TY - JOUR A1 - Traub, Jan A1 - Grondey, Katja A1 - Gassenmaier, Tobias A1 - Schmitt, Dominik A1 - Fette, Georg A1 - Frantz, Stefan A1 - Boivin-Jahns, Valérie A1 - Jahns, Roland A1 - Störk, Stefan A1 - Stoll, Guido A1 - Reiter, Theresa A1 - Hofmann, Ulrich A1 - Weber, Martin S. A1 - Frey, Anna T1 - Sustained increase in serum glial fibrillary acidic protein after first ST-elevation myocardial infarction JF - International Journal of Molecular Sciences N2 - Acute ischemic cardiac injury predisposes one to cognitive impairment, dementia, and depression. Pathophysiologically, recent positron emission tomography data suggest astroglial activation after experimental myocardial infarction (MI). We analyzed peripheral surrogate markers of glial (and neuronal) damage serially within 12 months after the first ST-elevation MI (STEMI). Serum levels of glial fibrillary acidic protein (GFAP) and neurofilament light chain (NfL) were quantified using ultra-sensitive molecular immunoassays. Sufficient biomaterial was available from 45 STEMI patients (aged 28 to 78 years, median 56 years, 11% female). The median (quartiles) of GFAP was 63.8 (47.0, 89.9) pg/mL and of NfL 10.6 (7.2, 14.8) pg/mL at study entry 0–4 days after STEMI. GFAP after STEMI increased in the first 3 months, with a median change of +7.8 (0.4, 19.4) pg/mL (p = 0.007). It remained elevated without further relevant increases after 6 months (+11.7 (0.6, 23.5) pg/mL; p = 0.015), and 12 months (+10.3 (1.5, 22.7) pg/mL; p = 0.010) compared to the baseline. Larger relative infarction size was associated with a higher increase in GFAP (ρ = 0.41; p = 0.009). In contrast, NfL remained unaltered in the course of one year. Our findings support the idea of central nervous system involvement after MI, with GFAP as a potential peripheral biomarker of chronic glial damage as one pathophysiologic pathway. KW - myocardial infarction KW - STEMI KW - glial fibrillary acidic protein KW - GFAP KW - neurofilament light chain KW - NfL KW - glial damage KW - cardiac magnetic resonance imaging KW - MRI KW - infarction size Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-288261 SN - 1422-0067 VL - 23 IS - 18 ER - TY - JOUR A1 - Traub, Jan A1 - Otto, Markus A1 - Sell, Roxane A1 - Göpfert, Dennis A1 - Homola, György A1 - Steinacker, Petra A1 - Oeckl, Patrick A1 - Morbach, Caroline A1 - Frantz, Stefan A1 - Pham, Mirko A1 - Störk, Stefan A1 - Stoll, Guido A1 - Frey, Anna T1 - Serum phosphorylated tau protein 181 and neurofilament light chain in cognitively impaired heart failure patients JF - Alzheimer's Research & Therapy N2 - Background Chronic heart failure (HF) is known to increase the risk of developing Alzheimer’s dementia significantly. Thus, detecting and preventing mild cognitive impairment, which is common in patients with HF, is of great importance. Serum biomarkers are increasingly used in neurological disorders for diagnostics, monitoring, and prognostication of disease course. It remains unclear if neuronal biomarkers may help detect cognitive impairment in this high-risk population. Also, the influence of chronic HF and concomitant renal dysfunction on these biomarkers is not well understood. Methods Within the monocentric Cognition.Matters-HF study, we quantified the serum levels of phosphorylated tau protein 181 (pTau) and neurofilament light chain (NfL) of 146 extensively phenotyped chronic heart failure patients (aged 32 to 85 years; 15.1% women) using ultrasensitive bead-based single-molecule immunoassays. The clinical work-up included advanced cognitive testing and cerebral magnetic resonance imaging (MRI). Results Serum concentrations of NfL ranged from 5.4 to 215.0 pg/ml (median 26.4 pg/ml) and of pTau from 0.51 to 9.22 pg/ml (median 1.57 pg/ml). We detected mild cognitive impairment (i.e., T-score < 40 in at least one cognitive domain) in 60% of heart failure patients. pTau (p = 0.014), but not NfL, was elevated in this group. Both NfL (ρ = − 0.21; p = 0.013) and pTau (ρ = − 0.25; p = 0.002) related to the cognitive domain visual/verbal memory, as well as white matter hyperintensity volume and cerebral and hippocampal atrophy. In multivariable analysis, both biomarkers were independently influenced by age (T = 4.6 for pTau; T = 5.9 for NfL) and glomerular filtration rate (T = − 2.4 for pTau; T = − 3.4 for NfL). Markers of chronic heart failure, left atrial volume index (T = 4.6) and NT-proBNP (T = 2.8), were further cardiological determinants of pTau and NfL, respectively. In addition, pTau was also strongly affected by serum creatine kinase levels (T = 6.5) and ferritin (T = − 3.1). Conclusions pTau and NfL serum levels are strongly influenced by age-dependent renal and cardiac dysfunction. These findings point towards the need for longitudinal examinations and consideration of frequent comorbidities when using neuronal serum biomarkers. KW - Alzheimer’s dementia KW - heart failure KW - cognitive impairment KW - neurofilament light chain KW - phosphorylated tau protein KW - renal function KW - age Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-300515 VL - 14 ER - TY - JOUR A1 - Traub, Jan A1 - Otto, Markus A1 - Sell, Roxane A1 - Homola, György A. A1 - Steinacker, Petra A1 - Oeckl, Patrick A1 - Morbach, Caroline A1 - Frantz, Stefan A1 - Pham, Mirko A1 - Störk, Stefan A1 - Stoll, Guido A1 - Frey, Anna T1 - Serum glial fibrillary acidic protein indicates memory impairment in patients with chronic heart failure JF - ESC Heart Failure N2 - Aims Cognitive dysfunction occurs frequently in patients with heart failure (HF), but early detection remains challenging. Serum glial fibrillary acidic protein (GFAP) is an emerging biomarker of cognitive decline in disorders of primary neurodegeneration such as Alzheimer's disease. We evaluated the utility of serum GFAP as a biomarker for cognitive dysfunction and structural brain damage in patients with stable chronic HF. Methods and results Using bead-based single molecule immunoassays, we quantified serum levels of GFAP in patients with HF participating in the prospective Cognition.Matters-HF study. Participants were extensively phenotyped, including cognitive testing of five separate domains and magnetic resonance imaging (MRI) of the brain. Univariable and multivariable models, also accounting for multiple testing, were run. One hundred and forty-six chronic HF patients with a mean age of 63.8 ± 10.8 years were included (15.1% women). Serum GFAP levels (median 246 pg/mL, quartiles 165, 384 pg/mL; range 66 to 1512 pg/mL) did not differ between sexes. In the multivariable adjusted model, independent predictors of GFAP levels were age (T = 5.5; P < 0.001), smoking (T = 3.2; P = 0.002), estimated glomerular filtration rate (T = −4.7; P < 0.001), alanine aminotransferase (T = −2.1; P = 0.036), and the left atrial end-systolic volume index (T = 3.4; P = 0.004). NT-proBNP but not serum GFAP explained global cerebral atrophy beyond ageing. However, serum GFAP levels were associated with the cognitive domain visual/verbal memory (T = −3.0; P = 0.003) along with focal hippocampal atrophy (T = 2.3; P = 0.025). Conclusions Serum GFAP levels are affected by age, smoking, and surrogates of the severity of HF. The association of GFAP with memory dysfunction suggests that astroglial pathologies, which evade detection by conventional MRI, may contribute to memory loss beyond ageing in patients with chronic HF. KW - Glial fibrillary acidic protein KW - GFAP KW - Chronic heart failure KW - Cognitive decline KW - Memory dysfunction KW - Brain atrophy Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-312736 VL - 9 IS - 4 ER - TY - JOUR A1 - Trifault, Barbara A1 - Mamontova, Victoria A1 - Burger, Kaspar T1 - In vivo proximity labeling of nuclear and nucleolar proteins by a stably expressed, DNA damage-responsive NONO-APEX2 fusion protein JF - Frontiers in Molecular