bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation and prediction of spread of COVID-19 in The Republic of Serbia by SEIRDS model of disease transmission
Authors: Stanojevic Slavoljub , Ponjavic Mirza , Stanojevic Slobodan , Stevanovic Aleksandar , Radojicic Sonja
Published: October 2020

As a response to the pandemic caused by SARS-Cov-2 virus, on 15 March, 2020, the Republic of Serbia introduced comprehensive anti-epidemic measures to curb COVID-19. After a slowdown in the epidemic, on 6 May, 2020, the regulatory authorities decided to relax the implemented measures. However, the epidemiological situation soon worsened again. As of 7 February, 2021, a total of 406,352 cases of SARSCov-2 infection have been reported in Serbia, 4,112 deaths caused by COVID-19. In order to better understand the epidemic dynamics and predict possible outcomes, we have developed an adaptive mathematical model SEAIHRDS (S-susceptible, E-exposed, A-asymptomatic, I-infected, H-hospitalized, R-recovered, D-dead due to COVID-19 infection, S-susceptible). The model can be used to simulate various scenarios of the implemented intervention measures and calculate possible epidemic outcomes, including the necessary hospital capacities. Considering promising results regarding the development of a vaccine against COVID-19, the model is extended to simulate vaccination among different population strata. The findings from various simulation scenarios have shown that, with implementation of strict measures of contact reduction, it is possible to control COVID-19 and reduce number of deaths. The findings also show that limiting effective contacts within the most susceptible population strata merits a special attention. However, the findings also show that the disease has a potential to remain in the population for a long time, likely with a seasonal pattern. If a vaccine, with efficacy equal or higher than 65%, becomes available it could help to significantly slow down or completely stop circulation of the virus in human population.

The effects of vaccination depend primarily on: 1. Efficacy of available vaccine(s), 2. Prioritization of the population categories for vaccination, and 3. Overall vaccination coverage of the population, assuming that the vaccine(s) develop solid immunity in vaccinated individuals. With expected basic reproduction number of Ro=2.46 and vaccine efficacy of 68%, an 87% coverage would be sufficient to stop the virus circulation.
Girding the loins? Direct evidence of the use of a medieval parchment birthing girdle from biomolecular analysis
Authors: Fiddyment Sarah , Goodison Natalie J. , Brenner Elma , Signorello Stefania , Price Kierri , Collins Matthew J.
Published: October 2020

In this paper we describe a dry non-invasive extraction method to detect palaeoproteomic evidence from stained manuscripts. The manuscript analysed in this study is a medieval parchment birth girdle (Wellcome Collection Western MS. 632) made in England and thought to be used by pregnant women while giving birth. Using a dry non-invasive sampling method we were able to extract both human and non-human peptides from the stains, including evidence for the use of honey, cereals, ovicaprine milk and legumes. In addition, a large number of human peptides were detected on the birth roll, many of which are found in cervico-vaginal fluid. This suggests that the birth roll was actively used during childbirth. This study is the first to extract and analyse non-collagenous peptides from a parchment document using a dry non-invasive sampling method and demonstrates the potential of this type of analysis for stained manuscripts, providing direct biomolecular evidence for active use.
Potential Achilles heels of SARS-CoV-2 are best displayed by the base order-dependent component of RNA folding energy
Authors: Zhang Chiyu , Forsdyke Donald R.
Published: October 2020

The base order-dependent component of folding energy has revealed a highly conserved region in HIV-1 genomes that associates with RNA structure. This corresponds to a packaging signal that is recognized by the nucleocapsid domain of the Gag polyprotein. Long viewed as a potential HIV-1 “Achilles heel,” the signal can be targeted by a new antiviral compound. Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. This indicates structural invariance (SI) sustained by natural selection. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions can be considered potential “Achilles heels” for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. The ribosomal frameshifting element scored well, but higher SI scores were obtained in other regions, including those encoding NSP13 and the nucleocapsid (N) protein.
A triple functional sensing chip for rapid detection of pathogenicListeria monocytogenes
Authors: Zhang Yachao , Wang Huimin , Xiao Sa , Wang Xia , Xu Ping
Published: October 2020

Here a triple functional sensing chip was created forL. monocytogenesdetection by integrating three biomarkers (Listeriolysin O (LLO) at protein level,hlygene at genetic level, and acetoin at metabolic level). Liposome encapsulated catechol was used for LLO detection via LLO pore-forming ability.hlygene was specifically captured by using a thiolated capture probe on nanoporous gold (NPG). As an electroactive label, methylene blue was embedded in double-stranded structures to generate an electrochemical signal forhlydetection. Combined with the electrocatalysis of NADH by NPG, the acetoin detection was achieved by measuring the consumption of NADH as a cofactor under acetoin reductase catalysis. Importantly, theL. monocytogenesdetection results obtained by detecting three biomarkers using the chip can be mutually verified, which reduces the probability of false positives based on a single marker. Moreover, the detection time was reduced to about 90 min, making it a rapid and reliable tool forL. monocytogenesdetection.
Following the footprints of variability during filopodia growth
Authors: Senra Daniela , Páez Alejandra , Gueron Geraldine , Bruno Luciana , Guisoni Nara
Published: October 2020

