Scholarly Works, Chemical Engineering

Permanent URI for this collection

https://hdl.handle.net/10919/24288

Research articles, presentations, and other scholarship

Browse

Now showing 1 - 20 of 155

18.1% single palladium atom catalysts on mesoporous covalent organic framework for gas phase hydrogenation of ethylene
Kuo, Chun-Te; Lu, Yubing; Arab, Pezhman; Weeraratne, K. Shamara; El-Kaderi, Hani; Karim, Ayman M. (2021-07-21)
Noble metal single-atom catalysts maximize metal utilization and offer opportunities to design heterogeneous catalysts at the molecular scale. Mesoporous covalent organic frameworks provide an ideal support to stabilize metal single atoms with specific ligand configuration similar to a homogeneous catalyst In this work, a high loading of single Pd atoms, 18.1 wt %, on mesoporous imine-linked covalent organic framework was synthesized, characterized, and evaluated for ethylene hydrogenation. X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, and diffuse-reflectance infrared Fourier transform spectroscopy of adsorbed CO demonstrate that the Pd is atomically dispersed with a highly homogeneous local coordination. The Pd single atoms are active for hydrogenation of ethylene to ethane at room temperature. The study demonstrates that mesoporous COFs provide a large number of identical metal binding sites that are good candidates for immobilizing metal single atoms and their use in gas-phase catalytic applications.
3D Hepatic Cultures Simultaneously Maintain Primary Hepatocyte and Liver Sinusoidal Endothelial Cell Phenotypes
Kim, Yeonhee; Rajagopalan, Padmavathy (PLOS, 2010-11-12)
Developing in vitro engineered hepatic tissues that exhibit stable phenotype is a major challenge in the field of hepatic tissue engineering. However, the rapid dedifferentiation of hepatic parenchymal (hepatocytes) and non-parenchymal (liver sinusoidal endothelial, LSEC) cell types when removed from their natural environment in vivo remains a major obstacle. The primary goal of this study was to demonstrate that hepatic cells cultured in layered architectures could preserve or potentially enhance liver-specific behavior of both cell types. Primary rat hepatocytes and rat LSECs (rLSECs) were cultured in a layered three-dimensional (3D) configuration. The cell layers were separated by a chitosan-hyaluronic acid polyelectrolyte multilayer (PEM), which served to mimic the Space of Disse. Hepatocytes and rLSECs exhibited several key phenotypic characteristics over a twelve day culture period. Immunostaining for the sinusoidal endothelial 1 antibody (SE-1) demonstrated that rLSECs cultured in the 3D hepatic model maintained this unique feature over twelve days. In contrast, rLSECs cultured in monolayers lost their phenotype within three days. The unique stratified structure of the 3D culture resulted in enhanced heterotypic cell-cell interactions, which led to improvements in hepatocyte functions. Albumin production increased three to six fold in the rLSEC-PEM-Hepatocyte cultures. Only rLSEC-PEM-Hepatocyte cultures exhibited increasing CYP1A1/2 and CYP3A activity. Well-defined bile canaliculi were observed only in the rLSEC-PEM-Hepatocyte cultures. Together, these data suggest that rLSEC-PEM-Hepatocyte cultures are highly suitable models to monitor the transformation of toxins in the liver and their transport out of this organ. In summary, these results indicate that the layered rLSEC-PEM-hepatocyte model, which recapitulates key features of hepatic sinusoids, is a potentially powerful medium for obtaining comprehensive knowledge on liver metabolism, detoxification and signaling pathways in vitro.
Algorithm-derived feature representations for explainable AI in catalysis
Omidvar, Noushin; Xin, Hongliang (Elsevier, 2021-12-01)
Machine learning (ML) has emerged as a critical tool in catalysis, attributed to its capability of finding complex patterns in high dimensional and heterogeneous data. A recently published article in Chem Catalysis (Esterhuizen et al.) used unsupervised ML for uncovering electronic and geometric descriptors of the surface reactivity of metal alloys and oxides.
