Modeling steric effects in antibody aggregation using rule-based methods

The allergic response is produced by the release of immune mediators by mast cells and basophils. This process, in turn, is initiated by the aggregation of antigens and IgE-FcεRI antibody-receptor complexes. Computational modeling of antibody- antigen aggregate formation as well as the size and structure of these aggregates is an important tool for greater understanding of the allergic response. In addition, the incorporation of molecular geometry into aggregation models can more accurately capture details of the aggregation process, and may lead to insights into how geom- etry affects aggregate formation. However, it is challenging to simulate aggregation due to the computational cost of simulating large molecules. Methods to geometri- cally model antibody aggregation inspired by rigid body robotic motion simulations have previously been developed; however, high computational cost mandates that the resolution of the 3D molecular models be reduced, which affects the results of the simulation. Rule-based modeling can be used to model aggregation with low computational cost, but traditional rule-based modeling approaches do not include details of molecular geometry. In this work, we propose a novel implementation of rule-based modeling that encodes details of molecular geometry into the rules and the binding rate constant associated with each rule. We demonstrate how the set of rules is constructed accord- ing to the curvature of the molecule. We then perform a study of antigen-antibody aggregation using our proposed method combined with a previously developed 3D rigid-body Monte Carlo simulation. We first simulate the binding of IgE antibodies bound to cell surface receptors FcεRI to various binding regions of the allergen Pen a 1 using the aforementioned Monte Carlo simulation, and we analyze the distribution of the sizes of the aggregates that form during the simulation. Then, using our novel rule-based approach, we optimize a rule-based model according to the geometry of the Pen a 1 molecule and the data from the Monte Carlo simulation. In particular, we use the distances between the binding regions of the Pen a 1 molecule to optimize the rules and associated binding rate constants. The optimized rule-based models provide information about the average steric hindrance between binding regions and the probability that IgE-FcεRI receptor complexes will bind to these regions. In ad- dition, the optimized rule-based models provide a means of quantifying the variation in aggregate size distribution that results from differences in molecular geometry. We perform this procedure for seven resolutions and three molecular conforma- tions of Pen a 1. We then analyze the impact of resolution and conformation on the aggregate size distribution and on the optimal rule-based model. In addition, we develop a predictive model by first fixing the rule set and varying only the binding rate constant for each resolution, and then fitting the resulting data to a function. This model is intended to enable the prediction of the aggregate size distribution for higher resolutions while requiring only data for lower resolution Monte Carlo models, thus enhancing computational efficiency. Finally, we use a simple rule-based model to fit experimental cell degranulation data for various concentrations of the shrimp allergen Pen a 1 and the IgE antibody

An Approach Based on Particle Swarm Optimization for Inspection of Spacecraft Hulls by a Swarm of Miniaturized Robots

The remoteness and hazards that are inherent to the operating environments of space infrastructures promote their need for automated robotic inspection. In particular, micrometeoroid and orbital debris impact and structural fatigue are common sources of damage to spacecraft hulls. Vibration sensing has been used to detect structural damage in spacecraft hulls as well as in structural health monitoring practices in industry by deploying static sensors. In this paper, we propose using a swarm of miniaturized vibration-sensing mobile robots realizing a network of mobile sensors. We present a distributed inspection algorithm based on the bio-inspired particle swarm optimization and evolutionary algorithm niching techniques to deliver the task of enumeration and localization of an a priori unknown number of vibration sources on a simplified 2.5D spacecraft surface. Our algorithm is deployed on a swarm of simulated cm-scale wheeled robots. These are guided in their inspection task by sensing vibrations arising from failure points on the surface which are detected by on-board accelerometers. We study three performance metrics: (1) proximity of the localized sources to the ground truth locations, (2) time to localize each source, and (3) time to finish the inspection task given a 75% inspection coverage threshold. We find that our swarm is able to successfully localize the present so

Evaluation of Novel Particle Detection Methods and their Application to Characterize the Process of Protein Aggregation

