Biomolecular Level Research Articles

Randomized maps for assessing the reliability of patients clusters in DNA microarray data analyses

Clustering algorithms may be applied to the analysis of DNA microarray data to identify novel subgroups that may lead to new taxonomies of diseases defined at bio-molecular level. A major problem related to the identification of biologically meaningful clusters is the assessment of their reliability, since clustering algorithms may find clusters even if no structure is present. Recently, methods based on random "perturbations" of the data, such as bootstrapping, noise injections techniques and random subspace methods have been applied to the problem of cluster validity estimation. In this framework, we propose stability measures that exploits the high dimensionality of DNA microarray data and the redundancy of information stored in microarray chips. To this end we randomly project the original gene expression data into lower dimensional subspaces, approximately preserving the distance between the examples according to the Johnson-Lindenstrauss (JL) theory. The stability of the clusters discovered in the original high dimensional space is estimated by comparing them with the clusters discovered in randomly projected lower dimensional subspaces. The proposed cluster-stability measures may be applied to validate and to quantitatively assess the reliability of the clusters obtained by a large class of clustering algorithms. We tested the effectiveness of our approach with high dimensional synthetic data, whose distribution is a priori known, showing that the stability measures based on randomized maps correctly predict the number of clusters and the reliability of each individual cluster. Then we showed how to apply the proposed measures to the analysis of DNA microarray data, whose underlying distribution is unknown. We evaluated the validity of clusters discovered by hierarchical clustering algorithms in diffuse large B-cell lymphoma (DLBCL) and malignant melanoma patients, showing that the proposed reliability measures can support bio-medical researchers in the identification of stable clusters of patients and in the discovery of new subtypes of diseases characterized at bio-molecular level.

Characterization of lung tumor subtypes through gene expression cluster validity assessment

The problem of assessing the reliability of clusters patients identified by clustering algorithms is crucial to estimate the significance of subclasses of diseases detectable at bio-molecular level, and more in general to support bio-medical discovery of patterns in gene expression data. In this paper we present an experimental analysis of the reliability of clusters discovered in lung tumor patients using DNA microarray data. In particular we investigate if subclasses of lung adenocarcinoma can be detected with high reliability at bio-molecular level. To this end we apply cluster validity measures based on random projections recently proposed by Bertoni and coworkers. The results show that at least two subclasses of lung adenocarcinoma can be detected with relatively high reliability, confirming and extending previous findings reported in the literature.

Physics models of centriole replication

Our previous pre-clinic experimental results have showed that the epithelialization can be enhanced by the externally applied rectangular pulsed electrical current stimulation (RPECS). The results are clinically significant for patients, especially for those difficult patients whose skin wounds need long periods to heal. However, the results also raise questions: How does the RPECS accelerate the epithelium cell proliferation? To answer these questions, we have previously developed several models for animal cells, in a view of physics, to explain mechanisms of mitosis and cytokinesis at a cellular level, and separation of nucleotide sequences and the unwinding of a double helix during DNA replication at a bio-molecular level. In this paper, we further model the mechanism of centriole replication during a natural and normal mitosis and cytokinesis to explore the mechanism of epithelialization enhanced with the externally applied RPECS at a bio-molecular level. Our models suggest: (1) Centriole replication is an information flowing. The direction of the information flowing is from centrioles to centrioles based on a cylindrical template of 9 x 3 protein microtubules (MTs) pattern. (2) A spontaneous and strong electromagnetic field (EMF) force is a pushing force that separates a mother and a daughter centrioles in centrosomes or in cells, while a pulling force of interacting fibers and pericentriolar materials delivers new babies. The newly born babies inherit the pattern information from their mother(s) and grow using microtubule fragments that come through the centrosome pores. A daughter centriole is always born and grows along stronger EMF. The EMF mostly determines centrioles positions and plays key role in centriole replication. We also hypothesize that the normal centriole replication could not been disturbed in centrosome in the epithelium cells by our RPECS, because the centrioles have two non-conducting envelope (cell and centrosome membranes), that protect the normal duplication. The induced electric field by externally applied RPECS could be mild compared with the spontaneous and natural electric field of the centrioles. Therefore, the centriole replication during the epithelium cellular proliferation may be directly, as well as indirectly (e.g., somatic reflex) accelerated by the RPECS.

