Improved serial analysis of V1 ribosomal sequence tags (SARST-V1) provides a rapid, comprehensive, sequence-based characterization of bacterial diversity and community composition

Serial analysis of ribosomal sequence tags (SARST) is a recently developed technology that can generate large 16S rRNA gene (rrs) sequence data sets from microbiomes, but there are numerous enzymatic and purification steps required to construct the ribosomal sequence tag (RST) clone libraries. We report here an improved SARST method, which still targets the V1 hypervariable region of rrs genes, but reduces the number of enzymes, oligonucleotides, reagents, and technical steps needed to produce the RST clone libraries. The new method, hereafter referred to as SARST-V1, was used to examine the eubacterial diversity present in community DNA recovered from the microbiome resident in the ovine rumen. The 190 sequenced clones contained 1055 RSTs and no less than 236 unique phylotypes (based on > or = 95% sequence identity) that were assigned to eight different eubacterial phyla. Rarefaction and monomolecular curve analyses predicted that the complete RST clone library contains 99% of the 353 unique phylotypes predicted to exist in this microbiome. When compared with ribosomal intergenic spacer analysis (RISA) of the same community DNA sample, as well as a compilation of nine previously published conventional rrs clone libraries prepared from the same type of samples, the RST clone library provided a more comprehensive characterization of the eubacterial diversity present in rumen microbiomes. As such, SARST-V1 should be a useful tool applicable to comprehensive examination of diversity and composition in microbiomes and offers an affordable, sequence-based method for diversity analysis.     

The stringent response mediator Rsh is required for Brucella melitensis and Brucella suis virulence, and for expression of the type IV secretion system virB

Physiological adaptation of intracellular bacteria is critical for timely interaction with eukaryotic host cells. One mechanism of adaptation, the stringent response, is induced by nutrient stress via its effector molecule (p)ppGpp, synthesized by the action of RelA/SpoT homologues. The intracellular pathogen Brucella spp., causative agent of brucellosis, possesses a gene homologous to relA/spoT, named rsh, encoding a (p)ppGpp synthetase as confirmed by heterologous complementation of a relA mutant of Sinorhizobium meliloti. The Rsh deletion mutants in Brucella suis and Brucella melitensis were characterized by altered morphology, and by reduced survival under starvation conditions and in cellular and murine models of infection. Most interestingly, we evidenced that expression of virB, encoding the type IV secretion system, a major virulence factor of Brucella, was Rsh-dependent. All mutant phenotypes, including lack of VirB proteins, were complemented with the rsh gene of Brucella. In addition, RelA of S. meliloti functionally replaced Brucella Rsh, describing the capacity of a gene from a plant symbiont to restore virulence in a mammalian pathogen. We therefore concluded that in the intramacrophagic environment encountered by Brucella, Rsh might participate in the adaptation of the pathogen to low-nutrient environments, and indirectly in the VirB-mediated formation of the final replicative niche.     

Reversible inactivation of the transcriptional function of P53 protein by farnesylation

Background  

The use of integrating viral vectors in Gene therapy clinical trials has pointed out the problem of the deleterous effect of the integration of the ectopic gene to the cellular genome and the safety of this strategy. We proposed here a way to induce the death of gene modified cells upon request by acting on a pro-apoptotic protein cellular localization and on the activation of its apoptotic function.     

Development of a new bicistronic retroviral vector with strong IRES activity

Background  

Internal Ribosome Entry Site (IRES)-based bicistronic vectors are important tools in today's cell biology. Among applications, the expression of two proteins under the control of a unique promoter permits the monitoring of expression of a protein whose biological function is being investigated through the observation of an easily detectable tracer, such as Green Fluorescent Protein (GFP). However, analysis of published results making use of bicistronic vectors indicates that the efficiency of the IRES-controlled expression can vary widely from one vector to another, despite their apparent identical IRES sequences. We investigated the molecular basis for these discrepancies.     