Biosciences N2 - Cellular stress can induce DNA lesions that threaten the stability of genes. The DNA damage response (DDR) recognises and repairs broken DNA to maintain genome stability. Intriguingly, components of nuclear paraspeckles like the non-POU domain containing octamer-binding protein (NONO) participate in the repair of DNA double-strand breaks (DSBs). NONO is a multifunctional RNA-binding protein (RBP) that facilitates the retention and editing of messenger (m)RNA as well as pre-mRNA processing. However, the role of NONO in the DDR is poorly understood. Here, we establish a novel human U2OS cell line that expresses NONO fused to the engineered ascorbate peroxidase 2 (U2OS:NONO-APEX2-HA). We show that NONO-APEX2-HA accumulates in the nucleolus in response to DNA damage. Combining viability assays, subcellular localisation studies, coimmunoprecipitation experiments and in vivo proximity labeling, we demonstrate that NONO-APEX2-HA is a stably expressed fusion protein that mimics endogenous NONO in terms of expression, localisation and bona fide interactors. We propose that in vivo proximity labeling in U2OS:NONO-APEX2-HA cells is capable for the assessment of NONO interactomes by downstream assays. U2OS:NONO-APEX2-HA cells will likely be a valuable resource for the investigation of NONO interactome dynamics in response to DNA damage and other stimuli. KW - APEX2 KW - proximity labeling KW - NONO KW - paraspeckles KW - nucleolus KW - DNA damage Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-276707 SN - 2296-889X VL - 9 ER - TY - JOUR A1 - Trivanović, Drenka T1 - Adult stem cells in aging JF - Journal of Personalized Medicine N2 - No abstract available KW - adult stem cells Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-275226 SN - 2075-4426 VL - 12 IS - 5 ER - TY - THES A1 - Trujillo Viera, Jonathan T1 - Protein kinase D2 drives chylomicron-mediate lipid transport in the intestine and promotes obesity T1 - Die Proteinkinase D2 treibt den Chylomicron-vermittelten Lipidtransport im Darm an und fördert Fettleibigkeit N2 - Obesity and associated metabolic syndrome are growing concerns in modern society due to the negative consequences for human health and well-being. Cardiovascular diseases and type 2 diabetes are only some of the pathologies associated to overweight. Among the main causes are decreased physical activity and food availability and composition. Diets with high content of fat are energy-dense and their overconsumption leads to an energy imbalance, which ultimately promotes energy storage as fat and obesity. Aberrant activation of signalling cascades and hormonal imbalances are characteristic of this disease and members of the Protein Kinase D (PKD) family have been found to be involved in several mechanisms mediating metabolic homeostasis. Therefore, we aimed to investigate the role of Protein Kinase D2 (PKD2) in the regulation of metabolism. Our investigation initiated with a mice model for global PKD2 inactivation, which allowed us to prove a direct involvement of this kinase in lipids homeostasis and obesity. Inactivation of PKD2 protected the mice from high-fat diet-induced obesity and improved their response to glucose, insulin and lipids. Furthermore, the results indicated that, even though there were no changes in energy intake or expenditure, inactivation of PKD2 limited the absorption of fat from the intestine and promoted energy excretion in feces. These results were verified in a mice model for specific deletion of intestinal PKD2. These mice not only displayed an improved metabolic fitness but also a healthier gut microbiome profile. In addition, we made use of a small-molecule inhibitor of PKD in order to prove that local inhibition of PKD2 in the intestine was sufficient to inhibit lipid absorption. The usage of the inhibitor not only protected the mice from obesity but also was efficient in avoiding additional body-weight gain after obesity was pre-established in mice. Mechanistically, we determined that PKD2 regulates lipids uptake in enterocytes by phosphorylation of Apolipoprotein A4 (APOA4) and regulation of chylomicron-mediated triglyceride absorption. PKD2 deletion or inactivation increased abundance of APOA4 and decreased the size of chylomicrons and therefore lipids absorption from the diet. Moreover, intestinal activation of PKD2 in human obese patients correlated with higher levels of triglycerides in circulation and a detrimental blood profile. In conclusion, we demonstrated that PKD2 is a key regulator of dietary fat absorption in murine and human context, and its inhibition might contribute to the treatment of obesity. N2 - Fettleibigkeit und das damit verbundene metabolische Syndrom stellt in der modernen Gesellschaft aufgrund der negativen Folgen für die menschliche Gesundheit und das Wohlbefinden ein zunehmendes Problem dar. Herz-Kreislauf-Erkrankungen und Typ- 2-Diabetes sind nur einige der mit Übergewicht verbundenen Pathologien. Zu den Hauptursachen zählen eine verminderte körperliche Aktivität sowie die Verfügbarkeit und Zusammensetzung von Nahrungsmitteln. Diäten mit hohem Fettgehalt haben eine hohe Energiedichte und ihr übermäßiger Konsum führt zu einem Energieungleichgewicht, das letztendlich die Energiespeicherung als Fett und Fettleibigkeit fördert. Aberrante Aktivierung von Signalkaskaden und hormonelle Ungleichgewichte sind charakteristisch für diese Krankheit, und es wurde festgestellt, dass Mitglieder der Protein Kinase D (PKD) -Familie an mehreren Mechanismen der metabolischen Homöostase beteiligt sind. Daher zielten wir darauf ab die Rolle der Proteinkinase D2 (PKD2) bei der Regulation des Stoffwechsels zu untersuchen. Unsere Untersuchung begann mit einem Mäusemodell für die globale PKD2- Inaktivierung, welches es uns ermöglichte, eine direkte Beteiligung dieser Kinase an der Lipidhomöostase und Fettleibigkeit nachzuweisen. Die Inaktivierung von PKD2 schützte die Mäuse vor fettreicher diätbedingter Fettleibigkeit und verbesserte ihre Reaktion auf Glukose, Insulin und Lipide. Darüber hinaus zeigten die Ergebnisse, dass die Inaktivierung von PKD2 die Absorption von Fett über den Darm begrenzte und die Energieausscheidung im Kot förderte, obwohl sich die Energieaufnahme oder der Energieverbrauch nicht änderten. Diese Ergebnisse wurden in einem Mäusemodell mit spezifischer Deletion von intestinaler PKD2 verifiziert. Diese Mäuse zeigten nicht nur eine verbesserte metabolische Fitness, sondern auch ein gesünderes Darmmikrobiomprofil. Zusätzlich verwendeten wir einen niedermolekularen PKD- Inhibitor, um zu beweisen, dass die lokale Hemmung von PKD2 im Darm ausreicht, um die Lipidabsorption zu hemmen. Die Verwendung des Inhibitors schützte die Mäuse nicht nur vor Fettleibigkeit, sondern verhinderte auch wirksam eine zusätzliche Gewichtszunahme, nachdem bei Mäusen bereits Fettleibigkeit festgestellt worden war. Mechanistisch haben wir festgestellt, dass PKD2 die Lipidaufnahme in Enterozyten durch Phosphorylierung von Apolipoprotein A4 (APOA4) und Regulation der Chylomicron-vermittelten Triglyceridabsorption reguliert. Die Deletion oder Inaktivierung von PKD2 erhöhte die Häufigkeit von APOA4 und verringerte die Größe der Chylomikronen und damit die Lipidabsorption aus der Nahrung. Darüber hinaus korrelierte die intestinale Aktivierung von PKD2 bei adipösen Patienten mit höheren Triglyceridspiegeln im Kreislauf und einem schädlichen Blutprofil. Zusammenfassend haben wir gezeigt, dass PKD2 ein Schlüsselregulator für die Aufnahme von Nahrungsfett im murinen und menschlichen Kontext ist und seine Hemmung zur Behandlung von Fettleibigkeit beitragen könnte KW - Chylomicrons KW - Übergewicht KW - Proteinkinase D KW - Darm KW - Protein Kinase D2 KW - Chylomicron KW - Obesity Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-265095 ER - TY - JOUR A1 - Truongvan, Ngoc A1 - Li, Shurong A1 - Misra, Mohit A1 - Kuhn, Monika A1 - Schindelin, Hermann T1 - Structures of UBA6 explain its dual specificity for ubiquitin and FAT10 JF - Nature Communications N2 - The covalent modification of target proteins with ubiquitin or ubiquitin-like modifiers is initiated by E1 activating enzymes, which typically transfer a single modifier onto cognate conjugating enzymes. UBA6 is an unusual E1 since it activates two highly distinct modifiers, ubiquitin and FAT10. Here, we report crystal structures of UBA6 in complex with either ATP or FAT10. In the UBA6-FAT10 complex, the C-terminal domain of FAT10 binds to where ubiquitin resides in the UBA1-ubiquitin complex, however, a switch element ensures the alternate recruitment of either modifier. Simultaneously, the N-terminal domain of FAT10 interacts with the 3-helix bundle of UBA6. Site-directed mutagenesis identifies residues permitting the selective activation of either ubiquitin or FAT10. These results pave the way for studies investigating the activation of either modifier by UBA6 in physiological and pathophysiological settings. KW - enzyme mechanisms KW - post-translational modifications KW - X-ray crystallography Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-301161 VL - 13 ER - TY - JOUR A1 - Tsoulias, Nikos A1 - Jörissen, Sven A1 - Nüchter, Andreas T1 - An approach for monitoring temperature on fruit surface by means of thermal point cloud JF - MethodsX N2 - Heat and excessive solar radiation can produce abiotic stresses during apple maturation, resulting fruit quality. Therefore, the monitoring of temperature on fruit surface (FST) over the growing period can allow to identify thresholds, above of which several physiological disorders such as sunburn may occur in apple. The current approaches neglect spatial variation of FST and have reduced repeatability, resulting in unreliable predictions. In this study, LiDAR laser scanning and thermal imaging were employed to detect the temperature on fruit surface by means of 3D point cloud. A process for calibrating the two sensors based on an active board target and producing a 3D thermal point cloud was suggested. After calibration, the sensor system was utilised to scan the fruit trees, while temperature values assigned in the corresponding 3D point cloud were based on the extrinsic calibration. Whereas a fruit detection algorithm was performed to segment the FST from each apple. • The approach allows the calibration of LiDAR laser scanner with thermal camera in order to produce a 3D thermal point cloud. • The method can be applied in apple trees for segmenting FST in 3D. Whereas the approach can be utilised to predict several physiological disorders including sunburn on fruit surface. KW - point cloud KW - thermal point cloud KW - fruit temperature KW - sunburn KW - food quality KW - precision horticulture Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-300270 SN - 2215-0161 VL - 9 ER - TY - JOUR A1 - Tuca, Alexandru-Cristian A1 - Bernardelli de Mattos, Ives A1 - Funk, Martin A1 - Winter, Raimund A1 - Palackic, Alen A1 - Groeber-Becker, Florian A1 - Kruse, Daniel A1 - Kukla, Fabian A1 - Lemarchand, Thomas A1 - Kamolz, Lars-Peter T1 - Orchestrating the dermal/epidermal tissue ratio during wound healing by controlling the moisture content JF - Biomedicines N2 - A balanced and moist wound environment and surface increases the effect of various growth factors, cytokines, and chemokines, stimulating cell growth and wound healing. Considering this fact, we tested in vitro and in vivo water evaporation rates from the cellulose dressing epicite\(^{hydro}\) when combined with different secondary dressings as well as the resulting wound healing efficacy in a porcine donor site model. The aim of this study was to evaluate how the different rates of water evaporation affected wound healing efficacy. To this end, epicite\(^{hydro}\) primary dressing, in combination with different secondary dressing materials (cotton gauze, JELONET\(^◊\), AQUACEL\(^®\) Extra\(^™\), and OPSITE\(^◊\) Flexifix), was placed on 3 × 3 cm-sized dermatome wounds with a depth of 1.2 mm on the flanks of domestic pigs. The healing process was analyzed histologically and quantified by morphometry. High water evaporation rates by using the correct secondary dressing, such as cotton gauze, favored a better re-epithelialization in comparison with the low water evaporation resulting from an occlusive secondary dressing, which favored the formation of a new and intact dermal tissue that nearly fully replaced all the dermis that was removed during wounding. This newly available evidence may be of great benefit to clinical wound management. KW - bacterial cellulose dressing KW - secondary wound dressing KW - moisture balance KW - wound healing KW - in vivo experiments Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-275115 SN - 2227-9059 VL - 10 IS - 6 ER - TY - JOUR A1 - Tütüncü, Serdar A1 - Olma, Manuel C. A1 - Kunze, Claudia A1 - Krämer, Michael A1 - Dietzel, Joanna A1 - Schurig, Johannes A1 - Filser, Paula A1 - Pfeilschifter, Waltraud A1 - Hamann, Gerhard F. A1 - Büttner, Thomas A1 - Heuschmann, Peter U. A1 - Kirchhof, Paulus A1 - Laufs, Ulrich A1 - Nabavi, Darius G. A1 - Röther, Joachim A1 - Thomalla, Götz A1 - Veltkamp, Roland A1 - Eckardt, Kai‐Uwe A1 - Haeusler, Karl Georg A1 - Endres, Matthias T1 - Levels and dynamics of estimated glomerular filtration rate and recurrent vascular events and death in patients with minor stroke or transient ischemic attack JF - European Journal of Neurology N2 - Background and purpose Impaired kidney function is associated with an increased risk of vascular events in acute stroke patients, when assessed by single measurements of estimated glomerular filtration rate (eGFR). It is unknown whether repeated measurements provide additional information for risk prediction. Methods The MonDAFIS (Systematic Monitoring for Detection of Atrial Fibrillation in Patients with Acute Ischemic Stroke) study randomly assigned 3465 acute ischemic stroke patients to either standard procedures or an additive Holter electrocardiogram. Baseline eGFR (CKD‐EPI formula) were dichotomized into values of < versus ≥60 ml/min/1.73 m\(^{2}\). eGFR dynamics were classified based on two in‐hospital values as “stable normal” (≥60 ml/min/1.73 m\(^{2}\)), “increasing” (by at least 15% from baseline, second value ≥ 60 ml/min/1.73 m\(^{2}\)), “decreasing” (by at least 15% from baseline of ≥60 ml/min/1.73 m\(^{2}\)), and “stable decreased” (<60 ml/min/1.73 m\(^{2}\)). The composite endpoint (stroke, major bleeding, myocardial infarction, all‐cause death) was assessed after 24 months. We estimated hazard ratios in confounder‐adjusted models. Results Estimated glomerular filtration rate at baseline was available in 2947 and a second value in 1623 patients. After adjusting for age, stroke severity, cardiovascular risk factors, and randomization, eGFR < 60 ml/min/1.73 m\(^{2}\) at baseline (hazard ratio [HR] = 2.2, 95% confidence interval [CI] = 1.40–3.54) as well as decreasing (HR = 1.79, 95% CI = 1.07–2.99) and stable decreased eGFR (HR = 1.64, 95% CI = 1.20–2.24) were independently associated with the composite endpoint. In addition, eGFR < 60 ml/min/1.732 at baseline (HR = 3.02, 95% CI = 1.51–6.10) and decreasing eGFR were associated with all‐cause death (HR = 3.12, 95% CI = 1.63–5.98). Conclusions In addition to patients with low eGFR levels at baseline, also those with decreasing eGFR have increased risk for vascular events and death; hence, repeated estimates of eGFR might add relevant information to risk prediction. KW - kidney function KW - prognosis KW - stroke Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-287271 VL - 29 IS - 9 SP - 2716 EP - 2724 ER - TY - JOUR A1 - Tütüncü, Serdar A1 - Olma, Manuel A1 - Kunze, Claudia A1 - Dietzel, Joanna A1 - Schurig, Johannes