Research and Publications - Department of Chemical & Biological Engineering

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Accessing the main-group metal formyl scaffold through CO-activation in beryllium hydride complexes
(Nature Portfolio, 2022) Hadlington, Terrance J.; Szilvasi, Tibor; Technical University of Munich; University of Alabama Tuscaloosa
Carbon monoxide (CO) is an indispensable C1 building block. For decades this abundant gas has been employed in hydroformylation and Pausen-Khand catalysis, amongst many related chemistries, where a single, non-coupled CO fragment is delivered to an organic molecule. Despite this, organometallic species which react with CO to yield C1 products remain rare, and are elusive for main group metal complexes. Here, we describe a range of amido-beryllium hydride complexes, and demonstrate their reactivity towards CO, in its mono-insertion into the Be-H bonds of these species. The small radius of the Be2+ ion in conjunction with the non-innocent pendant phosphine moiety of the developed ligands leads to a unique beryllium formyl complex with an ylidic P-C-CO fragment, whereby the carbon centre, remarkably, datively binds Be. This, alongside reactivity toward carbon dioxide, sheds light on the insertion chemistry of the Be-H bond, complimenting the long-known chemistry of the heavier Alkaline Earth hydrides. Stoichiometric carbon monoxide insertion processes leading to metal-formyl complexes are scarce, even for transition metals. Here, light is shed on the underexplored chemistry of beryllium hydrides leading to a stable example of a main group metal-formyl complex.
Amelioration of Alzheimer's disease pathology by mitophagy inducers identified via machine learning and a cross-species workflow
(Nature Portfolio, 2022) Xie, Chenglong; Zhuang, Xu-Xu; Niu, Zhangming; Ai, Ruixue; Lautrup, Sofie; Zheng, Shuangjia; Jiang, Yinghui; Han, Ruiyu; Sen Gupta, Tanima; Cao, Shuqin; Lagartos-Donate, Maria Jose; Cai, Cui-Zan; Xie, Li-Ming; Caponio, Domenica; Wang, Wen-Wen; Schmauck-Medina, Tomas; Zhang, Jianying; Wang, He-ling; Lou, Guofeng; Xiao, Xianglu; Zheng, Wenhua; Palikaras, Konstantinos; Yang, Guang; Caldwell, Kim A.; Caldwell, Guy A.; Shen, Han-Ming; Nilsen, Hilde; Lu, Jia-Hong; Fang, Evandro F.; Wenzhou Medical University; University of Oslo; Oujiang Laboratory; University of Macau; Sun Yat Sen University; Athens Medical School; National & Kapodistrian University of Athens; Royal Brompton Hospital; Imperial College London; University of Alabama Tuscaloosa; University of Alabama Birmingham; National University of Singapore; Zhengzhou University
A reduced removal of dysfunctional mitochondria is common to aging and age-related neurodegenerative pathologies such as Alzheimer's disease (AD). Strategies for treating such impaired mitophagy would benefit from the identification of mitophagy modulators. Here we report the combined use of unsupervised machine learning (involving vector representations of molecular structures, pharmacophore fingerprinting and conformer fingerprinting) and a cross-species approach for the screening and experimental validation of new mitophagy-inducing compounds. From a library of naturally occurring compounds, the workflow allowed us to identify 18 small molecules, and among them two potent mitophagy inducers (Kaempferol and Rhapontigenin). In nematode and rodent models of AD, we show that both mitophagy inducers increased the survival and functionality of glutamatergic and cholinergic neurons, abrogated amyloid-beta and tau pathologies, and improved the animals' memory. Our findings suggest the existence of a conserved mechanism of memory loss across the AD models, this mechanism being mediated by defective mitophagy. The computational-experimental screening and validation workflow might help uncover potent mitophagy modulators that stimulate neuronal health and brain homeostasis.
Appendices to: Addressing the importance of STEM to Public Science communication in engineering formation: an analysis of an educational innovation for an upper-level chemical engineering health and safety course
(2024) Simpson, Lance Michael; VanDyke, Matthew S.; Koh, Amanda S.
STEM-to-public science communication is recognized as an important skill, but a pedagogical framework for teaching these skills is lacking. Collaborating with safety and science communication experts, an educational innovation was developed in a health and safety course for chemical engineering students. Students attended three science communication workshops and conducted a mock town hall based on briefs from historical chemical incidents. Initial and follow-up surveys show that students’ self-efficacy around these skills improved following participation in the educational innovation.
