WorldCat Identities

Weber, Wilfried 1974-

Overview
Works: 33 works in 57 publications in 2 languages and 333 library holdings
Genres: Academic theses  Laboratory manuals 
Roles: dgs, Author, Editor, Other, Thesis advisor
Publication Timeline
.
Most widely held works by Wilfried Weber
Synthetic gene networks : methods and protocols by Wilfried Weber( )

11 editions published between 2011 and 2016 in English and held by 221 WorldCat member libraries worldwide

The rapid expansion of synthetic biology is due to the design and construction of synthetic gene networks that have opened many new avenues in fundamental and applied research. Synthetic Gene Networks: Methods and Protocols provides the necessary information to design and construct synthetic gene networks in different host backgrounds. Divided into four convenient sections, this volume focuses on design concepts to devise synthetic gene networks and how mathematical models can be applied to the predictable engineering of desired network features. The volume continues by highlighting the construction and validation of biologic tools, describing strategies to optimize and streamline the host cell for optimized network performance, and covering how optimally designed gene networks can be implemented in a large variety of host cells ranging from bacteria over yeast and insect cells to plant and mammalian cell culture. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Synthetic Gene Networks: Methods and Protocols serves as an invaluable resource for established biologists, engineers, and computer scientists or novices just entering into the rapidly growing field of synthetic biology
Single molecule imaging of the initial steps of EGFR activation in Mammalian cells by Shima Tahvildar Khazaneh( )

1 edition published in 2017 in English and held by 16 WorldCat member libraries worldwide

Abstract: The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that undergoes ligand mediated dimerization and activation. EGFRs regulate physiological processes such as cell migration, differentiation and proliferation, but their aberrant activation plays a pivotal role in cancer and neurodegenerative disease development. In resting cells, EGFRs are present as a population of inactive monomers and predimers that are laterally mobile and expressed uniformly across the cell surface. Ligand binding rapidly shifts the inactive monomer population to receptor dimers. Besides an increase in dimers, clusters of immobile EGF receptors have been observed shortly after activation. It remains unclear however, to what extent dimerization and clustering depend on one another, their role in receptor phosphorylation, and the intracellular proteins and endocytic compartments involved in facilitating their formation.<br><br>In the present work, the current model for EGFR activation is extended to include the role of EGFR predimers and clusters in receptor signaling. With a highly efficient fluorescent protein labeling approach, we image and track the majority of GFP-labeled EGF receptors at the plasma membrane of a living cell on a single molecule (SM) level. The focus on SM imaging of dynamic EGFR interactions affords in addition to determining diffusion coefficients of receptors, the quantification of their aggregation behavior in real time. The direct observation of EGFR interactions along with the use of several EGFR mutations and pharmacological inhibitors have led to three core findings in this work; (i) EGFR diffusion on the plasma membrane is tightly linked to its activation, where activated receptors have lower diffusion coefficients than unliganded receptors, (ii) EGF induced redistribution of EGFRs into clusters requires an active kinase domain and receptor clustering is non-essential for short-term receptor activation, and (iii) endocytic adaptor proteins provide a scaffold facilitating ligand-induced EGFR clustering. Ultimately, a better understanding of EGFR activation can aid the development of pharmacological targets for down-regulating aberrant EGFR activation
Engineering of prokaryotic transcription regulators for mammalian cell biotechnology by Wilfried Weber( )

6 editions published in 2003 in English and German and held by 11 WorldCat member libraries worldwide

Synthetic Gene Networks Methods and Protocols by Wilfried Weber( )

5 editions published in 2012 in English and held by 10 WorldCat member libraries worldwide

