Biology subjects

Lang, S.

Publications and source records attributed to Lang, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

The Quest to Identify USP8 Inhibitors for Parkinsons Disease, a PAINful Experience.

Pan Assay INterference compoundS (PAINS) are known to be a source of false positives in High Throughput Screening (HTS) campaigns. This has become a major problem in medicinal chemistry, often resulting in undesirable project outcomes and increased overall cost. Our recent campaign to identify inhibitors of USP8 that could be used in the treatment of Parkinsons disease identified several PAINS that worked via a variety of mechanisms. Herein, we discuss the process developed to identify not only the PAINS but also confirming the interference mechanism causing their activity. We found in this project that our USP8 assay was susceptible to multiple modes of interference, making it difficult to identify genuine hit molecules. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/556294v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@b917a6org.highwire.dtl.DTLVardef@1bfac47org.highwire.dtl.DTLVardef@c78e1dorg.highwire.dtl.DTLVardef@1434fdd_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2023

TIGIT drives the immunosuppressive environment by downregulation of metalloproteinases MMP2 and MMP14 in perihilar cholangiocarcinoma.

BackgroundCheckpoint blockade in cholangiocarcinoma (CCA) is promising; however, little is known about the response to treatment in CCA subtypes. In this study, we investigated the spatial immune environment in combination with checkpoint expression in perihilar CCA (pCCA). Materials & MethodsThe levels of checkpoint molecules (PD-1, PD-L1, PD-L2, LAG-3, ICOS, TIGIT, TIM-3, and CTLA-4), macrophages (CD68), and T cells (CD4 and CD8) were assessed by multiplex immunofluorescence (mIF) in 50 patients. We investigated the transcriptomic profile using the NanoString Cancer Progression Panel, and validation was performed by mIF on tissue sections from 24 patients. ResultsThe expression of checkpoint molecules TIGIT, CTLA-4, and LAG-3 alone and in combination with other checkpoint molecules was more abundant in the Central Tumor (CT) and Invasive Margin (IM) than in peritumoral tissue (PT) (CD4 and CD8 TIGIT p<0.0001 for both CD4 and CD8 CTLA-4, p<0.0001 and p < 0.001, respectively, and CD8 LAG-3 p < 0.05). MMP2 and MMP14 were differentially expressed in patients with high TIGIT expression. ConclusionThe immune environment in pCCA is characterized by the expression of multiple checkpoints, demonstrating the complexity of ICI treatment. High TIGIT expression drives an immunosuppressive environment by modulating the extracellular matrix. Future clinical trials in pCCA could consider TIGIT as a therapeutically relevant target for (combination) treatment.

cancer biology↗

bioRxiv2023

ExMove: An open-source toolkit for processing and exploring animal tracking data in R

O_LIOngoing technological advances have led to a rapid increase in the number, type, and scope of animal tracking studies. In response, many software tools have been developed to analyse animal movement data. These tools generally focus on movement modelling, but the steps required to clean raw data files from different tracking devices have been largely ignored. Such pre-processing steps are often time-consuming and involve a steep learning curve but are crucial for the creation of high quality, standardised, and shareable data. Moreover, decisions made at this early stage can substantially influence subsequent analyses, and in the current age of reproducibility crisis, the transparency of this process is vital. C_LIO_LIHere we present an open-access, reproducible toolkit written in the programming language R for processing raw data files into a single cleaned data set for analyses and upload to online tracking databases (found here: https://github.com/ExMove/ExMove). The toolkit comprises well documented and flexible code to facilitate data processing and user understanding, both of which can increase user confidence and improve the uptake of sharing open and reproducible code. Additionally, we provide an overview website (found here: https://exmove.github.io/) and a Shiny app to help users visualise tracking data and assist with parameter determination during data cleaning. C_LIO_LIThe toolkit is generalisable to different data formats and device types, uses modern tidy coding practices, and relies on few well-maintained packages. Amongst these, we perform spatial manipulations using the package sf, providing a timely resource for movement ecologists following the recent deprecation of the widely-used sp package. C_LIO_LIOverall, by collating all required steps from data collection to archiving on open access databases into a single, robust pipeline, our toolkit provides a valuable resource for anyone conducting animal movement analyses and represents an important step towards increased standardisation and reproducibility in animal movement ecology. C_LI

ecology↗

bioRxiv2023

Learning about neurodiversity from parents - auditory gestalt perception of prelinguistic vocalisations

