bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors affecting bacterial community dynamics and volatile metabolite profiles of Thai traditional salt fermented fish
Authors: Det-udom Rachatida , Settachaimongkon Sarn , Chancharoonpong Chuenjit , Suphamityotin Porrarath , Suriya Atchariya , Prakitchaiwattana Cheunjit 
Published: February 2021

AbstractBacterial diversity of the Thai traditional salt fermented fish with roasted rice bran or Pla-ra, in Thai, was investigated using classical and molecular approaches. Pla-ra fermentation could be classified into two types, i.e., solid-state fermentation (SSF) and submerged fermentation (SMF). Bacterial population ranged from 102-106and 106-109CFU/g in SSF and SMF, respectively. TherRNAdetection revealed thatHalanaerobiumspp. andLentibacillusspp. were the main genera present in all types and most stages of fermentation.Tetragenococcus halophilluswere dominant during final stage of fermentation in the samples in which sea salt was used as one of the ingredients whileBacillusspp. were found in those that rock salt was used. In contrast, cultural plating demonstrated thatBacillusspp. were the dominant genera.B. amyloliquefacienswere the main species found in all types of Pla-ra whereasB. pumilus, B. autrophaeus,B.subtilis andB. velezensiswere specifically associated with the samples in which rock salt was used. The main volatile metabolites in all Pla-ra samples were butanoic acid and its derivatives. Dimethyl disulfide was observed during earlier stage of fermentation under high salt condition with a long fermentation period. Key factors affected bacterial profiles and volatile compounds of salt fermented fish are type of salt, addition of roasted rice bran, and fermenting conditions.ImportanceProtein hydrolysates with high salt fermentation from soy, fish as sauces and pastes are important food condiments commonly found in Asian food cultures. In Thailand, an indigenous semi-paste product derived from salted fish fermentation also called Pla-ra is well recognized and extensively in demands. In-depth information on Pla-ra fermentation ecosystems, in which roasted rice bran and different types of salt are incorporated, are still limited. In this study, we found thatHalanaerobiumspp. was the key autochthonous microbe initiating Pla-ra fermentation. Addition of roasted rice brand and rock salt were associated with the prevalence ofBacillusspp. while sea salt was associated with the presence ofTetragenococcus halophillus, The risk of pathogenicStaphylococcusspp. andClostridiumspp. needed to be also concerned. Geographical origin authentication of Pla-ra products could be discriminated based on their distinctive volatile profiles. This research provides novel insights for quality and safety control fermentation together with conservation of its authenticity.
In vivoantigen expression regulates CD4 T cell differentiation and vaccine efficacy againstMycobacterium tuberculosisinfection
Authors: Clemmensen Helena Strand , Dube Jean-Yves , McIntosh Fiona , Rosenkrands Ida , Jungersen Gregers , Aagaard Claus , Andersen Peter , Behr Marcel A. , Mortensen Rasmus 
Published: February 2021

AbstractNew vaccines are urgently needed againstMycobacterium tuberculosis(Mtb), which kills more than 1.4 million people each year. CD4 T cell differentiation is a key determinant of protective immunity against Mtb, but it is not fully understood how host-pathogen interactions shape individual antigen-specific T cell populations and their protective capacity. Here, we investigated the immunodominant Mtb antigen, MPT70, which is upregulated in response to IFN-γ or nutrient/oxygen deprivation ofin vitroinfected macrophages. Using a murine aerosol infection model, we compared thein vivoexpression kinetics of MPT70 to a constitutively expressed antigen, ESAT-6, and analysed their corresponding CD4 T cell phenotype and vaccine-protection. For wild-type Mtb, we found thatin vivoexpression of MPT70 was delayed compared to ESAT-6. This delayed expression was associated with induction of less differentiated MPT70-specific CD4 T cells but, compared to ESAT-6, also reduced protection after vaccination. In contrast, infection with an MPT70-overexpressing Mtb strain promoted highly differentiated KLRG1+CX3CR1+CD4 T cells with limited lung-homing capacity. Importantly, this differentiated phenotype could be prevented by vaccination and, against the overexpressing strain, vaccination with MPT70 conferred similar protection as ESAT-6. Together our data indicate that highin vivoantigen expression drives T cells towards terminal differentiation and that targeted vaccination with adjuvanted protein can counteract this phenomenon by maintaining T cells in a protective less-differentiated state. These observations shed new light on host-pathogen interactions and provide guidance on how future Mtb vaccines can be designed to tip the immune-balance in favor of the host.ImportanceTuberculosis, caused by Mtb, constitutes a global health crisis of massive proportions and the impact of the current COVID-19 pandemic is expected to cause a rise in tuberculosis-related deaths. Improved vaccines are therefore needed more than ever, but a lack of knowledge on protective immunity hampers their development. The present study shows that constitutively expressed antigens with high availability drive highly differentiated CD4 T cells with diminished protective capacity, which could be a survival strategy by Mtb to evade T cell immunity against key antigens. We demonstrate that immunisation with such antigens can counteract this phenomenon by maintaining antigen-specific T cells in a state of low differentiation. Future vaccine strategies should therefore explore combinations of multiple highly expressed antigens and we suggest that T cell differentiation could be used as a readily measurable parameter to identify these in both preclinical and clinical studies.
Proximity-labeling reveals novel host and parasite proteins at theToxoplasmaparasitophorous vacuole membrane
Authors: Cygan Alicja M. , Jean Beltran Pierre M. , Branon Tess C. , Ting Alice Y. , Carr Steven A. , Boothroyd John C. 
Published: February 2021

