bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dual prokaryotic (E. coli) expression system (pdMAX)
Authors: Murakami Manabu , Murakami Agnieszka M. , Hirota Kazuyoshi , Itagaki Shirou 
Published: July 2020

AbstractIn this study, we introduced an efficient subcloning and expression system with two inducible prokaryotic expression promoters, arabinose and lac, in a single plasmid inEscherichia coli. This pdMAX system is a manageable size at 5811 bp. The arabinose promoter unit allows for the expression of a FLAG-tagged protein, while the isopropyl-β-D-thiogalactoside (IPTG)-inducible unit allows for the expression of a Myc-tagged protein. An efficient subcloning (DNA insertion) system (iUnit) follows each promoter. The iUnit, based on a toxin that targets DNA topoisomerase ofE. coli, allows for effective selection with arabinose or IPTG induction.Interestingly, the dual induction plasmid system shows limited protein expression. To analyze the expression of inserted genes, we performed anα-complementation assay, in which theα-peptide of the lacZ (β-galactosidase) gene is inserted in XL-10E. colicells.E. coliexpressing the recombinant plasmid form blue colonies when plated on ampicillin/IPTG- or arabinose/X-gal-containing plates if theα-peptide was correctly inserted in-frame to produce the tagged protein. This assay system assesses whether theα-peptide was inserted at the restriction sites (EcoRV or SmaI), whether the inserted peptide was expressed, and whether the insertedα-peptide sequence was ligated in-frame to produce a tagged protein. Frameshifts result in noα-complementation and white colonies.With the dual promoter plasmid (pdMAX) system, expressedlacZactivity was significantly decreased comparing with the solo expression (pgMAX) system. Despite this disadvantage, we believe the pdMAX system is still useful for the analysis of distinct genes inE. coli, which will enable different types of expression analysis. Overall, the novel pdMAX system allows for efficient subcloning of two different genes. Furthermore, the pdMAX system could be used to induce and analyze the expression of two distinct genes and adopted to various types of prokaryotic gene expression analyses.
Development and validation of a clinical risk score to predict the risk of SARS-CoV-2 infection from administrative data: a population-based cohort study from Italy
Authors: Orlando Valentina , Rea Federico , Savaré Laura , Guarino Ilaria , Mucherino Sara , Perrella Alessandro , Trama Ugo , Coscioni Enrico , Menditto Enrica , Corrao Giovanni 
Published: July 2020

AbstractBackgroundThe novel coronavirus (SARS-CoV-2) pandemic spread rapidly worldwide increasing exponentially in Italy. To date, there is lack of studies describing clinical characteristics of the population most at risk of infection. Hence, we aimed to identify clinical predictors of SARS-CoV-2 infection risk and to develop and validate a score predicting SARS-CoV-2 infection risk comparing it with unspecific surrogates.MethodsRetrospective case/control study using administrative health-related database was carried out in Southern Italy (Campania region) among beneficiaries of Regional Health Service aged over than 30 years. For each subject with Covid-19 confirmed diagnosis (case), up to five controls were randomly matched for gender, age and municipality of residence. Odds ratios and 90% confidence intervals for associations between candidate predictors and risk of infection were estimated by means of conditional logistic regression. SARS-CoV-2 Infection Score (SIS), was developed by generating a total aggregate score obtained from assignment of a weight at each selected covariate using coefficients estimated from the model. Finally, the score was categorized by assigning increasing values from 1 to 4. SIS was validated by comparison with specific and unspecific predictors of SARS-CoV-2 infection.ResultsSubjects suffering from diabetes, anaemias, Parkinson’s disease, mental disorders, cardiovascular and inflammatory bowel and kidney diseases showed increased risk of SARS-CoV-2 infection. Similar estimates were recorded for men and women and younger and older than 65 years. Fifteen conditions significantly contributed to the SIS. As SIS value increases, risk progressively increases, being odds of SARS-CoV-2 infection among people with the highest SIS value (SIS=4), 1.74 times higher than those unaffected by any SIS contributing conditions (SIS=1).ConclusionThis study identified conditions and diseases making individuals more vulnerable to SARS-CoV-2 infection. Our results are a decision-maker support tool for identifying population most at risk allowing adoption of preventive measures to minimize a potential new relapse damage.
Ecological memory mitigates negative impacts of disturbance on biomass production in benthic diatom metacommunities
Authors: Engel Friederike G. , Matthiessen Birte , Andriana Rosyta , Eriksson Britas Klemens 
Published: July 2020

