Effect and design of buffer zones in the Nordic climate: The influence of width, amount of surface runoff, seasonal variation and vegetation type on retention efficiency for nutrient and particle runoff

Loss of nutrients and sediments from agricultural runoff causes eutrophication in surface water. Vegetated buffer zones adjacent to a stream can effectively remove and retain nutrients and sediments. It is, therefore, important to study design criteria which optimise the effect of buffer zones (BZ). This paper describes the influence of four criteria: (i) buffer zone width, (ii) amount of surface runoff water entering the BZ, (iii) seasonal variation and (iv) vegetation type. These parameters were studied after simulated and natural runoff at four different sites in Southern Norway with cold temperate climate. Surface runoff was collected before entering and after passing the BZs. The simulation experiments were short-term experiments carried out over a few days in 1992 and 1993. In the natural runoff experiments, volume proportional mixed samples were collected after each runoff period during 1992–1999. The results show significantly higher removal efficiency (in %) from 10 m wide BZs compared to 5 m widths, however, the specific retention (per m²) is higher in 5 m BZ. Buffer zones can receive particle runoff over several days without a significant decrease in their removal level. Retention efficiency between summer and autumn varied depending on the measured parameter (phosphorus, particles and nitrogen), and there were no significant differences in removal efficiency between summer and winter. The results show no significant differences between forest buffer zones (FBZ) and grass buffer zones (GBZ) regarding their retention efficiency for nitrogen and phosphorus. There was significantly higher retention efficiency in FBZ for particles. Average removal efficiencies from both simulated and natural runoff experiments varied from 60–89%, 37–81% and 81–91% for phosphorus, nitrogen and particles, respectively.     

SIRT1 Activation by Small Molecules: KINETIC AND BIOPHYSICAL EVIDENCE FOR DIRECT INTERACTION OF ENZYME AND ACTIVATOR?

SIRT1 is a protein deacetylase that has emerged as a therapeutic target for the development of activators to treat diseases of aging. SIRT1-activating compounds (STACs) have been developed that produce biological effects consistent with direct SIRT1 activation. At the molecular level, the mechanism by which STACs activate SIRT1 remains elusive. In the studies reported herein, the mechanism of SIRT1 activation is examined using representative compounds chosen from a collection of STACs. These studies reveal that activation of SIRT1 by STACs is strongly dependent on structural features of the peptide substrate. Significantly, and in contrast to studies reporting that peptides must bear a fluorophore for their deacetylation to be accelerated, we find that some STACs can accelerate the SIRT1-catalyzed deacetylation of specific unlabeled peptides composed only of natural amino acids. These results, together with others of this study, are at odds with a recent claim that complex formation between STACs and fluorophore-labeled peptides plays a role in the activation of SIRT1 (Pacholec, M., Chrunyk, B., Cunningham, D., Flynn, D., Griffith, D., Griffor, M., Loulakis, P., Pabst, B., Qiu, X., Stockman, B., Thanabal, V., Varghese, A., Ward, J., Withka, J., and Ahn, K. (2010) J. Biol. Chem. 285, 8340–8351). Rather, the data suggest that STACs interact directly with SIRT1 and activate SIRT1-catalyzed deacetylation through an allosteric mechanism.     

Design,synthesis and biological activity evaluation of novel 2,6-difluorobenzamide derivatives through FtsZ inhibition

Novel series of 3-substituted 2,6-difluorobenzamide derivatives as FtsZ inhibitors were designed, synthesized and evaluated for their in vitro antibacterial activity against various phenotype of Gram-positive and Gram-negative bacteria, and their cell division inhibitory activity against three representative strains. As a result, 3-chloroalkoxy derivative 7, 3-bromoalkoxy derivative 12 and 3-alkyloxy derivative 17 were found to exhibit the best antibacterial activity against Bacillus subtilis with MICs of 0.25–1 μg/mL, and good activity (MIC < 10 μg/mL) against both susceptible and resistant Staphylococcus aureus. Additionally, all the three compounds displayed potent cell division inhibitory activity with MIC values of below 1 μg/mL against Bacillus subtilis and Staphylococcus aureus.     