Alterations in the molecular composition of COVID-19 patient urine, detected using Raman spectroscopic/computational analysis
Robertson, John L.; Senger, Ryan S.; Talty, Janine; Du, Pang; Sayed-Issa, Amr; Avellar, Maggie L.; Ngo, Lacy T.; Gomez de la Espriella, Mariana; Fazili, Tasaduq N.; Jackson-Akers, Jasmine Y.; Guruli, Georgi; Orlando, Giuseppe (PLOS, 2022-07-01)
We developed and tested a method to detect COVID-19 disease, using urine specimens. The technology is based on Raman spectroscopy and computational analysis. It does not detect SARS-CoV-2 virus or viral components, but rather a urine ‘molecular fingerprint’, representing systemic metabolic, inflammatory, and immunologic reactions to infection. We analyzed voided urine specimens from 46 symptomatic COVID-19 patients with positive real time-polymerase chain reaction (RT-PCR) tests for infection or household contact with test-positive patients. We compared their urine Raman spectra with urine Raman spectra from healthy individuals (n = 185), peritoneal dialysis patients (n = 20), and patients with active bladder cancer (n = 17), collected between 2016–2018 (i.e., pre-COVID-19). We also compared all urine Raman spectra with urine specimens collected from healthy, fully vaccinated volunteers (n = 19) from July to September 2021. Disease severity (primarily respiratory) ranged among mild (n = 25), moderate (n = 14), and severe (n = 7). Seventy percent of patients sought evaluation within 14 days of onset. One severely affected patient was hospitalized, the remainder being managed with home/ambulatory care. Twenty patients had clinical pathology profiling. Seven of 20 patients had mildly elevated serum creatinine values (>0.9 mg/dl; range 0.9–1.34 mg/dl) and 6/7 of these patients also had estimated glomerular filtration rates (eGFR) <90 mL/min/1.73m2 (range 59–84 mL/min/1.73m2). We could not determine if any of these patients had antecedent clinical pathology abnormalities. Our technology (Raman Chemometric Urinalysis—Rametrix®) had an overall prediction accuracy of 97.6% for detecting complex, multimolecular fingerprints in urine associated with COVID-19 disease. The sensitivity of this model for detecting COVID-19 was 90.9%. The specificity was 98.8%, the positive predictive value was 93.0%, and the negative predictive value was 98.4%. In assessing severity, the method showed to be accurate in identifying symptoms as mild, moderate, or severe (random chance = 33%) based on the urine multimolecular fingerprint. Finally, a fingerprint of ‘Long COVID-19’ symptoms (defined as lasting longer than 30 days) was located in urine. Our methods were able to locate the presence of this fingerprint with 70.0% sensitivity and 98.7% specificity in leave-one-out cross-validation analysis. Further validation testing will include sampling more patients, examining correlations of disease severity and/or duration, and employing metabolomic analysis (Gas Chromatography–Mass Spectrometry [GC-MS], High Performance Liquid Chromatography [HPLC]) to identify individual components contributing to COVID-19 molecular fingerprints.
Ambient ammonia synthesis via palladium-catalyzed electrohydrogenation of dinitrogen at low overpotential
Wang, Jun; Yu, Liang; Hu, Lin; Chen, Gang; Xin, Hongliang; Feng, Xiaofeng (Springer Nature, 2018-05-15)
Electrochemical reduction of N2 to NH3 provides an alternative to the Haber−Bosch process for sustainable, distributed production of NH3 when powered by renewable electricity. However, the development of such process has been impeded by the lack of efficient electrocatalysts for N2 reduction. Here we report efficient electroreduction of N2 to NH3 on palladium nanoparticles in phosphate buffer solution under ambient conditions, which exhibits high activity and selectivity with an NH3 yield rate of ~4.5 μg mg−1Pd h−1 and a Faradaic efficiency of 8.2% at 0.1 V vs. the reversible hydrogen electrode (corresponding to a low overpotential of 56 mV), outperforming other catalysts including gold and platinum. Density functional theory calculations suggest that the unique activity of palladium originates from its balanced hydrogen evolution activity and the Grotthuss-like hydride transfer mechanism on α-palladium hydride that lowers the free energy barrier of N2 hydrogenation to *N2H, the rate-limiting step for NH3 electrosynthesis.