BackgroundInfants with Rett syndrome (RTT) may have subtle anomalies in their prelinguistic vocalisations but the detection of these is difficult, since their conspicuous vocalisations are often interspersed with inconspicuous ones. Aims and methodsExtending a previous study with predominantly non-parents, the present study sampled parents of children with RTT and aimed to examine their gestalt perception of prelinguistic vocalisations. Methods and procedureParents (n = 76) of female children with RTT listened to vocalisation recordings from RTT and typically developing (TD) infants, including an inconspicuous vocalisation from a RTT girl. For each recording, parents indicated if the vocalisation was produced by a RTT or a TD child. ResultsOverall correct to incorrect identification rate was 2:1, which was comparable to that of the previous study. Intriguingly, parents of RTT children seemed to be sensitive to features characterising the vocalisations of RTT infants, which has especially influenced their perception of the inconspicuous vocalisation from a RTT girl. Conclusions and implicationsThese results invite further research on the potential characterising differences between vocalisations from TD infants and infants with divergent neurodevelopment. What this paper adds?Previous studies suggested that parents observations of their childrens behaviour are insightful and could aid clinical diagnosis. There is evidence that non-parents also seem to be sensitive to typical versus atypical characteristics in infant development. As normal and divergent developmental behaviours are often overlapping with each other, detecting deviant development is often difficult. For example, atypical vocalisations of infants later diagnosed with Rett syndrome (RTT) are often interspersed with their more typical and inconspicuous vocalisations. Can we learn extras from parents about divergences in prelinguistic vocalisations? The current study extended previous research and focused on the auditory gestalt perception of parents. We found parents of children with RTT were sensitive to the characterising differences between vocalisations from RTT and typically developing (TD) infants. They differentiated RTT vocalisations from TD vocalisations, even the RTT vocalisation was benchmarked as inconspicuous by speech-language experts. The characterising features that point to RTT, which seem to be perceptible to parents, might be more than the conspicuousness that could be readily classified by experts. What we have learned from parents perceptions motivates further research on the potential characterising features in prelinguistic vocalisations from different infants, especially in vocalisations that sound inconspicuous to experts and professionals, which may help to refine our understandings of diverse vocalisation patterns on the one hand, and to identify infants with neurodevelopmental divergences on the other hand.

developmental biology↗

bioRxiv2022

Proteomics identifies substrates and a novel component in hSnd2-dependent ER protein targeting

Protein import into the endoplasmic reticulum (ER) is essential for about 30% of the human proteome. It involves targeting of precursor proteins to the ER and insertion into or translocation across the ER membrane. Furthermore, it relies on signals in the precursor polypeptides and components, which read the signals and facilitate their targeting to a protein-conducting channel in the ER membrane, the Sec61 complex. Compared to the SRP- and TRC-dependent pathways, little is known about the SRP-independent/SND pathway. Our aim was to identify additional components and characterize the client spectrum of the human SND pathway. The established strategy of combining depletion of the central hSnd2-component from HeLa cells with proteomic- and differential protein abundance-analysis was used. The SRP and TRC targeting pathways were analyzed in comparison. TMEM109 was characterized as hSnd3. Unlike SRP but similar to TRC, the SND clients are predominantly membrane proteins with N-terminal, central, or C-terminal targeting signals.

cell biology↗

bioRxiv2022

How to resolve conflicting conservation objectives: A decision support tool for the global selection of multi-purpose protected areas

The establishment and maintenance of protected areas (PAs) is viewed as a key action in delivering post-2020 biodiversity targets. PAs often need to meet multiple objectives, ranging from biodiversity protection to ecosystem service provision and climate change mitigation, but available land and conservation funding is limited. Therefore, optimizing resources by selecting the most beneficial PAs is vital. Here, we advocate for a flexible and transparent approach to selecting protected areas based on multiple objectives, and illustrate this with a decision support tool on a global scale. The tool allows weighting and prioritization of different conservation objectives according to user-specified preferences, as well as real-time comparison of the selected areas that result from such different priorities. We apply the tool across 1347 terrestrial PAs and highlight frequent trade-offs among different objectives, e.g., between species protection and ecosystem integrity. Outputs indicate that decision makers frequently face trade-offs among conflicting objectives. Nevertheless, we show that transparent decision-support tools can reveal synergies and trade-offs associated with PA selection, thereby helping to illuminate and resolve land-use conflicts embedded in divergent societal and political demands and values.

