Ribosome association primes the stringent factor Rel for tRNA-dependent locking in the A-site and activation of (p)ppGpp synthesis

In the Gram-positive Firmicute bacterium Bacillus subtilis, amino acid starvation induces synthesis of the alarmone (p)ppGpp by the RelA/SpoT Homolog factor Rel. This bifunctional enzyme is capable of both synthesizing and hydrolysing (p)ppGpp. To detect amino acid deficiency, Rel monitors the aminoacylation status of the ribosomal A-site tRNA by directly inspecting the tRNA’s CCA end. Here we dissect the molecular mechanism of B. subtilis Rel. Off the ribosome, Rel predominantly assumes a ‘closed’ conformation with dominant (p)ppGpp hydrolysis activity. This state does not specifically select deacylated tRNA since the interaction is only moderately affected by tRNA aminoacylation. Once bound to the vacant ribosomal A-site, Rel assumes an ‘open’ conformation, which primes its TGS and Helical domains for specific recognition and stabilization of cognate deacylated tRNA on the ribosome. The tRNA locks Rel on the ribosome in a hyperactivated state that processively synthesises (p)ppGpp while the hydrolysis is suppressed. In stark contrast to non-specific tRNA interactions off the ribosome, tRNA-dependent Rel locking on the ribosome and activation of (p)ppGpp synthesis are highly specific and completely abrogated by tRNA aminoacylation. Binding pppGpp to a dedicated allosteric site located in the N-terminal catalytic domain region of the enzyme further enhances its synthetase activity.     

Microbiological and molecular assessment of bacteriophage ISP for the control of Staphylococcus aureus

The increasing antibiotic resistance in bacterial populations requires alternatives for classical treatment of infectious diseases and therefore drives the renewed interest in phage therapy. Methicillin resistant Staphylococcus aureus (MRSA) is a major problem in health care settings and live-stock breeding across the world. This research aims at a thorough microbiological, genomic, and proteomic characterization of S. aureus phage ISP, required for therapeutic applications. Host range screening of a large batch of S. aureus isolates and subsequent fingerprint and DNA microarray analysis of the isolates revealed a substantial activity of ISP against 86% of the isolates, including relevant MRSA strains. From a phage therapy perspective, the infection parameters and the frequency of bacterial mutations conferring ISP resistance were determined. Further, ISP was proven to be stable in relevant in vivo conditions and subcutaneous as well as nasal and oral ISP administration to rabbits appeared to cause no adverse effects. ISP encodes 215 gene products on its 138,339 bp genome, 22 of which were confirmed as structural proteins using tandem electrospray ionization-mass spectrometry (ESI-MS/MS), and shares strong sequence homology with the 'Twort-like viruses'. No toxic or virulence-associated proteins were observed. The microbiological and molecular characterization of ISP supports its application in a phage cocktail for therapeutic purposes.     

Lack of phylogeographic structure in the freshwater cyanobacterium Microcystis aeruginosa suggests global dispersal

Background

Free-living microorganisms have long been assumed to have ubiquitous distributions with little biogeographic signature because they typically exhibit high dispersal potential and large population sizes. However, molecular data provide contrasting results and it is far from clear to what extent dispersal limitation determines geographic structuring of microbial populations. We aimed to determine biogeographical patterns of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. Being widely distributed on a global scale but patchily on a regional scale, this prokaryote is an ideal model organism to study microbial dispersal and biogeography.

Methodology/Principal Findings

The phylogeography of M. aeruginosa was studied based on a dataset of 311 rDNA internal transcribed spacer (ITS) sequences sampled from six continents. Richness of ITS sequences was high (239 ITS types were detected). Genetic divergence among ITS types averaged 4% (maximum pairwise divergence was 13%). Preliminary analyses revealed nearly completely unresolved phylogenetic relationships and a lack of genetic structure among all sequences due to extensive homoplasy at multiple hypervariable sites. After correcting for this, still no clear phylogeographic structure was detected, and no pattern of isolation by distance was found on a global scale. Concomitantly, genetic differentiation among continents was marginal, whereas variation within continents was high and was mostly shared with all other continents. Similarly, no genetic structure across climate zones was detected.

Conclusions/Significance

The high overall diversity and wide global distribution of common ITS types in combination with the lack of phylogeographic structure suggest that intercontinental dispersal of M. aeruginosa ITS types is not rare, and that this species might have a truly cosmopolitan distribution.     

