bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial-temporal dynamics of a microbial cooperative behavior robust to cheating
Authors: Monaco Hilary , Sereno Tiago , Liu Kevin , Reagor Caleb , Deforet Maxime , Xavier Joao B.
Published: January 2020

Individuals living in dense populations control their behaviors by sensing, integrating and responding to many cues. How can these processes enable the evolution and stability of cooperative behaviors that could easily be exploited by cheaters? Here we shed light on how bacteria regulate cooperation by studying swarming inPseudomonas aeruginosa, a behavior requiring cooperative secretions of rhamnolipid surfactants to facilitate collective movement over surfaces. By combining fluorescent imaging and computational analyses we show, counterintuitively, that rhamnolipid expression peaks at swarming edges. We then show that the integration of competing diffusive cues—quorum sensing signals and growth-limiting nutrients—enablesP. aeruginosato communicate across centimeters and adopt expression patterns unseen in well-mixed liquid culture. Integration of multiple cues enables robustness against cheating even when we experimentally perturb the quorum sensing system. Taken together, these results illuminate how the integration of cues in spatially structured communities can stabilize cooperation.
A Spiking Neural Network Model for Category Learning
Authors: Iyer Laxmi R. , Basu Arindam
Published: January 2020

The creation of useful categories from data is an important cognitive ability, and from the extensive research on categorization, it is now known that the brain has distinct systems for category learning. In this paper, we present the first spiking neural network (SNN) model of human category learning. Here categories are combinations of features - such categories are observed in the prefrontal cortex (PFC). The system follows an architecture commonly used to model the cortex - features are arranged in a topological 2D grid with short range excitatory connectivity and long range inhibitory connectivity - however, here, this architecture is used differently from other models to model higher level cognition. Earlier we presented an artificial neural network (ANN) model of category learning; however, here, a simpler model was adequate, as desired functionality emerges from the SNN dynamics. We identified the objectives that had to be fulfilled for the model to achieve the desired functionality, and performed a design space exploration (DSE) to identify the parameter range in which each of the objectives was fulfilled, and the parameter range for which the system exhibits good performance. Finally, we compared triphasic STDP (a variant of spike time dependant plasticity (STDP)) with standard STDP and observed that triphasic STDP exhibited quicker convergence.
USP15 deubiquitinase safeguards hematopoiesis and genome integrity in hematopoietic stem cells and leukemia cells
Authors: van den Berk Paul , Lancini Cesare , Company Carlos , Serresi Michela , Hulsman Danielle , Pritchard Colin , Song Ji-Ying , Schmitt Matthias Jürgen , Tanger Ellen , Huijbers Ivo J. , Jacobs Heinz , van Lohuizen Maarten , Gargiulo Gaetano , Citterio Elisabetta
Published: January 2020

Altering ubiquitination by disruption of individual deubiquitinating enzymes (DUBs) has proven to affect hematopoietic stem cell (HSC) maintenance. However, comprehensive knowledge of DUB function during hematopoiesisin vivois lacking. To accomplish this goal, we systematically inactivated DUBs in mouse hematopoietic progenitors usingin vivosmall hairpin RNAs (shRNAs) screens. We found that multiple DUBs may be individually required for hematopoiesis and that the ubiquitin-specific protease 15 (USP15) is particularly important for the maintenance of murine hematopoietic stem and progenitor cellsin vitroandin vivo.Consistently,Usp15knockout mice exhibited a reduced HSC pool. The defect was intrinsic to HSCs, as demonstrated by competitive repopulation assays. Importantly, USP15 is highly expressed in normal human hematopoietic cells and leukemias, and USP15 depletion in murine early progenitors and myeloid leukemia cells impairedin vitroexpansion and increased genotoxic stress. Our study underscores the importance of DUBs in preserving normal hematopoiesis and uncovers USP15 as a critical DUB in safeguarding genome integrity in HSC and in leukemia cells.
Distinct neural variables underlie subjective reports of attention
Authors: Whitmarsh Stephen , Gitton Christophe , Jousmäki Veikko , Sackur Jérôme , Tallon-Baudry Catherine
Published: January 2020

Attention is subjectively experienced as a unified cognitive effort. This unitary experience of attention contrasts with the diversity of neural and peripheral correlates of attention. While the effects of attention on stimulus-evoked responses, alpha oscillations and pupil diameter, are well-known the relationship between these indices and thesubjectiveexperience of attention, has not yet been assessed. Participants performed a sustained (10 s to 30 s) attention task in which rare (10%) targets were detected within continuous tactile stimulation (16 Hz). Trials were followed by attention ratings on an 8-point Likert scale. Steady-state evoked fields (SSEFs) in response to tactile stimulation, as measured by magnetoencephalography, provided an objective measure of sensory processing. Beamformer source analysis of somatosensory alpha power was used as a measure of cortical excitability, while pupillometry provided a peripheral index of arousal. Attention ratings correlated negatively with contralateral somatosensory alpha power, and positively with pupil diameter. The effect of pupil diameter on attention ratings extended into the following trial, reflecting a sustained aspect of attention related to vigilance. The effect of alpha power did not carry over to the next trial, and furthermore mediated the effect of pupil diameter on attention ratings. Variation in SSEF power reflected stimulus processing under the influence of alpha oscillations, but were not readily expressed through subjective ratings of attention. Together, our results show that both alpha power and pupil diameter are reflected in the subjective experience of attention, albeit on different time spans, while continuous stimulus processing might not be metacognitively accessible.

