scholarly journals Analysis of Metabolic Network Disruption in Engineered Microbial Hosts due to Enzyme Promiscuity

2020 ◽  
Author(s):  
Vladimir Porokhin ◽  
Sara A. Amin ◽  
Trevor B. Nicks ◽  
Venkatesh Endalur Gopinarayanan ◽  
Nikhil U. Nair ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Experimental Testing ◽  
Biological Systems ◽  
Strain Engineering ◽  
Computational Method ◽  
Enzyme Promiscuity ◽  
Subsequent Formation ◽  
Wide Range ◽  
Network Disruption ◽  
Host Metabolism

AbstractBackgroundIncreasing understanding of metabolic and regulatory networks underlying microbial physiology has enabled creation of progressively more complex synthetic biological systems for biochemical, biomedical, agricultural, and environmental applications. However, despite best efforts, confounding phenotypes still emerge from unforeseen interplay between biological parts, and the design of robust and modular biological systems remains elusive. Such interactions are difficult to predict when designing synthetic systems and may manifest during experimental testing as inefficiencies that need to be overcome. Despite advances in tools and methodologies for strain engineering, there remains a lack of tools that can systematically identify incompatibilities between the native metabolism of the host and its engineered modifications.ResultsTransforming organisms such as Escherichia coli into microbial factories is achieved via a number of engineering strategies, used individually or in combination, with the goal of maximizing the production of chosen target compounds. One technique relies on suppressing or overexpressing selected genes; another involves on introducing heterologous enzymes into a microbial host. These modifications steer mass flux towards the set of desired metabolites but may create unexpected interactions. In this work, we develop a computational method, termed Metabolic Disruption Workflow (MDFlow), for discovering interactions and network disruption arising from enzyme promiscuity – the ability of enzymes to act on a wide range of molecules that are structurally similar to their native substrates. We apply MDFlow to two experimentally verified cases where strains with essential genes knocked out are rescued by interactions resulting from overexpression of one or more other genes. We then apply MDFlow to predict and evaluate a number of putative promiscuous reactions that can interfere with two heterologous pathways designed for 3-hydroxypropic acid (3-HP) production.ConclusionsUsing MDFlow, we can identify putative enzyme promiscuity and the subsequent formation of unintended and undesirable byproducts that are not only disruptive to the host metabolism but also to the intended end-objective of high biosynthetic productivity and yield. In addition, we show how enzyme promiscuity can potentially be responsible for the adaptability of cells to the disruption of essential pathways in terms of biomass growth.

scholarly journals Engineering the Interface between Inorganic Nanoparticles and Biological Systems through Ligand Design

Nanomaterials ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1001
Author(s):  
Rui Huang ◽  
David C. Luther ◽  
Xianzhi Zhang ◽  
Aarohi Gupta ◽  
Samantha A. Tufts ◽  
...  
Keyword(s):  
Organic Synthesis ◽  
Molecular Design ◽  
Biological Systems ◽  
Ligand Design ◽  
Inorganic Nanoparticles ◽  
Organic Ligands ◽  
Biological Applications ◽  
Wide Range ◽  
Insight Into

Nanoparticles (NPs) provide multipurpose platforms for a wide range of biological applications. These applications are enabled through molecular design of surface coverages, modulating NP interactions with biosystems. In this review, we highlight approaches to functionalize nanoparticles with ”small” organic ligands (Mw < 1000), providing insight into how organic synthesis can be used to engineer NPs for nanobiology and nanomedicine.

scholarly journals Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexey Bondar ◽  
Olga Rybakova ◽  
Josef Melcr ◽  
Jan Dohnálek ◽  
Petro Khoroshyy ◽  
...  
Keyword(s):  
Biological Systems ◽  
Linear Dichroism ◽  
Quantitative Information ◽  
Living Cells ◽  
Software Tools ◽  
Model Systems ◽  
Membrane Properties ◽  
Polarization Microscopy ◽  
Molecular Processes ◽  
Wide Range

AbstractFluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.

scholarly journals Continuum modeling perspectives of non-Fourier heat conduction in biological systems

