First passage times of driven DNA hairpin unzipping

We model the dynamics of voltage-driven transport of DNA hairpins through transmembrane channels. A two-dimensional stochastic model of the DNA translocation process is fit to the measurements of Mathé, who pulled self-hybridized DNA hairpins through lipid-embedded alpha-hemolysin channels. As the channel was too narrow to accommodate hybridized DNA, dehybridization of the hairpin became the rate-limiting step of the transport process. We show that the mean first passage time versus voltage curve for the escape of the DNA from the transmembrane channel can be divided into two regions: (1) a low-voltage region where the DNA slides out of the pore in reverse and without undergoing significant dehybridization, and (2) a region where the DNA dehybridizes under the influence of the applied voltage and translocates across the membrane.     

Structural rearrangements in active and inactive forms of hydrogenase from Thiocapsa roseopersicina.

The electrophoretic behavior of Thiocapsa roseopersicina hydrogenase on sodium dodecyl sulfate gels demonstrates that the protein exists in two active forms, A1 and A2, which may be interconverted. Each of these forms has a characteristic electrophoretic mobility and differs in its sensitivity to O2. Form A1 is O2-labile and converts to A2 under O2. Form A2 is less sensitive to O2 and may be converted into A1 under H2 atmosphere. Both active forms are present in aerobically isolated samples. Because the proteins are still active on 15% sodium dodecyl sulfate gels, they are not completely denatured, and the apparent molecular masses do not necessarily represent the true molecular masses of the enzymes. A1 has an Rf = 0.19, corresponding to an apparent molecular mass of 90 kDa, and A2 has an Rf = 0.35, corresponding to an apparent molecular mass of 49 kDa. A sedimentation equilibrium centrifugation study of the active enzyme shows that the holoenzyme has a molecular mass of 98 kDa. Form A2 may be separated into two subunits of molecular mass of 64 kDa and 34 kDa, respectively. Thus, form A2 represents the holoenzyme with a true molecular mass of 98 kDa. Amino acid compositions and N-terminal amino acid sequences of the A2 protein and these subunits are consistent with a heterodimeric holoenzyme. The relationship between the conformational changes detected in this study and a three-state scheme proposed on the basis of EPR spectroscopic studies of the metal-containing cofactors present in the enzyme is also discussed.     

H+ -mediated coupling of transmembrane Ca2+ fluxes in vegetative Trichoderma viride mycelia suggested by the study of ageing and adaptation to extreme Ca2+ concentrations

The adaptation to extreme concentrations of Ca(2+) and its consequence on the properties of the (45)Ca(2+) transport were studied in submerged mycelia of Trichoderma viride. The adaptation to low [Ca(2+)](o) did not cause changes in kinetic parameters of the (45)Ca(2+) influx but the adaptation to high [Ca(2+)](o) increased the K(M(Ca2+)). The V(max) of the (45)Ca(2+) influx decreased with the age of (non-adapted) mycelia with concomitant decrease of the K(M(Ca2+)) these changes were prevented in mycelia adapted to high Ca(2+). High [Ca(2+)](o) decreased the stimulation by the uncoupler, 3, 3', 4', 5-tetrachloro salicylanilide (TCS) (30 muM), as compared to the control, whereas the Ca(2+) chelator, EGTA, stimulated it. In the aged mycelia, the stimulation by TCS of the (45)Ca(2+) influx faded away, in parallel with the activity of the H(+)-ATPase. The (45)Ca(2+) efflux from mycelia was affected by TCS in a similar way as the (45)Ca(2+) influx. The results demonstrate the adaptive responses of transport processes participating in the mycelial Ca(2+) homeostasis and ageing are in agreement with a notion that both Ca(2+)-influx and-efflux are coupled by the H(+)-homeostasis at the plasma membrane.     

Nitrogen input by cyanobacterial biofilms of an inselberg into a tropical rainforest in French Guiana

Inselbergs are isolated rock outcrops displaying high heterogeneity in both soil formation and microclimatic condition with high variation in plant biodiversity. Vegetation patterns on inselbergs in the humid tropics range from rocks covered with dense biofilms predominated by cyanobacteria to high forest on deep soils. Along a similar transect, we investigated N supply to the vegetation using element and isotopic analyses of soil and biofilm samples from an inselberg in French Guiana. An increase in N content related to total dry weight (N%) in soils from the inselberg peak to surrounding habitats was related to changes in stable isotope composition (δ¹⁵N). At the inselberg peak cyanobacterial biofilms on bare rocks and soils within small vegetation islands had similar δ¹⁵N values of −1.9‰ and −1.3‰ while δ¹⁵N of soils progressively increased towards the primary rainforest up to 6‰. From the peak towards the base of the inselberg, the density of higher plants and soil depth increased. Hence, soil N cycling and N losses to the environment resulted in a progressive increase of soil δ¹⁵N. The distribution of N%, δ¹⁵N and δ¹³C values suggest that the main N supply for soils at and nearby the inselberg is derived from cyanobacterial N₂ fixation through leaching processes.     

