Chemical and Biomolecular Engineering Research Works

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RNA Interference mediated knockdown of genes in order to increase protein production using the baculovirus expression system
(Springer Nature, 2006-10-10) Hebert, Colin; Kim, Eun Jeong; Kramer, Shannon F; Valdes, James J; Bentley, William E
Microbial nar-GFP cell sensors reveal oxygen limitations in highly agitated and aerated laboratory-scale fermentors
(Springer Nature, 2009-01-15) Garcia, Jose R; Cha, Hyung J; Rao, Govind; Marten, Mark R; Bentley, William E
Small-scale microbial fermentations are often assumed to be homogeneous, and oxygen limitation due to inadequate micromixing is often overlooked as a potential problem. To assess the relative degree of micromixing, and hence propensity for oxygen limitation, a new cellular oxygen sensor has been developed. The oxygen responsive E. coli nitrate reductase (nar) promoter was used to construct an oxygen reporter plasmid (pNar-GFPuv) which allows cell-based reporting of oxygen limitation. Because there are greater than 109 cells in a fermentor, one can outfit a vessel with more than 109 sensors. Our concept was tested in high density, lab-scale (5 L), fed-batch, E. coli fermentations operated with varied mixing efficiency – one verses four impellers. In both cases, bioreactors were maintained identically at greater than 80% dissolved oxygen (DO) during batch phase and at approximately 20% DO during fed-batch phase. Trends for glucose consumption, biomass and DO showed nearly identical behavior. However, fermentations with only one impeller showed significantly higher GFPuv expression than those with four, indicating a higher degree of fluid segregation sufficient for cellular oxygen deprivation. As the characteristic time for GFPuv expression (approx 90 min.) is much larger than that for mixing (approx 10 s), increased specific fluorescence represents an averaged effect of oxygen limitation over time and by natural extension, over space. Thus, the pNar-GFPuv plasmid enabled bioreactor-wide oxygen sensing in that bacterial cells served as individual recirculating sensors integrating their responses over space and time. We envision cell-based oxygen sensors may find utility in a wide variety of bioprocessing applications.
Individual vs. combinatorial effect of elevated CO2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: Comparing the early molecular response using time-series transcriptomic and metabolomic analyses
(2010-12-29) Kanani, Harin; Dutta, Bhaskar; Klapa, Maria I
Background: In this study, we investigated the individual and combinatorial effect of elevated CO2 conditions and salinity stress on the dynamics of both the transcriptional and metabolic physiology of Arabidopsis thaliana liquid hydroponic cultures over the first 30 hours of continuous treatment. Both perturbations are of particular interest in plant and agro-biotechnological applications. Moreover, within the timeframe of this experiment, they are expected to affect plant growth to opposite directions. Thus, a major objective was to investigate whether this expected “divergence” was valid for the individual perturbations and to study how it is manifested under the combined stress at two molecular levels of cellular function, using high-throughput analyses. Results: We observed that a) high salinity has stronger effect than elevated CO2 at both the transcriptional and metabolic levels, b) the transcriptional responses to the salinity and combined stresses exhibit strong similarity, implying a robust transcriptional machinery acting to the salinity stress independent of the co-occurrence of elevated CO2 , c) the combinatorial effect of the two perturbations on the metabolic physiology is milder than of the salinity stress alone. Metabolomic analysis suggested that the beneficial role of elevated CO2 on salt-stressed plants within the timeframe of this study should be attributed to the provided additional resources; these allow the plants to respond to high salinity without having to forfeit other major metabolic functions, and d) 9 h-12 h and 24 h of treatment coincide with significant changes in the metabolic physiology under any of the investigated stresses. Significant differences between the acute and longer term responses were observed at both molecular levels. Conclusions: This study contributes large-scale dynamic omic data from two levels of cellular function for a plant system under various stresses. It provides an additional example of the power of integrated omic analyses for the comprehensive study of the molecular physiology of complex biological systems. Moreover, taking into consideration the particular interest of the two investigated perturbations in plant biotechnology, enhanced understanding of the molecular physiology of the plants under these conditions could lead to the design of novel metabolic engineering strategies to increase the resistance of commercial crops to salinity stress.