Applications of capillary action in drug delivery
(Cell Press, 2021) Li, Xiaosi; Zhao, Yue; Zhao, Chao; University of Alabama Tuscaloosa; Northwestern Polytechnical University
Contrary to the fact that capillary action is ubiquitous in our daily lives, its role in drug delivery has not attracted attention. Therefore, its application in medicine and disease treatment has not been actively developed. This perspective begins by reviewing the principles, advantages, and limitations of the three existing drug delivery strategies: non-covalent interaction, cavity loading, and covalent conjugation. Then, we discussed the principle of capillary action in drug delivery and the influencing factors that determine its performance. To illustrate the advantages of capillary action over existing drug delivery strategies and how the capillary action could potentially address the shortcomings of the existing drug delivery strategies, we described five examples of using capillary action to design drug delivery platforms for disease treatment: marker pen for topical and transdermal drug delivery, microneedle patch with a sponge container for pulsatile drug delivery, core- shell scaffold for sustained release of growth factors, oral bolus for insulin delivery to the esophagus, and semi-hollow floating ball for intravesical and gastroprotective drug delivery. Each of the five drug delivery platforms exhibits certain unique functions that existing drug delivery technologies cannot easily achieve, hence expected to solve specific practical medical problems that are not satisfactorily resolved. As people pay more attention to capillary action and develop more drug delivery platforms, more unique functions and characteristics of capillary action in drug delivery will be explored. Thus, capillary action could become an important choice for drug delivery systems to improve therapeutic drug efficacy, treat diseases, and improve human health.
Automatic food intake detection based on swallowing sounds
(Elsevier, 2012) Makeyev, Oleksandr; Lopez-Meyer, Paulo; Schuckers, Stephanie; Besio, Walter; Sazonov, Edward; University of Rhode Island; University of Alabama Tuscaloosa; Clarkson University
This paper presents a novel fully automatic food intake detectior methodology, an important step toward objective monitoring of ingestive behavior. The aim of such monitoring is to improve our understanding of eating behaviors associated with obesity and eating disorders. The proposed methodology consists of two stages. First, acoustic detection of swallowing instances based on mel-scale Fourier spectrum features and classification using support vector machines is performed. Principal component analysis and a smoothing algorithm are used to improve swallowing detection accuracy. Second, the frequency of swallowing is used as a predictor for detection of food intake episodes. The proposed methodology was tested on data collected from 12 subjects with various degrees of adiposity. Average accuracies of >80% and >75% were obtained for intra-subject and inter-subject models correspondingly with a temporal resolution of 30 s. Results obtained on 44.1 h of data with a total of 7305 swallows show that detection accuracies are comparable for obese and lean subjects. They also suggest feasibility of food intake detection based on swallowing sounds and potential of the proposed methodology for automatic monitoring of ingestive behavior. Based on a wearable non-invasive acoustic sensor the proposed methodology may potentially be used in free-living conditions. (C) 2012 Elsevier Ltd. All rights reserved.
Automatic identification of the number of food items in a meal using clustering techniques based on the monitoring of swallowing and chewing
(Elsevier, 2012) Lopez-Meyer, Paulo; Schuckers, Stephanie; Makeyev, Oleksandr; Fontana, Juan M.; Sazonov, Edward; University of Alabama Tuscaloosa; Clarkson University; University of Rhode Island
The number of distinct foods consumed in a meal is of significant clinical concern in the study of obesity and other eating disorders. This paper proposes the use of information contained in chewing and swallowing sequences for meal segmentation by food types. Data collected from experiments of 17 volunteers were analyzed using two different clustering techniques. First, an unsupervised clustering technique, Affinity Propagation (AP), was used to automatically identify the number of segments within a meal. Second, performance of the unsupervised AP method was compared to a supervised learning approach based on Agglomerative Hierarchical Clustering (AHC). While the AP method was able to obtain 90% accuracy in predicting the number of food items, the AHC achieved an accuracy >95%. Experimental results suggest that the proposed models of automatic meal segmentation may be utilized as part of an integral application for objective Monitoring of Ingestive Behavior in free living conditions. (C) 2011 Elsevier Ltd. All rights reserved.
