bluuebunny/crossref_metadata_2025_split huggingface dataset:
A targeted subgenomic approach for phylogenomics based on microfluidic PCR and high throughput sequencing
Authors: Uribe-Convers Simon , Settles Matthew L. , Tank David C. 
Published: June 2015

AbstractAdvances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses a Fluidigm microfluidic PCR array and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per microfluidic array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our subgenomic method and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genusBartsiaL. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ∼25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ∼13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ∼40,500bp for 349 samples.
A seasonal copepod ‘lipid pump’ promotes carbon sequestration in the deep North Atlantic
Authors: Jónasdóttir Sigrún H. , Visser André W. , Richardson Katherine , Heath Michael R. 
Published: June 2015

AbstractEstimates of carbon flux to the deep oceans are essential for our understanding for global carbon budgets. We identify an important mechanism, the lipid pump, that has been unrecorded in previous estimates. The seasonal lipid pump is highly efficient in sequestering carbon in the deep ocean. It involves the vertical transport and respiration of carbon rich compounds (lipids) by hibernating zooplankton. Estimates for one species, the copepodCalanus finmarchicusoverwintering in the North Atlantic, sequester around the same amount of carbon as does the flux of detrital material that is usually thought of as the main component of the biological pump. The efficiency of the lipid pump derives from a near complete decoupling between nutrient and carbon cycling and directly transports carbon through the meso-pelagic with very little attenuation to below the permanent thermocline. Consequently the seasonal transport of lipids by migrating zooplankton is overlooked in estimates of deep ocean carbon sequestration by the biological pump.
GAP Activity, but Not Subcellular Targeting, Is Required for Arabidopsis RanGAP Cellular and Developmental Functions
Authors: Boruc Joanna , Griffis Anna H.N. , Rodrigo-Peiris Thushani , Zhou Xiao , Tilford Bailey , Van Damme Daniël , Meier Iris 
Published: June 2015

AbstractThe Ran GTPase activating protein (RanGAP) is important to Ran signaling involved in nucleocytoplasmic transport, spindle organization, and postmitotic nuclear assembly. Unlike vertebrate and yeast RanGAP, plant RanGAP has an N-terminal WPP domain, required for nuclear envelope association and several mitotic locations of Arabidopsis thaliana RanGAP1. A double null mutant of the two Arabidopsis RanGAP homologs is gametophyte lethal. Here, we created a series of mutants with various reductions in RanGAP levels by combining a RanGAP1 null allele with different RanGAP2 alleles. As RanGAP level decreases, the severity of developmental phenotypes increases, but nuclear import is unaffected. To dissect whether the GAP activity and/or the subcellular localization of RanGAP are responsible for the observed phenotypes, this series of rangap mutants were transformed with RanGAP1 variants carrying point mutations abolishing the GAP activity and/or the WPP-dependent subcellular localization. The data show that plant development is differentially affected by RanGAP mutant allele combinations of increasing severity and requires the GAP activity of RanGAP, while the subcellular positioning of RanGAP is dispensable. In addition, our results indicate that nucleocytoplasmic trafficking can tolerate both partial depletion of RanGAP and delocalization of RanGAP from the nuclear envelope.
Do tutorials on application method enhance adapalene–benzoyl peroxide combination gel tolerability in the treatment of acne?
Authors: Kwon Hyuck Hoon , Park Seon Yong , Yoon Ji Young , Min Seonguk , Suh Dae Hun 
Published: June 2015

AbstractFixed‐dose combination adapalene 0.1% and benzoyl peroxide 2.5% gel (A‐BPO) has rarely been studied for Asian acne patients, while they have complained of local irritations more often when applying individual components. In this study, we compared A‐BPO gel with benzoyl peroxide (BPO) in terms of efficacy and tolerability in Korean patients first, and assessed the clinical benefit of a dermatological tutorial on application technique in reducing irritations for A‐BPO. This study was conducted as a single‐blind controlled split‐face trial for a 12‐week period. Each half facial side of 85 patients was randomly assigned to either A‐BPO or BPO. Success rate, lesion counts and safety profiles were evaluated (analysis I). During initial assignment, all patients were further randomized to either dermatological tutorial (DT) or non‐tutorial (NT) subgroups depending on the presence of dermatologists' tutorials for application methods to their A‐BPO sides. Clinical data of the A‐BPO side was compared between two subgroups (analysis II). As a result, A‐BPO gel outperformed BPO, demonstrating better efficacy in success rates and lesion counts as early as 1 week. However, A‐BPO proved significantly less tolerable compared with both BPO and previous A‐BPO data from Caucasians. Bioengineering measurements further confirmed clinical data (analysis I). The DT subgroup achieved much better tolerability with comparable therapeutic efficacies compared with the NT subgroup (analysis II). In conclusion, A‐BPO demonstrated higher efficacies in acne compared with BPO in Korean patients, while skin irritation levels were notable concurrently. Dermatologists' education for application methods would significantly decrease these side‐effects, maintaining superior efficacy levels.
Improvement in T helper 1‐related immune responses in BALB/c mice immunized with an HIV‐1 gag plasmid combined with a chimeric plasmid encoding interleukin‐18 and flagellin
Authors: Chen Ya‐Lei , Chen Yao‐Shen , Hung Yi‐Chien , Liu Pei‐Ju , Tasi Hsi‐Ying , Ni Wei‐Feng , Hseuh Pei‐Tan , Lin Hsi‐Hsun 
Published: June 2015

