Hairpin elements, the first family of foldback transposons (FTs) in Arabidopsis thaliana

We report here on the identification in Arabidopsis thaliana of a new family of transposable elements named Hairpin. These elements are related to foldback transposons (FTs), a large and heterogeneous group of transposable elements first described in Drosophila and recently in Solanaceae. Hairpin elements are the first family of FTs reported in Arabidopsis thaliana and the first family of FTs of type 3 to be described in the plant kingdom. In contrast to previous FTs described, Hairpin appears to be a homogeneous family in size (238 +/- 7 bp) as well as in structure. Hairpin elements are dispersed in the Arabidopsis genome and Southern hybridization revealed that they are present in relatively low copy numbers. Finally, we discuss the potential usefulness of these elements in studying the phylogenetic relationship between Arabidopsis ecotypes.     

Tropical soils degraded by slash‐and‐burn cultivation can be recultivated when amended with ashes and compost

In many tropical regions, slash‐and‐burn agriculture is considered as a driver of deforestation; the forest is converted into agricultural land by cutting and burning the trees. However, the fields are abandoned after few years because of yield decrease and weed invasion. Consequently, new surfaces are regularly cleared from the primary forest. We propose a reclamation strategy for abandoned fields allowing and sustaining re‐cultivation. In the dry region of south‐western Madagascar, we tested, according to a split‐plot design, an alternative selective slash‐and‐burn cultivation technique coupled with compost amendment on 30–year‐old abandoned fields. Corn plants (Zea mays L.) were grown on four different types of soil amendments: no amendment (control), compost, ashes (as in traditional slash‐and‐burn cultivation), and compost + ashes additions. Furthermore, two tree cover treatments were applied: 0% tree cover (as in traditional slash‐and‐burn cultivation) and 50% tree cover (selective slash‐and‐burn). Both corn growth and soil fertility parameters were monitored during the growing season 2015 up to final harvest. The amendment compost + ashes strongly increased corn yield, which was multiplied by 4–5 in comparison with ashes or compost alone, reaching 1.5 t/ha compared to 0.25 and 0.35 t/ha for ashes and compost, respectively. On control plots, yield was negligible as expected on these degraded soils. Structural equation modeling evidenced that compost and ashes were complementary fertilizing pathways promoting soil fertility through positive effects on soil moisture, pH, organic matter, and microbial activity. Concerning the tree cover treatment, yield was reduced on shaded plots (50% tree cover) compared to sunny plots (0% tree cover) for all soil amendments, except ashes. To conclude, our results provide empirical evidence on the potential of recultivating tropical degraded soils with compost and ashes. This would help mitigating deforestation of the primary forest by increasing lifespan of agricultural lands.     

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.     

Agricultural sustainability: concepts, principles and evidence

Concerns about sustainability in agricultural systems centre on the need to develop technologies and practices that do not have adverse effects on environmental goods and services, are accessible to and effective for farmers, and lead to improvements in food productivity. Despite great progress in agricultural productivity in the past half-century, with crop and livestock productivity strongly driven by increased use of fertilizers, irrigation water, agricultural machinery, pesticides and land, it would be over-optimistic to assume that these relationships will remain linear in the future. New approaches are needed that will integrate biological and ecological processes into food production, minimize the use of those non-renewable inputs that cause harm to the environment or to the health of farmers and consumers, make productive use of the knowledge and skills of farmers, so substituting human capital for costly external inputs, and make productive use of people's collective capacities to work together to solve common agricultural and natural resource problems, such as for pest, watershed, irrigation, forest and credit management. These principles help to build important capital assets for agricultural systems: natural; social; human; physical; and financial capital. Improving natural capital is a central aim, and dividends can come from making the best use of the genotypes of crops and animals and the ecological conditions under which they are grown or raised. Agricultural sustainability suggests a focus on both genotype improvements through the full range of modern biological approaches and improved understanding of the benefits of ecological and agronomic management, manipulation and redesign. The ecological management of agroecosystems that addresses energy flows, nutrient cycling, population-regulating mechanisms and system resilience can lead to the redesign of agriculture at a landscape scale. Sustainable agriculture outcomes can be positive for food productivity, reduced pesticide use and carbon balances. Significant challenges, however, remain to develop national and international policies to support the wider emergence of more sustainable forms of agricultural production across both industrialized and developing countries.     

