@article{beck_kleiner_garrell_2022, title={Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.910377}, abstractNote={With a growing world population and increasing frequency of climate disturbance events, we are in dire need of methods to improve plant productivity, resilience, and resistance to both abiotic and biotic stressors, both for agriculture and conservation efforts. Microorganisms play an essential role in supporting plant growth, environmental response, and susceptibility to disease. However, understanding the specific mechanisms by which microbes interact with each other and with plants to influence plant phenotypes is a major challenge due to the complexity of natural communities, simultaneous competition and cooperation effects, signalling interactions, and environmental impacts. Synthetic communities are a major asset in reducing the complexity of these systems by simplifying to dominant components and isolating specific variables for controlled experiments, yet there still remains a large gap in our understanding of plant microbiome interactions. This perspectives article presents a brief review discussing ways in which metabolic modelling can be used in combination with synthetic communities to continue progress toward understanding the complexity of plant-microbe-environment interactions. We highlight the utility of metabolic models as applied to a community setting, identify different applications for both flux balance and elementary flux mode simulation approaches, emphasize the importance of ecological theory in guiding data interpretation, and provide ideas for how the integration of metabolic modelling techniques with big data may bridge the gap between simplified synthetic communities and the complexity of natural plant-microbe systems.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Beck, Ashley E. and Kleiner, Manuel and Garrell, Anna-Katharina}, year={2022}, month={Jun} }
 @article{baker_blackman_cooper_smartt_walser_boland_kolar_beck_chinn_2021, title={Exploratory analysis of Spirulina platensis LB 2340 growth in varied concentrations of anaerobically digested pig effluent (ADPE)}, volume={7}, ISSN={["2405-8440"]}, DOI={10.1016/j.heliyon.2021.e08065}, abstractNote={There is a significant interest in novel waste management solutions to treat wastewater from swine operations. Anaerobic digestion is a rising and prominent solution, but this technology still generates highly concentrated effluent that requires further remediation. Therefore, the aim of this study was to explore the feasibility of cultivating the cyanobacterium Spirulina platensis in swine effluent for future applications in biological waste treatment and value-added fermentation. To accomplish this goal, growth of S. platensis was characterized in varying proportions of ideal, synthetic Zarrouk medium and anaerobically digested pig effluent (ADPE) to obtain growth rate models. Results yielded a positive correlation between S. platensis growth rate and Zarrouk medium proportion, with the highest growth rate in 100% Zarrouk media but comparable growth in the 50/50% Zarrouk/ADPE mixture. This study demonstrates the potential for S. platensis to further improve the treatment efficacy of anaerobic digestion systems, and the exploratory analysis also highlights that further testing is required to investigate possible carbon availability, chemical inhibition, and overall nutrient reduction in ADPE. This research contributes important data toward the feasibility of producing value-added cyanobacterial biomass while simultaneously consuming excess nutrients to aid in agricultural wastewater management efforts and generate cost-effective products in a more sustainable manner.}, number={9}, journal={HELIYON}, author={Baker, Matthew and Blackman, Sam and Cooper, Erin and Smartt, Kevin and Walser, David and Boland, Megan and Kolar, Praveen and Beck, Ashley E. and Chinn, Mari S.}, year={2021}, month={Sep} }
 @article{beck_2020, title={Metabolic Efficiency of Sugar Co-Metabolism and Phenol Degradation in <i>Alicyclobacillus acidocaldarius</i> for Improved Lignocellulose Processing}, url={https://www.mdpi.com/2227-9717/8/5/502}, DOI={10.3390/pr8050502}, abstractNote={Substrate availability plays a key role in dictating metabolic strategies. Most microorganisms consume carbon/energy sources in a sequential, preferential order. The presented study investigates metabolic strategies of Alicyclobacillus acidocaldarius, a thermoacidophilic bacterium that has been shown to co-utilize glucose and xylose, as well as degrade phenolic compounds. An existing metabolic model was expanded to include phenol degradation and was analyzed with both metabolic pathway and constraint-based analysis methods. Elementary flux mode analysis was used in conjunction with resource allocation theory to investigate ecologically optimal metabolic pathways