AbstractDisturbance events to coastal habitats such as extreme heat events, storms, or floods have increased in magnitude and frequency in recent years due to anthropogenic climate change and the destruction of habitats. These events constitute a major threat to many ecological communities and global biodiversity. Disturbance history influences ecosystem response to novel disturbances such that communities that have previously been exposed to disturbances should be more resilient to new disturbances compared to previously sheltered communities. This principle is defined as ecological memory. Resilience should also increase with access to a larger species pool, because a larger species pool increases species and response diversity of a community. One possibility of increasing the local species pool is connectivity via adequate dispersal between habitat patches with different species compositions in metacommunities. In a laboratory experiment, we exposed benthic diatom communities of different origin to a mechanical disturbance, simulated dispersal in half of the communities, and measured their chlorophyllaconcentration over time. The local diatom communities originated from different locations on an intertidal flat that varied in hydrodynamic exposure history. Hydrodynamic exposure disturbs the sediment, and thereby determines sediment properties and the composition of intertidal diatom communities. In the experiment, disturbance negatively affected chlorophyllaconcentration across all treatments. However, the response to disturbance depended on the ecological memory of the communities; the more exposed areas the communities originated from, the less negative was the effect of the mechanical disturbance. Interestingly, dispersal did not mitigate the negative impacts of disturbance in any of the communities. Our results highlight the importance of ecological memory for ecosystem functioning and demonstrate the limitations of patch connectivity to alleviate the impacts of disturbance events in metacommunities.
Vacuolar transporter Mnr2 safeguards mitochondrial integrity in aged cells
Authors: Reza Md. Hashim , Patkar Rajesh , Sanyal Kaustuv 
Published: July 2020

AbstractAging is associated with altered mitochondrial function. Mitochondrial function is dependent on the magnesium (Mg+2) ion flux. The molecular mechanism underlying Mg+2homeostasis, especially during aging has not been well understood. We previously demonstrated that the absence of a vacuolar ion transporter Mnr2 accelerates cell death in the older part of the colony inMagnaporthe oryzaepresumably due to an altered Mg+2homeostasis. Localization of Mnr2 as dynamic puncta at the vacuolar membrane especially in the olderMagnaporthecells further suggests its association with aged cells. Interestingly, such vacuolar Mnr2 puncta colocalized with the filamentous mitochondria in the aged cells. Further, we show that agedmnr2Δ null cells displayed loss of integrity of mitochondria and vacuoles. Remarkably, exogenously added Mg+2restored the mitochondrial structure as well as improved the lifespan ofmnr2Δ null cells. Thus, we uncover a mechanism of maintenance of mitochondrial integrity and function by the ion transporter Mnr2-based Mg+2homeostasis during aging.
The Latency of Spontaneous Eye Blinks Marks Relevant Visual and Auditory Information Processing
Authors: Murali Supriya , Händel Barbara 
Published: July 2020