Ammonium Bisphosphonate Polymeric Magnetic Nanocomplexes for Platinum Anticancer Drug Delivery and Imaging with Potential Hyperthermia and Temperature-Dependent Drug Release
Zhang, Rui; Fellows, Benjamin; Pothayee, Nikorn; Hu, Nan; Pothayee, Nipon; Jo, Ami; Bohórquez, Ana C.; Rinaldi, Carlos; Mefford, Olin Thompson; Davis, Richey M.; Riffle, Judy S. (Hindawi, 2018-08-05)
Novel magnetite-ammonium bisphosphonate graft ionic copolymer nanocomplexes (MGICs) have been developed for potential drug delivery, magnetic resonance imaging, and hyperthermia applications. The complexes displayed relatively uniform sizes with narrow size distributions upon self-assembly in aqueous media, and their sizes were stable under simulated physiological conditions for at least 7 days. The anticancer drugs, cisplatin and carboplatin, were loaded into the complexes, and sustained release of both drugs was observed. The transverse NMR relaxivities (s) of the complexes were 244 s−1 (mM Fe)−1 which is fast compared to either the commercial T2-weighted MRI agent Feridex IV® or our previously reported magnetite-block ionomer complexes. Phantom MRI images of the complexes demonstrated excellent negative contrast effects of such complexes. Thus, the bisphosphonate-bearing MGICs could be promising candidates for dual drug delivery and magnetic resonance imaging. Moreover, the bisphosphonate MGICs generate heat under an alternating magnetic field of 30 kA·m−1 at 206 kHz. The temperature of the MGIC dispersion in deionized water increased from 37 to 41°C after exposure to the magnetic field for 10 minutes, corresponding to a specific absorption rate of 77.0 W·g−1. This suggests their potential as hyperthermia treatment agents as well as the possibility of temperature-dependent drug release, making MGICs more versatile in potential drug delivery applications.
Anticancer nanoparticulate polymer-drug conjugate
Feng, Quanyou; Tong, Rong (Wiley, 2016-08-26)
We review recent progress in polymer-drug conjugate for cancer nanomedicine. Polymer-drug conjugates, including the nanoparticle prepared from these conjugates, are designed to release drug in tumor tissues or cells in order to improve drugs’ therapeutic efficacy. We summarize general design principles for the polymer-drug conjugate, including the synthetic strategies, the design of the chemical linkers between the drug and polymer in the conjugate, and the in vivo drug delivery barriers for polymer-drug conjugates. Several new strategies, such as the synthesis of polymerdrug conjugates and supramolecular-drug conjugates, the use of stimulus-responsive delivery, and triggering the change of the nanoparticle physiochemical properties to over delivery barriers, are also highlighted.
The assembly of integrated rat intestinal-hepatocyte cultures
Kothari, Anjaney; Rajagopalan, Padmavathy (2019-11)
The jejunum is the segment of the small intestine responsible for several metabolism and biotransformation functions. In this report, we have cultured rat jejunum explants in vitro and integrated them with hepatocyte cultures. We have also investigated the changes in jejunum function at different locations since spatial variations in intestinal functions have been reported previously. We divided the length of the rat jejunum into three distinct regions of approximately 9 cm each. We defined the regions as proximal (adjacent to the duodenum), medial, and distal (adjacent to the ileum). Spatiotemporal variations in functions were observed between these regions within the jejunum. Alkaline phosphatase activity (a marker of enterocyte function), decreased twofold between the proximal and distal regions at 4 hr. Lysozyme activity (a marker of Paneth cell function) increased from the proximal to the distal jejunum by 40% at 24 hr. Mucin-covered areas, a marker of goblet cell function, increased by twofold between the proximal and distal segments of the jejunum at 24 hr. When hepatocytes were integrated with proximal jejunum explants, statistically higher urea (similar to 2.4-fold) and mucin (57%) production were observed in the jejunum explants. The integrated intestine-liver cultures can be used as a platform for future investigations.