A core microbiome associated with the peritoneal tumors of pseudomyxoma peritonei
(Springer Nature, 2013-07-12) Gilbreath, Jeremy J; Semino-Mora, Cristina; Friedline, Christopher J; Liu, Hui; Bodi, Kip L; McAvoy, Thomas J; Francis, Jennifer; Nieroda, Carol; Sardi, Armando; Dubois, Andre; Lazinski, David W; Camilli, Andrew; Testerman, Traci L; Merrell, D Scott
Pseudomyxoma peritonei (PMP) is a malignancy characterized by dissemination of mucus-secreting cells throughout the peritoneum. This disease is associated with significant morbidity and mortality and despite effective treatment options for early-stage disease, patients with PMP often relapse. Thus, there is a need for additional treatment options to reduce relapse rate and increase long-term survival. A previous study identified the presence of both typed and non-culturable bacteria associated with PMP tissue and determined that increased bacterial density was associated with more severe disease. These findings highlighted the possible role for bacteria in PMP disease. To more clearly define the bacterial communities associated with PMP disease, we employed a sequenced-based analysis to profile the bacterial populations found in PMP tumor and mucin tissue in 11 patients. Sequencing data were confirmed by in situ hybridization at multiple taxonomic depths and by culturing. A pilot clinical study was initiated to determine whether the addition of antibiotic therapy affected PMP patient outcome. We determined that the types of bacteria present are highly conserved in all PMP patients; the dominant phyla are the Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. A core set of taxon-specific sequences were found in all 11 patients; many of these sequences were classified into taxonomic groups that also contain known human pathogens. In situ hybridization directly confirmed the presence of bacteria in PMP at multiple taxonomic depths and supported our sequence-based analysis. Furthermore, culturing of PMP tissue samples allowed us to isolate 11 different bacterial strains from eight independent patients, and in vitro analysis of subset of these isolates suggests that at least some of these strains may interact with the PMP-associated mucin MUC2. Finally, we provide evidence suggesting that targeting these bacteria with antibiotic treatment may increase the survival of PMP patients. Using 16S amplicon-based sequencing, direct in situ hybridization analysis and culturing methods, we have identified numerous bacterial taxa that are consistently present in all PMP patients tested. Combined with data from a pilot clinical study, these data support the hypothesis that adding antimicrobials to the standard PMP treatment could improve PMP patient survival.
Dynamic Modeling for the Design and Cyclic Operation of an Atomic Layer Deposition (ALD) Reactor
(MDPI, 2013-08-19) Travis, Curtisha D.; Adomaitis, Raymond A.
A laboratory-scale atomic layer deposition (ALD) reactor system model is derived for alumina deposition using trimethylaluminum and water as precursors. Model components describing the precursor thermophysical properties, reactor-scale gas-phase dynamics and surface reaction kinetics derived from absolute reaction rate theory are integrated to simulate the complete reactor system. Limit-cycle solutions defining continuous cyclic ALD reactor operation are computed with a fixed point algorithm based on collocation discretization in time, resulting in an unambiguous definition of film growth-per-cycle (𝑔𝑝𝑐). A key finding of this study is that unintended chemical vapor deposition conditions can mask regions of operation that would otherwise correspond to ideal saturating ALD operation. The use of the simulator for assisting in process design decisions is presented.
