IU Indianapolis ScholarWorks :: Browsing by Author "Naumann, Christoph A."

Browsing by Author "Naumann, Christoph A."

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Advances in Gas Chromatography, Thermolysis, Mass Spectrometry, and Vacuum Ultraviolet Spectrometry
(2021-05) Rael, Ashur; Goodpaster, John V.; Manicke, Nicholas E.; Naumann, Christoph A.; Minto, Robert E.
In the area of forensic chemistry, improved or new analysis methods are continually being investigated. One common and powerful technique used in forensic chemistry is wall-coated open-tubular column (WCOT) gas chromatography with electron ionization single quadrupole mass spectrometry (GC-MS). Improvements to and effectiveness of alternatives to this instrumental platform were explored in an array of parallel inquiries. The areas studied included the column for the chromatographic separation, the universal detection method employed, and the fragmentation method used to enhance molecular identification. Superfine-micropacked capillary (SFµPC) columns may provide an alternative to commercial packed GC columns and WCOT GC columns that combines the benefits of the larger sample capacity of packed columns and the benefits of the excellent separation capabilities and mass spectrometry (MS) flow rate compatibility of WCOT columns. SFµPC columns suffer from high inlet pressure requirements and prior reported work has required specialized instrumentation for their use. Fabrication of and chromatography with SFµPC GC columns was successfully achieved with typical GC-MS instrumentation and within the flow rate limit of a MS. Additionally, the use of higher viscosity carrier gasses was demonstrated to reduce the required inlet pressure for SFµPC GC columns. Recently, a new vacuum ultraviolet spectrometer (VUV) universal detector has been commercialized for GC. The ability of VUV detectors to acquire absorbance spectra from 125 nm to 430 nm poses a potential alternative to MS. As such, GC-VUV provides an exciting potential alternative approach to achieving excellent quantitative and qualitative analysis across a wide range of analytes. The performance of VUV and MS detectors for forensic analysis in terms of quantitative and qualitative analysis was compared. Analysis of alkylbenzenes in ignitable liquids was explored, which can be important evidence from suspected arson fires and are difficult to differentiate with MS. The VUV detector was found to have superior specificity and comparable sensitivity to the MS detector in scan mode. Addition of thermolysis (Th) as an orthogonal fragmentation pathway provides the opportunity to increase the differences between MS fragmentation patterns. Fragmentation has been widely established to aid in identification of molecules with MS by providing characteristic fragments at characteristic relative abundances. However, molecules with very similar structures do not result in sizable spectral differences in all cases with typical MS fragmentation techniques. A series of Th units were fabricated and integrated into GC-Th-MS instruments. Th-MS was conducted with the thermally labile nitrate esters across a range of instrumentation and thermal conditions.
Biomembrane-mimicking lipid bilayer system as a mechanically tunable cell substrate
(Elsevier B.V., 2014-03) Lautscham, Lena A.; Lin, Corey Y.; Auernheimer, Vera; Naumann, Christoph A.; Goldmann, Wolfgang H.; Fabry, Ben; Department of Chemistry & Chemical Biology, School of Science
Cell behavior such as cell adhesion, spreading, and contraction critically depends on the elastic properties of the extracellular matrix. It is not known, however, how cells respond to viscoelastic or plastic material properties that more closely resemble the mechanical environment that cells encounter in the body. In this report, we employ viscoelastic and plastic biomembrane-mimicking cell substrates. The compliance of the substrates can be tuned by increasing the number of polymer-tethered bilayers. This leaves the density and conformation of adhesive ligands on the top bilayer unaltered. We then observe the response of fibroblasts to these property changes. For comparison, we also study the cells on soft polyacrylamide and hard glass surfaces. Cell morphology, motility, cell stiffness, contractile forces and adhesive contact size all decrease on more compliant matrices but are less sensitive to changes in matrix dissipative properties. These data suggest that cells are able to feel and respond predominantly to the effective matrix compliance, which arises as a combination of substrate and adhesive ligand mechanical properties.
