Computer-aided design of polyketides with the required properties

An approach to rational design of new polyketides with the required spectrum of biological activity has been proposed. We have developed the BioGenPharm software, which generates combinatorial libraries of polyketides based on the user-defined input parameters, performs prediction of biological activity spectra for the generated structures and selection of molecuels with the required properties. PASS algorithm has been applied for prediction of polyketide activity spectra (http://www.ibmc.msk.ru/PASS). Validation of PASS prediction ability for polyketides was performed vs. the evaluation set containing 242 natural macrolides from the Dictionary of Natural Products. The mean prediction accuracy was 75.5%. The problem of choice of the cutting points for probability of the presence of activity (Pa), which provides optimal combination of such parameters as sensitivity, specificity, concordance has been considered. Applicability of the described method has been illustrated by generation of a virtual library of the erythromycin analogues and selection of substances with low probability of the hepatotoxic effect.     

Deep supercooling xylem parenchyma cells of katsura tree (Cercidiphyllum japonicum) contain flavonol glycosides exhibiting high anti-ice nucleation activity

Xylem parenchyma cells (XPCs) of boreal hardwood species adapt to sub-freezing temperatures by deep supercooling to maintain a liquid state of intracellular water near −40 °C. Our previous study found that crude xylem extracts from such tree species exhibited anti-ice nucleation activity to promote supercooling of water. In the present study, thus, we attempted to identify the causative substances of supercooling. Crude xylem extracts from katsura tree ( Cercidiphyllum japonicum ), of which XPCs exhibited deep supercooling to −40 °C, were prepared by methanol extraction. The crude extracts were purified by liquid–liquid extraction and then by silica gel column chromatography. Although all the fractions obtained after each purification step exhibited some levels of anti-ice nucleation activity, only the most active fraction was retained to proceed to the subsequent level of purification. High-performance liquid chromatography (HPLC) analysis of a fraction with the highest level of activity revealed four peaks with high levels of anti-ice nucleation activity in the range of 2.8–9.0 °C. Ultraviolet (UV), mass and nuclear magnetic resonance (NMR) spectra revealed that these four peaks corresponded to quercetin-3- O - β -glucoside (Q3G), kaempferol-7- O - β -glucoside (K7G), 8-methoxykaempferol-3- O - β -glucoside (8MK3G) and kaempferol-3- O - β -glucoside (K3G). Microscopic observations confirmed the presence of flavonoids in cytoplasms of XPCs. These results suggest that diverse kinds of anti-ice nucleation substances, including flavonol glycosides, may have important roles in deep supercooling of XPCs.     

Amelioration of cadmium-induced cardiac impairment by taurine

The present study has been designed to investigate the protective role of taurine (2-aminoethanesulfonic acid), a sulfur containing conditionally essential amino acid, against cadmium-induced cardiac dysfunction in mice. Cadmium chloride (CdCl(2)) was used as the source of cadmium and it was administered orally at a dose of 4mg/kg body weight for 6 days. Cadmium exposure caused significant accumulation of the cadmium and iron in mice hearts tissue. Levels of serum specific markers related to cardiac impairments, e.g. total cholesterol, HDL cholesterol and triglyceride were altered due to cadmium toxicity. Reduction in the activities of antioxidant enzymes, namely, superoxide dismutase (SOD), catalase (CAT), glutathione-S-transferase (GST), glutathione reductase (GR), glutathione peroxidase (GPx) and glucose-6-phosphate dehydrogenase (G6PD) have been observed in cadmium exposed mice. Cadmium intoxication also decreased the cardiac glutathione (GSH) and total thiols contents and increased the levels of oxidized glutathione (GSSG), lipid peroxidation end products, protein carbonyl content and the extent of DNA fragmentation. Oral administration of taurine at a dose of 100mg/kg body weight for 5 days, however, prevented all the toxin-induced oxidative impairments mentioned above. "Ferric Reducing/Antioxidant Power (FRAP) assay" showed that taurine could protect the cardiac tissue by preventing cadmium-induced reduction of the intracellular antioxidant power. Histological examination of cardiac segments also supported the beneficial role of taurine against cadmium-induced damages in the murine hearts. Effect of a well established antioxidant, vitamin C has been included in the study as a positive control. Combining all, results suggest that taurine attenuates cadmium-induced impairment in mice hearts.     

