The recent development of single molecule detection techniques has opened new horizons for the study of individual macromolecules under physiological conditions. Conformational subpopulations, internal dynamics and activity of single biomolecules, parameters that have so far been hidden in large ensemble averages, are now being unveiled. Herein, we review a particular attractive solution‐based single molecule technique, fluorescence correlation spectroscopy (FCS). This time‐averaging fluctuation analysis which is usually performed in Confocal setups combines maximum sensitivity with high statistical confidence. FCS has proven (...) to be a very versatile and powerful tool for detection and temporal investigation of biomolecules at ultralow concentrations on surfaces, in solution, and in living cells. The introduction of dual‐color cross‐correlation and two‐photon excitation in FCS experiments is currently increasing the number of promising applications of FCS to biological research. BioEssays 24:758–764, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Replication protein A (RPA), the major single‐stranded DNA‐binding protein in eukaryotic cells, is required for processing of single‐stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high‐affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single molecule studies showed (...) that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error‐prone repair of double‐stranded breaks and promote error‐free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis. (shrink)

Pointillistic based super‐resolution techniques, such as photoactivated localization microscopy (PALM), involve multiple cycles of sequential activation, imaging, and precise localization of single fluorescent molecules. A super‐resolution image, having nanoscopic structural information, is then constructed by compiling all the image sequences. Because the final image resolution is determined by the localization precision of detected single molecules and their density, accurate image reconstruction requires imaging of biological structures labeled with fluorescent molecules at high density. In such image datasets, stochastic variations in photon (...) emission and intervening dark states lead to uncertainties in identification of single molecules. This, in turn, prevents the proper utilization of the wealth of information on molecular distribution and quantity. A recent strategy for overcoming this problem is pair‐correlation analysis applied to PALM. Using rigorous statistical algorithms to estimate the number of detected proteins, this approach allows the spatial organization of molecules to be quantitatively described. (shrink)

Intensive research and development of electrophoresis methodology and instrumentation during past decades has resulted in unique methods widely implemented in bioanalysis. While two‐dimensional electrophoresis and denaturing polyacrylamide gel electrophoresis in sodium dodecylsulfate are still the most frequently used electrophoretic methods applied to analyses of proteins, new miniaturized capillary and microfluidic versions of electromigrational methods have been developed. High‐throughput electrophoretic instruments with hundreds of capillaries for parallel separations and laser‐induced fluorescence detection of labeled DNA strands have been of key importance for (...) the scientific and commercial success of the Human Genome Project. Another powerful method, capillary isoelectric focusing with pressurized and pH‐driven mobilization, provides efficient separations and on‐line sensitive detection of proteins, bacteria and viruses. Electrophoretic microfluidic devices can integrate single‐cell injection, cell lysis, separation of its components and fluorescence or mass spectrometry detection. These miniaturized devices also proved the capability of single‐molecule detection. (shrink)

Biological psychiatry has been dominated by a psychopharmacologically-driven neurotransmitter dysfunction paradigm. The objective of this paper is to explore a reductionist assumption underlying this paradigm, and to suggest an improvement on it. The methods used are conceptual analysis with a comparative approach, particularly using illustrations from the history of both biological psychiatry and molecular biology. The results are that complete reduction to physicochemical explanations is not fruitful, at least in the initial stages of research in the medical and life (...) sciences, and that an appropriate (non-reducible) integrative principle - addressing a property of the whole system under study - is required for each domain of research. This is illustrated in Pauling's use of a topological integrative principle for the discovery of the functioning of proteins and in Watson and Crick's use of the notion of a genetic code as an integrative principle for the discovery of the structure of genes. The neurotransmitter dysfunction paradigm addresses single molecules and their neural pathways, yet their interactions within the CNS as a whole seem most pertinent to mental disorders such as schizophrenia. The lack within biological psychiatry of an integrative principle addressing a property of the CNS as a whole may be responsible for the empirical failure of orthomolecular psychiatry, as well as for the central role that serendipity has played in the study of mental disorders, which is dominated by the neurotransmitter paradigm. The conclusion is that research in biological psychiatry may benefit from using, at least initially, some integrative principle(s) addressing a property of the CNS as a whole, such as connectionism or a hierarchical notion. (shrink)

