bluuebunny/crossref_metadata_2025 huggingface dataset:
CRK2 and C-terminal phosphorylation of NADPH oxidase RBOHD regulate ROS production in Arabidopsis
Authors: Kimura Sachie , Hunter Kerri , Vaahtera Lauri , Tran Huy Cuong , Citterico Matteo , Vaattovaara Aleksia , Rokka Anne , Stolze Sara Christina , Harzen Anne , Meißner Lena , Wilkens Maya Melina Tabea , Hamann Thorsten , Toyota Masatsugu , Nakagami Hirofumi , Wrzaczek Michael
Published: April 2019

Reactive oxygen species (ROS) are important messengers in eukaryotic organisms and their production is tightly controlled. Active extracellular ROS production by NADPH oxidases in plants is triggered by receptor-like protein kinase (RLK)-dependent signaling networks. Here we show that the cysteine-rich RLK CRK2 kinase activity is required for plant growth and CRK2 exists in a preformed complex with the NADPH oxidase RBOHD in Arabidopsis. Functional CRK2 is required for the full elicitor-induced ROS burst and consequently the crk2 mutant is impaired in defense against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Our work demonstrates that CRK2 regulates plant innate immunity. We identified in vitro CRK2-dependent phosphorylation sites in the C-terminal region of RBOHD. Phosphorylation of S703 RBOHD is enhanced upon flg22 treatment and substitution of S703 with alanine reduced ROS production in Arabidopsis. Phylogenetic analysis suggests that phospho-sites in C-terminal region of RBOHD are conserved throughout the plant lineage and between animals and plants. We propose that regulation of NADPH oxidase activity by phosphorylation of the C-terminal region might be an ancient mechanism and that CRK2 is an important element in regulating MAMP-triggered ROS production.

One-sentence summary

CRK2 associates with and activates RBOHD to trigger MAMP-induced ROS production and reveals a novel regulatory mechanism for plant NADPH oxidases through phosphorylation of the C-terminus.
Co-infections by non-interacting pathogens are not independent & require new tests of interaction
Authors: Hamelin Frédéric M. , Allen Linda J.S. , Bokil Vrushali A. , Gross Louis J. , Hilker Frank M. , Jeger Michael J. , Manore Carrie A. , Power Alison G. , Rúa Megan A. , Cunniffe Nik J.
Published: April 2019

If pathogen species, strains or clones do not interact, intuition suggests the proportion of co-infected hosts should be the product of the individual prevalences. Independence consequently underpins the wide range of methods for detecting pathogen interactions from cross-sectional survey data. However, the very simplest of epidemiological models challenge the underlying assumption of statistical independence. Even if pathogens do not interact, death of co-infected hosts causes net prevalences of individual pathogens to decrease simultaneously. The induced positive correlation between prevalences means the proportion of co-infected hosts is expected to be higher than multiplication would suggest. By modeling the dynamics of multiple non-interacting pathogens, we develop a pair of novel tests of interaction that properly account for non-independence. Our tests allow us to reinterpret data from previous studies including pathogens of humans, plants, and animals. Our work demonstrates how methods to identify interactions between pathogens can be updated using simple epidemic models.
Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)
Authors: VanWallendael Acer , Bonnette Jason , Juenger Thomas E. , Fritschi Felix B. , Fay Philip A. , Mitchell Robert B. , Lloyd-Reilley John , Rouquette Francis M. , Bergstrom Gary C. , Lowry David B.
Published: April 2019

Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described.

To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust (Puccinia spp.) severity in switchgrass (Panicum virgatum) plantings at eight locations across the central United States for three years and conducted quantitative trait locus (QTL) mapping for rust progression.

We mapped several variable QTLs, but two large-effect QTLs which we have namedPrr1andPrr2were consistently associated with rust severity in multiple sites and years, particularly in northern sites. In contrast, there were numerous small-effect QTLs at southern sites, indicating a genotype-by-environment interaction in rust resistance loci. Interestingly,Prr1andPrr2had a strong epistatic interaction, which also varied in strength and direction of effect across space.

Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Further, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.
REMoDNaV: Robust Eye-Movement Classification for Dynamic Stimulation
Authors: Dar Asim H. , Wagner Adina S. , Hanke Michael
Published: April 2019

Tracking of eye movements is an established measurement for many types of experimental paradigms. More complex and more prolonged visual stimuli have made algorithmic approaches to eye movement event classification the most pragmatic option. A recent analysis revealed that many current algorithms are lackluster when it comes to data from viewing dynamic stimuli such as video sequences. Here we present an event classification algorithm—built on an existing velocity-based approach—that is suitable for both static and dynamic stimulation, and is capable of classifying saccades, post-saccadic oscillations, fixations, and smooth pursuit events. We validated classification performance and robustness on three public datasets: 1) manually annotated, trial-based gaze trajectories for viewing static images, moving dots, and short video sequences, 2) lab-quality gaze recordings for a feature length movie, and 3) gaze recordings acquired under suboptimal lighting conditions inside the bore of a magnetic resonance imaging (MRI) scanner for the same full-length movie. We found that the proposed algorithm performs on par or better compared to state-of-the-art alternatives for static stimulation. Moreover, it yields eye movement events with biologically plausible characteristics on prolonged dynamic recordings. Lastly, algorithm performance is robust on data acquired under suboptimal conditions that exhibit a temporally varying noise level. These results indicate that the proposed algorithm is a robust tool with improved classification accuracy across a range of use cases. The algorithm is cross-platform compatible, implemented using the Python programming language, and readily available as free and open source software from public sources.
Brain BOLD MRI O2and CO2stress testing: Implications for perioperative neurocognitive disorder following surgery
Authors: Mutch W. Alan C. , El-Gabalawy Renée , Ryner Lawrence , Puig Josep , Essig Marco , Kilborn Kayla , Fidler Kelsi , Graham M. Ruth
Published: April 2019

Respiratory end-tidal (ET) gas control is fundamental to anaesthetic management. The range of ET O2and CO2during the conduct of anaesthesia can significantly deviate from values in the awake state. Recent work shows ET CO2influences the incidence of perioperative neurocognitive disorder (POND). We examine the effects of controlled alterations in both ET O2and CO2on cerebral blood flow (CBF) in awake adults using BOLD MRI. Twelve healthy adults had BOLD and CBF responses measured to alterations in ET CO2and O2in various combinations commonly observed under anaesthesia. Dynamic alterations in regional BOLD and CBF were seen in all subjects with expected and inverse responses to both stimuli. These effects were incremental and rapid (within seconds). The most dramatic effects were seen with combined hyperoxia and hypocapnia. Inverse responses increased with age. Here we show that human brain CBF responds dramatically to alterations in ET respiratory gas tensions commonly seen during anaesthesia. Such alterations may impact the observed incidence of POND following surgery and intensive care, and is an important area for further investigation.
Modeling the Switching behavior of Functional Connectivity Microstates (FCμstates) as a Novel Biomarker for Mild Cognitive Impairment
Authors: Dimitriadis SI , López María Eugenia , Maestu Fernando , Pereda Ernesto
Published: April 2019

It is evident the need for designing and validating novel biomarkers for the detection of mild cognitive impairment (MCI). MCI patients have a high risk of developing Alzheimer’s disease (AD), and for that reason the introduction of novel and reliable biomarkers is of significant clinical importance. Motivated by recent findings about the rich information of dynamic functional connectivity graphs (DFCGs) about brain (dys)function, we introduced a novel approach of identifying MCI based on magnetoencephalographic (MEG) resting state recordings.

