bluuebunny/crossref_metadata_2025_split huggingface dataset:
Partial prion cross-seeding between fungal and mammalian amyloid signaling motifs
Authors: Bardin Thierry , Daskalov Asen , Barrouilhet Sophie , Granger-Farbos Alexandra , Salin Bénédicte , Blancard Corinne , Saupe Sven J. , Coustou Virginie 
Published: July 2020

AbstractIn filamentous fungi, NLR-based signalosomes activate downstream membrane-targeting cell-death inducing proteins by a mechanism of amyloid templating. In the speciesPodospora anserina, two such signalosomes, NWD2/HET-S and FNT1/HELLF have been described. An analogous system, involving a distinct amyloid signaling motif termed PP was also identified in the genome of the speciesChaetomium globosumand studied using heterologous expression inPodospora anserina. The PP-motif bears resemblance to the RHIM and RHIM-like motifs controlling necroptosis in mammals and innate immunity in flies. We identified here, a third NLR signalosome inPodospora anserinacomprising a PP-motif and organized as a two-gene cluster encoding a NLR and a HELL-domain cell-death execution protein termed HELLP. We show that the PP-motif region of HELLP forms a prion we term [π] and that [π] prions trigger the cell-death inducing activity of full length HELLP. We detect no prion cross-seeding between HET-S, HELLF and HELLP amyloid motifs. In addition, we find that akin to PP-motifs, RHIM motifs from human RIP1 and RIP3 kinases are able to form prions inPodospora, and that [π] and [Rhim] prions partially cross-seed. Our study shows thatPodospora anserinadisplays three independent cell-death inducing amyloid signalosomes. Based on the described functional similarity between RHIM and PP, it appears likely that these amyloid motifs constitute evolutionary related cell-death signaling modules.ImportanceAmyloids are β-sheet-rich protein polymers that can be pathological or display a variety of biological roles. In filamentous fungi, specific immune receptors activate programmed cell-death execution proteins through a process of amyloid templating akin to prion propagation.Among these fungal amyloid signaling sequences, the PP-motif stands out because it shows similarity to RHIM, an amyloid sequence controlling necroptotic cell-death in mammals. We characterized an amyloid signaling system comprising a PP-motif in the model speciesPodospora anserinathus bringing to three the number of independent amyloid signaling cell death pathways described in that species. We then show that human RHIM motifs not only propagate as prions inP. anserinabut also partially cross-seed with fungal PP-prions. These results indicate that in addition to show sequence similarity, PP and RHIM-motif are at least partially functionally related, supporting a model of long-term evolutionary conservation of amyloid signaling mechanisms from fungi to mammals.
Genome-resolved viral ecology in a marine oxygen minimum zone (OMZ)
Authors: Vik Dean , Gazitúa Maria Consuelo , Sun Christine L. , Aldunate Montserrat , Mulholland Margaret R. , Ulloa Osvaldo , Sullivan Matthew B. 
Published: July 2020

SummaryOxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of surface oxygenated to anoxic waters (< 0.02 μmol/L O2) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46,127 viral populations (>5 kb), which augments the known viruses at this site by 10-fold. ETSP viral communities clustered into 6 groups that correspond to oceanographic features, with 3 clusters representing samples from suboxic to anoxic waters. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. Viruses were largely endemic as few (6% of viruses from this study) were found in at least another marine metagenome, and of those, most (77%) were restricted to other OMZs. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments.Originality-Significance StatementMarine oxygen minimum zones (OMZs) are unique and important ocean ecosystems where microbes drive climate-altering nutrient transformations. This study provides a baseline, deeply sequenced viral metagenomic dataset and reference viral genomes to assess ecological change and drivers across the oxygenated surface to de-oxygenated deep waters of the Eastern Tropical South Pacific (ETSP) OMZ. Community ecological assessment of the ETSP viromes reveals a relatively low diversity viral community with a high degree of endemic populations in the OMZ waters.
Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth’s crust
Authors: Rahlff Janina , Turzynski Victoria , Esser Sarah P. , Monsees Indra , Bornemann Till L.V. , Figueroa-Gonzalez Perla Abigail , Schulz Frederik , Woyke Tanja , Klingl Andreas , Moraru Cristina , Probst Alexander J. 
Published: July 2020