ecology↗

bioRxiv2022

Single-cell RNA sequencing identifies phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow

Hematopoiesis is regulated by the bone marrow (BM) stroma. However, cellular identities and functions of the different BM stromal elements in humans remain poorly defined. Based on single-cell RNA sequencing, we systematically characterized the BM stromal compartment which led to the identification of six transcriptionally and functionally distinct stromal cell populations. Stromal cell differentiation hierarchy was recapitulated based on RNA velocity analysis, in vitro proliferation capacities and differentiation potentials. Potential key factors that govern the transition from stem and progenitor cells to fate- committed cells were identified. In silico cell-cell communication prediction and in situ localization analyses demonstrated distinct hematopoietic stromal cell niches in specific BM locations, which used either the CXCL12 or SPP1 axis as the major hematopoiesis-regulating mechanism. These findings provide the basis for a comprehensive understanding of the cellular complexity of the human BM microenvironment and the intricate stroma- hematopoiesis crosstalk mechanisms, thus refining our current view on hematopoietic niche organization.

cell biology↗

bioRxiv2021

Adaptive subsets limit the anti-tumoral NK-cell activity in Hepatocellular Carcinoma

Background and AimsHepatocellular carcinoma (HCC) is a global health burden with increasing incidence, poor prognosis and limited therapeutic options. Natural killer (NK) cells exhibit potent anti-tumoral activity and therefore represent potential targets for immunotherapeutic approaches in HCC treatment. However, the human NK-cell repertoire is highly diverse including conventional and adaptive NK cells that differ in phenotype and effector function. Adaptive NK-cell frequencies are increased in association with HCMV (human cytomegalovirus) seropositivity that is also common in HCC patients. In this study, we aimed to gain a better understanding of the NK-cell repertoire and the associated anti-tumoral activity in HCC patients. MethodsIn-depth phenotypic and functional flow-cytometry analyses of the HCMV-associated NK cell-repertoire obtained from 57 HCC patients, 33 liver cirrhosis patients and 36 healthy donors (HD). ResultsFirst, adaptive subsets are present in all three cohorts with conserved characteristics in patients with liver cirrhosis and HCC. Second, adaptive NK cells can be isolated from HCC tissue however lack features of tissue-residency and thus probably represent circulating/infiltrating lymphocytes. Third, the anti-tumoral activity by adaptive NK cells is reduced compared to conventional NK-cell subsets, also in HCC. Lastly, frequencies of adaptive NK cells were increased in patients suffering from Hepatitis B virus-associated HCC providing a link between etiology and the NK-cell repertoire in HCC. ConclusionAdaptive NK cells limit the anti-tumoral activitity of NK cells in HCC, especially in association with HBV infection that is accompanied by an expansion of this NK cell subset. Lay summaryIn patients with liver cancer (HCC), a subset of natural killer cells, so called adaptive NK cells show a diminished anti-tumoral activity compared to other, called conventional NK cells. Adaptive NK cells are expanded in patients with HCC associated to Hepatitis B virus infection. Thus, presence of adaptive NK cells contributes to the immune escape in HCC.

immunology↗

bioRxiv2020

CECR2 Drives Breast Cancer Metastasis by Suppressing Macrophage Inflammatory Responses

Epigenetic and transcriptional changes are critical for metastasis, the major cause of cancer-related deaths. Metastatic tumor cells escape immune surveillance more efficiently than tumor cells in the primary sites, but the mechanisms controlling their immune evasion are poorly understood. We found that distal metastases are more immune inert with increased M2 macrophages compared to their matched primary tumors. Acetyl-lysine reader CECR2 is an epigenetic regulator upregulated in metastases and positively associated with M2 macrophages. CECR2 specifically promotes breast cancer metastasis in multiple mouse models, with more profound effect in the immunocompetent setting. Mechanistically, NF-{kappa}B family member RELA recruits CECR2 to activate CSF1 and CXCL1, which are critical for macrophage-mediated immunosuppression at the metastatic sites. Furthermore, pharmacological inhibition of CECR2 bromodomain impedes NF-{kappa}B-mediated immune suppression by macrophages and inhibits breast cancer metastasis. These results reveal novel therapeutic strategies to treat metastatic breast cancer. Statement of SignificanceComparison of matched primary breast tumors and distal metastases show that metastases are more immune inert with increased tumor promoting macrophages. Depletion or pharmacological inhibition of CECR2 inhibits breast cancer metastasis by suppressing macrophage inflammatory responses, nominating CECR2 as a promising therapeutic target for cancer metastasis.