Filopodia are actin-built finger-like dynamic structures that protrude from the cell cortex. These structures can sense the environment and play key roles in migration and cell-cell interactions. The growth-retraction cycle of filopodia is a complex process exquisitely regulated by intra- and extra-cellular cues, whose nature remains elusive. Filopodia present wide variation in length, lifetime and growth rate. Here, we investigate the features of filopodia patterns in fixed prostate cancer cells by confocal microscopy. Analysis of almost a thousand filopodia suggests the presence of two different populations: one characterized by a narrow distribution of lengths and the other with a much more variable pattern with very long filopodia. We explore a stochastic model of filopodia growth which takes into account diffusion and reactions involving actin and the regulatory proteins formin and capping, and retrograde flow. Interestingly, we found an inverse dependence between the filopodial length and the retrograde velocity. This result led us to propose that variations in the retrograde velocity could explain the experimental lengths observed for these tumor cells. In this sense, one population involves a wider range of retrograde velocities than the other population, and also includes low values of this velocity. It has been hypothesized that cells would be able to regulate retrograde flow as a mechanism to control filopodia length. Thus, we propound that the experimental filopodia pattern is the result of differential retrograde velocities originated from heterogeneous signaling due to cell-substrate interactions or prior cell-cell contacts.
Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre
Authors: Ashhurst Thomas Myles , Marsh-Wakefield Felix , Putri Givanna Haryono , Spiteri Alanna Gabrielle , Shinko Diana , Read Mark Norman , Smith Adrian Lloyd , King Nicholas Jonathan Cole
Published: October 2020

As the size and complexity of high-dimensional cytometry data continue to expand, comprehensive, scalable, and methodical computational analysis approaches are essential. Yet, contemporary clustering and dimensionality reduction tools alone are insufficient to analyze or reproduce analyses across large numbers of samples, batches, or experiments. Moreover, approaches that allow for the integration of data across batches or experiments are not well incorporated into computational toolkits to allow for streamlined workflows. Here we present Spectre, an R package that enables comprehensive end-to-end integration and analysis of high-dimensional cytometry data from different batches or experiments. Spectre streamlines the analytical stages of raw data pre-processing, batch alignment, data integration, clustering, dimensionality reduction, visualization and population labelling, as well as quantitative and statistical analysis. Critically, the fundamental data structures used within Spectre, along with the implementation of machine learning classifiers, allow for the scalable analysis of very large high-dimensional datasets, generated by flow cytometry, mass cytometry (CyTOF), or spectral cytometry. Using open and flexible data structures, Spectre can also be used to analyze data generated by single-cell RNA sequencing (scRNAseq) or high-dimensional imaging technologies, such as Imaging Mass Cytometry (IMC). The simple, clear, and modular design of analysis workflows allow these tools to be used by bioinformaticians and laboratory scientists alike. Spectre is available as an R package or Docker container. R code is available on Github (https://github.com/immunedynamics/spectre).
Computational response modeling reveals context dependent Akt activity in luminal breast cancer cells
Authors: Erdem Cemal , Lee Adrian V. , Taylor D. Lansing , Lezon Timothy R.
Published: October 2020

Aberrant signaling through insulin (Ins) and insulin-like growth factor I (IGF1) receptors contributes to the risk and advancement of many cancer types by activating cell survival cascades. Mechanistic computational modeling of such pathways provides insights into each component’s role in the cell response. In previous computational models, the two receptors were treated as indistinguishable, missing the opportunity to delineate their distinct roles in cancer progression. Here, a dual receptor (IGF1R & InsR) computational model elucidated new experimental hypotheses on how differential early responses emerge. Complementary to our previous findings, the model suggested that the regulation of insulin receptor substrate (IRS) is critical in inducing differential MAPK and Akt activation. As predicted, perturbing ribosomal protein S6 kinase (RPS6K) kinase activity led to an increased Akt activation with insulin stimulation compared to IGF1 stimulation. Being able to discern differential downstream signaling, we can explore improved anti-IGF1R cancer therapies by eliminating emergence of compensation mechanisms, without disrupting InsR signaling.

Implications

The study shows, both experimentally and through computational models, that IGF1 and insulin receptor signaling pathways respond differently to RPS6K inhibition.
Unified neural dynamics of decisions and actions in the cerebral cortex and basal ganglia
Authors: Thura David , Cabana Jean-François , Feghaly Albert , Cisek Paul
Published: October 2020

