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A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: 1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. 2) The highly different accessibility in the membrane and water regions are addressed with a two-step, two-probe grid labeling procedure, and 3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 {\AA} for globular proteins is a very reasonable default value for membrane protein simulations. It gives an overall minimum number of inconsistencies between the continuum and explicit representations of water distributions in membrane channel proteins, at least in the water accessible pore/channel regions that we focus on. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe a good agreement with experiment results.Comment: 40 pages, 6 figures, 5 table

A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome.

A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa

Hierarchical Structure with Highly Ordered Macroporous-Mesoporous Metal-Organic Frameworks as Dual Function for CO2 Fixation.

As a major greenhouse gas, the continuous increase of carbon dioxide (CO2) in the atmosphere has caused serious environmental problems, although CO2 is also an abundant, inexpensive, and nontoxic carbon source. Here, we use metal-organic framework (MOF) with highly ordered hierarchical structure as adsorbent and catalyst for chemical fixation of CO2 at atmospheric pressure, and the CO2 can be converted to the formate in excellent yields. Meanwhile, we have successfully integrated highly ordered macroporous and mesoporous structures into MOFs, and the macro-, meso-, and microporous structures have all been presented in one framework. Based on the unique hierarchical pores, high surface area (592 m2/g), and high CO2 adsorption capacity (49.51 cm3/g), the ordered macroporous-mesoporous MOFs possess high activity for chemical fixation of CO2 (yield of 77%). These results provide a promising route of chemical CO2 fixation through MOF materials

Experimental Study of Smoke Spread in Titled Urban Traffic Tunnels Fires

AbstractMore and more urban traffic tunnels are built due to the heavy traffic in dense urban areas. Fire safety in tunnels is a concern due to the large traffic flow. Most of the urban tunnels have slope. Knowledge on smoke spread in titled tunnel is still limited. Experimental studies on the smoke spread in a titled tunnel are carried out by the reduced-scale tunnel model tests and will be discussed in this paper. Effects of the titled gradients and longitudinal ventilation speed on the temperature distribution and smoke stratification downstream from the fire along the tunnel will be studied The results show that the smoke spread upwards much faster with the slop gradient increasing, and a thick smoke layer was formed when smoke moved to the upward part of the tunnel and filled it up. The ventilation speed had a great influence on temperature distribution along the tunnel, and the smoke stratification will be distributed when the longitudinal ventilation speed becomes large. Lower ventilation speed should be adopted at the beginning to ensure the smoke downstream of the fire keep stratified to give the tunnel users more time to escape

Direct Cr (VI) bio-reduction with organics as electron donor by anaerobic sludge

Industrial activities produce lots of Cr (VI)-containing wastewater. This study presented a detailed work on direct Cr (VI) bio-reduction (i.e. Cr (VI) is reduced with organics as electron donor directly) by anaerobic sludge through both batch and long-term experiments. Effects of pH and initial Cr (VI) concentrations on direct Cr (VI) bio-reduction activity were evaluated. The highest direct Cr (VI) bio-reduction rate was achieved at pH 8.0 at 104\ua0mg Cr (VI)/g MLVSS/d (MLVSS: mixed liquor volatile suspended solids), corresponding to the highest protein release (124\ua0mg/g MLVSS) and cell viability (71%). In contrast, the direct Cr (VI) bio-reduction rates were 46, 70 and 82\ua0mg Cr (VI)/g MLVSS/d, respectively, at pH 6.0, 7.0 and 9.0. Also, the direct Cr (VI) bio-reduction activity decreased by 74% when initial Cr (VI) concentration increased from 10\ua0mg/L to 50\ua0mg/L. The contribution of chemical adsorption to Cr (VI) removal was found to be negligible, whereas biosorption played a role in Cr (VI) removal although its role was insignificant. Indirect Cr (VI) bio-reduction (i.e. Cr (VI) is chemically reduced by sulfide produced from biological sulfate reduction) rate (990\ua0mg Cr (VI)/g MLVSS/d) was faster than that (210\ua0mg Cr (VI)/g MLVSS/d) of direct Cr (VI) bio-reduction, indicating that indirect Cr (VI) bio-reduction would dominate the Cr (VI) bio-reduction pathway if both Cr (VI) and sulfate were present. The direct Cr (VI) bio-reduction was then successfully demonstrated in an up-flow anaerobic sludge bed (UASB) reactor, where the Cr (VI) was completely removed with a Cr (VI) removal rate of 1.0\ua0mg Cr (VI)/L/h. 454 pyrosequencing results revealed that direct Cr (VI) bio-reduction related genera were Desulfovibrio, Ochrobactrum and Anaerovorax