Automatic Ingestion Monitor: A Novel Wearable Device for Monitoring of Ingestive Behavior
(IEEE, 2014) Fontana, Juan M.; Farooq, Muhammad; Sazonov, Edward; University of Alabama Tuscaloosa; Universidad Nacional Rio Cuarto
Objective monitoring of food intake and ingestive behavior in a free-living environment remains an open problem that has significant implications in study and treatment of obesity and eating disorders. In this paper, a novel wearable sensor system (automatic ingestion monitor, AIM) is presented for objective monitoring of ingestive behavior in free living. The proposed device integrates three sensor modalities that wirelessly interface to a smartphone: a jaw motion sensor, a hand gesture sensor, and an accelerometer. A novel sensor fusion and pattern recognition method was developed for subject-independent food intake recognition. The device and the methodology were validated with data collected from 12 subjects wearing AIM during the course of 24 h in which both the daily activities and the food intake of the subjects were not restricted in any way. Results showed that the system was able to detect food intake with an average accuracy of 89.8%, which suggests that AIM can potentially be used as an instrument to monitor ingestive behavior in free-living individuals.
Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252)
(Springer, 2015) Koo, Hyunmin; Mojib, Nazia; Huang, Jonathan P.; Donahoe, Rona J.; Bej, Asim K.; University of Alabama Birmingham; University of Alabama Tuscaloosa
In this study, we examined the responses by the indigenous bacterial communities in salt-marsh sediment microcosms in vitro following treatment with Mississippi Canyon Block 252 oil (MC252). Microcosms were constructed of sediment and seawater collected from Bayou La Batre located in coastal Alabama on the Gulf of Mexico. We used an amplicon pyrosequencing approach on microcosm sediment metagenome targeting the V3-V5 region of the 16S rRNA gene. Overall, we identified a shift in the bacterial community in three distinct groups. The first group was the early responders (orders Pseudomonadales and Oceanospirillales within class Gammaproteobacteria), which increased their relative abundance within 2 weeks and were maintained 3 weeks after oil treatment. The second group was identified as early, but transient responders (order Rhodobacterales within class Alphaproteobacteria; class Epsilonproteobacteria), which increased their population by 2 weeks, but returned to the basal level 3 weeks after oil treatment. The third group was the late responders (order Clostridiales within phylum Firmicutes; order Methylococcales within class Gammaproteobacteria; and phylum Tenericutes), which only increased 3 weeks after oil treatment. Furthermore, we identified oil-sensitive bacterial taxa (order Chromatiales within class Gammaproteobacteria; order Syntrophobacterales within class Deltaproteobacteria), which decreased in their population after 2 weeks of oil treatment. Detection of alkane (alkB), catechol (C2,3DO) and biphenyl (bph) biodegradation genes by PCR, particularly in oil-treated sediment metacommunity DNA, delineates proliferation of the hydrocarbon degrading bacterial community. Overall, the indigenous bacterial communities in our salt-marsh sediment in vitro microcosm study responded rapidly and shifted towards members of the taxonomic groups that are capable of surviving in an MC252 oil-contaminated environment.
Biomaterial Scaffolds as Pre-metastatic Niche Mimics Systemically Alter the Primary Tumor and Tumor Microenvironment
(Wiley, 2018) Aguado, Brian A.; Hartfield, Rachel M.; Bushnell, Grace G.; Decker, Joseph T.; Azarin, Samira M.; Nanavati, Dhaval; Schipma, Matthew J.; Rao, Shreyas S.; Oakes, Robert S.; Zhang, Yining; Jeruss, Jacqueline S.; Shea, Lonnie D.; Northwestern University; University of Michigan; University of Alabama Tuscaloosa
Primary tumor (PT) immune cells and pre-metastatic niche (PMN) sites are critical to metastasis. Recently, synthetic biomaterial scaffolds used as PMN mimics are shown to capture both immune and metastatic tumor cells. Herein, studies are performed to investigate whether the scaffold-mediated redirection of immune and tumor cells would alter the primary tumor microenvironment (TME). Transcriptomic analysis of PT cells from scaffold-implanted and mock-surgery mice identifies differentially regulated pathways relevant to invasion and metastasis progression. Transcriptomic differences are hypothesized to result from scaffold-mediated modulations of immune cell trafficking and phenotype in the TME. Culturing tumor cells with conditioned media generated from PT immune cells of scaffold-implanted mice decrease invasion in vitro more than two-fold relative to mock surgery controls and reduce activity of invasion-promoting transcription factors. Secretomic characterization of the conditioned media delineates interactions between immune cells in the TME and tumor cells, showing an increase in the pan-metastasis inhibitor decorin and a concomitant decrease in invasion-promoting chemokine (C-C motif) ligand 2 (CCL2) in scaffold-implanted mice. Flow cytometric and transcriptomic profiling of PT immune cells identify phenotypically distinct tumor-associated macrophages (TAMs) in scaffold-implanted mice, which may contribute to an invasion-suppressive TME. Taken together, this study demonstrates biomaterial scaffolds systemically influence metastatic progression through manipulation of the TME.
