Dam methylation controls O-antigen chain length in Salmonella enterica serovar enteritidis by regulating the expression of Wzz protein

We reported previously that a Salmonella enterica serovar Enteritidis dam mutant expressing a truncated Dam protein does not agglutinate in the presence of specific antibodies against O9 polysaccharide. Here we investigate the participation of Dam in lipopolysaccharide (LPS) synthesis in Salmonella. The LPS O-antigen profiles of a dam null mutant (SEDeltadam) and the Salmonella serovar Enteritidis parental strain were examined by using electrophoresis and silver staining. Compared to the parental strain, SEDeltadam produced LPS with shorter O-antigen polysaccharide chains. Since Wzz is responsible for the chain length distribution of the O antigen, we investigated whether Dam methylation is involved in regulating wzz expression. Densitometry analysis showed that the amount of Wzz produced by SEDeltadam is threefold lower than the amount of Wzz produced by the parental strain. Concomitantly, the activity of the wzz promoter in SEDeltadam was reduced nearly 50% in logarithmic phase and 25% in stationary phase. These results were further confirmed by reverse transcription-PCR showing that wzz gene expression was threefold lower in the dam mutant than in the parental strain. Our results demonstrate that wzz gene expression is downregulated in a dam mutant, indicating that Dam methylation activates expression of this gene. This work indicates that wzz is a new target regulated by Dam methylation and demonstrates that DNA methylation not only affects the production of bacterial surface proteins but also the production of surface polysaccharides.

Spatial and temporal ecology of Scots pine ectomycorrhizas

Spatial analysis was used to explore the distribution of individual species in an ectomycorrhizal (ECM) fungal community to address: whether mycorrhizas of individual ECM fungal species were patchily distributed, and at what scale; and what the causes of this patchiness might be. Ectomycorrhizas were extracted from spatially explicit samples of the surface organic horizons of a pine plantation. The number of mycorrhizas of each ECM fungal species was recorded using morphotyping combined with internal transcribed spacer (ITS) sequencing. Semivariograms, kriging and cluster analyses were used to determine both the extent and scale of spatial autocorrelation in species abundances, potential interactions between species, and change over time. The mycorrhizas of some, but not all, ECM fungal species were patchily distributed and the size of patches differed between species. The relative abundance of individual ECM fungal species and the position of patches of ectomycorrhizas changed between years. Spatial and temporal analysis revealed a dynamic ECM fungal community with many interspecific interactions taking place, despite the homogeneity of the host community. The spatial pattern of mycorrhizas was influenced by the underlying distribution of fine roots, but local root density was in turn influenced by the presence of specific fungal species.

Efficient differentiation into skin cells of bone marrow cells recovered in a pellet after density gradient fractionation

We had previously demonstrated the participation of whole bone marrow cells from adult mice in the reconstitution of skin, including the epidermis and hair follicles. To get an insight into cell populations that give rise to the epithelial components of the reconstituted skin, we fractionated bone marrow cells derived from green fluorescent protein-transgenic mice by density gradient. Unexpectedly, we found that a substantial amount of mononucleated cells (approximately 30%) was recovered in the pellet fraction and that the cells in the pellet fraction preferentially differentiated into epithelial components of skin, rather than the cells in the mononuclear cell fraction. The pellet fraction contained more CD45-negative (thus uncommitted to the hematopoietic cell lineage) cells than the mononuclear cell fraction. These results indicate that density gradient fractionation results in significant loss of specific progenitor cells into the usually discarded pellet fraction.

