Research and Publications - Department of Chemical & Biological Engineering

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Direct and Indirect Influence of Parental Bedrock on Streambed Microbial Community Structure in Forested Streams
(American Society of Microbiology, 2011) Mosher, Jennifer J.; Findlay, Robert H.; University of Alabama Tuscaloosa
A correlative study was performed to determine if variation in streambed microbial community structure in low-order forested streams can be directly or indirectly linked to the chemical nature of the parental bedrock of the environments through which the streams flow. Total microbial and photosynthetic biomass (phospholipid phosphate [PLP] and chlorophyll a), community structure (phospholipid fatty acid analysis), and physical and chemical parameters were measured in six streams, three located in sandstone and three in limestone regions of the Bankhead National Forest in northern Alabama. Although stream water flowing through the two different bedrock types differed significantly in chemical composition, there were no significant differences in total microbial and photosynthetic biomass in the sediments. In contrast, sedimentary microbial community structure differed between the bedrock types and was significantly correlated with stream water ion concentrations. A pattern of seasonal variation in microbial community structure was also observed. Further statistical analysis indicated dissolved organic matter (DOM) quality, which was previously shown to be influenced by geological variation, correlated with variation in bacterial community structure. These results indicate that the geology of underlying bedrock influences benthic microbial communities directly via changes in water chemistry and also indirectly via stream water DOM quality.
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 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.
U(VI) Reduction in Sulfate-Reducing Subsurface Sediments Amended with Ethanol or Acetate
(American Society of Microbiology, 2013) Converse, Brandon J.; Wu, Tao; Findlay, Robert H.; Rodena, Eric E.; University of Wisconsin Madison; University of Alabama Tuscaloosa
An experiment was conducted with subsurface sediments from Oak Ridge National Laboratory to determine the potential for reduction of U(VI) under sulfate-reducing conditions with either ethanol or acetate as the electron donor. The results showed extensive U(VI) reduction in sediments supplied with either electron donor, where geochemical and microbiological analyses demonstrated active sulfate reduction.
A novel approach for food intake detection using electroglottography
(IOP, 2014) Farooq, Muhammad; Fontana, Juan M.; Sazonov, Edward; University of Alabama Tuscaloosa
Many methods for monitoring diet and food intake rely on subjects self-reporting their daily intake. These methods are subjective, potentially inaccurate and need to be replaced by more accurate and objective methods. This paper presents a novel approach that uses an electroglottograph (EGG) device for an objective and automatic detection of food intake. Thirty subjects participated in a four-visit experiment involving the consumption of meals with self-selected content. Variations in the electrical impedance across the larynx caused by the passage of food during swallowing were captured by the EGG device. To compare performance of the proposed method with a well-established acoustical method, a throat microphone was used for monitoring swallowing sounds. Both signals were segmented into non-overlapping epochs of 30 s and processed to extract wavelet features. Subject-independent classifiers were trained, using artificial neural networks, to identify periods of food intake from the wavelet features. Results from leave-one-out cross validation showed an average per-epoch classification accuracy of 90.1% for the EGG-based method and 83.1% for the acoustic-based method, demonstrating the feasibility of using an EGG for food intake detection.
Linker-free conjugation and specific cell targeting of antibody functionalized iron-oxide nanoparticles
(Royal Society of Chemistry, 2014) Xu, Yaolin; Baiu, Dana C.; Sherwood, Jennifer A.; McElreath, Meghan R.; Qin, Ying; Lackey, Kimberly H.; Otto, Mario; Bao, Yuping; University of Alabama Tuscaloosa; University of Wisconsin Madison
Specific targeting is a key step to realize the full potential of iron oxide nanoparticles in biomedical applications, especially tumor-associated diagnosis and therapy. Here, we developed anti-GD2 antibody conjugated iron oxide nanoparticles for highly efficient neuroblastoma cell targeting. The antibody conjugation was achieved through an easy, linker-free method based on catechol reactions. The targeting efficiency and specificity of the antibody-conjugated nanoparticles to GD2-positive neuroblastoma cells were confirmed by flow cytometry, fluorescence microscopy, Prussian blue staining and transmission electron microscopy. These detailed studies indicated that the receptor-recognition capability of the antibody was fully retained after conjugation and the conjugated nanoparticles quickly attached to GD2-positive cells within four hours. Interestingly, longer treatment (12 h) led the cell membrane-bound nanoparticles to be internalized into cytosol, either by directly penetrating the cell membrane or escaping from the endosomes. Last but importantly, the uniquely designed functional surfaces of the nanoparticles allow for easy conjugation of other bioactive molecules.