Carbon Capture Utilization and Storage in Methanol Production Using a Dry Reforming-Based Chemical Looping Technology
(American Chemical Society, 2022) Ugwu, Ambrose; Osman, Mogahid; Zaabout, Abdelghafour; Amini, Shahriar; Norwegian University of Science & Technology (NTNU); SINTEF; University of Alabama Tuscaloosa
This further investigates the concept of gas switching dry reforming (GSDR) that efficiently converts the two major greenhouse gases (CO2 and CH4) into a valuable product (syngas) for gas-to-liquid (GTL) syntheses. The proposed GSDR is based on chemical looping technology but avoids external circulation of solids (metal oxides) by alternating the supply of reducing and oxidizing gas into a single fluidized bed reactor to achieve redox cycles. Each cycle consists of three steps where a metal oxide/catalyst is first reduced using GTL offgases to produce CO2 (and steam) that is supplied to the next reforming step to produce syngas for GTL processes. The metal oxide is then reoxidized in the third step associated with heat generation (through the exothermic oxidation reaction of the metal oxide and air) to provide the heat needed for the endothermic dry methane reforming step. Experimental demonstrations have shown that a syngas H-2/CO molar ratio between 1 and 2 suitable for methanol production could be achieved. A further demonstration shows that pressure has negative effects on gas conversion. Following the successful experimental campaign, process simulations were completed using ASPEN to show how the GSDR process can be integrated into a methanol (MeOH) production plant.
The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin
(BMC, 2015) Leliaert, Frederik; Lopez-Bautista, Juan M.; University of Alabama Tuscaloosa; Ghent University
Background: Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified). Results: Both DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region. Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta. Conclusions: The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta. The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae.
A CNN-LSTM neural network for recognition of puffing in smoking episodes using wearable sensors
(Springer Nature, 2020) Senyurek, Volkan Y.; Imtiaz, Masudul H.; Belsare, Prajakta; Tiffany, Stephen; Sazonov, Edward; University of Alabama Tuscaloosa; State University of New York (SUNY) Buffalo
A detailed assessment of smoking behavior under free-living conditions is a key challenge for health behavior research. A number of methods using wearable sensors and puff topography devices have been developed for smoking and individual puff detection. In this paper, we propose a novel algorithm for automatic detection of puffs in smoking episodes by using a combination of Respiratory Inductance Plethysmography and Inertial Measurement Unit sensors. The detection of puffs was performed by using a deep network containing convolutional and recurrent neural networks. Convolutional neural networks (CNN) were utilized to automate feature learning from raw sensor streams. Long Short Term Memory (LSTM) network layers were utilized to obtain the temporal dynamics of sensor signals and classify sequence of time segmented sensor streams. An evaluation was performed by using a large, challenging dataset containing 467 smoking events from 40 participants under free-living conditions. The proposed approach achieved an F1-score of 78% in leave-one-subject-out cross-validation. The results suggest that CNN-LSTM based neural network architecture sufficiently detect puffing episodes in free-living condition. The proposed model be used as a detection tool for smoking cessation programs and scientific research.
