Molecular dynamics simulation studies for DNA sequence recognition by reactive metabolites of anticancer compounds

The discovery of novel anticancer molecules 5F‐203 (NSC703786) and 5‐aminoflavone (5‐AMF, NSC686288) has addressed the issues of toxicity and reduced efficacy by targeting over expressed Cytochrome P450 1A1 (CYP1A1) in cancer cells. CYP1A1 metabolizes these compounds into their reactive metabolites, which are proven to mediate their anticancer effect through DNA adduct formation. However, the drug metabolite–DNA binding has not been explored so far. Hence, understanding the binding characteristics and molecular recognition for drug metabolites with DNA is of practical and fundamental interest. The present study is aimed to model binding preference shown by reactive metabolites of 5F‐203 and 5‐AMF with DNA in forming DNA adducts. To perform this, three different DNA crystal structures covering sequence diversity were selected, and 12 DNA‐reactive metabolite complexes were generated. Molecular dynamics simulations for all complexes were performed using AMBER 11 software after development of protocol for DNA‐reactive metabolite system. Furthermore, the MM‐PBSA/GBSA energy calculation, per‐nucleotide energy decomposition, and Molecular Electrostatic Surface Potential analysis were performed. The results obtained from present study clearly indicate that minor groove in DNA is preferable for binding of reactive metabolites of anticancer compounds. The binding preferences shown by reactive metabolites were also governed by specific nucleotide sequence and distribution of electrostatic charges in major and minor groove of DNA structure. Overall, our study provides useful insights into the initial step of mechanism of reactive metabolite binding to the DNA and the guidelines for designing of sequence specific DNA interacting anticancer agents. Copyright © 2014 John Wiley & Sons, Ltd.     

Effectiveness of mouse minute virus inactivation by high temperature short time treatment technology: A statistical assessment

Viral contamination of mammalian cell cultures in GMP manufacturing facility represents a serious safety threat to biopharmaceutical industry. Such adverse events usually require facility shutdown for cleaning/decontamination, and thus result in significant loss of production and/or delay of product development. High temperature short time (HTST) treatment of culture media has been considered as an effective method to protect GMP facilities from viral contaminations. Log reduction factor (LRF) has been commonly used to measure the effectiveness of HTST treatment for viral inactivation. However, in order to prevent viral contaminations, HTST treatment must inactivate all infectious viruses (100%) in the medium batch since a single virus is sufficient to cause contamination. Therefore, LRF may not be the most appropriate indicator for measuring the effectiveness of HTST in preventing viral contaminations. We report here the use of the probability to achieve complete (100%) virus inactivation to assess the effectiveness of HTST treatment. By using mouse minute virus (MMV) as a model virus, we have demonstrated that the effectiveness of HTST treatment highly depends upon the level of viral contaminants in addition to treatment temperature and duration. We believe that the statistical method described in this report can provide more accurate information about the power and potential limitation of technologies such as HTST in our shared quest to mitigate the risk of viral contamination in manufacturing facilities.     

神农架海拔梯度上4种典型森林的乔木叶片功能性状特征

研究植物群落叶片功能性状沿环境梯度的变化可以更好地认识群落对环境的适应机制,海拔梯度在较小的空间范围内浓缩了不同的群落类型和环境梯度,是研究和理解群落与环境关系的理想场所。以神农架海拔梯度上4种典型森林为研究对象,分析了4种典型森林优势乔木树种的LMA、LDMC、N_area、N_mass、叶片厚度及叶片叶绿素含量等主要叶片功能性状随海拔的变化规律及各功能性状之间的相关性,以期从叶片功能性状角度揭示群落适应环境的机制。研究结果表明:在780-1970 m范围内,神农架海拔梯度上典型森林乔木优势种叶片的、N_area和叶片厚度随海拔升高而下降,而海拔2570 m的亚高山针叶林的LMA、N_area和叶片厚度最高,分别为187.37 g/cm²、1.92 g/m²和385.31 um,且针叶林的LMA是常绿阔叶林的2倍、落叶阔叶林的3.7倍;除常绿落叶阔叶混交林的N_mass小于落叶阔叶林外,N_mass随海拔升高(780-2570 m)而下降;海拔最高(2570 m)的针叶林和海拔最低(780 m)的常绿阔叶林的LDMC和叶绿素含量最高,分别为454.93 g/kg、407.64 g/kg和48.84、44.12;而海拔介于二者之间的常绿落叶阔叶混交林和落叶阔叶林的LDMC和叶绿素含量则最低,分别为338.93 g/kg、337.3 g/kg和38.73、38.19。叶片各功能性状之间存在着显著的相关性:叶片厚度与LMA/LDMC及LMA显著正相关。叶片叶绿素含量与N_area显著正相关。LMA与LDMC、N_area、叶片厚度、叶绿素含量显著正相关,LDMC与N_area、叶绿素含量、叶片厚度显著正相关,N_area与叶片厚度、叶绿素含量显著正相关,叶片厚度、叶绿素含量显著正相关。本研究进一步表明,随着海拔梯度上升环境条件的变化,森林群落不同物种功能性状间的相互作用共同决定着森林群落对环境的适应性。     

Morpho-anatomical and physiological leaf traits of two alpine herbs, Podophyllum hexandrum and Rheum emodi in the Western Himalaya under different irradiances

Morpho-anatomical leaf traits and photosynthetic activity of two alpine herbs, Podophyllum hexandrum (shade-tolerant) and Rheum emodi (light-requiring), were studied under field (PAR>2 000 μmol m⁻² s⁻¹) and greenhouse (PAR 500 μmol m⁻² s⁻¹) conditions. Mesophyll thickness, surface area of mesophyll cells facing intercellular spaces (S_mes), surface area of chloroplasts facing intercellular spaces (S_c), intercellular spaces of mesophyll cells (porosity), photon-saturated rate of photosynthesis per unit leaf area (P _Nmax), and ribulose-1,5-bisphosphate carboxylase/oxygenase activity decreased in the greenhouse with respect to the field and the decreases were significantly higher in R. emodi than in P. hexandrum. P. hexandrum had lower intercellular CO₂ concentration than R. emodi under both irradiances. The differences in acclimation of the two alpine herbs to low irradiance were due to their highly unlikely changes in leaf morphology, anatomy, and P _Nmax which indicated that the difference in radiant energy requirement related to leaf acclimation had greater impact under low than high irradiance.     

