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The mutational dynamics of the SARS-CoV-2 virus in serial passages in vitro

Virologica Sinica 2022年第2期37卷 198-207页

作者： Sissy Therese Sonnleitner Stefanie Sonnleitner Eva Hinterbichler Hannah Halbfurter Dominik BCKopecky Stephan Koblmüller Christian Sturmbauer Wilfried Posch gernot walder dr.gernot walder gmbh Medical LaboratoryDepartment of VirologyAusservillgraten9931Austria Division of Hygiene and Medical Microbiology Medical University of InnsbruckInnsbruck6020Austria Institute of Biology University of GrazGraz8010Austria

Since its outbreak in 2019,Severe Acute Respiratory Syndrome Coronavirus 2(SARS-Co V-2)keeps surprising the medical community by evolving diverse immune escape mutations in a rapid and effective *** gain deeper insight into mutation frequency and dynamics,we isolated ten ancestral strains of SARS-Co V-2 and performed consecutive serial incubation in ten replications in a suitable and common cell line and subsequently analysed them using RT-q PCR and whole genome *** those lines we hoped to gain fundamental insights into the evolutionary capacity of SARS-Co V-2 in *** results identified a series of adaptive genetic changes,ranging from unique convergent substitutional mutations and hitherto undescribed *** region coding for spike proved to be a mutational hotspot,evolving a number of mutational changes including the already known substitutions at positions S:484 and S:*** discussed the evolution of all specific adaptations as well as possible reasons for the seemingly inhomogeneous potential of SARS-Co V-2 in the adaptation to cell *** combination of serial passage in vitro with whole genome sequencing uncovers the immense mutational potential of some SARS-Co V-2 *** observed genetic changes of SARS-Co V-2 in vitro could not be explained solely by selectively neutral mutations but possibly resulted from the action of directional selection accumulating favourable genetic changes in the evolving variants,along the path of increasing potency of the *** among a high number of quasi-species in the SARS-Co V-2 in vitro population gene pool may reinforce directional selection and boost the speed of evolutionary change.

关键词： SARS-CoV-2 Whole genome sequencing(WGS) Mutational dynamics Adaptation Serial passage in vitro

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Prevalence and Seroprevalence of Non-SARS Human Coronaviruses 229E and OC43 in East Tyrol/Austria

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Journal of Biosciences and Medicines 2023年第7期11卷 125-139页

作者： Sonnleitner Stefanie Sonnleitner Sissy Eva Hinterbichler gernot walder dr. gernot walder gmbh Medical Laboratory Department of Virology Ausservillgraten Austria Division of Hygiene and Medical Microbiology Medical University of Innsbruck Innsbruck Austria

The recent SARS-CoV-2 pandemic renewed interest in other previously discovered human coronaviruses—the non-severe acute respiratory syndrome human coronavirus (non-SARS hCoVs) and this study is a starting point for a closer investigation of those. With the pandemic behind us we believe it to be important to also examine the current and past respiratory pathogen landscape in the patient population in our care. Therefore, 954 nasopharyngeal swabs of patients with respiratory diseases collected between October 2018 and March 2020 were tested against the pathogens Mycoplasma pneumoniae, Bordetella pertussis, Influenza A and virus, Human metapneumovirus, respiratory syncytial virus, Parainfluenza virus, human Adenovirus and Polyoma virus BK/JC. Swabs negative against these pathogens were further tested for OC43 and 229E by RT-qPCR. Human coronaviruses 229E and OC43 were proven as the causative agents in a considerable number of cases, confirmed by PCR. Overall, our results show that those two non-SARS hCoVs were responsible for 13.9% (11 of 79) of infections with flu-like symptoms of unknown etiology in the study area. In the subsequent seroprevalence study, it was shown that the seroprevalence rate of IgG antibodies against 229E and OC43 was over 50%, indicating that a big part of the population in our study area has been in contact with these non-SARS-CoVs and has built the specific humoral immune response accordingly.

