Biology subjects

Wagner, S.

Publications and source records attributed to Wagner, S..

80 records · Page 5Linked to original sources

bioRxiv2019

Preserving cultural heritage: Analyzing the antifungal potential of ionic liquids tested in paper restoration

Early industrialization and the development of cheap production processes for paper have led to an exponential accumulation of paper-based documents during the last two centuries. Archives and libraries harbor vast amounts of ancient and modern documents and have to undertake extensive endeavors to protect them from abiotic and biotic deterioration. While services for mechanical preservation such as ex post de-acidification of historic documents are already commercially available, the possibilities for long-term protection of paper-based documents against fungal attack (apart from temperature and humidity control) are very limited. Novel processes for mechanical enhancement of damaged cellulosic documents use Ionic Liquids (IL) as essential process components. With some of these ILs having azole-functionalities similar to well-known fungicides such as Clotrimazole, the possibility of antifungal activities of these ILs was proposed but has not yet been experimentally confirmed.\n\nWe evaluated the potency of four ILs with potential application in paper restoration for suppression of fungal growth on five relevant paper-infesting molds. The results revealed a general antifungal activity of all ILs, which increased with the size of the non-polar group. Physiological experiments and ultimate elemental analysis allowed to determine the minimal inhibitory concentration of each IL as well as the residual IL concentration in process-treated paper. These results provide valuable guidelines for IL-applications in paper restoration processes with antifungal activity as an added benefit. With azoles remaining in the paper after the process, simultaneous repair and biotic protection in treated documents could be facilitated.

microbiology↗

bioRxiv2019

Redox-mediated Kick-Start of Mitochondrial Energy Metabolism drives Resource-efficient Seed Germination

Seeds preserve a far developed plant embryo in a quiescent state. Seed metabolism relies on stored resources and is re-activated to drive germination when the external conditions are favorable. Since the switchover from quiescence to re-activation provides a remarkable case of a cell physiological transition we investigated the earliest events in energy and redox metabolism of Arabidopsis seeds at imbibition. By developing fluorescent protein biosensing in intact seeds, we observed ATP accumulation and oxygen uptake within minutes, indicating rapid activation of mitochondrial respiration, which coincided with a sharp transition from an oxidizing to a more reducing thiol redox environment in the mitochondrial matrix. To identify individual operational protein thiol switches, we captured the fast release of metabolic quiescence in organello and devised quantitative iodoacetyl tandem mass tag-based (iodoTMT) thiol redox proteomics. The redox state across all Cys-peptides was shifted towards reduction from 27.1 % to 13.0 %. A large number of Cys-peptides (412) were redox-switched, representing central pathways of mitochondrial energy metabolism, including the respiratory chain and each enzymatic step of the tricarboxylic acid cycle (TCA). Active site Cys-peptides of glutathione reductase 2, NADPH-thioredoxin reductase a/b and thioredoxin-o1 showed the strongest responses. Germination of seeds lacking those redox proteins was associated with markedly enhanced respiration and deregulated TCA cycle dynamics suggesting decreased resource efficiency of energy metabolism. Germination in aged seeds was strongly impaired. We identify a global operation of thiol redox switches that is required for optimal usage of energy stores by the mitochondria to drive efficient germination.

plant biology↗

bioRxiv2019

TrackUSF, a novel methodology for automated analysis of ultrasonic vocalizations, reveals modified social communication in a rat model of autism

Rodents emit various social ultrasonic vocalizations (USVs), which reflect their emotional state and mediate social interaction. USVs are usually analyzed by manual or semi-automated methodologies categorizing discrete USVs according to their structure in the frequency-time domains. This laborious analysis hinders effective use of USVs for screening animal models of human pathologies associated with modified social behavior, such as autism spectrum disorder (ASD). Here we present a novel, automated methodology for analyzing USVs, termed TrackUSF. To validate TrackUSF, we analyzed a dataset of mouse mating calls and compared the results with a manual analysis by a trained observer. We found that TrackUSF was capable of detecting most USVs, with less than 1% of false-positive detections. We then employed TrackUSF to social vocalizations in Shank3-deficient rats, a rat model of ASD and found, for the first time, that these vocalizations exhibit a spectrum of deviations from pro-social calls towards aggressive calls.

animal behavior and cognition↗

bioRxiv2018

One and Two Year Visual Outcomes from the Moorfields AMD Database - an Open Science Resource for the Study of Neovascular Age-related Macular Degeneration

