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SLC19A1 is an importer of the immunotransmitter cGAMP [article]

Anthony F. Cordova, Christopher Ritchie, Gaelen T. Hess, Michael C. Bassik, Lingyin Li
2019 bioRxiv   pre-print
For [ 3 H]methotrexate import in U937 cell lines, p values were calculated using an unpaired t-test assuming a Gaussian distribution.  ...  In the case of cancer clearance, IFN-β promotes cross-priming of CD8 + T cells by tumor-infiltrating antigen presenting cells (Fuertes et al. 2011) .  ... 
doi:10.1101/539247 fatcat:iqzaqpclxbbnfa4ag6dfqr5cie

Translation readthrough mitigation

Joshua A. Arribere, Elif S. Cenik, Nimit Jain, Gaelen T. Hess, Cameron H. Lee, Michael C. Bassik, Andrew Z. Fire
2016 Nature  
Artiles for technical expertise, and T. Schedl, T. Inada, C. Joazeiro, L. Ling, A. Nager, and N. Spies for discussions. A. Sapiro and B. Li were instrumental in developing the RNA-seq2 protocol.  ...  Student's t-test two-tailed P value.  ...  Rand1-3(A, C, G, T) are random combinations of A, C, G, and T created in silico. CDS N-M is an arbitrary fragment of the respective coding DNA sequence of the gene (from amino acid N to M).  ... 
doi:10.1038/nature18308 pmid:27281202 pmcid:PMC5054982 fatcat:stzjnjkscjfbvexby2xgp65lue

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

Gaelen T. Hess, Josh Tycko, David Yao, Michael C. Bassik
2017 Molecular Cell  
Similar to the TAM system, the conversion of C to A, G, or T and G to A, C, or T showed only a slight preference for C>T. Mutations at A and T bases were also observed, but at a much lower frequency.  ...  As an initial proof-of-principle, wild-type GFP was evolved to EGFP using CRISPR-X (Hess et al., 2016) .  ... 
doi:10.1016/j.molcel.2017.09.029 pmid:28985508 pmcid:PMC5997582 fatcat:icxxt5au5ffejb77fcqhnyafvi

Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform [article]

Dirk H Siepe, Lukas T Henneberg, Steven C Wilson, Gaelen T Hess, Michael C Bassik, Kai Zinn, K. Christopher Garcia
2022 bioRxiv   pre-print
Its expression is restricted to naïve and memory regulatory T cells (T-regs), basophils, and neutrophils, with the highest expression levels being observed in basophils (Figure 5G ).  ...  LGI1_HUMAN FIGURE LEGENDS K R T D A P LY 6 H S C R G 1 V W C 2 L N R N 1 L N R N 1 Correlation -1.0 -0 LGI2_HUMAN LGI3_HUMAN LGI4_HUMAN Figure 1 . 1 Figure 1.  ... 
doi:10.1101/2022.06.22.497261 fatcat:ce2dommxivdyljakxc4pqvxo3u

Cellular binding, motion, and internalization of synthetic gene delivery polymers

Gaelen T. Hess, William H. Humphries, Nicole C. Fay, Christine K. Payne
2007 BBA - Molecular Cell Research  
Using fluorescence microscopy we have tracked the cellular binding, surface motion, and internalization of polyarginine and polyethylenimine, cationic ligands used for gene and protein delivery. Each ligand was complexed with a quantum dot to provide a photostable probe. Transfection with exogenous DNA was used to relate the observed motion to gene delivery. Cell surface motion was independent of sulfated proteoglycans, but dependent on cholesterol. Cellular internalization required sulfated
more » ... teoglycans and cholesterol. These observations suggest that sulfated proteoglycans act as cellular receptors for the cationic ligands, rather than only passive binding sites. Understanding the interaction of polyarginine and polyethylenimine with the plasma membrane may assist in designing more efficient gene delivery systems.
doi:10.1016/j.bbamcr.2007.07.009 pmid:17888530 pmcid:PMC2121221 fatcat:dt7us5lm6ben7a5e6i6ck376hi