Experimental evidence and isotopomer analysis of mixotrophic glucose metabolism in the marine diatom Phaeodactylum tricornutum
(Springer Nature, 2013-11-14) Zheng, Yuting; Quinn, Andrew H; Sriram, Ganesh
Heterotrophic fermentation using simple sugars such as glucose is an established and cost-effective method for synthesizing bioproducts from bacteria, yeast and algae. Organisms incapable of metabolizing glucose have limited applications as cell factories, often despite many other advantageous characteristics. Therefore, there is a clear need to investigate glucose metabolism in potential cell factories. One such organism, with a unique metabolic network and a propensity to synthesize highly reduced compounds as a large fraction of its biomass, is the marine diatom Phaeodactylum tricornutum (Pt). Although Pt has been engineered to metabolize glucose, conflicting lines of evidence leave it unresolved whether Pt can natively consume glucose. Isotope labeling experiments in which Pt was mixotrophically grown under light on 100% U-13C glucose and naturally abundant (~99% 12C) dissolved inorganic carbon resulted in proteinogenic amino acids with an average 13C-enrichment of 88%, thus providing convincing evidence of glucose uptake and metabolism. The dissolved inorganic carbon was largely incorporated through anaplerotic rather than photosynthetic fixation. Furthermore, an isotope labeling experiment utilizing 1-13C glucose and subsequent metabolic pathway analysis indicated that (i) the alternative Entner-Doudoroff and Phosphoketolase glycolytic pathways are active during glucose metabolism, and (ii) during mixotrophic growth, serine and glycine are largely synthesized from glyoxylate through photorespiratory reactions rather than from 3-phosphoglycerate. We validated the latter result for mixotrophic growth on glycerol by performing a 2-13C glycerol isotope labeling experiment. Additionally, gene expression assays showed that known, native glucose transporters in Pt are largely insensitive to glucose or light, whereas the gene encoding cytosolic fructose bisphosphate aldolase 3, an important glycolytic enzyme, is overexpressed in light but insensitive to glucose. We have shown that Pt can use glucose as a primary carbon source when grown in light, but cannot use glucose to sustain growth in the dark. We further analyzed the metabolic mechanisms underlying the mixotrophic metabolism of glucose and found isotopic evidence for unusual pathways active in Pt. These insights expand the envelope of Pt cultivation methods using organic substrates. We anticipate that they will guide further engineering of Pt towards sustainable production of fuels, pharmaceuticals, and platform chemicals.
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network
(Springer Nature, 2013-11-14) Misra, Ashish; Sriram, Ganesh
Gene regulatory networks (GRNs) are models of molecule-gene interactions instrumental in the coordination of gene expression. Transcription factor (TF)-GRNs are an important subset of GRNs that characterize gene expression as the effect of TFs acting on their target genes. Although such networks can qualitatively summarize TF-gene interactions, it is highly desirable to quantitatively determine the strengths of the interactions in a TF-GRN as well as the magnitudes of TF activities. To our knowledge, such analysis is rare in plant biology. A computational methodology developed for this purpose is network component analysis (NCA), which has been used for studying large-scale microbial TF-GRNs to obtain nontrivial, mechanistic insights. In this work, we employed NCA to quantitatively analyze a plant TF-GRN important in floral development using available regulatory information from AGRIS, by processing previously reported gene expression data from four shoot apical meristem cell types. The NCA model satisfactorily accounted for gene expression measurements in a TF-GRN of seven TFs (LFY, AG, SEPALLATA3 [SEP3], AP2, AGL15, HY5 and AP3/PI) and 55 genes. NCA found strong interactions between certain TF-gene pairs including LFY → MYB17, AG → CRC, AP2 → RD20, AGL15 → RAV2 and HY5 → HLH1, and the direction of the interaction (activation or repression) for some AGL15 targets for which this information was not previously available. The activity trends of four TFs - LFY, AG, HY5 and AP3/PI as deduced by NCA correlated well with the changes in expression levels of the genes encoding these TFs across all four cell types; such a correlation was not observed for SEP3, AP2 and AGL15. For the first time, we have reported the use of NCA to quantitatively analyze a plant TF-GRN important in floral development for obtaining nontrivial information about connectivity strengths between TFs and their target genes as well as TF activity. However, since NCA relies on documented connectivity information about the underlying TF-GRN, it is currently limited in its application to larger plant networks because of the lack of documented connectivities. In the future, the identification of interactions between plant TFs and their target genes on a genome scale would allow the use of NCA to provide quantitative regulatory information about plant TF-GRNs, leading to improved insights on cellular regulatory programs.