Production of polyclonal antibodies directed to recombinant methionyl bovine somatotropin

The administration of recombinant methionyl bovine somatotropin (rMbST) to dairy cows to increase milk yield remains a common practice in many countries including the USA, Brazil, Mexico, South Africa and Korea, whereas it has been forbidden within the European Union (EU) since 1999. A rapid screening immunoanalytical method capable of the unequivocal determination of rMbST in milk would be highly desirable in order to effectively monitor compliance with the EU-wide ban for home-made or imported dairy products. For decades, the production of specific antibodies for this recombinant isoform of bovine somatotropin (bST) has remained elusive, due to the high degree of sequence homology between both counterparts (e.g. methionine for rMbST in substitution of alanine in bST at the N-terminus). In this study, we compared several immunizing strategies for the production of specific polyclonal antibodies (pAbs), based on the use of the full-length recombinant protein, an rMbST N-terminus peptide fragment and a multiple antigen peptide (MAP) which consists of an oligomeric branching lysine core attached to the first two N-terminus amino acids of rMbST, methionine and phenylalanine (MF-MAP). The immunization with KLH-conjugated MF-MAP led to the production of the pAb with the highest rMbST/bST recognition ratio amongst the generated battery of antibodies. The pAb exhibited a specific binding ability to rMbST in a competitive antigen-coated ELISA format, which avidity was further improved after purification by rMbST N-terminus peptide-based affinity chromatography. These results suggest that immunodiscrimination between structurally related proteins can be achieved using immuno-enhanced immunogens such as MAPs. © 2012 Elsevier B.V.

Vibrational state-selected photodissociation of ClO+

We report on the UV photodissociation of specific vibrational states (v = 2–45) of ClO+ using velocity map
ion imaging. The high vibrational states of ClO+ are prepared via a double resonant scheme through the
ClO (A 2P) state and ion-pair states followed by photoionization with a third photon. The absorption of a
fourth photon results in photodissociation of the ClO+ into two dominant asymptotic channels. The Cl+
and O+ fragment ion images reveal information on both the energetics of high-lying cation vibrational
states and the low-lying dissociative electronic states that correlate to Cl+(3P) + O(3P) and Cl(2P) + O+(4S)
asymptotic channels. We also report ab initio potentials for the bound ClO+ and ion-pair states as well as
calculations of the ClO+ excited states relevant to the photodissociation process.

A mirage of genes

This paper examines the structure of popular conceptions of the new genetics, and assesses why genetics has been so readily accepted in medicine and in the public discourse. Adapting Rene Dubos' classic analysis, Mirage of Health, we examine the new genetics by comparing it to Dubos' analysis of the structure and limits of germ theory. Germ theory focuses on the internal rather than the external environment, emphasises a doctrine of specific aetiology, and adopts the metaphor of the body as a machine. The germ theory model narrowed our vision about disease aetiology, proved misleading in some cases, yet remained the basis for clinical medical models of disease. In recent years, genetics has moved to the cutting edge of medical research and thinking about disease and behaviour. The structure of popular conceptions of the new genetics shows remarkable parallels with germ theory. This has eased the acceptance of genetics but simultaneously raises questions about these genetic explanations. An appearance and allure of specificity privileges genetic explanations in the public discourse; on examination, this specificity may prove to be a mirage.

Impacts of Electric Vehicle charging under electricity market operations

The Irish government set a target in 2008 that 10% of all vehicles in the transport fleet be powered by electricity by 2020. Similar electric vehicle targets have been introduced in other countries. In this study the effects of 213,561 electric vehicles on the operation of the single wholesale electricity market for the Republic of Ireland and Northern Ireland is investigated. A model of Ireland’s electricity market in 2020 is developed using the power systems market model called PLEXOS for power systems. The amount of CO2 emissions associated with charging the EVs and the impacts with respect to Ireland’s target for renewable energy in transport is also quantified. A single generation portfolio and two different charging scenarios, arising from a peak and off-peak charging profile are considered. Results from the study confirm that offpeak charging is more beneficial than peak charging and that charging EVs will contribute 1.45% energy supply to the 10% renewable energy in transport target. The net CO2 reductions are 147 and 210 kt CO2 respectively.

The biology of habitat dominance; can microbes behave as weeds?

Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard-wired to behave in a vigorous and ecologically aggressive manner. These 'microbial weeds' are able to dominate the communities that develop in fertile but uncolonized - or at least partially vacant - habitats via traits enabling them to out-grow competitors; robust tolerances to habitat-relevant stress parameters and highly efficient energy-generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat-specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes, such as Escherichia coli, Mycobacterium smegmatis and Pseudoxylaria spp., exhibit characteristics of both weed and non-weed species. We propose that the concept of nonweeds represents a 'dustbin' group that includes species such as Synodropsis spp., Polypaecilum pisce, Metschnikowia orientalis, Salmonella spp., and Caulobacter crescentus. We show that microbial weeds are conceptually distinct from plant weeds, microbial copiotrophs, r-strategists, and other ecophysiological groups of microorganism. Microbial weed species are unlikely to emerge from stationary-phase or other types of closed communities; it is open habitats that select for weed phenotypes. Specific characteristics that are common to diverse types of open habitat are identified, and implications of weed biology and open-habitat ecology are discussed in the context of further studies needed in the fields of environmental and applied microbiology.

Development and Validation of a Forklift Truck Powertrain Simulation

Fuel economy has become an important consideration in forklift truck design, particularly in Europe. A simulation of the fuel consumption and performance of a forklift truck has been developed, validated and subsequently used to determine the energy consumed by individual powertrain components during drive cycles.
The truck used in this study has a rated lifting capacity of 2500kg, and is powered by a 2.6 litre naturally aspirated diesel engine with a fuel pump containing a mechanical variable-speed governor. The drivetrain consisted of a torque convertor, hydraulic clutch and single speed transmission.
AVL Cruise was used to simulate the vehicle powertrain, with coupled Mathworks Simulink models used to simulate the hydraulic and control systems and governor. The vehicle has been simulated on several performance and fuel consumption drive cycles with the main focus being the VDI 2198 fuel consumption drive cycle.
To validate the model, a truck was instrumented and measurements taken to compare the performance and instantaneous fuel consumption to simulated values. The fuel injector pump was modified and calibrated to enable instantaneous fuel flow to be measured.
The model has been validated to within acceptable limits and has been used to investigate the effect four different torque converters have on the fuel consumption and performance of the forklift truck. The study demonstrates how the model can be used to compare the fuel consumption and performance trade-offs when selecting drivetrain components.

Pattern of learning disabilities in children with extremely low birth weight and broadly average intelligence

To examine the prevalence and pattern of specific areas of learning disability (LD) in neurologically normal children with extremely low birth weight (ELBW) (<or = 800 g) who have broadly average intelligence compared with full-term children with normal birth weight of comparable sociodemographic background, and to explore concurrent cognitive correlates of the specific LDs.

Smooth Muscle Cells Differentiated from Reprogrammed Embryonic Lung Fibroblasts Through DKK3 Signalling are Potent for Tissue Engineering of Vascular Grafts

Rationale: Smooth muscle cells (SMCs) are a key component of tissue-engineered vessels. However, the sources by which they can be isolated are limited.

Objective: We hypothesized that a large number of SMCs could be obtained by direct reprogramming of fibroblasts, that is, direct differentiation of specific cell lineages before the cells reaching the pluripotent state.

Methods and Results: We designed a combined protocol of reprogramming and differentiation of human neonatal lung fibroblasts. Four reprogramming factors (OCT4, SOX2, KLF4, and cMYC) were overexpressed in fibroblasts under reprogramming conditions for 4 days with cells defined as partially-induced pluripotent stem (PiPS) cells. PiPS cells did not form tumors in vivo after subcutaneous transplantation in severe combined immunodeficiency mice and differentiated into SMCs when seeded on collagen IV and maintained in differentiation media. PiPS-SMCs expressed a panel of SMC markers at mRNA and protein levels. Furthermore, the gene dickkopf 3 was found to be involved in the mechanism of PiPS-SMC differentiation. It was revealed that dickkopf 3 transcriptionally regulated SM22 by potentiation of Wnt signaling and interaction with Kremen1. Finally, PiPS-SMCs repopulated decellularized vessel grafts and ultimately gave rise to functional tissue-engineered vessels when combined with previously established PiPS-endothelial cells, leading to increased survival of severe combined immunodeficiency mice after transplantation of the vessel as a vascular graft.