The rapid expansion of synthetic biology is due to the design and construction of synthetic gene networks that have opened many new avenues in fundamental and applied research. Synthetic Gene Networks: Methods and Protocols provides the necessary information to design and construct synthetic gene networks in different host backgrounds. Divided into four convenient sections, this volume focuses on design concepts to devise synthetic gene networks and how mathematical models can be applied to the predictable engineering of desired network features. The volume continues by highlighting the construction and validation of biologic tools, describing strategies to optimize and streamline the host cell for optimized network performance, and covering how optimally designed gene networks can be implemented in a large variety of host cells ranging from bacteria over yeast and insect cells to plant and mammalian cell culture. Written in the successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Synthetic Gene Networks: Methods and Protocols serves as an invaluable resource for established biologists, engineers, and computer scientists or novices just entering into the rapidly growing field of synthetic biology
Multiplexed protein caging: orthogonal and on-command release of angiogenesis-promoting factors by Natascha Hotz( )

1 edition published in 2015 in English and held by 10 WorldCat member libraries worldwide

Zusammenfassung: Materials that are capable of changing their physical, chemical or biological properties in response to an external stimulus are called smart materials and have broadened the field of material science for a new spectrum of technical applications. Especially interesting for biomedical applications are biohybrid materials. Such materials are composed of a biological polymer and a synthetic polymeric backbone. Once incorporated into a synthetic matrix such biomolecules act as biological switches and translate small changes in the environmental conditions into macromolecular changes of the materials. The advantages of using biological polymers with inherent switch functions are fairly obvious. Owing their biological origin, they perform best under physiological conditions and are able to react to physiologically relevant changes of a large variety of signals including small molecules such as drugs or metabolites. As standardization of biological molecules with diverse functions has been a major goal of synthetic biology, a large variety of well characterized biological switches is available to find their application in material science. Here, the development of new biohybrid materials which respond to the physiologically compatible stimulus fluorescein is presented. Two different approaches for the realization of this goal were pursued. First, a biohybrid hydrogel which translates changes in fluorescein concentrations into a gel-to-sol transition, which could find possible applications in drug delivery, has been developed on the basis of the fluorescein-responsive anticalin FluA and the highly specific interaction of the hexahistidine peptide motif with immobilized nickel ions. In addition it was investigated if the native chemical reaction might be used for the development of a fluorescein-responsive hydrogel. In the second approach the concept of controlled caging and uncaging of biological compounds was utilized. A protein cage with is capable of caging Fc.- tagged growth factors to an agarose matrix via the adaptor protein FluA was developed. Thus, the protein cage translates changes in fluorescein concentration into changes of growth factor concentrations. Further, this fluorescein-responsive protein cage was combined with a novobiocin-responsive protein cage previously reported by Karlsson et al.[1] for the development of a tool for the multiplexed uncaging of growth factors. Considering that the vast majority of cellular processes are regulated by proteins such as growth factors and that de-regulated signaling is the basis for major and chronic diseases, this tool is of interest in both, fundamental and applied biological research and we believe that it will be a valuable asset in various biomedical settings
Clinical on-site monitoring of ß-lactam antibiotics for a personalized antibiotherapy by Richard Bruch( )

1 edition published in 2017 in English and held by 4 WorldCat member libraries worldwide

Human atrial fibroblast adaptation to heterogeneities in substrate stiffness by Ramona Emig( )

1 edition published in 2020 in English and held by 3 WorldCat member libraries worldwide

