bluuebunny/crossref_metadata_2025_split huggingface dataset:
High speed, three-dimensional imaging reveals chemotactic behavior specific to human-infectiveLeishmaniaparasites
Authors: Findlay Rachel C. , Osman Mohamed , Spence Kirsten A. , Kaye Paul M. , Walrad Pegine B. , Wilson Laurence G. 
Published: August 2020

AbstractCellular motility is an ancient eukaryotic trait, ubiquitous across phyla with roles in predator avoidance, resource access and competition. Flagellar-dependent motility is seen in a variety of parasitic protozoans and morphological changes in flagellar structure and function have been qualitatively described during differentiation. However, whether the dynamics of flagellar motion vary across lifecycle stages and whether such changes serve to facilitate human infection is not known. Here we used holographic video microscopy to study the pattern of motility in insect midgut forms ofLeishmania(procyclic promastigotes; PCF) and differentiated human infective metacyclic promastigotes (META). We discovered that PCF swim in a slow, corkscrew motion around a gently curving axis while META display ‘run and tumble’ behaviour in the absence of stimulus, reminiscent of bacterial behaviour. In addition, we demonstrate that META specifically respond to a macrophage-derived stimulus, modifying swimming direction and speed to target host immune cells. Thus, the motility strategy employed byLeishmaniaappears as a random search that is replaced with a ballistic swimming motion in the presence of an immunological stimulus. These findings shed unique insights into how flagellar motion adapts to the particular needs of the parasite at different times in its lifecycle and define a new pre-adaptation for infection of the human host.
DPCfam: a new method for unsupervised protein family classification
Authors: Russo Elena Tea , Laio Alessandro , Punta Marco 
Published: August 2020

AbstractMotivationAs the UniProt database approaches the 200 million entries’ mark, the vast majority of proteins it contains lack any experimental validation of their functions. In this context, the identification of homologous relationships between proteins remains the single most widely applicable tool for generating functional and structural hypotheses in silico. Although many databases exist that classify proteins and protein domains into homologous families, large sections of the sequence space remain unassigned.ResultsWe introduce DPCfam, a new unsupervised procedure that uses sequence alignments and Density Peak Clustering to automatically classify homologous protein regions. Here, we present a proof-of-principle experiment based on the analysis of two clans from the Pfam protein family database. Our tests indicate that DPCfam automatically-generated clusters are generally evolutionary accurate corresponding to one or more Pfam families and that they cover a significant fraction of known homologs. Overall, DPCfam shows potential both for assisting manual annotation efforts (domain discovery, detection of classification inconsistencies, improvement of family coverage and boosting of clan membership) and as a stand-alone tool for unsupervised classification of sparsely annotated protein datasets such as those from environmental metagenomics studies (domain discovery, analysis of domain diversity).AvailabilityAlgorithm implementation used in this paper is available athttps://gitlab.com/ETRu/dpcfam(Requires Python 3, C++ compiler and runs on Linux systems.); data are available athttps://zenodo.org/record/3934399
The deep and slow breathing characterizing rest favors brain respiratory-drive
Authors: Girin Baptiste , Juventin Maxime , Garcia Samuel , Lefèvre Laura , Amat Corine , Fourcaud-Trocmé Nicolas , Buonviso Nathalie 
Published: August 2020

ABSTRACTA respiration-locked activity in the olfactory brain, mainly originating in the mechano-sensitivity of olfactory sensory neurons to air pressure, propagates from the olfactory bulb to the rest of the brain. Interestingly, changes in nasal airflow rate result in reorganization of olfactory bulb response. Therefore, if the respiratory drive of the brain originates in nasal airflow movements, then it should vary with respiration dynamics that occur spontaneously during natural conditions. We took advantage of the spontaneous variations of respiration dynamics during the different waking and sleep states to explore respiratory drive in various brain regions. We analyzed their local field potential activity relative to respiratory signal. We showed that respiration regime was state-specific, and that quiet waking was the only vigilance state during which all the recorded structures can be respiration-driven whatever the respiration frequency. We used a CO2-enriched air to change the respiratory regime associated to each state and, using a respiratory cycle-by-cycle analysis, we evidenced that the large and strong brain entrainment during quiet waking was the consequence of its associated respiration regime consisting in an optimal trade-off between deepness and duration of inspiration. These results show for the first time that changes in respiration regime alter the cortical dynamics and that the respiratory regime associated with rest is optimal for respiration to drive the brain.
The morphology and evolution of chondrichthyan cranial muscles: a digital dissection of the elephantfishCallorhinchus miliiand the catsharkScyliorhinus canicula
Authors: Dearden Richard P. , Mansuit Rohan , Cuckovic Antoine , Herrel Anthony , Didier Dominique , Tafforeau Paul , Pradel Alan 
Published: August 2020

AbstractThe anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates, due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups – holocephalans and elasmobranchs – have played a pivotal role in the formation of evolutionary hypotheses targeting major cranial structures such as the jaws and pharynx. However, despite the advent of digital dissections as a means of easily visualizing and sharing the results of anatomical studies in three dimensions, information on the musculoskeletal systems of the chondrichthyan head remains largely limited to traditional accounts, many of which are at least a century old. Here we use synchrotron tomography acquire 3D data which we used to carry out a digital dissection of a holocephalan and an elasmobranch widely used as model species: the elephantfish,Callorhinchus milii, and the small-spotted catshark, Scyliorhinus canicula. We describe and figure the skeletal anatomy of the head, labial, mandibular, hyoid, and branchial cartilages in both taxa as well as the muscles of the head and pharynx. We make new observations, particularly regarding the branchial musculature ofCallorhinchus, revealing several previously unreported or previously ambiguous structures. Finally, we review what is known about the evolution of chondrichthyan cranial muscles from their fossil record and discuss the implications for muscle homology and evolution, broadly concluding that the holocephalan pharynx is likely derived from a more elasmobranch-like form. This dataset has great potential as a resource, particularly for researchers using these model species for zoological research, functional morphologists requiring models of musculature and skeletons, as well as for palaeontologists seeking comparative models for extinct taxa.
THE REGULATORY EFFECT OF LIGHT OVER FRUIT DEVELOPMENT AND RIPENING IS MEDIATED BY EPIGENETIC MECHANISMS
Authors: Bianchetti Ricardo , Bellora Nicolas , de Haro Luis A , Zuccarelli Rafael , Rosado Daniele , Freschi Luciano , Rossi Magdalena , Bermudez Luisa 
Published: August 2020

