340 research outputs found
Structural modeling and functional analysis of the essential ribosomal processing protease Prp from Staphylococcus aureus
In Firmicutes and related bacteria, ribosomal large subunit protein L27 is encoded with a conserved N-terminal extension that is removed to expose residues critical for ribosome function. Bacteria encoding L27 with this N-terminal extension also encode a sequence-specific cysteine protease, Prp, which carries out this cleavage. In this work, we demonstrate that L27 variants with an un-cleavable N-terminal extension, or lacking the extension (pre-cleaved), are unable to complement an L27 deletion in Staphylococcus aureus. This indicates that N-terminal processing of L27 is not only essential but possibly has a regulatory role. Prp represents a new clade of previously uncharacterized cysteine proteases, and the dependence of S. aureus on L27 cleavage by Prp validates the enzyme as a target for potential antibiotic development. To better understand the mechanism of Prp activity, we analyzed Prp enzyme kinetics and substrate preference using a fluorogenic peptide cleavage assay. Molecular modeling and site-directed mutagenesis implicate several residues around the active site in catalysis and substrate binding, and support a structural model in which rearrangement of a flexible loop upon binding of the correct peptide substrate is required for the active site to assume the proper conformation. These findings lay the foundation for the development of antimicrobials that target this novel, essential pathway
A mixed-model moving-average approach to geostatistical modeling in stream networks
Spatial autocorrelation is an intrinsic characteristic in freshwater stream environments where nested watersheds and flow connectivity may produce patterns that are not captured by Euclidean distance. Yet, many common autocovariance functions used in geostatistical models are statistically invalid when Euclidean distance is replaced with hydrologic distance. We use simple worked examples to illustrate a recently developed moving-average approach used to construct two types of valid autocovariance models that are based on hydrologic distances. These models were designed to represent the spatial configuration, longitudinal connectivity, discharge, and flow direction in a stream network. They also exhibit a different covariance structure than Euclidean models and represent a true difference in the way that spatial relationships are represented. Nevertheless, the multi-scale complexities of stream environments may not be fully captured using a model based on one covariance structure. We advocate using a variance component approach, which allows a mixture of autocovariance models (Euclidean and stream models) to be incorporated into a single geostatistical model. As an example, we fit and compare ‘‘mixed models,’’ based on multiple covariance structures, for a biological indicator. The mixed model proves to be a flexible approach because many sources of information can be incorporated into a single model
Correcting misclassification errors in crowdsourced ecological data: A Bayesian perspective
Many research domains use data elicited from "citizen scientists" when a
direct measure of a process is expensive or infeasible. However, participants
may report incorrect estimates or classifications due to their lack of skill.
We demonstrate how Bayesian hierarchical models can be used to learn about
latent variables of interest, while accounting for the participants' abilities.
The model is described in the context of an ecological application that
involves crowdsourced classifications of georeferenced coral-reef images from
the Great Barrier Reef, Australia. The latent variable of interest is the
proportion of coral cover, which is a common indicator of coral reef health.
The participants' abilities are expressed in terms of sensitivity and
specificity of a correctly classified set of points on the images. The model
also incorporates a spatial component, which allows prediction of the latent
variable in locations that have not been surveyed. We show that the model
outperforms traditional weighted-regression approaches used to account for
uncertainty in citizen science data. Our approach produces more accurate
regression coefficients and provides a better characterization of the latent
process of interest. This new method is implemented in the probabilistic
programming language Stan and can be applied to a wide number of problems that
rely on uncertain citizen science data.Comment: 18 figures, 5 table
Bayesian spatio-temporal models for stream networks
Spatio-temporal models are widely used in many research areas including
ecology. The recent proliferation of the use of in-situ sensors in streams and
rivers supports space-time water quality modelling and monitoring in near
real-time. In this paper, we introduce a new family of dynamic spatio-temporal
models, in which spatial dependence is established based on stream distance and
temporal autocorrelation is incorporated using vector autoregression
approaches. We propose several variations of these novel models using a
Bayesian framework. Our results show that our proposed models perform well
using spatio-temporal data collected from real stream networks, particularly in
terms of out-of-sample RMSPE. This is illustrated considering a case study of
water temperature data in the northwestern United States.Comment: 26 pages, 10 fig
Increasing trust in new data sources: crowdsourcing image classification for ecology
Crowdsourcing methods facilitate the production of scientific information by
non-experts. This form of citizen science (CS) is becoming a key source of
complementary data in many fields to inform data-driven decisions and study
challenging problems. However, concerns about the validity of these data often
constrain their utility. In this paper, we focus on the use of citizen science
data in addressing complex challenges in environmental conservation. We
consider this issue from three perspectives. First, we present a literature
scan of papers that have employed Bayesian models with citizen science in
ecology. Second, we compare several popular majority vote algorithms and
introduce a Bayesian item response model that estimates and accounts for
participants' abilities after adjusting for the difficulty of the images they
have classified. The model also enables participants to be clustered into
groups based on ability. Third, we apply the model in a case study involving
the classification of corals from underwater images from the Great Barrier
Reef, Australia. We show that the model achieved superior results in general
and, for difficult tasks, a weighted consensus method that uses only groups of
experts and experienced participants produced better performance measures.
