bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cascade of destabilizations: combiningWolbachiaand Allee effects to eradicate insect pests
Authors: Blackwood Julie C. , Vargas Roger , Fauvergue Xavier 
Published: July 2016

SummaryThe management of insect pests has long been dominated by the use of chemical insecticides, with the aim of instantaneously killing enough individuals to limit their damage. To minimize unwanted consequences, environmentally-friendly approaches have been proposed that utilize biological control and take advantage of intrinsic demographic processes to reduce pest populations.We address the feasibility of a novel pest management strategy based on the release of insects infected withWolbachia, which causes cytoplasmic incompatibilities in its host population, into a population with a pre-existing Allee effect. We hypothesize that the transient decline in population size caused by a successful invasion ofWolbachiacan bring the population below its Allee threshold and, consequently, trigger extinction.We develop a stochastic population model that accounts forWolbachia-induced cytoplasmic incompatibilities in addition to an Allee effect arising from mating failures at low population densities. Using our model, we identify conditions under which cytoplasmic incompatibilities and Allee effects successfully interact to drive insect pest populations toward extinction. Based on our results, we delineate control strategies based on introductions ofWolbachia-infected insects.We extend this analysis to evaluate control strategies that implement successive introductions of two incompatibleWolbachiastrains. Additionally, we consider methods that combineWolbachiainvasion with mating disruption tactics to enhance the pre-existing Allee effect.We demonstrate that Wolbachia-induced cytoplasmic incompatibility and the Allee effect act independently from one another: the Allee effect does not modify theWolbachia-invasion threshold, and cytoplasmic incompatibilities only have a marginal effect on the Allee threshold. However, the interaction of these two processes can drive even large populations to extinction. The success of this method can be amplified by the introduction of multipleWolbachiacytotypes as well as the addition of mating disruption.Our study extends the existing literature by proposing the use ofWolbachiaintroductions to capitalize on pre-existing Allee effects and consequently eradicate insect pests. More generally, it highlights the importance of transient dynamics, and the relevance of manipulating a cascade of destabilizatons for pest management.
On phylogenetic branch lengths distribution and the late acquistion of mitochondria
Authors: Pittis Alexandros A. , Gabaldón Toni 
Published: July 2016

AbstractIn a recent article, Martin et. al. [1] criticize several methodological aspects of our recent study on the timing of the acquisition of mitochondria [2]. Here we show that our results are independent of the model-based partitioning of the data. In addition, we assess the robustness of our inferences by analyzing data from Martin et. al.
Quantitative, image-based phenotyping methods provide insight into spatial and temporal dimensions of plant disease
Authors: Mutka Andrew M. , Fentress Sarah J. , Sher Joel W. , Berry Jeffrey C. , Pretz Chelsea , Nusinow Dmitri A. , Bart Rebecca 
Published: July 2016

AbstractPlant disease symptoms exhibit complex spatial and temporal patterns that are challenging to quantify. Image-based phenotyping approaches enable multi-dimensional characterization of host-microbe interactions and are well suited to capture spatial and temporal data that are key to understanding disease progression. We applied image-based methods to investigate cassava bacterial blight, which is caused by the pathogenXanthomonas axonopodispv.manihotis(Xam). We generatedXamstrains in which individual predicted type III effector (T3E) genes were mutated and applied multiple imaging approaches to investigate the role of these proteins in bacterial virulence. Specifically, we quantified bacterial populations, water-soaking disease symptoms, and pathogen spread from the site of inoculation over time for strains with mutations inavrBs2,xopX, andxopKas compared to wild-typeXam. ΔavrBs2and ΔxopXboth showed reduced growth in planta and delayed spread through the vasculature system of cassava. ΔavrBs2exhibited reduced water-soaking symptoms at the site of inoculation. In contrast, ΔxopKexhibited enhanced induction of disease symptoms at the site of inoculation but reduced spread through the vasculature. Our results highlight the importance of adopting a multi-pronged approach to plant disease phenotyping to more fully understand the roles of T3Es in virulence. Finally, we demonstrate that the approaches used in this study can be extended to many host-microbe systems and increase the dimensions of phenotype that can be explored.Summary:Novel, image-based phenotyping methods enhance characterization of plant-pathogen interactions.
Massively multiplex single-cell Hi-C
Authors: Ramani Vijay , Deng Xinxian , Gunderson Kevin L , Steemers Frank J , Disteche Christine M , Noble William S , Duan Zhijun , Shendure Jay 
Published: July 2016

