bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient
Authors: Sorensen Jackson W. , Dunivin Taylor K. , Tobin Tammy C. , Shade Ashley 
Published: March 2018

SummarySmall bacterial and archaeal genomes provide insights into the minimal requirements for life1and seem to be widespread on the microbial phylogenetic tree2. We know that evolutionary processes, mainly selection and drift, can result in microbial genome reduction3,4. However, we do not know the precise environmental pressures that constrain genome size in free-living microorganisms. A study including isolates5has shown that bacteria with high optimum growth temperatures, including thermophiles, often have small genomes6. It is unclear how well this relationship may extend generally to microorganisms in nature7,8, and in particular to those microbes inhabiting complex and highly variable environments like soil3,6,9. To understand the genomic traits of thermally-adapted microorganisms, here we investigated bacterial and archaeal metagenomes from a 45°C gradient of temperate-to-thermal soils overlying the ongoing Centralia, Pennsylvania (USA) coal seam fire. There was a strong relationship between average genome size and temperature: hot soils had small genomes relative to ambient soils (Pearson’s r = −0.910, p < 0.001). There was also an inverse relationship between soil temperature and cell size (Pearson’s r = −0.65, p = 0.021), providing evidence that cell and genome size in the wild are together constrained by temperature. Notably, hot soils had different community structures than ambient soils, implicating ecological selection for thermo-tolerant cells that had small genomes, rather than contemporary genome streamlining within the local populations. Hot soils notably lacked genes for described two-component regulatory systems and antimicrobial production and resistance. Our work provides field evidence for the inverse relationship between microbial genome size and temperature requirements in a diverse, free-living community over a wide range of temperatures that support microbial life. Our findings demonstrate that ecological selection for thermophiles and thermo-tolerant microorganisms can result in smaller average genome sizesin situ, possibly because they have small genomes reminiscent of a more ancestral state.
Association of tamoxifen resistance and lipid reprogramming in breast cancer
Authors: Hultsch Susanne , Kankainen Matti , Paavolainen Lassi , Kovanen Ruusu-Maaria , Ikonen Elina , Kangaspeska Sara , Pietiäinen Vilja , Kallioniemi Olli 
Published: March 2018

AbstractBackgroundTamoxifen treatment of estrogen receptor (ER)-positive breast cancer reduces mortality by 31%. However, over half of advanced ER-positive breast cancers are intrinsically resistant to tamoxifen and about 40% will acquire the resistance during the treatment.MethodsIn order to explore mechanisms underlying endocrine therapy resistance in breast cancer and to identify new therapeutic opportunities, we created tamoxifen-resistant breast cancer cell lines that represent the luminal A or the luminal B. Gene expression patterns revealed by RNA-sequencing in seven tamoxifen-resistant variants were compared with their isogenic parental cells. We further examined those transcriptomic alterations in a publicly available patient cohort.ResultsWe show that tamoxifen resistance cannot simply be explained by altered expression of individual genes, common mechanism across all resistant variants, or the appearance of new fusion genes. Instead, the resistant cell lines shared altered gene expression patterns associated with cell cycle, protein modification and metabolism, especially with the cholesterol pathway. In the tamoxifen-resistant T-47D cell variants we observed a striking increase of neutral lipids in lipid droplets as well as an accumulation of free cholesterol in the lysosomes. Tamoxifen-resistant cells were also less prone to lysosomal membrane permeabilization (LMP) and not vulnerable to compounds targeting the lipid metabolism. However, the cells were sensitive to disulfiram, LCS-1, and dasatinib.ConclusionAltogether, our findings highlight a major role of LMP prevention in tamoxifen resistance, and suggest novel drug vulnerabilities associated with this phenotype.
On the regulatory evolution of new genes throughout their life history
Authors: Zhang Jia-yu , Zhou Qi 
Published: March 2018