Conclusions: We developed a protocol to generate SMCs from PiPS cells through a dickkopf 3 signaling pathway, useful for generating tissue-engineered vessels. These findings provide a new insight into the mechanisms of SMC differentiation with vast therapeutic potential.

Biomolecular mechanisms of staphylococcal biofilm formation

The multitude of biomolecular and regulatory factors involved in staphylococcal adhesion and biofilm formation owe much to their ability to colonize surfaces, allowing the biofilm form to become the preferential bacterial phenotype. Judging by total number, biomass and variety of environments colonized, bacteria can be categorized as the most successful lifeform on earth. This is due to the ability of bacteria and other microorganisms to respond phenotypically via biomolecular processes to the stresses of their surrounding environment. This review focuses on the specific pathways involved in the adhesion of the Gram-positive bacteria Staphylococcus epidermidis and Staphylococcus aureus with reference to the role of specific cell surface adhesins, the ica operon, accumulation-associated proteins and quorum-sensing systems and their significance in medical device-related infection.

The p-hub Model with Hub-catchment Areas, Existing Hubs, and Simulation: A Case Study of Serbian Intermodal Terminals

This paper addresses the problem of optimally locating intermodal freight terminals in Serbia. To solve this problem and determine the effects of the resulting scenarios, two modeling approaches were combined. The first approach is based on multiple-assignment hub-network design, and the second is based on simulation. The multiple-assignment p-hub network location model was used to determine the optimal location of intermodal terminals. Simulation was used as a tool to estimate intermodal transport flow volumes, due to the unreliability and unavailability of specific statistical data, and as a method for quantitatively analyzing the economic, time, and environmental effects of different scenarios of intermodal terminal development. The results presented here represent a summary, with some extension, of the research realized in the IMOD-X project (Intermodal Solutions for Competitive Transport in Serbia).

Participation of adult mouse bone marrow cells in reconstitution of skin

Results of recent studies have indicated that bone marrow cells can differentiate into various cells of ectodermal, mesodermal, and endodermal origins when transplanted into the body. However, the problems associated with those experiments such as the long latent period, rareness of the event, and difficulty in controlling the processes have hampered detailed mechanistic studies. In the present study, we examined the potency of mouse bone marrow cells to differentiate into cells comprising skin tissues using a skin reconstitution assay. Bone marrow cells from adult green fluorescent protein (GFP)-transgenic mice were transplanted in a mixture of embryonic mouse skin cells (17.5 days post-coitus) onto skin defects made on the backs of nude mice. Within 3 weeks, fully differentiated skin with hair was reconstituted. GFP-positive cells were found in the epidermis, hair follicles, sebaceous glands, and dermis. The localization and morphology of the cells, results of immunohistochemistry, and results of specific staining confirmed that the bone marrow cells had differentiated into epidermal keratinocytes, sebaceous gland cells, follicular epithelial cells, dendritic cells, and endothelial cells under the present conditions. These results indicate that this system is suitable for molecular and cellular mechanistic studies on differentiation of stem cells to various epidermal and dermal cells.

Quantitative detection of DNA by autocatalytic enlargement of hybridized gold nanoprobes

Quantitative detection of specific viral DNA has become a pressing issue for the earlier clinical diagnosis of viral infectious diseases. Therefore, in this paper, we report a simple, sensitive, and inexpensive quantitative approach for DNA detection based on the autocatalytic Au deposition of gold nanoprobes via the surface reduction of AuCl4- to Au0 on their surface in the presence of ascorbic acid (AA) and cetyltrimethylammonium bromide (CTAB). On this basis, signal enhancements in the absorbance intensity and kinetic behavior of gold enlargement in the aqueous phase have been well investigated and explained for the selection of analytical parameters. To achieve high sensitivity, magnetic particles conjugated with capture probes (PMPs) were employed for the collection of gold nanoprobes. After denaturated by ion a pH 11 solution, the amplified signals of gold nanoprobes, which is proportional to the concentration of the target DNA, could easily be confirmed by a UV-vis scanning spectrophotometer. Limit of detection could be obtained as low as 1.0 fM by this simple method.