The Legionella pneumophila F‐box protein Lpp2082 (AnkB) modulates ubiquitination of the host protein parvin B and promotes intracellular replication

The environmental pathogen Legionella pneumophila encodes three proteins containing F‐box domains and additional protein–protein interaction domains, reminiscent of eukaryotic SCF ubiquitin–protein ligases. Here we show that the F‐box proteins of L. pneumophila strain Paris are Dot/Icm effectors involved in the accumulation of ubiquitinated proteins associated with the Legionella‐containing vacuole. Single, double and triple mutants of the F‐box protein encoding genes were impaired in infection of Acanthamoeba castellanii, THP‐1 macrophages and human lung epithelial cells. Lpp2082/AnkB was essential for infection of the lungs of A/J mice in vivo , and bound Skp1, the interaction partner of the SCF complex in mammalian cells, similar to AnkB from strain AA100/130b. Using a yeast two‐hybrid screen and co‐immunoprecipitation analysis we identified ParvB a protein present in focal adhesions and in lamellipodia, as a target. Immunofluorescence analysis confirmed that ectopically expressed Lpp2082/AnkB colocalized with ParvB at the periphery of lamellipodia. Unexpectedly, ubiquitination tests revealed that Lpp2082/AnkB diminishes endogenous ubiquitination of ParvB. Based on these results we propose that L. pneumophila modulates ubiquitination of ParvB by competing with eukaryotic E3 ligases for the specific protein–protein interaction site of ParvB, thereby revealing a new mechanism by which L. pneumophila may employ translocated effector proteins to promote bacterial survival.     

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBD_L), among individuals without pedigree, given information on surrounding markers and population history. These IBD_L probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD_L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.     

The hERG K(+) channel S4 domain L532P mutation: characterization at 37°C

hERG (human Ether-à-go-go Related Gene) is responsible for ion channels mediating rapid delayed rectifier potassium current, I(Kr), which is key to cardiac action potential repolarization. Gain-of-function hERG mutations give rise to the SQT1 variant of the Short QT Syndrome (SQTS). Reggae mutant zebrafish, with a S4 zERG mutation (Leucine499Proline; L499P), display arrhythmic features analogous to those seen in the SQTS. The affected S4 domain ERG residue is highly conserved. This study was executed to determine how the homologous hERG mutation (L532P) influences channel function at 37°C. Whole-cell measurements of current (I(hERG)) were made from HEK 293 cells expressing WT or L532P hERG. The half maximal activation voltage (V(0.5)) of L532P I(hERG) was positively shifted by ~+36mV compared to WT I(hERG); however at negative voltages a pronounced L532P I(hERG) was observed. Both activation and deactivation time-courses were accelerated for L532P I(hERG). The inactivation V(0.5) for L532P I(hERG) was shifted by ~+32mV. Under action potential (AP) voltage-clamp, L532P I(hERG) exhibited a dome-shaped current peaking at ~+16mV, compared to ~-31mV for WT-I(hERG). The L532P mutation produced an ~5-fold increase in the IC(50) for dronedarone inhibition of I(hERG). Homology modeling indicated that the L532 residue within the S4 helix lies closely apposed to the S5 region of an adjacent hERG subunit. Alterations to the S4 domain structure and, potentially, to interactions between adjacent hERG subunits are likely to account for the functional effects of this mutation.     

A chicory cytochrome P450 mono-oxygenase CYP71AV8 for the oxidation of (+)-valencene

Chicory (Cichorium intybus L.), which is known to have a variety of terpene-hydroxylating activities, was screened for a P450 mono-oxygenase to convert (+)-valencene to (+)-nootkatone. A novel P450 cDNA was identified in a chicory root EST library. Co-expression of the enzyme with a valencene synthase in yeast, led to formation of trans-nootkatol, cis-nootkatol and (+)-nootkatone. The novel enzyme was also found to catalyse a three step conversion of germacrene A to germacra-1(10),4,11(13)-trien-12-oic acid, indicating its involvement in chicory sesquiterpene lactone biosynthesis. Likewise, amorpha-4,11-diene was converted to artemisinic acid. Surprisingly, the chicory P450 has a different regio-specificity on (+)-valencene compared to germacrene A and amorpha-4,11-diene.     

The Rockefeller University Hospital (1910-2010): creating the science of medicine

The year 2010 marked the centennial of the Rockefeller University Hospital, one of the great philanthropic achievements of 20th-century science. For 100 years, the Hospital played a central role in the development and growth of medical science by enabling physician-scientists to make intensive study of human biology and disease. With ingenuity and devotion, they greatly enriched clinical medicine as well as basic biological science. This account emphasizes the founding and first half-century of the Hospital as it became a germinal center for clinical investigation. The second half of the century saw rapid change in medicine and health care with vexing problems, many yet unsolved. This history should serve as a call to arms for maintaining the linkage of science and medicine, supporting patient-oriented research as a basic discipline of medicine.