Changes in Cholesterol Level Alter Integrin Sequestration in Raft-Mimicking Lipid Mixtures
(Elsevier, 2018-01-09) Ge, Yifan; Gao, Jiayun; Jordan, Rainer; Naumann, Christoph A.; Chemistry and Chemical Biology, School of Science
The influence of cholesterol (CHOL) level on integrin sequestration in raft-mimicking lipid mixtures forming coexisting liquid-ordered (lo) and liquid-disordered (ld) lipid domains is investigated using complementary, single-molecule-sensitive, confocal detection methods. Systematic analysis of membrane protein distribution in such a model membrane environment demonstrates that variation of CHOL level has a profound influence on lo-ld sequestration of integrins, thereby exhibiting overall ld preference in the absence of ligands and lo affinity upon vitronectin addition. Accompanying photon-counting histogram analysis of integrins in the different model membrane mixtures shows that the observed changes of integrin sequestration in response to variations of membrane CHOL level are not associated with altering integrin oligomerization states. Instead, our experiments suggest that the strong CHOL dependence of integrin sequestration can be attributed to CHOL-mediated changes of lipid packing and bilayer thickness in coexisting lo and ld domains, highlighting the significance of a biophysical mechanism of CHOL-mediated regulation of integrin sequestration. We envision that this model membrane study may help clarify the influence of CHOL in integrin functionality in plasma membranes, thus providing further insight into the role of lipid heterogeneities in membrane protein distribution and function in a cellular membrane environment.
Cholesterol-Induced Buckling in Physisorbed Polymer-Tethered Lipid Monolayers
(MDPI, 2013-04-06) Hussain, Noor F.; Siegel, Amanda P.; Johnson, Merrell A.; Naumann, Christoph A.; Chemistry and Chemical Biology, School of Science
The influence of cholesterol concentration on the formation of buckling structures is studied in a physisorbed polymer-tethered lipid monolayer system using epifluorescence microscopy (EPI) and atomic force microscopy (AFM). The monolayer system, built using the Langmuir-Blodgett (LB) technique, consists of 3 mol % poly(ethylene glycol) (PEG) lipopolymers and various concentrations of the phospholipid, 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC), and cholesterol (CHOL). In the absence of CHOL, AFM micrographs show only occasional buckling structures, which is caused by the presence of the lipopolymers in the monolayer. In contrast, a gradual increase of CHOL concentration in the range of 0–40 mol % leads to fascinating film stress relaxation phenomena in the form of enhanced membrane buckling. Buckling structures are moderately deficient in CHOL, but do not cause any notable phospholipid-lipopolymer phase separation. Our experiments demonstrate that membrane buckling in physisorbed polymer-tethered membranes can be controlled through CHOL-mediated adjustment of membrane elastic properties. They further show that CHOL may have a notable impact on molecular confinement in the presence of crowding agents, such as lipopolymers. Our results are significant, because they offer an intriguing prospective on the role of CHOL on the material properties in complex membrane architecture.
Collaborative Research from the Center for Membrane Biosciences
(Office of the Vice Chancellor for Research, 2010-04-09) Petrache, Horia I.; Justice, Matthew J.; Rogozea, Adriana L.; Patrusca, Daniela N.; Petrache, Irina; Wassall, Stephen R.; Siegel, Amanda; Murcia, Mike; Minner, Dan; Elmendorf, Jeffrey S.; Tackett, Lixuan; Naumann, Christoph A.
The Center for Membrane Biosciences has been facilitating new research activities between the IUPUI School of Science and IU School of Medicine in the structure, biochemistry, and physiology of biological membranes. Results from two projects resulting from these collaborations are presented. Project 1: Ceramides are sphingolipids involved in the development of lung alveolar cell apoptosis (programmed death) and possibly in the clearance of apoptotic cells by alveolar macrophages. We use a combination of molecular and cellular methods to determine the effect of ceramides on the ability of alveolar macrophages to engulf apoptotic cells. Engulfment experiments of labeled apoptotic Jurkat cells were performed with rat alveolar macrophages (AM) obtained via bronchoalveolar lavage. AM were treated with various ceramide species and efferocytosis was quantified by flow cytometry. Using small-angle X-ray scattering and solid state 2H NMR we determined how ceramides (C6:0, C18:1) affect the molecular organization and the physical properties of model membranes. These studies can lead to a better understanding of the molecular mechanisms responsible for apoptotic cell clearance. If the clearance process is impaired, apoptotic cells may progress to secondary necrosis, resulting in release of harmful cellular contents and tissue inflammation. Project 2: Highly-photostable quantum dots (QD) conjugated to lipids or antibodies can be utilized to explore changes in compartmentalization of the plasma membrane due to hyperinsulinemia using wide field single molecule fluorescence microscopy. Protocols describing the bio-inertness and monovalent binding of QDs to antibodies are outlined, as well as use of confocal fluorescence correlation spectroscopy to determine colloidal stability of CdSe/ZnS QDs in aqueous solution. Tracking experiments on QD-conjugated to transferrin receptors in healthy and insulin-resistant adipocytes detect changes in membrane compartmentalization. The impact of chromium picolinate on receptor mobility was also investigated.