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

Gaelen T Hess, Laure Frésard, Kyuho Han, Cameron H Lee, Amy Li, Karlene A Cimprich, Stephen B Montgomery, Michael C Bassik
2016 Nature Methods  
CRISPR-X tiling of GFP locus Hess et al. Page 18 Nat Methods.  ...  Importantly, we find a significant increase in mutation frequencies for all possible base changes except A>T for the AID*Δ treated samples.  ... 
doi:10.1038/nmeth.4038 pmid:27798611 pmcid:PMC5557288 fatcat:dtqrlp4runghjl4vic2guav2ja

Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions

Kyuho Han, Edwin E Jeng, Gaelen T Hess, David W Morgens, Amy Li, Michael C Bassik
2017 Nature Biotechnology  
A l l r i g h t s r e s e r v e d .  ...  Nature Biotechnol. http://dx.doi. org/10.1038/nbt.3834 (2017) © 2 0 1 7 M a c m i l l a n P u b l i s h e r s L i m i t e d , p a r t o f S p r i n g e r N a t u r e .  ... 
doi:10.1038/nbt.3834 pmid:28319085 pmcid:PMC5557292 fatcat:baahdehhrjdydiqmzygicfda5u

High-throughput discovery and characterization of human transcriptional effectors [article]

Josh Tycko, Nicole DelRosso, Gaelen T. Hess, Aradhana, Abhimanyu Banerjee, Aditya Mukund, Mike V. Van, Braeden K. Ego, David Yao, Kaitlyn Spees, Peter Suzuki, Georgi K Marinov (+3 others)
2020 bioRxiv   pre-print
High-throughput discovery and characterization of human transcriptional effectorsJosh Tycko 1 , Nicole DelRosso 2 , Gaelen T. Hess 1 , Aradhana 1 , Abhimanyu Banerjee 3 , Aditya Mukund 2 , Mike V.  ... 
doi:10.1101/2020.09.09.288324 fatcat:3lazhg4ut5dz5fnmqgmcqs66o4

Static And Dynamic DNA Loops Form AP-1 Bound Activation Hubs During Macrophage Development [article]

Douglas H. Phanstiel, Kevin Van Bortle, Damek V. Spacek, Gaelen T. Hess, Muhammad Saad Shamim, Ido Machol, Michael I. Love, Erez Lieberman Aiden, Michael C. Bassik, Michael P. Snyder
2017 bioRxiv   pre-print
Peaks were identified for each sample and biological replicate using MACS2 version 2.1.0 with command line options "macs2 callpeak -bdg -t -g hs".  ...  using trim galore version 0.40 with command-line settings "trim_galore -q 20 --trim1 --paired" and subsequently aligned to the hg19 reference genome using bowtie2 version 2.2.4 with settings "bowtie2 -t  ... 
doi:10.1101/142026 fatcat:cjzrfozvszgpvjgwka3h6itenu

A comprehensive portrait of cilia and ciliopathies from a CRISPR-based screen for Hedgehog signaling [article]

David K. Breslow, Sascha Hoogendoorn, Adam R. Kopp, David W. Morgens, Brandon K. Vu, Kyuho Han, Amy Li, Gaelen T. Hess, Michael C. Bassik, James K. Chen, Maxence V. Nachury
2017 bioRxiv   pre-print
Wang and T. Stearns, personal 27 communication).  ...  Wang and T. Stearns for sharing unpublished results and cDNA for Cby1; and M. 6 Scott for helpful discussions.  ... 
doi:10.1101/156059 fatcat:hksdcswrebaxvnawrjzd5ywcdm

Orthogonal Labeling of M13 Minor Capsid Proteins with DNA to Self-Assemble End-to-End Multiphage Structures

Gaelen T. Hess, Carla P. Guimaraes, Eric Spooner, Hidde L. Ploegh, Angela M. Belcher
2013 ACS Synthetic Biology  
building block for more complex multi-material devices such as transistors and diodes, because its major capsid protein (pVIII) can been engineered to bind and nucleate different materials. 2, 4, 6 T  ... 
doi:10.1021/sb400019s pmid:23713956 pmcid:PMC3905569 fatcat:gkaojgvzibaafbi3gf2cruuy6y

The LRRC8A:C Heteromeric Channel Is a cGAMP Transporter and the Dominant cGAMP Importer in Human Vasculature Cells [article]

