bluuebunny/crossref_metadata_2025_split huggingface dataset:
VIT1-dependent Fe distribution in seeds is conserved in dicots
Authors: Eroglu Seckin , Karaca Nur , Vogel-Mikus Katarina , Kavčič Anja , Filiz Ertugrul , Tanyolac Bahattin 
Published: December 2018

AbstractOne third of the people suffer from iron (Fe) Fe deficiency. An underlying factor for this malnutrition is insufficient Fe intake from the diet. A major part of the human diet includes seeds of staple crops, which contain Fe that is poorly bioavailable. One reason for the low bioavailability is these seeds store Fe in cellular compartments that also contain antinutrients, such as phytate. Thus, several studies focused on decreasing phytate concentrations. As an alternative approach to increase bioavailable Fe, Fe reserves might be directed to cellular compartments such as plastids that are free of phytate. Previous studies indicated that Fe reserves can be relocalized inside the seed to the desired compartment by genetic modification, provided that a suitable iron transporter protein is used. However, to the best of our knowledge, a Fe transporter localizing to plastids have not been identified in seeds to date. To discover novel Fe transporters, we screened Fe patterns in seeds of distinct plant lineages, hypothesizing Fe hyperaccumulating sites would indicate Fe transporter presence. To this end, metal localizations in seeds of more than twenty species were investigated using histochemical or X-ray based techniques. Results showed that in Rosids, the largest clade of eudicots, Fe reserves were primarily confined in the embryo part of the seeds. Furthermore, inside the embryos, Fe was enriched in the endodermal cell layer, a well-known feature that is mediated by vacuolar Fe transporter, VIT1 in model plantArabidopsis thaliana. This enrichment was well conserved in and beyond Rosid species. Finally, a few seeds showed novel Fe patterns, includingCarica papayawhich concentrated large Fe reserves exclusively in plastids called amyloplasts. Generally, Fe stored in amyloplast is considered bioavailable. Taken together, this study suggests dicot seeds store Fe mainly in the embryo, with a VIT1-dependent enrichment in its endodermal cell layer and indicateCarica papayapossess a strong Fe transporter at the plastid membrane. Once it is identified that might be useful in biofortification, as a novel tool to shift Fe to compartments where it is more bioavailable.
Analysis of Maize Profilin-4 Isoform as an allergen
Authors: Alam Saruar , Hasan Md. Kamrul , Hossain Md. Faruk 
Published: December 2018

AbstractProfilin is an actin monomer-binding protein that controls the dynamic turnover of actin filaments and is ubiquitously present in different organisms ranging from prokaryotes to higher eukaryotes. Maize (Zea mays) profilin-4 isoform is a pollen-specific protein. Birch profilin isoform is a known allergen but maize profilin is yet to be characterized. Due to the high cultivation rate of maize, the analysis of the properties of maize profilin-4 isoform as an allergen is a demand of time for developing an effective immune therapy. Here, we analyzed the allergenic potency of profilin-4 by studying of its physicochemical properties, including molecular weight (∼14kD) and theoretical pI (4.63). We tested the potential B cell epitope candidates of profilin-4 using different immune-informatics tools housed at IEDB analysis resource. For the B cell epitope prediction, potential antigenic sites on the protein surface were predicted by both propensity scale and machine learning method followed by their mapping of 3D structure prediction. We hereby claim that the profilin-4 is a potential allergen and is able to induce allergic responses. However, the wet lab experiments are needed to validate our claim that’s beyond our scope.
Mitochondrial cristae biogenesis coordinates with ETC complex IV assembly during Drosophila maturation
Authors: Jiang Yi-fan , Lin Hsiang-ling , Wang Li-jie , Hsu Tian , Fu Chi-yu 
Published: December 2018

