Bruce Ward

In situ measurement of coastal ocean movements and survival of juvenile Pacific salmon.

Many salmon populations in both the Pacific and Atlantic Oceans have experienced sharply decreasing returns and high ocean mortality in the past two decades, with some populations facing extirpation if current marine survival trends continue. Our inability to monitor the movements of marine fish or to directly measure their survival precludes experimental tests of theories concerning the factors regulating fish populations, and thus limits scientific advance in many aspects of fisheries management and conservation. Here we report a large-scale synthesis of survival and movement rates of free-ranging juvenile salmon across four species, 13 river watersheds, and 44 release groups of salmon smolts (>3,500 fish tagged in total) in rivers and coastal ocean waters, including an assessment of where mortality predominantly occurs during the juvenile migration. Of particular importance, our data indicate that, over the size range of smolts tagged, (i) smolt survival was not strongly related to size at release, (ii) tag burden did not appear to strongly reduce the survival of smaller animals, and (iii) for at least some populations, substantial mortality occurred much later in the migration and more distant from the river of origin than generally expected. Our findings thus have implications for determining where effort should be invested to improve the accuracy of salmon forecasting, to understand the mechanisms driving salmon declines, and to predict the impact of climate change on salmon stocks.

Rapid magnetosome formation shown by real-time x-ray magnetic circular dichroism.

Magnetosomes are magnetite nanoparticles formed by biomineralization within magnetotactic bacteria. Although there have been numerous genetic and proteomic studies of the magnetosome-formation process, there have been only limited and inconclusive studies of mineral-phase evolution during the formation process, and no real-time studies of such processes have yet been performed. Thus, suggested formation mechanisms still need substantiating with data. Here we report the examination of the magnetosome material throughout the formation process in a real-time in vivo study of Magnetospirillum gryphiswaldense, strain MSR-1. Transmission EM and x-ray absorption spectroscopy studies reveal that full-sized magnetosomes are seen 15 min after formation is initiated. These immature magnetosomes contain a surface layer of the nonmagnetic iron oxide-phase hematite. Mature magnetite is found after another 15 min, concurrent with a dramatic increase in magnetization. This rapid formation result is contrary to previously reported studies and discounts the previously proposed slow, multistep formation mechanisms. Thus, we conclude that the biomineralization of magnetite occurs rapidly in magnetotactic bacteria on a similar time scale to high-temperature chemical precipitation reactions, and we suggest that this finding is caused by a biological catalysis of the process.

Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium (Alphaproteobacteria: Rhodospirillaceae) isolated from a salt marsh

A magnetotactic bacterium, designated strain MV-1(T), was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1(T) were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1(T) was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10 % seawater were required for growth. Strain MV-1(T) exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin-Benson-Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26-28 °C. The genome of strain MV-1(T) consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9-53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1(T) belongs to the family Rhodospirillaceae within the Alphaproteobacteria, but is not closely related to the genus Magnetospirillum. The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1(T). The type strain of Magnetovibrio blakemorei is MV-1(T) ( = ATCC BAA-1436(T)  = DSM 18854(T)).

Quantitative proteomic analysis of the exoelectrogenic bacterium Arcobacter butzleri ED-1 reveals increased abundance of a flagellin protein under anaerobic growth on an insoluble electrode