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.
Formation mechanism of chalcogenide nanocrystals confined inside genetically engineered virus-like particles
(Nature Portfolio, 2014) Zhou, Ziyou; Bedwell, Gregory J.; Li, Rui; Prevelige, Peter E., Jr.; Gupta, Arunava; University of Alabama Tuscaloosa; University of Alabama Birmingham
Engineered virus-like particles (VLP) are attractive for fabricating nanostructured materials for applications in diverse areas such as catalysis, drug delivery, biomedicine, composites, etc. Basic understanding of the interaction between the inorganic guest and biomolecular host is thus important for the controlled synthesis of inorganic nanoparticles inside VLP and rational assembly of ordered VLP-based hierarchical nanostructures. We have investigated in detail the formation mechanism and growth kinetics of semiconducting nanocrystals confined inside genetically engineered bacteriophage P22 VLP using semiconducting CdS as a prototypical example. The selective nucleation and growth of CdS at the engineered sites is found to be uniform during the early stage, followed by a more stochastic growth process. Furthermore, kinetic studies reveal that the presence of an engineered biotemplate helps in significantly retarding the reaction rate. These findings provide guidance for the controlled synthesis of a wide range of other inorganic materials confined inside VLP, and are of practical importance for the rational design of VLP-based hierarchical nanostuctures.
Efficient Thermolysis Route to Monodisperse Cu2ZnSnS4 Nanocrystals with Controlled Shape and Structure
(Nature Portfolio, 2014) Zhang, Xiaoyan; Guo, Guobiao; Ji, Cheng; Huang, Kai; Zha, Chenyang; Wang, Yifeng; Shen, Liming; Gupta, Arunava; Bao, Ningzhong; Nanjing Tech University; University of Alabama Tuscaloosa
Monodisperse Cu2ZnSnS4 (CZTS) nanocrystals with tunable shape, crystalline phase, and composition are synthesized by efficient thermolysis of a single source precursor of mixed metal-oleate complexes in hot organic solvents with dissolved sulfur sources. Suitable tuning of the synthetic conditions and the Cu/(Zn + Sn) ratio of the precursor has enabled precise control of the crystalline phase in the form of kesterite, or a newly observed wurtzite structure. Nanocrystals with morphology in the form of spherical, rice-like, or rod-like shapes are obtained over a wide range of compositions (0.5 <= Cu/(Zn + Sn) <= 1.2). Both the final products and intermediates for each shape exhibit consistent composition and structure, indicating homogenous nucleation and growth of single-phase nanocrystals. Thin films prepared from colloidal nanocrystal suspensions display interesting shape-dependent photoresponse behavior under white light illumination from a solar simulator.
The genomes of two key bumblebee species with primitive eusocial organization
(BMC, 2015) Sadd, Ben M.; Barribeau, Seth M.; Bloch, Guy; de Graaf, Dirk C.; Dearden, Peter; Elsik, Christine G.; Gadau, Juergen; Grimmelikhuijzen, Cornelis J. P.; Hasselmann, Martin; Lozier, Jeffrey D.; Robertson, Hugh M.; Smagghe, Guy; Stolle, Eckart; Van Vaerenbergh, Matthias; Waterhouse, Robert M.; Bornberg-Bauer, Erich; Klasberg, Steffen; Bennett, Anna K.; Camara, Francisco; Guigo, Roderic; Hoff, Katharina; Mariotti, Marco; Munoz-Torres, Monica; Murphy, Terence; Santesmasses, Didac; Amdam, Gro V.; Beckers, Matthew; Beye, Martin; Biewer, Matthias; Bitondi, Marcia M. G.; Blaxter, Mark L.; Bourke, Andrew F. G.; Brown, Mark J. F.; Buechel, Severine D.; Cameron, Rossanah; Cappelle, Kaat; Carolan, James C.; Christiaens, Olivier; Ciborowski, Kate L.; Clarke, David F.; Colgan, Thomas J.; Collins, David H.; Cridge, Andrew G.; Dalmay, Tamas; Dreier, Stephanie; du Plessis, Louis; Duncan, Elizabeth; Erler, Silvio; Evans, Jay; Falcon, Tiago; Flores, Kevin; Freitas, Flavia C. P.; Fuchikawa, Taro; Gempe, Tanja; Hartfelder, Klaus; Hauser, Frank; Helbing, Sophie; Humann, Fernanda C.; Irvine, Frano; Jermiin, Lars S.; Johnson, Claire