bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome shuffling in a globalized bacterial plant pathogen: Recombination-mediated evolution inXanthomonas euvesicatoriaandX. perforans
Authors: Jibrin Mustafa O. , Potnis Neha , Timilsina Sujan , Minsavage Gerald V. , Vallad Gary E. , Roberts Pamela D. , Jones Jeffrey B. , Goss Erica M. 
Published: August 2017

ABSTRACTBacterial recombination and clonality underly the evolution and epidemiology of pathogenic lineages as well as their cosmopolitan spread. While the spread of stable clonal bacterial pathotypes drives disease epidemics, recombination leads to the evolution of new bacterial lineages. Recombinant lineages of plant bacterial pathogens are typically associated with colonization of novel hosts and emergence of new diseases. Here, we show that recombination between evolutionarily and phenotypically distinct plant pathogenic lineages has generated new recombinant lineages with unique combinations of pathogenicity and virulence factors.X. euvesicatoria(Xe) andX. perforans(Xp) are two closely related monophyletic species causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of strains representing populations on tomato in Nigeria and found shuffling of secretion systems and effectors such that these strains contain genes from bothXeandXp. Multiple strains, from populations in Nigeria, Italy, and Florida, USA, exhibited extensive genomewide homologous recombination and both species exhibited dynamic open pangenomes. Our results show that recombination is generating new lineages of bacterial spot pathogens on tomato with consequences for disease management strategies.ImportanceTheXanthomonaspathogens that cause bacterial spot of tomato and pepper have been model systems for plant-microbe interactions. Two of these pathogens,X. euvesicatoriaandX. perforans, are very closely related. Genome sequences of bacterial spot field strains from Nigeria, Italy, and the United States showed varying levels of homologous recombination that changed the amino sequence of effectors, secretion systems, and other proteins. This shuffling of genome content occurred betweenX. euvesicatoriaandX. perforans, while a Nigerian lineage also contained the lipopolysaccharide cluster of a distantly relatedXanthomonasspecies. Gene content varied among strains and the affected genes are important in the establishment of disease, therefore our findings point to global variation in the host-pathogen interaction driven by gene exchange among evolutionarily distinct lineages.
Inhibition of p53 improves CRISPR/Cas - mediated precision genome editing
Authors: Haapaniemi Emma , Botla Sandeep , Persson Jenna , Schmierer Bernhard , Taipale Jussi 
Published: August 2017

AbstractWe report here that genome editing by CRISPR/Cas9 induces a p53-mediated DNA damage response and cell cycle arrest. Transient inhibition of p53 prevents this response, and increases the rate of homologous recombination more than five-fold. This provides a way to improve precision genome editing of normal cells, but warrants caution in using CRISPR for human therapies until the mechanism of the activation of p53 is elucidated.
Induction of differentiation and metabolic reprogramming in human hepatoma cells by adult human serum
Authors: Steenbergen Rineke , Oti Martin , Horst Rob ter , Tat Wilson , Neufeldt Chris , Belovodskiy Alexandr , Chua Tiing Tiing , Cho Woo Jung , Joyce Michael , Dutilh Bas E. , Lorne Tyrrell D. 
Published: August 2017

AbstractTissue culture medium routinely contains fetal bovine serum (FBS). Here we show that culturing human hepatoma cells in their native, adult serum (human serum, HS) results in the restoration of key morphological and metabolic features of normal liver cells. When moved to HS, these cells show differential transcription of 22-32% of the genes, stop proliferating, and assume a hepatocyte-like morphology. Metabolic analysis shows that the Warburg-like metabolic profile, typical for FBS-cultured cells, is replaced by a diverse metabolic profile consistent within vivohepatocytes. We demonstrate the formation of large lipid and glycogen stores, increased glycogenesis, increased β-oxidation, increased ketogenesis, and decreased glycolysis. Finally, organ-specific functions are restored, including xenobiotics degradation and secretion of bile, very low density lipoprotein, and albumin. Thus, organ-specific functions are not necessarily lost in cell cultures, but might be merely suppressed in FBS. Together, we showed that cells that are representative of normal physiology can be produced from cancer cells simply by replacing FBS by HS in culture media. The effect of serum is often overseen in cell culture and we provide a detailed study in the changes that occur, provide insight in some of the serum components that may play a role in the establishment of the different phenotypes, and discuss how these finding might be beneficial to a variety of research fields.
The Geometry of Partial Fitness Orders and an Efficient Method for Detecting Genetic Interactions
Authors: Lienkaemper Caitlin , Lamberti Lisa , Drain James , Beerenwinkel Niko , Gavryushkin Alex 
Published: August 2017