AbstractToxoplasma gondiiis a ubiquitous, intracellular parasite that envelopes its parasitophorous vacuole with a protein-laden membrane (PVM). The PVM is critical for interactions with the infected host cell such as nutrient transport and immune defense. Only a few parasite and host proteins have so far been identified on the host-cytosolic side of the PVM. We report here the use of human foreskin fibroblasts expressing the proximity-labeling enzyme miniTurbo, fused to a domain that targets it to this face of the PVM, in combination with quantitative proteomics to specifically identify proteins present at this crucial interface. Out of numerous human and parasite proteins with candidate PVM localization, we validate three novel parasite proteins (TGGT1_269950, TGGT1_215360, and TGGT1_217530) and four new host proteins (PDCD6IP/ALIX, PDCD6, CC2D1A, and MOSPD2) as localized to the PVM in infected human cells through immunofluorescence microscopy. These results significantly expand our knowledge of proteins present at the PVM and, given that three of the validated host proteins are components of the ESCRT machinery, they further suggest that novel biology is operating at this crucial host-pathogen interface.ImportanceToxoplasmais an intracellular pathogen which resides and replicates inside a membrane-bound vacuole in infected cells. This vacuole is modified by both parasite and host proteins which participate in a variety of host-parasite interactions at this interface, including nutrient exchange, effector transport, and immune modulation. Only a small number of parasite and host proteins present at the vacuolar membrane and exposed to the host cytosol have thus far been identified. Here we report the identification of several novel parasite and host proteins present at the vacuolar membrane using enzyme-catalyzed proximity-labeling, significantly increasing our knowledge of the molecular players present and novel biology occurring at this crucial interface.
Identification of novel inner membrane complex and apical annuli proteins of the malaria parasitePlasmodium falciparum
Authors: Wichers Jan Stephan , Wunderlich Juliane , Heincke Dorothee , Pazicky Samuel , Strauss Jan , Schmitt Marius , Kimmel Jessica , Wilcke Louisa , Scharf Sarah , von Thien Heidrun , Burda Paul-Christian , Spielmann Tobias , Löw Christian , Filarsky Michael , Bachmann Anna , Gilberger Tim W. 
Published: February 2021

ABSTRACTThe inner membrane complex (IMC) is a defining feature of apicomplexan parasites, which confers stability and shape to the cell, functions as a scaffolding compartment during the formation of daughter cells and plays an important role in motility and invasion during different life cycle stages of these single celled organisms. To explore the IMC proteome of the malaria parasitePlasmodium falciparumwe applied a proximity-dependent biotin identification (BioID)-based proteomics approach, using the established IMC marker protein Photosensitized INA-Labelled protein 1 (PhIL1) as bait in asexual blood-stage parasites. Subsequent mass spectrometry-based peptide identification revealed enrichment of twelve known IMC proteins and several uncharacterized candidate proteins. We validated nine of these previously uncharacterized proteins by endogenous GFP-tagging. Six of these represent new IMC proteins, while three proteins have a distinct apical localization that most likely represent structures described as apical annuli inToxoplasma gondii. Additionally, various Kelch13 interacting candidates were identified, suggesting an association of the Kelch13 compartment and the IMC in schizont and merozoite stages. This work extends the number of validated IMC proteins in the malaria parasite and reveals for the first time the existence of apical annuli proteins inP. falciparum.Additionally, it provides evidence for a spatial association between the Kelch13 compartment and the IMC in late blood-stage parasites.
CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
Authors: Wittig Alice , Miranda Fábio , Hölzer Martin , Altenburg Tom , Bartoszewicz Jakub M. , Beyvers Sebastian , Dieckmann Marius A. , Genske Ulrich , Giese Sven H. , Nowicka Melania , Richard Hugues , Schiebenhoefer Henning , Schmachtenberg Anna-Juliane , Sieben Paul , Tang Ming , Tembrockhaus Julius , Renard Bernhard Y. , Fuchs Stephan 
Published: February 2021

