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Sinha, B.

Publications and source records attributed to Sinha, B..

At least 19 recordsLinked to original sources

Size-dependent membrane remodelling at Myomerger clusters during myoblast fusion

Myomerger drives fusion pore formation after hemifusion of membranes during myogenic cell-cell fusion in myogenesis, but its mechanical impact has been characterised largely in liposomes. In differentiating C2C12 cells, hemifusion began at 8 hr and peaked at 24 hr, whereas the earliest content-mixing events appeared only at 24 hr - Myomerger is therefore present much before it is competent to complete fusion. Using Interference Reflection Microscopy (IRM), we found that basal membrane tension in hemifusing cells was indistinguishable from that of non-fusing cells at 8-24 hr, and became significantly higher by 48 hr. Knockdown showed that Myomerger switched across this window from tension-reducing to enhancing cell-scale tension, unlike Myomaker, which enhanced tension in both the early and late phases. Addressing the local impact, Stimulated Emission Depletion microscopy (STED) imaging resolved Myomerger clusters built from a [~]40 nm basic unit that aggregate further. Small clusters induced nanometric outward bulges, a topology rare outside Myomerger-enriched regions; these bulges damped membrane fluctuations and showed higher lipid compaction at the centre, as deciphered by Flipper-TR FLIM, at the lateral as well as the basal membrane, and may be central to the hemifusion-to-pore transition. Larger clusters indented the membrane, showed enhanced fluctuations and associated with the clathrin-coated pits, consistent with surface clearance by endocytosis. Myomerger colocalized poorly with actin fibres and cholesterol-enriched nanodmains despite lying close to both. Together, these findings establish size-based clustering of Myomerger as a determinant of membrane topology and lipid compaction when hemifusion peaks and content mixing begins.

biophysics↗

Spatio-temporal regulation of ligand trafficking and TLR9 activation involves PIEZO1 mechanosensing in human plasmacytoid dendritic cells

Plasmacytoid dendritic cells (pDCs) are specialized innate immune cells which play a pivotal role in antiviral immunity by producing large quantities of type I interferons (IFNs) upon sensing nucleic acids via Toll-like receptor 9 (TLR9). Synthetic oligodeoxynucleotides (ODNs) such as CpGA and CpGB, both containing unmethylated CpG motifs, are commonly used experimental TLR9 agonists. Interestingly, CpGA and CpGB elicit markedly different responses in pDCs - CpGA induces robust IFN- production, whereas CpGB does not. The mechanistic basis underlying this ligand-specific functional divergence has remained unclear. Here, we identify PIEZO1, a mechanosensory ion channel, as a critical determinant of ligand-specific IFN responses in human primary pDCs. We demonstrate that unlike CpGB, CpGA self-associates into larger aggregates that generate membrane tension during cellular uptake, leading to activation of PIEZO1. This activation triggers localized calcium influx and cytoskeletal remodeling, resulting in the formation of local F-actin structures that retain CpGA within early endosomes enabling sustained IRF7 nuclear translocation and robust type I IFN production. Disruption of PIEZO1 or actin polymerization abrogates CpGA-induced IFN production, while pharmacological activation of Piezo1 enhances IFN production in response to CpGB. Thus, these findings uncover a previously unrecognized biophysical checkpoint in nucleic acid sensing, wherein membrane tension is transduced via PIEZO1 into spatially controlled TLR9 signaling. Overall, our study establishes PIEZO1 mechanosensing at the plasma membrane as a key regulatory event in nucleic acid-induced immunity, with different functional outcomes based on the cargo structure, opening potential new avenues for modulating type I IFN responses in infection and autoimmunity.

immunology↗

Inhibiting ezrin triggers formin-mediated actin remodelling reducing cellular mechano-protection

