Ecology of soils: a new science of the biosphere class

The history of a new science, ecology of soils, is described. Its object, subject, and methodology are discussed, with emphasis placed upon the top-priority problems. It has been proved that ecology of soils is among the sciences whose concern is the study of biosphere. Examples are given to illustrate rules and laws of the new science. It is shown in particular that humus components and their ratios are bearing on climate parameters and fall on definite ecological ranges of certain kinds of soils characterized by different ratios of humic acids.     

From the allocation debate to a substitution paradox in waste bioenergy life cycle assessment studies

The International Journal of Life Cycle Assessment -     

Chemiluminescence energy transfer: a new technique applicable to the study of ligand--ligand interactions in living systems

Chemiluminescent molecules can be readily detected in the range 10(-15) to 10(-18) mol, and potentially at least down to 10(-20) mol reacting/s. The chemiluminescent compound aminobutylethylisoluminol (ABEI) and its isothiocyanate derivative have been synthesized. The ABEI was coupled to rabbit immunoglobulin and cyclic AMP. These labeled antigens were stable for at least 9 months and were used to establish chemiluminescent immunoassays. When these chemiluminescent-labeled antigens bound to their respective fluorescein-labeled antibodies, a wavelength shift towards the green was detected in the chemiluminescence. This was due to chemiluminescence energy transfer and used to establish an homogenous immunoassay which could measure these antigens in biological samples at least as sensitively as conventional radioimmunoassays.     

The biosphere theory of V. I. Vernadsky and the Gaia theory of James Lovelock: a comparative analysis of the two theories and traditions

James Hutton (1726-1797) regarded Earth as a super-organism and physiology the science to study it. A strong line of evidence for an intimate relationship of biological and abiotic processes on Earth leads from Hutton to the Gaia theory of J. Lovelock. A less known in the West but important approach to the biosphere as a self-regulating system (the biosphere theory) was proposed V.I. Vernadsky (1863-1945). The main concern of this paper revolves around the question: What is the difference between Gaia and the biosphere? To approach the problem of Earth as a super-organism one can use also the biosphere theory of V. N. Beklemishev (1890-1962), who examined the biosphere from a morphological viewpoint.     

Organics in chimneys and water samples from deep-sea hydrothermal systems: implications for sub-vent biosphere.

Searching for life in extreme terrestrial environments can be a model of that for extraterrestrial life. Submarine hydrothermal system is one of promising sites for the frontier of life on the earth. Here seawater and vent chimnies were collected from deep-sea hydrothermal vents at Suiyo Seamount, Izu-bonin arc, Pacific Ocean as a part of Archaean Park Project. Pure seawater sample of 300 degrees C (purity>97%) could be collected. Dissolved and total hydrolyzable amino acids were determined by ion-exchange HPLC, and their enantiomeric ratio was measured by reversed-phase HPLC for the first time. Glycine and serine were two most abundant amino acids, followed by other proteinous amino acids such as alanine, glutamic acid and aspartic acid. Non-proteinous amino acids were detected as minor constituents. Most of the amino acids detected were of the L-form. Thus amino acids of abiotic origin were quite minor, and most of the amino acids detected were formed biologically. These results, together with analytical results of the vent chimney samples, suggest that there is active microbial activities near the hydrothermal systems.     

Hip extension, knee flexion paradox: a new mechanism for non-contact ACL injury

Considering that an athlete performs at-risk sports activities countless times throughout the course of his or her career prior to the instance of anterior cruciate ligament (ACL) injury, one may conclude that non-contact ACL injury is a rare event. Nevertheless, the overall number of non-contact ACL injuries, both in the US and worldwide, remains alarming due to the growing number of recreational and professional athletes participating in high-risk activities. To date, numerous non-contact ACL injury mechanisms have been proposed, but none provides a detailed picture of sequence of events leading to injury and the exact cause of this injury remains elusive. In this perspective article, we propose a new conception of non-contact ACL injury mechanism that comprehensively integrates risk factors inside and outside the knee joint. The proposed mechanism is robust in the sense that it is biomechanically justifiable and addresses a number of confounding issues related to ACL injury.     

