bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical metagenomics bioinformatics pipeline for the identification of hospital-acquired pneumonia pathogens antibiotic resistance genes from bronchoalveolar lavage samples
Authors: Tournoud Maud , Ruppé Etienne , Perrin Guillaume , Schicklin Stéphane , Guigon Ghislaine , Mahé Pierre , Lazarevic Vladimir , Hauser Sébastien , Mirande Caroline , Levrat Albrice , Louis Karen , Gervasi Gaspard , Schrenzel Jacques
Published: February 2020

Background

Shortening the time-to-result for pathogen detection and identification and antibiotic susceptibility testing for patients with Hospital-Acquired and Ventilator-Associated pneumonia (HAP-VAP) is of great interest. For this purpose, clinical metagenomics is a promising non-hypothesis driven alternative to traditional culture-based solutions: when mature, it would allow direct sequencing all microbial genomes present in a BronchoAlveolar Lavage (BAL) sample with the purpose of simultaneously identifying pathogens and Antibiotic Resistance Genes (ARG). In this study, we describe a new bioinformatics method to detect pathogens and their ARG with good accuracy, both in mono- and polymicrobial samples.

Methods

The standard approach (hereafter called TBo), that consists in taxonomic binning of metagenomic reads followed by an assembly step, suffers from lack of sensitivity for ARG detection. Thus, we propose a new bioinformatics approach (called TBwDM) with both models and databases optimized for HAP-VAP, that performs reads mapping against ARG reference database in parallel to taxonomic binning, and joint reads assembly.

Results

In in-silico simulated monomicrobial samples, the recall for ARG detection increased from 51% with TBo to 97.3% with TBwDM; in simulated polymicrobial infections, it increased from 41.8% to 82%. In real sequenced BAL samples (mono and polymicrobial), detected pathogens were also confirmed by traditional culture approaches. Moreover, both recall and precision for ARG detection were higher with TBwDM than with TBo (35 points difference for recall, and 7 points difference for precision).

Conclusions

We present a new bioinformatics pipeline to identify pathogens and ARG in BAL samples from patients with HAP-VAP, with higher sensitivity for ARG recovery than standard approaches and the ability to link ARG to their host pathogens.
Next-generation sequencing of pIJ101-basedStreptomyces-E. colishuttle vectors
Authors: Brown Katelyn , Nybo S. Eric
Published: February 2020

The sequences of two commonly used pIJ101-basedStreptomyces-E. colishuttle vectors, pEM4 and pUWL201, were determined using next-generation sequencing and mapped. pEM4 was found to be 8.3 kbp long, containing genes encoding β-lactamase, thiostrepton resistance, thelacZ□ fragment, anE. colipUC19 origin of replication, and theStreptomycespIJ101 origin of replication. pUWL201 was found to be 6.78 kbp long, containing genes encoding β-lactamase, thiostrepton resistance, thelacZ□ fragment, anE. colipUC19 origin of replication, and theStreptomycespIJ101 origin of replication. Interestingly, the sequences for both pEM4 and pUWL201 exceed their previously reported size by 1.1 kbp and 0.4 kbp, respectively. This report updates the literature with the corrected sequences for these two popular vectors, ensuring their compatibility with modern synthetic biology cloning methodologies.
Intermittent hypoxia promotes functional neuroprotection from retinal ischemia in untreated first-generation offspring
Authors: Harman Jarrod C. , Guidry Jessie J. , Gidday Jeffrey M.
Published: February 2020

Environmental stimuli can promote short- or long-lasting changes in phenotype through epigenetics. Under certain circumstances, induced phenotypes can be passed through the germline to subsequent generations, providing a novel mechanistic basis for disease heritability. In the present study, we tested the hypothesis that repetitively exposing parents to a nonharmful epigenetic stimulus can promote disease resilience in offspring. Male and female mice were mated following brief exposures to mild systemic hypoxia every other day for 16 weeks. Electroretinographic determinations of postischemic function in response to transient unilateral retinal ischemia in their 5-month-old F1 progeny revealed significant resilience to injury relative to animals derived from normoxic control parents. Mass spectrometry identified hundreds of differentially expressed proteins between protected and injured retinae; bioinformatic analyses of the pathways and networks these proteins comprise provided specific mechanistic insights into the molecular manifestation of this injury-resilient phenotype. Thus, epigenetics can modify heritability to promote disease resilience.
Model of ciprofloxacin subdiffusion inPseudomonas aeruginosabiofilm formed in artificial sputum medium
Authors: Kosztołowicz Tadeusz , Metzler Ralf , Wa̧sik Sławomir , Arabski Michał
Published: February 2020

