bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations
Authors: Paul Dhiraj , Jani Kunal , Kumar Janesh , Chauhan Radha , Seshadri Vasudevan , Lal Girdhari , Karyakarte Rajesh , Joshi Suvarna , Tambe Murlidhar , Sen Sourav , Karade Santosh , Anand Kavita Bala , Singh Shergill Shelinder Pal , Gupta Rajiv Mohan , Bhat Manoj Kumar , Sahu Arvind , Shouche Yogesh S
Published: August 2020

India has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4715Leu), and A23403G (Asp614Gly), located at 5’UTR, Orf1a, Orf1b, and Spike protein regions of the genome, respectively, were predominant and ubiquitous (90%). Phylogenetic analysis of the genomes revealed four distinct clusters, formed owing to different variants. The major cluster (cluster 4) is distinguished by mutations C313T, C5700A, G28881A are unique patterns and observed in 45% of samples. We thus report a newly emerging pattern of linked mutations. The predominance of these linked mutations suggests that they are likely a part of the viral fitness landscape. A novel and distinct pattern of mutations in the viral strains of each of the districts was observed. The Satara district viral strains showed mutations primarily at the 3′ end of the genome, while Nashik district viral strains displayed mutations at the 5′ end of the genome. Characterization of Pune strains showed that a novel variant has overtaken the other strains. Examination of the frequency of three mutations i.e., C313T, C5700A, G28881A in symptomatic versus asymptomatic patients indicated an increased occurrence in symptomatic cases, which is more prominent in females. The age-wise specific pattern of mutation is observed. Mutations C18877T, G20326A, G24794T, G25563T, G26152T, and C26735T are found in more than 30% study samples in the age group of 10-25. Intriguingly, these mutations are not detected in the higher age range 61-80. These findings portray the prevalence of unique linked mutations in SARS-CoV-2 in western India and their prevalence in symptomatic patients.

Importance

Elucidation of the SARS-CoV-2 mutational landscape within a specific geographical location, and its relationship with age and symptoms, is essential to understand its local transmission dynamics and control. Here we present the first comprehensive study on genome and mutation pattern analysis of SARS-CoV-2 from the western part of India, the worst affected region by the pandemic. Our analysis revealed three unique linked mutations, which are prevalent in most of the sequences studied. These may serve as a molecular marker to track the spread of this viral variant to different places.
Pursuing the Mechanisms Underlying Alcohol-Induced Changes in the Ghrelin System: New Insights from Preclinical and Clinical Investigations
Authors: Farokhnia Mehdi , Deschaine Sara L. , Gregory-Flores Adriana , Zallar Lia J. , You Zhi-Bing , Sun Hui , Harvey Deon M. , Marchette Renata C.N. , Tunstall Brendan J. , Mani Bharath K. , Moose Jacob E. , Lee Mary R. , Gardner Eliot , Akhlaghi Fatemeh , Roberto Marisa , Hougland James L. , Zigman Jeffrey M. , Koob George F. , Vendruscolo Leandro F. , Leggio Lorenzo
Published: August 2020

Ghrelin is a gastric-derived peptide hormone with demonstrated impact on alcohol intake and craving, but the reverse side of this bidirectional link, i.e., the effects of alcohol on the ghrelin system, remains to be fully established. To characterize the downstream effects of alcohol on the ghrelin system, we examined the following: (1) plasma ghrelin levels across four human laboratory alcohol administration experiments with non-treatment seeking, heavy-drinking participants, (2) expression of ghrelin, ghrelin receptor, and ghrelin-O-acyltransferase (GOAT) genes(GHRL, GHSR,andMBOAT4, respectively) in humanpost-mortembrain tissue from individuals with alcohol use disorder (AUD)vs.controls, (3) plasma ghrelin levels inGhsrknockout and wild-type rats following intraperitoneal (i.p.) ethanol administration, (4) effect of ethanol on ghrelin secretion from gastric mucosa cellsex vivoand GOAT enzymatic activityin vitro,and (5) plasma ghrelin levels in rats following i.p. ethanol administrationvs. an iso-caloric sucrose solution. Peripheral acyl- and total ghrelin levels significantly decreased following acute ethanol administration in humans. No difference inGHRL, GHSR,andMBOAT4mRNA expression in the brain was observed between AUDvs.controlpost-mortemsamples. In rats, acyl-ghrelin levels significantly decreased following i.p. ethanol administration in both genotype groups(Ghsrknockout and wild-type), while des-acyl-ghrelin was not affected by ethanol. No effect of ethanol was observedex vivoon ghrelin secretion from gastric mucosa cells orin vitroon GOAT acylation activity. Lastly, we observed different effects of i.p. ethanol and sucrose solution on acyl- and des-acyl-ghrelin in rats despite administering amounts with equivalent caloric value. Ethanol acutely decreases peripheral ghrelin concentrations in humans and rats, and our findings suggest that this effect does not occur through interaction with ghrelin-secreting gastric mucosal cells, the ghrelin receptor, or the GOAT enzyme. Moreover, this effect does not appear to be proportional to caloric load. Our findings, therefore, suggest that ethanol does not suppress circulating ghrelin through direct interaction with the ghrelin system, or in proportion to the caloric value of alcohol, and may differentially affect ghrelin acylation and ghrelin peptide secretion.
Host-mediated, cross-generational intraspecific competition in a herbivore species
Authors: Castagneyrol Bastien , Halder Inge van , Kadiri Yasmine , Schillé Laura , Jactel Hervé
Published: August 2020

