On the relevance of TCR rearrangement circles as molecular markers for thymic output during experimental graft-versus-host disease

Efficient reconstitution of the pool of peripheral T cells after hemopoietic stem cell transplantation (HSCT) is dependent on normal thymic function. However, the development of graft-vs-host disease (GVHD) in the context of allogeneic HSCT is associated with injurious effects on thymocyte development. In this study, we examined in models of syngeneic and allogeneic murine HSCT whether actual posttransplant thymic output is accurately reflected by analysis of signal-joint TCR rearrangement excision circles (sjTRECs). Our data demonstrate that the de novo generation of T cells following syngeneic HSCT of T cell-deficient B6.RAG2(-/-) (recombination-activating gene 2(-/-)) mice correlates firmly with an increase of sjTRECs in the thymus and spleen. However, the altered homeostasis of naive peripheral T cells in the presence of GVHD necessitates the combined analysis of cell division in vivo and determinations of sjTREC contents and total sjTREC numbers to draw informative conclusions. From our data, we substantiate that thymic output and peripheral division of newly generated T cells are diminished in the presence of acute GVHD in an experimental radiation/allogeneic HSCT model.     

Biological control of weeds: an analysis of introductions,rates of establishment and estimates of success,worldwide

The foremost document that comprehensively reports on biological control introductions against weeds—‘Biological control of weeds: a world catalogue of agents and their target weeds’—has been updated and now includes all deliberate releases made through 2012. It includes data on 1555 intentional releases of 468 biological control agent species used against 175 species of target weeds in 48 plant families, in 90 countries. For 55 (31.4%) of the target weed species, only one biocontrol agent was introduced. The largest number of agent species (44) was introduced for the biological control of Lantana camara (Verbenaceae). Three insect orders (Coleoptera, Lepidoptera and Diptera) comprised about 80% of all biocontrol agent species released and releases made. Of the 468 biocontrol agent species introduced, 332 (70.9%) established in at least one instance. Of the 313 species, for which impact could be categorized, 172 (55.0%) caused medium, variable or heavy levels of damage (impacts). Of all releases made through 2012, 982 (63.2%) led to establishment. Forty-two releases were judged too early post-release to categorize impact, leaving 940 releases for which impact analyses were conducted. Similar to agent species, approximately half of the established releases (503 or 53.5%) caused medium, variable or heavy levels of damage on the target weeds, and almost a quarter of releases (225 or 23.9%) caused heavy impact. Across all countries and regions, 65.7% of the weeds targeted for biological control experienced some level of control. These data indicate the value of this practice, on its own, or as a supplement to other methods, in the management of invasive plants.     

miRTrace reveals the organismal origins of microRNA sequencing data

We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately (>?99%) assigns real and simulated data to 14 important animal and plant groups, sensitively detects parasitic infection in mammals, and discovers the primate origin of single cells. Applying our algorithm to over 700 public datasets, we find evidence that over 7% are cross-contaminated and present a novel solution to clean these computationally, even after sequencing has occurred. miRTrace is freely available at https://github.com/friedlanderlab/mirtrace.     

In the presence of subunit A inhibitors DNA gyrase cleaves DNA fragments as short as 20 bp at specific sites.

A key step in the supercoiling reaction is the DNA gyrase-mediated cleavage and religation step of double-stranded DNA. Footprinting studies suggest that the DNA gyrase binding site is 100-150 bp long and that the DNA is wrapped around the enzyme with the cleavage site located near the center of the fragment. Subunit A inhibitors interrupt this cleavage and resealing cycle and result in cleavage occurring at preferred sites. We have been able to show that even a 30 bp DNA fragment containing a 20 bp preferred cleavage sequence from the pBR322 plasmid was a substrate for the DNA gyrase-mediated cleavage reaction in the presence of inhibitors. This DNA fragment was cleaved, although with reduced efficiency, at the same sites as a 122 bp DNA fragment. A 20 bp DNA fragment was cleaved with low efficiency at one of these sites and a 10 bp DNA fragment was no longer a substrate. We therefore propose that subunit A inhibitors interact with DNA at inhibitor-specific positions, thus determining cleavage sites by forming ternary complexes between DNA, inhibitors and DNA gyrase.     

Molecular Fingerprinting of the Fecal Microbiota of Children Raised According to Different Lifestyles

In this population-based study, 90 children from three European countries were examined to determine the impact of lifestyle on the fecal microbiota. The study was designed to assess the impact of two extreme lifestyles that we hypothesized could impact the microbial composition in the gut: i.e., an anthroposophic lifestyle (restricted use of antibiotics, greater consumption of fermented vegetables, etc.) versus living on a farm (greater consumption of farm milk, contact with animals, etc.). In previous studies, these lifestyles correlated with lower prevalence of allergies. Terminal restriction fragment length polymorphism (T-RFLP) was used to assess the bacterial composition in fecal samples since recent studies have shown that the majority of this community cannot be cultivated. The T-RFLP data were used to calculate richness and evenness of the fecal microbiota. Children that were attending Steiner schools (anthroposophic children) had a significantly higher diversity of microbes in their feces than farm children, who in turn also had lower diversity than the control groups. Specific primers were also used to focus on the Lactobacillus-like community (lactic acid bacteria [LAB]). Large differences were found in the LAB subpopulations in the sampled groups. In some children, the LAB subpopulation was dominated by a species that has not yet been cultivated.     

Zur Mechanik der Markballenbildung bei der Wallerschen Degeneration

Summary Wallerian degeneration was studied in frog single fibers. A new preparation for microscopic observation of peripheral motor fibers in living Rana esculenta was used. The authors studied proximally transected groups of fibers using the polarization technique.The results confirmed that the axon destruction preceds the breakdown of the myelin sheath, and the Schmidt-Lanterman incisures play an important role in the formation of ovoids. Details of the ovoid formation are demonstrated in serial photographs. It is suggested that the incisures of Schmidt-Lanterman are pathways for electrolyte and water transport in Wallerian degeneration.