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Judith Straimer,
Marcus C S Lee, Andrew H Lee,
Bryan Zeitler,
April E Williams,
Jocelynn R Pearl,
Lei Zhang,
Edward J Rebar,
Philip D Gregory,
Manuel Llinás,
Fyodor D Urnov,
David A Fidock
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ABSTRACT: Malaria afflicts over 200 million people worldwide, and its most lethal etiologic agent, Plasmodium falciparum, is evolving to resist even the latest-generation therapeutics. Efficient tools for genome-directed investigations of P. falciparum-induced pathogenesis, including drug-resistance mechanisms, are clearly required. Here we report rapid and targeted genetic engineering of this parasite using zinc-finger nucleases (ZFNs) that produce a double-strand break in a user-defined locus and trigger homology-directed repair. Targeting an integrated egfp locus, we obtained gene-deletion parasites with unprecedented speed (2 weeks), both with and without direct selection. ZFNs engineered against the parasite gene pfcrt, responsible for escape under chloroquine treatment, rapidly produced parasites that carried either an allelic replacement or a panel of specified point mutations. This method will enable a diverse array of genome-editing approaches to interrogate this human pathogen.
Nature Methods 08/2012; 9(10):993-8. · 19.28 Impact Factor
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Andrew J Wood,
Te-Wen Lo,
Bryan Zeitler,
Catherine S Pickle,
Edward J Ralston, Andrew H Lee,
Rainier Amora,
Jeffrey C Miller,
Elo Leung,
Xiangdong Meng,
Lei Zhang,
Edward J Rebar,
Philip D Gregory,
Fyodor D Urnov,
Barbara J Meyer
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ABSTRACT: Evolutionary studies necessary to dissect diverse biological processes have been limited by the lack of reverse genetic approaches in most organisms with sequenced genomes. We established a broadly applicable strategy using zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) for targeted disruption of endogenous genes and cis-acting regulatory elements in diverged nematode species.
Science 06/2011; 333(6040):307. · 31.20 Impact Factor
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John J Young,
Jennifer M Cherone,
Yannick Doyon,
Irina Ankoudinova,
Farhoud M Faraji, Andrew H Lee,
Catherine Ngo,
Dmitry Y Guschin,
David E Paschon,
Jeffrey C Miller,
Lei Zhang,
Edward J Rebar,
Philip D Gregory,
Fyodor D Urnov,
Richard M Harland,
Bryan Zeitler
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ABSTRACT: The frog Xenopus, an important research organism in cell and developmental biology, currently lacks tools for targeted mutagenesis. Here, we address this problem by genome editing with zinc-finger nucleases (ZFNs). ZFNs directed against an eGFP transgene in Xenopus tropicalis induced mutations consistent with nonhomologous end joining at the target site, resulting in mosaic loss of the fluorescence phenotype at high frequencies. ZFNs directed against the noggin gene produced tadpoles and adult animals carrying up to 47% disrupted alleles, and founder animals yielded progeny carrying insertions and deletions in the noggin gene with no indication of off-target effects. Furthermore, functional tests demonstrated an allelic series of activity between three germ-line mutant alleles. Because ZFNs can be designed against any locus, our data provide a generally applicable protocol for gene disruption in Xenopus.
Proceedings of the National Academy of Sciences 04/2011; 108(17):7052-7. · 9.68 Impact Factor
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Jeffrey B Doyon,
Bryan Zeitler,
Jackie Cheng,
Aaron T Cheng,
Jennifer M Cherone,
Yolanda Santiago, Andrew H Lee,
Thuy D Vo,
Yannick Doyon,
Jeffrey C Miller,
David E Paschon,
Lei Zhang,
Edward J Rebar,
Philip D Gregory,
Fyodor D Urnov,
David G Drubin
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ABSTRACT: Clathrin-mediated endocytosis (CME) is the best-studied pathway by which cells selectively internalize molecules from the plasma membrane and surrounding environment. Previous live-cell imaging studies using ectopically overexpressed fluorescent fusions of endocytic proteins indicated that mammalian CME is a highly dynamic but inefficient and heterogeneous process. In contrast, studies of endocytosis in budding yeast using fluorescent protein fusions expressed at physiological levels from native genomic loci have revealed a process that is very regular and efficient. To analyse endocytic dynamics in mammalian cells in which endogenous protein stoichiometry is preserved, we targeted zinc finger nucleases (ZFNs) to the clathrin light chain A and dynamin-2 genomic loci and generated cell lines expressing fluorescent protein fusions from each locus. The genome-edited cells exhibited enhanced endocytic function, dynamics and efficiency when compared with previously studied cells, indicating that CME is highly sensitive to the levels of its protein components. Our study establishes that ZFN-mediated genome editing is a robust tool for expressing protein fusions at endogenous levels to faithfully report subcellular localization and dynamics.