AbstractEvery gene has a birthplace and an age, i.e., a cis-regulatory environment and an evolution lifespan since its origination, yet how gene’s evolution trajectory is shaped by the two remains unclear. Here we address this basic question by comparing phylogenetically dated new genes of different ages among Drosophila and vertebrate species. For both, we find a clear ‘out of testis’ transition from the testis-specific young genes to the broadly expressed old housekeeping genes. Particularly, many new genes have evolved specific activation at maternal-zygotic transition, or distinctive spatiotemporal embryonic expression patterns from the parental genes. We uncover an age-dependent gain/loss of active/repressive histone modifications and cis-regulatory elements, with variations between species and between somatic/germline tissues, which together underpin the stepwise acquisition of novel and important function by new genes. These results illuminate the general evolution trajectory and the underlying regulatory mechanisms of genes throughout their life history.
Escherichia coliLrp regulates one-third of the genome via direct, cooperative, and indirect routes
Authors: Kroner Grace M. , Wolfe Michael B. , Freddolino Peter L. 
Published: March 2018

AbstractThe global regulator Lrp plays a crucial role in regulating metabolism, virulence and motility in response to environmental conditions. Lrp has previously been shown to activate or repress approximately 10% of genes inEscherichia coli. However, the full spectrum of targets, and how Lrp acts to regulate them, has stymied earlier study. We have combined matched ChIP-seq and RNA sequencing under nine physiological conditions to map the binding and regulatory activity of Lrp as it directs responses to nutrient abundance. In addition to identifying hundreds of novel Lrp targets, we observe two new global trends: first, that Lrp will often bind to promoters in a poised position under conditions when it has no regulatory activity, and second, that nutrient levels induce a global shift in the equilibrium between non-specific and sequence-specific DNA binding. The overall regulatory behavior of Lrp, which as we now show regulates 35% ofE. coligenes directly or indirectly under at least one condition, thus arises from the interaction between changes in Lrp binding specificity and cooperative action with other regulators.
A comparison of single-cell trajectory inference methods: towards more accurate and robust tools
Authors: Saelens Wouter , Cannoodt Robrecht , Todorov Helena , Saeys Yvan 
Published: March 2018

AbstractUsing single-cell-omics data, it is now possible to computationally order cells along trajectories, allowing the unbiased study of cellular dynamic processes. Since 2014, more than 50 trajectory inference methods have been developed, each with its own set of methodological characteristics. As a result, choosing a method to infer trajectories is often challenging, since a comprehensive assessment of the performance and robustness of each method is still lacking. In order to facilitate the comparison of the results of these methods to each other and to a gold standard, we developed a global framework to benchmark trajectory inference tools. Using this framework, we compared the trajectories from a total of 29 trajectory inference methods, on a large collection of real and synthetic datasets. We evaluate methods using several metrics, including accuracy of the inferred ordering, correctness of the network topology, code quality and user friendliness. We found that some methods, including Slingshot, TSCAN and Monocle DDRTree, clearly outperform other methods, although their performance depended on the type of trajectory present in the data. Based on our benchmarking results, we therefore developed a set of guidelines for method users. However, our analysis also indicated that there is still a lot of room for improvement, especially for methods detecting complex trajectory topologies. Our evaluation pipeline can therefore be used to spearhead the development of new scalable and more accurate methods, and is available at github.com/dynverse/dynverse.To our knowledge, this is the first comprehensive assessment of trajectory inference methods. For now, we exclusively evaluated the methods on their default parameters, but plan to add a detailed parameter tuning procedure in the future. We gladly welcome any discussion and feedback on key decisions made as part of this study, including the metrics used in the benchmark, the quality control checklist, and the implementation of the method wrappers. These discussions can be held at github.com/dynverse/dynverse/issues.
Reconstructing imagined letters from early visual cortex reveals tight topographic correspondence between visual mental imagery and perception
Authors: Senden Mario , Emmerling Thomas , Hoof Rick van , Frost Martin , Goebel Rainer 
Published: March 2018