ABSTRACTBoth flagellin (fliC) and IL‐18 (INF‐γ‐inducing factor) have been developed as adjuvants for improving immunogenicity in DNA‐vaccinated hosts. An HIV‐1 gag plasmid encodes a protein harboring broad epitopes for cytotoxic T‐lymphocytes. In this study, the immunogenicity of BALB/c mice immunized with an HIV‐1 gag plasmid (pVAX/gag) combined with a chimeric plasmid encoding IL‐18 fused to flagellin (pcDNA3/IL‐18_fliC) or a single plasmid encoding IL‐18 (pcDNA3/IL‐18) and/or flagellin (pcDNA3/fliC) was assessed. Through in vitro transcription and translation, it was demonstrated that both mRNA and protein were appropriately expressed by each construct. The IL‐18 and flagellin fusion protein, which could be detected in supernatants from transfected cells, was effective in inducing IFN‐γ by lymphocytes. Following i.m. immunization, expressions of flagellin or IL‐18 were detected in muscle cells by immunohistochemistry analysis from 72 hr. At 12 weeks post‐immunization, both gag‐specific IgG in sera and spleen cell proliferation were high in all murine groups. However, the IgG2a/IgG1 ratio, Th1 cytokine (IL‐2 and IFN‐γ) production and proportion of gag‐specific CD3+CD8+ IFN‐γ‐secreting cells were significantly higher in the murine group co‐immunized with pVAX/gag plasmid and pcDNA3/IL‐18_fliC than in the mice immunized with pVAX/gag plasmid combined with either pcDNA3/fliC or pcDNA3/IL‐18 plasmid or both. These findings suggest that a chimeric plasmid encoding IL‐18 fused to flagellin can be used as an adjuvant‐like plasmid to improve the Th1 immune response, particularly for induction of CD3+CD8+ IFN‐γ‐secreting cells in gag plasmid‐vaccinated mice.
Orientation to the sun by animals and its interaction with crypsis
Authors: Penacchio Olivier , Cuthill Innes C. , Lovell P. George , Ruxton Graeme D. , Harris Julie M. 
Published: June 2015

Summary

Orientation with respect to the sun has been observed in a wide range of species and has generally been interpreted in terms of thermoregulation and/or ultraviolet (UV) protection. For countershaded animals, orientation with respect to the sun may also result from the pressure to exploit the gradient of coloration optimally to enhance crypsis.

Here, we use computational modelling to predict the optimal countershading pattern for an oriented body. We assess how camouflage performance declines as orientation varies using a computational model that incorporates realistic lighting environments.

Once an optimal countershading pattern for crypsis has been chosen, we determine separately how UV protection/irradiation and solar thermal inflow fluctuate with orientation.

We show that body orientations that could optimally use countershading to enhance crypsis are very similar to those that allow optimal solar heat inflow and UV protection.

Our findings suggest that crypsis has been overlooked as a selective pressure on orientation and that new experiments should be designed to tease apart the respective roles of these different selective pressures. We propose potential experiments that could achieve this.
The downside of eDNA as a survey tool in water bodies
Authors: Roussel Jean‐Marc , Paillisson Jean‐Marc , Tréguier Anne , Petit Eric 
Published: June 2015

Summary

There is a growing literature on the detection of species‐specific DNA fragments in water to reveal animals' presence in aquatic environments.

Analysis of Rees et al. (Journal of Applied Ecology, 2014, 51, 1450) and additional publications highlight the downside of the method and suggest that some conclusions have to be toned down.

Non‐detection of species‐specific DNA fragments in a water sample does not automatically imply the absence of the target species. A positive signal does not necessarily mean the species is present because the environmental DNA (eDNA) could have been transported or preserved after an animal's death. Detection of aquatic invertebrates is weakly documented. The effect of species abundance on detection efficiency is not always established.

