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1. Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth

   https://doi.org/10.1128/mbio.03259-21  

   Wilkes, Rebecca A. ; Waldbauer, Jacob ; Aristilde, Ludmilla ( December 2021 , mBio)

   Dunn, Anne K. ; Ruby, Edward G. (Ed.)

   ABSTRACT Gluconeogenic carbon metabolism is not well understood, especially within the context of flux partitioning between energy generation and biomass production, despite the importance of gluconeogenic carbon substrates in natural and engineered carbon processing. Here, using multiple omics approaches, we elucidate the metabolic mechanisms that facilitate gluconeogenic fast-growth phenotypes in Pseudomonas putida and Comamonas testosteroni , two Proteobacteria species with distinct metabolic networks. In contrast to the genetic constraint of C. testosteroni , which lacks the enzymes required for both sugar uptake and a complete oxidative pentose phosphate (PP) pathway, sugar metabolism in P. putida is known to generate surplus NADPH by relying on the oxidative PP pathway within its characteristic cyclic connection between the Entner-Doudoroff (ED) and Embden-Meyerhoff-Parnas (EMP) pathways. Remarkably, similar to the genome-based metabolic decoupling in C. testosteroni , our 13 C-fluxomics reveals an inactive oxidative PP pathway and disconnected EMP and ED pathways in P. putida during gluconeogenic feeding, thus requiring transhydrogenase reactions to supply NADPH for anabolism in both species by leveraging the high tricarboxylic acid cycle flux during gluconeogenic growth. Furthermore, metabolomics and proteomics analyses of both species during gluconeogenic feeding, relative to glycolytic feeding, demonstrate a 5-fold depletion in phosphorylated metabolites and the absence of or up to a 17-fold decrease in proteins of the PP and ED pathways. Such metabolic remodeling, which is reportedly lacking in Escherichia coli exhibiting a gluconeogenic slow-growth phenotype, may serve to minimize futile carbon cycling while favoring the gluconeogenic metabolic regime in relevant proteobacterial species. IMPORTANCE Glycolytic metabolism of sugars is extensively studied in the Proteobacteria , but gluconeogenic carbon sources (e.g., organic acids, amino acids, aromatics) that feed into the tricarboxylic acid (TCA) cycle are widely reported to produce a fast-growth phenotype, particularly in species with biotechnological relevance. Much remains unknown about the importance of glycolysis-associated pathways in the metabolism of gluconeogenic carbon substrates. Here, we demonstrate that two distinct proteobacterial species, through genetic constraints or metabolic regulation at specific metabolic nodes, bypass the oxidative PP pathway during gluconeogenic growth and avoid unnecessary carbon fluxes by depleting protein investment into connected glycolysis pathways. Both species can leverage instead the high TCA cycle flux during gluconeogenic feeding to meet NADPH demand. Importantly, lack of a complete oxidative pentose phosphate pathway is a widespread metabolic trait in Proteobacteria with a gluconeogenic carbon preference, thus highlighting the important relevance of our findings toward elucidating the metabolic architecture in these bacteria. 

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2. Systems metabolic engineering design: Fatty acid production as an emerging case study

   https://doi.org/10.1002/bit.25205  

   Tee, Ting Wei ; Chowdhury, Anupam ; Maranas, Costas D. ; Shanks, Jacqueline V. ( February 2014 , Biotechnology and Bioengineering)

   Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C₆to C₁₆are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel‐like biofuels. The abundance of genetic information available forEscherichia coliand specifically, fatty acid metabolism inE. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high‐yielding medium chain fatty acid producingE. colistrains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high‐yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain‐length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain‐lengths and functionalities. Biotechnol. Biotechnol. Bioeng. 2014;111: 849–857. © 2014 Wiley Periodicals, Inc.

    

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3. RTD Light Emission around 1550 nm with IQE up to 6% at 300 K

   https://doi.org/10.1109/DRC50226.2020.9135175  

   Brown, E. R. ; Zhang, W-D. ; Fakhimi, P. ; Growden, T. A. ; Berger, P.R. ( June 2020 , IEEE Device Research Conference (DRC), Columbus, OH (June 22-24, 2020))

