Harnessing biocompatible chemistry for developing improved and novel microbial cell factories

White biotechnology relies on the sophisticated chemical machinery inside living cells for producing a broad range of useful compounds in a sustainable and environmentally friendly way. However, despite the impressive repertoire of compounds that can be generated using white biotechnology, this approach cannot currently fully replace traditional chemical production, often relying on petroleum as a raw material. One challenge is the limited number of chemical transformations taking place in living organisms. Biocompatible chemistry, that is non-enzymatic chemical reactions taking place under mild conditions compatible with living organisms, could provide a solution. Biocompatible chemistry is not a novel invention, and has since long been used by living organisms. Examples include Fenton chemistry, used by microorganisms for degrading plant materials, and manganese or ketoacids dependent chemistry used for detoxifying reactive oxygen species. However, harnessing biocompatible chemistry for expanding the chemical repertoire of living cells is a relatively novel approach within white biotechnology, and it could potentially be used for producing valuable compounds which living organisms otherwise are not able to generate. In this mini review, we discuss such applications of biocompatible chemistry, and clarify the potential that lies in using biocompatible chemistry in conjunction with metabolically engineered cell factories for cheap substrate utilization, improved cell physiology, efficient pathway construction and novel chemicals production.     

Bio-electrosprays: a novel electrified jetting methodology for the safe handling and deployment of primary living organisms

Electrohydrodynamic jetting (EHDJ) which is also known as electrosprays (ES) has recently been elucidated as a unique electrified biotechnique for the safe handling and deployment of living organisms. This high intensity electric field driven jetting methodology is now referred to as "bioelectrosprays" (BES). Previously these charged jets have only been shown to jet-process immortalized cells which have undergone expected cellular behavior when compared with control cells. In this paper we demonstrate the ability to jet process primary living organisms in the stable conejetting mode. Finally the viability of the bio-electrosprayed living organisms has been assessed employing a flow cytometry approach which forms the discussion in this paper. Our findings further establish BES as a competing biotechnique, which could be employed for the deposition of primary living organisms according to a predetermined active cellular architecture. One day this could be used for the fabrication of viable tissues and organs for repair or replacement. These advanced studies carried out on BES have direct widespread applications ranging from developmental biology to regenerative and therapeutic medicine, which are a few amongst several other areas of study within the life sciences.     

Are attractors 'strange', or is life more complicated than the simple laws of physics?

Interesting and intriguing questions involve complex systems whose properties cannot be explained fully by reductionist approaches. Last century was dominated by physics, and applying the simple laws of physics to biology appeared to be a practical solution to understand living organisms. However, although some attributes of living organisms involve physico-chemical properties, the genetic program and evolutionary history of complex biological systems make them unique and unpredictable. Furthermore, there are and will be 'unobservable' phenomena in biology which have to be accounted for.     

Development of energetics in evolution of the living world (Stages,Digits, Postulates)

This work deals with the current stage of study of energy exchange between living organ-isms and the environment. In the epoch of molecular biology, study of energy exchange might have seemed a study of old, well known concepts. However, the retrospective insight into the energy exchange of quite a few organisms allows obtaining new data about development of energetics of the living world, approaches to interesting comparisons, opens the earlier unknown quantitative relations in energetics of living organisms, provides a possibility of analyzing causes of very high values of energy consumption by living organisms, causes of different sensitivity of living organisms to deficit of energy, etc. Based on all these data, there have been noted 12 principal moments or postulates in development of energetics of the living world from the most ancient to the present time.     

Metagenomics: DNA sequencing of environmental samples

Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the living or once-living organisms of interest. Many species are difficult to study in isolation because they fail to grow in laboratory culture, depend on other organisms for critical processes, or have become extinct. Methods that are based on DNA sequencing circumvent these obstacles, as DNA can be isolated directly from living or dead cells in various contexts. Such methods have led to the emergence of a new field, which is referred to as metagenomics.     

To be or not to be rhythmic? A review of studies on organisms inhabiting constant environments

Abstract

Circadian clocks are endogenous time keeping mechanisms that drive near 24-h behavioural, physiological and metabolic rhythms in organisms. It is thought that organisms possess circadian clocks to facilitate coordination of essential biological events to the external day and night (extrinsic advantage) so as to enhance Darwinian fitness. However, on Earth, there are a number of habitats that are not subject to such robust daily cycling of geo-physical factors. Do organisms living under such conditions exhibit rhythmic behaviours that are driven by endogenous circadian clocks? We attempt to critically survey studies of rhythms (or the lack of them) in organisms living in a range of constant environments. Many such organisms do show rhythms in behaviour and/or physiological variables. We suggest that such presence of rhythms may be indicative of an underlying clock that facilitates, (a) internal synchrony among rhythms, and (b) temporal partitioning of incompatible cellular processes (intrinsic advantage). We then highlight reasons that limit our interpretations about the presence (or absence) of clocks in such organisms living under constant conditions, and suggest possible methods to conclusively test whether or not rhythms in these organisms are driven by endogenous circadian clocks with the hope that it may enhance our understanding of circadian clocks in organisms under constant environments.     