Abstract: Fibrosis is associated with aging and many cardiac pathologies. It is characterized both by myofibroblast differentiation and by excessive accumulation of extracellular matrix proteins. Fibrosis-related tissue remodeling results in significant changes in tissue structure and function, including passive mechanical properties. This research area has gained significant momentum with the recent development of new tools and approaches to better characterize and understand the ability of cells to sense and respond to their biophysical environment. We use a novel hydrogel, termed CyPhyGel, to provide an advanced in vitro model of remodeling-related changes in tissue stiffness. Based on light-controlled dimerization of a Cyanobacterial Phytochrome, it enables contactless and reversible tuning of hydrogel mechanical properties with high spatial and temporal resolution. Human primary atrial fibroblasts were cultured on CyPhyGels. After 4 days of culturing on stiff (~4.6 kPa) or soft (~2.7 kPa) CyPhyGels, we analyzed fibroblast cell area and stiffness. Cells grown on the softer substrate were smaller and softer, compared to cells grown on the stiffer substrate. This difference was absent when both soft and stiff growth substrates were combined in a single CyPhyGel, with the resulting cell areas being similar to those on homogeneously stiff gels and cell stiffnesses being similar to those on homogeneously soft substrates. Using CyPhyGels to mimic tissue stiffness heterogeneities in vitro, our results confirm the ability of cardiac fibroblasts to adapt to their mechanical environment, and suggest the presence of a paracrine mechanism that tunes fibroblast structural and functional properties associated with mechanically induced phenotype conversion toward myofibroblasts. In the context of regionally increased tissue stiffness, such as upon scarring or in diffuse fibrosis, such a mechanism could help to prevent abrupt changes in cell properties at the border zone between normal and diseased tissue. The light-tunable mechanical properties of CyPhyGels and their suitability for studying human primary cardiac cells make them an attractive model system for cardiac mechanobiology research. Further investigations will explore the interactions between biophysical and soluble factors in the response of cardiac fibroblasts to spatially and temporally heterogeneous mechanical cues
Data-driven modeling of intracellular auxin fluxes indicates a dominant role of the ER in controlling nuclear auxin uptake by Alistair Middleton( )

1 edition published in 2018 in English and held by 3 WorldCat member libraries worldwide

Abstract: In plants, the phytohormone auxin acts as a master regulator of developmental processes and environmental responses. The best characterized process in the auxin regulatory network occurs at the subcellular scale, wherein auxin mediates signal transduction into transcriptional programs by triggering the degradation of Aux/IAA transcriptional repressor proteins in the nucleus. However, whether and how auxin movement between the nucleus and the surrounding compartments is regulated remain elusive. Using a fluorescent auxin analog, we show that its diffusion into the nucleus is restricted. By combining mathematical modeling with time course assays on auxin-mediated nuclear signaling and quantitative phenotyping in single plant cell systems, we show that ER-to-nucleus auxin flux represents a major subcellular pathway to directly control nuclear auxin levels. Our findings propose that the homeostatically regulated auxin pool in the ER and ER-to-nucleus auxin fluxes underpin auxin-mediated downstream responses in plant cells
Design of a human rhinovirus-14 3C protease-inducible caspase-3 by Hanna Jeannine Wagner( )

1 edition published in 2019 in English and held by 3 WorldCat member libraries worldwide

Abstract: The engineering of enzymes for the purpose of controlling their activity represents a valuable approach to address challenges in both fundamental and applied research. Here, we describe and compare different design strategies for the generation of a human rhinovirus-14 (HRV14) 3C protease-inducible caspase-3 (CASP3). We exemplify the application potential of the resulting protease by controlling the activity of a synthetic enzyme cascade, which represents an important motif for the design of artificial signal transduction networks. In addition, we use our engineered CASP3 to characterize the effect of aspartate mutations on enzymatic activity. Besides the identification of mutations that render the enzyme inactive, we find the CASP3-D192E mutant (aspartate-to-glutamate exchange at position 192) to be inaccessible for 3C protease-mediated cleavage. This indicates a structural change of CASP3 that goes beyond a slight misalignment of the catalytic triad. This study could inspire the design of additional engineered proteases that could be used to unravel fundamental research questions or to expand the collection of biological parts for the design of synthetic signaling pathways
CRISPR/Cas13a powered electrochemical microfluidic biosensor for nucleic acid amplification-free miRNA diagnostics by Richard Bruch( )

1 edition published in 2019 in English and held by 3 WorldCat member libraries worldwide

