Biology subjects

Ulrich, H.

Publications and source records attributed to Ulrich, H..

7 recordsLinked to original sources

bioRxiv2023

Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease

Single-cell mRNA sequencing (scRNA-seq) allows deep molecular and cellular profiling of immunological processes. Longitudinal scRNA-seq datasets can be used for deterministic ordinary differential equation (ODE)-based modelling to mechanistically describe immune dynamics. Here, we derived longitudinal changes in the abundance of six colonic cell types during inflammatory bowel disease (IBD) from scRNA-seq data of a mouse model of colitis using ODE-based models. We then predicted the immune dynamics of a different mouse colitis protocol and confirmed these scRNA-seq-based predictions with our previously published single-cell-based flow cytometry data. We further hypothesised that the estimated model parameters reflect biological processes. We validated this prediction of cellular turnover rates with KI-67 staining and with gene expression information from the scRNA-seq data not used for model fitting. Finally, we tested the translational relevance of the model simulations by predicting genes indicative of treatment response in human IBD patients. The predictive power of IBD deterministic modelling from scRNA-seq data highlights its potential to advance our understanding of immune dynamics in health and disease.

systems biology↗

bioRxiv2022

The Nse5/6-like SIMC1-SLF2 Complex Localizes SMC5/6 to Viral Replication Centers

The human SMC5/6 complex is a conserved guardian of genome stability and an emerging component of antiviral responses. These disparate functions likely require distinct mechanisms of SMC5/6 regulation. In yeast, Smc5/6 is regulated by its Nse5/6 subunits, but such regulatory subunits for human SMC5/6 are poorly defined. Here, we identify a novel SMC5/6 subunit called SIMC1 that contains SUMO interacting motifs (SIMs) and an Nse5-like domain. We isolated SIMC1 from the proteomic environment of SMC5/6 within polyomavirus large T antigen (LT)-induced subnuclear compartments. SIMC1 uses its SIMs and Nse5-like domain to localize SMC5/6 to polyomavirus replication centers (PyVRCs) at SUMO-rich PML nuclear bodies. SIMC1s Nse5-like domain binds to the putative Nse6 orthologue SLF2 to form an anti-parallel helical dimer resembling the yeast Nse5/6 structure. SIMC1-SLF2 structure-based mutagenesis defines a conserved surface region containing the N-terminus of SIMC1s helical domain that regulates SMC5/6 localization to PyVRCs. Furthermore, SLF1, which recruits SMC5/6 to DNA lesions, binds SLF2 analogously to SIMC1 and forms a distinct Nse5/6-like complex. Thus, two Nse5/6-like complexes independently regulate human SMC5/6: SIMC1-SLF2 responding to viral challenge and SLF1/2 recognizing DNA damage.

cell biology↗

bioRxiv2021

Molecular dynamics analysis of fast-spreading severe acute respiratory syndrome coronavirus 2 variants and their effects in the interaction with human angiotensin-converting enzyme 2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolving with mutations in the Spike protein, especially in the receptor-binding domain (RBD). The failure of public health measures to contain the spread of the disease in many countries has given rise to novel viral variants with increased transmissibility. However, key questions about how quickly the variants can spread and whether they can cause a more severe disease remain unclear. Herein, we performed a structural investigation using molecular dynamics simulations and determined dissociation constant (KD) values using surface plasmon resonance (SPR) assays of three fastspreading SARS-CoV-2 variants, Alpha, Beta and Gamma ones, as well as genetic factors in the host cells that may be related to the viral infection. Our results suggest that the SARS-CoV-2 variants facilitate their entry into the host cell by moderately increased binding affinities to the human ACE2 receptor, different torsions in hACE2 mediated by RBD variants, and an increased Spike exposure time to proteolytic enzymes. We also found that other host cell aspects, such as gene and isoform expression of key genes for the infection (ACE2, FURIN and TMPRSS2), may have few contributions to the SARS-CoV-2 variants infectivity. In summary, we concluded that a combination of viral and host cell factors allows SARS-CoV-2 variants to increase their abilities to spread faster than wild-type. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

molecular biology↗

bioRxiv2020

Purinergic P2Y1 and P2Y2/4 receptors elicit distinct Ca2+ signaling patterns in hepatocytes via differential feedback regulation by Protein Kinase C

Extracellular nucleotides are key regulators of liver physiology. In primary rat hepatocytes, P2Y1 receptor (P2Y1R) activation by ADP generates cytosolic calcium ([Ca2+]c) oscillations with narrow spikes, whereas P2Y2/4R activation by UTP led to more complex broad [Ca2+]c oscillations. Both [Ca2+]c oscillation signatures were observed with the common agonist ATP. Inhibition of Gq signaling with YM-254890 abolished ATP-induced [Ca2+]c oscillations, indicating that they depend on inositol 1,4,5-trisphosphate (IP3), and are not mediated by P2X receptors. The narrow P2Y1-linked [Ca2+]c spikes and the broad P2Y2/4-linked [Ca2+]c spikes are shaped by differential and complex PKC-mediated feedback mechanisms. Downregulation of PKC broadened both ADP- and UTP-induced [Ca2+]c oscillations, with a more pronounced effect on the former. PKC downregulation also selectively elicited a more robust response to ADP stimulation, enhancing oscillatory and sustained [Ca2+]c responses. Acute PKC modulation confirmed the importance of the negative PKC feedback regulation of P2Y1R-linked [Ca2+]c signals; such that PKC activation decreased [Ca2+]c oscillation frequency and PKC inhibition increased [Ca2+]c spike width. However, both PKC activation and inhibition decreased the spike width of P2Y2/4R-induced [Ca2+]c oscillations, suggesting that multiple opposing PKC feedback mechanisms shape P2Y2/4R responses. Significantly, plasma membrane Ca2+ entry was required for negative PKC feedback on P2Y1R-linked [Ca2+]c oscillations, whereas P2Y2/4R-linked [Ca2+]c oscillations were less sensitive to negative regulation by PKC and independent of Ca2+ influx. Thus, differential feedback regulation by PKC gives rise to receptor-specific [Ca2+]c oscillation profiles, which can encode the diverse physiological and pathophysiological responses to distinct agonists that all act through the IP3 signaling cascade.