cancer biology↗

bioRxiv2020

A DNAmRep epigenetic fingerprint for determining cellular replication age

ii.Aging is known to elicit dramatic changes to DNA methylation (DNAm), although the causes and consequences of such alterations are not clear and require further exploration. Our ability to experimentally uncover mechanisms of epigenetic aging will be greatly enhanced by our ability to study and manipulate these changes using in vitro models. However, it remains unclear whether the changes elicited by cells in culture can serve as a model of what is observed in aging tissues in vivo. To test this, we serially passaged mouse embryonic fibroblasts (MEFs) and assessed changes in DNAm at each time-point via RRBS. By developing a measure that tracked cellular aging in vitro, we tested whether it tracked physiological aging in various mouse tissues and whether anti-aging interventions modulate this measure. Our measure, termed DNAmCULTURE, was shown to strongly increase with age when examined in multiple tissues (liver, lung, kidney, blood, and adipose). As a control, we confirmed that the measure was not a marker of cellular senescence, suggesting that it reflects a distinct yet progressive cellular aging phenomena that can be induced in vitro. Furthermore, we demonstrated slower epigenetic aging in animals undergoing caloric restriction and a resetting of our measure in lung and kidney fibroblasts when re-programmed to iPSCs. Enrichment and clustering analysis implicated SUZ12, EED and Polycomb group (PcG) factors as potentially important chromatin regulators in translational culture aging phenotypes. Overall, this study supports the concept that physiologically relevant aging changes can be induced in vitro and moving forward, used to uncover mechanistic insights into epigenetic aging.

pathology↗

bioRxiv2020

Nerve fibers in the Tumor Microenvironment are co-localized with Tertiary Lymphoid Structures

BackgroundB cells and tertiary lymphoid structures (TLS) are reported to be important in the improvement of survival of cancer patients. These secondary lymphoid organs have been associated with the generation of an anti-tumor response. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancer types and the stromal architecture shapes the intratumoral heterogeneity. The stroma of PDAC is a complex system in which crosstalk takes place between cancer-associated fibroblasts, immune cells, endothelial cells and the cancer cells. Besides immune cells and fibroblasts, there is some limited data about the influence of nerve fibers on cancer progression. Patients and methodsNerve Fiber Density (NFD) was analysed in our cohort of 188 patients with Pancreatic Ductal Adenocarcinoma who underwent pancreatic surgery. We used immunohistochemistry and multiplex imaging to phenotype the immune cell infiltrate. The cell detection classifier measured distance from immune cell to cancer gland and with a heat map we could count TLS. By using Machine learning we were able to define the spatial distribution and counting Tertiary Lymphoid Structures. ResultsHigh NFD is significantly associated with prolonged overall survival (HR 1.676 (95%CI 1.126,2.495) for low vs. high NFD, p-value 0.0109). The immune cells surrounding the nerve fibers were phenotyped in B cells, T cells and dendritic follicular cells, matching a TLS. Here we show that small nerve fibers are located at the TLS in Pancreatic Cancer and a high Nerve Fiber Density combined with more than 5 TLS is associated with a better survival (HR 0.388 (95%CI 0.218, 0.689). ConclusionThe co-localization of small nerve fibers with TLS is a new finding which has not been described before. However the precise roles of these TLS and nerve fibers remains unknown. These findings unravel future pathways and has the potential to reach new directions into already existing targeted therapy.

