bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of the myzozoan aquatic parasite Perkinsus marinus as a versatile experimental genetic model organism
Authors: Einarsson Elin , Lassadi Imen , Zielinski Jana , Guan Qingtian , Wyler Tobias , Pain Arnab , Gornik Sebastian G. , Waller Ross F. 
Published: June 2021

ABSTRACTThe phylum Perkinsozoa is an aquatic parasite lineage that has devastating effects on commercial and natural mollusc populations, and also comprises parasites of algae, fish and amphibians. They are related to, and share much of their biology with, dinoflagellates and apicomplexans and thus offer excellent genetic models for both parasitological and evolutionary studies. Genetic transformation has been previously achieved for select Perkinsus spp. but with few tools for transgene expression and only limited selection efficacy. We thus sought to expand the power of experimental genetic tools for Perkinsus marinus — the principal perkinsozoan model to date. We constructed a modular plasmid assembly system that enables expression of multiple genes simultaneously. We developed an efficient selection system for three drugs, puromycin, bleomycin and blasticidin, that achieves transformed cell populations in as little as three weeks. We developed and quantified eleven new promoters of variable expression strength. Furthermore, we identified that genomic integration of transgenes is predominantly via non-homologous recombination and often involves transgene fragmentation including deletion of some introduced elements. To counter these dynamic processes, we show that bi-cistronic transcripts using the viral 2A peptides can couple selection systems to the maintenance of the expression of a transgene of interest. Collectively, these new tools and insights provide new capacity to efficiently genetically modify and study Perkinsus as an aquatic parasite and evolutionary model.
A new method to identify global targets of RNA-binding proteins in plants
Authors: Cheng You-Liang , Hsieh Hsin-Yu , Tu Shih-Long 
Published: June 2021

AbstractBackgroundRNA-binding proteins (RBPs) play crucial roles in various aspects of post-transcriptional gene expression; their functions can vary between tissues, cell types, developmental stages, and environmental conditions. Identifying RBP target RNAs and investigating whether they are differentially bound by RBPs in different cell types, stages, or conditions could shed light on RBP functions. Although several strategies have been designed to identify RBP targets, they involve complicated biochemical steps and require large quantities of material, and only a few studies using these techniques have been performed in plants. The TRIBE (targets of RNA binding proteins identified by editing) method was recently developed to identify RBP targets using a RBP coupled to the catalytic domain of a Drosophila RNA editing enzyme and expressing this fusion protein in vivo. The resulting novel editing events can be identified by sequencing. This technique uses little material and does not require complex biochemical steps, however it is not yet adapted for use in plants.ResultsWe successfully applied an optimized genome-wide TRIBE method in plants. We selected the splicing regulator polypyrimidine tract-binding protein (PTB) as a model protein for testing the TRIBE system in the moss Physcomitrium patens. We demonstrated that 13.81% of protein-coding gene transcripts in P. patens are targets of PTB. Most potential PTB binding sites are located in coding sequences and 3’ untranslated regions, suggesting that PTB performs multiple functions besides pre-mRNA splicing in this moss. In addition, TRIBE showed reproducible results compared to other methods.ConclusionsWe have developed an alternative method based on the TRIBE system to identify RBP targets in plants globally, and we provide guidance here for its application in plants.
Stx2 induces differential gene expression by activating several pathways and disturbs circadian rhythm genes in the proximal tubule
Authors: Obata Fumiko , Ozuru Ryo , Tsuji Takahiro , Matsuba Takashi , Fujii Jun 
Published: June 2021

Abstract(1)BackgroundShiga toxin-producing Escherichia coli (STEC) causes proximal tubular defects in the kidney. However, factors altered by Shiga toxin (Stx) within the proximal tubules are yet to be shown.(2)MethodsWe determined Stx receptor Gb3 in murine and human kidneys and confirmed the receptor expression in the proximal tubules. Stx2-injected mouse kidney tissues and Stx2-treated human primary renal proximal tubular epithelial cell (RPTEC) were collected, and microarray analysis was performed.(3)ResultsWe compared murine kidney and RPTEC arrays and selected common 58 genes that are differentially expressed vs. control (0 h, no toxin-treated). We found that the most highly expressed gene was GDF15, which may be involved in Stx2-induced weight loss. Genes associated with previously reported Stx2 activities such as src kinase Yes phosphorylation pathway activation, unfolded protein response (UPR) and ribotoxic stress response (RSR) showed differential expressions. Moreover, circadian clock genes were differentially expressed suggesting Stx2-induced renal circadian rhythm disturbance. Circadian rhythm-regulated proximal tubular Na+-glucose transporter SGLT1(SLC5A1) was down-regulated, indicating proximal tubular functional deterioration, and mice developed glucosuria confirming proximal tubular dysfunction.(4)ConclusionsStx2 alters gene expression in murine and human proximal tubules through known activities and newly investigated circadian rhythm disturbance resulting in proximal tubular dysfunctions.
Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts
Authors: Christinaki Anastasia C. , Kanellopoulos Spyros G. , Kortsinoglou Alexandra M. , Theelen Bart , Boekhout Teun , Kouvelis Vassili N. 
Published: June 2021