E.; Johnson, Reed M.; Jones, Andrew K.; Kadowaki, Tatsuhiko; Kidner, Jonathan H.; Koch, Vasco; Koehler, Arian; Kraus, F. Bernhard; Lattorff, H. Michael G.; Leask, Megan; Lockett, Gabrielle A.; Mallon, Eamonn B.; Antonio, David S. Marco; Marxer, Monika; Meeus, Ivan; Moritz, Robin F. A.; Nair, Ajay; Napflin, Kathrin; Nissen, Inga; Niu, Jinzhi; Nunes, Francis M. F.; Oakeshott, John G.; Osborne, Amy; Otte, Marianne; Pinheiro, Daniel G.; Rossie, Nina; Rueppell, Olav; Santos, Carolina G.; Schmid-Hempel, Regula; Schmitt, Bjoern D.; Schulte, Christina; Simoes, Zila L. P.; Soares, Michelle P. M.; Swevers, Luc; Winnebeck, Eva C.; Wolschin, Florian; Yu, Na; Zdobnov, Evgeny M.; Aqrawi, Peshtewani K.; Blankenburg, Kerstin P.; Coyle, Marcus; Francisco, Liezl; Hernandez, Alvaro G.; Holder, Michael; Hudson, Matthew E.; Jackson, LaRonda; Jayaseelan, Joy; Joshi, Vandita; Kovar, Christie; Lee, Sandra L.; Mata, Robert; Mathew, Tittu; Newsham, Irene F.; Ngo, Robin; Okwuonu, Geoffrey; Pham, Christopher; Pu, Ling-Ling; Saada, Nehad; Santibanez, Jireh; Simmons, DeNard; Thornton, Rebecca; Venkat, Aarti; Walden, Kimberly K. O.; Wu, Yuan-Qing; Debyser, Griet; Devreese, Bart; Asher, Claire; Blommaert, Julie; Chipman, Ariel D.; Chittka, Lars; Fouks, Bertrand; Liu, Jisheng; O'Neill, Meaghan P.; Sumner, Seirian; Puiu, Daniela; Qu, Jiaxin; Salzberg, Steven L.; Scherer, Steven E.; Muzny, Donna M.; Richards, Stephen; Robinson, Gene E.; Gibbs, Richard A.; Schmid-Hempel, Paul; Worley, Kim C.; Illinois State University; Swiss Federal Institutes of Technology Domain; ETH Zurich; University of North Carolina; East Carolina University; Hebrew University of Jerusalem; Ghent University; University of Otago; University of Missouri Columbia; Georgetown University; Arizona State University; Arizona State University-Tempe; University of Copenhagen; University Hohenheim; University of Alabama Tuscaloosa; University of Illinois Urbana-Champaign; Martin Luther University Halle Wittenberg; University of Geneva; Swiss Institute of Bioinformatics; Massachusetts Institute of Technology (MIT); Harvard University; Broad Institute; University of Munster; Barcelona Institute of Science & Technology; Pompeu Fabra University; Centre de Regulacio Genomica (CRG); Ernst Moritz Arndt Universitat Greifswald; University of California Berkeley; United States Department of Energy (DOE); Lawrence Berkeley National Laboratory; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); University of East Anglia; Heinrich Heine University Dusseldorf; University of Cologne; Universidade de Sao Paulo; University of Edinburgh; University of London; Royal Holloway University London; University of Bristol; Commonwealth Scientific & Industrial Research Organisation (CSIRO); Trinity College Dublin; Zoological Society of London; United States Department of Agriculture (USDA); North Carolina State University; Kyoto University; Instituto Federal de Sao Paulo (IFSP); Ohio State University; Oxford Brookes University; University of Southampton; University of Leicester; Universidade Federal de Sao Carlos; Universidade Estadual Paulista; University of North Carolina Greensboro; National Centre of Scientific Research "Demokritos"; University of Munich; Baylor College of Medicine; UTMD Anderson Cancer Center; University of Chicago; Queen Mary University London; Guangzhou University; Johns Hopkins University
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
Direct conversion of theophylline to 3-methylxanthine by metabolically engineered E-coli
(BMC, 2015) Algharrawi, Khalid H. R.; Summers, Ryan M.; Gopishetty, Sridhar; Subramanian, Mani; University of Iowa; University of Alabama Tuscaloosa; University of Baghdad
