bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jumping back and forth: anthropozoonotic and zoonotic transmission of SARS-CoV-2 on mink farms
Authors: Oude Munnink Bas B. , Sikkema Reina S. , Nieuwenhuijse David F. , Molenaar Robert Jan , Munger Emmanuelle , Molenkamp Richard , van der Spek Arco , Tolsma Paulin , Rietveld Ariene , Brouwer Miranda , Bouwmeester-Vincken Noortje , Harders Frank , der Honing Renate Hakze-van , Wegdam-Blans Marjolein C.A. , Bouwstra Ruth J. , GeurtsvanKessel Corine , van der Eijk Annemiek A. , Velkers Francisca C. , Smit Lidwien A.M. , Stegeman Arjan , van der Poel Wim H.M. , Koopmans Marion P.G. 
Published: September 2020

AbstractThe zoonotic origin of the SARS-CoV-2 pandemic is still unknown. Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation of outbreaks on 16 mink farms and humans living or working on these farms, using whole genome sequencing. We conclude that the virus was initially introduced from humans and has evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. At the moment, despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, there is ongoing transmission between mink farms with three big transmission clusters with unknown modes of transmission. We also describe the first animal to human transmissions of SARS-CoV-2 in mink farms.One sentence summarySARS-CoV-2 transmission on mink farms.
Ongoing evolution of KRAB zinc finger protein-coding genes in modern humans
Authors: Thorball Christian W. , Planet Evarist , de Tribolet-Hardy Jonas , Coudray Alexandre , Fellay Jacques , Turelli Priscilla , Trono Didier 
Published: September 2020

AbstractBackgroundKrüppel-associated box (KRAB) zinc finger proteins (KZFPs) constitute the largest and fastest evolving family of gene regulators encoded by the human genome. Recent data indicate that many KZFPs serve as repressors of transposable element-embedded regulatory sequences (TEeRS) and that the evolutionary turnover of KZFP genes is mainly attributable to the changing transposable element (TE) load of their hosts. However, how natural selection and genetic variation are shaping this process is still poorly defined.MethodsGenetic information was collected from nine primate species and 138,500 human genomes. Gene-wide as well as functional amino acid position specific constraint was calculated across all human KZFPs.ResultsWe found that the most conserved KZFPs, some of which go back close to 400 million years, have been subjected to marked negative selection in the evolutionarily recent past and are very homogeneous within the human population. In contrast, younger, largely primate-restricted family members present evidence of less negative selection than the rest of genome and lower levels of coding constraint, particularly within the sequences encoding the functional sites of their zinc finger (ZF) arrays. We defined 33 sets of KZFP paralogs, which pairwise displayed a broad range of coding constraints differentials, with more recently emerged paralogs usually displaying a higher frequency of putatively deleterious mutations and missense variants within the functional sites of their ZF arrays than their source gene. Finally, we identified three KZFP genes more constrained in the genomes of individuals of African ancestry than in Europeans, with their modes of expression or DNA targets pointing to possible links between these inter-populational genetic differences and regional differences in the prevalence of some diseases.ConclusionsThis work shows how the ongoing selection of KZFPs contributes to modern human genetic variation, in particular through the constraint of putatively deleterious- and missense variants in functional protein sites, and how ongoing interplays between environment and KZFP genes might be impacting the biology of modern humans.
Confinement size determines the architecture of Ran-induced microtubule networks
Authors: Gai Ya , Setru Sagar , Cook Brian , Stone Howard A. , Petry Sabine 
Published: September 2020