1

Significance Statement

Attention is subjectively experienced as a unified cognitive effort, in contrast with a diversity of neural and peripheral measures shown to correlate with attention. We present the first comprehensive study on the complex inter-relationship between the most common bio-physiological indices of attention, and their association with the subjective experience of attention. We show that the subjective experience of attention correlates negatively with cortical alpha oscillations, and positively with pupil diameter. The latter reflected a sustained aspect of attention, spanning several tens of seconds, related to vigilance. Alpha power, representing cortical control, fluctuated faster and mediated the effect of pupil diameter on attention. Tactile steady-state power reflected stimulus processing, also under the influence of alpha oscillations, but did not contribute much to subjective ratings of attention.
Interleukin-35 pretreatment attenuates lipopolysaccharide-induced heart injury by inhibition of inflammation, apoptosis and fibrosis
Authors: Fu Yang , Hu Huan , Li Meng , Xia Huasong , Liu Yue , Sun Xiaopei , Hu Yang , Song Fulin , Cheng Xiaoshu , Li Ping , Wu Yanqing
Published: January 2020

Previous studies have demonstrated that targeting inflammation is a promising strategy for treating lipopolysaccharide (LPS)-induced sepsis and related heart injury. Interleukin-35 (IL-35), which consists of two subunits, Epstein–Barr virus-induced gene 3 (EBI3) and p35, is an immunosuppressive cytokine of the IL-12 family and exhibits strong anti-inflammatory activity. However, the role of IL-35 in LPS-induced heart injury remains obscure. In this study, we explored the role of IL-35 in heart injury induced by LPS and its potential mechanisms. Mice were treated with a plasmid encoding IL-35 (pIL-35) and then injected intraperitoneally (ip) with LPS (10 mg/kg). Cardiac function was assessed by echocardiography 12 h later. LPS apparently decreased the expression of EBI3 and p35 and caused cardiac dysfunction and pathological changes, which were significantly improved by pIL-35 pretreatment. Moreover, pIL-35 pretreatment significantly decreased the levels of cardiac proinflammatory cytokines including TNF-α, IL-6, and IL-1β, and the NLRP3 inflammasome. Furthermore, increased BCL-2 levels and decreased BAX levels inhibited apoptosis, and LPS-induced upregulation of the expression of pro-fibrotic genes (MMP2 and MMP9) was inhibited. Further investigation indicated that pIL-35 pretreatment suppressed the activation of the cardiac NF-κBp65 and TGF-β1/Smad2/3 signaling pathways in LPS-treated mice. Similar cardioprotective effects of IL-35 pretreatment were observed in mouse myocardial fibroblasts challenged with LPS in vitro. In summary, IL-35 pretreatment can attenuate cardiac inflammation, apoptosis, and fibrosis induced by LPS, implicating IL-35 as a promising therapeutic target in sepsis-related cardiac injury.
Natural selection maintains species despite widespread hybridization in the desert shrubEncelia
Authors: DiVittorio Christopher D , Singhal Sonal , Roddy Adam B , Zapata Felipe , Ackerly David D , Baldwin Bruce G , Brodersen Craig R , Burquez Alberto , Fine Paul VA , Padilla Flores Mayra , Solis Elizabeth , Morales-Villavicencio Jaime , Morales-Arce David , Kyhos Don W
Published: January 2020

Natural selection is an important driver of genetic and phenotypic differentiation between species. A powerful way to test the role of natural selection in the formation and maintenance of species is to study species complexes in which potential gene flow is high but realized gene flow is low. For a recent radiation of New World desert shrubs (Encelia: Asteraceae), we use fine-scale geographic sampling and population genomics to determine patterns of gene flow across two hybrid zones formed between two independent pairs of species with parapatric distributions. After finding evidence for extremely strong selection at both hybrid zones, we use a combination of field experiments, high-resolution imaging, and physiological measurements to determine the ecological basis for selection at one of the hybrid zones. Our results identify multiple ecological mechanisms of selection (drought, salinity, herbivory, and burial) that together are sufficient to maintain species boundaries despite high rates of hybridization. Given that multiple pairs of species hybridize at ecologically divergent parapatric boundaries in the adaptive radiation ofEncelia, such mechanisms may maintain species boundaries throughout this group.

