<Emphasis Type="Italic">In silico</Emphasis> identification and experimental validation of PmrAB targets in <Emphasis Type="Italic">Salmonella typhimurium</Emphasis>by regulatory motif detection

Background  

The PmrAB (BasSR) two-component regulatory system is required for Salmonella typhimurium virulence. PmrAB-controlled modifications of the lipopolysaccharide (LPS) layer confer resistance to cationic antibiotic polypeptides, which may allow bacteria to survive within macrophages. The PmrAB system also confers resistance to Fe³⁺-mediated killing. New targets of the system have recently been discovered that seem not to have a role in the well-described functions of PmrAB, suggesting that the PmrAB-dependent regulon might contain additional, unidentified targets.     

Reaction center and antenna processes in photosynthesis at low temperature

Around 1960 experiments of Arnold and Clayton, Chance and Nishimura and Calvin and coworkers demonstrated that the primary photosynthetic electron transfer processes are not abolished by cooling to cryogenic temperatures. After a brief historical introduction, this review discusses some aspects of electron transfer in bacterial reaction centers and of optical spectroscopy of photosynthetic systems with emphasis on low-temperature experiments.Abbreviations (B)Chl (bacterio)chlorophyll - (B)Phe (bacterio)pheophytin - FMO Fenna-Matthews-Olson - LH1, LH2 light harvesting complexes of purple bacteria - LHC II, CP47 light harvesting complexes of Photosystem II - P, P870 primary electron donor - RC reaction center     

INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis

INCLUSive is a suite of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. The tools allow normalization, filtering and clustering of microarray data, functional scoring of gene clusters, sequence retrieval, and detection of known and unknown regulatory elements using probabilistic sequence models and Gibbs sampling. All tools are available via different web pages and as web services. The web pages are connected and integrated to reflect a methodology and facilitate complex analysis using different tools. The web services can be invoked using standard SOAP messaging. Example clients are available for download to invoke the services from a remote computer or to be integrated with other applications. All services are catalogued and described in a web service registry. The INCLUSive web portal is available for academic purposes at http://www.esat.kuleuven.ac.be/inclusive.     

Use of antibodies to the lipopolysaccharide core region in the treatment of gram-negative sepsis and shock

In this paper we review evidence in favor of a protective role for antibodies directed at the lipopolysaccharide (LPS) core region of Gram-negative bacilli. It will be shown that, given the right animal model, polyclonal antisera raised against O-antigen lacking, rough mutant strains, can be shown to protect animals against lethal sepsis due to a variety a bacterial species. Evidence for a protective role obtained from clinical studies will also be discussed. It will be stressed how difficult it is to prove that the antibodies directed against the LPS-core, and not other proteins present in the polyclonal anti-rough strain antisera, were responsible for the observed protective effects. The solution to some of these problems is the production of monoclonal antibodies (Mabs). We will discuss the findings that purified anti-core Mabs may give false-positive outcomes of protection studies, due to the induction of tolerance by small amounts of contaminating endotoxin, present in the antibody preparation. The need to administer the Mab therapeutically instead of prophylactically to the test animals, will be stressed. It will be shown how we succeeded in determining the epitope-specificities of several anti-core antibodies. It will be shown also that use of Elisa alone for characterization of anti-core Mabs may lead to false conclusions concerning epitope specificities. We will prove that synthetic KDO-(=ketodeoxycctanate) and lipid A-containing antigens are indispensable tools for thorough characterization of Mabs. Using this methodology we were able to discriminate between specific antigen-antibody interactions, and the ability of some Mabs to bind “non-specifically” to hydrophobic surfaces. The relationship between epitope specificity and protective effects of anti-core Mabs will be described. Finally, we will demonstrate that a KDO-specific Mabs is capable of protecting mice against lethal sepsis; in other words, it will be shown conclusively that Mabs to defined epitopes in LPS core region are cross-protective.     