This thesis investigates the epistemological and metaphysical relations between chemistry and quantum mechanics. These relations are examined with respect to how chemistry and quantum mechanics each describe a single inert molecule. A review of how these relations are understood in the literature shows that there is a proliferation of positions which focus on how chemistry is separate from quantum mechanics. This proliferation is accompanied by a tendency within the philosophy of chemistry community to connect the legitimacy of the field with (...) the autonomy of chemistry. First, it is argued that this connection should not be made. Secondly, it is argued that chemistry and quantum mechanics are unified in accordance with Harold Kincaid’s model of non-reductive unity because the two theories exhibit particular epistemic and metaphysical interconnections. Thirdly, a metaphysical account is examined which is incompatible with Kincaid’s model of unity; namely strong emergence as understood by Robin Hendry. According to Hendry, the structure of a single inert molecule strongly emerges from its quantum mechanical entities in the sense that there is downward causation. However, Hendry’s defense of this account faces certain problems. Moreover, the putative empirical evidence for his understanding of strong emergence can be explained without invoking strong emergence. This is shown by considering how quantum mechanics assumes an idealized understanding of a molecule’s stability and structure. In the light of the philosophical literature on idealizations, this idealization can be interpreted in two different ways, both of which explain why quantum mechanics describes the structure of a single molecule the way it does, without assuming strong emergence in Hendry’s sense. Each interpretation has philosophical implications regarding the nature of chemical properties, and the relation of chemistry and quantum mechanics. These implications are consistent with Kincaid’s model of unity and thus further support chemistry’s unity with quantum mechanics (as per Kincaid). (shrink)

DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA‐topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single‐molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of (...) topoisomerase interactions with accessory proteins and other DNA‐associated proteins, supporting the idea that they often function as part of multi‐enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini‐A. These new findings are advancing our understanding of DNA‐related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism. (shrink)

Macromolecular interactions play a central role in many biological processes. Protein‐protein interactions have mostly been studied by co‐immunoprecipitation, which cannot provide quantitative information on all possible molecular connections present in the complex. We will review a new approach that allows cellular proteins and biomolecular complexes to be studied in real‐time at the single‐molecule level. This technique is called single‐molecule pull‐down (SiMPull), because it integrates principles of conventional immunoprecipitation with the powerful single‐molecule fluorescence microscopy. SiMPull is used to (...) count how many of each protein is present in the physiological complexes found in cytosol and membranes. Concurrently, it serves as a single‐molecule biochemical tool to perform functional studies on the pulled‐down proteins. In this review, we will focus on the detailed methodology of SiMPull, its salient features and a wide range of biological applications in comparison with other biosensing tools. (shrink)

Outer membrane proteins (OMPs) maintain the viability of Gram‐negative bacteria by functioning as receptors, transporters, ion channels, lipases, and porins. Folding and assembly of OMPs involves synchronized action of chaperones and multi‐protein machineries which escort the highly hydrophobic polypeptides to their target outer membrane in a folding competent state. Previous studies have identified proteins and their involvement along the OMP biogenesis pathway. Yet, the mechanisms of action and the intriguing ability of all these molecular machines to work without the typical (...) cellular energy source of ATP, but solely based on thermodynamic principles, are still not well understood. Here, we highlight how different single‐molecule studies can shed additional light on the mechanisms and kinetics of OMP biogenesis. (shrink)

The paper describes the change from molecular genetics to postgenomic biology. It focuses on phenomena in the regulation of gene expression that provide a break with the central dogma, according to which sequence specificity for a gene product must be template derived. In its place we find what is called here ‘constitutive molecular epigenesis’. Its three classes of phenomena, which I call sequence ‘activation’, ‘selection’ and ‘creation’, are exemplified by processes such as transcriptional activation, alternative cis- and trans-splicing, and RNA (...) editing. These phenomena support the following main theses of the paper: 1. Other molecular resources share the causal role of ‘genes’: the ‘causal specificity’ for the linear sequence of any gene product is distributed between the coding sequence, cis-acting sequences, trans-acting factors, environmental signals, and the contingent history of the cell (the cellular code) (thesis of distributed causal specificity). 2. These multiple and overlapping processing and targeting mechanisms amplify the repertoire of RNA and protein products specified through the eukaryotic genome, expanding the possibilities specified by the literal code of DNA (thesis of genetic underdeterminism). 3. These mechanisms of gene expression change the focus of postgenomic research from single molecules and their molecular, biochemical and intrinsic function to their cellular, constituent, component or contextual function due to their recruitment and organization in complex cellular networks. In other words, all agents involved in the regulation of gene expression, including DNA, must interact with other agents to achieve full specificity, which is imposed by regulated recruitment and combinatorial control (theses of regulated recruitment and of system analysis). I conclude from these three main theses that the complexity of higher organisms lies not in its number of genes but in the flexibility, versatility and reactivity of its whole genome. (shrink)

