Research and Publications - Department of Chemical & Biological Engineering

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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.
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.
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.
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.
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.
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.
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.
Growth and stress response mechanisms underlying post- feeding regenerative organ growth in the Burmese python
(BMC, 2017) Andrew, Audra L.; Perry, Blair W.; Card, Daren C.; Schield, Drew R.; Ruggiero, Robert P.; McGaugh, Suzanne E.; Choudhary, Amit; Secor, Stephen M.; Castoe, Todd A.; University of Texas Arlington; University of Minnesota Twin Cities; Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; University of Alabama Tuscaloosa
Background: Previous studies examining post-feeding organ regeneration in the Burmese python (Python molurus bivittatus) have identified thousands of genes that are significantly differentially regulated during this process. However, substantial gaps remain in our understanding of coherent mechanisms and specific growth pathways that underlie these rapid and extensive shifts in organ form and function. Here we addressed these gaps by comparing gene expression in the Burmese python heart, liver, kidney, and small intestine across pre- and post-feeding time points (fasted, one day post-feeding, and four days post-feeding), and by conducting detailed analyses of molecular pathways and predictions of upstream regulatory molecules across these organ systems. Results: Identified enriched canonical pathways and upstream regulators indicate that while downstream transcriptional responses are fairly tissue specific, a suite of core pathways and upstream regulator molecules are shared among responsive tissues. Pathways such as mTOR signaling, PPAR/LXR/RXR signaling, and NRF2-mediated oxidative stress response are significantly differentially regulated in multiple tissues, indicative of cell growth and proliferation along with coordinated cell-protective stress responses. Upstream regulatory molecule analyses identify multiple growth factors, kinase receptors, and transmembrane receptors, both within individual organs and across separate tissues. Downstream transcription factors MYC and SREBF are induced in all tissues. Conclusions: These results suggest that largely divergent patterns of post-feeding gene regulation across tissues are mediated by a core set of higher-level signaling molecules. Consistent enrichment of the NRF2-mediated oxidative stress response indicates this pathway may be particularly important in mediating cellular stress during such extreme regenerative growth.
Engineering the pre-metastatic niche
(Nature Portfolio, 2017) Aguado, Brian A.; Bushnell, Grace G.; Rao, Shreyas S.; Jeruss, Jacqueline S.; Shea, Lonnie D.; Northwestern University; University of Michigan; University of Alabama Tuscaloosa
The pre-metastatic niche -the accumulation of aberrant immune cells and extracellular-matrix proteins in target organs primes the initially healthy organ microenvironment and renders it amenable for subsequent colonization by metastatic cancer cells. By attracting metastatic cells, mimics of the pre-metastatic niche offer both diagnostic and therapeutic potential. However, deconstructing the complexity of the niche by identifying the interactions between cell populations as well as the mediatory roles of the immune system, soluble factors, extracellular-matrix proteins and stromal cells has proved challenging. Experimental models are needed to recapitulate niche-population biology in situ and to mediate in vivo tumour-cell homing, colonization and proliferation. In this Review, we outline the biology of the pre-metastatic niche and discuss advances in the engineering of niche-mimicking biomaterials that regulate the behaviour of tumour cells at an implant site. Such 'oncomaterials' offer strategies for the early detection of metastatic events, the inhibition of the formation of the pre-metastatic niche and the attenuation of metastatic progression.
Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation
(Biomed Central, 2017) Sun, Jian; Shi, Jian; Konda, N. V. S. N. Murthy; Campos, Dan; Liu, Dajiang; Nemser, Stuart; Shamshina, Julia; Dutta, Tanmoy; Berton, Paula; Gurau, Gabriela; Rogers, Robin D.; Simmons, Blake A.; Singh, Seema; United States Department of Energy (DOE); Joint BioEnergy Institute - JBEI; Sandia National Laboratories; University of Kentucky; Lawrence Berkeley National Laboratory; University of Alabama Tuscaloosa; McGill University
Background: Biomass pretreatment using certain ionic liquids (ILs) is very efficient, generally producing a substrate that is amenable to saccharification with fermentable sugar yields approaching theoretical limits. Although promising, several challenges must be addressed before an IL pretreatment technology can become commercially viable. One of the most significant challenges is the affordable and scalable recovery and recycle of the IL itself. Pervaporation (PV) is a highly selective and scalable membrane separation process for quantitatively recovering volatile solutes or solvents directly from non-volatile solvents that could prove more versatile for IL dehydration. Results: We evaluated a commercially available PV system for IL dehydration and recycling as part of an integrated IL pretreatment process using 1-ethyl-3-methylimidazolium acetate -([C(2)C(1)Im][OAc]) that has been proven to be very effective as a biomass pretreatment solvent. Separation factors as high as 1500 were observed. We demonstrate that > 99.9 wt% -[C(2)C(1)Im][OAc] can be recovered from aqueous solution (<= 20 wt% IL) and recycled five times. A preliminary technoeconomic analysis validated the promising role of PV in improving overall biorefinery process economics, especially in the case where other IL recovery technologies might lead to significant losses. Conclusions: These findings establish the foundation for further development of PV as an effective method of recovering and recycling ILs using a commercially viable process technology.
