Million-year lag times in a post-orogenic sediment conveyor.
Ontology highlight
ABSTRACT:
SUBMITTER: Fulop RH
PROVIDER: S-EPMC7304991 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Publications
Million-year lag times in a post-orogenic sediment conveyor.
Fülöp R-H RH Codilean A T AT Wilcken K M KM Cohen T J TJ Fink D D Smith A M AM Yang B B Levchenko V A VA Wacker L L Marx S K SK Stromsoe N N Fujioka T T Dunai T J TJ
Science advances 20200619 25
Understanding how sediment transport and storage will delay, attenuate, and even erase the erosional signal of tectonic and climatic forcings has bearing on our ability to read and interpret the geologic record effectively. Here, we estimate sediment transit times in Australia's largest river system, the Murray-Darling basin, by measuring downstream changes in cosmogenic <sup>26</sup>Al/<sup>10</sup>Be/<sup>14</sup>C ratios in modern river sediment. Results show that the sediments have experienc ...[more]
Similar Datasets
Project description:Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years. IMPORTANCE The nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor are unknown. Subseafloor populations have ultralow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits. Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting that the genome evolution of these bacteria has been dominated by genetic drift. Thus, reduced recombination, stemming from long-term physical isolation, resulted in small clonal populations of Thalassospira that have accumulated mutations in their genomes over millions of years.
| S-EPMC8406185 | biostudies-literature
Project description:Protein aggregation is linked to more than 30 human pathologies, including Alzheimer's and Parkinson's diseases. Since small oligomers that form at the beginning of the fibrillation process probably are the most toxic elements, therapeutic strategies involving fibril fragmentation could be detrimental. An alternative approach, named kinetic inhibition, aims to prevent fibril formation by using small ligands that stabilize the parent protein. The factors that govern fibrillation lag times during kinetic inhibition are largely unknown, notwithstanding their importance for designing effective long-term therapies. Inhibitor-bound species are not likely to be incorporated into the core of mature fibrils, although their presence could alter the kinetics of the fibrillation process. For instance, inhibitor-bound species may act as capping elements that impair the nucleation process and/or fibril growth. Here, we address this issue by studying the effect of two natural inhibitors on the fibrillation behavior of lysozyme at neutral pH. We analyzed a set of 79 fibrillation curves obtained in lysozyme alone and a set of 37 obtained in the presence of inhibitors. We calculated the concentrations of the relevant species at the beginning of the curves using the inhibitor-binding constants measured under the same experimental conditions. We found that inhibitor-bound protein species do not affect fibrillation onset times, which are mainly determined by the concentration of unbound protein species present in equilibrium. In this system, knowledge of the fibrillation kinetics and inhibitor affinities suffices to predict the effect of kinetic inhibitors on fibrillation lag times. In addition, we developed a new methodology to better estimate fibrillation lag times from experimental curves.
| S-EPMC4129507 | biostudies-literature
Project description:Internal feedback of nutrients may impede timely improvement in lake water quality. We describe a parsimonious, mechanistic framework for modeling lag times to recovery of phosphorus-enriched lakes, given decreases in external loading. The approach assumes first-order kinetics in a two-compartment system taking account of phosphorus storage in and loading from benthic sediments. Bayesian parameter modeling, published sediment phosphorus release rates, and a prior dynamic calibration for one lake are used to derive estimates of key parameters. Applications are developed for an example lake, as are maps displaying estimated times to attainment of a phosphorus criterion in lakes across a midwestern state, and lag time estimates for fractional water column concentration decrease averaged over HUC-8s. Mean lag times to 50 and 75% declines in water column phosphorus concentration were estimated as 13.1 and 39.0 years respectively, across more than 70,000 lentic water bodies in the continental United States.