Molecular interactions are at the origin of life. How molecules get at different locations in the cell and how they locate their partners is a major and partially unresolved question in biology that is paramount to signaling. Spatio‐temporal correlations of fluctuating fluorescently tagged molecules reveal how they move, interact, and bind in the different cellular compartments. Methods based on fluctuations represent a remarkable technical advancement in biological imaging. Here we discuss image analysis methods based on spatial and temporal correlation (...) of fluctuations, raster image correlation spectroscopy, number and brightness, and spatial cross‐correlations that give us information about how individual molecules move in cells and interact with partners at the single molecule level. These methods can be implemented with a standard laser scanning microscope and produce a cellular level spatio‐temporal map of molecular interactions. (shrink)

It is suggested that if Cultural-Historical Activity Theory (CHAT) is to fulfil its potential as an approach to cultural and historical science in general, then an interdisciplinary concept of activity is needed. Such a concept of activity would provide a common foundation for all the human sciences, underpinning concepts of, for example, state and social movement equally as, for example, learning and personality. For this is needed a clear conception of the ‘unit of analysis’ of activity, i.e., of what (...) constitutes ‘ an activity’, and a clear distinction between the unit of analysis and the substance , i.e., ultimate reality underlying all the human sciences: artifact-mediated joint activity. It is claimed that the concept of ‘project collaboration’ – the interaction between two or more persons in pursuit of a common objective – forms such a unit of activity, the single ‘molecule’ in terms of which both sociological and psychological phenomena can be theorised. It is suggested that such a clarification of the notion of activity allows us to see how individual actions and societal activities mutually constitute one another and are each construed in the light of the other. (shrink)

New imaging methodologies in quantitative fluorescence microscopy, such as Förster resonance energy transfer (FRET), have been developed in the last few years and are beginning to be extensively applied to biological problems. FRET is employed for the detection and quantification of protein interactions, and of biochemical activities. Herein, we review the different methods to measure FRET in microscopy, and more importantly, their strengths and weaknesses. In our opinion, fluorescence lifetime imaging microscopy (FLIM) is advantageous for detecting inter‐molecular interactions quantitatively, the (...) intensity ratio approach representing a valid and straightforward option for detecting intra‐molecular FRET. Promising approaches in single molecule techniques and data analysis for quantitative and fast spatio‐temporal protein‐protein interaction studies open new avenues for FRET in biological research. (shrink)

We present a quantum-mechanical analysis of Szilard's famous single-molecule engine, showing that it is analogous to the double-slit experiment. We further show that the energy derived from the engine's operation is provided by the act of observing the molecule's location. The engine can be operated with no increase in physical entropy, and the second law of thermodynamics does not compel us to relate physical entropy to informational entropy. We conclude that information per seis a subjective, idealized, concept separated from (...) the physical realm. Physical entropy depends on physical objects and physical interactions, and any entropy change owing to observations is entirely a result of the entropy created in the physical apparatus by the process of observation. (shrink)

While innovations in modern microscopy, spectroscopy, and nanoscopy techniques have made single molecule observation a standard in many laboratories, the actual design of meaningful fluorescence reporter systems now hinders major scientific breakthroughs. Even though the field of chemical biology is supercharging the fluorescence toolbox, surprisingly few strategies exist that make the transition from model systems to biologically relevant applications. At the same time, the number of microscopy techniques is growing dramatically. We explain our view on how the impact of modern (...) technologies is influenced not only by further hard‐ and software developments, but also by the availability and suitability of protein‐engineering tools. We identify how the largely independent research fields of chemical biology and fluorescence nanoscopy can influence each other to synergistically drive future technology that can visualize the localization, structure, and dynamics of molecular function without constraints. (shrink)

