Defining Life: Connecting Robotics and Chemistry

Life is commonly referred as open systems driven by organic chemistry capable to self reproduce and to evolve. The notion of life has also been extended to non chemical systems such as robots. The key characteristics of living systems, i.e. autonomy, self-replication, self-reproduction, self-organization, self-aggregation, autocatalysis, as defined in chemistry and in robotics, are compared in a dialogue between a chemist and a robotitian.     

Sudden Shifts in Ecological Systems: Intermittency and Transients in the Coupled Ricker Population Model

Many real ecological systems show sudden changes in behavior, phenomena sometimes categorized as regime shifts in the literature. The relative importance of exogenous versus endogenous forces producing regime shifts is an important question. These forces’ role in generating variability over time in ecological systems has been explored using tools from dynamical systems. We use similar ideas to look at transients in simple ecological models as a way of understanding regime shifts. Based in part on the theory of crises, we carefully analyze a simple two patch spatial model and begin to understand from a mathematical point of view what produces transient behavior in ecological systems. In particular, since the tools are essentially qualitative, we are able to suggest that transient behavior should be ubiquitous in systems with overcompensatory local dynamics, and thus should be typical of many ecological systems. This work has been supported by NSF Grant EF-0434266.     

VicRK(YycFG)双组分调节系统

细菌双组分调节系统,或称之为双组分信号转导系统,是细菌感应外界多变环境,维持自身存活和生长繁衍的重要感应系统.在这些调节系统中,最早发现于枯草芽孢杆菌的VicRK(YycFG)系统因与细胞存活密切相关而倍受关注.该系统存在于少数低G+C含量的革兰氏阳性菌中,包括金黄色葡萄球菌和肺炎链球菌等致病菌,高度保守.许多证据显示,VicRK(YycFG)具有调控细胞壁合成与代谢、胞膜完整、细胞分裂、脂类代谢、多糖合成与被膜形成以及细菌毒力等多种功能,参与细胞的生长、分裂与感染.该系统异常可导致细菌生活力严重下降,甚至死亡,因而成为防治该类病原菌的重要靶标.     

Hybrid semi-parametric mathematical systems: bridging the gap between systems biology and process engineering

Systems biology is an integrative science that aims at the global characterization of biological systems. Huge amounts of data regarding gene expression, proteins activity and metabolite concentrations are collected by designing systematic genetic or environmental perturbations. Then the challenge is to integrate such data in a global model in order to provide a global picture of the cell. The analysis of these data is largely dominated by nonparametric modelling tools. In contrast, classical bioprocess engineering has been primarily founded on first principles models, but it has systematically overlooked the details of the embedded biological system. The full complexity of biological systems is currently assumed by systems biology and this knowledge can now be taken by engineers to decide how to optimally design and operate their processes. This paper discusses possible methodologies for the integration of systems biology and bioprocess engineering with emphasis on applications involving animal cell cultures. At the mathematical systems level, the discussion is focused on hybrid semi-parametric systems as a way to bridge systems biology and bioprocess engineering.     

Bifurcations and Intrinsic Chaotic and 1/f Dynamics in an Isolated Perfused Rat Heart

The application of the theory of chaotic dynamical systems has gradually evolved from computer simulations to assessment of erratic behavior of physical, chemical, and biological systems. Whereas physical and chemical systems lend themselves to fairly good experimental control, biologic systems, because of their inherent complexity, are limited in this respect. This has not, however, prevented a number of investigators from attempting to understand many biologic periodicities. This has been especially true regarding cardiac dynamics: the spontaneous beating of coupled and non-coupled cardiac pacemakers provides a convenient comparison to the dynamics of oscillating systems of the physical sciences. One potentially important hypothesis regarding cardiac dynamics put forth by Goldberger and colleagues, is that normal heart beat fluctuations are chaotic, and are characterized by a 1/f-like power spectrum. To evaluate these conjectures, we studied the heart beat intervals (R wave toR wave of the electocardiogram) of isolated, perfused rat hearts and their response to a variety of external perturbations. The results indicate bifurcations between complex patterns, states with positive dynamical entropies, and low values of fractal dimensions frequently seen in physical, chemical and cellular systems, as well as power law scaling of the spectrum. Additionally, these dynamics can be modeled by a simple, discrete map, which has been used to describe the dynamics of the Belousov-Zhabotinsky reaction.     