关键词： NonSARS Human Coronavirus hCoV hCoV OC43 hCoV 229E Respiratory Pathogens

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Comparison of Pfizer/BioNTech BNT162b2 COVID-19 (Comirnaty) Vaccination Effects in Aged Adults with Special Consideration for the Effectiveness of the Three-Color iSpot in Assessing Immune Response

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Journal of Biosciences and Medicines 2023年第5期11卷 111-123页

作者： Stefanie Sonnleitner Sissy Therese Sonnleitner Simone Obererlacher gernot walder dr. gernot walder gmbh Medical Laboratory Department of Virology Ausservillgraten Austria Division of Hygiene and Medical Microbiology Medical University of Innsbruck Innsbruck Austria

Background: The roll-out of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was certainly among the fastest in medical history. Vaccination campaigns around the world began a year after the outbreak in 2019. When Austria started vaccinating the population in 2020, we took the opportunity to collect data from the first sets of patients receiving the vaccine in our study region of East Tyrol. Purpose: Many studies have been conducted examining the immunogenicity of the new vaccines using classic serological test methods in combination with an IFN-γ ELISpot. Undeniable disadvantages of using IFN-γ to characterize the status of the cellular immunity are that 1) being an acute phase cytokine, IFN-γ loses signal strength in the long run and 2) IFN-γ does not provide information about the involvement of T helper 2 (Th2) cells in the immune process. This implies that it can affect false negative data about the cell-mediated immune status. Method: Therefore, in addition to a chemiluminescent immunoassay and the enzymatic IFN-γ ELISpot, this study included a fluorescent ELISpot assay using precoated human SARS-CoV-2-specific IFN-γ/IL-2/IL-5 ELISpot kits to show a more holistic overview on the involvement of T helper 1 (Th1) cells as signal senders of IL-2 and Th2 cells as senders of IL-5. Results and Conclusion: Our study confirms good immunogenicity of Pfizer/BioNTech BNT162b2 COVID-19 (Comirnaty) with strong Th1 and vanishingly small Th2 participation. The fluorescent three color iSpot can improve the diagnostic results’ significance for the individual, especially when the infection has been longer in the past and the IFN-γ signal diminishes.

关键词： Three-Color iSpot Immune Response Vaccination

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Application of a simplified ADM1 for full-scale anaerobic co-digestion of cattle slurry and grass silage:assessment of input variability

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Frontiers of Environmental Science & Engineering 2024年第4期18卷 125-139页

作者： Sofia Tisocco Sören Weinrich Gary Lyons Michael Wills Xinmin Zhan Paul Crosson Civil Engineering College of Science and EngineeringUniversity of GalwayGalwayH91 TK33Ireland Teagasc Animal and Bioscience Research Department Animal and Grassland Research and Innovation CentreDunsanyC15 PW93Ireland Biochemical Conversion Department Deutsches Biomasseforschungszentrum gemeinnützige GmbHLeipzig 04347Germany Faculty of Energy·Building Services·Environmental Engineering Münster University of Applied SciencesSteinfurt 48565Germany Agri-Food and Biosciences Institute HillsboroughBT266DRUK Ryan Institute University of GalwayGalwayH91 TK33Ireland MaREI Research Centre for Energy Climate and MarineRyan InstituteUniversity of GalwayGalwayH91 TK33Ireland

Mathematical modeling of anaerobic digestion is a powerful tool to predict gas yields and optimize the *** Anaerobic Digestion Model No.1(ADM1)is a widely implemented model for this ***,modeling full-scale biogas plants is challenging due to the extensive substrate and parameter characterization *** study describes the modification of the ADM1 through a simplification of individual process phases,characteristic components and required ***,the ability of the simplified model to simulate the co-digestion of grass silage and cattle slurry was evaluated using data from a full-scale biogas *** impacts of substrate composition(crude carbohydrate,protein and lipid concentration)and variability of carbohydrate degradability on simulation results were assessed to identify the most influential *** indicated that the simplified version was able to depict biogas and biomethane production with average model efficiencies,according to the Nash-Sutcliffe efficiency(NSE)coefficient,of 0.70 and 0.67,respectively,and was comparable to the original ADM1(average model efficiencies of 0.71 and 0.63,respectively).The variability of crude carbohydrate,protein and lipid concentration did not significantly impact biogas and biomethane output for the data sets *** contrast,carbohydrate degradability seemed to explain much more of the variability in the biogas and methane ***,the application of simplified models provides a reliable basis for the process simulation and optimization of full-scale agricultural biogas plants.