In this pedagogical communication after demonstrating the legitimacy for using the quantum theory of atoms in molecules (QTAIM) to non-Coulombic systems, Hookean H2 +/H3 2+ species are used for AIM analysis. In these systems, in contrast to their Coulombic counterparts, electron density is atom-like and instead of expected two/three topological atoms, just a single topological atom emerges. This observation is used to demonstrate that what is really “seen” by the topological analysis of electron densities is the clustering of (...) electrons. The very trait of monotonic decay of electron density around the “centers” of clustering guarantees the appearance of topological atoms as basin of attraction of the gradient vector field of the electron density. Although observations with Hookean molecules may seem disappointing at first glance, a careful reasoning points to the fact that the QTAIM methodology is extendable to novel domains, by a knowledge of the morphology of underlying densities, beyond the typical Coulombic systems. (shrink)

The objects we encounter in ordinary life and scientific practice - cars, trees, people, houses, molecules, galaxies, and the like - have long been a fruitful source of perplexity for metaphysicians. The Structure of Objects gives an original analysis of those material objects to which we take ourselves to be committed in our ordinary, scientifically informed discourse. Koslicki focuses on material objects in particular, or, as metaphysicians like to call them "concrete particulars", i.e., objects which occupy a single region (...) of space-time at each time at which they exist and which have a certain range of properties that go along with space-occupancy, such as weight, shape, color, texture, and temperature. The Structure of Objects focuses in particular on the question of how the parts of such objects, assuming that they have parts, are related to the wholes which they compose. (shrink)

On a sunny Sunday afternoon in 2012 a conflict arose between two men riding a popular mountain biking track in New Zealand. The bulk of this was filmed from a helmet-mounted action camera, facilitating a single case analysis of the transition from an everyday trouble to an unexpected violent ending. The two riders come across each other travelling downhill at speed on a narrow track. Unease quickly develops for the camera-clad rider wants to pass the rider in front, but (...) except for an intriguing and brief interlude, the first rider will not let the other pass. The second rider grows frustrated, progressing to tailgate the ‘slower’ rider, in the midst of which he invokes a rule of mountain biking conduct. The reflexive implications of the rule-invocation need to be seen to be believed. The video is used as data to get close to such seeing, and despite some limitations, we can see a clear trajectory where the rule significantly contributes to a moment of phenomenological salience. Thereafter, it becomes witnessably relevant to the conflict that develops. (shrink)

The only RNA molecules known to be branched are circular structures with tails known as lariats that arise during nuclear pre‐mRNA splicing. Lariats accumulate within a large multicomponent particle called a spliceosome that forms upon the addition of unspliced mRNA to nuclear extracts. Recently an RNA molecule has been observed to catalyze branch formation. In this case a single intron of a yeast mitochondrial pre‐mRNA participates in a self‐splicing reaction that results in the accumulation of branched lariats that are processed (...) to correctly spliced exons.An enzyme highly specific for branch removal found in the same extracts that form branches during pre‐mRNA splicing can debranch RNA lariats to their linear forms without loss of nucleotides.The chemical synthesis of branched RNA has recently been achieved. High yields of sequence‐specific oligonucleotides are now available for the analysis of RNA splicing by techniques dependent on branch‐site recognition. (shrink)

Electronegativity, described by Linus Pauling described as “The power of an atom in a molecule to attract electrons to itself” (Pauling in The nature of the chemical bond, 3rd edn, Cornell University Press, Ithaca, p 88, 1960), is used to predict bond polarity. There are dozens of methods for empirically quantifying electronegativity including: the original thermochemical technique (Pauling in J Am Chem Soc 54:3570–3582, 1932), numerical averaging of the ionisation potential and electron affinity (Mulliken in J Chem Phys 2:782–784, 1934), (...) effective nuclear charge and covalent radius analysis (Sanderson in J Chem Phys 23:2467, 1955) and the averaged successive ionisation energies of an element’s valence electrons (Martynov and Batsanov in Zhurnal Neorganicheskoi Khimii 5:3171–3175, 1980), etc. Indeed, there are such strong correlations between numerous atomic parameters—physical and chemical—that the term “electronegativity” integrates them into a single dimensionless number between 0.78 and 4.00 that can be used to predict/describe/model much of an element’s physical character and chemical behaviour. The design of the common and popular medium form of the periodic table is in large part determined by four quantum numbers and four associated rules. However, adding electronegativity completes the construction so that it displays the multi-parameter periodic law operating in two dimensions, down the groups and across the periods, with minimal ambiguity. (shrink)