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Ákos Sudár ◽  
Gergely Futaki ◽  
Róbert Kovács
Keyword(s):  
Biological Systems ◽  
Phase Lag ◽  
Dual Phase ◽  
Continuum Modeling ◽  
Biological Origin ◽  
Ultrasound Surgery ◽  
Thermal Models ◽  
Wide Range ◽  
Fourier Heat Conduction ◽  
The Continuum

Abstract The thermal modeling of biological systems is increasingly important in the development of more advanced and more precise techniques such as ultrasound surgery. One of the primary barriers is the complexity of biological materials: the geometrical, structural, and material properties vary in a wide range. In the present paper, we focus on the continuum modeling of heterogeneous materials of biological origin. There are numerous examples in the literature for non-Fourier thermal models. However, as we realized, they are associated with a few common misconceptions. Therefore, we first aim to clarify the basic concepts of non-Fourier thermal models. These concepts are demonstrated by revisiting two experiments from the literature in which the Cattaneo–Vernotte and the dual phase lag models are utilized. Our investigation revealed that these non-Fourier models are based on misinterpretations of the measured data, and the seeming deviation from Fourier’s law originates from the source terms and boundary conditions.

scholarly journals Self-ordered nanospike porous alumina fabricated under a new regime by an anodizing process in alkaline media

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mana Iwai ◽  
Tatsuya Kikuchi ◽  
Ryosuke O. Suzuki
Keyword(s):  
Aspect Ratio ◽  
High Aspect Ratio ◽  
Porous Alumina ◽  
Three Dimensional ◽  
Alkaline Media ◽  
Alkaline Electrolyte ◽  
Subsequent Formation ◽  
Interpore Distance ◽  
Wide Range ◽  
Ordered Porous

AbstractHigh-aspect ratio ordered nanomaterial arrays exhibit several unique physicochemical and optical properties. Porous anodic aluminum oxide (AAO) is one of the most typical ordered porous structures and can be easily fabricated by applying an electrochemical anodizing process to Al. However, the dimensional and structural controllability of conventional porous AAOs is limited to a narrow range because there are only a few electrolytes that work in this process. Here, we provide a novel anodizing method using an alkaline electrolyte, sodium tetraborate (Na2B4O7), for the fabrication of a high-aspect ratio, self-ordered nanospike porous AAO structure. This self-ordered porous AAO structure possesses a wide range of the interpore distance under a new anodizing regime, and highly ordered porous AAO structures can be fabricated using pre-nanotexturing of Al. The vertical pore walls of porous AAOs have unique nanospikes measuring several tens of nanometers in periodicity, and we demonstrate that AAO can be used as a template for the fabrication of nanomaterials with a large surface area. We also reveal that stable anodizing without the occurrence of oxide burning and the subsequent formation of uniform self-ordered AAO structures can be achieved on complicated three-dimensional substrates.

scholarly journals Could metabolomics drive the fate of COVID-19 pandemic? A narrative review on lights and shadows

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michele Mussap ◽  
Vassilios Fanos
Keyword(s):  
Molecular Mechanisms ◽  
Vascular Dysfunction ◽  
Asymptomatic Infection ◽  
Multiple Organ ◽  
Therapeutic Interventions ◽  
Patient Specific ◽  
Wide Range ◽  
Life Threatening ◽  
The Individual ◽  
Host Metabolism

Abstract Human Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infection activates a complex interaction host/virus, leading to the reprogramming of the host metabolism aimed at the energy supply for viral replication. Alterations of the host metabolic homeostasis strongly influence the immune response to SARS-CoV-2, forming the basis of a wide range of outcomes, from the asymptomatic infection to the onset of COVID-19 and up to life-threatening acute respiratory distress syndrome, vascular dysfunction, multiple organ failure, and death. Deciphering the molecular mechanisms associated with the individual susceptibility to SARS-CoV-2 infection calls for a system biology approach; this strategy can address multiple goals, including which patients will respond effectively to the therapeutic treatment. The power of metabolomics lies in the ability to recognize endogenous and exogenous metabolites within a biological sample, measuring their concentration, and identifying perturbations of biochemical pathways associated with qualitative and quantitative metabolic changes. Over the last year, a limited number of metabolomics- and lipidomics-based clinical studies in COVID-19 patients have been published and are discussed in this review. Remarkable alterations in the lipid and amino acid metabolism depict the molecular phenotype of subjects infected by SARS-CoV-2; notably, structural and functional data on the lipids-virus interaction may open new perspectives on targeted therapeutic interventions. Several limitations affect most metabolomics-based studies, slowing the routine application of metabolomics. However, moving metabolomics from bench to bedside cannot imply the mere determination of a given metabolite panel; rather, slotting metabolomics into clinical practice requires the conversion of metabolic patient-specific data into actionable clinical applications.