The activity of different brain rhythms {δ, θ, α1, α2, β1, β2, γ1, γ2} was first beamformed with linear constrained minimum norm variance in the MEG data to determine ninety anatomical regions of interest (ROIs). A dynamic functional connectivity graph (DFCG) was then estimated using the imaginary part of phase lag value (iPLV) for both intra-frequency coupling (8) and also cross-frequency coupling pairs (28). We analyzed DFCG profiles of neuromagnetic resting state recordings of 18 Mild Cognitive Impairment (MCI) patients and 20 healthy controls. We followed our model of identifying the dominant intrinsic coupling mode (DICM) across MEG sources and temporal segments that further leads to the construction of an integrated DFCG (iDFCG). We then filtered statistically and topologically every snapshot of the iDFCG with data-driven approaches. Estimation of the normalized Laplacian transformation for every temporal segment of the iDFCG and the related eigenvalues created a 2D map based on the network metric time series of the eigenvalues (NMTSeigs). NMTSeigs preserves the non-stationarity of the fluctuated synchronizability of iDCFG for each subject. Employing the initial set of 20 healthy elders and 20 MCI patients, as training set, we built an overcomplete dictionary set of network microstates (nμstates). Afterward, we tested the whole procedure in an extra blind set of 20 subjects for external validation.

We succeeded a high classification accuracy on the blind dataset (85 %) which further supports the proposed Markovian modeling of the evolution of brain states. The adaptation of appropriate neuroinformatic tools that combine advanced signal processing and network neuroscience tools could manipulate properly the non-stationarity of time-resolved FC patterns revealing a robust biomarker for MCI.
Mutual Information Analysis of Neural Representations of Speech in Noise in the Aging Midbrain
Authors: Zan Peng , Presacco Alessandro , Anderson Samira , Simon Jonathan Z.
Published: April 2019

Younger adults with normal hearing can typically understand speech in the presence of a competing speaker without much effort, but this ability to understand speech in challenging conditions deteriorates with age. Older adults, even with clinically normal hearing, often have problems understanding speech in noise. Earlier auditory studies using the frequency-following response (FFR), primarily believed generated by the midbrain, have demonstrated age-related neural deficits when analyzed using traditional measures. Here we use a mutual information paradigm to analyze the FFR to speech (masked by a competing speech signal) by estimating the amount of stimulus information contained in the FFR. Our results show, first, a broad-band informational loss associated with aging for both FFR amplitude and phase. Second, this age-related loss of information is more severe in higher frequency FFR bands (several hundred Hz). Third, the mutual information between the FFR and the stimulus decreases as noise level increases for both age groups. Fourth, older adults benefit neurally, i.e., show a reduction in loss of information, when the speech masker is changed from meaningful (talker speaking a language that they can comprehend, such as English) to meaningless (talker speaking a language that they cannot comprehend, such as Dutch). This benefit is not seen in younger listeners, which suggests age-related informational loss may be more severe when the speech masker is meaningful than when it is meaningless. In summary, as a method, mutual information analysis can unveil new results that traditional measures may not have enough statistical power to assess.

New & Noteworthy

Older adults, even with clinically normal hearing, often have problems understanding speech in noise. Auditory studies using the frequency-following response (FFR) have demonstrated age-related neural deficits using traditional methods. Here we use a mutual information paradigm to analyze the FFR to speech masked by competing speech. Results confirm those using traditional analysis, but additionally show that older adults benefit neurally when the masker changes from a language that they comprehend to a language they cannot.
Efficient treatment of a preclinical inflammatory bowel disease model with engineered bacteria
Authors: Ferenczi Szilamer , Horváth István , Szeőcs Natália , Grózer Zsuzsanna , Kuti Dániel , Juhász Balázs , Winkler Zsuzsanna , Pankotai Tibor , Sükösd Farkas , Kovács Krisztina J. , Szallasi Zoltan
Published: April 2019

