Hydrodynamic multibead modeling: problems, pitfalls, and solutions. 2. Proteins

The shape of macromolecules can be approximated by filling models, if both hydrodynamic and scattering properties should be predicted. Modeling of complex biological macromolecules, such as oligomeric proteins, or of molecule details calls for usage of many beads to preserve the original features. However, the calculation of precise values for structural and hydrodynamic parameters has to consider many problems and pitfalls. Among these, the huge number of beads required for modeling details and the choice of appropriate volume corrections for the calculation of intrinsic viscosities are pestering problems to date. As a first step to tackle these problems, various tests with multibead models (ellipsoids of different axial ratios) were performed. The agreement of the predicted molecular properties with those derived from whole-body approaches can be used as evaluation criteria. Modification of previously available versions of García de la Torre’s program HYDRO allows hydrodynamic modeling of macromolecules composed of a maximum of about 11,000 beads. Moreover, application of our recently suggested “reduced volume correction” enables a fast and efficient anticipation of intrinsic viscosities. Correct parameter predictions were obtained for all models analyzed. The data obtained were compared to the results of calculations based on HYDRO programs available to the public. The calculations revealed some unexpected results and allowed founded conclusions of general importance for precise calculations on multibead models (e.g., the requirement of calculations in the double-precision mode).     

Hydrodynamic multibead modeling: problems, pitfalls, and solutions. 1. Ellipsoid models

The shape of macromolecules can be approximated by filling models, if both hydrodynamic and scattering properties should be predicted. Modeling of complex biological macromolecules, such as oligomeric proteins, or of molecule details calls for usage of many beads to preserve the original features. However, the calculation of precise values for structural and hydrodynamic parameters has to consider many problems and pitfalls. Among these, the huge number of beads required for modeling details and the choice of appropriate volume corrections for the calculation of intrinsic viscosities are pestering problems to date. As a first step to tackle these problems, various tests with multibead models (ellipsoids of different axial ratios) were performed. The agreement of the predicted molecular properties with those derived from whole-body approaches can be used as evaluation criteria. Modification of previously available versions of García de la Torre’s program HYDRO allows hydrodynamic modeling of macromolecules composed of a maximum of about 11,000 beads. Moreover, application of our recently suggested “reduced volume correction” enables a fast and efficient anticipation of intrinsic viscosities. Correct parameter predictions were obtained for all models analyzed. The data obtained were compared to the results of calculations based on HYDRO programs available to the public. The calculations revealed some unexpected results and allowed founded conclusions of general importance for precise calculations on multibead models (e.g., the requirement of calculations in the double-precision mode).     

Comparison of mechanistic and hybrid modeling approaches for characterization of a CHO cultivation process: Requirements,pitfalls and solution paths

Despite the advantages of mathematical bioprocess modeling, successful model implementation already starts with experimental planning and accordingly can fail at this early stage. For this study, two different modeling approaches (mechanistic and hybrid) based on a four-dimensional antibody-producing CHO fed-batch process are compared. Overall, 33 experiments are performed in the fractional factorial four-dimensional design space and separated into four different complex data partitions subsequently used for model comparison and evaluation. The mechanistic model demonstrates the advantage of prior knowledge (i.e., known equations) to get informative value relatively independently of the utilized data partition. The hybrid approach displayes a higher data dependency but simultaneously yielded a higher accuracy on all data partitions. Furthermore, our results demonstrate that independent of the chosen modeling framework, a smart selection of only four initial experiments can already yield a very good representation of a full design space independent of the chosen modeling structure. Academic and industry researchers are recommended to pay more attention to experimental planning to maximize the process understanding obtained from mathematical modeling.     

Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures.

