bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surveillance of densoviruses and mesomycetozoans inhabiting grossly normal tissues of three New Zealand asteroid species
Authors: Hewson Ian , Sewell Mary A. 
Published: October 2020

ABSTRACTAsteroid wasting events and mass mortality have occurred for over a century. We currently lack a fundamental understanding of the microbial ecology of asteroid disease, with disease investigations hindered by sparse information about the microorganisms associated with grossly normal specimens. We surveilled viruses and protists associated with grossly normal specimens of three asteroid species (Patiriella regularis, Stichaster australis, Coscinasterias muricata) on the North Island, New Zealand, using metagenomes prepared from virus and ribosome-sized material. We discovered several densovirus-like genome fragments in our RNA and DNA metagenomic libraries. Subsequent survey of their prevalence within populations by quantitative PCR (qPCR) demonstrated their occurrence in only a few (13 %) specimens (n = 36). Survey of large and small subunit rRNAs in metagenomes revealed the presence of a mesomycete (most closely matchingIchthyosporeasp.). Survey of large subunit prevalence and load by qPCR revealed that it is widely detectable (80%) and present predominately in body wall tissues across all 3 species of asteroid. Our results raise interesting questions about the roles of these microbiome constituents in host ecology and pathogenesis under changing ocean conditions.
A colony-level optimization model provides a potential mechanism for the evolution of novel castes in eusocial ant colonies
Authors: Nag Suryadeepto , Bhat Ananda Shikhara 
Published: October 2020

AbstractAnt species often have multiple morphologically distinct ‘castes’ within a single colony. Given that most of these castes are involved in non-reproductive tasks, and since such individuals thus never reproduce, the question of how ant castes can evolve is a non-trivial one. Over the years, several models have been proposed in order to explain the evolution of castes in ant colonies. Here, we attempt to answer this question using an economics-based approach, developing an optimization model that implements adaptation and selection at the colony level. We argue that due to the nature of ant colonies, selection is shifted to the group level, and, due to this, individual ants are sheltered from negative selection. We show that our framework can explain the evolution of novel castes in ant colonies, and discuss the novelty of our model with regard to previous models that have been proposed. We also show that our model is consistent with several empirical observations of ant colonies.
Phylogeny, classification, and character evolution of tribe Citharexyleae (Verbenaceae)
Authors: Frost Laura A. , O’Leary Nataly , Lagomarsino Laura P. , Tank David C. , Olmstead Richard G. 
Published: October 2020

AbstractPremise of the studyTribe Citharexyleae comprises three genera:Baillonia, Citharexylum, andRehdera. While there is good support for these genera as a clade, relationships between genera remain unresolved due to low sampling of the largest genus,Citharexylum. A molecular phylogenetic approach was taken to resolve intergeneric relationships in Citharexyleae and infrageneric relationships inCitharexylum.MethodsSeven chloroplast regions, two nuclear ribosomal spacers, and six low-copy nuclear loci were analyzed for 64 species of Citharexyleae. Phylogenetic analyses were conducted using maximum likelihood, Bayesian inference, and Bayesian multi-species coalescent approaches. Habit, presence/absence of thorns, inflorescence architecture, flower color, fruit color, and geography were examined to identify diagnostic characters for clades withinCitharexylum.Key resultsIntergeneric relationships resolvedRehderaas sister toCitharexylumandBaillonianested withinCitharexylum. Two species,C. oleinumandC. tetramerum, fell outside of Citharexyleae close to tribe Duranteae. There is strong support for seven clades withinCitharexylum, each characterized by a unique combination of geography, fruit color/maturation, and inflorescence architecture.ConclusionsBailloniais included inCitharexylum; Rehderais retained as a distinct genus. A subgeneric classification forCitharexylumis proposed.
Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwig
Authors: Van Meyel Sophie , Devers Séverine , Dupont Simon , Dedeine Franck , Meunier Joël 
Published: October 2020

