Now showing items 1-20 of 321

    • A 3D inᅠvitro model of patient-derived prostate cancer xenograft for controlled interrogation of inᅠvivo tumor-stromal interactions 

      Fong, Eliza L.S.; Wan, Xinhai; Yang, Jun; Morgado, Micaela; Mikos, Antonios G.; (2016)
      Patient-derived xenograft (PDX) models better represent human cancer than traditional cell lines. However, the complex in vivo environment makes it challenging to employ PDX models to investigate tumor-stromal interactions, such as those that mediate prostate cancer (PCa) bone metastasis. Thus, we engineered a defined three-dimensional (3D) hydrogel ...
    • A 3D inᅠvitro model of patient-derived prostate cancer xenograft for controlled interrogation of inᅠvivo tumor-stromal interactions 

      Fong, Eliza L.S.; Wan, Xinhai; Yang, Jun; Morgado, Micaela; Mikos, Antonios G.; (2016)
      Patient-derived xenograft (PDX) models better represent human cancer than traditional cell lines. However, the complex in vivo environment makes it challenging to employ PDX models to investigate tumor-stromal interactions, such as those that mediate prostate cancer (PCa) bone metastasis. Thus, we engineered a defined three-dimensional (3D) hydrogel ...
    • A Burrowing/Tunneling Assay for Detection of Hypoxia in Drosophila melanogaster Larvae 

      Qiang, Karen M.; Zhou, Fanli; Beckingham, Kathleen M. (2018)
      Oxygen deprivation in animals can result from exposure to low atmospheric oxygen levels or from internal tissue damage that interferes with oxygen distribution. It is also possible that aberrant behavior of oxygen-sensing neurons could induce hypoxia-like behavior in the presence of normal oxygen levels. In D. melanogaster, development at low oxygen ...
    • A collagen glucosyltransferase drives lung adenocarcinoma progression in mice 

      Guo, Hou-Fu; Bota-Rabassedas, Neus; Terajima, Masahiko; Leticia Rodriguez, B.; Gibbons, Don L.; (2021)
      Cancer cells are a major source of enzymes that modify collagen to create a stiff, fibrotic tumor stroma. High collagen lysyl hydroxylase 2 (LH2) expression promotes metastasis and is correlated with shorter survival in lung adenocarcinoma (LUAD) and other tumor types. LH2 hydroxylates lysine (Lys) residues on fibrillar collagen’s amino- and ...
    • A divide-and-conquer method for scalable phylogenetic network inference from multilocus data 

      Zhu, Jiafan; Liu, Xinhao; Ogilvie, Huw A.; Nakhleh, Luay K. (2019)
      Motivation: Reticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other processes, such as incomplete lineage sorting. However, these methods can only handle a ...
    • A facile forward-genetic screen for Arabidopsis autophagy mutants reveals twenty-one loss-of-function mutations disrupting six ATG genes 

      Young, Pierce G.; Passalacqua, Michael J.; Chappell, Kevin; Llinas, Roxanna J.; Bartel, Bonnie (2019)
      Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (ATG) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved ATG genes in plants, only a few atg mutants ...
    • A facile forward-genetic screen forᅠArabidopsisᅠautophagy mutants reveals twenty-one loss-of-function mutations disrupting sixᅠATGᅠgenes 

      Young, Pierce G.; Passalacqua, Michael J.; Chappell, Kevin; Llinas, Roxanna J.; Bartel, Bonnie (2019)
      Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (ATG) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved ATG genes in plants, only a few atg mutants ...
    • A High-throughput, High-content, Liquid-based C. elegans Pathosystem 

      Anderson, Quinton L.; Revtovich, Alexey V.; Kirienko, Natalia V. (2018)
      The number of new drugs identified by traditional, in vitro screens has waned, reducing the success of this approach in the search for new weapons to combat multiple drug resistance. This has led to the conclusion that researchers do not only need to find new drugs, but also need to develop new ways of finding them. Amongst the most promising candidate ...
    • A hybrid cyt c maturation system enhances the bioelectrical performance of engineered Escherichia coli by improving the rate-limiting step 

      Su, Lin; Fukushima, Tatsuya; Ajo-Franklin, Caroline M. (2020)
      Bioelectronic devices can use electron flux to enable communication between biotic components and abiotic electrodes. We have modified Escherichia coli to electrically interact with electrodes by expressing the cytochrome c from Shewanella oneidensis MR-1. However, we observe inefficient electrical performance, which we hypothesize is due to the ...
    • A maximum pseudo-likelihood approach for phylogenetic networks 

      Yu, Yun; Nakhleh, Luay (2015)
      Abstract Background Several phylogenomic analyses have recently demonstrated the need to account simultaneously for incomplete lineage sorting (ILS) and hybridization when inferring a species phylogeny. A maximum likelihood approach was introduced recently for inferring species phylogenies in the ...
    • A mechanism for increased sensitivity of acute myeloid leukemia to mitotoxic drugs 