ABSTRACTThe continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we used a combination of metagenomics and genome-informed microscopy to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches displayed resistances of Ca. Altiarchaea against eight predicted viral clades, which showed genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tagged and imaged a putatively viral genome rich in protospacers using fluorescence microscopy. Virus-targeted genomeFISH revealed a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.
Combination of high pressure treatment at 500 MPa and biopreservation with aLactococcus lactisstrain for lowering the bacterial growth during storage of diced cooked ham with reduced nitrite salt
Authors: Chaillou Stéphane , Ramaroson Mihanta , Coeuret Gwendoline , Rossero Albert , Anthoine Valérie , Champomier-Vergès Marie , Moriceau Nicolas , Rezé Sandrine , Martin Jean-Luc , Guillou Sandrine , Zagorec Monique 
Published: July 2020

AbstractWe investigated the combined effects of biopreservation and high pressure treatment on bacterial communities of diced cooked ham prepared with diminished nitrite salt. First, bacterial communities of four commercial brands of dice cooked ham from local supermarkets, were characterised and stored frozen. Second, sterile diced cooked ham, prepared with reduced level of nitrite was inoculated with two different microbiota collected from the aforementioned commercial samples together with a nisin producingLactococcus lactisprotective strain able to recover from a 500 MPa high pressure treatment. Dices were then treated at 500 MPa for 5 minutes and bacterial dynamics was monitored during storage at 8°C. Depending on samples, ham microbiota were dominated by different Proteobacteria (Pseudomonas, Serratia, Psychrobacter, orVibrio) or by Firmicutes (LatilactobacillusandLeuconostoc). Applied alone, none of the treatments stabilized durably the growth of hams microbiota. Nevertheless, the combination of biopreservation and high pressure treatment was efficient to reduce the growth of Proteobacteria spoilage species. However, this effect was dependent on the nature of the initial microbiota, showing that use of biopreservation and high pressure treatment as an alternative to nitrite reduction for ensuring cooked ham microbial safety merits attention but still requires improvement.
Neonatal hyperoxia enhances age-dependent expression of SARS-CoV-2 receptors in mice
Authors: Yee Min , Cohen E. David , Haak Jeannie , Dylag Andrew M. , O’Reilly Michael A. 
Published: July 2020

ABSTRACTThe severity of COVID-19 lung disease is higher in the elderly and people with pre-existing co-morbidities. People who were born preterm may be at greater risk for COVID-19 because their early exposure to oxygen at birth increases their risk of being hospitalized when infected with RSV and other respiratory viruses. Our prior studies in mice showed how high levels of oxygen (hyperoxia) between postnatal days 0-4 increases the severity of influenza A virus infections by reducing the number of alveolar epithelial type 2 (AT2) cells. Because AT2 cells express the SARS-CoV-2 receptors angiotensin converting enzyme (ACE2) and transmembrane protease/serine subfamily member 2 (TMPRSS2), we expected their expression would decline as AT2 cells were depleted by hyperoxia. Instead, we made the surprising discovery that expression ofAce2andTmprss2mRNA increases as mice age and is accelerated by exposing mice to neonatal hyperoxia. ACE2 is primarily expressed at birth by airway Club cells and becomes detectable in AT2 cells by one year of life. Neonatal hyperoxia increases ACE2 expression in Club cells and makes it detectable in 2-month-old AT2 cells. This early and increased expression of SARS-CoV-2 receptors was not seen in adult mice who had been administered the mitochondrial superoxide scavenger mitoTEMPO during hyperoxia. Our finding that early life insults such as hyperoxia enhances the age-dependent expression of SARS-CoV-2 receptors in the respiratory epithelium helps explain why COVID-19 lung disease is greater in the elderly and people with pre-existing co-morbidities.
Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons
Authors: Cetnar Daniel P. , Salis Howard M. 
Published: July 2020