AbstractMitochondrial cristae contain electron transport chain (ETC) complexes and are distinct from the inner boundary membrane (IBM) in both protein composition and function. While many details of mitochondrial membrane structure are known, the processes governing cristae biogenesis, including the organization of lipid membranes and assembly of proteins encoded by both nuclear and mitochondrial DNA, remain obscure. We followed cristae biogenesis in situ upon Drosophila eclosion using serial-section electron tomography and revealed that the morphogenesis of lamellar cristae coordinates with ETC complex IV assembly. The membrane morphogenesis and gain-of-function were intricately co-evolved during cristae biogenesis. Marf-knockdown flies formed lamellar cristae containing ATP synthase and functional COX. However, OPA1-knockdown flies showed impaired cristae biogenesis. Overall, this study revealed the multilevel coordination of protein-coupled membrane morphogenesis in building functional cristae.
qgg: an R package for large-scale quantitative genetic analyses
Authors: Rohde Palle Duun , Sørensen Izel Fourie , Sørensen Peter 
Published: December 2018

AbstractSummaryStudies of complex traits and diseases are strongly dependent on the availability of user-friendly software designed to handle large-scale genetic and phenotypic data. Here, we present the R package qgg, which provides an environment for large-scale genetic analyses of quantitative traits and disease phenotypes. The qgg package provides an infrastructure for efficient processing of large-scale genetic data and functions for estimating genetic parameters, performing single and multiple marker association analyses, and genomic-based predictions of phenotypes. In particular, we have developed novel predictive models that use information on functional features of the genome that enables more accurate predictions of complex trait phenotypes. We illustrates core facilities of the qgg package by analysing human standing height from the UK Biobank.Availability and implementationThe R package qgg is freely available. For latest updates, user guides and example scripts, consult the main page http://psoerensen.github.io/qgg/.
A unifying photocycle model for light adaptation and temporal evolution of cation conductance in Channelrhodopsin-2
Authors: Kuhne Jens , Vierock Johannes , Tennigkeit Stefan Alexander , Dreier Max-Aylmer , Wietek Jonas , Petersen Dennis , Gavriljuk Konstantin , El-Mashtoly Samir F. , Hegemann Peter , Gerwert Klaus 
Published: December 2018

AbstractAlthough Channelrhodopsin (ChR) is a widely applied light-activated ion channel, important properties such as light-adaptation, photocurrent inactivation, and alteration of the ion selectivity during continuous illumination are not well-understood from a molecular perspective. Herein, we address these open questions using single turn-over electrophysiology, time-resolved step-scan FTIR and Raman spectroscopy of fully dark adapted ChR2. This yields a unifying parallel photocycle model explaining all data: in dark-adapted ChR2, the protonated Schiff base retinal chromophore (RSBH+) adopts an all-trans,C=N-anti conformation only. Upon light activation, a branching reaction into either a 13-cis,C=N-anti or a 13-cis,C=N-syn retinal conformation occurs. The anti-cycle features sequential H+ and Na+ conductance in a late M-like state and an N-like open-channel state. In contrast, the 13-cis,C=N-syn isomer represents a second closed-channel state identical to the long lived P480-state, which has been previously assigned to a late intermediate in a single photocycle model. Light excitation of P480 induces a parallel syn-photocycle with an open channel state of small conductance and high proton selectivity. E90 becomes deprotonated in P480 and stays deprotonated in the C=N-syn-cycle and we show that deprotonation of E90 and successive pore hydration are crucial for late proton conductance following light-adaptation. Parallel anti- and syn-photocycles explain inactivation and ion selectivity changes of ChR2 during continuous illumination, fostering the future rational design of optogenetic tools.Significance statementUnderstanding the mechanisms of photoactivated biological processes facilitates the development of new molecular tools, engineered for specific optogenetic applications, allowing the control of neuronal activity with light. Here, we use a variety of experimental and theoretical techniques to examine the precise nature of the light-activated ion channel in one of the most important molecular species used in optogenetics, channelrhodopsin-2. Existing models for the photochemical and photophysical pathway after light absorption by the molecule fail to explain many aspects of its observed behavior including the inactivation of the photocurrent under continuous illumination. We resolve this by proposing a new branched photocycle explaining electrical and photochemical channel properties and establishing the structure of intermediates during channel turnover.
Impaired reliability and precision of spiking in adults but not juveniles in a mouse model of Fragile X Syndrome
Authors: Dwivedi Deepanjali , Chattarji Sumantra , Bhalla Upinder S. 
Published: December 2018