ABSTRACTThe SARS-CoV-2 pandemic underlined the importance of molecular surveillance to track the evolution of the virus and inform public health interventions. Fast analysis, easy visualization and convenient filtering of the latest virus sequences are essential for this purpose. However, access to computational resources, the lack of bioinformatics expertise, and the sheer volume of sequences in public databases complicate surveillance efforts. CovRadar combines an analytical pipeline and a web application designed for the molecular surveillance of the spike gene of SARS-CoV-2, an important vaccine target. The intuitive web front-end focuses on mutations rather than viral lineages and provides easy access to frequencies and spatio-temporal distributions from global sample collections. The data is regularly updated based on a scalable and reproducible analytical back-end. With this platform, we aim to give users, those with or without bioinformatics skills or sufficient computational resources, the possibility to track and explore mutational changes in the SARS-CoV-2 spike gene and to filter, download, and further analyze data that meet their questions and needs. Advanced computational users have the ability to apply the analytical pipeline and data visualization methods locally on their own data. CovRadar is freely accessible athttps://covradar.net, source code is available athttps://gitlab.com/dacs-hpi/covradar.GRAPHICAL ABSTRACT
Full Brain and Lung Prophylaxis against SARS-CoV-2 by Intranasal Lentiviral Vaccination in a New hACE2 Transgenic Mouse Model or Golden Hamsters
Authors: Ku Min-Wen , Authié Pierre , Bourgine Maryline , Anna François , Noirat Amandine , Moncoq Fanny , Vesin Benjamin , Nevo Fabien , Lopez Jodie , Souque Philippe , Blanc Catherine , Chardenoux Sébastien , Lafosse llta , Hardy David , Nemirov Kirill , Guinet Françoise , Vives Francina Langa , Majlessi Laleh , Charneau Pierre 
Published: February 2021

SummaryNon-integrative, non-cytopathic and non-inflammatory lentiviral vectors are particularly suitable for mucosal vaccination and recently emerge as a promising strategy to elicit sterilizing prophylaxis against SARS-CoV-2 in preclinical animal models. Here, we demonstrate that a single intranasal administration of a lentiviral vector encoding a prefusion form of SARS-CoV-2 spike glycoprotein induces full protection of respiratory tracts and totally avoids pulmonary inflammation in the susceptible hamster model. More importantly, we generated a new transgenic mouse strain, expressing the human Angiotensin Converting Enzyme 2, with unprecedent brain permissibility to SARS-CoV-2 replication and developing a lethal disease in <4 days post infection. Even though the neurotropism of SARS-CoV-2 is now well established, so far other vaccine strategies under development have not taken into the account the protection of central nervous system. Using our highly stringent transgenic model, we demonstrated that an intranasal booster immunization with the developed lentiviral vaccine candidate achieves full protection of both respiratory tracts and brain against SARS-CoV-2.
APICURON: a database to credit and acknowledge the work of biocurators
Authors: Hatos András , Quaglia Federica , Piovesan Damiano , Tosatto Silvio C.E. 
Published: February 2021

AbstractAPICURON is an open and freely accessible resource that tracks and credits the work of biocurators across multiple participating knowledgebases. Biocuration is essential to extract knowledge from research data and make it available in a structured and standardized way to the scientific community. However, processing biological data - mainly from literature - requires a huge effort which is difficult to quantify and acknowledge. APICURON collects biocuration events from third party resources and aggregates this information, spotlighting biocurator contributions. APICURON promotes biocurator engagement implementing gamification concepts like badges, medals and leaderboards and at the same time provides a monitoring service for registered resources and for biocurators themselves. APICURON adopts a data model that is flexible enough to represent and track the majority of biocuration activities. Biocurators are identified through their ORCID. The definition of curation events, scoring systems and rules for assigning badges and medals are resource-specific and easily customizable. Registered resources can transfer curation activities on the fly through a secure and robust Application Programming Interface (API). Here we show how simple and effective it is to connect a resource to APICURON describing the DisProt database of intrinsically disordered proteins as a use case. We believe APICURON will provide biological knowledgebases with a service to recognize and credit the effort of their biocurators, monitor their activity and promote curators engagement.Database URL:https://apicuron.org
Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography
Authors: Walsh C. , Tafforeau P. , Wagner Willi L. , Jafree D. J. , Bellier A. , Werlein C. , Kühnel M. P. , Boller E. , Walker-Samuel S. , Robertus J. L. , Long D. A. , Jacob J. , Marussi S. , Brown E. , Holroyd N. , Jonigk D. D. , Ackermann M. , Lee P. D. 
Published: February 2021

