Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae)

As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.

Direct iminization of PEEK

Semi-crystalline poly(ether ketone)s are important high-temperature engineering thermoplastics, but are difficult to characterize at the molecular level because of their insolubility in conventional organic solvents. Here we report that polymers of this type, including PEEK, react cleanly at high temperatures with low-volatility aralkyl amines to afford stable, noncrystalline poly(ether-imine)s, which are readily soluble in solvents such as chloroform, THF and DMF and so characterizable by conventional size-exclusion chromatography.

Asymmetric oligopoly and foreign direct investment: implications for host-country tax-setting

We present a duopoly model with heterogeneous firms that vary in cost-efficiency, each of which can choose to serve a foreign market by either exporting or local production. We do so to analyse the effects of a host-country corporate profit tax on both the scale and composition of FDI, and find that: strategic interaction between oligopolistic firms provides for a pattern of FDI that favours cost-inefficiency to the detriment of host-country welfare; and the host-country tax rate can be optimally used to avoid such patterns of FDI and instead promote direct investment by a relatively cost-efficient firm.

Direct Computation of Stochastic Flow in Reservoirs with Uncertain Parameters

A direct method is presented for determining the uncertainty in reservoir pressure, flow, and net present value (NPV) using the time-dependent, one phase, two- or three-dimensional equations of flow through a porous medium. The uncertainty in the solution is modelled as a probability distribution function and is computed from given statistical data for input parameters such as permeability. The method generates an expansion for the mean of the pressure about a deterministic solution to the system equations using a perturbation to the mean of the input parameters. Hierarchical equations that define approximations to the mean solution at each point and to the field covariance of the pressure are developed and solved numerically. The procedure is then used to find the statistics of the flow and the risked value of the field, defined by the NPV, for a given development scenario. This method involves only one (albeit complicated) solution of the equations and contrasts with the more usual Monte-Carlo approach where many such solutions are required. The procedure is applied easily to other physical systems modelled by linear or nonlinear partial differential equations with uncertain data.

Lighting energy saving due to the use of direct sunlight

This paper describe a simulation program, which uses Trengenza’s average room illuminance method in conjunction with hourly solar irradiance and luminous efficacy, to predict the potential lighting energy saving for a side-lit room. Two lighting control algorithms of photoelectric switching (on/off) and photoelectric dimming (top-up) have been coded in the program. A simulation for a typical UK office room has been conducted and the results show that energy saving due to the sunlight dependent on the various factors such as orientation, control methods, building depth, glazing area and shading types, etc. This simple tool can be used for estimating the potential lighting energy saving of the windows with various shading devices at the early design stage.

New direct payments scheme: targeting and redistribution in the future CAP

The Commission has proposed that a revised version of the present regime of direct payments should be rolled forward into the post-2013 CAP. There would be a limited redistribution of funds between Member States. Thirty per cent of the budget would be allocated to a new greening component, which would be problematic in the WTO. Non-active farmers would not qualify for aid; and payments would be capped. Special schemes would be introduced for small farmers, for young new entrants, and for disadvantaged regions.

The CtsR regulator of Listeria monocytogenes contains a variant glycine repeat region that affects piezotolerance, stress resistance, motility and virulence

A spontaneous high hydrostatic pressure (HHP)-tolerant mutant of Listeria monocytogenes ScottA, named AK01, was isolated previously. This mutant was immotile and showed increased resistance to heat, acid and H2O2 compared with the wild type (wt) (Karatzas, K.A.G. and Bennik, M.H.J. 2002 Appl Environ Microbiol 68: 3183–3189). In this study, we conclusively linked the increased HHP and stress tolerance of strain AK01 to a single codon deletion in ctsR (class three stress gene repressor) in a region encoding a highly conserved glycine repeat. CtsR negatively regulates the expression of the clp genes, including clpP, clpE and the clpC operon (encompassing ctsR itself), which belong to the class III heat shock genes. Allelic replacement of the ctsR gene in the wt background with the mutant ctsR gene, designated ctsRΔGly, rendered mutants with phenotypes and protein expression profiles identical to those of strain AK01. The expression levels of CtsR, ClpC and ClpP proteins were significantly higher in ctsRΔGly mutants than in the wt strain, indicative of the CtsRΔGly protein being inactive. Further evidence that the CtsRΔGly protein lacks its repressor function came from the finding that the Clp proteins in the mutant were not further induced upon heat shock, and that HHP tolerance of a ctsR deletion strain was as high as that of a ctsRΔGly mutant. The high HHP tolerance possibly results from the increased expression of the clp genes in the absence of (active) CtsR repressor. Importantly, the strains expressing CtsRΔGly show significantly attenuated virulence compared with the wt strain; however, no indication of disregulation of PrfA in the mutant strains was found. Our data highlight an important regulatory role of the glycine-rich region of CtsR in stress resistance and virulence.