cancer biology↗

bioRxiv2020

Prion Protein Folding Mechanism Revealed by Pulling Force Studies

The mammalian prion protein (PrP) engages with the ribosome-Sec61 translocation channel complex to generate different topological variants that are either physiological, or involved in neurodegenerative diseases. Here, we describe cotranslational folding and translocation mechanisms of PrP coupled to a Xbp1-based arrest peptide (AP) as folding sensor, to measure forces acting on PrP nascent chain. Our data reveal two main pulling events followed by a minor third one exerted on the nascent chains during their translocation. Using those force landscapes, we show that a specific sequence within an intrinsically disordered region, containing a polybasic and glycine-proline rich residues, modulates the second pulling event by interacting with TRAP complex. This work also delineates the sequence of events involved in generation of PrP toxic transmembrane topologies during its synthesis. Our results shed new insight into the folding of such topological complex protein, where marginal pulling by the signal sequence, together with the downstream sequence in the mature domain, primarily drives an overall inefficient translocation resulting in the nascent chain to adopt other topologies.

biochemistry↗

bioRxiv2019

LegoBody: facile generation of bispecific and multi-specific antibodies

Bispecific and multi-specific antibodies are capable of recognizing multiple ligands simultaneously or synergistically, creating complex biological interactions not achievable by monoclonal antibodies, thus expanding opportunities for novel therapy development. With the large number of monoclonal antibodies either approved or under clinical development, there are numerous opportunities to combine their specificities to further improve therapeutic potential. Although simple in concept, clinical development of bi- and multi-specific antibodies face several challenges, chief of which is how to efficiently and reliably produce bispecific and multi-specific antibodies with expected specificity and desired biophysical properties. In this study, we developed a modular approach that uses temporary linkers to enforce proper chain pairing and proteases such as thrombin to remove those linkers from the final product. Combined with the knob-into-hole design, we can generate IgG-like, bi- or multi-specific antibodies from any pre-existing monoclonal antibodies. The approach is highly versatile and applicable to any monoclonal antibody pair or panel, expediting evaluation and therapeutic development of bi- and multi-specific antibodies.

bioengineering↗

bioRxiv2019

Proteomics identifies signal peptide features determining the substrate specificity in human Sec62/Sec63-dependent ER protein import

In mammalian cells one-third of all polypeptides are integrated into the membrane or translocated into the lumen of the endoplasmic reticulum (ER) via the Sec61-channel. While the Sec61-complex facilitates ER-import of most precursor polypeptides, the Sec61-associated Sec62/Sec63-complex supports ER-import in a substrate-specific manner. So far, mainly posttranslationally imported precursors and the two cotranslationally imported precursors of ERj3 and prion protein were found to depend on the Sec62/Sec63-complex in vitro. Therefore, we determined the rules for engagement of Sec62/Sec63 in ER-import in intact human cells using a recently established unbiased proteomics approach. In addition to confirming ERj3, we identified twenty-two novel Sec62/Sec63-substrates under these in vivo-like conditions. As a common feature, those previously unknown substrates share signal peptides with comparatively longer but less hydrophobic H-region and lower C-region polarity. Further analyses with four substrates, and ERj3 in particular, revealed the combination of a slowly-gating signal peptide and a downstream translocation-disruptive positively charged cluster of amino acid residues as decisive for the Sec62-/Sec63-requirement. In the case of ERj3, these features were found to be responsible for an additional BiP-requirement and to correlate with sensitivity towards the Sec61-channel inhibitor CAM741. Thus, the human Sec62/Sec63-complex may support Sec61-channel opening for precursor polypeptides with slowly-gating signal peptides by direct interaction with the cytosolic amino-terminal peptide of Sec61 or via recruitment of BiP and its interaction with the ER-lumenal loop 7 of Sec61. These novel insights into the mechanism of human ER protein import contribute to our understanding of the etiology of SEC63-linked Polycystic Liver Disease. DatabasesThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (http://www.ebi.ac.uk/pride/archive/projects/Identifiers) with the dataset identifiers: PXD008178, PXD011993, and PXD012078. Supplementary information was deposited at Mendeley Data under the DOI:10.17632/6s5hn73jcv.1 (http://dx.doi.or/10.17632/6s5hn73jcv.1).

biochemistry↗

bioRxiv2019

Epigenetic contributions to hemisphere asymmetry in healthy brain, aging, and Parkinson’s disease

Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinsons disease (PD), but its molecular determinants are unknown. Here, we determine epigenetic differences involved in hemispheric asymmetry in the healthy and the PD brain. Neurons of the healthy brain exhibit numerous hemispheric differences in DNA methylation, which affect genes implicated in neurodegenerative diseases. In PD patients, hemispheric asymmetry in DNA methylation is even greater and involves many PD risk genes. The lateralization of clinical PD symptoms involves epigenetic, transcriptional, and proteomic differences across hemispheres that affect neurodevelopment, immune activation, and synaptic transmission. During aging, healthy neurons show a progressive loss of hemispheric asymmetry in the epigenome, which is amplified in PD. For PD patients, a long disease course is associated with greater hemispheric asymmetry in neuronal epigenomes than a short disease course. Hemispheric differences in epigenetic gene regulation are prevalent in neurons and may affect the progression and symptoms of PD.

neuroscience↗

bioRxiv2019

Brain tissue properties and morphometry assessment after chronic complete spinal cord injury

There is much controversy about the potential impact of spinal cord injury (SCI) on brains anatomy and function, which is mirrored in the substantial divergence of findings between animal models and human imaging studies. Given recent advances in quantitative magnetic resonance imaging (MRI) we sought to tackle the unresolved question about the link between the presumed injury associated volume differences and underlying brain tissue property changes in a cohort of chronic complete SCI patients. Using the established computational anatomy methods of voxel-based morphometry (VBM) and voxel-based quantification (VBQ) we performed statistical analyses of grey matter volume and parameter maps indicative for brains myelin, iron and free tissue water content in complete SCI patients (n=14) and healthy individuals (n=14). Our whole-brain analysis showed significant white matter volume loss in the rostral and dorsal part of the spinal cord consistent with Wallerian degeneration of proprioceptive axons in the lemniscal tract in SCI subjects, which correlated with spinal cord atrophy assessed with quantification of the spinal cord cross-sectional area at cervical level. The latter finding suggests that Wallerian degeneration of the lemniscal tract represents a main contributor to the observed spinal cord atrophy, which is highly consistent with preclinical ultrastructural/histological evidence of remote changes in the central nervous system secondary to SCI. Structural changes in the brain representing remote changes in the course of chronic SCI could not be confirmed with conventional VBM or VBQ statistical analysis. Whether and how MRI based brain morphometry and brain tissue property analysis will inform clinical decision making and clinical trial outcomes in spinal cord medicine remains to be determined.

neuroscience↗

bioRxiv2019

Complete genome sequence of Escherichia coli C - an old model organism with a new application in biofilm research

Escherichia coli C forms more robust biofilms than the other laboratory strains. Biofilm formation and cell aggregation under a high shear force depends on temperature and salt concentrations. It is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43, waaSBOJYZUL for LPS synthesis, and cpsB for curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the -35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of the csgD gene, which may drive its overexpression in biofilm. And finally, E. coli C encodes an additional sigma70 subunit overexpressed in biofilm and driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions and total expression profiles using RNA-seq analyses comparing planktonic and biofilm envirovars provided insights into understanding this regulatory pathway in E. coli. IMPORTANCEBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains of E. coli grown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain of E. coli C produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence as well as gene expression profiles of both the biofilm and planktonic envirovars of this classic strain, which provide for a base level of characterization and make it useful for many biofilm-based applications.

microbiology↗

bioRxiv2018

Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor binding head domains

Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from emergence of a new pandemic influenza strain might have potentially even more devastating consequences. As such, there is intense interest in isolating and characterizing potent neutralizing antibodies that target the hemagglutinin (HA) viral surface glycoprotein. Here, we use cryo-electron microscopy to decipher the mechanism of action of a potent HA head-directed monoclonal antibody bound to an influenza H7 HA. The epitope of the antibody is not solvent accessible in the compact, pre-fusion conformation that typifies all HA structures to date. Instead, the antibody binds between HA head protomers to an epitope that must be partly or transiently exposed in the pre-fusion conformation. The \"breathing\" of the HA protomers is implied by the exposure of this epitope, which is consistent with metastability of class I fusion proteins. This structure likely therefore represents an early structural intermediate in the viral fusion process. Understanding the extent of transient exposure of conserved neutralizing epitopes also may lead to new opportunities to combat influenza that have not been appreciated previously.\n\nAuthor SummaryA transiently exposed epitope on influenza H7 hemagglutinin represents a new target for neutralizing antibodies.

immunology↗