ABSTRACTThe organization of microtubules (MTs) within cells is critical for its internal organization during interphase and mitosis. During mitotic spindle assembly, MTs are made and organized around chromosomes in a process regulated by RanGTP. The role of RanGTP has been explored inXenopusegg extracts, which are not limited by a cell membrane. Here, we investigated whether cell-sized confinements affect the assembly of RanGTP-induced MT networks inXenopusegg extracts. We used microfluidics to encapsulate extract within monodisperse extract-in-oil droplets. Importantly, we find that the architecture of Ran-induced MT networks depends on the droplet diameter and the Ran concentration, and differs from structures formed in bulk extract. Our results highlight that both MT nucleation and physical confinement play critical roles in determining the spatial organization of the MT cytoskeleton.STATEMENT OF SIGNIFICANCEDuring cell division, chromosomes are segregated by the mitotic spindle, whose framework consists of up to hundreds of thousands of microtubules (MTs). Spindle MTs are generated via several pathways, one of which is regulated by RanGTP. Yet, how Ran-induced MTs self-organize within cell-sized confinement remains unclear. This work reports unexpected architectures of Ran-induced MT networks confined in cell-sized droplets, which depend on the droplet diameter and the RanGTP concentration. Thus, MT nucleation and confinement together give rise to specific MT network architectures, which are otherwise not observed in unconfined assays. The findings provide a simple strategy to engineer the architectures of MT networks and could have direct implications in nucleation-controlled soft material processing.
Strong reduction of the chain rigidity of hyaluronan by selective binding of Ca2+ions
Authors: Giubertoni G. , Pérez de Alba Ortíz A. , Bano F. , Zhang X. , Linhardt R.J. , Green D. E. , DeAngelis P. L. , Koenderink G.H. , Richter R. P. , Ensing B. , Bakker H.J. 
Published: September 2020

ABSTRACTThe biological functions of natural polyelectrolytes are strongly influenced by the presence of ions, which bind to the polymer chains and thereby modify their properties. Although the biological impact of such modifications is well-recognized, a detailed molecular picture of the binding process and of the mechanisms that drive the subsequent structural changes in the polymer is lacking. Here, we study the molecular mechanism of the condensation of calcium, a divalent cation, on hyaluronan, a ubiquitous polymer in human tissues. By combining two-dimensional infrared spectroscopy experiments with molecular dynamics simulations, we find that calcium specifically binds to hyaluronan at millimolar concentrations. Because of its large size and charge, the calcium cation can bind simultaneously to the negatively charged carboxylate group and the amide group of adjacent saccharide units. Molecular dynamics simulations and single-chain force spectroscopy measurements provide evidence that the binding of the calcium ions weakens the intra-molecular hydrogen-bond network of hyaluronan, increasing the flexibility of the polymer chain. We also observe that the binding of calcium to hyaluronan saturates at a maximum binding fraction of ~10-15 mol %. This saturation indicates that the binding of Ca2+strongly reduces the probability of subsequent binding of Ca2+at neighboring binding sites, possibly as a result of enhanced conformational fluctuations and/or electrostatic repulsion effects. Our findings provide a detailed molecular picture of ion condensation, and reveal the severe effect of a few, selective and localized electrostatic interactions on the rigidity of a polyelectrolyte chain.TOC
New shallow water species of CaribbeanIrciniaNardo, 1833 (Porifera: Irciniidae)
Authors: Kelly Joseph B. , Thacker Robert W. 
Published: September 2020

AbstractSevenIrciniagrowth forms were collected from three sites in the Caribbean (Bocas del Toro, Panama; the Mesoamerican Barrier Reef, Belize; and the Florida Keys, United States of America). Previous research used an integrative taxonomic framework to delimit species boundaries among these growth forms. Here, we present descriptions for these species, six of which are new to science (Ircinia lowisp. nov.,Ircinia bocatorensissp. nov.,Ircinia radixsp. nov.,Ircinia laeviconulosasp. nov.,Ircinia vansoestisp. nov.,Ircinia rutzlerisp. nov.) in addition to one speciesconferre(Irciniacf.reteplanaTopsent, 1923).
High-Quality Genome Assembly and Annotation of the California Harvester AntPogonomyrmex californicus(Buckley, 1867)
Authors: Bohn Jonas , Halabian Reza , Schrader Lukas , Shabardina Victoria , Steffen Raphael , Suzuki Yutaka , Ernst Ulrich R. , Gadau Jürgen R. , Makałowski Wojciech 
Published: September 2020

