Temperature acquisition as a function of the computer-based biofeedback system utilized: An exploratory analysis

Thermal biofeedback is widely used to treat various clinical disorders. Given its widespread utility, and the variability among the biofeedback systems currently on the market, it is important to investigate which systems are most effective for training various skills. This study compared the performance of normal subjects on two different computer-biofeedback systems. Results indicated a significant difference in subject performance between the two systems. Limitations and implications of these findings are discussed.     

Systems Biology,Systems Medicine,Systems Pharmacology: The What and The Why

Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences.     

The Csr/Rsm system of Yersinia and related pathogens: A post-transcriptional strategy for managing virulence

This review emphasizes the function and regulation of the Csr regulatory system in the human enteropathogen Yersinia pseudotuberculosis and compares its features with the homologous Csr/Rsm systems of related pathogens. The Csr/Rsm systems of eubacteria form a complex regulatory network in which redundant non-translated Csr/Rsm-RNAs bind the RNA-binding protein CsrA/RsmA, thereby preventing its interaction with mRNA targets. The Csr system is controlled by the BarA/UvrY-type of two-component sensor-regulator systems. Apart from that, common or pathogen-specific regulators control the abundance of the Csr components. The coordinate control of virulence factors and infection-linked physiological traits by the Csr/Rsm systems helps the pathogens to adapt individually to rapidly changing conditions to which they are exposed during the different stages of an infection. As Csr/Rsm function is relevant for full virulence, it represents a target suitable for antimicrobial drug development.     

Systems biology as a foundation for genome-scale synthetic biology

As the ambitions of synthetic biology approach genome-scale engineering, comprehensive characterization of cellular systems is required, as well as a means to accurately model cell-scale molecular interactions. These requirements are coincident with the goals of systems biology and, thus, systems biology will become the foundation for genome-scale synthetic biology. Systems biology will form this foundation through its efforts to reconstruct and integrate cellular systems, develop the mathematics, theory and software tools for the accurate modeling of these integrated systems, and through evolutionary mechanisms. As genome-scale synthetic biology is so enabled, it will prove to be a positive feedback driver of systems biology by exposing and forcing researchers to confront those aspects of systems biology which are inadequately understood.     

Extending the viability theory framework of resilience to uncertain dynamics,and application to lake eutrophication

Resilience, the capacity for a system to recover from a perturbation so as to keep its properties and functions, is of growing concern to a wide range of environmental systems. The challenge is often to render this concept operational without betraying it, nor diluting its content. The focus here is on building on the viability theory framework of resilience to extend it to discrete-time stochastic dynamical systems. The viability framework describes properties of the system as a subset of its state space. This property is resilient to a perturbation if it can be recovered and kept by the system after a perturbation: its trajectory can come back and stay in the subset. This is shown to reflect a general definition of resilience. With stochastic dynamics, the stochastic viability kernel describes the robust states, in which the system has a high probability of staying in the subset for a long time. Then, probability of resilience is defined as the maximal probability that the system reaches a robust state within a time horizon. Management strategies that maximize the probability of resilience can be found through dynamic programming. It is then possible to compute a range of statistics on the time for restoring the property. The approach is illustrated on the example of lake eutrophication and shown to foster the use of different indicators that are adapted to distinct situations. Its relevance for the management of ecological systems is also discussed.     

Free Energy Calculations of Pharmaceutically Important Properties

When determining the biochemical function of a proposed new drug it is useful to be able to calculate a number of properties which regulate its behaviour. By using the Free Energy Perturbation method incorporated into molecular dynamics, both on its own and in conjunction with quantum mechanical calculations, we have calculated redox potentials, pK_a s, tautomer ratios and partition coefficients on model systems.

This paper reviews the techniques currently being used to perform such calculations and presents the results for a number of different systems. The accuracy with which the properties are determined is most encouraging and suggests that useful calculations on realistic systems are now possible, and will play a major role in drug-design in the future.     