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.
Tissue Anisotropy Modeling Using Soft Composite Materials
(Hindawi, 2018) Chanda, Arnab; Callaway, Christian; University of Alabama Tuscaloosa; University of Pittsburgh
Soft tissues in general exhibit anisotropic mechanical behavior, which varies in three dimensions based on the location of the tissue in the body. In the past, there have been few attempts to numerically model tissue anisotropy using composite-based formulations (involving fibers embedded within a matrix material). However, so far, tissue anisotropy has not been modeled experimentally. In the current work, novel elastomer-based soft composite materials were developed in the form of experimental test coupons, to model the macroscopic anisotropy in tissue mechanical properties. A soft elastomer matrix was fabricated, and fibers made of a stiffer elastomer material were embedded within the matrix material to generate the test coupons. The coupons were tested on a mechanical testing machine, and the resulting stress-versus-stretch responses were studied. The fiber volume fraction (FVF), fiber spacing, and orientations were varied to estimate the changes in the mechanical responses. The mechanical behavior of the soft composites was characterized using hyperelastic material models such as Mooney-Rivlin's, Humphrey's, and VerondaWestmann's model and also compared with the anisotropic mechanical behavior of the human skin, pelvic tissues, and brain tissues. This work lays the foundation for the experimental modelling of tissue anisotropy, which combined with microscopic studies on tissues can lead to refinements in the simulation of localized fiber distribution and orientations, and enable the development of biofidelic anisotropic tissue phantom materials for various tissue engineering and testing applications.
Host-associated microbiomes are predicted by immune system complexity and climate
(BMC, 2020) Woodhams, Douglas C.; Bletz, Molly C.; Becker, C. Guilherme; Bender, Hayden A.; Buitrago-Rosas, Daniel; Diebboll, Hannah; Huynh, Roger; Kearns, Patrick J.; Kueneman, Jordan; Kurosawa, Emmi; LaBumbard, Brandon C.; Lyons, Casandra; McNally, Kerry; Schliep, Klaus; Shankar, Nachiket; Tokash-Peters, Amanda G.; Vences, Miguel; Whetstone, Ross; University of Massachusetts Boston; Smithsonian Institution; Smithsonian Tropical Research Institute; University of Alabama Tuscaloosa; University of Rwanda; Braunschweig University of Technology
Background Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors. Results Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate. Conclusions Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.
Semicontinuous sophorolipid fermentation using a novel bioreactor with dual ventilation pipes and dual sieve-plates coupled with a novel separation system
(Wiley, 2018) Zhang, Yaguang; Jia, Dan; Sun, Wanqi; Yang, Xue; Zhang, Chuanbo; Zhao, Fanglong; Lu, Wenyu; Tianjin University; University of Alabama Tuscaloosa
Sophorolipids (SLs) are biosurfactants with widespread applications. The yield and purity of SLs are two important factors to be considered during their commercial large-scale production. Notably, SL accumulation causes an increase in viscosity, decrease in dissolved oxygen and product inhibition in the fermentation medium. This inhibits the further production and purification of SLs. This describes the development of a novel integrated system for SL production using Candida albicans O-13-1. Semicontinuous fermentation was performed using a novel bioreactor with dual ventilation pipes and dual sieve-plates (DVDSB). SLs were separated and recovered using a newly designed two-stage separation system. After SL recovery, the fermentation broth containing residual glucose and oleic acid was recycled back into the bioreactor. This novel approach considerably alleviated the problem of product inhibition and accelerated the rate of substrate utilization. Production of SLs achieved was 477gl(-1), while their productivity was 1.59gl(-1)h(-1). Purity of SLs improved by 23.3%, from 60% to 74%, using DVDSB with the separation system. The conversion rate of carbon source increased from 0.5gg(-1) (in the batch fermentation) to 0.6gg(-1). These results indicated that the integrated system could improve the efficiency of production and purity of SLs.