| S-EPMC10116841 | biostudies-literature
Project description:ObjectiveWe assessed the extent of lag times in the publication and indexing of network meta-analyses (NMAs).Study designThis was a survey of published NMAs on drug interventions.SettingNMAs indexed in PubMed (searches updated in May 2020).Primary and secondary outcome measuresLag times were measured as the time between the last systematic search and the article submission, acceptance, online publication, indexing and Medical Subject Headings (MeSH) allocation dates. Time-to-event analyses were performed considering independent variables (geographical origin, Journal Impact Factor, Scopus CiteScore, open access status) (SPSS V.24, R/RStudio).ResultsWe included 1245 NMAs. The median time from last search to article submission was 6.8 months (204 days (IQR 95-381)), and to publication was 11.6 months. Only 5% of authors updated their search after first submission. There is a very slightly decreasing historical trend of acceptance (rho=-0.087; p=0.010), online publication (rho=-0.080; p=0.008) and indexing (rho=-0.080; p=0.007) lag times. Journal Impact Factor influenced the MeSH allocation process, but not the other lag times. The comparison between open access versus subscription journals confirmed meaningless differences in acceptance, online publication and indexing lag times.ConclusionEfforts by authors to update their search before submission are needed to reduce evidence production time. Peer reviewers and editors should ensure authors' compliance with NMA standards. The accuracy of these findings depends on the accuracy of the metadata used; as we evaluated only NMA on drug interventions, results may not be generalisable to all types of studies.
| S-EPMC8422315 | biostudies-literature
Project description:Recent studies have revealed new insights into the endocytosis of vaccinia virus (VACV). However, the mechanism of fusion between viral and cellular membranes remains unknown. We developed a microfluidic device with a cell-trap array for immobilization of individual cells, with which we analyzed the acid-dependent fusion of single virions. VACV particles incorporating enhanced green fluorescent protein (EGFP) and labeled with self-quenching concentrations of R18 membrane dye were used in combination with total internal reflection fluorescence microscopy to measure the kinetics of R18 dequenching and thus single hemifusion events initiated by a fast low-pH trigger. These studies revealed unexpectedly long lag phases between pH change and hemifusion. In addition, we found that EGFP fluorescence in the virus was quenched upon acidification, indicating that protons could access the virus core, possibly through a proton channel. In a fraction of virus particles, EGFP fluorescence was recovered, presumably after fusion-pore formation and exposure of the core to the physiological pH of the host-cell cytosol. Given that virus-encoded cation channels play a crucial role in the life cycle of many viruses and can serve as antiviral drug targets, further investigations into a potential VACV viroporin are justified. Our findings indicate that the microfluidic device described may be highly beneficial to similar studies requiring fast kinetic measurements.
| S-EPMC3714929 | biostudies-literature
Project description:We lack a comprehensive understanding of evolutionary pattern and process because short-term and long-term data have rarely been combined into a single analytical framework. Here we test alternative models of phenotypic evolution using a dataset of unprecedented size and temporal span (over 8,000 data points). The data are body-size measurements taken from historical studies, the fossil record, and among-species comparative data representing mammals, squamates, and birds. By analyzing this large dataset, we identify stochastic models that can explain evolutionary patterns on both short and long timescales and reveal a remarkably consistent pattern in the timing of divergence across taxonomic groups. Even though rapid, short-term evolution often occurs in intervals shorter than 1 Myr, the changes are constrained and do not accumulate over time. Over longer intervals (1-360 Myr), this pattern of bounded evolution yields to a pattern of increasing divergence with time. The best-fitting model to explain this pattern is a model that combines rare but substantial bursts of phenotypic change with bounded fluctuations on shorter timescales. We suggest that these rare bursts reflect permanent changes in adaptive zones, whereas the short-term fluctuations represent local variations in niche optima due to restricted environmental variation within a stable adaptive zone.