The Candidate Oncogene CYP24A1: A Potential Biomarker for Colorectal Tumorigenesis

The main autocrine/paracrine role of the active metabolite of vitamin D₃, 1α,25-dihydroxyvitamin D₃ (1,25-D₃), is inhibition of cell growth and induction of cell differentiation and/or apoptosis. Synthesis and degradation of the secosteroid occurs not only in the kidney but also in normal tissue or malignant extrarenal tissues such as the colon. Because 25-hydroxyvitamin D₃ 24-hydroxylase (CYP24A1) is considered to be the main enzyme determining the biological half-life of 1,25-D₃, we have examined expression of the CYP24A1 mRNA (by real-time RT-PCR) and protein (by immunohistochemistry) in normal human colon mucosa, colorectal adenomas, and adenocarcinomas in 111 patients. Although 76% of the normal and benign colonic tissue was either completely devoid of or expressed very low levels of CYP24A1, in the majority of the adenocarcinomas (69%), the enzyme was present at high concentrations. A parallel increased expression of the proliferation marker Ki-67 in the same samples suggests that overexpression of CYP24A1 reduced local 1,25-D₃ availability, decreasing its antiproliferative effect. (J Histochem Cytochem 58:277–285, 2010)     

Gene expression and activity of cartilage degrading glycosidases in human rheumatoid arthritis and osteoarthritis synovial fibroblasts

Introduction

Similar to matrix metalloproteinases, glycosidases also play a major role in cartilage degradation. Carbohydrate cleavage products, generated by these latter enzymes, are released from degrading cartilage during arthritis. Some of the cleavage products (such as hyaluronate oligosaccharides) have been shown to bind to Toll-like receptors and provide endogenous danger signals, while others (like N-acetyl glucosamine) are reported to have chondroprotective functions. In the current study for the first time we systematically investigated the expression of glycosidases within the joints.

Methods

Expressions of β-D-hexosaminidase, β-D-glucuronidase, hyaluronidase, sperm adhesion molecule 1 and klotho genes were measured in synovial fibroblasts and synovial membrane samples of patients with rheumatoid arthritis and osteoarthritis by real-time PCR. β-D-Glucuronidase, β-D-glucosaminidase and β-D-galactosaminidase activities were characterized using chromogenic or fluorogenic substrates. Synovial fibroblast-derived microvesicles were also tested for glycosidase activity.

Results

According to our data, β-D-hexosaminidase, β-D-glucuronidase, hyaluronidase, and klotho are expressed in the synovial membrane. Hexosaminidase is the major glycosidase expressed within the joints, and it is primarily produced by synovial fibroblasts. HexA subunit gene, one of the two genes encoding for the alpha or the beta chains of hexosaminidase, was characterized by the strongest gene expression. It was followed by the expression of HexB subunit gene and the β-D-glucuronidase gene, while the expression of hyaluronidase-1 gene and the klotho gene was rather low in both synovial fibroblasts and synovial membrane samples. Tumor growth factor-β1 profoundly downregulated glycosidase expression in both rheumatoid arthritis and osteoarthritis derived synovial fibroblasts. In addition, expression of cartilage-degrading glycosidases was moderately downregulated by proinflammatory cytokines including TNFα, IL-1β and IL-17.

Conclusions

According to our present data, glycosidases expressed by synovial membranes and synovial fibroblasts are under negative regulation by some locally expressed cytokines both in rheumatoid arthritis and osteoarthritis. This does not exclude the possibility that these enzymes may contribute significantly to cartilage degradation in both joint diseases if acting in collaboration with the differentially upregulated proteases to deplete cartilage in glycosaminoglycans.     

Water bird guilds and their feeding connections in the Bodrogzug, Hungary

Thalli of the intertidal Phaeophyte Fucus spiralis L. and the subtidal Chlorophyte Ulva olivascens Dangeard were exposed to artificial UV-A, UV-B and photosynthetically active radiation (PAR) by combination of PAR + UV-A + UV-B (PAB), PAR + UV-A (PA) and PAR (P) treatments. UV-A enhanced photosynthesis and stimulated carbonic anhydrase (CA) and nitrate reductase (NR) in F. spiralis whilst PAR only had an inhibitory effect in this species. U. olivascens suffered chronic photoinhibition in all the treatments as evidenced by reduced maxima photosynthesis (P_max) and photosynthetic efficiency (α). Non stimulatory effect was observed upon CA and NR in this species. Our results showed that artificial UV radiation triggered opposite responses in both species. We suggest that differences shown by both species might be related to their location in the rocky shore and their ability to sense UV. We propose that the ratio UV:PAR acts as an environmental signal involved in the control of photosynthesis as shown by pronounced inhibition in samples exposed to only PAR. We also suggest that UV-regulated photosynthesis would be related to carbon (C) and nitrogen (N) cycles, regulating feedback processes that control C and N assimilation.     

Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree

Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F₂ offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001) but negatively correlated with skeletonizer damage (P<0.01) in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast-growing forest tree.     

DIATOMS LIVING INSIDE THE THALLUS OF THE GREEN ALGAL LICHEN COENOGONIUM LINKII IN NEOTROPICAL LOWLAND RAIN FORESTS1

Coenogonium linkii Ehrenb. is a very common filamentous lichen, growing on stems, hanging roots, and lianas in the understory of neotropical lowland rain forests. We investigated several thalli of this species from locations in Panama and French Guiana. All thalli were inhabited by various species of terrestrial diatoms, which were found between the thallus filaments on extracellular material of the mycobiont. We identified 18 species of diatoms belonging to nine genera: Diadesmis, Eunotia, Hantzschia, Luticola, Melosira, Nitzschia, Orthoseira, Pinnularia, and Stauroneis. The potential benefits both diatoms and lichens could derive from symbiosis in relation to water, irradiance, and nitrogen availability are discussed.