Molecular classification of living organisms

Recent studies in molecular evolution have generated strong conflicts in opinion as to how world living organisms should be classified. The traditional classification of life into five kingdoms has been challenged by the molecular analysis carried out mostly on rRNA sequences, which supported the division of the extant living organisms into three major groups: Archaebacteria, Eubacteria, and Eukaryota. As to the problem of placing the root of the tree of life, the analysis carried out on a few genes has provided discrepant results. In order to measure the genetic distances between species, we have carried out an evolutionary analysis of the glutamine synthetase genes, which previously have been revealed to be good molecular clocks, and of the small and large rRNA genes. All data demonstrate that archaebacteria are more closely related to eubacteria than to eukaryota, thus supporting the classical division of living organisms into two main superkingdoms, Prokaryota and Eukaryota.Abbreviations Mya million years ago - GS glutamine synthetase - Isu large subunit - ssu small subunit - SMC Stationary Markov clock Correspondence to: G. Pesole     

Luminescence microscopy determination of the survival of yeasts after dehydration

The technique of luminescent microscopy can be used to determine the survival rate of yeast organisms dehydrated by the convective method. If the cells were subjected to more severe extreme actions, the technique should be combined with the direct microscopy to follow the growth of reactivated organisms and to count the number of microcolonies being formed. The authors propose to classify the state of living organisms after the action of sublethal factors basing on the ability of cells to grow after reactivation.     

Leishmania parasites: could we consider them as living organisms per se?

Over the last 10 years - in Microbes and Infection - the publications dealing with protozoan parasites were mainly providing insights on the pathogenic processes leading to the local or systemic damages in the mammals, these parasitic organisms exploit/subvert as hosts. As a result, many investigators introduced the objectives of their analysis by referring to "host-pathogen" interactions. Though we, as investigators, are all determined to decipher the pathogenic processes which can indeed be coupled to the parasite uncontrolled development, I think that the parasites - alike the living organisms they subvert as hosts - need to be considered as living organisms per se, instead of being considered as "pathogens". Such a conceptual frame will promote research on the processes on which relies their perpetuation whatever the level under investigations - individual and/or population level. Only the unicellular protozoan parasites of the genus Leishmania known to be hosted by blood-feeding insects and mammals will be further considered in this brief contribution.     

Nitric Oxide Cycle in Mammals and the Cyclicity Principle

This paper continues a series of reports considering nitric oxide (NO) and its cyclic conversions in mammals. Numerous facts are summarized with the goal of developing a general concept that would allow the statement of the multiple effects of NO on various systems of living organisms in the form of a short and comprehensive law. The current state of biological aspects of NO research is analyzed in term of elucidation of possible role of these studies in the system of biological sciences. The general concept is based on a notion on cyclic conversions of NO and its metabolites. NO cycles in living organisms and nitrogen turnover in the biosphere and also the Bethe nitrogen–carbon cycle in star matter are considered. A hypothesis that the cyclic organization of processes in living organisms and the biosphere reflects the evolution of life is proposed: the development of physiological functions and metabolism are suggested to be closely related to space and evolution of the Earth as a planet of the Solar System.     

Where is Darwin 200 years later?

The theory of evolution is perceived by many people, particularly but not only in the United States, as a controversial theory not yet fully demonstrated. Yet, that living organisms, including humans, have evolved from ancestors who were very different from them is beyond reasonable doubt, confirmed by at least as much evidence as any other widely accepted scientific theory. I argue that Darwin’s contribution to science goes much beyond the theory of evolution in itself. The theory of natural selection explains the adaptations of organisms, their ‘design’. The ‘Copernican Revolution’ brought the phenomena of the physical universe into the realm of science: explanations by natural causes that can be tested by observation and experiment. However, the scientific revolution that occurred in the 16th and 17th centuries had left the living world out of scientific explanations, because organisms seemingly show that they are ‘designed,’ and thus call for an intentional designer. It was Darwin’s greatest contribution to science, to demonstrate that the adaptations of organisms, their apparent ‘design’, can be explained by natural processes governed by natural laws. At that point, science came into maturity, because all natural phenomena in the universe, living as well as nonliving, could be investigated scientifically, and explained as matter in motion governed by natural laws.     