Analysis of Direct Outdoor Air Cooling Efficency for Combined Variable Air Volume Air-conditioning System in Stores in Cold Climates of China

Direct outdoor air cooling contributes a lot not only to the improvement of the indoor air quality but also to the energy saving. Its full use will reduce the water chiller’s running time especially in some stores where cooling load keeps much higher and longer than that in other buildings. A novel air-conditioning system named Combined Variable Air Volume system (CVAV), combining a normal AHU with a separate outdoor air supply system, was proposed firstly by the authors. The most attractive feature of the system is its full utilization of cooling capacity and freshness of outdoor air in the transition period of the year round. On the basis of the obtain of the dynamic cooling loads of the typical shopping malls in different four cities located in cold climates in China with the aid of DOE-2, the possibility of increasing the amount of outdoor air volume of CVAV system in the transition period instead of operating the water chillers was confirmed. Moreover, a new concept, Direct Outdoor Air Cooling Efficiency (DOACE), was defined as the ratio of cooling capacity of outdoor air to the water chiller, indicating the degree of outdoor air’s utilization. And the DOACE of the CVAV was calculated and compared with that of conventional all-air constant volume air-conditioning systems, the results showed that CVAV bear much more energy saving potential with the 10%~19% higher DOACE and it is a kind of energy efficient systems and can improve the indoor air quality as well.

Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of Parkinson's disease (PD). LRRK2 contains a Ras of complex proteins (ROC) domain that may act as a GTPase to regulate its protein kinase activity. The structure of ROC and the mechanism(s) by which it regulates kinase activity are not known. Here, we report the crystal structure of the LRRK2 ROC domain in complex with GDP-Mg2+ at 2.0-Å resolution. The structure displays a dimeric fold generated by extensive domain-swapping, resulting in a pair of active sites constructed with essential functional groups contributed from both monomers. Two PD-associated pathogenic residues, R1441 and I1371, are located at the interface of two monomers and provide exquisite interactions to stabilize the ROC dimer. The structure demonstrates that loss of stabilizing forces in the ROC dimer is likely related to decreased GTPase activity resulting from mutations at these sites. Our data suggest that the ROC domain may regulate LRRK2 kinase activity as a dimer, possibly via the C-terminal of ROC (COR) domain as a molecular hinge. The structure of the LRRK2 ROC domain also represents a signature from a previously undescribed class of GTPases from complex proteins and results may provide a unique molecular target for therapeutics in PD.

Updated estimate of aerosol direct radiative forcing from satellite observations and comparison against the Hadley Centre climate model

The fourth assessment report of the Intergovernmental Panel on Climate Change (IPCC) includes a comparison of observation-based and modeling-based estimates of the aerosol direct radiative forcing. In this comparison, satellite-based studies suggest a more negative aerosol direct radiative forcing than modeling studies. A previous satellite-based study, part of the IPCC comparison, uses aerosol optical depths and accumulation-mode fractions retrieved by the Moderate Resolution Imaging Spectroradiometer (MODIS) at collection 4. The latest version of MODIS products, named collection 5, improves aerosol retrievals. Using these products, the direct forcing in the shortwave spectrum defined with respect to present-day natural aerosols is now estimated at −1.30 and −0.65 Wm−2 on a global clear-sky and all-sky average, respectively, for 2002. These values are still significantly more negative than the numbers reported by modeling studies. By accounting for differences between present-day natural and preindustrial aerosol concentrations, sampling biases, and investigating the impact of differences in the zonal distribution of anthropogenic aerosols, good agreement is reached between the direct forcing derived from MODIS and the Hadley Centre climate model HadGEM2-A over clear-sky oceans. Results also suggest that satellite estimates of anthropogenic aerosol optical depth over land should be coupled with a robust validation strategy in order to refine the observation-based estimate of aerosol direct radiative forcing. In addition, the complex problem of deriving the aerosol direct radiative forcing when aerosols are located above cloud still needs to be addressed.

Acetone enhances the direct analysis of procyanidin- and prodelphinidin-based condensed tannins in lotus species by the butanol-HCl-iron assay

The butanol-HCl spectrophotometric assay is widely used for quantifying extractable and insoluble condensed tannins (CT, syn. proanthocyanidins) in foods, feeds, and foliage of herbaceous and woody plants, but the method underestimates total CT content when applied directly to plant material. To improve CT quantitation, we tested various cosolvents with butanol-HCl and found that acetone increased anthocyanidin yields from two forage Lotus species having contrasting procyanidin and prodelphinidin compositions. A butanol-HCl-iron assay run with 50% (v/v) acetone gave linear responses with Lotus CT standards and increased estimates of total CT in Lotus herbage and leaves by up to 3.2-fold over the conventional method run without acetone. The use of thiolysis to determine the purity of CT standards further improved quantitation. Gel-state 13C and 1H–13C HSQC NMR spectra of insoluble residues collected after butanol-HCl assays revealed that acetone increased anthocyanidin yields by facilitating complete solubilization of CT from tissue.