Nature Cell Biology 02/2011; 13(3):331-7. · 19.49 Impact Factor
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ABSTRACT: Recent histological studies suggest relatively rapid growth in dinosaurs. However, the timing of reproductive maturity (RM) in dinosaurs is poorly known because unambiguous indicators of RM are rare. One exception is medullary bone (MB), which is an ephemeral bony tissue that forms before ovulation in the marrow cavities of birds as a calcium source for eggshelling. Recently, MB also was described in a single specimen of the saurischian dinosaur Tyrannosaurus rex. Here, we report two other occurrences of MB: in another saurischian dinosaur, Allosaurus, and in the ornithischian dinosaur Tenontosaurus. We show by counting lines of arrested growth and performing growth curve reconstructions that Tenontosaurus, Allosaurus, and Tyrannosaurus were reproductively mature by 8, 10, and 18 years, respectively. RM in these dinosaurs coincided with a transition from growth acceleration to deceleration. It also far precedes predictions based on the growth rates of living reptiles scaled to similar size. Despite relatively rapid growth, dinosaurs were similar to reptiles in that RM developed before reaching asymptotic size. However, this reproductive strategy also occurs in medium- to large-sized mammals and correlates with a strategy of prolonged multiyear growth. RM in actively growing individuals suggests that these dinosaurs were born relatively precocial and experienced high adult mortality. The origin of the modern avian reproductive strategy in ornithuran birds likely coincided with their extreme elevations in growth rate and truncations to growth duration.
Proceedings of the National Academy of Sciences 02/2008; 105(2):582-7. · 9.68 Impact Factor
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Andrew H Lee
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ABSTRACT: Histological analysis of a growth series of alligator femora tests the correlation between strain milieu and microstructure. From mid-diaphyseal cross-sections of these femora (n = 7), vascular canal orientation and density as well as collagen fibre organization were recorded. Throughout ontogeny, the proportion of transverse-spiral (TS) collagen in the dorsal cortex is significantly greater than it is in the ventral cortex (P = 0.008). This regional difference in the proportion of TS collagen is correlated with a regional difference in the state of peak principal strain (compressive or tensile). Nevertheless, the predominant orientation of collagen fibres is longitudinal, which is inconsistent with biomechanical hypotheses that involve peak principal or shear strains. Although the density and orientation of vascular canals do not show significant regional differences (P = 0.26 and P = 0.26, respectively), as with collagen orientation, the vascular canal orientation is predominantly longitudinal. The longitudinal organization of both the vascular canals and the collagen fibres is probably a consequence of longitudinal shifting of subperiosteal osteoid during femoral lengthening. When taken together, these data suggest that growth dynamics is the dominant influence on the histological organization of primary bony tissues in alligator femora.
Journal of Anatomy 04/2004; 204(Pt 3):197-207. · 2.37 Impact Factor
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ABSTRACT: Variants of rhodopsin, a complex of 11-cis retinal and opsin, cause retinitis pigmentosa (RP), a degenerative disease of the retina. Trafficking defects due to rhodopsin misfolding have been proposed as the most likely basis of the disease, but other potentially overlapping mechanisms may also apply. Pharmacological therapies for RP must target the major disease mechanism and contend with overlap, if it occurs. To this end, we have explored the molecular basis of rhodopsin RP in the context of pharmacological rescue with 11-cis retinal. Stable inducible cell lines were constructed to express wild-type opsin; the pathogenic variants T4R, T17M, P23A, P23H, P23L, and C110Y; or the nonpathogenic variants F220L and A299S. Pharmacological rescue was measured as the fold increase in rhodopsin or opsin levels upon addition of 11-cis retinal during opsin expression. Only Pro23 and T17M variants were rescued significantly. C110Y opsin was produced at low levels and did not yield rhodopsin, whereas the T4R, F220L, and A299S proteins reached near-wild-type levels and changed little with 11-cis retinal. All of the mutant rhodopsins exhibited misfolding, which increased over a broad range in the order F220L, A299S, T4R, T17M, P23A, P23H, P23L, as determined by decreased thermal stability in the dark and increased hydroxylamine sensitivity. Pharmacological rescue increased as misfolding decreased, but was limited for the least misfolded variants. Significantly, pathogenic variants also showed abnormal photobleaching behavior, including an increased ratio of metarhodopsin-I-like species to metarhodopsin-II-like species and aberrant photoproduct accumulation with prolonged illumination. These results, combined with an analysis of published biochemical and clinical studies, suggest that many rhodopsin variants cause disease by affecting both biosynthesis and photoactivity. We conclude that pharmacological rescue is promising as a broadly effective therapy for rhodopsin RP, particularly if implemented in a way that minimizes the photoactivity of the mutant proteins.
Journal of Molecular Biology.
