Multimodal Networks: Structure and Operations

A multimodal network (MMN) is a novel graph-theoretic formalism designed to capture the structure of biological networks and to represent relationships derived from multiple biological databases. MMNs generalize the standard notions of graphs and hypergraphs, which are the bases of current diagrammatic representations of biological phenomena and incorporate the concept of mode. Each vertex of an MMN is a biological entity, a biot, while each modal hyperedge is a typed relationship, where the type is given by the mode of the hyperedge. The current paper defines MMNs and concentrates on the structural aspects of MMNs. A companion paper develops MMNs as a representation of the semantics of biological networks and discusses applications of the MMNs in managing complex biological data. The MMN model has been implemented in a database system containing multiple kinds of biological networks.     

Optically active molecule-based magnets: enantioselective self-assembling, optical, and magnetic properties.

In this short communication we describe the synthesis and the optical and magnetic properties of optically active three dimensional (3D) bimetallic [Cr-Mn] networks [[Delta Cr(III) Delta Mn(II)(ox)(3)][Delta Ru(II)(bpy)(3)]ClO(4)](n)1 - Delta, [[Lambda Cr(III)Lambda Mn(II)(ox)(3)][Lambda Ru(II) (bpy)(3)]ClO(4)](n) 1 - Lambda and [[Delta Cr(III)Delta Mn(II)(ox)(3)][Delta Ru(II)(bpy)(2)p p y]](n) 2 - Delta,[[Lambda Cr(III)Lambda Mn(II)(ox)(3)][Lambda Ru(II)(bpy)(2)ppy]](n) 2 - Lambda (ox = oxalate, bpy = bipyridine, ppy = phenyl-pyridine).     

Biocompatibility: Nanomaterials for cell- and tissue engineering

The reaction of cells to varying topographic surfaces has been investigated ever since the beginnings of cell culture technology, as these features influence the cells principle behaviours such as adhesion, spreading, morphology, motility and proliferation. Interest in this aspect of cell biology was renewed when advanced fabrication methods became more widespread. This paper tries to briefly summarise the current state of knowledge regarding the use of nanostructured surfaces for cell- and tissue engineering.     

Penetration of Cell Membranes and Synthetic Lipid Bilayers by Nanoprobes

Nanoscale devices have been proposed as tools for measuring and controlling intracellular activity by providing electrical and/or chemical access to the cytosol. Unfortunately, nanostructures with diameters of 50–500 nm do not readily penetrate the cell membrane, and rationally optimizing nanoprobes for cell penetration requires real-time characterization methods that are capable of following the process of membrane penetration with nanometer resolution. Although extensive work has examined the rupture of supported synthetic lipid bilayers, little is known about the applicability of these model systems to living cell membranes with complex lipid compositions, cytoskeletal attachment, and membrane proteins. Here, we describe atomic force microscopy (AFM) membrane penetration experiments in two parallel systems: live HEK293 cells and stacks of synthetic lipid bilayers. By using the same probes in both systems, we were able to clearly identify membrane penetration in synthetic bilayers and compare these events with putative membrane penetration events in cells. We examined membrane penetration forces for three tip geometries and 18 chemical modifications of the probe surface, and in all cases the median forces required to penetrate cellular and synthetic lipid bilayers with nanoprobes were greater than 1 nN. The penetration force was sensitive to the probe's sharpness, but not its surface chemistry, and the force did not depend on cell surface or cytoskeletal properties, with cells and lipid stacks yielding similar forces. This systematic assessment of penetration under various mechanical and chemical conditions provides insights into nanoprobe-cell interactions and informs the design of future intracellular nanoprobes.     

