Calculating glucose fluxes during meal tolerance test: a new computational approach

A new calculation method is proposed to quantify the endogenous glucose production (EGP), the glucose appearance rate due to meal ingestion (R(a meal)), and the glucose disposal (R(d)) during a three-tracer study design. The method utilizes the maximum likelihood theory combined with a regularization method to achieve a theoretically coherent computational framework. The method uses the two-compartment formulation of the glucose kinetics. Instead of assuming smoothness of unlabeled and labeled glucose concentrations, the method assumes that the EGP, the R(a meal), and the fractional glucose clearance are smooth, increasing plausibility of their individual estimates. The method avoids transformation of the measurement errors, which may skew the estimates of the EGP, R(a meal), and R(d) with the traditional approach. Finally, the sequential nature of the calculations is replaced by calculating the EGP, R(a meal), and R(d) in "one go" to avoid the propagation of the errors from the EGP and R(a meal) into R(d). An example study is shown demonstrating the utility of the approach. A better performance of the new method is demonstrated in a simulation study.     

Somatostatin-dopamine chimeras: a novel approach to treatment of neuroendocrine tumors

A combination of basic research observations concerning the interaction of somatostatin (SST) and dopamine (DA) receptors, and clinical reports of enhanced efficacy of combined SST and DA analogue treatment in suppressing GH hypersecretion, lead to the concept of creating chimeric molecules combining structural features of both compound classes. The resulting SST/DA chimeras retain the ability to interact with receptors of both families and display greatly enhanced potency and efficacy, as compared with that of individual SST or DA receptor agonists. In vitro studies with pituitary adenoma cells from acromegalic patients have demonstrated that the chimeric molecules have exceptional activity with regard to suppression of GH and prolactin secretion. Similarly, potent suppression of ACTH secretion from Cushing's-causing corticotroph tumors, and suppression of nonfunctioning pituitary adenoma proliferation has been observed. The chimeric SST/DA compounds are also quite potent and efficacious in suppressing both GH and IGF1 in vivo when tested in nonhuman primates, with no effect on either insulin secretion or glycemic control. Initial clinical studies examining acute, subcutaneous administration of the chimeric SST/DA compound, BIM-23A760, revealed both prolonged circulating half-life and extended duration of biological effect. With chronic administration, however, BIM-23A760 was found to produce a metabolite with dopaminergic activity that gradually accumulates and interferes with the activity of the parent compound. Consequently, efforts are currently underway to produce a second-generation chimera for treatment of neuroendocrine disease.     

Positioning of proteins in membranes: a computational approach

A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water to the lipid bilayer. The membrane hydrocarbon core was approximated as a planar slab of adjustable thickness with decadiene-like interior and interfacial polarity profiles derived from published EPR studies. Applicability and accuracy of the method was verified for a set of 24 transmembrane proteins whose orientations in membranes have been studied by spin-labeling, chemical modification, fluorescence, ATR FTIR, NMR, cryo-microscopy, and neutron diffraction. Subsequently, the optimal rotational and translational positions were calculated for 109 transmembrane, five integral monotopic and 27 peripheral protein complexes with known 3D structures. This method can reliably distinguish transmembrane and integral monotopic proteins from water-soluble proteins based on their transfer energies and membrane penetration depths. The accuracies of calculated hydrophobic thicknesses and tilt angles were approximately 1 A and 2 degrees, respectively, judging from their deviations in different crystal forms of the same proteins. The hydrophobic thicknesses of transmembrane proteins ranged from 21.1 to 43.8 A depending on the type of biological membrane, while their tilt angles with respect to the bilayer normal varied from zero in symmetric complexes to 26 degrees in asymmetric structures. Calculated hydrophobic boundaries of proteins are located approximately 5 A lower than lipid phosphates and correspond to the zero membrane depth parameter of spin-labeled residues. Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database:http://opm.phar.umich.edu/.     

Understanding the melanocyte distribution in human epidermis: an agent-based computational model approach

The strikingly even color of human skin is maintained by the uniform distribution of melanocytes among keratinocytes in the basal layer of the human epidermis. In this work, we investigated three possible hypotheses on the mechanism by which the melanocytes and keratinocytes organize themselves to generate this pattern. We let the melanocyte migration be aided by (1) negative chemotaxis due to a substance produced by the melanocytes themselves, or (2) positive chemotaxis due to a substance produced by keratinocytes lacking direct physical contact with a melanocyte, or (3) positive chemotaxis due to a substance produced by keratinocytes in a distance-to-melanocytes dependent manner. The three hypotheses were implemented in an agent-based computational model of cellular interactions in the basal layer of the human epidermis. We found that they generate mutually exclusive predictions that can be tested by existing experimental protocols. This model forms a basis for further understanding of the communication between melanocytes and other skin cells in skin homeostasis.     