AbstractEye blinks are influenced by several external sensory and internal cognitive factors. However, neither the precise temporal effects of these factors on blinking nor how their timing compares between modalities is known. Our aim was to understand the influence of sensory input vs task-relevant information on blinks in the visual and auditory domain.Using a visual and an auditory temporal judgement task, we found that blinks were suppressed during stimulus presentation in both domains and the overall input length had a significant positive relationship with blink latency i.e. the end of blink suppression. Indeed, the effect of sensory input duration on blink latency was not significantly different between visual and auditory stimuli. The precise timing of blink latency was further modulated by the duration of the task relevant input, which was independent of the overall length of sensory input. The influence of task related changes embedded in the overall stimulation suggests an additional influence of top-down processes on blink timing. Intriguingly, embedded changes as short as 40 ms in the auditory domain and 100 ms in the visual domain are reflected in blink latency differences. Importantly, we could show that task accuracy and motor response was not the driving factor of blink modulation.Our results show a sensory domain independent modulation of blink latencies introduced by changes in the length of task-relevant information. Therefore, blinks not only mark the time of sensory input but also can act as precise indicator for periods of cognitive processing and attention.
Integration of sleep homeostasis and navigation inDrosophila
Authors: Valle Andres Flores , Gonçalves Pedro J. , Seelig Johannes D. 
Published: July 2020

ABSTRACTDuring sleep, the brain undergoes dynamic and structural changes. InDrosophila, such changes have been observed in the central complex, a brain area important for sleep control and navigation. The connectivity of the central complex raises the question about how navigation, and specifically the head direction system, can operate in the face of sleep related plasticity.To address this question, we develop a model that integrates sleep homeostasis and head direction. We show that by introducing plasticity, the head direction system can function in a stable way by balancing plasticity in connected circuits that encode sleep pressure. With increasing sleep pressure, the head direction system nevertheless becomes unstable and a sleep phase with a different plasticity mechanism is introduced to reset network connectivity.The proposed integration of sleep homeostasis and head direction circuits captures features of their neural dynamics observed in flies and mice.
Epidermal PAR-6 and PKC-3 are essential for postembryonic development ofCaenorhabditis elegansand control non-centrosomal microtubule organization
Authors: Castiglioni Victoria G. , Pires Helena R. , Bertolini Rodrigo Rosas , Riga Amalia , Kerver Jana , Boxem Mike 
Published: July 2020

AbstractThe cortical polarity regulators PAR-6, PKC-3 and PAR-3 are essential for the polarization of a broad variety of cell types in multicellular animals, from the first asymmetric division of theC. eleganszygote to apical–basal polarization of epithelial cells. InC. elegans, the roles of the PAR proteins in embryonic development have been extensively studied, yet little is known about their functions during larval development. Using auxin-inducible protein depletion, we here show that PAR-6 and PKC-3, but not PAR-3, are essential for postembryonic development. We also demonstrate that PAR-6 and PKC-3 are required in the epidermal epithelium to support animal growth and molting, and the proper timing and pattern of seam cell divisions. Finally, we uncovered a novel role for PAR-6 in controlling the organization of non-centrosomal microtubule arrays in the epidermis. PAR-6 was required for the localization of the microtubule organizer NOCA-1/Ninein, and microtubule defects in anoca-1mutant are highly similar to those caused by epidermal PAR-6 depletion. As NOCA-1 physically interacts with PAR-6, we propose that PAR-6 promotes non-centrosomal microtubule organization through localization of NOCA-1/Ninein.SummaryUsing inducible protein degradation, we show that PAR-6 and PKC-3/aPKC are essential for postembryonic development ofC. elegansand control the organization of non-centrosomal microtubule bundles in the epidermis, likely through recruitment of NOCA-1/Ninein.
Zinc shapes the folding landscape of p53 and establishes a new pathway for reactivating structurally diverse p53 mutants
Authors: Blanden Adam R. , Yu Xin , Blayney Alan J. , Demas Christopher , Ha Jeung-Hoi , Liu Yue , Withers Tracy , Carpizo Darren R. , Loh Stewart N. 
Published: July 2020