A1 - Fiessler, Cornelia A1 - Malsch, Carolin A1 - Haas, Tobias Eberhard A1 - Dimitrijeski, Boris A1 - Doehner, Wolfram A1 - Hagemann, Georg A1 - Hamilton, Frank A1 - Honermann, Martin A1 - Jungehulsing, Gerhard Jan A1 - Kauert, Andreas A1 - Koennecke, Hans-Christian A1 - Mackert, Bruno-Marcel A1 - Nabavi, Darius A1 - Nolte, Christian H. A1 - Reis, Joschua Mirko A1 - Schmehl, Ingo A1 - Sparenberg, Paul A1 - Stingele, Robert A1 - Völzke, Enrico A1 - Waldschmidt, Carolin A1 - Zeise-Wehry, Daniel A1 - Heuschmann, Peter U. A1 - Endress, Matthias A1 - Haeusler, Karl Georg T1 - Off-label-dosing of non-vitamin K-dependent oral antagonists in AF patients before and after stroke: results of the prospective multicenter Berlin Atrial Fibrillation Registry JF - Journal of Neurology N2 - Aims We aimed to analyze prevalence and predictors of NOAC off-label under-dosing in AF patients before and after the index stroke. Methods The post hoc analysis included 1080 patients of the investigator-initiated, multicenter prospective Berlin Atrial Fibrillation Registry, designed to analyze medical stroke prevention in AF patients after acute ischemic stroke. Results At stroke onset, an off-label daily dose was prescribed in 61 (25.5%) of 239 NOAC patients with known AF and CHA2DS2-VASc score ≥ 1, of which 52 (21.8%) patients were under-dosed. Under-dosing was associated with age ≥ 80 years in patients on rivaroxaban [OR 2.90, 95% CI 1.05-7.9, P = 0.04; n = 29] or apixaban [OR 3.24, 95% CI 1.04-10.1, P = 0.04; n = 22]. At hospital discharge after the index stroke, NOAC off-label dose on admission was continued in 30 (49.2%) of 61 patients. Overall, 79 (13.7%) of 708 patients prescribed a NOAC at hospital discharge received an off-label dose, of whom 75 (10.6%) patients were under-dosed. Rivaroxaban under-dosing at discharge was associated with age ≥ 80 years [OR 3.49, 95% CI 1.24-9.84, P = 0.02; n = 19]; apixaban under-dosing with body weight ≤ 60 kg [OR 0.06, 95% CI 0.01-0.47, P < 0.01; n = 56], CHA2DS2-VASc score [OR per point 1.47, 95% CI 1.08-2.00, P = 0.01], and HAS-BLED score [OR per point 1.91, 95% CI 1.28-2.84, P < 0.01]. Conclusion At stroke onset, off-label dosing was present in one out of four, and under-dosing in one out of five NOAC patients. Under-dosing of rivaroxaban or apixaban was related to old age. In-hospital treatment after stroke reduced off-label NOAC dosing, but one out of ten NOAC patients was under-dosed at discharge. KW - NOAC KW - ischemic stroke KW - atrial fibrillation KW - under-dosing Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-266969 SN - 1432-1459 VL - 269 IS - 1 ER - TY - JOUR A1 - Uereyen, Soner A1 - Bachofer, Felix A1 - Kuenzer, Claudia T1 - A framework for multivariate analysis of land surface dynamics and driving variables — a case study for Indo-Gangetic river basins JF - Remote Sensing N2 - The analysis of the Earth system and interactions among its spheres is increasingly important to improve the understanding of global environmental change. In this regard, Earth observation (EO) is a valuable tool for monitoring of long term changes over the land surface and its features. Although investigations commonly study environmental change by means of a single EO-based land surface variable, a joint exploitation of multivariate land surface variables covering several spheres is still rarely performed. In this regard, we present a novel methodological framework for both, the automated processing of multisource time series to generate a unified multivariate feature space, as well as the application of statistical time series analysis techniques to quantify land surface change and driving variables. In particular, we unify multivariate time series over the last two decades including vegetation greenness, surface water area, snow cover area, and climatic, as well as hydrological variables. Furthermore, the statistical time series analyses include quantification of trends, changes in seasonality, and evaluation of drivers using the recently proposed causal discovery algorithm Peter and Clark Momentary Conditional Independence (PCMCI). We demonstrate the functionality of our methodological framework using Indo-Gangetic river basins in South Asia as a case study. The time series analyses reveal increasing trends in vegetation greenness being largely dependent on water availability, decreasing trends in snow cover area being mostly negatively coupled to temperature, and trends of surface water area to be spatially heterogeneous and linked to various driving variables. Overall, the obtained results highlight the value and suitability of this methodological framework with respect to global climate change research, enabling multivariate time series preparation, derivation of detailed information on significant trends and seasonality, as well as detection of causal links with minimal user intervention. This study is the first to use multivariate time series including several EO-based variables to analyze land surface dynamics over the last two decades using the causal discovery algorithm PCMCI. KW - time series analysis KW - trends KW - seasonality KW - partial correlation KW - causal networks KW - NDVI KW - snow cover area KW - surface water area KW - Indus-Ganges-Brahmaputra-Meghna KW - Himalaya Karakoram Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-255295 SN - 2072-4292 VL - 14 IS - 1 ER - TY - JOUR A1 - Uhler, Johannes A1 - Haase, Peter A1 - Hoffmann, Lara A1 - Hothorn, Torsten A1 - Schmidl, Jürgen A1 - Stoll, Stefan A1 - Welti, Ellen A. R. A1 - Buse, Jörn A1 - Müller, Jörg T1 - A comparison of different Malaise trap types JF - Insect Conservation and Diversity N2 - Recent reports on insect decline have highlighted the need for long‐term data on insect communities towards identifying their trends and drivers. With the launch of many new insect monitoring schemes to investigate insect communities over large spatial and temporal scales, Malaise traps have become one of the most important tools due to the broad spectrum of species collected and reduced capture bias through passive sampling of insects day and night. However, Malaise traps can vary in size, shape, and colour, and it is unknown how these differences affect biomass, species richness, and composition of trap catch, making it difficult to compare results between studies. We compared five Malaise trap types (three variations of the Townes and two variations of the Bartak Malaise trap) to determine their effects on biomass and species richness as identified by metabarcoding. Insect biomass varied by 20%–55%, not strictly following trap size but varying with trap type. Total species richness was 20%–38% higher in the three Townes trap models compared to the Bartak traps. Bartak traps captured lower richness of highly mobile taxa but increased richness of ground‐dwelling taxa. The white roofed Townes trap captured a higher richness of pollinators. We find that biomass, total richness, and taxa group specific richness are all sensitive to Malaise trap type. Trap type should be carefully considered and aligned to match monitoring and research questions. Additionally, our estimates of trap type effects can be used to adjust results to facilitate comparisons across studies. KW - Bartak KW - biodiversity KW - insect communities KW - insect monitoring KW - Malaise trap KW - Townes KW - trap selectivity Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-293694 VL - 15 IS - 6 SP - 666 EP - 672 ER - TY - JOUR A1 - Ullherr, Maximilian A1 - Diez, Matthias A1 - Zabler, Simon T1 - Robust image reconstruction strategy for multiscalar holotomography JF - Journal of Imaging N2 - Holotomography is an extension of computed tomography where samples with low X-ray absorption can be investigated with higher contrast. In order to achieve this, the imaging system must yield an optical resolution