bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the impact of mindfulness attitudes on attentional quality through focused breath induction
Authors: França M , Tanaka GK , Cagy M , Ribeiro P , Velasques B , Gamboa OL 
Published: April 2019

AbstractMindfulness attitudes, as gentleness, openness, acceptance, curiosity and being non-judgmental have been related to improvement in cognitive and emotional functions, but few studies have focused on its specific contribution. The present study investigated the effect of the mindfulness attitudes on top-down attentional control abilities. Twenty one healthy participants were submitted to two conditions: a Mindfulness induction session where participants practiced focusing on the sensory sensations of breathing while encouraged to incorporate the five mindfulness attitudes and an attentional control session in which participants were repeatedly instructed to merely attend to the breath, without any mindfulness attitude component. Before and after each condition, participants performed two blocks of the oddball task while EEG was recorded. Contrary to our expectations, attentional control assessed through amplitude and latency of the P3b ERP component and oddball task accuracy did not show any changes in any of the conditions. These results suggest that a low dose of mindfulness training in naive individuals, through a focused breath induction, is not enough to improve the allocation of attentional resources towards task-relevant stimuli.
Evolutionary dynamics of culturally transmitted, fertility-reducing traits
Authors: Wodarz Dominik , Stipp Shaun , Hirshleifer David , Komarova Natalia L. 
Published: April 2019

AbstractHuman populations in many countries have undergone a phase of demographic transition, characterized by a major reduction in fertility at a time of increased resource availability. A key stylized fact is that the reduction in fertility is preceded by a reduction in mortality and a consequent increase in population density. Various theories have been proposed to account for the demographic transition process, including maladaptation, increased parental investment in fewer offspring, and cultural evolution. None of these approaches, including formal cultural evolutionary models of the demographic transitions, have addressed a possible direct causal relationship between a reduction in mortality and the subsequent decline in fertility. We provide mathematical models in whichlow mortalityfavors the cultural selection of low fertility traits. This occurs because reduced mortality slows turnover in the model, which allows the cultural transmission advantage of low fertility traits to out-race their reproductive disadvantage. For mortality to be a crucial determinant of outcome, a cultural transmission bias is required where slow reproducers exert higher social influence. Computer simulations of our models that allow for exogenous variation in the death rate can reproduce the central features of the demographic transition process, including substantial reductions in fertility within only 1-3 generations. A model assuming continuous evolution of reproduction rates through imitation errors predicts fertility to fall below replacement levels, if death rates are sufficiently low. This can potentially explain the very low preferred family sizes in Western Europe.
Supercoiling DNA optically
Authors: King Graeme A. , Burla Federica , Peterman Erwin J. G. , Wuite Gijs J.L. 
Published: April 2019

AbstractCellular DNA is regularly subject to torsional stress during genomic processes, such as transcription and replication, resulting in a range of supercoiled DNA structures.1,2,3 For this reason, methods to prepare and study supercoiled DNA at the single-molecule level are widely used, including magnetic,4,5,6 angular-optical,7,8,9 micro-pipette,10 and magneto-optical tweezers.11 However, in order to address many open questions, there is a growing need for new techniques that can combine rapid torque control with both spatial manipulation and fluorescence microscopy. Here we present a single-molecule assay that can rapidly and controllably generate negatively supercoiled DNA using a standard dual-trap optical tweezers instrument. Supercoiled DNA formed in this way is amenable to fast buffer exchange, and can be interrogated with both force spectroscopy and fluorescence imaging of the whole DNA. We establish this method as a powerful platform to study both the biophysical properties and biological interactions of negatively supercoiled DNA.
Population genomics reveals complex patterns of immune gene evolution in monarch butterflies (Danaus plexippus)
Authors: Tan Wen-Hao , Mongue Andrew J. , de Roode Jacobus C. , Gerardo Nicole M. , Walters James R. 
Published: April 2019