Transients: the key to long-term ecological understanding?

Ecological theory has been dominated by a focus on long-term or asymptotic behavior as a way to understand natural systems. Yet experiments are done on much shorter timescales, and the relevant timescales for ecological systems can also be relatively short. Thus, there is a mismatch between the timescales of most experiments and the timescales of many theoretical investigations. However, recent work has emphasized the importance of transient dynamics rather than long-term behavior in ecological systems, enabling the examination of forces that allow coexistence on ecological timescales. Through an examination of what leads to transients in ecological systems, a deeper appreciation of the forces leading to persistence or coexistence in ecological systems emerges, as well as a general understanding of how population levels can change through time.     

Light elicited isolation of the complementary visual input systems in white-eye Drosophila.

Evidence is presented to show that the spectral sensitivity of the white-eye of Drosophila, indicated by the residual ERG following blue irradiation which renders the eye dark-depolarized, has a maximum around 460 nm, and represents the activity of R7 and possibly that of R8. Whereas the ERG of the repolarized dark-adapted white-eye, effected by orange irradiation, indicates a spectral sensitivity having a maximum around 490 to 500 nm, and represents the activity of R1 to 6 preferentially. Manipulation of these two visual input systems is achieved using various régimes of irradiation, the systems being switched at will. The critical flicker fusion frequency respectively for the two systems has been measured, that of R1 to 6 being twice as high as that of R7±8.Implications for the visual function of the eye are considered, in particular the significance of the wildtype red-eye colour. The ease of manipulation has considerable value to the experimentalist wishing to study the input systems in isolation and concomitantly.     

Developmental selection and self-organization

Developmental selection is the differential survival and proliferation of developmental units, such as cellular lineages. This type of internal selection has been proposed as an explanation for diverse examples of self-organization, from the wiring of brains to the formation of pores on leaf surfaces. A general understanding of developmental selection has been slowed by failure to understand its relationship to familiar forms of genetical selection and evolution. I show the formal analogies between models of developmental selection and genetical selection. The general method I outline for the analysis of selective systems partitions self-organizing selective systems into generative rules that create variation and selective filters that move the population toward a target design. The method also emphasizes aggregate statistical measures of evolving systems, such as the covariance between particular traits and fitness. The identification of useful aggregate measures is a crucial step in the analysis of selective systems. I apply these concepts to a model of self-organization in ant colonies.     

Artificial activation of toxin-antitoxin systems as an antibacterial strategy

Toxin-antitoxin (TA) systems are unique modules that effect plasmid stabilization via post-segregational killing of the bacterial host. The genes encoding TA systems also exist on bacterial chromosomes, and it has been speculated that these are involved in a variety of cellular processes. Interest in TA systems has increased dramatically over the past 5 years as the ubiquitous nature of TA genes on bacterial genomes has been revealed. The exploitation of TA systems as an antibacterial strategy via artificial activation of the toxin has been proposed and has considerable potential; however, efforts in this area remain in the early stages and several major questions remain. This review investigates the tractability of targeting TA systems to kill bacteria, including fundamental requirements for success, recent advances, and challenges associated with artificial toxin activation.     

Soil macrofauna diversity as a key element for building sustainable agriculture in Argentine Pampas

The agricultural activity in the Argentine Pampas, characterized by an important trend towards no-till soybean monocropping, has completely transformed the original Pampas landscape into a monotonous scenario with a continuous succession of farms of very low crop diversity. This process has led to soil physical, chemical and biological degradation in those systems. The increase of crop rotation rates in no-till and reduced tillage systems has been proposed as an alternative with reduced negative impact on soils in the context of conventional agriculture. On the other hand, extensive organic farming is also suggested as an alternative to high-input agriculture systems. In this article, we aim to explore how different variations of farming practices and systems impact soil macrofauna, along an edaphoclimatic gradient in the Pampas region. We studied the following systems: natural grassland (Gr) as indicator of the original community, extensive organic farming (Org), conventional agriculture with no-tillage and three crop rotation levels (Nt-R1, Nt-R2 and Nt-R3), and reduced tillage with two levels of crop rotation (Til and Til-R). We assessed soil macrofauna, with emphasis on earthworm, beetle and ant communities; and soil physical and chemical properties. Macrofaunal taxa composition was significantly affected by both management systems and edaphoclimatic conditions. The Gr community had pronounced differences from all the agricultural systems. The earthworm community from Gr had distinctive features from those of most agricultural systems, with Org and Nt-R3 being the most similar to Gr in native and exotic earthworm species, respectively. The beetle community in Org was the most different one, and the communities from the other systems did not show a pattern related to management. Ant community composition was not determined by management systems, but it was affected by edaphoclimatic conditions. All the studied macrofauna groups had a significant co-variation with soil physical and chemical properties, showing that both the characteristics of each soil relative to the geographic location and the effect of management on abiotic soil attributes have an important effect on soil macrofauna. This study confirms that biodiversity is being lost in Pampas soils, which implies a possible threat to the soil capacity to perform the processes that sustain soil functioning and hence plant productivity. Further considerations about the sustainability of the current agricultural model applied in the Argentine Pampas are needed.     