Microarray analysis of ageing-related signatures and their expression in tumors based on a computational biology approach

Ageing and cancer have been associated with genetic and genomic changes.The identification of common signatures between ageing and cancer can reveal shared molecular mechanisms underlying them.In this study,we collected ageing-related gene signatures from ten published studies involved in six different human tissues and an online resource.We found that most of these gene signatures were tissuespecific and a few were related to multiple tissues.We performed a genome-wide examination of the expression of these signatures in various human tumor types,and found that a large proportion of these signatures were universally differentially expressed among normal vs.tumor phenotypes.Functional analyses of the highly-overlapping genes between ageing and cancer using DAVID tools have identified important functional categories and pathways linking ageing with cancer.The convergent and divergent mechanisms between ageing and cancer are discussed.This study provides insights into the biology of ageing and cancer,suggesting the possibility of potential interventions aimed at postponing ageing and preventing cancer.     

Evaluation of a computational model used to predict the patellofemoral contact pressure distribution

One possible cause of patellofemoral pain syndrome is excessive lateral force acting on the patella. Although several treatment methods focus on decreasing the lateral force acting on the patella, the relationship between the lateral force and the patellofemoral contact pressure distribution is unclear. A computational model has been developed to determine how loading variations alter the patellofemoral force and pressure distributions for individual knees. The model allows variation in the quadriceps and patella tendon forces, and calculates the predicted contact pressure distribution using the discrete element analysis technique. To characterize the accuracy of the model, four cadaver knees were flexed on a knee simulator with three initial Q-angles, while recording the force and pressure distributions with a pressure sensor. A model of each knee was created from CT data. Using the external force applied to the knee, the geometry of the knee, and the quadriceps origin as input, the pressure distribution was calculated during flexion. Similar trends were noted for the computational and experimental results. The percentage of the total force applied to the lateral cartilage increased with the Q-angle. The maximum contact pressure increased during flexion. The maximum lateral contact pressure increased with the Q-angle for three knees. For the other knee, increasing the Q-angle decreased the maximum lateral pressure. The maximum medial contact pressure decreased as the Q-angle increased. By characterizing the influence of patellofemoral loading on the force and pressure distributions, the computational model could be used to evaluate treatment methods prescribed for patellofemoral pain.     

The role of neuronal death during the development of topographically ordered projections: a computational approach

At the time of synaptogenesis typically 50% of the neurons die. The biological role of this is still unclear, but there is evidence in the visual system that many neurons projecting to topographically inappropriate parts of their target are eliminated to improve the accuracy of the mapping. The signaling that determines neuronal survival involves electrical activity and trophic factors. Based on these observations, we have elaborated a computational model for the self-organization of a two-layered neural network. We observe changes in the topographical organization between the two layers. In layer 1, a traveling wave of electrical activity is used as input. Activity transmission to layer 2 can generate, according to a Hebbian rule, a retrograde death signal that is compensated by a trophic survival signal generated by the target cells. Approximately 50% of the neurons die, and we observe refinement in the topography between the two layers. In alternative versions of the model, we show that an equivalent reorganization can occur through Hebbian synaptic modification alone, but with less precision and efficiency. When the two mechanisms are combined, synaptic modification provides no further improvement over that produced by neuronal death alone. This computational study supports the hypothesis that neuronal death during development can play a role in the refinement of topographical projections in the nervous system. Received: 9 November 1998 / Accepted in revised form: 14 April 1999     

dCLIP: a computational approach for comparative CLIP-seq analyses

Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at http://qbrc.swmed.edu/software/.     

Effect of initial core temperature on hyperthermic hyperventilation during prolonged submaximal exercise in the heat

We investigated whether a core temperature threshold for hyperthermic hyperventilation is seen during prolonged submaximal exercise in the heat when core temperature before the exercise is reduced and whether the evoked hyperventilatory response is affected by altering the initial core temperature. Ten male subjects performed three exercise trials at 50% of peak oxygen uptake in the heat (37°C and 50% relative humidity) after altering their initial esophageal temperature (T(es)). Initial T(es) was manipulated by immersion for 25 min in water at 18°C (Precooling), 35°C (Control), or 40°C (Preheating). T(es) after the water immersion was significantly higher in the Preheating trial (37.5 ± 0.3°C) and lower in the Precooling trial (36.1 ± 0.3°C) than in the Control trial (36.9 ± 0.3°C). In the Precooling trial, minute ventilation (Ve) showed little change until T(es) reached 37.1 ± 0.4°C. Above this core temperature threshold, Ve increased linearly in proportion to increasing T(es). In the Control trial, Ve increased as T(es) increased from 37.0°C to 38.6°C after the onset of exercise. In the Preheating trial, Ve increased from the initially elevated levels of T(es) (from 37.6 to 38.6°C) and Ve. The sensitivity of Ve to increasing T(es) above the threshold for hyperventilation (the slope of the T(es)-Ve relation) did not significantly vary across trials (Precooling trial = 10.6 ± 5.9, Control trial = 8.7 ± 5.1, and Preheating trial = 9.2 ± 6.9 L·min(-1)·°C(-1)). These results suggest that during prolonged submaximal exercise at a constant workload in humans, there is a clear core temperature threshold for hyperthermic hyperventilation and that the evoked hyperventilatory response is unaffected by altering initial core temperature.     