Strain-engineering in AlGaN/GaN HEMTs: impact of silicon nitride passivation layer on electrical performance

2021 ◽  
Author(s):  
Sanghamitra Das ◽  
Taraprasanna Dash ◽  
Devika Jena ◽  
Eleena Mohapatra ◽  
C K Maiti
Keyword(s):  
Experimental Data ◽  
Compressive Strain ◽  
Cutoff Frequency ◽  
Strain Engineering ◽  
Electrical Performance ◽  
Current Gain ◽  
Great Promise ◽  
High Electron ◽  
Wide Range ◽  
Gan Hemts

Abstract In this work, we present a physics-based analysis of two-dimensional electron gas (2DEG) sheet carrier density and other microwave characteristics such as transconductance and cutoff frequency of AlxGa1-xN/GaN high electron mobility transistors (HEMT). An accurate polarization-dependent charge control-based analysis is performed for microwave performance assessment in terms of current, transconductance, gate capacitances, and cutoff frequency of lattice-mismatched AlGaN/GaN HEMTs. The influence of stress on spontaneous and piezoelectric polarization is included in the simulation of an AlGaN/GaN HEMT. We have shown the change in threshold voltage (Vt) due to tensile and compressive strain with different gate lengths. Also, the influence of stress due to the change in nitride thickness is presented. Our simulation results for drain current, transconductance, and current-gain cutoff frequency for various gate length devices are calibrated and verified with experimental data over a wide range of gate and drain applied voltages, which are expected to be useful for microwave circuit design. The predicted transconductance, drain conductance, and operation frequency are quite close to the experimental data. The AlGaN/GaN heterostructure HEMTs with nitride passivation layers show great promise as a candidate in future high speed and high power applications.

scholarly journals Experimental Issues in Testing a Semiactive Technique to Control Earthquake Induced Vibration

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Nicola Caterino ◽  
Mariacristina Spizzuoco ◽  
Julian M. Londoño ◽  
Antonio Occhiuzzi
Keyword(s):  
Large Scale ◽  
Experimental Testing ◽  
Practical Experience ◽  
Structural Testing ◽  
Frame Structure ◽  
Semiactive Control ◽  
Electrical Currents ◽  
Wide Range ◽  
And Control ◽  
Steel Frame Structure

This work focuses on the issues to deal with when approaching experimental testing of structures equipped with semiactive control (SA) systems. It starts from practical experience authors gained in a recent wide campaign on a large scale steel frame structure provided with a control system based on magnetorheological dampers. The latter are special devices able to achieve a wide range of physical behaviours using low-power electrical currents. Experimental activities involving the use of controllable devices require special attention in solving specific aspects that characterize each of the three phases of the SA control loop: acquisition, processing, and command. Most of them are uncommon to any other type of structural testing. This paper emphasizes the importance of the experimental assessment of SA systems and shows how many problematic issues likely to happen in real applications are also present when testing these systems experimentally. This paper highlights several problematic aspects and illustrates how they can be addressed in order to achieve a more realistic evaluation of the effectiveness of SA control solutions. Undesired and unavoidable effects like delays and control malfunction are also remarked. A discussion on the way to reduce their incidence is also offered.

Experimental Measurements and CFD Evaluation of the Onset Flow Boiling at Low Pressure and High Subcooling Flow of R-11 Within Vertical Annulus

2014 ◽  
Author(s):  
Y. Bouaichaoui ◽  
R. Kibboua ◽  
M. Matkovič
Keyword(s):  
Heat Flux ◽  
Liquid Velocity ◽  
Flow Boiling ◽  
Fluid Model ◽  
Computer Code ◽  
Computational Method ◽  
Subcooled Boiling ◽  
Two Phase ◽  
Local Flow ◽  
Wide Range