Ezrin plays a crucial role in linking the cortical actin cytoskeleton to the plasma membrane in animal cells. Inactivated by small molecule ezrin inhibitors (EzrInh), ezrin is known to regulate cellular functions like adhesion and motility. However, whether ezrin plays any significant role in protecting cells against mechanical stresses is less explored. We use hypo-osmotic shock (HS) to challenge cells and study the mechano-protective role of ezrin. Inhibition of ezrin phosphorylation led to increased cell rupture rates on hypo-shock, with a greater impact at later time points ([~] 10 min). The time scales match with that of enhanced tension contrast at edges at the basal plane. We also observed a lowered relative retraction rate at protrusions created by hypo-shock and a less contractile mid-plane cortex - both indicate the role of a weakening of the cortex by EzrInh in compromising membrane integrity on hypo-shock. Concomitantly, EzrInh also increased stress fibres (SFs), traction forces and cell spreading clearly indicative of additional cellular pre-stress. Utilizing formin inhibitor (SMIFH2), we showed that formin-mediated actin polymerization was critical for the SF response to EzrInh while it also prevented the subsequent EzrInh-treatment from enhancing cell rupture rates. Together EzrInh reduced mechano-protection in cells by tilting of balance of actins organization from the cortex to SF enhancing formin-mediated SF assembly. HighlightsO_LIHypo-osmotically shocked CHO cells rupture more on ezrin inhibition C_LIO_LIEzrin inhibition weakens contractility of cortical actin but enhances stress fibre numbers at the base C_LIO_LIHypo-osmotic shock creates basal protrusions that are also retracted. C_LIO_LIRetractive potential in cells is weakened by ezrin inhibition C_LIO_LIFormin inhibitor prevents net increase in stress fibres by inhibition of ezrin C_LIO_LIOn pre-treatment with formin inhibitor, subsequent inhibition of ezrin doesnot render cells more vulnerable to hypo-osmotic shock C_LI

biophysics↗

Molecular Basis of Ionic Suppression of ZAP-70 Dependent T Cell Receptor Activation

Ionic imbalance in the tumor microenvironment alters the tumor-infiltrating T lymphocyte function. High extracellular K+ suppresses T cell function by negatively regulating T cell receptor (TCR) signaling. In contrast, elevated extracellular Na+ enhances T cell effector function by boosting the phosphorylation of TCR signaling modules. Here, we presented a mechanism explaining how the two monovalent cations differently regulate TCR function. At rest, high intracellular K+ uncouples allosteric recruitment of ZAP-70, a key signaling module, to the TCR complex. The formation of antigen TCR complex induces K+ efflux, causing spontaneous recruitment of ZAP-70 to the TCR. Increasing extracellular K+ perturbs K+ efflux and slows ZAP-70 recruitment to the TCR complex, even upon antigen binding. This leads to defects in T cell development and arthritis-like symptoms in juvenile mice. We conclude that K+ dynamics is integral to T cell ligand discrimination and fundamental to turning off the signaling during T cell quiescence.

immunology↗

Non-canonical regulation of the plasma membrane copper transporter CTR1 through modulation of membrane mechanical properties

We describe a non-canonical, membrane receptor-like regulation of the human copper transporter CTR1 in response to copper stimuli. CTR1 is the sole high-affinity trimeric plasma-membrane copper-importing channel that self-regulates by undergoing endocytosis to limit copper uptake. We observed that preceding copper-induced endocytosis, CTR1 forms clusters on the plasma membrane, a phenomenon that is typically observed in membrane receptors. We deciphered the mechanism of CTR1 clustering and studied its ramifications on plasma membrane physical properties harboring the clusters that favors endocytosis. Membrane tension and fluctuation are fundamental regulators of pre- and post-endocytic events. Using coarse-grain MD simulation and coupled Interference Reflection Microscopy-Total Internal Reflection Fluorescence Microscopy we demonstrated that CTR1 clusters induce positive membrane curvature, increase in local membrane tension and decrease in local membrane fluctuation; alterations that favors formation of endocytic pits. Clustering is facilitated by copper-sequestering Methionine rich extracellular amino-terminus of CTR1. MD-simulations and IRM-TIRF imaging revealed that CTR1 clustering is facilitated by membrane cholesterol, depletion of which delays CTR1 endocytosis. CTR1 clustering promotes clathrin-coated pit formation that engages recruitment of adapter protein AP-2. To summarize, we report a hitherto unknown pre-endocytic receptor-like phenomenon of ligand-induced clustering of a metal channel, that in-turn regulates self-endocytosis by modulating membrane properties.

cell biology↗

Actin contractility and endocytosis create apico-basal tension gradient in HeLa cells