Integrated Biological-Semiconductor Devices

The advent of semiconductor devices with nanoscale dimensions creates the potential to integrate nanoelectronics and optoelectronic devices with a great variety of biological systems. Moreover, the advances in nanotechnology are opening the way to achieving direct electrical contact of nanoelectronic structures with electrically and electrochemically active subcellular structures-including ion channels, receptors, and transmembrane proteins such as bacteriorhodopsin. Direct electrical interfacing at the biomolecular level opens the possibility of monitoring and controlling critical biological functions and processes in unprecedented ways, and portends a vast array of possibilities such as new classes of prosthetic devices, medical monitoring devices, medical delivery systems, and patient monitoring systems, as well as other applications. This article describes the salient properties of relevant biological structures and nanostructures. Advances in integrating man-made nanostructures with biological structures, including biomolecules, are described as well as the properties,characteristics, and functions of integrated nanoelectronic-biological structures. Future directions based on these prototype systems are highlighted.

Small Heat Shock Proteins, Morphological and Physiological Characteristics Associated with Heat Tolerance in Salvia (Salvia splendens)

Small heat shock proteins (sHSP) are a specific group of highly conserved proteins produced in almost all living organisms under heat stress. These sHSP have been shown to help prevent damage at the biomolecular level in plants. One of the greatest impediments to production of marketable herbaceous plants and their longevity is high temperature stress. The objectives of this experiment were to study the plant responses in terms of sHSP synthesis, single leaf net photosynthesis, total water-soluble carbohydrates (WSC), and overall growth for two S. splendens cultivars differing in performance under heat stress. `Vista Red' (heat tolerant) and `Sizzler Red' (heat sensitive) were exposed to short duration (3 hours) high temperature stresses of 30, 35, and 40 °C in growth chambers. Increasing the temperature to about 10 to 15 °C above the optimal growth temperature (25 °C, control) induced the synthesis of sHSP 27 in S. splendens. Expression of these proteins was significantly greater in the heat-tolerant vs. the heat-sensitive cultivar. Soluble carbohydrate content was greater in `Vista Red', and in both the cultivars raffinose was the primary soluble carbohydrate in heat-stressed plants. Overall growth of plants was significantly different in the two cultivars studied in terms of plant height, stem thickness, number of days to flower, and marketable quality. The better performance of `Vista Red' under heat stress was attributed to its morphological characteristics, including short stature, thicker stems and leaves. sHSPs and WSC are also found to be associated with heat tolerance and heat adaptation in S. splendens.

Modelling biological complexity: a physical scientist's perspective.

We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the integration of molecular and more coarse-grained representations of matter. The scope of such integrative approaches to complex systems research is circumscribed by the computational resources available. Computational grids should provide a step jump in the scale of these resources; we describe the tools that RealityGrid, a major UK e-Science project, has developed together with our experience of deploying complex models on nascent grids. We also discuss the prospects for mathematical approaches to reducing the dimensionality of complex networks in the search for universal systems-level properties, illustrating our approach with a description of the origin of life according to the RNA world view.

