Functional genomic hypothesis generation and experimentation by a robot scientist

King R. D., Whelan, K. E., Jones, F. M., Reiser, P. G. K., Bryant, C. H., Muggleton, S., Kell, D. B. and Oliver, S. G. (2004) Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 427 (6971) p247-252

Ethylene rapidly up-regulates the activities of both monomeric GTP-binding proteins and protein kinase(s) in epicotyls of pea

Igor E. Moshkov, Galina V. Novikova, Luis A.J. Mur, Aileen R. Smith, and Michael A. Hall. (2003). Ethylene rapidly up-regulates the activities of both monomeric GTP-binding proteins and protein kinase(s) in epicotyls of pea. Plant Physiology, 131(4), 1718-1726 RAE2008

Salicylic acid dependent signaling promotes basal thermotolerance but is not essential for acquired thermotolerance in Arabidopsis thaliana

Clarke, S. M., Mur, L. A. J., Wood, J. E., & Scott, I. M. (2004). Salicylic acid dependent signaling promotes basal thermotolerance but is not essential for acquired thermotolerance in Arabidopsis thaliana. The Plant Journal, 38(3), 432-447. Sponsorship: BBSRC RAE2008

Porównawcza analiza udziału pokrewnych kinaz MAPK (MKK1, MKK2, MKK4 i MKK5) Arabidopsis thaliana w odpowiedzi na stres suszy

Wydział Biologii: Instytut Biologii Molekularnej i Biotechnologii

The extradomain a of fibronectin enhances the efficacy of lipopolysaccharide defective Salmonella bacterins as vaccines in mice

The Extradomain A from fibronectin (EDA) has an immunomodulatory role as fusion protein with viral and tumor antigens, but its effect when administered with bacteria has not been assessed. Here, we investigated the adjuvant effect of EDA in mice immunizations against Salmonella enterica subspecies enterica serovar Enteritidis (Salmonella Enteritidis). Since lipopolysaccharide (LPS) is a major virulence factor and the LPS O-polysaccharide (O-PS) is the immunodominant antigen in serological diagnostic tests, Salmonella mutants lacking O-PS (rough mutants) represent an interesting approach for developing new vaccines and diagnostic tests to differentiate infected and vaccinated animals (DIVA tests). Here, antigenic preparations (hot-saline extracts and formalin-inactivated bacterins) from two Salmonella Enteritidis rough mutants, carrying either intact (SE Delta waaL) or deep-defective (SE Delta gal) LPS-Core, were used in combination with EDA. Biotinylated bacterins, in particular SE Delta waaL bacterin, decorated with EDAvidin (EDA and streptavidin fusion protein) improved the protection conferred by hot-saline or bacterins alone and prevented significantly the virulent infection at least to the levels of live attenuated rough mutants. These findings demonstrate the adjuvant effect of EDAvidin when administered with biotinylated bacterins from Salmonella Enteritidis lacking O-PS and the usefulness of BEDA-SE Delta waaL as non-live vaccine in the mouse model.

Udział miRNA w regulacji alternatywnego splicingu u roślin

Wydział Biologii

TCP over CDMA2000 Networks: A Cross-Layer Measurement Study

Modern cellular channels in 3G networks incorporate sophisticated power control and dynamic rate adaptation which can have a significant impact on adaptive transport layer protocols, such as TCP. Though there exists studies that have evaluated the performance of TCP over such networks, they are based solely on observations at the transport layer and hence have no visibility into the impact of lower layer dynamics, which are a key characteristic of these networks. In this work, we present a detailed characterization of TCP behavior based on cross-layer measurement of transport, as well as RF and MAC layer parameters. In particular, through a series of active TCP/UDP experiments and measurement of the relevant variables at all three layers, we characterize both, the wireless scheduler in a commercial CDMA2000 network and its impact on TCP dynamics. Somewhat surprisingly, our findings indicate that the wireless scheduler is mostly insensitive to channel quality and sector load over short timescales and is mainly affected by the transport layer data rate. Furthermore, we empirically demonstrate the impact of the wireless scheduler on various TCP parameters such as the round trip time, throughput and packet loss rate.

TCP over CDMA2000 Networks: A Cross-Layer Measurement Study

Modern cellular channels in 3G networks incorporate sophisticated power control and dynamic rate adaptation which can have significant impact on adaptive transport layer protocols, such as TCP. Though there exists studies that have evaluated the performance of TCP over such networks, they are based solely on observations at the transport layer and hence have no visibility into the impact of lower layer dynamics, which are a key characteristic of these networks. In this work, we present a detailed characterization of TCP behavior based on cross-layer measurement of transport layer, as well as RF and MAC layer parameters. In particular, through a series of active TCP/UDP experiments and measurement of the relevant variables at all three layers, we characterize both, the wireless scheduler and the radio link protocol in a commercial CDMA2000 network and assess their impact on TCP dynamics. Somewhat surprisingly, our findings indicate that the wireless scheduler is mostly insensitive to channel quality and sector load over short timescales and is mainly affected by the transport layer data rate. Furthermore, with the help of a robust correlation measure, Normalized Mutual Information, we were able to quantify the impact of the wireless scheduler and the radio link protocol on various TCP parameters such as the round trip time, throughput and packet loss rate.