ABSTRACTHuman organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique utilising the European Synchrotron Radiation Facility’s Extremely Brilliant Source: the world’s first high-energy 4thgeneration X-ray source. HiP-CT enabled three-dimensional and non-destructive imaging at near-micron resolution in soft tissues at one hundred thousand times the voxel size whilst maintaining the organ’s structure. We applied HiP-CT to image five intact human parenchymal organs: brain, lung, heart, kidney and spleen. These were hierarchically assessed with HiP-CT, providing a structural overview of the whole organ alongside detail of the organ’s individual functional units and cells. The potential applications of HiP-CT were demonstrated through quantification and morphometry of glomeruli in an intact human kidney, and identification of regional changes to the architecture of the air-tissue interface and alveolar morphology in the lung of a deceased COVID-19 patient. Overall, we show that HiP-CT is a powerful tool which can provide a comprehensive picture of structural information for whole intact human organs, encompassing precise details on functional units and their constituent cells to better understand human health and disease.
Energy-harnessing problem solving of primordial life: modeling the emergence of catalytic host-parasite life cycles
Authors: Conrad Bernard , Pirovino Magnus 
Published: February 2021

AbstractAll life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energy required for survival, and an evolvable, informational polymer – the genome – conferring heredity. Genome replication invariably generates essential and ubiquitous genetic parasites. Here we model the energetic, replicative conditions of LUCA-like organisms and their parasites, as well as adaptive problem solving of host-parasite pairs. We show using the Lotka-Volterra equations that three host-parasite pairs – individually a unit of a host and a parasite that is itself parasitized – are sufficient for robust and stable homeostasis, forming a life cycle. This catalytic life cycle efficiently captures, channels and transforms energy, enabling dynamic host survival and adaptation. We propose a Malthusian fitness model for an original quasispecies evolving through a host-parasite life cycle.
Horizontal gene transfer of a uniquenifisland drives convergent evolution of free-living N2-fixingBradyrhizobium
Authors: Tao Jinjin , Wang Sishuo , Liao Tianhua , Luo Haiwei 
Published: February 2021

SummaryThe alphaproteobacterial genusBradyrhizobiumhas been best known as N2-fixing members that nodulate legumes, supported by thenifandnodgene clusters. Recent environmental surveys show thatBradyrhizobiumrepresents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding ofBradyrhizobiumcomes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88Bradyrhizobiumstrains derived from diverse soil samples, including bothnif-carrying and non-nif-carrying free-living (nodfree) members. Phylogenomic analyses of these and 252 publicly availableBradyrhizobiumgenomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, thenifphylogeny shows that allnif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotesnifexpansion among the free-livingBradyrhizobiumand that the free-livingnifcluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that thenifin free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-livingBradyrhizobium nifand the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance ofBradyrhizobiumin world’s soils, our findings have implications for global nitrogen cycles and agricultural research.
Enzyme kinetics of CRISPR molecular diagnostics
Authors: Ramachandran Ashwin , Santiago Juan G. 
Published: February 2021

AbstractCRISPR diagnostic assays have gained significant interest in the last few years. This interest has grown rapidly during the current COVID-19 pandemic where CRISPR diagnostics have been frontline contenders for rapid testing solutions. This surge in CRISPR diagnostics research prompts the following question: What exactly are the achievable limits of detection and associated assay times enabled by the kinetics of Cas12 and Cas13 enzymes? To address this question, we here present a model based on Michaelis-Menten enzyme kinetics theory applied to Cas enzymes. We use the model to develop analytical solutions for reaction kinetics and develop back-of-the­ envelope criteria to validate and check for consistency in reported enzyme kinetics parameters. We applied our analyses to all studies known to us which report Michaelis-Menten-type kinetics data for CRISPR associated enzymes. These studies include all subtypes of Cas12 and Cas13 and orthologs. We found all studies but one clearly violate at least two of our three rules of consistency. We further use our model to explore ranges of reaction time scales and degree of reaction completion for practically relevant target concentrations applicable to CRISPR-diagnostic assays.
Chimpanzees use numerous flexible vocal sequences with more than two vocal units: A step towards language?
Authors: Girard-Buttoz Cédric , Zaccarella Emiliano , Bortolato Tatiana , Friederici Angela D. , Wittig Roman M. , Crockford Catherine 
Published: February 2021

AbstractA major question in evolutionary science is how did language evolve? Syntax, as the core of language, combines meaning-bearing units (words) into hierarchical structures, thereby creating new meanings. Some other mammals and birds combine meaning-bearing vocalisations, but no documented examples exist of non-human animals combining more than two meaning-bearing vocalisations. Was the two-unit threshold only surpassed in the hominid lineage? Here, we examine the positional patterning of vocal sequences of chimpanzees. We analysed 4826 vocal utterances of 46 wild adult female and male chimpanzees. We found a flexible system with 390 multi-unit vocal sequences, some showing positional or transitional regularities. Two-unit pairs embedded in three-unit sequences predictably occurred either in head or tail positions, and co-occurred with specific other elements. The capacity to organise vocal output beyond the two-unit level may thus exist in species other than humans and could be viewed as an important evolutionary step towards language.