Crossing forest thresholds: inertia and collapse in a Holocene sequence from south-central Spain

A Holocene palaeoecological sequence from Villaverde, south-central Spain, is presented. The pollen stratigraphy is used to infer past vegetation changes within a catchment area that represents the boundary between semi-arid, plateau and mountain vegetation. From c. 9700–7530 cal. yr BP, Pinus is dominant, probably as a result of a combination of a relatively dry climate and natural fire disturbance. From c. 7530–5900 cal. yr BP, moderate invasion by Quercus appears to be a migrational response following increased moisture and temperature, but in part shaped by competitive adjustments. From c. 5900–5000 cal. yr BP, the pine forests are replaced by deciduous-Quercus forests with an important contribution from Corylus, Betula, Fraxinus and Alnus. Mediterranean-type forests spread from c. 5000 to 1920 cal. yr BP coincident with expansions of Artemisia, Juniperus and other xerophytes. From c. 1920–1160 cal. yr BP, Pinus becomes dominant after a disturbance- mediated invasion of the oak forests. Human impact upon the regional landscape was negligible during the Neolithic, and limited in the Bronze and Iron Ages. Local deforestation and the expansion of agro-pastoral activities occur after c. 1600 cal. yr BP.

Pilgrimstad revisited - a multi-proxy reconstruction of Early/Middle Weichselian climate and environment at a key site in central Sweden

The site Pilgrimstad in central Sweden has often been cited as a key locality for discussions of ice-free/ice-covered intervals during the Early and Middle Weichselian. Multi-proxy investigations of a recently excavated section at Pilgrimstad now provide a revised picture of the climatic and environmental development between similar to 80 and 36 ka ago. The combination of sedimentology, geochemistry, OSL and 14C dating, and macrofossil, siliceous microfossil and chironomid analyses shows: (i) a lower succession of glaciofluvial/fluvial, lacustrine and glaciolacustrine sediments; (ii) an upper lacustrine sediment sequence; and (iii) Last Glacial Maximum till cover. Microfossils in the upper lacustrine sediments are initially characteristic for oligo- to mesotrophic lakes, and macrofossils indicate arctic/sub-arctic environments and mean July temperatures > 8 degrees C. These conditions were, however, followed by a return to a low-nutrient lake and a cold and dry climate. The sequence contains several hiatuses, as shown by the often sharp contacts between individual units, which suggests that ice-free intervals alternated with possible ice advances during certain parts of the Early and Middle Weichselian.

Isolation and characterization of a novel simazine-degrading bacterium from agricultural soil of central Chile, Pseudomonas sp MHP41

s-Triazine herbicides are used extensively in South America in agriculture and forestry. In this study, a bacterium designated as strain MHP41, capable of degrading simazine and atrazine, was isolated from agricultural soil in the Quillota valley, central Chile. Strain MHP41 is able to grow in minimal medium, using simazine as the sole nitrogen source. In this medium, the bacterium exhibited a growth rate of mu = 0.10 h(-1), yielding a high biomass of 4.2 x 10(8) CFU mL(-1). Resting cells of strain MHP41 degrade more than 80% of simazine within 60 min. The atzA, atzB, atzC, atzD, atzE and atzF genes encoding the enzymes of the simazine upper and lower pathways were detected in strain MHP41. The motile Gram-negative bacterium was identified as a Pseudomonas sp., based on the Biolog microplate system and comparative sequence analyses of the 16S rRNA gene. Amplified ribosomal DNA restriction analysis allowed the differentiation of strain MHP41 from Pseudomonas sp. ADP. The comparative 16S rRNA gene sequence analyses suggested that strain MHP41 is closely related to Pseudomonas nitroreducens and Pseudomonas multiresinovorans. This is the first s-triazine-degrading bacterium isolated in South America. Strain MHP41 is a potential biocatalyst for the remediation of s-triazine-contaminated environments.