Exoelectrogens have the ability to generate electricity in mediator-less microbial fuel cells (MFCs) by extracellular electron transfer to the anode. We investigate the anode-specific responses of Arcobacter butzleri ED-1, the first identified exoelectrogenic Epsilonproteobacterium. iTRAQ and 2D-LC MS/MS driven proteomics were used to compare protein abundances in A. butzleri ED-1 when generating an electronegative potential (-225 mV) in an anaerobic half-cell - either growing as an electrogenic biofilm or suspended in the liquid medium - versus a microaerobic culture. This is the first quantitative proteomic study concentrating on growth of an exoelectrogen during current generation. From 720 proteins identified and quantified (soluble and insoluble sub-proteomes), statistical analysis reveals 75 differentially-expressed proteins. This dataset was enriched in proteins regulating energy and intermediary metabolism, electron and protein transport. Flagellin up-regulation was concomitant with electron transport in the anodic cells, while decreased abundance of a methyl-accepting chemotaxis protein suggested that flagella were involved in communication with the anode surface and electrogenesis, rather than motility. Two novel cytochromes potentially related to electron transport were up-regulated in anaerobic cultures. We demonstrate that employing an insoluble extracellular electron acceptor for anaerobic growth regulates multiple proteins involved in cell surface properties, electron transport and the methylcitrate cycle.

Stochastic EM-based TFBS motif discovery with MITSU

Motivation: The Expectation–Maximization (EM) algorithm has been successfully applied to the problem of transcription factor binding site (TFBS) motif discovery and underlies the most widely used motif discovery algorithms. In the wider field of probabilistic modelling, the stochastic EM (sEM) algorithm has been used to overcome some of the limitations of the EM algorithm; however, the application of sEM to motif discovery has not been fully explored. Results: We present MITSU (Motif discovery by ITerative Sampling and Updating), a novel algorithm for motif discovery, which combines sEM with an improved approximation to the likelihood function, which is unconstrained with regard to the distribution of motif occurrences within the input dataset. The algorithm is evaluated quantitatively on realistic synthetic data and several collections of characterized prokaryotic TFBS motifs and shown to outperform EM and an alternative sEM-based algorithm, particularly in terms of site-level positive predictive value. Availability and implementation: Java executable available for download at http://www.sourceforge.net/p/mitsu-motif/, supported on Linux/OS X. Contact: a.m.kilpatrick@sms.ed.ac.uk

MCOIN: a novel heuristic for determining transcription factor binding site motif width

BackgroundIn transcription factor binding site discovery, the true width of the motif to be discovered is generally not known a priori. The ability to compute the most likely width of a motif is therefore a highly desirable property for motif discovery algorithms. However, this is a challenging computational problem as a result of changing model dimensionality at changing motif widths. The complexity of the problem is increased as the discovered model at the true motif width need not be the most statistically significant in a set of candidate motif models. Further, the core motif discovery algorithm used cannot guarantee to return the best possible result at each candidate width.ResultsWe present MCOIN, a novel heuristic for automatically determining transcription factor binding site motif width, based on motif containment and information content. Using realistic synthetic data and previously characterised prokaryotic data, we show that MCOIN outperforms the current most popular method (E-value of the resulting multiple alignment) as a predictor of motif width, based on mean absolute error. MCOIN is also shown to choose models which better match known sites at higher levels of motif conservation, based on ROC analysis.ConclusionsWe demonstrate the performance of MCOIN as part of a deterministic motif discovery algorithm and conclude that MCOIN outperforms current methods for determining motif width.

Bacterial Energy Metabolism

The bacteria described in this book on molecular medical microbiology are chemoorganotrophs which gain energy by utilization of organic substrates using either aerobic respiration, anaerobic respiration or fermentation. The theory of chemiosmosis is the essential link between energy generation, its coupling to ATP synthesis and the utilization of energy for metabolism. The chapter discusses the principles of chemiosmosis, the respiratory components of electron transport chains and the H+- and Na+-translocating ATPases. Fermentation is covered, with emphasis on fermentation in the human gut. As oxygen availability in host tissue is both variable and often limited, discussion of aerobic recitation is focused on cytochrome oxidases whilst for anaerobic respiration denitrification is the main topic. Regulation of the switch between aerobic and anaerobic metabolism regulation covers the sensory and regulatory functions of regulators, illustrated with examples from Escherichia coli and Paracoccus denitrificans. This is extended into our current understanding of regulatory networks. The energy metabolism of five pathogens is discussed in relation to their cell physiology and their growth and survival in their host.