927,848 research outputs found

    Unstandard Standardization: The Case of Biology

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    How applicable are the approaches adopted by information and communication technology standards-setting organizations to biological standards? Most engineering-based industries construct products from standard, well understood components. By contrast, despite the early attachment of the moniker “genetic engineering” to biotechnology, standardization in the biological sciences has been relatively rare

    Developments in the tools and methodologies of synthetic biology.

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    Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a body of knowledge from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community

    On engineering reliability concepts and biological aging

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    Some stochastic approaches to biological aging modeling are studied. We assume that an organism acquires a random resource at birth. Death occurs when the accumulated dam-age (wear) exceeds this initial value, modeled by the discrete or continuous random vari-ables. Another source of death of an organism is also taken into account, when it occurs as a consequence of a shock or of a demand for energy, which is a generalization of the Strehler-Mildwan’s model (1960). Biological age based on the observed degradation is also defined. Finally, aging properties of repairable systems are discussed. We show that even in the case of imperfect repair, which is certainly the case for organisms, aging slows down with age and eventually can even fade out. This presents another possible explanation for the human mortality rate plateaus.mortality

    Biological Systems Engineering

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    The present work studied the optimization of aeration rate, agitation rate and oxygen transfer and the use of various batch fermentation strategies for xylanase production from a recombinant Aspergillus nidulans strain in a 3 L stirred tank reactor. Maximum xylanase production of 1250 U/mL with productivity of 313 U/mL/day was obtained under an aeration rate of 2 vvm and an agitation rate of 400 rpm using batch fermentation. The optimum volumetric oxygen transfer coefficient (kLa) for efficient xylanase production was found to be 38.6 h1. Fed batch mode and repeated batch fermentation was also performed with kLa was 38.6 h1. Xylanase enzyme productivity increased to 327 with fed batch fermentation and 373 U/mL/ day with repeated batch fermentation. Also, maximum xylanase activity increased to 1410 U/mL with fed batch fermentation and 1572 U/mL with repeated batch fermentation

    Synthetic biology—putting engineering into biology

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    Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis—synthetic biology’s system fabrication process—supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.

    Imaging 3D tissue fiber organization using optical polarization tractography

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    Field of study: Biological engineering.Dr. Gang Yao, Dissertation Supervisor.Includes vita."July 2017."Optical polarization tractography (OPT) is a new imaging technology developed based on an advanced Jones matrix implementation of polarization-sensitive optical coherence tomography (PSOCT). OPT can acquire high-resolution, three-dimensional (3D), depth-resolved images of fiber organization in tissue. To validate OPT's accuracy in measuring fiber orientation, a comprehensive histology comparison study was conducted using heart tissues which are known to have a depth-dependent fiber orientation change. A systematic image processing procedure was developed to register histology images with OPT images so that the pixel-wise difference between the two measurements can be compared in details. The validation results indicated that OPT can reveal the tissue fiber tractography with histology-like resolution. OPT was then applied to image freshly excised heart samples of the mdx mouse model of Duchene muscular dystrophies (DMD). A rotational imaging platform was developed to obtain OPT images of the excised whole mouse heart. The imaging light was repetitively scanned along the long axis of the heart while the heart was rotated continuously on the imaging platform. The acquired 3D image data were then transformed to construct the 3D whole heart image. The "cross-helical" laminar architecture of the myocardial fibers can be clearly visualized. More importantly, the OPT results revealed significant global and microscopic structural remodeling in the heart of the mdx mouse. OPT can also be applied to image fiber organization in other fibrous tissue samples. For example, OPT revealed focal fiber disorganization in the tibialis anterior (TA) muscle of the mdx mouse, which was confirmed in histology as muscle damage. The 3D OPT images of the TA muscle can be quantified by analyzing the randomness of the fiber orientation distribution. A "fiber disarray" index can be computed to automatically identify and visualize all damaged tissues in the 3D TA muscle. Since the OPT only images the projected fiber orientation within a plane perpendicular to the light propagation, a dual-angle imaging procedure was developed to obtain the absolute 3D fiber orientation. The two 3D OPT images of the same tissue acquired at two different view angles were registered to reconstruct the image of the absolute 3D fiber orientation. This new method was validated by imaging a mouse extensor digitorum longus (EDL) muscle placed at various known positions. The capability of this dual-angle OPT method was demonstrated by visualizing the absolute 3D muscle fiber structure in mouse TA muscles and the unique arcade collagen fiber architecture in a piece of articular cartilage. In summary, the results presented in this dissertation study indicated that the newly developed OPT technology can obtain high-resolution 3D image of tissue fiber organization. OPT may provide a practical tool for studying disease related fiber structural changes in many fibrous tissues.Includes bibliographical references (pages 116-129)