Synthesis and applications. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration.
Applications and limitations of measuring environmental DNA as indicators of the presence of aquatic animals
Authors: Rees Helen C. , Gough Kevin C. , Middleditch David J. , Patmore James R. M. , Maddison Ben C. 
Published: June 2015

Summary

In Rees et al. (2014b), we reviewed the current status of environmental DNA (eDNA) to monitor aquatic populations. Our aim was to focus on discussion of methodologies used, application of eDNA analysis as a survey tool in ecology, and to include some innovative ideas for using eDNA in conservation and management.

Roussel et al. (2015) claim that analysis of Rees et al. (2014b) and other publications highlights the downsides of the method, and they suggest that some conclusions should be toned down. Many of their arguments were covered in our original paper (Rees et al., 2014b); however, they make the point that modelling approaches should be encouraged, and we fully agree with this suggestion.

Roussel et al. (2015) also claim that we neglected to recognize that there are two sources of imperfect detection (at the field level and at the laboratory level). We feel that our review paper implies this point.

Synthesis and applications. Roussel et al. (2015) reiterate many of the points made in the original paper but do cover some additional areas that improve the debate on the use of environmental DNA (eDNA). Both the comment (Roussel et al., 2015) and our rebuttal clearly highlight that detailed laboratory protocols and rigorous field sampling design are crucial factors which require sufficient reporting in the literature to allow for experimental comparison and replication. Any development of a new method for eDNA detection should be compared directly with established ‘gold standard’ methods for the detection of the species or habitat under investigation. None of the issues raised in Roussel et al. (2015) would alter our main conclusions.
Avoiding the crowds: the evolution of plastic responses to seasonal cues in a density‐dependent world
Authors: Metcalf C. Jessica E. , Burghardt Liana T. , Koons David N. 
Published: June 2015

Summary

Across a range of organisms, life‐history transitions can be triggered by specific levels of seasonal cues, such as day length or temperature. This acts to regulate the life cycle relative to seasonal fluctuations, so that, for example, reproduction occurs when resources are most abundant.

At an environmentally optimal cue level, individuals might be selected to respond in a similar way, and consequently abruptly increase population density through, for example, the production of offspring. However, if density dependence is operating, crowding will reduce individual fitness, and selection will then favour life‐history transitions at different cue levels.

We explore the eco‐evolutionary dynamics that result from the interaction between density dependence and phenology using a life‐history model of an annual plant and focus on the timing of seed germination within the year. We characterize the adaptive dynamics of the mean and variance across the year of germination timing.

Our results indicate that, even in predictably varying environments, mean timing of germination is not evolutionarily stable, but may experience evolutionary branching if variance in germination timing is sufficiently constrained. Unpredictably varying environments extend contexts where this is the case.

Synthesis. Even if there is a restricted time period in the year during which environmental conditions are most appropriate for germination, observed timing of germination might be very diverse. Density dependence selects for persistence of traits conferring variance in timing across the year and additionally can lead to evolutionary branching of mean germination timing, resulting in multiple coexisting genotypes corresponding to different mean germination timings.
The susceptibility of Echinacea angustifolia to a specialist aphid: eco‐evolutionary perspective on genotypic variation and demographic consequences
Authors: Shaw Ruth G. , Wagenius Stuart , Geyer Charles J. 
Published: June 2015

Summary

Plants and their herbivores may influence each other's fitness and, hence, genetic dynamics, as well as their demography. Conversely, variation in fitness‐related traits may influence the occurrence or intensity of the interaction. Disentangling the fitness consequences of an interaction in nature from the influence of fitness variation on it is challenging, but important to clarifying the ecological and evolutionary dynamics of plants with their herbivores.

As part of a larger effort to elucidate eco‐evolutionary dynamics in a population of Echinacea angustifolia that is subject to severe fragmentation, we initiated an experiment in 2001 to evaluate differences in fitness among plants of three genotypic classes resulting from matings of plants from different remnant populations (‘between’, B), plants randomly chosen from the same remnant (‘within’, W) and maternal siblings (‘inbreds’, I). The experiment was planted into a field undergoing restoration to a prairie community. Fitness components of individual plants were recorded through 2012. During 2004–2010, each plant was also monitored for its load of Aphis echinaceae, a specialist insect herbivore.