What chemists take as molecular structure is a theoretical construct based on the concepts of chemical bond, atoms in molecules, etc. and hence it should be distinguished from tangible structures around us. The practical adequacy of it has been demonstrated by the established method of retro-synthetic analysis, for instance. But it is not derived a priori from quantum mechanical treatments of the molecule and criticized for being irrelevant to the reality of the molecule. There is persistent skepticism about it. (...) The present study aims to overcome this skepticism by having recourse to the concepts of affordance and phenomenal field. The basic idea of our approach is suggested by the following statement of Niels Bohr: ‘evidence obtained under different experimental conditions cannot be comprehended within a single picture but must be regarded as complementary in the sense that only the totality of the phenomena exhausts the possible information about the objects’. This implies that we should take account of a context in which the cognition of a fact arises when we think about human activities including science. This can be realized by invoking affordances of a complex such as {agent, devices, methods, substances, surroundings}. That is to say, affordances are context-relative dispositional attributes of {agent-material world} complexes as is asserted by Harré and Llored. The phenomenal field is a conceptual device which schematizes the contextual aspect of affordance and, more importantly, serves as a link between the concept of affordance and Kant’s theory of knowledge, by which alone affordances are realized as the dispositional properties of {agent-material world} complexes. Because affordances become actualized in various phenomenal fields, affordances of one and the same object may well be distinct from one another. In conclusion we can take that molecular structure is the affordance of a complex that includes a chemist who is engaged in organic synthesis, whereas a quantum mechanical picture of the molecule may be one of the possible affordances of a complex that includes a quantum chemist who cares about electronic states of the molecule. (shrink)

What chemists take as molecular structure is a theoretical construct based on the concepts of chemical bond, atoms in molecules, etc. and hence it should be distinguished from tangible structures around us. The practical adequacy of it has been demonstrated by the established method of retro-synthetic analysis, for instance. But it is not derived a priori from quantum mechanical treatments of the molecule and criticized for being irrelevant to the reality of the molecule. There is persistent skepticism about it. (...) The present study aims to overcome this skepticism by having recourse to the concepts of affordance and phenomenal field. The basic idea of our approach is suggested by the following statement of Niels Bohr: ‘evidence obtained under different experimental conditions cannot be comprehended within a single picture but must be regarded as complementary in the sense that only the totality of the phenomena exhausts the possible information about the objects’. This implies that we should take account of a context in which the cognition of a fact arises when we think about human activities including science. This can be realized by invoking affordances of a complex such as {agent, devices, methods, substances, surroundings}. That is to say, affordances are context-relative dispositional attributes of {agent-material world} complexes as is asserted by Harré and Llored. The phenomenal field is a conceptual device which schematizes the contextual aspect of affordance and, more importantly, serves as a link between the concept of affordance and Kant’s theory of knowledge, by which alone affordances are realized as the dispositional properties of {agent-material world} complexes. Because affordances become actualized in various phenomenal fields, affordances of one and the same object may well be distinct from one another. In conclusion we can take that molecular structure is the affordance of a complex that includes a chemist who is engaged in organic synthesis, whereas a quantum mechanical picture of the molecule may be one of the possible affordances of a complex that includes a quantum chemist who cares about electronic states of the molecule. (shrink)

What chemists take as molecular structure is a theoretical construct based on the concepts of chemical bond, atoms in molecules, etc. and hence it should be distinguished from tangible structures around us. The practical adequacy of it has been demonstrated by the established method of retro-synthetic analysis, for instance. But it is not derived a priori from quantum mechanical treatments of the molecule and criticized for being irrelevant to the reality of the molecule. There is persistent skepticism about it. (...) The present study aims to overcome this skepticism by having recourse to the concepts of affordance and phenomenal field. The basic idea of our approach is suggested by the following statement of Niels Bohr: ‘evidence obtained under different experimental conditions cannot be comprehended within a single picture but must be regarded as complementary in the sense that only the totality of the phenomena exhausts the possible information about the objects’. This implies that we should take account of a context in which the cognition of a fact arises when we think about human activities including science. This can be realized by invoking affordances of a complex such as {agent, devices, methods, substances, surroundings}. That is to say, affordances are context-relative dispositional attributes of {agent-material world} complexes as is asserted by Harré and Llored. The phenomenal field is a conceptual device which schematizes the contextual aspect of affordance and, more importantly, serves as a link between the concept of affordance and Kant’s theory of knowledge, by which alone affordances are realized as the dispositional properties of {agent-material world} complexes. Because affordances become actualized in various phenomenal fields, affordances of one and the same object may well be distinct from one another. In conclusion we can take that molecular structure is the affordance of a complex that includes a chemist who is engaged in organic synthesis, whereas a quantum mechanical picture of the molecule may be one of the possible affordances of a complex that includes a quantum chemist who cares about electronic states of the molecule. (shrink)