Background: Methylxanthines are natural and synthetic compounds found in many foods, drinks, pharmaceuticals, and cosmetics. Aside from caffeine, production of many methylxanthines is currently performed by chemical synthesis. This process utilizes many chemicals, multiple reactions, and different reaction conditions, making it complicated, environmentally dissatisfactory, and expensive, especially for monomethylxanthines and paraxanthine. A microbial platform could provide an economical, environmentally friendly approach to produce these chemicals in large quantities. The recently discovered genes in our laboratory from Pseudomonas putida, ndmA, ndmB, and ndmD, provide an excellent starting point for precisely engineering Escherichia coli with various gene combinations to produce specific high-value paraxanthine and 1-, 3-, and 7-methylxanthines from any of the economical feedstocks including caffeine, theobromine or theophylline. Here, we show the first example of direct conversion of theophylline to 3-methylxanthine by a metabolically engineered strain of E. coli. Results: Here we report the construction of E. coli strains with ndmA and ndmD, capable of producing 3-methylxanthine from exogenously fed theophylline. The strains were engineered with various dosages of the ndmA and ndmD genes, screened, and the best strain was selected for large-scale conversion of theophylline to 3-methylxanthine. Strain pDdA grown in super broth was the most efficient strain; 15 mg/mL cells produced 135 mg/L (0.81 mM) 3-methylxanthine from 1 mM theophylline. An additional 21.6 mg/L (0.13 mM) 1-methylxanthine were also produced, attributed to slight activity of NdmA at the N-3-position of theophylline. The 1- and 3-methylxanthine products were separated by preparative chromatography with less than 5 % loss during purification and were identical to commercially available standards. Purity of the isolated 3-methylxanthine was comparable to a commercially available standard, with no contaminant peaks as observed by liquid chromatography-mass spectrophotometry or nuclear magnetic resonance. Conclusions: We were able to biologically produce and separate 100 mg of highly pure 3-methylxanthine from theophylline (1,3-dimethylxanthine). The N-demethylation reaction was catalyzed by E. coli engineered with N-demethylase genes, ndmA and ndmD. This microbial conversion represents a first step to develop a new biological platform for the production of methylxanthines from economical feedstocks such as caffeine, theobromine, and theophylline.
Endoplasmic reticulum stress impairment in the spinal dorsal horn of a neuropathic pain model
(Nature Portfolio, 2015) Zhang, Enji; Yi, Min-Hee; Shin, Nara; Baek, Hyunjung; Kim, Sena; Kim, Eunjee; Kwon, Kisang; Lee, Sunyeul; Kim, Hyun-Woo; Bae, Yong Chul; Kim, Yonghyun; Kwon, O. -Yu; Lee, Won Hyung; Kim, Dong Woon; Chungnam National University; Chungnam National University Hospital; Kyungpook National University; Yanbian University; University of Alabama Tuscaloosa
Endoplasmic reticulum (ER) stress has been implicated in neurodegenerative diseases, but its role in neuropathic pain remains unclear. In this study, we examined the ER stress and the unfolded protein response (UPR) activation in a L5 spinal nerve ligation (SNL)-induced rat neuropathic pain model. SNL-induced neuropathic pain was assessed behaviorally using the CatWalk system, and histologically with microglial activation in the dorsal spinal horn. L5 SNL induced BIP upregulation in the neuron of superficial laminae of dorsal spinal horn. It also increased the level of ATF6 and intracellular localization into the nuclei in the neurons. Moreover, spliced XBP1 was also markedly elevated in the ipsilateral spinal dorsal horn. The PERK-elF2 pathway was activated in astrocytes of the spinal dorsal horn in the SNL model. In addition, electron microscopy revealed the presence of swollen cisternae in the dorsal spinal cord after SNL. Additionally, inhibition of the ATF6 pathway by intrathecal treatment with ATF6 siRNA reduced pain behaviors and BIP expression in the dorsal horn. The results suggest that ER stress might be involved in the induction and maintenance of neuropathic pain. Furthermore, a disturbance in UPR signaling may render the spinal neurons vulnerable to peripheral nerve injury or neuropathic pain stimuli.