Microvessel rupture induced by high-intensity therapeutic ultrasound—a study of parameter sensitivity in a simple in vivo model
(Springer Nature, 2017-03-02) Kim, Yeonho; Nabili, Marjan; Acharya, Priyanka; Lopez, Asis; Myers, Matthew R.
Safety analyses of transcranial therapeutic ultrasound procedures require knowledge of the dependence of the rupture probability and rupture time upon sonication parameters. As previous vessel-rupture studies have concentrated on a specific set of exposure conditions, there is a need for more comprehensive parametric studies. Probability of rupture and rupture times were measured by exposing the large blood vessel of a live earthworm to high-intensity focused ultrasound pulse trains of various characteristics. Pressures generated by the ultrasound transducers were estimated through numerical solutions to the KZK (Khokhlov-Zabolotskaya-Kuznetsov) equation. Three ultrasound frequencies (1.1, 2.5, and 3.3 MHz) were considered, as were three pulse repetition frequencies (1, 3, and 10 Hz), and two duty factors (0.0001, 0.001). The pressures produced ranged from 4 to 18 MPa. Exposures of up to 10 min in duration were employed. Trials were repeated an average of 11 times. No trends as a function of pulse repetition rate were identifiable, for either probability of rupture or rupture time. Rupture time was found to be a strong function of duty factor at the lower pressures; at 1.1 MHz the rupture time was an order of magnitude lower for the 0.001 duty factor than the 0.0001. At moderate pressures, the difference between the duty factors was less, and there was essentially no difference between duty factors at the highest pressure. Probability of rupture was not found to be a strong function of duty factor. Rupture thresholds were about 4 MPa for the 1.1 MHz frequency, 7 MPa at 3.3 MHz, and 11 MPa for the 2.5 MHz, though the pressure value at 2.5 MHz frequency will likely be reduced when steep-angle corrections are accounted for in the KZK model used to estimate pressures. Mechanical index provided a better collapse of the data (less separation of the curves pertaining to the different frequencies) than peak negative pressure, for both probability of rupture and rupture time. The results provide a database with which investigations in more complex animal models can be compared, potentially establishing trends by which bioeffects in human vessels can be estimated.
Shape-Changing Tubular Hydrogels
(MDPI, 2018-02-22) Raghavan, Srinivasa R.; Fernandes, Neville J.; Cipriano, Bani H.
We describe the creation of hollow tubular hydrogels in which different zones along the length of the tube are composed of different gels. Our method to create these gels is adapted from a technique developed previously in our lab for creating solid hybrid hydrogels. The zones of our tubular gel are covalently bonded at the interfaces; as a result, these interfaces are highly robust. Consequently, the tube can be picked up, manipulated and stretched without suffering any damage. The hollow nature of these gels allows them to respond 2–30-fold faster to external stimuli compared to a solid gel of identical composition. We study the case where one zone of the hybrid tube is responsive to pH (due to the incorporation of an ionic monomer) while the other zones are not. Initially, the entire tube has the same diameter, but when pH is changed, the diameter of the pH-responsive zone alone increases (i.e., this zone bulges outward) while the other zones maintain their original diameter. The net result is a drastic change in the shape of the gel, and this can be reversed by reverting the pH to its original value. Similar localized changes in gel shape are shown for two other stimuli: temperature and solvent composition. Our study points the way for researchers to design three-dimensional soft objects that can reversibly change their shape in response to stimuli.