We study theoretically and empirically ciprofioxacin antibiotic diffusion through a gel-like artificial sputum medium (ASM) mimicking physiological conditions typical for a cystic fibrosis layer, in which regions occupied byPseudomonas aeruginosabacteria are present. Our theoretical model is based on the subdiffusion-absorption equation with a fractional time derivative that describes molecules diffusion in a medium structured as Thompson’s plumpudding model; the pudding ‘background’ represents ASM and the plums represent the bacterial biofilm. We show that the process can be divided into three successive stages: (1) only antibiotic subdiffusion with constant biofilm parameters, (2) subdiffusion and absorption of antibiotic molecules with variable biofilm parameters, (3) subdiffusion and absorption in the medium but biofilm parameters are constant. Stage 2 is interpreted as the appearance of an intensive defence bulid-up of bacteria against the action of an antibiotic, in the stage 3 it is likely that the bacteria have been inactivated. Times at which stages change are determined from the experimentally obtained temporal evolution of the amount of substance that has diffused through the ASM with bacteria. Our analysis shows good agreement between experimental and our theoretical results.
Natural selection influenced the genetic architecture of brain structure, behavioral and neuropsychiatric traits
Authors: Wendt Frank R , Pathak Gita A , Overstreet Cassie , Tylee Daniel S , Gelernter Joel , Atkinson Elizabeth G , Polimanti Renato
Published: February 2020

Natural selection has shaped the phenotypic characteristics of human populations. Genome-wide association studies (GWAS) have elucidated contributions of thousands of common variants with small effects on an individual’s predisposition to complex traits (polygenicity), as well as wide-spread sharing of risk alleles across traits in the human phenome (pleiotropy). It remains unclear how the pervasive effects of natural selection influence polygenicity in brain-related traits. We investigate these effects by annotating the genome with measures of background (BGS) and positive selection, indications of Neanderthal introgression, measures of functional significance including loss-of-function (LoF) intolerant and genic regions, and genotype networks in 75 brain-related traits. Evidence of natural selection was determined using binary annotations of top 2%, 1%, and 0.5% of selection scores genome-wide. We detected enrichment (q<0.05) of SNP-heritability at loci with elevated BGS (7 phenotypes) and in genic (34 phenotypes) and LoF-intolerant regions (67 phenotypes). BGS (top 2%) significantly predicted effect size variance for trait-associated loci (σ2parameter) in 75 brain-related traits (β=4.39×10−5,p=1.43×10−5, modelr2=0.548). By including the number of DSM-5 diagnostic combinations per psychiatric disorder, we substantially improved model fit (σ2~ BTop2%× Genic × diagnostic combinations; modelr2=0.661). We show that GWAS with larger variance in risk locus effect sizes are collectively predicted by the effects of loci under strong BGS and in regulatory regions of the genome. We further show that diagnostic complexity exacerbates this relationship and perhaps dampens the ability to detect psychiatric risk loci.
The cue-reactivity paradigm: An ensemble of networks driving attention and cognition when viewing drug and natural reward-related stimuli
Authors: Hill-Bowen Lauren D. , Riedel Michael C. , Poudel Ranjita , Salo Taylor , Flannery Jessica S. , Camilleri Julia A. , Eickhoff Simon B. , Laird Angela R. , Sutherland Matthew T.
Published: February 2020

Background

The cue-reactivity paradigm is a widely adopted neuroimaging probe engendering brain activity linked with attentional, affective, and reward processes following presentation of appetitive stimuli. Given the multiple mental operations invoked, we sought to decompose cue-related brain activity into constituent components employing emergent meta-analytic techniques when considering drug and natural reward-related cues.

Methods

We conducted multiple coordinate-based meta-analyses delineatingcommonanddistinctbrain activity convergence across cue-reactivity studies (N=196 articles) involving drug (n=133) or natural reward-related (n=63) visual stimuli. Subsequently, we characterized the connectivity profiles of identified brain regions by using them as seeds in task-independent and task-dependent functional connectivity analyses. Using hierarchical clustering on these connectivity profiles, we grouped cue-related brain regions into subnetworks. Functional decoding was then employed to characterize mental operations linked with each subnetwork.

Results

Across all studies,pooledactivity convergence was observed in the striatum, amygdala, thalamus, cingulate, insula, and multiple frontal, parietal, and occipital regions.Drug-distinctconvergence (drug>natural) was observed notably in the posterior cingulate cortex (PCC), dorsolateral prefrontal cortex (dlPFC), and temporal and parietal regions, whereasdistinct naturalreward convergence (natural>drug) was observed in thalamic, insular, orbitofrontal, and occipital regions. Hierarchical clustering using each regions’ connectivity profiles identified six subnetworks, involving: 1) occipital and thalamic (lateral geniculate nucleus) regions functionally linked with early visual processing, 2) occipital-temporal regions associated with higher level visual association, 3) parietal-frontal regions linked with cognitive control mechanisms, 4) posterior and ventral insula as well as anterior cingulate cortex (ACC) functionally linked with salient event detection, 5) nucleus accumbens, PCC, precuneus, ACC, and thalamus (mediodorsal) associated with subjective valuation, and 6) bilateral amygdalae, orbitofrontal, and dorsal insula regions linked with affective processes.

Conclusions

These outcomes suggest multifaceted brain activity during the cue-reactivity paradigm can be decomposed into more elemental processes and indicate that while drugs of abuse usurp the brain’s natural reward processing system, some regions appear distinctly related to drug cue-reactivity (e.g., PCC, dlPFC).
Tissue mimetic hyaluronan bioink containing collagen fibers with controlled orientation modulating cell morphology and alignment
Authors: Schwab Andrea , Helary Christophe , Richards Geoff , Alini Mauro , Eglin David , D’Este Matteo
Published: February 2020

Biofabrication is providing scientists and clinicians the ability to produce engineered tissues with desired shapes, and gradients of composition and biological cues. Typical resolutions achieved with extrusion-based bioprinting are at the macroscopic level. However, for capturing the fibrillar nature of the extracellular matrix (ECM), it is necessary to arrange ECM components at smaller scales, down to the micron and the molecular level.