Degradation of lyophilized lipid/DNA complexes during storage: The role of lipid and reactive oxygen species

The presence of trace amounts of metal ions in nonviral vector formulations can significantly affect the stability of lipid/DNA complexes (lipoplexes) during acute freeze-drying. The goal of the present study was to evaluate the generation of reactive oxygen species (ROS) in dried formulations of lipoplexes and in their individual components (lipid or naked DNA). The experiments were conducted in the presence or absence of a transition metal (Fe²⁺). Lipoplexes and their individual components were formulated in trehalose and subjected to lyophilization and stored for a period of up to 2 months at + 60 °C. Physico-chemical characteristics and biological activity were evaluated at different time intervals. Generation of ROS during storage was determined by adding a fluorescence probe to the formulations prior to freeze-drying. We also monitored the formation of thiobarbituric reactive substances (TBARS). Our results show that ROS and TBARS form during storage in the dried state. Our findings also suggest that degradation is more rapid in the presence of lipid, even in the absence of metal. We also showed that dried naked DNA formulations are more stable without the lipid component. Effective strategies are then needed to minimize the formation and accumulation of oxidative damage of lipoplexes during storage.     

酶降解烟叶中细胞壁物质

烟叶中以细胞壁物质存在的碳水化合物在燃吸时产生不良影响,在一定条件下向烟叶中施加一定量的纤维素酶和果胶酶,使部分细胞壁物质降解为水溶性糖,烟质得到改善,纤维素酶和果胶酶最佳用量均为每克烟叶30u酶量（活力）,最佳作用条件为;烟叶水分25%,作用温度50℃,作用时间4h,且在真空条件下可使细胞壁物质降解更有效,可降解烟叶中细胞壁物质10%左右,烟叶的评吸质量得到明显改善。     

Spatial distribution,size structure,and prey of Craspedacusta sowerbyi Lankester in a shallow New Zealand lake

Solar ultraviolet radiation both degrades and alters the quality of natural organic matter as well as organic pollutants in surface waters. Still, it is only recently that this indirect influence of photochemical processes on aquatic organisms (e.g. bacteria) has received attention. We experimentally studied the photochemical degradation of three PAHs; anthracene, phenanthrene and naphthalene, in water. Anthracene and phenanthrene were rapidly photodegraded (half-lives of 1 and 20.4 hours, respectively), while the photochemical half-life of naphthalene exceeded 100 hours. Hence photodegradation is most likely a less important removal mechanism for the latter compound. The influence of humic substance additions (0–25 mg C l^–1) on degradation rates was also assessed, and while photodegradation of anthracene was not affected by these additions, phenanthrene photodegradation slowed down considerably at the higher humic substance concentrations. These differential responses of anthracene and phenanthrene can at least partially be explained by differences in the spectral absorbance of the two compounds. In contrast, ionic strength did not have any appreciable effect on the estimated photodegradation rates of either compound. The influence of PAHs on growth of aquatic bacteria was assessed in dilution cultures with and without exposure to PAHs and simulated solar UV radiation. Separately, neither PAHs nor simulated solar UV radiation had any effect on bacterial growth. However, when combined, a marked inhibition of bacterial growth could be observed in water obtained from a clearwater lake. This could be due to the formation of toxic photodegradation products such as quinones (detected in our incubations) or other reactive species that affect bacteria negatively. Hence, in addition to influencing the fate and persistence of PAHs in aquatic systems, solar radiation and natural organic matter and regulate the toxicity of these compounds to indigenous micro-organisms.     

Organic matter chemistry and dynamics in clear-cut and unmanaged hardwood forest ecosystems

Forest harvesting alters the organic matter cycle by changing litter inputs and the decomposition regime. We hypothesized that these changes would result in differences in organic matter chemistry between clear-cut and uncut watershed ecosystems. We studied the chemistry of soil organic matter (SOM), and dissolved organic carbon (DOC) in soil solutions and stream samples in clear-cut and uncut sites at the Hubbard Brook Experimental Forest in New Hampshire using DOC fractionation techniques and solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy.Alkyl-C (aliphatic compounds) and O-alkyl-C (carbohydrates) were the largest C fractions in soil and dissolved organic matter at Hubbard Brook. Alkyl-C ranged from 29–48% of soil C, 25–42% of soil solution C, and 22–42% of streamwater DOC. Carbohydrates comprised 32–49%, 36–43%, and 29–60% of C in soils, solutions, and streamwater, respectively. In both soils and soil solutions, the carbohydrate fraction decreased with increasing soil depth, while the aromaticity of organic matter increased with depth. There were no significant differences in the structural chemistry of SOM between clear-cut and uncut watersheds.The aromatic-C fractions in soil solutions at the clear-cut site ranged from 12–16%, approximately 40% greater than at the uncut site (8.5–11%). Thus, clear-cutting has resulted in the leaching of more highly decomposed organic matter, and depletion of more aliphatic compounds in the soluble organic pool. Because DOC fluxes are small compared to the SOM pool, large differences in soil solution chemistry do not substantially alter the overall composition of SOM. While the organic chemistry of stream DOC varied greatly among 3 sampling dates, there were no obvious clear-cutting effects. Thus, temporal variations in flowpaths and/or in-stream processes appear to be more important than disturbance in regulating the organic carbon chemistry of these streams.     

