Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

Evaluating use of an ultrasound device to measure distances to foliar and woody targets.

RM-RN-46

Middle Miocene carnivorans from the Monarch Mill Formation, Nevada

The lowest part of the Monarch Mill Formation in the Middlegate basin, west-central Nevada, has yielded a middle Miocene (Barstovian Land Mammal Age) vertebrate assemblage, the Eastgate local fauna. Paleobotanical evidence from nearby, nearly contemporaneous fossil leaf assemblages indicates that the Middle Miocene vegetation in the area was mixed coniferous and hardwood forest and chaparral-sclerophyllous shrubland, and suggests that the area had been uplifted to 2700–2800 m paleoaltitude before dropping later to near its present elevation of 1600 m. Thus, the local fauna provides a rare glimpse at a medium- to high-altitude vertebrate community in the intermountain western interior of North America. The local fauna includes the remains of fish, amphibians, reptiles, birds, and 25 families of mammals. Carnivorans, the focus of this study, include six taxa (three of which are new) belonging to four families. Canidae are represented by the borophagine Tomarctus brevirostris and the canine Leptocyon sp. indet. The earliest record and second North American occurrence of the simocyonine ailurid Actiocyon is represented by A. parverratis sp. nov. Two new mustelids, Brevimalictis chikasha gen. et sp. nov. and Negodiaetictis rugatrulleum gen. et sp. nov., may represent Galictinae but are of uncertain subfamilial and tribal affinity. The fourth family is represented by the felid Pseudaelurus sp. indet. Tomarctus brevirostris is limited biochronologically to the Barstovian land mammal age and thus is consistent with the age indicated by other members of the Eastgate local fauna as well as by indirect tephrochronological dates previously associated with the Monarch Mill Formation. Actiocyon parverratis sp. nov. extends the temporal range of the genus Actiocyon from late Clarendonian back to the Barstovian. The Eastgate local fauna improves our understanding of mammalian successions and evolution, during and subsequent to the Mid-Miocene Climatic Optimum (~14–17 Ma)

A new genus of eomyid rodent from the Miocene of Nevada

The description of a new genus (Apeomyoides) of eomyid rodent from the Miocene of Nevada increases the diversity of known taxa, enhances the geographic range, and extends the biochronology for the Apeomyinae (Eomyidae). Three groups of Eomyidae are known from the fossil record of North America. Of the three groups, Neogene taxa include four genera representing the Eomyinae and two genera representing the Apeomyinae; no genera of the subfamily Yoderimyinae are known from the Neogene of the continent. This diversity represents a significant reduction of eomyid taxa compared to the Paleogene, from which 17 genera of eomyines and three genera of yoderimyines are known. In Eurasia, 11 genera of eomyids occurred during the Neogene, with a few taxa that persisted until about 2 million years before present. At present, there are no known eomyids from the last 4.5 million years of the Neogene in North America. Apeomyoides savagei is referable to the subfamily Apeomyinae based on several key structures of the teeth and mandible. This new eomyid is part of the Eastgate local fauna, collected from volcanic ash deposits of the Monarch Mill Formation, Churchill County, Nevada. Apeomyoides has an occlusal pattern that shares characteristics of apeomyines from both North America (Megapeomys and Arikareeomys) and Eurasia (Apeomys and Megapeomys). The unique occlusal pattern and large size of Apeomyoides demonstrates that not all eomyids from North America were small or that their lineages decreased in size through time. Apeomyoides also may provide evidence, which challenges the hypothesis that eomyids within a single lineage from North America became more lophodont in geologically younger genera