Engineering topics
Wei, Hui
Publications and source records attributed to Wei, Hui.
Reconstruction of the complex angle-dependent photoionization transition dipole from a laser-dressed streaking experiment
We study the retrieval of the angular dependence of the photoionization transition dipole phase of an attosecond XUV pulse in order to reconstruct the whole photoelectron wave packet after the photoemission process. Using a one-electron model Ar atom, we show that the full electron wave packet can be reconstructed from IR-free photoelectron angular distributions and the streaking electron spectra in an IR-dressed XUV photoionization, with photoelectrons along the common polarization direction of the two pulses. The method relies on the validity of the strong-field approximation so it is valid only for higher energy photoelectrons. Here, we also point out that a single photoionization group time delay is not enough to represent a photoemission process; instead, a complete characterization of the electron wave packet requires the retrieval of the spectral phase over the whole bandwidth of the wave packet.
Role of the Transition Dipole Amplitude and Phase on the Generation of Odd and Even High-Order Harmonics in Crystals
Since the first observation of odd and even high-order harmonics generated from ZnO crystals in 2011, the dependence of the harmonic yields on the orientation of the laser polarization with respect to the crystal axis has never been properly interpreted. This failure has been traced to the lack of a correct account of the phase of the transition dipole moment between the valence band and the conduction band. Using a simple one-dimensional two-band model, here we demonstrate that the observed odd harmonics is directly related to the orientation dependence of the magnitude of the transition dipole, while even harmonics is directly related to the phase of the transition dipole. Our result points out the essential role of the complex transition dipole moment in understanding harmonic generation from solids that has long been overlooked so far.
Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1
A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses, suggesting translatability. In conclusion, the N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.
Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme
Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes peptides that tend to form amyloid fibrils remained unsolved. We used cryoEM to understand both the apo- and insulin-bound dimeric IDE states, revealing that IDE displays a large opening between the homologous ~55 kDa N- and C-terminal halves to allow selective substrate capture based on size and charge complementarity. We also used cryoEM, X-ray crystallography, SAXS, and HDX-MS to elucidate the molecular basis of how amyloidogenic peptides stabilize the disordered IDE catalytic cleft, thereby inducing selective degradation by substrate-assisted catalysis. Furthermore, our insulin-bound IDE structures explain how IDE processively degrades insulin by stochastically cutting either chain without breaking disulfide bonds. Together, our studies provide a mechanism for how IDE selectively degrades amyloidogenic peptides and offers structural insights for developing IDE-based therapies.
Kinetic Modelling and Experimental Studies for the Effects of Fe 2+ Ions on Xylan Hydrolysis with Dilute-Acid Pretreatment and Subsequent Enzymatic Hydrolysis
High-temperature (150-170 degrees C) pretreatment of lignocellulosic biomass with mineral acids is well established for xylan breakdown. Fe 2+ is known to be a cocatalyst of this process although kinetics of its action remains unknown. The present work addresses the effect of ferrous ion concentration on sugar yield and degradation product formation from corn stover for the entire two-step treatment, including the subsequent enzymatic cellulose hydrolysis. The feedstock was impregnated with 0.5% acid and 0.75 mM iron cocatalyst, which was found to be optimal in preliminary experiments. The detailed kinetic data of acid pretreatment, with and without iron, was satisfactorily modelled with a four-step linear sequence of first-order irreversible reactions accounting for the formation of xylooligomers, xylose and furfural as intermediates to provide the values of Arrhenius activation energy. Based on this kinetic modelling, Fe 2+ turned out to accelerate all four reactions, with a significant alteration of the last two steps, that is, xylose degradation. Consistent with this model, the greatest xylan conversion occurred at the highest severity tested under 170 ⁰C/30 min with 0.75 mM Fe 2+ , with a total of 8% xylan remaining in the pretreated solids, whereas the operational conditions leading to the highest xylose monomer yield, 63%, were milder, 150 degrees C with 0.75 mM Fe 2+ for 20 min. Furthermore, the subsequent enzymatic hydrolysis with the prior addition of 0.75 mM of iron(II) increased the glucose production to 56.3% from 46.3% in the control (iron-free acid). The detailed analysis indicated that conducting the process at lower temperatures yet long residence times benefits the yield of sugars. The above kinetic modelling results of Fe 2+ accelerating all four reactions are in line with our previous mechanistic research showing that the pretreatment likely targets multiple chemistries in plant cell wall polymer networks, including those represented by the C-O-C and C-H bonds in cellulose, resulting in enhanced sugar solubilization and digestibility.
Effect of transition dipole phase on high-order-harmonic generation in solid materials
High-order harmonic spectra from solid materials driven by single-color multicycle laser fields sometimes contain even harmonics. In this work we attribute the appearance of even harmonics to the nonzero transition dipole phase (TDP) when the solid system has broken symmetry. By calculating the harmonic efficiency from graphene and gapped graphene by using the semiconductor Bloch equations under the tight-binding approximation, we demonstrate the role of the TDP, which has been ignored for a long time. Furthermore, when the crystal has inversion symmetry, or reflection symmetry with the symmetry plane perpendicular to the laser polarization direction, the TDP can be neglected. Without such symmetry, however, the TDP will lead to the appearance of even harmonics. We further show that the TDP is sensitive to the crystal geometry. To extract the structure information from the harmonic spectra of a solid the TDP cannot be ignored.