Within a season, aphid‐load depended consistently on a plant's location and on its load the previous season. Further, flowering individuals generally harboured more aphids than non‐flowering plants. In analyses of overall plant fitness, within each genotypic class, fitness was greatest for plants with the greatest aphid‐loads, consistent with the preference of aphids for flowering individuals. Inbreeding depression was severe, with I plants producing 60% fewer achenes than W or B plants, and varied with aphid‐load. To distinguish the role of aphid choice from the effect of aphid herbivory in the relationship between plant fitness and aphid‐load, we evaluated how components of fitness varied with prior aphid‐load. Notably, genotype I plants with high aphid‐loads the previous year produced far fewer achenes per flower head than those that carried fewer aphids.

Synthesis. Sibmating reduces individuals’ demographic contribution by 60% over the first 12 years. Outbred individuals tolerate this aphid; each produces on average about 200 achenes per head in a year, despite a heavy aphid‐load the previous year. However, inbreeding, which is greater in severely fragmented prairie habitat, results in poor tolerance. Aphid herbivory exacerbates inbreeding depression, further reducing the contribution of those individuals to population growth. This study illustrates an approach that helps to distinguish fitness‐dependent attraction of herbivores from the effects of herbivory on plant fitness and demography, a goal that is critically important to eco‐evolutionary understanding.
Eco‐evolutionary dynamics in plants: interactive processes at overlapping time‐scales and their implications
Authors: Shefferson Richard P. , Salguero‐Gómez Roberto 
Published: June 2015

Summary

Evolution can happen rapidly and frequently. This realization has motivated a rethinking of ecological and evolutionary time‐scales and their overlap, and stimulated research on processes at their interface. This premise lays at the heart of eco‐evolutionary dynamics, a relatively recent field redeveloping how we conceive of ecological and evolutionary processes.

Classical evolutionary theory and empirical evidence has generally supported a gradualist view of evolution as occurring on much longer time‐scales than ecological processes. The systematic documentation of rapid evolution beginning in the 1970s served as a catalyst to question this basic assumption. The commonness of rapid evolution suggests that ecological and evolutionary processes often occur at the same time‐scale, which may allow them to interact.

As a new field, eco‐evolutionary dynamics faces some important challenges. First, the field is primarily driven by theoretical research and empirical work on organisms with simple, short life cycles, typically animals, and mostly performed under controlled conditions. Secondly, it is unclear whether interactions between ecology and evolution are driven through a few common mechanisms, or whether all interactions are context dependent. Thirdly, there is a lack of eco‐evolutionary research at higher organizational levels (e.g. ecosystem and landscape), although it is at those levels that the impact of evolution on our greatest conservation challenges may be most acute. Finally, it remains unclear how genetic diversity impacts eco‐evolutionary dynamics, although the strong relationships between additive genetic variance, fitness and the speed of evolution suggest that it is important.

Summary. This Special Feature includes five research manuscripts expanding our knowledge of eco‐evolutionary dynamics in plants and the organisms they interact with. Its contributors address the aforementioned challenges outlined above, ranging from demonstrating the impacts of genetic variation on plant and herbivore populations, to exploring the role of density in the evolution of plant life‐history traits and to documenting genetic covariation among co‐occurring communities. This Special Feature highlights the cutting‐edge exploration of the dynamic effects of interacting ecological and evolutionary processes, including the potential for complex life histories to influence eco‐evolutionary interactions, for common mechanisms to underlie most eco‐evolutionary dynamics, for evolution to impact higher organizational levels and for genetic changes to cascade through communities.
High‐throughput SNPs for all: genotyping‐in‐thousands
Authors: Pavey Scott A. 
Published: June 2015

Understanding the genetic structure of species is essential for conservation. It is only with this information that managers, academics, user groups and land‐use planners can understand the spatial scale of migration and local adaptation, source‐sink dynamics and effective population size. Such information is essential for a multitude of applications including delineating management units, balancing management priorities, discovering cryptic species and implementing captive breeding programmes. Species can range from locally adapted by hundreds of metres (Pavey et al. ) to complete species panmixia (Côté et al. ). Even more remarkable is that this essential information can be obtained without fully sequenced or annotated genomes, but from mere (putatively) nonfunctional variants. First with allozymes, then microsatellites and now SNPs, this neutral genetic variation carries a wealth of information about migration and drift. For many of us, it may be somewhat difficult to remember our understanding of species conservation before the widespread usage of these useful tools. However most species on earth have yet to give us that ‘peek under the curtain’. With the current diversity on earth estimated to be nearly 9 million species (Mora et al. ), we have a long way to go for a comprehensive meta‐phylogeographic understanding. A method presented in this issue by Campbell and colleagues (Campbell et al. ) is a tool that will accelerate the pace in this area. Genotyping‐in‐thousands (GT‐seq) leverages recent advancements in sequencing technology to save many hours and dollars over previous methods to generate this important neutral genetic information.