AbstractWe present combinatorial single cell Hi-C, a novel method that leverages combinatorial cellular indexing to measure chromosome conformation in large numbers of single cells. In this proof-of-concept, we generate and sequence combinatorial single cell Hi-C libraries for two mouse and four human cell types, comprising a total of 9,316 single cells across 5 experiments. We demonstrate the utility of single-cell Hi-C data in separating different cell types, identify previously uncharacterized cell-to-cell heterogeneity in the conformational properties of mammalian chromosomes, and demonstrate that combinatorial indexing is a generalizable molecular strategy for single-cell genomics.
High Phylogenetic Utility of an Ultraconserved Element Probe Set Designed for Arachnida
Authors: Starrett James , Derkarabetian Shahan , Hedin Marshal , Bryson Robert W. , McCormack John E. , Faircloth Brant C. 
Published: July 2016

AbstractArachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite this applied importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have confounded these attempts. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved genomic regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, even down to the level of species differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods.
A Rationally Designed Aminoacyl-tRNA Synthetase for Genetically Encoded Fluorescent Amino Acids
Authors: Steinberg Ximena , Galpin Jason , Nasir Gibran , Sepulveda-Ugarte Jose , Sepúlveda Romina V. , Gonzalez-Nilo Fernando , Islas Leon D. , Ahern Christopher A. , Brauchi Sebastian 
Published: July 2016

AbstractThe incorporation of non-canonical amino acids into proteins has emerged as a promising strategy to manipulate and study protein structure-function relationships with superior precisionin vitroandin vivo. To date, fluorescent non-canonical amino acids (f-ncAA) have been successfully incorporated in proteins expressed in bacterial systems,Xenopusoocytes, and HEK-293T cells. Here, we describe the rational generation of an orthogonal aminoacyltRNA synthetase based on theE. colityrosine synthetase that is capable of encoding the f-ncAA tyr-coumarin in HEK-293T cells.
Neuroendocrine Modulation Sustains theC. elegansForward Motor State
Authors: Lim Maria A. , Chitturi Jyothsna , Laskova Valeriya , Meng Jun , Findeis Daniel , Wiekenberg Anne , Mulcahy Ben , Luo Linjiao , Li Yan , Lu Yangning , Hung Wesley , Qu Yixin , Ho Chi-Yip , Holmyard Douglas , Ji Ni , McWhirter Rebecca , Samuel Aravinthan D. T. , Miller David M. , Schnabel Ralf , Calarco John A. , Zhen Mei 
Published: July 2016

AbstractNeuromodulators shape neural circuit dynamics. Combining electron microscopy, genetics, transcriptome profiling, calcium imaging, and optogenetics, we discovered a peptidergic neuron that modulatesC. elegansmotor circuit dynamics. The Six/SO-family homeobox transcription factor UNC-39 governs lineage-specific neurogenesis to give rise to a neuron RID. RID bears the anatomic hallmarks of a specialized endocrine neuron: it harbors near-exclusive dense core vesicles that cluster periodically along the axon, and expresses multiple neuropeptides, including the FMRF-amide-related FLP-14. RID activity increases during forward movement. Ablating RID reduces the sustainability of forward movement, a phenotype partially recapitulated by removing FLP-14. Optogenetic depolarization of RID prolongs forward movement, an effect reduced in the absence of FLP-14. Together, these results establish the role of a neuroendocrine cell RID in sustaining a specific behavioral state inC. elegans.
Probabilistic adaptation in changing microbial environments
Authors: Katz Yarden , Springer Michael 
Published: July 2016

AbstractMicrobes growing in animal host environments face fluctuations that have elements of both randomness and predictability. In the mammalian gut, fluctuations in nutrient levels and other physiological parameters are structured by the animal host’s behavior, diet, health and microbiota composition. Microbial cells that are able to anticipate these fluctuations by exploiting this structure would likely gain a fitness advantage, by adapting their internal state in advance. We propose that the problem of adaptive growth in these structured changing environments can be viewed as probabilistic inference. We analyze environments that are “meta-changing”: where there are changes in the way the environment fluctuates, governed by a mechanism unobservable to cells. We develop a dynamic Bayesian model of these environments and show that a real-time inference algorithm (particle filtering) for this model can be used as a microbial growth strategy implementable in molecular circuits. The growth strategy suggested by our model outperforms heuristic strategies, and points to a class of algorithms that could support real-time probabilistic inference in natural or synthetic cellular circuits.
The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core
Authors: Deco Gustavo , Kringelbach Morten L. , Jirsa Viktor K. , Ritter Petra 
Published: July 2016