ABSTRACTImmune genes presumably rapidly evolve as pathogens exert strong selection pressures on host defense, but the evolution of immune genes is also constrained by trade-offs with other biological functions and shaped by the environmental context. Thus, immune genes may exhibit complex evolutionary patterns, particularly when organisms disperse to or live in variable environments. We examined the evolutionary patterns of the full set of known canonical immune genes within and among populations of monarch butterflies (Danaus plexippus), and relative to a closely related species (D. gilippus). Monarchs represent a system with a known evolutionary history, in which North American monarchs dispersed to form novel populations across the world, providing an opportunity to explore the evolution of immunity in the light of population expansion into novel environments. By analyzing a whole-genome resequencing dataset across populations, we found that immune genes as a whole do not exhibit consistent patterns of selection, differentiation, or genetic variation, but that patterns are specific to functional classes. Species comparisons betweenD. plexippusandD. gilippusand analyses of monarch populations both revealed consistently low levels of genetic variation in signaling genes, suggesting conservation of these genes over evolutionary time. Modulation genes showed the opposite pattern, with signatures of relaxed selection across populations. In contrast, recognition and effector genes exhibited less consistent patterns. When focusing on genes with exceptionally strong signatures of selection or differentiation, we also found population-specific patterns, consistent with the hypothesis that monarch populations do not face uniform selection pressures with respect to immune function.
Rapid sensory integration in orexin neurons governs probability of future movements
Authors: Karnani Mahesh M. , Schöne Cornelia , Bracey Edward F. , Antonio González J. , Viskaitis Paulius , Adamantidis Antoine , Burdakov Denis 
Published: April 2019

AbstractInternally and externally triggered movement is crucial for survival and is controlled by multiple interconnected neuronal populations spanning many brain areas. Lateral hypothalamic orexin/hypocretin neurons are thought to play a slow, modulatory part in this scheme through their key role in promoting metabolism and wakefulness. However, it is unknown whether orexin/hypocretin neurons participate in rapid neural processing, leading to immediate movement. Furthermore, their role in sensorimotor transformations remains unknown. Here we use cellular-resolution Ca2+ imaging and optogenetics to show that orexin/hypocretin cells are instantaneous regulators of self-generated and sensory-evoked movement. They are activated before and during movement, preventing this activation reduces self-generated locomotion, and optogenetic mimicry of this transient activation rapidly initiates locomotion. We find that the same orexin neurons whose activity predicts movement initiation are rapidly controllable by external sensory stimuli, and silencing orexin cells during sensation prevents normal motor performance. These findings place orexin neurons in a physiological position of unexpectedly rapid and strong sensorimotor control.
Anterior cingulate cortex and ventral hippocampal inputs to the basolateral amygdala selectively control generalized fear
Authors: Ortiz Samantha , Latsko Maeson S. , Fouty Julia L. , Dutta Sohini , Adkins Jordan M. , Jasnow Aaron M. 
Published: April 2019

AbstractNearly one third of Americans have been afflicted with an anxiety disorder. A common symptom of anxiety disorders is the over generalization of fear across a broad range of contextual cues. We previously found that the anterior cingulate cortex and ventral hippocampus (vHPC) regulate generalized fear. Here, we investigate the functional projections from the ACC and vHPC to the amygdala and their role in governing generalized fear in a preclinical rodent model. A chemogenetic approach (DREADDs) was used to inhibit glutamatergic projections from the ACC or vHPC that terminate within the basolateral amygdala (BLA) at recent (1 day) or remote (28 days) time points after contextually fear conditioning male mice. Inactivating ACC or vHPC projections to the BLA significantly reduced generalized fear to a novel, nonthreatening context but had no effect on fear to the training context. Further, our data indicate that the ACC-BLA circuit supports generalization in a time-independent manner. We also identified for the first time a strictly time-dependent role of the vHPC-BLA circuit in supporting remote generalized contextual fear. Dysfunctional signaling to the amygdala from the ACC or the hippocampus could underlie over-generalized fear responses that are associated with anxiety disorders. Our findings demonstrate that the ACC and vHPC regulate fear expressed in novel, nonthreatening environments via projections to the BLA but do so as a result of training intensity or time, respectively.Significance StatementAnxiety disorders are characterized by a common symptom that promotes overgeneralization of fear in non-threatening environments. Dysregulation of the amygdala, anterior cingulate cortex (ACC), or hippocampus has been hypothesized to contribute to increased fear associated with anxiety disorders. Our findings show that the ACC and HPC projections to the basolateral amygdala regulate generalized fear in non-threatening, environments. However, descending ACC projections control fear generalization independent of time, whereas HPC projections play a strictly time-dependent role in regulating generalized fear. Thus, dysfunctional ACC/HPC signaling to the BLA may be a predominant underlying mechanism of non-specific fear associated with anxiety disorders. Our data have important implications for predictions made by theories about aging memories and interactions between the hippocampus and cortical regions.
An anticipated optimization approach to macromolecular crystallization
Authors: Gorrec Fabrice 
Published: April 2019