ObjectivesTo analyse treatment outcomes and share clinical data from a large, single-center, well-curated database (8174 eyes / 6664 patients with 120,756 single entries) of patients with neovascular age related macular degeneration (AMD) treated with anti-vascular endothelial growth factor (VEGF). By making our depersonalised raw data openly available, we aim to stimulate further research in AMD, as well as setting a precedent for future work in this area.\n\nSettingRetrospective, comparative, non-randomised electronic medical record (EMR) database cohort study of the UK Moorfields AMD database with data extracted between 2008 and 2018.\n\nParticipants3357 eyes/patients (61% female). Extraction criteria were [≥] 1 ranibizumab or aflibercept injection, entry of \"AMD\" in the diagnosis field of the EMR, and a minimum of one year of follow-up. Exclusion criteria were unknown date of first injection and treatment outside of routine clinical care at Moorfields before the first recorded injection in the database.\n\nMain outcome measuresPrimary outcome measure was change in VA at one and two years from baseline as measured in Early Treatment Diabetic Retinopathy Study (ETDRS) letters. Secondary outcomes were the number of injections and predictive factors for VA gain.\n\nResultsMean VA gain at one-year and two years were +5.5{+/-}0.5 and +4.9{+/-}0.68 letters respectively. Fifty-four percent of eyes gained [≥]5 letters at two years, 63% had stable VA ({+/-}[≤]14 letters), forty-four percent of eyes maintained good VA ([≥]70 letters). Patients received a mean of 7.7{+/-}0.06 injections during year one and 13.0{+/-}0.2 injections over two years.\n\nYounger age, lower baseline VA, and more injections were associated with higher VA gain at two years.\n\nConclusionThis study benchmarks high quality EMR study results of real life AMD treatment and promotes open science in clinical AMD research by making the underlying data publicly available.\n\nStrengths and limitations of this study- Large sample size, retrospective, single centre, electronic medical record database study\n- High quality real life data\n- Open science approach with sharing of depersonalised raw data

epidemiology↗

bioRxiv2018

Structure of the Core of the Type Three Secretion System ExportApparatus

Export of proteins through type three secretion systems is critical for bacterial motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP/FliQ/FliR) are suggested to form the core of an export gate in the inner membrane, but their structure, assembly and location within the final nanomachine remain unclear. We here present the structure of this complex at 4.2 [A] by cryo-electron microscopy. None of the subunits adopt canonical integral membrane protein topologies and common helix-turn-helix structural elements allow them to form a helical assembly with 5:4:1 stoichiometry. Fitting of the structure into reconstructions of intact secretion systems localize the export gate as a core component of the periplasmic portion of the machinery, and cross-linking experiments confirm this observation. This study thereby identifies the export gate as a key element of the secretion channel and implies that it primes the helical architecture of the components assembling downstream.\n\nOne Sentence SummaryThe core of the T3SS export gate forms a supra-membrane helical assembly

microbiology↗

bioRxiv2017

ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology

Growth and development of plants is ultimately driven by light energy captured through photosynthesis. ATP acts as universal cellular energy cofactor fuelling all life processes, including gene expression, metabolism, and transport. Despite a mechanistic understanding of ATP biochemistry, ATP dynamics in the living plant have been largely elusive. Here we establish live MgATP2- assessment in plants using the fluorescent protein biosensor ATeam1.03-nD/nA. We generate Arabidopsis sensor lines and investigate the sensor in vitro under conditions appropriate for the plant cytosol. We establish an assay for ATP fluxes in isolated mitochondria, and demonstrate that the sensor responds rapidly and reliably to MgATP2- changes in planta. A MgATP2- map of the Arabidopsis seedling highlights different MgATP2- concentrations between tissues and in individual cell types, such as root hairs. Progression of hypoxia reveals substantial plasticity of ATP homeostasis in seedlings, demonstrating that ATP dynamics can be monitored in the living plant.\n\nOne-sentence SummarySensing of MgATP2- by fluorimetry and microscopy allows dissection of ATP fluxes of isolated organelles, and dynamics of cytosolic MgATP2- in vivo.\n\nFunding AgenciesThis work was supported by the Deutsche Forschungsgemeinschaft (DFG) through the Emmy-Noether programme (SCHW1719/1-1; M.S. and GR4251/1-1; C.G.), the Research Training Group GRK 2064 (M.S.; A.J.M.), the Priority Program SPP1710 (A.J.M.) and a grant (SCHW1719/5-1; M.S.) as part of the package PAK918. The Seed Fund grant CoSens from the Bioeconomy Science Center, NRW (A.J.M.; M.S.) is gratefully acknowledged. The scientific activities of the Bioeconomy Science Center were financially supported by the Ministry of Innovation, Science and Research within the framework of the NRW Strategieprojekt BioSC (No. 313/323-400-002 13). A.Co. received funding by the Ministero dellIstruzione, dellUniversita e della Ricerca through the FIRB 2010 programme (RBFR10S1LJ_001) and Piano di Sviluppo di Ateneo 2015 (Universita degli Studi di Milano). M.Z. received funding by the Ministero dellIstruzione, dellUniversita e della Ricerca (Italy) through the PRIN 2010 programme (PRIN2010CSJX4F). S.W. and T.N. received travel support by the Deutscher Akademischer Austauschdienst (DAAD). V.D.C. was supported by the European Social Fund, Operational Programme 2007/2013, and an Erasmus+ Traineeship grant. M.D.F was supported by The Human Frontier Science Program (RPG0053/2012), and the Leverhulme Foundation (RPG-2015-437). I.M.M. was supported by a grant from the Danish Council for Independent Research - Natural Sciences. V.C.P. was supported by the Innovation and Technology Fund (Funding Support to Partner State Key Laboratories in Hong Kong) of the HKSAR.\n\nAbbreviationsAAC - ADP/ATP carrier; AK - adenylate kinase; cAT - carboxyatractyloside; CCCP - carbonyl cyanide m-chlorophenyl hydrazone; CFP - cyan fluorescent protein; CLSM - confocal laser scanning microscopy; ETC - electron transport chain; FRET - Forster Resonance Energy Transfer; LSFM - light sheet fluorescence microscopy.