AbstractIn the human brain, spontaneous activity during resting state consists of rapid transitions between functional network states over time but the underlying mechanisms are not understood. We use connectome based computational brain network modeling to reveal fundamental principles of how the human brain generates large-scale activity observable by noninvasive neuroimaging. By including individual structural and functional neuroimaging data into brain network models we construct personalized brain models. With this novel approach, we reveal that the human brain during resting state operates at maximum metastability, i.e. in a state of maximum network switching. In addition, we investigate cortical heterogeneity across areas. Optimization of the spectral characteristics of each local brain region revealed the dynamical cortical core of the human brain, which is driving the activity of the rest of the whole brain. Personalized brain network modelling goes beyond correlational neuroimaging analysis and reveals non-trivial network mechanisms underlying non-invasive observations. Our novel findings significantly pertain to the important role of computational connectomics in understanding principles of brain function.
Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks
Authors: Didelot Xavier , Fraser Christophe , Gardy Jennifer , Colijn Caroline 
Published: July 2016

AbstractGenomic data is increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom - a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by colouring the branches of a phylogeny according to which host those branches were in. Here we extend this approach and show that it can be applied to partially sampled and ongoing outbreaks. This requires computing the correct probability of an observed transmission tree and we herein demonstrate how to do this for a large class of epidemiological models. We also demonstrate how the branch colouring approach can incorporate a variable number of unique colours to represent unsampled intermediates in transmission chains. The resulting algorithm is a reversible jump Monte-Carlo Markov Chain, which we apply to both simulated data and real data from an outbreak of tuberculosis. By accounting for unsampled cases and an outbreak which may not have reached its end, our method is uniquely suited to use in a public health environment during real-time outbreak investigations. We implemented our technique in an R package called TransPhylo, which is freely available fromhttps://github.com/xavierdidelot/TransPhylo.
Morphological structure of ant assemblages in tropical and temperate forests
Authors: Silva Rogério R. , Toro Israel Del , Brandão Carlos Roberto F. , Ellison Aaron M. 
Published: July 2016

AbstractMorphological variation in co-occurring species often is used to infer species assembly rules and other processes structuring ecological assemblages. We compared the morphological structure of ant assemblages in two biogeographic regions along two extensive latitudinal gradients to examine common patterns and unique characteristics of trait distribution. We sampled ant assemblages along extensive latitudinal gradients in Tropical Atlantic Forest in eastern Brazil and temperate forests in the eastern United States. We quantified 14 morphological traits related to the ecology and life history of each of 599 ant species and defined the morphological space occupied by different ant assemblages. Null models were used to test whether tropical and temperate ant assemblages differed from random expectation in morphological structure. Correlations between traits and climate were used to infer associations between habitat characteristics and morphological space occupied by ant assemblages. Tropical ant assemblages had higher morphological diversity and variation in the space of occupied morphospace, whereas temperate assemblages had higher variance in size. Although tropical ant assemblages had smaller morphological distances among species, species packing (i.e., mean nearest-neighbor distance) did not differ between regions. Null model analysis revealed scant evidence of habitat filtering or niche differentiation within assemblages. Different traits had different means, variances, skewness, and kurtosis values along each environmental gradient. Mean trait values within assemblages were associated mainly with region and correlated with temperature but trait variances had more complex responses to climate, including interactions between temperature and precipitation in the models. The higher functional diversity in tropical ant assemblages occurs by expansion of the morphospace rather than through an increase in species packing. Different traits vary independently along environmental gradients. Analysis of individual traits together with categorization of the moments of trait distributions (statistical central tendencies) provide new directions for quantifying morphological diversity in ant assemblages.
Genome size variation and species diversity in salamanders
Authors: Herrick John , Sclavi Bianca 
Published: July 2016

AbstractSalamanders (Urodela) have among the largest vertebrate genomes, ranging in size from 10 to 120 pg. Although changes in genome size often occur randomly and in the absence of selection pressure, non-random patterns of genome size variation are evident among specific vertebrate lineages. Several reports suggest a relationship between species richness and genome size, but the exact nature of that relationship remains unclear both within and across different taxonomic groups. Here we report i) a negative relationship between haploid genome size (C-value) and species richness at the family taxonomic level in salamander clades; ii) a correlation of C-value and species richness with clade crown-age but not with diversification rates; iii) strong associations between C-value and either geographical area or climatic niche rate. Finally, we report a relationship between C-value diversity and species diversity at both the family and genus level clades in urodeles.
Patterns of individual variation in visual pathway structure and function in the sighted and blind
Authors: Aguirre Geoffrey K. , Datta Ritobrato , Benson Noah C. , Prasad Sashank , Jacobson Samuel G. , Cideciyan Artur V. , Bridge Holly , Watkins Kate E. , Butt Omar H. , Dain Alexsandra S. , Brandes Lauren , Gennatas Efstathios D. 
Published: July 2016