Enhanced endoxylanase production by Myceliophthora thermophila using rice straw and its synergism with phytase in improving nutrition

The goal of the present investigation was to attain the enhanced production of endoxylanase in submerged fermentation using different approaches followed by its utility in improving nutrition of wheat and rice flours along with phytase. Myceliophthora thermophila BJTLRMDU3 produced 51.70 U/mL of xylanase using rice straw as a substrate after optimization with ‘one variable at a time’ approach. After Plackett-Burman design study, sodium nitrate, K₂HPO₄ and Tween 20 were selected as critical factors and further optimized by response surface methodology. Increased xylanase production (80.15 U/mL) was attained with 2.5 % (w/v) sodium nitrate, 1.25 % (w/v) K₂HPO₄, and 2 % (v/v) Tween 20 at 40 °C. An overall 1.5-fold increase in xylanase production was achieved after statistical optimization. Applicability of M. thermophila xylanase (200 U/g flour) alone and in combination with phytase (15 U/g flour) from Aspergillus oryzae SBS50 in wheat and rice flours showed enhancement in nutritional qualities of both flours. About 45.67 %, 29.73 %, and 107.91 % increase in reducing sugars, soluble proteins and inorganic phosphate, respectively in wheat flour, while 94.16 %, 134.52 %, and 473.33 % increase in reducing sugars, soluble proteins and inorganic phosphate, respectively in rice flour was achieved at 60 °C and pH 5.0 by synergistic action of xylanase and phytase as compared to control having only xylanase.     

Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology

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Engineering A-kinase Anchoring Protein (AKAP)-selective Regulatory Subunits of Protein Kinase A (PKA) through Structure-based Phage Selection

PKA is retained within distinct subcellular environments by the association of its regulatory type II (RII) subunits with A-kinase anchoring proteins (AKAPs). Conventional reagents that universally disrupt PKA anchoring are patterned after a conserved AKAP motif. We introduce a phage selection procedure that exploits high-resolution structural information to engineer RII mutants that are selective for a particular AKAP. Selective RII (R_Select) sequences were obtained for eight AKAPs following competitive selection screening. Biochemical and cell-based experiments validated the efficacy of R_Select proteins for AKAP2 and AKAP18. These engineered proteins represent a new class of reagents that can be used to dissect the contributions of different AKAP-targeted pools of PKA. Molecular modeling and high-throughput sequencing analyses revealed the molecular basis of AKAP-selective interactions and shed new light on native RII-AKAP interactions. We propose that this structure-directed evolution strategy might be generally applicable for the investigation of other protein interaction surfaces.     

Kinetic cooperativity in the concerted model for allosteric enzymes.

The cooperativity of enzyme-substrate interactions is investigated in the concerted allosteric model of Monod, Wyman and Changeux. The general case of K-V systems is considered, in which the two protomer conformational states R and T postulated in the theory differ in catalytic and binding properties. An expression for the Hill coefficient nH defined with respect to the asymptotic velocity V infinity to is analyzed in conditions which exclude substrate inhibition. Kinetic cooperativity is always positive (nH greater than 1) in the case of a dimer enzyme, and in the case of an inactive T state. Slight kinetic negative cooperativity (nH less than 1) occurs under restrictive conditions for larger numbers of protomers when the substrate binds significantly to the less active state of the enzyme, but the phenomenon remains negligible for trimers and tetramers. These conclusions differ from those obtained [A. Goldbeter, J. Mol.Biol.90 (1974) 185] with the Hill coefficient based on the absolute maximum velocity, which may exceed the experimental value V infinity to in K-V systems. The results extend those of Paulus and DeRiel [J. Mol. Biol. 97 (1975) 667] and support the view that in most cases, negative cooperativity is not compatible with a mechanism based on a concerted and conservative allosteric transition. The Hill coefficients for binding and catalysis are compared in K-V systems.     

Population ecology of the endangered butterflies Maculinea teleius and M. nausithous and the implications for conservation

Butterflies of the genus Maculinea are highly endangered in Europe. The cuckoo species M. rebeli has been thoroughly investigated through both empirical and modelling studies, but less is known about the population ecology of predatory Maculinea. We present the findings of a 2-year research study on sympatric populations of two endangered butterflies: Maculinea teleius and M. nausithous in the Kraków region, southern Poland. The study comprised mark–release–recapture sampling and laboratory rearing of butterflies from larvae collected in the field. For both species the sex ratio was slightly, but consistently, female-biased and there was little year-to-year change in the seasonal population sizes. Daily numbers showed greater variation between the 2 years of the study due to the differences in daily survival rate. The average life span of laboratory-raised butterflies kept in ideal conditions was more than 6 days, compared to only 2–3 days in the field. The recruitment of both males and females consistently followed a bimodal pattern. A small proportion of individuals (maximum 25%) changed sites, in spite of relatively short distances of ca. 100 m separating them. The results indicate that populations of both species are typically stable within their sites, possibly due to larval polymorphism, but there is little inter-site mobility and thus landscape corridors seem necessary to enhance metapopulation viability. A further problem to be considered in the conservation of Maculinea butterflies is the fact that their very short life span in relation to flight-period length reduces the effective population size.