Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Functional catalysts by design for renewable fuels and chemicals production

Doctor of PhilosophyDepartment of Chemical EngineeringBin LiuIn the course of mitigating our dependence on fossil energy, it has become an urgent issue to develop unconventional and innovative technologies based on renewable energy utilization for fuels and chemicals production. Due to the lack of fundamental understanding of catalytic behaviors of the novel chemical compounds involved, the task to design and engineer effective catalytic systems is extremely challenging and time-consuming. One central challenge is that an intricate balance among catalytic reactivity, selectivity, durability, and affordability must be achieved pertinent to any successful design. In this dissertation, density functional theory (DFT), coupled with modeling techniques derived from DFT, is employed to gain insights into molecular interactions between elusive intermediates and targeted functional catalytic materials for novel electrochemical and heterogeneous catalytic processes. Two case studies, i.e., electroreduction of furfural and step-catalysis for cyclic ammonia production, will be discussed to demonstrate the capability and utility of DFT-based theoretical modeling toolkits and strategies. Transition metal cathodes such as silver, lead, and nickel were evaluated for furfuryl alcohol and 2-methylfuran production through detailed DFT modeling. Investigation of the molecular mechanisms revealed that two intermediates, mh6 and mh7 from mono-hydrogenation of furfural, are the key intermediates that will determine the product formation activities and selectivities. Nickel breaks the trends from other metals as DFT calculations suggested the 2-methylfuran formation pathway is most likely different from other cathodes. In this work, the Brønsted–Evans–Polanyi relationship, derived from DFT energy barrier calculations, has been found to be particularly reliable and computationally efficient for C-O bond activation trend predictions. To obtain the solvation effect on the adsorptions of biomass-derived compounds (e.g., furfural and glycerol), influence of explicit solvent was probed using periodic DFT calculations. The adsorptions of glycerol and its dehydrogenation intermediates at the water-platinum surface were understood via various water–adsorbate, water–water, and water–metal interactions. Interestingly, the bond-order-based scaling relationship established in solvent-free environment is found to remain valid based on our explicit solvent models. In the second case study, step-catalysis that relies on manganese’s ability to dissociate molecular nitrogen and as a nitrogen carrier emerges as an alternative route for ammonia production to the conventional Haber-Bosch process. In this collaborative project, DFT was used as the primary tool to produce the mechanistic understanding of NH3 formation via hydrogen reduction on various manganese nitride systems (e.g., Mn4N and Mn2N). Both nickel and iron dopants have the potential to facilitate NH3 formation. A broader consideration of a wide range of nitride configurations revealed a rather complex pattern. Materials screening strategies, supported by linear scaling relationships, suggested the linear correlations between NHx (x=0, 1, 2) species must be broken in the development of optimal step catalysis materials. These fundamental findings are expected to significantly guide and accelerate the experimental material design. Overall, molecular modeling based on DFT has clearly demonstrated its remarkable value beyond just a validation tool. More importantly, its unique predictive power should be prized as an avenue for scientific advance through the fundamental knowledge in novel catalysts design

TREM2 deficiency impairs the energy metabolism of Schwann cells and exacerbates peripheral neurological deficits

Abstract Triggering receptor expressed on myeloid cells-2 (TREM2) has been implicated in susceptibility to neurodegenerative disease. Schwann cells (SCs), the predominant glial cell type in the peripheral nervous system (PNS), play a crucial role in myelination, providing trophic support for neurons and nerve regeneration. However, the function of TREM2 in SCs has not been fully elucidated. Here, we found that TREM2 is expressed in SCs but not in neurons in the PNS. TREM2 deficiency leads to disruption of glycolytic flux and oxidative metabolism in SCs, impairing cell proliferation. The energy crisis caused by TREM2 deficiency triggers mitochondrial damage and autophagy by activating AMPK and impairing PI3K-AKT-mTOR signaling. Combined metabolomic analysis demonstrated that energic substrates and energy metabolic pathways were significantly impaired in TREM2-deficient SCs. Moreover, TREM2 deficiency impairs energy metabolism and axonal growth in sciatic nerve, accompanied by exacerbation of neurological deficits and suppression of nerve regeneration in a mouse model of acute motor axonal neuropathy. These results indicate that TREM2 is a critical regulator of energy metabolism in SCs and exerts neuroprotective effects on peripheral neuropathy. TREM2 deficiency impairs glycolysis and oxidative metabolism in Schwann cells, resulting in compromised cell proliferation. The energy crisis caused by TREM2 deficiency induces mitochondrial damage and autophagy by activating AMPK and impairing PI3K-AKT-mTOR signaling. Moreover, TREM2 deficiency disrupts the energy metabolism of the sciatic nerve and impairs support for axonal regeneration, accompanied by exacerbation of neurological deficits and suppression of nerve regeneration in a mouse model of acute motor axonal neuropathy (by FigDraw)