ABSTRACTSaccharomycotina yeasts contain diverse clades within the kingdom of Fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 141 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions’ diversity, genetic code alterations and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout Saccharomycotina evolution. Overall, this work shows that phylogenetic studies that employ the mt genome of yeasts highlight major evolutionary events.
HOXB8 counteracts MAPK/ERK oncogenic signaling in a chicken embryo model of neoplasia
Authors: Wilmerding Axelle , Bouteille Lauranne , Rinaldi Lucrezia , Caruso Nathalie , Graba Yacine , Delfini Marie-Claire 
Published: June 2021

ABSTRACTHOX transcription factors are members of an evolutionarily conserved family of proteins required for the establishment of the anteroposterior body axis during bilaterian development. Although they are often deregulated in cancers, the molecular mechanisms by which they act as oncogenes or tumor suppressor genes are only partially understood. Since the MAPK/ERK signaling pathway is deregulated in most cancers, we aimed at apprehending if and how Hox proteins interact with ERK oncogenicity.Using an in vivo neoplasia model in the chicken embryo that we have developed, consisting in the overactivation of the ERK1/2 kinases in the trunk neural tube, we analyzed the consequences of HOXB8 gain of function at morphological and transcriptional level in this model. We found that HOXB8 acts as a tumor suppressor, counteracting ERK-induced neoplasia. HOXB8 tumor suppressor function in this model relies on a large reversion of the oncogenic transcriptome induced by ERK. In addition to showing that HOXB8 protein controls the transcriptional responsiveness to ERK oncogenic signaling, our study identified new downstream targets of ERK oncogenic activation in an in vivo context that could provide clues for therapeutic strategies.
The acquisition of additional feedback loops may optimize and speed up the response of quorum sensing
Authors: Fondi Marco , Di Patti Francesca , Perrin Elena 
Published: June 2021

1.AbstractBacterial quorum sensing (QS) is a cell-to-cell communication system in which specific signals are activated to coordinate, for example, pathogenic behaviors and help bacteria collectively respond to perturbations. QS in Gram-negative bacteria is typically regulated by a N-acyl-homoserine lactone (AHL) molecules-mediated system, homologous of Vibrio fischeri LuxI-R. In many cases, bacteria possess more than one QS system, based on different types of molecules, that interact through a complex regulatory network. Presumably, these configurations have emerged over time from simpler ones through the acquisition of novel players (e.g. transcription factors) that have been successfully integrated into the native regulatory systems. However, the advantages provided by these alternative/additional configurations on QS-related phenotypes is poorly predictable only based on their underlying network structure. Here, we have adopted a modelling approach to infer the possible improvements conferred by the acquisition of additional control over bacterial regulation of QS. We use the Burkholderia genus as a case study because some of these strains, besides the LuxIR-like system (named CepIR), possess an integrated regulatory module named CciIR that interferes with the CepIR system through the implementation of several positive and negative control loops. Being associated to a genomic island (cci island), this additional module is prone to being horizontally transferred, giving rise to a potentially patchy genomic distribution and, in turn, to a complete (CepIR and CciIR systems together) vs. core (CepIR only) organization of QS regulation in this group of microorganisms. By using both deterministic and stochastic modelling we show that, upon their activation, the two regulatory schemes may lead to different phenotypes and to distinct responses to the extracellular concentration of signalling molecules. In particular, our simulations show that the presence of the additional regulatory module may confer specific improvements, including a faster response time and optimized control of QS regulation. Interestingly, some of these features may be particularly advantageous during host invasion, thus highlighting once more the importance of QS in the establishment and maintenance of bacterial infections.
Salivary oxytocin co-varies with parturition and nursing behavior in domestic pigs (Sus scrofa domesticus)
Authors: Moscovice Liza R. , Sobczak Birgit , Gimsa Ulrike , Kanitz Ellen 
Published: June 2021