Fluorinated solid electrolyte interphase enables highly reversible solid-state Li metal battery
(AAAS, 2018-12-21) Fan, Xiulin; Ji, Xiao; Han, Fudong; Yue, Jie; Chen, Ji; Chen, Long; Deng, Tao; Jiang, Jianjun; Wang, Chunsheng
Solid-state electrolytes (SSEs) are receiving great interest because their high mechanical strength and transference number could potentially suppress Li dendrites and their high electrochemical stability allows the use of high-voltage cathodes, which enhances the energy density and safety of batteries. However, the much lower critical current density and easier Li dendrite propagation in SSEs than in nonaqueous liquid electrolytes hindered their possible applications. Herein, we successfully suppressed Li dendrite growth in SSEs by in situ forming an LiF-rich solid electrolyte interphase (SEI) between the SSEs and the Li metal. The LiF-rich SEI successfully suppresses the penetration of Li dendrites into SSEs, while the low electronic conductivity and the intrinsic electrochemical stability of LiF block side reactions between the SSEs and Li. The LiF-rich SEI enhances the room temperature critical current density of Li3PS4 to a record-high value of >2 mA cm−2. Moreover, the Li plating/stripping Coulombic efficiency was escalated from 88% of pristine Li3PS4 to more than 98% for LiF-coated Li3PS4. In situ formation of electronic insulating LiF-rich SEI provides an effective way to prevent Li dendrites in the SSEs, constituting a substantial leap toward the practical applications of next-generation high-energy solid-state Li metal batteries.
Turnover versus Treadmilling in Actin Network Assembly and Remodeling
(2019) Ni, Qin; Papoian, Garegin
Actin networks are highly dynamic cytoskeletal structures that continuously undergo structural remodeling. One prominent way to probe these processes is via Fluorescence Recovery After Photobleaching (FRAP), which can be used to estimate the rate of turnover for filamentous actin monomers. It is thought that head-to-tail treadmilling and de novo filament nucleation constitute two primary mechanisms underlying turnover kinetics. More generally, these self-assembly activities are responsible for many important cellular functions such as force generation, cellular shape dynamics and cellular motility. In what relative proportions filament treadmilling and \textit{de novo} filament nucleation contribute to actin network turnover is still not fully understood. We used an advanced stochastic reaction-diffusion model in three dimensions, MEDYAN, to study turnover dynamics of actin networks containing Arp2/3, formin and capping protein at experimentally meaningful length- and timescales. Our results reveal that, most commonly, treadmilling of older filaments is the main contributor to actin network turnover. On the other hand, although turnover and treadmilling are often used interchangeably, we show clear instances where this assumption would not be justified, for example, finding that rapid turnover is accompanied by slow treadmilling in highly dendritic Arp2/3 networks.
Effect of a Cationic Surfactant on Microemulsion Globules and Drug Release from Hydrogel Contact Lenses
(MDPI, 2019-06-06) Torres-Luna, Cesar; Hu, Naiping; Koolivand, Abdollah; Fan, Xin; Zhu, Yuli; Domszy, Roman; Yang, Jeff; Yang, Arthur; Wang, Nam Sun
The present study evaluates the in vitro release of diclofenac sodium (DFNa) from contact lenses based on poly-2-hydroxyethyl methacrylate (pHEMA) hydrogels containing an embedded microemulsion to extend release duration. The oil (ethyl butyrate)-in-water microemulsion systems are prepared with two non-ionic surfactants, Brij 97 or Tween 80, together with a long-alkyl chain cationic surfactant, cetalkonium chloride (CKC). Without CKC, Brij 97 or Tween 80-based microemulsions showed average droplet sizes of 12 nm and 18 nm, respectively. The addition of CKC decreased the average droplet sizes to 2–5 nm for both non-ionic surfactants. Such significant reduction in the average droplet size corresponds to an increase in the DFNa release duration as revealed by the in vitro experiments. Contact lens characterization showed that important properties such as optical transparency and water content of Brij 97-based contact lenses with cationic microemulsions was excellent. However, the optical transparency of the corresponding Tween 80 based contact lenses was unsatisfactory. The results indicate that cationic microemulsion-laden contact lenses can benefit from combinatory effects of microemulsions and cationic surfactant at low CKC weight percentage, e.g., with the release of 70% of the drug in 45, 10, and 7 h for B97-CKC-0.45%, CKC-0.45%, and control lenses, respectively. However, the microemulsion effect on extending DFNa release became negligible at the highest CKC weight percentage (1.8%).
