Person:
Davoli, Teresa

Profile Picture

Email Address

AA Acceptance Date

Birth Date

Research Projects

Organizational Units

Job Title

Last Name

Davoli

First Name

Teresa

Name

Davoli, Teresa
Author's Publications: search.filters.isAuthorOfPublication.778601ea-ba85-4fa8-9fde-aa1b230899f6

Search Results

Now showing 1 - 2 of 2
  • Thumbnail Image
    Publication
    Comprehensive Identification of Host Modulators of HIV-1 Replication using Multiple Orthologous RNAi Reagents
    (2016) Zhu, Jian; Davoli, Teresa; Perriera, Jill M.; Chin, Christopher R.; Gaiha, Gaurav; John, Sinu P.; Sigiollot, Frederic D.; Gao, Geng; Xu, Qikai; Qu, Hongjing; Pertel, Thomas; Sims, Jennifer S.; Smith, Jennifer A.; Baker, Richard E.; Maranda, Louise; Ng, Aylwin; Elledge, Stephen; Brass, Abraham L.
    SUMMARY RNAi screens have implicated hundreds of host proteins as HIV-1 dependency factors (HDFs). While informative, these early studies overlap poorly due to false positives and false negatives. To ameliorate these issues, we combined information from the existing HDF screens together with new screens performed with multiple orthologous RNAi reagents (MORR). In addition to being traditionally validated, the MORR screens and the historical HDF screens were quantitatively integrated by the adaptation of an established analysis program, RIGER, for the collective interpretation of each gene’s phenotypic significance. False positives were addressed by the removal of poorly expressed candidates through gene expression filtering, as well as with GESS, which identifies off-target effects. This workflow produced a quantitatively integrated network of genes that modulate HIV-1 replication. We further investigated the roles of GOLGI49, SEC13, and COG in HIV-1 replication. Collectively, the MORR-RIGER method minimized the caveats of RNAi screening and improved our understanding of HIV-1–host cell interactions.
  • Thumbnail Image
    Publication
    Sources of Error in Mammalian Genetic Screens
    (Genetics Society of America, 2016) Sack, Laura; Davoli, Teresa; Xu, Qikai; Li, Mamie Z.; Elledge, Stephen
    Genetic screens are invaluable tools for dissection of biological phenomena. Optimization of such screens to enhance discovery of candidate genes and minimize false positives is thus a critical aim. Here, we report several sources of error common to pooled genetic screening techniques used in mammalian cell culture systems, and demonstrate methods to eliminate these errors. We find that reverse transcriptase-mediated recombination during retroviral replication can lead to uncoupling of molecular tags, such as DNA barcodes (BCs), from their associated library elements, leading to chimeric proviral genomes in which BCs are paired to incorrect ORFs, shRNAs, etc. This effect depends on the length of homologous sequence between unique elements, and can be minimized with careful vector design. Furthermore, we report that residual plasmid DNA from viral packaging procedures can contaminate transduced cells. These plasmids serve as additional copies of the PCR template during library amplification, resulting in substantial inaccuracies in measurement of initial reference populations for screen normalization. The overabundance of template in some samples causes an imbalance between PCR cycles of contaminated and uncontaminated samples, which results in a systematic artifactual depletion of GC-rich library elements. Elimination of contaminating plasmid DNA using the bacterial endonuclease Benzonase can restore faithful measurements of template abundance and minimize GC bias.