Acetate addition to an immobilized yeast column of ethanol production

Acetate, a by-product of ethanol fermentation by Saccharomyces cerevisiae, has been shown to inhibit cell growth if present in high concentrations. Consequently, acetate has been considered undesirable in systems where the production rate depends upon steady-state growth. Acetate, however, may be desirable in some systems since it increases the specific rate of ethanol production by increasing the maintenance requirements of yeast. In immobilized cell reactors using the crosslinking method, steady state is not achieved and cell overgrowth is a problem. This article presents the results of a study aimed at taking advantage of the use of acetate, both to reduce cell overgrowth and to increase productivity. Various concentrations of acetate were added to batch and plug flow systems, while monitoring the effects on cell growth and ethanol production. The productivity was increased by as much as 50% in an immobilized cell reactor (ICR), while cell growth was greatly reduced.     

Development of enzyme immunoassay for the herbicide chlorsulfuron

Antibodies against the herbicide chlorsulfuron have been raised and characterized. Enzyme immunoassays (EIAs) for chlorsulfuron, involving labeled antigen or labeled antibodies, have been developed. The kinetics of antigen-antibody interactions in the EIA systems developed has been studied. Both systems exhibit equal sensitivity (1 ng/ml). The values of the coefficient of variation (CV), determined within the range of chlorsulfuron concentrations 1-100 ng/ml to be measured by the systems, are not in excess of 8%. The possibility of using glucose oxidase as a label in EIAs for chlorsulfuron has been demonstrated. Lack of cross-reactivity with a series of sulfonyl- and arylurea derivatives and triazines makes it possible to recommend the EIA systems developed for chlorsulfuron determination in the environment.     

The diagnostic value of different test systems for the screening determination of antibodies to the human immunodeficiency virus]

Evaluation of the quality of enzyme immunoassay (EIA) systems by their sensitivity and specificity is inadequate, mainly due to the impossibility of detecting early or latent HIV infection in humans as it manifests by seroconversion only to a few HIV proteins. The additional evaluation criterion (confirmation rate) has been introduced, and an original method for the integral evaluation of the quality of assay systems intended for the diagnosis of HIV infection by EIA techniques has been proposed.     

Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies

Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR. We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.     

Iron acquisition in Vibrio cholerae

Vibrio cholerae, the causative agent of cholera, has an absolute requirement for iron and must obtain this element in the human host as well as in its varied environmental niches. It has multiple systems for iron acquisition, including the TonB-dependent transport of heme, the endogenous siderophore vibriobactin and several siderophores that are produced by other microorganisms. There is also a Feo system for the transport of ferrous iron and an ABC transporter, Fbp, which transports ferric iron. There appears to be at least one additional high affinity iron transport system that has not yet been identified. In iron replete conditions, iron acquisition genes are repressed by Fur. Fur also represses the synthesis of a small, regulatory RNA, RyhB, which negatively regulates genes for iron-containing proteins involved in the tricarboxylic acid cycle and respiration as well as genes for motility and chemotaxis. The redundancy in iron transport systems has made it more difficult to determine the role of individual systems in vivo and in vitro, but it may reflect the overall importance of iron in the growth and survival of V. cholerae.     

Amino acid incorporation by preparations from the developing rat brain

1. A study has been made of the ability of cerebral microsome-cell sap systems, taken from rats at various ages, to incorporate [(14)C]valine. 2. The systems appear to follow Michaelis-Menten kinetics when cell sap is considered as substrate, microsomes as enzyme and total counts/mg. of microsomal protein as a measure of reaction velocity. 3. Reproducible ;affinity constant' values are obtained, and the system from 4-day-old rats has a higher V(max.) and affinity constant than the system from adult rats. 4. It is suggested the the amino acid-incorporating ability of different systems may be compared by this means.     