Assessment of a closed wash system developed for processing living donor femoral heads

NHS Blood and Transplant Tissue and Eye Services (TES) and Scottish National Blood Transfusion Services Tissues and Cells Directorate (TCD) currently bank whole, frozen femoral head bone from living donors who are undergoing primary hip replacement surgery. When required, the bone is issued to a surgeon still frozen on dry ice (? 79 °C). Consequently, the femoral head bone is not processed, is not sterilised and at the time of issue, it contains donor blood, bone marrow and associated cells. We have previously shown that, cut, shaped and washed bone from deceased donors can be processed to remove up to 99.9% of blood, bone marrow and associated cells (Eagle et al. 2015). However, cut and shaped bone is not suitable for some orthopaedic procedures and some orthopaedic surgeons do not wish to use irradiated bone; therefore in this report, a method has been developed in which whole femoral heads can be washed to remove donor blood and bone marrow components. Processing results in excess of 99% bone marrow component removal—soluble protein, haemoglobin and DNA; the procedure is performed inside a closed system, thereby eliminating the need for terminal sterilisation by irradiation. In addition, uniaxial testing demonstrated no difference in compressive strength between washed and unwashed bone. We suggest that this washed bone may be capable of improving incorporation after grafting without disturbing biomechanical properties of the graft.     

The first living systems: a bioenergetic perspective.

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.     

Factors governing algal growth in photobioreactors: the “open” versus “closed” debate

Until recently, most large commercial scale microalgal production systems employed open systems. However, several large-scale closed systems have now been built and, for the first time, actual comparisons can be made. There are major operational differences between open and closed photobioreactors and, consequently, the growth physiology of the microalgae is different between the two systems. Several of the factors governing growth can, within certain boundaries, be manipulated while others are specific to the cultivation system. Crucial factors are the optical depth, turbulence, light acclimated state of the organism, nutrient availability and metabolite accumulation. In the final analyses, systems are used for specific purposes and each will determine which system is the most suitable, since there is no universal all-purpose photobioreactor.     

Chance vs. necessity in living systems: a false antinomy

The concepts of order and randomness are crucial to understand 'living systems' structural and dynamical rules. In the history of biology, they lay behind the everlasting debate on the relative roles of chance and determinism in evolution. Jacques Monod [1970] built a theory where chance (randomness) and determinism (order) were considered as two complementary aspects of life. In the present paper, we will give an up to date version of the problem going beyond the dichotomy between chance and determinism. To this end, we will first see how the view on living systems has evolved from the mechanistic one of the 19th century to the one stemming from the most recent literature, where they emerge as complex systems continuously evolving through multiple interactions among their components and with the surrounding environment. We will then report on the ever increasing evidence of "friendly" co-existence in living beings between a number of "variability generators", fixed by evolution, and the "spontaneous order" derived from interactions between components. We will propose that the "disorder" generated is "benevolent" because it allows living systems to rapidly adapt to changes in the environment by continuously changing, while keeping their internal harmony.     

Cryptococcus stepposus,a new filobasidiaceous yeast species found in the Prioksko-terrasny biosphere reserve in Russia

Mycocinotyping of cryptococci from the Prioksko-terrasny reserve (Russia) has revealed three strains that have a unique mycocin-sensitivity profile. Sequencing results of the D1/D2 domain of the 26S rDNA and of the complete ITS region placed them in the Floriforme clade of the Filobasidiales lineage (Hymenomycetes). The three strains had identical sequences, which differed from those of known Filobasidium and Cryptococcus species. A novel species named Cryptococcus stepposus (type strain VKM Y-2918) is proposed to accommodate these isolates. Physiological characteristics distinguishing the novel species from other Cryptococcus species in the Floriforme clade are presented.     