The functions of the plasma membrane of a cell are coupled to its mechanical state. To understand the players that contribute to the tight regulation of membrane mechanics with its local heterogeneities, the tension of the cell membrane requires to be mapped out from the basal to the apical membrane. In this work, optical-trap-based tension measurements performed at two axial (z) planes per cell reveal an apico-basal gradient, that is understood better on comparison with basal membrane mechanics and membrane compaction measurements by a combination of high resolution microscopy (IRM) and fluorescence lifetime (Flipper-TR) measurements, respectively. While the apico-basal gradient in the apparent tension (low to high) was found to depend on an intact actin cytoskeleton, analysing the colocalization of the cortical actin with the motor protein myosin and the actin-membrane linker ezrin suggested that cytoskeleton contractility is a major determinant of the patterned tension. Tension-sensitive lifetime of Flipper-TR, validated the gradient but failed to catch the dependence on actin due to the dual and opposite effects of tension on lifetime. Finally, measurements utilizing fluorescently tagged transferrin (Tf) demonstrated that the functional state of the membrane also showed similar height dependence. Thus, planes where tension maximized showed a peak in accumulation of Tf colocalizing with clathrin indicative of the presence of more pits. This enabled us to demonstrate that cells exist in tightly regulated patterned tension states that is coupled to their cytoskeleton as well membrane functions like endocytosis. Significance StatementThe cell membrane is protective but also highly dynamic - performing a diverse set of functions usually via membrane shape changes. These functions affect membrane mechanics but are also mechano-regulated. Mapping the state of cell surface mechanics or tension of live cells is therefore of fundamental importance. Interestingly, recent works have suggested that membrane tension can be non-uniform. However, no single tension-measuring technique can truly reach every part of the cell. Our work addresses this issue where we map tension in live HeLa cells using multifarious approaches including the measurement of tether forces, membrane fluctuations, and lipid compaction. We show that at the top/apical surface, the membrane-tension is lower than that at the midplane. The observed gradient resembles that of the state of endocytosis and controlled acto-myosin contractility.

biophysics↗

Enhancing antimicrobial resistance monitoring: Core Plasmid Multi-Locus sequence typing (cpMLST) with Oxford Nanopore sequencing technology (ONT)

BackgroundThe spread of antimicrobial resistance (AMR) poses a significant threat to global public health, primarily driven by the horizontal gene transfer of resistance genes via plasmids. Understanding the dynamics of plasmid transmission within (intra) and between (inter) bacterial species is crucial for developing effective countermeasures. In this study, we utilize long-read sequencing technology to develop an innovative approach called core plasmid Multi-Locus Sequence Typing (cpMLST) and track the global plasmid transmission pathways. MethodsWe collected wastewater samples from six different hospitals in Germany. Within 24 hours of collection, we isolated extensively drug-resistant (XDR) bacteria using CHROMagar plates (CHROMagar, Paris, France). Species identification was done using MALDI-TOF MS (Bruker Daltonics, Bremen, Germany). Genomic DNA from the isolates was extracted using the PureLink Genomic DNA Mini Kit (Invitrogen, Carlsbad, USA) and subsequently sequenced using Oxford Nanopore Technologies (ONT) sequencing (Oxford Nanopore Technologies). We employed the SQK-RBK114.24 kit on an R10.4.1 flow cell, achieving a minimum of 250 Mb of raw data for each isolate with an accuracy of 98.9%. The reads were assembled using Unicycler, and the quality of the assemblies was assessed using QUAST and Bandage. The assembled genomes were then uploaded to the Center for Genomic Epidemiology (CGE) https://www.genomicepidemiology.org/ platform to determine incompatibility (Inc) types and antimicrobial resistance (AMR) genes. Additionally, we performed core plasmid analysis using chewBBACA v.3.3.10 to assess plasmid relatedness. ResultsThe analysis confirmed the identification of various bacterial isolates. Among the most prevalent XDR isolate were Enterobacter roggenkampii (n=38), Serratia marcescens (n=12), Klebseilla oxytoca (n=11), Klebseilla michiganensis (n=8), and Citrobacter freundii (n=7). We conducted a cpMLST analysis to examine the highly prevalent plasmids and reveal evolutionary relationships and transmission patterns. Each isolate harbored different types of complete plasmids. Among those were the IncFII (n=45), IncHI (n=26), IncX3 (n=21), and other incompatibility groups. By focusing on shared Inc types among the bacterial species, their transfer within a single bacterial species (intra-species transfer) and between different species (inter-species transfer) were identified. The allelic differences ranged from 3-55 (IncHI), 2-32 (IncFII) and 2-24 (IncX3). Moreover, these plasmids, typically identified as smaller plasmids (IncX3), were larger than their commonly reported sizes. The analysis of plasmid dynamics across diverse bacterial hosts provides valuable insight into the mechanisms driving the spread of antimicrobial resistance, offering potential strategies for better controlling the dissemination of antimicrobial resistance and its transmission in clinical environments. ConclusionIn conclusion, long-read sequencing technologies emerge as an essential tool for investigating the transmission dynamics of antimicrobial resistance genes among plasmids. By implementing cp-MLST, we anticipate achieving an unparalleled understanding of the global dissemination and evolutionary patterns of resistance-carrying plasmids. This approach offers superior resolution to conventional plasmid typing methods, potentially opening new avenues for innovative strategies to combat the escalating AMR crisis.

