Browsing by Author "Silver, Pamela"

Now showing items 1-20 of 37

    • Alternative Splicing Regulation in Programmed Cell Death and Neurological Disorders: A Systems Biology Approach 

      Wang, Qingqing (2013-09-30)
      Alternative splicing (AS) is a major source of biological diversity and a crucial determinant of cell fate and identity. Characterizing the role of AS regulatory networks in physiological and pathological processes remains ...

    • The Bacterial Carbon-Fixing Organelle Is Formed by Shell Envelopment of Preassembled Cargo 

      Chen, Anna H.; Robinson-Mosher, Avi; Savage, David F.; Silver, Pamela A.; Polka, Jessica K. (Public Library of Science, 2013)
      Background: Cyanobacteria play a significant role in the global carbon cycle. In Synechococcuselongatus, the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is concentrated into polyhedral, ...

    • A BioBrick compatible strategy for genetic modification of plants 

      Boyle, Patrick M; Burrill, Devin Rene; Inniss, Mara Christine; Agapakis, Christina M; Deardon, Aaron; dewerd, Jonathan G; Gedeon, Michael A; Quinn, Jacqueline Y; Paull, Morgan L; Raman, Anugraha M; Theilmann, Mark R; Wang, Lu; Winn, Julia C; Medvedik, Oliver; Schellenberg, Kurt William; Haynes, Karmella; Viel, Alain; Brenner, Tamara Jane; Church, George McDonald; Shah, Jagesh V.; Silver, Pamela A. (BioMed Central, 2012)
      Background: Plant biotechnology can be leveraged to produce food, fuel, medicine, and materials. Standardized methods advocated by the synthetic biology community can accelerate the plant design cycle, ultimately making ...

    • Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities 

      Polka, Jessica; Hays, Stephanie Grace; Silver, Pamela A. (Cold Spring Harbor Laboratory Press, 2016)
      Traditional views of synthetic biology often treat the cell as an unstructured container in which biological reactions proceed uniformly. In reality, the organization of biological molecules has profound effects on cellular ...

    • A Conserved CCCH-type Zinc Finger Protein Regulates mRNA Nuclear Adenylation and Export 

      Hurt, Jessica A.; Obar, Robert Alan; Zhai, Bo; Farny, Natalie G.; Gygi, Steven P.; Silver, Pamela A. (The Rockefeller University Press, 2009)
      Coupling of messenger RNA (mRNA) nuclear export with prior processing steps aids in the fidelity and efficiency of mRNA transport to the cytoplasm. In this study, we show that the processes of export and polyadenylation ...

    • Controlling fluxes for microbial metabolic engineering 

      Sachdeva, Gairik (2014-10-21)
      This thesis presents novel synthetic biology tools and design principles usable for microbial metabolic engineering. Controlling metabolic fluxes is essential for biological manufacturing of fuels, materials, and high value ...

    • A distributed cell division counter reveals growth dynamics in the gut microbiota 

      Myhrvold, Cameron; Kotula, Jonathan W.; Hicks, Wade M.; Conway, Nicholas J.; Silver, Pamela A. (Nature Pub. Group, 2015)
      Microbial population growth is typically measured when cells can be directly observed, or when death is rare. However, neither of these conditions hold for the mammalian gut microbiota, and, therefore, standard approaches ...

    • Engineering acyl carrier protein to enhance production of shortened fatty acids 

      Liu, Xueliang; Hicks, Wade M.; Silver, Pamela A.; Way, Jeffrey C. (BioMed Central, 2016)
      Background: The acyl carrier protein (ACP) is an essential and ubiquitous component of microbial synthesis of fatty acids, the natural precursor to biofuels. Natural fatty acids usually contain long chains of 16 or more ...

    • Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution 

      Liu, Xueliang; Lopez, Paola A.; Giessen, Tobias W.; Giles, Michael; Way, Jeffrey C.; Silver, Pamela A. (Nature Publishing Group, 2016)
      Genetically encoding the synthesis of functional nanomaterials such as magnetic nanoparticles enables sensitive and non-invasive biological sensing and control. Via directed evolution of the natural iron-sequestering ...

    • Engineering Synthetic TAL Effectors with Orthogonal Target Sites 

      Garg, Abhishek; Lohmueller, Jason Jakob; Silver, Pamela A.; Armel, Thomas Z. (Oxford University Press, 2012)
      The ability to engineer biological circuits that process and respond to complex cellular signals has the potential to impact many areas of biology and medicine. Transcriptional activator-like effectors (TALEs) have emerged ...