On-line fluorescent monitoring of the degradation of polymeric scaffolds for tissue engineering

Tissue engineering involves culturing, growing and assembling cells and newly generated matrix in polymeric scaffolds. To achieve a functional tissue in vitro, the cell-scaffold constructs are subjected to various stimulations during an incubation phase, which mimics the in vivo environment. In order to monitor the progression of tissue formation, there is a need for on-line and non-destructive methods of monitoring at the cellular and biomolecular level, for example, the assessment of scaffold degradation alongside the measure of matrix production. This study presents a proof of concept for monitoring scaffold degradation on-line within a culture environment. Using a mesoporous silica based approach, a pH sensitive fluorescent probe, fluorescein isothiocyanate (FITC), was incorporated into degradable polymeric scaffolds made from poly(L-lactic acid) which has a slow degradation rate, and poly(lactide-co-glycolide) which has a rapid degradation rate. The fluorescent probe was incorporated into thin films and three dimensional porous scaffolds demonstrating the capabilities of monitoring on-line. Following incubation, the intensity of fluorescence in the rapidly degrading scaffolds reduced with culture time in comparison to slow degrading polymeric scaffolds when observed qualitatively using fluorescent microscopy. The relationship between pH and fluorescent intensity was assessed, and the use of this technique for monitoring by-products via the solid scaffold by microscopy or through culture medium by a luminescence spectrometer is discussed. This study demonstrates that endowing scaffolds with a sensing element could provide an on-line and non-destructive monitoring method for tissue engineering.

Oxidativer Stress und kardiovaskuläre Erkrankungen

A number of diseases like hypercholesterolemia and atherosclerosis, hypertension, congestive heart failure, diabetes, ischemia-reperfusion, neurodegenerative diseases as well as acute and chronic inflammatory diseases are characterized by an increased steady-state concentration of reactive oxygen species (ROS). On a biomolecular level an enhanced oxidative stress causes damage of proteins, lipids and nucleic acids. Both the experimental and therapeutic efficiency of different antioxidative compounds (like various antioxidative enzymes) , drugs, metabolites and vitamins for the maintenance of an appropriate intracellular redox potential underline the importance of an excessive ROS-formation for these diseases. Control of excessive ROS-formation can be obtained by angiotensin converting enzyme (ACE-) inhibitors, by AT (1)-receptor blockers, by statins and other lipid lowering compounds, by improved expression of antioxidative enzymes (superoxide dismutase, catalase etc.), by compounds such as probucol, certain vitamins, pyruvate, by lipid apheresis and by physical exercise training, which displays surprising efficacy.

Characterization of particulate proteins in Pacific surface waters

We investigated molecular characteristics of particulate proteins in Pacific surface waters using two‐dimensional electrophoresis (2DE). Most proteinaceous materials estimated by dye‐binding methods were characterized by the 2DE unresolved acidic materials with a broad range of molecular mass and the 2DE unresolved low molecular mass materials with a broad range of isoelectric point. The 2DE unresolved acidic and low molecular mass materials were considered to comprise peptides conjugated with acidic saccharides and degradation products (peptides) of proteins, respectively, which indicates that almost all proteins in living organisms failed to survive in detrital particulate organic matter (POM). Nevertheless, 23 discrete proteins were distinguished by the 2DE. Electrophoretic patterns of the discrete proteins indicated that they were a component of detrital POM. Three discrete proteins were subjected to N terminal amino acid sequence analysis. Two proteins out of three could not be determined because their N termini were blocked, and one protein was determined from the N terminus to the ninth amino acid residue. A homology search revealed that the N terminal amino acid sequence of the protein agreed completely with that of 70 kDa heat shock protein (HSP70) derived from photosynthetic organisms. HSP70 is a major member of the molecular chaperones that protect or repair proteins from damage under conditions of environmental stress. The occurrence of HSP70 in this study demonstrated that phytoplankton were able to induce the molecular chaperone(s). Clarification of factor(s) controlling induction of chaperones will enable us to assess the actual environmental stress on phytoplankton at the biomolecular level.