What chemists take as molecular structure is a theoretical construct based on the concepts of chemical bond, atoms in molecules, etc. and hence it should be distinguished from tangible structures around us. The practical adequacy of it has been demonstrated by the established method of retro-synthetic analysis, for instance. But it is not derived a priori from quantum mechanical treatments of the molecule and criticized for being irrelevant to the reality of the molecule. There is persistent skepticism about it. (...) The present study aims to overcome this skepticism by having recourse to the concepts of affordance and phenomenal field. The basic idea of our approach is suggested by the following statement of Niels Bohr: ‘evidence obtained under different experimental conditions cannot be comprehended within a single picture but must be regarded as complementary in the sense that only the totality of the phenomena exhausts the possible information about the objects’. This implies that we should take account of a context in which the cognition of a fact arises when we think about human activities including science. This can be realized by invoking affordances of a complex such as {agent, devices, methods, substances, surroundings}. That is to say, affordances are context-relative dispositional attributes of {agent-material world} complexes as is asserted by Harré and Llored. The phenomenal field is a conceptual device which schematizes the contextual aspect of affordance and, more importantly, serves as a link between the concept of affordance and Kant’s theory of knowledge, by which alone affordances are realized as the dispositional properties of {agent-material world} complexes. Because affordances become actualized in various phenomenal fields, affordances of one and the same object may well be distinct from one another. In conclusion we can take that molecular structure is the affordance of a complex that includes a chemist who is engaged in organic synthesis, whereas a quantum mechanical picture of the molecule may be one of the possible affordances of a complex that includes a quantum chemist who cares about electronic states of the molecule. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...) separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)

Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information – one replicating with each cell division and the other cycling with a period of one generation – coevolve (...) while perpetuating an organism. Unlike the genome sequence, the arrangement of molecules, including DNA, RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome sequence are transmitted together from one generation to the next, analysis of both is necessary to understand evolution and origins of inherited diseases. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation. Life relies on the information for making organisms that is encoded in single cells and transmitted between generations. These cell codes include interdependent stores of information that replicate and that cycle. Understanding evolution and the origins of inherited diseases requires analysis of cell codes. (shrink)

The goal of synthetic biology is to create artificial organisms. To achieve this it is essential to understand what life is. Metabolism-replacement systems, or (M, R)-systems, constitute a theory of life developed by Robert Rosen, characterized in the statement that organisms are closed to efficient causation, which means that they must themselves produce all the catalysts they need. This theory overlaps in part with other current theories, including autopoiesis, the chemoton, and autocatalytic sets, all of them invoking some idea of (...) closure. A simple model of an (M, R)-system has been implemented in the computer, and behaves in ways that may shed light on the requirements for a prebiotic self-organizing system. In addition to a trivial steady state in which nothing happens, it can establish a non-trivial steady state in which all intermediates have finite concentrations, with their rates of degradation balanced by their rates of synthesis. The system can be regenerated from the set of food components plus a single intermediate, and maintain itself in that state indefinitely, despite continuous degradation. At the very low compartment volumes that may have existed in prebiotic conditions, for example in cavities in minerals, or in micelles formed by simple amphiphiles, statistical fluctuations in the numbers of molecules need to be taken into account. With the stochastic approach there is no non-trivial steady state in strict mathematical terms, because the system will always collapse to the trivial state after sufficient time. However, the average time before collapse is so long for volumes greater than $10^{-19}\;{\textsc{l}}$ (much smaller than the volume of the order of $10^{-15}\;{\textsc{l}}$ for a typical bacterial cell) that for practical purposes the self-maintaining state of non-null concentrations becomes significant, recalling the situation of bistability that is observed in deterministic analysis. In turn, there exists a minimum size below which the self-organizing system cannot maintain itself on chemically relevant time scales. The value of the critical volume depends on the particular concentrations and rate constants assumed, but the principle could apply generally. (shrink)