AbstractThe microbes residing within the gut of an animal host often increase their own fitness by modifying their host’s physiological, reproductive, and behavioural functions. Whereas recent studies suggest that they may also shape host sociality and therefore have critical effects on animal social evolution, the impact of the gut microbiota on maternal care remains unexplored. This is surprising, as this behaviour is widespread among animals, often determines the fitness of both juveniles and parents, and is essential in the evolution of complex animal societies. Here, we tested whether life-long alterations of the gut microbiota with rifampicin - a broad-spectrum antibiotic - impair pre- and post-hatching maternal care in the European earwig. Our results first confirm that rifampicin altered the mothers’ gut microbial communities and indicate that the composition of the gut microbiota differs before and after egg care. Contrary to our predictions, however, the rifampicin-induced alterations of the gut microbiota did not modify pre- or post-hatching care. Independent of maternal care, rifampicin increased the females’ feces production and resulted in lighter eggs and juveniles. By contrast, rifampicin altered none of the other 21 physiological, reproductive and longevity traits measured over the 300 days of a female’s lifetime. Overall, these findings reveal that altering the gut microbiota with a large spectrum antibiotic such as rifampicin does not necessarily affect host sociality. They also emphasize that not all animals have evolved a co-dependence with their microbiota and call for caution when generalizing the central role of gut microbes in host biology.
Sleuthing biochemical evidence to elucidate unassigned electron density in a CBL/SLAP2 crystal complex
Authors: Wybenga-Groot Leanne E. , McGlade C. Jane 
Published: October 2020

AbstractThe Src-like adaptor proteins (SLAP/SLAP2) bind to CBL E3 ubiquitin ligase to downregulate antigen, cytokine, and tyrosine kinase receptor signaling. In contrast to phospho-tyrosine dependent binding of CBL substrates through its tyrosine kinase binding domain (TKBD), CBL TKBD associates with the C-terminal tail of SLAP2 in a phospho-independent manner. To understand the distinct nature of this interaction, a purification protocol for SLAP2 in complex with CBL TKBD was established and the complex crystallized. However, determination of the complex crystal structure was hindered by apparent SLAP2 degradation during the crystallization process, such that only CBL TKBD residues could be modeled initially. Close examination of the CBL TKBD structure revealed a unique dimer interface that included two short segments of electron density of unknown origin. To elucidate which residues of SLAP2 to model in this unassigned density, a co-expression system was generated to test SLAP2 deletion mutants and define the minimal SLAP2 binding region. As well, SLAP2 degradation products were analyzed by mass spectrometry. Model building and map generation features of the Phenix software package were employed, leading to successful modeling of the C-terminal tail of SLAP2 in the unassigned electron density segments.
Insights on Poster Preparation Practices in Life Sciences
Authors: Jambor Helena Klara 
Published: October 2020

AbstractPosters are intended to spark scientific dialogue and omnipresent at biological conferences. Guides and how-to articles help life scientists in preparing informative visualizations in poster format. However, those posters shown at conferences are at present often overloaded with data and text and are poorly designed, which in sum hinder, rather than spark communication. Here, we surveyed life scientists themselves to understand why posters are such a struggle and to shed light on poster preparation from their subjective perspectives. We find that biologist spend on average two entire days preparing one poster, with half of the time devoted to visual design aspects. Most respond that they receive no design or software training and also receive little to no feedback when preparing their visualizations. In conclusion, our data suggests that some training, beyond providing literature, of life scientists in visualization principles and tools would likely improve conference poster quality. In addition, this would also improve other common visuals such as figures and slides, and thus overall benefit the science communication of researchers.
Preferential recognition and antagonism of SARS-CoV-2 spike glycoprotein binding to 3-O-sulfated heparan sulfate
Authors: Tiwari Vaibhav , Tandon Ritesh , Sankaranarayanan Nehru Viji , Beer Jacob C. , Kohlmeir Ellen K. , Swanson-Mungerson Michelle , Desai Umesh R. 
Published: October 2020