AbstractFragile X Syndrome (FXS) is the most common source of intellectual disability and autism. Extensive studies have been performed on the network and behavioral correlates of the syndrome but our knowledge about intrinsic conductance changes is still limited. In this study we show a differential effect of FMRP Knock Out (KO) in different sub-sections of hippocampus using whole cell patch clamp in mouse hippocampal slices. We observed no significant change in spike numbers in the CA1 region of hippocampus but a significant increase in CA3, in juvenile mice. However, in adult mice we see a reduction in spike number in the CA1 with no significant difference in CA3. In addition, we see increased variability in spike number in CA1 cells following a variety of steady and modulated current step protocols. This effect emerges in adult (8 weeks) but not juvenile (4 weeks) mice. This increased spiking variability was correlated with reduced spike number and with elevated AHP. The increased AHP arose from elevated SK currents (small conductance calcium activated potassium channels) but other currents involved in mAHP, such as Ih and M, were not significantly different. We obtained a partial rescue of the cellular variability phenotype when we blocked SK current using the specific blocker apamin. Our observations provide a single cell correlate of the network observations of response variability and loss of synchronization, and suggest that elevation of SK currents in FXS may provide a partial mechanistic explanation for this difference.Significance StatementFragile-X syndrome leads to a range of intellectual disability effects and autism. We have found differential effect of FMRP KO in different sub sections of hippocampus where it caused an increased spiking in CA3 in juveniles and reduced spiking in CA1, in adults. We have also found that even individual neurons with this mutation exhibit increased variability in their activity patterns. Importantly, this effect emerges after six weeks of age in mice. We showed that a specific ion channel protein, SK channel, was partially responsible, and blockage of these channels led to a partial restoration of cellular activity. This is interesting as it provides a possible molecular link between activity variability in single cells, and reported irregularity in network activity.
Are Zinc oxide nanoparticles safe? A structural study on human serum albumin using in vitro and in silico methods
Authors: Hassanian Marziyeh , Aryapour Hassan , Goudarzi Alireza , Javan Masoud Bezi 
Published: December 2018

AbstractWith due attention to adsorption of proteins on the nanoparticles surface and the formation of nanoparticle-protein corona, investigation of nanoparticles toxicity on the structure of proteins is important. Therefore, this work was done to evaluate toxicity of Zinc oxide nanoparticles (ZnO NPs) on the structure of human serum albumin (HSA) through in vitro and in silico studies. First, ZnO NPs were synthesized using hydrothermal method and their size and morphology were determined by SEM and TEM methods and then to study its toxicity on the HSA structure were used UV-Vis and fluorescence spectroscopy. Also, in order to investigate interaction mechanism of ZnO NP with HSA at the atomistic level was used molecular dynamics (md) simulation. The obtained images from SEM and TEM showed that ZnO NPs were nanosheet with size of less than 40 nm. The results of spectroscopic studies showed ZnO NPs lead to significant conformational changes in the protein’s absorption and emission spectra. Moreover, md results showed the minor structure changes in HSA due to interaction with ZnO NP during the 100 ns simulation and the formation of nanoparticle-protein corona complex that is mainly because of electrostatic interactions between charge groups of HSA and ZnO NP.
Continent-scale phenotype mapping using citizen scientists’ photographs
Authors: Drury Jonathan P. , Barnes Morgan , Finneran Ann E. , Harris Maddie , Grether Gregory F. 
Published: December 2018