Abstract

Conspecific insect herbivores co-occurring on the same host plant interact both directly through interference competition and indirectly through exploitative competition, plant-mediated interactions and enemy-mediated interactions. However, the situation is less clear when the interactions between conspecific insect herbivores are separated in time within the same growing season, as it is the case for multivoltine species. We hypothesized that early season herbivory would result in reduced egg laying and reduced performance of the next generation of herbivores on previously attacked plants. We tested this hypothesis in a choice experiment with box tree moth females (Cydalima perspectalisWalker, Lepidoptera: Crambidae). These females were exposed to box trees (Buxus sempervirensL., Buxaceae) that were either undamaged or attacked by conspecific larvae earlier in the season. We then compared the performance of the next generation larvae on previously damagedvsundamaged plants. Previous herbivory had no effect on oviposition behaviour, but the weight of next generation larvae was significantly lower in previously damaged plants. There was a negative correlation between the number of egg clutches laid on plants by the first generation and the performance of the next generation larvae. Overall, our findings reveal that early season herbivory reduces the performance of conspecific individuals on the same host plant later in the growing season, and that this time-lagged intraspecific competition results from a mismatch between the oviposition preference of females and the performance of its offspring.
Parasitism and host dispersal plasticity in an aquatic model system
Authors: Zilio Giacomo , Nørgaard Louise S. , Petrucci Giovanni , Zeballos Nathalie , Gougat-Barbera Claire , Fronhofer Emanuel A. , Kaltz Oliver
Published: August 2020

Dispersal is a central determinant of spatial dynamics in communities and ecosystems, and various ecological factors can shape the evolution of constitutive and plastic dispersal behaviours. One important driver of dispersal plasticity is the biotic environment. Parasites, for example, influence the internal condition of infected hosts and define external patch quality. Thus state-dependent dispersal may be determined by infection status and context-dependent dispersal by the abundance of infected hosts in the population. A prerequisite for such dispersal plasticity to evolve is a genetic basis on which natural selection can act. Using interconnected microcosms, we investigated dispersal in experimental populations of the freshwater protistParamecium caudatumin response to the bacterial parasiteHolospora undulata. For a collection of 20 natural host strains, we found substantial variation in constitutive dispersal, and to a lesser degree in dispersal plasticity. First, infection tended to increase or decrease dispersal relative to uninfected controls, depending on strain identity, potentially indicative of state-dependent dispersal plasticity. Infection additionally decreased host swimming speed compared to the uninfected counterparts. Second, for certain strains, there was a weak negative association between dispersal and infection prevalence, such that uninfected hosts tended to disperse less when infection was more frequent in the population, indicating context-dependent dispersal plasticity. Future experiments may test whether the observed differences in dispersal plasticity are sufficiently strong to react to natural selection. The evolution of dispersal plasticity as a strategy to mitigate parasite effects spatially may have important implications for epidemiological dynamics.
Motor cortical dynamics are shaped by multiple distinct subspaces during naturalistic behavior
Authors: Perich Matthew G. , Conti Sara , Badi Marion , Bogaard Andrew , Barra Beatrice , Rajan Kanaka , Bloch Jocelyne , Courtine Gregoire , Micera Silvestro , Capogrosso Marco , Milekovic Tomislav
Published: August 2020

Behavior relies on continuous influx of sensory information about the body. In primates, motor cortex must integrate somatic feedback to accurately reach and manipulate objects. Yet, prior work demonstrates that motor cortex is well-described with deterministic, rather than input-driven, dynamics. Deterministic dynamics facilitate robust movement generation, but flexible motor output requires rapid responses to unexpected inputs. Here, we resolved this paradox by simultaneously recording neural population activity in motor and somatosensory cortex from four monkeys performing a naturalistic object interaction behavior resulting in occasional errors. Motor cortex was strikingly input-driven surrounding behavioral error correction. Intriguingly, input-driven dynamics were isolated to a subspace of the population activity that putatively captured somatosensory feedback. Using electrical stimulation of ascending somatosensory tracts, we causally verified that this feedback subspace captured peripheral inputs to cortex. Our results demonstrate that cortical activity is compartmentalized within distinct subspaces, enabling flexible integration of salient inputs for robust behavior.
Deep Learning Based Segmentation of Brain Tissue from Diffusion MRI
Authors: Zhang Fan , Breger Anna , Kevin Cho Kang Ik , Ning Lipeng , Westin Carl-Fredrik , O’Donnell Lauren J. , Pasternak Ofer
Published: August 2020