SIGNIFICANCE STATEMENT

In Baja California, the deserts meet the coastal dunes in a narrow transition visible even from satellite images. We study two species pairs of desert shrubs (Encelia) that occur across this transition. Although these species can interbreed, they remain distinct. Using a combination of genetics, field experiments, 3D-imaging, and physiological measurements, we show that natural selection counteracts the homogenizing effects of gene exchange. The different habitats of these species create multiple mechanisms of selection - drought, salinity, herbivory, and burial, which together maintain these species in their native habitats and their hybrids in intermediate habitats. This study illustrates how environmental factors influence traits and fitness and how this in turn maintain species, highlighting the importance of natural selection in speciation.
A high-density narrow-field inhibitory retinal interneuron with direct coupling to Müller glia
Authors: Grimes William N , Aytürk Didem Göz , Hoon Mrinalini , Yoshimatsu Takeshi , Gamlin Clare , Carrera Daniel , Ahlquist Richard M , Sabnis Adit , Diamond Jeffrey S , Wong Rachel O. , Cepko Connie , Rieke Fred
Published: January 2020

Amacrine cells are interneurons comprising the most diverse cell type in the mammalian retina. They help encode visual features such as edges or directed motion by mediating excitatory and inhibitory interactions between input (i.e. bipolar) and output (i.e. ganglion) neurons in the inner plexiform layer (IPL). Like other brain regions, the retina also contains glial cells that contribute to neurotransmitter uptake, neurovascular control and metabolic regulation. Here, we report that a previously poorly characterized, but relatively abundant, inhibitory amacrine cell type in the mouse retina is coupled directly to Müller glia. Electron microscopic reconstructions of this amacrine type revealed extensive associations with Müller glia, whose processes often completely ensheathe the neurites of this amacrine cell type. Microinjections of small tracer molecules into the somas of these amacrine cells led to selective labelling of nearby Müller glia, leading us to suggest the name “Müller glia-coupled amacrine cell” or MAC. Our electrophysiological data also indicate that MACs release glycine at conventional chemical synapses with amacrine, bipolar and retinal ganglion cells (RGCs), and viral transsynaptic tracing showed connections to several known RGC types. Visually-evoked responses revealed a strong preference for light increments; these “ON” responses were primarily mediated by excitatory chemical synaptic input and direct electrical coupling to other cells. This initial characterization of the MAC provides the first evidence for neuron-glia coupling in the mammalian retina and identifies the MAC as a potential link between inhibitory processing and glial function.

Significance Statement

Gap junctions between pairs of neurons or glial cells are commonly found throughout the nervous system, and play a myriad of roles including electrical coupling and metabolic exchange. In contrast, gap junctions between neurons and glia cells are rare and poorly understood. Here we report the first evidence for neuron-glia coupling in the mammalian retina, specifically between an abundant (but previously unstudied) inhibitory interneuron and Müller glia.
Molecular evolution of luciferase diversified bioluminescent signals in sea fireflies
Authors: Hensley Nicholai M. , Ellis Emily A. , Leung Nicole Y. , Coupart John , Mikhailovsky Alexander , Taketa Daryl A. , Tessler Michael , Gruber David F. , De Tomaso Anthony W. , Mitani Yasuo , Rivers Trevor J. , Gerrish Gretchen A. , Torres Elizabeth , Oakley Todd H.
Published: January 2020

Understanding the genetic causes of evolutionary diversification is challenging because differences across species are complex, often involving many genes. However, cases where single or few genetic loci affect a feature that varies dramatically across a radiation of species would provide tractable opportunities to understand the genetics of diversification. Here, we show the diversification of bioluminescent signals in cypridinid ostracods (“sea fireflies”) to be strongly influenced by a single gene, cypridinid-luciferase. We find different evolutionary processes, including selection, drift, and constraint, each acted on c-luciferase at different times during evolutionary history and impacted different phenotypes, diversifying behavioral signals across species. In particular, some amino acid sites in c-luciferase evolved under episodic diversifying selection, and are associated significantly with phenotypic changes in both enzyme kinetics and color, which impact signals directly. We also find that multiple other amino acid positions in c-luciferase evolved neutrally or under purifying selection and may have impacted the variation of color of bioluminescent signals across genera. This work provides a rare glimpse into the genetic basis of diversification across many species, showing how multiple evolutionary processes may act at different times during a radiation of species to diversify phenotypes. These results indicate not only selection but also drift and constraint may be important evolutionary drivers of species diversification.

Significance statement

A hallmark of life is its astounding diversity. While we are beginning to understand the drivers of biodiversity, uncovering the genetic basis remains challenging. As such, how different molecular evolutionary processes act to diversify phenotypes is a major question in biology. Here we show a single gene to be important in a riotous diversity of fantastical behaviors - the bioluminescent signals of sea fireflies - allowing us to demonstrate multiple evolutionary forces including selection, drift, and constraint contributed to diversification. Our work highlights that not only selection but also neutral processes and constraint have each worked at different times to shape phenotypic diversity.
VINYL: Variant prIoritizatioN bY survivaL analysis
Authors: Chiara Matteo , Mandreoli Pietro , Tangaro Marco Antonio , D’Erchia Anna Maria , Sorrentino Sandro , Forleo Cinzia , Horner David S. , Zambelli Federico , Pesole Graziano
Published: January 2020

Motivation

Clinical applications of genome re-sequencing technologies typically generate large amounts of data that need to be carefully annotated and interpreted to identify genetic variants associated with pathological conditions. In this context, accurate and reproducible methods for the functional annotation and prioritization of genetic variants are of fundamental importance, especially when large volumes of data - like those produced by modern sequencing technologies - are involved.

