Living off the Sun: chlorophylls,bacteriochlorophylls and rhodopsins

Pigments absorbing 350–1,050 nm radiation have had an important role on the Earth for at least 3.5 billion years. The ion pumping rhodopsins absorb blue and green photons using retinal and pump ions across cell membranes. Bacteriochlorophylls (BChl), absorbing in the violet/blue and near infra red (NIR), power anoxygenic photosynthesis, with one photoreaction centre; and chlorophylls (Chl), absorbing in the violet/blue and red (occasionally NIR) power oxygenic photosynthesis, with two photoreaction centres. The accessory (bacterio)chlorophylls add to the spectral range (bandwidth) of photon absorption, e.g., in algae living at depth in clear oceanic water and in algae and photosynthetic (PS) bacteria in microbial mats. Organism size, via the package effect, determines the photon absorption benefit of the costs of synthesis of the pigment–protein complexes. There are unresolved issues as to the evolution of Chls vs. BChls and the role of violet/blue and NIR radiation in PS bacteria.     

On the Emergence of Living Systems

If the problem of the origin of life is conceptualized as a process of emergence of biochemistry from proto-biochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, then the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to living systems and biosemiosis. In such a view the emergence of life, and concomitantly of natural selection and biosemiosis, is the result of deep natural laws (the outlines of which we are only beginning to perceive) and reflects a degree of holism in those systems that led to life. Further, such an approach may lead to the development of a more general theory of biology and of natural organization, one informed by semiotic concepts.     

Information Theory in Living Systems,Methods, Applications,and Challenges

Living systems are distinguished in nature by their ability to maintain stable, ordered states far from equilibrium. This is despite constant buffeting by thermodynamic forces that, if unopposed, will inevitably increase disorder. Cells maintain a steep transmembrane entropy gradient by continuous application of information that permits cellular components to carry out highly specific tasks that import energy and export entropy. Thus, the study of information storage, flow and utilization is critical for understanding first principles that govern the dynamics of life. Initial biological applications of information theory (IT) used Shannon’s methods to measure the information content in strings of monomers such as genes, RNA, and proteins. Recent work has used bioinformatic and dynamical systems to provide remarkable insights into the topology and dynamics of intracellular information networks. Novel applications of Fisher-, Shannon-, and Kullback–Leibler informations are promoting increased understanding of the mechanisms by which genetic information is converted to work and order. Insights into evolution may be gained by analysis of the the fitness contributions from specific segments of genetic information as well as the optimization process in which the fitness are constrained by the substrate cost for its storage and utilization. Recent IT applications have recognized the possible role of nontraditional information storage structures including lipids and ion gradients as well as information transmission by molecular flux across cell membranes. Many fascinating challenges remain, including defining the intercellular information dynamics of multicellular organisms and the role of disordered information storage and flow in disease.     

Biophysics and Thermodynamics: The Scientific Building Blocks of Bio-inspired Drug Delivery Nano Systems

Biophysics and thermodynamics are considered as the scientific milestones for investigating the properties of materials. The relationship between the changes of temperature with the biophysical variables of biomaterials is important in the process of the development of drug delivery systems. Biophysics is a challenge sector of physics and should be used complementary with the biochemistry in order to discover new and promising technological platforms (i.e., drug delivery systems) and to disclose the ‘silence functionality’ of bio-inspired biological and artificial membranes. Thermal analysis and biophysical approaches in pharmaceuticals present reliable and versatile tools for their characterization and for the successful development of pharmaceutical products. The metastable phases of self-assembled nanostructures such as liposomes should be taken into consideration because they represent the thermal events can affect the functionality of advanced drug delivery nano systems. In conclusion, biophysics and thermodynamics are characterized as the building blocks for design and development of bio-inspired drug delivery systems.KEY WORDS: biophysics, drug delivery nano systems, pharmaceutics, thermal analysis, thermodynamics     

Biophysics of the subgenual organ of the honeybee, Apis mellifera

The subgenual organ of the honeybee (Apis mellifera) is suspended in a haemolymph channel in the tibia of each leg. When the leg is accelerated, inertia causes the haemolymph (and the subgenual organ) to lag behind the movement of the rest of the leg. The magnitude of this phase lag determines the displacement of the subgenual organ relative to the leg and to the proximal end of the organ, which is connected to the cuticle. Oscillations of the subgenual organ are visualised during vibration stimulation of the leg, by means of stroboscopic light. Video analysis provides fairly accurate values of the amplitude and phase of the oscillations, which are compared with the predictions of a model.   The model comparison shows that the haemolymph channel can be described as an oscillating fluid-filled tube occluded by an elastic structure (probably the subgenual organ). The mechanical properties of the subgenual organ and haemolymph channel resemble those of an overdamped mass-spring system. A comparison of the threshold curve of the subgenual organ determined using electrophysiology with that predicted by the oscillating tube model suggests that the sensory cells respond to displacements of the organ relative to the leg. Accepted: 10 May 1997     

