp arboreal substrates. Both Pan species possess a disto-dorsal distribution of RBV/TV, compatible with multiple hand postures associated with a more varied locomotor regime. Further inter-ray comparisons reveal RBV/TV patterns consistent with varied knuckle-walking postures in Pan species in contrast to higher RBV/TV values toward the midline of the hand in Mc2 and Mc5 of Gorilla, consistent with habitual palm-back knuckle-walking. These patterns of trabecular bone distribution and structure reflect different behavioural signals that could be useful for determining the behaviours of fossil hominins
Working paper analysing the economic implications of the proposed 30% target for areal protection in the draft post-2020 Global Biodiversity Framewor
58 pages, 5 figures, 3 tables- The World Economic Forum now ranks biodiversity loss as a top-five risk to the global economy, and the draft post-2020 Global Biodiversity Framework proposes an expansion of conservation areas to 30% of the earth’s surface by 2030 (hereafter the “30% target”), using protected areas (PAs) and other effective area-based conservation measures (OECMs). - Two immediate concerns are how much a 30% target might cost and whether it will cause economic losses to the agriculture, forestry and fisheries sectors. - Conservation areas also generate economic benefits (e.g. revenue from nature tourism and ecosystem services), making PAs/Nature an economic sector in their own right. - If some economic sectors benefit but others experience a loss, high-level policy makers need to know the net impact on the wider economy, as well as on individual sectors. [...]A. Waldron, K. Nakamura, J. Sze, T. Vilela, A. Escobedo, P. Negret Torres, R. Button, K. Swinnerton, A. Toledo, P. Madgwick, N. Mukherjee were supported by National Geographic and the Resources Legacy Fund. V. Christensen was supported by NSERC Discovery Grant RGPIN-2019-04901. M. Coll and J. Steenbeek were supported by EU Horizon 2020 research and innovation programme under grant agreement No 817578 (TRIATLAS). D. Leclere was supported by TradeHub UKRI CGRF project. R. Heneghan was supported by Spanish Ministry of Science, Innovation and Universities, Acciones de Programacion Conjunta Internacional (PCIN-2017-115). M. di Marco was supported by MIUR Rita Levi Montalcini programme. A. Fernandez-Llamazares was supported by Academy of Finland (grant nr. 311176). S. Fujimori and T. Hawegawa were supported by The Environment Research and Technology Development Fund (2-2002) of the Environmental Restoration and Conservation Agency of Japan and the Sumitomo Foundation. V. Heikinheimo was supported by Kone Foundation, Social Media for Conservation project. K. Scherrer was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682602. U. Rashid Sumaila acknowledges the OceanCanada Partnership, which funded by the Social Sciences and Humanities Research Council of Canada (SSHRC). T. Toivonen was supported by Osk. Huttunen Foundation & Clare Hall college, Cambridge. W. Wu was supported by The Environment Research and Technology Development Fund (2-2002) of the Environmental Restoration and Conservation Agency of Japan. Z. Yuchen was supported by a Ministry of Education of Singapore Research Scholarship Block (RSB) Research FellowshipPeer reviewe
Bostonia: The Boston University Alumni Magazine. Volume 15
Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs
Long-term thermal sensitivity of Earth’s tropical forests
The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (−9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth’s climate
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