Results

In this paper, we present VINYL, a highly accurate and fully automated system for the functional annotation and prioritization of genetic variants in large scale clinical studies. Extensive analyses of both real and simulated datasets suggest that VINYL show higher accuracy and sensitivity when compared to equivalent state of the art methods, allowing the rapid and systematic identification of potentially pathogenic variants in different experimental settings.
LRRK2 mediates tubulation and vesicle sorting from membrane damaged lysosomes
Authors: Bonet-Ponce Luis , Beilina Alexandra , Williamson Chad D. , Lindberg Eric , Kluss Jillian H. , Saez-Atienzar Sara , Landeck Natalie , Kumaran Ravindran , Mamais Adamantios , Bleck Christopher K. E. , Li Yan , Cookson Mark R.
Published: January 2020

Mutations in the leucine rich repeat kinase 2 (LRRK2) gene are a cause of familial and sporadic Parkinson’s disease (PD). Nonetheless, the biological functions of LRRK2 remain incompletely understood. Here, we observed that LRRK2 is recruited to lysosomes that have a ruptured membrane. Using unbiased proteomics, we observed that LRRK2 is able to recruit the motor adaptor protein JIP4 to permeabilized lysosomes in a kinase-dependent manner through the phosphorylation of RAB35 and RAB10. Super-resolution live cell imaging microscopy and FIB-SEM revealed that once at the lysosomal membrane, JIP4 promotes the formation of LAMP1-negative lysosomal tubules that release membranous content from ruptured lysosomes. Released vesicular structures are able to interact with other lysosomes. Thus, we described a new process that uses lysosomal tubulation to release vesicular structures from permeabilized lysosomes. LRRK2 orchestrates this process that we name LYTL (LYsosomal Tubulation/sorting driven by LRRK2) that, given the central role of the lysosome in PD, is likely to be disease relevant.
Identification of a blood test-based biomarker of aging through deep learning of aging trajectories in large phenotypic datasets of mice
Authors: Avchaciov Konstantin , Antoch Marina P. , Andrianova Ekaterina L. , Tarkhov Andrei E. , Menshikov Leonid I. , Burmistrova Olga , Gudkov Andrei V. , Fedichev Peter O.
Published: January 2020

We proposed and characterized a novel biomarker of aging and frailty in mice trained from the large set of the most conventional, easily measured blood parameters such as Complete Blood Counts (CBC) from the open-access Mouse Phenome Database (MPD). Instead of postulating the existence of an aging clock associated with any particular subsystem of an aging organism, we assumed that aging arises cooperatively from positive feedback loops spanning across physiological compartments and leading to an organism-level instability of the underlying regulatory network. To analyze the data, we employed a deep artificial neural network including auto-encoder (AE) and auto-regression (AR) components. The AE was used for dimensionality reduction and denoising the data. The AR was used to describe the dynamics of an individual mouse’s health state by means of stochastic evolution of a single organism state variable, the “dynamic frailty index” (dFI), that is the linear combination of the latent AE features and has the meaning of the total number of regulatory abnormalities developed up to the point of the measurement or, more formally, the order parameter associated with the instability. We used neither the chronological age nor the remaining lifespan of the animals while training the model. Nevertheless, dFI fully described aging on the organism level, that is it increased exponentially with age and predicted remaining lifespan. Notably, dFI correlated strongly with multiple hallmarks of aging such as physiological frailty index, indications of physical decline, molecular markers of inflammation and accumulation of senescent cells. The dynamic nature of dFI was demonstrated in mice subjected to aging acceleration by placement on a high-fat diet and aging deceleration by treatment with rapamycin.
Comprehensive bioinformatic analysis of newly sequencedTurdoides affinismitogenome reveals the persistence of translational efficiency and dominance of NADH dehydrogenase complex-I in electron transport system over Leiothrichidae family
Authors: Sarkar Indrani , Dey Prateek , Sharma Sanjeev Kumar , Ray Swapna Devi , Singh Ram Pratap
Published: January 2020

Mitochondrial genome provides useful information about species with respect to its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based andde-novoassemblies of mitogenome were performed and observed thatde-novoassembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembledde-novo) was 17,671 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with 2 rRNAs and 22 tRNAs were detected along with duplicated control regions. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over all the thirteen protein-coding genes in yellow-billed babbler mitogenome. Moreover, genetic distance and variation analysis indicated the dominance of NADH dehydrogenase complex-I in the electron transport system ofT. affinis. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogenetics results suggest thatT. affinisis closer toGarrulax.
Diversity and Structural Variability of Bacterial Microbial Communities in Rhizocompartments of Desert Leguminous Plants
Authors: Zhou Ziyuan , Ding Guodong , Yu Minghan , Gao Guanglei , Wang Genzhu
Published: January 2020

By assessing diversity variations of bacterial communities under different rhizocompartment types (i.e., roots, rhizosphere soil, root zone soil, and inter-shrub bulk soil), we explore the structural variability of bacterial communities in different root microenvironments under desert leguminous plant shrubs. Results will enable the influence of niche differentiation of plant roots and root soil on the structural stability of bacterial communities under three desert leguminous plant shrubs to be examined. High-throughput 16S rRNA genome sequencing was used to characterize diversity and structural differences of bacterial microbes in the rhizocompartments of three xeric leguminous plants. Results from this study confirm previous findings relating to niche differentiation in rhizocompartments under related shrubs, and they demonstrate that diversity and structural composition of bacterial communities have significant hierarchical differences across four rhizocompartment types under leguminous plant shrubs. Desert leguminous plants had significant effects on the enrichment and filtration of specific bacterial microbiomes across different rhizocompartments (P<0.05). The core bacterial microbiomes causing structure and composition variability of bacterial communities across different niches of desert leguminous plants are also identified. By investigating the influence of niches on the structural variability of soil bacterial communities with the differentiation of rhizocompartments under desert leguminous plant shrubs, we provide data support for the identification of dominant bacteria and future preparation of inocula, and provide a foundation for further study of the host plants-microbial interactions.