An atomic force microscope tip as a light source
Lulevich, V.; Honig, Christopher D. F.; Ducker, William A. (AIP Publishing, 2005-12-01)
We present a simple method for causing the end of a silicon nitride atomic force microscope (AFM) tip to emit light, and we use this emitted light to perform scanning near-field optical microscopy. Illumination of a silicon nitride AFM tip by blue (488 nm) or green (532 nm) laser light causes the sharp part of the tip to emit orange light. Orange light is emitted when the tip is immersed in either air or water; and while under illumination, emission continues for a period of many hours without photobleaching. By careful alignment of the incident beam, we can arrange the scattered light to decay as a function of the tip-substrate separation with a decay length of 100-200 nm. The exponential decay of the intensity means that the emitted light is dominated by contributions from parts of the tip that are near the sample, and therefore the emitted orange light can be used to capture high-resolution near-field optical images in air or water. (c) 2005 American Institute of Physics.
Bayesian learning of chemisorption for bridging the complexity of electronic descriptors
Wang, Siwen; Pillai, Hemanth Somarajan; Xin, Hongliang (Springer Nature, 2020)
Building upon the d-band reactivity theory in surface chemistry and catalysis, we develop a Bayesian learning approach to probing chemisorption processes at atomically tailored metal sites. With representative species, e.g., *O and *OH, Bayesian models trained with ab initio adsorption properties of transition metals predict site reactivity at a diverse range of intermetallics and near-surface alloys while naturally providing uncertainty quantification from posterior sampling. More importantly, this conceptual framework sheds light on the orbitalwise nature of chemical bonding at adsorption sites with d-states characteristics ranging from bulk-like semi-elliptic bands to free-atom-like discrete energy levels, bridging the complexity of electronic descriptors for the prediction of novel catalytic materials.
Bayesian-optimization-assisted discovery of stereoselective aluminum complexes for ring-opening polymerization of racemic lactide
Wang, Xiaoqian; Huang, Yang; Xie, Xiaoyu; Liu, Yan; Huo, Ziyu; Lin, Maverick; Xin, Hongliang; Tong, Rong (Nature Research, 2023-06-20)
Stereoselective ring-opening polymerization catalysts are used to produce degradable stereoregular poly(lactic acids) with thermal and mechanical properties that are superior to those of atactic polymers. However, the process of discovering highly stereoselective catalysts is still largely empirical.We aim to develop an integrated computational and experimental framework for efficient, predictive catalyst selection and optimization. As a proof of principle, we have developed a Bayesian optimization workflow on a subset of literature results for stereoselective lactide ring-opening polymerization, and using the algorithm, we identify multiple new Al complexes that catalyze either isoselective or heteroselective polymerization. In addition, feature attribution analysis uncovers mechanistically meaningful ligand descriptors, such as percent buried volume (%Vbur) and the highest occupied molecular orbital energy (Eₕₒₘₒ), that can access quantitative and predictivemodels for catalyst development.