In this study, we introduce a bioink containing hyaluronan (HA) as tyramine derivative (THA) and collagen type 1 (Col 1). Similarly to other connective tissues, in this bioink Col is present in fibrillar form and HA as viscoelastic space filler. THA was enzymatically crosslinked under mild conditions allowing simultaneous Col fibrillogenesis, thus achieving a homogeneous distribution of Col fibrils within the viscoelastic HA-based matrix. THA-Col composite displayed synergistic properties in terms of storage modulus and shear-thinning, translating into good printability.

Shear-induced alignment of the Col fibrils along the printing direction was achieved and quantified via immunofluorescence and second harmonic generation. Cell-free and cell-laden constructs were printed and characterized, analyzing the influence of the controlled microscopic anisotropy on human bone marrow derived mesenchymal stromal cells (hMSC) migration.

THA-Col showed cell instructive properties modulating hMSC adhesion, morphology and sprouting from spheroids stimulated by the presence and the orientation of Col fibers. Actin filament staining showed that hMSCs embedded into aligned constructs displayed increased cytoskeleton alignment along the fibril direction. Based on gene expression of cartilage/bone markers and ECM production, hMSCs embedded into the bioink displayed chondrogenic differentiation comparable to standard pellet culture by means of proteoglycan production (Safranin O staining and proteoglycan quantification).

The possibility of printing matrix components with control over microscopic alignment brings biofabrication one step closer to capturing the complexity of native tissues.
Drosha Regulates Oogenesis and microRNAs Germline Autonomously and Non-autonomously inC. elegans
Authors: Minogue Amanda L. , Trimmer Kenneth A. , Seemann Jacob H. , Kalia Awdhesh , Arur Swathi
Published: February 2020

Small non-coding RNAs regulate multiple aspects of development including germ cell development. The microRNA pathway genes Dicer, Drosha and Pasha have been shown to regulate oocyte meiotic maturation inC. elegans. However, Dicer controls oocyte meiotic maturation through endo-siRNAs, rather than microRNAs. A repertoire of Drosha-dependent oocyte-expressed microRNAs were identified which regulate various aspects of oogenesis but not oocyte meiotic maturation. These data lead to the following models: (a) microRNAs function redundantly to regulate oocyte meiotic maturation, (b) Drosha and microRNAs function germline non-autonomously to regulate meiotic maturation. We investigated these models and observed that Drosha regulates oocyte meiotic maturation in a germline non-autonomous manner. Additionally, we uncovered a role for Drosha in regulating pachytene progression and oocyte development in a germline autonomous manner through miR-35 family and miR-51 respectively. Interestingly we also find that though Drosha-dependent oocyte-expressed microRNAs, miR-61 and miR-72, are sufficient to regulate pachytene progression and oocyte development respectively, they are generated in a germline non-autonomous manner. Collectively these data reveal a Drosha-dependent microRNA circuit, which coordinates oocyte development germline autonomously as well as through soma-germline communication.
Long-term in vivo Monitoring of Gliotic Sheathing of Ultrathin Entropic Coated Brain Microprobes with Fiber-based Optical Coherence Tomography
Authors: Dryg Ian , Xie Yijing , Bergmann Michael , Urban Gerald , Shain William , Hofmann Ulrich G.
Published: February 2020

Microfabricated neuroprosthetic devices have made possible important observations on neuron activity; however, long-term high-fidelity recording performance of these devices has yet to be realized. Tissue-device interactions appear to be a primary source of lost recording performance. The current state of the art for visualizing the tissue response surrounding brain implants in animals is Immunohistochemistry + Confocal Microscopy, which is mainly performed after sacrificing the animal. Monitoring the tissue response as it develops could reveal important features of the response which may inform improvements in electrode design. Optical Coherence Tomography (OCT), an imaging technique commonly used in ophthalmology, has already been adapted for imaging of brain tissue. Here, we use OCT to achieve real-time,in vivomonitoring of the tissue response surrounding chronically implanted neural devices. The employed tissue-response-provoking implants are coated with a plasma-deposited nanofilms, which have been demonstrated as a biocompatible and anti-inflammatory interface for indwelling devices. We evaluate the method by comparing the OCT results to traditional histology qualitatively and quantitatively. The differences in OCT signal across the implantation period between the plasma group and the control reveal that the Parylene-type coating of otherwise rigid brain probes (glass and silicon) does not improve the glial encapsulation in the brain parenchyma.
Languages, evolution and statistics: human sound systems were shaped by changes in bite configuration.Response to Tarasov & Uyeda (2020)
Authors: Blasi Damián E. , Moran Steven , Moisik Scott R. , Widmer Paul , Dediu Dan , Bickel Balthasar
Published: February 2020

In Blasi et al. (2019) we have shown, through a series of statistical analyses and models, that human sound systems have been affected by a transition in bite configuration starting from the Neolithic. Tarasov and Uyeda (2020) (henceforth T&U) raise a number of observations in relation to our article. We appreciate T&U’s engagement with our work and their sharing of the code and data of the analyses reported. In brief, their technical comment involves five analyses:

Binomial Causal Models (BCM)

Linear Regression of across-area variation in labiodentals and subsistence

Predictive Posterior Simulations (PPS)

Poisson Linear Regression (PLR): model comparison

Phylogenetic Analyses

In what follows, we show that the discrepancies they report between our findings and theirs are due mostly to ill-specified models, weak (or missing) statistical evidence, and a misinterpretation of our results. After these issues are addressed, we conclude that T&U’s claims do not hold.
Recovery plans need better science to support decisions that allow species to decline in abundance but be recovered
Authors: Li Ya-Wei , Malcom Jacob W. , Che-Castaldo Judy P. , Neel Maile C.
Published: February 2020

The U.S. Endangered Species Act (ESA) is widely considered the strongest biodiversity conservation law in the world. Part of its strength comes from the mandate to use the best available science to make decisions under the law, including whether to list a species, setting the criteria for when a species can be considered recovered, and determining when those criteria have been met and a species can be delisted. Both biological status and threat factors are considered at each stage of the listing and delisting process. In most cases, conservation science would suggest that species at risk enough to be listed under the Act should be more abundant and secure at delisting than they were at listing. Surprisingly, we identified 130 ESA-listed species that the U.S. Fish and Wildlife Service could consider recovered with fewer populations or individuals than existed at the time of listing. We ask whether their ESA recovery plans present scientific data, rationale, or evidence to support a decline in abundance as part of recovery. We find that almost no plan clearly explains why a decline is allowed. Fewer than half of the plans provide scientific support for a decline in the form of literature references or modeling results. We recommend that the U.S. Fish and Wildlife Service and the National Marine Fisheries Service create a decision support system to inform when species can decline in abundance and still recover, including guidance on (a) the need to explicitly address the declines and (b) the science used to support the decisions.
Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies
Authors: Klein Steffen , Wimmer Benedikt H. , Winter Sophie L. , Kolovou Androniki , Laketa Vibor , Chlanda Petr
Published: February 2020

Lamellar bodies (LBs) are surfactant-rich organelles in alveolar cells. LBs disassemble into a lipid-protein network that reduces surface tension and facilitates gas exchange in the alveolar cavity. Current knowledge of LB architecture is predominantly based on electron microscopy studies using disruptive sample preparation methods. We established and validated a post-correlation on-lamella cryo-correlative light and electron microscopy approach for cryo-FIB milled cells to structurally characterize and validate the identity of LBs in their unperturbed state. Using deconvolution and 3D image registration, we were able to identify fluorescently labeled membrane structures analyzed by cryo-electron tomography. In situ cryo-electron tomography of A549 cells as well as primary Human Small Airway Epithelial Cells revealed that LBs are composed of membrane sheets frequently attached to the limiting membrane through “T”-junctions. We report a so far undescribed outer membrane dome protein complex (OMDP) on the limiting membrane of LBs. Our data suggest that LB biogenesis is driven by parallel membrane sheet import and by the curvature of the limiting membrane to maximize lipid storage capacity.
Propagation of Hippocampal Ripples to the Neocortex by Way of a Subiculum-Retrosplenial Pathway
Authors: Nitzan Noam , McKenzie Sam , Beed Prateep , English Daniel Fine , Oldani Silvia , Tukker John Jan , Buzsáki György , Schmitz Dietmar
Published: February 2020

Bouts of high frequency activity known as sharp wave ripples (SPW-Rs) facilitate communication between the hippocampus and neocortex. However, the paths and mechanisms by which SPW-Rs broadcast their content are not well understood. Due to its anatomical positioning, the granular retrosplenial cortex (gRSC) may be a bridge for this hippocampo-cortical dialogue. Using silicon probe recordings in awake, head-fixed mice, we show the existence of SPW-R analogues in gRSC and demonstrate their coupling to hippocampal SPW-Rs. gRSC neurons reliably distinguished different subclasses of hippocampal SPW-Rs according to ensemble activity patterns in CA1. We demonstrate that this coupling is brain state-dependent, and delineate a topographically-organized anatomical pathway via VGlut2-expressing, bursty neurons in the subiculum. Optogenetic stimulation or inhibition of bursty subicular cells induced or reduced responses in superficial gRSC, respectively. These results identify a specific path and underlying mechanisms by which the hippocampus can convey neuronal content to the neocortex during SPW-Rs.
Rtrack: a software package for reproducible automated water maze analysis
Authors: Overall Rupert W , Zocher Sara , Garthe Alexander , Kempermann Gerd
Published: February 2020

Rtrackis an open-source software package for the analysis of spatial exploration data from behavioural tests such as the Morris water maze. The software provides an easy-to-use interface for data import, analysis and visualisation. A parameter-free machine learning model allows rapid and reproducible classification of spatial search strategies. We also propose a standard export format to enable cross-platform data sharing for the first time in the field.
Genome-wide study identifies association between HLA-B*55:01 and penicillin allergy
Authors: Krebs Kristi , Bovijn Jonas , Lepamets Maarja , Censin Jenny C , Jürgenson Tuuli , Särg Dage , Luo Yang , Skotte Line , Geller Frank , Feenstra Bjarke , Wang Wei , Auton Adam ,   23andMe Research Team, Raychaudhuri Soumya , Esko Tõnu , Metspalu Andres , Laur Sven , Holmes Michael V , Lindgren Cecilia M , Mägi Reedik , Milani Lili , Fadista João
Published: February 2020

Background

Hypersensitivity reactions to drugs are often unpredictable and can be life-threatening, underscoring a need for understanding their underlying mechanisms and risk factors. The extent to which germline genetic variation influences the risk of commonly reported drug allergies such as penicillin allergy remains largely unknown.