plant biology↗

bioRxiv2017

Low-Cost HPV Screening And The Prevalence Of Cervical Infection In Asymptomatic Populations In Guatemala

BackgroundA low cost and accurate method for detecting high-risk (HR) HPV is important to permit HPV testing for cervical cancer prevention. We validated a low-cost commercially available HPV method (H13, Hybribio, Hong Kong) and determined the distribution of HPV infections in over 1717 cancer-free women in Guatemala.\n\nMethodsH13 results were compared with two more established HPV tests: (Xpert (Cepheid) and SPF10-LIPA25 (DDL)) in 40 mainly known positive specimens. HR-HPV was detected in cervical samples from 1717 cancer-free women receiving Pap smears using the Hybribio realtime PCR assay of 13 HR types. Selected HPV positive samples were sequenced to determine viral type.\n\nResultsThe Hybribio H13 Assay showed 93% identical results with Xpert, and 89% with SPF10-LIPA25. A total of 13% (226/1717) of women tested HPV+. The highest prevalence was found in younger women (<30 years, 22 %) and older ones ([≥]60 years, 15%). The six most common HR-HPV types among the 148 HPV+ typed were HPV16 (22%), HPV18 (11%), HPV39 (11%), HPV58 (10%), HPV52 (8%), and HPV45 (8%).\n\nConclusionsThe Hybribio Assay was low cost, and accurate in testing for HR-HPV infection. As in most places, HPV16 was the most prevalent HR type in Guatemala and the age-specific prevalence curve peaked in younger ages.\n\nHighlightsO_LIA low cost and accurate method, Hybribio Assay, could be used for CC testing in low income regions.\nC_LIO_LIA total of 13% of cancer-free women were HPV+ and positivity was associated with younger age (<30 years old) in Guatemala.\nC_LIO_LIHPV16 was the major prevalent type.\nC_LI

molecular biology↗

bioRxiv2017

Resolving Drug Effects In Patient-Derived Cancer Cells Links Organoid Responses To Genome Alterations

Cancer drug screening in patient-derived cells holds great promise for personalized oncology and drug discovery but lacks standardization. Whether cells are cultured as conventional monolayer or advanced organoid cultures influences drug effects and thereby drug selection and clinical success. To precisely compare drug profiles in differently cultured primary cells, we developed DeathPro, an automated microscopy-based assay to resolve drug-induced cell death and proliferation inhibition. Using DeathPro, we screened cells from ovarian cancer patients in monolayer or organoid culture with clinically relevant drugs. Drug-induced growth arrest and efficacy of cytostatic drugs differed between the two culture systems. Interestingly, drug effects in organoids were more diverse and had lower therapeutic potential. Genomic analysis revealed novel links between drug sensitivity and DNA repair deficiency in organoids that were undetectable in monolayers. Thus, our results highlight the dependency of cytostatic drugs and pharmacogenomic associations on culture systems, and guide culture selection for drug tests.

cancer biology↗