2011–12 Seasonal Influenza Vaccines Effectiveness against Confirmed A(H3N2) Influenza Hospitalisation: Pooled Analysis from a European Network of Hospitals. A Pilot Study

Background

Influenza vaccination strategies aim at protecting high-risk population from severe outcomes. Estimating the effectiveness of seasonal vaccines against influenza related hospitalisation is important to guide these strategies. Large sample size is needed to have precise estimate of influenza vaccine effectiveness (IVE) against severe outcomes. We assessed the feasibility of measuring seasonal IVE against hospitalisation with laboratory confirmed influenza through a network of 21 hospitals in the European Union.

Methods

We conducted a multicentre study in France (seven hospitals), Italy (one hospital), and Navarra (four hospitals) and Valencia (nine hospitals) regions in Spain. All ≥18 years hospitalised patients presenting an influenza-like illness within seven days were swabbed. Cases were patients RT-PCR positive for influenza A (H3N2); controls were patients negative for any influenza virus. Using logistic regression with study site as a fixed effect we calculated IVE adjusted for potential confounders. We restricted the analyses to those swabbed within four days.

Results

We included, 375 A(H3N2) cases and 770 controls. The overall adjusted IVE was 24.9% (95%CI–1.8;44.6). Among the target group for vaccination (N = 1058) the adjusted IVE was 28.8% (95%CI:2.8;47.9); it was respectively 36.8% (95%CI:−48.8; 73.1), 42.6% (95%CI:−16.5;71.7), 17.8%(95%CI:−40.8; 52.1) and 37.5% (95%CI:−22.8;68.2) in the age groups 18–64, 65–74, 75–84 and more than 84 years.

Discussion

Estimation of IVE based on the pooling of data obtained through a European network of hospitals was feasible. Our results suggest a low IVE against hospitalised confirmed influenza in 2011–12. The low IVE may be explained by a poor immune response in the high-risk population, imperfect match between vaccine and circulating strain or waning immunity due to a late season. Increased sample size within this network would allow more precise estimates and stratification of the IVE by time since vaccination and vaccine types or brands.     

Intraperitoneal versus subcutaneous telemetry devices in young Mongolian gerbils (Meriones unguiculatus)

Radiotelemetry has become a very popular biotelemetric tool for measuring physiological parameters such as heart rate, blood pressure, body temperature and muscle activity, as well as general behavioural activity in undisturbed, freely moving animals. In most studies using this technique, adult subjects are used. However, sometimes an ontogenetic approach is required to clarify whether changes in one parameter are preceeded or followed by changes in another parameter. Tracking physiological changes in young, developing individuals could explain given states of these animals as adults. Implanting telemetry devices can be done subcutaneously and intraperitoneally, the former method posing less of a challenge on the animal and its recovery from surgery. Because telemetry will be used in weanling gerbils during subsequent studies, we needed to investigate whether subcutaneous implantation of telemetric devices is preferable to intraperitoneal surgery with respect to animal welfare. This is a technical paper describing anaesthetic and surgical techniques in detail during a pre-trial involving subcutaneous (n=10, aged 21-29 days) and intraperitoneal (n=10, aged 19-34 days) implantation of dummy telemetry transmitters (1.9 cm3, 3.6 g after shortening of leads) in weanling gerbils, Meriones unguiculatus. Body weight was measured and analysed over four-day intervals. Optimizing anaesthetic dosages was a first step in this pilot trial. This occurred during the first few subcutaneous implantations. Three animals died while anaesthetized during the subcutaneous procedure but none post-surgery. All animals survived anaesthesia during the intraperitoneal implantation, but two died in the first three days post-surgery. In the former method, the tension on the dermal sutures caused by the presence of the transmitters was too great, resulting in the animals opening the sutures by chewing them. The animals died during the latter procedure probably due to strangulation of the intestine by the excess lead that was coiled in the abdomen. Furthermore, placement of the exposed negative lead of the transmitter on the underlying muscle had to be done on the m. pectoralis transversus in order for it to stay in place as the animal developed. This paper showed that the implantation of a telemetric device in weanling gerbils is feasible and is best executed through the intraperitoneal technique.     