Methods

We extracted data from the electronic health records of 52,000 Estonian and 500,000 UK biobank participants to study the role of genetic variation in the occurrence of penicillin hypersensitivity reactions. We used imputed SNP to HLA typing data from up to 22,554 and 488,377 individuals from the Estonian and UK cohorts, respectively, to further fine-map the human leukocyte antigen (HLA) association and replicated our results in two additional cohorts involving a total of 1.14 million individuals.

Results

Genome-wide meta-analysis of penicillin allergy revealed a significant association located in the HLA region on chromosome 6. The signal was further fine-mapped to the HLA-B*55:01 allele (OR 1.47 95% CI 1.37-1.58, P-value 4.63×10-26) and confirmed by independent replication in two cohorts. The meta-analysis of all four cohorts in the study revealed a strong association of HLA-B*55:01 allele with penicillin allergy (OR 1.33 95% CI 1.29-1.37, P-value 2.23×10-72).In silicofollow-up suggests a potential effect on T lymphocytes at HLA-B*55:01.

Conclusion

We present the first robust evidence for the role of an allele of the major histocompatibility complex (MHC) I gene HLA-B in the occurrence of penicillin allergy.
Hook shape of growing leaves results from an active regulation
Authors: Rivière Mathieu , Corre Yoann , Peaucelle Alexis , Derr Julien , Douady Stéphane
Published: February 2020

The rachis of most growing compound leaves observed in nature exhibit a stereotyped hook shape. In this study, we focus on the canonical case ofAverrhoa carambola. Combining kinematics and mechanical investigation, we characterize this hook shape and shed light on its establishment and maintenance. We show quantitatively that the hook shape is a conserved bent zone propagating at constant velocity and constant distance from the apex throughout development. A simple mechanical test first reveals non-zero spontaneous curvature profiles for the growing leaves, indicating that the hook shape is actively regulated. It then evidences the robust spatial organization of growth, curvature, rigidity and lignification and their interplay. Regulation processes appear to be specifically localized: in particular, differential growth occurs where the elongation rate drops. Finally, impairing the graviception of the leaf on a clinostat led to reduced hook curvatures but not to its loss. Altogether our results suggest a role for proprioception in the regulation of the apical hook, likely mediated via mechanical strain.
Antarctic cryptoendolithic bacterial lineages of pre-Cambrian origin as proxy for Mars colonization
Authors: Albanese Davide , Coleine Claudia , Rota-Stabelli Omar , Onofri Silvano , Tringe Susannah G. , Stajich Jason E. , Selbmann Laura , Donati Claudio
Published: February 2020

Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks. They are able to persist at the edge of the biological potential for life in the ice-free areas of continental Antarctica. These areas include the McMurdo Dry Valleys, often cited as a Terrestrial analog of the Martian environment. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity and genetic makeup of bacterial species that reside in these environments. We performed metagenomic sequencing of 18 communities from rocks collected in Antarctic desert areas over a distance of about 350 km. A total of 469 draft bacterial genome sequences were assembled, and clustered into 269 candidate species that lack a representative genome in public databases. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma, much earlier than the glaciation of Antarctica, and that are functionally distinct from known related taxa. The hypothesis that Antarctic cryptoendolithic bacterial lineages were generated by the selection of pre-existing cold-tolerant organisms whose origin dates back to the Tonian glaciations gives new insights for the possibility of life on Mars.
Integrin-mediated adhesion in the unicellular holozoanCapsaspora owczarzaki
Authors: Parra-Acero Helena , Harcet Matija , Sánchez-Pons Núria , Casacuberta Elena , Brown Nicholas H. , Dudin Omaya , Ruiz-Trillo Iñaki
Published: February 2020

In animals, cell-matrix adhesion is mainly mediated by integrins and their associated proteins. Comparative genomic analyses have shown that core components of the integrin adhesome pre-date the emergence of animals, however, whether it mediates cell adhesion in non-metazoan taxa remains unknown. Here, we investigate cell-substrate adhesion inCapsaspora owczarzaki, the closest unicellular relative of animals with the most complete integrin adhesome. Using an adhesion assay, we show thatC. owczarzakiadheres to surfaces using actin-dependent filopodia. We show that integrin β2 and its associated protein vinculin localise as distinct patches in the filopodia. We also demonstrate that substrate adhesion and integrin localisation are enhanced by the ligand fibronectin. Finally, using a specific antibody for Integrin β2, we inhibited cell adhesion to a fibronectin-coated surface. Our results show that adhesion to the substrate inC. owczarzakiis mediated by integrins. This suggests that integrin-mediated adhesion pre-dates the emergence of animals.
Short and Long-read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and its Host
Authors: Olasz Ferenc , Tombácz Dóra , Torma Gábor , Csabai Zsolt , Moldován Norbert , Dörmő Ákos , Prazsák István , Mészáros István , Magyar Tibor , Tamás Vivien , Zádori Zoltán , Boldogkői Zsolt
Published: February 2020