    • Eukaryotic Systems Broaden the Scope of Synthetic Biology 

      Haynes, Karmella A.; Silver, Pamela A. (The Rockefeller University Press, 2009)
      Synthetic biology aims to engineer novel cellular functions by assembling well-characterized molecular parts (i.e., nucleic acids and proteins) into biological “devices” that exhibit predictable behavior. Recently, efforts ...

    • Exon expression profiling reveals stimulus-mediated exon use in neural cells 

      McKee, Adrienne E; Neretti, Nicola; Carvalho, Luis E; Brodsky, Alexander S; Meyer, Clifford; Meyer, Clifford; Fox, Edward Alvin; Silver, Pamela A. (BioMed Central, 2007)
      Background: Neuronal cells respond to changes in intracellular calcium ([Ca2+]i) by affecting both the abundance and architecture of specific mRNAs. Although calcium-induced transcription and transcript variation have ...

    • Genome-Wide Identification of Functionally Distinct Subsets of Cellular mRNAs Associated with Two Nucleocytoplasmic-Shuttling Mammalian Splicing Factors 

      Gama-Carvalho, Margarida; Barbosa-Morais, Nuno L; Brodsky, Alexander S; Silver, Pamela A.; Carmo-Fonseca, Maria (BioMed Central, 2006)
      Background: Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome ...

    • A Genome-Wide In Situ Hybridization Map of RNA-Binding Proteins reveals Anatomically Restricted Expression in the Developing Mouse Brain 

      McKee, Adrienne E.; Minet, Emmanuel; Stern, Charlene; Riahi, Shervin; Stiles, Charles Dean; Silver, Pamela A. (BioMed Central, 2005)
      Background: In eukaryotic cells, RNA-binding proteins (RBPs) contribute to gene expression by regulating the form, abundance, and stability of both coding and non-coding RNA. In the vertebrate brain, RBPs account for many ...

    • Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells 

      Brodsky, Alexander S; Meyer, Clifford; Swinburne, Ian A; Hall, Giles; Keenan, Benjamin J; Liu, Xiaole Shirley; Fox, Edward Alvin; Silver, Pamela A. (BioMed Central, 2005)
      Background: Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be ...

    • Identification and selective expansion of functionally superior T cells expressing chimeric antigen receptors 

      Chang, ZeNan L.; Silver, Pamela A.; Chen, Yvonne Y. (BioMed Central, 2015)
      Background: T cells expressing chimeric antigen receptors (CARs) have shown exciting promise in cancer therapy, particularly in the treatment of B-cell malignancies. However, optimization of CAR-T cell production remains ...

    • In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner 

      Sachdeva, Gairik; Garg, Abhishek; Godding, David; Way, Jeffrey C.; Silver, Pamela A. (Oxford University Press, 2014)
      Co-localization of biochemical processes plays a key role in the directional control of metabolic fluxes toward specific products in cells. Here, we employ in vivo scaffolds made of RNA that can bind engineered proteins ...

    • Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway 

      Nishida, Keiji; Silver, Pamela A. (Public Library of Science, 2012)
      Most organisms are simply diamagnetic, while magnetotactic bacteria and migratory animals are among organisms that exploit magnetism. Biogenic magnetization not only is of fundamental interest, but also has industrial ...

    • LanTERN: A Fluorescent Sensor That Specifically Responds to Lanthanides 

      Jones, Ethan; Su, Yang; Sander, Chris; Justman, Quincey A.; Springer, Michael; Silver, Pamela A; Silver, Pamela (American Chemical Society (ACS), 2024-02-20)
      Lanthanides, a series of 15 f-block elements, are crucial in modern technology, and their purification by conventional chemical means comes at a significant environmental cost. Synthetic biology offers promising solutions. ...

    • Learning a Prior on Regulatory Potential from eQTL Data 

      Lee, Su-In; Dudley, Aimée M.; Drubin, David; Silver, Pamela A.; Krogan, Nevan J.; Pe'er, Dana; Koller, Daphne (Public Library of Science, 2009)
      Genome-wide RNA expression data provide a detailed view of an organism's biological state; hence, a dataset measuring expression variation between genetically diverse individuals (eQTL data) may provide important insights ...