ABSTRACTmRNA degradation is a central process that affects all gene expression levels, and yet the determinants that control mRNA decay rates remain poorly characterized. Here, we applied a synthetic biology, learn-by-design approach to elucidate the sequence and structural determinants that control mRNA stability in bacterial operons. We designed, constructed, and characterized 82 operons, systematically varying RNAse binding site characteristics, translation initiation rates, and transcriptional terminator efficiencies in the 5’ UTR, intergenic, and 3’ UTR regions, and measuring their mRNA levels using RT-qPCR assays. We show that introducing long single-stranded RNA into 5’ UTRs reduced mRNA levels by up to 9.4-fold and that lowering translation rates reduced mRNA levels by up to 11.8-fold. We also found that RNAse binding sites in intergenic regions had much lower effects on mRNA levels. Surprisingly, changing transcriptional termination efficiency or introducing long single-stranded RNA into 3’ UTRs had no effect on upstream mRNA levels. From these measurements, we developed and validated biophysical models of ribosome protection and RNAse activity with excellent quantitative correspondence. We also formulated design rules to rationally control a mRNA’s stability, facilitating the automated design of engineered genetic systems with desired functionalities.
Modular cell-free expression plasmids to accelerate biological design in cells
Authors: Karim Ashty S. , Liew Fungmin Eric , Garg Shivani , Vögeli Bastian , Rasor Blake J. , Gonnot Aislinn , Pavan Marilene , Juminaga Alex , Simpson Séan D. , Köpke Michael , Jewett Michael C. 
Published: July 2020

AbstractIndustrial biotechnology aims to produce high-value products from renewable resources. This can be challenging because model microorganisms—organisms that are easy to use likeEscherichia coli—often lack the machinery required to utilize desired feedstocks like lignocellulosic biomass or syngas. Non-model organisms, such asClostridium, are industrially proven and have the desired metabolic features but have several hurdles to mainstream use. Namely, these species grow more slowly than conventional laboratory microbes and genetic tools for engineering them are far less prevalent. To address these hurdles for accelerating cellular design, cell-free synthetic biology has emerged as an approach for characterizing non-model organisms and rapidly testing metabolic pathwaysin vitro. Unfortunately, cell-free systems can require specialized DNA architectures with minimal regulation that are not compatible with cellular expression. In this work, we develop a modular vector system that allows for T7 expression of desired enzymes for cell-free expression and direct Golden Gate assembly intoClostridiumexpression vectors. Utilizing the Joint Genome Institute’s DNA Synthesis Community Science Program, we designed and synthesized these plasmids and genes required for our projects allowing us to shuttle DNA easily between ourin vitroandin vivoexperiments. We next validated that these vectors were sufficient for cell-free expression of enzymes, performing on par with the previous state-of-the-art. Lastly, we demonstrated automated six-part DNA assemblies forC. autoethanogenumexpression with efficiencies ranging from 68-90%. We anticipate this system of plasmids will enable a framework for facile testing of biosynthetic pathwaysin vitroandin vivoby shortening development cycles.
CglB adhesins secreted at bacterial focal adhesions mediate gliding motility
Authors: Islam Salim T. , My Laetitia , Jolivet Nicolas Y. , Belgrave Akeisha M. , Fleuchot Betty , Brasseur Gael , Faure Laura M. , Sharma Gaurav , Lemon David J. , Saïdi Fares , Fiche Jean-Bernard , Bratton Benjamin P. , Singer Mitchell , Garza Anthony G. , Nollmann Marcelo , Shaevitz Joshua W. , Mignot Tâm 
Published: July 2020