African swine fever virus (ASFV) is an important animal pathogen causing substantial economic losses in the swine industry globally. At present, little is known about the molecular biology of ASFV, including its transcriptome organization. In this study, we applied cutting-edge sequencing approaches, namely the Illumina short-read sequencing (SRS) and the Oxford Nanopore Technologies long-read sequencing (LRS) techniques, together with several library preparation chemistries to analyze the ASFV dynamic transcriptome. SRS can generate a large amount of high-precision sequencing reads, but it is inefficient for identifying long RNA molecules, transcript isoforms and overlapping transcripts. LRS can overcome these limitations, but this approach also has shortcomings, such as its high error rate and the low coverage. Amplification-based LRS techniques produce relatively high read counts but also high levels of spurious transcripts, whereas the non-amplified cDNA and direct RNA sequencing techniques are more precise but achieve lower throughput. The drawbacks of the various technologies can be circumvented by the combined use of these approaches.
Dampened PI3K/AKT signaling contributes to cancer resistance of the naked mole rat
Authors: Zhao Jing , Tian Xiao , Zhu Yabing , Zhang Zhihui , Rydkina Elena , Yuan Yongxuan , Zhang Hongyun , Roy Bhaskar , Cornwell Adam , Nevo Eviatar , Shang Xiaoxiao , Huang Runyue , Kristiansen Karsten , Seluanov Andrei , Fang Xiaodong , Gorbunova Vera
Published: February 2020

Mammalian species have a dramatically different susceptibility to cancer. However, how cancer-resistant species resist oncogenic transformation is not fully understood. Here, we performed a comprehensive analysis of oncogene-induced transcriptional changes in the fibroblasts of a cancer-prone species, the mouse, and three cancer-resistant species, the human, the blind mole rat, and the naked mole rat. We report that multiple cellular processes are more refractory to oncogene-induced transcriptional changes in blind mole-rat, naked mole-rat, or human cells compared to mouse cells, such as cell division, cell adhesion, extracellular matrix organization, and metabolism. Strikingly, naked mole rat cells are more resistant to Ras-induced transcriptional changes compared to the other three species. As a mechanism, we found that critical genes in the PI3K pathway includingAkt1andPik3caare downregulated in naked mole rat cells. Activating the PI3K/AKT pathway in the naked mole rat cells renders them susceptible to tumorigenic transformation. This study provides multiple new insights into anti-cancer mechanisms in cancer-resistant species of mammals.

Significance statement

Animal species differ greatly in their cancer susceptibility. Cancer rates in the mouse range from 50-90%, while two other rodent species, the naked mole rat and the blind mole rat have only a few cancer cases ever reported. Here we examined the mechanisms responsible these differences by comparing changes in transcription patters in response to oncoproteins in the mouse, naked mole rat, blind mole rat and human cells. The most striking finding was that the naked mole rat cells were resistant to transcriptional changes induced by oncogenic Ras. We found that pathways downstream of Ras were naturally attenuated in the naked mole rat. This finding identifies a novel mechanism that evolved to provide tumor resistance to the naked mole rat.
mTOR-driven widespread exon skipping renders multifaceted gene regulation and proteome complexity
Authors: Cheng Sze , Fahmi Naima Ahmed , Park Meeyeon , Chang Jae-Woong , Sun Jiao , Thao Kaitlyn , Yeh Hsin-Sung , Zhang Wei , Yong Jeongsik
Published: February 2020

The mammalian target of rapamycin (mTOR) pathway is crucial in cell proliferation. Previously, we reported transcriptome-wide 3’-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon-skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: alternative splicing (AS) in the 5’-UTR controls translation efficiency while AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.
Gradient of Tactile Properties in the Rat Whisker Pad
Authors: Gugig Erez , Sharma Hariom , Azouz Rony
Published: February 2020

The array of vibrissae on a rat’s face is the first stage in a high-resolution tactile sensing system. Progressing from rostral to caudal in any vibrissae row results in an increase in whisker length and thickness. This in turn may provide a systematic map of separate tactile channels governed by the mechanical properties of the whiskers. To examine whether this map is expressed in a location-dependent transformation of tactile signals into whisker vibrations and neuronal responses, we monitored whiskers’ movements across various surfaces and edges. We found a robust rostral-caudal gradient of tactile information transmission in which rostral shorter vibrissae displayed a higher sensitivity and a bigger differences in response to the different textures, whereas longer caudal vibrissae were less sensitive to the different textures. Nonetheless, we found that texture identity is not represented spatially across the whisker pad. Based on the responses of first-order sensory neurons, we found that neurons innervating rostral whiskers were better suited for textures discrimination, whereas neurons innervating caudal whiskers were more suited for edge detection. To examine the functional role of this organization, we monitored the whisking activity of awake rats foraging for food. We found a caudal-rostral gradient of whisking angle movements in which the longer caudal vibrissae spanned a larger space making them more suitable for object localization, whereas the rostral shorter vibrissae hardly moved. These results suggest that the whisker array in rodents forms a sensory structure in which different facets of tactile information are transmitted through location-dependent gradient of vibrissae on the rat’s face.
LC-Based Metabolomics and Multivariate Analyses Reveal Metabolite Variations in Different Propagation Methods ofEurycoma longifoliaRoots Harvested at Different Ages and Locations
Authors: Alias Nur Nabilah , Azizan Kamalrul Azlan , Basherudin Norlia , Hassan Nor Hasnida , Abdullah Nazirah
Published: February 2020