Several theoretical models suggest that deciding about actions and executing them are not completely distinct neural mechanisms but instead two modes of an integrated dynamical system. Here, we investigate this proposal by examining how neural activity unfolds during a dynamic decision-making task within the high-dimensional space defined by the activity of cells in monkey dorsal premotor (PMd), primary motor (M1), and dorsolateral prefrontal cortex (dlPFC) as well as the external and internal segments of the globus pallidus (GPe, GPi). Dimensionality reduction shows that the four strongest components of neural activity are functionally interpretable, reflecting a state transition between deliberation and commitment, the transformation of sensory evidence into a choice, and the baseline and slope of the rising urgency to decide. Analysis of the contribution of each population to these components shows differences between regions but no distinct clusters within each region. During deliberation, cortical activity unfolds on a two-dimensional “decision manifold” defined by sensory evidence and urgency, and falls off this manifold at the moment of commitment into a choice-dependent trajectory leading to movement initiation. The structure of the manifold varies between regions: In PMd it is curved, in M1 it is nearly perfectly flat, and in dlPFC it is almost entirely confined to the sensory evidence dimension. In contrast, pallidal activity during deliberation is primarily defined by urgency. We suggest that these findings reveal the distinct dynamics of different regions, supporting a unified recurrent attractor model of action selection and execution.
Learning to leverage salient regions in neuro-oncology using Deep Learning
Authors: Grigis A. , Alentorn A. , Frouin V.
Published: October 2020

Developing an automatic tumor detector for MRI medical images is a major challenge in neuro-oncology. The availability of such a tool would be a valuable assistance for the radiologists. Numerous works have tried to segment the tumor tissues, others have attempted to localize the tumor globally. In this work we focus on this second class of methods and we compare two drastically different strategies. The first one is an assumption-free anomaly detector build over a Variational Auto-Encoder (VAE), and the second one is a VGG classifier that embed Attention-Gated (AG) units to focus on the target structures at almost no additional computational cost. This comparison is first conducted on the publicly available BraTS glioma dataset for which published performance results can serve as reference, and extended as such (ie., without transfer learning) to two internal image datasets, namely Primary Central Nervous System Lymphoma (PCNSL) and Metastasis. The results demonstrate that the VAE and AG-VGG strategies can be used, up to a certain extent, to localize brain tumors.
Mass mortality of foundation species on rocky shores: another reason why monitoring programs are relevant
Authors: Mendez María M. , Livore Juan P. , Márquez Federico , bigatti Gregorio
Published: October 2020

Global concern around substantial losses of biodiversity has led to the development of a number of large-scale long-term monitoring programs. In the past few decades, networks were established to obtain appropriate data on the spatial and temporal variation of marine species on rocky shores. Recently, the Marine Biodiversity Observation Network Pole to Pole of the Americas program (MBON P2P) was established and is coordinating biodiversity surveys along coastal areas throughout the continent. In this context, the goal of this paper was to demonstrate whether the proposed MBON P2P sampling protocol is capable of detecting rapid declines in cover of foundation species on Patagonian rocky shores. Changes in mussel beds cover were studied on monitored sites in northern Patagonia. Concurrently, long-term mussel bed dynamics were assessed based on existing data. Results showed that a mussel mortality event could be detected with this methodology. It took less than a year for mussel cover to drop from 90 to almost 0% despite the fact that significant changes in mussel bed cover were not registered in the previous 20 years at the study area. Therefore, yearly monitoring is needed, as a minimum, in order to timely perceive this kind of process. Real-time detection offers the opportunity of properly understanding the causes that lead to the loss of key community components such as these foundation species. Furthermore, it would provide early warning to decision makers enhancing the chances of conservation of natural environments and their key ecosystem services.
Single-cell secretion analysis reveals a dual role for IL-10 in restraining and resolving the TLR4-induced inflammatory response
Authors: Alexander Amanda F. , Forbes Hannah , Miller-Jensen Kathryn
Published: October 2020

Following TLR4 stimulation of macrophages, negative feedback mediated by the anti-inflammatory cytokine IL-10 limits the inflammatory response. However, extensive cell-to-cell variability in TLR4-stimulated cytokine secretion raises questions about how negative feedback is robustly implemented. To explore this, we characterized the TLR4-stimulated secretion program in primary murine macrophages using a single-cell microwell assay that enabled evaluation of functional autocrine IL-10 signaling. High-dimensional analysis of single-cell data revealed three distinct tiers of TLR4-induced proinflammatory activation based on levels of cytokine secretion. Surprisingly, while IL-10 inhibits TLR4-induced activation in the highest tier, it also contributes to the TLR4-induced activation threshold by regulating which cells transition from non-secreting to secreting states. This role for IL-10 in restraining TLR4 inflammatory activation is largely mediated by intermediate IFN-β signaling, while TNF-a likely mediates response resolution by IL-10. Thus, cell-to-cell variability in cytokine regulatory motifs provides a means to tailor the TLR4-induced inflammatory response.
Mapping the Antibody Repertoires in Ferrets with Repeated Influenza A/H3 Infections: Is Original Antigenic Sin Really “Sinful”?
Authors: Einav Tal , Kosikova Martina , Radvak Peter , Kuo Yuan-Chia , Kwon Hyung Joon , Xie Hang
Published: October 2020

