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UFGI Publications Round-Up Week 7/25/2016

Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences.

Author information: Hosner PA1, Braun EL2, Kimball RT2.
1Department of Biology, University of Florida, Gainesville, FL, United States; Florida Museum of Natural History, University of Florida, Gainesville, FL, United States. Electronic address: hosner@ufl.edu.
2Department of Biology, University of Florida, Gainesville, FL, United States.

Journal: Molecular Phylogenetics and Evolution

Date of e-pub: June 28, 2016

Abstract: The Cracidae (curassows, guans, and chachalacas) include some of the most spectacular and endangered Neotropical bird species. They lack a comprehensive phylogenetic hypothesis, hence their geographic origin and the history of their diversification remain unclear. We present a species-level phylogeny of Cracidae inferred from a matrix of 430 ultraconserved elements (UCEs; at least one species sampled per genus) and eight more variable loci (introns and mtDNA; all available species). We use this phylogeny along with probabilistic biogeographic modeling to test whether Gondwanan vicariance, ancient dispersal to South America, ancient dispersal from South America, or massive global cooling isolated cracids in the Neotropics. Contrary to previous estimates that extant cracids diversified in the Cretaceous, our fossil-calibrated divergence time estimates instead support that crown Cracidae originated in the late Miocene. Species-rich genera Crax, Penelope, and Ortalis began diversifying as recently as 3Mya. Biogeographic reconstructions indicate that modern cracids originated in Mesoamerica and were isolated from a widespread Laurasian ancestor, consistent with the massive global cooling hypothesis. Current South American diversity is the result of multiple colonization events following uplift of the Panamanian Isthmus, coupled with rapid diversification and evolution of secondary sympatry. Of the four major cracid lineages (curassows, chachalacas, typical guans, horned guan), the only lineage that has failed to colonize and diversify South America is the unique horned guan (Oreophasis derbianus), which is sister to curassows and chachalacas rather than typical guans.

 

Cryo-electron microscopy reconstruction and stability studies of Wild-Type and R432A Variant of AAV2 Reveals Capsid Structural Stability is a Major Factor in Genome Packaging.

Author information: Drouin LM1, Lins B1, Janssen M2, Bennett A1, Chipman P1, McKenna R1, Chen W3, Muzyczka N3, Cardone G2, Baker TS4, Agbandje-McKenna M5.
1Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
2Department of Chemistry and Biochemistry, and Division of Biological Sciences, University of California-San Diego, San Diego, California, USA 92093.
3Department of Molecular Genetics and Microbiology, University of Florida Genetics Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
4Department of Chemistry and Biochemistry, and Division of Biological Sciences, University of California-San Diego, San Diego, California, USA 92093 tsb@ucsd.edu.
5Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA mckenna@ufl.edu.

Journal: Journal of Virology

Date of e-pub: July 20, 2016

Abstract: The Adeno-associated viruses (AAV) are promising therapeutic gene delivery vectors, and better understanding of their capsid assembly and genome packaging mechanism is needed for improved vector production. Empty AAV capsids assemble in the nucleus prior to genome packaging by virally encoded Rep proteins. To elucidate the capsid determinants of this process, structural differences between wild-type (wt) AAV2 and a packaging deficient variant, AAV2-R432A, were examined using cryo-electron microscopy and three-dimensional image reconstruction both at ∼5.0 Å (medium) and also 3.8 and 3.7 Å (high) resolution, respectively. The high resolution structures showed that removal of the arginine side-chain in AAV2-R432A eliminated hydrogen bonding interactions resulting in altered intramolecular and intermolecular interactions propagated from under the 3-fold axis towards the 5-fold channel. Consistent with these observations, differential scanning calorimetry showed an ∼10° C decrease in thermal stability for AAV2-R432A compared to wt-AAV2. Additionally, the medium resolution structures revealed differences in the juxtaposition of the less ordered, N-terminal region of their capsid proteins, VP1/2/3. A structural rearrangement in AAV2-R432A repositioned the βA strand region under the icosahedral 2-fold axis rather than anti-parallel to the βB strand, eliminating many intramolecular interactions. Thus, a single amino acid substitution can significantly alter the AAV capsid integrity to the extent of reducing its stability and possibly rendering it unable to tolerate the stress of genome packaging. Furthermore, the data show that the 2-, 3-, and 5-fold regions of the capsid contributed to producing the packaging defect and highlight a tight connection between the entire capsid in maintaining packaging efficiency.

NOTE: These abstracts were retrieved from the U.S. National Library of Medicine website managed in collaboration with the U.S. National Library of Medicine 

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