Comparing the performance of one-column process and four-zone simulated moving bed by computer simulation

A new one-column chromatography process, analogous to a four-zone simulated moving bed (SMB), was presented. The basic principle of the process was identical to that of a four-zone SMB. The process consisted of one chromatographic column and four tanks, instead of the four columns in the four-zone SMB (1-1-1-1), and has been used for the separation of two amino acids, phenylalanine and tryptophan, using an ion exchange resin. The operating parameters for the one-column process and four-zone SMB were obtained from equilibrium theory. Computer simulations were used to compare the performances of the new one column process to that of the general four-zone SMB, using Aspen Chromatography^™ v 11.1. The differences between the one-column and SMB processes in terms of the purities and yields of phenylalanine and tryptophan were less than 4 and about 6%, respectively. The lower purities of the one-column process were due to the loss of the developed concentration profiles in the column when the liquid was stored in tanks. The one-column process gave great flexibility, and would be useful for reconstructing an existing conventional chromatography process to one of a SMB.     

Enhancement of oxygen mass transfer in stirred bioreactors using oxygen-vectors. 1. Simulated fermentation broths

Oxygen mass transfer represents the most important parameter involved in the design and operation of mixing-sparging equipment for bioreactors. It can be described and analyzed by means of the mass transfer coefficient, k_La. The k_La values are affected by many factors such as geometrical and operational characteristics of the vessels, media composition, type, concentration and microorganism morphology, and biocatalysts properties. The efficiency of oxygen transfer could be enhanced by adding oxygen-vectors in broths, such as hydrocarbons or fluorocarbons, without increasing the energy consumption for mixing or aeration. The experimental results obtained for simulated broths indicated a considerable increase of k_La in the presence of n-dodecane, and the existence of a certain value of n-dodecane concentration that corresponds to a maximum mass transfer rate of oxygen. The magnitude of the positive effect of n-dodecane depends both on the broths characteristics and operational conditions of the bioreactor.Notation d stirrer diameter, mm - d oxygen electrode diameter, mm - D bioreactor diameter, mm - h distance from the inferior stirrer to the bioreactor bottom, mm - H bioreactor height, mm - k_La oxygen mass transfer coefficient, s^-1 - l impeller blade length, mm - I oxygen electrode immersed length, mm - P power consumption for mixing of non-aerated broths, W - P_a power consumption for mixing of aerated broths, W - (P_a/V) specific power input, W/m³ - s baffle width, mm - v_S superficial air velocity, m/s - V volume of medium, m³ - w impeller blade height, mm - volumetric fraction of oxygen-vector - _a apparent viscosity, Pa*s - density, kg/m³     

Experimental study of rat beta islet cells cultured under simulated microgravity conditions

To observe the effects of simulated microgravity on beta islet cell culture, we have compared the survival rates and the insulin levels of the isolated rat islet cells cultured at micro- and normal gravity conditions. The survival rates of the cells cultured were determined by acridine orange-propidium iodide double-staining on day 3, 7 and 14. The morphology of the cells was observed by electron microscopy. Insulin levels were measured by radio immuno assays. Our results show that the cell number cultured under the microgravity condition is significantly higher than that under the routine condition (P<0.01). Some tubular structure shown by transmission electron microscopy, possibly for the transport of nutrients, were formed intercellularly in the microgravity cultured group on day 7. There were also abundant secretion particles and mitochondria in the cytoplasm of the cells. Scanning electron microscopy showed that there were holes formed between each islet, possibly connecting with the nutrient trans     

Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library

Accurate prediction of the placement and comformations of protein side chains given only the backbone trace has a wide range of uses in protein design, structure prediction, and functional analysis. Prediction has most often relied on discrete rotamer libraries so that rapid fitness of side-chain rotamers can be assessed against some scoring function. Scoring functions are generally based on experimental parameters from small-molecule studies or empirical parameters based on determined protein structures. Here, we describe the NCN algorithm for predicting the placement of side chains. A predominantly first-principles approach was taken to develop the potential energy function incorporating van der Waals and electrostatics based on the OPLS parameters, and a hydrogen bonding term. The only empirical knowledge used is the frequency of rotameric states from the PDB. The rotamer library includes nearly 50,000 rotamers, and is the most extensive discrete library used to date. Although the computational time tends to be longer than most other algorithms, the overall accuracy exceeds all algorithms in the literature when placing rotamers on an accurate backbone trace. Considering only the most buried residues, 80% of the total residues tested, the placement accuracy reaches 92% for chi(1), and 83% for chi(1 + 2), and an overall RMS deviation of 1 A. Additionally, we show that if information is available to restrict chi(1) to one rotamer well, then this algorithm can generate structures with an average RMS deviation of 1.0 A for all heavy side-chains atoms and a corresponding overall chi(1 + 2) accuracy of 85.0%.     