Automatic moving object detection and tracking is very important task in video surveillance applications. In the present work the well known background subtraction model and use of Gaussian Mixture Models have been used to implement a robust automated single object tracking system. In this implementation, background subtraction on subtracting consecutive frame-by-frame basis for moving object detection is done. Once the object has been detected it is tracked by employing an efficient GMM technique. After successful completion of tracking, moving object recognition (...) of those objects using well known Principal Component Analysis, which is used for extracting features and Manhattan based distance metric is used for subsequent classification purpose. The system is capable of handling entry and exit of an object. Such a tracking system is cost effective and can be used as an automated video conferencing system and also has applications like human tracking, vehicles monitoring, and event recognition for video surveillance. The proposed algorithm was tested on standard database on complex environments and the results were satisfactory. (shrink)

A recent single cell mRNA sequencing study by Dueck et al. compares neuronal transcriptomes to the transcriptomes of adipocytes and cardiomyocytes. Single cell ‘omic approaches such as those used by the authors are at the leading edge of molecular and biophysical measurement. Many groups are currently employing single cell sequencing approaches to understand cellular heterogeneity in cancer and during normal development. These single cell approaches also are beginning to address long‐standing questions regarding nervous system diversity. Beyond an innate interest in (...) cataloging cell type diversity in the brain, single cell neuronal diversity has important implications for neurotypic neural circuit function and for neurological disease. Herein, we review the authors’ methods and findings, which most notably include evidence of unique expression profiles in some single neurons. (shrink)

In this paper, we formulate and investigate a two-microorganism and single nutrient chemostat model with Monod-Haldane response function and random perturbation. First, for the corresponding deterministic system, we introduce the conditions of the stability of the equilibrium points. Then, using Lyapunov function and Itô’s formula, we investigate the existence and uniqueness of the global positive solution of the stochastic chemostat model. Furthermore, we explore and obtain the criterions of the extinction and the permanence for the stochastic model. Finally, numerical simulations (...) are carried out to illustrate our main results. (shrink)

In the name of safeguarding public interests and ethical principles, China’s National Health Commission bans unmarried women from using assisted reproductive technology (ART), including egg freezing. Supported by local governments, the ban has restricted single women’s reproductive rights nationwide. Although some courts bypassed the ban to allow widowed single women to use ART, they have not adopted a position in favour of single women’s reproductive autonomy, but quite the contrary. Faced with calls to relax the ban and allow single women (...) to freeze eggs electively, the National Health Commission refused to amend their policy, partly to protect women’s well-being paternalistically and partly to implement the central government’s policies to boost the birthrate and maintain traditional family structures. While the government’s concerns about elective egg freezing are not entirely unfounded, they have failed to demonstrate that banning single women’s egg freezing is a suitable, necessary and proportionate means to safeguard societal interests and ethical principles. The authority’s assumptions that women cannot make rational decisions for their health even with adequate informed consent procedures, that banning egg freezing by single women promotes a culture of having children ‘at a proper age’, and that egg freezing by single women offends China’s public moralities have not been substantiated. (shrink)

To explore how molecules became signs I will ask: “What sort of process is necessary and sufficient to treat a molecule as a sign?” This requires focusing on the interpreting system and its interpretive competence. To avoid assuming any properties that need to be explained I develop what I consider to be a simplest possible molecular model system which only assumes known physics and chemistry but nevertheless exemplifies the interpretive properties of interest. Three progressively more complex variants of this model (...) of interpretive competence are developed that roughly parallel an icon-index-symbol hierarchic scaffolding logic. The implication of this analysis is a reversal of the current dogma of molecular and evolutionary biology which treats molecules like DNA and RNA as the original sources of biological information. Instead I argue that the structural characteristics of these molecules have provided semiotic affordances that the interpretive dynamics of viruses and cells have taken advantage of. These molecules are not the source of biological information but are instead semiotic artifacts onto which dynamical functional constraints have been progressively offloaded during the course of evolution. (shrink)

Within the schema therapy model, schema modes are the shifting experiential states that individuals experience, and identification of these is central to case conceptualization and the planning of interventions. Differences in the naming and descriptions of modes in the literature suggest the need for systematic phenomenological investigation. This paper presents the first part of an interpretative phenomenological analysis of schema modes within the single case of Linda, a young woman with anorexia nervosa. The analysis, which is based largely (...) on transcripts of seven therapy sessions, yielded phenomenological accounts of her experience of a number of modes. In this, the first of two papers, a phenomenological account of her Child and Parent modes are presented and discussed. (shrink)

