Chemical and Biomolecular Engineering Research Works

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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.
Cell-Like Capsules with “Smart” Compartments
(Wiley, 2023-03-09) Ahn, So Hyun; Borden, Leah K.; Bentley, William E.; Raghavan, Srinivasa R.
Eukaryotic cells have inner compartments (organelles), each with distinct properties and functions. One mimic of this architecture, based on biopolymers, is the multicompartment capsule (MCC). Here, MCCs in which the inner compartments are chemically unique and “smart,” i.e., responsive to distinct stimuli in an orthogonal manner are created. Specifically, one compartment alone is induced to degrade when the MCC is contacted with an enzyme while other compartments remain unaffected. Similarly, just one compartment gets degraded upon contact with reactive oxygen species generated from hydrogen peroxide (H2O2). And thirdly, one compartment alone is degraded by an external, physical stimulus, namely, by irradiating the MCC with ultraviolet (UV) light. All these specific responses are achieved without resorting to complicated chemistry to create the compartments: the multivalent cation used to crosslink the biopolymer alginate (Alg) is simply altered. Compartments of Alg crosslinked by Ca2+ are shown to be sensitive to enzymes (alginate lyases) but not to H2O2 or UV, whereas the reverse is the case with Alg/Fe3+ compartments. These results imply the ability to selectively burst open a compartment in an MCC “on-demand” (i.e., as and when needed) and using biologically relevant stimuli. The results are then extended to a sequential degradation, where compartments in an MCC are degraded one after another, leaving behind an empty MCC lumen. Collectively, this work advances the MCC as a platform that not only emulates key features of cellular architecture, but can also begin to capture rudimentary cell-like behaviors.
COMSOL fracture model
(2024-08-06) Jung, Taeho; Carmona, Eric A; Song, Yueming; Albertus, Paul
Solid-electrolyte (SE) fracture initiation model at the lithium/SE interface during lithium plating.
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.
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%).
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.
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.
Electrically Induced Bursting of Aqueous Capsules Made from Biopolymers: ‘Switching On’ the Release of Payloads
(Wiley, 2022-10-30) Gargava, Ankit; Xu, Wenhao; Raghavan, Srinivasa R.
The use of electric fields to stimulate the delivery of drugs or other active ingredients is of great interest for wearable electronics and other applications. Most attempts at electrically induced delivery with soft materials in water have focused on electronically conducting polymers (e.g., polypyrroles) or conductive nanocomposites (e.g., polymers with carbon nanotubes). Here, electrical responses are induced even in structures made from nonconducting biopolymers that are widely available, biocompatible, and biodegradable. The materials studied here are spherical capsules created from the anionic polysaccharide alginate by cross-linking with cations like Ca2+ or Cu2+. When these capsules are placed in an aqueous solution and subjected to an electric field (direct current) of ≈8 V cm−1, they deform within a couple of minutes and then burst and disintegrate into pieces within ≈5 min. Capsules across a range of length scales (200 µm to 2 cm) respond in the above manner, and the electroresponse persists even if the capsules are embedded in a nonionic gel matrix. This electroresponse is due to electrophoretic migration of charged species (ions and/or polyelectrolyte chain-segments) within (or out of) the capsules. In an alginate capsule, the cations are induced to migrate away from the positive electrode, which creates a weakly cross-linked region of the capsule that swells appreciably. This anisotropic swelling continues until the capsule eventually bursts. Applications for electroresponsive capsules that highlight the spatial and temporal accuracy possible with an electrical stimulus are discussed. The bursting of capsules can be used to release solutes loaded inside these structures. Also, even the deformation of intact capsules can be used to create electrically actuatable valves, where a liquid flows out through the valve only when a capsule plug is dislodged.
Examining the Electrochemical Properties of Hybrid Aqueous/Ionic Liquid Solid Polymer Electrolytes through the Lens of Composition-Function Relationships
(Wiley, 2023-07-04) Ludwig, Kyle B.; Correll-Brown, Riordan; Freidlin, Max; Garaga, Mounesha N.; Bhattacharyya, Sahana; Gonzales, Patricia M.; Cresce, Arthur V.; Greenbaum, Steven; Wang, Chunsheng; Kofinas, Peter
Solid polymer electrolytes (SPEs) have the potential to meet evolving Li-ion battery demands, but for these electrolytes to satisfy growing power and energy density requirements, both transport properties and electrochemical stability must be improved. Unfortunately, improvement in one of these properties often comes at the expense of the other. To this end, a “hybrid aqueous/ionic liquid” SPE (HAILSPE) which incorporates triethylsulfonium-TFSI (S2,2,2) or N-methyl-N-propylpyrrolidinium-TFSI (Pyr1,3) ionic liquid (IL) alongside H2O and LiTFSI salt to simultaneously improve transport and electrochemical stability is studied. This work focuses on the impact of HAILSPE composition on electrochemical performance. Analysis shows that an increase in LiTFSI content results in decreased ionic mobility, while increasing IL and water content can offset its impact. pfg-NMR results reveal that preferential lithium-ion transport is present in HAILSPE systems. Higher IL concentrations are correlated with an increased degree of passivation against H2O reduction. Compared to the Pyr1,3 systems, the S2,2,2 systems exhibit a stronger degree of passivation due to the formation of a multicomponent interphase layer, including LiF, Li2CO3, Li2S, and Li3N. The results herein demonstrate the superior electrochemical stability of the S2,2,2 systems compared to Pyr1,3 and provide a path toward further enhancement of HAILSPE performance via composition optimization.
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.
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.
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.