Segmentation of brain tissue types from diffusion MRI (dMRI) is an important task, required for quantification of brain microstructure and for improving tractography. Current dMRI segmentation is mostly based on anatomical MRI (e.g., T1- and T2-weighted) segmentation that is registered to the dMRI space. However, such inter-modality registration is challenging due to more image distortions and lower image resolution in the dMRI data as compared with the anatomical MRI data. In this study, we present a deep learning method that learns tissue segmentation from high-quality imaging datasets from the Human Connectome Project (HCP), where registration of anatomical data to dMRI is more precise. The method is then able to predict a tissue segmentation directly from new dMRI data, including data collected with a different acquisition protocol, without requiring anatomical data and inter-modality registration. We train a convolutional neural network (CNN) to learn a tissue segmentation model using a novel augmented target loss function designed to improve accuracy in regions of tissue boundary. To further improve accuracy, our method adds diffusion kurtosis imaging (DKI) parameters that characterize non-Gaussian water molecule diffusion to the conventional diffusion tensor imaging parameters. The DKI parameters are calculated from the recently proposed mean-kurtosis-curve method that corrects implausible DKI parameter values and provides additional features that discriminate between tissue types. We demonstrate high tissue segmentation accuracy on HCP data, and also when applying the HCP-trained model on dMRI data from a clinical acquisition with lower resolution and fewer gradient directions.
Sexual dimorphism of synaptonemal complex length among populations of threespine stickleback fish
Authors: Madison Barquiesha S. , Nath Shivangi , Flanagan Mary K. , Dorsey Brittany A. , White Michael A.
Published: August 2020

Crossover frequencies often differ substantially between sexes (i.e. heterochiasmy). Although this phenomenon is widespread throughout taxa, the mechanisms that lead to heterochiasmy remain unclear. One pattern that has emerged is that the overall length of the synaptonemal complex likely has a direct influence on the total number of crossovers in each sex. However, this has only been investigated in a handful of species. The threespine stickleback fish (Gasterosteus aculeatus) is an excellent species to explore whether synaptonemal complex length is associated with differences in the total number of crossovers, as females have much longer linkage maps than males. We used an immunocytological approach to quantify synaptonemal complex length in late pachytene female and male meiocytes in two different populations of threespine stickleback fish. Overall, the freshwater population had shorter synaptonemal complex lengths than the marine population. In both populations we observed sexual dimorphism, with females possessing longer axes. Our results support a model where chromosome axis length determines overall crossover frequency and establish the threespine stickleback as a useful species to explore the mechanistic basis of heterochiasmy as well as the genetic basis underlying variation in synaptonemal complex length.
Optically pumped magnetometers disclose magnetic field components of the muscular action potential
Authors: Broser Philip J. , Middelmann Thomas , Sometti Davide , Braun Christoph
Published: August 2020

Aim

To track the magnetic field generated by the propagating muscle action potential (MAP).

Method

In this prospective, proof of principle study, the magnetic activity of the intrinsic foot muscle after electric stimulation of the tibial nerve was measured using optically pumped magnetometers (OPMs). A classical biophysical electric dipole model of the propagating MAP was implemented to model the source of the data.

Results

The signal profile generated by the activity of the intrinsic foot muscles was measured by four OPM devices. Three devices were located above the same muscle to compare the direction and the strength of the magnetic signal while propagating along the muscle.

Interpretation

OPM devices allow for a new, non-invasive way to study MAP patterns. Since magnetic fields are less altered by the tissue surrounding the dipole source compared to electric activity, a precise analysis of the spatial characteristics and temporal dynamics of the MAP is possible. The classic electric dipole model explains major but not all aspects of the magnetic field. The field has longitudinal components generated by intrinsic structures of the muscle fibre. By understanding these magnetic components, new methods could be developed to analyse the muscular signal transduction pathway in greater detail.

What this paper adds

- Technological concepts to record and analyse the small magnetic fields generated by electric muscular activity

- Model to link the signals measured by the OPM sensors to the underlying physiology

- Insights into the propagation of muscle action potential and the sequential control of motor activity
Deep learning-enhanced light-field imaging with continuous validation
Authors: Wagner Nils , Beuttenmueller Fynn , Norlin Nils , Gierten Jakob , Boffi Juan Carlos , Wittbrodt Joachim , Weigert Martin , Hufnagel Lars , Prevedel Robert , Kreshuk Anna
Published: August 2020

Light-field microscopy (LFM) has emerged as a powerful tool for fast volumetric image acquisition in biology, but its effective throughput and widespread use has been hampered by a computationally demanding and artefact-prone image reconstruction process. Here, we present a novel framework consisting of a hybrid light-field light-sheet microscope and deep learning-based volume reconstruction, where single light-sheet acquisitions continuously serve as training data and validation for the convolutional neural network reconstructing the LFM volume. Our network delivers high-quality reconstructions at video-rate throughput and we demonstrate the capabilities of our approach by imaging medaka heart dynamics and zebrafish neural activity.
Genetics of resistance to common root rot (spot blotch),Fusariumcrown rot, and sharp eyespot in wheat
Authors: Su Jun , Zhao Jiaojie , Zhao Shuqing , Li Mengyu , Pang Shuyong , Chen Shisheng , Chen Feng , Zhen Wenchao , Kang Zhensheng , Wang Xiaodong
Published: August 2020