IMPORTANCE

Colonization by plant communities make valued contribution to sand-fixing in poor ecological desert environments, thereby reducing the effects of wind erosion in these areas. Our study revealed that specific core bacterial microbiomes in under-shrub soil microbial communities had a significant hierarchical enrichment effect among rhizocompartments, and were filtered into roots. The root endophyte microbiomes thus formed had low abundance and diversity, but their structural variability was the highest. In addition, our data also verified that the rhizocompartments of under desert leguminous plant shrubs had a significant differentiation effect for the core bacterial microbiomes enriched and filtered by host plants, and that each rhizocompartment represented a unique niche of bacterial communities. Understanding the interactions between xeric shrubs and soil microbial communities is a fundamental step for describing desert soil ecosystems, which in turn can offer a microbe-associated reference for evaluating the restoration of desert vegetation.
When enemies do not become friends: Experimental evolution of heat-stress adaptation in a vertically transmitted parasite
Authors: Dusi Eike , Krenek Sascha , Petzoldt Thomas , Kaltz Oliver , Berendonk Thomas U.
Published: January 2020

Strict vertical (parent-to-offspring) transmission of symbionts may be associated with benevolence and mutualism, because host reproduction and symbiont transmission are linked. Nonetheless, many such symbionts do reduce host fitness costs and the factors driving their evolution are unclear. Using microcosm populations ofCaedibacter taeniospiralis, a vertically transmitted bacterial symbiont of the protozoanParamecium tetraurelia, we investigated evolutionary change under permissive conditions (26°C) and under heat stress (32°C), over 150 host generations. We found evidence for symbiont adaptation to heat stress, involving increased infection persistence and, consequently, higher rates of vertical transmission. For certain genetic backgrounds, heat-stress adaptation was associated with higher proliferation of infected lines at 26°C, suggesting cost-free evolution of super-generalists. Despite a general decrease in symbiont virulence relative to ancestral strains, infected evolved lines still showed substantial reductions (>20%) in population growth. There was no sign of a temperature-specific reduction in virulence or protection of the host against heat stress. Our results show that obligately vertically transmitted symbionts can still qualify as ‘parasites’ and evolve adaptations that do not help their hosts. Long-term infection persistence might require additional mechanisms, such as the symbiont-mediated ’killer trait’ in this system, allowing the selective elimination of uninfected individuals in the population.
Plasmid diversity among genetically relatedKlebsiella pneumoniae blaKPC-2andblaKPC-3isolates collected in the Dutch national surveillance
Authors: Hendrickx Antoni P.A. , Landman Fabian , de Haan Angela , Borst Dyogo , Witteveen Sandra , van Santen Marga , van der Heide Han , Schouls Leo M. ,   the Dutch CPE surveillance Study Group
Published: January 2020

Carbapenemase-producingKlebsiella pneumoniaeemerged over the past decades as an important pathogen causing morbidity and mortality in hospitalized patients. For infection prevention and control, it is important to track the spread of bacterial strains in humans including the plasmids they contain. However, little is known concerning the plasmid repertoire amongK. pneumoniaestrains. Therefore, the major aim was to recapitulate the size, contents and diversity of the plasmids of genetically relatedK. pneumoniaestrains harboring the beta-lactamase geneblaKPC-2orblaKPC-3to determine their dissemination in the Netherlands and the former Dutch Caribbean islands from 2014-2019. Next-generation sequencing was combined with long-read third-generation sequencing to reconstruct 18 plasmids ofK. pneumoniae. wgMLST revealed five genetic clusters (termed KpnClusters) comprised ofK. pneumoniae blaKPC-2isolates and four clusters consisted ofblaKPC-3isolates. Each cluster was characterized by a distinct resistome and plasmidome. KpnCluster-019blaKPC-2isolates were found both in the Netherlands and the Caribbean islands.K. pneumoniae blaKPC-3isolates were found in the collection of the Netherlands. The 18 plasmids were mostly unrelated and varied betweenK. pneumoniae blaKPC-2andblaKPC-3clusters. However, the large and medium sized plasmids contained a variety of antibiotic resistance genes, transposons, insertion sequence elements, conjugal transfer systems, cation transport systems, toxin/antitoxin systems, and prophage-related sequence elements. The small plasmids carried genes implicated in virulence. Thus, implementing long-read plasmid sequencing analysis forK. pneumoniaesurveillance provided important insights in the success and understanding of transmission of a KpnCluster-019blaKPC-2strain between the Netherlands and the Caribbean.