Penetration of Cell Membranes and Synthetic Lipid Bilayers by Nanoprobes

Nanoscale devices have been proposed as tools for measuring and controlling intracellular activity by providing electrical and/or chemical access to the cytosol. Unfortunately, nanostructures with diameters of 50–500 nm do not readily penetrate the cell membrane, and rationally optimizing nanoprobes for cell penetration requires real-time characterization methods that are capable of following the process of membrane penetration with nanometer resolution. Although extensive work has examined the rupture of supported synthetic lipid bilayers, little is known about the applicability of these model systems to living cell membranes with complex lipid compositions, cytoskeletal attachment, and membrane proteins. Here, we describe atomic force microscopy (AFM) membrane penetration experiments in two parallel systems: live HEK293 cells and stacks of synthetic lipid bilayers. By using the same probes in both systems, we were able to clearly identify membrane penetration in synthetic bilayers and compare these events with putative membrane penetration events in cells. We examined membrane penetration forces for three tip geometries and 18 chemical modifications of the probe surface, and in all cases the median forces required to penetrate cellular and synthetic lipid bilayers with nanoprobes were greater than 1 nN. The penetration force was sensitive to the probe''s sharpness, but not its surface chemistry, and the force did not depend on cell surface or cytoskeletal properties, with cells and lipid stacks yielding similar forces. This systematic assessment of penetration under various mechanical and chemical conditions provides insights into nanoprobe-cell interactions and informs the design of future intracellular nanoprobes.     

Evolution, Ecology, and Multimodal Distributions of Body Size

The sizes of organisms are determined by their interactions with their environment and related ecological and evolutionary processes. Recent studies of body size distributions across communities show evidence for multimodality. The multiple modes were originally explained as a consequence of textural discontinuities in habitat structure. Because communities consist of species that are drawn from lineages, body size patterns within lineages will affect those that are expressed in communities. We used a cellular automation model to argue that multimodality in body sizes within lineages can arise from a few fundamental evolutionary mechanisms alone. We tested the hypothesis using body size data for 138 fish genera and found strong support for the idea that evolution structures body size distributions. The results suggest, first, that we should expect the distribution of body sizes within lineages to be multimodal and second, that a coherent theory of community body size distributions will need to combine both evolutionary and ecological perspectives. Received 28 January 2002; accepted 21 March 2002     

Multimodal silica-shelled quantum dots: direct intracellular delivery, photosensitization, toxic, and microcirculation effects

In the present study, we describe a multimodal QD probe with combined fluorescent and paramagnetic properties, based on silica-shelled single QD micelles with incorporated paramagnetic substances [tris(2,2,6,6-tetramethyl-3,5-heptanedionate)/gadolinium] into the micelle and/or silica coat. The probe was characterized with high photoluminescence quantum yield and good positive MRI contrast, low cytotoxicity, and easy intracellular delivery in viable cells. The intravenous administration of the probe in experimental animals did not affect significantly the physiological parameters and microcirculation (e.g., heart rate, blood pressure, diameter and shape of blood vessels), which makes it appropriate for tracing of blood circulation and in vivo multimodal imaging using fluorescent confocal microscopy, two-photon microscopy, and MRI.     

Multimodal Holographic Microscopy: Distinction between Apoptosis and Oncosis

Identification of specific cell death is of a great value for many scientists. Predominant types of cell death can be detected by flow-cytometry (FCM). Nevertheless, the absence of cellular morphology analysis leads to the misclassification of cell death type due to underestimated oncosis. However, the definition of the oncosis is important because of its potential reversibility. Therefore, FCM analysis of cell death using annexin V/propidium iodide assay was compared with holographic microscopy coupled with fluorescence detection - “Multimodal holographic microscopy (MHM)”. The aim was to highlight FCM limitations and to point out MHM advantages. It was shown that the annexin V+/PI− phenotype is not specific of early apoptotic cells, as previously believed, and that morphological criteria have to be necessarily combined with annexin V/PI for the cell death type to be ascertained precisely. MHM makes it possible to distinguish oncosis clearly from apoptosis and to stratify the progression of oncosis.     

