bluuebunny/crossref_metadata_2025_split huggingface dataset:
Near-Atomic Cryo-EM Imaging of a Small Protein Displayed on a Designed Scaffolding System
Authors: Liu Yuxi , Gonen Shane , Gonen Tamir , Yeates Todd O. 
Published: November 2017

AbstractCurrent single particle electron cryo-microscopy (cryo-EM) techniques can produce images of large protein assemblies and macromolecular complexes at atomic level detail without the need for crystal growth. However, proteins of smaller size, typical of those found throughout the cell, are not presently amenable to detailed structural elucidation by cryo-EM. Here we use protein design to create a modular, symmetrical scaffolding system to make protein molecules of typical size amenable to cryo-EM. Using a rigid continuous alpha-helical linker, we connect a small 17 kDa protein (DARPin) to a protein subunit that was designed to self-assemble into a cage with cubic symmetry. We show that the resulting construct is amenable to structural analysis by single particle cryo-EM, allowing us to identify and solve the structure of the attached small protein at near-atomic detail, ranging from 3.5 to 5 Å resolution. The result demonstrates that proteins considerably smaller than the theoretical limit of 50 kDa for cryo-EM can be visualized clearly when arrayed in a rigid fashion on a symmetric designed protein scaffold. Furthermore, because the amino acid sequence of a DARPin can be chosen to confer tight binding to various other protein or nucleic acid molecules, the system provides a future route for imaging diverse macromolecules, potentially broadening the application of cryoEM to proteins of typical size in the cell.Significance statementNew electron microscopy methods are making it possible to view the structures of large proteins and nucleic acid complexes at atomic detail, but the methods are difficult to apply to molecules smaller than about 50 kDa, which is larger than the size of the average protein in the cell. The present work demonstrates that a protein much smaller than that limit can be successfully visualized when it is attached to a large protein scaffold designed to hold 12 copies of the attached protein in symmetric and rigidly defined orientations. The small protein chosen for attachment and visualization can be modified to bind to other diverse proteins, opening up a new avenue for imaging cellular proteins by cryo-EM.
Inferring the Evolutionary Reduction of Corm Lobation inIsoëtesusing Bayesian Model-Averaged Ancestral State Reconstruction
Authors: Freund Forrest D. , Freyman William A. , Rothfels Carl J. 
Published: November 2017

ABSTRACTInferring the evolution of characters inIsoëteshas been problematic, as these plants are morphologically conservative and yet highly variable and homoplasious within that conserved base morphology. However, molecular phylogenies have given us a valuable tool to test hypothesis of character evolution within the genus. One such hypothesis is that extantIsoëteshave undergone a morphological reduction from larger arborescent lycophyte ancestors. In this work we examine the reduction in lobe numbers on the underground trunk, or corm, over evolutionary time. Using reversible-jump MCMC and Bayesian inference, our results support the hypothesis of a directional reduction in lobe number inIsoëtes, with the best-supported model of character evolution being one of irreversible reduction. Furthermore, the most probable ancestral corm lobe number of extantIsoëtesis three, and a reduction to two lobes has occurred at least six times. From our results, we can infer that corm lobation, like many other traits inIsoëtes, shows a degree of homoplasy, yet also shows ongoing evolutionary reduction.
An essential post-developmental role for Lis1 in mice
Authors: Hines Timothy J. , Gao Xu , Sahu Subhshri , Lange Meghann M. , Turner Jill R. , Twiss Jeffery L. , Smith Deanna S. 
Published: November 2017