Diagenetic Alterations and Reservoir Quality Evolution of Lower Cretaceous Fluvial Sandstones: Nubian Formation, Sirt Basin, North-Central Libya

Lower Cretaceous meandering and braided fluvial sandstones of the Nubian Formation form some of the most important subsurface reservoir rocks in the Sirt Basin, north-central Libya. Mineralogical, petrographical and geochemical analyses of sandstone samples from well BB6-59, Sarir oilfield, indicate that the meandering fluvial sandstones are fine- to very fine-grained subarkosic arenites (av. Q91F5L4), and that braided fluvial sandstones are medium- to very coarse-grained quartz arenites (av. Q96F3L1). The reservoir qualities of these sandstones were modified during both eodiagenesis (ca. <70oC; <2 km) and mesodiagenesis (ca. >70oC; >2km). Reservoir quality evolution was controlled primarily by the dissolution and kaolinitization of feldspars, micas and mud intraclasts during eodiagenesis, and by the amount and thicknessof grain-coating clays, chemical compaction and quartz overgrowths during mesodiagenesis. However, dissolution and kaolinitization of feldspars, micas and mud intraclasts resulted in the creation of intercrystalline micro- and mouldic macro-porosity and permeability during eodiagenesis, which were more widespread in braided fluvial than in meandering fluvial sandstones. This was because of the greater depositional porosity and permeability in the braided fluvial sandstones which enhanced percolation of meteoric waters. The development of only limited quartz overgrowths in the braided fluvial sandstones, in which quartz grains are coated by thick illite layers, retained high porosity and permeability (12-23 % and 30- 600 mD). By contrast, meandering fluvial sandstones underwent porosity loss as a result of quartz overgrowth development on quartz grains which lack or have thin and incomplete grain-coating illite (2-15 % and 0-0.1mD). Further loss of porosity in the meandering fluvial sandstones occurred as a result of chemical compaction (pressuredissolution) induced by the occurrence of micas along grains contacts. Otherdiagenetic alterations, such as the growth of pyrite, siderite, dolomite/ankerite and albitization, had little impact on reservoir quality. The albitization of feldspars may have had minor positive influence on reservoir quality throughthe creation of intercrystalline micro-porosity between albite crystals.The results of this study show that diagenetic modifications of the braided and meandering fluvial sandstones in the Nubian Formation, and resulting changes in reservoir quality, are closely linked to depositional porosity and permeability. They are also linked to the thickness of grain-coating infiltrated clays, and to variations in detrital composition, particularly the amounts of mud intraclasts, feldspars and mica grains as well as climatic conditions.

Post-depositional modification of atmospheric dust on a granite building in central Rio de Janeiro: implications for surface induration and subsequent stone decay

Extensive contour scaling of a 200 year old granite church is associated with the breaching of an apparently iron-rich crust and the widespread deposition of atmospheric dust within the canyon-like streetscape of Rio de Janeiro. Contemporary dust, accumulated dust from within the a depression on the building surface, the surface crust and the underlying granite are examined by a combination of total element analysis and sequential extraction, X-ray diffraction and energy dispersive X-ray fluorescence. Results indicate an increase in total organic carbon and a marked decrease in pH within the accumulated dust, and a rapid mobilization of anions and cations from the water-soluble and carbonate phases. It is considered that the latter is linked to salt accumulation within and eventual salt weathering of the granite. Post-depositional alteration of the dust is also linked with the de-silicification of clay minerals (Illite to kaolinite) and the loss of silica from the amorphous Fe/Mn phase of the accumulated dust under the initially saline and progressively more acidic conditions experienced at the stone - atmosphere interface. This mobilization of silica is associated with the formation of what is, in effect, a thin silica-rich surface crust or glaze. Within the glaze, assessory amounts of extractable iron are concentrated within the amorphous and crystalline Fe/Mn phases at levels that are significantly elevated with respect to the underlying granite, but much lower than the equivalent phases of the accumulated dust from which it is principally assumed to derive. The protection afforded to the stone work by the crust is not, however, permanent and within the last 15 years it has been possible to observe a rapid increase in the surface delamination of the church close to street level.

Mice lacking alpha-tocopherol transfer protein gene have severe alpha-tocopherol deficiency in multiple regions of the central nervous system

Ataxia with vitamin E deficiency is caused by mutations in a-tocopherol transfer protein (a-TTP) gene and it can be experimentally generated in mice by a-TTP gene inactivation (a-TTP-KO). This study compared a-tocopherol (a-T) concentrations of five brain regions and of four peripheral organs from 5 months old, male and female, wild-type (WT) and a-TTP-KO mice. All brain regions of female WT mice contained significantly higher a-T than those from WT males. a-T concentration in the cerebellum was significantly lower than that in other brain regions of WT mice. These sex and regional differences in brain a-T concentrations do not appear to be determined by a-TTP expression which was undetectable in all brain regions. All the brain regions of a-TTP-KO mice were severely depleted in a-T. The concentration of another endogenous antioxidant, total glutathione, was unaffected by gender but was decreased slightly but significantly in most brain regions of a-TTP-KO mice. The results show that both gender and the hepatic a-TTP, but not brain a-TTP gene expression are important in determining a-T concentrations within the brain. Interestingly, functional abnormality (ataxia) develops only very late in a-TTP-KO mice in spite of the severe a-tocopherol deficiency in the brain starting at an early age.

