bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global invasion history of the world’s most abundant pest butterfly: a citizen science population genomics study
Authors: Ryan Sean F. , Lombaert Eric , Espeset Anne , Vila Roger , Talavera Gerard , Dincă Vlad , Renshaw Mark A. , Eng Matthew W. , Doellman Meredith M. , Hornett Emily A. , Li Yiyuan , Pfrender Michael E. , Shoemaker DeWayne 
Published: December 2018

AbstractA major goal of invasion and climate change biology research is to understand the ecological and evolutionary responses of organisms to anthropogenic disturbance, especially over large spatial and temporal scales. One significant, and sometimes unattainable, challenge of these studies is garnering sufficient numbers of relevant specimens, especially for species spread across multiple continents. We developed a citizen science project, “Pieris Project”, to successfully amass thousands of specimens of the invasive agricultural pestPieris rapae, the small cabbage white butterfly, from 32 countries worldwide. We then generated and analyzed genomic (ddRAD) and mitochondrial DNA sequence data for these samples to reconstruct and compare different global invasion history scenarios. Our results bolster historical accounts of the global spread and timing ofP. rapaeintroductions. The spread ofP. rapaeover the last ∼160 years followed a linear series of at least four founding events, with each introduced population serving as the source for the next. We provide the first molecular evidence supporting the hypothesis that the ongoing divergence of the European and Asian subspecies ofP. rapae(∼1,200 yrBP) coincides with the domestication of brassicaceous crops. Finally, the international success of the Pieris Project allowed us to nearly double the geographic scope of our sampling (i.e., add >1,000 specimens from 13 countries), demonstrating the power of the public to aid scientists in collections-based research addressing important questions in ecology and evolutionary biology.Non-technical summaryWe provide genetic evidence that the success of the small cabbage white butterfly—its rise to one of the most widespread and abundant butterflies on the planet— was largely facilitated by human activities, through the domestication of its food plants and the accidental movement of the butterfly by means of trade and human movement (migration). Through an international citizen science project—Pieris Project—people from around the world helped to unravel the global invasion history of this agricultural pest butterfly by collecting samples for DNA analysis. The success of this citizen science project demonstrates the power of the public to aid in collections-based research that address important questions related to ecology and evolutionary biology.
A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells
Authors: Fonseca João Pedro , Bonny Alain R. , Kumar G. Renuka , Ng Andrew H. , Town Jason , Wu Qiu Chang , Aslankoohi Elham , Chen Susan Y. , Harrigan Patrick , Osimiri Lindsey C. , Kistler Amy L. , El-Samad Hana 
Published: December 2018

AbstractThe ability to rapidly assemble and prototype cellular circuits is vital for biological research and its applications in biotechnology and medicine. Current methods that permit the assembly of DNA circuits in mammalian cells are laborious, slow, expensive and mostly not permissive of rapid prototyping of constructs. Here we present the Mammalian ToolKit (MTK), a Golden Gate-based cloning toolkit for fast, reproducible and versatile assembly of large DNA vectors and their implementation in mammalian models. The MTK consists of a curated library of characterized, modular parts that can be easily mixed and matched to combinatorially assemble one transcriptional unit with different characteristics, or a hierarchy of transcriptional units weaved into complex circuits. MTK renders many cell engineering operations facile, as showcased by our ability to use the toolkit to generate single-integration landing pads, to create and deliver libraries of protein variants and sgRNAs, and to iterate through Cas9-based prototype circuits. As a biological proof of concept, we used the MTK to successfully design and rapidly construct in mammalian cells a challenging multicistronic circuit encoding the Ebola virus (EBOV) replication complex. This construct provides a non-infectious biosafety level 2 (BSL2) cellular assay for exploring the transcription and replication steps of the EBOV viral life cycle in its host. Its construction also demonstrates how the MTK can enable important and time sensitive applications such as the rapid testing of pharmacological inhibitors of emerging BSL4 viruses that pose a major threat to human health.
A Rat Model of Somatosensory-Evoked Reflex Seizures Induced by Peripheral Stimulation
Authors: Bortel Aleksandra , Yao Ze Shan , Shmuel Amir 
Published: December 2018

