D6.7 Report on the experience of conducting the case studies

One of the main aims of the case studies was to publish improved market reports. The data collected as part of the six case studies have been, or will shortly be, published in the five improved national organic market reports and one first regional market report (MOAN case study). This will make a contribution towards filling the many gaps that continue to exist in organic market data collection in Europe

Timing Calibration and Windowing Technique Comparison for Lightning Mapping Arrays

Since their introduction 22 years ago, lightning mapping arrays (LMA) have played a central role in the investigation of lightning physics. Even in recent years with the proliferation of digital interferometers and the introduction of the LOw Frequency ARray (LOFAR) radio telescope, LMAs still play an important role in lightning science. LMA networks use a simple windowing technique that records the highest pulse in either 80 μs or 10 μs fixed windows in order to apply a time-of-arrival location technique. In this work, we develop an LMA-emulator that uses lightning data recorded by LOFAR to simulate an LMA, and we use it to test three new styles of pulse windowing. We show that they produce very similar results as the more traditional LMA windowing, implying that LMA lightning mapping results are relatively independent of windowing technique. In addition, each LMA station has its GPS-conditioned clock. While the timing accuracy of GPS receivers has improved significantly over the years, they still significantly limit the timing measurements of the LMA. Recently, new time-of-arrival techniques have been introduced that can be used to self-calibrate systematic offsets between different receiving stations. Applying this calibration technique to a set of data with 32 ns uncertainty, observed by the Colorado LMA, improves the timing uncertainty to 19 ns. This technique is not limited to LMAs and could be used to help calibrate future multi-station lightning interferometers

Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors

We investigate the application of hierarchical classification schemes to the annotation of gene function based on several characteristics of protein sequences including phylogenic descriptors, sequence based attributes, and predicted secondary structure. We discuss three Bayesian models and compare their performance in terms of predictive accuracy. These models are the ordinary multinomial logit (MNL) model, a hierarchical model based on a set of nested MNL models, and a MNL model with a prior that introduces correlations between the parameters for classes that are nearby in the hierarchy. We also provide a new scheme for combining different sources of information. We use these models to predict the functional class of Open Reading Frames (ORFs) from the E. coli genome. The results from all three models show substantial improvement over previous methods, which were based on the C5 algorithm. The MNL model using a prior based on the hierarchy outperforms both the non-hierarchical MNL model and the nested MNL model. In contrast to previous attempts at combining these sources of information, our approach results in a higher accuracy rate when compared to models that use each data source alone. Together, these results show that gene function can be predicted with higher accuracy than previously achieved, using Bayesian models that incorporate suitable prior information

Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages

The evolutionary history of biological pathways is of general interest, especially in this post-genomic era, because it may provide clues for understanding how complex systems encoded on genomes have been organized. To explain how pathways can evolve de novo, some noteworthy models have been proposed. However, direct reconstruction of pathway evolutionary history both on a genomic scale and at the depth of the tree of life has suffered from artificial effects in estimating the gene content of ancestral species. Recently, we developed an algorithm that effectively reconstructs gene-content evolution without these artificial effects, and we applied it to this problem. The carefully reconstructed history, which was based on the metabolic pathways of 160 prokaryotic species, confirmed that pathways have grown beyond the random acquisition of individual genes. Pathway acquisition took place quickly, probably eliminating the difficulty in holding genes during the course of the pathway evolution. This rapid evolution was due to massive horizontal gene transfers as gene groups, some of which were possibly operon transfers, which would convey existing pathways but not be able to generate novel pathways. To this end, we analyzed how these pathways originally appeared and found that the original acquisition of pathways occurred more contemporaneously than expected across different phylogenetic clades. As a possible model to explain this observation, we propose that novel pathway evolution may be facilitated by bidirectional horizontal gene transfers in prokaryotic communities. Such a model would complement existing pathway evolution models

