bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Tricks for an old molecule: Preserved antibacterial activity of ribosomal protein S15 during evolution
Authors: Qu Baozhen , Ma Zengyu , Yao Lan , Gao Zhan , Zhang Shicui 
Published: February 2020

AbstractPrevious studies show that some ribosomal proteins possess antimicrobial peptide (AMP) activity. However, information as such remains rather fragmentary and limited. Here we demonstrated for the first time that amphioxus RPS15, BjRPS15, was a previously uncharacterized AMP, which was not only capable of identifying Gram-negative and -positive bacteria via interaction with LPS and LTA but also capable of killing the bacteria. We also showed that both the sequence and 3D structure of RPS15 and its prokaryotic homologs were highly conserved, suggesting its antibacterial activity is universal across widely separated taxa. Actually this was supported by the facts that the residues positioned at 45-67 formed the core region for the antimicrobial activity of BjRPS15, and its prokaryotic counterparts, includingNitrospiraeRPS1933-55,AquificaeRPS1933-55andP. syringaeRPS1950-72,similarly displayed antibacterial activities. BjRPS15 functioned by both interaction with bacterial membrane via LPS and LTA and membrane depolarization as well as induction of intracellular ROS. Moreover, we showed that RPS15 existed extracellularly in amphioxus, shrimp, zebrafish and mice, hinting it may play a critical role in systematic immunity in different animals. In addition, we found that neither BjRPS15 nor its truncated form BjRPS1545-67were toxic to mammalian cells, making them promising lead molecules for the design of novel peptide antibiotics against bacteria. Collectively, these indicate that RPS15 is a new member of AMP with ancient origin and high conservation throughout evolution.Author summaryRibosomal protein, a component of ribonucleoprotein particles, is traditionally known involved in protein synthesis in a cell. Here we demonstrated for the first time that amphioxus ribosomal protein 15 was a novel antibacterial protein, capable of recognizing Gram-negative and -positive bacteria as well as killing them. It killed the bacteria by a combined mode of action of disrupting bacterial membrane integrity and inducing radical oxygen species production. We also showed that both eukaryotic ribosomal protein 15 and its prokaryotic counterpart ribosomal protein 19 possessed antibacterial activity, indicating that the antibacterial property is universal for this family of molecules. Moreover, we found that ribosomal protein 15 was present in the circulation system of various animals including shrimp, amphioxus, zebrafish and mice, suggesting it may physiologically play a key role in systematic immunity. Altogether, our study provides a new angle for understanding the biological function of ribosomal proteins.
Autophagy-associated Production of Antimicrobial Peptides hBD1 and LL37 Exhibits Anti-Bacillus Calmette-Guérin Effects in Lung Epithelial Cells
Authors: Wang Rui-ning , Liu Hong-lin , Chen Yao-xin , Wen Qian , Zhou Xin-ying , Wang Jin-li , Yang Jia-hui , Li Yan-fen , Han Zhen-yu , Ma Li 
Published: February 2020

AbstractAntimicrobial peptides (AMPs) constitute important groups of bactericidal polypeptides against various microorganisms that exhibit their anti-bacteria activity through cleavage of precursor peptides into the active form of 50–100 amino acids in length. Various AMP cleavage mechanisms have been reported in different cell types; however, those inMycobacterium tuberculosis(MTB)-infected lung epithelial cells remain unknown. In the present study, we found that MTB-infected lung epithelial cells expressed high level of the AMPs hBD1 and LL37 to kill intracellular MTB as the first-line immune barrier against MTB infection. Notably, their production in the lung epithelial cells was closely related to the function of autophagosomes and lysosomes. Experimental induction of autophagy in lung epithelial cells could enhance the expression of active hBD1 and LL37 at the post-transcriptional level, whereas silencing of these two active AMPs could decrease the bactericidal effect of autophagy. These findings indicated that cleavage of peptide precursors to form active AMPs might constitute a previously unrecognized antibacterial mechanism of autophagy.Author summaryLM and RW conceived and designed the experiments; RW performed the experiments and analyzed the data; QW analyzed the data and contributed reagents/materials/analysis tools; HL performed the experiments; XZ, JY, YL and ZH analyzed the data. LM and RW drafted the manuscript.
Junctional and cytoplasmatic contributions in wound healing
Authors: Mosaffa Payman , Tetley Robert J. , Rodríguez-Ferran Antonio , Mao Yanlan , Muñoz José J. 
Published: February 2020