Novel dermaseptin, adenoregulin and caerin homologs from the Central American red-eyed leaf frog, Agalychnis callidryas, revealed by functional peptidomics of defensive skin secretion

By integrating systematic peptidome and transcriptome studies of the defensive skin secretion of the Central American red-eyed leaf frog, Agalychnis callidryas, we have identified novel members of three previously described antimicrobial peptide families, a 27-mer dermaseptin-related peptide (designated DRP-AC4), a 33-mer adenoregulin-related peptide (designated ARP-AC1) and most unusually, a 27-mer caerin-related peptide (designated CRP-AC1). While dermaseptin and adenoregulin were originally isolated from phyllomedusine leaf frogs, the caerins, until now. had only been described in Australian frogs of the genus, Litoria. Both the dermaseptin and adenoregulin were C-terminally amidated and lacked the C-terminal tripeptide of the biosynthetic precursor sequence. In contrast, the caerin-related peptide, unlike the majority of Litoria analogs. was not C-terminally amidated. The present data emphasize the need for structural characterization of mature peptides to ensure that unexpected precursor cleavages and/or post-translational modifications do not produce mature peptides that differ in structure to those predicted from cloned biosynthetic precursor cDNA. Additionally, systematic study of the secretory peptidome can produce unexpected results such as the CRP described here that may have phylogenetic implications. It is thus of the utmost importance in the functional evaluation of novel peptides that the primary structure of the mature peptide is unequivocally established - something that is often facilitated by cloning biosynthetic precursor cDNAs but obviously not reliable using such data alone. (C) 2008 Elsevier Masson SAS. All rights reserved.

Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations

Due to their maternal mode of inheritance, mitochondrial markers can be regarded as almost 'ideal' tools in evolutionary studies of conifer populations. In the present study, polymorphism was analysed at one mitochondrial intron (nad 1, exon B/C) in 23 native European Pinus sylvestris populations. In a preliminary screening for variation using a polymerase chain reaction-restriction fragment length polymorphism approach, two length variants were identified. By fully sequencing the 2.5 kb region, the observed length polymorphism was found to result from the insertion of a 31 bp sequence, with no other mutations observed within the intron. A set of primers was designed flanking the observed mutation, which identified a novel sequence-tagged-site mitochondrial marker for P. sylvestris. Analysis of 747 trees from the 23 populations using these primers revealed the occurrence of two distinct haplotypes in Europe. Within the Iberian Peninsula, the two haplotypes exhibited extensive population differentiation (Phi(ST) = 0.59; P less than or equal to 0.001) and a marked geographical structuring. In the populations of central and northern Europe, one haplotype largely predominated, with the second being found in only one individual of one population.

DNA-dependent Protein Kinase-mediated Phosphorylation of Protein Kinase B Requires a Specific Recognition Sequence in the C-terminal Hydrophobic Motif

DNA-dependent protein kinase (DNA-PK) has been implicated in a variety of nuclear processes including DNA double strand break repair, V(D)J recombination, and transcription. A recent study showed that DNA-PK is responsible for Ser-473 phosphorylation in the hydrophobic motif of protein kinase B (PKB/Akt) in genotoxic-stressed cells, suggesting a novel role for DNA-PK in cell signaling. Here, we report that DNA-PK activity toward PKB peptides is impaired in DNA-PK knock-out mouse embryonic fibroblast cells when compared with wild type. In addition, human glioblastoma cells expressing a mutant form of DNA-PK (M059J) displayed a lower DNA-PK activity when compared with glioblastoma cells expressing wild-type DNA- PK (M059K) when PKB peptide substrates were tested. DNA- PK preferentially phosphorylated PKB on Ser-473 when compared with its known in vitro substrate, p53. A consensus hydrophobic amino acid surrounding the Ser-473 phospho-acceptor site in PKB containing amino acids Phe at position +1 and +4 and Tyr at position -1 are critical for DNA- PK activity. Thus, these data define the specificity of DNA- PK action as a Ser-473 kinase for PKB in DNA repair signaling.