The influenza-specific antibody repertoire is continuously reshaped by infection and vaccination. The host immune response to contemporary viruses can be redirected to preferentially boost antibodies specific for viruses encountered early in life, a phenomenon called original antigenic sin (OAS) that is suggested to be responsible for diminished vaccine effectiveness after repeated vaccination. In this study, we used a new computational tool called Neutralization Map to determine the hemagglutination inhibition profiles of individual antibodies within ferret antisera elicited by repeated influenza A/H3 infections. Our results suggest that repeated infections continuously reshape the ferret antibody repertoire, but that a broadly neutralizing antibody signature can nevertheless be induced irrespective of OAS. Overall, our study offers a new way to visualize how immune history shapes individual antibodies within a repertoire, which may help inform future vaccine design.
The mechanism of motor inhibition by microtubule-associated proteins
Authors: Ferro Luke S , Eshun-Wilson Lisa , Gölcük Mert , Fernandes Jonathan , Huijben Teun , Gerber Eva , Jack Amanda , Costa Katelyn , Gür Mert , Fang Qianglin , Nogales Eva , Yildiz Ahmet
Published: October 2020

Microtubule (MT)-associated proteins (MAPs) regulate intracellular transport by selectively recruiting or excluding kinesin and dynein motors from MTs. We used single-molecule and cryo-electron imaging to determine the mechanism of MAP-motor interactionsin vitro. Unexpectedly, we found that the regulatory role of a MAP cannot be predicted based on whether it overlaps with the motor binding site or forms liquid condensates on the MT. Although the MT binding domain (MTBD) of MAP7 overlaps with the kinesin-1 binding site, tethering of kinesin-1 by the MAP7 projection domain supersedes this inhibition and results in biphasic regulation of kinesin-1 motility. Conversely, the MTBD of tau inhibits dynein motility without overlapping with the dynein binding site or by forming tau islands on the MT. Our results indicate that MAPs sort intracellular cargos moving in both directions, as neither dynein nor kinesin can walk on a MAP-coated MT without favorably interacting with that MAP.

HIGHLIGHTS

MAP7 binds to a novel site and can coexist with tau on the MT.

Kinesin-1 motility is biphasically regulated by MAP7 accumulation on the microtubule.

MT decoration of MAPs inhibits motors even when they do not block the motor binding site.

Motors need to interact with a MAP to walk on MAP-decorated MTs
Distributed Phase Oscillatory Excitation Efficiently Produces Attractors Using Spike Timing Dependent Plasticity
Authors: Wong Eric C.
Published: October 2020

The brain is thought to represent information in the form of activity in distributed groups of neurons known as attractors, but it is not clear how attractors are formed or used in processing. We show here that in a randomly connected network of simulated spiking neurons, periodic stimulation of neurons with distributed phase offsets, along with standard spike timing dependent plasticity (STDP), efficiently creates distributed attractors. These attractors may have a consistent ordered firing pattern, or become disordered, depending on the conditions. We also show that when two such attractors are stimulated in sequence, the same STDP mechanism can create a directed association between them, forming the basis of an associative network. We find that for an STDP time constant of 20ms, the dependence of the efficiency of attractor creation on the driving frequency has a broad peak centered around 8Hz. Upon restimulation, the attractors selfoscillate, but with an oscillation frequency that is higher than the driving frequency, ranging from 10-100Hz.
A Transgenic System for Targeted Ablation of Reproductive and Maternal-Effect genes
Authors: Bertho Sylvain , Kaufman Odelya , Lee KathyAnn , Santos-Ledo Adrian , Dellal Daniel , Marlow Florence L.
Published: October 2020

Maternally provided gene products regulate the earliest events of embryonic life, including formation of the oocyte that will develop into an egg, and eventually an embryo. Forward genetic screens have provided invaluable insights into the molecular regulation of embryonic development, including essential contributions of some genes whose products must be provided to the transcriptionally silent early embryo for normal embryogenesis, maternal-effect genes. However, other maternal-effect genes are not accessible due to their essential zygotic functions during embryonic development. Identifying these regulators is essential to fill the large gaps in our understanding of the mechanisms and molecular pathways contributing to fertility and maternally regulated developmental processes. To identify these maternal factors, it is necessary to bypass the earlier requirement for these genes so that their potential later functions can be investigated. Here we report reverse genetic systems to identify genes with essential roles in reproductive and maternal-effect processes, as proof of principal and to assess the efficiency and robustness of mutagenesis we used these transgenic systems to disrupt two genes with known maternal-effect functions,kif5Baandbucky ball.

Summary Statement

We report reverse genetic systems to identify essential regulators of reproductive and maternal-effect processes, as proof of principal we used these transgenic systems to disrupt genes with known maternal-effect functions.
Transient light-activated gene expression in Chinese hamster ovary cells
Authors: Minami Shiaki A. , Shah Priya S.
Published: October 2020

Background

Chinese hamster ovary (CHO) cells are widely used for industrial production of biopharmaceuticals. Many genetic, chemical, and environmental approaches have been developed to modulate cellular pathways to improve titers. However, these methods are often irreversible or have off-target effects. Development of techniques which are precise, tunable, and reversible will facilitate temporal regulation of target pathways to maximize titers. In this study, we investigate the use of optogenetics in CHO cells. The light-activated CRISPR-dCas9 effector (LACE) system was first transiently transfected to express eGFP in a light-inducible manner. Then, a stable system was tested using lentiviral transduction.

