DIEL RHYTHM OF ALGAL PHOSPHATE UPTAKE RATES IN P‐LIMITED CYCLOSTATS AND SIMULATION OF ITS EFFECT ON GROWTH AND COMPETITION1

Oscillations in the phosphate (P_i) uptake rates for three species of green algae were examined in a P‐limited cyclostat. For Ankistrodesmus convolutus Corda and Chlorella vulgaris Beyerinck, the P_i uptake rates increased during the daytime and decreased at night. In contrast, Chlamydomonas sp. exhibited the opposite uptake pattern. Cell densities also oscillated under a light:dark cycle, dividing at a species‐specific timing rather than continuously. In general, the cell densities exhibited an inverse relationship with the P_i uptake rates. A competition experiment between A. convolutus and C. vulgaris in a P‐limited cyclostat resulted in the dominance of C. vulgaris, regardless of the relative initial cell concentrations. Chlorella vulgaris also dominated in a mixed culture with Chlamydomonas sp., irrespective of the initial seeding ratio and dilution rate. However, Chlamydomonas sp. and A. convolutus coexisted in the competition experiment with gradual decrease of Chlamydomonas sp. when equally inoculated. Mathematical expressions of the oscillations in the P_i uptake rate and species‐specific cell division gate were used to develop a simulation model based on the Droop equation. The simulation results for each of the species conformed reasonably well to the experimental data. The results of the competition experiments also matched the competition simulation predictions quite well, although the experimental competition was generally more delayed than the simulations. In conclusion, the model simulation that incorporated the effect of diel rhythms in nutrient uptake clearly demonstrated that species diversity could be enhanced by different oscillation patterns in resource uptake, even under the condition of limitation by the same resource.     

A system to simulate gas exchange in humans to control quality of metabolic measurements

We have developed a gas exchange simulation system (GESS) to assess the quality control in measurements of metabolic gas exchange. The GESS simulates human breathing from rest to maximal exercise. It approximates breath-by-breath waveforms, ventilatory output, gas concentrations, temperature and humidity during inspiration and expiration. A programmable motion control driving two syringes allows the ventilation to be set at any tidal volume (V _T), respiratory frequency (f), flow waveform and period of inspiration and expiration. The GESS was tested at various combinations of V _T (0.5–2.5 l) and f (10–60 stroke · min⁻¹) and at various fractional concentrations of expired oxygen (0.1294–0.1795); and carbon dioxide (0.0210–0.0690) for a pre-set flow waveform and for expired gases at the same temperature and humidity as room air. Expired gases were collected in a polyethylene bag for measurement of volume and gas concentrations. Accuracy was assessed by calculating the absolute and relative errors on parameters (error = measured−predicted). The overall error in the gas exchange values averaged less than 2% for oxygen uptake and carbon dioxide output, which is within the accuracy of the Douglas bag method. Accepted: 4 June 1998     

Design,synthesis and molecular docking of thiazolidinedione based benzene sulphonamide derivatives containing pyrazole core as potential anti-diabetic agents

We herein report the design, synthesis and molecular docking studies of 2,4-thiazolidinedione derivatives containing benzene sulphonyl group which are docked against the Peroxisome Proliferator Activated Receptor (PPARγ) target. Compound 7p was most effective in lowering the blood glucose level as compared to standard drugs pioglitazone and rosiglitazone. Compound 7p exhibited potent PPAR-γ transactivation of 61.2% with 1.9 folds increase in gene expression. In molecular docking studies 7p showed excellent interactions with amino acids TYR 473, SER 289, HIE 449, TYR 327, ARG 288, MET 329 and LEU 228. Compound 7p did not cause any damage to the liver without any noteworthy weight gain and may be considered as promising candidates for the development of new antidiabetic agents.     

A molecular dynamics simulation investigation of the relative stability of the cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents

The cyclic octa-peptide octreotide and its derivatives are used as diagnostics and therapeutics in relation to particular types of cancers. This led to investigations of their conformational properties using spectroscopic, NMR and CD, methods. A CF₃-substituted derivative, that was designed to stabilize the dominant octreotide conformer responsible for receptor binding, turned out to have a lower affinity. The obtained spectroscopic data were interpreted as to show an increased flexibility of the CF₃ derivative compared to the unsubstituted octreotide, which could then explain the lower affinity.In this article, we use MD simulation without and with time-averaged NOE distance and time-averaged local-elevation ³J-coupling restraining representing experimental NMR data to determine the conformational properties of the different peptides in the different solvents for which experimental data are available, that are compatible with the NOE atom–atom distance bounds and the ³J_HNHα-couplings as derived from the NMR measurements. The conformational ensembles show that the CF₃ substitution in combination with the change of solvent from water to methanol leads to a decrease in flexibility and a shift in the populations of the dominant conformers that are compatible with the experimental data.     