AbstractWound healing is characterised by the re-epitheliation of a tissue through the activation of contractile forces concentrated mainly at the wound edge. While the formation of an actin purse string has been identified as one of the main mechanisms, far less is known about the effects of the viscoelastic properties of the surrounding cells, and the different contribution of the junctional and cytoplasmic contractilities.In this paper we simulate the wound healing process, resorting to a hybrid vertex model that includes cell boundary and cytoplasmatic contractilities explicitly, together with a differentiated viscoelastic rheology based on an adaptive rest-length. From experimental measurements of the recoil and closure phases of wounds in theDrosophilawing disc epithelium, we fit tissue viscoelastic properties. We then analyse in terms of closure rate and energy requirements the contributions of junctional and cytoplasmatic contractilities.Our results suggest that reduction of junctional stiffness rather than cytoplasmatic stiffness has a more pronounced effect on shortening closure times, and that intercalation rate has a minor effect on the stored energy, but contributes significantly to shortening the healing process, mostly in the later stages.Author summaryWe simulate the wound healing process of epithelia in the absence of substrate. By analysing the recoil process we are able to fit the viscoelastic properties of the monolayer, and study the influence of contractility at junctions and at the interior polymer network. We numerically simulate the whole wound opening and closure process, and inspect which mechanism has a more pronounced effect in terms of energy barrier and wound closure rate. We conclude that while junctional stiffness seems to be more effective than bulk stiffness at speeding up the closure, the increase of intercalation process is the mechanism with the lowest energy cost.
Redundant Trojan horse and endothelial-circulatory mechanisms for host-mediated spread ofCandida albicansyeast
Authors: Scherer Allison K. , Blair Bailey A. , Park Jieun , Seman Brittany G. , Kelley Joshua B. , Wheeler Robert T. 
Published: February 2020

AbstractThe host innate immune system has developed elegant processes for the detection and clearance of invasive fungal pathogens. These strategies may also aid in the spread of pathogensin vivo, although technical limitations have previously hindered our ability to view the host innate immune and endothelial cells to probe their roles in spreading disease. Here, we have leveraged zebrafish larvae as a model to view the interactions of these host processes with the fungal pathogenCandida albicans in vivo. We examined three potential host-mediated mechanisms of fungal spread: movement inside phagocytes in a “Trojan Horse” mechanism, inflammation-assisted spread, and endothelial barrier passage. Utilizing both chemical and genetic tools, we systematically tested the loss of neutrophils and macrophages and the loss of blood flow on yeast cell spread. Both neutrophils and macrophages respond to yeast-locked and wild typeC. albicansin our model and time-lapse imaging revealed that macrophages can support yeast spread in a “Trojan Horse” mechanism. Surprisingly, loss of immune cells or inflammation does not alter dissemination dynamics. On the other hand, when blood flow is blocked, yeast can cross into blood vessels but they are limited in how far they travel. Blockade of both phagocytes and circulation reduces rates of dissemination and significantly limits fungal spread distance from the infection site. Together, this data suggests a redundant two-step process whereby (1) yeast cross the endothelium inside phagocytes or via direct uptake, and then (2) they utilize blood flow or phagocytes to travel to distant sites.Author summaryAlthoughCandida albicansis the most common cause of fungal bloodstream infection, we know little about how it spreads from one tissue to another. Host processes often inadvertently assist pathogens that can hijack immune cells or induce endothelial endocytosis. Here we have used transparent zebrafish to visualize how specific host cells and processes contribute to yeast spreadin vivo.We find thatCandidais a sophisticated pathogen that uses redundant strategies to disseminate in the host: it can either use host immune cells or cross into the circulatory system and use blood flow. These data suggest that both of these mechanisms must be targeted to limitCandidadissemination during infection.
Loss of Corneal Raver2 Expression in Aniridia Associated Keratopathy
Authors: Das Subrata K. , Carroll Lara , Holt Derick , Zhang Xiaohui , Uehara Hironori , Archer Bonnie , Ambati Jayakrishna , Ambati Balamurali K. 
Published: February 2020