ABSTRACTLIS1 mutations cause lissencephaly (LIS), a severe developmental brain malformation. Much less is known about its role in the mature nervous system. LIS1 regulates the microtubule motor cytoplasmic dynein 1 (dynein), and as LIS1 and dynein are both expressed in the adult nervous system, Lis1 could potentially regulate dynein-dependent processes such as axonal transport. We therefore knocked out Lis1 in adult mice using tamoxifen-induced, Cre-ER-mediated recombination. When an actin promoter was used to drive Cre-ER expression (Act-Cre-ER), heterozygous Lis1 KO caused no obvious change in viability or behavior, despite evidence of widespread recombination by a Cre reporter three weeks after tamoxifen exposure. In contrast, homozygous Lis1 KO caused the rapid onset of neurological symptoms in both male and female mice. One tamoxifen-dosing regimen caused prominent recombination in the midbrain/hindbrain, PNS, and cardiac/skeletal muscle within a week; these mice developed severe symptoms in that time frame and were euthanized. A different tamoxifen regimen resulted in delayed recombination in midbrain/hindbrain, but not in other tissues, and also delayed the onset of symptoms. This indicates that Lis1 loss in the midbrain/hindbrain causes the severe phenotype. In support of this, brainstem regions known to house cardiorespiratory centers showed signs of axonal dysfunction in KO animals. Transport defects, neurofilament alterations, and varicosities were observed in axons in cultured DRG neurons from KO animals. Because no symptoms were observed when a cardiac specific Cre-ER promoter was used, we propose a vital role for Lis1 in autonomic neurons and implicate defective axonal transport in the KO phenotype.SIGNIFICANCE STATEMENTMammalian Lis1 is best known for its role in brain development. Lis1 binds to and regulates the microtubule motor, cytoplasmic dynein. We show that Lis1 function is needed post-developmentally and provide evidence that loss of Lis1 in the hindbrain leads to death. The effect is dose dependent in mice, as loss of only one allele does not produce an overt phenotype. However, since LIS1 haploinsufficiency causes lissencephaly (LIS) in humans, our study raises the possibility that post-developmental axonal transport defects could contribute to worsening symptoms in children with LIS1 mutations. Our data are consistent with the hypothesis is that Lis1 regulates dynein-dependent axon transport in the mature nervous system.
The Fluid Membrane determines Mechanics of Red Blood Cell Extracellular Vesicles and is Softened in Hereditary Spherocytosis
Authors: Vorselen Daan , Dommelen Susan M. van , Sorkin Raya , Schiller Jürgen , Wijk Richard van , Schiffelers Raymond M. , Wuite Gijs J.L. , Roos Wouter H. 
Published: November 2017

AbstractExtracellular vesicles (EVs) are widely studied regarding their role in cell-to-cell communication and disease, as well as for applications as biomarker or drug delivery vehicle. EVs contain both membrane and intraluminal proteins, affecting their structural properties and thereby likely their functioning. Here, we use atomic force microscopy for the mechanical characterization of red blood cell (RBC) EVs from healthy individuals as well as from a patient with hereditary spherocytosis (HS) due to ankyrin deficiency. We show that the EVs are packed with proteins, yet their response to indentation is similar to that of a fluid lipid vesicle lacking proteins. The bending modulus of RBC EVs of healthy donors is ~15kbT, agreeing well with the bending modulus of the RBC membrane. Surprisingly, whereas RBCs become more rigid in HS, the excreted vesicles of a patient with this blood disorder have a significantly (~50%) lower bending modulus than donor EVs. These results shed new light on the mechanism and effects of EV budding and may underlie the reported increase in vesiculation and stiffening of RBCs in hereditary spherocytosis patients.
Junction-based lamellipodia drive endothelial cell rearrangements in vivo via a VE-cadherin/F-actin based oscillatory ratchet mechanism
Authors: Paatero Ilkka , Sauteur Loïc , Lee Minkyoung , Lagendijk Anne K. , Heutschi Daniel , Bieli Dimitri , Hogan Benjamin M. , Affolter Markus , Belting Heinz-Georg 
Published: November 2017