The catalytic potency of β-glucosidase from Pyrococcus furiosus in the direct glucosylation reaction

Enzymes from extremophiles operate at conditions that are different from their ‘normal’ counterparts, and are therefore a useful extension of the enzyme toolbox. In this paper, the direct glucosylation reaction mediated by a hyperthermophilic β-glucosidase from Pyrocuccus furiosus was investigated. Hexanol was successfully coupled to glucose with this enzyme. A preliminary study was conducted to improve the product yield. A maximum product concentration of 12.9 g.l⁻¹ was attainable by increasing the glucose concentration to the maximum solubility of 2000 g.(kg buffer solution)⁻¹ at the reaction temperature. The highest glucose based yield of 2.64% was achieved with a glucose concentration of 900 g.(kg buffer solution)⁻¹ at a reaction temperature of 65°C and a pH of 6.0. Performing the reaction at higher pH and temperature led to lower product concentrations. This was caused by deactivation of the enzyme accompanied by browning of the reaction mixture. A pH of 4.4 did have a negative effect on both the storage and the operational stability of the enzyme.     

Polarity of meiotic gene conversion is 5′ to 3′ within the niaD gene of Aspergillus nidulans

We have examined polarity of meiotic gene conversion in the niiA-niaD gene cluster of Aspergillus nidulans in two-point crosses. The type and position of the mutations represented by the niaD alleles and the correlation between the relative frequency of gene conversion and the physical position of these mutations were determined. We show that polarity of meiotic gene conversion is 5′ to 3′ (transcribed strand) within the niaD gene. Additional crosses involving a niiA allele and a niaD allele show little polarity of gene conversion, which suggests that the recombination events leading to restoration of the niaD gene are initiated upstream of the coding region of the niaD gene but within the niiA-niaD gene cluster, possibly within the intergenic promoter region.     

Aquatic plant shows flexible avoidance by escape from tuber predation by swans

Deeper burial of bulbs and tubers has been suggested as an escape against below-ground herbivory by vertebrates, but experimental evidence is lacking. As deep propagule burial can incur high costs of emergence after dormancy, burial depth may represent a trade-off between sprouting survival and herbivore avoidance. We tested whether burial depth of subterraneous tubers is a flexible trait in fennel pondweed (Potamogeton pectinatus), facing tuber predation by Bewick's swans (Cygnus columbianus bewickii) in shallow lakes in winter. In a four-year experiment involving eight exclosures, winter herbivory by swans and all vertebrate summer herbivory were excluded in a full-factorial design; we hence controlled for aboveground vertebrate herbivory in summer, possibly influencing tuber depth. Tuber depth was measured each September before swan arrival and each March before tuber sprouting. In accordance with our hypothesis, tuber depth in September decreased after excluding Bewick's swans in comparison to control plots. The summer exclosure showed an increase in tuber biomass and the number of shallow tubers, but not a significant effect on the mean burial depth of tuber mass. Our results suggest that a clonal plant like P. pectinatus can tune the tuber burial depth to predation pressure, either by phenotypic plasticity or genotype sorting, hence exhibiting flexible avoidance by escape. We suggest that a flexible propagule burial depth can be an effective herbivore avoidance strategy, which might be more widespread among tuber forming plant species than previously thought.     

PFGE diversity within the methicillin-resistant <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> clonal lineage ST398

Background  

Livestock has recently been identified as a new reservoir of methicillin-resistant Staphylococcus aureus (MRSA). Most isolates belong to ST398 and are non-typeable with PFGE using SmaI, making it difficult to study transmission and outbreaks. Therefore, a new PFGE using Cfr9I, a neoschizomer of SmaI was optimized and evaluated to investigate ST398 isolates.     

Asymptomatic Middle East Respiratory Syndrome Coronavirus Infection in Rabbits

The ability of Middle East respiratory syndrome coronavirus (MERS-CoV) to infect small animal species may be restricted given the fact that mice, ferrets, and hamsters were shown to resist MERS-CoV infection. We inoculated rabbits with MERS-CoV. Although virus was detected in the lungs, neither significant histopathological changes nor clinical symptoms were observed. Infectious virus, however, was excreted from the upper respiratory tract, indicating a potential route of MERS-CoV transmission in some animal species.