A unified mixed-model method for association mapping that accounts for multiple levels of relatedness

As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by population structure. We have developed a unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers. We applied this new approach to two samples: a family-based sample of 14 human families, for quantitative gene expression dissection, and a sample of 277 diverse maize inbred lines with complex familial relationships and population structure, for quantitative trait dissection. Our method demonstrates improved control of both type I and type II error rates over other methods. As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping.     

Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy

The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), CA (capsid) and NC (nucleocapsid). Assembly of an infectious virion proceeds in two stages. In the first stage, Gag oligomerization into a hexameric protein lattice leads to the formation of an incomplete, roughly spherical protein shell that buds through the plasma membrane of the infected cell to release an enveloped immature virus particle. In the second stage, cleavage of Gag by the viral protease leads to rearrangement of the particle interior, converting the non-infectious immature virus particle into a mature infectious virion. The immature Gag shell acts as the pivotal intermediate in assembly and is a potential target for anti-retroviral drugs both in inhibiting virus assembly and in disrupting virus maturation. However, detailed structural information on the immature Gag shell has not previously been available. For this reason it is unclear what protein conformations and interfaces mediate the interactions between domains and therefore the assembly of retrovirus particles, and what structural transitions are associated with retrovirus maturation. Here we solve the structure of the immature retroviral Gag shell from Mason-Pfizer monkey virus by combining cryo-electron microscopy and tomography. The 8-? resolution structure permits the derivation of a pseudo-atomic model of CA in the immature retrovirus, which defines the protein interfaces mediating retrovirus assembly. We show that transition of an immature retrovirus into its mature infectious form involves marked rotations and translations of CA domains, that the roles of the amino-terminal and carboxy-terminal domains of CA in assembling the immature and mature hexameric lattices are exchanged, and that the CA interactions that stabilize the immature and mature viruses are almost completely distinct.     

Temperature responses and habitat sharing in two sympatric species of Okanagana (Homoptera: Cicadoidea)

Okanagana striatipes and O. utahensis are species synchronous in location of activity and utilization of host plants. They possess similar acoustic behavior. Analysis of calling songs shows that calls overlap in frequency but differ in temporal pattern. Based on characteristics of the cicada auditory system and the species recognition mechanism, the potential for acoustic interference exists. Both species are ectothermic behavioral thermoregulators. Measurements of thermal preference and body temperature during singing show that although thermal preferences are similar, O. utahensis sings at a significantly higher body temperature. Differences in body temperature required to coordinate singing in the 2 species provide a partial temporal separation of acoustic signaling. We suggest the physiological mechanisms that permit synchronous utilization of a habitat by the 2 species are the production of calling songs of different temporal patterns and the presence of different thermal requirements, which may permit and/or facilitate temporal separation of the acoustic environment during the day.     

Alpine and subalpine wetland plant communities of the Uinta Mountains, Utah

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Triiodothyronine and thyroxine: Induction of mitosis in adult forgs

Zusammenfassung Nachweis, dass bei adulten, reifen Fröschen Thyroxin und Triiodothyronin die mitotische Aktivität und die DNS-Synthese in verschiedenen Organen (Augenlinse, mit Epithel, Niere Darm, Leber, Milz, Haut, Horn-und Nickhaut) zu stimulieren vermag.

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This work was supported by USPHS Grant No. EY 00281-09 from the National Eye Institute, and Fight for Sight Grant-in-Aid No. G-496.     

Single-species models for many-species food webs

Most species live in species-rich food webs; yet, for a century, most mathematical models for population dynamics have included only one or two species. We ask whether such models are relevant to the real world. Two-species population models of an interacting consumer and resource collapse to one-species dynamics when recruitment to the resource population is unrelated to resource abundance, thereby weakening the coupling between consumer and resource. We predict that, in nature, generalist consumers that feed on many species should similarly show one-species dynamics. We test this prediction using cyclic populations, in which it is easier to infer underlying mechanisms, and which are widespread in nature. Here we show that one-species cycles can be distinguished from consumer resource cycles by their periods. We then analyse a large number of time series from cyclic populations in nature and show that almost all cycling, generalist consumers examined have periods that are consistent with one-species dynamics. Thus generalist consumers indeed behave as if they were one-species populations, and a one-species model is a valid representation for generalist population dynamics in many-species food webs.