AbstractCrystallization is an essential step for determining macromolecular structures at atomic resolution with X-ray crystallography. Crystals of diffraction quality obtained from purified samples of proteins, RNAs, DNAs and their complexes enable our understanding of biological processes and structure-based design of drugs. Targets of interest for researchers are however increasingly challenging to produce and crystallise. Progress in crystallization methods applicable to limiting amount of sample while increasing the yield of useful crystals are hence urgently needed. In this context, an Anticipated Optimization Approach was investigated. For this approach, it is assumed that samples are highly unstable and will most probably not produce useful crystals (‘hits’). By selecting leads very early, what remains from the initial sample can be used for follow-up optimization experiments. Subsequently, the reproducibility issues caused by sample variability are bypassed. An initial crystallization screen that failed to produce hits becomes a well-suited solubility assay that is a starting point for optimization. The approach was tested with a straightforward and cost-effective protocol developed elsewhere. The yield of useful crystals was increased and accelerated for three targets of pharmacologic studies.SynopsisThis study suggests that the yield of useful crystals obtained from challenging protein samples can be increased by using an initial crystallization screen as solubility assay.
Membrane remodeling by the lytic fragment of sticholysin II: implications for the toroidal pore model
Authors: Mesa-Galloso H. , Valiente P.A. , Epand R.F. , Lanio M.E. , Epand R.M. , Alvarez C. , Tieleman D.P. , Ros U. 
Published: April 2019

AbstractSticholysins are pore-forming toxins of biomedical interest and represent a prototype of proteins acting through the formation of protein-lipid or toroidal pores. Peptides spanning the N-terminus of sticholysins can mimic their permeabilizing activity and together with the full-length toxins have been used as a tool to understand the mechanism of pore formation in membranes. However, the lytic mechanism of these peptides and the lipid shape modulating their activity are not completely clear. In this paper, we combine molecular dynamics (MD) simulations and experimental biophysical tools to dissect different aspects of the pore-forming mechanism of StII1-30, a peptide derived from the N-terminus of sticholysin II. With this combined approach, membrane curvature induction and flip-flop movement of the lipids were identified as two important membrane remodeling steps mediated by StII1-30-pore forming activity. Pore-formation by this peptide was enhanced by the presence of the negatively-curved lipid phosphatidylethanolamine (PE) in membranes. This lipid emerged not only as a facilitator of membrane interactions but also as a structural element of the StII1-30-pore that is recruited to the pore ring upon its assembly. Collectively, these new findings support a toroidal model for the architecture of the pore formed by this peptide and provide new molecular insight into the role of PE as a membrane component that easily accommodates into the ring of toroidal pores aiding in its stabilization. This study contributes to a better understanding of the molecular mechanism underlying the permeabilizing activity of StII1-30 and peptides or proteins acting via a toroidal pore mechanism and offers an informative framework for the optimization of the biomedical application of this and similar molecules.State of significanceWe provide evidence about the ability of StII1-30 to form toroidal pores. Due to pore assembly, StII1-30-pore induces membrane curvature and facilitates flip-flop movement of the lipids. The negatively-curved lipid PE relocates from the membrane into the pore ring, being also a structural element of the pore StII1-30 forms. This peptide emerged as a new tool, together with the full-length toxin, to understand the mechanism of toroidal pore formation in membranes. This study provides new molecular insight into the role of curved lipids as co-factors of toroidal pores, which could aid in its stabilization by easily accommodating into the ring. This framework could underpin strategies for the rational use of peptides or proteins acting via toroidal pores.
“De novo Classification of Mouse B Cell Types using Surfaceome Proteotype Maps”
Authors: van Oostrum Marc , Müller Maik , Klein Fabian , Bruderer Roland , Zhang Hui , Pedrioli Patrick G. A. , Reiter Lukas , Tsapogas Panagiotis , Rolink Antonius , Wollscheid Bernd 
Published: April 2019

AbstractSystem-wide quantification of the cell surface proteotype and identification of extracellular glycosylation sites is challenging when sample is limiting. We miniaturized and automated the previously described Cell Surface Capture technology increasing sensitivity, reproducibility, and throughput. We used this technology, which we call autoCSC, to create population-specific surfaceome maps of developing mouse B cells and used targeted flow cytometry to uncover developmental cell subpopulations.
Direct Nucleosome Binding of Borealin Secures Chromosome Association and Function of the Chromosomal Passenger complex
Authors: Abad M. A. , Ruppert J. G. , Buzuk L. , Wear M. , Zou J. , Webb K. M. , Kelly D. A. , Voigt P. , Rappsilber J. , Earnshaw W. C. , Jeyaprakash A. A. 
Published: April 2019