AbstractField investigations of phenotypic variation in free-living organisms are often limited in scope owing to time and funding constraints. By collaborating with online communities of amateur naturalists, investigators can greatly increase the amount and diversity of phenotypic data in their analyses while simultaneously engaging with a public audience. Here, we present a method for quantifying phenotypes of individual organisms in citizen scientists’ photographs. We then show that our protocol for measuring wing phenotypes from photographs yields accurate measurements in two species of Calopterygid damselflies. Next, we show that, while most observations of our target species were made by members of the large and established community of amateur naturalists at iNaturalist.org, our efforts to increase recruitment through various outreach initiatives were successful. Finally, we present results from two case studies: (1) an analysis of wing pigmentation in male smoky rubyspots (Hetaerina titia) showing previously undocumented geographical variation in a seasonal polyphenism, and (2) an analysis of variation in the relative size of the wing spots of male banded demoiselles (Calopteryx splendens) in Great Britain questioning previously documented evidence for character displacement. Our results demonstrate that our protocol can be used to create high quality phenotypic datasets using citizen scientists’ photographs, and, when combined with metadata (e.g., date and location), can greatly broaden the scope of studies of geographical and temporal variation in phenotypes. Our analyses of the recruitment and engagement process also demonstrate that collaborating with an online community of amateur naturalists can be a powerful way to conduct hypothesis-driven research aiming to elucidate the processes that impact trait evolution at landscape scales.
Aspects of invasiveness of Ludwigia and Nelumbo in shallow temperate fluvial lakes
Authors: Tóth Viktor R. , Villa Paolo , Pinardi Monica , Bresciani Mariano 
Published: December 2018

AbstractThe relationship between invasive plant functional traits and their invasiveness is still the subject of scientific investigation, and the backgrounds of transition from non-native to invasive species in ecosystems are therefore poorly understood. Furthermore, our current knowledge on species invasiveness is heavily biased toward terrestrial species; we know much less about the influence of allochthonous plant traits on their invasiveness in aquatic ecosystems. We studied physiological and ecological traits of two introduced and three native macrophyte species in the Mantua lakes system (northern Italy). We compared their photophysiology, pigment content, leaf reflectance, and phenology in order to assess how the invasive Nelumbo nucifera and Ludwigia hexapetala perform compared to native species, Nuphar lutea, Nymphaea alba, and Trapa natans. We found L. hexapetala to have higher photosynthetic efficiency and able to tolerate higher light intensities than N. nucifera and the native species especially at extreme weather conditions (prolonged exposure to high light and higher temperatures). Chlorophyll a and b, and carotenoid contents of both allochthonous species was substantially higher than that of the native plants suggesting adaptive response to the ecosystem of Mantua lakes system. Higher variability of recorded data in invasive species also was observed. These observations suggest advanced photosynthetic efficiency of the invasive species, especially L. hexapetala, resulting in faster growth rates and higher productivity. This was supported by the evaluation of seasonal dynamics mapped from satellite remote sensing data. This study provides empirical evidence for the relationship between specific plant physiological traits and invasiveness of aquatic plant species, highlighting the importance of trait studies in predicting ecosystem-level impacts of invasive plant species.
To integrate or not to integrate: Temporal dynamics of hierarchical Bayesian Causal Inference
Authors: Aller Máté , Noppeney Uta 
Published: December 2018