Paclitaxel delivery to brain tumors from hydrogels: a computational study

Malignant gliomas are aggressive forms of primary brain tumors characterized by a poor prognosis. The most successful treatment so far is the local implantation of polymer carriers (Gliadel® wafers) for the sustained release of carmustine. To improve the effectiveness of local drug treatment, new polymer carriers and pharmacological agents are currently being investigated. Of particular interest is a set of novel thermo‐gelling polymers for the controlled release of hydrophobic drugs such as paclitaxel (e.g., OncoGel?). Herein, we use computational mass transport simulations to investigate the effectiveness of paclitaxel delivery from hydrogel‐forming polymer carriers. We found similar (within 1–2 mm) therapeutic penetration distances of paclitaxel when released from these hydrogels as compared with carmustine released from Gliadel® wafers. Effective therapeutic concentrations were maintained for >30 days for paclitaxel when released from the hydrogel as compared with 4 days for carmustine released from Gliadel® wafers. Convection in brain tissue prevented the formation of a uniform drug concentration gradient around the implant. In addition, the surface area to volume ratio of the gel is an important factor that should be considered to maintain a controlled release of paclitaxel within the degradation lifetime of the polymer matrix. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011     

Analysis and 3D reconstruction of heterogeneity in malignant brain tumors: an interdisciplinary case study using a novel computational visualization approach

OBJECTIVE: To explore how a multidisciplinary approach, combining modern visualization and image processing techniques with innovative experimental studies, can augment the understanding of tumor development. STUDY DESIGN: We analyzed histologic sections of a microscopic brain tumor and reconstructed these slices into a 3D representation. We processed these slices to: (1) identify tumor boundaries, (2) isolate proliferating tumor cells, and (3) segment the tumor into regions based on the density of proliferating cells. We then reconstructed the 3D shape of the tumor using a constrained deformable surface approach. RESULTS: This novel method allows the analyst to (1) see specific properties of histologic slices in the 3D environment with animation, (2) switch 2D "views" dynamically, and (3) see relationships between the 3D structure and structure on a plane. CONCLUSION: Using this method to analyze a specific "case," we were also able to shed light on the limitations of a widely held assumption about the shape of expanding microscopic solid tumors as well as find more indications that such tumors behave as adaptive biosystems. Implications of these case study results, as well as future applications of the method for tumor biology research, are discussed.     

EXAMINE: a computational approach to reconstructing gene regulatory networks

Reverse-engineering of gene networks using linear models often results in an underdetermined system because of excessive unknown parameters. In addition, the practical utility of linear models has remained unclear. We address these problems by developing an improved method, EXpression Array MINing Engine (EXAMINE), to infer gene regulatory networks from time-series gene expression data sets. EXAMINE takes advantage of sparse graph theory to overcome the excessive-parameter problem with an adaptive-connectivity model and fitting algorithm. EXAMINE also guarantees that the most parsimonious network structure will be found with its incremental adaptive fitting process. Compared to previous linear models, where a fully connected model is used, EXAMINE reduces the number of parameters by O(N), thereby increasing the chance of recovering the underlying regulatory network. The fitting algorithm increments the connectivity during the fitting process until a satisfactory fit is obtained. We performed a systematic study to explore the data mining ability of linear models. A guideline for using linear models is provided: If the system is small (3-20 elements), more than 90% of the regulation pathways can be determined correctly. For a large-scale system, either clustering is needed or it is necessary to integrate information in addition to expression profile. Coupled with the clustering method, we applied EXAMINE to rat central nervous system development (CNS) data with 112 genes. We were able to efficiently generate regulatory networks with statistically significant pathways that have been predicted previously.     

Gating and conduction of nano-channel forming proteins: a computational approach

Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used to measure the possible amplitude of vibration in channel forming proteins. The current approach complements theoretical and experimental techniques including HOLE, Molecular Dynamics (MD), and voltage clamp used to address the channel’s structure and dynamics and provides the means to conduct a theoretical simultaneous study of the structure and function of the channel.