The hydrodynamic properties of rigid particles are calculated from models composed of spherical elements (beads) using theories developed by Kirkwood, Bloomfield, and their coworkers. Bead models have usually been built in such a way that the beads fill the volume occupied by the particles. Sometimes the beads are few and of varying sizes (bead models in the strict sense), and other times there are many small beads (filling models). Because hydrodynamic friction takes place at the molecular surface, another possibility is to use shell models, as originally proposed by Bloomfield. In this work, we have developed procedures to build models of the various kinds, and we describe the theory and methods for calculating their hydrodynamic properties, including approximate methods that may be needed to treat models with a very large number of elements. By combining the various possibilities of model building and hydrodynamic calculation, several strategies can be designed. We have made a quantitative comparison of the performance of the various strategies by applying them to some test cases, for which the properties are known a priori. We provide guidelines and computational tools for bead modeling.     

Evaluation of a palliative care service: problems and pitfalls.

OBJECTIVE--To evaluate a palliative care home support team based on an inpatient unit. DESIGN--Randomised controlled trial with waiting list. Patients in the study group received the service immediately, those in the control group received it after one month. Main comparison point was at one month. SETTING--A city of 300,000 people with a publicly funded home care service and about 200 general practitioners, most of whom provide home care. MAIN OUTCOME MEASURES--Pain and nausea levels were measured at entry to trial and at one month, as were quality of life for patients and care givers'' health. RESULTS--Because of early deaths, problems with recruitment, and a low compliance rate for completion of questionnaires, the required sample size was not attained. CONCLUSION--In designing evaluations of palliative care services, investigators should be prepared to deal with the following issues: attrition due to early death, opposition to randomisation by patients and referral sources, ethical problems raised by randomisation of dying patients, the appropriate timing of comparison points, and difficulties of collecting data from sick or exhausted patients and care givers. Investigators may choose to evaluate a service from various perspectives using different methods: controlled trials, qualitative studies, surveys, and audits. Randomised trials may prove to be impracticable for evaluation of palliative care.     

Microsatellite based typing of Aspergillus fumigatus: strengths, pitfalls and solutions

Microsatellites, or short tandem repeats (STR's), are popular tools to discriminate between microbial isolates. Here, we report on the robustness of a microsatellite panel for discrimination of Aspergillus fumigatus isolates. Two major PCR artefacts (stutter peaks and minus-A peaks) can complicate correct interpretation of STR data. We investigated the effect of alterations to the various components of the PCR amplification mixtures on these PCR artefacts and on the reproducibility of this assay. Some extreme conditions led to a loss of signal, but, under all conditions where a signal was obtained, identical typing results were produced. Furthermore, pitfalls with the exchange of results between labs are discussed. These pitfalls are primarily associated with sizing of the obtained PCR fragments.     

Image-based modeling for better understanding and assessment of atherosclerotic plaque progression and vulnerability: Data,modeling, validation,uncertainty and predictions

Medical imaging and image-based modeling have made considerable progress in recent years in identifying atherosclerotic plaque morphological and mechanical risk factors which may be used in developing improved patient screening strategies. However, a clear understanding is needed about what we have achieved and what is really needed to translate research to actual clinical practices and bring benefits to public health. Lack of in vivo data and clinical events to serve as gold standard to validate model predictions is a severe limitation. While this perspective paper provides a review of the key steps and findings of our group in image-based models for human carotid and coronary plaques and a limited review of related work by other groups, we also focus on grand challenges and uncertainties facing the researchers in the field to develop more accurate and predictive patient screening tools.     

Psychophysics of sweet and fat perception in obesity: problems, solutions and new perspectives

Psychophysical comparisons seem to show that obese individuals experience normal sweet and fat sensations, they like sweetness the same or less, but like fat more than the non-obese do. These psychophysical comparisons have been made using scales (visual analogue or category) that assume intensity labels (e.g. extremely) which denote the same absolute perceived intensity to all. In reality, the perceived intensities denoted by labels vary because they depend on experiences with the substances to be judged. This variation makes comparisons invalid. Valid comparisons can be made by asking the subjects to rate their sensory/hedonic experiences in contexts that are not related to the specific experiences of interest. Using this methodology, we present the evidence that the sensory and hedonic properties of sweet and fat vary with body mass index. The obese live in different orosensory and orohedonic worlds than do the non-obese; the obese experience reduced sweetness, which probably intensifies fat sensations, and the obese like both sweet and fat more than the non-obese do. Genetic variation as well as taste pathology contribute to these results. These psychophysical advances will impact experimental as well as clinical studies of obesity and other eating disorders.     