Lignocellulose deconstruction in the biosphere
Microorganisms have evolved different and yet complementary mechanisms to degrade biomass in the biosphere. The chemical biology of lignocellulose deconstruction is a complex and intricate process that appears to vary in response to specific ecosystems. These microorganisms rely on simple to complex arrangements of glycoside hydrolases to conduct most of these polysaccharide depolymerization reactions and also, as discovered more recently, oxidative mechanisms via lytic polysaccharide monooxygenases or non-enzymatic Fenton reactions which are used to enhance deconstruction. It is now clear that these deconstruction mechanisms are often more efficient in the presence of the microorganisms. In general, a major fraction of the total plant biomass deconstruction in the biosphere results from the action of various microorganisms, primarily aerobic bacteria and fungi, as well as a variety of anaerobic bacteria. Beyond carbon recycling, specialized microorganisms interact with plants to manage nitrogen in the biosphere. Understanding the interplay between these organisms within or across ecosystems is crucial to further our grasp of chemical recycling in the biosphere and also enables optimization of the burgeoning plant-based bioeconomy.
Biomass Conversion
Biomass constitutes all the plant matter found on our planet, and is produced directly by photosynthesis, the fundamental engine of life on earth. It is the photosynthetic capability of plants to utilize carbon dioxide from the atmosphere that leads to its designation as a 'carbon neutral' fuel, meaning that it does not introduce new carbon into the atmosphere. This article discusses the life cycle assessments of biomass use and the magnitude of energy captured by photosynthesis in the form of biomass on the planet to appraise approaches to tap this energy to meet the ever-growing demand for energy.
Theory of retrieving orientation-resolved molecular information using time-domain rotational coherence spectroscopy
We provide a unified theoretical framework for recently emerging experiments that retrieve fixed-in-space molecular information through time-domain rotational coherence spectroscopy. Unlike a previous approach by Makhija et al. (V. Makhija et al., arXiv:1611.06476), our method can be applied to the retrieval of both real-valued (e.g., ionization yield) and complex-valued (e.g., induced dipole moment) molecular response information. It is also a direct retrieval method without using iterations. We also demonstrate that experimental parameters, such as the fluence of the aligning laser pulse and the rotational temperature of the molecular ensemble, can be quite accurately determined using a statistical method.
Towards an Understanding of Enhanced Biomass Digestibility by In Planta Expression of a Family 5 Glycoside Hydrolase
In planta expression of a thermophilic endoglucanase (AcCel5A) reduces recalcitrance by creating voids and other irregularities in cell walls of Arabidopsis thaliana that increase enzyme accessibility without negative impacts on plant growth or cell wall composition. Furthermore, our results suggest that cellulose β-1–4 linkages can be cut sparingly in the assembling wall and that these minimal changes, made at the proper time, have an impact on plant cell wall recalcitrance without negative effects on overall plant development.
Phase-retrieval algorithm for the characterization of broadband single attosecond pulses
Recent progress in high-order harmonic generation with few-cycle mid-infrared wavelength lasers has pushed light pulses into the water-window region and beyond. These pulses have the bandwidth to support single attosecond pulses down to a few tens of attoseconds. However, the present available techniques for attosecond pulse measurement are not applicable to such pulses. Here we report a phase-retrieval method using the standard photoelectron streaking technique where an attosecond pulse is converted into its electron replica through photoionization of atoms in the presence of a time-delayed infrared laser. The iterative algorithm allows accurate reconstruction of the spectral phase of light pulses, from the extreme-ultraviolet (XUV) to soft x-rays, with pulse durations from hundreds down to a few tens of attoseconds. At the same time, the streaking laser fields, including short pulses that span a few octaves, can also be accurately retrieved. Furthermore, such well-characterized single attosecond pulses in the XUV to the soft-x-ray region are required for time-resolved probing of inner-shell electronic dynamics of matter at their own timescale of a few tens of attoseconds.