ABSTRACTObjectiveWe introduce a novel animal model of somatosensory stimulation-induced reflex seizures which generates focal seizures without causing damage to the brain.MethodsSpecifically, we electrically stimulated digits or forepaws of adult rats sedated with dexmedetomidine while imaging cerebral blood volume and recording neurophysiological activity in cortical area S1FL. For the recordings, we either inserted a linear probe into the D3 digit representation or we performed surface electrocorticography (ECoG) recordings.ResultsPeripheral stimulation of a digit or the forepaw elicited seizures that were followed by a refractory period with decreased neuronal activity, or another seizure or a normal response. LFP amplitudes in response to electrical pulses during the seizures (0.28 ± 0.03 mV) were higher than during normal evoked responses (0.25 ± 0.05 mV) and refractory periods (0.2 ± 0.08 mV). Seizures generated during the stimulation period showed prolonged after-discharges that were sustained for 20.9±1.9 s following the cessation of the stimulus. High-frequency oscillations were observed prior to and during the seizures, with amplitudes higher than those associated with normal evoked responses. The seizures were initially focal. Optical imaging of the cerebral blood volume response showed that they propagated from the onset zone to adjacent cortical areas, beyond the S1FL representation of the stimulated digit or forepaw. The spatial extent during seizures was on average 1.74 times larger during the stimulation and 4.1 times following its cessation relative to normal evoked responses. Seizures were recorded not only by probes inserted into cortex but also with ECoG arrays (24.1±5.8 seizures per rat) placed over the dura matter, indicating that the seizures were not induced by damage caused by inserting the probes to cortex. Stimulation of the forepaw elicited more seizures (18.8±8.5 seizures per rat) than stimulation of a digit (1.7±0.7). Unlike rats sedated with dexmedetomidine, rats anesthetized with urethane showed no seizures, indicating that the seizures may depend on the use of the mild sedative dexmedetomidine.SignificanceOur proposed animal model generates seizures induced by electrical sensory stimulation free of artifacts and brain damage. It can be used for studying the mechanisms underlying the generation and propagation of reflex seizures and for evaluating antiepileptic drugs.HIGHLIGHTSPeripheral stimulation of the rat forepaw or digits induces seizuresSeizures are evoked with no direct application of convulsants, electro-stimulation or damage to the brainSeizures are focal at onset, then spread beyond the spatial representation of the digit or forepawSeizures persist following the cessation of the stimulusProposed animal model may support the study of reflex seizures and improving therapeutic interventions
Anticipatory coadaptation of ankle stiffness and sensorimotor gain for standing balance
Authors: Le Mouel Charlotte , Brette Romain 
Published: December 2018