Moreover, we found that participants learn as they have more classification
opportunities, which substantially increases their abilities over time.
Overall, the paper demonstrates the feasibility of CS for answering complex and
challenging ecological questions when these data are appropriately analysed.
This serves as motivation for future work to increase the efficacy and
trustworthiness of this emerging source of data.Comment: 25 pages, 10 figure
Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing bisphosphonates
Nitrogen-containing-bisphosphonates (N-BPs) are widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here we implemented a CRISPRi-mediated genome-wide screen and identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We observed that SLC37A3 forms a complex with ATRAID (all-trans retinoic acid-induced differentiation factor), a previously identified genetic target of N-BPs. SLC37A3 and ATRAID localize to lysosomes and are required for releasing N-BP molecules that have trafficked to lysosomes through fluid-phase endocytosis into the cytosol. Our results elucidate the route by which N-BPs are delivered to their molecular target, addressing a key aspect of the mechanism of action of N-BPs that may have significant clinical relevance
Using virtual reality and thermal imagery to improve statistical modelling of vulnerable and protected species.
Biodiversity loss and sparse observational data mean that critical conservation decisions may be based on little to no information. Emerging technologies, such as airborne thermal imaging and virtual reality, may facilitate species monitoring and improve predictions of species distribution. Here we combined these two technologies to predict the distribution of koalas, specialized arboreal foliovores facing population declines in many parts of eastern Australia. For a study area in southeast Australia, we complemented ground-survey records with presence and absence observations from thermal-imagery obtained using Remotely-Piloted Aircraft Systems. These field observations were further complemented with information elicited from koala experts, who were immersed in 360-degree images of the study area. The experts were asked to state the probability of habitat suitability and koala presence at the sites they viewed and to assign each probability a confidence rating. We fit logistic regression models to the ground survey data and the ground plus thermal-imagery survey data and a Beta regression model to the expert elicitation data. We then combined parameter estimates from the expert-elicitation model with those from each of the survey models to predict koala presence and absence in the study area. The model that combined the ground, thermal-imagery and expert-elicitation data substantially reduced the uncertainty around parameter estimates and increased the accuracy of classifications (koala presence vs absence), relative to the model based on ground-survey data alone. Our findings suggest that data elicited from experts using virtual reality technology can be combined with data from other emerging technologies, such as airborne thermal-imagery, using traditional statistical models, to increase the information available for species distribution modelling and the conservation of vulnerable and protected species
Acknowledging uncertainty in evolutionary reconstructions of ecological niches
Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods may infer the history of ecological niche evolution inaccurately because (a) species' niches are often poorly characterized; and (b) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species' environmental tolerances. Here, we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty introduced by incomplete niche characterization. Then, we modify existing ancestral state inference methods to leverage full estimates of environmental tolerances. We provide a worked empirical example of our method, investigating ecological niche evolution in the New World orioles (Aves: Passeriformes: Icterus spp.). Temperature and precipitation tolerances were generally broad and conserved among orioles, with niche reduction and specialization limited to a few terminal branches. Tools for performing these reconstructions are available in a new R package called nichevol
- …