Abstract: Noncoding small RNAs, such as microRNAs, are becoming the biomarkers of choice for multiple diseases in clinical diagnostics. A dysregulation of these microRNAs can be associated with many different diseases, such as cancer, dementia, and cardiovascular conditions. The key for effective treatment is an accurate initial diagnosis at an early stage, improving the patient's survival chances. In this work, the first clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a-powered microfluidic, integrated electrochemical biosensor for the on-site detection of microRNAs is introduced. Through this unique combination, the quantification of the potential tumor markers microRNA miR-19b and miR-20a is realized without any nucleic acid amplification. With a readout time of 9 min and an overall process time of less than 4 h, a limit of detection of 10 pm is achieved, using a measuring volume of less than 0.6 µL. Furthermore, the feasibility of the biosensor platform to detect miR-19b in serum samples of children, suffering from brain cancer, is demonstrated. The validation of the obtained results with a standard quantitative real-time polymerase chain reaction method shows the ability of the electrochemical CRISPR-powered system to be a low-cost, easily scalable, and target amplification-free tool for nucleic acid based diagnostics
A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication by Katja Kolar( )

2 editions published in 2015 in English and held by 3 WorldCat member libraries worldwide

Abstract: Background<br><br>Multicellular organisms depend on the exchange of information between specialized cells. This communication is often difficult to decipher in its native context, but synthetic biology provides tools to engineer well-defined systems that allow the convenient study and manipulation of intercellular communication networks.<br><br>Results<br><br>Here, we present the first mammalian synthetic network for reciprocal cell-cell communication to compute the border between a sender/receiver and a processing cell population. The two populations communicate via L-tryptophan and interleukin-4 to highlight the population border by the production of a fluorescent protein. The sharpness of that visualized edge can be adjusted by modulating key parameters of the network.<br><br>Conclusions<br><br>We anticipate that this network will on the one hand be a useful tool to gain deeper insights into the mechanisms of tissue formation in nature and will on the other hand contribute to our ability to engineer artificial tissues.<br><br>Keywords<br><br>Synthetic biology - Intercellular communication - Population borders - Edge-detect
A chemical switch for controlling viral infectivity by Maximilian Hörner( )

2 editions published in 2014 in English and held by 3 WorldCat member libraries worldwide

Abstract: Chemically triggered molecular switches for controlling the fate and function of biological systems are fundamental to the emergence of synthetic biology and the development of biomedical applications. We here present the first chemically triggered switch for controlling the infectivity of adeno-associated viral (AAV) vectors
Designed miniaturization of microfluidic biosensor platforms using the stop-flow technique by Can Dincer( )

2 editions published in 2016 in English and held by 3 WorldCat member libraries worldwide

Abstract: Here, we present a novel approach to increase the degree of miniaturization as well as the sensitivity of biosensor platforms by the optimization of microfluidic stop-flow techniques independent of the applied detection technique (e.g. electrochemical or optical). The readout of the labeled bioassays, immobilized in a microfluidic channel, under stop-flow conditions leads to a rectangular shaped peak signal. Data evaluation using the peak height allows for a high level miniaturization of the channel geometries. To study the main advantages and limitations of this method by numerical simulations, a universally applicable model system is introduced for the first time. Consequently, proof-of-principle experiments were successfully performed with standard and miniaturized versions of an electrochemical biosensor platform utilizing a repressor protein-based assay for tetracycline antibiotics. Herein, the measured current peak heights are the same despite the sextuple reduction of the channel dimensions. Thus, this results in a 22-fold signal amplification compared to the constant flow measurements in the case of the miniaturized version
Optogenetic control shows that kinetic proofreading regulates the activity of the T cell receptor by Omid Sascha Yousefi( )

1 edition published in 2019 in English and held by 3 WorldCat member libraries worldwide

Cell and tissue reaction engineering by Regine Eibl( Book )

2 editions published between 2008 and 2009 in English and held by 3 WorldCat member libraries worldwide