城市热环境定量评价技术研究进展及发展趋势

自“城市热岛”概念提出以来,城市热环境定量评价一直是城市气候与环境研究领域的重要内容.随着空间信息技术与计算机模拟技术的不断发展,城市热环境定量评价的技术手段和方法也取得了长足进步.从最初单一利用气象站历史数据对城市宏观尺度热环境进行数理统计分析,逐步发展到综合利用地面气象观测、热红外遥感、数值模式模拟等多种技术对不同尺度热环境进行动态模拟与预测.本文系统回顾了地面气象观测、热红外遥感、数值模式模拟3类城市热环境定量评价技术的发展历程,并总结了各类技术的优缺点、适用性及发展趋势,以期为今后的城市热环境评价与优化研究提供参考.     

Molecular docking and dynamics simulations on the interaction of cationic porphyrin–anthraquinone hybrids with DNA G-quadruplexes

A series of cationic porphyrin–anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.     

Thermoregulation in premature infants: A mathematical model

PurposeIn 2010, approximately 14.9 million babies (11.1%) were born preterm. Because preterm infants suffer from an immature thermoregulatory system they have difficulty maintaining their core body temperature at a constant level. Therefore, it is essential to maintain their temperature at, ideally, around 37 °C. For this, mathematical models can provide detailed insight into heat transfer processes and body-environment interactions for clinical applications.MethodsA new multi-node mathematical model of the thermoregulatory system of newborn infants is presented. It comprises seven compartments, one spherical and six cylindrical, which represent the head, thorax, abdomen, arms and legs, respectively. The model is customizable, i.e. it meets individual characteristics of the neonate (e.g. gestational age, postnatal age, weight and length) which play an important role in heat transfer mechanisms. The model was validated during thermal neutrality and in a transient thermal environment.ResultsDuring thermal neutrality the model accurately predicted skin and core temperatures. The difference in mean core temperature between measurements and simulations averaged 0.25±0.21 °C and that of skin temperature averaged 0.36±0.36 °C. During transient thermal conditions, our approach simulated the thermoregulatory dynamics/responses. Here, for all infants, the mean absolute error between core temperatures averaged 0.12±0.11 °C and that of skin temperatures hovered around 0.30 °C.ConclusionsThe mathematical model appears able to predict core and skin temperatures during thermal neutrality and in case of a transient thermal conditions.     

Macromolecular crowding and its influence on possible reaction mechanisms in photosynthetic electron flow

The diffusion of plastoquinol and its binding to the Qo site of the cyt bf complex in the course of photosynthetic electron transport was studied by following the sigmoidal flash-induced re-reduction kinetics of P700 after previous oxidation of the intersystem electron carriers. The data resulting from these experiments were matched with a simulation of electron transport using Monte Carlo techniques. The simulation was able to account for the experimental observations. Two different extreme cases of reaction mechanism at the Qo site were compared: a diffusion limited collisional mechanism and a non-diffusion limited tight binding mechanism. Assuming a tight binding mechanism led to best matches due to the high protein density in thylakoids. The varied parameters resulted in values well within the range of published data. The results emphasise the importance of structural characteristics of thylakoids in models of electron transport.     

Phase behavior and dynamic heterogeneities in lipids: A coarse-grained simulation study of DPPC-DPPE mixtures

The coarse-grained Marrink-model for biomembrane simulation is used to study mixtures of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylethanolamine (DPPE) at various concentrations and temperatures. At high temperatures close to ideal mixing is observed. In the low temperature ordered phase dynamic heterogeneities are identified under some conditions. These are correlated with heterogeneities in the local order and define local neighborhoods.     

A joint frailty model for survival and gap times between recurrent events

Therapy for patients with a recurrent disease focuses on delaying disease recurrence and prolonging survival. A common analysis approach for such data is to estimate the distribution of disease-free survival, that is, the time to the first disease recurrence or death, whichever happens first. However, treating death similarly as disease recurrence may give misleading results. Also considering only the first recurrence and ignoring subsequent ones can result in loss of statistical power. We use a joint frailty model to simultaneously analyze disease recurrences and survival. Separate parameters for disease recurrence and survival are used in the joint model to distinguish treatment effects on these two types of events. The correlation between disease recurrences and survival is taken into account by a shared frailty. The effect of disease recurrence on survival can also be estimated by this model. The EM algorithm is used to fit the model, with Markov chain Monte Carlo simulations in the E-steps. The method is evaluated by simulation studies and illustrated through a study of patients with heart failure. Sensitivity analysis for the parametric assumption of the frailty distribution is assessed by simulations.