We developed an engineered bacterium based, RNA interference mediated therapeutic method to significantly reduce the symptoms in the most frequently used animal model of inflammatory bowel disease. This transkingdom RNA interference strategy was based on the non-pathogenic E. coli MDS42 strain, which was engineered to constitutively produce invasin and histeriolysin cytolysin. These proteins enabled the bacteria first to invade the colon epithelium and then degrade in the phagosome. This allowed the delivery of a plasmid encoding shRNA targeting TNF alpha into the cytoplasm of the target cells. The expression levels of TNF alpha and other cytokines significantly decreased and the inflammatory symptoms were significantly reduced. With further safety modifications this method could serve as a safe and side-effect free alternative to biologicals targeting TNF-alpha.
Adapterama II: Universal amplicon sequencing on Illumina platforms (TaggiMatrix)
Authors: Glenn Travis C. , Pierson Todd W. , Bayona-Vásquez Natalia J. , Kieran Troy J. , Hoffberg Sandra L. , Thomas Jesse C. , Lefever Daniel E. , Finger John W. , Gao Bei , Bian Xiaoming , Louha Swarnali , Kolli Ramya T. , Bentley Kerin , Rushmore Julie , Wong Kelvin , Shaw Timothy I. , Rothrock Michael J. , McKee Anna M. , Guo Tai L. , Mauricio Rodney , Molina Marirosa , Cummings Brian S. , Lash Lawrence H. , Lu Kun , Gilbert Gregory S. , Hubbell Stephen P. , Faircloth Brant C.
Published: April 2019

Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. Most NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5’ end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (eight forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy.
N-WASP regulates the mobility of the B cell receptor and co-receptors during signaling activation
Authors: Rey-Suarez Ivan , Wheatley Brittany , Koo Peter , Shu Zhou , Mochrie Simon , Song Wenxia , Shroff Hari , Upadhyaya Arpita
Published: April 2019

Regulation of membrane receptor mobility is important in tuning the cell’s response to external signals. This is particularly relevant in the context of immune receptor signaling. The binding of B cell receptors (BCR) to antigen induces B cell receptor activation. While actin dynamics and BCR signaling are known to be linked, the role of actin dynamics in modulating receptor mobility is not well understood. Here, we use single molecule imaging to examine BCR movement during signaling activation and examine the role of actin dynamics on BCR mobility. We use a novel machine learning based method to classify BCR trajectories into distinct diffusive states and show that the actin regulatory protein N-WASP regulates receptor mobility. Constitutive loss or acute inhibition of N-WASP, which is associated with enhanced signaling, leads to a predominance of BCR trajectories with lower diffusivity and is correlated with a decrease in actin dynamics. Furthermore, loss of N-WASP reduces diffusivity of CD19, a stimulatory co-receptor of the BCR but not that of unstimulated FcγRIIB, an inhibitory co-receptor. The effect of N-WASP is mirrored by inhibition of the Arp2/3 complex and formins. Our results implicate the dynamic actin network in fine-tuning receptor mobility and receptor-ligand interactions, thereby modulating B cell signaling.
An Optimized Registration Workflow and Standard Geometric Space for Small Animal Brain Imaging
Authors: Ioanas Horea-Ioan , Marks Markus , Zerbi Valerio , Yanik Mehmet Fatih , Rudin Markus
Published: April 2019

The reliability of scientific results critically depends on reproducible and transparent data processing. Cross-subject and cross-study comparability of imaging data in general, and magnetic resonance imaging (MRI) data in particular, is contingent on the quality of registration to a standard reference space. In small animal MRI this is not adequately provided by currently used processing workflows, which utilize high-level scripts optimized for human data, and adapt animal data to fit the scripts, rather than vice-versa. In this fully reproducible article we showcase a generic workflow optimized for the mouse brain, alongside a standard reference space suited to harmonize data between analysis and operation. We introduce four separate metrics for automated quality control (QC), and a visualization method to aid operator inspection. Benchmarking this workflow against common legacy practices reveals that it performs more consistently, better preserves variance across subjects while minimizing variance across sessions, and improves both volume and smoothness conservation RMSE approximately 2-fold. We propose this open source workflow and the QC metrics as a new standard for small animal MRI registration, ensuring workflow robustness, data comparability, and region assignment validity, all of which are indispensable prerequisites for the comparability of scientific results across experiments and centers.
Immunodietica: A data-driven approach to investigate interactions between diet and autoimmune disorders
Authors: Gershteyn Iosif M. , Ferreira Leonardo M.R.
Published: April 2019