AbstractExternal perturbation forces may compromise standing balance. The nervous system can intervene only after a delay greater than 100 ms, during which the body falls freely. With ageing, sensorimotor delays are prolonged, posing a critical threat to balance. We study a generic model of stabilisation with neural delays to understand how the organism should adapt to challenging balance conditions. The model suggests that ankle stiffness should be increased in anticipation of perturbations, for example by muscle co-contraction, so as to slow down body fall during the neural response delay. Increased ankle muscle co-contraction is indeed observed in young adults when standing in challenging balance conditions, and in older relative to young adults during normal stance. In parallel, the analysis of the model shows that increases in either stiffness or neural delay must be coordinated with decreases in spinal sensorimotor gains, otherwise the feedback itself becomes destabilizing. Accordingly, a decrease in spinal feedback is observed in challenging conditions, and with age-related increases in neural delay. These observations have been previously interpreted as indicating an increased reliance on cortical rather than spinal control of balance, despite the fact that cortical responses have a longer latency. Our analysis challenges this interpretation by showing that these observations are consistent with a functional coadaptation of spinal feedback gains to functional changes in stiffness and neural delay.Author summaryBeing able to stand still can be difficult when faced with an unexpected push. It takes the nervous system more than a tenth of a second to respond to such a perturbation, and during this delay the body falls under the influence of its own weight. By co-contracting their ankle muscles in anticipation of a perturbation, subjects can increase their ankle stiffness, which slows down their fall during the neural delay. Young subjects indeed adopt this strategy when they need to remain particularly still (for example when they stand in front of a cliff). Older subjects adopt this strategy even during normal standing. We present a model of standing balance that shows that this postural strategy provides partial compensation for the increase in neural delays with ageing. According to our model, increasing ankle stiffness only improves balance if it is accompanied by a decrease in sensorimotor gain. This provides a novel and functional interpretation for the decrease in spinal feedback observed during ageing, and observed in young subjects when they stand in challenging balance conditions.
A Darwinian Uncertainty Principle
Authors: Gascuel Olivier , Steel Mike 
Published: December 2018

AbstractReconstructing ancestral characters and traits along a phylogenetic tree is central to evolutionary biology. It is the key to understanding morphology changes among species, inferring ancestral biochemical properties of life, and recovering migration routes in phylogeography. The goal is twofold: to reconstruct the character state at the tree root (e.g. the region of origin of some species), and to understand the process of state changes along the tree (e.g. species flow between countries). Although each goal can be achieved with high accuracy individually, we use mathematics and simulations to demonstrate that it is generally impossible to accurately estimate both the root state and the rates of state changes along the tree branches from the observed data at the tips of the tree. This inherent ‘Darwinian uncertainty principle’ concerning the simultaneous estimation of ‘pattern’ and ‘process’ governs ancestral reconstructions in biology. Increasing the number of tips improves the joint estimation accuracy for certain tree shapes that arise in evolutionary models, however, for other trees shapes it does not.
Pedigree-based estimation of human mobile element retrotransposition rates
Authors: Feusier Julie , Watkins W. Scott , Thomas Jainy , Farrell Andrew , Witherspoon David J. , Baird Lisa , Ha Hongseok , Xing Jinchuan , Jorde Lynn B. 
Published: December 2018

AbstractGermline mutation rates in humans have been estimated for a variety of mutation types, including single nucleotide and large structural variants. Here we directly measure the germline retrotransposition rate for the three active retrotransposon elements: L1, Alu, and SVA. We utilized three tools for calling Mobile Element Insertions (MEIs) (MELT, RUFUS, and TranSurVeyor) on blood-derived whole genome sequence (WGS) data from 603 CEPH individuals, comprising 33 three-generation pedigrees. We identified 27 de novo MEIs in 440 births. The retrotransposition rate estimates for Alu elements, one in 40, is roughly half the rate estimated using phylogenetic analyses, a difference in magnitude similar to that observed for single nucleotide variants. The L1 retrotransposition rate is one in 62 births and is within range of previous estimates (1:20-1:200 births). The SVA retrotransposition rate, one in 55 births, is much higher than the previous estimate of one in 900 births. Our large, three-generation pedigrees allowed us to assess parent-of-origin effects and the timing of insertion events in either gametogenesis or early embryonic development. We find a statistically significant paternal bias in Alu retrotransposition. Our study represents the first in-depth analysis of the rate and dynamics of human retrotransposition from WGS data in three-generation human pedigrees.
Searching the optimal folding routes of a Complex Lasso protein
Authors: Perego Claudio , Potestio Raffaello 
Published: December 2018

