bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutagenesis and homology modeling reveal a predicted pocket of lysophosphatidylcholine acyltransferase 2 to catch Acyl-CoA
Authors: Hamano Fumie , Matoba Kazuaki , Hashidate-Yoshida Tomomi , Suzuki Tomoyuki , Miura Kiyotake , Hishikawa Daisuke , Harayama Takeshi , Yuki Koichi , Kita Yoshihiro , Noda Nobuo N. , Shimizu Takao , Shindou Hideo 
Published: November 2020

AbstractPlatelet-activating factor (PAF) is a potent proinflammatory phospholipid mediator that elicits various cellular functions and promotes several pathological conditions, including anaphylaxis and neuropathic pain. PAF is biosynthesized by two types of lyso-PAF acetyltransferases: lysophosphatidylcholine acyltransferase 1 (LPCAT1) and LPCAT2, which are constitutive and inducible forms of lyso-PAF acetyltransferase, respectively. Because LPCAT2 mainly produces PAF under inflammatory conditions, understanding the structure of LPCAT2 is important for developing specific drugs against PAF-related inflammatory diseases. Although the structure of LPCAT2 has not been determined, the crystal structure was reported forThermotoga maritimaPlsC, an enzyme in the same enzyme family as LPCAT2. In this study, we identified residues in mouse LPCAT2 essential for its enzymatic activity and a potential acyl-coenzyme A (CoA)-binding pocket, based on homology modeling of mouse LPCAT2 with PlsC. We also found that Ala115 of mouse LPCAT2 was important for acyl-CoA selectivity. In conclusion, these results predict the structure of mouse LPCAT2. Our findings have implications for the future development of new drugs against PAF-related diseases.
Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice
Authors: Hamza Bashar , Miller Alex B. , Meier Lara , Stockslager Max , King Emily M. , Ng Sheng Rong , DeGouveia Kelsey L. , Mulugeta Nolawit , Calistri Nicholas L. , Strouf Haley , Lin Lin , Chin Christopher R. , Weinberg Robert A. , Shalek Alex K. , Jacks Tyler , Manalis Scott 
Published: November 2020

AbstractExisting pre-clinical methods for acquiring dissemination kinetics of rare circulating tumor cells (CTCs) en route to forming metastases have not been capable of providing a direct measure of CTC intravasation rate and subsequent half-life in the circulation. Here, we demonstrate an approach for measuring endogenous CTC kinetics by continuously exchanging CTC-containing blood over several hours between un-anesthetized, tumor-bearing mice and healthy, tumor-free counterparts. By tracking CTC transfer rates using an autochthonous small cell lung cancer model, we extrapolated half-life times in the circulation of 50-100 seconds and intravasation rates between 4,000 and 27,000 CTCs/hour – an average daily shedding rate equivalent to ∼0.07% of the total number of primary tumor cells in the lung. Additionally, transfer of 1-2% of daily-shed CTCs from late-stage tumor-bearing mice generated macrometastases in healthy recipient mice. We envision that our technique will help further elucidate the role of CTCs and the rate-limiting steps in metastasis.
Sequential dynein effectors regulate axonal autophagosome motility in a maturation-dependent pathway
Authors: Cason Sydney E. , Carman Peter , Duyne Claire Van , Goldsmith Juliet , Dominguez Roberto , Holzbaur Erika L.F. 
Published: November 2020

AbstractAutophagy is a degradative pathway required to maintain neuronal homeostasis. Neuronal autophagosomes form constitutively at the axon terminal and mature via lysosomal fusion during dynein-mediated transport to the soma. How the dynein-autophagosome interaction is regulated during maturation is unknown. Here, we identify a series of handoffs between dynein effectors as autophagosomes transit along the axons of primary neurons. In the distal axon, JIP1 initiates autophagosomal transport, while autophagosomes in the mid-axon require HAP1 and Huntingtin for motility. We demonstrate that HAP1 is a bonafide dynein activator, binding the dynein-dynactin complex via canonical and noncanonical interactions. JIP3 is found on most axonal autophagosomes but specifically regulates the transport of acidified autolysosomes. Inhibiting autophagosomal transport disrupts maturation, while inhibiting autophagosomal maturation perturbs the association and function of dynein effectors. Thus maturation and transport are tightly linked. These results describe a novel maturation-based dynein effector handoff on neuronal autophagosomes that is key to autophagosomal motility, cargo degradation, and the maintenance of axonal health.SummaryNeuronal autophagosomes form in the distal axon and mature via fusion with lysosomes during their dynein-driven transport to the soma. Dynein is regulated on autophagosomes by distinct effector proteins—JIP1, HAP1, and JIP3—depending on location and autophagosomal maturity. In this sequential pathway, transport and maturation state are tightly linked to maintain neuronal health.
Light-inducible Deformation of Mitochondria in Live Cells
Authors: Song Yutong , Huang Peiyuan , Liu Xiaoying , Cui Bianxiao , Duan Liting 
Published: November 2020

