Brain Radiation Information Data Exchange (BRIDE): Integration of experimental data from low-dose ionising radiation research for pathway discovery

Background: The underlying molecular processes representing stress responses to low-dose ionising radiation (LDIR) in mammals are just beginning to be understood. In particular, LDIR effects on the brain and their possible association with neurodegenerative disease are currently being explored using omics technologies. Results: We describe a light-weight approach for the storage, analysis and distribution of relevant LDIR omics datasets. The data integration platform, called BRIDE, contains information from the literature as well as experimental information from transcriptomics and proteomics studies. It deploys a hybrid, distributed solution using both local storage and cloud technology. Conclusions: BRIDE can act as a knowledge broker for LDIR researchers, to facilitate molecular research on the systems biology of LDIR response in mammals. Its flexible design can capture a range of experimental information for genomics, epigenomics, transcriptomics, and proteomics. The data collection is available at:

Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species

The mechanisms of stress tolerance in sessile animals, such as molluscs, can offer fundamental insights into the adaptation of organisms for a wide range of environmental challenges. One of the best studied processes at the molecular level relevant to stress tolerance is the heat shock response in the genus Mytilus. We focus on the upstream region of Mytilus galloprovincialis Hsp90 genes and their structural and functional associations, using comparative genomics and network inference. Sequence comparison of this region provides novel evidence that the transcription of Hsp90 is regulated via a dense region of transcription factor binding sites, also containing a region with similarity to the Gamera family of LINE-like repetitive sequences and a genus-specific element of unknown function. Furthermore, we infer a set of gene networks from tissue-specific expression data, and specifically extract an Hsp class-associated network, with 174 genes and 2,226 associations, exhibiting a complex pattern of expression across multiple tissue types. Our results (i) suggest that the heat shock response in the genus Mytilus is regulated by an unexpectedly complex upstream region, and (ii) provide new directions for the use of the heat shock process as a biosensor system for environmental monitoring

STUDY OF THE SALIVARY GLAND POLYTENE CHROMOSOMES OF DROSOPHILA AURARIA

DROSOPHILA AURARIA AND ITS SIBLING SPECIES D. BIAURARIA, D. QUADRARIA AND D. TRIAURARIA ARE UNIQUE AMONG DROSOPHILA SPECIES IN THAT THEIR SALIVARY GLAND CHROMOSOMES EXHIBIT BALBIANI RING (BRS). WE PRESENT HERE A CYTOLOGICAL MAP OF D. AURARIA AND INFORMATION ON THE DEVELOPMENTAL PROFILES OF ITS PUFFS AND BRS. AUTORADIOGRAPHY HAS BEEN PERFORMED IN ORDER TO CONFIRM THE RNA SYNTHESIS OF THE BRS DURING DEVELOPMENT. INFORMATION IS PRESENTED ON THE EXISTENCE OF TANDEM INVERTED DUPLICATIONS INVOLVING THE BRS REGIONS AND OTHERS OF THE CHROMOSOMES, AND DATA ARE GIVEN CONCERNING THE PUFFING PATTERNS OF THE DUPLICATED BONDS. THE INTERCALARY HETEROCHROMATIN SITES OF THE GENOMA ARE GIVEN, AND THE POSSIBLE ROLE OF THEIR TYPE OF HETEROCHROMATIN ARE DISCUSSED. POSSIBLE HOMOLOGIES BETWEEN PUFFS OF D. MELANOGASTER AND D. AURARIA AND CERTAIN DIFFERENCIES BETWEEN THE TWO SPECIES IN THE DEVELOPMENTAL SEQUENCES OF THE ACTIVA LOCI ARE ALSO DISCUSSED.Η DROSOPHILA AURARIA ΚΑΙ ΤΑ ΑΔΕΛΦΑ ΤΗΣ ΕΙΔΗ: D. BIAURARIA, D. TRIAURARIA ΚΑΙ D. QUADRARIA ΕΙΝΑΙ ΜΟΝΑΔΙΚΑ ΜΕΤΑΞΥ ΤΩΝ ΕΙΔΩΝ ΤΗΣ DROSOPHILA, ΣΤΟ ΟΤΙ ΤΑ ΠΟΛΥΤΑΙΝΙΚΑ ΧΡΩΜΟΣΩΜΑΤΑ ΤΩΝ ΣΙΑΛΟΓΟΝΩΝ ΑΔΕΝΩΝ ΤΟΥΣ ΠΑΡΟΥΣΙΑΖΟΥΝ ΔΑΚΤΥΛΙΟΥΣ BALBIANI (BRS). ΣΤΗ ΔΙΑΤΡΙΒΗ ΑΥΤΗ ΠΑΡΟΥΣΙΑΖΟΝΤΑΙ ΚΑΙ ΣΥΖΗΤΟΥΝΤΑΙ: Α) Ο ΚΥΤΤΑΡΟΛΟΓΙΚΟΣ ΧΑΡΤΗΣ ΤΗΣ D. AURARIA, Β) ΤΑ ΑΝΑΠΤΥΞΙΑΚΑ ΠΡΟΤΥΠΑ ΤΩΝ ΒΡΟΧΩΝ ΚΑΙ ΤΩΝ ΔΑΚΤΥΛΙΩΝ BALBIANI ΣΕ ΔΙΑΦΟΡΑ ΑΝΑΠΤΥΞΙΑΚΑ ΣΤΑΔΙΑ, Γ) ΧΡΩΜΟΣΩΜΑΤΙΚΟΙ ΔΙΠΛΑΣΙΑΣΜΟΙ ΠΟΥ ΠΕΡΙΛΑΜΒΑΝΟΥΝ ΤΟΥΣ BRS ΚΑΙ ΑΛΛΕΣ ΠΕΡΙΟΧΕΣ ΤΟΥ ΓΟΝΙΔΙΩΜΑΤΟΣ, Δ) ΑΥΤΟΡΑΔΙΟΓΡΑΦΙΚΗ ΜΕΛΕΤΗ ΤΩΝ BRS, E) ΟΙ ΘΕΣΕΙΣ ΤΗΣ ΠΑΡΕΜΒΑΛΛΟΜΕΝΗΣ ΕΤΕΡΟΧΡΩΜΑΤΙΚΗΣ ΚΑΘΩΣ ΚΑΙ ΤΗΣ ΣΥΣΤΑΤΙΚΗΣ, ΣΤ) ΟΙ ΠΙΘΑΝΕΣ ΟΜΟΛΟΓΙΕΣ ΜΕΤΑΞΥ ΤΩΝ ΒΡΟΧΩΝ ΤΗΣ D. MELANOGASTER ΚΑΙ ΤΗΣ D. AURARIA