AbstractWe present an efficient computational approach for detecting genetic interactions from fitness comparison data together with a geometric interpretation using polyhedral cones associated to partial orderings. Genetic interactions are defined by linear forms with integer coefficients in the fitness variables assigned to genotypes. These forms generalize several popular approaches to study interactions, including Fourier-Walsh coefficients, interaction coordinates, and circuits. We assume that fitness measurements come with high uncertainty or are even unavailable, as is the case for many empirical studies, and derive interactions only from comparisons of genotypes with respect to their fitness, i.e. from partial fitness orders. We present a characterization of the class of partial fitness orders that imply interactions, using a graph-theoretic approach. Our characterization then yields an efficient algorithm for testing the condition when certain genetic interactions, such as sign epistasis, are implied. This provides an exponential improvement of the best previously known method. We also present a geometric interpretation of our characterization, which provides the basis for statistical analysis of partial fitness orders and genetic interactions.
The lawful imprecision of human surface tilt estimation in natural scenes
Authors: Kim Seha , Burge Johannes 
Published: August 2017

AbstractEstimating local surface orientation (slant and tilt) is fundamental to recovering the three-dimensional structure of the environment, but it is unknown how well humans perform this task in natural scenes. Here, with a high-fidelity database of natural stereo-images with groundtruth surface orientation at each pixel, we find dramatic differences in human tilt estimation with natural and artificial stimuli. With artificial stimuli, estimates are precise and unbiased. With natural stimuli, estimates are imprecise and strongly biased. An image-computable normative model grounded in natural scene statistics predicts human bias, precision, and trial-by-trial errors without fitting parameters to the human data. These similarities suggest that the complex human performance patterns with natural stimuli are lawful, and that human visual systems have internalized local image and scene statistics to optimally infer the three-dimensional structure of the environment. The current results help generalize our understanding of human vision from the lab to the real world.
Nuclear transcriptomes at high resolution using retooled INTACT
Authors: Reynoso Mauricio A. , Pauluzzi Germain C. , Kajala Kaisa , Cabanlit Sean , Velasco Joel , Bazin Jérémie , Deal Roger , Sinha Neelima R. , Brady Siobhan M. , Bailey-Serres Julia 
Published: August 2017

AbstractIsolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation ofNuclei fromTAgged specificCellTypes (INTACT) to the monocot rice (Oryza sativaL.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear envelope-targeting domain of the Nuclear Tagging Fusion (NTF) protein with an outer nuclear envelope-anchored domain. This modified NTF was combined with codon optimizedE. coli BirAin a single T-DNA construct. We also developed inexpensive methods for INTACT, T-DNA insertion mapping and profiling of the complete nuclear transcriptome, including a rRNA degradation procedure that minimizes pre-rRNA transcripts. A high-resolution comparison of nuclear and steady-state poly (A)+transcript populations of seedling root tips confirmed the capture of pre-mRNA and exposed distinctions in diversity and abundance of the nuclear and total transcriptomes. This retooled INTACT can enable high-resolution monitoring of the nuclear transcriptome and chromatin in specific cell-types of rice and other species.Summary:Improved technology and methodology for affinity purification of nuclei and analysis of nuclear transcriptomes, chromatin and other nuclear components.
Preparation of H-Ras GTPase conjugated to lipid nanodiscs for NMR spectroscopy
Authors: Kovrigina Elizaveta A , Shah Sneha , Kovrigin Evgenii L 
Published: August 2017