microbiology↗

Intra-cluster receptor density (IRD) dictates TNFR1 clusters' signaling efficacy

Tumor Necrosis Factor Receptor 1 (TNFR1) signaling regulates cell fate in inflammation, immune responses, and tumorigenesis. While TNF--mediated TNFR1 pathways are well known, the role of receptor clustering remains unclear. Utilizing homo-FRET using fluorescence anisotropy, we show that intra-cluster receptor density (IRD) governs TNFR1 signaling outcomes. Soluble TNF- (sTNF-) increases IRD at cluster cores but decreases it at rims via receptor reorganization. Reducing IRD through membrane tension, zafirlukast, actin depolymerization, or cholesterol depletion suppresses sTNF- signaling, whereas increasing IRD by lowering membrane tension or exposing cells in a 3D gel-like microenvironment triggers ligand-independent activation. These findings reveal IRD as a key regulator of receptor signaling, with potential relevance across related receptor families and innovative strategies in modulating TNFR1 signaling. TeaserIntra-cluster receptor density (IRD) is critical for TNFR1 signal modulation, with higher IRD activating and lower IRD impairing the TNFR1 signaling.

biophysics↗

Influence of different landscape configurations on insect pollinators of important horticultural crops in a western Himalayan landscape

Pollinators play critical roles in ecosystem stability and agricultural productivity, and their decline has become a global concern. One of the main reasons for pollinators decline is changing landscape configuration. We conducted this study in Kullu Valley, Himachal Pradesh, India to evaluate varied landscape configuration impacts on the diversity, richness, and abundance of insect pollinators in apple and plum orchards. Five different landscape configurations were considered for the study. The survey spanned 28 orchards across the valley during the blooming periods of 2021 and 2022. Standard sampling protocols were used to collect the pollinator specimen. We recorded a total of 107 insect species across 67 genera, 29 families and five orders (Hymenoptera, Lepidoptera, Diptera, Coleoptera, and Thysanoptera) from different orchards. Hymenoptera and Diptera were the most abundant pollinators in the study area. Pollinator richness and diversity were higher in orchards located within 1-km of natural forests and in lower elevations (>1500 meters). Orchards near large settlements, agricultural lands and complete modernised management practice showed comparative less pollinator diversity and abundance. This study demonstrates the influence of diverse land-use practices on pollinators on a landscape scale and provides insights for developing effective conservation strategies in the Himalaya.

ecology↗

Formation of clathrin-pits and ATP-independent cholesterol-dependent tubules initiates mechano-regulation on de-adhesion.

Adherent cells ensure membrane homeostasis during de-adhesion by various mechanisms including endocytosis. Although mechano-chemical feedbacks involved in this process have been studied, the step-by-step build-up and resolution of the mechanical changes by endocytosis is not well understood. To investigate this, we study the de-adhesion of HeLa cells using a combination of interference reflection microscopy, optical-trapping and fluorescence experiments. We found that de-adhesion enhanced membrane height fluctuations of the basal membrane in the presence of an intact cortex. A reduction in the tether-force was also noted at the apical side. However, membrane fluctuations reveal phases of an initial drop in effective tension followed by a saturation. The area fractions of early (Rab5-labelled) and recycling (Rab4-labelled) endosomes as well as transferrin-labelled pits close to the basal plasma membrane also transiently increased. On blocking dynamin-dependent scission of endocytic pits, the regulation of fluctuations was not blocked but proceeded uncontrolled. Interestingly, the regulation could not be suppressed by ATP or cholesterol depletion individually but was arrested on depleting both. The data strongly supports pit-formation to be central to the reduction in fluctuations whether in normal or ATP depleted condition. Furthermore, while in normal conditions the contribution of clathrin-mediated endocytosis is clear, under ATP-depleted conditions we propose that cholesterol-dependent pits spontaneously regulate tension. SummaryWe show that during de-adhesion, cell edges retract, creating membrane folds and increasing fluctuations. Cells increase the rate of endocytosis to regulate back their membrane fluctuations. This is achieved by forming invaginations. Dynamin-dependent pathways are majorly involved, while cholesterol-dependent ATP-independent mechanisms also contribute.

