bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accumulation and retention of radioactive elements in biofilm communities surrounding the accident site of the Fukushima Daiichi Nuclear Power Plant
Authors: Moriya Shigeharu , Otsu Hideaki , Kihara Kumiko , Kato Yukari , Itouga Misao , Sakata Kenji , Kikuchi Jun , Yamakawa Hiroshi , Suga Jiro 
Published: February 2017

AbstractAfter the Fukushima Daiichi Nuclear Power Plant accident, various surveys have been performed to measure the extent of radioactive contamination in marine sediments, surface waters, plankton, and fish. However, the radioactive contamination of one of the most important ecological niches, biofilms, has not been investigated. Therefore, in this study, we sampled biofilms from sea floor stones around Hisanohama Port, which is less than 30 km south of the accident site, and then analyzed the microbial community structure and element profiles, including those of radioactive elements, of these biofilms in order to determine the accumulation and retention of radioactive elements in them. Our results showed that the biofilm samples contained relatively high levels of radioactive cesium even when the sampling was performed 8–11 months after the accident. Our results also suggested that the structure of the biofilm organismal community is related to the element profile of radioactive cesium. Thus, our study suggests that biofilms are a possible radioactive compound accumulator in the natural environment and that they can retain radioactive material for at least 8–11 months.
Phenotype and gene ontology enrichment as guides for disease modeling inC. elegans
Authors: Angeles-Albores David , Lee Raymond YN , Chan Juancarlos , Sternberg Paul W 
Published: February 2017

AbstractGenome-wide experiments have the capacity to generate massive amounts of unbiased data about an organism. In order to interpret this data, dimensionality reduction techniques are required. One approach is to annotate genes using controlled languages and to test experimental datasets for term enrichment using probabilistic methods. Although gene, phenotype and anatomy ontologies exist forC. elegans, no unified software offers enrichment analyses of all the ontologies using the same methodology. Here, we present the WormBase Enrichment Suite, which offers users the ability to test all nematode ontologies simultaneously. We show that the WormBase Enrichment Suite provides valuable insight into different biological problems. Briefly, we show that phenotype enrichment analysis (PEA) can help researchers identify disease phenologs, phenotypes that are homologous across species, which can inform disease modeling inC. elegans. The WormBase Enrichment Suite analysis can also shed light on RNA-seq datasets by showing what molecular functions are enriched, which phenotypes these functions are implicated in and what tissues are overrepresented in the dataset. Finally, we explore the phenotype-anatomy relationship, showing that a small subset of highly specific tissues are disproportionately likely to cause an Egl phenotype, but inferring tissue expression from an Egl phenotype is limited to the largest tissues.
Resistance genes in global crop breeding networks
Authors: Garrett K. A. , Andersen K. F. , Asche F. , Bowden R. L. , Forbes G. A. , Kulakow P. A. , Zhou B. 
Published: February 2017

AbstractResistance genes are a major tool for managing crop diseases. The crop breeder networks that exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks. We evaluate the general structure of crop breeding networks for cassava, potato, rice, and wheat, which illustrate a range of public and private configurations. These systems must adapt to global change in climate and land use, the emergence of new diseases, and disruptive breeding technologies. Principles for maintaining system resilience can be applied to global resistance gene deployment. For example, both diversity and redundancy in the roles played by individual crop breeding groups (public versus private, global versus local) may support societal goals for crop production. Another principle is management of connectivity. Enhanced connectivity among crop breeders may benefit resistance gene deployment, but increase risks to the durability of resistance genes without effective policies regarding deployment.
Composite Likelihood Method for Inferring Local Pedigrees
Authors: Ko Amy , Nielsen Rasmus 
Published: February 2017