PurposeThe aim of this study was to evaluate downstream factors of Pax6 associated with the aniridic corneal phenotype. We characterize the ocular expression ofRaver2, a novel heterogeneous ribonucleoprotein (hnRNP).MethodsGenome wide microarrays of corneal RNA from non-aniridic mice (C57BL/6J and MRL/MpJ) and corneas from aniridia model, Pax6+/-(SEY) mice were performed.Raver2expression profiles were validated using qPCR and western blot. Raver2 immunohistochemistry on corneas of Pax6+/-mice and aniridic humans were compared to control specimens, and insitu-hybridization was used to analyze developmental expression ofRaver2.ResultsMicroarray analysis of corneal RNA identifiedRaver2as the gene with the strongest differential expression profile across non-aniridic and aniridic mouse strains. Consistent with mouse data, we found thatRaver2is expressed at high levels in healthy human corneal epithelium, and is downregulated in the corneas of human aniridia patients.ConclusionsThese findings suggest thatRaver2has an evolutionarily conserved developmental role downstream ofPax6in corneal development and maintenance.
A non-canonical Hippo pathway regulates spindle disassembly and cytokinesis during meiosis inSaccharomyces cerevisiae
Authors: Paulissen Scott M. , Hunt Cindy A. , Slubowski Christian J. , Yu Yao , Truong Dang , Mucelli Xheni , Nguyen Hung T. , Newman-Toledo Shayla , Neiman Aaron M. , Huang Linda S. 
Published: February 2020

ABSTRACTMeiosis in the budding yeastSaccharomyces cerevisiaeis used to create haploid yeast spores from a diploid mother cell. During meiosis II, cytokinesis occurs by closure of the prospore membrane, a membrane that initiates at the spindle pole body and grows to surround each of the haploid meiotic products. Timely prospore membrane closure requiresSPS1, which encodes a STE20-family GCKIII kinase. To identify genes that may activateSPS1, we utilized a histone phosphorylation defect ofsps1mutants to screen for genes with a similar phenotype and found thatcdc15shared this phenotype.CDC15encodes a Hippo-like kinase that is part of the mitotic exit network. We find that Sps1 complexes with Cdc15, that Sps1 phosphorylation requires Cdc15, and thatCDC15is also required for timely prospore membrane closure. We also find thatSPS1, likeCDC15, is required for meiosis II spindle disassembly and sustained anaphase II release of Cdc14 in meiosis. However, the NDR-kinase complex encoded byDBF2/DBF20 MOB1which functions downstream ofCDC15in mitotic cells, does not appear to play a role in spindle disassembly, timely prospore membrane closure, or sustained anaphase II Cdc14 release. Taken together, our results suggest that the mitotic exit network is rewired for exit from meiosis II, such thatSPS1replaces the NDR-kinase complex downstream ofCDC15.
Drosophilalarval epidermal cells only exhibit epidermal aging when they persist to the adult stage
Authors: Wang Yan , Burra Sirisha , Galko Michael J. 
Published: February 2020

AbstractHolometabolous insects undergo a complete transformation of the body plan from the larval to the adult stage. InDrosophila, this transformation includes replacement of larval epidermal cells (LECs) by adult epidermal cells (AECs). AECs inDrosophilaundergo a rapid and stereotyped aging program where they lose both cell membranes and nuclei. Whether LEC’s are capable of undergoing aging in a manner similar to AECs remains unknown. Here, we address this question in two ways. First, we looked for hallmarks of epidermal aging in larvae that have a greatly extended third instar and/or carry mutations that would cause premature epidermal aging at the adult stage. Such larvae, irrespective of genotype, did not show any of the signs of epidermal aging observed in the adult. Second, we developed a procedure to effect a heterochronic persistence of LECs into the adult epidermal sheet. LECs embedded within the adult epidermal sheet undergo clear signs of epidermal aging; they form multinucleate cells with each other and with the surrounding AECs on the same schedule as the AECs themselves. Our data reveals that epidermal aging in holometabolousDrosophilais a stage-specific phenomenon and that the capacity of LECs to respond to aging signals does exist.Summary StatementWe show thatDrosophilalarval epidermal cells do not age at the larval stage. They do, however, exhibit signs of aging if they persist into the adult.
Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform
Authors: Nhu Thao Tran Thi , Labroussaa Fabien , Ebert Nadine , V’kovski Philip , Stalder Hanspeter , Portmann Jasmine , Kelly Jenna , Steiner Silvio , Holwerda Melle , Kratzel Annika , Gultom Mitra , Laloli Laura , Hüsser Linda , Wider Manon , Pfaender Stephanie , Hirt Dagny , Cippà Valentina , Crespo-Pomar Silvia , Schröder Simon , Muth Doreen , Niemeyer Daniela , Müller Marcel A. , Drosten Christian , Dijkman Ronald , Jores Joerg , Thiel Volker 
Published: February 2020