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.
Genetic characterization of caffeine degradation by bacteria and its potential applications
(Wiley, 2015) Summers, Ryan M.; Mohanty, Sujit K.; Gopishetty, Sridhar; Subramanian, Mani; University of Alabama Tuscaloosa; University of Iowa
The ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. Extensive research into this subject has revealed two distinct pathways, N-demethylation and C-8 oxidation, for bacterial caffeine degradation. However, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. This review article discusses the recent discoveries of the genes responsible for both N-demethylation and C-8 oxidation. All of the genes for the N-demethylation pathway, encoding enzymes in the Rieske oxygenase family, reside on 13.2-kb genomic DNA fragment found in Pseudomonas putidaCBB5. A nearly identical DNA fragment, with homologous genes in similar orientation, is found in Pseudomonas sp. CES. Similarly, genes for C-8 oxidation of caffeine have been located on a 25.2-kb genomic DNA fragment of Pseudomonas sp. CBB1. The C-8 oxidation genes encode enzymes similar to those found in the uric acid metabolic pathway of Klebsiella pneumoniae. Various biotechnological applications of these genes responsible for bacterial caffeine degradation, including bio-decaffeination, remediation of caffeine-contaminated environments, production of chemical and fuels and development of diagnostic tests have also been demonstrated.
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.
Synthesis of Hierarchical Nanoporous Microstructures via the Kirkendall Effect in Chemical Reduction Process
(Nature Portfolio, 2015) Gao, Ling; Pang, Chao; He, Dafang; Shen, Liming; Gupta, Arunava; Bao, Ningzhong; Nanjing Tech University; University of Alabama Tuscaloosa
A series of novel hierarchical nanoporous microstructures have been synthesized through one-step chemical reduction of micron size Cu2O and Co3O4 particles. By controlling the reduction time, nonporous Cu2O microcubes sequentially transform to nanoporous Cu/Cu2O/Cu dented cubic composites and hollow eightling-like Cu microparticles. The mechanism involved in the complex structural evolution is explained based on oxygen diffusion and Kirkendall effect. The nanoporous Cu/Cu2O/Cu dented cubic composites exhibit superior electrochemical performance as compared to solid Cu2O microcubes. The reduction of nonporous Co3O4 also exhibits a uniform sequential reduction process from nonporous Co3O4 to porous Co3O4/CoO composites, porous CoO, porous CoO/Co composites, and porous foam-like Co particles. Nanoscale channels originate from the particle surface and eventually develop inside the entire product, resulting in porous foam-like Co microparticles. The Kirkendall effect is believed to facilitate the formation of porous structures in both processes.
ROCK Inhibition Facilitates In Vitro Expansion of Glioblastoma Stem-Like Cells
(PLOS, 2015) Tilson, Samantha G.; Haley, Elizabeth M.; Triantafillu, Ursula L.; Dozier, David A.; Langford, Catherine P.; Gillespie, G. Yancey; Kim, Yonghyun; University of Alabama Tuscaloosa; University of Alabama Birmingham
Due to their stem-like characteristics and their resistance to existing chemo-and radiation therapies, there is a growing appreciation that cancer stem cells (CSCs) are the root cause behind cancer metastasis and recurrence. However, these cells represent a small subpopulation of cancer cells and are difficult to propagate in vitro. Glioblastoma is an extremely deadly form of brain cancer that is hypothesized to have a subpopulation of CSCs called glioblastoma stem cells (GSCs; also called brain tumor initiating cells, BTICs). We propose the use of selective Rho-kinase (ROCK) inhibitors, Y-27632 and fasudil, to promote GSC/BTIC-like cell survival and propagation in vitro. ROCK inhibitors have been implicated in suppressing apoptosis, and it was hypothesized that they would increase the number of GSC/BTIC-like cells grown in vitro and improve cloning efficiencies. Indeed, our data demonstrate that transient and continuous supplementation of non-toxic concentrations of Y-27632 and fasudil inhibited apoptosis, enhanced the cells' ability to form spheres, and increased stem cell marker expressing GSC/BTIC-like cell subpopulation. Our data indicated that pharmacological and genetic (siRNA) inhibitions of the ROCK pathway facilitates in vitro expansion of GSC/BTIC-like cells. Thus, ROCK pathway inhibition shows promise for future optimization of CSC culture media.