Design of Biomembrane-Mimicking Substrates of Tunable Viscosity to Regulate Cellular Mechanoresponse
(2012-03-20) Minner, Daniel Eugene; Naumann, Christoph A.; Long, Eric C. (Eric Charles); Suter, Daniel; Shah, Kavita
Tissue cells display mechanosensitivity in their ability to discern and respond to changes in the viscoelastic properties of their surroundings. By anchoring and pulling, cells are capable of translating mechanical stimuli into a biological response through a process known as mechanotransduction, a pathway believed to critically impact cell adhesion, morphology and multiple cellular processes from migration to differentiation. While previous studies on polymeric gels have revealed the influence of substrate elasticity on cellular shape and function, a lack of suitable substrates (i.e. with mobile cell-substrate linkers) has hindered research on the role of substrate viscosity. This work presents the successful design and characterization of lipid-bilayer based cell substrates of tunable viscosity affecting cell-substrate linker mobility through changes in viscous drag. Here, two complementary membrane systems were employed to span a wide range of viscosity. Single polymer-tethered lipid bilayers were used to generate subtle changes in substrate viscosity while multiple, polymer-interconnected lipid bilayer stacks were capable of producing dramatic changes in substrate viscosity. The homogeneity and integrity of these novel multibilayer systems in the presence of adherent cells was confirmed using optical microscopy techniques. Profound changes in cellular growth, phenotype and cytoskeletal organization confirm the ability of cells to sense changes in viscosity. Moreover, increased migration speeds coupled with rapid area fluctuations suggest a transition to a different migration mode in response to the dramatic changes in substrate viscosity.
Development of Polymer Gel-Supported Lipid Bilayer Using Capillary-Assisted Assembly
(2024-12) Chuduang, Kridnut; Naumann, Christoph A.; Long, Eric C.; Sardar, Rajesh; Lin, Chien-Chi
The modern view of the plasma membrane is that of a complex, highly dynamic, compartmentalized system that critically impacts multiple important cellular functions. Supported model membranes of well-defined compositions have emerged as attractive experimental platforms to determine the underlying molecular processes that regulate membrane-associated cellular functions using advanced biophysical detection methods with up to single molecule resolution. However, membrane properties of previously employed supported membrane systems, such as solid-supported lipid bilayer (SLB) and polymer-supported lipid bilayer with a polymer layer thickness of several nm, were found to be perturbed by the nearby solid substrate. To overcome this limitation, the present work describes for the first time the capillary-assisted formation of a lipid bilayer (CA-PGB) on the surface of a fully hydrated, several micrometers thick polyacrylamide gel. CA-PGB formation can be accomplished by physisorption or specific chemical linkages (tethering) between polymer gel and bilayer. Not dissimilar to conditions found in plasma membranes, membrane properties of CA-PGB are found to be solely influenced by the attached polymer layer. The successful formation and lipid fluidity of CA-PGB is confirmed using confocal microscopy and fluorescence correlation spectroscopy (FCS). Lipid bilayer spreading on the hydrogel surface by capillary-assisted assembly is not altered when the polymer gel stiffness or bilayer bending stiffness are varied, illustrating the robustness and versatility of the assembly process. This work also shows that, unlike other supported membrane systems, the capillary-assisted assembly approach causes the formation of a lipid reservoir at the edge of the capillary. This lipid reservoir provides a lipid supply for the CA-PGB, enabling bilayer self-healing and superior bilayer stability relative to SLB. Experimental data are presented that support an assembly process, in which bilayer spreading on the gel surface inside the water capillary between two substrates is caused by monolayer collapse of suddenly accumulated lipids at the air-water interface of the capillary during sandwiching. A key aspect of the monolayer collapse-induced bilayer spreading is its rapid kinetics, which appears to be faster than the polymer gel swelling kinetics. The importance of the fast kinetics of bilayer spreading during capillary-assisted assembly is supported by the observation that attempts to build polymer gel-supported lipid bilayer using traditional lipid assembly methods [i. e., Langmuir-Blodgett (LB)/Langmuir-Schaefer (LS), LB- vesicle fusion, and spontaneous bilayer spreading from a hydrated lipid source], characterized by slower bilayer spreading kinetics, are unable to form a homogeneous fluid lipid bilayer on the polymer gel surface. The experimental results obtained in this work strongly suggest that the CA-PGB not only represents a powerful experimental model membrane platform for the analysis of membrane-associated processes relevant in cellular membranes, but also serves as promising cell surface mimetic to probe the cellular mechanosensitivity of adherend cells.