The knowledge of the onset of subcooled boiling in forced convective flow at high liquid velocity and subcooling is of importance in thermal hydraulic studies. Measurements were performed under various conditions of mass flux, heat flux, and inlet subcooling, which enabled to study the influence of different boundary conditions on the development of local flow parameters. Also, some measurements have been compared to the predictions by the three-dimensional two-fluid model of subcooled boiling flow carried out with the computer code ANSYS-CFX-13. A computational method based on theoretical studies of steady state two phase forced convection along a test section loop was released. The calculation model covers a wide range of two phase flow conditions. It predicts the heat transfer rates and transitions points such as the Onset of Critical Heat Flux.

scholarly journals Engineering and experimental testing of two-wavelength laser-assisted device for photocoagulation of eye tissue

2013 ◽  
Vol 6 (2) ◽  
pp. 10-15
Author(s):  
Yury Sergeevich Astakhov ◽  
Yevgeny Leonidovich Akopov ◽  
Aleksandr Anatolevich Ivanov ◽  
Mariya Alexeevna Smirnova ◽  
Leonid Nikolaevich Panteleev ◽  
...  
Keyword(s):  
High Efficiency ◽  
Experimental Testing ◽  
Wide Spectrum ◽  
Retinal Disease ◽  
Primary Objective ◽  
3D Analysis ◽  
Potential Candidate ◽  
Living Tissue ◽  
Wide Range ◽  
Retinal Photocoagulation

Retinal photocoagulation is believed to be one of most efficient methods to treat many retinal abnormalities. By now, a number of lasers operating at different wavelengths, irradiation intensities, and exposure times have been tested in search of optimal parameters for each type of retinal photocoagulation. Taking into consideration a wide range of such parameters, the primary objective of the present study was to develop a device that would combine the potentials of different lasers into a single universal laser-assisted coagulator (ULAC) equally suitable for a wide diversity of retinal disease. Important issue would be the creation of an experimental model allowing an operative evaluation of the coagulating effect induced by the ULAC. The sources of coherent irradiation to be combined were DPSS and diode lasers (532 and 810 nm, respectively). Through two individual fibers, irradiation generated by each of the lasers entered the optical blender to be further directed to the target, now via a single fiber. The target termed the “surrogate of living tissue” was a mixture of donor human blood and chicken egg white, which corresponded, respectively, to the chromophore and thermocoagulating agent, both sensitive to laser beams at 532 and 810 nm. As a result, irradiation of surrogate of living tissue by a laser under the trial caused the formation of a coagulate and its firm adhesion to the coverslip, after that the coagulate was separated from the unaffected surrogate of living tissue followed by its 3D-analysis. In conclusion, the whole procedure, while being relatively non-expensive and easy to perform, has proved to be simple enough for testing of a wide spectrum of coagulation-inducing parameters, whatever laser was used. Moreover, even the initial experiments have shown the high efficiency of the ULAC as a potential candidate for the application in ophthalmological practice.

scholarly journals Constraint-based metabolic control analysis for rational strain engineering

2020 ◽  
Author(s):  
Sophia Tsouka ◽  
Meric Ataman ◽  
Tuure Hameri ◽  
Ljubisa Miskovic ◽  
Vassily Hatzimanikatis
Keyword(s):  
Metabolic Engineering ◽  
Genome Editing ◽  
Metabolic Control ◽  
Metabolic Flux ◽  
Strain Engineering ◽  
Metabolic Control Analysis ◽  
Physiological Data ◽  
Response Analysis ◽  
Control Analysis ◽  
Wide Range

AbstractThe advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering interventions on flows in metabolic networks and metabolic concentrations, it fails to account for the physiological limitations of the cellular environment and metabolic engineering design constraints. We report here a constraint-based framework based on MCA, Network Response Analysis (NRA), for the rational genetic strain design that incorporates biologically relevant constraints, as well as genome editing restrictions. The NRA core constraints being similar to the ones of Flux Balance Analysis, allow it to be used for a wide range of optimization criteria and with various physiological constraints. We show how the parametrization and introduction of biological constraints enhance the NRA formulation compared to the classical MCA approach, and we demonstrate its features and its ability to generate multiple alternative optimal strategies given several user-defined boundaries and objectives. In summary, NRA is a sophisticated alternative to classical MCA for rational metabolic engineering that accommodates the incorporation of physiological data at metabolic flux, metabolite concentration, and enzyme expression levels.

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