Host-associated microbiomes are predicted by immune system complexity and climate (vol 21, 23, 2020)
(BMC, 2020) Woodhams, Douglas C.; Bletz, Molly C.; Becker, C. Guilherme; Bender, Hayden A.; Buitrago-Rosas, Daniel; Diebboll, Hannah; Huynh, Roger; Kearns, Patrick J.; Kueneman, Jordan; Kurosawa, Emmi; LaBumbard, Brandon C.; Lyons, Casandra; McNally, Kerry; Schliep, Klaus; Shankar, Nachiket; Tokash-Peters, Amanda G.; Vences, Miguel; Whetstone, Ross; University of Massachusetts Boston; Smithsonian Institution; Smithsonian Tropical Research Institute; University of Alabama Tuscaloosa; University of Rwanda; Braunschweig University of Technology
Improved computational method to generate properly equilibrated atomistic microstructures
(Elsevier, 2021) Gupta, Ankit; Rajaram, Satish S.; Thompson, Gregory B.; Tucker, Garritt J.; Colorado School of Mines; Drexel University; University of Alabama Tuscaloosa
Atomistic simulations play an important role in unravelling the fundamental behavior of nanocrystalline (NC) metals/alloys. To ensure the validity of the simulated results, the initial NC structures must be representative of a real material to the extent possible. Using proper equilibration techniques, it must also be ensured that these NC structures reach a state of metastable equilibrium before probing their response. To this effect, the influence of simulated thermal equilibration of atomistic NC Ni structures on the resulting mechanical behavior is discussed in this work. It is shown that the well-equilibrated NC structures become stiffer in terms of both elastic response and yielding behavior and accumulate less residual strain upon unloading, thus, signifying the importance of proper equilibration. However, it is found that the regular equilibration method of thermal relaxations at 300 K, typically employed in atomistic modeling studies, takes significantly longer to drive the NC structures towards a metastable equilibrium state. Finally, an improved two-step equilibration method is presented that drastically expedites the equilibration process while resulting in the structural and mechanical properties comparable with the regular equilibration method performed for significantly larger simulation times. The major modification in the improved method involves: Subjecting only the grain boundary and the surrounding atoms to thermal relaxations at relatively higher temperature. (C) 2021 The Authors. Published by Elsevier B.V.
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.
In-situ observation of trapped carriers in organic metal halide perovskite films with ultra-fast temporal and ultra-high energetic resolutions
(Nature Portfolio, 2021) Kobbekaduwa, Kanishka; Shrestha, Shreetu; Adhikari, Pan; Liu, Exian; Coleman, Lawrence; Zhang, Jianbing; Shi, Ying; Zhou, Yuanyuan; Bekenstein, Yehonadav; Yan, Feng; Rao, Apparao M.; Tsai, Hsinhan; Beard, Matthew C.; Nie, Wanyi; Gao, Jianbo; Clemson University; United States Department of Energy (DOE); Los Alamos National Laboratory; Huazhong University of Science & Technology; Jilin University; Hong Kong Baptist University; Technion Israel Institute of Technology; University of Alabama Tuscaloosa; National Renewable Energy Laboratory - USA
We in-situ observe the ultrafast dynamics of trapped carriers in organic methyl ammonium lead halide perovskite thin films by ultrafast photocurrent spectroscopy with a sub-25 picosecond time resolution. Upon ultrafast laser excitation, trapped carriers follow a phonon assisted tunneling mechanism and a hopping transport mechanism along ultra-shallow to shallow trap states ranging from 1.72-11.51 millielectronvolts and is demonstrated by time-dependent and independent activation energies. Using temperature as an energetic ruler, we map trap states with ultra-high energy resolution down to < 0.01 millielectronvolt. In addition to carrier mobility of similar to 4 cm(2)V(-1)s(-1) and lifetime of similar to 1 nanosecond, we validate the above transport mechanisms by highlighting trap state dynamics, including trapping rates, de-trapping rates and trap properties, such as trap density, trap levels, and capture-cross sections. In this work we establish a foundation for trap dynamics in high defect-tolerant perovskites with ultra-fast temporal and ultra-high energetic resolution.
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.
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.

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