ABSTRACTThe harvester ant genusPogonomyrmexis endemic to arid and semiarid habitats and deserts of North and South America and California harvester antPogonomyrmex californicusis the most widely distributedPogonomyrmexspecies in the North America.P. californicuscolonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present high quality genome assembly and annotation ofP. californicus. The size of the assembly is 241 Mb, which is in good agreement with previously estimated genome size and we were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO completeness at the 95% level. This high quality genome will pave the way for investigations of the genomic underpinnings of social polymorphism in queen number, regulation of aggression, and the evolution of adaptations to dry habitats inP. californicus.
Bacteriophage activity against and characterisation of avian pathogenicEscherichia coliisolated from colibacillosis cases in Uganda
Authors: Kazibwe George , Katami Phionah , Alinaitwe Ruth , Alafi Stephen , Nanteza Ann , Nakavuma Jesca Lukanga 
Published: September 2020

AbstractA laboratory-based study aimed at establishing a stock of avian pathogenicEscherichia coli(APEC) lytic bacteriophages, for future development of cocktail products for controlling colibacillosis as well as minimizing use of antimicrobial drugs in the poultry production systems in Uganda. Specifically, the study determined the antibiotic susceptibility; phylogenetic categories, occurrence of selected virulence genes amongEscherichia colistock isolates from cases of chicken colibacillosis; and isolation of specific bacteriophages. Fifty six isolates were confirmed asE. coliby standard phenotypic tests. All the 56 (100%) isolates were resistant to at least one antibiotic while 50 (89.3%) isolates were resistant to at least three classes of antimicrobial drugs and were therefore designated as multi-drug resistant. Phylogenetically, APEC isolates mainly belonged to phylogroups A and D which represented 44.6% and 39.3%, respectively. Virulence genes,ompTandiutAwere the most frequent with 33 (58.9%) and 32 (57.1%) isolates respectively; whileiroNleast occurred in 23 (41.1%) isolates. Of the 56 isolates, 69.6% harbored at least one virulence gene, while 50% had at least four virulence genes; hence confirmed as APEC. None of the isolates belonged to the selected serotypes O1, O2 and O78. Seven specific bacteriophages were isolated and their host range, varied from 1.8% to 17.9% (n=56 APEC isolates), while the combined lytic spectrum of all the phages was 25%. Phage stability was negatively affected by increasing temperatures with both UPEC04 and UPEC10 phages becoming undetectable at 70°C; however activity was detected between pH 2 and 12. The high occurrence of APEC isolates with resistance against the commonly used antibiotics supports the need for alternative strategies of bacterial infections control in poultry. The low host range exhibited by the phages calls for search for more candidates before more in-depth studies are done for phage characterization and application.
Ccr2 suppression by minocycline in Cx3cr1/Ccr2-visualized inherited retinal degeneration
Authors: Terauchi Ryo , Kohno Hideo , Watanabe Sumiko , Saito Saburo , Watanabe Akira , Nakano Tadashi 
Published: September 2020

AbstractRetinal inflammation accelerates photoreceptor cell death (PCD) caused by retinal degeneration. Minocycline, a semisynthetic broad-spectrum tetracycline antibiotic, has previously been reported to show PCD rescue effect in retinal degeneration. The purpose of this study was to assess the effect of minocycline on Cx3cr1 and Ccr2 expression in retinal degeneration.Mertk-/-Cx3cr1GFP/+Ccr2RFP/+mice, which enabled observation ofCx3cr1- andCcr2-expression pattern in inherited retinal degeneration, were used to test the effect of minocycline. Minocycline was systemically administered toMertk-/-Cx3cr1GFP/+Ccr2RFP/+mice. For observing the effect of minocycline on Cx3cr1 and Ccr2 expression, administration was started on 4-week-old mice and continued for 2 weeks. To assess the PCD rescue effect, minocycline was administered to 6-week-old mice for 2 weeks. The expression pattern of Cx3cr1-GFP and Ccr2-RFP were observed on retinal and retinal pigment epithelium (RPE) flat-mounts. The severity of retinal degeneration was assessed on retinal sections. Minocycline administration suppressedCcr2expression inMertk-/-Cx3cr1GFP/+Ccr2RFP/+mice as observed in retinal and RPE flat-mounts. On the contrary, Cx3cr1 expression was not affected by minocycline administration. Retinal degeneration is ameliorated in minocycline administeredMertk-/-Cx3cr1GFP/+Ccr2RFP/+mice. In conclusions, Minocycline suppression of Ccr2 expression correlates to amelioration of retinal degeneration.
Light dependent morphological changes can tune light absorption in iridescent plant chloroplasts
Authors: Castillo Miguel A. , Wardley William P. , Lopez-Garcia Martin 
Published: September 2020