AbstractMitochondria, the powerhouse of the cell, are dynamic organelles that undergo constant morphological changes. Increasing evidence indicates that mitochondria morphologies and functions can be modulated by mechanical cues. However, the mechano-sensing and -responding properties of mitochondria and the correlation between mitochondrial morphologies and functions are unclear due to the lack of methods to precisely exert mechano-stimulation on and deform mitochondria inside live cells. Here we present an optogenetic approach that uses light to induce deformation of mitochondria by recruiting molecular motors to the outer mitochondrial membranevialight-activated protein-protein hetero-dimerization. Mechanical forces generated by motor proteins distort the outer membrane, during which the inner mitochondrial membrane can also be deformed. Moreover, this optical method can achieve subcellular spatial precision and be combined with other optical dimerizers and molecular motors. This method presents a novel mitochondria-specific mechano-stimulator for studying mitochondria mechanobiology and the interplay between mitochondria shapes and functions.
Differential response of macrophages and neutrophils to trypanosome infections in zebrafish: occurrence of foamy macrophages
Authors: Jacobs Sem H. , Dóró Éva , Hammond Ffion R. , Nguyen-Chi Mai E. , Lutfalla Georges , Wiegertjes Geert F. , Forlenza Maria 
Published: November 2020

AbstractA tightly regulated innate immune response to trypanosome infections is critical to strike a balance between parasite control and inflammation-associated pathology. In the present study, we make use of the recently establishedTrypanosoma carassiiinfection model in larval zebrafish to study the early response of macrophages and neutrophils to trypanosome infectionsin vivo. We consistently identified high- and low-infected individuals and were able to simultaneously characterize their differential innate response. Not only did macrophage and neutrophil number and distribution differ between the two groups, but also macrophage morphology and activation state. Exclusive to high-infected zebrafish, was the appearance of macrophages rich in lipid droplets, confirmed to be foamy macrophages and characterized by a strong pro-inflammatory profile. Altogether, we provide anin vivocharacterization of the differential response of macrophage and neutrophil to trypanosome infection and identify foamy macrophages as potentially associated with an exacerbated immune response and susceptibility to the infection. To our knowledge this is the first report of the occurrence of foamy macrophages during an extracellular trypanosome infection.
TAD cliques predict key features of chromatin organization
Authors: Liyakat Ali Tharvesh M. , Brunet Annaël , Collas Philippe , Paulsen Jonas 
Published: November 2020

AbstractProcesses underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and interactions with the nuclear lamina dynamically act on chromatin at multiple levels. Here, we explore long-range interaction patterns between topologically associated domains (TADs) in several cell types. We find that this is connected to many key features of chromatin organization, including open and closed compartments, compaction and loop extrusion processes. We find that domains that form large TAD cliques tend to be repressive across cell types, when comparing gene expression, LINE/SINE repeat content and chromatin subcompartments. Further, TADs in large cliques are larger in genomic size, less dense and depleted of convergent CTCF motifs, in contrast to smaller and denser TADs formed by a loop extrusion processes. Our results shed light on the organizational principles that govern repressive and active domains in the human genome.
Comprehensive single cell analyses of the nutritional environment of intracellularSalmonella enterica
Authors: Röder Jennifer , Felgner Pascal , Hensel Michael 
Published: November 2020

AbstractThe facultative intracellular pathogenSalmonella entericaTyphimurium (STM) resides in a specific membrane-bound compartment termed theSalmonella-containing vacuole (SCV). STM is able to obtain all nutrients required for rapid proliferation, although being separated from direct access to host cell metabolites. The formation of specific tubular membrane compartment, calledSalmonella-induced filaments (SIFs) are known to provides bacterial nutrition by giving STM access to endocytosed material and enabling proliferation. Additionally, STM expresses a range of nutrient uptake system for growth in nutrient limited environments to overcome the nutrition depletion inside the host. By utilizing dual fluorescence reporters, we shed light on the nutritional environment of intracellular STM in various host cells and distinct intracellular niches. We showed that STM uses nutrients of the host cell and adapts uniquely to the different nutrient conditions. In addition, we provide further evidence for improved nutrient supply by SIF formation or presence in the cytosol of epithelial cells, and the correlation of nutrient supply to bacterial proliferation.
Mutations in an intracellular vestibule that bifurcates from the pore of ClC-1 chloride ion channels affect anion permeation
Authors: Bennetts Brett , Morton Craig J. , Parker Michael W. 
Published: November 2020