Co-culturing experiments reveal the uptake of myo-inositol phosphate synthase (EC 5.5.1.4) in an inositol auxotroph of Saccharomyces cerevisiae
(BMC, 2021) Steele, Erika; Alebous, Hana D.; Vickers, Macy; Harris, Mary E.; Johnson, Margaret D.; University of Alabama Tuscaloosa; University of Jordan
BackgroundMyo-Inositol Phosphate Synthase (MIP) catalyzes the conversion of glucose 6- phosphate into inositol phosphate, an essential nutrient and cell signaling molecule. Data obtained, first in bovine brain and later in plants, established MIP expression in organelles and in extracellular environments. A physiological role for secreted MIP has remained elusive since its first detection in intercellular space. To provide further insight into the role of MIP in intercellular milieus, we tested the hypothesis that MIP may function as a growth factor, synthesizing inositol phosphate in intercellular locations requiring, but lacking ability to produce or transport adequate quantities of the cell-cell communicator. This idea was experimentally challenged, utilizing a Saccharomyces cerevisiae inositol auxotroph with no MIP enzyme, permeable membranes with a 0.4 mu m pore size, and cellular supernatants as external sources of inositol isolated from S. cerevisiae cells containing either wild-type enzyme (Wt-MIP), no MIP enzyme, auxotroph (Aux), or a green fluorescent protein (GFP) tagged reporter enzyme (MIP- GFP) in co- culturing experiments.ResultsResulting cell densities and microscopic studies with corroborating biochemical and molecular analyses, documented sustained growth of Aux cells in cellular supernatant, concomitant with the uptakeof MIP, detected as MIP-GFP reporter enzyme. These findings revealed previously unknown functions, suggesting that the enzyme can: (1) move into and out of intercellular space, (2) traverse cell walls, and (3) act as a growth factor to promote cellular proliferation of an inositol requiring cell.ConclusionsCo-culturing experiments, designed to test a probable function for MIP secreted in extracellular vesicles, uncovered previously unknown functions for the enzyme and advanced current knowledge concerning spatial control of inositol phosphate biosynthesis. Most importantly, resulting data identified an extracellular vesicle (a non-viral vector) that is capable of synthesizing and transporting inositol phosphate, a biological activity that can be used to enhance specificity of current inositol phosphate therapeutics.
Combined Syngas and Hydrogen Production using Gas Switching Technology
(American Chemical Society, 2021) Ugwu, Ambrose; Zaabout, Abdelghafour; Donat, Felix; van Diest, Geert; Albertsen, Knuth; Muller, Christoph; Amini, Shahriar; SINTEF; Swiss Federal Institutes of Technology Domain; ETH Zurich; University of Alabama Tuscaloosa; Norwegian University of Science & Technology (NTNU)
This paper focuses on the experimental demonstration of a threestage GST (gas switching technology) process (fuel, steam/CO2, and air stages) for syngas production from methane in the fuel stage and H-2/CO production in the steam/ CO2 stage using a lanthanum- based oxygen carrier (La0.85Sr0.15Fe0.95Al0.05O3). Experiments were performed at temperatures between 750-950 degrees C and pressures up to 5 bar. The results show that the oxygen carrier exhibits high selectivity to oxidizing methane to syngas at the fuel stage with improved process performance with increasing temperature although carbon deposition could not be avoided. Co-feeding CO2 with CH4 at the fuel stage reduced carbon deposition significantly, thus reducing the syngas H-2/CO molar ratio from 3.75 to 1 (at CO2/CH4 ratio of 1 at 950 degrees C and 1 bar). The reduced carbon deposition has maximized the purity of the H-2 produced in the consecutive steam stage thus increasing the process attractiveness for the combined production of syngas and pure hydrogen. Interestingly, the cofeeding of CO2 with CH4 at the fuel stage showed a stable syngas production over 12 hours continuously and maintained the H-2/CO ratio at almost unity, suggesting that the oxygen carrier was exposed to simultaneous partial oxidation of CH4 with the lattice oxygen which was restored instantly by the incoming CO2. Furthermore, the addition of steam to the fuel stage could tune up the H-2/CO ratio beyond 3 without carbon deposition at H2O/ CH4 ratio of 1 at 950 degrees C and 1 bar; making the syngas from gas switching partial oxidation suitable for different downstream processes, for example, gas-to-liquid processes. The process was also demonstrated at higher pressures with over 70% fuel conversion achieved at 5 bar and 950 degrees C.
Comparative proteomic analysis of three Chinese hamster ovary (CHO) host cells
(Elsevier, 2017) Xu, Ningning; Ma, Chao; Ou, Jianfa; Sun, Wanqi Wendy; Zhou, Lufang; Hu, Hui; Liu, Xiaoguang Margaret; University of Alabama Birmingham; University of Alabama Tuscaloosa
Chinese hamster ovary (CHO)1 cells have been widely used to express heterologous genes and produce therapeutic proteins in biopharmaceutical industry. Different CHO host cells have distinct cell growth rates and protein expression characteristics. In this study, the expression of about 1307 host proteins in three sublines, i.e. CHO K1, CHO S and CHO/dihydrofolate reductase (dhfr)(-), were investigated and compared using proteomic analysis. The proteins involved in cell growth, glycolysis, tricarboxylic acid cycle, transcription, translation and glycosylation were quantitated using Liquid chromatography tandem-mass spectrometry (LC-MS/MS). The key host cell proteins that regulate the kinetics of cell growth and the magnitude of protein expression levels were identified. Furthermore, several rational cell engineering strategies on how to combine the desired features of fast cell growth and efficient production of therapeutic proteins into one new super CHO host cell have been proposed. (C) 2017 Elsevier B.V. All rights reserved.