Due to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch),Fusariumcrown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot,Fusariumcrown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized.
Failure of vergence size constancy challenges our understanding of visual scale
Authors: Linton Paul
Published: August 2020

The closer an object is, the more the eyes have to rotate to fixate on it. This degree of eye rotation (or vergence) is thought to play an essential role in size constancy, the process of perceiving an object as having a constant physical size despite changes in distance. But vergence size constancy has never been tested divorced from confounding cues such as changes in the retinal image. We control for these confounding cues and find no evidence of vergence size constancy. This has three important implications. First, we need a new explanation for binocular vision’s contribution to visual scale. Second, the vergence modulation of neurons in V1 can no longer be responsible for size constancy. Third, given the role attributed to vergence in multisensory integration, multisensory integration appears to be more reliant on cognitive factors than previous thought.
Nucleotide usage biases distort inferences of the species tree
Authors: Borges Rui , Boussau Bastien , Szöllősi Gergely J. , Kosiol Carolin
Published: August 2020

Despite the importance of natural selection in species’ evolutionary history, phylogenetic methods that take into account population-level processes typically ignore selection. The assumption of neutrality is often based on the idea that selection occurs at a minority of loci in the genome and is unlikely to compromise phylogenetic inferences significantly. However, genome-wide processes like GC-bias and some variation segregating at the coding regions are known to evolve in the nearly neutral range. As we are now using genome-wide data to estimate species trees, it is natural to ask whether weak but pervasive selection is likely to blur species tree inferences. We developed a polymorphism-aware phylogenetic model tailored for measuring signatures of nucleotide usage biases to test the impact of selection in the species tree. Our analyses indicate that while the inferred relationships among species are not significantly compromised, the genetic distances are systematically underestimated in a node-height dependent manner: i.e., the deeper nodes tend to be more underestimated than the shallow ones. Such biases have implications for molecular dating. We dated the evolutionary history of 30 worldwide fruit fly populations, and we found signatures of GC-bias considerably affecting the estimated divergence times (up to 23%) in the neutral model. Our findings call for the need to account for selection when quantifying divergence or dating species evolution.

Significance statement

Although little is known about the impact of natural selection on species tree estimation, expectations are that it occurs at a minority of loci in eukaryotic genomes and is thus unlikely to affect the divergence process. However, growing evidence suggests that a large amount of the genomic variation evolves under weak but pervasive selection (e.g., fixation biases created by GC-bias gene conversion). We tested the impact of unaccounted-for nearly neutral selection on species tree estimation and found that the estimated branch lengths are systematically biased. Our results highlight the need for selection-aware models in species tree estimation and molecular dating.
Multiscale integration of environmental stimuli in plant tropism produces complex behaviors
Authors: Moulton Derek E. , Oliveri Hadrien , Goriely Alain
Published: August 2020

Plant tropism refers to the directed movement of an organ or organism in response to external stimuli. Typically, these stimuli induce hormone transport that triggers cell growth or deformation. In turn, these local cellular changes create mechanical forces on the plant tissue that are balanced by an overall deformation of the organ, hence changing its orientation with respect to the stimuli. This complex feedback mechanism takes place in a three-dimensional growing plant with varying stimuli depending on the environment. We model this multiscale process in filamentary organs for an arbitrary stimulus by linking explicitly hormone transport to local tissue deformation leading to the generation of mechanical forces and the deformation of the organ in three dimensions. We show, as examples, that the gravitropic, phototropic, nutational, and thigmotropic dynamic responses can be easily captured by this framework. Further, the integration of evolving stimuli and/or multiple contradictory stimuli can lead to complex behavior such as sun following, canopy escape, and plant twining.

Significance Statement

To survive and to thrive, plants rely on their ability to sense multiple environmental signals, such as gravity or light, and respond to them by growing and changing their shape. To do so, the signals must be transduced down to the cellular level to create the physical deformations leading to shape changes. We propose a multiscale theory of tropism that takes multiple stimuli and transforms them into auxin transport that drives tissue-level growth and remodeling, thus modifying the plant shape and position with respect to the stimuli. This feedback loop can be dynamically updated to understand the response to individual stimuli or the complex behavior generated by multiple stimuli such as canopy escape or pole wrapping for climbing plants.
Covert attention increases the gain of stimulus-evoked population codes
Authors: Foster Joshua J. , Thyer William , Wennberg Janna W. , Awh Edward
Published: August 2020

Covert spatial attention has a variety of effects on the responses of individual neurons. However, relatively little is known about the net effect of these changes on sensory population codes, even though perception ultimately depends on population activity. Here, we measured the electroencephalogram (EEG) in human observers (male and female), and isolated stimulus-evoked activity that was phase-locked to the onset of attended and ignored visual stimuli. Using an encoding model, we reconstructed spatially selective population tuning functions from the pattern of stimulus-evoked activity across the scalp. Our EEG-based approach allowed us to measure very early visually evoked responses occurring ~100 ms after stimulus onset. In Experiment 1, we found that covert attention increased the amplitude of spatially tuned population responses at this early stage of sensory processing. In Experiment 2, we parametrically varied stimulus contrast to test how this effect scaled with stimulus contrast. We found that the effect of attention on the amplitude of spatially tuned responses increased with stimulus contrast, and was well-described by an increase in response gain (i.e., a multiplicative scaling of the population response). Together, our results show that attention increases the gain of spatial population codes during the first wave of visual processing.