Secretome identification of immune cell factors mediating metastatic cell homing
(Nature Portfolio, 2015) Aguado, Brian A.; Wu, Jia J.; Azarin, Samira M.; Nanavati, Dhaval; Rao, Shreyas S.; Bushnell, Grace G.; Medicherla, Chaitanya B.; Shea, Lonnie D.; Northwestern University; University of Minnesota Twin Cities; University of Alabama Tuscaloosa; University of Michigan; Feinberg School of Medicine
Metastatic cell homing is a complex process mediated in part by diffusible factors secreted from immune cells found at a pre-metastatic niche. We report on connecting secretomics and TRanscriptional Activity CEll aRray (TRACER) data to identify functional paracrine interactions between immune cells and metastatic cells as novel mediators of homing. Metastatic breast cancer mouse models were used to generate a diseased splenocyte conditioned media (D-SCM) containing immune cell secreted factors. MDA-MB-231 metastatic cell activity including cell invasion, migration, transendothelial migration, and proliferation were increased in D-SCM relative to control media. Our D-SCM secretome analysis yielded 144 secreted factor candidates that contribute to increased metastatic cell activity. The functional mediators of homing were identified using MetaCore software to determine interactions between the immune cell secretome and the TRACER-identified active transcription factors within metastatic cells. Among the 5 candidate homing factors identified, haptoglobin was selected and validated in vitro and in vivo as a key mediator of homing. Our studies demonstrate a novel systems biology approach to identify functional signaling factors associated with a cellular phenotype, which provides an enabling tool that complements large-scale protein identification provided by proteomics.
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.
Extracellular matrix mediators of metastatic cell colonization characterized using scaffold mimics of the pre-metastatic niche
(Elsevier, 2016) Aguado, Brian A.; Gaffe, Jordan R.; Nanavati, Dhaval; Rao, Shreyas S.; Bushnell, Grace G.; Azarin, Samira M.; Shea, Lonnie D.; Northwestern University; University of Alabama Tuscaloosa; University of Michigan; University of Minnesota Twin Cities
Metastatic tumor cells colonize the pre-metastatic niche, which is a complex microenvironment consisting partially of extracellular matrix (ECM) proteins. We sought to identify and validate novel contributors to tumor cell colonization using ECM-coated poly(epsilon-caprolactone) (PCL) scaffolds as mimics of the pre metastatic niche. Utilizing orthotopic breast cancer mouse models, fibronectin and collagen IV-coated scaffolds implanted in the subcutaneous space captured colonizing tumor cells, showing a greater than 2-fold increase in tumor cell accumulation at the implant site compared to uncoated scaffolds. As a strategy to identify additional ECM colonization contributors, decellularized matrix (DCM) from lungs and livers containing metastatic tumors were characterized. In vitro, metastatic cell adhesion was increased on DCM coatings from diseased organs relative to healthy DCM. Furthermore, in vivo implantations of diseased DCM-coated scaffolds had increased tumor cell colonization relative to healthy DCM coatings. Mass-spectrometry proteomics was performed on healthy and diseased DCM to identify candidates associated with colonization. Myeloperoxidase was identified as abundantly present in diseased organs and validated as a contributor to colonization using myeloperoxidase-coated scaffold implants. This work identified novel ECM proteins associated with colonization using decellularization and proteomics techniques and validated candidates using a scaffold to mimic the pre-metastatic niche. Statement of Significance The pre-metastatic niche consists partially of ECM proteins that promote metastatic cell colonization to a target organ. We present a biomaterials-based approach to mimic this niche and identify ECM mediators of colonization. Using murine breast cancer models, we implanted microporous PCL scaffolds to recruit colonizing tumor cells in vivo. As a strategy to modulate colonization, we coated scaffolds with various ECM proteins, including decellularized lung and liver matrix from tumor-bearing mice. After characterizing the organ matrices using proteomics, myeloperoxidase was identified as an ECM protein contributing to colonization and validated using our scaffold. Our scaffold provides a platform to identify novel contributors to colonization and allows for the capture of colonizing tumor cells for a variety of downstream clinical applications. (C) 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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