AbstractThe predatory deltaproteobacteriumMyxococcus xanthususes a helically-trafficked motor at bacterial focal adhesion (bFA) sites to power gliding motility. Using TIRF and force microscopy, we herein identify the integrin αI-domain-like outer-membrane (OM) lipoprotein CglB as an essential substratum-coupling protein of the gliding motility complex. Similar to most known OM lipoproteins, CglB is anchored on the periplasmic side of the OM and thus a mechanism must exist to secrete it to the cell surface in order for it to interact with the underlying substratum. We reveal this process to be mediated by a predicted OM β-barrel structure of the gliding complex. This OM platform was found to regulate the conformational activation and secretion of CglB across the OM. These data suggest that the gliding complex promotes surface exposure of CglB at bFAs, thus explaining the manner by which forces exerted by inner-membrane motors are transduced across the cell envelope to the substratum; they also uncover a novel protein secretion mechanism, highlighting the ubiquitous connection between secretion and bacterial motility.
Rescue of SARS-CoV-2 from a single bacterial artificial chromosome
Authors: Ye Chengjin , Chiem Kevin , Park Jun-Gyu , Oladunni Fatai , Platt Roy Neal , Anderson Tim , Almazan Fernando , de la Torre Juan Carlos , Martinez-Sobrido Luis 
Published: July 2020

ABSTRACTAn infectious coronavirus disease 2019 (COVID-19) emerged in the city of Wuhan (China) in December 2019, causing a pandemic that has dramatically impacted public health and socioeconomic activities worldwide. A previously unknown coronavirus, Severe Acute Respiratory Syndrome CoV-2 (SARS-CoV-2), has been identified as the causative agent of COVID-19. To date, there are no United States (US) Food and Drug Administration (FDA)-approved vaccines or therapeutics available for the prevention or treatment of SARS-CoV-2 infection and/or associated COVID-19 disease, which has triggered a large influx of scientific efforts to develop countermeasures to control SARS-CoV-2 spread. To contribute to these efforts, we have developed an infectious cDNA clone of the SARS-CoV-2 USA-WA1/2020 strain based on the use of a bacterial artificial chromosome (BAC).Recombinant (r)SARS-CoV-2 was readily rescued by transfection of the BAC into Vero E6 cells. Importantly, the BAC-derived rSARS-CoV-2 exhibited growth properties and plaque sizes in cultured cells comparable to those of the SARS-CoV-2 natural isolate. Likewise, rSARS-CoV-2 showed similar levels of replication to that of the natural isolate in nasal turbinates and lungs of infected golden Syrian hamsters. This is, to our knowledge, the first BAC based reverse genetics system for the generation of infectious rSARS-CoV-2 that displays similar featuresin vivoto that of a natural viral isolate. This SARS-CoV-2 BAC-based reverse genetics will facilitate studies addressing several important questions in the biology of SARS-CoV-2, as well as the identification of antivirals and development of vaccines for the treatment of SARS-CoV-2 infection and associated COVID-19 disease.
Ovariectomy as a Management Technique in Suburban Deer Populations
Authors: DeNicola Anthony J. , DeNicola Vickie L. 
Published: July 2020