Phenotype Characterisation Using Integrated Gene Transcript, Protein and Metabolite Profiling

Multifactorial diseases present a significant challenge for functional genomics. Owing to their multiple compartmental effects and complex biomolecular activities, such diseases cannot be adequately characterised by changes in single components, nor can pathophysiological changes be understood by observing gene transcripts alone. Instead, a pattern of subtle changes is observed in multifactorial diseases across multiple tissues and organs with complex associations between corresponding gene, protein and metabolite levels. This article presents methods for exploratory and integrative analysis of pathophysiological changes at the biomolecular level. In particular, novel approaches are introduced for the following challenges: (i) data processing and analysis methods for proteomic and metabolomic data obtained by electrospray ionisation (ESI) liquid chromatography-tandem mass spectrometry (LC/MS); (ii) association analysis of integrated gene, protein and metabolite patterns that are most descriptive of pathophysiological changes; and (iii) interpretation of results obtained from association analyses in the context of known biological processes. These novel approaches are illustrated with the apolipoprotein E3-Leiden transgenic mouse model, a commonly used model of atherosclerosis. We seek to gain insight into the early responses of disease onset and progression by determining and identifying--well in advance of pathogenic manifestations of disease--the sets of gene transcripts, proteins and metabolites, along with their putative relationships in the transgenic model and associated wild-type cohort. Our results corroborate previous findings and extend predictions for three processes in atherosclerosis: aberrant lipid metabolism, inflammation, and tissue development and maintenance.

Effects of traditional chinese medicine on congestive heart failure

CHF is a common cardiovascular complication, and also is a result of all kinds of cardiopathies. Common cardiotonic and diuretic treatment don’t have a good effect and patients could easily get digitalism because of poor tolerance of digitalis. Recently, good curative effects have been achieved by the therapy of integrative Chinese and western medicine. Especially in recent few years, Chinese medicine has reached a fairly depth and achieved positive results in studying CHF with the raising level of medical research. Even so, because of lacking n a great many controlled observation, further research of the effect on CHF with Chinese medicine is remained to be studied from biochemical and biomolecular level, or from clinical practice.

The priority of basic research on ageing vulnerability in a comprehensive research agenda on ageing for the 21st century.

The prospects for individual and population ageing as we enter a new century pose some of the greatest social, economic and humanitarian challenges humankind as a whole has ever faced. The basic biological mechanisms that control human ageing remain ill understood but it is clear that for many individuals exhibiting predisposition to risk factors for certain chronic diseases, such as coronary heart disease, diabetes, osteoporosis, certain cancers and Alzheimer's disease, such predisposition is mediated through genetic processes that operate at a most fundamental biomolecular level interacting with nongenetic attributes. The prospect of improved understanding of the fundamental processes underlying the pathogenesis of common age-related diseases that may lead to identification of interventions that are effective in preventing, delaying or ameliorating the diseases and their consequences is compelling. It is this prospect that provides the prime justification for giving high priority to research on ageing vulnerability in a comprehensive research agenda on ageing for the 21st century.

Angiotensin-Converting Enzyme Gene Deletion Polymorphism Determines an Increase in Frequency of Migraine Attacks in Patients Suffering from Migraine without Aura

Many authors have reported an association between the angiotensin-converting enzyme (ACE)-D allele and coronary heart disease and other cardiovascular diseases. The mechanism underlying the positive associations between the ACE-D alleles and diseases are not yet clear. Previous reports showed an association between migraine without aura and ACE-D allele polymorphism. The study is aimed to evaluate if the DD genotype could also be associated with the frequency and duration of migraine without aura. In 302 patients suffering from migraine without aura (at least for 1 year), with no history of cardiovascular diseases and major risk factors for ischemic events, the genotypes of the ACE gene, plasma ACE activity, and the frequency (weekly) and duration of migraine attacks were evaluated. No drugs were given before (4 weeks) and during the study. The same evaluations were performed in 201 subjects without migraine. The molecular biologist and the physician evaluating the patient data were blinded to the clinical history and ACE-DD gene determination. Genotypes were determined by polymerase chain reaction amplification. Plasma ACE activity was performed by the HPLC method. The groups were similar for sex, age and smoking habit (migraines: 302 patients (200 F/102 M), mean age 37.8 ± 8.2 years; control: 201 subjects (127 F/74 M), mean age 37.5 ± 9.3 years). Patients with migraine without aura showed higher incidence of the ACE-DD gene (48.34%) than control subjects (37.32%), p < 0.05. The frequency of migraine (average attacks per week) was higher in patients with DD (2.11 ± 1.9) than in patients with ID (1.54 ± 1.44), p < 0.05. No difference in duration of migraine attacks (hours per week) was observed. Plasma ACE activity was increased in patients with the ACE-DD gene. Our data suggest that ACE-DD gene polymorphism could have an important role in determining migraine attacks and the frequency of these attacks. Further data are needed through further studies, especially on the biomolecular level.