      Panina, Svetlana B.; Baran, Natalia; da Costa, Fabio H. Brasil; Konopleva, Marina; Kirienko, Natalia V. (2019)
      Mitochondria play a central and multifunctional role in the progression of tumorigenesis. Although many recent studies have demonstrated correlations between mitochondrial function and genetic makeup or originating tissue, it remains unclear why some cancers are more susceptible to mitocans (anticancer drugs that target mitochondrial function to ...
    • A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling 

      Bocci, Federico; Jolly, Mohit Kumar; George, Jason Thomas; Levine, Herbert; Onuchic, José Nelson; (2018)
      Epithelial-mesenchymal transition (EMT) and cancer stem cell (CSCs) formation are two fundamental and well-studied processes contributing to cancer metastasis and tumor relapse. Cells can undergo a partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype or a complete EMT to attain a mesenchymal one. Similarly, cells can reversibly gain ...
    • A molecular dynamics approach towards evaluating osmotic and thermal stress in the extracellular environment 

      Fuentes, David; Muñoz, Nina M.; Guo, Chunxiao; Polak, Urzsula; Minhaj, Adeeb A.; (2018)
      OBJECTIVE: A molecular dynamics approach to understanding fundamental mechanisms of combined thermal and osmotic stress induced by thermochemical ablation (TCA) is presented. METHODS: Structural models of fibronectin and fibronectin bound to its integrin receptor provide idealized models for the effects of thermal and osmotic stress in the extracellular ...
    • A pex1 missense mutation improves peroxisome function in a subset of Arabidopsis pex6 mutants without restoring PEX5 recycling 

      Gonzalez, Kim L.; Ratzel, Sarah E.; Burks, Kendall H.; Danan, Charles H.; Wages, Jeanne M.; (2018)
      Peroxisomes are eukaryotic organelles critical for plant and human development because they house essential metabolic functions, such as fatty acid β-oxidation. The interacting ATPases PEX1 and PEX6 contribute to peroxisome function by recycling PEX5, a cytosolic receptor needed to import proteins targeted to the peroxisomal matrix. Arabidopsis pex6 ...
    • A PEX5 missense allele preferentially disrupts PTS1 cargo import into Arabidopsis peroxisomes 

      Patel, Khushali J.; Kao, Yun‐Ting; Llinas, Roxanna J.; Bartel, Bonnie; BioSciences (2019-03-20)
      The sorting of eukaryotic proteins to various organellar destinations requires receptors that recognize cargo protein targeting signals and facilitate transport into the organelle. One such receptor is the peroxin PEX5, which recruits cytosolic cargo carrying a peroxisome‐targeting signal (PTS) type 1 (PTS1) for delivery into the peroxisomal lumen ...
    • A platform for post-translational spatiotemporal control of cellular proteins 

      Jayanthi, Brianna; Bachhav, Bhagyashree; Wan, Zengyi; Martinez Legaspi, Santiago; Segatori, Laura; (2021)
      Mammalian cells process information through coordinated spatiotemporal regulation of proteins. Engineering cellular networks thus relies on efficient tools for regulating protein levels in specific subcellular compartments. To address the need to manipulate the extent and dynamics of protein localization, we developed a platform technology for the ...
    • A protocol for whole-mount immuno-coupled hybridization chain reaction (WICHCR) in zebrafish embryos and larvae 

      Ibarra-García-Padilla, Rodrigo; Howard, Aubrey Gaylon Adam; Singleton, Eileen Willey; Uribe, Rosa Anna (2021)
      Characterizing mRNA and protein expression with temporal and spatial resolution is a valuable component of nearly every developmental study. Here, we describe a protocol that combines in situ hybridization chain reaction (HCR) and immunofluorescence, allowing for the detection of mRNAs and proteins simultaneously, in zebrafish embryos and larvae. ...
    • A Simple Nematode Infection Model for Studying Candida albicans Pathogenesis 

      Kim, Grace H.; Rosiana, Sierra; Kirienko, Natalia V.; Shapiro, Rebecca S. (2020)
      Candida albicans is an opportunistic fungal pathogen and a model organism to study fungal pathogenesis. It exists as a harmless commensal organism and member of the healthy human microbiome, but can cause life‐threatening mucosal and systemic infections. A model host to study C. albicans infection and pathogenesis is the nematode Caenorhabditis ...
    • A strategy to apply quantitative epistasis analysis on developmental traits 

      Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei (2017)
      Abstract Background Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such ...
    • A suppressor tRNA-mediated feedforward loop eliminates leaky gene expression in bacteria 

      Ho, Joanne M.L.; Miller, Corwin A.; Parks, Sydney E.; Mattia, Jacob R.; Bennett, Matthew R. (2021)
      Ligand-inducible genetic systems are the mainstay of synthetic biology, allowing gene expression to be controlled by the presence of a small molecule. However, ‘leaky’ gene expression in the absence of inducer remains a persistent problem. We developed a leak dampener tool that drastically reduces the leak of inducible genetic systems while retaining ...