Recovery of hand function through mental practice: A study protocol

Background  

The study aims to assess the therapeutic benefits of motor imagery training in stroke patients with persistent motor weakness. There is evidence to suggest that mental rehearsal of movement can produce effects normally attributed to practising the actual movements. Imagining hand movements could stimulate the redistribution of brain activity, which accompanies recovery of hand function, thus resulting in a reduced motor deficit.     

Functional integration of adult-born neurons

Over the past decade, it has become clear that neural stem cells in the adult mammalian brain continuously generate new neurons, predominantly in the hippocampus and olfactory bulb. However, the central issue of whether these new neurons participate in functional synaptic circuitry has yet to be resolved. Here, we use virus-based transsynaptic neuronal tracing and c-Fos mapping of odor-induced neuronal activity to demonstrate that neurons generated in the adult functionally integrate into the synaptic circuitry of the brain.     

Effect of inhibition of phenylpropanoid biosynthesison peroxidase and IAA-oxidase activities and auxin contentin alfalfa suspension cultures

The inhibition of phenylpropanoid biosynthesis by 2-aminoindan-2-phosphonic acid (AIP) in alfalfa suspension cultures (Medicago sativa L.) was associated with a marked decline in the content of cinnamic acid derivatives during the whole subculture interval. The levels of all investigated forms of phenolic acids in AIP-treated cells were lower than those of control with the exception of free phenolic acids on days 1 and 2. The dynamics of free IAA content in AIP-treated cells was similar to that of the control but its peak was significantly lower. The auxin content in AIP-treated cells on days 9 and 11 represented only 35 and 40 % of control values, respectively. AIP-treatment stimulated soluble peroxidase (EC 1.11.1.7) activity in the first 2 d after cell inoculation. Time-course of soluble IAA-oxidase activities was similar to that of soluble peroxidases (with the exception of the drop in peroxidase activity on day 3) but beginning day 6, the enzyme activities in AIP-treated cells were significantly lower until the end of the subculture interval.     

Relationships between bone mass and micro-architecture at the mandible and iliac bone in edentulous subjects: a dual X-ray absorptiometry, computerised tomography and microcomputed tomography study

doi: 10.1111/j.1741‐2358.2011.00527.x Relationships between bone mass and micro‐architecture at the mandible and iliac bone in edentulous subjects: a dual X‐ray absorptiometry, computerised tomography and microcomputed tomography study Objectives: To compare bone volume, bone mineral density, cortical thickness and bone micro‐architecture in a series of paired mandibular and iliac bone samples analysed by various imagery techniques to see whether relationships exist between the various techniques and between mandibular and iliac bone. Materials and methods: Bone samples from the mandible and ilium were harvested in 20 cadavers and analysed by dual energy X‐ray absorptiometry (DXA), computerised tomography (CT) on a conventional hospital machine and microCT. Results: Significant correlations were found between Hounsfield density obtained by CT, and bone mass determined by microCT but not with DXA values. Cortical thickness measurements were well correlated between CT and microCT. No relationships were found between mandibular and iliac bone, when considering mineral density, cortical thickness, bone volume or micro‐architecture. Conclusion: In clinical practice, CT remains the most appropriate routine means for bone qualitative and quantitative evaluation at the mandible. In this ex vivo study, these results confirm that mandibular bone status does not reflect the axial skeletal one and assist in the placement of implants with dental prostheses in old or osteoporotic patients.     

Epidemiological studies based on medical and administrative databases : a potential strength in France

Population-based epidemiological cohorts may include nowadays hundreds of thousands of subjects, followed-up during decades. France has a major potential strength: nationwide medical and social databases set up for administrative purposes. The main databases useful for epidemiology are the social security database which contains individual medical data from different sources, and the retirement fund database on employment and social benefits. These databases have several advantages: they cover the whole French population, with no lost to follow-up, data are often of good quality and it is possible to link them with individual surveys. However medical data are not always ascertained and an important methodological and practical work has to be done, and some legal and practical problems have to be solved for an optimal use.