The biopharmaceutical sector is one of most promising and profitable sectors in medical treatment of a multitude of severe diseases. Biological molecules, however, lead to new challenges for the manufacturing companies. This thesis focused on one of the main challenges for therapeutic proteins: protein aggregation and the detection of the resulting particles. Within this thesis, three main tasks have been addressed: (1) the evaluation of emerging particle detection and characterization techniques, (2) the evaluation of novel technologies for aggregation and unfolding process characterization and (3) the investigation of the aggregation process of current therapeutic proteins (mABs). For the evaluation of particle detection and characterization techniques for the application on protein samples, the following three techniques have been selected: Nanoparticle tracking analysis (NTA), Tunable resistive pulse (TRPS) and STEP-technology® (space and time-resolved extinction profiles) applied in the LUMiSizer®. All techniques rely on different measurement principles and can be claimed as orthogonal methods. These techniques have been shown to be applicable for polystyrene particle suspensions and showed high agreement for the size and/ or concentration determinations of these particles. In the first step, all techniques have been evaluated in two comparative studies analyzing protein BSA standard particle suspensions and monoclonal antibody suspensions. In a second step, a more detailed evaluation of the NTA and the STEP-technology® was performed for monoclonal antibody samples. For the evaluation of novel technologies for the investigation and characterization of protein unfolding and aggregation processes, the following two techniques have been selected: Zetasizer Helix system and the SwitchSENSE®. The Zetasizer Helix system is an instrument combining dynamic light scattering and Raman spectroscopy. The three measurement modes (sample series, isothermal incubation, temperature ramp) have been successfully evaluated for selected therapeutic mABs. The outcome indicated differences in the aggregation mechanism. The same applies to the thermal ramp experiments. In addition, the obtained melting temperatures and aggregation onset fit to the results of orthogonal methods (DSC, ITF, SwitchSENSE). In conclusion, the Zetasizer Helix is an instrument that is not applicable in a high throughput manner, but it gives valuable information for better understanding the correlation between structural changes and aggregation behavior. The SwitchSENSE® technology is a chip-based analytical platform using a specific DNA-based biosurface system to investigate molecular interactions, such as binding kinetics and affinities or enzymatic activities. Out of the various applications of the SwitchSENSE technology, the following applications were evaluated for therapeutic proteins: protein sizing, protein interaction and thermal melting approaches. The most promising approach was the usage of the SwitchSENSE system as orthogonal method for the characterization of the thermal melting behavior. The combination of sizing step and thermal melting step gave information about the refolding potential. Comparative investigations with DSC and ITF showed good coincidence of unfolding start and melting temperature determinations. The system development and application identification is ongoing and continuous updates are necessary for further potential approaches. For the protein aggregation case studies, three monoclonal antibodies (mAB1, mAB2 and mAB3) have been selected. Following these model systems have been investigated considering their biophysical characterization, stability and aggregation behaviour using established and novel techniques and technologies. For the aggregation studies three approaches have been addressed, temperature ramp experiments, isothermal experiments and further protein stress factors, such as extreme temperature, mechanical stirring, extreme acidic pH, reducing stress. In summary, the results of these case studies describe the stability and aggregation processes of the three monoclonal antibodies. Depending on different stress factors (temperature, pH, reducing conditions, etc.) and different approaches (temperature ramp, isothermal incubation and extreme conditions), molecule specific aggregation mechanisms were postulated. The application of the evaluated technologies in the case studies outline their suitability for practical stability studies.Der Einsatz von Biopharmazeutika ist ein vielversprechender Ansatz für die Behandlung einer Vielzahl von Krankheiten. Diese biologischen Moleküle, bspw. therapeutische Antikörper, führen allerdings zu neuen Herausforderungen, denen sich die Pharmaindustrie stellen muss. Eine Herausforderung