关键词： ADM1 Agricultural feedstocks Biogas technology Input variability Parameter estimation

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A statistical reappraisal of the relationship between liquid limit and specific surface area, cation exchange capacity and activity of clays

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Journal of Rock Mechanics and Geotechnical Engineering 2019年第4期11卷 874-881页

作者： Giovanni Spagnoli Satoru Shimobe BASF Construction Solutions gmbh Dr.-Albert-Frank-StraBe 3283308Germany College of Science and Technology Nihon UniversityFunabashi274-8501Japan

More than 500 datasets from the literature have been used to evaluate the relationships of specific surface area (SSA),cation exchange capacity (CEC) and activity versus the liquid limit (LL).The correlations gave R^2 values ranging between 0.71 and *** data were also used to validate the *** SSA values slightly overestimate the measured SSA up to 100 m^2/*** the estimated CEC values,they overestimated the measured CEC values up to 20 meq/(100 g).A probabilistic approach was performed for the correlations of SSA,CEC and activity versus *** analysis shows that the relations of SSA,CEC and activity with LL are *** the LL values,it is possible to assess other basic engineering properties of clays.

关键词： Liquid limit(LL) Specific surface area(SSA) Cation exchange capacity(CEC) Activity statistical analysis

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Fall cone tests considering water content, cone penetration index, and plasticity angle of fine-grained soils

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Journal of Rock Mechanics and Geotechnical Engineering 2020年第6期12卷 1347-1355页

作者： Satoru Shimobe Giovanni Spagnoli College of Science and Technology Nihon UniversityFunabashi274-8501Japan BASF Construction Solutions gmbh Dr.-Albert-Frank-Straße 32Trostberg83308Germany

This paper analyzed the consistency of some parameters of soils in the literature and experimental results from fall cone test and its application to soil plasticity *** 500 data from both literatures and experiments using fall cone and Casagrande methods were compiled to assess the relationships among specified water content,cone penetration index ebT,and plasticity angle eaT of finegrained *** results indicate that no unique correlation exists among b,liquid limit of the fall cone test(LLc)and *** water content at 1 mm cone penetration eC0T correlates well with b,plasticity ratio eRpT(*** ratio of plastic limit to liquid limit),and ***,the potential of using the btan a diagram to classify soil plasticity was also discussed.

关键词： Atterberg limits Fall cone test Plasticity angle Water content Cone penetration index Plasticity ratio

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A Setup for a Scenario-driven Water Balance at Landscape Scale—Assessment with AKWA-M~-Embedded in a Model Framework for Land-Use Planning’s Decision Support in Mountainous Southwest China

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Journal of Earth Science 2010年第6期21卷 974-978页

作者： Andreas Wahren Karin Berkhoff Albrecht Münch Sylvia Herrmann Karl-Heinz Feger Insitute of Soil Science and Site Ecology Technische Universitt Dresden dr. Dittrich & Partner Hydro-Consult gmbh Institute of Environmental Planning Leibniz University Hannover

Land-cover changes cause a loss of natural vegetation in many parts of the world. In the Xishuangbanna （西双版纳） district （Yunnan （云南） Province）, rubber plantations replace tropical rainforests covering already an area of about 10% of the study area （2007）. There, land-use allocation is mostly driven by economic considerations. Thus, local planning authorities need decision support for land-use planning issues, which integrate socio-economic and ecological aspects. Within the NabanFrame, an agro-economic, ecological and social model was applied, which, altogether, interacted with a land allocation model via defined interfaces. Effects on the water cycle, ecological conditions as well as socio-economic should be considered by integrating the spatially distributed rainfali-runoff and water balance model AKWA-M in the model setup.