Significance Statement

We know relatively little about how attention improves population codes, even though perception is thought to critically depend on population activity. In this study, we used an encoding-model approach to test how attention modulates the spatial tuning of stimulus-evoked population responses measured with EEG. We found that attention multiplicatively scales the amplitude of spatially tuned population responses. Furthermore, this effect was present within 100 ms of stimulus onset. Thus, our results show that attention improves spatial population codes by increasing their gain at this early stage of processing.
Reinforcement Learning approaches to hippocampus-dependent flexible spatial navigation
Authors: Tessereau Charline , O’Dea Reuben , Coombes Stephen , Bast Tobias
Published: August 2020

Humans and non-human animals show great flexibility in spatial navigation, including the ability to return to specific locations based on as few as one single experience. To study spatial navigation in the laboratory, watermaze tasks, in which rats have to find a hidden platform in a pool of cloudy water surrounded by spatial cues, have long been used. Analogous tasks have been developed for human participants using virtual environments. Spatial learning in the watermaze is facilitated by the hippocampus. In particular, rapid, one-trial, allocentric place learning, as measured in the Delayed-Matching-to-Place (DMP) variant of the watermaze task, which requires rodents to learn repeatedly new locations in a familiar environment, is hippocampal dependent. In this article, we review some computational principles, embedded within a Reinforcement Learning (RL) framework, that utilise hippocampal spatial representations for navigation in watermaze tasks. We consider which key elements underlie their efficacy, and discuss their limitations in accounting for hippocampus-dependent navigation, both in terms of behavioural performance (i.e., how well do they reproduce behavioural measures of rapid place learning) and neurobiological realism (i.e., how well do they map to neurobiological substrates involved in rapid place learning). We discuss how an actor-critic architecture, enabling simultaneous assessment of the value of the current location and of the optimal direction to follow, can reproduce one-trial place learning performance as shown on watermaze and virtual DMP tasks by rats and humans, respectively, if complemented with map-like place representations. The contribution of actor-critic mechanisms to DMP performance is consistent with neurobiological findings implicating the striatum and hippocampo-striatal interaction in DMP performance, given that the striatum has been associated with actor-critic mechanisms. Moreover, we illustrate that hierarchical computations embedded within an actor-critic architecture may help to account for aspects of flexible spatial navigation. The hierarchical RL approach separates trajectory control via a temporal-difference error from goal selection via a goal prediction error and may account for flexible, trial-specific, navigation to familiar goal locations, as required in some arm-maze place memory tasks, although it does not capture one-trial learning of new goal locations, as observed in open field, including watermaze and virtual, DMP tasks. Future models of one-shot learning of new goal locations, as observed on DMP tasks, should incorporate hippocampal plasticity mechanisms that integrate new goal information with allocentric place representation, as such mechanisms are supported by substantial empirical evidence.
Trophic niche of the invasive gregarious speciesCrepidula fornicata, in relation to ontogenic changes
Authors: Androuin Thibault , Dubois Stanislas F. , Hubas Cédric , Lefebvre Gwendoline , Le Grand Fabienne , Schaal Gauthier , Carlier Antoine
Published: August 2020

Abstract

The slipper limpetCrepidula fornicatais a common and widespread invasive gregarious species along the European coast. Among its life-history traits, well documented ontogenic changes in behavior (i.e., motile male to sessile female) suggests a potential shift in feeding strategy across its life stages. Considering the ecological significance of this species in colonized areas, understanding how conspecifics share the trophic resource is crucial. Using fatty acids (FA) and stable isotopes (SI) as complementary trophic markers, we conducted a field survey between late winter and spring to investigate the trophic niche of three ontogenic stages ofC. fornicatathat bear different sexual (male/female) and motility (motile/sessile) traits. Potential trophic sources were characterized by their pigment, FA and SI compositions and discriminated well over the study period. We showed that the biofilm coveringC. fornicatashells harbored a higher biomass of primary producers (i.e., chlorophytes and diatoms) than the surrounding sediment surface. Over the study period, we observed a covariation between the three ontogenic stages for both FA and SI compositions which suggest that the trophic niche ofC. fornicatadoes not change significantly across its benthic life. During periods of low food availability, slipper limpets displayed an opportunistic suspension-feeding behaviour, relying on both fresh and detrital organic matter, likely coming from superficial sedimentary organic matter. During high food availability (i.e., spring phytoplankton bloom), all ontogenic stages largely benefited from this fresh supply of organic matter (pelagic diatoms in this case). However, the three ontogenic stages showed consistent differences in FA composition, and to a lesser extent in SI composition. These differences persist over time, as they originate more likely from ontogenic physiological changes (e.g., differential growth rates, metabolic rate or gametogenesis) rather than diet discrepancies.
It’s not just poverty: unregulated global market and bad governance explain unceasing deforestation in Western Madagascar
Authors: Vieilledent Ghislain , Nourtier Marie , Grinand Clovis , Pedrono Miguel , Clausen Alison , Rabetrano Tsiky , Rakotoarijaona Jean-Roger , Rakotoarivelo Bruno , Rakotomalala Fety A. , Rakotomalala Linjanantenaina , Razafimpahanana Andriamandimbisoa , Ralison José M. , Achard Frédéric
Published: August 2020