| S-EPMC3179053 | biostudies-literature
Project description:The assembly of regional biotas and organismal responses to anthropogenic climate change both depend on the capacity of organisms to adapt to novel ecological conditions. Here we demonstrate the concept of evolutionary lag time, the time between when a climatic regime or habitat develops in a region and when it is colonized by a given clade. We analyzed the time of colonization of four clades (three plant genera and one lizard genus) into the Atacama-Sechura Desert of South America, one of Earth's driest and oldest deserts. We reconstructed time-calibrated phylogenies for each clade and analyzed the timing of shifts in climatic distributions and biogeography and compared these estimates to independent geological estimates of the time of origin of these deserts. Chaetanthera and Malesherbia (plants) and Liolaemus (animal) invaded arid regions of the Atacama-Sechura Desert in the last 10 million years, some 20 million years after the initial onset of aridity in the region. There are also major lag times between when these clades colonized the region and when they invaded arid habitats within the region (typically 4-14 million years). Similarly, hyperarid climates developed ∼8 million years ago, but the most diverse plant clade in these habitats (Nolana) only colonized them ∼2 million years ago. Similar evolutionary lag times may occur in other organisms and habitats, but these results are important in suggesting that many lineages may require very long time scales to adapt to modern desertification and climatic change.
| S-EPMC3710863 | biostudies-literature
Project description:Sparse microbial populations persist from seafloor to basement in the slowly accumulating oxic sediment of the oligotrophic South Pacific Gyre (SPG). The physiological status of these communities, including their substrate metabolism, is previously unconstrained. Here we show that diverse aerobic members of communities in SPG sediments (4.3‒101.5 Ma) are capable of readily incorporating carbon and nitrogen substrates and dividing. Most of the 6986 individual cells analyzed with nanometer-scale secondary ion mass spectrometry (NanoSIMS) actively incorporated isotope-labeled substrates. Many cells responded rapidly to incubation conditions, increasing total numbers by 4 orders of magnitude and taking up labeled carbon and nitrogen within 68 days after incubation. The response was generally faster (on average, 3.09 times) for nitrogen incorporation than for carbon incorporation. In contrast, anaerobic microbes were only minimally revived from this oxic sediment. Our results suggest that microbial communities widely distributed in organic-poor abyssal sediment consist mainly of aerobes that retain their metabolic potential under extremely low-energy conditions for up to 101.5 Ma.
| S-EPMC7387439 | biostudies-literature
Project description:Understanding the lag time between land management and impacts on riverine nitrate-nitrogen (N) loads is critical to understand when action to mitigate nitrate-N leaching losses from the soil profile may start improving water quality. These lags occur due to leaching of nitrate-N through the subsurface (soil and groundwater). Actions to mitigate nitrate-N losses have been mandated in New Zealand policy to start showing improvements in water quality within five years. We estimated annual rates of nitrate-N leaching and annual nitrate-N loads for 77 river catchments from 1990 to 2018. Lag times between these losses and riverine loads were determined for 34 catchments but could not be determined in other catchments because they exhibited little change in nitrate-N leaching losses or loads. Lag times varied from 1 to 12 years according to factors like catchment size (Strahler stream order and altitude) and slope. For eight catchments where additional isotope and modelling data were available, the mean transit time for surface water at baseflow to pass through the catchment was on average 2.1 years less than, and never greater than, the mean lag time for nitrate-N, inferring our lag time estimates were robust. The median lag time for nitrate-N across the 34 catchments was 4.5 years, meaning that nearly half of these catchments wouldn't exhibit decreases in nitrate-N because of practice change within the five years outlined in policy.
| S-EPMC8360963 | biostudies-literature
Project description:The current study examines the effect of tannins and tannin extracts on the lag phase duration, growth rate, and generation time of Escherichia coli. Effects of castalagin, vescalagin, gallic acid, Colistizer, tannic acid as well as chestnut, mimosa, and quebracho extracts were determined on E. coli's growth phases using the broth microdilution method and obtained by turbidimetric measurements. E. coli responds to the stress caused by the investigated antimicrobial agents with reduced growth rates, longer generation times, and extended lag phases. Prolongation of the lag phase was relatively small at low tannin concentrations, while it became more pronounced at concentrations above half the MIC. Moreover, for the first time, it was observed that lag time extensions follow a strict exponential relationship with increasing tannin concentrations. This feature is very likely a direct consequence of the tannin complexation of certain essential ions from the growth medium, making them unavailable to E. coli for its growth.
| S-EPMC7760653 | biostudies-literature