AbstractVisual mental imagery is the quasi-perceptual experience of “seeing in the mind’s eye”. While a tight correspondence between imagery and perception in terms of subjective experience is well established, their correspondence in terms of neural representations remains insufficiently understood. In the present study, we exploit the high spatial resolution of functional magnetic resonance imaging (fMRI) at 7T, the retinotopic organization of early visual cortex, and machine learning techniques to investigate whether visual imagery of letter shapes preserves the topographic organization of perceived shapes. Sub-millimeter resolution fMRI images were obtained from early visual cortex in six subjects performing visual imagery of four different letter shapes. Predictions of imagery voxel activation patterns based on a population receptive field encoding model and physical letter stimuli provided first evidence in favor of detailed topographic organization. Subsequent visual field reconstructions of imagery data based on the inversion of the encoding model further showed that visual imagery preserves the geometric profile of letter shapes. These results open new avenues for decoding as we show that a denoising autoencoder can be used to pretrain a classifier purely based on perceptual data before fine-tuning it on imagery data. Finally, we show that the autoencoder can project imagery-related voxel activations onto their perceptual counterpart allowing for visually recognizable reconstructions even at the single-trial level. The latter may eventually be utilized for the development of content-based BCI letter-speller systems.
Conversion of degraded agricultural landscapes to a smallholder agroforestry system and carbon sequestration in drylands
Authors: Chiemela Stella Nwawulu , Noulèkoun Florent , Chiemela Chinedum Jachinma , Zenebe Amanuel , Abadi Nigussie , Birhane Emiru 
Published: March 2018

Purpose
This paper aims at providing the evidence about how carbon sequestration in terrestrial ecosystems could contribute to the decrease of atmospheric CO2 rates through the adoption of appropriate cropping systems such as agroforestry.

Design/methodology/approach
Stratified randomly selected plots were used to collect data on tree diameter at breast height (DBH). Composite soil samples were collected from three soil depths for soil carbon analysis. Above ground biomass estimation was made using an allometric equation. The spectral signature of each plot was extracted to study the statistical relationship between carbon stock and selected vegetation indices.

Findings
There was a significant difference in vegetation and soil carbon stocks among the different land use/land cover types (P < 0.05). The potential carbon stock was highest in the vegetation found in sparsely cultivated land (13.13 ± 1.84 tons ha−1) and in soil in bushland (19.21 ± 3.79 tons ha−1). Carbon sequestration potential of the study area significantly increased (+127174.5 tons CO2e) as a result of conversion of intensively cultivated agricultural lands to agroforestry systems. The amount of sequestered carbon was found to be dependent on species diversity, tree density and tree size. The vegetation indices had a better correlation with soil and total carbon.

Originality/value
The paper has addressed an important aspect in curbing greenhouse gases in integrated land systems. The paper brings a new empirical insight of carbon sequestration potentials of agroforestry systems with a focus on drylands.
The resilient retail entrepreneur: dynamic capabilities for facing natural disasters
Authors: Martinelli Elisa , Tagliazucchi Giulia , Marchi Gianluca 
Published: March 2018

Purpose
The purpose of this paper is to investigate the formative dimensions of organizational resilience – namely dynamic capabilities (DCs) and social capital – displayed by retail entrepreneurs in the face of natural disasters (i.e. the 2012 Emilia earthquake). The paper evaluates social capital and the various types of DCs that support small entrepreneurs’ resilience during three temporal units of analysis: before the earthquake, during the emergency period, and during the recovery process.

Design/methodology/approach
The study was performed by applying a qualitative approach based on two focus groups and a double set of semi-structured interviews administered to a sample of eight small retail entrepreneurs hit by the 2012 Emilia earthquake. Content analysis was then applied.