biophysics↗

Connexin 43 mediated collective cell migration is independent of Golgi orientation

Cell migration is vital for multiple physiological functions and is involved in the metastatic dissemination of tumour cells in various cancers. For effective directional migration, cells often reorient their secretory traffic towards the leading edge by reorienting the Golgi apparatus. However, conflicting results on the positioning of the Golgi relative to the migrating cell raise questions about its regulation. Herein, we address the role of gap junction protein Connexin 43, which connects cells allowing the direct exchange of molecules and also controls the distribution of microtubules. We utilized HeLa WT (wild-type cells lacking Connexin 43) and HeLa 43 cells (stably expressing Connexin 43). We found that functional Connexin 43 channels affected Golgi morphology and reduced the ability of reorientation of Golgi (towards the leading edge) during cell migration. Although Connexin 43 also reduced migration velocity, the front displayed enhanced coherence in movement, implying an augmented collective nature of migration compared to HeLa WT cells lacking the cell-cell connectivity evidenced in HeLa 43. The increase in vimentin and basal actin in HeLa 43 shows that Connexin 43 expression alters the cytoskeleton. Non-invasive measurement of basal membrane height fluctuations revealed that HeLa 43 had a lower membrane tension and a more uniform intra- and inter-cellular distribution than HeLa WT, similar to their coherence in migration. We, therefore, propose that the reduced Golgi reorientation in HeLa 43 might be linked to lesser dependence on directed secretory trafficking, which is believed to be required to buffer the increasing tension caused by migration.

biophysics↗

Piezo1 mechanosensing regulates integrin-dependent chemotactic migration in human T cells

T cells are crucial for efficient antigen-specific immune responses and thus their migration within the body, to inflamed tissues from circulating blood or to secondary lymphoid organs, play a very critical role. T cell extravasation in inflamed tissues depends on chemotactic cues and interaction between endothelial adhesion molecules and cellular integrins. A migrating T cell is expected to sense diverse external and membrane-intrinsic mechano-physical cues, but molecular mechanisms of such mechanosensing in cell migration are not established. We explored if the professional mechanosensor Piezo1 play any role during integrin-dependent chemotaxis of human T cells. We found that deficiency of Piezo1 in human T cells interfered with integrin-dependent cellular motility on ICAM-1-coated surface. Piezo1 recruitment at the leading edge of moving T cells is dependent on and follows focal adhesion formation at the leading edge and local increase in membrane tension on chemokine receptor activation. Piezo1 recruitment and activation, followed by calcium influx and calpain activation, in turn are crucial for the integrin LFA-1 (CD11a/CD18) recruitment at the leading edge of the chemotactic human T cells. Thus, we find that Piezo1 activation in response to local mechanical cues constitutes a membrane-intrinsic component of the outside-in signaling in human T cells, migrating in response to chemokines, that mediates integrin recruitment to the leading edge.

immunology↗

Probing the role of macromolecular crowding in cell volume regulation using fluorescence anisotropy

Cytoplasmic macromolecular crowding (MMC) influences multiple cellular functions. Using fluorescence anisotropy of EGFP, we explore the homeostasis of MMC in the cytoplasm and its role in cell volume regulation. Individual cells of different lineages maintain a distinctly unique average cytoplasmic MMC for considerably long durations. Despite diffusion, actin cytoskeleton facilitates spatially heterogeneous MMC in the cytoplasm. While hypertonic-stress triggers regulatory volume increase (RVI), other methods of increasing cytoplasmic MMC fail to start RVI, suggesting that cells lack capabilities for MMC homeostasis. During spreading or microtubule-depolymerized state, cells neglect changes in cytoplasmic MMC to undergo volume regulation. Inhibition of TNFR1 increases the membrane tension and deprives cells of their ability to undergo volume regulation. Current understanding contemplates that cytoplasmic MMC, the mechanical state of the plasma membrane or the actin cytoskeleton, could be sensors for cell volume regulation. Our observations establish the irrelevance of cytoplasmic MMC and the significance of plasma membrane tension in setting off the cell volume regulation machinery.