DNA Recognition and Cleavage by Phenyl-Benzimidazole Modified Gly-Gly-His-Derived Metallopeptides
(2010-04-08T16:20:15Z) Wang, Tianxiu; Long, Eric C. (Eric Charles); Blacklock, Brenda J.; Naumann, Christoph A.
Metallopeptides of the general form M(II)∙Gly1-Gly2-His induce DNA strand scission via minor groove interactions. This peptide system can serve as a nucleic acid-targeted cleavage agent – either as an appendage to other DNA binding agents, or as a stand alone complex. In an effort to further our knowledge of DNA recognition and cleavage, a novel series of phenyl-benzimidazole modified Gly-Gly-His-derived metallopeptides was synthesized via solid phase methods and investigated. The new systems allow the formation of additional contacts to the DNA minor groove through the incorporation of a DNA binding phenyl-benzimidazole moiety, thus strengthening the overall binding interaction and further stabilizing the metal complex-DNA association. In addition, how Lys side chains and an amidinium group influence the efficiency of DNA cleavage was also studied. DNA cleavage studies suggested that the phenyl-benzimidazole-modified Gly-Gly-His metallopeptides possess enhanced DNA cleavage abilities. In particular, when amidines are placed on the benzimidazole moieties, these moieties appeared to play an important role in increasing the DNA cleavage activity of the metal complex, most likely through an enhanced electrostatic attraction to the DNA.
Functionalization of Polymeric Beads as Optical Reporters of Biomembrane Mimicking Cell Substrate Properties
(Office of the Vice Chancellor for Research, 2013-04-05) Moretti, Leandro; Minner, Daniel E.; Herring, Vincent L.; Naumann, Christoph A.
Novel biomembrane-mimicking cell substrates based on a polymer-tethered multi-lipid bilayer stack have been recently developed in the Naumann lab. These novel substrates have been shown to induce profound changes in cellular behavior dependent on the number of bilayers in the stack. However, the underlying mechanical substrate properties remain unclear. To overcome this problem, the central goal of my research is the development of a nanoparticle-based optical reporter that provides insight into the dynamic and viscoelastic properties of the multibilayer system. To achieve this goal, fluorescent polystyrene beads and magnetic polystyrene beads were functionalized for use in confocal microscopy and magnetic tweezers (MT) assays, respectively. Both kinds of beads were specifically tailored and functionalized to link the bilayer system to cellular adhesion proteins recognized by plated cells, thus acting as fluorescent cell-substrate linkages. To assure the correct surface functionalization of nanoparticles, Zetasizer assays were run on both kinds of beads to verify expected changes in hydrodynamic radius and zeta potential as reactions progressed. Fluorescent beads were specifically linked to lipid bilayers using maleimide-thiol coupling chemistry, thus allowing subsequent experiments in the presence of plated cells. As confirmed by analysis of cellular nanoparticle uptake, the cellular uptake kinetics of the newly synthesized fluorescent beads could be controlled through adjustment of nanoparticle coating composition. These results are significant because they validate the new nanobead design, which shows enhanced reporter efficiency for confocal microscopy and MT based assays.
Investigating spatial distribution and dynamics of membrane proteins in polymer-tethered lipid bilayer systems using single molecule-sensitive imaging techniques
(2016-12) Ge, Yifan; Naumann, Christoph A.