AbstractThe COVID-19 pandemic caused by SARS-CoV-2 is in immediate need of an effective antidote. Although the Spike glycoprotein (SgP) of SARS-CoV-2 has been shown to bind to heparins, the structural features of this interaction, the role of a plausible heparan sulfate proteoglycan (HSPG) receptor, and the antagonism of this pathway through small molecules remain unaddressed. Using an in vitro cellular assay, we demonstrate HSPGs modified by the 3-O-sulfotransferase isoform-3, but not isoform-5, preferentially increased SgP-mediated cell-to-cell fusion in comparison to control, unmodified, wild-type HSPGs. Computational studies support preferential recognition of the receptor-binding domain of SgP by 3-O-sulfated HS sequences. Competition with either fondaparinux, a 3-O-sulfated HS-binding oligopeptide, or a synthetic, non-sugar small molecule, blocked SgP-mediated cell-to-cell fusion. Finally, the synthetic, sulfated molecule inhibited fusion of GFP-tagged pseudo SARS-CoV-2 with human 293T cells with sub-micromolar potency. Overall, overexpression of 3-O-sulfated HSPGs contribute to fusion of SARS-CoV-2, which could be effectively antagonized by a synthetic, small molecule.
A general decoding strategy explains the relationship between behavior and correlated variability
Authors: Ni Amy M. , Huang Chengcheng , Doiron Brent , Cohen Marlene R. 
Published: October 2020

ABSTRACTImprovements in perception are frequently accompanied by decreases in correlated variability in sensory cortex. This relationship is puzzling because overall changes in correlated variability should minimally affect optimal information coding. We hypothesize that this relationship arises because instead of using optimal strategies for decoding the specific stimuli at hand, observers prioritizegenerality: a single set of neuronal weights to decode any stimuli. We tested this using a combination of multineuron recordings in the visual cortex of behaving rhesus monkeys and a cortical circuit model. We found that general decoders optimized for broad rather than narrow sets of visual stimuli better matched the animals’ decoding strategy, and that their performance was more related to the magnitude of correlated variability. In conclusion, the inverse relationship between perceptual performance and correlated variability can be explained by observers using a general decoding strategy, capable of decoding neuronal responses to the variety of stimuli encountered in natural vision.IMPACT STATEMENTThe frequently observed relationship between perceptual performance and correlated variability in sensory cortex can be explained by observers using a decoding strategy that prioritizes generality for many stimuli over precision.
Developing Human Pluripotent Stem Cell-Based Cerebral Organoids with a Controllable Microglia Ratio for Modeling Brain Development and Pathology
Authors: Xu Ranjie , Boreland Andrew J. , Li Xiaoxi , Erickson Caroline , Jin Mengmeng , Atkins Colm , Pang Zhiping , Daniels Brian P. , Jiang Peng 
Published: October 2020

AbstractMicroglia, as brain-resident macrophages, play critical roles in brain development, homeostasis, and disease. Microglia in animal models cannot accurately model the properties of human microglia due to notable transcriptomic and functional differences between human and other animal microglia. Efficient generation of microglia from human pluripotent stem cells (hPSCs) provides unprecedented opportunities to study the function and behavior of human microglia. Particularly, incorporating hPSCs-derived microglia into brain organoids facilitates their development in a 3-dimensional context, mimicking the brain environment. However, an optimized method that integrates an appropriate amount of microglia into brain organoids at a proper time point, resembling in vivo brain development, is still lacking. Here, we report the development of a new brain region-specific, microglia-containing organoid model by co-culturing hPSCs-derived primitive neural progenitor cells (pNPCs) and primitive macrophage progenitors (PMPs). In these organoids, hPSCs-derived pNPCs and PMPs interact with each other and develop into functional neurons, astroglia, and microglia, respectively. Importantly, the numbers of human microglia in the organoids can be controlled, resulting in a cell type ratio similar to that seen in the human brain. Using super-resolution microscopy, we demonstrate that these human microglia are able to phagocytize neural progenitor cells (NPCs) and apoptotic cells, as well as to prune synapses at different developmental stages of the organoids. Furthermore, these human microglia respond to Zika virus infection of the organoids, as indicated by amoeboid-like morphology, increased expression of gene transcripts encoding inflammatory cytokines, and excessive pruning of synaptic materials. Together, our findings establish a new microglia-containing brain organoid model that will serve to study human microglial function in a variety of neurological disorders.
The human brain vasculature shows a distinct expression pattern of SARS-CoV-2 entry factors
Authors: Ghobrial Moheb , Charish Jason , Takada Shigeki , Valiante Taufik , Monnier Philippe P. , Radovanovic Ivan , Bader Gary D. , Wälchli Thomas 
Published: October 2020