AbstractAngiogenesis and vascular remodeling are driven by a wide range of endothelial cell behaviors, such as cell divisions, cell movements, cell shape and polarity changes. To decipher the cellular and molecular mechanism of cell movements, we have analyzed the dynamics of different junctional components during blood vessel anastomosis in vivo. We show that endothelial cell movements are associated with oscillating lamellipodia-like structures, which are orientated in the direction of these movements. These structures emerge from endothelial cell junctions and we thus call them junction-based lamellipodia (JBL). High-resolution time-lapse imaging shows that JBL are formed by F-actin based protrusions at the front end of moving cells. These protrusions also contain diffusely distributed VE-cadherin, whereas the junctional protein ZO-1 (Zona occludens 1) remains at the junction. Subsequently, a new junction is formed at the front of the JBL and the proximal junction is pulled towards the newly established distal junction. JBL function is highly dependent on F-actin dynamics. Inhibition of F-actin polymerization prevents JBL formation, whereas Rac-1 inhibition interferes with JBL oscillations. Both interventions disrupt endothelial junction formation and cell elongation. To examine the role of VE-cadherin (encoded by cdh5 gene) in this process, we generated a targeted mutation in VE-cadherin gene (cdh5ubs25), which prevents VE-cad/F-actin interaction. Although homozygous ve-cadherin mutants form JBL, these JBL are less dynamic and do not promote endothelial cell elongation. Taken together, our observations suggest a novel oscillating ratchet-like mechanism, which is used by endothelial cells to move along or over each other and thus provides the physical means for cell rearrangements.
IDENTIFICATION OF AN EARLY SUBSET OF CEREBELLAR NUCLEI NEURONS IN MICE
Authors: Rahimi-Balaei Maryam , Amiri Shayan , Lamonerie Thomas , Wu Sih-Rong , Zoghbi Huda Y. , Consalez G. Giacomo , Goldowitz Daniel , Marzban Hassan 
Published: November 2017

ABSTRACTCerebellar nuclei (CN) neurons serve as the primary output of the cerebellum and originate from the cerebellar primordium at early stages of cerebellar development. These neurons are diverse, integrating information from the cerebellar cortex and relaying it to various brain regions. Employing various methodologies, we have characterized a specific subset of CN neurons that do not originate from the rhombic lip or ventricular zone of the cerebellar primordium. Embryos were collected at early stages of development and processed for immunohistochemistry (IHC), Western blotting,in situhybridization (ISH), embryonic culture, DiI labeling, and flow cytometry analysis (FCM). Our findings indicate that a subset of CN neurons expressing α-synuclein (SNCA), OTX2, MEIS2, and p75NTR (NGFR) are located in the rostroventral region of the nuclear transitory zone (NTZ). While CN neurons derived from the rhombic lip are positioned in the caudodorsal area of the NTZ in the cerebellar primordium. Utilizing Otx2-GFP andAtoh1−/−mice, we have determined that these cells do not originate from the germinal zone of the cerebellar primordium. These results suggest the existence of a novel extrinsic germinal zone for the cerebellar primordium, possibly the mesencephalon, from which early CN neurons originate.SIGNIFICANCE STATEMENTThe cerebellum contains a variety of distinct neuronal populations, each playing a significant role in its function within the brain. This research demonstrates that a particular subset of cerebellar nuclei neurons originates from a previously unrecognized germinal zone specific to the cerebellar primordium, independently of Atoh1’s influence.
Functional categories in macaque frontal eye field
Authors: Lowe Kaleb A. , Schall Jeffrey D. 
Published: November 2017