AbstractThe ubiquitous CLC protein superfamily consists of channels, that permit passive diffusion of Cl ions across biological membranes, and pumps, that can actively transport Cl ions against their electrochemical gradient; yet, puzzlingly, both types share a strongly conserved Cl ion transport pathway comprised of three consecutive binding sites. This raises the question; how does the same pathway support passive diffusion in CLC channels and active transport in CLC pumps? Based on high-resolution structural data current theories suggest that subtle structural differences in the conserved pathway allow CLC channels to ‘leak’ Cl ions. A recent cryo-electron microscopy structure of the human ClC-1 channel does not show occupancy of the central Cl ion binding site but reveals a wide intracellular vestibule that bifurcates from the conserved pathway in this region. Here we show that replacing residues that line the ClC-1 intracellular vestibule with the corresponding residues of CLC pumps resulted in interactions between permeating anions at neighbouring binding sites and altered anion selectivity. Removing the side chain of a strictly conserved tyrosine residue, that coordinates Cl ion at the central binding site of CLC pumps, removed multi-ion behaviour in ClC-1 mutants. In contrast, removing the side chain of a highly conserved glutamate residue that transiently occupies Cl ion binding sites, as part of the transport mechanism of CLC pumps and the mechanism that opens and closes CLC channels, only partially removed multi-ion behaviour in ClC-1 mutants. Our findings show that structural differences between CLC channels and pumps, outside of the conserved Cl ion transport pathway, fundamentally affect anion permeation in ClC-1 channels.SummarySome CLC proteins are passive Cl-channels while others are active Cl-pumps but, paradoxically, both share a conserved, canonical, Cl-permeation pathway. Here Bennetts, Morton and Parker show that ‘pump-like’ mutations in a poorly conserved region, located remotely from the canonical pathway, affect anion permeation in human ClC-1 channels.
Rational tuning of a membrane-perforating antimicrobial peptide to selectively target membranes of different lipid composition
Authors: Chen Charles H. , Starr Charles G. , Guha Shantanu , Wimley William C. , Ulmschneider Martin B. , Ulmschneider Jakob P. 
Published: November 2020

AbstractThe use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure-function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We demonstrate that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore forming peptide into a selective pore former for different lipid types. A library of 2,916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.
Triblock copolymer micelle model of spherical paraspeckles
Authors: Yamamoto Tetsuya , Yamazaki Tomohiro , Hirose Tetsuro 
Published: November 2020

ABSTRACTParaspeckles are nuclear bodies composed of architectural RNA (arcRNA) and RNA-binding proteins. In the wild type, the blocks at the two terminal regions of arcRNAs compose the shell of paraspeckles and the middle region between the two terminal blocks composes the core, analogous to micelles of ABC triblock copolymers. We here use an extension of the theory of polymer micelles to predict the structure and size of paraspeckles as one decreases the length of one of the terminal blocks of arcRNA by CRISPR/Cas9, assuming that paraspeckles are spherical. Our theory predicts that when the length of the edited terminal blocks is larger than a critical value, paraspeckles show discontinuous transitions between the structure in which all the edited terminal blocks are localized in the shell and the structure in which all the edited terminal blocks are localized in the core at a threshold value of the transcription rate of arcRNA. In contrast, when the length of the edited terminal blocks is smaller than the critical value, the population of edited terminal blocks in the shell decreases continuously as one increases the transcription rate of arcRNA. The size of paraspeckles increases as one decreases the length of the edited terminal blocks. These predictions are consistent with our experiments.
Dermal EZH2 simultaneously orchestrates dermal differentiation and epidermal proliferation during murine skin development
Authors: Thulabandu Venkata , Nehila Timothy , Ferguson James W. , Atit Radhika P. 
Published: November 2020