ABSTRACTA large number of hospitalized COVID-19 patients show neurological symptoms such as ischemic- and hemorrhagic stroke as well as encephalitis, and SARS-CoV-2 can directly infect endothelial cells leading to endotheliitis across multiple vascular beds. These findings suggest an involvement of the brain- and peripheral vasculature in COVID-19, but the underlying molecular mechanisms remain obscure. To understand the potential mechanisms underlying SARS-CoV-2 tropism for brain vasculature, we constructed a molecular atlas of the expression patterns of SARS-CoV-2 viral entry-associated genes (receptors and proteases) and SARS-CoV-2 interaction partners in human (and mouse) adult and fetal brain as well as in multiple non-CNS tissues in single-cell RNA-sequencing data across various datasets. We observed a distinct expression pattern of the cathepsins B (CTSB) and -L (CTSL) - which are able to substitute for the ACE2 co-receptor TMPRSS2 - in the human vasculature with CTSB being mainly expressed in the brain vasculature and CTSL predominantly in the peripheral vasculature, and these observations were confirmed at the protein level in the Human Protein Atlas and using immunofluorescence stainings. This expression pattern of SARS-CoV-2 viral-entry associated proteases and SARS-CoV-2 interaction partners was also present in endothelial cells and microglia in the fetal brain, suggesting a developmentally established SARS-CoV-2 entry machinery in the human vasculature. At both the adult and fetal stages, we detected a distinct pattern of SARS-CoV-2 entry associated genes’ transcripts in brain vascular endothelial cells and microglia, providing a potential explanation for an inflammatory response in the brain endothelium upon SARS-CoV-2 infection. Moreover, CTSB was co-expressed in adult and fetal brain endothelial cells with genes and pathways involved in innate immunity and inflammation, angiogenesis, blood-brain-barrier permeability, vascular metabolism, and coagulation, providing a potential explanation for the role of brain endothelial cells in clinically observed (neuro)vascular symptoms in COVID-19 patients. Our study serves as a publicly available single-cell atlas of SARS-CoV-2 related entry factors and interaction partners in human and mouse brain endothelial- and perivascular cells, which can be employed for future studies in clinical samples of COVID-19 patients.
Universal enzyme-linked immunosorbent assays (ELISA) and utility in the detection of antibodies against Salmonella spp. in several animal species
Authors: Justiz-Vaillant Angel A , Ferrer-Cosme Belkis , Curtello Suzette 
Published: October 2020

