Research

There are many different research projects being run on The Lattice Project Grid system. This page explains these projects in more detail.

NOTE: If you are a researcher using The Lattice Project for your work, please cite The Lattice Project in your papers and publications using these guidelines.

• The Cummings Laboratory, the LepTree project, and others are using GARLI to infer evolutionary relationships based on DNA sequence data.

  Miriam Reyna-Fabián aims to solve the intra- and inter-genus relationships of more than 15 species of rotifers, currently assigned to the family Brachionidae. Species of this family are free-living organisms and they compose part of the zooplankton in freshwater and marine systems. Variation in morphological characters has traditionally been used to differentiate species. However, the taxonomic positions of 3 species — Brachionus patulus, B. macracanthus and B. polyacanthus — have been controversial. A study based on scanning electron microscopy of the trophy (Segers el al., 1993) proposed erecting these 3 species to a new genus: Plationus.

  The phylogenetic analyses of the family Brachionidae were carried out through the analysis of genes encoding cytochrome oxidase subunit 1 (Cox 1) and the domains (D2-D3) of the 28S rRNA. A total of 23 sequences, including 8 outgroups, were aligned. The phylogenies derived from this study were used to evaluate the validity of the new genus Plationus. Our analyses support the hypothesis that Plationus patulus and P. macracanthus compose a distinct clade from Brachionus and Platyias with high bootstrap values.
  

  • Reyna-Fabián M, Laclette JP, Cummings MP, Sarma SSS and M García-Varela. Molecular phylogeny of some species of the genus Brachionus and the systematic position of Plationus based on nuclear and mitochondrial gene sequences. To appear.
  
  

  The Neel lab is studying phylogenetic relationships among North American members of the genus Agalinis Raf. These species represent a taxonomically challenging group and there have been extensive historical revisions at the species, section, and subsection levels of classification. The genus contains many rare species, including the federally listed endangered species Agalinis acuta. In addition to evaluating the degree to which historical classifications at the section and subsection levels are supported by molecular data sampled from 79 individuals representing 29 Agalinis species, we assessed the monophyly of 27 species by sampling multiple individuals representing different populations of those species. Twenty-one of these species are of conservation concern in at least some part of their range.
  

  • James B Pettengill and Maile C Neel. 2008. Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae). BMC Evolutionary Biology 8:264.
  
  

  Silvana Marten-Rodriguez aims to understand the role of pollinators in the evolution of floral traits and breeding systems in the Antillean tribe Gesnerieae by combining phylogenetic approaches with ecological studies. The tribe Gesnerieae encompasses species specialized for hummingbird or bat pollination as well as some generalized species pollinated by bats, hummingbirds and insects. Preliminary phylogenies suggest various independent pollination system transitions well as the evolution of reproductive assurance mechanisms (i.e. autonomous self-pollination). Low frequencies of hummingbird visitation and high pollen limitation in specialized hummingbird pollinated species might be responsible for these transitions.
  

  • Marten-Rodriguez S, Fenster CB and Zimmer LA. Evolution of pollination and breeding systems in Antillean Gesneriaceae. To appear.
  
  

• The Edwards Laboratory is using the HMMPfam service to compute Pfam assignments for all bacterial, plasmid, and virus protein sequences from Swiss-Prot, TrEMBL, GenBank, RefSeq, and TIGR's CMR, plus an inclusive set of all plausible Glimmer predictions from RefSeq bacterial genomes. These protein sequences, and their Pfam assignments, are used in the Rapid Microorganism Identification Database (www.RMIDb.org). The HMMPfam service is also being used as a model for "data-heavy" bioinformatics applications on the Lattice Grid infrastructure, a collaboration between the Cummings and Edwards laboratories.
  

  • N.J. Edwards and F. Pineda. Poster at ASMS (2006). Rapid Microorganism Identification Database (www.RMIDb.org), 2006.
  
  

• Dr. Catherine Dibble's Computational Laboratories Group uses agent-based simulation models to study the geographic spread of Avian Influenza across the United States, to quantify the relative pandemic risk of US cities and determine optimal intervention strategies. The Grid service being used is Complab.
  

  • Catherine Dibble, Stephen Wendel, and Kristofor Carle (University of Maryland). Simulating Pandemic Influenza Risks of U.S. Cities. In Proceedings of the 2007 Winter Simulation Conference, 2007.
  
  

• The Cummings Laboratory is using gsi to assess the performance of the statistic in a variety of situations.
  

  • Cummings, M. P., M. C. Neel and K. L. Shaw. 2008. A genealogical approach to quantifying lineage divergence. Evolution 62:2411-2422.
  
  

• Maile Neel and Joanna Grand are using Marxan to quantify the effects of poor and incomplete data on the ability to capture biological diversity in nature reserves.
  

  • Grand, J., M. P. Cummings, A. G. Rebelo, T. H. Ricketts, and M. C. Neel. 2007. Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology Letters 10:364-374.
  
  

• The Laboratory of David Fushman runs protein:protein docking algorithms on Lattice. When driven by experimentally derived constraints, these will help in modeling the structures of large multi-subunit proteins, and the interactions of such proteins with various ligands. CNS is the featured Grid service in this project.
  

  • Varadan, R., Assfalg, M., Raasi, S., Pickart, C. & Fushman, D. Structural Determinants for Selective Recognition of a Lys48-Linked Polyubiquitin Chain by a UBA Domain. Mol Cell 18, 687-98 (2005).
  
  

• Floyd Reed and Holly Mortensen from the Laboratory of Sarah Tishkoff have run a number of MDIV and IM simulations through The Lattice Project. These are studies in molecular population genetics that seek to use DNA sequence polymorphism to estimate the times of divergence and migration rates among ethnically diverse human populations in Africa.
  

  • Tishkoff, S. A., Gonder, M. K., Henn, B. M., Mortensen, H., Knight, A., Gignoux, C., Fernandopulle, N., Lema, G., Nyambo, T. B., Ramakrishnan, U., Floyd A. Reed, F. A. & Mountain, J. L. History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution 24(10), 2180-2195 (2007).