AbstractChloroplasts, the organelles responsible for photosynthesis in most plants and algae, exhibit a variety of morphological adaption strategies to changing light environments which can have important yet overlooked light scattering effects. This can be even more significant for iridoplasts, specialized chloroplasts whose tissue is arranged as a photonic multilayer producing a characteristic strong blue reflectance associated to a wavelength selective absorption enhancement relevant for photosynthesis.In this work, we study how the photonic properties of iridoplasts are affected by light induced dynamic changes using realistic data extracted from previous reports. Our results show a reflectance red-shift from blue to green under increasing light intensity. Consequently, the light absorption enhancement induced by the photonic nanostructure is also redshifted. We also show that the photonic properties are resilient to biologically realistic levels of disorder in the structure. We extended this analysis to another photonic nanostructure-containing chloroplast, known as a bisonoplast, and found similar results, pointing towards similar properties in different plant species. We finally found that all types of chloroplasts can tune light absorption depending on light conditions. In general, our study opens the door to understanding how dynamic morphologies in chloroplasts can affect light scattering and absorption.
First evidence for an Amazonian insect migration in the butterflyPanacea prola(Lepidoptera: Nymphalidae)
Authors: Gallice Geoffrey , Mattea Riccardo , Stoiser Allison 
Published: September 2020

ABSTRACTInsect migrations rival those of vertebrates in terms of numbers of migrating individuals and even biomass, although instances of the former are comparatively poorly documented. This is especially true in the world’s tropics, which harbor the vast majority of Earth’s insect species. Understanding these mass movements is of critical and increasing importance as global climate and land use change accelerate and interact to alter the environmental cues that underlie migration, particularly in the tropics. Here, we provide the first evidence for an insect migration for the nymphalid butterflyPanacea prolain the Amazon, the world’s largest and most biodiverse rainforest that is experiencing a shifting climate and rapid forest loss.
High transmissibility and fetal pathogenicity of recent Zika virus strains from the African lineage
Authors: Aubry Fabien , Jacobs Sofie , Darmuzey Maïlis , Lequime Sebastian , Delang Leen , Fontaine Albin , Jupatanakul Natapong , Miot Elliott F. , Dabo Stéphanie , Manet Caroline , Montagutelli Xavier , Baidaliuk Artem , Gambaro Fabiana , Simon-Lorière Etienne , Gilsoul Maxime , Romero-Vivas Claudia M. , Cao-Lormeau Van-Mai , Jarman Richard G. , Diagne Cheikh T. , Faye Oumar , Faye Ousmane , Sall Amadou A. , Neyts Johan , Nguyen Laurent , Kaptein Suzanne J. F. , Lambrechts Louis 
Published: September 2020

SummaryThe global emergence of Zika virus (ZIKV) in the last decade revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects such as microcephaly. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compared the transmissibility and pathogenicity of seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We found that recent African ZIKV strains largely outperformed their Asian counterparts in mosquito transmission kinetics experiments, which translated into a markedly higher epidemic potential in outbreak computer simulations. In addition, African ZIKV strains were significantly more lethal than Asian ZIKV strains in immunocompromised adult mice. Finally, prenatal infection of immunocompetent mouse embryos with an African ZIKV strain resulted in embryonic death whereas it caused microcephaly with Asian ZIKV strains. Together, our results demonstrate the high epidemic potential and pathogenicity of recent ZIKV strains from Africa. Importantly, they also imply that the African ZIKV lineage could more easily go unnoticed by public health surveillance systems than the Asian ZIKV lineage due to its propensity to cause fetal loss rather than birth defects.
The importance of charge in perturbing the aromatic glue stabilizing the protein-protein interface of homodimeric tRNA-guanine transglycosylase
Authors: Nguyen Andreas , Nguyen Dzung , Nguyen Tran Xuan Phong , Sebastiani Maurice , Dörr Stefanie , Hernandez-Alba Oscar , Debaene François , Cianférani Sarah , Heine Andreas , Klebe Gerhard , Reuter Klaus 
Published: September 2020

AbstractBacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine and tyrosine. Inactivation of thetgtgene leads to decreased pathogenicity ofShigellabacteria. Therefore, Tgt constitutes a putative target for Shigellosis drug therapy. Since only active as homodimer, interference with dimer-interface formation may, in addition to active-site inhibition, provide further means to disable this protein. A cluster of four aromatic residues seems important to stabilize the homodimer. We mutated residues of this aromatic cluster and analyzed each exchange with respect to dimer and thermal stability or enzyme activity applying native mass spectrometry, thermal shift assay, enzyme kinetics, and X-ray crystallography. Our structural studies indicate strong influence of pH on homodimer stability. Obviously, protonation of a histidine within the aromatic cluster promotes the collapse of an essential structural motif within the dimer interface at slightly acidic pH.TOC GraphicFor table of contents use only.
Rabaptin5 targets autophagy to damaged endosomes and SCVs by interaction with FIP200 and ATG16L1
Authors: Millarte Valentina , Schlienger Simon , Kälin Simone , Spiess Martin 
Published: September 2020

SummarySelective autophagy of damaged organelles is an important process for cellular homeostasis. The mechanisms how autophagy selects specific targets is often poorly understood. Rabaptin5 was previously known as a major regulator of early endosome identity and maturation. Here we identified two novel Rabaptin5 interactors: FIP200, a subunit of the ULK1 autophagy initiator complex, and ATG16L1, a central component of the E3-like enzyme in LC3 lipidation. Indeed, autophagy of early endosomes damaged by chloroquine or monensin treatment was found to require Rabaptin5 and particularly a specific short sequence motif binding to the WD domain of ATG16L1. Rabaptin5 and this interaction with ATG16L1 is further required for much of autophagic elimination ofSalmonella entericain phagosomes with early endosomal characteristics early after infection. Our results demonstrate a novel function of Rabaptin5 in quality control of early endosomes in the selective recruitment of autophagy to damaged early endosomes and phagosomes.
Gradual development of non-adjacent dependency learning during early childhood
Authors: Paul Mariella , Männel Claudia , van der Kant Anne , Mueller Jutta L. , Höhle Barbara , Wartenburger Isabell , Friederici Angela D. 
Published: September 2020

AbstractIn order to become proficient native speakers, children have to learn the morpho-syntactic relations between distant elements in a sentence, so-called non-adjacent dependencies (NADs). Previous research suggests that NAD learning in children comprises different developmental stages, where until 2 years of age children are able to learn NADs associatively under passive listening conditions, while starting around the age of 3 to 4 years children fail to learn NADs during passive listening. To test whether the transition between these developmental stages occurs gradually, we tested children’s NAD learning in a foreign language using event-related potentials (ERPs). We found ERP evidence of NAD learning across the ages of 1, 2 and 3 years. The amplitude of the ERP effect indexing NAD learning, however, decreased with age. These findings might indicate a gradual transition in children’s ability to learn NADs associatively. Cognitively, this transition might be driven by children’s increasing knowledge of their native language, hindering NAD learning in novel contexts. Neuroanatomically, maturation of the prefrontal cortex might play a crucial role, promoting top-down learning, affecting bottom-up, associative learning. In sum, our study suggests that NAD learning under passive listening conditions undergoes a gradual transition between different developmental stages during early childhood.Research HighlightsTransition between developmental stages of non-adjacent dependency (NAD) learningChildren between 1 and 3 years of age showed learning of NADs in a foreign languageBrain responses revealed associative NAD learning, triggered by passive listeningGradual decrease of the strength of associative non-adjacent dependency learning