Characterization of the particulate protein in Pacific surface waters

We investigated molecular characteristics of particulate proteins in Pacific surface waters using two-dimensional electrophoresis (2DE). Most proteinaceous materials estimated by dye-binding methods were characterized by the 2DE unresolved acidic materials with a broad range of molecular mass and the 2DE unresolved low molecular mass materials with a broad range of isoelectric point. The 2DE unresolved acidic and low molecular mass materials were considered to comprise peptides conjugated with acidic saccharides and degradation products (peptides) of proteins, respectively, which indicates that almost all proteins in living organisms failed to survive in detrital particulate organic matter (POM). Nevertheless, 23 discrete proteins were distinguished by the 2DE. Electrophoretic patterns of the discrete proteins indicated that they were a component of detrital POM. Three discrete proteins were subjected to N terminal amino acid sequence analysis. Two proteins out of three could not be determined because their N termini were blocked, and one protein was determined from the N terminus to the ninth amino acid residue. A homology search revealed that the N terminal amino acid sequence of the protein agreed completely with that of 70 kDa heat shock protein (HSP70) derived from photosynthetic organisms. HSP70 is a major member of the molecular chaperones that protect or repair proteins from damage under conditions of environmental stress. The occurrence of HSP70 in this study demonstrated that phytoplankton were able to induce the molecular chaperone(s). Clarification of factor(s) controlling induction of chaperones will enable us to assess the actual environmental stress on phytoplankton at the biomolecular level. The particulate organic matter (POM) in surface water is a complex mixture of living biomass and nonliving detritus. The contribution of living biomass to the bulk POM is generally 1 order of magnitude lower than that of detrital organic matter (e.g., Volkman and Tanoue 2002). The particulate combined amino acids (PCAA) are the largest identified fraction in surface POM (e.g., Wakeham et al. 1997), and dye-binding colorimetric methods demonstrated that proteinaceous materials were a major component of POM (Setchell 1981; Long and Azam 1996). Phytoplankton is a primary producer of organic matter in the sea, and most combined amino acids in phytoplankton are in the form of proteins. However, heterotrophic processing may convert cellular proteins of phytoplankton to other forms before its incorporation into detrital pool. At present the chemical nature of the detrital combined amino acids and proteinaceous materials is not well documented, and the processes by which organic matter produced by phytoplankton is transferred to detrital POM are not clear. The characterization of proteinaceous materials in POM at the molecular level is 1

Enantioselective autocatalysis. IV. Implications for parity violation effects.

Historically, parity violation at the contemporary biomolecular level (i.e., only L-amino acids in proteins and D-sugars in DNA and RNA) has been postulated to be the inevitable result of parity violations at the elementary particle level, involving either beta-decay electrons or parity violating energy differences (PVEDs) between enantiomers. These two chiral biases have in turn allegedly impressed a small but persistent chirality onto prebiotic chemistry which, after appropriate amplification, has culminated in our contemporary homochiral biopolymers. Experiments and controversies pertaining to the efficacy of these two chiral biases are reviewed briefly, with the conclusions that: a) there is no experimental evidence supporting the capability of beta-decay electrons or other spin-polarized chiral particles to generate chiral molecules, and b) only theoretical calculations, but no experimental evidence, support the allegation of a causal relation between PVEDs and biomolecular homochirality. We here attempt to examine the latter allegation experimentally. Spontaneous resolution under racemization conditions (SRURC) during the crystallization of the bromofluoro-1,4-benzodiazepinooxazole derivative I is capable of affording products of high enantiomeric purity. This process, which involves very efficient stereoselective autocatalysis, has now been examined statistically. If PVED effects are operative, the SRURC of racemic I should provide, either exclusively or with a strong and consistent bias, only one enantiomer of crystalline I. However, crystallization experiments of racemic I showed no bias in its SRURC, leading to the conclusion that PVED effects are ineffective in dictating a preferred chirality in this system. Several earlier experiments in the literature leading to a similar conclusion as to the inefficacy of PVED effects in promoting a preferred chirality are noted.