Restriction-modification systems in Bacillus strains related to Bacillus subtilis

127 strains of bacilli sensitive to different phages of Bacillus subtilis were isolated from the soil of Moscow and its country-side. In 6 strains, restriction and modification systems were discovered which differed from these previously described for Bac. subtilis BsuR system. Two strains has identical restriction-modification systems, and one strain possessed two different systems. Using DNA from all 6 strains, it was possible to transform competent cells of Bac. subtilis RUB834. Two of these 6 strains could serve as recipients in transformation and transfection experiments.     

Ultrastructural investigations on the muscular systems in the barnacle, Tetraclita squamosa japonica

Four muscular systems of the Tetraclita squamosa barnacle were observed by means of an electron microscope and it was revealed that these systems each bore different types of muscle cells. The four systems were the adductor (A), the lateral scutal depressor (LSD), the ventral scutal depressor (VSD), and the tergal depressor (TD). The A-system included cross stiated muscle cells which showed long sarcomeres (about 10 mum) and rather disordered arrays of myofilaments. The LSD-system included cross striated muscles which had medium length sarcomeres (about 6.7 mum) and rather ordered myofilamental arrays. The VSD-system was constructed of cross striated muscle cells which bore shorter sarcomeres (4.6 mum) than the previous three systems and ordered myofilamental arrays. This last type of cell also bore well-developed sarcoplasmic reticular systems. The TD-system included smooth muscle cells which showed rather ordered arrays of myofilaments and dense-bodies. Each muscular system, as described above, included to its advantage one type of cross striated or smooth muscle cell for its characteristic contraction. The relations between ultrastructures and functions of each muscular system will now be discussed.     

Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems.

It has recently been shown through DNA microarray analysis of Bacillus subtilis two-component regulatory systems (DegS-DegU, ComP-ComA, and PhoR-PhoP) that overproduction of a response regulator of the two-component systems in the background of a deficiency of its cognate sensor kinase affects the regulation of genes, including its target ones. The genome-wide effect on gene expression caused by the overproduction was revealed by DNA microarray analysis. In the present work, we newly analyzed 24 two-component systems by means of this strategy, leaving out 8 systems to which it was unlikely to be applicable. This analysis revealed various target gene candidates for these two-component systems. It is especially notable that interesting interactions appeared to take place between several two-component systems. Moreover, the probable functions of some unknown two-component systems were deduced from the list of their target gene candidates. This work is heuristic but provides valuable information for further study toward a comprehensive understanding of the B. subtilis two-component regulatory systems. The DNA microarray data obtained in this work are available at the KEGG Expression Database website (http://www.genome.ad.jp/kegg/expression).     

VirB8: a conserved type IV secretion system assembly factor and drug target.

Type IV secretion systems are used by many gram-negative bacteria for the translocation of macromolecules (proteins, DNA, or DNA-protein complexes) across the cell envelope. Among them are many pathogens for which type IV secretion systems are essential virulence factors. Type IV secretion systems comprise 8-12 conserved proteins, which assemble into a complex spanning the inner and the outer membrane, and many assemble extracellular appendages, such as pili, which initiate contact with host and recipient cells followed by substrate translocation. VirB8 is an essential assembly factor for all type IV secretion systems. Biochemical, cell biological, genetic, and yeast two-hybrid analyses showed that VirB8 undergoes multiple interactions with other type IV secretion system components and that it directs polar assembly of the membrane-spanning complex in the model organism Agrobacterium tumefaciens. The availability of the VirB8 X-ray structure has enabled a detailed structure-function analysis, which identified sites for the binding of VirB4 and VirB10 and for self-interaction. Due to its multiple interactions, VirB8 is an excellent model for the analysis of assembly factors of multiprotein complexes. In addition, VirB8 is a possible target for drugs that target its protein-protein interactions, which would disarm bacteria by depriving them of their essential virulence functions.     