Combination of pharmacological analgesics and microwave irradiation of an acupuncture point for suppression of visceral pain in mice: Role of the opioid and serotonergic cerebral systems

We studied suppression of pain-related reactions induced in mice by i.p. injection of 0.08 ml of a 2% solution of acetic acid using pharmacological analgesics (analgin and tramadol) combined with low-intensity microwave irradiation of an acupuncture point (AP) E-36 (frequency 30 to 300 GHz and power rate density 3·10⁻⁹ W/cm²). The respective effects were also observed under conditions of suppression of the functions of opioid and serotonergic cerebral systems using injections of, respectively, naloxone and DL-p-chlorophenylalanine (p-CPA). We found that antinociceptive effects provided by analgesics used in a 50% mean single dose in the combination with microwave irradiation of the AP were significantly more intense than those induced by isolated injection of analgesics used in both 50% and full mean single doses and isolated microwave irradiation of the AP E-36. After injections of naloxone, analgesic effects caused by the combined action of analgin and microwave irradiation of the AP were considerably smaller. At the same time, after injection of p-CPA, analgesic effects, provided by the combination of injection of pharmacological agents and microwave irradiation of the AP, weakened in the case of use of both analgesics. This was manifested in a significant increase in the total duration of pain-related behavioral reactions. Therefore, the studied analgesic effects observed in the examined animal groups are realized due to the involvement of the opioid and serotonergic cerebral systems. Neirofiziologiya/Neurophysiology, Vol. 39, No. 6, pp. 468–477, November–December, 2007.     

Expression, purification and characterization of full-length RNA-free hepatitis B core particles

The nucleocapsid or core particle of the hepatitis B virus has become one of the favourite recombinant vaccine carriers for foreign peptides, proteins and stimulatory oligonucleotides. The core protein consists of three regions: an N-terminal, a central and a C-terminal region that can accommodate the addition or insertion of the foreign sequences. The protamine-like C-terminal region that binds host RNA randomly during recombinant particle formation is often truncated. It is commonly thought that these truncations do not affect particle assembly. Recent studies have demonstrated that the C-terminal domains mediate a glycosaminoglycan-dependent attachment of nucleocapsids to the plasma membranes of host cells. This interaction might well contribute to the immunogenicity of nucleocapsids. Testing the hypothesis that full-length particles might be safer and superior for the induction of an immune response against the nucleocapsids and inserted sequences, requires the availability of purified particles. In this report, we detail a novel method for the synthesis and purification of full-length core particles essentially free of RNA from Escherichia coli.     

Autovaccination Confers Protection against Devriesea agamarum Associated Septicemia but Not Dermatitis in Bearded Dragons (Pogona vitticeps)

Devrieseasis caused by Devriesea agamarum is a highly prevalent disease in captive desert lizards, resulting in severe dermatitis and in some cases mass mortality. In this study, we assessed the contribution of autovaccination to devrieseasis control by evaluating the capacity of 5 different formalin-inactivated D. agamarum vaccines to induce a humoral immune response in bearded dragons (Pogona vitticeps). Each vaccine contained one of the following adjuvants: CpG, incomplete Freund''s, Ribi, aluminium hydroxide, or curdlan. Lizards were administrated one of the vaccines through subcutaneous injection and booster vaccination was given 3 weeks after primo-vaccination. An indirect ELISA was developed and used to monitor lizard serological responses. Localized adverse effects following subcutaneous immunization were observed in all but the Ribi adjuvanted vaccine group. Following homologous experimental challenge, the incomplete Freund''s as well as the Ribi vaccine were observed to confer protection in bearded dragons against the development of D. agamarum associated septicemia but not against dermatitis. Subsequently, two-dimensional gelelectrophoresis followed by immunoblotting and mass spectrometry was conducted with serum obtained from 3 lizards that showed seroconversion after immunisation with the Ribi vaccine. Fructose-bisphosphate aldolase and aldo-keto reductase of D. agamarum reacted with serum from the latter lizards. Based on the demonstrated seroconversion and partial protection against D. agamarum associated disease following the use of formalin-inactivated vaccines as well as the identification of target antigens in Ribi vaccinated bearded dragons, this study provides promising information towards the development of a vaccination strategy to control devrieseasis in captive lizard collections.     

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

ChIP-seq is a powerful method for obtaining genome-wide maps of protein-DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq quality control and protocol optimization. Our user-friendly graphical software quickly estimates the strength and quality of immunoprecipitations, identifies biases, compares the user's data with ENCODE's large collection of published datasets, performs multi-sample normalization, checks against quantitative PCR-validated control regions, and produces informative graphical reports. CHANCE is available at https://github.com/songlab/chance.