Biophysics and Structure of the Patch and the Gigaseal

Interpreting channel behavior in patches requires an understanding of patch structure and dynamics, especially in studies of mechanosensitive channels. High resolution optical studies show that patch formation occurs via blebbing that disrupts normal membrane structure and redistributes in situ components including ion channels. There is a 1-2 μm region of the seal below the patch where proteins are excluded and this may consist of extracted lipids that form the gigaseal. Patch domes often have complex geometries with inhomogeneous stresses due to the membrane-glass adhesion energy (E_a), cytoskeletal forces, and possible lipid subdomains. The resting tension in the patch dome ranges from 1-4 mN/m, a significant fraction of the lytic tension of a bilayer (∼10 mN/m). Thus, all patch experiments are conducted under substantial, and uneven, resting tension that may alter the kinetics of many channels. E_a seems dominated by van der Waals attraction overlaid with a normally repulsive Coulombic force. High ionic strength pipette saline increased E_a and, surprisingly, increased cytoskeletal rigidity in cell-attached patches. Low pH pipette saline also increased E_a and reduced the seal selectivity for cations, presumably by neutralizing the membrane surface charge. The seal is a negatively charged, cation selective, space with a resistance of ∼7 gigohm/μm in 100 mM KCl, and the high resistivity of the space may result from the presence of high viscosity glycoproteins. Patches creep up the pipette over time with voltage independent and voltage dependent components. Voltage-independent creep is expected from the capillary attraction of E_a and the flow of fresh lipids from the cell. Voltage-dependent creep seems to arise from electroosmosis in the seal. Neutralization of negative charges on the seal membrane with low pH decreased the creep rate and reversed the direction of creep at positive pipette potentials.     

Systems Biology in Aging: Linking the Old and the Young

Aging can be defined as a process of progressive decline in the physiological capacity of an organism, manifested by accumulated alteration and destabilization at the whole system level. Systems biology approaches offer a promising new perspective to examine the old problem of aging. We begin this review by introducing the concepts of systems biology, and then illustrate the application of systems biology approaches to aging research, from gene expression profiling to network analysis. We then introduce the network that can be constructed using known lifespan and aging regulators, and conclude with a look forward to the future of systems biology in aging research. In summary, systems biology is not only a young field that may help us understand aging at a higher level, but also an important platform that can link different levels of knowledge on aging, moving us closer to a more comprehensive control of systematic decline during aging.     

Stepwise Evolution of Nonliving to Living Chemical Systems

Steps by which a nonliving chemical system could have transformed into a living system are described and discussed, assuming general features of Wächtershäuser's chemo-autotrophic surface theory of the origin of life. Environmental species such as CO₂ and H₂S are proposed to have reacted to form a quasi-steady state metal-bound intermediate (CH₃-M) that slowly decayed into waste (CH₄). Unpredictable dispersive reactions expanded the system to include surface-bound forms of the citric acid cycle intermediates (oxaloacetate → citrate). Further reaction yielded an autocatalytic system in which raw materials are converted into the system at exponential rates. Combinatorial dispersive reactions that improved the performance of this system were automatically selected and incorporated into it. Systems evolved critical features of living systems (proteins, membranes, proteins, nucleic acids, etc.) using two related mechanisms called grafting and waste-conversion. Such living systems were transformed from less recognizable types (characterized by autocatalytic spreading, decentralization, poorly defined boundaries, etc.) into more recognizable ones (encapsulated by membranes, controlled by single-molecule genomes, etc.) that self-replicated by a cell division cycle and could evolve by the standard gene-based Darwinian mechanism. The resulting systems are viewed as having an autocatalytic network composed of three linked autocatalytic subreactions.     

The Sensory Canal Systems of the Living Coelacanth, Latimeria Chalumnae: A New Instalment

Entire sensory canal systems of the coelacanth, Latimeria chalumnae, are described: not only the course of principal canals with their primary and secondary collaterals, but also the course and branches of the pit-line and reticular canals. The number of pores on the left side of the head were found to be 296 in an early (yolksac) embryo, 321 in a late term fetus, 485 in a juvenile, and 2974 in adults. This means that in latimeria most of the lateral-line canal system develop after parturition. Pit lines of the living coelacanth are not rows of superficial neuromasts but canals covered by a thin epidermis like in other sensory canals of the lateral line. These pit-line canals, however, have a very specific structure and branching pattern: the medial dorsal pit-line canal is connected by fine branches on top of the head. The infra-dentary pit-line canal connects via these branches with canals deep inside the bones. Several fine and richly branched canaliculi of unknown function radiate from each quadratojugal pit-line canal. The gular plate pit-line canal has superficially branching arms as well as connections to numerous deeper canals inside the bone. These canals consist of fine branches that in turn lead to and open on the ventral surface of the gular plates as small pores. The system is reminiscent of the reticular (pore) canal system known only from some fossil agnathans and fishes. Thus latimeria combines the reticular system of ancient vertebrates with the lateral-line system of modern fishes. The significance of this gular (possibly electro-sensory) system for feeding by the coelacanth will be discussed.