Results

Transient transfections resulted in increasing eGFP expression as a function of LED intensity, and activation for 48 hours yielded up to 4-fold increased eGFP expression compared to cells kept in the dark. Fluorescence decreased once the LACE system was deactivated, and a half-life of 14.9 hours was calculated, which is in agreement with values reported in the literature. In cells stably expressing the LACE system, eGFP expression was confirmed, but there was no significant increase in expression following light activation.

Conclusions

Taken together, these results suggest that optogenetics can regulate CHO cell cultures, but development of stable cell lines requires optimized expression levels of the LACE components to maintain high dynamic range.
ATAC-seq with unique molecular identifiers improves quantification and footprinting
Authors: Zhu Tao , Liao Keyan , Zhou Rongfang , Xia Chunjiao , Xie Weibo
Published: October 2020

ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces an increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. In our study, UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq, which helps identify an additional 50% or more of footprints. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available athttps://github.com/tzhu-bio/UMI-ATAC-seq.
Specificities of modeling membrane proteins using multi-template homology modeling
Authors: Leman Julia Koehler , Bonneau Richard
Published: October 2020

Structures of membrane proteins are challenging to determine experimentally and currently represent only about 2% of the structures in the ProteinDataBank. Because of this disparity, methods for modeling membrane proteins are fewer and of lower quality than those for modeling soluble proteins. However, better expression, crystallization, and cryo-EM techniques have prompted a recent increase in experimental structures of membrane proteins, which can act as templates to predict the structure of closely related proteins through homology modeling. Because homology modeling relies on a structural template, it is easier and more accurate than fold recognition methods orde novomodeling, which are used when the sequence similarity between the query sequence and the sequence of related proteins in structural databases is below 25%. In homology modeling, a query sequence is mapped onto the coordinates of a single template and refined. With the increase in available templates, several templates often cover overlapping segments of the query sequence. Multi-template modeling can be used to identify the best template for local segments and join them into a single model. Here we provide a protocol for modeling membrane proteins from multiple templates in the Rosetta software suite. This approach takes advantage of several integrated frameworks, namely RosettaScripts, RosettaCM, and RosettaMP with the membrane scoring function.
A Wnt5a-Cdc42 axis controls aging and rejuvenation of hair-follicle stem cells
Authors: Tiwari Rajiv L , Mishra Pratibha , Martin Nicola , George Nikhil Oommen , Sakk Vadim , Soller Karin , Nalapareddy Kodandaramireddy , Nattamai Kalpana , Scharffetter-Kochanek Karin , Florian Maria Carolina , Geiger Hartmut
Published: October 2020

Normal hair growth occurs in cycles, comprising growth (anagen), cessation (catagen) and rest (telogen). Upon aging, the initiation of anagen is significantly delayed, which results in impaired hair regeneration. Hair regeneration is driven by hair follicle stem cells (HFSCs). We show here that aged HFSCs present with a decrease in canonical Wnt signaling and a shift towards non-canonical Wnt5a driven signaling which antagonizes canonical Wnt signaling. Elevated expression of Wnt5a in HFSCs upon aging results in elevated activity of the small RhoGTPase Cdc42 as well as a change in the spatial distribution of Cdc42 within HFSCs. Treatment of aged HFSC with a specific pharmacological inhibitor of Cdc42 activity termed CASIN to suppress the aging-associated elevated activity of Cdc42 restored canonical Wnt signaling in aged HFSCs. Treatment of aged mice in vivo with CASIN induced anagen onset and increased the percentage of anagen skin areas. Aging-associated functional deficits of HFSCs are at least in part intrinsic to HFSCs and can be restored by rational pharmacological approaches.
Mesoscale phase separation of chromatin in the nucleus
Authors: Bajpai Gaurav , Amiad-Pavlov Daria , Lorber Dana , Volk Talila , Safran Samuel
Published: October 2020

Intact-organism imaging ofDrosophilalarvae reveals and quantifies chromatin-aqueous phase separation. The chromatin can be organized near the lamina layer of the nuclear envelope, conventionally fill the nucleus, be organized centrally, or as a wetting droplet. These transitions are controlled by changes in nuclear volume and the interaction of chromatin with the lamina (part of the nuclear envelope) at the nuclear periphery. Using a simple polymeric model that includes the key features of chromatin self-attraction and its binding to the lamina, we demonstrate theoretically that it is the competition of these two effects that determines the mode of chromatin distribution. The qualitative trends as well as the compositional profiles obtained in our simulations compare well with the observed intact-organism imaging and quantification. Since the simulations contain only a small number of physical variables we can identify the generic mechanisms underlying the changes in the observed phase separations.
Goblet cell LRRC26 regulates BK channel activation and protects against colitis in mice
Authors: Gonzalez-Perez Vivian , Martinez-Espinosa Pedro L. , Sala-Rabanal Monica , Bharadwaj Nikhil , Xia Xiao-Ming , Chen Albert C. , Alvarado David , Gustafsson Jenny K. , Hu Hongzhen , Ciorba Matthew A. , Lingle Christopher J.
Published: October 2020