An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:3     

Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach

In order to understand the structural basis of Factor Xa (FXa) specificity, structural complexes of FXa with its synthetic inhibitors are determined using a computational docking approach. The AutoDock suite of programs is used to determine the binding modes of the synthetic inhibitors such as 3- and 4-amidinobenzylphenyl ether (ABP), amidinophenyl pyruvic acid (APPA), diamidinobenzofuranyl ethene (DABE), and DX-9065a 2-(5'-amidino-2'-benzofuranyl)-3-(7'amidino-2'-napthyl)-propionic acid (ABAP) to FXa. The synthetic inhibitors docked in the present study are different in size, nature of linkage, and properties. Two sets of simulations were carried out for synthetic inhibitors docking to FXa. In the first set of simulations, no explicit water molecules were included. In the second set of simulations two explicit solvent molecules were considered. In all the computationally predicted synthetic inhibitor complexes of FXa, the specificity pocket residue Asp-189 is involved in hydrogen bonding with the bound inhibitor. The active site water molecule WAT522 is involved in hydrogen bonding with all the bound inhibitors. The computed energies clearly discriminate the high affinity from low affinity binders.     

Comprehensive mutagenesis of HIV-1 protease: a computational geometry approach

A computational geometry technique based on Delaunay tessellation of protein structure, represented by C(alpha) atoms, is used to study effects of single residue mutations on sequence-structure compatibility in HIV-1 protease. Profiles of residue scores derived from the four-body statistical potential are constructed for all 1881 mutants of the HIV-1 protease monomer and compared with the profile of the wild-type protein. The profiles for an isolated monomer of HIV-1 protease and the identical monomer in a dimeric state with an inhibitor are analyzed to elucidate changes to structural stability. Protease residues shown to undergo the greatest impact are those forming the dimer interface and flap region, as well as those known to be involved in inhibitor binding.     

Scaling, growth and cyclicity in biology: a new computational approach

Background

The Phenomenological Universalities approach has been developed by P.P. Delsanto and collaborators during the past 2–3 years. It represents a new tool for the analysis of experimental datasets and cross-fertilization among different fields, from physics/engineering to medicine and social sciences. In fact, it allows similarities to be detected among datasets in totally different fields and acts upon them as a magnifying glass, enabling all the available information to be extracted in a simple way. In nonlinear problems it allows the nonscaling invariance to be retrieved by means of suitable redefined fractal-dimensioned variables.

Results

The main goal of the present contribution is to extend the applicability of the new approach to the study of problems of growth with cyclicity, which are of particular relevance in the fields of biology and medicine.

Conclusion

As an example of its implementation, the method is applied to the analysis of human growth curves. The excellent quality of the results (R ² = 0.988) demonstrates the usefulness and reliability of the approach.     

Lymphocyte HSP72 following exercise in hyperthermic runners: The effect of temperature

Heat shock protein 72 (HSP72) is the most inducible HSP, but is not always increased in lymphocytes following exercise. This field study examined whether lymphocyte HSP72 was increased in hyperthermic (T_rec>39.0 °C) male athletes following a 14 km competitive race in cool conditions (ambient temperature 11.2 °C). A comparison was also made between control runners (n=7) and those treated for exertional heat illness (n=9). Lymphocyte HSP72 was not increased in control runners immediately post- compared with pre-race, and there was no difference between both groups of runners. A second study of the race (ambient temperature 14.6 °C) found that lymphocyte HSP72 in control (n=7) and treated (n=9) athletes was higher 2 days post- compared with immediately post-race (p<0.01) and these increases were correlated with post-exercise T_rec (p<0.05).     

Novel families of toxin-like peptides in insects and mammals: a computational approach

Most animal toxins are short proteins that appear in venom and vary in sequence, structure and function. A common characteristic of many such toxins is their apparent structural stability. Sporadic instances of endogenous toxin-like proteins that function in non-venom context have been reported. We have utilized machine learning methodology, based on sequence-derived features and guided by the notion of structural stability, in order to conduct a large-scale search for toxin and toxin-like proteins. Application of the method to insect and mammalian sequences revealed novel families of toxin-like proteins. One of these proteins shows significant similarity to ion channel inhibitors that are expressed in cone snail and assassin bug venom, and is surprisingly expressed in the bee brain. A toxicity assay in which the protein was injected to fish induced a strong yet reversible paralytic effect. We suggest that the protein may function as an endogenous modulator of voltage-gated Ca(2+) channels. Additionally, we have identified a novel mammalian cluster of toxin-like proteins that are expressed in the testis. We suggest that these proteins might be involved in regulation of nicotinic acetylcholine receptors that affect the acrosome reaction and sperm motility. Finally, we highlight a possible evolutionary link between venom toxins and antibacterial proteins. We expect our methodology to enhance the discovery of additional novel protein families.