Findings
The findings show that DCs and social capital are instrumental to enhancing organizational resilience; moreover the contribution of each category of DCs (reconfiguration, leveraging, sensing and interpreting, learning and knowledge integration) and social capital to entrepreneurs’ resilience changes according to the temporal phase of the natural disaster under analysis.

Research limitations/implications
This study will provide small retailer entrepreneurs and public authorities with useful insights on how DCs and social capital can practically support recovery paths at different times in the occurrence of a natural disaster.

Originality/value
This study contributes to the scientific debate on organizational resilience in disaster management, studying it through the lens of DCs and social capital, and analyzing the role of different types of DCs in developing entrepreneurs’ resilience during the various periods of a natural disaster. Moreover, it contributes by applying the concepts of resilience and DCs to a poorly investigated entrepreneurial context such as the retail one.
Prey adaptive behaviour under predation risk modify stoichiometry predictions of predator‐induced stress paradigms
Authors: Guariento Rafael Dettogni , Luttbeg Barney , Carneiro Luciana Silva , Caliman Adriano 
Published: March 2018

AbstractPrey responses to predation risk can affect multiple phenotypic traits that have significant implications for population‐to‐ecosystem‐level properties. The general stress paradigm (hereafterGSP) proposes integrating the principles of ecological stoichiometry and prey physiological plasticity in response to predation risk to provide an explicit mechanistic framework to evaluate the direct influence of predation risk on ecosystem functioning.However, theoretical attempts evaluating theGSPhave focused on only one component of phenotypic plasticity, neglecting the fact that multiple phenotypic responses can affect nutrient demand and consumption, and therefore, the overall animal effect on nutrient cycling rates and stoichiometry.In this study, we used a dynamic state variable model to examine how variation in predation and starvation risk on a landscape of patch types that vary in food quality affects the behavioural and physiological phenotypic responses of prey and the linked nutrient and carbon recycling.We found that the stress imposed by predation risk promotes prey carbon limitation, which leads to increased nutrient release and carbon uptake due to a stoichiometric mismatch between an animal's demand and food stoichiometry. Such effects can be altered by prey shifting spatially to carbon‐ or nutrient‐rich patches. However, the abilities of prey to cope with new physiological demands can be affected by absolute stress level or the predation risk distribution on a spatially implicit landscape of stoichiometric‐divergent patch type availability. Overall, starvation risk can act as a selective force favouring individuals that maximize their growth, thus reducing their nutrient release, but increasing their exposure to predation risk.Our results provide an important connection between predator‐induced stress ecology and ecosystem functioning, linking organism nutrition and ecological stoichiometry to fitness outcomes, thus improving our understanding of how non‐consumptive predator effects can scale up to ecosystems.Aplain language summaryis available for this article.
Response of bluebunch wheatgrass to invasion: Differences in competitive ability among invader‐experienced and invader‐naïve populations
Authors: Gibson Alexis , Nelson Cara R. , Atwater Daniel Z. 
Published: March 2018

Abstract

Invasive species may alter selective pressures on native plant populations. Although there is some evidence that competition with invasive plants may lead to differences in competitive ability between populations that have experienced invasion and those that have not, previous results have varied among species but also among populations of the same species.

We conducted a glasshouse experiment to determine whether there was variation in traits or in ability to tolerate or suppress an invasive species among populations of a common native grass that had different histories of exposure to competition from an invasive species. Specifically, we grew seeds of a native grass (Pseudoroegneria spicata) collected from 14 wild populations (six from invaded populations and eight from uninvaded populations) and a cultivar (Anatone) alone or in competition with the invasive aster (Centaurea stoebe) and measured traits of both species during and at the end of a 100‐day growing period.

Pseudoroegneria spicata seedlings from invader‐experienced populations had more leaves than invader‐naïve populations, and juvenile plants from experienced populations were less affected by competition with C. stoebe than were plants from naïve populations.

There were significant differences in traits among populations at the seedling and juvenile life stages, and at both life stages variation among populations was greater than variation among experience types.

