Marguerite C. Murphy

Draft genome of the red harvester ant Pogonomyrmex barbatus

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant (Linepithema humile), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of >1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ants biology, as well as similarities to Apis mellifera and Nasonia vitripennis. Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes (>110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium, which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.

The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colonys primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ants lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host–microbe symbioses.

Execution plan balancing

A novel relational query optimization technique for use in shared memory multiprocessor database systems is described. A collection of practical algorithms for allocating computational resources to parallel select-project filter (SPJ) query execution plans is presented. The computational resources considered include disk bandwidth, memory buffers and general-purpose processors. The goal of the allocation algorithms is to produce minimum duration execution strategies with computational resource requirements that are less than the given system bounds. Preliminary experimental results indicate that the algorithms can be realized and are effective in producing good execution plans. Disk bandwidth appears to be the critical system resource. The most effective means to decrease complex query response time appears to be by reducing disk contention. This can be achieved by increasing the total number of disks and/or rearranging the placement of data on disks.<<ETX>>

Work in progress - testing right from the start

Writing syntactically correct code and understanding algorithm development are two essential skills mastered by most introductory computer science students. Another important component of professional programming is thorough testing to verify correct design and accurate coding; however this topic is frequently covered with less emphasis than it deserves in the core programming curricula. In this paper we describe instructional software that we are developing to support introductory level programming students in collaboratively and incrementally developing test cases for the class libraries they implement, as well as to automatically validate their implementations. This software is structured as an Internet application with a simplified user interface that allows distributed generation of a common library of test cases as well as remote testing of each students individual implementation. By integrating testing and validation into the earliest stages of programming instruction, we anticipate that students will develop a better understanding of not only the syntax of the programming languages they are using but, more importantly, a deeper understanding of the semantics of the code they author and better success in debugging initial versions of their program solutions. Furthermore, using an Internet based infrastructure allows students to become familiar with having different aspects of the program development process itself performed by different (teams) of individuals, each of whom might be geographically distributed: an important practical component of global software engineering. A fully functional on-line version of our software is expected by the end of Summer 2007 and Human Subjects Protocol approval is expected for Fall 2007 evaluation of the effectiveness of our software in instructing introductory level programming students.

Integrating bioinformatic data sources over the SFSU ER design tools XML databus

The SFSU ER Design Tools were developed to support database design and data integration over multiple implementation data models. These tools allow users to enter and view Entity Relationship (ER) schemas and to translate ER schemas into a variety of equivalent implementation schemas, including Relational (ANSI SQL2), Object Oriented (ODMG 3.0), Spreadsheet (Universal Relation with associated functional dependencies) and W3C XML DTD. In addition, for each implementation data model, the Tools generate DDL statements to create a database, as well as simple JDBC/ODBC based code to dump stored data into an XML file and to load data from an XML file into a database. Data can be transferred from one data store to another over an HTTP based XML Databus. In this paper we describe the design and implementation of our XML Databus using Web Services, as well as a new strategy to support integration of bioinformatics data sets. We first manually identify semantically equivalent attributes in both schemas, then automatically join the corresponding data sets into a single integrated collection of XML formatted data. Our software is operational, and preliminary performance measurements over DTD and data downloaded from the NIH-NCBI Web site show that our strategy is feasible for moderately sized data sets.

GO Visual Browser

Biologists commonly annotate genome and protein properties using ontology terms. While biologists have a deep understanding of the underlying biology, they rarely have a good understanding of the semantic networks used to represent domain ontologies. This paper presents the design and implementation of the GO Visual Browser: a new tool to provide visualization of Gene Ontology terms and relationships, as well as retrieval of associated genomic data. Browsing involves selecting a term and type of ontology relationship, and then displaying an interactive map with all of the related terms. This map can then be used to search a genome database for all features, related sequences, and metadata annotated with the selected ontology terms. Our code is fully functional and is being distributed as open source software.