Importance

Carbapenemase-producingKlebsiella pneumoniaehas spread globally and is of great concern for debilitated patients.K.pneumoniaeis notorious for spreading antimicrobial resistance genes by plasmids amongEnterobacterales. Combining short and long read sequencing enables reconstruction of plasmids containing antibiotic resistance genes, conjugation machinery, transposons, toxins and/or virulence determinants and thereby enhancing international pathogen surveillance.
Genome Sequences ofBurkholderia thailandensis strains E421, E426, and DW503
Authors: Mageeney Catherine M. , Sinha Anupama , Williams Kelly P. , Branda Steven S.
Published: January 2020

We present the draft genome sequences of threeBurkholderia thailandensisstrains: E421, E426, and DW503. E421 consists of 90 contigs of 6,639,935bp and 67.73% GC content. E426 consists of 106 contigs of 6,587,853bp and 67.73% GC content. DW503 consists of 102 contigs of 6,458,767bp and 67.64% GC content.
Swine ANP32A supports avian influenza virus polymerase
Authors: Peacock Thomas P. , Swann Olivia C. , Staller Ecco , Leung P. Brian , Goldhill Daniel H. , Zhou Hongbo , Long Jason S. , Barclay Wendy S.
Published: January 2020

Avian influenza viruses occasionally infect and adapt to mammals, including humans. Swine are often described as ‘mixing vessels’, being susceptible to both avian and human origin viruses, which allows the emergence of novel reassortants, such as the precursor to the 2009 H1N1 pandemic. ANP32 proteins are host factors that act as influenza virus polymerase cofactors. In this study we describe how swine ANP32A, uniquely among the mammalian ANP32 proteins tested, supports some, albeit limited, activity of avian origin influenza virus polymerases. We further show that after the swine-origin influenza virus emerged in humans and caused the 2009 pandemic it evolved polymerase gene mutations that enabled it to more efficiently use human ANP32 proteins. We map the super pro-viral activity of swine ANP32A to a pair of amino acids, 106 and 156, in the LRR and central domains and show these mutations enhance binding to influenza virus trimeric polymerase. These findings help elucidate the molecular basis for the ‘mixing vessel’ trait of swine and further our understanding of the evolution and ecology of viruses in this host.
A Fob1 independent role for the Smc5/6 complex in the rDNA that modulates lifespan
Authors: Moradi-Fard Sarah , Mojumdar Aditya , Chan Megan , Harkness Troy A. A. , Cobb Jennifer A.
Published: January 2020

The ribosomal DNA (rDNA) inSaccharomyces cerevisiaeis in one tandem repeat array on Chromosome XII. Two spacer regions within each repetitive element, callednon-transcribedspacer1(NTS1) and NTS2, are important in nucleolar organization. Smc5/6 localizes to both NTS1 and NTS2 and is involved in the regulation of Sir2 and Cohibin binding at NTS1, whereas Fob1 and Sir2 are required for optimal binding of the complex to NTS1 and NTS2, respectively. We demonstrate that Smc5/6 functions in chromatin silencing at NTS1 independently of its role in homologous recombination (HR) when forks pause at the replication fork barrier (RFB). In contrast, when the complex does not localize to the rDNA innse3-1 mutants, the shortened lifespan correlates with NTS2 homeostasis independently ofFOB1status. Our data identify the importance of Smc5/6 integrity in NTS2 transcriptional silencing and repeat tethering, which in turn underscores rDNA stability and replicative lifespan.

Highlights

Smc5/6 is important for transcriptional silencing in the rDNA.

Smc5/6 tethers the rDNA array to the periphery.

Transcriptional silencing of ncRNA at NTS1 and NTS2 is differentially regulated.

Smc5/6 has a role in rDNA maintenance independent of HR processing at the RFB.

Fob1-independent disruption of Smc5/6 at NTS2 leads to lifespan reduction.
Transcriptional analysis supports the expression of human snRNA variants and reveals U2 snRNA homeostasis by an abundant U2 variant
Authors: Kosmyna Brian , Gupta Varun , Query Charles
Published: January 2020

Although expansion of snRNA genes in the human genome and sequence variation in expressed transcripts were both identified long ago, no study has comprehensively analyzed which genes are transcriptionally active. Here, we use comprehensive bioinformatic analysis to differentiate between similar or identical genomic loci to determine that 49 snRNA genes are actively transcribed. This greatly expands on previous observation of sequence variation within snRNA transcripts. Further analysis of U2 snRNA variants reveals sequence variation maintains conserved secondary structures, yet sensitizes these U2 snRNAs to modulation of assembly factors. Homeostasis of total U2 snRNA level is maintained by altering the ratio of canonical and an abundant U2 snRNA variant. Both canonical and variant snRNA promoters respond to MYC and appear differentially sensitive to increased MYC levels. Thus, we identify transcribed snRNA variants and the sequence variation within, and propose mechanisms of transcriptional and post-transcriptional regulation of snRNA levels and pre-mRNA splicing.

