Welcome to the Rhubarb talks website
Upcoming seminars are posted below and cover a whole range of scientific exploits. Talks are held every other Monday afternoon at 4.30pm in the postgrad lounge (node 086) and are accompanied by nibbles and refreshments.
For more info or to volunteer for a talk, please contact The Rhubarb Team: Liz (E.Sargent@noc.soton.ac.uk), Rosanna (R.Greenop@noc.soton.ac.uk), Maike (firstname.lastname@example.org) or Sara (Sara.Cregeen@noc.soton.ac.uk)
Friday, November 2, 2012
26th of November Marcello Passaro presents: The new challenges of Coastal Altimetry presents;The new challenges of Coastal Altimetry: a 20-year-old database still unknown
Friday, October 26, 2012
29th October, Cathy Cole: "Adaptations to a heavy metal lifestyle: the molecular detoxification strategies of Mytilus edulis, and implications for life in extreme environments. "
Thursday, October 25, 2012
29th October, Cathy Cole: "Adaptations to a heavy metal lifestyle: the molecular detoxification strategies of Mytilus edulis, and implications for life in extreme environments."
"Adaptations to a heavy metal lifestyle: the molecular detoxification strategies of Mytilus edulis, and implications for life in extreme environments."
Hydrothermal vents support life in extreme abundance, yet fluids emanating from these vents are highly enriched in many metals compared with seawater. Animals are exposed to metal concentrations on the order of a thousand times higher than in oceanic waters and must have evolved specialised mechanisms of detoxification. To understand faunal colonisation of these metalliferous environments, it is important to investigate pre-adaptations for detoxification in their non-vent relatives. The common blue mussel, Mytilus edulis, is the closest shallow-water taxonomic relative of the deep-sea hydrothermal vent mussel subfamily, the Bathymodiolinae. Using biochemical techniques learnt this summer during a GSNOCS exchange placement to University College Cork, Ireland, I investigated the proteomic response of M. edulis to experimental metal enrichment.
Monday, August 6, 2012
Next Monday, 13th of August, Liz Sargent will do a practice run of her talk for the Challenger Conference: Novel molecular insights into the fate of N2 fixed by diazotrophic plankton
Marine diazotrophs play an important role in oligotrophic surface oceans by fixing N2 into bioavailable forms. To date, studies of the three main groups of N2-fixing organisms in the ocean (i.e. filamentous, heterocystous, and unicellular diazotrophs) have generally been limited to assessment of their presence and function in the euphotic zone, while the role these organisms have in the export of material to the ocean's interior has seldom been addressed. Optical assessments of sinking particulate material from the eastern subtropical and tropical Atlantic demonstrated that Trichodesmium and Richelia intracellularis were commonly present below 100 m and as deep as 500 m. Real-time quantitative PCR analysis with TaqMan probes was carried out on extracts of sinking particulate samples to 500 m to assess the presence of 5 nifH phylotypes: a single filamentous cyanobacterial probe specific to Trichodesmium, two heterocystous cyanobacterial probes specific to Richelia-Rhizosolenia and ¬Richelia¬-Hemiaulus (diazotrophic diatom associations), and two unicellular cyanobacterial probes specific to the uncultured Group A and Group C cyanobacteria. These analyses revealed the presence of all of these diazotrophs below the mixed layer, which indicates previous assessments of the vertical distributions of these organisms may have overlooked the presence of diazotrophs at depth. Contrary to previous expectations, results suggest that all three groups of marine diazotrophs are constituents of sinking material and are exported out of the euphotic zone in the subtropical and tropical Atlantic Ocean, providing novel insight into the cycling of fixed nitrogen in the oligotrophic ocean.
Sunday, July 22, 2012
23 July, Chris Cave-Ayland: Hybrid quantum and classical free energy methods in computational drug optimisation
A long-term aim of the pharmceutical industry is the development for computer
based approaches for the development of new drugs. There are a range of approaches
to this problem the most rigourous of which are known as free energy techniques.
These make use of the theory of thermodynamics and statistical mechanics to
allow detailed treatments of such systems and can be highly effective under appropriate
conditions. Application of these requires the ability to accurately calculate the energies
of proteins in complex with potential drug molecules. Two contrasting ways of making
energy calculations are through classical and quantum approaches.
Classical approaches are highly paramaterised, however comparatively cheap, and
effectively attempt to approximate the chemical bonds within a system with idealised
potentials. Quantum approaches on the other hand provide a theoretically exact representation
of the chemistry of the system, allowing them to capture effects that are lost in classical
representations, although at a far greater computational expense.
My project focuses on so called hybrid classical and quantum methods, in
partnership with Professor Jon Essex and Chris Skylaris from the department of
chemistry. These approches attempt to gain the best of both worlds in terms of
accuracy and computational tractability of both models. This effectively
involves switching between the two different levels of description of the
system and the presents novel practical and theoretical difficulties.