Preterm EEG: A Multimodal Neurophysiological Protocol

Since its introduction in early 1950s, electroencephalography (EEG) has been widely used in the neonatal intensive care units (NICU) for assessment and monitoring of brain function in preterm and term babies. Most common indications are the diagnosis of epileptic seizures, assessment of brain maturity, and recovery from hypoxic-ischemic events. EEG recording techniques and the understanding of neonatal EEG signals have dramatically improved, but these advances have been slow to penetrate through the clinical traditions. The aim of this presentation is to bring theory and practice of advanced EEG recording available for neonatal units. In the theoretical part, we will present animations to illustrate how a preterm brain gives rise to spontaneous and evoked EEG activities, both of which are unique to this developmental phase, as well as crucial for a proper brain maturation. Recent animal work has shown that the structural brain development is clearly reflected in early EEG activity. Most important structures in this regard are the growing long range connections and the transient cortical structure, subplate. Sensory stimuli in a preterm baby will generate responses that are seen at a single trial level, and they have underpinnings in the subplate-cortex interaction. This brings neonatal EEG readily into a multimodal study, where EEG is not only recording cortical function, but it also tests subplate function via different sensory modalities. Finally, introduction of clinically suitable dense array EEG caps, as well as amplifiers capable of recording low frequencies, have disclosed multitude of brain activities that have as yet been overlooked.In the practical part of this video, we show how a multimodal, dense array EEG study is performed in neonatal intensive care unit from a preterm baby in the incubator. The video demonstrates preparation of the baby and incubator, application of the EEG cap, and performance of the sensory stimulations.     

Multimodal communication and language origins: integrating gestures and vocalizations

The presence of divergent and independent research traditions in the gestural and vocal domains of primate communication has resulted in major discrepancies in the definition and operationalization of cognitive concepts. However, in recent years, accumulating evidence from behavioural and neurobiological research has shown that both human and non‐human primate communication is inherently multimodal. It is therefore timely to integrate the study of gestural and vocal communication. Herein, we review evidence demonstrating that there is no clear difference between primate gestures and vocalizations in the extent to which they show evidence for the presence of key language properties: intentionality, reference, iconicity and turn‐taking. We also find high overlap in the neurobiological mechanisms producing primate gestures and vocalizations, as well as in ontogenetic flexibility. These findings confirm that human language had multimodal origins. Nonetheless, we note that in great apes, gestures seem to fulfil a carrying (i.e. predominantly informative) role in close‐range communication, whereas the opposite holds for face‐to‐face interactions of humans. This suggests an evolutionary shift in the carrying role from the gestural to the vocal stream, and we explore this transition in the carrying modality. Finally, we suggest that future studies should focus on the links between complex communication, sociality and cooperative tendency to strengthen the study of language origins.     

Synthesis and Calibration of Phosphorescent Nanoprobes for Oxygen Imaging in Biological Systems

Oxygen measurement by phosphorescence quenching [1, 2] consists of the following steps: 1) the probe is delivered into the medium of interest (e.g. blood or interstitial fluid); 2) the object is illuminated with light of appropriate wavelength in order to excite the probe into its triplet state; 3) the emitted phosphorescence is collected, and its time course is analyzed to yield the phosphorescence lifetime, which is converted into the oxygen concentration (or partial pressure, pO₂). The probe must not interact with the biological environment and in some cases to be 4) excreted from the medium upon the measurement completion. Each of these steps imposes requirements on the molecular design of the phosphorescent probes, which constitute the only invasive component of the measurement protocol. Here we review the design of dendritic phosphorescent nanosensors for oxygen measurements in biological systems. The probes consist of Pt or Pd porphyrin-based polyarylglycine (AG) dendrimers, modified peripherally with polyethylene glycol (PEG''s) residues. For effective two-photon excitation, termini of the dendrimers may be modified with two-photon antenna chromophores, which capture the excitation energy and channel it to the triplet cores of the probes via intramolecular FRET (Förster Resonance Energy Transfer). We describe the key photophysical properties of the probes and present detailed calibration protocols.Download video file.^{(126M, mp4)}     

Nanomaterials modulate stem cell differentiation: biological interaction and underlying mechanisms

Stem cells are unspecialized cells that have the potential for self-renewal and differentiation into more specialized cell types. The chemical and physical properties of surrounding microenvironment contribute to the growth and differentiation of stem cells and consequently play crucial roles in the regulation of stem cells’ fate. Nanomaterials hold great promise in biological and biomedical fields owing to their unique properties, such as controllable particle size, facile synthesis, large surface-to-volume ratio, tunable surface chemistry, and biocompatibility. Over the recent years, accumulating evidence has shown that nanomaterials can facilitate stem cell proliferation and differentiation, and great effort is undertaken to explore their possible modulating manners and mechanisms on stem cell differentiation. In present review, we summarize recent progress in the regulating potential of various nanomaterials on stem cell differentiation and discuss the possible cell uptake, biological interaction and underlying mechanisms.     