   Resonant tunneling diodes (RTDs) have come full-circle in the past 10 years after their demonstration in the early 1990s as the fastest room-temperature semiconductor oscillator, displaying experimental results up to 712 GHz and fmax values exceeding 1.0 THz [1]. Now the RTD is once again the preeminent electronic oscillator above 1.0 THz and is being implemented as a coherent source [2] and a self-oscillating mixer [3], amongst other applications. This paper concerns RTD electroluminescence – an effect that has been studied very little in the past 30+ years of RTD development, and not at room temperature. We present experiments and modeling of an n-type In0.53Ga0.47As/AlAs double-barrier RTD operating as a cross-gap light emitter at ~300K. The MBE-growth stack is shown in Fig. 1(a). A 15-μm-diam-mesa device was defined by standard planar processing including a top annular ohmic contact with a 5-μm-diam pinhole in the center to couple out enough of the internal emission for accurate free-space power measurements [4]. The emission spectra have the behavior displayed in Fig. 1(b), parameterized by bias voltage (VB). The long wavelength emission edge is at  = 1684 nm - close to the In0.53Ga0.47As bandgap energy of Ug ≈ 0.75 eV at 300 K. The spectral peaks for VB = 2.8 and 3.0 V both occur around  = 1550 nm (h = 0.75 eV), so blue-shifted relative to the peak of the “ideal”, bulk InGaAs emission spectrum shown in Fig. 1(b) [5]. These results are consistent with the model displayed in Fig. 1(c), whereby the broad emission peak is attributed to the radiative recombination between electrons accumulated on the emitter side, and holes generated on the emitter side by interband tunneling with current density Jinter. The blue-shifted main peak is attributed to the quantum-size effect on the emitter side, which creates a radiative recombination rate RN,2 comparable to the band-edge cross-gap rate RN,1. Further support for this model is provided by the shorter wavelength and weaker emission peak shown in Fig. 1(b) around = 1148 nm. Our quantum mechanical calculations attribute this to radiative recombination RR,3 in the RTD quantum well between the electron ground-state level E1,e, and the hole level E1,h. To further test the model and estimate quantum efficiencies, we conducted optical power measurements using a large-area Ge photodiode located ≈3 mm away from the RTD pinhole, and having spectral response between 800 and 1800 nm with a peak responsivity of ≈0.85 A/W at  =1550 nm. Simultaneous I-V and L-V plots were obtained and are plotted in Fig. 2(a) with positive bias on the top contact (emitter on the bottom). The I-V curve displays a pronounced NDR region having a current peak-to-valley current ratio of 10.7 (typical for In0.53Ga0.47As RTDs). The external quantum efficiency (EQE) was calculated from EQE = e∙IP/(∙IE∙h) where IP is the photodiode dc current and IE the RTD current. The plot of EQE is shown in Fig. 2(b) where we see a very rapid rise with VB, but a maximum value (at VB= 3.0 V) of only ≈2×10-5. To extract the internal quantum efficiency (IQE), we use the expression EQE= c ∙i ∙r ≡ c∙IQE where ci, and r are the optical-coupling, electrical-injection, and radiative recombination efficiencies, respectively [6]. Our separate optical calculations yield c≈3.4×10-4 (limited primarily by the small pinhole) from which we obtain the curve of IQE plotted in Fig. 2(b) (right-hand scale). The maximum value of IQE (again at VB = 3.0 V) is 6.0%. From the implicit definition of IQE in terms of i and r given above, and the fact that the recombination efficiency in In0.53Ga0.47As is likely limited by Auger scattering, this result for IQE suggests that i might be significantly high. To estimate i, we have used the experimental total current of Fig. 2(a), the Kane two-band model of interband tunneling [7] computed in conjunction with a solution to Poisson’s equation across the entire structure, and a rate-equation model of Auger recombination on the emitter side [6] assuming a free-electron density of 2×1018 cm3. We focus on the high-bias regime above VB = 2.5 V of Fig. 2(a) where most of the interband tunneling should occur in the depletion region on the collector side [Jinter,2 in Fig. 1(c)]. And because of the high-quality of the InGaAs/AlAs heterostructure (very few traps or deep levels), most of the holes should reach the emitter side by some combination of drift, diffusion, and tunneling through the valence-band double barriers (Type-I offset) between InGaAs and AlAs. The computed interband current density Jinter is shown in Fig. 3(a) along with the total current density Jtot. At the maximum Jinter (at VB=3.0 V) of 7.4×102 A/cm2, we get i = Jinter/Jtot = 0.18, which is surprisingly high considering there is no p-type doping in the device. When combined with the Auger-limited r of 0.41 and c ≈ 3.4×10-4, we find a model value of IQE = 7.4% in good agreement with experiment. This leads to the model values for EQE plotted in Fig. 2(b) - also in good agreement with experiment. Finally, we address the high Jinter and consider a possible universal nature of the light-emission mechanism. Fig. 3(b) shows the tunneling probability T according to the Kane two-band model in the three materials, In0.53Ga0.47As, GaAs, and GaN, following our observation of a similar electroluminescence mechanism in GaN/AlN RTDs (due to strong polarization field of wurtzite structures) [8]. The expression is Tinter = (2/9)∙exp[(-2 ∙Ug 2 ∙me)/(2h∙P∙E)], where Ug is the bandgap energy, P is the valence-to-conduction-band momentum matrix element, and E is the electric field. Values for the highest calculated internal E fields for the InGaAs and GaN are also shown, indicating that Tinter in those structures approaches values of ~10-5. As shown, a GaAs RTD would require an internal field of ~6×105 V/cm, which is rarely realized in standard GaAs RTDs, perhaps explaining why there have been few if any reports of room-temperature electroluminescence in the GaAs devices. [1] E.R. Brown,et al., Appl. Phys. Lett., vol. 58, 2291, 1991. [5] S. Sze, Physics of Semiconductor Devices, 2nd Ed. 12.2.1 (Wiley, 1981). [2] M. Feiginov et al., Appl. Phys. Lett., 99, 233506, 2011. [6] L. Coldren, Diode Lasers and Photonic Integrated Circuits, (Wiley, 1995). [3] Y. Nishida et al., Nature Sci. Reports, 9, 18125, 2019. [7] E.O. Kane, J. of Appl. Phy 32, 83 (1961). [4] P. Fakhimi, et al., 2019 DRC Conference Digest. [8] T. Growden, et al., Nature Light: Science & Applications 7, 17150 (2018). [5] S. Sze, Physics of Semiconductor Devices, 2nd Ed. 12.2.1 (Wiley, 1981). [6] L. Coldren, Diode Lasers and Photonic Integrated Circuits, (Wiley, 1995). [7] E.O. Kane, J. of Appl. Phy 32, 83 (1961). [8] T. Growden, et al., Nature Light: Science & Applications 7, 17150 (2018). 