ABSTRACTRas GTPase is a peripheral membrane protein central to cellular signaling of growth and proliferation. Membrane attachment is critical for a range of Ras activities, therefore, ability to make faithfulin-vitrosamples of a mem-brane-bound Ras for detailed biophysical studies is a highly desirable goal. In this manuscript, we are describing preparation of a large-scale sample of isotopically labeled H-Ras conjugated to lipid nanodiscs. We demonstrate that the Ras-nanodisc sample is fairly stable to allow for a range of Nuclear Magnetic Resonance (NMR) and other biophysical measurements. The need to achieve a homogeneous protein-nanodisc ratio is also emphasized.
Somatic maintenance impacts the evolution of mutation rate
Authors: Rozhok Andrii , DeGregori James 
Published: August 2017

AbstractThe evolution of multi-cellular animals has produced a conspicuous trend toward increased body size. This trend has introduced at least two novel problems: an elevated risk of somatic disorders, such as cancer, and declining evolvability due to reduced population size, lower reproduction rate and extended generation time. Low population size is widely recognized to explain the high mutation rates in animals by limiting the presumed universally negative selection acting on mutation rates. Here, we present evidence from stochastic modeling that the direction and strength of selection acting on mutation rates is highly dependent on the evolution of somatic maintenance, and thus longevity, which modulates the cost of somatic mutations. We argue that this mechanism may have been critical in facilitating animal evolution.
Redistributive policies in decentralised systems: The effect of decentralisation on subnational social spending
Authors: KLEIDER HANNA 
Published: August 2017

AbstractThis article uses cross‐national data to examine the effects of fiscal and political decentralisation on subnational governments’ social expenditures. It revisits the benefit competition hypothesis put forward by fiscal federalism research, which posits that subnational governments in decentralised countries match welfare benefit reductions by their peers to keep taxes low and avoid an in‐migration of welfare dependents. As a consequence, subnational social expenditures are assumed to plateau at similar and low levels. Using a new cross‐national dataset on social expenditures in 334 subnational units across 14 countries and 21 years, the author explores whether benefit competition causes subnational governments to converge on similar levels of social spending. The analysis reveals that as countries decentralise, subnational social spending levels begin to diverge rather than converge, with some subnational governments reducing their social expenditures and others increasing them. Furthermore, decentralisation is not likely to be associated with lowest common denominator social policies, but with more variability in social expenditure. The article also examines the effects of other macro‐level institutions and demonstrates that policy coordination influences the relationship between decentralisation and subnational social spending levels.
Insect–plant–pathogen interactions as shaped by future climate: effects on biology, distribution, and implications for agriculture
Authors: Trębicki Piotr , Dáder Beatriz , Vassiliadis Simone , Fereres Alberto 
Published: August 2017

AbstractCarbon dioxide (CO2) is the main anthropogenic gas which has drastically increased since the industrial revolution, and current concentrations are projected to double by the end of this century. As a consequence, elevated CO2 is expected to alter the earths’ climate, increase global temperatures and change weather patterns. This is likely to have both direct and indirect impacts on plants, insect pests, plant pathogens and their distribution, and is therefore problematic for the security of future food production. This review summarizes the latest findings and highlights current knowledge gaps regarding the influence of climate change on insect, plant and pathogen interactions with an emphasis on agriculture and food production. Direct effects of climate change, including increased CO2 concentration, temperature, patterns of rainfall and severe weather events that impact insects (namely vectors of plant pathogens) are discussed. Elevated CO2 and temperature, together with plant pathogen infection, can considerably change plant biochemistry and therefore plant defense responses. This can have substantial consequences on insect fecundity, feeding rates, survival, population size, and dispersal. Generally, changes in host plant quality due to elevated CO2 (e.g., carbon to nitrogen ratios in C3 plants) negatively affect insect pests. However, compensatory feeding, increased population size and distribution have also been reported for some agricultural insect pests. This underlines the importance of additional research on more targeted, individual insect–plant scenarios at specific locations to fully understand the impact of a changing climate on insect–plant–pathogen interactions.
High nymphal host density and mortality negatively impact parasitoid complex during an insect herbivore outbreak
Authors: Hall Aidan A. G. , Johnson Scott N. , Cook James M. , Riegler Markus 
Published: August 2017