AbstractReverse genetics has been an indispensable tool revolutionising our insights into viral pathogenesis and vaccine development. Large RNA virus genomes, such as from Coronaviruses, are cumbersome to clone and to manipulate inE. colihosts due to size and occasional instability1-3. Therefore, an alternative rapid and robust reverse genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform for the genetic reconstruction of diverse RNA viruses, including members of theCoronaviridae, FlaviviridaeandParamyxoviridaefamilies. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples, or synthetic DNA, and reassembled in one step inSaccharomyces cerevisiaeusing transformation associated recombination (TAR) cloning to maintain the genome as a yeast artificial chromosome (YAC). T7-RNA polymerase has been used to generate infectious RNA, which was then used to rescue viable virus. Based on this platform we have been able to engineer and resurrect chemically-synthetized clones of the recent epidemic SARS-CoV-24in only a week after receipt of the synthetic DNA fragments. The technical advance we describe here allows to rapidly responding to emerging viruses as it enables the generation and functional characterization of evolving RNA virus variants - in real-time - during an outbreak.
Silencing branched-chain ketoacid dehydrogenase or treatment with branched-chain ketoacids ex vivo inhibits muscle insulin signaling
Authors: Biswas Dipsikha , Dao Khoi T. , Mercer Angella , Cowie Andrew , Duffley Luke , El Hiani Yassine , Kienesberger Petra C. , Pulinilkunnil Thomas 
Published: February 2020

AbstractBranched-chain α-keto acids (BCKAs) are downstream catabolites of branched-chain amino acids (BCAAs). Mitochondrial oxidation of BCKAs is catalyzed by branched-chain ketoacid dehydrogenase (BCKDH), an enzyme sensitive to inhibitory phosphorylation by BCKD kinase (BCKDK). Emerging studies show that defective BCAA catabolism and elevated BCKAs levels correlate with glucose intolerance and cardiac dysfunction. However, if/how BCKDH and BCKDK exert control on the availability and flux of intramyocellular BCKAs and if BCKA reprograms nutrient metabolism by influencing insulin action remains unexplored. We observed altered BCAA catabolizing enzyme expression in the murine heart and skeletal muscle during physiological fasting and diet-induced obesity and after ex vivo exposure of C2C12 cells to increasing concentration of saturated fatty acid, palmitate. BCKAs per se impaired insulin-induced AKT phosphorylation and AKT activity in skeletal myotubes and cardiomyocytes. In skeletal muscle cells, mTORC1 and protein translation signaling was enhanced by BCKA with concomitant suppression of mitochondrial respiration. Lowering intracellular BCKA levels by genetic and pharmacological activation of BCKDHA enhanced insulin signaling and activated pyruvate dehydrogenase, an effector of glucose oxidation and substrate metabolism. Our findings suggest that BCKAs profoundly influence muscle insulin function, providing new insight into the molecular nexus of BCAA metabolism and signaling with cellular insulin action and respiration.
Reprogramming of Human Cells to Pluripotency Induces CENP-A Chromatin Depletion
Authors: Milagre Inês , Pereira Carolina , Oliveira Raquel , Jansen Lars E.T. 
Published: February 2020

SummaryPluripotent stem cells (PSCs) are central to development as they are the precursors of all cell types in the embryo. Therefore, maintaining a stable karyotype is essential, both for their physiological role as well as for use in regenerative medicine. In culture, an estimated 10-30% of PSC lines present karyotypic abnormalities, but the underlying causes remain unknown. To gain insight into the mitotic capacity of human embryonic stem cells and induced pluripotent stem cells, we explore the structure of the centromere and kinetochore. Centromere function depends on CENP-A nucleosome-defined chromatin. We show that while PSCs maintain abundant pools of CENP-A, CENP-C and CENP-T, these essential centromere components are strongly reduced at stem cell centromeres. Outer kinetochore recruitment is also impaired to a lesser extent, indicating an overall weaker kinetochore. This impairment is specific for the kinetochore forming centromere complex while the inner centromere protein Aurora B remains unaffected. We further show that, similar to differentiated human cells, CENP-A chromatin assembly in PSCs requires transition into G1 phase. Finally, reprogramming experiments indicate that reduction of centromeric CENP-A levels is an early event during dedifferentiation, coinciding with global chromatin remodelling. Our characterisation of centromeres in human stem cells drives new hypotheses including a possible link between impaired centromere function and stem cell aneuploidies.
Automated continuous evolution of proteinsin vivo
Authors: Zhong Ziwei , Wong Brandon G. , Ravikumar Arjun , Arzumanyan Garri A. , Khalil Ahmad S. , Liu Chang C. 
Published: February 2020