for different carbon substrate combinations. Additionally, a dynamic version of flux balance analysis was used to generate time-resolved simulations of growth on phenol and xylose. Results showed that availability of xylose along with glucose did not predict enhanced growth efficiency beyond that of glucose alone, but did predict some differences in pathway utilization and byproduct profiles. In contrast, addition of phenol as a co-substrate with xylose predicted lower growth efficiency. Dynamic simulations predicted co-consumption of xylose and phenol in a similar pattern as previously reported experiments. Altogether, this work serves as a case study for combining both elementary flux mode and flux balance analyses to probe unique metabolic features, and also demonstrates the versatility of A. acidocaldarius for lignocellulosic biomass processing applications.}, journal={Processes}, author={Beck, Ashley}, year={2020}, month={Apr} }
 @article{hughes_power_beck_betz_goodell_hopwood_jaramillo_lanigan_martinez_micheli_et al._2020, title={Short-Term Effects of an Obesity Prevention Program Among Low-Income Hispanic Families With Preschoolers}, volume={52}, ISSN={["1878-2620"]}, DOI={10.1016/j.jneb.2019.12.001}, abstractNote={Objective To assess the short-term effects of an obesity prevention program promoting eating self-regulation and healthy food preferences in low-income Hispanic children. Design Randomized controlled trial with pretest, posttest, and 6- and 12-month assessments. Setting and Participants Head Start and similar early learning institutions in Houston, TX, and Pasco, WA. A total of 255 families with preschoolers randomized into prevention (n = 136) and control (n = 119) groups. Intervention Multicomponent family-based prevention program. Fourteen waves lasted 7 weeks each with 8–10 mother–child dyads in each group. Main Outcome Measures Parent assessments included feeding practices, styles, and knowledge. Child assessments included child eating self-regulation, willingness to try new foods, and parent report of child fruit and vegetable preferences. Parent and child heights and weights were measured. Analysis Multilevel analyses were employed to consider the nested nature of the data: time points within families within waves. Results The program had predicted effects on parental feeding practices, styles, and knowledge in the pre- to post-comparisons. Effects on child eating behavior were minimal; only the number of different vegetables tried showed significant pre-post differences. Conclusions and Implications Short-term effects of this prevention program highlight the importance of family-focused feeding approaches to combating child overweight and obesity.}, number={3}, journal={JOURNAL OF NUTRITION EDUCATION AND BEHAVIOR}, author={Hughes, Sheryl O. and Power, Thomas G. and Beck, Ashley and Betz, Drew and Goodell, L. Suzanne and Hopwood, Veronica and Jaramillo, J. Andrea and Lanigan, Jane and Martinez, AnaMaria Diaz and Micheli, Nilda and et al.}, year={2020}, month={Mar}, pages={224–239} }
 @article{schmitt-wilson_vaterlaus_beck_2019, title={Adolescent life values: An exploratory study of differences and similarities by urbanicity}, volume={2}, DOI={10.1016/j.soscij.2019.02.001}, abstractNote={This exploratory correlational study examined whether life values (i.e., goals or principles that guide peoples’ lives) differed by urbanicity. The nationally representative sample included adolesc...}, journal={The Social Science Journal}, publisher={Informa UK Limited}, author={Schmitt-Wilson, Sarah and Vaterlaus, J. Mitchell and Beck, Ashley}, year={2019}, month={Feb} }
 @article{schepens_carlson_heys_beck_gedeon_2019, title={Role of resource allocation and transport in emergence of cross-feeding in microbial consortia}, volume={467}, DOI={10.1016/j.jtbi.2019.01.030}, abstractNote={Microbial communities that implement mutual cross-feeding are commonly observed in nature and with synthetic constructs in laboratory experiments. A mathematical model of competition in a chemostat is developed to investigate the role that resource allocation and transport of metabolites play in cooperation. The model contains four cell types that differ by whether they produce two, one, or none of two essential metabolites. Producing cell types may export these resources into the environment, and those that do not produce both metabolites must import the missing resource. The contribution to the emergence of a collaborative consortium of single resource producers from the transport rate of these metabolites and the type of transport used by the cell (active vs. passive) is studied. Multiple instances of bi-stability and tri-stability are observed, and the effect of the initial concentration of a non-cooperative cheater cell type on the final outcome of the competition is examined. When the cost of producing metabolites is introduced into the model, significant changes to the outcome of the competition are observed, including coexistence of multiple cell types.}, journal={Journal of Theoretical Biology}, publisher={Elsevier BV}, author={Schepens, Diana and Carlson, Ross P. and Heys, Jeff and Beck, Ashley E. and Gedeon, Tomáš}, year={2019}, month={Apr}, pages={150–163} }