Formation of Drug-Participating Catanionic Aggregates for Extended Delivery of Non-Steroidal Anti-Inflammatory Drugs from Contact Lenses
(MDPI, 2019-10-10) Torres-Luna, Cesar; Koolivand, Abdollah; Fan, Xin; Agrawal, Niti R.; Hu, Naiping; Zhu, Yuli; Domszy, Roman; Briber, Robert M.; Wang, Nam Sun; Yang, Arthur
This paper focuses on extending drug release duration from contact lenses by incorporating catanionic aggregates. The aggregates consist of a long-chain cationic surfactant, i.e., cetalkonium chloride (CKC), and an oppositely charged anti-inflammatory amphiphilic drug. We studied three non-steroidal anti-inflammatory (NSAID) drugs with different octanol–water partition coefficients; diclofenac sodium (DFNa), flurbiprofen sodium (FBNa), and naproxen sodium (NPNa). Confirmation of catanionic aggregate formation in solution was determined by steady and dynamic shear rheology measurements. We observed the increased viscosity, shear thinning, and viscoelastic behavior characteristic of wormlike micelles; the rheological data are reasonably well described using a Maxwellian fluid model with a single relaxation time. In vitro release experiments demonstrated that the extension in the drug release time is dependent on the ability of a drug to form viscoelastic catanionic aggregates. Such aggregates retard the diffusive transport of drug molecules from the contact lenses. Our study revealed that the release kinetics depends on the CKC concentration and the alkyl chain length of the cationic surfactant. We demonstrated that more hydrophobic drugs such as diclofenac sodium show a more extended release than less hydrophobic drugs such as naproxen sodium.
Two-Dimensional Zeolite Materials: Structural and Acidity Properties
(MDPI, 2020-04-12) Schulman, Emily; Wu, Wei; Liu, Dongxia
Zeolites are generally defined as three-dimensional (3D) crystalline microporous aluminosilicates in which silicon (Si4+) and aluminum (Al3+) are coordinated tetrahedrally with oxygen to form large negative lattices and consequent Brønsted acidity. Two-dimensional (2D) zeolite nanosheets with single-unit-cell or near single-unit-cell thickness (~2–3 nm) represent an emerging type of zeolite material. The extremely thin slices of crystals in 2D zeolites produce high external surface areas (up to 50% of total surface area compared to ~2% in micron-sized 3D zeolite) and expose most of their active sites on external surfaces, enabling beneficial effects for the adsorption and reaction performance for processing bulky molecules. This review summarizes the structural properties of 2D layered precursors and 2D zeolite derivatives, as well as the acidity properties of 2D zeolite derivative structures, especially in connection to their 3D conventional zeolite analogues’ structural and compositional properties. The timeline of the synthesis and recognition of 2D zeolites, as well as the structure and composition properties of each 2D zeolite, are discussed initially. The qualitative and quantitative measurements on the acid site type, strength, and accessibility of 2D zeolites are then presented. Future research and development directions to advance understanding of 2D zeolite materials are also discussed.
Motion of an Elastic Capsule in a Trapezoidal Microchannel under Stokes Flow Conditions
(MDPI, 2020-05-17) Koolivand, Abdollah; Dimitrakopoulos, Panagiotis
Even though the research interest in the last decades has been mainly focused on the capsule dynamics in cylindrical or rectangular ducts, channels with asymmetric cross-sections may also be desirable especially for capsule migration and sorting. Therefore, in the present study we investigate computationally the motion of an elastic spherical capsule in an isosceles trapezoidal microchannel at low and moderate flow rates under the Stokes regime. The steady-state capsule location is quite close to the location where the single-phase velocity of the surrounding fluid is maximized. Owing to the asymmetry of the trapezoidal channel, the capsule’s steady-state shape is asymmetric while its membrane slowly tank-treads. In addition, our investigation reveals that tall trapezoidal channels with low base ratios produce significant off-center migration for large capsules compared to that for smaller capsules for a given channel length. Thus, we propose a microdevice for the sorting of artificial and physiological capsules based on their size, by utilizing tall trapezoidal microchannels with low base ratios. The proposed sorting microdevice can be readily produced via glass fabrication or as a microfluidic device via micromilling, while the required flow conditions do not cause membrane rupture.