of a few micrometers or less, which reduces the measurement area (field of view = FOV) to a few mm at most. If the sample size, however, exceeds the field of view (called local tomography or region of interest = ROI CT), filter problems arise during the CT reconstruction and phase retrieval in holotomography. In this paper, we will first investigate the practical impact of these filter problems and discuss approximate solutions. Secondly, we will investigate the effectiveness of a technique we call “multiscalar holotomography”, where, in addition to the ROI CT, a lower resolution non-ROI CT measurement is recorded. This is used to avoid the filter problems while simultaneously reconstructing a larger part of the sample, albeit with a lower resolution in the additional area. KW - reconstruction KW - region of interest KW - ROI KW - multiscalar holotomography KW - holotomography KW - computed tomography KW - CT KW - X-ray Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-262112 SN - 2313-433X VL - 8 IS - 2 ER - TY - JOUR A1 - Ullmann, Tobias A1 - Möller, Eric A1 - Baumhauer, Roland A1 - Lange-Athinodorou, Eva A1 - Meister, Julia T1 - A new Google Earth Engine tool for spaceborne detection of buried palaeogeographical features – examples from the Nile Delta (Egypt) JF - E&G Quaternary Science Journal N2 - No abstract available. KW - Google Earth KW - Nile Delta (Egypt) KW - paleogeography Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-300164 VL - 71 IS - 2 ER - TY - JOUR A1 - Umstätter, Florian A1 - Werner, Julia A1 - Zerlin, Leah A1 - Mühlberg, Eric A1 - Kleist, Christian A1 - Klika, Karel D. A1 - Hertlein, Tobias A1 - Beijer, Barbro A1 - Domhan, Cornelius A1 - Zimmermann, Stefan A1 - Ohlsen, Knut A1 - Haberkorn, Uwe A1 - Mier, Walter A1 - Uhl, Philipp T1 - Impact of linker modification and PEGylation of vancomycin conjugates on structure-activity relationships and pharmacokinetics JF - Pharmaceuticals N2 - As multidrug-resistant bacteria represent a concerning burden, experts insist on the need for a dramatic rethinking on antibiotic use and development in order to avoid a post-antibiotic era. New and rapidly developable strategies for antimicrobial substances, in particular substances highly potent against multidrug-resistant bacteria, are urgently required. Some of the treatment options currently available for multidrug-resistant bacteria are considerably limited by side effects and unfavorable pharmacokinetics. The glycopeptide vancomycin is considered an antibiotic of last resort. Its use is challenged by bacterial strains exhibiting various types of resistance. Therefore, in this study, highly active polycationic peptide-vancomycin conjugates with varying linker characteristics or the addition of PEG moieties were synthesized to optimize pharmacokinetics while retaining or even increasing antimicrobial activity in comparison to vancomycin. The antimicrobial activity of the novel conjugates was determined by microdilution assays on susceptible and vancomycin-resistant bacterial strains. VAN1 and VAN2, the most promising linker-modified derivatives, were further characterized in vivo with molecular imaging and biodistribution studies in rodents, showing that the linker moiety influences both antimicrobial activity and pharmacokinetics. Encouragingly, VAN2 was able to undercut the resistance breakpoint in microdilution assays on vanB and vanC vancomycin-resistant enterococci. Out of all PEGylated derivatives, VAN:PEG1 and VAN:PEG3 were able to overcome vanC resistance. Biodistribution studies of the novel derivatives revealed significant changes in pharmacokinetics when compared with vancomycin. In conclusion, linker modification of vancomycin-polycationic peptide conjugates represents a promising strategy for the modulation of pharmacokinetic behavior while providing potent antimicrobial activity. KW - glycopeptide antibiotics KW - antimicrobial resistance KW - vancomycin KW - polycationic peptides KW - linker influence KW - pharmacokinetics KW - PEGylation Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-255197 SN - 1424-8247 VL - 15 IS - 2 ER - TY - THES A1 - Upcin, Berin T1 - Contribution of vascular adventitia-resident progenitor cells to new vessel formation in \(ex\) \(vivo\) 3D models T1 - Der Beitrag der Gefäßwandadventitia-residenten Vorläuferzellen zur Neovaskularisation in \(ex\) \(vivo\) 3D Modellen N2 - Ongoing research to fight cancer, one of the dominant diseases of the 21st century has led to big progress especially when it comes to understanding the tumor growth and metastasis. This includes the discovery of the molecular mechanisms of tumor vascularization, which is critically required for establishment of tumor metastasis. Formation of new blood vessels is the first step in tumor vascularization. Therefore, understanding the molecular and cellular basis of tumor vascularization attracted a significant effort studying in biomedical research. The blood vessels for supplying tumor can be formed by sprouting from pre-existing vessels, a process called angiogenesis, or by vasculogenesis, that is de novo formation of blood vessels from not fully differentiated progenitor cell populations. Vasculogenic endothelial progenitor cells (EPCs) can either be activated from populations in the bone marrow reaching the pathological region via the circulation or they can be recruited from local reservoirs. Neovessel formation influences tumor progression, hence therapeutic response model systems of angiogenesis/vasculogenesis are necessary to study the underlying mechanisms. Although, initially the research in this area focused more on angiogenesis, it is now well understood that both angiogenesis and postnatal vasculogenesis contribute to neovessel formation in adult under both most pathological as well as physiological conditions. Studies in the last two decades demonstrate that in addition to the intimal layer of fully differentiated mature endothelial cells (ECs) and various smaller supplying vessels (vasa vasorum) that can serve as a source for new vessels by angiogenesis, especially the adventitia of large and medium size blood vessels harbors various vascular wall-resident stem and progenitor cells (VW-SPCs) populations that serve as a source for new vessels by postnatal vasculogenesis. However, little is known about the potential role of VW-SPCs in tumor vascularization. To this end, the present work started first to establish a modified aortic ring assay (ARA) using mouse aorta in order to study the contribution of vascular adventitia-resident VW-SPCs to neovascularization in general and in presence of tumor cells. ARA is already established an ex vivo model for neovascularization allows to study the morphogenetic events of complex new vessel formation that includes all layers of mature blood vessels, a significant advantage over the assays that employ monolayer endothelial cell cultures. Moreover, in contrast to assays employing endothelial cells monocultures, both angiogenic and vasculogenic events take place during new vessel formation in ARA although the exact contribution of these two processes to new vessel formation cannot be easily distinguished in conventional ARA. Thus, in this study, a modified protocol for the ARA (mdARA) was established by either removing or keeping the aortic adventitia in place. The mdARA allows to distinguish the role of VW-SPCs from those of other aortic layers. The present data show that angiogenic sprouting from mature aortic endothelium was markedly delayed when the adventitial layer was removed. Furthermore, the network between the capillary-like sprouts was significantly reduced in absence of aortic adventitia. Moreover, the stabilization of new sprouts by assembling the NG2+ pericyte-like cells that enwrapped the endothelial sprouts from the outside was improved when the