Autoimmunity is on the rise around the globe. Diet has been proposed as a risk factor for autoimmunity and shown to modulate the severity of several autoimmune disorders. Yet, the interaction between diet and autoimmunity in humans remains largely unstudied. Here, we systematically interrogated commonly consumed animals and plants for peptide epitopes previously implicated in human autoimmune disease. A total of fourteen species investigated could be divided into three broad categories regarding their content in human autoimmune epitopes, which we represented using a new metric, the Gershteyn-Ferreira index (GF index). Strikingly, pig contains a disproportionately high number of unique autoimmune epitopes compared to all other species analyzed. This work uncovers a potential new link between pork consumption and autoimmunity in humans and lays the foundation for future studies on the impact of diet on the pathogenesis and progression of autoimmune disorders.
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

Mindfulness 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

Human 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

Cellular 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

Immune 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

Internally 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

Nearly 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 Statement

Anxiety 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

Crystallization 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.

Synopsis

This 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

Sticholysins 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 significance

We 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

System-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

Chromosome 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

Introduction

HIV 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.

Methods

We 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.

Results

The 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

Motile 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 STATEMENT

Basal 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

Although 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.
Plant uses in a traditional fisherman community in northeastern Brazil
Authors: Tng DYP , Apgaua DMG , Lisboa MDS , El-Hani CN
Published: April 2019

Background

Knowledge of traditional plant use in rural communities is under threat from urbanization and also land use change. Hence, elucidating region-specific patterns traditional knowledge of habitat resource use is crucial for assisting policy making with regard to nature conservation, human nutrition, and human health. Using original data from northeast Bahia, Brazil, we aim to document the collective knowledge of plant use possessed by artisanal fishermen and women in fishing communities, related to medicinal, construction, technology and ritualistic/religious uses.

Methods

Data were collected through interviews with and opportunistic guided tours by local specialists to record the local knowledge of plant use and methods of use.

Results

Through interviews, 116 species of plants from 104 genera and 47 botanical families were identified along with their local names, plant parts utilized, habitats, and preparation methods, and an additional 26 spp. for which only local names were available. Of these, 72 spp. are used as medicine, 48 spp. as non-conventional edibles, 31 spp. for construction and 11 for religious/mystical purposes. Female informants generally cited more food and medicinal plants than male informants. All interviewees unanimously expressed that the use of plants for medicines and fishing technology has significantly reduced or been superseded by modern materials.

Conclusion

The present study demonstrates that the rich collective plant use knowledge of an artisanal fishing community in northeast Brazil. The results of this study serves as a framework for to extend ethnobotanical investigations to other traditional fishing communities in the vicinity, and also to examine more social and demographic factors influencing traditional knowledge related to uses of plants. Finally, the rich tradition of plant use in the region underpins the need to encourage measures to preserve this cultural knowledge and conserve the natural environments that are a source of these plants.
A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance ofAchromobacter xylosoxidans
Authors: Cameron Lydia C. , Bonis Benjamin , Phan Chi Q. , Kent Leslie A. , Lee Alysha K. , Hunter Ryan C.
Published: April 2019

Achromobacter xylosoxidanshas attracted increasing attention as an emerging pathogen in patients with cystic fibrosis. Intrinsic resistance to several classes of antimicrobials and the ability to form robust biofilmsin vivocontribute to the clinical manifestations of persistentA. xylosoxidansinfection. Still, much ofA. xylosoxidansbiofilm formation remains uncharacterized due to the scarcity of existing genetic tools. Here we demonstrate a promising genetic system for use inA. xylosoxidans; generating a transposon mutant library which was then used to identify genes involved in biofilm developmentin vitro. We further described the effects of one of the genes found in the mutagenesis screen, encoding a putative enoyl-CoA hydratase, on biofilm structure and tolerance to antimicrobials. Through additional analysis, we find that a cis-2 fatty acid signaling compound is essential toA. xylosoxidansbiofilm ultrastructure and maintenance. This work describes methods for the genetic manipulation ofA. xylosoxidansand demonstrated their use to improve our understanding ofA. xylosoxidanspathophysiology.