title: Three-Dimensional Encapsulation of Saccharomyces cerevisiae in Silicate Matrices Creates Distinct Metabolic States as Revealed by Gene Chip Analysis.
abstract: In order to design hybrid cellular/synthetic devices such as sensors and vaccines, it is important to understand how the metabolic state of living cells changes upon physical confinement within three-dimensional (3D) matrices. We analyze the gene expression patterns of stationary phase Saccharomyces cerevisiae (S. cerevisiae) cells encapsulated within three distinct nanostructured silica matrices and relate those patterns to known naturally occurring metabolic states. Silica encapsulation methods employed were lipid-templated mesophase silica thin films formed by cell-directed assembly (CDA), lipid-templated mesophase silica particles formed by spray drying (SD), and glycerol-doped silica gel monoliths prepared from an aqueous silicate (AqS+g) precursor solution. It was found that the cells for all three-encapsulated methods enter quiescent states characteristic of response to stress, albeit to different degrees and with differences in detail. By the measure of enrichment of stress-related gene ontology categories, we find that the AqS+g encapsulation is more amenable to the cells than CDA and SD encapsulation. We hypothesize that this differential response in the AqS+g encapsulation is related to four properties of the encapsulating gel: (1) oxygen permeability, (2) relative softness of the material, (3) development of a protective sheath around individual cells (visible in TEM micrographs vide infra), and (4) the presence of glycerol in the gel, which has been previously noted to serve as a protectant for encapsulated cells and can serve as the sole carbon source for S. cerevisiae under aerobic conditions. This work represents a combination of experiment and analysis aimed at the design and development of 3D encapsulation procedures to induce, and perhaps control, well-defined physiological behaviors.
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology , Park Road, Tarlai Kalan, Islamabad 45550, Pakistan.
authors.forename: Zeeshan
authors.initials: Z
authors.lastname: Fazal
authors.forename: Jennifer
authors.initials: J
authors.lastname: Pelowitz
authors.forename: Patrick E
authors.initials: PE
authors.lastname: Johnson
authors.forename: Jason C
authors.initials: JC
authors.lastname: Harper
authors.forename: C Jeffrey
authors.initials: CJ
authors.lastname: Brinker
authors.forename: Eric
authors.identifier: 0000-0002-7892-5295
authors.initials: E
authors.lastname: Jakobsson
mesh_terms: D002478:Cells, Cultured; D049329:Nanostructures / Q000737:chemistry*; D020411:Oligonucleotide Array Sequence Analysis; D010316:Particle Size; D016062:Porosity; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics* / Q000378:metabolism*; D017640:Silicates / Q000737:chemistry*; D012996:Solutions; D013499:Surface Properties; D014867:Water / Q000737:chemistry
chemical_list: D017640:Silicates; D012996:Solutions; D014867:Water
keywords: cell-directed assembly; glycerol modified silanes; living hybrid biomaterials; sol−gel; spray drying; yeast quiescent state; yeast stress response