cell biology↗

bioRxiv2020

Molecular dynamics reveals complex compensatory effects of ionic strength on the SARS-CoV-2 Spike/hACE-2 interaction

The SARS-CoV-2 pandemic has already killed more than 800,000 people worldwide. To gain entry, the virus uses its spike protein to bind to host hACE-2 receptors on the host cell surface and mediate fusion between viral and cell membranes. As initial steps leading to virus entry involves significant changes in protein conformation as well as in the electrostatic environment in the vicinity of the spike-hACE-2 complex, we explored the sensitivity of the interaction to changes in ionic strength through computational simulations and surface plasmon resonance. We identified two regions in the receptor-binding domain (RBD), E1 and E2, which interact differently with hACE-2. At high salt concentration, E2-mediated interactions are weakened but are compensated by strengthening E1-mediated hydrophobic interactions. These results provide a detailed molecular understanding of spike RBD/hACE-2 complex formation and stability under a wide range of ionic strengths. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/267351v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1a7dc02org.highwire.dtl.DTLVardef@15d3c78org.highwire.dtl.DTLVardef@2d09c1org.highwire.dtl.DTLVardef@db78a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2020

Hypertonic saline solution inhibits SARS-CoV-2 in vitro assay

We are facing an unprecedented global health crisis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At this date more than 680 thousand people have died due to coronavirus disease 2019 (COVID-19). Unfortunately, until now no effective treatment to combat the virus and vaccine are available. We performed experiments to test if hypertonic saline solution is able to inhibit virus replication in vitro. Our data shows that 260 mM NaCl (1.5%) inhibits 100% SARS-CoV-2 replication in Vero cells. Furthermore, our results suggest that the virus replication inhibition is due to an intracellular mechanism and not due to the dissociation between spike SARS-CoV-2 protein and its human receptor angiotensin-converting enzyme 2 interaction. NaCl depolarizes the plasma membrane supposedly associated with the inhibition of the SARS-CoV-2 life cycle. This observation could lead to simple, safe and low cost interventions at various stages of COVID-19 treatment, improving the prognosis of infected patients, thereby mitigating the social and economic costs of the pandemic.

microbiology↗

bioRxiv2019

A novel decellularization method to produce brain scaffolds

Scaffolds composed of extracellular matrix (ECM) can assist tissue remodeling and repair following injury. The ECM is a complex biomaterial composed of proteins, glycoproteins, proteoglycans, and glycosaminoglycans, secreted by cells. The ECM contains fundamental biological cues that modulate cell behavior and serves as a structural scaffold for cell adhesion and growth. For clinical applications, where immune rejection is a constraint, ECM can be processed using decellularization methods intended to remove cells and donor antigens from tissue or organs, while preserving native biological cues essential for cell growth and differentiation. Recent studies show bioengineered organs composed by a combination of a diversity of materials and stem cells as a possibility of new therapeutic strategies to treat diseases that affect different tissues and organs, including the central nervous system (CNS). Nevertheless, the methodologies currently described for brain decellularization involve the use of several chemical reagents with many steps that ultimately limit the process of organ or tissue recellularization. Here, we describe for the first time a fast and straightforward method for complete decellularization of mice brain by the combination of rapid freezing and thawing following the use of only one detergent (Sodium dodecyl sulfate (SDS)). Our data show that using the protocol we describe here the brain can be entirely decellularized, while still maintaining ECM components that are essential for cell survival and repopulation of the scaffold. Our results also show the repopulation of the decellularized brain matrix with Neuro2a cells, that were identified by immunohistochemistry in their undifferentiated form. We conclude that this novel and simple method for brain decellularization can be used as a biocompatible scaffold for cell repopulation.\n\nImpact StatementFor the first time we describe an easy, effective and low cost method for complete decellularization of murine brain by the use of only one detergent (SDS) combined with rapid freezing and thawing, that can be used as a 3D scaffold for cell culture of neuronal cells. The results show that the decellularized brains still maintain ECM components essential for cell survival and repopulation of the scaffold. Moreover, we found that the decellularized brain matrix can be repopulated with neural cells, showing its biocompatibility.\n\nGRAFICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC=\"FIGDIR/small/680702v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@15fd027org.highwire.dtl.DTLVardef@15acfeborg.highwire.dtl.DTLVardef@1087d2eorg.highwire.dtl.DTLVardef@529309_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