ABSTRACTUnderstanding how polypeptides can efficiently and reproducibly attain a self-entangled conformation is a compelling biophysical challenge, which might shed new light on our general knowledge of protein folding. Complex Lassos, namely self-entangled protein structures characterized by a covalent loop sealed by a cysteine bridge, represent an ideal test system in the framework of entangled folding. Indeed, as cysteine bridges form in oxidizing conditions, they can be used as on/off switches of the structure topology, to investigate the role played by the backbone entanglement in the process.In the present work we have used molecular dynamics to simulate the folding of a complex lasso glycoprotein, Granulocyte-macrophage colony-stimulating factor, modeling both reducing and oxidizing conditions. Together with a well-established Go-like description, we have employed the elastic folder model, a Coarse-Grained, minimalistic representation of the polypeptide chain, driven by a structure-based angular potential. The purpose of this study is to assess the kinetically optimal pathways, in relation to the formation of the native topology. To this end we have implemented an evolutionary strategy that tunes the elastic folder model potentials to maximize the folding probability within the early stages of the dynamics. The resulting protein model is capable of folding with high success rate, avoiding the kinetic traps that hamper the efficient folding in the other tested models. Employing specifically designed topological descriptors, we could observe that the selected folding routes avoid the topological bottleneck by locking the cysteine bridge after the topology is formed.These results provide valuable insights on the selection of mechanisms in self-entangled protein folding while, at the same time, the proposed methodology can complement the usage of established minimalistic models, and draw useful guidelines for more detailed simulations.
Black spruce (Picea mariana) colonization of subarctic snowpatches in response to warmer climate
Authors: Truchon‐Savard Alexandre , Jean Mélanie , Payette Serge 
Published: December 2018

Abstract

Snowpatches are disjunct arctic ecosystems scattered across the subarctic, particularly on wind‐protected lee slopes, where a thick snow cover accumulates during the winter. These snow‐rich treeless ecosystems are affected by delayed snowmelt, causing shorter growing seasons. Snow‐tolerant plants occupy the centre of subarctic snowpatches, whereas black spruce trees grow at the margins. Snowpatches have shown sporadic expansion and shrinkage phases from tree establishment and mortality linked to climatic trends. Field surveys in the subarctic of eastern Canada are showing an afforestation process occurring in snowpatches. The origin and nature of this afforestation were investigated based on the hypothesis that tree colonization and growth were closely associated with recent changes in climate.

Snowpatches were categorized into three types based on border trees: forested, semi‐forested and tundra‐like. In eight randomly selected snowpatches of each type, snowpatch borders and areas covered by deciduous shrubs or trees were mapped and chionophilous plants and frost‐associated soil disturbances were recorded. Radial (tree‐ring) and vertical growth were measured on stems to evaluate the impact of climate and local factors on snowpatch black spruce populations.

Two waves of spruce colonization occurred in all forested and semi‐forested snowpatches in the 1960s and in the 1980s to present. Spruce establishment was more frequent and abundant in recent years, near the forest margins and on moss and barren seedbeds. Expanding shrub (dwarf birch) cover inhibited spruce seedling establishment. Tree establishment and growth were positively correlated with growing season temperature and negatively correlated with annual maximum snow depth. More recently established spruce seedlings exhibited faster vertical growth than those established in the 20th century.

Synthesis. Due to warmer conditions and earlier snowmelt in eastern Canada, black spruce trees and dwarf birch shrubs are racing through subarctic snowpatches. This afforestation could change biodiversity in the subarctic and affect watershed dynamics through a change in snowmelt pattern. Subarctic snowpatches are climate‐sensitive ecosystems of the forest–tundra landscape, forming ideal biotopes for snow‐tolerant, arctic–alpine species. Further tree encroachment in snowpatches in this century is potentially a threat to plant diversity, especially chionophilous species that have no corridors to migrate towards arctic ecosystems.
Soil nutrients and dispersal limitation shape compositional variation in secondary tropical forests across multiple scales
Authors: van Breugel Michiel , Craven Dylan , Lai Hao Ran , Baillon Mario , Turner Benjamin L. , Hall Jefferson S. 
Published: December 2018

Abstract

Soil resource partitioning and dispersal limitation have been shown to shape the tree community structure of mature tropical forests, but are poorly studied in the context of forest succession. We examined the relative contributions of both ecological processes to the variation in the species composition of young tropical secondary forests at different spatial scales, and if the relative importance of these two ecological processes changed during succession. At the species level, we examined if the association between species abundances and soil fertility differed between early and late successional species and/or changed over the course of succession.