Estimating Sensor Motion from Wide-Field Optical Flow on a Log-Dipolar Sensor

Log-polar image architectures, motivated by the structure of the human visual field, have long been investigated in computer vision for use in estimating motion parameters from an optical flow vector field. Practical problems with this approach have been: (i) dependence on assumed alignment of the visual and motion axes; (ii) sensitivity to occlusion form moving and stationary objects in the central visual field, where much of the numerical sensitivity is concentrated; and (iii) inaccuracy of the log-polar architecture (which is an approximation to the central 20°) for wide-field biological vision. In the present paper, we show that an algorithm based on generalization of the log-polar architecture; termed the log-dipolar sensor, provides a large improvement in performance relative to the usual log-polar sampling. Specifically, our algorithm: (i) is tolerant of large misalignmnet of the optical and motion axes; (ii) is insensitive to significant occlusion by objects of unknown motion; and (iii) represents a more correct analogy to the wide-field structure of human vision. Using the Helmholtz-Hodge decomposition to estimate the optical flow vector field on a log-dipolar sensor, we demonstrate these advantages, using synthetic optical flow maps as well as natural image sequences.

The What-And-Where Filter: A Spatial Mapping Neural Network for Object Recognition and Image Understanding

The What-and-Where filter forms part of a neural network architecture for spatial mapping, object recognition, and image understanding. The Where fllter responds to an image figure that has been separated from its background. It generates a spatial map whose cell activations simultaneously represent the position, orientation, ancl size of all tbe figures in a scene (where they are). This spatial map may he used to direct spatially localized attention to these image features. A multiscale array of oriented detectors, followed by competitve and interpolative interactions between position, orientation, and size scales, is used to define the Where filter. This analysis discloses several issues that need to be dealt with by a spatial mapping system that is based upon oriented filters, such as the role of cliff filters with and without normalization, the double peak problem of maximum orientation across size scale, and the different self-similar interpolation properties across orientation than across size scale. Several computationally efficient Where filters are proposed. The Where filter rnay be used for parallel transformation of multiple image figures into invariant representations that are insensitive to the figures' original position, orientation, and size. These invariant figural representations form part of a system devoted to attentive object learning and recognition (what it is). Unlike some alternative models where serial search for a target occurs, a What and Where representation can he used to rapidly search in parallel for a desired target in a scene. Such a representation can also be used to learn multidimensional representations of objects and their spatial relationships for purposes of image understanding. The What-and-Where filter is inspired by neurobiological data showing that a Where processing stream in the cerebral cortex is used for attentive spatial localization and orientation, whereas a What processing stream is used for attentive object learning and recognition.

Cortical Dynamics of Visual Motion Perception: Short-Range and Long-Range Apparent Motion

This article describes further evidence for a new neural network theory of biological motion perception. The theory clarifies why parallel streams Vl --> V2, Vl --> MT, and Vl --> V2 --> MT exist for static form and motion form processing among the areas Vl, V2, and MT of visual cortex. The theory suggests that the static form system (Static BCS) generates emergent boundary segmentations whose outputs are insensitive to direction-ofcontrast and insensitive to direction-of-motion, whereas the motion form system (Motion BCS) generates emergent boundary segmentations whose outputs are insensitive to directionof-contrast but sensitive to direction-of-motion. The theory is used to explain classical and recent data about short-range and long-range apparent motion percepts that have not yet been explained by alternative models. These data include beta motion; split motion; gamma motion and reverse-contrast gamma motion; delta motion; visual inertia; the transition from group motion to element motion in response to a Ternus display as the interstimulus interval (ISI) decreases; group motion in response to a reverse-contrast Ternus display even at short ISIs; speed-up of motion velocity as interflash distance increases or flash duration decreases; dependence of the transition from element motion to group motion on stimulus duration and size; various classical dependencies between flash duration, spatial separation, ISI, and motion threshold known as Korte's Laws; dependence of motion strength on stimulus orientation and spatial frequency; short-range and long-range form-color interactions; and binocular interactions of flashes to different eyes.

A What-and-Where Neural Network for Invariant Image Preprocessing

A feedforward neural network for invariant image preprocessing is proposed that represents the position1 orientation and size of an image figure (where it is) in a multiplexed spatial map. This map is used to generate an invariant representation of the figure that is insensitive to position1 orientation, and size for purposes of pattern recognition (what it is). A multiscale array of oriented filters followed by competition between orientations and scales is used to define the Where filter.