Goblet cells (GCs) are specialized cells of the intestinal epithelium contributing critically to mucosal homeostasis. One of the functions of GCs is to produce and secrete MUC2, the mucin that forms the scaffold of the intestinal mucus layer coating the epithelium and separates the luminal pathogens and commensal microbiota from the host tissues. Although a variety of ion channels and transporters are thought to impact on MUC2 secretion, the specific cellular mechanisms that regulate GC function remain incompletely understood. Previously, we demonstrated that leucine-rich-repeat-containing protein 26 (LRRC26), a known regulatory subunit of the Ca2+-and voltage-activated K+channel (BK channel), localizes specifically to secretory cells within the intestinal tract. Here, utilizing a mouse model in which MUC2 is fluorescently tagged allowing visualization of single GCs in intact colonic crypts, we show that murine colonic GCs have functional LRRC26-associated BK channels. In the absence of LRRC26, BK channels are present in GCs, but are not activated at physiological conditions. In contrast, all tested MUC2-negative cells completely lacked BK channels. Moreover, LRRC26-associated BK channels underlie the BK channel contribution to the resting transepithelial current across mouse distal colonic mucosa. Genetic ablation of either LRRC26 or BK-pore forming α-subunit in mice results in a dramatically enhanced susceptibility to colitis induced by dextran sodium sulfate (DSS). These results demonstrate that normal potassium flux through LRRC26-associated BK channels in GCs has protective effects against colitis in mice.

Significance

A primary function of goblet cells (GCs) of the intestinal epithelium is to generate a protective mucus layer lining the intestinal lumen. GC dysfunction is linked to Inflammatory Bowel Disease (IBD). GC mucus secretion is thought to be dependent on contributions of an ensemble of anion and cation fluxes, although understanding remains limited. Here, it is shown in mouse colon that the Ca2+- and voltage-dependent BK-type K+channel, specifically in association with the LRRC26 regulatory subunit, plays a critical role in normal GC function, protecting mice against chemically-induced colitis. The results demonstrate that normal K+fluxes mediated by LRRC26-containing BK channels are required for normal GC function, potentially providing insights into the potential role of BK channels in IBD.
Surfactant-free production of biomimetic artificial cells using PDMS-based microfluidics
Authors: Yandrapalli Naresh , Petit Julien , Bäumchen Oliver , Robinson Tom
Published: October 2020

Microfluidic-based production of cellular mimics (e.g. giant vesicles) presents a paradigm-shift in the development of artificial cells. While encapsulation rates are high and vesicles are mono-disperse compared to swelling-based techniques, current microfluidic emulsion-based methods heavily rely on the addition of additives such as surfactants, glycerol and even ethanol to produce stable vesicles. In this work, we present a microfluidic platform designed for the production of cellular mimics in the form of giant unilamellar vesicles (GUVs). Our PDMS-based device comprises a double cross-junction and a serpentine-shaped shear inducing module to produce surfactant-free and additive-free monodisperse biomimetic GUVs. Vesicles can be made with neutral and charged lipids in physiological buffers and, unlike previous works, it is possible to produce them with pure water both inside and outside. By not employing surfactants such as block co-polymers, additives like glycerol, and long-chain poly-vinyl alcohol that are known to alter the properties of lipid membranes, the vesicles are rendered truly biomimetic. The membrane functionality and stability are validated by lipid diffusion, membrane protein incorporation, and leakage assays. To demonstrate the usability of the GUVs using this method, various macromolecules such as DNA, smaller liposomes, mammalian cells and even microspheres are encapsulated within the GUVs.
Habitat patch size and tree species richness shape the bird community in urban green spaces of rapidly urbanizing region of India
Authors: Kaushik Monica , Tiwari Samakshi , Manisha Kumari
Published: October 2020

Rapid urbanization and associated biodiversity loss is rampant globally but especially a cause of concern for developing countries. However, numerous studies investigating the role of urban green spaces have established their key role in conserving larger suites of species in urban area. Yet our knowledge is lopsided due to lag in research in developing countries. We examined how landscape and local scale features of urban green spaces influence bird species richness, density, fine-foraging guild richness and composition during breeding and non-breeding season. This is the first study of this nature in one the Himalayan states of India. We quantified landscape level variables in the 250m buffer around 18 urban green spaces. We sampled vegetation and bird community during breeding and non-breeding season through 52 intensive sampling point spread across 18 urban green spaces. Size of the urban green space at landscape level and tree richness at the local scale emerged as important predictor variables influencing bird species richness, density and richness of imperiled insectivorous guild across seasons. Urban green spaces within education institutions and offices experiencing much less management supported higher bird richness and density whereas city parks were the most species poor. Community composition was affected more strongly by built-up cover and barren area in the matrix and also by tree species richness within urban green spaces. City planners should focus on establishing larger city parks during design stage whereas biodiversity potential of the existing urban green spaces could be enhanced by selecting native tree and shrub species to increase overall habitat complexity.
Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using CRISPR-targeted ultra-long read sequencing (CTLR-Seq)
Authors: Zhou Bo , Shin GiWon , Greer Stephanie U. , Vervoort Lisanne , Huang Yiling , Pattni Reenal , Ho Marcus , Wong Wing H. , Vermeesch Joris R. , Ji Hanlee P. , Urban Alexander E.
Published: October 2020