ABSTRACTFrontal eye field (FEF) in macaque monkeys contributes to visual attention, visual-motor transformations and production of eye movements. Traditionally, neurons in FEF have been classified by the magnitude of increased discharge rates following visual stimulus presentation, during a waiting period, and associated with eye movement production. However, considerable heterogeneity remains within the traditional visual, visuomovement and movement categories. Cluster analysis is a data-driven method of identifying self-segregating groups within a dataset. Because many cluster analysis techniques exist and cluster outcomes vary with analysis assumptions, consensus clustering aggregates over multiple cluster analyses, identifying robust groups. To describe more comprehensively the neuronal composition of FEF, we applied a consensus clustering technique for unsupervised categorization of patterns of spike rate modulation measured during a memory-guided saccade task. We report ten functional categories, expanding on the traditional three. Categories were distinguished by latency, magnitude, and sign of visual response, presence of sustained activity, and dynamics, magnitude and sign of saccade-related modulation. Consensus clustering can include other metrics and can be applied to datasets from other brain regions to provides better information guiding microcircuit models of cortical function.SIGNIFICANCE STATEMENTThe contribution of a brain region cannot be understood without knowing the diversity, arrangement, and circuitry of constituent neurons. Traditional descriptions of frontal eye field include visual, visuo-saccadic, and saccadic categories. Here, we employ a novel consensus clustering method to identify more reliably functional categories in neural data. While confirming the traditional categories, consensus clustering distinguishes additional, previously unappreciated diversity in neural activity patterns. Such information is necessary to formulate correct microcircuit models of cortical function.
Membrane curvature and the Tol-Pal complex determine polar localization of the chemoreceptor Tar inE. coli
Authors: Saaki Terrens N. V. , Strahl Henrik , Hamoen Leendert W. 
Published: November 2017

AbstractChemoreceptors are localized at the cell poles ofEscherichia coliand other rod-shaped bacteria. Over the years different mechanisms have been put forward to explain this polar localization; from stochastic clustering, membrane curvature driven localization, interactions with the Tol-Pal complex, to nucleoid exclusion. To evaluate these mechanisms, we monitored the cellular localization of the aspartate chemoreceptor Tar in different deletion mutants. We did not find any indication for either stochastic cluster formation or nucleoid exclusion. However, the presence of a functional Tol-Pal complex appeared to be essential to retain Tar at cell poles. This finding also implies that the curvature of cell poles does not attract chemoreceptor complexes. Interestingly, Tar still accumulated at midcell intoland inpaldeletion mutants. In these mutants, the protein appears to gather at the base of division septa, a region characterised by strong membrane curvature. Chemoreceptors, like Tar, form trimer-of-dimers that bend the cell membrane due to a rigid tripod structure with an estimated curvature of approximately 37 nm. This curvature approaches the curvature of the cell membrane generated during cell division, and localization of chemoreceptor tripods at curved membrane areas is therefore energetically favourable as it lowers membrane tension. Indeed, when we introduced mutations in Tar that abolish the rigid tripod structure, the protein was no longer able to accumulate at midcell or cell poles. These findings favour a model where chemoreceptor localization inE. coliis driven by strong membrane curvature and association with the Tol-Pal complex.ImportanceBacteria have exquisite mechanisms to sense and to adapt to the environment they live in. One such mechanism involves the chemotaxis signal transduction pathway, in which chemoreceptors specifically bind certain attracting or repelling molecules and transduce the signals to the cell. In different rod-shaped bacteria, these chemoreceptors localize specifically to cell poles. Here, we examined the polar localization of the aspartate chemoreceptor Tar inE. coli, and found that membrane curvature at cell division sites and interaction with the Tal-pol protein complex, localize Tar at cell division sites, the future cell poles. This study shows how membrane curvature can guide localization of proteins in a cell.
Prefrontal control of visual distraction
Authors: Cosman Joshua D. , Woodman Geoffrey F. , Schall Jeffrey D. 
Published: November 2017

