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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
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Posts
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Blog Post number 4
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Blog Post number 1
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portfolio
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publications
Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli
Published in PLoS ONE, 2016
We present results of the first large-scale interlaboratory study carried out in synthetic biol- ogy, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest pro- moter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.
Recommended citation: Beal J, Haddock-Angelli T, Gershated M, de Mora K, Lizarazo M, Hollenhorst J, Randy Rettberg, iGEM Interlab Study Contributors. (2015). "Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli." PLoS ONE. 11(3), e0150182. DOI: https://doi:10.1371/journal.pone.0150182 http://fahsan.github.io/files/Beal-PLoSOne-2016.pdf
Initial B Cell Activation Induces Metabolic Reprogramming and Mitochondrial Remodeling
Published in iScience, 2018
B lymphocytes provide adaptive immunity by generating antigen-specific antibodies and supporting the activation of T cells. Little is known about how global metabolism supports naive B cell activation to enable an effective immune response. By coupling RNA sequencing (RNA-seq) data with glucose isotopomer tracing, we show that stimulated B cells increase programs for oxidative phosphorylation (OXPHOS), the tricarboxylic acid (TCA) cycle, and nucleotide biosynthesis, but not glycolysis. Isotopomer tracing uncovered increases in TCA cycle intermediates with almost no contribution from glucose. Instead, glucose mainly supported the biosynthesis of ribonucleotides. Glucose restriction did not affect B cell functions, yet the inhibition of OXPHOS or glutamine restriction markedly impaired B cell growth and differentiation. Increased OXPHOS prompted studies of mitochondrial dynamics, which revealed extensive mitochondria remodeling during activation. Our results show how B cell metabolism adapts with stimulation and reveals unexpected details for carbon utilization and mitochondrial dynamics at the start of a humoral immune response.
Recommended citation: Waters LR, Ahsan FM, Wolf DM, Shirihai O, Teitell MA. (2018). "Initial B Cell Activation Induces Metabolic Reprogramming and Mitochondrial Remodeling." iScience. 5(1), P99-109. DOI:https://doi.org/10.1016/j.isci.2018.07.005 http://fahsan.github.io/files/Waters-iScience-2018.pdf
PNPase knockout results in mtDNA loss and an altered metabolic gene expression program
Published in PLoS ONE, 2018
Polynucleotide phosphorylase (PNPase) is an essential mitochondria-localized exoribonu- clease implicated in multiple biological processes and human disorders. To reveal role(s) for PNPase in mitochondria, we established PNPase knockout (PKO) systems by first shifting culture conditions to enable cell growth with defective respiration. Interestingly, PKO estab- lished in mouse embryonic fibroblasts (MEFs) resulted in the loss of mitochondrial DNA (mtDNA).
Recommended citation: Shimada E, Ahsan FM, Nili M, Huang D, Atamdede S, TeSlaa T, Case D, Yu X, Gregory BD, Perrin BJ, Koehler CM, Teitell MA. (2018). "PNPase knockout results in mtDNA loss and an altered metabolic gene expression program." PLoS ONE. 13(7), e0200925. DOI: https://doi.org/10.1371/journal.pone.0200925 http://fahsan.github.io/files/ShimadaAhsan-PLoSOne-2018.pdf
Ampk regulates IgD expression but not energy stress with B cell activation
Published in Scientific Reports, 2019
Ampk is an energy gatekeeper that responds to decreases in ATP by inhibiting energy-consuming anabolic processes and promoting energy-generating catabolic processes. Recently, we showed that Lkb1, an understudied kinase in B lymphocytes and a major upstream kinase for Ampk, had critical and unexpected roles in activating naïve B cells and in germinal center formation. Therefore, we examined whether Lkb1 activities during B cell activation depend on Ampk and report surprising Ampk activation with in vitro B cell stimulation in the absence of energy stress, coupled to rapid biomass accumulation. Despite Ampk activation and a controlling role for Lkb1 in B cell activation, Ampk knockout did not significantly affect B cell activation, differentiation, nutrient dynamics, gene expression, or humoral immune responses. Instead, Ampk loss specifically repressed the transcriptional expression of IgD and its regulator, Zfp318. Results also reveal that early activation of Ampk by phenformin treatment impairs germinal center formation but does not significantly alter antibody responses. Combined, the data show an unexpectedly specific role for Ampk in the regulation of IgD expression during B cell activation.
Recommended citation: Waters LR, Ahsan FM, ten Hoeve J, Hong JS, Kim DNH, Minasyan A, Braas D, Graeber TG, Zangle TA, Teitell MA. (2019). "Ampk regulates IgD expression but not energy stress with B cell activation." Scientific Reports. 9(8176), 1-14. DOI: https://doi.org/10.1038/s41598-019-43985-y http://fahsan.github.io/files/Waters-ScientificReports-2019.pdf
Mitochondrial metabolism and glutamine are essential for mesoderm differentiation of human pluripotent stem cells.
Published in Cell Research, 2019
Human pluripotent stem cells (hPSCs) generate energy mainly by aerobic glycolysis, with glutamine oxidation in the tricarboxylic acid (TCA) cycle providing additional ATP required for survival. During the exit from pluripotency and initial differentiation into multiple germ lineage precursors, energy production shifts from mainly aerobic glycolysis to mitochondrial oxidative phosphorylation (OXPHOS). Until recently, consensus in the field was that as PSCs exit pluripotency, a metabolic switch from aerobic glycolysis to OXPHOS is required.
Recommended citation: Lu V, Dahan P, Ahsan FM, Patananan AN, Roy IJ, Torres Jr. A, Nguyen RMT, Huang D, Braas D, Teitell MA. (2019). "Mitochondrial metabolism and glutamine are essential for mesoderm differentiation of human pluripotent stem cells." Cell Research. 29, 596–598. DOI: https://doi.org/10.1038/s41422-019-0191-2 http://fahsan.github.io/files/LuDahan-CellResearch-2019.pdf
talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
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Teaching experience 2
Workshop, University 1, Department, 2015
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