We have developed a generally applicable method based on CRISPR/Cas9-targeted ultra-long read sequencing (CTLR-Seq) to completely and haplotype-specifically resolve, at base-pair resolution, large, complex, and highly repetitive genomic regions that had been previously impenetrable to next-generation sequencing analysis such as large segmental duplication (SegDup) regions and their associated genome rearrangements that stretch hundreds of kilobases. Our method combinesin vitroCas9-mediated cutting of the genome and pulse-field gel electrophoresis to haplotype-specifically isolate intact large (200-550 kb) target regions that encompass previously unresolvable genomic sequences. These target fragments are then sequenced (amplification-free) to produce ultra-long reads at up to 40x on-target coverage using Oxford nanopore technology, allowing for the complete assembly of the complex genomic regions of interest at single base-pair resolution. We applied CTLR-Seq to resolve the exact sequence of SegDup rearrangements that constitute the boundary regions of the 22q11.2 deletion CNV and of the 16p11.2 deletion and duplication CNVs. These CNVs are among the strongest known risk factors for schizophrenia and autism. We then performde novoassembly to resolve, for the first time, at single base-pair resolution, the sequence rearrangements of the 22q11.2 and 16p11.2 CNVs, mapping out exactly the genes and non-coding regions that are affected by the CNV for different carriers.
Imaging α-synuclein pathologies in animal models and patients with Parkinson’s and related diseases
Authors: Endo Hironobu , Ono Maiko , Takado Yuhei , Matsuoka Kiwamu , Takahashi Manami , Tagai Kenji , Kataoka Yuko , Hirata Kosei , Takahata Keisuke , Seki Chie , Kokubo Naomi , Fujinaga Masayuki , Mori Wakana , Nagai Yuji , Mimura Koki , Kumata Katsushi , Kikuchi Tatsuya , Shimozawa Aki , Mishra Sushil K. , Yamaguchi Yoshiki , Shimizu Hiroshi , Kakita Akiyoshi , Takuwa Hiroyuki , Shinotoh Hitoshi , Shimada Hitoshi , Kimura Yasuyuki , Ichise Masanori , Suhara Tetsuya , Minamimoto Takafumi , Sahara Naruhiko , Kawamura Kazunori , Zhang Ming-Rong , Hasegawa Masato , Higuchi Makoto
Published: October 2020

Deposition of α-synuclein fibrils is implicated in Parkinson’s disease (PD) and dementia with Lewy bodies (DLB), whilein vivodetection of α-synuclein pathologies in these illnesses has been challenging. Here, we have developed a small-molecule ligand, C05-05, for visualizing α-synuclein deposits in the brains of living subjects.In vivooptical and positron emission tomography (PET) imaging of mouse and marmoset models demonstrated that C05-05 captured a dynamic propagation of fibrillogenesis along neural pathways followed by disruptions of these structures. High-affinity binding of18F-C05-05 to α-synuclein aggregates in human brain tissues was also proven byin vitroassays. Notably, PET-detectable18F-C05-05 signals were intensified in the midbrains of PD and DLB patients as compared to healthy controls, providing the first demonstration of visualizing α-synuclein pathologies in these illnesses. Collectively, we propose a new imaging technology offering neuropathology-based translational assessments of PD and allied disorders towards diagnostic and therapeutic research and development.
Transferrin receptor is another receptor for SARS-CoV-2 entry
Authors: Tang Xiaopeng , Yang Mengli , Duan Zilei , Liao Zhiyi , Liu Lei , Cheng Ruomei , Fang Mingqian , Wang Gan , Liu Hongqi , Xu Jingwen , Kamau Peter M , Zhang Zhiye , Yang Lian , Zhao Xudong , Peng Xiaozhong , Lai Ren
Published: October 2020