ABSTRACTOverabundant suburban deer (Odocoileusspp.) are a source of human-wildlife conflict in many communities throughout the United States. Deer-vehicle collisions, tick-borne pathogens, impacts on local vegetation, and other negative interactions are the typical reasons cited for initiating a deer management program. Social attitudes, legal constraints, and perceived safety concerns lead many communities to examine nonlethal management options. Surgical sterilization is currently the only nonlethal method available to permanently sterilize females with a single treatment. There are limited data demonstrating methods and outcomes in management programs that sterilize a high percentage (>90%) of the local population, particularly regarding the impact of immigration on non-isolated populations. We present data from 6 surgical sterilization sites with geographically open populations in California, Maryland, Michigan, New York, Ohio, and Virginia, USA. From 2012–2020, we sterilized 493 deer primarily via ovariectomy. We conducted annual or periodic population estimates using camera surveys, road-based distance sampling, and intensive field observations to assess population trends. Initial densities ranged from about 6–63 deer/km2. Study sites ranged from 1.2 km2to 16.5 km2, and initial populations ranged from ~47 to 169 individuals. For our 6 study sites, we noted an average reduction in deer abundance of approximately 25% (range: 16.2%–36.2%) from Year 1 to Year 2. Four years after the first treatment, at monitored sites (n= 4) using this management method, we noted an average total population reduction of about 45% (range: 28%–56%). During the first year, the average cost per deer handled was $1,221 (range: $864–$1,998). These projects demonstrate that significant reductions in local deer densities using high percentage surgical sterilization programs can be achieved in non-insular locations. Sustained sterilization efforts are necessary, as is the case with all deer management programs in open landscapes.
Electrochemical corrosion behavior and surface passivation of bulk nanocrystalline copper in alkaline solution
Authors: Luo Wei , Hu Lei , Xv Yimin , Zhou Jian , Xv Wentao , Yan Mi 
Published: July 2020

PurposeThis paper aims to focus on an assessment of the electrochemical corrosion performance of bulk NC copper in a variety of corrosion environments.Design/methodology/approachThe electrochemical corrosion behavior of bulk nanocrystalline (NC) copper prepared by inert gas condensation andin situwarm compress technique was studied by using potentiodynamic polarization and electrochemical impedance spectroscopy tests in de-aerated 0.1 M NaOH solution.FindingsNC copper exhibited a typical active-passive-transpassive behavior with the formation of duplex passive films, which was qualitatively similar to coarse-grain (CG) copper. Although a compact passive film formed on NC copper surface, the corrosion resistance of NC copper was lower in comparison with CG copper. The increase in corrosion rate for NC copper was mainly attributed to the high activity of surface atoms and intergranular atoms. These atoms led to an enhancement of passive ability and an increase of dissolution rate of passive film in oxygen-deficiency solution. For NC copper, the corrosion resistance decreased as grain size increased in NC range.Originality/valueThe difference in corrosion resistance between bulk NC copper and its CG counterpart is dependent upon the corrosion solution. In a previous work, the potentiodynamic polarization tests revealed that NC copper bulks (grain size 48, 68, 92 nm) had identical corrosion resistance to CG copper bulk in naturally aerated 0.1 M NaOH solution. The results might be related to the dissolved oxygen in the medium.
Corporate brand management in a charity context: the internal communications challenge
Authors: Ramjaun Tauheed Ahmad 
Published: July 2020

PurposeThe purpose of this paper was to investigate the practical issues and challenges faced when managing a corporate brand internally within a charity context from perspectives of both senior managers and grassroots volunteers.Design/methodology/approachAn interpretive exploratory approach was adopted, where emphasis was placed on giving voice to participants considered as knowledge agents. Data collection methods included a combination of interviews and participatory observation. In-depth qualitative interviews were carried out with seven volunteers (including five branch chairs and one trustee) and five senior managers (chief executive officer [CEO], head of fundraising, national and regional directors and head of information and helplines). Participatory observations included visits in five branches as well as participation in two volunteer-targeted events.FindingsFindings from this study revealed the complexities of managing a charity brand internally with several issues and challenges relating to internal communications. Also, three major themes emerged from insights gathered from both senior managers and volunteers, which are as follows: (1) internal brand clarity, (2) internal relational communications and (3) internal brand presence.Originality/valueThe key contribution of the paper lies in exploring the challenges of managing a corporate brand internally from both the perspectives of senior management and volunteers within a unique charity context. The study adds insights on the issues and tension faced by charities in managing their brands internally and provides a series of practical recommendations that might help charities in strengthening their brands from inside.