cell biology↗

The Visual Dictionary of Antimicrobial Stewardship, Infection Control, and Institutional Surveillance

ObjectivesData and data visualization are integral parts of (clinical) decision-making in general and stewardship (antimicrobial stewardship, infection control, and institutional surveillance) in particular. However, systematic research on the use of data visualization in stewardship is lacking. This study aimed at filling this gap by creating a visual dictionary of stewardship through an assessment of data visualization in stewardship research. MethodsA random sample of 150 data visualizations from published research articles on stewardship were assessed. The visualization vocabulary (content) and design space (design elements) were combined to create a visual dictionary. Additionally, visualization errors, chart junk, and quality were assessed to identify problems in current visualizations and to provide improvement recommendations. ResultsDespite a heterogeneous use of data visualization, distinct combinations of graphical elements to reflect stewardship data were identified. In general, bar (n=54; 36.0%) and line charts (n=42; 28.1%) were preferred visualization types. Visualization problems comprised colour scheme mismatches, double y-axis, hidden data points through overlaps, and chart junk. Recommendations were derived that can help to clarify visual communication, improve colour use for grouping/stratifying, improve the display of magnitude, and match visualizations to scientific standards. ConclusionsResults of this study can be used to guide data visualization creators in designing visualizations that fit the data and visual habits of the stewardship target audience. Additionally, the results can provide the basis to further expand the visual dictionary of stewardship towards more effective visualizations that improve data insights, knowledge, and clinical decision-making.

scientific communication and education↗

Mapping Twenty Years of Antimicrobial Resistance Research Trends

BackgroundAntimicrobial resistance (AMR) is a global threat to health and healthcare. In response to the growing AMR burden, research funding also increased. However, a comprehensive overview of the research output, including conceptual, temporal, and geographical trends, is missing. Therefore, this study uses topic modelling, a machine learning approach, to reveal the scientific evolution of AMR research and its trends, and provides an interactive user interface for further analyses. MethodsStructural topic modelling (STM) was applied on a text corpus resulting from a PubMed query comprising AMR articles (1999-2018). A topic network was established and topic trends were analysed by frequency, proportion, and importance over time and space. FindingsIn total, 88 topics were identified in 158616 articles from 166 countries. AMR publications increased by 450% between 1999 and 2018, emphasizing the vibrancy of the field. Prominent topics in 2018 were Strategies for emerging resistances and diseases, Nanoparticles, and Stewardship. Emerging topics included Water and environment, and Sequencing. Geographical trends showed prominence of Multidrug-resistant tuberculosis (MDR-TB) in the WHO African Region, corresponding with the MDR-TB burden. China and India were growing contributors in recent years, following the United States of America as overall lead contributor. InterpretationThis study provides a comprehensive overview of the AMR research output thereby revealing the AMR research response to the increased AMR burden. Both the results and the publicly available interactive database serve as a base to inform and optimise future research. FundingINTERREG-VA EurHealth-1Health (202085); European Commission Horizon 2020 Framework Research in contextO_ST_ABSEvidence before this studyC_ST_ABSPrior to this study, PubMed, Web of Science, Scopus, and IEEE Xplore were queried to find studies providing a conceptual overview of antimicrobial resistance (AMR) research over time and space. The search string included keywords ("antimicrobial" OR antibiotic*) AND (resistan*) AND ("science mapping" OR bibliometric OR scientometric) in the title and abstract and focused on articles published before 2019 without language restrictions. Few studies were found relying on scientometric and bibliometric methods to assess either subfields of AMR research (e.g., AMR among uropathogens) or AMR-related fields (e.g., microbiology). No studies were found that focus on the entire AMR field. Therefore, this science mapping study using topic modelling was performed to provide an overview of the AMR field by identifying and assessing topics, trends, and geographical differences over time. Added value of this studyTo the best of our knowledge, this study is the first to use a science mapping approach to provide a comprehensive overview of the entire AMR research field, covering over 150 thousand articles published between 1999 and 2018. Our findings revealed important (e.g., Strategies for emerging resistances and diseases, Nanoparticles, and Stewardship) and emerging (e.g., Water and environment, and Sequencing) topics in AMR research. Lastly, this study resulted in an interactive user interface where all data are presented for further analyses. Implications of all the available evidenceOur comprehensive overview of the AMR field, including its conceptual structure, and temporal and geographical trends revealed the response of the research community to the AMR burden. The results and the openly available supporting data provide the base to guide future funding and research directions to tackle AMR.