Angiotensin-converting enzyme 2 (ACE2) has been suggested as a receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry to cause coronavirus disease 2019 (COVID-19). However, no ACE2 inhibitors have shown definite beneficiaries for COVID-19 patients, applying the presence of another receptor for SARS-CoV-2 entry. Here we show that ACE2 knockout dose not completely block virus entry, while TfR directly interacts with virus Spike protein to mediate virus entry and SARS-CoV-2 can infect mice with over-expressed humanized transferrin receptor (TfR) and without humanized ACE2. TfR-virus co-localization is found both on the membranes and in the cytoplasma, suggesting SARS-CoV-2 transporting by TfR, the iron-transporting receptor shuttling between cell membranes and cytoplasma. Interfering TfR-Spike interaction blocks virus entry to exert significant anti-viral effects. Anti-TfR antibody (EC50 ~16.6 nM) shows promising anti-viral effects in mouse model. Collectively, this report indicates that TfR is another receptor for SARS-CoV-2 entry and a promising anti-COVID-19 target.
Patient iPSC-astrocytes show transcriptional and functional dysregulation in schizophrenia
Authors: Koskuvi Marja , Lehtonen Šárka , Trontti Kalevi , Keuters Meike , Wu Ying Chieh , Koivisto Hennariikka , Ludwig Anastasia , Plotnikova Lidiia , Virtanen Pekka L. J. , Räsänen Noora , Kaipainen Satu , Hyötyläinen Ida , Dhungana Hiramani , Giniatullina Raisa , Ojansuu Ilkka , Vaurio Olli , Cannon Tyrone D. , Lönnqvist Jouko , Therman Sebastian , Suvisaari Jaana , Kaprio Jaakko , Lähteenvuo Markku , Tohka Jussi , Giniatullin Rashid , Rivera Claudio , Hovatta Iiris , Tanila Heikki , Tiihonen Jari , Koistinaho Jari
Published: October 2020

Human astrocytes are multifunctional brain cells and may contribute to the pathophysiology of schizophrenia (SCZ). We differentiated astrocytes from induced pluripotent stem cells of monozygotic twins discordant for SCZ, and found sex-specific gene expression and signaling pathway alterations related particularly to inflammation and synaptic functions. While Ingenuity Pathway Analysis identified SCZ disease and synaptic transmission pathway changes in SCZ astrocytes, the most consistent findings were related to collagen and cell adhesion associated pathways. Neuronal responses to glutamate and GABA differed between astrocytes from control persons, affected twins, and their unaffected co-twins, and were normalized by clozapine treatment. SCZ astrocyte cell transplantation to the mouse forebrain caused gene expression changes in demyelination, synaptic dysfunction and inflammation pathways of mouse brain cells and resulted in behavioral changes in cognitive and olfactory functions. Altogether, our results show that astrocytes contribute to both familial risk and clinical manifestation of SCZ in a sex-specific manner.
An extended reconstruction of human gut microbiota metabolism for personalized nutrition
Authors: Blasco Telmo , Pérez-Burillo Sergio , Balzerani Francesco , Lerma-Aguilera Alberto , Hinojosa-Nogueira Daniel , Pastoriza Silvia , Gosalbes María José , Jiménez-Hernández Nuria , Francino M. Pilar , Rufián-Henares José Ángel , Apaolaza Iñigo , Planes Francisco J.
Published: October 2020

Understanding how diet and gut microbiota interact in the context of human health is a key question in personalized nutrition. Genome-scale metabolic networks and constraint-based modeling approaches are promising to systematically address this complex question. However, when applied to nutritional questions, a major issue in existing reconstructions is the lack of information about degradation pathways of relevant nutrients in the diet that are metabolized by the gut microbiota. Here, we present AGREDA, an extended reconstruction of the human gut microbiota metabolism for personalized nutrition. AGREDA includes the degradation pathways of 231 nutrients present in the human diet and allows us to more comprehensively simulate the interplay between food and gut microbiota. We show that AGREDA is more accurate than existing reconstructions in predicting output metabolites of the gut microbiota. Finally, using AGREDA, we established relevant metabolic differences among clinical subgroups of Spanish children: lean, obese, allergic to foods and celiac.
Structural classification of proteins based on the computationally efficient recurrence quantification analysis and horizontal visibility graphs
Authors: Areti Zervou Michaela , Doutsi Effrosyni , Pavlidis Pavlos , Tsakalides Panagiotis
Published: October 2020

Motivation

Protein structure prediction is one of the most significant problems in bioinformatics, as it has a prominent role in understanding the function and evolution of proteins. Designing a computationally efficient but at the same time accurate prediction method remains a pressing issue, especially for sequences that we cannot obtain a sufficient amount of homologous information from existing protein sequence databases. Several studies demonstrate the potential of utilizing chaos game representation (CGR) along with time series analysis tools such as recurrence quantification analysis (RQA), complex networks, horizontal visibility graphs (HVG) and others. However, the majority of existing works involve a large amount of features and they require an exhaustive, time consuming search of the optimal parameters. To address the aforementioned problems, this work adopts the generalized multidimensional recurrence quantification analysis (GmdRQA) as an efficient tool that enables to process concurrently a multidimensional time series and reduce the number of features. In addition, two data-driven algorithms, namely average mutual information (AMI) and false nearest neighbors (FNN), are utilized to define in a fast yet precise manner the optimal GmdRQA parameters.

Results

The classification accuracy is improved by the combination of GmdRQA with the HVG. Experimental evaluation on a real benchmark dataset demonstrates that our methods achieve similar performance with the state-of-the-art but with a smaller computational cost.

Availability

The code to reproduce all the results is available athttps://github.com/aretiz/protein_structure_classification/tree/main.

Contact

edoutsi@ics.forth.gr

Supplementary information

Supplementary data are available atBioinformaticsonline.