The completion of the Human Genome Project and the rapid progress in cell bi- ogy and biochemical engineering, are major forces driving the steady increase of approved biotech products, especially biopharmaceuticals, in the market. Today mammalian cell products ("products from cells"), primarily monoclonals, cytokines, recombinant glycoproteins, and, increasingly, vaccines, dominate the biopharmaceutical industry. Moreover, a small number of products consisting of in vitro cultivated cells ("cells as product") for regenerative medicine have also been introduced in the market. Their efficient production requires comprehensive knowledge of biological as well as biochemical mammalian cell culture fundamentals (e.g., cell characteristics and metabolism, cell line establishment, culture medium optimization) and related engineering principles (e.g., bioreactor design, process scale-up and optimization). In addition, new developments focusing on cell line development, animal-free c- ture media, disposables and the implications of changing processes (multi-purpo- facilities) have to be taken into account. While a number of excellent books treating the basic methods and applications of mammalian cell culture technology have been published, only little attention has been afforded to their engineering aspects. The aim of this book is to make a contribution to closing this gap; it particularly focuses on the interactions between biological and biochemical and engineering principles in processes derived from cell cultures. It is not intended to give a c- prehensive overview of the literature. This has been done extensively elsewhere
A two-step approach for the design and generation of nanobodies by Hanna Jeannine Wagner( )

1 edition published in 2018 in English and held by 3 WorldCat member libraries worldwide

Abstract: Nanobodies, the smallest possible antibody format, have become of considerable interest for biotechnological and immunotherapeutic applications. They show excellent robustness, are non-immunogenic in humans, and can easily be engineered and produced in prokaryotic hosts. Traditionally, nanobodies are selected from camelid immune libraries involving the maintenance and treatment of animals. Recent advances have involved the generation of nanobodies from naïve or synthetic libraries. However, such approaches demand large library sizes and sophisticated selection procedures. Here, we propose an alternative, two-step approach for the design and generation of nanobodies. In a first step, complementarity-determining regions (CDRs) are grafted from conventional antibody formats onto nanobody frameworks, generating weak antigen binders. In a second step, the weak binders serve as templates to design focused synthetic phage libraries for affinity maturation. We validated this approach by grafting toxin- and hapten-specific CDRs onto frameworks derived from variable domains of camelid heavy-chain-only antibodies (VHH). We then affinity matured the hapten binder via panning of a synthetic phage library. We suggest that this strategy can complement existing immune, naïve, and synthetic library based methods, requiring neither animal experiments, nor large libraries, nor sophisticated selection protocols
A red light-controlled synthetic gene expression switch for plant systems by Konrad Müller( )

2 editions published in 2014 in English and held by 3 WorldCat member libraries worldwide

Abstract: On command control of gene expression in time and space is required for the comprehensive analysis of key plant cellular processes. Even though some chemical inducible systems showing satisfactory induction features have been developed, they are inherently limited in terms of spatiotemporal resolution and may be associated with toxic effects. We describe here the first synthetic light-inducible system for the targeted control of gene expression in plants. For this purpose, we applied an interdisciplinary synthetic biology approach comprising mammalian and plant cell systems to customize and optimize a split transcription factor based on the plant photoreceptor phytochrome B and one of its interacting factors (PIF6). Implementation of the system in transient assays in tobacco protoplasts resulted in strong (95-fold) induction in red light (660 nm) and could be instantaneously returned to the OFF state by subsequent illumination with far-red light (740 nm). Capitalizing on this toggle switch-like characteristic, we demonstrate that the system can be kept in the OFF state in the presence of 740 nm-supplemented white light, opening up perspectives for future application of the system in whole plants. Finally we demonstrate the system's applicability in basic research, by the light-controlled tuning of auxin signalling networks in N. tabacum protoplasts, as well as its biotechnological potential for the chemical-inducer free production of therapeutic proteins in the moss P. patens
CRISPR-powered electrochemical microfluidic multiplexed biosensor for target amplification-free miRNA diagnostics by Richard Bruch( )

1 edition published in 2021 in English and held by 3 WorldCat member libraries worldwide