 @article{carlson_beck_phalak_fields_gedeon_hanley_harcombe_henson_heys_2018, title={Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia}, volume={46}, DOI={10.1042/bst20170242}, abstractNote={Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning.}, number={2}, journal={Biochemical Society Transactions}, publisher={Portland Press Ltd.}, author={Carlson, Ross P. and Beck, Ashley E. and Phalak, Poonam and Fields, Matthew W. and Gedeon, Tomas and Hanley, Luke and Harcombe, William R. and Henson, Michael A. and Heys, Jeffrey J.}, year={2018}, month={Feb}, pages={269–284} }
 @article{beck_hunt_carlson_2018, title={Measuring Cellular Biomass Composition for Computational Biology Applications}, volume={6}, DOI={10.3390/pr6050038}, abstractNote={Computational representations of metabolism are increasingly common in medical, environmental, and bioprocess applications. Cellular growth is often an important output of computational biology analyses, and therefore, accurate measurement of biomass constituents is critical for relevant model predictions. There is a distinct lack of detailed macromolecular measurement protocols, including comparisons to alternative assays and methodologies, as well as tools to convert the experimental data into biochemical reactions for computational biology applications. Herein is compiled a concise literature review regarding methods for five major cellular macromolecules (carbohydrate, DNA, lipid, protein, and RNA) with a step-by-step protocol for a select method provided for each macromolecule. Additionally, each method was tested on three different bacterial species, and recommendations for troubleshooting and testing new species are given. The macromolecular composition measurements were used to construct biomass synthesis reactions with appropriate quality control metrics such as elemental balancing for common computational biology methods, including flux balance analysis and elementary flux mode analysis. Finally, it was demonstrated that biomass composition can substantially affect fundamental model predictions. The effects of biomass composition on in silico predictions were quantified here for biomass yield on electron donor, biomass yield on electron acceptor, biomass yield on nitrogen, and biomass degree of reduction, as well as the calculation of growth associated maintenance energy; these parameters varied up to 7%, 70%, 35%, 12%, and 40%, respectively, between the reference biomass composition and ten test biomass compositions. The current work furthers the computational biology community by reviewing literature regarding a variety of common analytical measurements, developing detailed procedures, testing the methods in the laboratory, and applying the results to metabolic models, all in one publicly available resource.}, number={5}, journal={Processes}, publisher={MDPI AG}, author={Beck, Ashley and Hunt, Kristopher and Carlson, Ross}, year={2018}, month={Apr}, pages={38} }
 @article{power_garcia_beck_goodell_johnson_hughes_2018, title={Observed and self-reported assessments of caregivers' feeding styles: Variable- and person-centered approaches for examining relationships with children's eating behaviors}, volume={130}, ISSN={["1095-8304"]}, DOI={10.1016/j.appet.2018.08.010}, abstractNote={Demandingness and responsiveness are dimensions used in general parenting as well as the feeding literature to measure parent attitudes and behaviors. These dimensions can be treated as continuous variables (variable-centered) or used to form groups of parents based on scores on each dimension (person-centered). Research focusing on these dimensions in the feeding domain has relied exclusively on maternal self-reports; observational studies of feeding styles have yet to be conducted. The purpose of this study was to investigate the effectiveness of variable-centered versus person-centered analyses in examining relationships between maternal feeding styles, child eating behaviors, and child weight status using both self-reported and observational methods for assessing parental feeding style. Participants included 137 low-income Head Start mothers and their preschoolers. Mothers completed the Caregiver's Feeding Styles Questionnaire and the Children's Eating Behavior Questionnaire. Parent/child interactions were observed during dinner meals at home and were coded using a previously developed coding system. Maternal demandingness during feeding was negatively associated with child BMI z-scores and positively associated with slowness in