Eurycoma longifoliais a well-known medicinal plant with pharmacological effects and important bioactive compounds such as alkaloids and quassinoids. The suitable age of harvestingE. longifoliaroot for commercial use is relatively unknown and could influence the overall bioactive compounds present in the plant. In this study, non-targeted liquid chromatography mass spectrometer (LC-MS) and multivariate analyses (MVA) were performed to determine the chemical constituent of aqueous extract of 3-month-oldE. longifoliahairy root (HR) culture, 1-, 4- and 11-year-old harvestedE. longifoliaroots. Unsupervised principle component analysis (PCA) and supervised partial least square discriminant analysis (PLSDA) were applied to evaluate metabolic similarities and differences inE. longifoliaroots and hairy root in response to different harvesting age, locations and propagation methods. A total of 34 significant buckets with variable importance in projection (VIP) exceeding 1 were selected and identified. It was found that putatively identified quassinoids were significantly higher in 1-, 4- and 11-year-oldE. longifoliaroots whereas putative canthin-6-one alkaloids were abundantly present in 3-month-oldE. longifoliahairy root (HR). These findings may be applicable to improve the harvesting age and increase the content of bioactive compounds inE. longifoliaroots.
Cerebral organoid model reveals excessive proliferation of human caudal late interneuron progenitors in Tuberous Sclerosis Complex
Authors: Eichmüller Oliver L. , Corsini Nina S. , Vértesy Ábel , Scholl Theresa , Gruber Victoria-Elisabeth , Peer Angela M. , Chu Julia , Novatchkova Maria , Paredes Mercedes F. , Feucht Martha , Knoblich Jürgen A.
Published: February 2020

Although the intricate and prolonged development of the human brain critically distinguishes it from other mammals1, our current understanding of neurodevelopmental diseases is largely based on work using animal models. Recent studies revealed that neural progenitors in the human brain are profoundly different from those found in rodent animal models2–5. Moreover, post-mortem studies revealed extensive migration of interneurons into the late-gestational and post-natal human prefrontal cortex that does not occur in rodents6. Here, we use cerebral organoids to show that overproduction of mid-gestational human interneurons causes Tuberous Sclerosis Complex (TSC), a severe neuro-developmental disorder associated with mutations inTSC1andTSC2. We identify a previously uncharacterized population of caudal late interneuron progenitors, the CLIP-cells. In organoids derived from patients carrying heterozygousTSC2mutations, dysregulation of mTOR signaling leads to CLIP-cell over-proliferation and formation of cortical tubers and subependymal tumors. Surprisingly, second-hit events resulting from copy-neutral loss-of-heterozygosity (cnLOH) are not causative for but occur during the progression of tumor lesions. Instead, EGFR signaling is required for tumor proliferation, opening up a promising approach to treat TSC lesions. Our study demonstrates that the analysis of developmental disorders in organoid models can lead to fundamental insights into human brain development and neuropsychiatric disorders.
Prediction of the receptorome for the human-infecting virome
Authors: Zhang Zheng , Ye Sifan , Wu Aiping , Jiang Taijiao , Peng Yousong
Published: February 2020

The virus receptors are key for the viral infection of host cells. Identification of the virus receptors is still challenging at present. Our previous study has shown that human virus receptor proteins have some unique features including high N-glycosylation level, high number of interaction partners and high expression level. Here, a random-forest model was built to identify human virus receptorome from human cell membrane proteins with an accepted accuracy based on the combination of the unique features of human virus receptors and protein sequences. A total of 1380 human cell membrane proteins were predicted to constitute the receptorome of the human-infecting virome. In addition, the combination of the random-forest model with protein-protein interactions between human and viruses predicted in previous studies enabled further prediction of the receptors for 693 human-infecting viruses, such as the Enterovirus, Norovirus and West Nile virus. As far as we know, this study is the first attempt to predict the receptorome for the human-infecting virome and would greatly facilitate the identification of the receptors for viruses.
ULK1 and ULK2 are less redundant than previously thought: Computational analysis uncovers distinct regulation and functions of these autophagy induction proteins
Authors: Demeter Amanda , Romero-Mulero Mari Carmen , Csabai Luca , Ölbei Márton , Sudhakar Padhmanand , Haerty Wilfried , Korcsmáros Tamás
Published: February 2020