adventitial layer remained in place. Next, mimicking the tumor-vessel adventitia-interaction, multicellular tumor spheroids (MCTS) and aortic rings (ARs) with or without adventitia of C57BL/6-Tg (UBC-GFP) mice were confronted within the collagen gel and cultured ex vivo. This 3D model enabled analysis of the mobilization, migration and capillary-like sprouts formation by VW-SPCs within tumor-vessel wall-interface in comparison to tumor-free side of the ARs. Interestingly, while MCTS preferred the uptake of single vascular adventitia-derived cells, neural spheroids were directly penetrated by capillary-like structures that were sprouted from the aortic adventitia. In summary, the model established in this work allows to study new vessel formation by both postnatal vasculogenesis and angiogenesis under same conditions. It can be applied in various mouse models including reporter mouse models, e.g. Cxcr1 CreER+/mTmG+/- mice, in which GFP-marked macrophages of the vessel wall were directly observed as they mobilized from their niche and migrated into collagen gel. Another benefit of the model is that it can be used for testing different factors such as small molecules, growth factors, cytokines, and drugs with both pro- and anti-angiogenic/vasculogenic effects. N2 - Die Forschungsarbeiten der letzten Jahrzehnte zur Bekämpfung der Krebserkrankung, einer der dominierenden Krankheiten des 21. Jahrhunderts, haben zu großen Fortschritten, insbesondere im Verständnis bezüglich der Tumormetastasierung geführt. Dies schließt die Prozesse der Tumorvaskularisierung als einen der initialen Schritte der Metastasierung mit ein, die nach wie vor nicht ausreichend geklärt sind. Die Blutgefäßbildung zur Versorgung des Tumorgewebes kann durch die Anagiogenese, die als Einsprießen neuer Gefäße aus den bereits vorhandenen Blutgefäßen definiert wird, oder durch die Vaskulogenese, die als Gefäßneubildung aus Stamm- und Vorläuferzellen beschrieben wird, sichergestellt werden. Noch nicht vollständig ausdifferenzierte endotheliale Vorläuferzellen (EPCs) werden dabei nach dem bisherigen Kenntnistand aus dem Knochenmark rekrutiert und erreichen die Regionen der Gefäßneubildung über die Blutzirkulation und können dort zur de novo Formierung neuer Blutgefäße auch beim Erwachsenen beitragen. Untersuchungen der letzten zwei Dekaden haben gezeigt, dass solche Vorläuferzellen auch aus lokalen Reservoiren, wie z.B. aus der Gefäßwandadventitia der bereits existierenden Blutgefäße mobilisiert werden. Da die Bildung neuer Gefäße einen direkten Einfluss auf die Tumorprogression hat, sind entsprechende Modellsysteme notwendig, um die zugrundeliegenden Mechanismen möglichst präzise zu untersuchen. Obwohl sich die Forschung der Tumorvaskularisierung zunächst auf Prozesse der Angiogenese konzentrierte, ist es mittlerweile ausreichend belegt, dass auch die Vaskulogenese zur Tumorvaskularisierung beiträgt und somit die Tumorprogression beeinflusst. Anhand einer Vielzahl an Studien der letzten zwei Jahrzehnte konnte demonstriert werden, dass sich, neben der Intimaschicht, die vollständig differenzierte Endothelzellen (ECs) enthält und kleineren Gefäßwand-versorgenden Blutgefäßen, der sogenannten Vasa vasorum in der Adventitia der großen Gefäße, auch Populationen gefäßwandresidenter Stamm- und Vorläuferzellen (VW-SPCs) in der äußeren Gefäßwandschicht, nämlich der Adventitia fast aller Gefäßabschnitte nachweisen lassen. Obwohl diese als Quelle neuer Gefäße in der postnatalen Vaskulogenese beschrieben sind, ist nach wie vor wenig über die potenzielle Rolle von VW-SPCs in der Tumorvaskularisation bekannt. Daher wurde im Rahmen dieser Arbeit zuerst ein modifiziertes Aortic Ringassay (ARA) unter Verwendung der Mausaorta etabliert, um den Beitrag der VW-SPCs zur Neovaskularisierung im Allgemeinen und zur Tumorvaskularisierung im Speziellen ex vivo untersuchen zu können. ARA ist ein bereits seit einigen Jahrzehnten etabliertes ex vivo Modell zur Untersuchung der Gefäßneubildung durch Angiogenese. Mittels ARA kann die Bildung komplexer vaskulärer Strukturen in Präsenz aller Wandschichten reifer Blutgefäße untersucht werden, was einen wesentlichen Vorteil gegenüber der Verwendung von Endothelzellkulturen in Monolayer bedeutet. Hierbei ist jedoch anzumerken, dass in ARA sowohl angiogene als auch vaskulogene Prozesse zur Gefäßbildung beitragen, aber der genaue Beitrag beider Prozesse schwer oder kaum voneinander unterscheidbar ist. Daher wurde im Rahmen dieser Arbeit ein modifiziertes ARA-Protokoll etabliert (mdARA), in welchem die aortale Adventitia vor dem Beginn des ARA entweder entfernt oder belassen wurde und somit die Rolle der VW-SPCs bei der Gefäßsprossung von den Zellen anderer Aortenwandschichten differenziert studiert werden konnte. Die dabei generierten Daten zeigen, dass sich die angiogene Aussprossung aus dem reifen Aortenendothel nach Entfernung der adventitialen Schicht deutlich verzögerte. Darüber hinaus war das Netzwerk zwischen den kapillarartigen Sprossen in Abwesenheit der Aortenadventitia signifikant reduziert. Mehr noch, das Belassen der adventitialen Wandstruktur führte zu einer verbesserten Stabilisierung neuer Gefäßsprossen. Als sichtbares Korrelat hierfür zeigte sich eine stärkere und bessere Anlagerung der NG2+ Perizyten-ähnlichen Zellen zu den endothelialen Kapillar-ähnlichen Aussprossungen von außen, wie Perizyten an der Kapillarwand in situ. Als nächstes wurden die Aortenringe (ARs) von C57BL/6-Tg (UBC-GFP)-Mäusen mit multizellulären Tumor-Sphäroiden (MCTS) in Kollagengel ko-kultiviert, um die Interaktion zwischen Tumor und Gefäßwand-Adventitia ex vivo nachzuahmen. Dieses 3D Modell ermöglichte die Analyse der Mobilisierung und Migration der VW-SPCs von der aortalen Adventitia sowohl zu der Tumorseite in den Tumor-Gefäßwand-Interfaces als auch zu der tumorfreien Seite der Aortenringe. Interessanterweise wurde die Kapillarsprossung im Tumor-Gefäßwand-Interface an der Grenze zum MCTS gestoppt und die VW-SPCs als Einzelzellen in die MCTS aufgenommen. Demgegenüber wurde auf der tumor-freien Seite der Aortenringe eine deutlich längere Kapillaraussprossung beobachtet. Im Gegensatz zu MCTS resultierte die Ko-Kultivierung der ARs mit neuronalen Spheroiden darin, dass die aus der aortalen Adventitia aussprossenden Kapillar-ähnlichen Strukturen direkt in die neuronalen Spheroide penetrierten. Zusammenfassend berücksichtigt dieses neuartige in vitro 3D-Modell sowohl Angiogenese als auch Vaskulogenese und bietet vielfältige Vorteile, wie zum Beispiel die Kompatibilität zu verschiedenen Mausmodellen einschließlich der Reporter-Mausmodelle, wie z.B. die in dieser Arbeit gezeigte Verwendung der Aorta von Cxcr1 CreER+/mTmG+/- um die GFP-markierten Makrophagen aus der Gefäßwand bei der Gefäßaussprossung studieren zu können. Des Weiteren ist dieses Model auch für Testung unterschiedlicher Faktoren und Therapeutika einschließlich der anti-angiogenen und -vasculogenen Substanzen unter ex vivo Bedingungen geeignet.   KW - Progenitor KW - Adventitia Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-255070 ER - TY - JOUR A1 - Uttinger, Konstantin L. A1 - Riedmeier, Maria A1 - Reibetanz, Joachim A1 - Meyer, Thomas A1 - Germer, Christoph Thomas A1 - Fassnacht, Martin A1 - Wiegering, Armin A1 - Wiegering, Verena T1 - Adrenalectomies in children and adolescents in Germany – a diagnose related groups based analysis from 2009-2017 JF - Frontiers in Endocrinology N2 - Background Adrenalectomies are rare procedures especially in childhood. So far, no large cohort study on this topic has been published with data on to age distribution, operative procedures, hospital volume and operative outcome. Methods This is a retrospective analysis of anonymized nationwide hospital billing data (DRG data, 2009-2017). All adrenal surgeries (defined by OPS codes) of patients between the age 0 and 21 years in Germany were included. Results A total of 523 patient records were identified. The mean age was 8.6 ± 7.7 years and 262 patients were female (50.1%). The majority of patients were between 0 and 5 years old (52% overall), while 11.1% were between 6 and 11 and 38.8% older than 12 years. The most common diagnoses were malignant neoplasms of the adrenal gland (56%, mostly neuroblastoma) with the majority being younger than 5 years. Benign neoplasms in the adrenal gland (D350) account for 29% of all cases with the majority of affected patients being 12 years or older. 