eating and satiety responsiveness. Maternal responsiveness was associated positively with enjoyment of food and associated negatively with food fussiness. Significant demandingness by responsiveness interactions showed that children of authoritarian mothers showed the highest levels of food fussiness and the lowest enjoyment of food. Overall, the findings were stronger for the self-report than for the observational measures and the variable-centered approach was clearly superior to the person-centered approach. The current results indicate that for research purposes the variable-centered approach may be the most powerful for examining relationships between maternal feeding and child eating. However, for clinical purposes, the person-centered approach might be most informative.}, journal={APPETITE}, author={Power, Thomas G. and Garcia, Karina Silva and Beck, Ashley D. and Goodell, L. Suzanne and Johnson, Susan L. and Hughes, Sheryl O.}, year={2018}, month={Nov}, pages={174–183} }
 @article{schmitt-wilson_downey_beck_2018, title={Rural educational attainment: The importance of context}, volume={33}, url={http://jrre.psu.edu/wp-content/uploads/2018/02/33-1.pdf}, number={1}, journal={Journal of Research in Rural Education}, author={Schmitt-Wilson, S. and Downey, J. and Beck, A.E.}, year={2018}, pages={1–14} }
 @article{beck_bernstein_carlson_2017, title={Stoichiometric Network Analysis of Cyanobacterial Acclimation to Photosynthesis-Associated Stresses Identifies Heterotrophic Niches}, volume={5}, DOI={10.3390/pr5020032}, abstractNote={Metabolic acclimation to photosynthesis-associated stresses was examined in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 using integrated computational and photobioreactor analyses. A genome-enabled metabolic model, complete with measured biomass composition, was analyzed using ecological resource allocation theory to predict and interpret metabolic acclimation to irradiance, O2, and nutrient stresses. Reduced growth efficiency, shifts in photosystem utilization, changes in photorespiration strategies, and differing byproduct secretion patterns were predicted to occur along culturing stress gradients. These predictions were compared with photobioreactor physiological data and previously published transcriptomic data and found to be highly consistent with observations, providing a systems-based rationale for the culture phenotypes. The analysis also indicated that cyanobacterial stress acclimation strategies created niches for heterotrophic organisms and that heterotrophic activity could enhance cyanobacterial stress tolerance by removing inhibitory metabolic byproducts. This study provides mechanistic insight into stress acclimation strategies in photoautotrophs and establishes a framework for predicting, designing, and engineering both axenic and photoautotrophic-heterotrophic systems as a function of controllable parameters.}, number={4}, journal={Processes}, publisher={MDPI AG}, author={Beck, Ashley and Bernstein, Hans and Carlson, Ross}, year={2017}, month={Jun}, pages={32} }
 @inbook{schepens_beck_heys_gedeon_carlson_2017, title={The benefits of resource partitioning and division of labor in microbial consortia}, booktitle={Advances in systems and synthetic biology}, publisher={EDP Sciences Publishing}, author={Schepens, D. and Beck, A.E. and Heys, J.J. and Gedeon, T. and Carlson, R.P.}, editor={Amar, P. and Kepes, F. and Norris, V.Editors}, year={2017}, pages={137–148} }
 @article{beck_hunt_bernstein_carlson_2016, title={Interpreting and Designing Microbial Communities for Bioprocess Applications, from Components to Interactions to Emergent Properties}, DOI={10.1016/b978-0-444-63475-7.00015-7}, abstractNote={Interest in microbial communities for bioprocessing has surged in recent years based on the potential to optimize multiple tasks simultaneously and to enhance process productivity and stability. The presence and magnitude of these desirable properties often result from interactions between community members. The importance of interactions has gained interest due to improving omics techniques, polymicrobial culturing approaches, and computational methods, which have made the systems-level analysis of interacting components more tractable. This review defines and categorizes natural and engineered system components, interactions, and emergent properties, as well as presents three ecological theories relevant to microbial communities. Case studies are interpreted to illustrate components, interactions, emergent properties, and theoretical context. A general foundation is laid to facilitate interpretation of current systems and to aid the design of next generation bioprocesses.}, journal={Biotechnology for Biofuel Production and Optimization}, publisher={Elsevier}, author={Beck, A.E. and Hunt, K.A. and Bernstein, H.C. and Carlson, R.P.}, year={2016}, pages={407–432} }