Madagascar is recognized both for its unparalleled biodiversity and the high level of threat suffered by this biodiversity, associated in particular with anthropogenic deforestation. Despite sustained efforts to fight poverty and curb deforestation, forest cover in Madagascar is rapidly decreasing. To try to explain why it is so difficult to stop deforestation in Madagascar, we analysed the recent deforestation process in Western Madagascar through satellite image analysis and field surveys. We show that deforestation has increased from less than 0.9%/yr on 2000–2010 to more than 2%/yr on 2010–2017. We identified two major causes of deforestation, which were not associated with subsistence agriculture: slash-and-burn agriculture for the cultivation of cash crops (maize and peanut), and uncontrolled fires to create open pasture. Maize production is mainly at the destination of the domestic market and is used in particular for livestock feeding. Peanut production has boomed since 2013 and more than half of it is now exported towards asiatic countries. The money earned by farmers is principally invested into zebu herd acquisition. Trade of agricultural commodities benefits several intermediaries, some of whom have political responsibilities thus creating conflicts of interest. On the other hand, agents from institutions in charge of the management of the protected areas have no means to enforce laws against deforestation. In the absence of an efficient strategy to stop deforestation, we predicted that 38-93% of the forest present in 2000 will have disappeared in 2050. Forest loss, apart from biodiversity loss and climate-change global issues, will be at the expense of local population. In order to stop deforestation, international aid should be used to improve local governance to enforce environmental laws and pressure should be put on trading companies to buy certified agricultural commodities that are not derived from deforestation.
A Newcastle disease virus (NDV) expressing membrane-anchored spike as a cost-effective inactivated SARS-CoV-2 vaccine
Authors: Sun Weina , McCroskery Stephen , Liu Wen-Chun , Leist Sarah R. , Liu Yonghong , Albrecht Randy A. , Slamanig Stefan , Oliva Justine , Amanat Fatima , Schäfer Alexandra , Dinnon Kenneth H. , Innis Bruce L. , García-Sastre Adolfo , Krammer Florian , Baric Ralph S. , Palese Peter
Published: August 2020

A successful SARS-CoV-2 vaccine must be not only safe and protective but must also meet the demand on a global scale at low cost. Using the current influenza virus vaccine production capacity to manufacture an egg-based inactivated Newcastle disease virus (NDV)/SARS-CoV-2 vaccine would meet that challenge. Here, we report pre-clinical evaluations of an inactivated NDV chimera stably expressing the membrane-anchored form of the spike (NDV-S) as a potent COVID-19 vaccine in mice and hamsters. The inactivated NDV-S vaccine was immunogenic, inducing strong binding and/or neutralizing antibodies in both animal models. More importantly, the inactivated NDV-S vaccine protected animals from SARS-CoV-2 infections or significantly attenuated SARS-CoV-2 induced disease. In the presence of an adjuvant, antigen-sparing could be achieved, which would further reduce the cost while maintaining the protective efficacy of the vaccine.
Validation and Application of a Bench Top Cell Sorter in a BSL-3 Containment Setting
Authors: Roberts Lydia M , Anderson Rebecca , Carmody Aaron , Bosio Catharine M
Published: August 2020

Rigorous assessment of the cellular and molecular changes during infection typically requires isolation of specific immune cell subsets for downstream application. While there are numerous options for enrichment/isolation of cells from tissues, fluorescent activated cell sorting (FACS) is accepted as a method that results in superior purification of a wide variety of cell types. Flow cytometry requires extensive fluidics and aerosol droplets can be generated during collection of target cells. Pathogens such asFrancisella tularensis,Mycobacterium tuberculosis,Yersinia pestis, and SARS-CoV-2 require manipulation at biosafety level-3 (BSL-3). Due to the concern of potential aerosolization of these pathogens, use of flow cytometric-based cell sorting in these laboratory settings requires placement of the equipment in dedicated biosafety cabinets within the BSL-3. For many researchers, this is often not possible due to expense, space, or expertise available. Here we describe the safety validation and utility of a completely closed cell sorter that results in gentle, rapid, high purity, and safe sorting of cells on the benchtop at BSL-3. We also provide data demonstrating the need for cell sorting versus bead purification and the applicability of this technology for BSL-3 and potentially BSL-4 related infectious disease projects. Adoption of this technology will significantly expand our ability to uncover important features of the most dangerous infectious diseases leading to faster development of novel vaccines and therapeutics.
Intrinsic neural timescales related to sensory processing: Evidence from abnormal behavioural states
Authors: Zilio Federico , Gomez-Pilar Javier , Cao Shumei , Zhang Jun , Zang Di , Qi Zengxin , Tan Jiaxing , Hiromi Tanigawa , Wu Xuehai , Fogel Stuart , Huang Zirui , Hohmann Matthias R. , Fomina Tatiana , Synofzik Matthis , Grosse-Wentrup Moritz , Owen Adrian M. , Northoff Georg
Published: August 2020