AbstractDomestic pigs produce twice as many offspring as wild boars, but little is known about the effects of selection pressures for increased productivity on pig behavior and welfare. From an evolutionary perspective, producing larger litters is expected to increase parent-offspring conflict, which may help to explain why piglets from larger litters are more likely to die by starvation or infant-crushing. Our goals were to identify behavioral and physiological correlates of variation in maternal care that may be useful as selection criteria in breeding programs to improve pig welfare. We observed eleven sows regularly during their lactational period and recorded their hourly postural changes and the proportion of time that piglets had contact with teats (nursing contact) or any physical contact with the sow (social contact). As a potential physiological indicator of maternal care, we measured oxytocin concentrations in 119 saliva samples from sows following observations. Samples were extracted and measured in an Enzyme Immunoassay. As a biological validation, we measured changes in salivary oxytocin during parturition in an additional eleven sows. Laboratory validations confirmed that the assay is suitable for measuring salivary oxytocin in pigs, and oxytocin increased almost three-fold during parturition. Sows’ nursing contact was positively correlated with social contact and negatively correlated with postural changes. Sow oxytocin concentrations were predicted by their nursing contact, but not by their overall social contact with piglets. We compare our results with current evidence regarding best practice methods for salivary oxytocin measurements and discuss the potential to use indicators of maternal care as selection criteria to improve pig welfare.
The emergence of a birth-dependent mutation rate in asexuals: causes and consequences
Authors: Patout Florian , Forien Raphaël , Alfaro Matthieu , Papaïx Julien , Roques Lionel 
Published: June 2021

AbstractIn unicellular organisms such as bacteria and in most viruses, mutations mainly occur during reproduction. Thus, genotypes with a high birth rate should have a higher mutation rate. However, standard models of asexual adaptation such as the ‘replicator-mutator equation’ often neglect this generation-time effect. In this study, we investigate the emergence of a positive dependence between the birth rate and the mutation rate in models of asexual adaptation and the consequences of this dependence. We show that it emerges naturally at the population scale, based on a large population limit of a stochastic time-continuous individual-based model with elementary assumptions. We derive a reaction-diffusion framework that describes the evolutionary trajectories and steady states in the presence of this dependence. When this model is coupled with a phenotype to fitness landscape with two optima, one for birth, the other one for survival, a new trade-off arises in the population. Compared to the standard approach with a constant mutation rate, the symmetry between birth and survival is broken. Our analytical results and numerical simulations show that the trajectories of mean phenotype, mean fitness and the stationary phenotype distribution are in sharp contrast with those displayed for the standard model. The reason for this is that the usual weak selection limit does not hold in a complex landscape with several optima associated with different values of the birth rate. Here, we obtain trajectories of adaptation where the mean phenotype of the population is initially attracted by the birth optimum, but eventually converges to the survival optimum, following a hook-shaped curve which illustrates the antagonistic effects of mutation on adaptation.
Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium
Authors: Neumann Mareike , Steimle Alex , Grant Erica T. , Wolter Mathis , Parrish Amy , Willieme Stéphanie , Brenner Dirk , Martens Eric C. , Desai Mahesh S. 
Published: June 2021

AbstractThe change of dietary habits in Western societies, including reduced consumption of fiber, is linked to alterations in gut microbial ecology. Nevertheless, mechanistic connections between diet-induced microbiota changes that affect colonization resistance and enteric pathogen susceptibility are still emerging. We sought to investigate how a diet devoid of soluble plant fibers impacts the structure and function of a conventional gut microbiota in specific-pathogen-free (SPF) mice and how such changes alter susceptibility to a rodent enteric pathogen. We show that absence of dietary fiber intake leads to shifts in the abundances of specific taxa, microbiome-mediated erosion of the colonic mucus barrier, a reduction of intestinal barrier-promoting short-chain fatty acids, and increases in markers of mucosal barrier integrity disruption. Importantly, our results highlight that these low fiber diet-induced changes in the gut microbial ecology collectively contribute to a lethal colitis by the mucosal pathogen Citrobacter rodentium, which is used as a mouse model for enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively). Our study indicates that modern, low-fiber Western diets might make individuals more prone to infection by enteric pathogens via the disruption of mucosal barrier integrity by diet-driven changes in the gut microbiota, illustrating possible implications for EPEC and EHEC infections.
Effect of levodopa on human brain connectome in Parkinson’s disease
Authors: Farashi Sajjad , Khazaei Mojtaba 
Published: June 2021