A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF

<p>Abstract</p> <p>Background</p> <p>New strategies for high-throughput sequencing are constantly appearing, leading to a great increase in the number of completely sequenced genomes. Unfortunately, computational genome annotation is out of step with this progress. Thus, the accurate annotation of these genomes has become a bottleneck of knowledge acquisition.</p> <p>Results</p> <p>We exploited a proteogenomic approach to improve conventional genome annotation by integrating proteomic data with genomic information. Using <it>Shigella flexneri </it>2a as a model, we identified total 823 proteins, including 187 hypothetical proteins. Among them, three annotated ORFs were extended upstream through comprehensive analysis against an in-house N-terminal extension database. Two genes, which could not be translated to their full length because of stop codon 'mutations' induced by genome sequencing errors, were revised and annotated as fully functional genes. Above all, seven new ORFs were discovered, which were not predicted in <it>S. flexneri </it>2a str.301 by any other annotation approaches. The transcripts of four novel ORFs were confirmed by RT-PCR assay. Additionally, most of these novel ORFs were overlapping genes, some even nested within the coding region of other known genes.</p> <p>Conclusions</p> <p>Our findings demonstrate that current <it>Shigella </it>genome annotation methods are not perfect and need to be improved. Apart from the validation of predicted genes at the protein level, the additional features of proteogenomic tools include revision of annotation errors and discovery of novel ORFs. The complementary dataset could provide more targets for those interested in <it>Shigella </it>to perform functional studies.</p

Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli

Gene order in some bacterial metabolic operons reflects ordering in the metabolic pathway. That this is true uniquely for operons expressed at low levels highlights the selective importance of fluctuations in protein levels

Geology, geochemistry and earthquake history of Lō`ihi Seamount, Hawai`i

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Chemie der Erde - Geochemistry 66 (2006): 81-108, doi:10.1016/j.chemer.2005.09.002.A half century of investigations are summarized here on the youngest Hawaiian volcano, Lō`ihi Seamount. It was discovered in 1952 following an earthquake swarm. Surveying in 1954 determined it has an elongate shape, which is the meaning of its Hawaiian name. Lō`ihi was mostly forgotten until two earthquake swarms in the 1970’s led to a dredging expedition in 1978, which recovered young lavas. This led to numerous expeditions to investigate the geology, geophysics, and geochemistry of this active volcano. Geophysical monitoring, including a realtime submarine observatory that continuously monitored Lō`ihi’s seismic activity for three months, captured some of the volcano’s earthquake swarms. The 1996 swarm, the largest recorded in Hawai`i, was preceded by at least one eruption and accompanied by the formation of a ~300-m deep pit crater, renewing interest in this submarine volcano. Seismic and petrologic data indicate that magma was stored in a ~8-9 km deep reservoir prior to the 1996 eruption. Studies on Lō`ihi have altered conceptual models for the growth of Hawaiian and other oceanic island volcanoes and led to a refined understanding of mantle plumes. Petrologic and geochemical studies of Lō`ihi lavas showed that the volcano taps a relatively primitive part of the Hawaiian plume, producing a wide range of magma compositions. These compositions have become progressively more silica-saturated with time reflecting higher degrees of partial melting as the volcano drifts towards the center of the hotspot. Seismic and bathymetric data have highlighted the importance of landsliding in the early formation of an ocean island volcano. Lō`ihi’s internal structure and eruptive behavior, however, cannot be fully understood without installing monitoring equipment directly on the volcano. The presence of hydrothermal activity at Lō`ihi was initially proposed based on nontronite deposits on dredged samples that indicated elevated temperatures (31oC), and on the detection of water temperature, methane and 3He anomalies, and clumps of benthic micro-organisms in the water column over the volcano in 1982. Submersible observations in 1987 confirmed a low temperature system (15-30oC) prior to the 1996 formation of Pele’s Pit. The sulfide mineral assemblage (wurtzite, pyrrhotite, and chalcopyrite) deposited after the pit crater collapsed are consistent with hydrothermal fluids >250oC. Vent temperatures have decreased to ~60oC during the 2004 dive season indicating the current phase of hydrothermal activity may be waning.This work was supported by a NSF grant to M. Garcia (OCE 97-29894)