AbstractSkin development and patterning is dependent on factors that regulate the stepwise differentiation of dermal fibroblasts concomitant with dermal-epidermal reciprocal signaling, two processes that are poorly understood. Here we show that dermal EZH2, the methyltransferase enzyme of the epigenetic Polycomb Repressive Complex 2 (PRC2), is a new coordinator of both these processes. Dermal EZH2 activity is present during dermal fibroblast differentiation and is required for spatially restricting Wnt/β-catenin signaling to reinforce dermal fibroblast cell fate. Later in development, dermal EZH2 regulates the differentiation to reticular dermal fibroblasts and initiation of secondary hair follicles. Embryos lacking dermal Ezh2 have elevated epidermal proliferation and differentiation that can be rescued by small molecule inhibition of retinoic acid (RA) signaling. Together, our study reveals that dermal EZH2 acts as a rheostat to control the levels of Wnt/β-catenin and RA signaling to impact fibroblast differentiation cell autonomously and epidermal keratinocyte development non-cell autonomously, respectively.
RNA-seq analysis of laser micro-dissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments
Authors: Berkowitz Oliver , Xu Yue , Wang Yan , Liew Lim Chee , Zhu Yanqiao , Lewsey Mathew G. , Whelan James 
Published: November 2020

ABSTRACTAcclimation of plants to adverse environmental conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have largely focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of diverse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and UV light in Arabidopsis. Profiling stimuli-dependent changes after treatments revealed an overall reduction in the tissue-specific expression of genes, with only a limited number gaining or changing their tissue-specificity. We find no evidence of a common stress response, with only a few genes responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap across tissues for individual treatments. Further analyses provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we generated an extensive reference data set and results enable the tailoring of the tissue-specific engineering of stress tolerant plants.
Analysis of enterprise resource planning (ERP) system workarounds with a resilience perspective
Authors: Yılmaz Börekçi Dilek , Büyüksaatçı Kiriş Sinem , Batmaca Sinem 
Published: November 2020

PurposeWorkarounds are defined as user-formulated solutions that overcome the obstacles preventing the system's execution from the users' lenses. In this paper, the authors aim to analyze the workarounds in system implementations and post-implementations with reflections on different levels of resilience in the workplace.Design/methodology/approachIn this paper, the authors conduct a critical review of enterprise resource planning (ERP) system workarounds by evaluating whether the workarounds are treated as resilience enhancers or as hinderers at multiple levels. While doing this evaluation, the authors try to understand the nature of the workarounds (self-serving, social-serving) with respective levels of analysis for resilience (ERP resilience, organizational resilience, team resilience, employee resilience) and to integrate the assessment of similar concepts to resilience such as adaptability, flexibility and agility (in survival and sustainability dimensions).FindingsWorkaround solutions can be treated as resilience enhancers when the alternative solutions overcome some systemic problems and prevent system failures in the short run, but in the long term, they should motivate positive change and organizational dynamics. Otherwise, weaknesses of informal workarounds may become embedded in practice, and prevent confronting and correcting the shortcomings of the system and thus harm resilience.Originality/valueThe differentiation of workarounds as self-serving or social-serving and the resilience perspective toward workarounds with different levels of analysis and integrating resilience relevant concepts such as adaptability, agility and flexibility are new as far as the authors know.
Scaling procedure for designing accidental gas release experiment
Authors: Moscatello Alberto , Uggenti Anna Chiara , Iuso Gaetano , D'Ambrosio Domenic , Cafiero Gioacchino , Gerboni Raffaella , Carpignano Andrea 
Published: November 2020

PurposeThe purpose of this paper is to present a procedure to design an experimental setup meant to validate an innovative approach for simulating, via computational fluid dynamics, a high-pressure gas release from a rupture (e.g. on an offshore oil and gas platform). The design is based on a series of scaling exercises, some of which are anything but trivial.Design/methodology/approachThe experimental setup is composed of a wind tunnel, the instrumented scaled (1:10) mock-up of an offshore platform and a gas release system. A correct scaling approach is necessary to define the reference speed in the wind tunnel and the conditions of the gas release to maintain similarity with respect to the real-size phenomena. The scaling of the wind velocity and the scaling of the gas release were inspired by the approach proposed by Hallet al.(1997): a dimensionless group was chosen to link release parameters, wind velocity and geometric scaling factor.FindingsThe theoretical scaling approaches for each different part of the setup were applied to the design of the experiment and some criticalities were identified, such as the existence of a set of case studies with some release parameters laying outside the applicability range of the developed scaling methodology, which will be further discussed.Originality/valueThe resulting procedure is one of a kind because it involves a multi-scaling approach because of the different aspects of the design. Literature supports for the different scaling theories but, to the best of the authors’ knowledge, fails to provide an integrated approach that considers the combined effects of scaling.