Human Cytokinome: a new challenge for systems biology

Cytokines play an important role in the evolution of inflammatory processes. Therefore, they are also key components of the cancer evolution, a disease recognized to depend on chronic inflammation. On the whole, we define cytokinome as the totality of these proteins and their interactions in and around biological cells. Understanding the complex interaction network of cytokines in patients affected from cancers should be very useful both to follow the cancer evolution from its early steps and to define innovative therapeutic strategies by using systems biology approaches.     

Mode coupling in living systems: implications for biology and medicine

Complex systems, and in particular biological ones, are characterized by large numbers of oscillations of widely differing frequencies. Various prejudices tend to lead to the assumption that such oscillators should generically be very weakly interacting. This paper reviews the basic ideas of linearity and nonlinearity as seen by a physicist, but with a view to biological systems. In particular, it is argued that large couplings between different oscillators of disparate frequencies are common, being present even in rather simple systems which are well-known in physics, although this issue is often glossed over. This suggests new experiments and investigations, as well as new approaches to therapies and human-environment interactions which, without the concepts described here, may otherwise seem unlikely to be interesting. The style of the paper is conversational with a minimum of mathematics, and no attempt at a complete list of references.     

The nitrodibenzofuran chromophore: a new caging group for ultra-efficient photolysis in living cells

Photochemical uncaging of bio-active molecules was introduced in 1977, but since then, there has been no substantial improvement in the properties of generic caging chromophores. We have developed a new chromophore, nitrodibenzofuran (NDBF) for ultra-efficient uncaging of second messengers inside cells. Photolysis of a NDBF derivative of EGTA (caged calcium) is about 16-160 times more efficient than photolysis of the most widely used caged compounds (the quantum yield of photolysis is 0.7 and the extinction coefficient is 18,400 M(-1) cm(-1)). Ultraviolet (UV)-laser photolysis of NDBF-EGTA:Ca(2+) rapidly released Ca(2+) (rate of 20,000 s(-1)) and initiated contraction of skinned guinea pig cardiac muscle. NDBF-EGTA has a two-photon cross-section of approximately 0.6 GM and two-photon photolysis induced localized Ca(2+)-induced Ca(2+) release from the sarcoplasmic recticulum of intact cardiac myocytes. Thus, the NDBF chromophore has great promise as a generic and photochemically efficient protecting group for both one- and two-photon uncaging in living cells.     

Structure for energy cycle: a unique status of the second law of thermodynamics for living systems

Distinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schr?dinger's neg-entropy and I. Prigogine's dissipative structure, we propose a chemical kinetic view that the earliest "live" process is embedded essentially in a special interaction between a pair of specific components under a particular, corresponding environmental conditions. The interaction exists as an inter-molecular-force-bond complex(IMFBC) that couples two separate chemical processes: one is the spontaneous formation of the IMFBC driven by a decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two chemical processes coupled by the IMFBC originated independently and were considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: the first landmark on the path from things to a being. The dynamic formation and disassembly of the IMFBC, as a composite individual, follows a principle designated as "… structure for energy for structure for energy…", the cycle continues; and for short it will be referred to as "structure for energy cycle". With additional features derived from this starting point, the IMFBC-centered "live" process spontaneously evolved into more complex living organisms with the characteristics currently known.     

Vendozoa: Organismic construction in the Proterozoic biosphere

Seilacher, Adolf 1989 07 15: Vendozoa: Organismic construction in the Proterozoic biosphere. Lethaia , Vol. 22. pp. 229–239. Oslo. ISSN 0024–1164.
Ediacara-type impressions of large, but flat and soft-bodied organisms in Late Proterozoic rocks are here interpreted not as ancestors of modern animal phyla, but as foliate pneu constructions, whose quilting patterns had to be accommodated with various modes of growth. In this view Vendozoa represent an evolutionary experiment that failed with the coming of macropbagous predators. True Metazoa are also represented, but in the form of trace fossils rather than body impressions. * Precambrian fossils, evolution, constructional morphology .