Structural genomics of proteins from conserved biochemical pathways and processes

During the past year, X-ray crystallographers and solution NMR spectroscopists have made significant progress towards the complete structural characterization of conserved biochemical pathways and processes. Some of these advances were made in the context of nascent structural genomics programs, which promise to accelerate structural studies of biologically and medically important proteins. The results of high-throughput protein production, crystallization, structure determination, homology modeling and functional annotation published by two such programs have provided insight into the evolution and function of enzymes in the isoprenoid biosynthesis and ribulose monophosphate pathways.     

The USDA Barley Core Collection: Genetic Diversity,Population Structure,and Potential for Genome-Wide Association Studies

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define ‘mini-core’ sets of accessions capturing the majority of the allelic diversity present in the core collection. These ‘mini-core’ sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of ‘hull cover’, ‘spike row number’, and ‘heading date’ demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.     

Carolina Chickadee (Aves, Paridae, Poecile carolinensis) Vocalization Rates: Effects of Body Mass and Food Availability under Aviary Conditions

We evaluated the effect of body mass and several environmental factors on vocalization rates of Carolina chickadees ( Poecile carolinensis ) housed in an aviary. Two different nonsong vocalizations (tseet and chick-a-dee) and song (fee-bee fee-bay) were recorded. Food was delivered from a feeder and three different levels of food access were presented to each bird: 10, 40 and 55 min/d. Two scales of body mass were measured: 'dawn mass' and 'focal mass' (mass during a focal observation divided by dawn mass). Across all birds, there was a significant negative correlation between both nonsong vocalization rates and body mass (both dawn and focal mass) and the effect of mass on call rate was greatest for days when food was relatively abundant. Nonsong vocalizations were also given at higher rates when food was limited (10 min/d) than when food was more abundant (40 and 55 min/d). No changes in call rates with time of day were observed. Overall, song rates were substantially lower than nonsong rates. Unlike nonsong rates, song rates were highest in birds that had relatively high dawn mass. No significant correlation between song rates and focal mass was observed, and no significant correlation between song rates and time of day was observed. Finally, vocalizations from nonfocal birds had little effect on vocalization rates of focal birds. Our results suggest that nonsong communicative signals are more important for birds facing energetic stress, while song is more important for birds that are not energetically stressed.     

Playing with bone and fat

The relationship between bone and fat formation within the bone marrow microenvironment is complex and remains an area of active investigation. Classical in vitro and in vivo studies strongly support an inverse relationship between the commitment of bone marrow-derived mesenchymal stem cells or stromal cells to the adipocyte and osteoblast lineage pathways. In this review, we focus on the recent literature exploring the mechanisms underlying these differentiation events and discuss their implications relevant to osteoporosis and regenerative medicine.     

Role of Smad2/3 and p38 MAP kinase in TGF-β1-induced epithelial-mesenchymal transition of pulmonary epithelial cells

Idiopathic pulmonary fibrosis is characterized by myofibroblast accumulation, extracellular matrix (ECM) remodeling, and excessive collagen deposition. ECM-producing myofibroblasts may originate from epithelial cells through epithelial to mesenchymal transition (EMT). TGF-β1 is an inducer of EMT in pulmonary epithelial cells in vitro and in vivo, though the mechanisms are unclear. We hypothesized that TGF-β1 induced EMT through Smad-dependent and -independent processes. To test this hypothesis, we studied the roles and mechanisms of TGF-β1-induced Smad and p38 mitogen-activated protein kinase (MAPK) signaling in EMT-related changes in pulmonary epithelial cells. Exposure of pulmonary epithelial 1HAEo(-) cells to TGF-β1 resulted in morphological and molecular changes of EMT over a 96-h period; loss of cell-cell contact, cell elongation, down-regulation of E-cadherin, up-regulation of fibronectin, and up-regulation of collagen I. Both Smad2/3 and p38 MAPK signaling pathways were activated by TGF-β1. However, neither Smad2/3 nor p38 MAPK were required for the down-regulation of E-cadherin, yet p38 MAPK was associated with fibronectin up-regulation. Both Smad2/3 and p38 MAPK had a role in regulation of TGF-β1-induced collagen expression. Furthermore, these data demonstrate that Smads and p38 MAPK differentially regulate EMT-related changes in pulmonary epithelial cells.     

Phytoalexin induction in the sapwood of plants of the Maloideae (Rosaceae): Biphenyls or dibenzofurans

Following fungal inoculation or natural infection, five biphenyl phytoalexins (aucuparin and its 2′ and 4′ oxygenated derivatives) were induced variously in the sapwood of Aronia, Chaenomeles, Eriobotrya, Malus(three spp.) and of Sorbus aucuparia. By contrast, 14 dibenzofuran phytoalexins were induced variously in sapwood of Cotoneaster (7 spp.), Crateagus, Cydonia, Mespilus, Photinia, Pseudocydonia, Pyracantha, Pyrus and two Sorbus spp. (S. chamaemespilum and S. domestica). These were five cotonefurans, three eriobofurans, five pyrufurans and a 2,3,4,7,8-pentaoxygenated dibenzofuran trimethyl ether. No plant has yet been found to produce both types of phytoalexin, although o-hydroxybiphenyls are theoretically precursors of the dibenzofurans. The ability to synthesize either biphenyls or dibenzofurans appears to be genus-specific, except in the case of Sorbus. In 18 of the 38 species tested, these phytoalexins were accompanied by constitutive antifungal phenolics, most of which appeared to be released from bound (glycosidic) forms during the infection process. These were identified variously as hydroquinone, p-hydroxyacetophenone, acetovanillone, 5,7-dihydroxychromone, chrysin, sakuranetin and naringenin. Woody members of the subfamilies Prunoideae and Spiraeoideae failed to yield any phytoalexins on induction, but did contain constitutive antifungal compounds. The limited frequency of the phytoalexin response within the family as a whole is considered in relation to the accumulation of constitutive antifungal agents in these plants.     

Structure of artemin complexed with its receptor GFRalpha3: convergent recognition of glial cell line-derived neurotrophic factors

Artemin (ARTN) is a member of the glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) which regulate the development and maintenance of many neuronal populations in the mammalian nervous system. Here we report the 1.92 A crystal structure of the complex formed between ARTN and its receptor GFRalpha3, which is the initiating step in the formation of a ternary signaling complex containing the shared RET receptor. It represents a new receptor-ligand interaction mode for the TGF-beta superfamily that reveals both conserved and specificity-determining anchor points for all GFL-GFRalpha pairs. In tandem with the complex structure, cellular studies using receptor chimeras implicate dyad-symmetric composite interfaces for recruitment and dimerization of RET, leading to intracellular signaling. These studies should facilitate the functional dissection of the specific versus pleiotropic roles of this system in neurobiology, as well as its exploitation for therapeutic applications.