关键词： land-use water balance model rubber integrated land-use planning land-use prognosis.

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Error Corrected Sub-Monolayer Ellipsometry for Measurement of Biomolecular Interactions

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Open Journal of Biophysics 2013年第1期3卷 76-85页

作者： Udo Riss drE-dr. Riss Ellipsometerbau gmbh Ratzeburg Germany

Already in 1946 Alexandre Rothen from the Rockefeller Institute for Medical Research, New York published the use of ellipsometry for the measurement of antigen-antibody interactions. And he found some effects that could not be explained by the assumption that the interaction of the molecules is only of chemical nature. 55 years later we started research on antibody-antigen interaction and found similar results. To make sure that these measurements are not produced by measurement artifacts, each component of our measurement technique is error analyzed and error corrected if necessary. With such type of error corrected instrumentation we found, that there must be an interaction between antigens and antibodies that is based on longitudinal electromagnetic waves, which are able to work through thin 7 nm membranes. A similar interaction is found for the virus-antigen interaction. Our measurement results are in contrast to the assumption that the antigen-antibody and antigen-virus interaction is only of chemical nature.

关键词： Ellipsometry Ellipsometer Antibody Antigen Virus Membrane Kinetics Electrodynamics

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Theory of affinity maturation of antibodies

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Advances in Bioscience and Biotechnology 2013年第4期4卷 67-72页

作者： Udo Riss drE-dr. Riss Ellipsometerbau gmbh Ratzeburg Germany

Based on the theory of long distance interaction between antibodies and antigens we developed a theory of affinity maturation of antibodies that is based on longitudinale electric waves. Early stage antibodies show a wide frequency spectrum for antigens and are polyspecific. After affinity maturation the antibody shows a very narrow band spectrum, the antibodies become monospecific. The feedback between antibody and antibody producing cell is done via messenger molecules that are also communicating with help of longitudinal electric waves. These messenger molecules transfer information from antibody arms and are informing cells whether the epitopes are switched on or off. The folding of antibody is done via eigen frequency resonances.

关键词： Affinity Maturation Somatic Mutation THz Waves Antibody Antigen

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Effects of a Food Supplement with a Wild Thyme (Thymus serpyllum L.) Extract on Gut Health and the Microbiome in Humans: A Randomized, Double-Blinded, Placebo-Controlled Clinical Trial

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Food and Nutrition Sciences 2022年第11期13卷 931-949页

作者： Katharina Knaub Christiane Schön Cynthia G. Suarez Ivo Pischel BioTeSys gmbh Esslingen Germany Finzelberg gmbh & Co. KG Andernach Germany dr. Ivo Pischel Consulting Rossbach Germany

Background: Based on the scientific and traditional knowledge, benefits for gut and digestive health were expected from Wild Thyme (Thymus serpyllum L.) extract (WThE) consumption, but no controlled human studies were performed yet to prove the proposed health benefits. Method: The aim of this human randomized, double-blind parallel arm pilot study was to explore the impact of aqueous Wild Thyme extract, a food supplement, in a healthy but overweight study collective (N = 40). In detail, the impact on digestion, gastrointestinal symptoms, gut microbiome, and quality of life by employing an essential oil-free WThE preparation or a matching placebo was investigated. Results: The study results indicate that WThE has the potential to improve gastrointestinal symptoms and increase stool frequency, thus an improved quality of life was observed. The stool microbiome of study collective was characterized by a high Firmicutes to Bacteroidetes ratio. A decrease in the mean Firmicutes/Bacteroidetes ratio was seen in WThE group. Conclusion: The data support the potential applications of WThE as a food supplement with benefits on gut health.

关键词： Wild Thyme (Thymus serpyllum L.) Extract Gut Health Gut Microbiome Abdominal Comfort Bowel Movement Mental Well-Being Quality of Life

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