系统生物学对医学的影响

系统生物学是21世纪最前沿的科学之一,它是随着生命科学飞速发展而产生的一门新兴生物学分支[1],它综合数学、信息科学和生物学的各种工具来阐明和理解大量的数据所包含的生物医学意义,从而使人们能够从整体上理解生物医学系统并精确、量化地预测生物医学系统的行为。随着系统生物学的发展及其理论的突破,将在疾病诊治、新药开发、预防医学方面发挥重要的作用,有助于弥补传统医学缺陷并促进其发展。     

Biocomplexity: adaptive behavior in complex stochastic dynamical systems

Existing methods of complexity research are capable of describing certain specifics of bio systems over a given narrow range of parameters but often they cannot account for the initial emergence of complex biological systems, their evolution, state changes and sometimes-abrupt state transitions. Chaos tools have the potential of reaching to the essential driving mechanisms that organize matter into living substances. Our basic thesis is that while established chaos tools are useful in describing complexity in physical systems, they lack the power of grasping the essence of the complexity of life. This thesis illustrates sensory perception of vertebrates and the operation of the vertebrate brain. The study of complexity, at the level of biological systems, cannot be completed by the analytical tools, which have been developed for non-living systems. We propose a new approach to chaos research that has the potential of characterizing biological complexity. Our study is biologically motivated and solidly based in the biodynamics of higher brain function. Our biocomplexity model has the following features, (1) it is high-dimensional, but the dimensionality is not rigid, rather it changes dynamically; (2) it is not autonomous and continuously interacts and communicates with individual environments that are selected by the model from the infinitely complex world; (3) as a result, it is adaptive and modifies its internal organization in response to environmental factors by changing them to meet its own goals; (4) it is a distributed object that evolves both in space and time towards goals that is continually re-shaping in the light of cumulative experience stored in memory; (5) it is driven and stabilized by noise of internal origin through self-organizing dynamics. The resulting theory of stochastic dynamical systems is a mathematical field at the interface of dynamical system theory and stochastic differential equations. This paper outlines several possible avenues to analyze these systems. Of special interest are input-induced and noise-generated, or spontaneous state-transitions and related stability issues.     

Ultrastructural investigations on the muscular systems in the barnacle, Tetraclita squamosa japonica

Four muscular systems of the Tetraclita squamosa barnacle were observed by means of an electron microscope and it was revealed that these systems each bore different types of muscle cells. The four systems were the adductor (A), the lateral scutal depressor (LSD), the ventral scutal depressor (VSD), and the tergal depressor (TD). The A-system included cross stiated muscle cells which showed long sarcomeres (about 10 μm) and rather disordered arrays of myofilaments. The LSD-system included cross striated muscles which had medium length sarcomeres (about 6.7 μm) and rather ordered myofilamental arrays. The VSD-system was constructed of cross striated muscle cells which bore shorter sarcomeres (4.6 μm) than the previous three systems and ordered myofilamental arrays. This last type of cell also bore well-developed sarcoplasmic reticular systems. The TD-system included smooth muscle cells which showed rather ordered arrays of myofilaments and dense-bodies. Each muscular system, as described above, included to its advantage one type of cross striated or smooth muscle cell for its characteristic contraction. The relations between ultrastructures and functions of each muscular system will now be discussed.     

Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440

A major challenge in microbiology is the elucidation of the genetic and ecophysiological basis of habitat specificity of microbes. Pseudomonas putida is a paradigm of a ubiquitous metabolically versatile soil bacterium. Strain KT2440, a safety strain that has become a laboratory workhorse worldwide, has been recently sequenced and its genome annotated. By drawing on both published information and on original in silico analysis of its genome, we address here the question of what genomic features of KT2440 could explain or are consistent with its ubiquity, metabolic versatility and adaptability. The genome of KT2440 exhibits combinations of features characteristic of terrestrial, rhizosphere and aquatic bacteria, which thrive in either copiotrophic or oligotrophic habitats, and suggests that P. putida has evolved and acquired functions that equip it to thrive in diverse, often inhospitable environments, either free-living, or in close association with plants. The high diversity of protein families encoded by its genome, the large number and variety of small aralogous families, insertion elements, repetitive extragenic palindromic sequences, as well as the mosaic structure of the genome (with many regions of 'atypical' composition) and the multiplicity of mobile elements, reflect a high functional diversity in P. putida and are indicative of its evolutionary trajectory and adaptation to the diverse habitats in which it thrives. The unusual wealth of determinants for high affinity nutrient acquisition systems, mono- and di-oxygenases, oxido-reductases, ferredoxins and cytochromes, dehydrogenases, sulfur metabolism proteins, for efflux pumps and glutathione-S-transfereases, and for the extensive array of extracytoplasmatic function sigma factors, regulators, and stress response systems, constitute the genomic basis for the exceptional nutritional versatility and opportunism of P. putida , its ubiquity in diverse soil, rhizosphere and aquatic systems, and its renowned tolerance of natural and anthropogenic stresses. This metabolic diversity is also the basis of the impressive evolutionary potential of KT2440, and its utility for the experimental design of novel pathways for the catabolism of organic, particularly aromatic, pollutants, and its potential for bioremediation of soils contaminated with such compounds as well as for its application in the production of high-added value compounds.     