Computation of Cigarette Smoke Exposure Metrics From Breathing
(IEEE, 2020) Belsare, Prajakta; Senyurek, Volkan Yusuf; Imtiaz, Masudul H.; Tiffany, Stephen; Sazonov, Edward; University of Alabama Tuscaloosa; State University of New York (SUNY) Buffalo
Traditional metrics of smoke exposure in cigarette smokers are derived either from self-report, biomarkers, or puff topography. Methods involving biomarkers measure concentrations of nicotine, nicotine metabolites, or carbon monoxide. Puff-topography methods employ portable instruments to measure puff count, puff volume, puff duration, and inter-puff interval. In this article, we propose smoke exposure metrics calculated from the breathing signal and describe a novel algorithm for the computation of these metrics. The Personal Automatic Cigarette Tracker v2 (PACT-2) sensors, puff topography devices (CReSS), and video observation were used in a study of 38 moderate to heavy smokers in a controlled environment. Parameters of smoke inhalation including the start and end of each puff, inhale and exhale cycle, and smoke holding were computed from the breathing signal. From these, the traditional metrics of puff duration, inhale-exhale cycle duration, smoke holding duration, inter-puff interval, and novel Respiratory Smoke Exposure Metrics (RSEMs) such as inhale-exhale cycle volume, and inhale-exhale volume over time were calculated. The proposed RSEM algorithm to extract smoke exposure metrics named generated interclass correlations (ICCs) of 0.85 and 0.87 and Pearson's correlations of 0.97 and 0.77 with video observation and CReSS, respectively, for puff duration. Similarly, for the inhale-exhale duration, an ICC of 0.84 and Pearson's correlation of 0.81 was obtained with video observation. The RSEMs provided measures previously unavailable in research that are proportional to the depth and duration of smoke inhalation. The results suggest that the breathing signal may be used to compute smoke exposure metrics.
Confinement Effects on Carbon Dioxide Methanation: A Novel Mechanism for Abiotic Methane Formation
(Nature Portfolio, 2017) Le, Thu; Striolo, Alberto; Turner, C. Heath; Cole, David R.; University of London; University College London; University of Alabama Tuscaloosa; Ohio State University
An important scientific debate focuses on the possibility of abiotic synthesis of hydrocarbons during oceanic crust-seawater interactions. While on-site measurements near hydrothermal vents support this possibility, laboratory studies have provided data that are in some cases contradictory. At conditions relevant for sub-surface environments it has been shown that classic thermodynamics favour the production of CO2 from CH4, while abiotic methane synthesis would require the opposite. However, confinement effects are known to alter reaction equilibria. This report shows that indeed thermodynamic equilibrium can be shifted towards methane production, suggesting that thermal hydrocarbon synthesis near hydrothermal vents and deeper in the magma-hydrothermal system is possible. We report reactive ensemble Monte Carlo simulations for the CO2 methanation reaction. We compare the predicted equilibrium composition in the bulk gaseous phase to that expected in the presence of confinement. In the bulk phase we obtain excellent agreement with classic thermodynamic expectations. When the reactants can exchange between bulk and a confined phase our results show strong dependency of the reaction equilibrium conversions, XCO2, on nanopore size, nanopore chemistry, and nanopore morphology. Some physical conditions that could shift significantly the equilibrium composition of the reactive system with respect to bulk observations are discussed.
