PUNCH: An architecture for Web-enabled wide-area network-computing

This paper addresses the architectural issues that arise in the design of a universally accessible wide-area network-computing system that is capable of making automatic cost/performance tradeoff decisions at run-time. The core system is designed around a three-level hierarchically distributed architecture, a choice driven by the dynamic, incremental, and distributed nature of the information associated with run-time cost/performance tradeoff decisions. Support for independent replication of each component in the hierarchy contributes to the overall scalability and reliability of the architecture. Meta-information is managed in a scalable manner by employing self-encoded resource identifiers that allow O(1) access to all managed information. Security and access control across administrative domains are provided by partitioning the infrastructure into independently-managed cells, and by giving administrators the ability to customize user-views directly at the location at which the request is processed. Demand-driven resource management is achieved by predicting the run-specific resource usage characteristics of tools via machine learning techniques. The concepts described in this paper are embodied in the Purdue University Network-Computing Hubs (PUNCH), a demand-based network-computing system that allows users to access and run unmodified tools via standard World Wide Web browsers. Tools do not have to be written in any particular language, and access to the source or object code is not required. The PUNCH infrastructure can be distributed in a manner that allows tools to be (user-transparently) executed wherever they reside. Currently, PUNCH contains over thirty tools developed by eight universities and four vendors, and serves more than five hundred users. During the past three years, PUNCH users have logged more than one million hits and have performed over seventy thousand simulations. This revised version was published online in July 2006 with corrections to the Cover Date.     

Expression of lipoxygenase during organogenic nodule formation from hop internodes.

Study of lipoxygenase expression (LOX; EC 1.13.11.12) during organogenic nodule formation in hop (Humulus lupulus var. Nugget) showed that LOXs are developmentally regulated throughout the process, suggesting their involvement in the response of internodes to wounding, nodule formation, and plantlet regeneration from these nodules. LOX activity and lipid peroxides exhibited a huge increase during the first week of culture, which may indicate a role for LOX and LOX products in response to wounding in hop, as reported for other systems. Western blotting analysis showed a de novo synthesis of LOX isoenzymes in response to wounding and the detection of three different isoenzymes. Confocal analysis of LOX immunofluorescence revealed the presence of the enzyme in cortical cells of induced internodes and in prenodular cells, mostly appearing as cytoplasmic spots. Some of them were identified as lipid bodies by cytochemical and double immunofluorescence assays, suggesting the involvement of a lipid body LOX during nodule formation. Immunogold labeling detected LOX in peroxisomes, lipid bodies, and plastids of nodular cells. Quantification of the labeling density provided statistical significance for the localization of LOX (three different isoenzymes) in the three compartments, which suggested a possible involvement of LOX in metabolic functions of these organelles during organogenic nodule formation and plantlet regeneration.     

Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle

A putative functional mutation (rs109231213) near PLAG1 (BTA14) associated with stature was studied in beef cattle. Data from 8199 Bos taurus, Bos indicus and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF‐I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P < 10^?4). Frequency of the mutant C allele of rs109231213 differed among B. indicus (0.52), B. taurus (0.96) and Tropical Composite (0.68). Most chromosomes carrying the C allele had the same surrounding 10 SNP haplotype, probably because the C allele was introgressed into Brahman from B. taurus cattle. A region of reduced heterozygosity surrounds the C allele; this is small in B. taurus but 20 Mb long in Brahmans, indicating recent and strong selection for the mutant allele. Thus, the C allele appears to mark a mutation that has been selected almost to fixation in the B. taurus breeds studied here and introduced into Brahman cattle during grading up and selected to a frequency of 0.52 despite its negative effects on fertility.     

Molecular phylogeny and evolution of inflorescence types in Eperua

Premise

The Amazonian hyperdominant genus Eperua (Fabaceae) currently holds 20 described species and has two strongly different inflorescence and flower types, with corresponding different pollination syndrome. The evolution of these vastly different inflorescence types within this genus was unknown and the main topic in this study.

Methods

We constructed a molecular phylogeny, based on the full nuclear ribosomal DNA and partial plastome, using Bayesian inference and maximum likelihood methods, to test whether the genus is monophyletic, whether all species are monophyletic and if the shift from bat to bee pollination (or vice versa) occurred once in this genus.

Results

All but two species are well supported by the nuclear ribosomal phylogeny. The plastome phylogeny, however, shows a strong geographic signal suggesting strong local hybridization or chloroplast capture, rendering chloroplast barcodes meaningless in this genus.

Conclusions

With our data, we cannot fully resolve the backbone of the tree to clarify sister genera relationships and confirm monophyly of the genus Eperua. Within the genus, the shift from bat to bee and bee to bat pollination has occurred several times but, with the bee to bat not always leading to a pendant inflorescence.