An analytical model on static smoke exhaust in Atria

Static smoke exhaust systems with natural vents are starting to be installed in big shopping complexes, ware‐houses and cargo terminals in the Far East. These systems are used for natural ventilation as well as for letting out smoke. This paper responds to concerns over the performance of static smoke exhaust systems, which remain less popular than dynamic smoke exhaust systems with mechanical fans. We propose a modification of a simple flow model found in the literature, adapting this to study smoke layer interface height with natural vents opened. We compare and justify our results, as generated by both Computational Fluid Dynamics and zone models, alongside reports of historical field tests. The model of smoke exhaust is applied in an illustrative example of a large hall, leading to the suggestion that a flow model could be used for designing natural vents. As the key driving force in removing smoke through natural vents is smoke's own buoyancy, the system might only be effective for bigger fires. Santrauka Tolimuosiuose Rytuose statines dūmu šalinimo sistemos su natūralios ventiliacijos angomis pradedamos irengti dideliuose prekybos kompleksuose, sandeliuose ir kroviniu terminaluose. Tokios sistemos naudojamos ir natūraliai ventiliacijai, ir dūmams šalinti. Šis straipsnis parengtas susirūpinus, kad statines dūmu išmetimo sistemos yra ne tokios populiarios nei dinamines dūmu išmetimo sistemos su mechaniniais ventiliatoriais. Autoriai siūlo literatūroje aprašomo paprasto srauto modelio modifikacija, pritaikant ši modeli dūmu sluoksnio salyčio su natūralios ventiliacijos angomis aukščiui tirti. Straipsnyje palyginti ir pagristi rezultatai, gauti taikant tiek skaičiuojamosios skysčiu dinamikos, tiek zonavimo modelius kartu su eksperimentiniais tyrimais vietoveje. Pateiktas dūmu šalinimo modelio taikymo pavyzdys dideleje saleje ir padaryta išvada, kad srauto modelis galetu būti taikomas irengiant natūralia ventiliacija. Kadangi pagrindine varomoji jega šalinant dūmus per natūralias ventiliacijos angas yra dūmu plūdrumas, sistema gali būti veiksminga tik esant didesniems gaisrams. First Published Online: 10 Feb 2011 Reikšminiai žodžiai: dūmu šalinimo sistemos, natūralios ventiliacijos angos, plūdrumas, dūmu sluoksnio salyčio aukšti

ADME Evaluation in Drug Discovery. 8. The Prediction of Human Intestinal Absorption by a Support Vector Machine

Human intestinal absorption (HIA) is an important roadblock in the formulation of new drug substances. In silico models for predicting the percentage of HIA based on calculated molecular descriptors are highly needed for the rapid estimation of this property. Here, we have studied the performance of a support vector machine (SVM) to classify compounds with high or low fractional absorption (%FA > 30% or %FA ≤ 30%). The analyzed data set consists of 578 structural diverse druglike molecules, which have been divided into a 480-molecule training set and a 98-molecule test set. Ten SVM classification models have been generated to investigate the impact of different individual molecular properties on %FA. Among these studied important molecule descriptors, topological polar surface area (TPSA) and predicted apparent octanol−water distribution coefficient at pH 6.5 (logD_(6.5)) show better classification performance than the others. To obtain the best SVM classifier, the influences of different kernel functions and different combinations of molecular descriptors were investigated using a rigorous training-validation procedure. The best SVM classifier can give satisfactory predictions for the training set (97.8% for the poor-absorption class and 94.5% for the good-absorption class). Moreover, 100% of the poor-absorption class and 97.8% of the good-absorption class in the external test set could be correctly classified. Finally, the influence of the size of the training set and the unbalanced nature of the data set have been studied. The analysis demonstrates that large data set is necessary for the stability of the classification models. Furthermore, the weights for the poor-absorption class and the good-absorption class should be properly balanced to generate unbiased classification models. Our work illustrates that SVMs used in combination with simple molecular descriptors can provide an extremely reliable assessment of intestinal absorption in an early in silico filtering process