Macroautophagy, the degradation of cytoplasmic content by lysosomal fusion, is an evolutionary conserved process promoting homeostasis and intracellular defence. Macroautophagy is initiated primarily by a complex containing ULK1 or ULK2 (two paralogs of the yeast Atg1 protein). Deletion of ULK1 is sufficient to interrupt autophagy, while ULK2 seems expendable. To understand the differences between ULK1 and ULK2, we compared the human ULK1 and ULK2 proteins and their regulation. Despite the high similarity in their enzymatic domain, we found that ULK1 and ULK2 have major differences in their post-translational and transcriptional regulators. We identified 18 ULK1-specific and 7 ULK2-specific protein motifs serving as different interaction interfaces. We identified threeULK1-specific and oneULK2-specific transcription factor binding sites, and eight sites shared by the regulatory region of both genes. Importantly, we found that both their post-translational and transcriptional regulators are involved in distinct biological processes - suggesting separate functions for ULK1 and ULK2. For example, we found a condition-specific, opposite effect on apoptosis regulation for the two ULK proteins. Given the importance of autophagy in diseases such as inflammatory bowel disease and cancer, unravelling differences between ULK1 and ULK2 could lead to a better understanding of how autophagy is dysregulated in diseased conditions.
Sensory input drives rapid homeostatic scaling of the axon initial segment in mouse barrel cortex
Authors: Jamann Nora , Dannehl Dominik , Wagener Robin , Corcelli Corinna , Schultz Christian , Staiger Jochen , Kole Maarten H.P. , Engelhardt Maren
Published: February 2020

The axon initial segment (AIS) is an important axonal microdomain for action potential initiation and implicated in the regulation of neuronal excitability during activity-dependent cortical plasticity. While structural AIS plasticity has been suggested to fine-tune neuronal activity when network states change, whether it acts as a homeostatic regulatory mechanism in behaviorally relevant contexts remains poorly understood. Using anin vivomodel of the mouse whisker-to-barrel pathway in combination with immunofluorescence, confocal analysis and patch-clamp electrophysiological recordings, we observed bidirectional AIS plasticity. Furthermore, we find that structural and functional AIS remodeling occurs in distinct temporal domains: long-term sensory deprivation elicits an AIS length increase, accompanied with an increase in neuronal excitability, while sensory enrichment results in a rapid AIS shortening, accompanied by a decrease in action potential generation. Our findings highlight a central role of the AIS in the homeostatic regulation of neuronal input-output relations.
Elevated soluble Galectin-3 as a marker of chemotherapy efficacy in Breast cancer patients; a prospective study
Authors: Shafiq Arooj , Moore January , Suleman Aliya , Faiz Sabeen , Farooq Omar , Arshad Adnan , Tehseen Mohammad , Zafar Ammarah , Ali Syed Haider , Din Nasir Ud , Loya Asif , Siddiqui Neelam , Rehman Fatima K.
Published: February 2020

Purpose

Galectin-3 (Gal-3) is a glycan-binding lectin with a debated role in cancer progression due to its various functions and patterns of expression. The current study investigates the relationship between breast cancer prognosis and secreted Gal-3.

Methods

Breast cancer patients with first time cancer diagnosis and no prior treatment (n=88) were placed in either adjuvant or neoadjuvant setting based on their treatment modality. Stromal and plasma Gal-3 levels were measured in each patient at the time of diagnosis and then throughout treatment using immunohistochemistry (IHC) and ELISA respectively. Healthy women (>18 years of age,n=63) were used to establish baseline levels of plasma Gal-3. Patients were followed for 84 months for disease free survival analysis.

Results

Enhanced levels of plasma (adjuvant) and stromal (neo-adjuvant) Gal-3 were found to be markers of chemotherapy efficacy. The patients with chemotherapy induced increase in extracellular Gal-3 had longer disease-free interval and significantly lower rate of recurrence during 84-month follow-up compared to patients with unchanged or decreased secretion.

Conclusion

The findings support the use of plasma Gal-3 as a marker for chemotherapy efficacy when no residual tumor is visible through imaging. Furthermore, stromal levels in any remaining tumors post chemotherapy can also be used to predict long term prognosis in patients.

Key points

Increased Gal-3 secretion due to chemotherapy leads to better prognosis and longer disease-free survival.

The analysis of soluble Gal-3 expression could be useful as a support tool in predicting treatment efficacy in patients with no visible tumor remaining for follow up through imaging.
Alteration of brain dynamics during natural dual-task walking
Authors: Nenna Federica , Do Cao-Tri , Protzak Janna , Gramann Klaus
Published: February 2020

While walking in our natural environment, we continuously solve additional cognitive tasks. This increases the demand of resources needed for both the cognitive and motor systems, resulting in Cognitive-Motor Interference (CMI). While it is well known that a performance decrease in one or both tasks can be observed, little is known about human brain dynamics underlying CMI during dual-task walking. Moreover, a large portion of previous investigations on CMI took place in static settings, emphasizing the experimental rigor but overshadowing the ecological validity. To address these problems, we developed a dual-task walking scenario in virtual reality (VR) combined with Mobile Brain/Body Imaging (MoBI). We aimed at investigating how brain dynamics are modulated during natural overground walking while simultaneously performing a visual discrimination task in an ecologically valid scenario. Even though the visual task did not affect performance while walking, a P3 amplitude reduction along with changes in power spectral densities (PSDs) during dual-task walking were observed. Replicating previous results, this reflects the impact of walking on the parallel processing of visual stimuli, even when the cognitive task is particularly easy. This standardized and easy to modify VR-paradigm helps to systematically study CMI, allowing researchers to control the complexity of different tasks and sensory modalities. Future investigations implementing an improved virtual design with more challenging cognitive and motor tasks will have to investigate the roles of both cognition and motion, allowing for a better understanding of the functional architecture of attention reallocation between cognitive and motor systems during active behavior.