AbstractPedigrees contain information about the genealogical relationships among individuals and are of fundamental importance in many areas of genetic studies. However, pedigrees are often unknown and must be inferred from genetic data. Despite the importance of pedigree inference, existing methods are limited to inferring only close relationships or analyzing a small number of individuals or loci. We present a simulated annealing method for estimating pedigrees in large samples of otherwise seemingly unrelated individuals using genome-wide SNP data. The method supports complex pedigree structures such as polygamous families, multi-generational families, and pedigrees in which many of the member individuals are missing. Computational speed is greatly enhanced by the use of a composite likelihood function which approximates the full likelihood. We validate our method on simulated data and show that it can infer distant relatives more accurately than existing methods. Furthermore, we illustrate the utility of the method on a sample of Greenlandic Inuit.Author SummaryPedigrees contain information about the genealogical relationships among individuals. This information can be used in many areas of genetic studies such as disease association studies, conservation efforts, and learning about the demographic history and social structure of a population. Despite their importance, pedigrees are often unknown and must be estimated from genetic information. However, pedigree inference remains a difficult problem due to the high cost of likelihood computation and the enormous number of possible pedigrees we must consider. These difficulties limit existing methods in their ability to infer pedigrees when the sample size or the number of markers is large, or when the sample contains only distant relatives. In this report, we present a method that circumvents these computational barriers in order to infer pedigrees of complex structure for a large number of individuals. From our simulation studies, we found that our method can infer distant relatives much more accurately than existing methods. Our ability to infer pedigrees with a greater accuracy opens up possibilities for developing or improving pedigree-based methods in many areas research such as linkage analysis, demographic inference, association studies, and conservation.
A simple centrifugation protocol leads to a 55-fold mitochondrial DNA enrichment and paves the way for future mitogenomic research
Authors: Macher Jan Niklas , Zizka Vera , Weigand Alexander Martin , Leese Florian 
Published: February 2017

AbstractDNA (meta)barcoding is used to study biodiversity and is available for standardised assessments. However, it suffers from PCR bias, which can lead to the loss of specific taxa. PCR-free techniques such as shotgun metagenomics are therefore thought to be more suited for biodiversity assessments, but are currently limited by incomplete reference libraries.The technique of ‘mitogenome-skimming’ or ‘mitogenomics’, in which complete mitochondrial genomes are sequenced, is ideal to bridge the techniques of (meta)barcoding and metagenomics. However, without the enrichment of mitochondria, roughly 99 % of all sequencing reads are of non-mitochondrial origin and mostly useless for common applications, e.g. species identification.Here, we present a simple centrifugation protocol that leads to an average 140-fold enrichment of mitochondrial DNA. By sequencing six ‘mock’- communities – comprising the freshwater taxaCorbicula fluminea, Gammarus roeseliiandHydropsyche exocellataeach – we recovered whole mitochondrial genomes of these species and the acanthocephalan endoparasitePomphorhynchus laevis.The presented protocol will greatly speed up building reference libraries for whole mitochondrial genomes, as dozens of species could be sequenced on a single MiSeq run. Subsequently, it will also allow biodiversity assessments using mitogenomics at greatly reduced costs in comparison to mitogenomic approaches without prior enrichment for mitochondria.
Deconvolution of membrane currents for low-crosstalk high-resolution membrane capacitance measurements
Authors: Hot’ka Matej , Zahradník Ivan 
Published: February 2017

AbstractMany cellular activities involving cell membrane manifest through changes in membrane capacitance. The accuracy and precision of cell membrane capacitance measurement is limited by the measuring system, which distorts membrane current responses used for analysis of impedance parameters. We developed a practical deconvolution procedure for reconstruction of the time course of membrane current and applied it to current responses recorded at step voltage changes by the whole-cell patch-clamp technique. In contrast to the recorded current responses, the reconstructed current responses could be exactly described by adequate impedance models of the recorded circuit. Deconvolution of membrane currents improved the performance of the square-wave method of high-resolution membrane capacitance recording by providing higher accuracy in a wider range of cell sizes and by eliminating cross-talk errors in parameter estimates. This allowed resolving instabilities in the recording conditions arising from parasitic capacitance and seal resistance variation. Complex tests on hardware models, on simulated data sets, and on living cells confirmed reliability of the deconvolution method for membrane capacitance recording. The aptitude of the method was demonstrated in isolated cardiac myocytes by recording spontaneous vesicular events, by discerning formation of a fusion pore, and by revealing artefacts due to unstable seal resistance.
Engineered shell proteins confer improved encapsulated pathway behavior in a bacterial microcompartment
Authors: Slininger Lee Marilyn F. , Jakobson Christopher M. , Tullman-Ercek Danielle 
Published: February 2017