15% were not defined regarding tumor behavior. Overall complication rate was 27% with a clear higher complication rate in resection for malignant neoplasia of the adrenal gland. Bleeding occurrence and transfusions are the main complications, followed by the necessary of relaparotomy. There was an uneven patient distribution between hospital tertiles (low volume, medium and high volume tertile). While 164 patients received surgery in 85 different “low volume” hospitals (0.2 cases per hospital per year), 205 patients received surgery in 8 different “high volume” hospitals (2.8 cases per hospital per year; p<0.001). Patients in high volume centers were significant younger, had more extended resections and more often malignant neoplasia. In multivariable analysis younger age, extended resections and open procedures were independent predictors for occurrence of postoperative complications. Conclusion Overall complication rate of adrenalectomies in the pediatric population in Germany is low, demonstrating good therapeutic quality. Our analysis revealed a very uneven distribution of patient volume among hospitals. KW - pediatric KW - neuroblastoma – diagnosis KW - therapy KW - adrenocortical adenocarcinoma KW - outcome KW - volume KW - adrenalectomia Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-282280 SN - 1664-2392 VL - 13 ER - TY - THES A1 - Vafadarnejad, Ehsan T1 - Implementation and application of bioinformatics methods to analyze and visualize single-cell RNA-sequencing data T1 - Implementierung und Anwendung von bioinformatischen Methoden zur Analyse und Visualisierung von Einzelzell-Sequenzierungsdaten N2 - RNA sequencing (RNA-seq) has become a transformative method to profile genome-wide gene expression and whole transcriptome analysis over the last decade. In recent years, with the development of new technologies, it has become possible to study gene expression at single-cell level. This new advances in single-cell RNA-sequencing has revolutionized the way scientists study biological processes. Single-cell RNA-sequencing has been used in different areas to better understand the underlying mechanisms of biological processes. In particular, single-RNA-sequencing is a suitable method to study infectious diseases. Infection is composed of heterogeneous mechanisms on either the host or pathogen side and the best way to understand the heterogeneity of these mechanisms and how they interact with each other is to study infectious diseases at the single-cell level. Studying infection processes at the single-cell level can reveal not only the heterogeneity but also the dynamics of infection and the interplay between the host and pathogen at the molecular level. In this thesis, we implemented and applied different single-cell RNA-seq technologies to better understand infectious diseases. In the present work, we conducted four independent but related research works to shed light on different aspects of infection biology: ● We took advantage of this novel technology to study the consequences of RSV infection on primary human epithelial cells. The primary human epithelial cells were collected from six donors and cultured in air liquid interface (ALI) cell culture inoculated with respiratory syncytial virus (RSV). In this project, we discovered ciliated cells as the susceptible cell types in RSV infection. We applied viral load as an indicator of infection progression and used it to reconstruct the dynamics of host response to RSV infection. Reconstruction of the dynamics of infection revealed many host genes and pathways that were suppressed or induced as a result of RSV infection. Pathways related to innate immune response and interferon response were suppressed during the progression of infection and on the other hand pathways like protein targeting to endoplasmic reticulum and apoptosis were induced. ● We developed a new method which is capable of sequencing the transcriptome of a bacterium at the single-cell level and potentially can help us to characterize the bacterial heterogeneity during the course of infection. In this research project, bacteria were cultured in three different culture conditions namely Late stationary phase, Anaerobic shock and NaCl shock and we used a poly(A)-independent single-cell RNA-sequencing protocol to sequence bacteria at the single-cell level. In this work, we report the faithful capture of growth-dependent gene expression patterns in individual Salmonella and Pseudomonas bacteria. The results of our analysis showed that not only we could capture transcripts across different RNA classes but also our method is capable of discerning the transcriptome of bacteria across different culture conditions. ● We used single-cell RNA-sequencing technology to characterize the immune cells landscape over the course of atherosclerosis. Atherosclerosis is considered a cardiac disease which is highly related to infections and previous infections with bacteria or viruses is considered as a risk factor for atherosclerosis. We performed single-cell RNA sequencing of aortic CD45+ cells extracted from healthy and atherosclerotic aorta of mice. We managed to find certain cell populations which were specifically present in atherosclerotic mice. One of the atheroschelorotic populations was previously undescribed TREM2high macrophages showing enrichment in Trem2 gene expression. This population of macrophages seemed to be involved in functions like lipid metabolism and catabolism and lesion calcification. This work revealed the phenotypic heterogeneity and immune cells landscape of different immune cell populations at different stages of atherosclerosis. Our work paves the way to better describe the relation between different infectious diseases and cardiovascular diseases. ● We developed a web-based platform called Infection Atlas to browse and visualize single-cell RNA-sequencing data. Infection Atlas platform provides a user-friendly interface to study different aspects of infectious diseases at the single-cell level and can potentially promote targeted approaches to intervene in infectious diseases. This platform which is available at infection-atlas.org in the short term provides a user-friendly interface to browse and visualize different aspects of infectious diseases and in the long-term is expected to be a comprehensive atlas of infection in human and mouse across different tissues and different pathogens. Overall, in this thesis we provide a framework to study infectious diseases at the single cell level with providing novel data analysis methods and this thesis paves the way for future studies to study host-pathogen encounters at the single-cell level. N2 - RNA-Sequenzierung (RNA-Seq) ist in den letzten zehn Jahren zu einer revolutionären Technik für genomweite Genexpressionsanalysen, sowie für Gesamt-Transkriptom-Analysen geworden. In den letzten Jahren ist es mit der Entwicklung neuer Technologien möglich geworden die Genexpression auf Einzelzell-Niveau zu untersuchen. Diese Fortschritte in der Einzelzell-RNA- Sequenzierung haben die Art wie Wissenschaftler biologische Prozesse betrachten von Grund auf verändert. Einzelzell-Sequenzierung wird in unterschiedlichen Bereichen angewendet, um die grundlegenden Mechanismen biologischer Prozesse besser zu verstehen. Besonders