Mechanistic Insights Evaluating Ag, Pb, and Ni as Electrocatalysts for Furfural Reduction from First-Principles Methods

Electrochemical reduction of furfural (ECRFF) emerges as an efficient and sustainable means to obtain high-value chemicals and biofuels with the activity and product selectivity being sensitive to cathode materials. In this work, elementary steps describing furfuryl alcohol (FA) and 2-methylfuran (MF) production routes in ECRFF are studied by using periodic density functional theory on Ag, Pb, and Ni, as alternative cathode materials. The established Brønsted–Evans–Polanyi (BEP) relationship has been proven to be reliable to estimate energy barriers of C–O bond cleavage. The intrinsic characters of Ag, Pb, and Ni are then summarized in free energy diagrams to reflect the FA and MF production trends as future guidelines to evaluate ECRFF activity and selectivity on these metals. On all metal surfaces, at both terrace and stepped sites, the first C–H or O–H hydrogenation step, producing respective mh6 or mh7 intermediates, influences overall FA production. On Ag and Pb, pathways involving the mh6 intermediate are thermodynamically and kinetically favored, whereas on Ni, both mh6 and mh7 routes are competitive due to strong interactions between the furan ring and the substrate. In addition, these partially hydrogenated intermediates can also undergo C–O bond cleavage with reduced energy barriers (compared to direct C–O bond cleavage in furfural), which opens potential paths for parallel MF production. Conversion of FA into MF catalyzed by these metallic cathodes was considered as well, although the high C–O bond cleavage energy barrier is likely to hinder this process

Empirical Analysis of Subsidy Industrial Policy’s Effect on Export Innovation in the Chinese Manufacturing

The relatively low export innovation capacity is not conductive to the steady transformation and upgrading of China’s manufacturing industry, and it is necessary to implement suitable policies to enhance export innovation capacity. This study empirically analyzes the data of 827,471 manufacturing enterprises from 2000 till 2013 to investigate the impact of subsidy policy on export innovation. The overall results show that China’s subsidy policy has a significant crowding-out effect on export innovation, and subsidy for relatively small enterprises is more conducive to promoting export innovation; however, enterprises’ independent investment does not own much impact on export innovation. The econometric results made from perspectives of the sub-region and the industry reveal that subsidy policy is not conducive to export innovation, independent investment is not beneficial to export innovation, and export innovation ability is positively correlated with enterprise scale, but the influence coefficient shows obvious differences

Fe and Ni Dopants Facilitating Ammonia Synthesis on Mn₄N and Mechanistic Insights from First-Principles Methods

Cyclic step-catalysis enables intermittent, atmospheric ammonia production, and can be integrated with sustainable and renewable energy sources. By employing metal (e.g., Mn) nitride, a nitrogen carrier, the rate-limiting N₂ activation step is bypassed. In this work, molecular-level pathways, describing the reduction of Mn₄N by dissociatively adsorbed hydrogen, were investigated using periodic density functional theory (DFT). The established mechanism confirmed that Fe and Ni doped in the nitride sublayer and top layer can disturb local electronic structures and be exploited to tune the ammonia production activity. The strength of N–M (M = Mn, Fe, Ni) and H–M bonds both determine the overall reduction thermochemistry. DFT-based modeling further showed that the low concentration of Fe or Ni in the Mn₄N sublayer facilitates N diffusion by lowering the diffusion energy barrier. Also, these heteroatom dopant species, particularly Ni, decrease the reduction endergonicity, thanks to the strong hydrogen binding with the surface Ni dopant. The Brønsted–Evans–Polanyi relationship and linear scaling relationships have been developed to reveal ammonia evolution kinetic and energetic trends for a series of idealized Fe- and Ni-doped Mn₄N. Deviations from the linear scaling relationship have been observed for certain doped systems, indicating potentially more complex behaviors of metal nitrides and intriguing promises for greater ammonia synthesis materials design opportunities