The Innate Immune Database (IIDB)

<p>Abstract</p> <p>Background</p> <p>As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site <url>http://www.innateImmunity-systemsbiology.org</url>. Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens.</p> <p>Description</p> <p>We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser.</p> <p>Conclusion</p> <p>We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at <url>http://db.systemsbiology.net/IIDB</url>.</p

Shannon Information Theory and Molecular Biology

The role and the contribution of Shannon Information Theory to the development of Molecular Biology has been the object of stimulating debates during the last thirty years. This seems to be connected with some semantic charms associated with the use of the word \u201cinformation\u201d in the biological context. Furthermore information itself, if viewed in a broader perspective, is far from being completely defined in a fashion that overcomes the technical level at which the classical Information Theory has been conceived. This review aims at building on the acknowledged contribution of Shannon Information Theory to Molecular Biology, so as to discover if it is only a technical tool to analyze DNA and proteinic sequences, or if it can rise, at least in perspective, to a higher role that exerts an influence on the construction of a suitable model for handling the genetic information in Molecular Biology

Independent Origins of Cultivated Coconut (Cocos nucifera L.) in the Old World Tropics

As a portable source of food, water, fuel, and construction materials, the coconut (Cocos nucifera L.) played a fundamental role in human migrations and the development of civilization across the humid tropics. Here we investigated the coconut's domestication history and its population genetic structure as it relates to human dispersal patterns. A sample of 1,322 coconut accessions, representing the geographical and phenotypic diversity of the species, was examined using ten microsatellite loci. Bayesian analyses reveal two highly genetically differentiated subpopulations that correspond to the Pacific and Indo-Atlantic oceanic basins. This pattern suggests independent origins of coconut cultivation in these two world regions, with persistent population structure on a global scale despite long-term human cultivation and dispersal. Pacific coconuts show additional genetic substructure corresponding to phenotypic and geographical subgroups; moreover, the traits that are most clearly associated with selection under human cultivation (dwarf habit, self-pollination, and “niu vai” fruit morphology) arose only in the Pacific. Coconuts that show evidence of genetic admixture between the Pacific and Indo-Atlantic groups occur primarily in the southwestern Indian Ocean. This pattern is consistent with human introductions of Pacific coconuts along the ancient Austronesian trade route connecting Madagascar to Southeast Asia. Admixture in coastal east Africa may also reflect later historic Arab trading along the Indian Ocean coastline. We propose two geographical origins of coconut cultivation: island Southeast Asia and southern margins of the Indian subcontinent

New dicynodonts (Therapsida, Anomodontia) from near the Permo-Triassic boundary of Laos: implications for dicynodont survivorship across the Permo-Triassic mass extinction and the paleobiogeography of Southeast Asian blocks

The dicynodonts are an emblematic group of herbivorous therapsids that survived the Permo-Triassic (P-Tr) crisis. Laotian dicynodonts from stratigraphically constrained beds, recently dated using the U-Pb zircon method, yield new insights into terrestrial faunas of Southeast Asia during the latest Permian and earliest Triassic. Summarily described, they were originally attributed to the genus Dicynodon. We provide a new phylogenetic analysis for Laotian dicynodonts, based on three well-preserved skulls, indicating that they belong to two new taxa: Counillonia superoculis, gen. et sp. nov., and Repelinosaurus robustus, gen. et sp. nov. Our phylogenetic analysis of Dicynodontia indicates that (1) Counillonia is closely related to some ‘Dicynodon’-grade taxa and (2) Repelinosaurus is a kannemeyeriiform. The phylogenetic affinities of these new Laotian dicynodonts allow discussion of the survivorship of multiple lineages (Kannemeyeriiformes and ‘Dicynodon’-grade dicynodontoids) across the P-Tr crisis. The Laotian dicynodonts also shed new light on the paleobiogeography of Southeast Asia from the late Paleozoic to the early Mesozoic, particularly the timing of collisions between the Indochina, the South China, and the North China blocks. The presence of dicynodonts in Laos, most likely in the Early Triassic, thus implies that the connection between the Indochina Block and the South China Block occurred no later than the latest Permian or earliest Triassic (i.e., when the dicynodonts provide direct evidence for a connection)