Bioactive Cellulose Nanocrystal-Poly(epsilon-Caprolactone) Nanocomposites for Bone Tissue Engineering Applications
Hong, Jung Ki; Cooke, Shelley L.; Whittington, Abby R.; Roman, Maren (2021-02-25)
3D-printed bone scaffolds hold great promise for the individualized treatment of critical-size bone defects. Among the resorbable polymers available for use as 3D-printable scaffold materials, poly(epsilon-caprolactone) (PCL) has many benefits. However, its relatively low stiffness and lack of bioactivity limit its use in load-bearing bone scaffolds. This study tests the hypothesis that surface-oxidized cellulose nanocrystals (SO-CNCs), decorated with carboxyl groups, can act as multi-functional scaffold additives that (1) improve the mechanical properties of PCL and (2) induce biomineral formation upon PCL resorption. To this end, an in vitro biomineralization study was performed to assess the ability of SO-CNCs to induce the formation of calcium phosphate minerals. In addition, PCL nanocomposites containing different amounts of SO-CNCs (1, 2, 3, 5, and 10 wt%) were prepared using melt compounding extrusion and characterized in terms of Young's modulus, ultimate tensile strength, crystallinity, thermal transitions, and water contact angle. Neither sulfuric acid-hydrolyzed CNCs (SH-CNCs) nor SO-CNCs were toxic to MC3T3 preosteoblasts during a 24 h exposure at concentrations ranging from 0.25 to 3.0 mg/mL. SO-CNCs were more effective at inducing mineral formation than SH-CNCs in simulated body fluid (1x). An SO-CNC content of 10 wt% in the PCL matrix caused a more than 2-fold increase in Young's modulus (stiffness) and a more than 60% increase in ultimate tensile strength. The matrix glass transition and melting temperatures were not affected by the SO-CNCs but the crystallization temperature increased by about 5.5 degrees C upon addition of 10 wt% SO-CNCs, the matrix crystallinity decreased from about 43 to about 40%, and the water contact angle decreased from 87 to 82.6 degrees. The abilities of SO-CNCs to induce calcium phosphate mineral formation and increase the Young's modulus of PCL render them attractive for applications as multi-functional nanoscale additives in PCL-based bone scaffolds.
Biomass Valorization to Bioenergy: Assessment of Biomass Residues' Availability and Bioenergy Potential in Nigeria
Ezealigo, Uchechukwu Stella; Ezealigo, Blessing Nonye; Kemausuor, Francis; Achenie, Luke Ekem Kweku; Onwualu, Azikiwe Peter (MDPI, 2021-12)
The bioenergy sector in Nigeria currently lacks a proper assessment of resource availability. In this study, we investigated the bioenergy potential of agricultural residues and municipal solid and liquid waste using data from 2008 to 2018, and we applied a computational and analytical approach with mild assumptions. The technical potential for the production of cellulosic ethanol and biogas was estimated from the available biomass. It was discovered that higher energy was generated from biogas than cellulosic ethanol for the same type of residue. The available crop residue technical potential of 84 Mt yielded cellulosic ethanol and biogas of 14,766 ML/yr (8 Mtoe) and 15,014 Mm(3)/yr (13 Mtoe), respectively. Biogas has diverse applications ranging from heat to electric power generation and therefore holds great potential in solving the current electricity crisis in Nigeria. It will also position the nation towards achieving the 7th sustainable development goal (SDG 7) on clean and affordable energy.
Blood Serum Affects Polysaccharide Production and Surface Protein Expression in S. Aureus
Islam, Nazrul; Hossain, Khwaja G.; Ross, Julia M.; Marten, Mark R. (Juniper Publishers, 2017-01)
S. aureus biofilm serves a major role in pathogenesis. Two of the major components of bacterial biofilm are Polysaccharides intercellular adhesions (PIA) and surface proteins. It is not known how PIA and surface proteins expressions are affected in presence of blood serum. Analyses of surface proteins expressions will provide more effective biomarker discovery that might lead to development of antimicrobial therapeutics to meet the challenges of biofilm-related infections.Secondary cultures of S. aureus Philips, a biofilm-forming bacterium, were generated by inoculating 1 ml of overnight culture into 50 ml of TSB. Bacteria were cultured at several concentrations of blood serum and found that 12.5% supplemented blood serum provide s similar growth curve as normal TSB (100%). One and 2 D SASPAGE were used to separate proteins and the differentially expressed proteins were identified by nano-LC/MS.Polysaccharide intercellular adhesions production was significantly increased due to the addition of blood serum in the media. We also identified two serum proteins, apolipoprotein and globulin (Fc and Fab), that remained attached with the membrane fraction of bacterial proteins.These results have strongly demonstrated that blood serum influences the exopolysaccharide expression in S. aureus.
BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells
Zhang, Xiaowen; Wang, Yao; Chiang, Huai-Chin; Hsieh, Yuan-Pang; Lu, Chang; Park, Ben H.; Jatoi, Ismail; Jin, Victor X.; Hu, Yanfen; Li, Rong (2019-04-17)
Background BRCA1-associated breast cancer originates from luminal progenitor cells. BRCA1 functions in multiple biological processes, including double-strand break repair, replication stress suppression, transcriptional regulation, and chromatin reorganization. While non-malignant cells carrying cancer-predisposing BRCA1 mutations exhibit increased genomic instability, it remains unclear whether BRCA1 haploinsufficiency affects transcription and chromatin dynamics in breast epithelial cells. Methods H3K27ac-associated super-enhancers were compared in primary breast epithelial cells from BRCA1 mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+). Non-tumorigenic MCF10A breast epithelial cells with engineered BRCA1 haploinsufficiency were used to confirm the H3K27ac changes. The impact of BRCA1 mutations on enhancer function and enhancer-promoter looping was assessed in MCF10A cells. Results Here, we show that primary mammary epithelial cells from women with BRCA1 mutations display significant loss of H3K27ac-associated super-enhancers. These BRCA1-dependent super-enhancers are enriched with binding motifs for the GATA family. Non-tumorigenic BRCA1mut/+ MCF10A cells recapitulate the H3K27ac loss. Attenuated histone mark and enhancer activity in these BRCA1mut/+ MCF10A cells can be partially restored with wild-type BRCA1. Furthermore, chromatin conformation analysis demonstrates impaired enhancer-promoter looping in BRCA1mut/+ MCF10A cells. Conclusions H3K27ac-associated super-enhancer loss is a previously unappreciated functional deficiency in ostensibly normal BRCA1 mutation-carrying breast epithelium. Our findings offer new mechanistic insights into BRCA1 mutation-associated transcriptional and epigenetic abnormality in breast epithelial cells and tissue/cell lineage-specific tumorigenesis.
Breaking adsorption-energy scaling limitations of electrocatalytic nitrate reduction on intermetallic CuPd nanocubes by machine-learned insights
Gao, Qiang; Pillai, Hemanth Somarajan; Huang, Yang; Liu, Shikai; Mu, Qingmin; Han, Xue; Yan, Zihao; Zhou, Hua; He, Qian; Xin, Hongliang; Zhu, Huiyuan (Nature Portfolio, 2022-04-29)
Machine learning is a powerful tool for screening electrocatalytic materials. Here, the authors reported a seamless integration of machine-learned physical insights with the controlled synthesis of structurally ordered intermetallic nanocrystals and well-defined catalytic sites for efficient nitrate reduction to ammonia. The electrochemical nitrate reduction reaction (NO3RR) to ammonia is an essential step toward restoring the globally disrupted nitrogen cycle. In search of highly efficient electrocatalysts, tailoring catalytic sites with ligand and strain effects in random alloys is a common approach but remains limited due to the ubiquitous energy-scaling relations. With interpretable machine learning, we unravel a mechanism of breaking adsorption-energy scaling relations through the site-specific Pauli repulsion interactions of the metal d-states with adsorbate frontier orbitals. The non-scaling behavior can be realized on (100)-type sites of ordered B2 intermetallics, in which the orbital overlap between the hollow *N and subsurface metal atoms is significant while the bridge-bidentate *NO3 is not directly affected. Among those intermetallics predicted, we synthesize monodisperse ordered B2 CuPd nanocubes that demonstrate high performance for NO3RR to ammonia with a Faradaic efficiency of 92.5% at -0.5 V-RHE and a yield rate of 6.25 mol h(-1) g(-1) at -0.6 V-RHE. This study provides machine-learned design rules besides the d-band center metrics, paving the path toward data-driven discovery of catalytic materials beyond linear scaling limitations.
Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues
Hsieh, Yuan-Pang; Naler, Lynette B.; Ma, Sai; Lu, Chang (Oxford University Press, 2022-01-13)
BRCA1 germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variations and potentially mediate biochemical cascades involved in tumorigenesis. Due to the cell-type specificity of epigenomic features, profiling of individual cell types is critical for understanding the molecular events in various cellular compartments within complex breast tissue. Here, we produced cell-type-specific profiles of genome-wide histone modifications including H3K27ac and H3K4me3 in basal, luminal progenitor, mature luminal and stromal cells extracted from a small pilot cohort of pre-cancer BRCA1 mutation carriers (BRCA1(mut/+)) and non-carriers (BRCA1(+/+)), using a low-input ChIP-seq technology that we developed. We discovered that basal and stromal cells present the most extensive epigenomic differences between mutation carriers (BRCA1(mut/+)) and non-carriers (BRCA1(+/+)), while luminal progenitor and mature luminal cells are relatively unchanged with the mutation. Furthermore, the epigenomic changes in basal cells due to BRCA1 mutation appear to facilitate their transformation into luminal progenitor cells. Taken together, epigenomic regulation plays an important role in the case of BRCA1 mutation for shaping the molecular landscape that facilitates tumorigenesis.
Characterizing glucose, illumination, and nitrogen-deprivation phenotypes of Synechocystis PCC6803 with Raman spectroscopy
Tanniche, Imen; Collakova, Eva; Denbow, Cynthia J.; Senger, Ryan S. (2020-03-30)
Background. Synechocystis sp. PCC6803 is a model cyanobacterium that has been studied widely and is considered for metabolic engineering applications. Here, Raman spectroscopy and Raman chemometrics (Rametrix (TM)) were used to (i) study broad phenotypic changes in response to growth conditions, (ii) identify phenotypic changes associated with its circadian rhythm, and (iii) correlate individual Raman bands with biomolecules and verify these with more accepted analytical methods. Methods. Synechocystis cultures were grown under various conditions, exploring dependencies on light and/or external carbon and nitrogen sources. The Rametrix (TM) LITE Toolbox for MATLAB (R) was used to process Raman spectra and perform principal component analysis (PCA) and discriminant analysis of principal components (DAPC). The Rametrix (TM) PRO Toolbox was used to validate these models through leave-oneout routines that classified a Raman spectrum when growth conditions were withheld from the model. Performance was measured by classification accuracy, sensitivity, and specificity. Raman spectra were also subjected to statistical tests (ANOVA and pairwise comparisons) to identify statistically relevant changes in Synechocystis phenotypes. Finally, experimental methods, including widely used analytical and spectroscopic assays were used to quantify the levels of glycogen, fatty acids, amino acids, and chlorophyll a for correlations with Raman data. Results. PCA and DAPC models produced distinct clustering of Raman spectra, representing multiple Synechocystis phenotypes, based on (i) growth in the presence of 5 mM glucose, (ii) illumination (dark, light/dark [12 h/12 h], and continuous light at 20 mE), (iii) nitrogen deprivation (0-100%NaNO3 of native BG-11 medium in continuous light), and (iv) throughout a 24 h light/dark (12 h/12 h) circadian rhythm growth cycle. Rametrix (TM) PRO was successful in identifying glucose-induced phenotypes with 95.3% accuracy, 93.4% sensitivity, and 96.9% specificity. Prediction accuracy was above random chance values for all other studies. Circadian rhythm analysis showed a return to the initial phenotype after 24 hours for cultures grown in light/dark (12 h/12 h) cycles; this did not occur for cultures grown in the dark. Finally, correlation coefficients (R > 0.7) were found for glycogen, all amino acids, and chlorophyll a when comparing specific Raman bands to other experimental results.