In schema therapy, the identification of schema modes is central to case conceptualization and the planning of interventions. Differences in the naming and description of specific modes in the literature suggest the need for systematic phenomenological investigation. This paper presents the second part of an interpretative phenomenological analysis of schema modes within the single case of Linda, a young woman with anorexia nervosa. In this paper, the focus is on Linda’s Coping modes and on several important superordinate themes: mode (...) dyads, mode conflicts and balance of power, mode differentiation, and mode sequences. The findings support the value of the mode framework that is standard in schema therapy, based on Child modes, Parent modes, Coping modes, and the Healthy Adult. They furthermore highlight the idiosyncratic nature of schema modes within an individual case. Research and clinical implications of the findings are discussed, and links are made to the phenomenological perspective of Merleau-Ponty. (shrink)

This dissertation investigates the plausibility of metaethical relativism, or more specifically, what I call “moral truth-value relativism”: the idea that the truth of a moral statement or belief depends on who utters or has it, or who assesses it. According to the most prevalent variants of this view in philosophical literature – “standard relativism” – the truth-values are relative to people’s moralities, often understood as some subset of their affective or desirelike attitudes. Standard relativism has two main contenders: absolutism – (...) the view that the truth-values of moral statements and beliefs do not vary in that way – and non-cognitivism – the view that moral judgements do not have truth-values, since they express affective or desire-like attitudes rather than beliefs. Almost the entire dissertation concerns the plausibility of standard relativism in contrast to absolutism. Part 1 examines first the two main arguments for standard relativism: that it accounts for the connection between moral judgements and motivation (chapter 2), and for the prevalence of diversity of moral opinion (chapter 3). Then the most common objection is considered: that it is inconsistent with the existence of genuine moral disagreements (chapter 4). I argue that these arguments are inconclusive. Both relativism and absolutism can account for the features discussed. Part 2 focuses on the fact that different people have different strongly held intuitions about the relative or absolute nature of morality. I argue that given a common methodological approach in philosophy and metaethics, which takes such intuitions as evidence of correct analyses, this difference in intuitions suggests that neither a relativist nor absolutist analysis can be correct for everyone’s moral judgements. I argue that this result holds both given semantic internalism (chapter 6) and given semantic externalism (chapter 7). To get one single analysis of everyone’s moral judgements we would have to abandon the intuitionbased methodology. In chapter 8, however, I argue that we can maintain this methodology if we accept analysis pluralism, the view that different analyses hold for different people’s moral judgements. (shrink)

One of the conundrums of Wittgenstein’s so-called ‘1914–1916 Notebooks’ concerns the role played by the visual instances of logical analysis. As a matter of fact, in discussing in that work the requirement that the logical analysis of meaningful sentences be complete, Wittgenstein often takes as examples statements about the colored parts of the subject's visual image (Gesichtsbild). In view of this, it might be thought that the requirement is not laid down in the Notebooks on logical grounds, but (...) somehow on psychological or psychophysical ones. In this paper I argue this is not so and that the requirement is exemplified rather than justified by the analysis of statements about the products of the subject’s visual imagination. I also argue that, on Wittgenstein’s syntactic notion of a complete logical analysis, our unanalyzed statements embody as they are the requirement that their sense be fully determinate; which is just what is meant by the idea that the analysis must be complete. (shrink)

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and (...) concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease. (shrink)

Conformational changes of proteins and other biomolecules play a fundamental role in their functional mechanism. Single pair Förster resonance energy transfer offers the possibility to detect these conformational changes and dynamics, and to characterize their underlying kinetics. Using spFRET on microscopes with different modes of detection, dynamic timescales ranging from nanoseconds to seconds can be quantified. Confocal microscopy can be used as a means to analyze dynamics in the range of nanoseconds to milliseconds, while total internal reflection fluorescence microscopy offers (...) information about conformational changes on timescales of milliseconds to seconds. While the existence of dynamics can be directly inferred from the FRET efficiency time trace or the correlation of FRET efficiency and fluorescence lifetime, additional computational approaches are required to extract the kinetic rates of these dynamics, a short overview of which is given in this review. The functional mechanism of proteins is often driven by underlying conformational changes. These intramolecular changes and dynamics can be investigated using single pair Förster resonance energy transfer. The kinetic timescales of the dynamics in the range of nanoseconds to seconds is then quantified using different experimental and analytical implementations. (shrink)