Overlaps and parallels in the regulation of intrinsic multiple-antibiotic resistance in Escherichia coli

Chromosomally encoded systems present in a variety of bacteria appear to play a central role in determining the intrinsic level of resistance to many commonly used antibiotics. Work with the Gram-negative bacterium Escherichia coli has shown that there is significant similarity at the amino acid sequence level among the structural components of these resistance systems as well as among their genetic regulators. This review describes two of the better-studied regulatory systems, marRAB and soxRS, as well as two regulated multidrug-efflux systems, encoded by emrAB and acrAB, and focuses on conserved themes in their primary structures and environmental stimuli. The observed resistance to clinically important antibiotics appears to reflect an overlap with broad-ranged adaptive responses by free-living bacteria to noxious plant materials in their natural environment.     

A Bayesian framework for combining gene predictions

MOTIVATION: Gene identification and gene discovery in new genomic sequences is one of the most timely computational questions addressed by bioinformatics scientists. This computational research has resulted in several systems that have been used successfully in many whole-genome analysis projects. As the number of such systems grows the need for a rigorous way to combine the predictions becomes more essential. RESULTS: In this paper we provide a Bayesian network framework for combining gene predictions from multiple systems. The framework allows us to treat the problem as combining the advice of multiple experts. Previous work in the area used relatively simple ideas such as majority voting. We introduce, for the first time, the use of hidden input/output Markov models for combining gene predictions. We apply the framework to the analysis of the Adh region in Drosophila that has been carefully studied in the context of gene finding and used as a basis for the GASP competition. The main challenge in combination of gene prediction programs is the fact that the systems are relying on similar features such as cod on usage and as a result the predictions are often correlated. We show that our approach is promising to improve the prediction accuracy and provides a systematic and flexible framework for incorporating multiple sources of evidence into gene prediction systems.     

Landfill methane oxidation in soil and bio-based cover systems: a review

Mitigation of landfill gases has gained the utmost importance in recent years due to the increase in methane (CH₄) emissions from landfills worldwide. This, in turn, can contribute to global warming and climatic changes. The concept of microbially mediated methane oxidation in landfill covers by using methanotrophic microorganisms has been widely adopted as a method to counter the rise in methane emissions. Traditionally, landfill soil covers were used to achieve methane oxidation, thereby reducing methane emissions. Meanwhile, the continual rise of CH₄ emissions from landfills and the significant need to and importance of developing a better technology has led researchers to explore different methods to enhance microbial methane oxidation by using organic rich materials such as compost in landfill covers. The development and field application of such bio-based systems, explored by various researches worldwide, eventually led to more widely accepted and better performing cover systems capable of reducing CH₄ emissions from landfills. However, the long-term performance of bio-based cover systems were found to be negatively affected by factors such as the material’s ability to self-degrade, causing CH₄ to be generated rather than oxidized as well as the greater potential for forming pore-clogging exopolymeric substances. In order to design an effective cover system for landfills, it is essential to have a thorough understanding of the concepts incorporated into methodologies currently in favor along with their pros and cons. This review summarizes previous laboratory and field-scale studies conducted on various soil and bio-based cover systems, along with the modeling mechanisms adopted for quantifying CH₄ oxidation rates. Finally, several issues and challenges in developing effective and economical soil and bio-based cover systems are presented.     

Development of Enzyme Immunoassays for the Herbicide Chlorsulfuron

Antibodies against the herbicide chlorsulfuron have been raised and characterized. Enzyme immunoassays (EIAs) for chlorsulfuron, involving labeled antigen or labeled antibodies, have been developed. The kinetics of antigen–antibody interactions in the EIA systems developed has been studied. Both systems exhibit equal sensitivity (1 ng/ml). The values of the coefficient of variation (CV), determined within the range of chlorsulfuron concentrations to be measured by the systems (1–100 ng/ml), are not in excess of 8%. The possibility of using glucose oxidase as a label in EIAs for chlorsulfuron has been demonstrated. Lack of cross-reactivity with a series of sulfonyl-/arylurea derivatives and triazines makes it possible to recommend the EIA systems developed for chlorsulfuron determination in the environment.