Bayesian inference phylogenetic tree based on Hsp90 protein sequences from Mollusca.

<p>Species in which multiple <i>hsp90</i> genes have been detected are in dark blue. Filled diamonds denote putative species-specific duplication events, predicted by this study. Numbers at nodes represent Posterior Probability (PP) values. Scale bar: substitutions/site.</p

Bayesian inference phylogenetic tree based on Hsp90 protein sequences from Chordata.

<p>Species in which multiple <i>hsp90</i> genes have been detected are in dark blue. Filled diamonds denote putative species-specific duplication events, predicted by this study. Filled square denotes the duplication event resulting in the cognate and inducible isoforms of vertebrates. Numbers at nodes represent Posterior Probability (PP) values. Scale bar: substitutions/site.</p

Assessment and Reconstruction of Novel HSP90 Genes: Duplications, Gains and Losses in Fungal and Animal Lineages

<div><p>Hsp90s, members of the Heat Shock Protein class, protect the structure and function of proteins and play a significant task in cellular homeostasis and signal transduction. In order to determine the number of <i>hsp90</i> gene copies and encoded proteins in fungal and animal lineages and through that key duplication events that this family has undergone, we collected and evaluated Hsp90 protein sequences and corresponding Expressed Sequence Tags and analyzed available genomes from various taxa. We provide evidence for duplication events affecting either single species or wider taxonomic groups. With regard to Fungi, duplicated genes have been detected in several lineages. In invertebrates, we demonstrate key duplication events in certain clades of Arthropoda and Mollusca, and a possible gene loss event in a hymenopteran family. Finally, we infer that the duplication event responsible for the two (a and b) isoforms in vertebrates occurred probably shortly after the split of Hyperoartia and Gnathostomata.</p></div

Bayesian inference phylogenetic tree based on Hsp90 protein sequences from Arthropoda.

<p>Species in which multiple <i>hsp90</i> genes have been detected are in dark blue. Filled diamonds denote putative species-specific duplication events predicted by this study. Filled squares denote duplication events in the common ancestor of a wide taxonomic group (e.g. Pleocyemata), predicted by this study. Filled circle shows the gain of type 2 isoform in Hymenoptera; empty-strikethrough circle shows loss of type 1 isoform in Formicidae. Numbers at nodes represent Posterior Probability (PP) values. Scale bar: substitutions/site.</p