AbstractTo form a percept of the environment, the brain needs to solve the binding problem – inferring whether signals come from a common cause and be integrated, or come from independent causes and be segregated. Behaviourally, humans solve this problem near-optimally as predicted by Bayesian Causal Inference; but, the neural mechanisms remain unclear. Combining Bayesian modelling, electroencephalography (EEG), and multivariate decoding in an audiovisual spatial localization task, we show that the brain accomplishes Bayesian Causal Inference by dynamically encoding multiple spatial estimates. Initially, auditory and visual signal locations are estimated independently; next, an estimate is formed that combines information from vision and audition. Yet, it is only from 200 ms onwards that the brain integrates audiovisual signals weighted by their bottom-up sensory reliabilities and top-down task-relevance into spatial priority maps that guide behavioural responses. Critically, as predicted by Bayesian Causal Inference, these spatial priority maps take into account the brain’s uncertainty about the world’s causal structure and flexibly arbitrate between sensory integration and segregation. The dynamic evolution of perceptual estimates thus reflects the hierarchical nature of Bayesian Causal Inference, a statistical computation, crucial for effective interactions with the environment.
Extensive recombination suppression and chromosome-wide differentiation of a segregation distorter in Drosophila
Authors: Fuller Zachary L. , Koury Spencer A. , Leonard Christopher J. , Young Randee E. , Ikegami Kobe , Westlake Jonathan , Richards Stephen , Schaeffer Stephen W. , Phadnis Nitin 
Published: December 2018

AbstractSegregation distorters violate Mendelian Inheritance by over-representing themselves in the progeny of carrier individuals and are commonly associated with chromosomal inversions. When distorting alleles are found on sex chromosomes, the progeny of carrier individuals will exhibit skewed sex ratios, as exemplified by the array ofSex-Ratio(SR) distorting chromosomes found in Drosophila. Because of the strong selective pressures such chromosomes are thought to inflict on genomes, segregation distorters and their associated inversions are expected to experience rapid turn-over. However, theSRX-chromosome ofDrosophila pseudoobscurais found at high frequencies in natural populations, forms stable latitudinal clines, appears to be unsuppressed, and shows evidence of being quite long-lived. Despite being a historically significant and well-studied segregation distortion system, the mechanisms allowing for the long-term persistence of theD.pseudoobscura SRchromosome remain unclear. Here, we perform a comparative genomic analysis betweenSRand uninverted standard X-chromosomes inD.pseudoobscurato study its evolutionary history and dynamics. We find a substantial level of differentiation between theSRand standard chromosome and estimate that the associated inversions have likely existed for the entire lifetime of the species (>2 million generations). Through direct recombination experiments and population genetic analyses, we infer that this high level of differentiation is maintained by a combination of suppressed recombination and epistatic selection. Finally, our data reveal a massive mutational target size for protein and expression level changes specific toSRgenerated by its three non-overlapping inversions. Together our results imply that the entireSRchromosome inD.pseudoobscurabehaves as a single co-adapted gene complex and has been maintained through a combination of suppressed recombination and epistatic selection. This finding highlights the dramatic consequences segregation distorters can have in shaping chromosome-wide patterns of recombination, nucleotide variation, and gene expression.
The Bayesian Superorganism: externalised memories facilitate distributed sampling
Authors: Hunt Edmund R. , Franks Nigel R. , Baddeley Roland J. 
Published: December 2018

AbstractA key challenge for any animal (or sampling technique) is to avoid wasting time by searching for resources (information) in places already found to be unprofitable. In biology, this challenge is particularly strong when the organism is a central place forager – returning to a nest between foraging bouts – because it is destined repeatedly to cover much the same ground. This problem will be particularly acute if many individuals forage from the same central place, as in social insects such as the ants. Foraging (sampling) performance may be greatly enhanced by coordinating movement trajectories such that each ant (‘walker’) visits separate parts of the surrounding (unknown) space. We find experimental evidence for an externalised spatial memory in Temnothorax albipennis ants: chemical markers (either pheromones or cues such as cuticular hydrocarbon footprints) that are used by nestmates to mark explored space. We show these markers could be used by the ants to scout the space surrounding their nest more efficiently through indirect coordination. We also develop a simple model of this marking behaviour that can be applied in the context of Markov chain Monte Carlo methods (Baddeley et al. 2019). This substantially enhances the performance of standard methods like the Metropolis–Hastings algorithm in sampling from sparse probability distributions (such as those confronted by the ants) with little additional computational cost. Our Bayesian framework for superorganismal behaviour motivates the evolution of exploratory mechanisms such as trail marking in terms of enhanced collective information processing.