AbstractBacterial microcompartments are a class of proteinaceous organelles comprising a characteristic protein shell enclosing a set of enzymes. Compartmentalization can prevent escape of volatile or toxic intermediates, prevent off-pathway reactions, and create private cofactor pools. Encapsulation in synthetic microcompartment organelles will enhance the function of heterologous pathways, but to do so, it is critical to understand how to control diffusion in and out of the microcompartment organelle. To this end, we explored how small differences in the shell protein structure result in changes in the diffusion of metabolites through the shell. We found that the ethanolamine utilization (Eut) protein EutM properly incorporates into the 1,2-propanediol utilization (Pdu) microcompartment, altering native metabolite accumulation and the resulting growth on 1,2-propanediol as the sole carbon source. Further, we identified a single pore-lining residue mutation that confers the same phenotype as substitution of the full EutM protein, indicating that small molecule diffusion through the shell is the cause of growth enhancement. Finally, we show that the hydropathy index and charge of pore amino acids are important indicators to predict how pore mutations will affect growth on 1,2- propanediol, likely by controlling diffusion of one or more metabolites. This study highlights the success of two strategies to engineer microcompartment control over metabolite transport: altering the existing shell protein pore via mutation of the pore-lining residues, and generating chimeras using shell proteins with the desired pores.TOC Abstract Graphic
A whole-genome-based approach for estimation and characterization of individual inbreeding
Authors: Druet T. , Gautier M. 
Published: February 2017

AbstractInbreeding results from the mating of related individuals and has negative consequence because it brings together deleterious variants in one individual. Inbreeding is associated with recessive diseases and reduced production or fitness. In general, inbreeding is estimated with respect to a base population that needs to be defined. Ancestors in generations anterior to the base population are considered unrelated. We herein propose a model that estimates inbreeding relative to multiple age-based classes. Each inbreeding distribution is associated to a different time in the past: recent inbreeding generating longer homozygous stretches than more ancient. Our model is a mixture of exponential distribution implemented in a hidden Markov model framework that uses marker allele frequencies, genetic distances, genotyping error rates and the sequences of observed genotypes. Based on simulations studies, we show that the inbreeding coefficients and the age of inbreeding are correctly estimated. Mean absolute errors of estimators are low, the efficiency depending on the available information. When several inbreeding classes are simulated, the model captures them if their ages are sufficiently different. Genotyping errors or low-fold sequencing data are easily accommodated in the hidden Markov model framework. Application to real data sets illustrate that the method can reveal recent different demographic histories among populations, some of them presenting very recent bottlenecks or founder effects. The method also clearly identifies individuals resulting from extreme consanguineous matings.
Slow development as an evolutionary cost of long life
Authors: Lind Martin I. , Chen Hwei‐yen , Meurling Sara , Guevara Gil Ana Cristina , Carlsson Hanne , Zwoinska Martyna K. , Andersson Johan , Larva Tuuli , Maklakov Alexei A. 
Published: February 2017

Summary

Life‐history theory predicts a trade‐off between early‐life fitness and life span. While the focus traditionally has been on the fecundity‐life span trade‐off, there are strong reasons to expect trade‐offs with growth rate and/or development time.

We investigated the roles of growth rate and development time in the evolution of life span in two independent selection experiments in the outcrossing nematode Caenorhabditis remanei.

First, we found that selection under heat‐shock leads to the evolution of increased life span without fecundity costs, but at the cost of slower development.

Thereafter, the putative evolutionary links between development time, growth rate, fecundity, heat‐shock resistance and life span were independently assessed in the second experiment by directly selecting for fast or slow development. This experiment confirmed our initial findings, since selection for slow development resulted in the evolution of long life span and increased heat‐shock resistance.

Because there were no consistent trade‐offs with growth rate or fecundity, our results highlight the key role of development rate – differentiation of the somatic cells per unit of time – in the evolution of life span.

Since development time is under strong selection in nature, reduced somatic maintenance resulting in shorter life span may be a widespread cost of rapid development.

