Persons, Places, and times: the meanings of repetition in an STD clinic

In this article we work the tensions between the way clinical medicine and public health necessarily construct the problem of "repetition" in the context of a sexually transmitted disease (STD) clinic and the ways patients narrate their illness experiences. This tension-between clinical and epidemiological exigencies and the messiness of lived experience-is a recurring theme of work conducted at the intersections of epidemiology, anthropology, and clinical medicine. Clinically, repeated infections are a threat to the individual body and to "normal" biological processes like reproduction. From a public health perspective, "repeaters" are imagined to be part of a "core group" that keeps infections in circulation, endangering the social body. Yet patients' accounts are anchored in particular social histories, and their experiences rely on different time scales than those implicated in either of these types of readings. Extended analyses are provided of two such accounts: one in which repetition can be "read" as part of a performance of recovery, and one in which repetition is bound up in the effort to avoid becoming the involuntary subject of institutionally administered intervention. We argue the need to open up the category of repeaters to include the social and draw on work by Cheryl Mattingly to suggest that one way to do this in the context of the STD clinic might be to adopt forms of therapeutic practice that make use of interpretive, in addition to technical, skills.     

A synthesis of the biological quality elements for the implementation of the European Water Framework Directive in the Mediterranean ecoregion: The case of Saronikos Gulf

Benthic macroinvertebrates, macroalgae and phytoplankton constitute the biological quality elements proposed in the Water Framework Directive (WFD, 2000/60/EC) to be used for the classification of the ecological status of a water body. In the context of the preparation for the implementation of WFD, classification schemes for all three elements have been developed and tested for all the European ecoregions. In the present work, the classification schemes, with the corresponding metric tools and the interpretations of the class boundaries according to the normative definitions of WFD, are presented for each biological element in Saronikos Gulf, as case study in the Mediterranean ecoregion. The combination of the three biological elements into an integrated classification for coastal water bodies has been one of the major issues addressed in the context of WFD guidelines. Results are interpreted and validated, through an ecological viewpoint, on the basis of relevant environmental data. Moreover, this work presents a way to combine the EUNIS system to the typology of water bodies in the Mediterranean ecoregion.     

Synthetic biology and the technicity of biofuels

The principal existing real-world application of synthetic biology is biofuels. Several ‘next generation biofuel’ companies—Synthetic Genomics, Amyris and Joule Unlimited Technologies—claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon’s notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic.     

Relationship between the structures of taxane derivatives and their microtubule polymerization activity

Paclitaxel (Taxol), one of the most potent anticancer drugs, is a microtubule-stabilizing compound that inhibits microtubule depolymerization within the cell. The structure of paclitaxel is composed of two key elements, a taxane ring and an N-benzoylphenylisoserine side chain at C-13. A number of natural and artificial compounds with taxane skeletons have been isolated, but almost none of their bioactivities have been evaluated. In this study, we focused on compounds having a taxane skeleton structure and examined their effects on tubulin dynamics. Although none of these compounds had an N-benzoylphenylisoserine side chain, three were found to promote tubulin assembly. On the other hand, one compound inhibited tubluin assembly in a way similar to nocodazole. These compounds exhibited novel structure-activity relationships of taxane compounds.     

From the salt marsh to the ID-card: Bacteriorhodopsin as a functional material in nanobiotechnology

Bacteriorhodopsin (BR) is an evolutionary highly optimized photochromic retinal protein, which is found in extremely halophilic bacteria, e.g., in salt marshes. We demonstrated that starting from the wildtype as a blueprint by means of gene technology and biotechnology a versatile material for optical information recording can be developed. BR is structurally related to the visual pigment rhodopsin. It is the key molecule in the halobacterial photosynthetic system — an alternative to the chlorophyll-dependent photosynthesis. Its biological function ist that of a light-driven proton pump. In the halobacterial cell — which are found e.g. in salt marshes — it converts light energy into chemical energy, i.e. a proton gradient over the cell membrane, which finally supplies ATP to the cell. The photochromic properties of BR are very attractive compared to those of known organic photochromic compounds, in particular as far as longevity under exposure to oxygen and light is concerned. This is one of the reasons why we try to utilized this evolutionary optimized biomaterial for technical applications in particular in optical data storage and processing. As the biological function of BR is optimized for energy conversion, the physical properties of BR need to be tuned to turn this molecule into a material which matches the requirements of optical applications in data storage and processing. Gene technology is a powerful tool for the controlled modification of physical properties of a biomolecule like BR. In technical applications water needs to be omitted. However, the function of biomaterials strictly depends on the presence of water. Membrane proteins are much less dependent on the presence of water which makes them good candidates for technical applications. We showed that BR can be processed into dry polymeric films where its function is preserved. In a field test where ID-cards comprising BR-based inks as security elements it has been demonstrated that biomaterials may be integrated in active form as functional components into conventional technical applications. Conventional nanomaterials supply properties to a product, biomaterials supply functions.     