Controlling Electron Transfer between the Two Cofactor Chains of Photosystem I by the Redox State of One of Their Components
(Cell Press, 2015) Santabarbara, Stefano; Bullock, Bradford; Rappaport, Fabrice; Redding, Kevin E.; Arizona State University; Arizona State University-Tempe; UDICE-French Research Universities; Sorbonne Universite; Centre National de la Recherche Scientifique (CNRS); CNRS - National Institute for Biology (INSB); Consiglio Nazionale delle Ricerche (CNR); Istituto di Biofisica (IBF-CNR); University of Alabama Tuscaloosa
Two functional electron transfer (ET) chains, related by a pseudo-C-2 symmetry, are present in the reaction center of photosystem I (PSI). Due to slight differences in the environment around the cofactors of the two branches, there are differences in both the kinetics of ET and the proportion of ET that occurs on the two branches. The strongest evidence that this is indeed the case relied on the observation that the oxidation rates of the reduced phylloquinone (PhQ) cofactor differ by an order of magnitude. Site-directed mutagenesis of residues involved in the respective PhQ-binding sites resulted in a specific alteration of the rates of semiquinone oxidation. Here, we show that the PsaA-F689N mutation results in an similar to 100-fold decrease in the observed rate of PhQ(A)(-) oxidation. This is the largest change of PhQ(A)(-) oxidation kinetics observed so far for a single-point mutation, resulting in a lifetime that exceeds that of the terminal electron donor, P-700(+). This situation allows a second photochemical charge separation event to be initiated before PhQ(A)(-) has decayed, thereby mimicking in PSI a situation that occurs in type II reaction centers. The results indicate that the presence of PhQ(A)(-) does not impact the overall quantum yield and leads to an almost complete redistribution of the fractional utilization of the two functional ET chains, in favor of the one that does not bear the charged species. The evolutionary implications of these results are also briefly discussed.
Detection of Diazotrophy in the Acetylene-Fermenting Anaerobe Pelobacter sp Strain SFB93
(American Society of Microbiology, 2017) Akob, Denise M.; Baesman, Shaun M.; Sutton, John M.; Fierst, Janna L.; Mumford, Adam C.; Shrestha, Yesha; Poret-Peterson, Amisha T.; Bennett, Stacy; Dunlap, Darren S.; Haase, Karl B.; Oremland, Ronald S.; United States Department of the Interior; United States Geological Survey; University of Alabama Tuscaloosa; United States Department of Agriculture (USDA); Boeing
Acetylene (C2H2) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C2H2 block assays of N2O reductase, and Pelobacter acetylenicus was shown to grow on C2H2 via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N(2)ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N(2)ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N(2)ase. Diazotrophic growth was observed under N-2 but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N(2)ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days. IMPORTANCE Here we show that a single Pelobacter strain can grow via acetylene fermentation and carry out nitrogen fixation, using the only two enzymes known to transform acetylene. These findings provide new insights into acetylene transformations and adaptations for nutrient (C and N) and energy acquisition by microorganisms. Enhanced understanding of acetylene transformations (i.e., extent, occurrence, and rates) in modern environments is important for the use of acetylene as a potential biomarker for extraterrestrial life and for degradation of anthropogenic contaminants.
Determining iron oxide nanoparticle heating efficiency and elucidating local nanoparticle temperature for application in agarose gel-based tumor model
(Elsevier, 2016) Shah, Rhythm R.; Dombrowsky, Alexander R.; Paulson, Abigail L.; Johnson, Margaret P.; Nikles, David E.; Brazel, Christopher S.; University of Alabama Tuscaloosa
Magnetic iron oxide nanoparticles (MNPs) have been developed for magnetic fluid hyperthermia (MFH) cancer therapy, where cancer cells are treated through the heat generated by application of a high frequency magnetic field. This heat has also been proposed as a mechanism to trigger release of chemotherapy agents. In each of these cases, MNPs with optimal heating performance can be used to maximize therapeutic effect while minimizing the required dosage of MNPs. In this study, the heating efficiencies (or specific absorption rate, SAR) of two types of MNPs were evaluated experimentally and then predicted from their magnetic properties. MNPs were also incorporated in the core of poly(ethylene glycol-b-caprolactone) micelles, co-localized with rhodamine B fluorescent dye attached to polycaprolactone to monitor local, nanoscale temperatures during magnetic heating. Despite a relatively high SAR produced by these MNPs, no significant temperature rise beyond that observed in the bulk solution was measured by fluorescence in the core of the magnetic micelles. MNPs were also incorporated into a macro-scale agarose gel system that mimicked a tumor targeted by MNPs and surrounded by healthy tissues. The agarose-based tumor models showed that targeted MNPs can reach hyperthermia temperatures inside a tumor with a sufficient MNP concentration, while causing minimal temperature rise in the healthy tissue surrounding the tumor. (C) 2016 Elsevier B.V. All rights reserved.

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