HIGHLIGHTS

ChIP-seq of active promoters identifies uncharacterized snRNA genes

Transcribed repetitive snRNA genes are distinguished from falsely-mapped snRNA loci

U2 snRNA variants are sensitive to modulations in snRNP assembly

Widely expressed U2 snRNA variants provide homeostasis for total U2 snRNP levels
Cell to cell communication is an early event in glioblastoma
Authors: Portela Marta , Mitchell Teresa , Casas-Tintó Sergio
Published: January 2020

Glioblastoma (GB) is the most aggressive and lethal tumour of the central nervous system (CNS). GB cells proliferate rapidly and display a network of ultra-long tumour microtubes (TMs) that mediate cell to cell communication. GB TMs infiltrate into the brain, enwrap neurons and facilitate the depletion of Wingless (Wg)/WNT from the neighbouring neurons. GB cells establish a positive feedback loop including Wg signalling upregulation that activates the JNK pathway and matrix metalloproteases (MMPs), in turn, these signals promote TMs infiltration, GB progression and neuronal synapse loss and degeneration. Thus, cellular and molecular signals other than primary mutations emerge as central players of GB. Here we describe the temporal organization of the events that occur in GB. We define the progressive activation of JNK pathway signalling mediated by Grindelwald (Grnd) receptor, is caused by the ligand Eiger (Egr)/TNFα produced by the healthy tissue. We propose that cellular interactions of GB with the rest of the brain is an early event that precedes GB proliferation and expansion. We conclude that non-autonomous signals facilitate GB progression and contribute to the complexity and versatility of these incurable tumours.
PAKC: A novel Panel of HLA class I Antigen presentation machinery Knockout Cells from the same genetic origin
Authors: de Waard Antonius A. , Verkerk Tamara , Jongsma Marlieke L.M. , Hoefakker Kelly , Sethumadhavan Sunesh , Gerke Carolin , Bliss Sophie , Janssen George M.C. , de Ru Arnoud H. , Claas Frans H.J. , Mulder Arend , Tampé Robert , van Veelen Peter A. , Halenius Anne , Spaapen Robbert M.
Published: January 2020

With the emergence of immunotherapies, the understanding of functional HLA class I antigen presentation to T cells is more relevant than ever. Current knowledge on antigen presentation is based on decades of research in a wide variety of cell types with varying antigen presentation machinery (APM) expression patterns, proteomes and HLA haplotypes. This diversity complicates the establishment of individual APM contributions to antigen generation, selection and presentation. Therefore, we generated a novel Panel of APM Knockout Cell lines (PAKC) from the same genetic origin. After CRISPR/Cas9 genome-editing of ten individual APM components in a human cell line, we derived clonal cell lines and confirmed their knockout status and phenotype. We then show how PAKC will accelerate research on the functional interplay between APM components and their role in antigen generation and presentation. This will lead to improved understanding of peptide-specific T cell responses in infection, cancer and autoimmunity.

Key points

We generated a panel of cell lines to study HLA class I antigen presentation

We show how this will spark research in infection, tumor biology and autoimmunity
Differential effects of aquaporin-4 channel inhibition on BOLD fMRI and Diffusion fMRI responses in rat visual cortex
Authors: Komaki Yuji , Debacker Clément , Djemai Boucif , Ciobanu Luisa , Tsurugizawa Tomokazu , Le Bihan Denis
Published: January 2020

The contribution of astrocytes to the BOLD fMRI and DfMRI responses in visual cortex of mice following visual stimulation were investigated an aquaporin 4 (AQP4) channel blocker, TGN-020, acting as an astrocyte function perturbator. Under TGN-020 injection the amplitude of the BOLD fMRI response became significantly higher. In contrast no significant changes in the DfMRI responses and the electrophysiological responses were observed. Those results further confirm the implications of astrocytes in the neurovascular coupling mechanism underlying BOLD fMRI, while DfMRI relies on other, not astrocyte-mediated mechanisms.
SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription
Authors: Bergenholtz Seth , Yang Xiaoyu , Maliskova Lenka , Yun Li , Shen Yin
Published: January 2020

Accurate RNA quantification at the single-cell level is critical for understanding the dynamics of gene expression and regulation across space and time. Single molecule FISH (smFISH), such as RNAscope, provides spatial and quantitative measurements of individual transcripts, therefore, can be used to explore differential gene expression among a heterogeneous cell population if combined with cell identify information. However, such analysis is not straightforward, and existing image analysis pipelines cannot integrate both RNA transcripts and cellular staining information to automatically output cell type-specific gene expression. We developed an efficient and customizable analysis method, Single-Molecule Automatic RNA Transcription Quantification (SMART-Q), to enable the analysis of gene transcripts in a cell type-specific manner. SMART-Q efficiently infers cell identity information from multiplexed immuno-staining and quantifies cell type-specific transcripts using a 3D Gaussian fitting algorithm. Furthermore, we have optimized SMART-Q for user experiences, such as flexible parameters specification, batch data outputs, and visualization of analysis results. SMART-Q meets the demands for efficient quantification of single-molecule RNA and can be widely used for cell type-specific RNA transcript analysis.
Comparison of Anorectal Function Measured using Wearable Digital Manometry and a High Resolution Manometry System
Authors: Attari Ali , Chey William D. , Baker Jason R. , Ashton-Miller James A.
Published: January 2020