Conformational analysis of endomorphin-2 by molecular dynamics methods

Endomorphin-2 (EM2, H-Tyr-Pro-Phe-Phe-NH(2)) is a highly potent and selective mu-opioid receptor agonist. A conformational analysis of EM2 was carried out by simulated annealing (SA) and molecular dynamics (MD) methods. Molecular modeling was conducted on both neutral (N-terminal NH(2)) and charged (N-terminal NH(3) (+)) molecules. Based on the results of NMR investigations showing an equilibrium mixture of cis and trans Tyr(1)-Pro(2) peptide bonds for EM2 in solution, simulations were performed with restrained cis-Pro and trans-Pro peptide bonds, too. A separate SA study with unrestrained Pro peptide bonds was also conducted. Preferred conformational states are presented in Ramachandran plots. The g(+), g(-), and trans populations of the aromatic amino acid residue side chains were determined in chi(1) space. The distances between the N-terminal N atom and the other backbone N and O atoms, and the distances between the centers of the aromatic rings and the Pro(2) ring, were determined. The energy distribution of the structures obtained by SA was calculated. The preferred secondary structural elements were different kinds of beta-turns, an inverse gamma-turn located in the N-terminal region, and regular and inverse gamma-turns located in the C-terminal region. These turns were stabilized by intramolecular H-bonds and bifurcated H-bonds.     

间断性人工重力作用对模拟失重大鼠股骨的防护效应

目的：比较三种间断性人工重力对抗措施对模拟失重大鼠的影响。方法：SD雄性大鼠30只,按体重配对后随机等分为5组：对照组（C）,悬吊组（S）,站立组（G1）,1.5G（G2）和2.6G人工重力组（G3）。对抗组大鼠每日分别给予1h的站立、1.5和2.6G人工重力作用。利用物理测量和三点弯曲等实验,观察了3周间断性人工重力对大鼠股骨生长、生物力学特性的影响。结果：与S组大鼠比较：G1组弹性载荷、最大和刚性系数显著恢复（P＜0.05）;G2组直径（P＜0.01）和干重、密度（P＜0.05）,弹性载荷和最大载荷显著提高（P＜0.05）;G3组弹性载荷和最大载荷显著恢复（P＜0.01）。结论：三种对抗措施均显著改善了尾吊大鼠承重骨的生长力学特性,而1.5G的1h/d人工重力作用是较理想的对抗方法。     

Regeneration in fringe mangrove forests damaged by Hurricane Andrew

Mangrove forests along many tropical coastlines are frequently andseverely damaged by hurricanes. The ability of mangrove forests to regeneratefollowing hurricanes has been noted, but changes that occur in vegetationfollowing disturbance by hurricane winds and storm tides have not been studied.We measured changes in plant community structure and environmental variables intwo fringe mangrove forests in south Florida, USA that experienced high windvelocities and storm tides associated with Hurricane Andrew (August1992). Loss of the forest canopy stimulated regeneration via seedlinggrowth and recruitment, as well as resprouting of some trees that survived thehurricane. Initial regeneration differed among species in both forests:Rhizophora mangle L. regenerated primarily via growth ofseedlings present at the time of the hurricane (i.e., release of advancerecruits), but many trees of Avicennia germinans(L.) Stearn and Laguncularia racemosa Gaertn.f.resprouted profusely from dormant epicormic buds. In one forest, which wasformerly dominated by Laguncularia, high densities ofRhizophora seedlings survived the hurricane and grew toform dense stands of saplings and small trees ofRhizophora. In the other forest, there were lowerdensitiesof surviving Rhizophora seedlings (possibly due tohigher storm tide), and extensive bare areas that were colonized byAvicennia, Laguncularia, andherbaceous species. This forest, predominantly Rhizophoraat the time of the hurricane, now contains stands of saplings and small treesofall three species, interspersed with patches dominated by herbaceous plants.These findings indicate that moderately damaged fringe forests may regenerateprimarily via release of Rhizophora advance recruits,leading to single-species stands. In severely damaged forests, seedlingrecruitment may be more important and lead to mixed-species stands.Regeneration of mangrove forests following hurricanes can involve differentpathways produced by complex interactions between resprouting capability,seedling survival, post-hurricane seedling recruitment, and colonizationby herbaceous vegetation. These differences in relative importance ofregeneration pathways, which may result in post-hurricane forestsdifferent from their pre-hurricane structure, suggest that models forregeneration of mangrove forests will be more complex than directregeneration models proposed for other tropical forests whereregeneration after hurricanes is dominated by resprouting.     