Mass spectrometry-based proteomics for systems biology

Mass spectrometry (MS)-based proteomics has significantly contributed to the development of systems biology, a new paradigm for the life sciences in which biological processes are addressed in terms of dynamic networks of interacting molecules. Because of its advanced analytical capabilities, MS-based proteomics has been used extensively to identify the components of biological systems, and it is the method of choice to consistently quantify the effects of network perturbation in time and space. Herein, we review recent contributions of MS to systems biology and discuss several examples that illustrate the importance of mass spectrometry to elucidate the components and interactions of molecular networks.     

A novel alkali-tolerant Yarrowia lipolytica strain for dissecting Na+-coupled phosphate transport systems in yeasts

The newly isolated osmo-, salt- and alkali-tolerant Yarrowia lipolytica yeast strain is remarkable by its capacity to grow at alkaline pH values (pH 9.7), which makes it an excellent model system for studying Na(+)-coupled phosphate transport systems in yeast cells grown at alkaline conditions. In cells Y. lipolytica grown at pH 9.7, phosphate uptake was mediated by several kinetically discrete Na(+)-dependent systems that are specifically activated by Na(+) ions. One of these, a low-affinity transporter, operated at high-phosphate concentrations. The other two, derepressible, high-affinity, high-capacity systems, functioned during phosphate starvation. Both H(+)- and Na(+)-coupled high-affinity phosphate transport systems of Y. lipolytica cells were under the dual control of the prevailing extracellular phosphate concentrations and pH values. The contribution of the Na(+)/P(i)-cotransport systems into the total cellular phosphate uptake activity was progressively increased with increasing pH, reaching its maximum at pH > or = 9.     

Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3

Shewanella species are widespread in various environments. Here, the genome sequence of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea sediment was determined with related functional analysis to study its environmental adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or gene clusters which help it to cope with extreme living conditions such as genes for two sets of flagellum systems, structural RNA modification, eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and synthesis. And WP3 contains 55 open reading frames encoding putative c-type cytochromes which are substantial to its wide environmental adaptation ability. The mtr-omc gene cluster involved in the insoluble metal reduction in the Shewanella genus was identified and compared. The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature.     

Distortion of effects caused by indirect confounding

Undetected confounding may severely distort the effect of anexplanatory variable on a response variable, as defined by astepwise data-generating process. The best known type of distortion,which we call direct confounding, arises from an unobservedexplanatory variable common to a response and its main explanatoryvariable of interest. It is relevant mainly for observationalstudies, since it is avoided by successful randomization. Bycontrast, indirect confounding, which we identify in this paper,is an issue also for intervention studies. For general stepwise-generatingprocesses, we provide matrix and graphical criteria to decidewhich types of distortion may be present, when they are absentand how they are avoided. We then turn to linear systems withoutother types of distortion, but with indirect confounding. Forsuch systems, the magnitude of distortion in a least-squaresregression coefficient is derived and shown to be estimable,so that it becomes possible to recover the effect of the generatingprocess from the distorted coefficient.     

Engineering life through Synthetic Biology

Synthetic Biology is a field involving synthesis of novel biological systems which are not generally found in nature. It has brought a new paradigm in science as it has enabled scientists to create life from the scratch, hence helping better understand the principles of biology. The viability of living organisms that use unnatural molecules is also being explored. Unconventional projects such as DNA playing tic-tac-toe, bacterial photographic film, etc. are taking biology to its extremes. The field holds a promise for mass production of cheap drugs and programming bacteria to seek-and-destroy tumors in the body. However, the complexity of biological systems make the field a challenging one. In addition to this, there are other major technical and ethical challenges which need to be addressed before the field realizes its true potential.