Fatty alcohol production in Lipomyces starkeyi and Yarrowia lipolytica
Not Available
Directed plant cell-wall accumulation of iron: Embedding co-catalyst for efficient biomass conversion
Plant lignocellulosic biomass is an abundant, renewable feedstock for the production of biobased fuels and chemicals. Previously, we showed that iron can act as a co-catalyst to improve the deconstruction of lignocellulosic biomass. However, directly adding iron catalysts into biomass prior to pretreatment is diffusion limited, and increases the cost of biorefinery operations. Recently, we developed a new strategy for expressing iron-storage protein ferritin intracellularly to accumulate iron as a catalyst for the downstream deconstruction of lignocellulosic biomass. In this study, we extend this approach by fusing the heterologous ferritin gene with a signal peptide for secretion into Arabidopsis cell walls (referred to here as FerEX). The transgenic Arabidopsis plants. FerEX. accumulated iron under both normal and iron-fertilized growth conditions; under the latter (iron-fertilized) condition, FerEX transgenic plants showed an increase in plant height and dry weight by 12 and 18 %, respectively, compared with the empty vector control plants. The SDS- and native-PAGE separation of cell-wall protein extracts followed by Western blot analyses confirmed the extracellular expression of ferritin in FerEX plants. Meanwhile, Perls' Prussian blue staining and X-ray fluorescence microscopy (XFM) maps revealed iron depositions in both the secondary and compound middle lamellae cell-wall layers, as well as in some of the corner compound middle lamella in FerEX. Remarkably, their harvested biomasses showed enhanced pretreatability and digestibility, releasing, respectively, 21 % more glucose and 34 % more xylose than the empty vector control plants. These values are significantly higher than those of our recently obtained ferritin intracellularly expressed plants. This study demonstrated that extracellular expression of ferritin in Arabidopsis can produce plants with increased growth and iron accumulation, and reduced thermal and enzymatic recalcitrance. Here, the results are attributed to the intimate colocation of the iron co-catalyst and the cellulose and hemicellulose within the plant cell-wall region, supporting the genetic modification strategy for incorporating conversion catalysts into energy crops prior to harvesting or processing at the biorefinery.
Comparison of nitrogen depletion and repletion on lipid production in yeast and fungal species
Although it is well known that low nitrogen stimulates lipid accumulation, especially for algae and some oleaginous yeast, few studies have been conducted in fungal species, especially on the impact of different nitrogen deficiency strategies. In this study, we use two promising consolidated bioprocessing (CBP) candidates to examine the impact of two nitrogen deficiency strategies on lipid production, which are the extensively investigated oleaginous yeast Yarrowia lipolytica , and the commercial cellulase producer Trichoderma reesei . We first utilized bioinformatics approaches to reconstruct the fatty acid metabolic pathway and demonstrated the presence of a triacylglycerol (TAG) biosynthesis pathway in Trichoderma reesei . We then examined the lipid production of Trichoderma reesei and Y. lipomyces in different media using two nitrogen deficiency strategies of nitrogen natural repletion and nitrogen depletion through centrifugation. Our results demonstrated that nitrogen depletion was better than nitrogen repletion with about 30% lipid increase for Trichoderma reesei and Y. lipomyces , and could be an option to improve lipid production in both oleaginous yeast and filamentous fungal species. The resulting distinctive lipid composition profiles indicated that the impacts of nitrogen depletion on yeast were different from those for fungal species. Under three types of C/N ratio conditions, C16 and C18 fatty acids were the predominant forms of lipids for both Trichoderma reesei and Y. lipolytica . In addition, while the overall fatty acid methyl ester (FAME) profiles of Trichoderma reesei were similar, the overall FAME profiles of Y. lipolytica observed a shift. The fatty acid metabolic pathway reconstructed in this work supports previous reports of lipid production in T. reesei , and provides a pathway for future omics studies and metabolic engineering efforts. Further investigation to identify the genetic targets responsible for the effect of nitrogen depletion on lipid production improvement will facilitate strain engineering to boost lipid production under more optimal conditions for productivity than those required for nitrogen depletion.
Prospect for Developing a Consolidated Bioprocessing (CBP) Strain Using Xylan as the Substrate: the Case Study of Yarrowia lipolytica
To achieve the goal of developing a direct microbial sugar conversion platform for the production of lipids and drop-in fuels from cellulosic biomass substrate, Yarrowia lipolytica was used to investigate its potential for being developed as CBP strain by expressing cellulase and xylanase enzymes. Y. lipolytica is known to accumulate lipids intracellularly and is capable of metabolizing glucose and xylose to produce lipids; however, due to the lack of the biomass degrading enzymes, it cannot directly utilize lignocellulosic substrates as carbon sources. While research is continuing on the development of a Y. lipolytica strain able to degrade cellulose, in this study, we present successful expression of several xylanases in Y. lipolytica. To the best of our knowledge, this is the first study introducing heterologous hemicellulose genes into the genome of Y. lipolytica. SDS-PAGE and western blotting analysis showed that the endo-xylanase gene XynII and exo-xylosidase gene XlnD were successfully expressed and secreted, and the expressed xylanases were likely either not or sparsely glycosylated, which is advantageous for expression of heterologous proteins from any species. Enzymatic activity tests further demonstrated active expression of XynII and XlnD in Y. lipolytica. Furthermore, synergistic action on converting xylan to xylose was observed when XlnD worked in concert with XynII. XlnD was able to work on the xylo-oligomers generated by XynII, enhancing the xylan conversion to monomeric xylose. The successful expression of these xylanases in Yarrowia further advances us towards our goal to develop a direct microbial conversion process using this organism. and xylose to produce lipids; however, due to the lack of the biomass degrading enzymes, it cannot directly utilize lignocellulosic substrates as carbon sources. While research is continuing on the development of a Y. lipolytica strain able to degrade cellulose, in this study, we present successful expression of several xylanases in Y. lipolytica.