Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.     

Copper isotopes as possible neoplasia biomarkers in captive wild felids

The longevity of zoo animals is increasing due to continuous improvement in husbandry and veterinary medicine. However, increasing age is correlated to a higher prevalence of neoplasia. Despite tremendous improvement in diagnoses and monitoring capacities, cancers are still a challenge for veterinarians within the global zoo community. The recent use of copper isotopes as biomarkers for neoplasia in both human and veterinary medicine is a promising and cost‐effective diagnostic tool. Two hundred and twenty‐nine serum samples from 10 different species of wild felids under human care were processed through mass spectrometry to determine the ratio of heavy and light copper isotopes (⁶⁵Cu/⁶³Cu). The results of this preliminary study exhibit an important variability between felid species, with a ratio ranging between ?1.71 and 0.63. Additionally, copper isotopes seem to be a promising diagnostic tool in monitoring cancer in wild animals, as in human medicine, where the isotopic ratio decreases significantly with time in the presence of a tumor.     

Aerosolization of cationic lipid-DNA complexes: lipoplex characterization and optimization of aerosol delivery conditions

This study deals with the development of gene therapy in the treatment of lung diseases. It reports on the use of ultrasonic nebulization to administer plasmid-lipid complexes to the lungs of mice to transfect their epithelial cells. A plasmid complexed to cationic lipids was aerosolized using an ultrasonic nebulizer. We then characterized the lipoplex size and visualized the lipoplex by electron microscopy. Finally, we assessed the in vivo transgene expression in the lungs further to the aerosolization of different lipid-plasmid formulations. The nebulizer-generated particles were small and looked like a string composed of little and more or less cubic units. Transgene expression was detected in the lungs of mice further to a 20-min exposure to aerosol particles produced with the ultrasonic nebulizer. The results obtained with our optimized plasmid-lipid-NaCl formulation suggest that this route can be used to administer an appropriate gene to the airways for the treatment of respiratory disorders.     

Distinct patterns of insulin-like growth factor binding protein (IGFBP)-2 and IGFBP-3 expression in oxidant exposed lung epithelial cells

Oxygen (O(2)) species are involved in a large variety of pulmonary diseases. Among the various cell types that compose the lung, the epithelial cells of the alveolar structure appear to be a major target for oxidant injury. Despite their importance in the repair processes, the mechanisms which regulate the replication of the stem cells of the alveolar epithelium, the type 2 cells, remain poorly understood. Based on the results of several studies which have documented the involvement of the insulin-like growth factor (IGF) system in lung epithelial cell replication, and which have also suggested a role for IGF binding proteins (IGFBPs) in the control of cell proliferation, the aim of the present work was to determine whether IGFBPs could be involved in the modulation of growth of human lung epithelial cells exposed to oxidants. Experiments were performed using a human lung adenocarcinoma cell line (A549) which was exposed for various durations to hyperoxia (95% O(2)). We observed a rapid and reversible growth arrest of the cells after only 24 h of O(2) exposure. When oxidant injury was prolonged, growth arrest was followed by induction of apoptosis with activation of the Fas pathway. These effects were associated with an increased expression of IGFBP-2 and IGFBP-3. In addition, study of localization of these proteins revealed distinct patterns of distribution. IGFBP-3 was mainly present in the extracellular compartment. In comparison, the fraction of IGFBP-2 secreted was less abundant whereas the IGFBP-2 fraction in the intracellular compartment appeared stronger. In addition, analysis of the subcellular localization provided data indicating the presence of IGFBP-2 in the nucleus. Taken together these data support a role for IGFBP-2 and IGFBP-3 in the processes of growth arrest and apoptosis in lung epithelial cells upon oxidant exposure. They also suggest that distinct mechanisms may link IGFBP-2 and IGFBP-3 to the key regulators of the cell cycle.     