SummaryAvoiding distraction by salient irrelevant stimuli is critical to accomplishing daily tasks. Regions of prefrontal cortex control attention by enhancing the representation of task-relevant information in sensory cortex, which can be measured directly in modulation of both single neurons and averaging of the scalp-recorded electroencephalogram [1,2]. However, when irrelevant information is particularly conspicuous, it may distract attention and interfere with the selection of behaviorally relevant information. Many studies have shown that that distraction can be minimized via top-down control [3–5], but the cognitive and neural mechanisms giving rise to this control over distraction remain uncertain and vigorously debated [6–8]. Bridging neurophysiology to electrophysiology, we simultaneously recorded neurons in prefrontal cortex and event-related potentials (ERPs) over extrastriate visual cortex to track the processing of salient distractors during a visual search task. Critically, we observed robust suppression of salient distractor representations in both cortical areas, with suppression arising in prefrontal cortex before being manifest in the ERP signal over extrastriate cortex. Furthermore, only prefrontal neurons that participated in selecting the task-relevant target also showed suppression of the task-irrelevant distractor. This suggests a common prefrontal mechanism for target selection and distractor suppression, with input from prefrontal cortex being responsible for both selecting task-relevant and suppressing task-irrelevant information in sensory cortex. Taken together, our results resolve a long-standing debate over the mechanisms that prevent distraction, and provide the first evidence directly linking suppressed neural firing in prefrontal cortex with surface ERP measures of distractor suppression.
Nearly Neutral Evolution Across theDrosophila melanogasterGenome
Authors: Castellano David , James Jennifer , Eyre-Walker Adam 
Published: November 2017

AbstractUnder the nearly neutral theory of molecular evolution the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here we investigate whether this is the case across the genome ofDrosophila melanogasterusing polymorphism data from North American and African lines. We show that the ratio of the number of non-synonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the non-independence is accounted for. The relationship is such that the proportion of effectively neutral non-synonymous mutations increases by ~45% asNeis halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitch-hiking: genetic hitch-hiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.
British values and identity among young British Muslims in Tower Hamlets: understandings and connections
Authors: Green Finlay 
Published: November 2017

Purpose
The purpose of this paper is to provide a platform for young British Muslims in Tower Hamlets to share their perspectives on British values and identity, in light of the increased pressure schools are facing to actively promote “British values”.

Design/methodology/approach
Three focus groups were convened of 16-18 year olds, two all-male (one with five and one with six participants) and one all-female (five participants). Discussions were audio recorded with the data subjected to a form of thematic analysis that divided the raw data into three different categories: individual, group and group interaction data.

Findings
All but one of the participants defined themselves as British, largely due to a strong connection with British values. A minority felt this understanding was reflected back to them by society. However, the majority felt that, as ethnically Bengali and as Muslims, the opposite was the case. By judging the strength of an individual’s Britishness against the strength of their adherence to British values the government’s British values agenda is only serving to reinforce the isolation of those that feel excluded.

Originality/value
While the identities of young people, British people, and Muslims have been widely explored, there is little research that looks at the intersection of all three.
The environment-strategy-structure fit and performance of industrial servitized SMEs
Authors: Ambroise Laure , Prim-Allaz Isabelle , Teyssier Christine , Peillon Sophie 
Published: November 2017

PurposeThe purpose of this paper is to examine the environment-strategy-structure fit in the context of industrial servitization and its impact on the profitability of manufacturing SMEs.Design/methodology/approachData were collected from face-to-face interviews with the CEOs of 184 French manufacturing SMEs. These primary data were complemented by the indicators extracted from a financial database to ensure objective measures of financial performance. Analyses were conducted by means of partial least squares structural equation modeling.FindingsThe research tests the impact of the organizational design (customer interface, service delivery system and service culture (SC)) on financial performance. It also tests the moderating effect on this relationship of servitization strategies adopted by the firm (added services (AS), activities reconfiguration (AR) and business model reconfiguration (BMR)) and the environment in which the firm is situated (industry dynamism, competitive intensity and industry munificence).Research limitations/implicationsThis study considers the coalescence of the environment-strategy-structure to be a driver of firm performance in the context of industrial firms’ servitization. Three specific servitization strategies (AS, AR and BMR) are suggested based on the service offering’s impact on the customer’s activity chain or business model.Practical implicationsThe research proposes some optimal organizational design depending on servitization strategy and environmental factors; for example, SC has a strong impact on financial performance when BMR is adopted.Originality/valueThis empirical study is based on an extended sample of 184 SMEs and provides quantitative support for the claim that good alignment between strategy and organizational design based on environmental factors increases profitability.