AbstractThe aim of this study was to confirm the feasibility of using hybrid immunoglobulin-binding reagents in ELISAs for IgG/IgY detection and detection of specific antibodies against an infectious microorganism (Salmonella spp.) in various animal species using a universal diagnostic ELISA. Hybrid immunoglobulin-binding bacterial proteins (IBP), including recombinant protein LA, recombinant protein LG, and recombinant protein AG, have been produced to improve their binding affinity to a much larger number of immunoglobulins. Thus, this hybrid bacterial protein represents a powerful tool for the binding, detection, and purification of immunoglobulins and their fragments. However, SpLA-LG-peroxidase and SpLAG-anti-IgYperoxidase were produced using the periodate method. These compounds have been shown to be effective as reagents. Their binding affinity to immunoglobulins surpasses that of previously reported hybrid IgG-binding proteins, including the most known SpAG, SpLA, and SpLG. The IgY fraction was isolated from the egg yolks of various birds, including chicken, bantam hen, guinea hen, quail, goose, duck, wild and domestic pigeons, parakeets, cattle egrets, pheasants, and ostrich. The IgY fraction was isolated using the chloroform-polyethylene glycol (PEG) method. An ELISA for anti-Salmonella spp. antibodies was employed with some modifications to determine the presence of antibodies in humans, laying hens, geese, quails, and pigeons. Salmonella is a motile, flagellated, rod-shaped zoonotic pathogen that can survive in the presence or absence of oxygen. They belong to the family Enterobacteriaceae and are implicated in typhoid fever and food-borne illnesses. This pathogen is associated with several diseases, which may become fatal and negatively impact the health of individuals and various economies globally. The poultry industry is most vulnerable to the influence of this pernicious microbe. The authors concluded that universal enzyme-linked immunosorbent assays were effective and reproducible in detecting immunoglobulins from both avian and mammalian species, but ELISA using the SpLAG-anti-IgY-HRP conjugate only reacted with the whole panel of animal antibodies. This conjugate was further used to standardize a universal ELISA for the determination of anti-Salmonella antibodies, in which human and avian species were serologically assessed.
Acquisition of a type 3 secretion signal in an housekeeping enzyme shaped glycogen metabolism inChlamydia
Authors: Triboulet Sébastien , N’Gadjaga Maimouna D. , Niragire Béatrice , Köstlbacher Stephan , Horn Matthias , Subtil Agathe 
Published: October 2020

ABSTRACTThe obligate intracellular bacteriaChlamydia trachomatisstore glycogen in the lumen of the vacuoles in which they grow. Glycogen catabolism generates glucose-1-phosphate (Glc1P), while the bacteria are capable of taking up only glucose-6-phosphate (Glc6P). We tested whether the conversion of Glc1P into Glc6P could be catalyzed by a phosphoglucomutase (PGM) of host or bacterial origin. We found no evidence for the presence of the host enzyme in the vacuole. InC. trachomatis, two proteins are potential PGMs. By reconstituting the reaction, and by complementing PGM deficient fibroblasts, we demonstrated that only CT295 displayed robust PGM activity. Furthermore, we showed that glycogen accumulation by a subset ofChlamydiaspecies correlated with the presence of a type three secretion (T3S) signal in their PGM. In conclusion, we established that the conversion of Glc1P into Glc6P was accomplished by a bacterial PGM, through the acquisition of a T3S signal in a “housekeeping” gene.
Schemas provide a scaffold for neocortical integration at the cost of memory specificity over time
Authors: Audrain Sam , McAndrews Mary Pat 
Published: October 2020

SUMMARYMemory transformation is increasingly acknowledged in theoretical accounts of systems consolidation, yet how memory quality and neural representation change over time and how schemas influence this process remains unclear. In this fMRI study, participants encoded and retrieved schema-congruent and incongruent object-scene pairs using a paradigm that probed coarse and detailed memories over 10-minutes and 72-hours. When a congruent schema was available, details were lost over time as representations were integrated in the medial prefrontal cortex (mPFC), and enhanced post-encoding coupling between the anterior hippocampus and mPFC was associated with coarser memories. Over time, pattern similarity in the hippocampus changed such that the posterior hippocampus represented specific details and the anterior hippocampus represented the general context of specific memories, irrespective of congruency. Our findings suggest schemas are used as a scaffold for accelerated consolidation of congruent information, and illustrate change in hippocampal organization of detailed contextual memory over time.