The current focus of my work is the validation of a technique known as a free energy
perturbation (FEP) that can be used to transition between different descriptions of a
molecular system. Examining the implicit assumptions of an FEP and determing its
limitations are key to its successful application.
Thursday, May 31, 2012
Thursday, March 29, 2012
Tuesday 3rd of April Liz Sargent will present: Assessing the direct contribution of TRICHODESMIUM TO exportTrichodesmium, a colonial marine cyanobacterium, is integrally involved in ocean biogeochemical cycling as it is a significant supplier of fixed nitrogen to the warm surface ocean. Recent reports have suggested that Trichodesmium is also important in the subsurface layer, and actively fixes nitrogen in the deep chlorophyll maximum (DCM); however, the role Trichodesmium plays in the biogeochemistry of deeper waters has yet to be described. This study focuses on Trichodesmium’s involvement in the direct export process. Contrary to previous expectations, results suggest that despite its buoyancy this organism is a constituent of sinking material. Sampling on research cruises in the eastern subtropical and tropical Atlantic, and in the Gulf of Mexico showed Trichodesmium was commonly present below 100 m in three forms: tufted colonies, free filaments, and free filaments included in aggregations with other organisms/faecal matter. The Marine Snow Catcher (MSC), a 100 L messenger-operated PVC closing water bottle, and in situ Stand Alone Pumping Systems (SAPS) were used to collect sinking particles, which were imaged and preserved for post-cruise assessment. All sub-DCM MSC collections between 80-250 m in areas where Trichodesmium was a significant counterpart of the surface population included negatively buoyant colonies sinking at 12 - 120 m d-1, as well as free filaments; SAPS collections also revealed the presence of free filaments in low concentrations as deep as 500 m. Further microscopic analysis of these colonies will allow for the elucidation of the mechanism of sinking in Trichodesmium, such as gas vacuole collapse, as well as aiding in describing its involvement in the export flux of POC and PON.
Monday, March 12, 2012
Wednesday, February 22, 2012
Monday, February 20, 2012
Want to know more about a particular method of collection or analysis? Or perhaps you have experience with a technique not known to many?
Rhubarb talks are expanding to include a Rhubarb Methods session.
We are looking for speakers willing to give ≥5 minute talks about any method they are familiar with that others might like to know more about. These talks would be grouped in 3 or 4 to fill a 30 minute Rhubarb slot.
Possible topics include, but are not limited to: Electron microscopy, qPCR, elemental analysis, field collections/sampling techniques, biogeochemical models, etc.
Please get in touch if you are interested in speaking or have other ideas for topics.
The Rhubarb Team
Monday, February 13, 2012
In preparation for an upcoming conference, Maike Sonnewald will present a Rhubarb talk next Monday, 20.2.12 at 4:30pm in the PG lounge.
Oceanic dominance of interannual subtropical North Atlantic heat content variability
Ocean heat content varies on a range of timescales, with significant impact on the local climate through interactions with the atmosphere. This variability can be driven either by oceanic or atmospheric heat transport for a local body of water. To diagnose the relative contributions and respective timescales, this study uses a box model forced with GCM output to investigate the heat content variability of the upper 800 m of the subtropical North Atlantic from 26oN to 36oN. The ocean and air-sea heat flux data needed to force the box model is taken from a 19 year (1985 to
2006) simulation performed with the 1/12o version of OCCAM. The box model heat content is compared to the corresponding heat content in OCCAM for verification. The main goal of the study is to identify to what extent the interannual to subannual ocean heat content variability is of atmospheric or oceanic origin. To this end, the box model was subject to a range of scenarios forced either with the full (detrended) ocean and air-sea fluxes, or their deseasoned counterparts. This revealed that in all cases, the seasonal variability was dominated by the subannual component of the air-sea flux, which produced a seasonal range of ~0.41oC. However, on longer timescales the interannual oceanic heat transport dominates, with changes of up to ~0.16oC.
The technique is subsequently appplied to observational data. For the ocean heat fluxes, we use data from the RAPID programme at 26oN, and at 36oN heat transport is inferred using a linear regression model from the oceanic low-frequency transport in OCCAM. The air-sea flux from OCCAM is used for the period 2004 to 2006 when the RAPID timeseries and the OCCAM simulation overlap, and a climatology is used for the air-sea flux from
2006 onwards. The results confirm that on longer (>2 years) timescales the ocean dominates the ocean heat content variability. This work illustrates that oceanic divergence significantly impacts the ocean heat content variability on timescales relevant for applications such as hurricane forecasts, and thus that understanding the underlying mechanisms is of great socioeconomic importance.