SummaryPhytochrome-mediated light and temperature perception has been shown to be a major regulator of fruit development. Furthermore, chromatin remodelling via DNA demethylation has been described as a crucial mechanism behind the fruit ripening process; however, the molecular basis underlying the triggering of this epigenetic modification remains largely unknown. Here, through integrative analyses of the methylome, siRNAome and transcriptome of tomato fruits fromphyAandphyB1B2null mutants, we report that PHYB1 and PHYB2 control genome-wide DNA methylation during fruit development from green towards ripe stages. The experimental evidence indicates that PHYB1B2 signal transduction is mediated by a gene expression network involving chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes and remodelling factors) and transcriptional regulators leading in the altered mRNA profile of photosynthetic and ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits.
Predicting the future development of mild cognitive impairment in the cognitively healthy elderly
Authors: Strange Bryan A. , Zhang Linda , Sierra-Marcos Alba , Alfayate Eva , Tohka Jussi , Medina Miguel 
Published: August 2020

ABSTRACTIdentifying measures that predict future cognitive impairment in healthy individuals is necessary to inform treatment strategies for candidate dementia-preventative and modifying interventions. Here, we derive such measures by studying “converters” who transitioned from cognitively normal at baseline to mild-cognitive impairment (MCI) in a longitudinal study of 1213 elderly participants. We first establish reduced grey matter density (GMD) in left entorhinal cortex (EC) as a biomarker for impending cognitive decline in healthy individuals, employing a matched sampling control for several dementia risk-factors, thereby mitigating the potential effects of bias on our statistical tests. Next, we determine the predictive performance of baseline demographic, genetic, neuropsychological and MRI measures by entering these variables into an elastic net-regularized classifier. Our trained statistical model classified converters and controls with validation Area-Under-the-Curve>0.9, identifying only delayed verbal memory and left EC GMD as relevant predictors for classification. This performance was maintained on test classification of out-of-sample converters and controls. Our results suggest a parsimonious but powerful predictive model for MCI development in the cognitively healthy elderly.
The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range
Authors: Techer Maeva A. , Roberts John M. K. , Cartwright Reed A , Mikheyev Alexander S. 
Published: August 2020

AbstractBackgroundHost switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and also may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in real-time and their demographic parameters remain poorly understood. As a result, fundamental factors that control subsequent parasite evolution, such as the size of the switching population or the extent of immigration from the original host, remain largely unknown. To shed light on the host switching process, we explored how host switches occur in independent host shifts by two ectoparasitic honey bee mites (Varroa destructor and V. jacobsoni).ResultsBoth switched to the western honey bee (Apis mellifera) after it was brought into contact with their ancestral host (Apis cerana), ∼70 and ∼12 years ago, respectively. Varroa destructor subsequently caused worldwide collapses of honey bee populations. Using whole-genome sequencing on 63 mites collected in their native ranges from both the ancestral and novel hosts, we were able to reconstruct the known temporal dynamics of the switch. We further found multiple previously undiscovered mitochondrial lineages on the novel host, along with the genetic equivalent of tens of individuals that were involved in the initial host switch. Despite being greatly reduced, some gene flow remains between mites adapted to different hosts.ConclusionOur findings suggest that while reproductive isolation may facilitate the fixation of traits beneficial for exploitation of the new host, ongoing genetic exchange may allow genetic amelioration of inbreeding effects.
Root electrotropism in Arabidopsis does not depend on auxin distribution but requires cytokinin biosynthesis
Authors: Salvalaio Maddalena , Oliver Nicholas , Tiknaz Deniz , Schwarze Maximillian , Kral Nicolas , Kim Soo-Jeong , Sena Giovanni 
Published: August 2020

ABSTRACTAn efficient foraging strategy for plant roots relies on the ability to sense multiple physical and chemical cues in soil and to reorient growth accordingly (tropism). Root tropisms range from sensing gravity (gravitropism), light (phototropism), water (hydrotropism), touch (thigmotropism) and more. Electrotropism, also known as galvanotropism, is the phenomenon of aligning growth with external electric fields and currents. Although observed in a few species since the end of the 19thcentury, the molecular and physical mechanism of root electrotropism remains elusive, limiting the comparison to more defined sensing pathways in plants.Here we provide a first quantitative and molecular characterisation of root electrotropism in the model systemArabidopsis thaliana, showing that it does not depend on an asymmetric distribution of the plant hormone auxin, but that instead it requires the biosynthesis of a second hormone, cytokinin. We also show that the dose-response kinetics of the early steps of root electrotropism follows a power law analogous to the one observed in some physiological reactions in animals.A future full molecular and quantitative characterisation of root electrotropism would represent a step forward towards a better understanding of signal integration in plants, and an independent outgroup for comparative analysis of electroreception in animals and fungi.
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

AbstractIndia 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.ImportanceElucidation 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

AbstractGhrelin 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

AbstractConspecific 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

AbstractDispersal 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.