AbstractInsect herbivore outbreaks frequently occur and this may be due to factors that restrict top‐down control by parasitoids, for example, host–parasitoid asynchrony, hyperparasitization, resource limitation and climate. Few studies have examined host–parasitoid density relationships during an insect herbivore outbreak in a natural ecosystem with diverse parasitoids. We studied parasitization patterns of Cardiaspina psyllids during an outbreak in a Eucalyptus woodland. First, we established the trophic roles of the parasitoids through a species‐specific multiplex PCR approach on mummies from which parasitoids emerged. Then, we assessed host–parasitoid density relationships across three spatial scales (leaf, tree and site) over one year. We detected four endoparasitoid species of the family Encyrtidae (Hymenoptera); two primary parasitoid and one heteronomous hyperparasitoid Psyllaephagus species (the latter with female development as a primary parasitoid and male development as a hyperparasitoid), and the hyperparasitoid Coccidoctonus psyllae. Parasitoid development was host–synchronized, although synchrony between sites appeared constrained during winter (due to temperature differences). Parasitization was predominantly driven by one primary parasitoid species and was mostly inversely host‐density dependent across the spatial scales. Hyperparasitization by C. psyllae was psyllid‐density dependent at the site scale, however, this only impacted the rarer primary parasitoid. High larval parasitoid mortality due to density‐dependent nymphal psyllid mortality (a consequence of resource limitation) compounded by a summer heat wave was incorporated in the assessment and resulted in density independence of host–parasitoid relationships. As such, high larval parasitoid mortality during insect herbivore outbreaks may contribute to the absence of host density‐dependent parasitization during outbreak events.
MiR‐155 inhibits proliferation and invasion by directly targeting PDCD4 in non‐small cell lung cancer
Authors: Liu Feng , Song Dalong , Wu Yanhu , Liu Xiang , Zhu Jinfu , Tang Yihu 
Published: August 2017

BackgroundMicroRNAs are often abnormally expressed in human non‐small cell lung cancer (NSCLC) and are thought to play a critical role in the emergence or maintenance of NSCLC by binding to its target messenger RNA. We assessed the effects of miR‐155 on cell proliferation and invasion to elucidate the role played by miR‐155/PDCD4 in NSCLC.MethodsQuantitative reverse transcription‐PCR, Western blotting, and cell counting kit‐8, luciferase, and transwell invasion assays were conducted on a normal human bronchial epithelial cell line (BEAS‐2B) and three NSCLC cell lines (SPC‐A‐1, A549, and H2170).ResultsWe confirmed that miR‐155 was upregulated, while PDCD4 messenger RNA and protein levels were downregulated in NSCLC cell lines. miR‐155 negatively regulated PDCD4 at both transcriptional and post‐transcriptional levels. Moreover, PDCD4 was forecast as an assumed target of miR‐155 using bioinformatic methods and we demonstrated that PDCD4 was a direct target of miR‐155 using luciferase reporter assays. Furthermore, PDCD4 overexpression could restrain NSCLC proliferation and invasion induced by miR‐155.ConclusionOur results collectively demonstrate that miR‐155 exerts an oncogenic role in NSCLC by directly targeting PDCD4.
Climate warming effects on grape and grapevine moth (Lobesia botrana) in thePalearcticregion
Authors: Gutierrez Andrew Paul , Ponti Luigi , Gilioli Gianni , Baumgärtner Johann 
Published: August 2017

AbstractThe grapevine mothLobesia botrana(Den. & Schiff.) (Lepidoptera: Tortricidae) is the principal native pest of grape in thePalearctic region. In the present study, we assessed prospectively the relative abundance of the moth inEurope and theMediterraneanBasin using linked physiologically‐based demographic models for grape andL. botrana. The model includes the effects of temperature, day‐length and fruit stage on moth development rates, survival and fecundity.Daily weather data for 1980–2010 were used to simulate the dynamics of grapevine andL. botranain 4506 lattice cells across the region. Average grape yield and pupae per vine were used as metrics of favourability. The results were mapped using thegrassGeographic Information System (http://grass.osgeo.org).The model predicts a wide distribution forL. botranawith highest populations in warmer regions in a wide band along latitude 40°N.The effects of climate warming on grapevine andL. botranawere explored using regional climate model projections based on theA1Bscenario of an average +1.8 °C warming during the period 2040–2050 compared with the base period (1960–1970). Under climate change, grape yields increase northwards and with a higher elevation but decrease in hotter areas. Similarly,L. botranalevels increase in northern areas but decrease in the hot areas where summer temperatures approach its upper thermal limit.
Keep Burning Coal or the Manatee Gets It: Rendering the Carbon Economy Invisible through Endangered Species Protection
Authors: Carr John , Milstein Tema 
Published: August 2017