Biological markers of environmental and ecological contamination: an overview.

An approach, using biomarkers (biological responses) for assessing the biological and ecological significance of contaminants present in the environment is described. Living organisms integrate exposure to contaminants in their environment and respond in some measurable and predictable way. Responses are observed at several levels of biological organization from the biomolecular level, where pollutants can cause damage to critical cellular macromolecules and elicit defensive strategies such as detoxication and repair mechanisms, to the organismal level, where severe disturbances are manifested as impairment in growth, reproduction, developmental abnormalities, or decreased survival. Biomarkers can provide not only evidence of exposure to a broad spectrum of anthropogenic chemicals, but also a temporally integrated measure of bioavailable contaminant levels. A suite of biomarkers are evaluated over time to determine the magnitude of the problem and possible consequences. Relationships between biomarker response and adverse ecological effects are determined from estimates of animal health and population structure.

Biomolecular absorption of ultrasound

Understanding of the mechanisms of the interaction of ultrasound and biomolecules is essential to a thorough understanding of the present biophysical and medical applications of ultrasound and to the systematic and efficient accomplishment of future advances. Experimental evidence indicates that the biomolecules present in tissues play an important role in the ultrasonic propagaTion properties of tissues. Classical absorption mechanisms apparently play no significant role at the biomolecular level. Chemical and structural relaxation mechanisms have been proposed to explain the acoustic behavior observed, although generalized dispersion relationships have been reported to apply as well. Specific mechanisms of absorption for biomolecules in suspension at neutral pH have not been determined. Molecular size plays a role (in a “threshold” sense) in absorption but not in propagation speed. Molecular conformation appears to be important in some cases but not in others. Biomolecular‐solvent equilibria and biomolecule‐biomolecule interactions apparently are involved in the absorption processes.

Cell metabolism in uremia

We hypothesize that the metabolic abnormalities of uremia, including carbohydrate intolerance and impaired protein synthesis result from a disturbed balance between normally occurring positive and negative effectors of enzyme activity at the biomolecular level, superimposed on malnutrition. To test this hypothesis circulating polymorphonuclear leukocytes were used as an experimental cell model. Leukocytes were isolated from pre- and postdialysis blood of 31 adult uremic subjects undergoing chronic hemodialysis. A 6 hr dialysis was associated with significant (P< 0.05) increases in activities of the glycolytic enzymes pyruvic kinase, phosphofructokinase, and glucose-6-phosphate dehydrogenase. Protein synthesis (3H-leucine incorporation) also increased. Urea, added to the postdialysis leukocytes did not significantly affect the activities. Nor was the energy state of the cell significantly altered by dialysis, although levels of fructose 1–6 diphosphate and of 3 phosphoglycerate increased—suggesting an increased glycolytic flux at the step catalyzed by phosphofructokinase. Leukocyte amino acid levels increased suggesting decreased utilization for gluconeogenesis since both glycolysis and protein synthesis increased. Leukocyte phosphofructokinase activity and protein synthesis increased significantly only in patients having carbohydrate intolerance (predialysis blood glucose averaging 160 mg/dl), but not in those with normal glucose (averaging 108 mg/dl), although both groups had similar dialysis treatment. These observations support the hypothesis that imbalance of enzyme effectors at the molecular level, rather than dialyzable toxins, may account for the carbohydrate intolerance and impaired protein synthesis in uremia.