Separation of VUV/UV photons and reactive particles in the effluent of a He/O2 atmospheric pressure plasma jet

Cold atmospheric pressure plasmas can be used for treatment of living tissues or for inactivation of bacteria or biological macromolecules. The treatment is usually characterized by a combined effect of UV and VUV radiation, reactive species, and ions. This combination is usually beneficial for the effectiveness of the treatment but it makes the study of fundamental interaction mechanisms very difficult. Here we report on an effective separation of VUV/UV photons and heavy reactive species in the effluent of a micro scale atmospheric pressure plasma jet ($\mu$-APPJ). The separation is realized by an additional flow of helium gas under well-defined flow conditions, which deflects heavy particles in the effluent without affecting the VUV and UV photons. Both components of the effluent, the photons and the reactive species, can be used separately or in combination for sample treatment. The results of treatment of a model plasma polymer film and vegetative Bacillus subtilis and Escherichia coli cells are shown and discussed. A simple model of the He gas flow and reaction kinetics of oxygen atoms in the gas phase and at the surface is used to provide a better understanding of the processes in the plasma effluent. The new jet modification, called X-Jet for its appearance, will simplify the investigation of interaction mechanisms of atmospheric pressure plasmas with biological samples.Comment: 10 pages, 7 figures, submitted to Journal of Physics D: Applied Physic

Target prediction and a statistical sampling algorithm for RNA-RNA interaction

It has been proven that the accessibility of the target sites has a critical influence for miRNA and siRNA. In this paper, we present a program, rip2.0, not only the energetically most favorable targets site based on the hybrid-probability, but also a statistical sampling structure to illustrate the statistical characterization and representation of the Boltzmann ensemble of RNA-RNA interaction structures. The outputs are retrieved via backtracing an improved dynamic programming solution for the partition function based on the approach of Huang et al. (Bioinformatics). The $O(N^6)$ time and $O(N^4)$ space algorithm is implemented in C (available from \url{http://www.combinatorics.cn/cbpc/rip2.html})Comment: 7 pages, 10 figure

Small but crucial : the novel small heat shock protein Hsp21 mediates stress adaptation and virulence in Candida albicans

Peer reviewedPublisher PD

Is Thermosensing Property of RNA Thermometers Unique?

A large number of studies have been dedicated to identify the structural and sequence based features of RNA thermometers, mRNAs that regulate their translation initiation rate with temperature. It has been shown that the melting of the ribosome-binding site (RBS) plays a prominent role in this thermosensing process. However, little is known as to how widespread this melting phenomenon is as earlier studies on the subject have worked with a small sample of known RNA thermometers. We have developed a novel method of studying the melting of RNAs with temperature by computationally sampling the distribution of the RNA structures at various temperatures using the RNA folding software Vienna. In this study, we compared the thermosensing property of 100 randomly selected mRNAs and three well known thermometers - rpoH, ibpA and agsA sequences from E. coli. We also compared the rpoH sequences from 81 mesophilic proteobacteria. Although both rpoH and ibpA show a higher rate of melting at their RBS compared with the mean of non-thermometers, contrary to our expectations these higher rates are not significant. Surprisingly, we also do not find any significant differences between rpoH thermometers from other -proteobacteria and E. coli non-thermometers

Practical issues affecting the utility of field survey data for biodiversity monitoring

There is growing emphasis on monitoring biodiversity in European waters not least due to the EC’s recent Marine Strategy Framework Directive (MSFD) listing biodiversity as one descriptor of ‘Good Environmental Status’ (GES). Member States already have various monitoring surveys in place, in particular groundfish and other fisheries surveys, which may provide a cost-effective way of assessing some elements of biodiversity. The MSFD recognises the “need to ensure, as far as possible, compatibility with existing programmes”. Although existing field surveys are a potential source of quantitative data for examining spatial and temporal biodiversity patterns, it must be acknowledged that such surveys were often not originally designed to monitor ‘biodiversity’, and long-term surveys may have had changes in survey design at some point, and/or subtle changes in survey protocols over time. Field surveys for infauna and plankton typically collect and preserve samples at sea, and subsequent laboratory work includes the use of reference collections, quality assurance and longer-term sample storage. Surveys with towed gears can collect large amounts of complex biological material which is typically processed at sea, and so different forms of quality assurance are required. The taxonomic knowledge, experience and enthusiasm of sea-going staff can also influence the biodiversity information collected (e.g. time spent sorting complex catches, species identification). Hence, matrices of species-station data can contain ‘artefacts’ that need to be understood and addressed before deriving biodiversity metrics, and may even necessitate some degree of data filtering. This paper uses field data from selected surveys to illustrate how various factors can affect ‘biodiversity information’

Regulation of Translation in Haloarchaea: 5′- and 3′-UTRs Are Essential and Have to Functionally Interact In Vivo