The relationship between nuclear DNA content and leaf strategy in seed plants

BACKGROUND AND AIMS: Species' 2C-values (mass of DNA in G(1) phase 2n nuclei) vary by at least four orders of magnitude among seed plants. The 2C-value has been shown to be co-ordinated with a number of other species traits, and with environmental variables. A prediction that species 2C-values are negatively related to leaf life span (LL) and leaf mass per area (LMA) is tested. These leaf traits are components of a major dimension of ecological variation among plant species. METHODS: Flow cytometry was used to measure the 2C-values for 41 Australian seed plant species, 40 of which were new to the literature. Where possible, LL and LMA data from the global literature were combined with 2C-values from our data set and online C-value databases. KEY RESULTS: Across all species, weak positive relationships were found between 2C-values and both LL and LMA; however, these did not reflect the relationships within either angiosperms or gymnosperms. Across 59 angiosperm species, there were weak negative relationships between 2C-values and both LL (r2 = 0.13, P = 0.005) and LMA (r2 = 0.15, P = 0.002). These relationships were the result of shifts to longer LL and greater LMA in woody compared with herbaceous growth forms, with no relationships present within growth forms. It was not possible to explain a positive relationship between 2C-values and LMA (r2 = 0.30, P = 0.024) across 17 gymnosperm species. The 2C-value was not related to LL or LMA either across species within orders (except for LMA among Pinales), or as radiation divergences in a model phylogeny. CONCLUSIONS: Gymnosperms appear to vary along a spectrum different from angiosperms. Among angiosperms, weak negative cross-species relationships were associated with growth form differences, and traced to a few divergences deep in the model phylogeny. These results suggest that among angiosperms, nuclear DNA content and leaf strategy are unrelated.     

Oxidative changes of lipids monitored by MALDI MS

Oxidation processes of lipids are of paramount interest from many viewpoints. For instance, oxidation processes are highly important under in vivo conditions because molecules with regulatory functions are generated by oxidation of lipids or free fatty acids. Additionally, many inflammatory diseases are accompanied by lipid oxidation and, therefore, oxidation products are also useful disease (bio)markers. Thus, there is also considerable interest in methods of (oxidized) lipid analysis.Nowadays, soft ionization mass spectrometric (MS) methods are regularly used to study oxidative lipid modifications due to their high sensitivities and the extreme mass resolution. Although electrospray ionization (ESI) MS is so far most popular, applications of matrix-assisted laser desorption and ionization (MALDI) MS are increasing. This review aims to summarize the so far available data on MALDI analyses of oxidized lipids. In addition to model systems, special attention will be paid to the monitoring of oxidized lipids under in vivo conditions, particularly the oxidation of (human) lipoproteins. It is not the aim of this review to praise MALDI as the “best” method but to provide a critical survey of the advantages and drawbacks of this method.     

Leaf economics and hydraulic traits are decoupled in five species‐rich tropical‐subtropical forests

Leaf economics and hydraulic traits are critical to leaf photosynthesis, yet it is debated whether these two sets of traits vary in a fully coordinated manner or there is room for independent variation. Here, we tested the relationship between leaf economics traits, including leaf nitrogen concentration and leaf dry mass per area, and leaf hydraulic traits including stomatal density and vein density in five tropical‐subtropical forests. Surprisingly, these two suites of traits were statistically decoupled. This decoupling suggests that independent trait dimensions exist within a leaf, with leaf economics dimension corresponding to light capture and tissue longevity, and the hydraulic dimension to water‐use and leaf temperature maintenance. Clearly, leaf economics and hydraulic traits can vary independently, thus allowing for more possible plant trait combinations. Compared with a single trait dimension, multiple trait dimensions may better enable species adaptations to multifarious niche dimensions, promote diverse plant strategies and facilitate species coexistence.     

Development of antler-type fruiting bodies of Ganoderma lucidum and determination of its biochemical properties

Following the importance of antler-type fruiting bodies of Ganoderma lucidum, in this study, the impact of main growth parameters such as ventilation and light on the development of antler-type fruiting bodies has been investigated together with the determination of physico-chemical properties of antler fruiting bodies. For this, the primordia bags of G. lucidum were kept under controlled ventilation to adjust the CO₂ produced by the mushrooms owing to its respiration under light and dark conditions. The bioactive compounds such as phenolics, flavonoids, water-soluble polysaccharides and ganoderic acid showed a two-fold increase in the antler-type fruiting bodies as compared to normal kidney-shaped fruiting bodies. It is assumed from this study that the antler type fruiting bodies are developed due to restricted ventilation which causes an increase in the level of CO₂ gas in the air as a result of respiration of mushroom. The shape and colour of antler fruiting bodies again dependent on the light provided in the growth chamber. This study also proves that with the manipulation of light and ventilation antler-type fruiting bodies of G. lucidum could be developed with higher quantity of bioactive compounds and with higher antioxidant potential.