There is a need for a lower cost manometry system for assessing anorectal function in primary and secondary care settings. We developed an index finger-based system (termed “digital manometry”) and tested it in healthy volunteers, patients with chronic constipation, and fecal incontinence. Anorectal pressures were measured in 16 participants with the digital manometry system and a 23-channel high-resolution anorectal manometry system. The results were compared using a Bland-Altman analysis at rest as well as during maximum squeeze and simulated defecation maneuvers. Myoelectric activity of the puborectalis muscle was also quantified simultaneously using the digital manometry system. The limits of agreement between the two methods were −7.1 ± 25.7 mmHg for anal sphincter resting pressure, 0.4 ± 23.0 mmHg for the anal sphincter pressure change during simulated defecation, −37.6 ± 50.9 mmHg for rectal pressure changes during simulated defecation, and −20.6 ± 172.6 mmHg for anal sphincter pressure during the maximum squeeze maneuver. The change in the puborectalis myoelectric activity was proportional to the anal sphincter pressure increment during a maximum squeeze maneuver (slope = 0.6, R2= 0.4). Digital manometry provided a similar evaluation of anorectal pressures and puborectalis myoelectric activity at an order of magnitude less cost than high-resolution manometry, and with a similar level of patient comfort. Digital Manometry provides a simple, inexpensive, point of service means of assessing anorectal function in patients with chronic constipation and fecal incontinence.
Information processing in biological molecular machines
Authors: Kurzynski M. , Chelminiak P.
Published: January 2020

ABSTRACT

Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics of conformational transitions which often manifests in fluctuating rates of the catalyzed processes and the presence of short-term memory resulting from the preference of certain conformations. For arbitrarily complex stochastic dynamics of protein machines, we proved the generalized fluctuation theorem predicting the possibility of reducing free energy dissipation at the expense of creating some information stored in memory. That this may be the case has been shown by interpreting results of computer simulations for a complex model network of stochastic transitions. The subject of the analysis was the time course of the catalyzed processes expressed by sequences of jumps at random moments of time. Since similar signals can be registered in the observation of real systems, all theses of the paper are open to experimental verification.

STATEMENT OF SIGNIFICANCE

The transient utilization of memory for storing information turns out to be crucial for the movement of protein motors and the reason for most protein machines to operate as dimers or higher organized assemblies. From a broader physical point of view, the division of free energy into the operation and organization energies is worth emphasizing. Information can be assigned a physical meaning of a change in the value of both these functions of state.
Structural insights into the insecticidal Vip3A toxin ofBacillus thuringiensis
Authors: Jiang Kun , Zhang Yan , Chen Zhe , Wu Dalei , Cai Jun , Gao Xiang
Published: January 2020

The vegetative insecticidal proteins (Vips) secreted byBacillus thuringiensisare regarded as the new generation of insecticidal toxins because they have different insecticidal properties compared with commonly applied insecticidal crystal proteins (Cry toxins). Vip3A toxin, representing the vast majority of Vips, has been used commercially in transgenic crops and bio-insecticides. However, the lack of both structural information of Vip3A and a clear understanding of its insecticidal mechanism at the molecular level, limits its further development and broader application. Here we present the first crystal structure of the Vip3A toxin in an activated form. Since all members of this insecticidal protein family are highly conserved, the structure of Vip3A provides unique insight into the general domain architecture and protein fold of the Vip3 family of insecticidal toxins. Our structural analysis reveals a four-domain organization, featuring a potential membrane insertion region, a receptor binding domain, and two glycan binding domains of activated Vip3A. We further identify the specific glycan moieties recognized by Vip3A through a glycan array screen. Taken together, these findings provide insights into the mode of action of Vip3 family of insecticidal toxins, and will boost the development of Vip3 into more efficient bio-insecticides.
Climate change will drive novel cross-species viral transmission
Authors: Carlson Colin J. , Albery Gregory F. , Merow Cory , Trisos Christopher H. , Zipfel Casey M. , Eskew Evan A. , Olival Kevin J. , Ross Noam , Bansal Shweta
Published: January 2020

At least 10,000 species of mammal virus are estimated to have the potential to spread in human populations, but the vast majority are currently circulating in wildlife, largely undescribed and undetected by disease outbreak surveillance1–3. In addition, changing climate and land use are already driving geographic range shifts in wildlife, producing novel species assemblages and opportunities for viral sharing between previously isolated species4, 5. In some cases, this will inevitably facilitate spillover into humans6, 7—a possible mechanistic link between global environmental change and emerging zoonotic disease8. Here, we map potential hotspots of viral sharing, using a phylogeographic model of the mammal-virus network, and projections of potential geographic range shifts for 3,139 mammal species under climate change and land use scenarios for the year 2070. Range-shifting mammal species are predicted to aggregate at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, driving the novel cross-species transmission of their viruses an estimated 4,000 times. Counter to expectations, holding warming under 2°C within the century does not reduce new viral sharing, due to greater potential range expansions— highlighting the need to invest in surveillance even in a low-warming future. Most projected viral sharing is driven by diverse hyperreservoirs (rodents and bats) and large-bodied predators (carnivores). Because of their unique dispersal capacity, bats account for the majority of novel viral sharing, and are likely to share viruses along evolutionary pathways that could facilitate future emergence in humans. Our findings highlight the urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking species’ range shifts, especially in tropical countries that harbor the most emerging zoonoses.