von therapeutischen Proteinen sind bspw. Aggregationsprozesse und folglich die Detektion der resultierenden Proteinpartikel mit geeigneten Methoden. Die Ziele dieser Arbeit waren daher die Evaluierung neuaufkommender Techniken für die Partikeldetektion und - charakterisierung, die Evaluierung neuer Technologien zur Untersuchung von Proteinentfaltungs- und Aggregationsprozessen und die Untersuchung des Aggregationsverhalten von drei therapeutischen Modellproteinen (monoklonale Antikörper). Für die Evaluierung neuaufkommender Techniken für die Partikeldetektion wurden drei Technologien untersucht: Nanoparticle Tracking Analysis (NTA), Tunable Resistive Pulse Sensing angewendet in dem Gerät qNano (TRPS) und die STEP-technology® angewendet in dem Gerät LUMiSizer®. Die initiale Vergleichbarkeit der Technologien und der Analyseergebnisse wurde zunächst gezeigt mit Hilfe von Latexpartikel Standard Suspensionen. Die anschließende Analyse von drei BSA (bovine serum albumin) Proteinpartikel Standard Suspensionen (mit nominalen Partikelgröße BSA1~150 nm; BSA2~500 nm und BSA3~750 nm) zeigte, vor allem für die heterogeneren Suspensionen BSA2 und BSA3 mit höherer Polydispersität, schon erste Herausforderungen für die Techniken. Während der TRPS-Analyse (Coulter Counter Prinzip) traten die Blockade der Pore sowie eine Proteinschicht auf der Membran auf. Diese Probleme wurden während der Analyse von gestressten therapeutischen Antikörperproben bestätigt und das TRPS-Gerät wurde für die Anwendung für Proteinproben als ungeeignet bewertet. Für NTA und den LUMiSizer® konnte in einer detaillierten Evaluierung hingegen die Anwendbarkeit demonstriert werden. Das NTA, eine Lichtstreu-basierte Methode, bietet dabei eine quantitative Methode zur Bestimmung der Partikelgrößenverteilung im nanometer-Größenbereich (150 nm bis ca. 1000 nm). Die Herausforderung bildet dabei die Einstellung geeigneter Messparameter (z.B. Detection Threshold). Der LUMiSizer®, eine Photozentrifuge, ist hingegen nicht für Konzentrationsbestimmungen geeignet, ermöglicht allerdings eine non-destruktive Analyse der Partikelgrößenverteilung über den nanometer und mikrometer Größenbereich. Die Herausforderung der Methode ist eine ausreichende Trübung der Probe, um die Partikelbewegung detektieren zu können. Zur Untersuchung von Proteinentfaltungs- und Aggregationsprozessen wurden zwei Technologien evaluiert: der Zetasizer Helix, eine Kombination aus Dynamischer Lichtstreuung und Raman Spektroskopie und die SwitchSENSE Technologie, eine chip-basierter Biosensorplattform. Der Zetasizer Helix ermöglicht die simultane Untersuchung von Partikelbildung (kolloidaler Stabilität) und Proteinstrukturänderungen (konformative Stabilität). Es konnte in dieser Arbeit gezeigt werden, dass dieser Ansatz für Proteinaggregationsstudien gut geeignet ist. Die SwitchSENSE Technologie bietet ein breites Einsatzgebiet. In dieser Arbeit konnte eine orthogonale Methode für die Untersuchung des Entfaltungsprozesses von mABs evaluiert werden. Für weitere Anwendungen zur Untersuchung von Proteinaggregation konnten keine neuen Vorteile durch die Verwendung der SwitchSENSE Technologie aufgezeigt werden. Im dritten Abschnitt der Arbeit wurden Aggregationsprozesse der Modellantikörper mAB1, mAB2 und mAB3 untersucht. Die Proteinsuspensionen wurden zunächst biophysikalisch untersucht, um die kolliodale und konformative Stabilität zu beschreiben. Während mAB1 und mAB2 vergleichbar stabil waren, zeigte mAB3 eine signifikant geringere Stabilität. Anschließend wurden die Aggregationsprozesse unter verschiedenen Stresskonditionen (u.a. Temperaturrampen, isothermer Stress oder extrem saurer pH-Wert) untersucht. Der Aggregationsprozess von mAB1 ist gekennzeichnet durch einen langsamen Verlauf, als rate-limiting Schritt kann der Entfaltungsschritt angenommen werden und der gesamte Prozess scheint entfaltungsgetrieben. Der Aggregationsprozess von mAB2 ist gekennzeichnet durch einen schnellen Verlauf, als rate-limiting Schritt kann die Formation eines irreversiblen Nukleus (Nukleationskontrolliert) angenommen werden und der Einfluss der Entfaltung scheint nach dem Aggregationsstart reduziert. Der Aggregationsprozess von mAB3 scheint hingegen gekennzeichnet durch Selbstassoziation der Monomere, einen schnellen Verlauf und als rate-limiting Schritt kann die Monomeraddition angenommen werden. Zusammenfassend konnten fünf neue Technologien evaluiert und in Aggregationsstudien implementiert werden, um die Aggregationsprozesse/-charakteristika von drei Modellantikörpern zu beschreiben. Die Beschreibung und das Verständnis von Aggregationsprozessen unterstützen die Entwicklung einer stabilen Formulierung von therapeutischen Proteinen und bildet daher einen wertvollen Beitrag für die Entwicklung solcher Biopharmazeutika

