Xenopus and Zebrafish Annotation in the UniProt Knowledgebase (UniProtKB)

The African clawed frog Xenopus laevis and the zebrafish Danio rerio have both proved to be good model organisms for studying early vertebrate cellular and developmental biology. More recently, the related western clawed frog Xenopus tropicalis has become a popular choice in the laboratory, since its shorter life style and diploid genome make it more amenable to genetic analysis. Ongoing sequencing of the X. tropicalis and D. rerio genomes, together with the growing number of EST/cDNA projects, is generating large amounts of sequence data and revealing many human developmental and disease genes that have counterparts in fish and frog.

UniProtKB/Swiss-Prot curates Xenopus and zebrafish proteins with functional and sequence annotation from the literature and sequence analysis tools, using both controlled vocabularies (including GO terms) and free text. The tetraploid nature of the X. laevis and D. rerio genomes complicates annotation since the protein copies need to be identified and curated as separate UniProtKB/Swiss-Prot entries. The recent addition of Xenbase cross-references in Xenopus UniProtKB entries has been the result of cross-talk with Xenbase, and we continue to collaborate with ZFIN to ensure consistency between databases. 

UniProt is mainly supported by the NIH, European Commission FELICS, Swiss Federal Government, PATRIC BRC and NSF grants.
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Research into how different stakeholders value geodiversity within Malta's coastal environment

Geodiversity refers to the variety of geological, geomorphological and soil features, and their assemblages, properties, relationships, systems and interpretations[1].For years geodiversity conservation has come second to biodiversity, with many finding it difficult to define the two separately[2].The research conducted aimed to explore the diverse set of ways geodiversity was valued between tourists and locals, and whether coastal sites were treated differently to others. The question ‘Do tourists and locals value geodiversity differently in three separate coastal environments’ was used throughout the study

A study into how stakeholders value geodiversity within Malta’s coastal environment

This research is about geodiversity. It takes the case study of coastal landscapes in Malta to consider the way that geodiversity is valued and how it might be conserved. Geodiversity refers to the variety of geological (rocks, fossils, minerals), geomorphological (landforms and processes) and soil features (Gray, 2004). Conservation is crucial to protect the value that tourists and locals hold for places and geodiversity. This research concentrates on five main place-based values; Functional, Appearance, Cultural, Research, and Educational. Coastal environments were explored as 96% of all accessible coastline in the Malta being developed and 21% of its total coastline no longer retains its natural features (Deidun, 2010; MEPA, 2006; Anderson & Schembri, 1989. The need for the Maltese people to protect their geodiversity is enhanced by the fact that global tourists specifically travel to the island to visit its coastal environments. There is no previous research into people’s values of geodiversity in Malta. The objective was to identify stakeholder views of Malta’s geodiversity. This resulted in the following aims (1) discover the values stakeholders associate with geodiversity (2) discover the threats stakeholders notice to geodiversity (3) discover conservation needs recognised by stakeholders. The research contrasted the views of locals and residents, female’s vs males and identified site specific differences

Fabrication of Hydrogel Microparticles for Acute Treatment of Penetrating Brain Injuries

Traumatic brain injuries (TBIs) are a type of acquired head trauma that results from an external force to the head. The development and severity of the secondary injury increases the risk of neurodegeneration and reduced cognitive recovery. Glucocorticoids are potent antiinflammatory therapeutics that have been investigated for potential treatment of TBIs, strokes, and other neuroinflammatory pathologies. However, their clinical application has been limited due to their ability to induce a variety of side effects, including adrenal suppression, edema, and reduced plasticity of the hippocampus. The use of a localized drug delivery system would overcome these systemic concerns. In previous studies, semi-interpenetrating networks (semi- IPNs) incorporating dexamethasone-conjugated hyaluronic acid (HA-DXM) as a macromolecular prodrug were developed. These semi-IPNs reduced neuroinflammation and improved motor function when applied to the cortical surface following a TBI. A subtype of TBIs are penetrating brain injuries (PBIs), which occur when a foreign object, such as a bullet, strikes the cranial cavity creating an opened wound. Due to the irregular geometry of PBIs, there is a need for hydrogels to be fabricated in an injectable, or dispersible, microparticulate form. The previous studies utilized a photo-initiated, radical polymerization crosslinking method that was found not to be effective or scalable in this form. Therefore, the objective of this work was to develop a new hydrogel formulation compatible with fabrication of microgels. Thiolated gelatin (gelatin-SH) and poly(ethylene glycol) diacrylate (PEGdA) were synthesized, characterized, and then successfully crosslinked utilizing a Michael-type reaction to form hydrogels. Additionally, native hyaluronic acid (HA) was incorporated to model HA-based macromolecular prodrugs, such as HA-DXM. The effects of gelatin-SH concentration and HA (700 kDA and 1.5 MDa) on crosslinking time, storage modulus, swelling, and degradation were investigated using bulk hydrogel samples. Both the addition of HA and increasing gelatin-SH concentrations produced an increased hydrogel storage modulus. Hydrogel microparticles were then fabricated in a water-in-oil emulsion system, producing particles with an average diameter ranging from approximately 125 to 250 microns depending on composition and stir rate. These studies demonstrate that gelatin-SH/PEGdA can create microparticles capable of conforming to the irregular geometry of PBIs. Future work will focus on the incorporation of HA-DXM into the hydrogel microparticles and the evaluation of drug-release and therapeutic efficacy in an animal PBI model

Seismological studies at the hengill geothermal area SW Iceland

Iceland is a sub-aerial part of the mid-Atlantic Ridge which has formed above an E migrating ridge centred hotspot. The Hengill area is a ridge-ridge-transform triple point that contains a central volcano-fissure swarm system and a large geothermal area. A seismological study of this triple point was conducted with the main emphasis on natural earthquake studies. The aims were to study the geothermal prospect and tectonic structure and to evaluate the passive seismic method as a geothermal prospecting tool. The area exhibits continuous small magnitude earthquake activity that correlates positively with surface geothermal displays, and negatively with surface faulting. The log (cumulative frequency) magnitude relationship is linear and indicates a b value of 0.74 ± 0.06. Focal mechanisms for 178 events indicated both shear and tensile crack type movements, the latter being confined to the high temperature geothermal area. Teleseismic and explosion data indicate a low velocity body beneath the central volcano in the depth range 0 - 10 km, flanked by higher velocity bodies to the W and E. Two volcanic systems occupy the Hengill area : the presently active Hengill system and the extinct Grensdalur system. The ongoing seismicity of the area is attributed to contraction cracking due to the action of cool groundwater fluids on hot rook, which, in a tensile stress regime, results in tensile crack formation. The high temperature area is fuelled by two heat sources associated with the two volcanic systems and may be divided into two separate fields that exhibit contrasting reservoir characteristics. Local seismioity studies may be applied to other Icelandic high temperature geothermal areas as a tool to map those volumes of rock that are fueling the geothermal reservoirs. The continuous formation of small tensile cracks on accretionary plate boundaries offers an explanation for the mechanism of dyke injection