Effects of Protein Unfolding on Aggregation and Gelation in Lysozyme Solutions
(MDPI, 2020-09-02) Nikfarjam, Shakiba; Jouravleva, Elena V.; Anisimov, Mikhail A.; Woehl, Taylor J.
In this work, we investigate the role of folding/unfolding equilibrium in protein aggregation and formation of a gel network. Near the neutral pH and at a low buffer ionic strength, the formation of the gel network around unfolding conditions prevents investigations of protein aggregation. In this study, by deploying the fact that in lysozyme solutions the time of folding/unfolding is much shorter than the characteristic time of gelation, we have prevented gelation by rapidly heating the solution up to the unfolding temperature (~80 °C) for a short time (~30 min.) followed by fast cooling to the room temperature. Dynamic light scattering measurements show that if the gelation is prevented, nanosized irreversible aggregates (about 10–15 nm radius) form over a time scale of 10 days. These small aggregates persist and aggregate further into larger aggregates over several weeks. If gelation is not prevented, the nanosized aggregates become the building blocks for the gel network and define its mesh length scale. These results support our previously published conclusion on the nature of mesoscopic aggregates commonly observed in solutions of lysozyme, namely that aggregates do not form from lysozyme monomers in their native folded state. Only with the emergence of a small fraction of unfolded proteins molecules will the aggregates start to appear and grow.
Capsule Migration and Deformation in a Converging Micro-Capillary
(MDPI, 2021-03-03) Wang, Yiyang; Dimitrakopoulos, Panagiotis
The lateral migration of elastic capsules towards a microchannel centerline plays a major role in industrial and physiological processes. Via our computational investigation, we show that a constriction connecting two straight microchannels facilitates the lateral capsule migration considerably, which is relatively slow in straight channels. Our work reveals that the significant cross-streamline migration inside the constriction is dominated by the strong hydrodynamic forces due to the capsule size. However, in the downstream straight channel, the increased interfacial deformation at higher capillary numbers or a lower viscosity ratio and lower membrane hardness results in increased lateral cross-streamline migration. Thus, our work highlights the different migration mechanisms occurring over curved and straight streamlines.
NetFlow: A tool for isolating carbon flows in genome-scale metabolic networks
(Elsevier, 2021-06) Mack, Sean G.; Sriram, Ganesh
Genome-scale stoichiometric models (GSMs) have been widely utilized to predict and understand cellular metabolism. GSMs and the flux predictions resulting from them have proven indispensable to fields ranging from metabolic engineering to human disease. Nonetheless, it is challenging to parse these flux predictions due to the inherent size and complexity of the GSMs. Several previous approaches have reduced this complexity by identifying key pathways contained within the genome-scale flux predictions. However, a reduction method that overlays carbon atom transitions on stoichiometry and flux predictions is lacking. To fill this gap, we developed NetFlow, an algorithm that leverages genome-scale carbon mapping to extract and quantitatively distinguish biologically relevant metabolic pathways from a given genome-scale flux prediction. NetFlow extends prior approaches by utilizing both full carbon mapping and context-specific flux predictions. Thus, NetFlow is uniquely able to quantitatively distinguish between biologically relevant pathways of carbon flow within the given flux map. NetFlow simulates 13C isotope labeling experiments to calculate the extent of carbon exchange, or carbon yield, between every metabolite in the given GSM. Based on the carbon yield, the carbon flow to or from any metabolite or between any pair of metabolites of interest can be isolated and readily visualized. The resulting pathways are much easier to interpret, which enables an in-depth mechanistic understanding of the metabolic phenotype of interest. Here, we first demonstrate NetFlow with a simple network. We then depict the utility of NetFlow on a model of central carbon metabolism in E. coli. Specifically, we isolated the production pathway for succinate synthesis in this model and the metabolic mechanism driving the predicted increase in succinate yield in a double knockout of E. coli. Finally, we describe the application of NetFlow to a GSM of lycopene-producing E. coli, which enabled the rapid identification of the mechanisms behind the measured increases in lycopene production following single, double, and triple knockouts.