Lauren J. Lahey, Xianlan Wen, Rachel E. Mardjuki, Volker Böhnert, Christopher Ritchie, Jacqueline A. Carozza, Gaelen T. Hess, Merritt Maduke, Michael C. Bassik, Lingyin Li
2020 bioRxiv   pre-print
Significance calculated using ratio paired t-test; *P ≤ 0.05. See also Figure S3 .  ...  Significance calculated using ratio paired t-test; *P ≤ 0.05. See also Figure S5 .  ... 
doi:10.1101/2020.02.13.948273 fatcat:areynik52bg5bof5vc3k7cath4

M13 Bacteriophage Display Framework That Allows Sortase-Mediated Modification of Surface-Accessible Phage Proteins

Gaelen T. Hess, Juan J. Cragnolini, Maximilian W. Popp, Mark A. Allen, Stephanie K. Dougan, Eric Spooner, Hidde L. Ploegh, Angela M. Belcher, Carla P. Guimaraes
2012 Bioconjugate chemistry  
We exploit bacterial sortases to attach a variety of moieties to the capsid proteins of M13 bacteriophage. We show that pIII, pIX, and pVIII can be functionalized with entities ranging from small molecules (e.g., fluorophores, biotin) to correctly folded proteins (e.g., GFP, antibodies, streptavidin) in a site-specific manner, and with yields that surpass those of any reported using phage display technology. A case in point is modification of pVIII. While a phage vector limits the size of the
more » ... sert into pVIII to a few amino acids, a phagemid system limits the number of copies actually displayed at the surface of M13. Using sortase-based reactions, a 100-fold increase in the efficiency of display of GFP onto pVIII is achieved. Taking advantage of orthogonal sortases, we can simultaneously target two distinct capsid proteins in the same phage particle and maintain excellent specificity of labeling. As demonstrated in this work, this is a simple and effective method for creating a variety of structures, thus expanding the use of M13 for materials science applications and as a biological tool.
doi:10.1021/bc300130z pmid:22759232 pmcid:PMC3564602 fatcat:sp4sfr7ygjbwzgzpytmghhdqde

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

Douglas H. Phanstiel, Kevin Van Bortle, Damek Spacek, Gaelen T. Hess, Muhammad Saad Shamim, Ido Machol, Michael I. Love, Erez Lieberman Aiden, Michael C. Bassik, Michael P. Snyder
2017 Molecular Cell  
Peaks were identified for each sample and biological replicate using MACS2 version 2.1.0 with command line options "macs2 callpeak -bdg -t -g hs".  ...  using trim galore version 0.40 with command-line settings "trim_galore -q 20 --trim1 --paired" and subsequently aligned to the hg19 reference genome using bowtie2 version 2.2.4 with settings "bowtie2 -t  ... 
doi:10.1016/j.molcel.2017.08.006 pmid:28890333 fatcat:k6bav5clqvhordahh4kaczq7ua

A CRISPR-based screen for Hedgehog signaling provides insights into ciliary function and ciliopathies

David K. Breslow, Sascha Hoogendoorn, Adam R. Kopp, David W. Morgens, Brandon K. Vu, Margaret C. Kennedy, Kyuho Han, Amy Li, Gaelen T. Hess, Michael C. Bassik, James K. Chen, Maxence V. Nachury
2018 Nature Genetics  
The primary cilium organizes Hedgehog signaling and shapes embryonic development, and its dysregulation is the unifying cause of ciliopathies. We conducted a functional genomic screen for Hedgehog signaling by engineering antibiotic-based selection of Hedgehog-responsive cells and applying genome-wide CRISPR-mediated gene disruption. The screen robustly identifies factors required for ciliary signaling with few false positives or false negatives. Characterization of hit genes uncovers novel
more » ... onents of several ciliary structures, including a protein complex containing δand ε-tubulin that is required for centriole maintenance. The screen also provides an unbiased tool for classifying ciliopathies and reveals that many congenital heart disorders are caused by loss of ciliary signaling. Collectively, our study enables a systematic analysis of ciliary Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:
doi:10.1038/s41588-018-0054-7 pmid:29459677 pmcid:PMC5862771 fatcat:hajwqonh3jf4pdkqroitjgk3g4
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