Computer modeling and molecular dynamics simulations of ligand bound complexes of bovine angiogenin: dinucleotide topology at the active site of RNase a family proteins

We have undertaken the modeling of substrate-bound structures of angiogenin. In our recent study, we modeled the dinucleotide ligand binding to human angiogenin. In the present study, the substrates CpG, UpG, and CpA were docked onto bovine angiogenin. This was achieved by overcoming the problem of an obstruction to the B1 site by the C-terminus and identifying residues that bind to the second base. The modeled complexes retain biochemically important interactions. The docked models were subjected to 1 ns of molecular dynamics, and structures from the simulation were refined by using simulated annealing. Our models explained the enzyme's specificity for both B1 and B2 bases as observed experimentally. The nature of binding of the dinucleotide substrate was compared with that of the mononucleotide product. The models of these complexes were also compared with those obtained earlier with human angiogenin. On the basis of the simulations and annealed structures, we came up with a consensus topology of dinucleotide ligands that binds to human and bovine angiogenins. This dinucleotide conformation can serve as a starting model for ligand-bound complex structures for RNase A family of proteins. We demonstrated this capability by generating the complex structure of CpA bound to eosinophil-derived neurotoxin (EDN) by fitting the consensus topology of CpA to the crystal structure of native EDN.     

Refined structure of a flexible heptasaccharide using 1H-13C and 1H-1H NMR residual dipolar couplings in concert with NOE and long range scalar coupling constants

The heptasaccharide isolated from the cell wall polysaccharide of Streptococcus mitis J22 serves as an important model for the dynamics and conformation of complex polysaccharides, illustrating the nature of flexibility with rigid epitopes joined by flexible hinges. One-bond C-H residual dipolar couplings (¹D_CH) and long-range H-H residual dipolar couplings (ⁿD_HH) were measured for the heptasaccharide in a cetylpyridinium chloride/hexanol/brine lamellar liquid crystal medium. A method is proposed to determine the ⁿD_HH in natural abundance based on a ¹³C resolved ¹H TOCSY pulse sequence previously published to determine the homonuclear scalar couplings. Different methods for interpretation of the ¹D_CH and the ⁿD_HH residual dipolar coupling data obtained were compared and combined with the NOE and long-range H,C and C,C scalar couplings available for this heptasaccharide. A flexible model of the heptasaccharide was determined in which two structurally well-defined regions involving four and two sugar residues, respectively are joined by a flexible hinge which involves two 16 glycosidic linkages.     

MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases

A new paradigm is proposed for modeling biomacromolecular interactions and complex formation in solution (protein-protein interactions so far in this report) that constitutes the scaffold of the automatic system MIAX (acronym for Macromolecular Interaction Assessment X). It combines in a rational way a series of computational methodologies, the goal being the prediction of the most native-like protein complex that may be formed when two isolated (unbound) protein monomers interact in a liquid environment. The overall strategy consists of first inferring putative precomplex structures by identification of binding sites or epitopes on the proteins surfaces and a simultaneous rigid-body docking process using geometric instances alone. Precomplex configurations are defined here as all those decoys the interfaces of which comply substantially with the inferred binding sites and whose free energy values are lower. Retaining all those precomplex configurations with low energies leads to a reasonable number of decoys for which a flexible treatment is amenable. A novel algorithm is introduced here for automatically inferring binding sites in proteins given their 3-D structure. The procedure combines an unsupervised learning algorithm based on the self-organizing map or Kohonen network with a 2-D Fourier spectral analysis. To model interaction, the potential function proposed here plays a central role in the system and is constituted by empirical terms expressing well-characterized factors influencing biomacromolecular interaction processes, essentially electrostatic, van der Waals, and hydrophobic. Each of these procedures is validated by comparing results with observed instances. Finally, the more demanding process of flexible docking is performed in MIAX embedding the potential function in a simulated annealing optimization procedure. Whereas search of the entire configuration hyperspace is a major factor precluding hitherto systems from efficiently modeling macromolecular interaction modes and complex structures, the paradigm presented here may constitute a step forward in the field because it is shown that a rational treatment of the information available from the 3-D structure of the interacting monomers combined with conveniently selected computational techniques can assist to elude search of regions of low probability in configuration space and indeed lead to a highly efficient system oriented to solve this intriguing and fundamental biologic problem.