Browsing by Subject "Biofilms"

Now showing 1 - 7 of 7
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    Atomic force microscopy for the investigation of molecular and cellular behavior
    (Elsevier, 2016-10) Ozkan A.D.; Topal, A. E.; Dana, A.; Güler, Mustafa O.; Tekinay, A. B.
    The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.
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    Cellular biocatalysts using synthetic genetic circuits for prolonged and durable enzymatic activity
    (Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim, 2019) Ahan, Recep Erdem; Şaltepe, Behide; Apaydın, Onur; Şeker, Urartu Özgür Şafak
    Cellular biocatalysts hold great promise for the synthesis of difficult to achieve compounds, such as complex active molecules. Whole‐cell biocatalysts can be programmed through genetic circuits to be more efficient, but they suffer from low stability. The catalytic activity of whole cells decays under stressful conditions, such as prolonged incubation times or high temperatures. In nature, microbial communities cope with these conditions by forming biofilm structures. In this study, it is shown that the use of biofilm structures can enhance the stability of whole‐cell biocatalysts. We employed two different strategies to increase the stability of whole‐cell catalysts and decrease their susceptibility to high temperature. In the first approach, the formation of a biofilm structure is induced by controlling the expression of one of the curli component, CsgA. The alkaline phosphatase (ALP) enzyme was used to monitor the catalytic activity of cells in the biofilm structure. In the second approach, the ALP enzyme was fused to the CsgA curli fiber subunit to utilize the protective properties of the biofilm on enzyme biofilms. Furthermore, an AND logic gate is introduced between the expression of CsgA and ALP by toehold RNA switches and recombinases to enable logical programming of the whole‐cell catalyst for biofilm formation and catalytic action with different tools. The study presents viable approaches to engineer a platform for biocatalysis processes.
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    Design and applications of self-assembled soft living materials using synthetic biology
    (Elsevier, 2022-01-01) Özkul, Gökçe; Yavuz, Merve; Hacıosmanoğlu, Nedim; Kırpat, Büşra Merve; Şeker, Urartu Özgür Şafak
    In nature, the cells are unique biofactories of various kinds of macroscale structures. These biofactories are as old as the earth. However, as technology developed and new areas of research fields developed these cellular biofactories became the center of attention. The motive was the question if we can engineer them according to the world’s needs. At that point, approaches and tools of synthetic biology came into the picture. After its development, people started to engineer biofactories and produce materials with new properties. One of those materials is classified as self-assembled soft living materials with their specific features and usage areas. To be more specific, biofilms are examples of self-assembled soft living materials due to their self-sustaining and self-assembling properties. They can be engineered starting from genetic circuits leading to creation of their building blocks and finally formation of complex biofilm systems. With the diversity in their engineering aspects, their application areas also vary. In this chapter, the design of biofilm structures from genetic circuits until the formation of complex biofilm structures and their various applications will be investigated.
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    Genetically encoded conductive protein nanofibers secreted by engineered cells
    (Royal Society of Chemistry, 2017-06) Kalyoncu, E.; Ahan, R. E.; Olmez, T. T.; Safak Seker, U. O.
    Bacterial biofilms are promising tools for functional applications as bionanomaterials. They are synthesized by well-defined machinery, readily form fiber networks covering large areas, and can be engineered for different functionalities. In this work, bacterial biofilms have been engineered for use as conductive biopolymers to interface with electrodes and connect bacterial populations to electronic gadgets. Bacterial biofilms are designed with different conductive peptide motifs, as the aromatic amino acid content of fused peptide motifs has been suggested to contribute to electronic conductivity by influencing monomer stacking behavior. To select the best candidates for constructing conductive peptide motifs, conductivity properties of aromatic amino acids are measured using two different fiber scaffolds, an amyloid-like fiber (ALF) forming peptide, and the amyloidogenic R5T peptide of CsgA protein. Three repeats of aromatic amino acids are added to fiber-forming peptide sequences to produce delocalized π clouds similar to those observed in conductive polymers. Based on the measurements, tyrosine and tryptophan residues provide the highest conductivity. Therefore, the non-conductive E. coli biofilm is switched into a conductive form by genetically inserted conductive peptide motifs containing different combinations of tyrosine and tryptophan. Finally, synthetic biofilm biogenesis is achieved with conductive peptide motifs using controlled biofilm production. Conductive biofilms on living cells are formed for bioelectronics and biosensing applications.