A biologically inspired validity measure for comparison of clustering methods over metabolic data sets

In the biological domain, clustering is based on the assumption that genes or metabolites involved in a common biological process are coexpressed/coaccumulated under the control of the same regulatory network. Thus, a detailed inspection of the grouped patterns to verify their memberships to well-known metabolic pathways could be very useful for the evaluation of clusters from a biological perspective. The aim of this work is to propose a novel approach for the comparison of clustering methods over metabolic data sets, including prior biological knowledge about the relation among elements that constitute the clusters. A way of measuring the biological significance of clustering solutions is proposed. This is addressed from the perspective of the usefulness of the clusters to identify those patterns that change in coordination and belong to common pathways of metabolic regulation. The measure summarizes in a compact way the objective analysis of clustering methods, which respects coherence and clusters distribution. It also evaluates the biological internal connections of such clusters considering common pathways. The proposed measure was tested in two biological databases using three clustering methods.     

烟草废弃物在堆肥领域的研究进展

在烟草生产及加工过程中,通常会产生大量的烟草废弃物,如何有效利用这些废弃物以避免环境污染和资源浪费,已成为烟草行业亟需解决的问解。研究发现,烟草废弃物堆肥化处理是规模化利用废弃资源的有效途径之一,对烟草农业的绿色、低碳、循环、可持续发展具有重要意义。从有机肥堆肥制备技术、肥效研究等方面进行了系统综述,从整体上展示了烟草废弃物堆肥技术的发展现状,以期为国内烟草废弃物源堆肥未来技术的研发及产业化提供一定的参考。通过分析发现,在堆肥制备技术方面,主要有微生物菌剂添加技术、共堆肥技术和烟草材料预处理技术3种,此外还衍生出液态有机肥和厌氧发酵联产有机肥技术;在堆肥肥效研究方面,烟草废弃物堆肥可明显改善土壤的物性参数、化学参数以及生物学参数,显著钝化土壤重金属元素,进而提高作物的产量或品质,其中堆肥与化学肥料配施的效果相对较好;堆肥的多功能化是未来堆肥创新利用的重要途径。     

Peroxisome-desmosome complexes in mouse hepatic cells

Summary In addition to mitochondrion-desmosome complexes, peroxisome-desmosome complexes were present in mouse hepatocytes. The latter complexes consisted of a desmosome which was flanked on one or both sides by a peroxisome. Occasional desmosomes were confronted on one side by a peroxisome and on the other by a mitochondrion. It is suggested that the association between organelles and desmosomes is fortuitous, and that no functional significance can be inferred from this association.This work was supported in part by grants from the Heart Association of Northeastern Ohio, Inc., by grant 3C179 from the Cleveland Foundation, by American Cancer Society Institutional Grant In-57-H, and by grant 5 SO1 FR05335-09 from the National Institutes of Health. The expert technical assistance of Merry A. Hetrick and Jeanne Luschin is acknowledged.     

Learning and evolution in bacterial taxis: an operational amplifier circuit modeling the computational dynamics of the prokaryotic 'two component system' protein network

Adaptive behavior in unicellular organisms (i.e., bacteria) depends on highly organized networks of proteins governing purposefully the myriad of molecular processes occurring within the cellular system. For instance, bacteria are able to explore the environment within which they develop by utilizing the motility of their flagellar system as well as a sophisticated biochemical navigation system that samples the environmental conditions surrounding the cell, searching for nutrients or moving away from toxic substances or dangerous physical conditions. In this paper we discuss how proteins of the intervening signal transduction network could be modeled as artificial neurons, simulating the dynamical aspects of the bacterial taxis. The model is based on the assumption that, in some important aspects, proteins can be considered as processing elements or McCulloch-Pitts artificial neurons that transfer and process information from the bacterium's membrane surface to the flagellar motor. This simulation of bacterial taxis has been carried out on a hardware realization of a McCulloch-Pitts artificial neuron using an operational amplifier. Based on the behavior of the operational amplifier we produce a model of the interaction between CheY and FliM, elements of the prokaryotic two component system controlling chemotaxis, as well as a simulation of learning and evolution processes in bacterial taxis. On the one side, our simulation results indicate that, computationally, these protein 'switches' are similar to McCulloch-Pitts artificial neurons, suggesting a bridge between evolution and learning in dynamical systems at cellular and molecular levels and the evolutive hardware approach. On the other side, important protein 'tactilizing' properties are not tapped by the model, and this suggests further complexity steps to explore in the approach to biological molecular computing.     

Non-uniformities and superimposed competition in a model of an autocatalytic network formed by error-prone self-replicative species

The particular dynamics of the previously proposed model of a catalytic network formed byn error-prone self-replicative species without and with superimposed competition is analysed. In the first case, two situations are studied in detail: a uniform network in which all the species are inter-coordinated in the same way, and a network with a species differentiated in its catalytic relation with the remaining elements. In the second case, the superimposed competition is introduced at two levels: first, as an asymmetry in one of the network species amplification factor considering a null self-catalytic vector, and secondly, as a non-null self-catalytic vector with no asymmetry in the other propertics of the species. This kind of system does not present complex behaviour and can be adequately deseribed by performing a standard linear analysis, which gives direct information on the asymptotic behaviour of the sytem. Finally, the biological implications of this analysis within the framework of biological evolution are discussed.     