Characterizing metabolic stress-induced phenotypes of Synechocystis PCC6803 with Raman spectroscopy
Tanniche, Imen; Collakova, Eva; Denbow, Cynthia J.; Senger, Ryan S. (2020-03-30)
Background. During their long evolution, Synechocystis sp. PCC6803 developed a remarkable capacity to acclimate to diverse environmental conditions. In this study, Raman spectroscopy and Raman chemometrics tools (Rametrix (TM)) were employed to investigate the phenotypic changes in response to external stressors and correlate specific Raman bands with their corresponding biomolecules determined with widely used analytical methods. Methods. Synechocystis cells were grown in the presence of (i) acetate (7.5-30 mM), (ii) NaCl (50-150 mM) and (iii) limiting levels of MgSO4 (0-62.5 mM) in BG-11 media. Principal component analysis (PCA) and discriminant analysis of PCs (DAPC) were performed with the Rametrix (TM) LITE Toolbox for MATLABR (R). Next, validation of these models was realized via Rametrix (TM) PRO Toolbox where prediction of accuracy, sensitivity, and specificity for an unknown Raman spectrum was calculated. These analyses were coupled with statistical tests (ANOVA and pairwise comparison) to determine statistically significant changes in the phenotypic responses. Finally, amino acid and fatty acid levels were measured with well-established analytical methods. The obtained data were correlated with previously established Raman bands assigned to these biomolecules. Results. Distinguishable clusters representative of phenotypic responses were observed based on the external stimuli (i.e., acetate, NaCl, MgSO4, and controls grown on BG-11 medium) or its concentration when analyzing separately. For all these cases, Rametrix (TM) PRO was able to predict efficiently the corresponding concentration in the culture media for an unknown Raman spectra with accuracy, sensitivity and specificity exceeding random chance. Finally, correlations (R > 0.7) were observed for all amino acids and fatty acids between well-established analytical methods and Raman bands.
Clearance of Biodegradable Polymer and Polyethylene Films from the Rumens of Holstein Bull Calves
Galyon, Hailey; Vibostok, Samuel; Duncan, Jane; Ferreira, Gonzalo; Whittington, Abby; Havens, Kirk; McDevitt, Jason; Cockrum, Rebecca R. (MDPI, 2023-03-03)
Due to the occurrence of plastic impaction in ruminants and its deleterious effects on health and production, it is necessary to determine the suitability of biodegradable polymers to replace polyethylene-based agricultural plastics, such as hay netting. The objectives of this study were to evaluate the clearance of a polyhydroxyalkanoate (PHA) and poly(butylene succinate-co-adipate) (PBSA) melt-blend polymer from the rumen when fed to cattle and subsequent animal health. Twelve Holstein bull calves were dosed with an encapsulated 13.6 g of PBSA:PHA (Blend), 13.6 g of low-density polyethylene (LDPE), or four empty gelatin capsules (Control) for 30 d. The feed intake, body weight, and body temperature were evaluated, and hemograms were run on d 0 and d 30. On d 31, calves were euthanized to evaluate gross rumen measurements and pathology, papillae length, and polymer residues in rumen contents. No calves presented any signs related to plastic impaction. The feed intake; body weight; rectal temperature; hematological parameters; gross rumen measurements and pathology; and rumen pH and temperature were not affected by treatments. Calves dosed with LDPE had 27 g of undegraded polymer retained in the rumen while Blend calves had only 2 g of fragmented polymers that were 10% of their original size. Agricultural plastics developed from PBSA:PHA may be a suitable alternative to LDPE-based products in the case of animal ingestion and may reduce the incidence of plastic impaction.

Browse

Browsing Scholarly Works, Chemical Engineering by Title

Results Per Page

Sort Options