microbiology↗

Heterogenous adhesion of follower cells affects tension profile and velocity of leader cells in primary keratocyte collective cell migration

Single cell studies demonstrate membrane tension to be a central regulator of lamellipodia-driven motility bringing in front-coherence. During collective cell migration, however, tension mapping or existence of intracellular tension-gradients and the effect of cell-cell interactions have remained unexplored. In this study of membrane fluctuations and fluctuation-tension of migrating primary keratocyte cell-sheets, we first show that some leader cells are followed by followers which remain de-adhered from the substrate while being attached to other cells and thus appear to be "taking a ride". A subtle yet significant enhanced long-timescale velocity in these leaders indicate increased directionality. Intriguingly, such leaders mostly have front-high tension gradients like single keratocytes, while followers and other leaders usually display front-low membrane tension gradients. The front-high tension gradient and higher membrane tension observed in these leaders, despite the high cell-to-cell variability in membrane tension demonstrate how leader-follower interactions and heterogenous adhesion profiles are key in collective cell migration.

biophysics↗

Nuclear deformation and anchorage defect induced by DCM mutants in lamin A

Dilated Cardiomyopathy (DCM) is one of the different types of laminopathies caused by the mutations in A-type lamins in somatic cells. The involuntary cyclic stretching of cardiac muscle cells, as observed in normal physiological conditions is perturbed in DCM which afflict patients globally. As A-type lamins are principal components in nuclear mechanics, we have investigated the effect of the DCM causing mutants- K97E, E161K and R190W on nuclear stretching and deformation by static and dynamic strain inducing experiments. All the mutants exhibited differential nuclear structural aberrations along with a tilt in the nuclear axis compared to the direction of the cell axis and a significant decrease in the lamina thickness which reflected the lower mechanical rigidity. These phenotypes could potentially lead to defects in nuclear anchorage to the actin filaments thereby resulting in the misshapen and misaligned nucleus.

cell biology↗

Development of an interactive open source software application (RadaR) for infection management / antimicrobial stewardship

ObjectivesAnalysing process and outcome measures for patients suspected of or having an infection in an entire hospital requires processing large datasets and accounting for numerous patient parameters and treatment guidelines. Rapid, reproducible and adaptable analyses usually need substantial technical expertise but can yield valuable insight for infection management and antimicrobial stewardship (AMS) teams. We describe a software application (RadaR - Rapid analysis of diagnostic and antimicrobial patterns in R) for infection management allowing user-friendly, intuitive and interactive analysis of large datasets without prior in-depth statistical or software knowledge.\n\nMethods and ResultsRadaR was built in R, an open source programming language, making it free to use and adaptable to different settings. Shiny, an additional open source package to implement web-application frameworks in R, was used to develop the application. RadaR was developed in the context of a 1339-bed academic tertiary referral hospital to handle data of more than 180,000 admissions.\n\nRadaR visualizes analytical graphs and statistical summaries in an interactive manner within seconds. Users can filter large patient groups by 17 different criteria and investigate antimicrobial use, microbiological diagnostic use and results, and outcome in length of stay. Results can easily be stratified and grouped to compare individually defined patient groups. Finally, datasets of identified patients / groups can be downloaded for further analyses.\n\nConclusionRadaR facilitates understanding and communication of trends in antimicrobial use, diagnostic use and patient outcome by linking and aggregating individual patient data in one user-friendly application. RadaR can produce aggregated data analysis while preserving patients features in the data to adjust and stratify results in detail. AMS teams can use RadaR to identify areas, both for diagnostic and therapeutic procedures, within their institutions that might benefit from increased support and to target their interventions.

bioinformatics↗