We used vegetation and soil data from 47 secondary forest sites with two plots each in a tropical agricultural landscape. A distance‐based redundancy analysis and variation partitioning were employed to examine the relative importance of spatial distance (proxy for dispersal limitation) and heterogeneity in soil nutrients (proxy for soil nutrient partitioning) at the landscape scale, and a linear regression to test their effects at the local scale. We examined interspecific variation in species’ responses to successional age and soil nutrients with a joint species distribution model.

Dispersal limitation and soil niche partitioning drove considerable variation in the composition of plant communities at local and landscape scales. The relative contribution of these two ecological processes changed with scale (local vs. landscape) and topography (lower slope vs. upper slope plots). At the species level, significant abundance–soil fertility associations were mostly positive. Most species became less responsive to soil nutrients over the first few decades of tropical forest succession, probably because light became the main limiting resource in older forests.

Synthesis. Our key finding is that spatial heterogeneity in soil resources and spatial distance jointly drive compositional variation within and across early successional forests. Our results highlight that a network of forest fragments enhances the resilience of ecological processes and the potential of secondary forests to restore and preserve biodiversity in human‐modified landscapes. To advance our understanding of ecological succession, we need to move beyond single‐factor and local‐scale studies and examine the effects of multiple variables on succession at different spatial scales.
Metacaspase involvement in programmed cell death of the marine cyanobacterium Trichodesmium
Authors: Spungin Dina , Bidle Kay D. , Berman‐Frank Ilana 
Published: December 2018

SummaryMetacaspases are cysteine specific proteases implicated in cell‐signalling, stress acclimation and programmed cell death (PCD) pathways in plants, fungi, protozoa, bacteria and algae. We investigated metacaspase‐like gene expression and biochemical activity in the bloom‐forming, N2‐fixing, marine cyanobacterium Trichodesmium, which undergoes PCD under low iron and high‐light stress. We examined these patterns with respect to in‐silico analyses of protein domain architectures that revealed a diverse array of regulatory domains within Trichodesmium metacaspases‐like (TeMC) proteins. Experimental manipulations of laboratory cultures and oceanic surface blooms of Trichodesmium from the South Pacific Ocean triggered PCD under Fe‐limitation and high light along with enhanced TeMC activity and upregulated expression of diverse TeMC representatives containing different regulatory domains. Furthermore, TeMC activity was significantly and positively correlated with caspase‐like activity, which has been routinely observed to increase with PCD induction in Trichodesmium. Although both TeMC and caspase‐like activities were stimulated upon PCD induction, inhibitor treatments of these proteolytic activities provided further evidence of largely distinct substrate specificities, even though some inhibitory crossover was observed. Our findings are the first results linking metacaspase expression and activity in PCD induced mortality in Trichodesmium. Yet, the role/s and specific activities of these different proteins remain to be elucidated.
Body Transportation after Homicides: Offender and Offense Characteristics
Authors: Lee Seo Jin , Park Jisun 
Published: December 2018

AbstractBody transportation is defined as moving the body of the victim from the scene of a homicide to another location. We analyzed data on 513 South Korean homicide cases with convictions to compare 104 homicides involving the transportation of victims’ bodies with 409 homicides that did not. Offenders who transported their victims’ bodies were significantly younger and more likely to be related to the victims and were less likely to use sharp instruments and more likely to use blunt instruments or strangle the victims than offenders who did not. Victims of homicide involving body transportation were more likely to suffer injuries to the neck and head and less likely to suffer injuries to the torso. Finally, offenders who transported victims’ bodies were more likely to have planned the offense and destroyed evidence. The present findings have practical implications for police investigations.