What research with stored samples teaches us about research with human subjects

There is widespread discussion concerning the safeguards appropriate for human research subjects. Less discussed is the fact that the safeguards one deems appropriate depend, in large part, on the model of research participation that one assumes. Therefore, to determine what safeguards are appropriate, it is necessary first to clarify the competing models of research participation. The ostensibly obscure debate over informed consent for research on stored biological samples is of particular interest in this regard because such research can involve varying subsets of the three central elements of research involvement. As a result, analysis of this debate provides an opportunity to identify the competing models of research participation. Based on this analysis, this paper describes a new model of research participation that is emerging, and considers its implications for clinical research.     

Mechanisms of cytokinin action

Cytokinins are involved in the control of numerous and important processes associated with plant growthand development. They take part in the control of cell division, chloroplast development, bud differentiation, shoot initiationand growth or leaf senescence. In contrast to the wide knowledge of cytokinin effects, the mechanisms of cytokinin actionremain largely unknown. Therefore, it is still difficult to explain how a group of molecules can control so many different biological responses. In this review, we propose some arguments in order to solve this question. In a first part, we underline that cytokinins act in concert with other signals for the control of biological responses. Therefore, the effects observed in responses to cytokinins would be not only related to cytokinins but would also be dependent on all other environmental and hormonal signals perceived by plant cells. In a second part, we present the different actors which could be involved in the signalling pathways of cytokinins. It is very likely that these different elements could be implicated in different cytokinin signalling pathways. Therefore, we propose that the diversity of the cytokinin responses could be also correlated with a diversity of cytokinin signalling pathways.     

The competition controversy in community ecology

There is a long history of controversy in ecology over the role of competition in determining patterns of distribution and abundance, and over the significance of the mathematical modeling of competitive interactions. This paper examines the controversy. Three kinds of considerations have been involved at one time or another during the history of this debate. There has been dispute about the kinds of regularities ecologists can expect to find, about the significance of evolutionary considerations for ecological inquiry, and about the empirical credentials of theoretical studies of competition. Each of these elements is examined with an eye toward gaining philosophical clarification of the issues involved. In the process, certain shortcomings of contemporary philosophical theories are revealed. In particular, I argue that plausibility arguments based on background considerations are an important part of the model building tradition, but that current accounts of the structure and evaluation of scientific theories do little to illuminate this side of theoretical ecology.     

One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations

Successfully modeling electrostatic interactions is one of the key factors required for the computational design of proteins with desired physical, chemical, and biological properties. In this paper, we present formulations of the finite difference Poisson-Boltzmann (FDPB) model that are pairwise decomposable by side chain. These methods use reduced representations of the protein structure based on the backbone and one or two side chains in order to approximate the dielectric environment in and around the protein. For the desolvation of polar side chains, the two-body model has a 0.64 kcal/mol RMSD compared to FDPB calculations performed using the full representation of the protein structure. Screened Coulombic interaction energies between side chains are approximated with an RMSD of 0.13 kcal/mol. The methods presented here are compatible with the computational demands of protein design calculations and produce energies that are very similar to the results of traditional FDPB calculations.     

P element-mediated duplications of genomic regions in Drosophila melanogaster

Previously we have described highly unstable yellow mutations induced by chimeric elements that consist of genomic sequences originating from different regions of the X chromosome flanked by identical copies of an internally deleted 1.2 kb P element. To study further the origin and the mechanism of formation of chimeric mobile elements, we analyzed complex y-sc mutations, induced by inversions between P elements located in the neighboring yellow and scute loci. The breakpoints of the inversions are flanked by two P elements in head-to-head orientation on one side and by one P element on the other side. Such an arrangement of P elements leads to frequent duplication into the site between the two P element copies located in head-to-head orientation of the yellow sequences adjacent to the single P element. The duplicated yellow sequences either partly replace the sequence of one of the P elements or are inserted between the conserved head-to-head oriented P elements. In some cases two copies of the yellow sequence are duplicated between the P elements in inverted tail-to-tail orientation. The structure of the P elements at the place of duplication and of the P element- yellow junction suggests that the described duplications, which form chimeric mobile elements, are generated through the previously proposed synthesis-dependent strand annealing mechanism.     

Human Proteome Organisation’s 7th World Congress, 2008

The annual world congress of Human Proteome Organisation (HUPO) is one of the premier meetings in proteomics. Rotating between Europe, North America and Asia/Oceana, this year’s host city was Amsterdam, The Netherlands. Proteomics still being a rapidly evolving field, HUPO meetings provide a platform for technical advancements in protein purification and separation techniques, innovations in mass spectrometry and applications in bioinformatics and computational biology. A special focus of this year’s meeting was on proteome biology, indicating that the state of technology has progressed to a level permitting interrogation of biological systems in a meaningful way.