Late Holocene climate change in central Sweden inferred from lacustrine stable isotope data

Stable isotopes (delta O-18 and delta C-13) of lacustrine carbonates (Chara spp. algae and Pisidium spp. molluscs) from a lake sedimentary sequence in central Sweden were analysed to infer changes in lake hydrology and climate during the late Holocene. Results from analysis of lake water isotopes (delta O-18 and delta H-2) show that Lake Blektjarnen water isotope composition is responsive to the balance between evaporation and input water (E/l ratio). A high E/l ratio results from a dry and probably warmer climate, decreasing the relative importance of precipitation input. Under such conditions evaporation and atmospheric equilibration probably enrich lake water in O-18 and C-13, respectively, which is reflected in the isotopic composition of the carbonates in the lake. From the relatively positive Chara delta O-18 values we infer that conditions were dry and warm between 4400 and 4000 cal. a BP, whereas more negative values indicate that conditions were wetter and probably cooler between 4000 and 3000 cal. a BP. A drier climate is inferred from more positive values between 2500 and 1000 cal. a BP. However, a successive depletion after ca. 1750 cal. a BP, also detected in several other delta O-18 records (carbonate and diatom), suggest increasingly wetter conditions in Scandinavia after that time, which is probably related to increased strength of the zonal flow.

Complete Genome Sequence of Propionibacterium acnes Type IB Strain 6609

Propionibacterium acnes is an anaerobic Gram-positive bacterium that forms part of the normal human cutaneous microbiota and is thought to play a central role in acne vulgaris, a chronic inflammatory disease of the pilosebaceous unit (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). Here we present the whole genome sequence of P. acnes type IB strain 6609, which was recovered from a skin sample from a woman with no recorded acne history and is thus considered a nonpathogenic strain (I. Nagy, Microbes Infect. 8:2195-2205, 2006).

Sequence-Specific and Strand-Specific Cleavage In Oligodeoxyribonucleotides and DNA Containing 3'-Thiothymidine

Oligonucleotides containing a 3'-thiothymidine residue (T3's) at the cleavage site for the EcoRV restriction endonuclease (between the central T and A residues of the sequence GATATC) have been prepared on an automated DNA synthesizer using 5'-O-monomethoxytritylthymidine 3'-S-(2-cyanoethyl N,N-di-isopropylphosphorothioamidite). The self-complementary sequence GACGAT3'sATCGTC was completely resistant to cleavage by EcoRV, while the heteroduplex composed of 5'-TCTGAT3'sATCCTC and 5'-GAGGATATCAGA (duplex 4) was cleaved only in the unmodified strand (5'-GAGGATATCAGA). In contrast, strands containing a 3'-S-phosphorothiolate linkage could be chemically cleaved specifically at this site with Ag+. A T3's residue has also been incorporated in the (-) strand of double-stranded closed circular (RF IV) M13mp18 DNA at the cleavage site of a unique EcoRV recognition sequence by using 5'-pCGAGCTCGAT3'sATCGTAAT as a primer for polymerization on the template (+) strand of M13mp18 DNA. On treatment of this substrate with EcoRV, only one strand was cleaved to produce the RF II or nicked DNA. Taken in conjunction with the cleavage studies on the oligonucleotides, this result demonstrates that the 3'-S-phosphorothiolate linkage is resistant to scission by EcoRV. Additionally, the phosphorothiolate-containing strand of the M13mp18 DNA could be cleaved specifically at the point of modification using iodine in aqueous pyridine. The combination of enzymatic and chemical techniques provides, for the first time, a demonstrated method for the sequence-specific cleavage of either the (+) or (-) strand.

A lower mass for the exoplanet WASP-21b

We present high-precision transit observations of the exoplanet WASP-21b, obtained with the Rapid Imager to Search for Exoplanets instrument mounted on the 2.0-m Liverpool Telescope. A transit model is fitted, coupled with a Markov chain Monte Carlo routine, to derive accurate system parameters. The two new high-precision transits allow us to estimate the stellar density directly from the light curve. Our analysis suggests that WASP-21 is evolving off the main sequence which led to a previous overestimation of the stellar density. Using isochrone interpolation, we find a stellar mass of 0.86 ± 0.04 Msun, which is significantly lower than previously reported (1.01 ± 0.03 Msun). Consequently, we find a lower planetary mass of 0.27 ± 0.01 MJup. A lower inclination (87?4 ± 0?3) is also found for the system than previously reported, resulting in a slightly larger stellar (R*= 1.10 ± 0.03 Rsun) and planetary radius (Rp= 1.14 ± 0.04 RJup). The planet radius suggests a hydrogen/helium composition with no core which strengthens the correlation between planetary density and host star metallicity. A new ephemeris is determined for the system, i.e. T0= 245 5084.519 74 ± 0.000 20 (HJD) and P= 4.322 5060 ± 0.000 0031 d. We found no transit timing variations in WASP-21b.