The most predictive traits of P. spicata tolerance to competition were number of leaves (seedling and juvenile stage) and total and root biomass (juvenile only). No traits significantly predicted suppression of C. stoebe.

There was not a significant relationship between a population's suppression of C. stoebe and its tolerance of competition.

Our results suggest that, in P. spicata, invasion selects for larger plants and traits that can influence tolerance of competition. If land managers are interested in identifying highly competitive seed sources for revegetation in invaded areas, both population and invader experience type should be considered. As tolerance and suppression do not appear to be related in P. spicata, seed source selection should be driven by the element of competitive ability (either tolerance or suppression) that is most important to project goals.

A plain language summary is available for this article.
Observed Changes in Climate and Streamflow in the Upper Rio Grande Basin
Authors: Chavarria Shaleene B. , Gutzler David S. 
Published: March 2018

AbstractObserved streamflow and climate data are used to test the hypothesis that climate change is already affecting Rio Grande streamflow volume derived from snowmelt runoff in ways consistent with model‐based projections of 21st‐Century streamflow. Annual and monthly changes in streamflow volume and surface climate variables on the Upper Rio Grande, near its headwaters in southern Colorado, are assessed for water years 1958–2015. Results indicate winter and spring season temperatures in the basin have increased significantly, April 1 snow water equivalent (SWE) has decreased by approximately 25%, and streamflow has declined slightly in the April–July snowmelt runoff season. Small increases in precipitation have reduced the impact of declining snowpack on trends in streamflow. Changes in the snowpack–runoff relationship are noticeable in hydrographs of mean monthly streamflow, but are most apparent in the changing ratios of precipitation (rain + snow, and SWE) to streamflow and in the declining fraction of runoff attributable to snowpack or winter precipitation. The observed changes provide observational confirmation for model projections of decreasing runoff attributable to snowpack, and demonstrate the decreasing utility of snowpack for predicting subsequent streamflow on a seasonal basis in the Upper Rio Grande Basin.
NHR‐49/HNF4 integrates regulation of fatty acid metabolism with a protective transcriptional response to oxidative stress and fasting
Authors: Goh Grace Y. S. , Winter Johnathan J. , Bhanshali Forum , Doering Kelsie R. S. , Lai Regina , Lee Kayoung , Veal Elizabeth A. , Taubert Stefan 
Published: March 2018

SummaryEndogenous and exogenous stresses elicit transcriptional responses that limit damage and promote cell/organismal survival. Like its mammalian counterparts, hepatocyte nuclear factor 4 (HNF4) and peroxisome proliferator‐activated receptor α (PPARα), Caenorhabditis elegans NHR‐49 is a well‐established regulator of lipid metabolism. Here, we reveal that NHR‐49 is essential to activate a transcriptional response common to organic peroxide and fasting, which includes the pro‐longevity gene fmo‐2/flavin‐containing monooxygenase. These NHR‐49‐dependent, stress‐responsive genes are also upregulated in long‐lived glp‐1/notch receptor mutants, with two of them making critical contributions to the oxidative stress resistance of wild‐type and long‐lived glp‐1 mutants worms. Similar to its role in lipid metabolism, NHR‐49 requires the mediator subunit mdt‐15 to promote stress‐induced gene expression. However, NHR‐49 acts independently from the transcription factor hlh‐30/TFEB that also promotes fmo‐2 expression. We show that activation of the p38 MAPK, PMK‐1, which is important for adaptation to a variety of stresses, is also important for peroxide‐induced expression of a subset of NHR‐49‐dependent genes that includes fmo‐2. However, organic peroxide increases NHR‐49 protein levels, by a posttranscriptional mechanism that does not require PMK‐1 activation. Together, these findings establish a new role for the HNF4/PPARα‐related NHR‐49 as a stress‐activated regulator of cytoprotective gene expression.