The brain exhibits a complex temporal structure which translates into a hierarchy of distinct neural timescales. An open question is how these intrinsic timescales are related to sensory or motor information processing and whether these dynamics have common patterns in different behavioural states. We address these questions by investigating the brain’s intrinsic timescales in healthy controls, motor (amyotrophic lateral sclerosis, locked-in syndrome), sensory (anaesthesia, unresponsive wakefulness syndrome), and progressive reduction of sensory processing (from awake states over N1, N2, N3). We employed a combination of measures from EEG resting-state data: auto-correlation window (ACW), power spectral density (PSD), and power-law exponent (PLE). Prolonged neural timescales accompanied by a shift towards slower frequencies were observed in the conditions with sensory deficits, but not in conditions with motor deficits. Our results establish that the spontaneous activity’s intrinsic neural timescale is related to specifically sensory rather than motor information processing in the healthy brain.

Highlights

EEG resting-state shows a hierarchy of intrinsic neural timescales.

Sensory deficits as in disorders of consciousness lead to prolonged intrinsic neuraltimescales.

Clinical conditions with motor deficits do not show changes in intrinsic neural timescales.20

Graphical Abstract
Estimating Genetic Similarity Matrices using Phylogenies
Authors: Wang Shijia , Ge Shufei , Colijn Caroline , Biller Priscila , Wang Liangliang , Elliott Lloyd T
Published: August 2020

Genetic similarity is a measure of the genetic relatedness among individuals. The standard method for computing these matrices involves the inner product of observed genetic variants. Such an approach is inaccurate or impossible if genotypes are not available, or not densely sampled, or of poor quality (for example, genetic analysis of extinct species). We provide a new method for computing genetic similarities among individuals using phylogenetic trees. Our method can supplement (or stand in for) computations based on genotypes. We provide simulations suggesting that the genetic similarity matrices computed from trees are consistent with those computed from genotypes. With our methods, quantitative analysis on genetic traits and analysis of heritability and co-heritability can be conducted directly using genetic similarity matrices and so in the absence of genotype data, or under uncertainty in the phylogenetic tree. We use simulation studies to demonstrate the advantages of our method, and we provide applications to data.
dadi.CUDA: Accelerating population genetic inference with Graphics Processing Units
Authors: Gutenkunst Ryan N.
Published: August 2020

Extracting insight from population genetic data often demands computationally intensive modeling. dadi is a popular program for fitting models of demographic history and natural selection to such data. Here, I show that running dadi on a Graphics Processing Unit (GPU) can speed computation by orders of magnitude compared to the CPU implementation, with minimal user burden. This speed increase enables the analysis of more complex models, which motivated the extension of dadi to four- and five-population models. Remarkably, dadi performs almost as well on inexpensive consumer-grade GPUs as on expensive server-grade GPUs. GPU computing thus offers large and accessible benefits to the community of dadi users. This functionality is available in dadi version 2.1.0,https://bitbucket.org/gutenkunstlab/dadi/.
Genome fractionation and loss of heterozygosity in hybrids and polyploids: mechanisms, consequences for selection, and link to gene function
Authors: Janko Karel , Bartoš Oldřich , Kočí Jan , Roslein Jan , Drdová Edita Janková , Kotusz Jan , Eisner Jan , Štefková-Kašparová Eva
Published: August 2020

Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. During their evolution, the subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that may enforce specific evolutionary pathways.

We studied the genome evolution in asexual diploid and polyploid hybrids between fish from the genusCobitis. Comparing exome sequencing with published cytogenetic and RNAseq data revealed that clonal genomes remain static on chromosome-scale levels but undergo considerable small-scale restructurations owing to two major processes; hemizygous deletions and gene conversions. Interestingly, polyploids were much more tolerant to accumulating deletions than diploid asexuals where gene conversions prevailed. The genomic restructurations accumulated preferentially in genes characterized by high transcription levels, relatively strong purifying selection and some specific functions such as interacting with intracellular membranes. The likelihood of an ortholog’s retention or loss correlated with its parental-species ancestry, GC content, and expression. Furthermore, all hybrids showed a strong bias towards the retention of one parental subgenome. Contrary to expectations, however, the preferentially retained subgenome was not transcriptionally dominant as all hybrids were phenotypically more similar to the other parent.