SummaryChromosome association of the Chromosomal Passenger Complex (CPC; consisting of Borealin, Survivin, INCENP and the Aurora B kinase) is essential to achieve error-free chromosome segregation during cell division. Hence, understanding the mechanisms driving the chromosome association of the CPC is of paramount importance. Here using a multifaceted approach, we show that the CPC binds nucleosomes through a multivalent interaction predominantly involving Borealin. Strikingly, Survivin, previously suggested to target the CPC to centromeres [1–3] failed to bind nucleosomes on its own and requires Borealin and INCENP for its binding. Disrupting Borealin-nucleosome interactions excluded the CPC from chromosomes and caused chromosome congression defects. We also show that Borealin-mediated chromosome association of the CPC is critical for Haspin- and Bub1-mediated centromere enrichment of the CPC and works upstream of the latter. Our work thus establishes Borealin as a master regulator determining the chromosome association and function of the CPC.
Clusters of sub-Saharan African countries based on sociobehavioural characteristics and associated HIV incidence
Authors: Merzouki Aziza , Estill Janne , Orel Erol , Tal Kali , Keiser Olivia 
Published: April 2019

AbstractIntroductionHIV incidence varies widely between sub-Saharan African (SSA) countries. This variation coincides with a substantial sociobehavioural heterogeneity, which complicates the design of effective interventions. In this study, we investigated how sociobehavioural heterogeneity in sub-Saharan Africa could account for the variance of HIV incidence between countries.MethodsWe analysed aggregated data, at the national-level, from the most recent Demographic and Health Surveys of 29 SSA countries [2010-2017], which included 594’644 persons (183’310 men and 411’334 women). We preselected 48 demographic, socio-economic, behavioural and HIV-related attributes to describe each country. We used Principal Component Analysis to visualize sociobehavioural similarity between countries, and to identify the variables that accounted for most sociobehavioural variance in SSA. We used hierarchical clustering to identify groups of countries with similar sociobehavioural profiles, and we compared the distribution of HIV incidence (estimates from UNAIDS) and sociobehavioural variables within each cluster.ResultsThe most important characteristics, which explained 69% of sociobehavioural variance across SSA among the variables we assessed were: religion; male circumcision; number of sexual partners; literacy; uptake of HIV testing; women’s empowerment; accepting attitude toward people living with HIV/AIDS; rurality; ART coverage; and, knowledge about AIDS. Our model revealed three groups of countries, each with characteristic sociobehavioural profiles. HIV incidence was mostly similar within each cluster and different between clusters (median(IQR); 0.5/1000(0.6/1000), 1.8/1000(1.3/1000) and 5.0/1000(4.2/1000)).
Microtubule glycylation promotes basal body attachment to the cell cortex
Authors: Junker Anthony D. , Soh Adam W. J. , O’Toole Eileen T. , Meehl Janet B. , Guha Mayukh , Winey Mark , Honts Jerry E. , Gaertig Jacek , Pearson Chad G. 
Published: April 2019

ABSTRACTMotile cilia generate directed hydrodynamic flow that is important for the motility of cells and extracellular fluids. To optimize directed hydrodynamic flow, motile cilia are organized and oriented into a polarized array. Basal bodies (BB) nucleate and position motile cilia at the cell cortex. Cytoplasmic BB-associated microtubules are conserved structures that extend from BBs. Using the ciliate,Tetrahymena thermophila, combined with EM-tomography and light microscopy, we show that BB-appendage microtubules assemble coincident with new BB assembly and are attached to the cell cortex. These BB-appendage microtubules are specifically marked with post translational modifications of tubulin, including glycylation. Mutations that prevent glycylation shorten BB-appendage microtubules and disrupt BB positioning and cortical attachment. Consistent with the attachment of BB-appendage microtubules to the cell cortex for BB positioning, mutations that disrupt the cellular cortical cytoskeleton similarly disrupt the cortical attachment and positioning of BBs. In summary, BB-appendage microtubules promote the organization of ciliary arrays through attachment to the cell cortex.SUMMARY STATEMENTBasal bodies position motile cilia at the cell cortex. This study finds tubulin glycylation to promote BB-associated microtubule elongation and structural attachment of basal bodies to the cell’s cortical cytoskeleton.
Environmental DNA facilitates accurate, indigenous-led, inexpensive, and multi-year population estimates of millions of Eulachon fish
Authors: Pochardt Meredith , Allen Jennifer M. , Hart Ted , Miller Sophie D. L. , Yu Douglas W. , Levi Taal 
Published: April 2019

AbstractAlthough environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends rather than simply assessing presence or absence. However, the efficacy of environmental-DNA-based indices of abundance for long-term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark-recapture population estimates for eulachon (Thaleichthys pacificus) and ‘eDNA rates,’ which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark-recapture population estimate, explaining 84.96% and 92.53% of the deviance respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark-recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark-recapture is infeasible.