Imprints of glacial refugia in the modern genetic diversity of Pinus sylvestris

Aim To understand the impact of glacial refugia and migration pathways on the modern genetic diversity of Pinus sylvestris. Location The study was carried out throughout Europe. Methods An extended set of data of pollen and macrofossil remains was used to locate the glacial refugia and reconstruct the migrating routes of P. sylvestris throughout Europe. A vegetation model was used to simulate the extent of the potential refugia during the last glacial period. At the same time a genetic survey was carried out on this species. Results The simulated distribution of P. sylvestris during the last glacial period is coherent with the observed fossil data, which showed a patchy distribution of the refugia between c. 40° N and 50° N. Several migrational fronts were detected within the Iberian and the Italian peninsulas, and outside the Hungarian plain and around the Alps. The modern mitochondrial DNA depicted three different haplotypes for P. sylvestris. Two distinct haplotypes were restricted to northern Spain and Italy, and the third haplotype dominated most of the present‐day remaining distribution range of P. sylvestris in Europe. Main conclusions During the last glacial period P. sylvestris was constrained under severe climatic conditions to survive in scattered and restricted refugial areas. Combining palaeoenvironmental data, vegetation modelling and the genetic data, we have shown that the long‐term isolation in the glacial refugia and the migrational process during the Holocene have played a major role in shaping the modern genetic diversity of P. sylvestris in Europe.     

Computer programs for population genetics data analysis: a survival guide

The analysis of genetic diversity within species is vital for understanding evolutionary processes at the population level and at the genomic level. A large quantity of data can now be produced at an unprecedented rate, requiring the use of dedicated computer programs to extract all embedded information. Several statistical packages have been recently developed, which offer a panel of standard and more sophisticated analyses. We describe here the functionalities, special features and assumptions of more than 20 such programs, indicate how they can interoperate, and discuss new directions that could lead to improved software and analyses.     

Modulation of 5' splice site selection using tailed oligonucleotides carrying splicing signals

Background  

We previously described the use of tailed oligonucleotides as a means of reprogramming alternative pre-mRNA splicing in vitro and in vivo. The tailed oligonucleotides that were used interfere with splicing because they contain a portion complementary to sequences immediately upstream of the target 5' splice site combined with a non-hybridizing 5' tail carrying binding sites for the hnRNP A1/A2 proteins.     

Leaching of contaminated leaves following uptake and phytoremediation of RDX, HMX, and TNT by poplar

The uptake and fate of 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) by hybrid poplars in hydroponic systems were compared and exposed leaves were leached with water to simulate potential exposure pathways from groundwater in the field. TNT was removed from solution more quickly than nitramine explosives. Most of radioactivity remained in root tissues for 14C-TNT, but in leaves for 14C-RDX and 14C-HMX. Radiolabel recovery for TNT and HMX was over 94%, but that of RDX decreased over time, suggesting a loss of volatile products. A considerable fraction (45.5%) of radioactivity taken up by whole plants exposed to 14C-HMX was released into deionized water, mostly as parent compound after 5 d of leaching. About a quarter (24.0%) and 1.2% were leached for RDX and TNT, respectively, mostly as transformed products. Leached radioactivity from roots was insignificant in all cases (< 2%). This is the first report in which small amounts of transformation products of RDX leach from dried leaves following uptake by poplars. Such behavior for HMX was reported earlier and is reconfirmed here. All three compounds differ substantially in their fate and transport during the leaching process.     

The interplay between environmental and host factors during an outbreak of visceral leishmaniasis in eastern Sudan

Parasitic diseases, including human visceral leishmaniasis, are multifactorial. Factors that are expected to play an important role in the parasite-human interaction are exposure, parasite "virulence" and host resistance factors. In populations exposed to Leishmania donovani most subjects do not allow the parasites to establish themselves or remain asymptomatic. Some individuals, however, fail to control parasite expansion and dissemination and develop a visceral disease. We report here the results of a longitudinal survey whose aims were to identify risk factors underlying visceral leishmaniasis (VL) susceptibility during an outbreak that occurred in a Sudanese village between 1995 and 1999. Most of the 660 subjects (90%) living in the central district were exposed to Leishmania and 20.9% (n = 138), mostly teenagers, developed VL. VL cases increased markedly in adults late in the outbreak, suggesting some changes in adult resistance status or in Leishmania "virulence" during the epidemic. Age and ethnic origin of the patients were the most important critical risk factors to account for the distribution of the VL cases that were recorded during the whole epidemic. This and the high frequency of VL in certain families suggest that host genetic factors played an important role in shaping the outbreak in this village. However, environmental factors (the presence of cows and neems in the households) that increase/decrease exposure to the parasite had significant effects on the distribution of VL cases in the village in the first phase of the outbreak.     