PROGRAM, THE NEBRASKA ACADEMY OF SCIENCES: One Hundred-Thirty-First Annual Meeting, APRIL 23-24, 2021. ONLINE

AFFILIATED SOCIETIES OF THE NEBRASKA ACADEMY OF SCIENCES, INC. 1.American Association of Physics Teachers, Nebraska Section: Web site: http://www.aapt.org/sections/officers.cfm?section=Nebraska 2.Friends of Loren Eiseley: Web site: http://www.eiseley.org/ 3.Lincoln Gem & Mineral Club: Web site: http://www.lincolngemmineralclub.org/ 4.Nebraska Chapter, National Council for Geographic Education 5.Nebraska Geological Society: Web site: http://www.nebraskageologicalsociety.org Sponsors of a $50 award to the outstanding student paper presented at the Nebraska Academy of SciencesAnnual Meeting, Earth Science /Nebraska Chapter, National Council Sections 6.Nebraska Graduate Women in Science 7.Nebraska Junior Academy of Sciences: Web site: http://www.nebraskajunioracademyofsciences.org/ 8.Nebraska Ornithologists’ Union: Web site: http://www.noubirds.org/ 9.Nebraska Psychological Association: http://www.nebpsych.org/ 10.Nebraska-Southeast South Dakota Section Mathematical Association of America: Web site: http://sections.maa.org/nesesd/ 11.Nebraska Space Grant Consortium: Web site: http://www.ne.spacegrant.org/ CONTENTS AERONAUTICS & SPACE SCIENCE ANTHROPOLOGY APPLIED SCIENCE & TECHNOLOGY BIOLOGICAL & MEDICAL SCIENCES COLLEGIATE ACADEMY: BIOLOGY COLLEGIATE ACADEMY: CHEMISTRY & PHYSICS EARTH SCIENCES ENVIRONMENTAL SCIENCES GENERAL CHEMISTRY GENERAL PHYSICS TEACHING OF SCIENCE & MATHEMATICS 2020-2021 PROGRAM COMMITTEE 2020-2021 EXECUTIVE COMMITTEE FRIENDS OF THE ACADEMY NEBRASKA ACADEMY OF SCIENCS FRIEND OF SCIENCE AWARD WINNERS FRIEND OF SCIENCE AWARD TO DR PAUL KAR

ReSCon '09, Research Student Conference: Book of Abstracts

The second SED Research Student Conference (ReSCon2009) was hosted over three days, 22-24 June 2009, in the Lecture Centre at Brunel University. The conference consisted of technical presentations, a poster session and social events. The abstracts and presentations were the result of ongoing research by postgraduate research students from the School of Engineering and Design at Brunel University. The conference is held annually, and ReSCon plays a key role in contributing to research and innovations within the School

Women in Science 2015

Women in Science 2015 summarizes research done by Smith College’s Summer Research Fellowship (SURF) Program participants. Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. In 2015, 162 students participated in SURF (153 hosted on campus and nearby eld sites), supervised by 60 faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants were asked to summarize their research experiences for this publication.https://scholarworks.smith.edu/clark_womeninscience/1002/thumbnail.jp

2016 IMSAloquium, Student Investigation Showcase

Welcome to the twenty-eighth year of the Student Inquiry and Research Program (SIR)! This is a program that is as old as IMSA. The SIR program represents our unending dedication to enabling our students to learn what it is to be an innovator and to make contributions to what is known on Earth.https://digitalcommons.imsa.edu/archives_sir/1026/thumbnail.jp