Nanomaterials for cancer therapy and imaging

A variety of organic and inorganic nanomaterials with dimensions below several hundred nanometers are recently emerging as promising tools for cancer therapeutic and diagnostic applications due to their unique characteristics of passive tumor targeting. A wide range of nanomedicine platforms such as polymeric micelles, liposomes, dendrimers, and polymeric nanoparticles have been extensively explored for targeted delivery of anti-cancer agents, because they can accumulate in the solid tumor site via leaky tumor vascular structures, thereby selectively delivering therapeutic payloads into the desired tumor tissue. In recent years, nanoscale delivery vehicles for small interfering RNA (siRNA) have been also developed as effective therapeutic approaches to treat cancer. Furthermore, rationally designed multi-functional surface modification of these nanomaterials with cancer targeting moieties, protective polymers, and imaging agents can lead to fabrication versatile theragnostic nanosystems that allow simultaneous cancer therapy and diagnosis. This review highlights the current state and future prospects of diverse biomedical nanomaterials for cancer therapy and imaging.     

Electrospun Nanomaterials for Supercapacitor Electrodes: Designed Architectures and Electrochemical Performance

Electrospinning is the most facile and highly versatile approach to produce 1D polymeric, inorganic, and hybrid nanomaterials with a small diameter, controllable dimensions, and designed architectures. In particular, with large surface area, high porosity, low density, good directionality, and tunable composition, electrospun nanofibers and mats are regarded as ideal candidates for various kinds of electrochemical energy storage devices such as supercapacitors (SCs). In this review, the recent progress in electrospun electrode materials for SCs is presented, covering the architecture design and their electrochemical performance. After a brief introduction about SCs, the basic principles of the electrospinning technique are discussed. Following, attention is paid to the discussion of various electrospun nanofibers and mats including 1D carbons, metal oxides, metal sulfides, metal nitrides, conducting polymers and composite nanomaterials with various types of architectures as electrodes for SCs. The relationship between the composition, architecture, and the electrochemical performance is discussed in detail. Finally, some challenges and perspectives of future research of the electrospun nanofibers and mats for high performance SCs are highlighted. It is anticipated that this review would provide the researchers some inspiration for constructing new types of energy storage devices.     

Tunable, monochromatic X-rays: an enabling technology for molecular/cellular imaging and therapy

Pulsed, tunable, monochromatic X-rays hold great potential as a cellular and molecular probe. These beams can be tuned to the binding energy of orbital electrons in atoms, making them extremely useful in diagnostic k-edge imaging and Auger cascade radiotherapy. Their wide tunability makes them ideal for the performance of various techniques as disparate as protein crystallography and three-dimensional, compressionless, monochromatic mammography. Since only the frequency best suited to the task at hand is used, radiation exposure to patients or animals is exceedingly low when compared to standard X-ray techniques.     

Multimodal interneurones in the polyclad flatworm,Alloeoplana californica

Summary Two morphological types of interneurones were found in the brainof Alloeoplana californica (Figs. 1, 2). Both respond to water vibration and to light offset (Fig. 3). These responses are blocked by Mg⁺⁺ or Cd⁺⁺ (Fig. 4), and habituate to repetitive stimuli (Figs. 6, 10). Even when the light response is habituated, light offset will dishabituate the vibration response (Figs. 7, 10); no other regime tested produced dishabituation of either response. These neurones receive higher-order sensory input, and make subthreshold excitatory synapses on motor pathways; intracellular tetraethylammonium lengthens the time course of the spikes (Fig. 5), and each such spike elicits a contraction in the anterior margin of the animal. We believe that they form part of the neuronal circuitry underlying arousal.Abbreviation TEA tetraethylammonium     

Optically inducible membrane recruitment and signaling systems

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Preparation and Derivatives of Optically Inactive Isopulegols

The unknown three isomers of optically inactive isopulegol, (±)-isopulegol(II), (±)-neo-isopulegol(III), and (±)-iso-isopulegol(IV) were isolated; then 3,5-dinitrobenzoates and p-nitrobenzoates were prepared from them.