Formation of LiF-rich Cathode-Electrolyte Interphase by Electrolyte Reduction
(Wiley, 2022-04-08) Bai, Panxing; Ji, Xiao; Zhang, Jiaxun; Zhang, Weiran; Hou, Singyuk; Su, Hai; Li, Mengjie; Deng, Tao; Cao, Longsheng; Liu, Sufu; He, Xinzi; Xu, Yunhua; Wang, Chunsheng
The capacityof transitionmetal oxide cathodefor Li-ionbatteriescan be furtherenhancedby increas-ing the chargingpotential.However,these high voltagecathodessufferfrom fast capacitydecaybecausethelargevolumechangeof cathodebreaksthe activematerialsand cathode-electrolyteinterphase(CEI),resultingin electrolytepenetrationinto brokenactivematerialsand continuousside reactionsbetweencath-ode and electrolytes.Herein,a robustLiF-richCEI wasformedby potentiostaticreductionof fluorinatedelec-trolyteat a low potentialof 1.7 V. By takingLiCoO2asa modelcathode,we demonstratethat the LiF-richCEImaintainsthe structuralintegrityand suppresseselectro-lyte penetrationat a high cut-offpotentialof 4.6 V. TheLiCoO2with LiF-richCEI exhibiteda capacityof198 mAhg
Gradient Structural and Compositional Design of Conductive MXene Aerogels for Stable Zn Metal Anodes
(Wiley, 2023-11-12) Li, Yang; Pang, Zhenqian; Ghani, Awais; Little, Joshua M.; Wang, Liping; Yang, Haochen; Zhao, Yusheng; Chen, Po-Yen
Aqueous rechargeable zinc-ion batteries (ZIBs) are a safe and low-cost energy storage technology. However, practical ZIB exploitation faces critical challenges in achieving stable Zn metal anodes, which suffer from hydrogen evolution reaction (HER) corrosion and Zn dendrite growth. To address these challenges, a Zn2+-induced assembly process to fabricate Ti3C2Tx MXene-reduced graphene oxide aerogels with ZnO crust layers on Zn plates (abbreviated as ZnO/MG aerogel–Zn) that serve as stable Zn metal anodes is reported. By applying a constant voltage to a Zn plate, Zn2+ is gradually released to ionically crosslink MG nanosheets. After spontaneous hydrolysis and freeze-drying, a crust layer composed of ZnO nanoparticles is in situ formed. Additionally, the gradient Zn−O/Zn−F profiles across the ZnO/MG aerogel can facilitate Zn2+ transport and collectively suppress HER, enabling fast electrochemical kinetics and dendrite-free Zn deposition. Symmetric cells with ZnO/MG aerogel–Zn electrodes present stable cycling for 1200 h at 10 mA cm−2, and full cells achieve long lifespans at high rates (>500 cycles at 1.0 A g−1). Combining the advantages of an insulating protective layer and a conductive structured host, the ZnO/MG aerogel–Zn electrode with gradient structures and compositions creates synergistic advances in stable Zn metal anodes.
High-energy and low-cost membrane-free chlorine flow battery
(Springer Nature, 2022-03-11) Hou, Singyuk; Chen, Long; Fan, Xiulin; Fan, Xiaotong; Ji, Xiao; Wang, Boyu; Cui, Chunyu; Chen, Ji; Yang, Chongyin; Wang, Wei; Li, Chunzhong; Wang, Chunsheng
Grid-scale energy storage is essential for reliable electricity transmission and renewable energy integration. Redox flow batteries (RFB) provide affordable and scalable solutions for stationary energy storage. However, most of the current RFB chemistries are based on expensive transition metal ions or synthetic organics. Here, we report a reversible chlorine redox flow battery starting from the electrolysis of aqueous NaCl electrolyte and the as-produced Cl2 is extracted and stored in the carbon tetrachloride (CCl4) or mineral spirit flow. The immiscibility between the CCl4 or mineral spirit and NaCl electrolyte enables a membrane-free design with an energy efficiency of >91% at 10 mA/cm2 and an energy density of 125.7 Wh/L. The chlorine flow battery can meet the stringent price and reliability target for stationary energy storage with the inherently low-cost active materials (~$5/kWh) and the highly reversible Cl2/Cl− redox reaction.
High-Performance Lithium Metal Batteries Enabled by a Fluorinated Cyclic Ether with a Low Reduction Potential
(Wiley, 2023-01-02) Wu, Min; Wang, Zeyi; Zhang, Weiran; Jayawardana, Chamithri; Li, Yue; Chen, Fu; Nan, Bo; Lucht, Brett L.; Wang, Chunsheng
Electrolyte engineering is crucial for developing high-performance lithium metal batteries (LMB). Here, we synthesized two cosolvents methyl bis(fluorosulfonyl)imide (MFSI) and 3,3,4,4-tetrafluorotetrahydrofuran (TFF) with significantly different reduction potentials and add them into LiFSI-DME electrolytes. The LiFSI/TFF-DME electrolyte gave an average Li Coulombic efficiency (CE) of 99.41 % over 200 cycles, while the average Li CEs for MFSI-based electrolyte is only 98.62 %. Additionally, the TFF-based electrolytes exhibited a more reversible performance than the state-of-the-art fluorinated 1,4-dimethoxylbutane electrolyte in both Li||Cu half-cell and anode-free Cu||LiNi0.8Mn0.1Co0.1O2 full cell. More importantly, the decomposition product from bis(fluorosulfonyl)imide anion could react with ether solvent, which destroyed the SEI, thus decreasing cell performance. These key discoveries provide new insights into the rational design of electrolyte solvents and cosolvents for LMB.
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.
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.
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.

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