Hydrodynamic properties of a double-helical model for DNA.

The translational and rotational diffusion coefficients of very short DNA fragments have been calculated using a double-helical bead model in which each nucleotide is represented by one bead. The radius of the helix is regarded as an adjustable parameter. The translational coefficient and the perpendicular rotation coefficient agree very well with experimental values for oligonuclotides with 8, 12, and 20 base pairs, for a single value of the helical radius of about 10 A. We have also calculated a nuclear magnetic resonance relaxation time in which the coefficient for rotation about the main axis is involved. As found previously with cylindrical models, the results deviate from experimental values, indicating that the internal motion of the bases has a remarkable amplitude. An attempt to quantify the extent of internal motions is presented.     

Pharmacophore modeling, molecular docking, and molecular dynamics simulation approaches for identifying new lead compounds for inhibiting aldose reductase 2

Aldose reductase 2 (ALR2), which catalyzes the reduction of glucose to sorbitol using NADP as a cofactor, has been implicated in the etiology of secondary complications of diabetes. A pharmacophore model, Hypo1, was built based on 26 compounds with known ALR2-inhibiting activity values. Hypo1 contains important chemical features required for an ALR2 inhibitor, and demonstrates good predictive ability by having a high correlation coefficient (0.95) as well as the highest cost difference (128.44) and the lowest RMS deviation (1.02) among the ten pharmacophore models examined. Hypo1 was further validated by Fisher's randomization method (95%), test set (r = 0.91), and the decoy set shows the goodness of fit (0.70). Furthermore, during virtual screening, Hypo1 was used as a 3D query to screen the NCI database, and the hit leads were sorted by applying Lipinski's rule of five and ADME properties. The best-fitting leads were subjected to docking to identify a suitable orientation at the ALR2 active site. The molecule that showed the strongest interactions with the critical amino acids was used in molecular dynamics simulations to calculate its binding affinity to the candidate molecules. Thus, Hypo1 describes the key structure-activity relationship along with the estimated activities of ALR2 inhibitors. The hit molecules were searched against PubChem to find similar molecules with new scaffolds. Finally, four molecules were found to satisfy all of the chemical features and the geometric constraints of Hypo1, as well as to show good dock scores, PLPs and PMFs. Thus, we believe that Hypo1 facilitates the selection of novel scaffolds for ALR2, allowing new classes of ALR2 inhibitors to be designed.     

Enzymatic conversions of polar lipids. Principles, problems and solutions

This text provides a brief overview of the principles of enzymatic lipid conversion and some recent advances in the enzymatic conversion of glycerophospholipids and galactolipids. Lipases and phospholipases are used to exchange fatty acids or the polar group in the lipids. The reactions can be carried out either as hydrolysis–esterification sequences or as one-step transferase reactions. The scope and limitations of the different methods are discussed.     

Dielectric properties of glucose in bulk aqueous solutions: Influence of electrode polarization and modeling

Impedance spectroscopy was applied to determine glucose concentration in the interstitial fluid for its potential use in diabetic monitoring. For this purpose, the changes in the measured dielectric properties due to the presence of glucose in water and saline solutions were examined between 40 Hz and 110 MHz. Electrode polarization (EP) was a dominant factor which shaped the spectrum at low frequencies. A theoretical model of EP using a constant phase-angle-element produced excellent matches to the measured data. By fitting the measured data to the model, the relative permittivity (?(h)) and conductivity (σ(l)) were obtained. For deionized water, the relative permittivity dropped from 80.1 to 73.2 and conductivity ranged between 0.142 and 0.212 mS/m when the glucose concentration was increased from 0 to 32 g/dl. For the same variation of glucose level in 0.15 M NaCl, ?(h) was reduced from 79.8 to 71.5 and σ(l) decreased from 1.384 to 0.522 S/m. Glucose level produced a definite change in dielectric properties. However, the changes within the physiological range of glucose (less than a few hundred mg/dl) were small and appeared to be within the measurement error.