Einzelzell-Sequenzierung ist eine geeignete Methode, um Infektionskrankheiten zu untersuchen. Infektionen sind durch heterogene Mechanismen auf Wirts- und Erreger Seite gekennzeichnet. Der beste Weg die Heterogenität dieser Mechanismen zu verstehen und wie sie interagieren ist die Analyse von Infektionskrankheiten auf Einzelzell-Niveau. Untersuchungen von Infektionsprozessen auf Einzelzell-Ebene können nicht nur die Heterogenität, sondern auch die Dynamik einer Infektion und das Wechselspiel zwischen Wirt und Pathogen auf molekularer Stufe aufzeigen. In dieser Dissertation wurden unterschiedliche Einzelzell-RNA-Sequenzierung Technologien implementiert und angewandt um ein besseres Verständnis von Infektionskrankheiten zu erlangen. In der vorliegenden Arbeit haben wir vier unabhängige, aber verwandte Forschungsarbeiten durchgeführt, um unterschiedliche Aspekte von Infektionsbiologie näher zu betrachten. ● Wir nutzten die Vorteile dieser neuen Technologie, um die Konsequenzen einer RSV Infektion bei primären humanen Epithelzellen zu untersuchen. Die primären humanen Epithelzellen stammten von sechs Spendern und wurden in Luft-Flüssigkeits-Grenzflächen (ALI) Zellkultur mit dem Respiratorischen Syncytial-Virus (kurz RS-Virus) infiziert. In diesem Projekt konnten wir ciliierte Zellen als anfällige Zelltypen einer RSV Infektion zeigen. Wir haben die Viruslast als Indikator für den Fortschritt der Infektion herangezogen, als auch für die Rekonstruktion der Wirtsantwort Dynamik gegenüber einer RSV Infektion. Die Rekonstruktion der Infektionsdynamik zeigte viele Wirtsgene und Signalwege, die durch die RSV Infektion unterdrückt oder induziert wurden. Signalwege, die mit der angeborenen Immunantwort und der Interferonantwort assoziiert waren, wurden durch die fortschreitende Infektion unterdrückt und andererseits waren Signalwege, wie die Zielsteuerung von Proteinen zum endoplasmatischen Retikulum und Apoptose induziert. ● Wir haben eine neue Methode entwickelt, die es ermöglicht das Transkriptom eines Bakteriums auf Einzelzell-Niveau zu sequenzieren und potenziell helfen könnte die bakterielle Heterogenität während des Verlaufs einer Infektion zu charakterisieren. In diesem Forschungsprojekt wurden Bakterien unter folgenden drei unterschiedlichen Konditionen angezogen: Späte stationäre Phase, anaerober Schock und Natriumchlorid Schock. Anschließend wendeten wir ein poly(A) unabhängiges Einzelzell-RNA Sequenzier-Protokoll an, um Bakterien auf Einzelzell-Niveau zu sequenzieren. In dieser Arbeit berichten wir die von wachstumsabhängigen Genexpressionsmustern in einzelnen Salmonellen und Pseudomonaden. Das Ergebnis unserer Analyse zeigte, dass wir nicht nur Transkripte unterschiedlicher RNA-Klassen, sondern auch das Transkriptom von Bakterien in unterschiedlichen Wachstumsbedingungen erfassen können. ● Wir haben Einzelzell-RNA Sequenzierungs-Technologien verwendet, um die Immunzellen Zusammensetzung während des Verlaufs der Athereosklerose zu betrachten. Die Atherosklerose wird als Herzkrankheit betrachtet, die eng mit Infektionen in Zusammenhang gebracht wird. Vorherige Infektionen mit Bakterien oder Viren werden als Risikofaktor für Atherosklerose angenommen. Wir haben für aortische CD45 Zellen von der gesunden und atherosklerotischen Aorta von Mäusen Einzelzell-RNA-Sequenzierungen durchgeführt. Hierbei konnten wir bestimmte Zellpopulationen identifizieren, die spezifisch in atherosklerotischen Mäusen vorkommen. Eine der athereosklerotischen Populationen war eine zuvor unbeschriebene TREM2high Makrophagen Population, die eine erhöhte Trem2 Genexpression zeigte. Diese Population von Makrophagen schien in Funktionen wie Lipid Metabolismus, Katabolismus, sowie Kalzifizierung von Verletzungen involviert zu sein. Diese Arbeit hat die phänotypische Heterogenität und das Feld unterschiedlicher Immunzellpopulationen in unterschiedlichen Stadien der Atherosklerose aufgezeigt. Unsere Arbeit bereitet den Weg, um die Beziehung zwischen unterschiedlichen Infektionskrankheiten und kardiovaskulären Krankheiten besser zu beschreiben. ● Wir haben eine webbasierte Plattform namens „Infektionsatlas“ entwickelt, um Einzelzell-RNA-Sequenzierungsdaten zu visualisieren und zu durchsuchen. Die „Infektionsatlas“ Plattform stellt eine nutzerfreundliche Oberfläche zur Untersuchung von unterschiedlichen Aspekten von Infektionskrankheiten auf Einzelzell-Niveau bereit und kann möglicherweise zielgerichtete Ansätze voranzutreiben, um Infektionskrankheiten zu verhindern. Diese Plattform, die unter „infection-atlas.org“ verfügbar ist, bietet im Moment eine nutzerfreundliche Oberfläche zum Durchsuchen und Darstellen unterschiedlicher Aspekte von Infektionskrankheiten. Langfristig soll es ein umfangreicher Atlas für Infektionen in Maus und Mesch in unterschiedlichen Geweben und unterschiedlichen Pathogenen. Insgesamt stellen wir in dieser Dissertation einen Rahmen zur Untersuchung von Infektionskrankheiten auf Einzelzell-Ebene mit neuen Methoden für die Datenanalyse zur Verfügung und bereiten den Weg für weitere Studien um Wirts-Pathogen Interaktionen auf Einzellzell-Niveau zu untersuchen. KW - Einzelzellanalyse Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-269258 ER - TY - JOUR A1 - Vansynghel, Justine A1 - Ocampo-Ariza, Carolina A1 - Maas, Bea A1 - Martin, Emily A. A1 - Thomas, Evert A1 - Hanf-Dressler, Tara A1 - Schumacher, Nils-Christian A1 - Ulloque-Samatelo, Carlos A1 - Tscharntke, Teja A1 - Steffan-Dewenter, Ingolf T1 - Cacao flower visitation: Low pollen deposition, low fruit set and dominance of herbivores JF - Ecological Solutions and Evidence N2 - 1. Pollination services of cacao are crucial for global chocolate production, yet remain critically understudied, particularly in regions of origin of the species. Notably, uncertainties remain concerning the identity of cacao pollinators, the influence of landscape (forest distance) and management (shade cover) on flower visitation and the role of pollen deposition in limiting fruit set. 2. Here, we aimed to improve understanding of cacao pollination by studying limiting factors of fruit set in Peru, part of the centre of origin of cacao. Flower visitors were sampled with sticky insect glue in 20 cacao agroforests in two biogeographically distinct regions of Peru, across gradients of shade cover and forest distance. Further, we assessed pollen quantities and compared fruit set between naturally and manually pollinated flowers. 3. The most abundant flower visitors were aphids, ants and thrips in the north and thrips, midges and parasitoid wasps in the south of Peru. We present some evidence of increasing visitation rates from medium to high shade (40%–95% canopy closure) in the dry north, and opposite patterns in the semi-humid south, during the wet season. 4. Natural pollination resulted in remarkably low fruit set rates (2%), and very low pollen deposition. After hand pollination, fruit set more than tripled (7%), but was still low. 5. The diversity and high relative abundances of herbivore flower visitors limit our ability to draw conclusions on the functional role of different flower visitors. The remarkably low fruit set of naturally and even hand pollinated flowers indicates that other unaddressed factors limit cacao fruit production. Such factors could be, amongst others, a lack of effective pollinators, genetic incompatibility or resource limitation. Revealing efficient pollinator species and other causes of low fruit set rates is therefore key to establish location-specific management strategies and develop high yielding native cacao agroforestry systems in regions of origin of cacao KW - agroforestry KW - cocoa KW - flower visitors KW - forest proximity KW - hand pollination KW - pollen KW - pollination services KW - shade cover Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-312722 SN - 2688-8319 VL - 3 IS - 2 ER -