Identification, gene cloning and expression of serine proteases in the extracellular medium of Nicotiana tabacum cells

Recombinant proteins secreted from plant suspension cells into the medium are susceptible to degradation by host proteases secreted during growth. Some degradation phenomena are inhibited in the presence of various protease inhibitors, such as EDTA or AEBSF/PMSF, suggesting the presence of different classes of proteases in the medium. Here, we report the results of a proteomic analysis of the extracellular medium of a Nicotiana tabacum bright yellow 2 culture. Several serine proteases belonging to a Solanaceae-specific subtilase subfamily were identified and the genes for four cloned. Their expression at the RNA level during culture growth varied depending on the gene. An in-gel protease assay (zymography) demonstrated serine protease activity in the extracellular medium from cultures. This was confirmed by testing the degradation of an antibody added to the culture medium. This particular subtilase subfamily, therefore, represents an interesting target for gene silencing to improve recombinant protein production. Key message The extracellular medium of Nicotiana tabacum suspension cells contains serine proteases that degrade antibodies.     

Consequences of range contractions and range shifts on molecular diversity

Due to past and current climatic changes, range contractions and range shifts are essential stages in the history of a species. However, unlike range expansions, the molecular consequences of these processes have been little investigated. In order to fill this gap, we simulated patterns of molecular diversity within and between populations for various types of range contractions and range shifts. We show that range contractions tend to decrease genetic diversity as compared with population with stable ranges but quite counterintuitively fast range contractions preserve higher levels of diversity and induce lower levels of genetic differentiation among refuge areas than slow contractions. Contrastingly, fast range shifts lead to lower levels of diversity than slow range shifts. At odds with our expectations, we find that species actively migrating toward refuge areas can only preserve higher levels of diversity in refugia if the contraction is rapid. Under slow range contraction or slow range shift, active migration toward refugia lead to a larger loss of diversity as compared with scenarios with isotropic migration and may thus not be a good evolutionary strategy. These results suggest that the levels of diversity preserved after a climate change both within and between refuge areas will not only depend on the dispersal abilities of a species but also on the speed of the change. It also implies that a given episode of climatic change will impact differently species with different generation times.     

Toll-like receptor 8: the awkward TLR

Toll-like receptors (TLR) sense a variety of microbial products and play an important role in the mounting of innate and adaptive immune responses. TLR1 to TLR9 are common in mice and humans and recognize similar ligands in both species, with the exception of TLR8. Human TLR7 and TLR8 and mouse TLR7 detect viral single-stranded RNA and imidazoquinoline compounds, while mouse TLR8 not. Based on this discrepancy, for long time it was believed that mouse TLR8 is not functional and as a consequence the contribution of TLR8 to innate immunity remained poorly understood. Our recent studies revealed an important role for TLR8 in the regulation of TLR7-mediated autoimmunity in the mouse. This review illustrates our current understanding regarding the function of TLR8 and its potential for future clinical use for the treatment and/or prevention of various pathological conditions.     

Context-related vocalizations in African grey parrots (Psittacus erithacus)

A few animal species are capable of vocal learning. Parrots are well known for their vocal imitation abilities. In this study, we investigated whether African grey parrots (Psittacus erithacus) emit specific vocalizations in specific contexts. We first described the vocal repertoire and its ontogenesis of four captive grey parrots. After a comparison with vocalizations emitted by wild and other captive African grey parrots, we observed that only three call categories were shared by all grey parrots populations, suggesting that isolated populations of parrots develop population-specific calls. Then, we artificially provoked ten different contexts and recorded vocalizations of four captive grey parrots in these situations. Parrots predominantly emitted call categories in some contexts: distress, protestation, alarm, asking (i.e. emitted when a bird wanted something from an experimenter) and contact calls. These results suggest that some calls are learned and can be used in specific contexts.