Plasma membranes are complex supramolecular assemblies comprised of lipids and membrane proteins. Both types of membrane constituents are organized in highly dynamic patches with profound impact on membrane functionality, illustrating the functional importance of plasma membrane ﬂuidity. Exemplary, dynamic processes of membrane protein oligomerization and distribution are of physiological and pathological importance. However, due to the complexity of the plasma membrane, the underlying regulatory mechanisms of membrane protein organization and distribution remain elusive. To address this shortcoming, in this thesis work, different mechanisms of dynamic membrane protein assembly and distribution are examined in a polymer-tethered lipid bilayer system using comple-mentary confocal optical detection techniques, including 2D confocal imaging and single molecule-sensitive confocal ﬂuorescence intensity analysis methods [ﬂuorescence correlation spectroscopy (FCS) autocorrelation analysis and photon counting histogram (PCH) method]. Speciﬁcally, this complementary methodology was applied to investigate mechanisms of membrane protein assembly and distribution, which are of signiﬁcance in the areas of membrane biophysics and cellular mechanics. From the membrane biophysics perspective, the role of lipid heterogeneities in the distribution and function of membrane proteins in the plasma membrane has been a long-standing problem. One of the most well-known membrane heterogeneities are known as lipid rafts, which are domains enriched in sphingolipids and cholesterol (CHOL). A hallmark of lipid rafts is that they are important regulators of membrane protein distribution and function in the plasma membrane. Unfortunately, progress in deciphering the mechanisms of raft-mediated regulation of membrane protein distribution has been sluggish, largely due to the small size and transient nature of raft domains in cellular membranes. To overcome this challenge, the current thesis explored the distribution and oligomerization of membrane proteins in raft-mimicking lipid mixtures, which form stable coexisting CHOL-enriched and CHOL-deﬁcient lipid domains of micron-size, which can easily be visualized using optical microscopy techniques. In particular, model membrane experiments were designed, which provided insight into the role of membrane CHOL level versus binding of native ligands on the oligomerization state and distribution of GPI-anchored urokinase plasminogen activator receptor (uPAR) and the transmembrane protein αvβ3 integrin. Experiments on uPAR showed that receptor oligomerization and raft sequestration are predominantly inﬂuenced by the binding of natural ligands, but are largely independent of CHOL level changes. In contrast, through a presumably different mechanism, the sequestration of αvβ3 integrin in raft-mimicking lipid mixtures is dependent on both ligand binding and CHOL content changes without altering protein oligomerization state. In addition, the signiﬁcance of membrane-embedded ligands as regulators of integrin sequestration in raft-mimicking lipid mixtures was explored. One set of experiments showed that ganglioside GM3 induces dimerization of α5β1 integrins in a CHOL-free lipid bilayer, while addition of CHOL suppresses such a dimerization process. Furthermore, GM3 was found to recruit α5β1 integrin into CHOL-enriched domains, illustrating the potential sig-niﬁcance of GM3 as a membrane-associated ligand of α5β1 integrin. Similarly, uPAR was observed to form complexes with αvβ3 integrin in a CHOL dependent manner, thereby causing the translocation of the complex into CHOL-enriched domains. Moreover, using a newly developed dual color FCS and PCH assay, the composition of uPAR and integrin within complexes was determined for the ﬁrst time. From the perspective of cell mechanics, the characterization of the dynamic assembly of membrane proteins during formation of cell adhesions represents an important scientiﬁc problem. Cell adhesions play an important role as force transducers of cellular contractile forces. They may be formed between cell and extracellular matrix, through integrin-based focal adhesions, as well as between different cells, through cadherin-based adherens junctions (AJs). Importantly, both types of cell adhesions act as sensitive force sensors, which change their size and shape in response to external mechanical signals. Traditionally, the correlation between adhesion linker assembly and external mechanical cues was investigated by employing polymeric substrates of adjustable substrate stiffness containing covalently attached linkers. Such systems are well suited to mimic the mechanosensitive assembly of focal adhesions (FAs), but fail to replicate the rich dynamics of cell-cell linkages, such as treadmilling of adherens junctions, during cellular force sensing. To overcome this limitation, the 2D confocal imaging methodology was applied to investigate the dynamic assembly of N-cadherin-chimera on the surface of a polymer-tethered lipid multi-bilayer in the presence of plated cells. Here, the N-cadherin chimera-functionalized polymer-tethered lipid bilayer acts as a cell surface-mimicking cell substrate, which: (i) allows the adjustment of substrate stiffness by changing the degree of bilayer stacking and (ii) enables the free assembly of N-cadherin chimera linkers into clusters underneath migrating cells, thereby forming highly dynamic cell-substrate linkages with remarkable parallels to adherens junctions. By applying the confocal methodology, the dynamic assembly of dye-labeled N-cadherin chimera into clusters was monitored underneath adhered cells. Moreover, the long-range mobility of N-cadherin chimera clusters was analyzed by tracking the cluster positions over time using a MATLAB-based multiple-particle tracking method. Disruption of the cytoskeleton organization of plated cells conﬁrmed the disassembly of N-cadherin chimera clusters, emphasizing the important role of the cytoskeleton of migrating cells during formation of cadherin-based cell-substrate linkages. Size and dynamics of N-cadherin chimera clusters were also analyzed as a function of substrate stiffness.

Browsing by Author "Naumann, Christoph A."

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