ABSTRACTMissense mutations in the DNA binding domain (DBD) of the p53 tumor suppressor contribute to approximately half of new cancer cases each year worldwide. A primary goal in cancer therapy is to develop drugs that rescue the transcription function of mutant p53. Here we present a thermodynamic model that quantifies and links the major pathways by which mutations inactivate p53. The model is constructed by measuring folding free energies, zinc dissociation constants, and DNA dissociation constants of 20 of the most common DBD mutations in the p53 database. We report here that DBD possesses two unusual properties——one of the highest zinc binding affinities of any eukaryotic protein and extreme instability in the absence of zinc—which are predicted to cause p53 to be poised on the edge of folding/unfolding in the cell, with a major determinant being the concentration of available zinc. Eighty percent of the mutations examined impair either thermodynamic stability, zinc binding affinity, or both. Using a combination of biophysical experiments, cell based assays, and murine cancer models, we demonstrate for the first time that a synthetic zinc metallochaperone not only rescues mutants with decreased zinc affinities, but also mutants that destabilize DBD without impairing zinc binding. The latter is a broad class of p53 mutants of which only one member (Y220C) has been successfully targeted by small molecules. The results suggest that zinc metallochaperones have the capability to treat 120,500 patients per year in the U.S.SUMMARYRestoring tumor suppressing function to mutant p53 has the capability of treating millions of new cancer patients worldwide each year. An important step toward this goal is to categorize the spectrum of mutations based on how they inactivate p53. This study finds that the majority of the most common tumorigenic mutations compromise p53’s thermodynamic stability or its interaction with zinc, and demonstrates for the first time that members of both classes can be reactivated in cells by synthetic zinc metallochaperones. These results serve to stratify patients for potential zinc metallochaperone therapy.
Brain activation lateralization in monkeys (Papio Anubis) following asymmetric motor and auditory stimulations through functional Near Infrared Spectroscopy
Authors: Debracque C. , Gruber T. , Lacoste R. , Grandjean D. , Meguerditchian A. 
Published: July 2020

AbstractHemispheric asymmetries have long been seen as characterizing the human brain; yet, an increasing number of reports suggest the presence of such brain asymmetries in our closest primate relatives. However, most available data in non-human primates have so far been acquired as part of neurostructural approaches such as MRI, while comparative data in humans are often dynamically acquired as part of neurofunctional studies. In the present exploratory study in baboons (Papio Anubis), we tested whether brain lateralization could be recorded non-invasively using a functional Near-Infrared Spectroscopy (fNIRS) device in two contexts: motor and auditory passive stimulations. Under light propofol anaesthesia monitoring, three adult female baboons were exposed to a series of (1) left-versusright-arm passive movement stimulations; and (2) left-versusright-earversusstereo auditory stimulations while recording fNIRS signals in the related brain areas (i.e., motor central sulcus and superior temporal cortices respectively). For the motor condition our results show that left-armversusright-arm stimulations induced typical contralateral difference in hemispheric activation asymmetries in the three subjects for all three channels. For the auditory condition, we also revealed typical human-like patterns of hemispheric asymmetries in one subject for all three channels, namely (1) typical contralateral differences in hemispheric asymmetry between left-earversusright-ear stimulations, and (2) a rightward asymmetry for stereo stimulations. Overall, our findings support the use of fNIRS to investigate brain processing in non-human primates from a functional perspective, opening the way for the development of non-invasive procedures in non-human primate brain research.
The formin Fmn2 is required for the development of an excitatory interneuron module in the zebrafish acoustic startle circuit
Authors: Nagar Dhriti , James Tomin K , Mishra Ratnakar , Guha Shrobona , Ghose Aurnab 
Published: July 2020