The present study demonstrated that the fate of subgenomes in asexual hybrids and polyploids depends on the complex interplay of selection and several molecular mechanisms whose impact depends on ploidy, sequence composition, gene expression as well as parental ancestry.
CoCoNet: Boosting RNA contact prediction by convolutional neural networks
Authors: Zerihun Mehari B. , Pucci Fabrizio , Schug Alexander
Published: August 2020

Physics-based co-evolutionary models such as direct coupling analysis (DCA) in combination with machine learning (ML) techniques based on deep neural networks are able to predict protein contact maps with astonishing accuracy. Such contacts can be used as constraints in structure prediction and massively increase prediction accuracy. Unfortunately, the same ML methods cannot readily be applied to RNA as they rely on large structural datasets only available for proteins but not for RNAs. Here, we demonstrate how the small amount of data available for RNA can be used to significantly improve prediction of RNA contact maps. We introduce an algorithm calledCoCoNetthat is based on a combination of aCoevolutionary model and a shallowConvolutional NeuralNetwork. Despite its simplicity and the small number of trained parameters, the method boosts the contact prediction accuracy by about 70% with respect to straightforward DCA as tested by cross-validation on a dataset of about sixty RNA structures. Both our extensive robustness tests and the limited number of parameters allow the generalization properties of our model. Finally, applications to other RNAs highlight the power of our approach. CoCoNet is freely available and can be found athttps://github.com/KIT-MBS/coconet.
Towards understanding how we pay attention in naturalistic visual search settings
Authors: Turoman Nora , Tivadar Ruxandra I. , Retsa Chrysa , Murray Micah M. , Matusz Pawel J.
Published: August 2020

Research on attentional control has largely focused on single senses and the importance of behavioural goals in controlling attention. However, everyday situations are multisensory and contain regularities, both likely influencing attention. We investigated how visual attentional capture is simultaneously impacted by top-down goals, the multisensory nature of stimuli,andthe contextual factors of stimuli’s semantic relationship and temporal predictability. Participants performed a multisensory version of the Folk et al. (1992) spatial cueing paradigm, searching for a target of a predefined colour (e.g. a red bar) within an array preceded by a distractor. We manipulated: 1) stimuli’s goal-relevance via distractor’s colour (matching vs. mismatching the target), 2) stimuli’s multisensory nature (colour distractors appearing alone vs. with tones), 3) the relationship between the distractor sound and colour (arbitrary vs. semantically congruent) and 4) the temporal predictability of distractor onset. Reaction-time spatial cueing served as a behavioural measure of attentional selection. We also recorded 129-channel event-related potentials (ERPs), analysing the distractor-elicited N2pc component both canonically and using a multivariate electrical neuroimaging framework. Behaviourally, arbitrary target-matching distractors captured attention more strongly than semantically congruent ones, with no evidence for context modulating multisensory enhancements of capture. Notably, electrical neuroimaging of surface-level EEG analyses revealed context-based influences on attention to both visual and multisensory distractors, in how strongly they activated the brain and type of activated brain networks. For both processes, the context-driven brain response modulations occurred long before the N2pc time-window, with topographic (network-based) modulations at ~30ms, followed by strength-based modulations at ~100ms post-distractor onset. Our results reveal that both stimulus meaning and predictability modulate attentional selection, and they interact while doing so. Meaning, in addition to temporal predictability, is thus a second source of contextual information facilitating goal-directed behaviour. More broadly, in everyday situations, attention is controlled by an interplay between one’s goals, stimuli’s perceptual salience, meaning and predictability. Our study calls for a revision of attentional control theories to account for the role of contextual and multisensory control.
Rapid Online Assessment of Reading Ability
Authors: Yeatman Jason D. , Tang Kenny An , Donnelly Patrick M. , Yablonski Maya , Ramamurthy Mahalakshmi , Karipidis Iliana I. , Caffarra Sendy , Takada Megumi E. , Kanopka Klint , Ben-Shachar Michal , Domingue Benjamin W.
Published: August 2020

An accurate model of the factors that contribute to individual differences in reading ability depends on data collection in large, diverse and representative samples of research participants. However, that is rarely feasible due to the constraints imposed by standardized measures of reading ability which require test administration by trained clinicians or researchers. Here we explore whether a simple, two-alternative forced choice, time limited lexical decision task (LDT), self-delivered through the web-browser, can serve as an accurate and reliable measure of reading ability. We found that performance on the LDT is highly correlated with scores on standardized measures of reading ability such as the Woodcock-Johnson Letter Word Identification test (r = 0.91, disattenuated r = 0.94). Importantly, the LDT reading ability measure is highly reliable (r = 0.97). After optimizing the list of words and pseudowords based on item response theory, we found that a short experiment with 76 trials (2-3 minutes) provides a reliable (r = 0.95) measure of reading ability. Thus, the self-administered, Rapid Online Assessment of Reading ability (ROAR) developed here overcomes the constraints of resource-intensive, in-person reading assessment, and provides an efficient and automated tool for effective online research into the mechanisms of reading (dis)ability.