Uptake of 5 9Fe from soluble 5 9Fe-humate complexes by cucumber and barley plants

The capability of cucumber (Cucumis sativus L., cv. Serpente cinese), a Strategy I plant and barley (Hordeum vulgaris L., cv. Europa), a Strategy II plant to use Fe complexed by a water-soluble humic fraction (WEHS) extracted from a peat, was studied. Uptake of ⁵⁹Fe from ⁵⁹Fe-WEHS by cucumber plants was higher at pH 6.0 than at pH 7.5. Roots of intact cucumber plants were able to reduce the Fe^III-WEHS complex either at pH 6.0 or 7.5, rates being higher in the assay medium buffered at pH 6.0. After supply of ⁵⁹Fe-WEHS, a large pool of root extraplasmatic ⁵⁹Fe was formed, which could be used to a large extent by Fe-deficient plants, particularly under acidic conditions. Uptake of ⁵⁹Fe from ⁵⁹Fe-WEHS by Fe-sufficient and Fe-deficient barley plants was examined during periods of high (morning) and low (evening) PS release. Uptake paralleled the diurnal rhythm of PS release. Furthermore, ⁵⁹Fe uptake was strongly enhanced by addition of PS to the uptake solution in both Fe-sufficient and Fe-deficient plants. High amount of root extraplasmatic ⁵⁹Fe was formed upon supply of Fe-WEHS, particularly in the evening experiment. Fe-deficient barley plants were able to utilize Fe from the root extraplasmatic pool, conceivably as a result of high rates of PS release. The results of the present work together with previous observations indicate that cucumber plants (Strategy I) utilize Fe complexed to WEHS, presumably via reduction of Fe^III-WEHS by the plasma membrane-bound reductase, while barley plants (Strategy II) use an indirect mechanism involving ligand exchange between WEHS and PS.     

Fe enriched biosolids as fertilizers for orange and peach trees grown in field conditions

Iron enriched biosolids (FEB) from water treatment facilities are being used as an alternative to synthetic chelates in order to improve Fe uptake. The impact of this type of products on iron nutrition is not fully understood. Plant response depends on FEB composition, soil and climatic conditions and crop response. In order to study the effectiveness of FEB as fertilisers, two field experiments have been carried out. Two different commercial formulations of FEB (unmodified u-FEB and modified m-FEB) produced as a by-product of a drinking water treatment facility in Tampa (Florida, USA) were used. An orange tree (Citrus sinensis, cv. Navelina) and a peach tree (Prunus persica cv. Sudanell) field experiments took place in different locations in Spain. Macro and micronutrients were evaluated to assess mineral status of orange and peach leaf samples. Yield and fruit size were also determined. Despite the large amount of Fe bound by the organic matter on FEB, these products were less effective than synthetic chelates to improve iron uptake. No differences were found in orange yield or size. Results show that the ferric treatments improve fruit calibre, but not yield in peaches.     

Hormonal factors controlling the initiation and development of lateral roots

As the first part of a comprehensive study of the hormonal control of lateral root initiation and development, the effect of surgical treatments such as removal of the root tip, one or more cotyledons, the young epicotyl, or combination of these treatments, on the induction and emergence of lateral roots on the primary root of pea seedlings has been examined. Results show that removal of the root tip leads to a rapid but transitory increase in the number of lateral primordia, the largest number arising in the most apical segment of decapitated roots suggesting the accumulation of acropetally moving promoter substances in this region. The cotyledons appear to be the main source of promoter substances for both the induction and emergence of lateral roots, although one or more promoters also appear to be produced in the epicotyl. The data further indicate that the root tip is possibly the source of a substance which moves basipetally and interacts with acropetally moving promoters to regulate the zone for lateral primordia initiation; the root tip also appears to be the source of a powerful inhibitor of lateral root emergence.