Effect of Carbon Chain Length, Ionic Strength, and pH on the In Vitro Release Kinetics of Cationic Drugs from Fatty-Acid-Loaded Contact Lenses
(MDPI, 2021-07-10) Torres-Luna, Cesar; Hu, Naiping; Domszy, Roman; Fan, Xin; Yang, Jeff; Briber, Robert M.; Wang, Nam Sun; Yang, Arthur
This paper explores the use of fatty acids in silicone hydrogel contact lenses for extending the release duration of cationic drugs. Drug release kinetics was dependent on the carbon chain length of the fatty acid loaded in the lens, with 12-, 14- and 18-carbon chain length fatty acids increasing the uptake and the release duration of ketotifen fumarate (KTF) and tetracaine hydrochloride (THCL). Drug release kinetics from oleic acid-loaded lenses was evaluated in phosphate buffer saline (PBS) at different ionic strengths (I = 167, 500, 1665 mM); the release duration of KTF and THCL was decreased with increasing ionic strength of the release medium. Furthermore, the release of KTF and THCL in deionized water did not show a burst and was significantly slower compared to that in PBS. The release kinetics of KTF and THCL was significantly faster when the pH of the release medium was decreased from 7.4 towards 5.5 because of the decrease in the relative amounts of oleate anions in the lens mostly populated at the polymer–pore interfaces. The use of boundary charges at the polymer–pore interfaces of a contact lens to enhance drug partition and extend its release is further confirmed by loading cationic phytosphingosine in contact lenses to attract an anionic drug.
Understanding the Impact of Hydrogen Activation by SrCe 0.8Zr0.2O 3−δ Perovskite Membrane Material on Direct Non-Oxidative Methane Conversion
(Frontiers, 2022-01-10) Cheng, Sichao; Oh, Su Cheun; Sakbodin, Mann; Qiu, Limei; Diao, Yuxia; Liu, Dongxia
Understanding the Impact of Hydrogen Activation by SrCe 0.8Zr0.2O 3−δ Perovskite Membrane Material on Direct Non-Oxidative Methane Conversion Sichao Cheng 1†, Su Cheun Oh 1†, Mann Sakbodin 1 , Limei Qiu 2 , Yuxia Diao 2 and Dongxia Liu 1 * 1 Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, United States, 2 Research Institute of Petroleum Processing, SINOPEC, Beijing, China Direct non-oxidative methane conversion (DNMC) converts methane (CH 4 ) in one step to olefin and aromatic hydrocarbons and hydrogen (H 2) co-product. Membrane reactors comprising methane activation catalysts and H 2 -permeable membranes can enhance methane conversion by in situ H 2 removal via Le Chatelier’s principle. Rigorous description of H 2 kinetic effects on both membrane and catalyst materials in the membrane reactor, however, has been rarely studied. In this work, we report the impact of hydrogen activation by hydrogen-permeable SrCe 0.8Zr 0.2O 3−δ (SCZO) perovskite oxide material on DNMC over an iron/silica catalyst. The SCZO oxide has mixed ionic and electronic conductivity and is capable of H2 activation into protons and electrons for H 2 permeation. In the fixed- bed reactor packed with a mixture of SCZO oxide and iron/silica catalyst, stable and high methane conversion and low coke selectivity in DNMC was achieved by co-feeding of H 2 in methane stream. The characterizations show that SCZO activates H 2 to favor “soft coke” formation on the catalyst. The SCZO could absorb H 2 in situ to lower its local concentration to mitigate the reverse reaction of DNMC in the tested conditions. The co-existence of H 2 co-feed, SCZO oxide, and DNMC catalyst in the present study mimics the conditions of DNMC in the H2 -permeable SCZO membrane reactor. The findings in this work offer the mechanistic understanding of and guidance for the design of H2 -permeable membrane reactors for DNMC and other alkane dehydrogenation reactions.

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