Investigation of global regulators influencing styrene metabolism and bioplastic synthesis in Pseudomonas putida CA-3

The genetics and biochemistry involved in the biodegradation of styrene and the production of polyhydroxyalkanoates in Pseudomonas putida CA-3 have been well characterised to date. Knowledge of the role played by global regulators in controlling these pathways currently represents a critical knowledge gap in this area. Here we report on our efforts to identify such regulators using mini-Tn5 transposon mutagenesis of the P. putida CA-3 genome. The library generated was subjected to phenotypic screening to identify mutants exhibiting a reduced sensitivity to the effects of carbon catabolite repression of aromatic pathway activity. Our efforts identified a clpX disrupted mutant which exhibited wild-type levels of growth on styrene but significantly reduced growth on phenylacetic acid. RT-PCR analysis of key PACoA catabolon genes necessary for phenylacetic acid metabolism, and SDS-PAGE protein profile analyses suggest that no direct alteration of PACoA pathway transcriptional or translational activity was involved. The influence of global regulators affecting the accumulation of PHAs in P. putida CA-3 was also studied. Phenotypic screening of the mini-Tn5 library revealed a gacS sensor kinase gene disruption resulting in the loss of PHA accumulation capacity in P. putida CA-3. Subsequent SDS-PAGE protein analyses of the wild type and gacS mutant strains identified post-transcriptional control of phaC1 synthase as a key point of control of PHA synthesis in P. putida CA-3. Disruption of the gacS gene in another PHA accumulating organism, P. putida S12, also demonstrated a reduction of PHA accumulation capacity. PHA accumulation was observed to be disrupted in the CA-3 gacS mutant under phosphorus limited growth conditions. Over-expression studies in both wild type CA-3 and gacS mutant demonstrated that rsmY over-expression in gacS disrupted P. putida CA-3 is insufficient to restore PHA accumulation in the cell however in wild type cells, over-expression of rsmY results in an altered PHA monomer compositions.

Investigation of growth and stress tolerance characteristics of Cronobacter spp.

Cronobacter spp. are opportunistic pathogens which can be isolated from a wide variety of foods and environments. They are Gram negative, motile, non-spore forming, peritrichous rods of the Enterobacteriaceae family. This food-borne pathogen is associated with the ingestion of contaminated infant milk formula (IMF), causing necrotizing enterocolitis, sepsis and meningitis in neonatal infants. The work presented in this thesis involved the investigation and characterisation of a bank of Cronobacter strains for their ability to tolerate physiologically relevant stress conditions that are commonly encountered in the gastrointestinal tract. While all strains were able to endure the suboptimal conditions tested, noteworthy variations were observed between strains. A collection of these strains were Lux-tagged to determine if their growth could be tracked in IMF by measuring bioluminescence. The resulting strains could be easily and reproducibly monitored in real time by measuring light emission. Following this a transposon mutagenesis library was created in one of the Lux-tagged strains of Cronobacter sakazakii. This library was screened for mutants with affected growth in milk. The majority of mutants identified were associated with amino acid metabolism. The final section of this thesis identified genes involved in the tolerance of C. sakazakii to the milk derived antimicrobial peptide, Lactoferricin B (Lfcin B). This was achieved by creating a transposon mutagenesis library in C. sakazakii and screening for mutants with increased susceptibility to Lfcin B. Overall this thesis demonstrates the variation between Cronobacter strains. It also identifies genes required for growth of the bacteria in milk, as well as genes needed for antimicrobial peptide tolerance.

Molecular characterisation of the mechanisms of compatible solute accumulation in Listeria monocytogenes

The ability of the Gram-positive foodborne pathogen Listeria monocytogenes to survive and grow in environments of elevated osmolarity can be attributed, at least in part, to the accumulation of a restricted range of low molecular mass solutes compatible with cellular function. Accumulated to high internal concentrations in hyper-saline environments, compatible solutes, either transported into the cell or synthesized de novo, play a dual role: helping to stabilize protein structure and function while also counterbalancing external osmotic strength, thus preventing water loss from the cell and plasmolysis. While previous physiological investigations identified glycine betaine, carnitine, and proline as the principal compatible solutes in the listerial osmostress response, genetic alanysis of the uptake/synthesis systems governing the accumulation of these compounds has, until now, remained largely unexplored. Representing the first genetic analysis of compatible solute accumulation in L. monocytogenes, this thesis describes the molecular characterization of BetL; a highly specific secondary glycine betaine transport system, OpuC; a multicomponent carnitine/glycine betaine transporter, and finally proBA; a two-gene operon encoding the first two enzymes of the listerial proline piosynthesis pathway. In addition to their role in osmotolerance, the potential of each system in contributing to listerial pathogenesis was investigated. While mutations in each gene cluster exhibited dramatic reductions in listerial osmotolerance, OpuC- mutants were additionally shown to exhibit reduced virulence when admisistered via the oral route. This represents the first direct link between the salt stress response and virulence in L. monocytogenes.