ABSTRACTThe formin family member, Fmn2, is a neuronally enriched cytoskeletal remodelling protein conserved across vertebrates. Recent studies have implicated Fmn2 in neurodevelopmental disorders, including sensory processing dysfunction and intellectual disability in humans. Cellular characterization of Fmn2 in primary neuronal cultures has identified its function in the regulation of cell-substrate adhesion and consequently growth cone translocation. However, the role of Fmn2 in the development of neural circuitsin vivo, and its impact on associated behaviours have not been tested.Using automated analysis of behaviour and systematic investigation of the associated circuitry, we uncover the role of Fmn2 in zebrafish neural circuit development. As reported in other vertebrates, the zebrafish ortholog of Fmn2 is also enriched in the developing zebrafish nervous system. We find that Fmn2 is required for the development of an excitatory interneuron pathway, the spiral fiber neuron, which is an essential circuit component in the regulation of the Mauthner cell-mediated acoustic startle response. Consistent with the loss of the spiral fiber neurons tracts, high-speed video recording revealed a reduction in the short latency escape events while responsiveness to the stimuli was unaffected.Taken together, this study provides evidence for a circuit-specific requirement of Fmn2 in eliciting an essential behaviour in zebrafish. Our findings underscore the importance of Fmn2 in neural development across vertebrate lineages and highlight zebrafish models in understanding neurodevelopmental disorders.SIGNIFICANCE STATEMENTFmn2 is a neuronally enriched cytoskeletal remodelling protein linked to neurodevelopment and cognitive disorders in humans. Recent reports have characterized its function in growth cone motility and chemotaxis in cultured primary neurons. However, the role of Fmn2 in the development of neural circuitsin vivoand its implications in associated behaviours remain unexplored. This study shows that Fmn2 is required for the development of neuronal processes in the acoustic startle circuit to ensure robust escape responses to aversive stimuli in zebrafish. Our study underscores the crucial role of the non-diaphanous formin, Fmn2, in establishing neuronal connectivity and related behaviour in zebrafish.
The evolution of social dominance through reinforcement learning
Authors: Leimar Olof 
Published: July 2020

AbstractGroups of social animals are often organised into dominance hierarchies that are formed through pairwise interactions. There is much experimental data on hierarchies, examining such things as winner, loser, and bystander effects, as well as the linearity and replicability of hierarchies, but there is a lack evolutionary analyses of these basic observations. Here I present a game-theory model of hierarchy formation in which individuals adjust their aggressive behaviour towards other group members through reinforcement learning. Individual traits such as the tendency to generalise learning between interactions with different individuals, the rate of learning, and the initial tendency to be aggressive are genetically determined and can be tuned by evolution. I find that evolution favours individuals with high social competence, making use of individual recognition, bystander learning and, to a limited extent, generalising learned behaviour between opponents when adjusting their behaviour towards other group members. The results are in good agreement with experimental data, for instance in finding weaker winner effects compared to loser effects.
Testing the CRISPR-Cas9 andglmSribozyme systems inLeishmania tarentolae
Authors: Turra Gino L. , Schneider Luzia , Liedgens Linda , Deponte Marcel 
Published: July 2020

AbstractLeishmaniaparasites include important pathogens and model organisms and are even used for the production of recombinant proteins. However, functional genomics and the characterization of essential genes are often limited inLeishmaniabecause of low-throughput technologies for gene disruption or tagging and the absence of components for RNA interference. Here, we tested the T7 RNA polymerase-dependent CRISPR-Cas9 system by Benekeet al. and theglmSribozyme-based knock-down system in the model parasiteLeishmania tarentolae. We successfully deleted two reference genes encoding the flagellar motility factor Pf16 and the salvage-pathway enzyme adenine phosphoribosyltransferase, resulting in immotile and drug-resistant parasites, respectively. In contrast, we were unable to disrupt the gene encoding the mitochondrial flavoprotein Erv. Cultivation ofL. tarentolaein standard BHI medium resulted in a constitutive down-regulation of an episomalmCherry-glmSreporter by 40 to 60%. For inducible knock-downs, we evaluated the growth ofL. tarentolaein alternative media and identified supplemented MEM, IMDM and McCoy’s 5A medium as candidates. Cultivation in supplemented MEM allowed an inducible, glucosamine concentration-dependent down-regulation of the episomalmCherry-glmSreporter by more than 70%. However, chromosomalglmS-tagging of the genes encoding Pf16, adenine phosphoribosyltransferase or Erv did not reveal a knock-down phenotype. Our data demonstrate the suitability of the CRISPR-Cas9 system for the disruption and tagging of genes inL. tarentolaeas well as the limitations of theglmSsystem, which was restricted to moderate efficiencies for episomal knock-downs and caused no detectable phenotype for chromosomal knock-downs.