Biomedical subjects

Anton Montsant

Publications and source records attributed to Anton Montsant.

4 recordsLinked to original sources

PubMed2005

Comparative genomics of the pennate diatom Phaeodactylum tricornutum.

Diatoms are one of the most important constituents of phytoplankton communities in aquatic environments, but in spite of this, only recently have large-scale diatom-sequencing projects been undertaken. With the genome of the centric species Thalassiosira pseudonana available since mid-2004, accumulating sequence information for a pennate model species appears a natural subsequent aim. We have generated over 12,000 expressed sequence tags (ESTs) from the pennate diatom Phaeodactylum tricornutum, and upon assembly into a nonredundant set, 5,108 sequences were obtained. Significant similarity (E < 1E-04) to entries in the GenBank nonredundant protein database, the COG profile database, and the Pfam protein domains database were detected, respectively, in 45.0%, 21.5%, and 37.1% of the nonredundant collection of sequences. This information was employed to functionally annotate the P. tricornutum nonredundant set and to create an internet-accessible queryable diatom EST database. The nonredundant collection was then compared to the putative complete proteomes of the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the centric diatom T. pseudonana. A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism. Finally, codon usage and utilization of C and G relative to gene expression (as measured by EST redundance) were studied, and preferences for utilization of C and CpG doublets were noted among the P. tricornutum EST coding sequences.

Animals↗

PubMed2005

The Diatom EST Database.

The Diatom EST database provides integrated access to expressed sequence tag (EST) data from two eukaryotic microalgae of the class Bacillariophyceae, Phaeodactylum tricornutum and Thalassiosira pseudonana. The database currently contains sequences of close to 30,000 ESTs organized into PtDB, the P.tricornutum EST database, and TpDB, the T.pseudonana EST database. The EST sequences were clustered and assembled into a non-redundant set for each organism, and these non-redundant sequences were then subjected to automated annotation using similarity searches against protein and domain databases. EST sequences, clusters of contiguous sequences, their annotation and analysis with reference to the publicly available databases, and a codon usage table derived from a subset of sequences from PtDB and TpDB can all be accessed in the Diatom EST Database. The underlying RDBMS enables queries over the raw and annotated EST data and retrieval of information through a user-friendly web interface, with options to perform keyword and BLAST searches. The EST data can also be retrieved based on Pfam domains, Cluster of Orthologous Groups (COG) and Gene Ontologies (GO) assigned to them by similarity searches. The Database is available at http://avesthagen.sznbowler.com.

DNA, Algal↗

PubMed2005

Diatomics: toward diatom functional genomics.

For diatom biologists one of the most interesting research areas over the next years will be in linking mathematical models for pattern formation with information derived from molecular genetic, biochemical, and physiological studies. A major goal of this research is to exploit diatom proficiency in biogenic silica formation to develop strategies for bio-inspired nanofabrication of silicon based materials. Development of high-throughput methods for the functional analysis of diatom genes is a key step toward this goal. In this article we review the different techniques available to investigate gene and protein function in diatoms. Furthermore, to make diatom research as effective as possible the research community must address the question of which diatom species should be developed as a model. Choice of a diatom model organism should be made on the basis of several criteria, such as the ease of genetic manipulation, ecological relevance, or biomineralization capability. Phaeodactylum tricornutum is one of the principal three species that are candidates for such a model. For this species we have accomplished the first large-scale analysis of 12000 expressed sequence tags (ESTs) and have organized it in a queryable database, Phaeodactylum tricornutum database (PtDB). A summary of the functional analysis of this EST collection is presented, and genes of particular interest are highlighted.

Chromosome Mapping↗

PubMed2004

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

Adaptation, Physiological↗