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4. Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations

   https://doi.org/10.1128/msystems.00588-22  

   Dufault-Thompson, Keith ; Nie, Chang ; Jian, Huahua ; Wang, Fengping ; Zhang, Ying ( August 2022 , mSystems)

   Mackelprang, Rachel (Ed.)

   ABSTRACT Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (Δ r G ′), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism’s ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism. 

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5. Enhanced Piezoelectric, Ferroelectric, and Electrostrictive Properties of Lead‐Free (1‐ x )BCZT‐( x )BCST Electroceramics with Energy Harvesting Capability

   https://doi.org/10.1002/smll.202300549  

   Baraskar, Bharat G. ; Kolekar, Yesappa D. ; Thombare, Balu. R. ; James, Ajit. R. ; Kambale, Rahul C. ; Ramana, C. V. ( May 2023 , Small)

   Next‐generation electronics and energy technologies can now be developed as a result of the design, discovery, and development of novel, environmental friendly lead (Pb)‐free ferroelectric materials with improved characteristics and performance. However, there have only been a few reports of such complex materials’ design with multi‐phase interfacial chemistry, which can facilitate enhanced properties and performance. In this context, herein, novel lead‐free piezoelectric materials (1‐x)Ba_0.95Ca_0.05Ti_0.95Zr_0.05O₃‐(x)Ba_0.95Ca_0.05Ti_0.95Sn_0.05O₃, are reported, which are represented as (1‐x)BCZT‐(x)BCST, with demonstrated excellent properties and energy harvesting performance. The (1‐x)BCZT‐(x)BCST materials are synthesized by high‐temperature solid‐state ceramic reaction method by varyingxin the full range (x= 0.00–1.00). In‐depth exploration research is performed on the structural, dielectric, ferroelectric, and electro‐mechanical properties of (1‐x)BCZT‐(x)BCST ceramics. The formation of perovskite structure for all ceramics without the presence of any impurity phases is confirmed by X‐ray diffraction (XRD) analyses, which also reveals that the Ca²⁺, Zr⁴⁺, and Sn⁴⁺are well dispersed within the BaTiO₃lattice. For all (1‐x)BCZT‐(x)BCST ceramics, thorough investigation of phase formation and phase‐stability using XRD, Rietveld refinement, Raman spectroscopy, high‐resolution transmission electron microscopy (HRTEM), and temperature‐dependent dielectric measurements provide conclusive evidence for the coexistence of orthorhombic + tetragonal (Amm2+P4mm) phases at room temperature. The steady transition ofAmm2crystal symmetry toP4mmcrystal symmetry with increasingxcontent is also demonstrated by Rietveld refinement data and related analyses. The phase transition temperatures, rhombohedral‐orthorhombic (T_R‐O), orthorhombic‐ tetragonal (T_O‐T), and tetragonal‐cubic (T_C), gradually shift toward lower temperature with increasingxcontent. For (1‐x)BCZT‐(x)BCST ceramics, significantly improved dielectric and ferroelectric properties are observed, including relatively high dielectric constantε_r≈ 1900–3300 (near room temperature),ε_r≈ 8800–12 900 (near Curie temperature), dielectric loss, tanδ≈ 0.01–0.02, remanent polarizationP_r≈ 9.4–14 µC cm⁻², coercive electric fieldE_c≈ 2.5–3.6 kV cm⁻¹. Further, high electric field‐induced strainS≈ 0.12–0.175%, piezoelectric charge coefficientd₃₃≈ 296–360 pC N⁻¹, converse piezoelectric coefficient ≈ 240–340 pm V⁻¹, planar electromechanical coupling coefficientk_p≈ 0.34–0.45, and electrostrictive coefficient (Q₃₃)_avg≈ 0.026–0.038 m⁴C⁻²are attained. Output performance with respect to mechanical energy demonstrates that the (0.6)BCZT‐(0.4)BCST composition (x= 0.4) displays better efficiency for generating electrical energy and, thus, the synthesized lead‐free piezoelectric (1‐x)BCZT‐(x)BCST samples are suitable for energy harvesting applications. The results and analyses point to the outcome that the (1‐x)BCZT‐(x)BCST ceramics as a potentially strong contender within the family of Pb‐free piezoelectric materials for future electronics and energy harvesting device technologies.

    

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