AbstractMany structural and functional brain alterations accompany blindness, with substantial individual variation in these effects. In normally sighted people, there is correlated individual variation in some visual pathway structures. Here we examined if the changes in brain anatomy produced by blindness alter the patterns of anatomical variation found in the sighted. We derived eight measures of central visual pathway anatomy from a structural image of the brain from 59 sighted and 53 blind people. These measures showed highly significant differences in mean size between the sighted and blind cohorts. When we examined the measurements across individuals within each group we found three clusters of correlated variation, with V1 surface area and pericalcarine volume linked, and independent of the thickness of V1 cortex. These two clusters were in turn relatively independent of the volumes of the optic chiasm and lateral geniculate nucleus. This same pattern of variation in visual pathway anatomy was found in the sighted and the blind. Anatomical changes within these clusters were graded by the timing of onset of blindness, with those subjects with a post-natal onset of blindness having alterations in brain anatomy that were intermediate to those seen in the sighted and congenitally blind. Many of the blind and sighted subjects also contributed functional MRI measures of cross-modal responses within visual cortex, and a diffusion tensor imaging measure of fractional anisotropy within the optic radiations and the splenium of the corpus callosum. We again found group differences between the blind and sighted in these measures. The previously identified clusters of anatomical variation were also found to be differentially related to these additional measures: across subjects, V1 cortical thickness was related to cross-modal activation, and the volume of the optic chiasm and lateral geniculate was related to fractional anisotropy in the visual pathway. Our findings show that several of the structural and functional effects of blindness may be reduced to a smaller set of dimensions. It also seems that the changes in the brain that accompany blindness are on a continuum with normal variation found in the sighted.
Global population divergence and admixture of the brown rat (Rattus norvegicus)
Authors: Puckett Emily E. , Park Jane , Combs Matthew , Blum Michael J. , Bryant Juliet E. , Caccone Adalgisa , Costa Federico , Deinum Eva E. , Esther Alexandra , Himsworth Chelsea G. , Keightley Peter D. , Ko Albert , Lundkvist Åke , McElhinney Lorraine M. , Morand Serge , Robins Judith , Russell James , Strand Tanja M. , Suarez Olga , Yon Lisa , Munshi-South Jason 
Published: July 2016

ABSTRACTOnce restricted to northern China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution due to the evolution of commensalism with humans. In contrast to black rats and the house mouse, which have tracked the regional and global development of human agricultural settlements, brown rats do not appear in the European historical record until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade and modern sea-faring. We inferred the global phylogeography of brown rats using 32k SNPs to reconstruct invasion routes from estimates of population divergence and admixture. Globally, we detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Rapid westward expansion resulted in the colonization of Europe from which subsequent colonization of Africa, the Americas, and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering found both between and within our sampling sites underscored the extent to which urban heterogeneity can shape the genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants despite continual global transport, suggesting that recruitment into established populations is limited. Understanding the global population structure ofR. norvegicusoffers novel perspectives on the forces driving the spread of zoonotic disease, and yields greater capacity to develop targeted rat eradication programs.
Construction of thousands of single cell genome sequencing libraries using combinatorial indexing
Authors: Vitak Sarah A. , Torkenczy Kristof A. , Rosenkrantz Jimi L. , Fields Andrew J. , Christiansen Lena , Wong Melissa H. , Carbone Lucia , Steemers Frank J. , Adey Andrew 
Published: July 2016

AbstractSingle cell genome sequencing has proven to be a valuable tool for the detection of somatic variation, particularly in the context of tumor evolution and neuronal heterogeneity. Current technologies suffer from high per-cell library construction costs which restrict the number of cells that can be assessed, thus imposing limitations on the ability to quantitatively measure genomic heterogeneity within a tissue. Here, we present Single cell Combinatorial Indexed Sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single cell libraries for the purpose of somatic copy number variant detection. In total, we constructed libraries for 16,698 single cells from a combination of cultured cell lines, frontal cortex tissue fromMacaca mulatta, and two human adenocarcinomas. This novel technology provides the opportunity for low-cost, deep characterization of somatic copy number variation in single cells, providing a foundational knowledge across both healthy and diseased tissues.