Abstract: Recently the use of microRNAs (miRNAs) as biomarkers for a multitude of diseases has gained substantial significance for clinical as well as point-of-care diagnostics. Amongst other challenges, however, it holds the central requirement that the concentration of a given miRNA must be evaluated within the context of other factors in order to unambiguously diagnose one specific disease. In terms of the development of diagnostic methods and devices, this implies an inevitable demand for multiplexing in order to be able to gauge the abundance of several components of interest in a patient's sample in parallel. In this study, we design and implement different multiplexed versions of our electrochemical microfluidic biosensor by dividing its channel into subsections, creating four novel chip designs for the amplification-free and simultaneous quantification of up to eight miRNAs on the CRISPR-Biosensor X ('X' highlighting the multiplexing aspect of the device). We then use a one-step model assay followed by amperometric readout in combination with a 2-min-stop-flow-protocol to explore the fluidic and mechanical characteristics and limitations of the different versions of the device. The sensor showing the best performance, is subsequently used for the Cas13a-powered proof-of-concept measurement of two miRNAs (miRNA-19b and miRNA-20a) from the miRNA-17-92 cluster, which is dysregulated in the blood of pediatric medulloblastoma patients. Quantification of the latter, alongside simultaneous negative control measurements are accomplished on the same device. We thereby confirm the applicability of our platform to the challenge of amplification-free, parallel detection of multiple nucleic acids
Light-controlled affinity purification of protein complexes exemplified by the resting ZAP70 interactome by Maximilian Hörner( )

1 edition published in 2019 in English and held by 3 WorldCat member libraries worldwide

Abstract: Multiprotein complexes control the behavior of cells, such as of lymphocytes of the immune system. Methods to affinity purify protein complexes and to determine their interactome by mass spectrometry are thus widely used. One drawback of these methods is the presence of false positives. In fact, the elution of the protein of interest (POI) is achieved by changing the biochemical properties of the buffer, so that unspecifically bound proteins (the false positives) may also elute. Here, we developed an optogenetics-derived and light-controlled affinity purification method based on the light-regulated reversible protein interaction between phytochrome B (PhyB) and its phytochrome interacting factor 6 (PIF6). We engineered a truncated variant of PIF6 comprising only 22 amino acids that can be genetically fused to the POI as an affinity tag. Thereby the POI can be purified with PhyB-functionalized resin material using 660 nm light for binding and washing, and 740 nm light for elution. Far-red light-induced elution is effective but very mild as the same buffer is used for the wash and elution. As proof-of-concept, we expressed PIF-tagged variants of the tyrosine kinase ZAP70 in ZAP70-deficient Jurkat T cells, purified ZAP70 and associating proteins using our light-controlled system, and identified the interaction partners by quantitative mass spectrometry. Using unstimulated T cells, we were able to detect the known interaction partners, and could filter out all other proteins
Optogenetic approaches for the spatiotemporal control of signal transduction pathways by Markus M Kramer( )

1 edition published in 2021 in English and held by 2 WorldCat member libraries worldwide

Abstract: Biological signals are sensed by their respective receptors and are transduced and processed by a sophisticated intracellular signaling network leading to a signal-specific cellular response. Thereby, the response to the signal depends on the strength, the frequency, and the duration of the stimulus as well as on the subcellular signal progression. Optogenetic tools are based on genetically encoded light-sensing proteins facilitating the precise spatiotemporal control of signal transduction pathways and cell fate decisions in the absence of natural ligands. In this review, we provide an overview of optogenetic approaches connecting light-regulated protein-protein interaction or caging/uncaging events with steering the function of signaling proteins. We briefly discuss the most common optogenetic switches and their mode of action. The main part deals with the engineering and application of optogenetic tools for the control of transmembrane receptors including receptor tyrosine kinases, the T cell receptor and integrins, and their effector proteins. We also address the hallmarks of optogenetics, the spatial and temporal control of signaling events
 
moreShow More Titles
fewerShow Fewer Titles
Audience Level
0
Audience Level
1
  Kids General Special  
Audience level: 0.71 (from 0.51 for Cell and t ... to 0.97 for Optogeneti ...)

Synthetic gene networks : methods and protocols Synthetic Gene Networks Methods and Protocols
Covers
Synthetic Gene Networks Methods and ProtocolsCell and tissue reaction engineering
Alternative Names
Wilfried Weber wetenschapper

Languages
English (43)

German (1)