AbstractWe present automated continuous evolution (ACE), a platform for the hands-free directed evolution of biomolecules. ACE pairs OrthoRep, a genetic system for continuous targeted mutagenesis of user-selected genesin vivo, with eVOLVER, a scalable and automated continuous culture device for precise, multi-parameter regulation of growth conditions. By implementing real-time feedback-controlled tuning of selection stringency with eVOLVER, genes of interest encoded on OrthoRep autonomously traversed multi-mutation adaptive pathways to reach desired functions, including drug resistance and improved enzyme activity. The durability, scalability, and speed of biomolecular evolution with ACE should be broadly applicable to protein engineering as well as prospective studies on how selection parameters and schedules shape adaptation.
Salvage logging changes the taxonomic, phylogenetic and functional successional trajectories of forest bird communities
Authors: Georgiev Kostadin B. , Chao Anne , Castro Jorge , Chen Yan‐Han , Choi Chang‐Yong , Fontaine Joseph B. , Hutto Richard L. , Lee Eun‐Jae , Müller Jörg , Rost Josep , Żmihorski Michal , Thorn Simon 
Published: February 2020

Abstract

Salvage logging following natural disturbances may alter the natural successional trajectories of biological communities by affecting the occurrences of species, functional groups and evolutionary lineages. However, few studies have examined whether dissimilarities between bird communities of salvaged and unsalvaged forests are more pronounced for rare species, functional groups and evolutionary lineages than for their more common counterparts.

We compiled data on breeding bird assemblages from nine study areas in North America, Europe and Asia, covering a 17‐year period following wildfire or windstorm disturbances and subsequent salvage logging. We tested whether dissimilarities based on non‐shared species, functional groups and evolutionary lineages (a) decreased or increased over time and (b) the responses of rare, common and dominant species varied, by using a unified statistical framework based on Hill numbers and null models.

We found that dissimilarities between bird communities caused by salvage logging persisted over time for rare, common and dominant species, evolutionary lineages and for rare functional groups. Dissimilarities of common and dominant functional groups increased 14 years post disturbance.

Salvage logging led to significantly larger dissimilarities than expected by chance. Functional dissimilarities between salvaged and unsalvaged sites were lower compared to taxonomic and phylogenetic dissimilarities. In general, dissimilarities were highest for rare, followed by common and dominant species.

Synthesis and applications. Our research demonstrates that salvage logging did not decrease dissimilarities of bird communities over time and taxonomic, functional and phylogenetic dissimilarities persisted for over a decade. We recommend resource managers and decision makers to reserve portions of disturbed forest to enable unmanaged post‐disturbance succession of bird communities, particularly to conserve rare species found in unsalvaged disturbed forests.
Drawing a line in the sand: affect and testimony in autism assessment teams in the UK
Authors: Hayes Jennie , McCabe Rose , Ford Tamsin , Russell Ginny 
Published: February 2020

AbstractDiagnosis of autism in the UK is generally made within a multidisciplinary team setting and is primarily based on observation and clinical interview. We examined how clinicians diagnose autism in practice by observing post‐assessment meetings in specialist autism teams. Eighteen meetings across four teams based in the south of England and covering 88 cases were audio‐recorded, transcribed and analysed using thematic analysis. We drew out two themes, related to the way in which clinicians expressed their specialist disciplinary knowledge to come to diagnostic consensus: Feeling Autism in the Encounter; and Evaluating Testimonies of Non‐present Actors. We show how clinicians produce objective accounts through their situated practices and perform diagnosis as an act of interpretation, affect and evaluation to meet the institutional demands of the diagnostic setting. Our study contributes to our understanding of how diagnosis is accomplished in practice.