Proline betaine accumulation and metabolism in alfalfa plants under sodium chloride stress. Exploring its compartmentalization in nodules

The osmoprotectant Pro betaine is the main betaine identified in alfalfa (Medicago sativa). We have investigated the long-term responses of nodulated alfalfa plants to salt stress, with a particular interest for Pro betaine accumulation, compartmentalization, and metabolism. Exposure of 3-week-old nodulated alfalfa plants to 0.2 m NaCl for 4 weeks was followed by a 10-, 4-, and 8-fold increase in Pro betaine in shoots, roots, and nodules, respectively. Isotope-labeling studies in alfalfa shoots indicate that [14C]Pro betaine was synthesized from l-[14C]Pro. [14C]Pro betaine was efficiently catabolized through sequential demethylations via N-methylPro and Pro. Salt stress had a minor effect on Pro betaine biosynthesis, whereas it strongly reduced Pro betaine turnover. Analysis of Pro betaine and Pro compartmentalization within nodules revealed that 4 weeks of salinization of the host plants induced a strong increase in cytosol and bacteroids. The estimated Pro betaine and Pro concentrations in salt-stressed bacteroids reached 7.4 and 11.8 mm, respectively, compared to only 0.8 mm in control bacteroids. Na+ content in nodule compartments was also enhanced under salinization, leading to a concentration of 14.7 mm in bacteroids. [14C]Pro betaine and [14C]Pro were taken up by purified symbiosomes and free bacteroids. There was no indication of saturable carrier(s), and the rate of uptake was moderately enhanced by salinization. Ultrastructural analysis showed a large peribacteroid space in salt-stressed nodules, suggesting an increased turgor pressure inside the symbiosomes, which might partially be due to an elevated concentration in Pro, Pro betaine, and Na+ in this compartment.     

A full saturated linkage map of<Emphasis Type="Italic"> Picea abies</Emphasis> including AFLP,SSR, ESTP, 5S rDNA and morphological markers

Based on an F₁ progeny of 73 individuals, two parental maps were constructed according to the double pseudo-test cross strategy. The paternal map contained 16 linkage groups for a total genetic length of 1,792 cM. The maternal map covered 1,920 cM, and consisted of 12 linkage groups. These parental maps were then integrated using 66 intercross markers. The resulting consensus map covered 2,035 cM and included 755 markers (661 AFLPs, 74 SSRs, 18 ESTPs, the 5S rDNA and the early cone formation trait) on 12 linkage groups, reflecting the haploid number of chromosomes of Picea abies. The average spacing between two adjacent markers was 2.6 cM. The presence of 39 of the SSR and/or ESTP markers from this consensus map on other published maps of different Picea and Pinus species allowed us to establish partial linkage group homologies across three P. abies maps (up to five common markers per linkage group). This first saturated linkage map of P. abies could be therefore used as a support for developing comparative genome mapping in conifers.Communicated by O. Savolainen     

The synthesis and SAR of 2-arylsulfanyl-phenyl piperazinyl acetic acids as glyT-1 inhibitors

Elevation of glycine levels and activation of the NMDA receptor by inhibition of the glycine transporter 1 (GlyT-1) is a potential strategy for the treatment of schizophrenia. A novel series of GlyT-1 inhibitors have been identified containing the 2-arylsulfanyl-phenylpiperazine motif. The most prominent member of this series, (R)-4-[5-chloro-2-(4-methoxy-phenylsulfanyl)-phenyl]-2-methyl-piperazin-1-yl-acetic acid (31) is a potent glycine transporter-1 inhibitor (IC(50)=150 nM), which elevated glycine levels in rat ventral hippocampus as measured by microdialysis in vivo at doses of 1.2-4.6 mg/kg s.c.     

SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history

We present an extension of the program SIMCOAL, which allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias. AVAILABILITY: http://cmpg.unibe.ch/software/simcoal2/.     

A practical approach to assess the native status of a rare plant species: the controverse of Buxus sempervirens L. in northern France revisited

Whether a species is native or introduced in a given geographic area is of major interest within the framewok of biological conservation. A practical approach combining phytosociological, ecological, phytogeographical and historical data is proposed to explore this status for rare plant species, and applied to Boxtree in northern France. Buxus sempervirens L. is an evergreen sub-mediterranean species whose wild populations in northern France are very rare and threatened. Its status – native or introduced – has long been be controversial. Three types of Box-woodland were found in the study area: 1) a Taxus baccata – Buxus sempervirens community which is strongly linked to post-Renaissance castles, 2) a Fraxinus excelsior–Mercurialis perennis community which may be related both to steep chalk slopes where Box was expected to be native and to Medieval castles, 3) a Quercus pubescens–Buxus sempervirens community which may be considered as an immature anthropogenic woodland. In all cases Buxus sempervirens was observed close to archaeological sites and together with exotic and/or nitrophilous plant species. Consequently Box is probably originally an introduced species in northern France and should be considered as both an archaeophyte and a feudal plant. This method offers an interesting alternative to determine the indigenity status of a rare plant species in its localities that would provide sufficiently accurate criteria in most of the cases.