AbstractObjectiveLevodopa-based drugs are widely used for mitigating the complications induced by PD. Despite the positive effects, several issues regarding the way that levodopa changes brain activities have remained unclear.MethodsA combined strategy using EEG data and graph theory was used for investigating how levodopa changed connectome and processing hubs of the brain during resting-state. Obtained results were subjected to ANOVA test and multiple-comparison post-hoc correction procedure.ResultsResults showed that graph topology of PD patients was not significantly different with the healthy group during eyes-closed condition while in eyes-open condition statistical significant differences were found. The main effect of levodopa medication was observed for gamma-band activity of the brain in which levodopa changed the brain connectome toward a star-like topology. Considering the beta subband of EEG data, graph leaf number increased following levodopa medication in PD patients. Enhanced brain connectivity in gamma band and reduced beta band connections in basal ganglia were also observed after levodopa medication. Furthermore, source localization using dipole fitting showed that levodopa prescription suppressed the activity of collateral trigone.ConclusionOur combined EEG and graph analysis showed that levodopa medication changed the brain connectome, especially in the high-frequency range of EEG (beta and gamma).HighlightsNo differences were found between graph features between ON and OFF PD cases in eyes-closed.Levodopa enhanced connectivity in gamma band in PD patients.Levodopa inhibited brain connectivity in beta band.
Highly potent photoinactivation of bacteria using a water soluble, cell permeable, DNA-binding photosensitizer
Authors: Digby Elyse M. , Ma Tianyi , Milstein Joshua N. , Beharry Andrew A. 
Published: June 2021

ABSTRACTAntimicrobial photodynamic therapy (APDT) employs a photosensitizer, light, and molecular oxygen to treat infectious diseases via oxidative damage, with a low likelihood for the development of resistance. For optimal APDT efficacy, photosensitizers with cationic charges that can permeate bacteria cells and bind intracellular targets are desired to not limit oxidative damage to the outer bacterial structure. Here we report the application of brominated DAPI (Br-DAPI), a water-soluble, DNA-binding photosensitizer for eradication of both gram-negative and gram-positive bacteria (as demonstrated on N99 E. coli and B. subtilis, respectively). We observe intracellular uptake of Br-DAPI, ROS-mediated bacterial cell death via 1- and 2-photon excitation, and selective photocytotoxicity of bacteria over mammalian cells. Photocytotoxicity of both N99 E. coli and B. subtilis occurred at sub-micromolar concentrations (IC50 = 0.2 μM – 0.4 μM) and low light doses (5-minute irradiation times, 4.5 J cm−2 dose) making it superior to commonly employed APDT phenothiazinium photosensitizers such as methylene blue. Given its high potency and 2-photon excitability, Br-DAPI is a promising novel photosensitizer for in vivo APDT applications.
Differential growth is a critical determinant of zebrafish pigment pattern formation
Authors: Owen Jennifer P. , Yates Christian A. , Kelsh Robert N. 
Published: June 2021

AbstractThe skin patterns of vertebrates are formed by complex interactions between pigment-producing cells during development. Adult zebrafish (Danio rerio), a model organism for investigating the underlying patterning processes, display alternating horizontal blue and golden stripes, generated by the self-organisation of three pigment cell-types. Mathematical studies in which these cells are modelled as individual agents communicating via short- and long-range interactions have produced breakthroughs in the understanding of pattern development. These models, incorporating all experimentally evidenced cell-cell interactions, replicate many aspects of wild-type and mutant zebrafish patterns. Although received wisdom suggested that initial iridophore distribution was pivotal in orienting patterning, here we show that growth can override its influence. Altered growth sequences can generate further pattern modulation, including vertical stripes and maze-like patterns. We demonstrate that ventrally-biased (asymmetric) growth of the skin field explains two key zebrafish pattern development features which are otherwise obscure (dorso-ventral pattern asymmetry, and predominant ventral-to-dorsal migration of melanophores) in wild-type and multiple zebrafish mutants, and in the related species Danio nigrofasciatus. By identifying biased growth as a novel patterning mechanism, our study will inform future investigations into the mechanisms and evolution of fish pigment patterning and vertebrate pigment pattern formation. Furthermore, our work has implications for the mechanistic basis of human pigmentation defects.
Antimicrobial Agent Triclosan Inhibits Acetylcholinesterase Activityin Vitroin a Dose-Dependent Manner
Authors: Pullaguri Narasimha , Andrea Kagoo R , Bhargava Anamika 
Published: June 2021

ABSTRACTThe antimicrobial agent, Triclosan, is widely used in many consumer products. It has been designated as a “contaminant of emerging concern (CEC)” because its exposure is known to cause adverse ecological and human health effects. Triclosan is not labelled as GRAS/GRAE (generally recognized as safe and effective), but its use is still prevailing.In vivostudies have revealed that exposure to triclosan results in a decreased acetylcholinesterase (AChE) activity. However mechanistic insights into AChE inhibition by triclosan are missing. Usingin vitroAChE activity assay with purified AChE, we show that triclosan acts as a direct inhibitor of AChE and inhibits AChE activity in a dose-dependent manner. Given the function of AChE, any alteration in its activity can be neurotoxic. Our results provide important mechanistic insights into triclosan induced neurotoxicity with AChE as a target.