AbstractAs ever expanding accretions of human industrial and residential development pave over endangered Florida manatees’ warm water springs winter habitat, more than half of the manatees have come to depend upon fossil fuel‐burning power plant hot water effluent channels for survival. In an effort to save these manatees, environmental activists have leveraged the US Endangered Species Act to protect the effluent streams and, by extension, have enshrined the power plants themselves as ecological saviors. This study interrogates the paradoxes within the resulting spatio‐legal regime. Recognizing the problematic human/nature binary at the heart of dominant Western practices, our study suggests spatial and legal regimes do not simply reify and reproduce this binary but also produce invisible ecocultural spaces that are essential to prop up an inherently unstable, illusory, and ultimately destructive definition of human existence.
Understanding Epigenetic Effects of Endocrine Disrupting Chemicals: From Mechanisms to Novel Test Methods
Authors: Alavian‐Ghavanini Ali , Rüegg Joëlle 
Published: August 2017

AbstractEndocrine‐disrupting chemicals (EDCs) are man‐made chemicals that interfere with hormonal signalling pathways. They are used in, for example, production of common household materials, in resin‐based medical supplies and in pesticides. Thus, they are environmentally ubiquitous and human beings and wildlife are exposed to them on a daily basis. Early‐life exposure to EDCs has been associated with later‐life adversities such as obesity, diabetes and cancer. Mechanisms underlying such associations are unknown but are likely to be mediated by epigenetic changes induced by EDCs. Epigenetics is the study of changes in gene function that are heritable but do not entail a change in DNA sequence. EDCs have been shown to affect epigenetic marks such as DNA methylation and histone modifications. The scope of this article was to review today's knowledge about mechanisms involved in EDC‐induced epigenetic changes and to discuss how this knowledge could be used for designing novel methods addressing epigenetic effects of EDCs.
Clinical and social characteristics associated with reduced visual acuity at presentation in Australian patients with neovascular age‐related macular degeneration: a prospective study from a long‐term observational data set. The Fight Retinal Blindness! Project
Authors: Nguyen Vuong , Daien Vincent , Guymer Robyn H , McAllister Ian L , Morlet Nigel , Barthelmes Daniel , Gillies Mark C 
Published: August 2017

AbstractImportanceIdentifying variables that influence presenting visual acuity (VA) in patients with neovascular age‐related macular degeneration (nAMD) is important because it is a strong predictor of long‐term outcomes.BackgroundTo assess the clinical and social characteristics associated with low presenting VA in nAMD patients.DesignThe present study is a cross‐sectional analysis from a prospective, observational database.ParticipantsWe identified 3242 treatment‐naïve patients from 54 Australian practices in the Fight Retinal Blindness! registry.MethodsAge, gender, ethnicity and VA were recorded at the baseline visit. Socio‐economic status was determined using the Australian Bureau of Statistics socio‐economic indexes for areas.Main Outcome MeasuresAssociation between clinical and socio‐economic characteristics with presenting VA was identified.ResultsPoor VA (≤35 letters) in the presenting eye was associated with older age (adjusted odds ratio [AOR]: 1.33 for patients aged ≥80 years vs. <80 years [95% confidence interval, CI: 1.04, 1.71]), treatment at a public practice (AOR: 1.91 for public vs. private practices [95% CI: 1.46, 2.50]) and intermediate (36–69 letters) VA in the fellow eye (AOR: 0.67 [95% CI: 0.47, 0.95] and 0.64 [95% CI: 0.48, 0.85] for poor [≤35 letters] and good [≥70 letters] VA vs. intermediate VA in the fellow eye). Gender, ethnicity and socio‐economic status were not independently associated with VA at presentation.Conclusions and RelevancePoor presenting vision is detrimental to the long‐term outcomes of nAMD. Poor presentation of nAMD in Australia may not be related to socio‐economic circumstances, but due to systems of care. Further research is warranted to determine why patients at public practices present with worse vision compared with private practices in Australia.