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    Genetically-tunable mechanical properties of bacterial functional amyloid nanofibers
    (American Chemical Society, 2017) Abdelwahab, M. T.; Kalyoncu, E.; Onur, T.; Baykara, M. Z.; Seker U.O.S.
    Bacterial biofilms are highly ordered, complex, dynamic material systems including cells, carbohydrates, and proteins. They are known to be resistant against chemical, physical, and biological disturbances. These superior properties make them promising candidates for next generation biomaterials. Here we investigated the morphological and mechanical properties (in terms of Young’s modulus) of genetically-engineered bacterial amyloid nanofibers of Escherichia coli (E. coli) by imaging and force spectroscopy conducted via atomic force microscopy (AFM). In particular, we tuned the expression and biochemical properties of the major and minor biofilm proteins of E. coli (CsgA and CsgB, respectively). Using appropriate mutants, amyloid nanofibers constituting biofilm backbones are formed with different combinations of CsgA and CsgB, as well as the optional addition of tagging sequences. AFM imaging and force spectroscopy are used to probe the morphology and measure the Young’s moduli of biofilm protein nanofibers as a function of protein composition. The obtained results reveal that genetically-controlled secretion of biofilm protein components may lead to the rational tuning of Young’s moduli of biofilms as promising candidates at the bionano interface.
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    Synthetic biogenesis of bacterial amyloid nanomaterials with tunable inorganic-organic interfaces and electrical conductivity
    (American Chemical Society, 2017) Seker U.O.S.; Chen, A. Y.; Citorik, R. J.; Lu, T. K.
    Amyloids are highly ordered, hierarchal protein nanoassemblies. Functional amyloids in bacterial biofilms, such as Escherichia coli curli fibers, are formed by the polymerization of monomeric proteins secreted into the extracellular space. Curli is synthesized by living cells, is primarily composed of the major curlin subunit CsgA, and forms biological nanofibers with high aspect ratios. Here, we explore the application of curli fibers for nanotechnology by engineering curli to mediate tunable biological interfaces with inorganic materials and to controllably form gold nanoparticles and gold nanowires. Specifically, we used cell-synthesized curli fibers as templates for nucleating and growing gold nanoparticles and showed that nanoparticle size could be modulated as a function of curli fiber gold-binding affinity. Furthermore, we demonstrated that gold nanoparticles can be preseeded onto curli fibers and followed by gold enhancement to form nanowires. Using these two approaches, we created artificial cellular systems that integrate inorganic-organic materials to achieve tunable electrical conductivity. We envision that cell-synthesized amyloid nanofibers will be useful for interfacing abiotic and biotic systems to create living functional materials.
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    Synthetic genetic circuits for self-actuated cellular nanomaterial fabrication devices
    (American Chemical Society, 2019) Ölmez, Tolga Tarkan; Şahin-Kehribar, Ebru; Işılak, Musa Efe; Lu, T. K.; Şeker, Urartu Özgür Şafak
    Genetically controlled synthetic biosystems are being developed to create nanoscale materials. These biosystems are modeled on the natural ability of living cells to synthesize materials: many organisms have dedicated proteins that synthesize a wide range of hard tissues and solid materials, such as nanomagnets and biosilica. We designed an autonomous living material synthesizing system consisting of engineered cells with genetic circuits that synthesize nanomaterials. The circuits encode a nanomaterial precursor-sensing module (sensor) coupled with a materials synthesis module. The sensor detects the presence of cadmium, gold, or iron ions, and this detection triggers the synthesis of the related nanomaterial-nucleating extracellular matrix. We demonstrate that when engineered cells sense the availability of a precursor ion, they express the corresponding extracellular matrix to form the nanomaterials. This proof-of-concept study shows that endowing cells with synthetic genetic circuits enables nanomaterial synthesis and has the potential to be extended to the synthesis of a variety of nanomaterials and biomaterials using a green approach.