A lay summary is available for this article.
Selective plant foraging and the top‐down suppression of native diversity in a restored prairie
Authors: Schneider Stefan , Steeves Royce , Newmaster Steve , MacDougall Andrew S. 
Published: February 2017

SummaryClarifying what species are being consumed at what times can improve our understanding of how anthropogenic change affects food web dynamics, with implications for community assembly including restoration. This includes human‐based changes to plant communities via species introductions, which can interact with consumer feeding preferences to indirectly alter assembly outcomes including reduced restoration success if planted species are preferentially targeted.We used DNA barcoding of plant material in rodent scat, combined with field‐based feeding trials, rodent trapping, and rodent exclosures to test for dietary preferences and assembly impacts of native rodents on a restored and regionally rare tallgrass prairie of central North America. We examined whether native rodents preferred non‐targeted and mostly non‐native oldfield plants that are more locally abundant, thus protecting the rarer native planted species from consumption, or if rodents preferred native plants regardless of abundance.Our results supported the latter outcome. Barcoding revealed that native rodents consumed mostly non‐planted oldfield species for 10 months of the year (92% of the diet). The exceptions were August–September, when planted prairie species accounted for 87% of plants consumed and coincided with their peak seed production. Cafeteria trials suggested diet seasonality to be explained by food limitation – native prairie seeds were consumed year‐round when made available. Non‐targeted oldfield species thus appeared to be of sufficient quality to support rodent populations (peaking at 23 individuals ha−1in summer), but without rescuing rarer prairie species from targeted granivory and resulting in reduced prairie diversity outside of experimental exclosures.Synthesis and applications. Our work illustrates how anthropogenic‐based changes to producer communities may affect feeding pathways in grassland food webs, potentially facilitating establishment by non‐target species via indirect consumer effects that can be difficult to detect. These findings suggest that rodents may reduce the restoration success of tallgrass prairie in our region, with some planted species likely to suffer future recruitment difficulties due to granivory. Managers may need to consider multiple trophic levels with restoration, not just the commonly planted producer communities but also the consumers and predators associated with them.
Declines in low‐elevation subalpine tree populations outpace growth in high‐elevation populations with warming
Authors: Conlisk Erin , Castanha Cristina , Germino Matthew J. , Veblen Thomas T. , Smith Jeremy M. , Kueppers Lara M. 
Published: February 2017

Summary

Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long life spans, the importance of climate‐sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively.

Using spatially explicit, stochastic population models combined with data from long‐term forest surveys, we explored whether the climate‐sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two widely distributed, high‐elevation North American conifers.

Empirically observed, warming‐driven declines in recruitment led to rapid modelled population declines at the low‐elevation, ‘warm edge’ of subalpine forest and slow emergence of populations beyond the high‐elevation, ‘cool edge’. Because population declines in the forest occurred much faster than population emergence in the alpine, we observed range contraction for both species. For Engelmann spruce, this contraction was permanent over the modelled time horizon, even in the presence of increased moisture. For limber pine, lower sensitivity to warming may facilitate persistence at low elevations – especially in the presence of increased moisture – and rapid establishment above tree line, and, ultimately, expansion into the alpine.

Synthesis. Assuming 21st century warming and no additional moisture, population dynamics in high‐elevation forests led to transient range contractions for limber pine and potentially permanent range contractions for Engelmann spruce. Thus, limitations to seedling recruitment with warming can constrain the pace of subalpine tree range shifts.
Transmission and temporal dynamics of anther‐smut disease (Microbotryum) on alpine carnation (Dianthus pavonius)
Authors: Bruns Emily L. , Antonovics Janis , Carasso Valentina , Hood Michael 
Published: February 2017

Summary

Theory has shown that sterilizing diseases with frequency‐dependent transmission (characteristics shared by many sexually transmitted diseases) can drive host populations to extinction.

Anther‐smut disease (caused by Microbotryum sp.) has become a model plant pathogen system for studying the dynamics of vector‐ and sexually transmitted diseases: infected individuals are sterilized, producing spores instead of pollen, and the disease is spread between reproductive individuals by insect pollinators. We investigated anther‐smut disease in a heavily infected population of Dianthus pavonius (alpine carnation) over an 8‐year period to determine disease impacts on host population dynamics.

Over the 8 years, disease prevalence remained consistently high (>40%), while the host population numbers declined by over 50%.

The observed rate of vector transmission to reproductive, adult hosts was inadequate to explain the high disease prevalence. Additional density‐dependent aerial transmission to highly susceptible juveniles, indicated from experimental field and greenhouse studies, is likely to play a key role in maintaining the high disease prevalence.

Epidemiological models that accounted for the mixed transmission mode predicted an eventual decline in disease.

Synthesis. Our results demonstrate that high prevalence of a sterilizing disease does not necessarily drive host populations towards extinction and also highlights the importance of demographic studies for establishing the presence of alternative transmission modes.