Recently a first genome-wide analysis of translational regulation using prokaryotic species had been performed which revealed that regulation of translational efficiency plays an important role in haloarchaea. In fact, the fractions of genes under differential growth phase-dependent translational control in the two species Halobacterium salinarum and Haloferax volcanii were as high as in eukaryotes. However, nothing is known about the mechanisms of translational regulation in archaea. Therefore, two genes exhibiting opposing directions of regulation were selected to unravel the importance of untranslated regions (UTRs) for differential translational control in vivo

Remodeling of the Streptococcus agalactiae Transcriptome in Response to Growth Temperature

BACKGROUND: To act as a commensal bacterium and a pathogen in humans and animals, Streptococcus agalactiae (group B streptococcus, GBS) must be able to monitor and adapt to different environmental conditions. Temperature variation is a one of the most commonly encountered variables. METHODOLOGY/PRINCIPAL FINDINGS: To understand the extent to which GBS modify gene expression in response to temperatures encountered in the various hosts, we conducted a whole genome transcriptome analysis of organisms grown at 30 degrees C and 40 degrees C. We identified extensive transcriptome remodeling at various stages of growth, especially in the stationary phase (significant transcript changes occurred for 25% of the genes). A large proportion of genes involved in metabolism was up-regulated at 30 degrees C in stationary phase. Conversely, genes up-regulated at 40 degrees C relative to 30 degrees C include those encoding virulence factors such as hemolysins and extracellular secreted proteins with LPXTG motifs. Over-expression of hemolysins was linked to larger zones of hemolysis and enhanced hemolytic activity at 40 degrees C. A key theme identified by our study was that genes involved in purine metabolism and iron acquisition were significantly up-regulated at 40 degrees C. CONCLUSION/SIGNIFICANCE: Growth of GBS in vitro at different temperatures resulted in extensive remodeling of the transcriptome, including genes encoding proven and putative virulence genes. The data provide extensive new leads for molecular pathogenesis research

Functions of Some Capsular Polysaccharide Biosynthetic Genes in Klebsiella pneumoniae NTUH K-2044

The growing number of Klebsiella pneumoniae infections, commonly acquired in hospitals, has drawn great concern. It has been shown that the K1 and K2 capsular serotypes are the most detrimental strains, particularly to those with diabetes. The K1 cps (capsular polysaccharide) locus in the NTUH-2044 strain of the pyogenic liver abscess (PLA) K. pneumoniae has been identified recently, but little is known about the functions of the genes therein. Here we report characterization of a group of cps genes and their roles in the pathogenesis of K1 K. pneumoniae. By sequential gene deletion, the cps gene cluster was first re-delimited between genes galF and ugd, which serve as up- and down-stream ends, respectively. Eight gene products were characterized in vitro and in vivo to be involved in the syntheses of UDP-glucose, UDP-glucuronic acid and GDP-fucose building units. Twelve genes were identified as virulence factors based on the observation that their deletion mutants became avirulent or lost K1 antigenicity. Furthermore, deletion of kp3706, kp3709 or kp3712 (ΔwcaI, ΔwcaG or Δatf, respectively), which are all involved in fucose biosynthesis, led to a broad range of transcriptional suppression for 52 upstream genes. The genes suppressed include those coding for unknown regulatory membrane proteins and six multidrug efflux system proteins, as well as proteins required for the K1 CPS biosynthesis. In support of the suppression of multidrug efflux genes, we showed that these three mutants became more sensitive to antibiotics. Taken together, the results suggest that kp3706, kp3709 or kp3712 genes are strongly related to the pathogenesis of K. pneumoniae K1

Behavioral Defects in Chaperone-Deficient Alzheimer's Disease Model Mice

Molecular chaperones protect cells from the deleterious effects of protein misfolding and aggregation. Neurotoxicity of amyloid-beta (Aβ) aggregates and their deposition in senile plaques are hallmarks of Alzheimer's disease (AD). We observed that the overall content of αB-crystallin, a small heat shock protein molecular chaperone, decreased in AD model mice in an age-dependent manner. We hypothesized that αB-crystallin protects cells against Aβ toxicity. To test this, we crossed αB-crystallin/HspB2 deficient (CRYAB-/-HSPB2-/-) mice with AD model transgenic mice expressing mutant human amyloid precursor protein. Transgenic and non-transgenic mice in chaperone-sufficient or deficient backgrounds were examined for representative behavioral paradigms for locomotion and memory network functions: (i) spatial orientation and locomotion was monitored by open field test; (ii) sequential organization and associative learning was monitored by fear conditioning; and (iii) evoked behavioral response was tested by hot plate method. Interestingly, αB-crystallin/HspB2 deficient transgenic mice were severely impaired in locomotion compared to each genetic model separately. Our results highlight a synergistic effect of combining chaperone deficiency in a transgenic mouse model for AD underscoring an important role for chaperones in protein misfolding diseases