The Evolution of Oxygen As a Biosynthetic Reagent

The biosynthesis of certain cell constituents: monounsaturated fatty acids, tyrosine, and nicotinic acid, is oxygen-dependent in many higher organisms. The same compounds can be synthesized by different, oxygen-independent pathways in lower organisms. The general outlines of these pathways are described and the importance of the compounds synthesized is discussed. An examination of the distribution of these pathways among living organisms reveals that oxygen-dependent pathways replaced the "anaerobic" pathways at different branch points on the evolutionary tree. Other groups of compounds are discussed, which are not distributed as widely among living organisms, but are found in all higher organisms. These compounds have specialized functions and their biosynthesis requires molecular oxygen. The oxygen-dependent portions of the biosynthetic pathways leading to porphyrins, quinone coenzymes, carotenoids, sterols, and polyunsaturated fatty acids are summarized. The distribution and functions of these compounds are also considered and an attempt is made to place them in the framework of evolution. While sterols and polyunsaturated fatty acids are found exclusively in the higher Protista and multicellular organisms, carotenoids, porphyrins, and quinones are also found in bacteria. The possibility of oxygen-independent mechanisms for their biosynthesis is discussed.     

Bio-electrosprays: the next generation of electrified jets

Biological electrosprays are rapidly becoming a robust means by which to engineer living organisms for applications ranging from tissue repair to developmental biology. We previously reported the ability to electrospray living organisms without compromising their viability, but found it challenging to achieve stability in the jetting of these organisms as a result of the chemical properties of the living cellular suspensions. Jet stability is required for the generation of a near-mono distribution of droplets, which is necessary for the development of electrospray technology as a "drop and place" biotechnique. Recently, we determined the conditions needed to achieve jet stability and were able to generate droplets with a near-mono distribution (<50 microm). In this communication, we elucidate the relationship between jet behaviour and droplet size under stable jetting conditions, with a view to further reducing the droplet size to deposit a single living cell within a droplet. We believe that this level of resolution will make electrospray jetting superior amongst the jet-based biotechnologies presently being developed for the engineering of biological architectures comprised of living cells.     

Origin of the scaling rule for fundamental living organisms based on thermodynamics

The regular relationships between metabolic energy and body mass M of unicellular organisms, poikilotherms and homeotherms were well known as general equations. The metabolic energy rate and the life span are proportional to M(0.75) and to M(0.25), respectively. As a result, the product of the metabolic energy rate and the life time, namely, life metabolic energy, is proportional to the mass of the living organism. The origin of the scaling rules for environmental organizing systems is as follows: (1) the scaling rules for internal energy, activation energy and free energy as a function of temperature and mass of a mole of molecules. (2) The majority of species of the living organisms have the same molecules such as polysaccharides, lipids, proteins and nucleic acids in nearly same the ratio. (3) The internal energy of reactants in living organisms is equilibrium with the internal energy of water. Then, the integrated metabolic energy over the synthesizing time depends on internal energy of water and is proportional to mass M, despite the synthesizing time of the system depending on reaction rate. The proportional constant is obtained based on the thermodynamics for fundamental living organisms such as unicellular organisms and plants. Information on the environmental organizing system is also discussed.     

Fundamental taboos of biology

This paper formulates some taboos relating to living systems and cognition of these systems: in nature, there exist no two identical living complex multicellular organisms; there is no way to create an exact copy of a multicellular organism; there is no way to obtain two identical clones of a unicellular organism if they contain a sufficiently large number of cells; based on comparing present-day organisms, it is impossible to restore the structure of the first living cell and the processes that have led to its emergence; it is impossible to create a living cell from its separate simple constituents; the mechanisms determining cell vitality are essentially incognizable.     

Single-Molecule Microscopy Reveals Membrane Microdomain Organization of Cells in a Living Vertebrate

It has been possible for several years to study the dynamics of fluorescently labeled proteins by single-molecule microscopy, but until now this technology has been applied only to individual cells in culture. In this study, it was extended to stem cells and living vertebrate organisms. As a molecule of interest we used yellow fluorescent protein fused to the human H-Ras membrane anchor, which has been shown to serve as a model for proteins anchored in the plasma membrane. We used a wide-field fluorescence microscopy setup to visualize individual molecules in a zebrafish cell line (ZF4) and in primary embryonic stem cells. A total-internal-reflection microscopy setup was used for imaging in living organisms, in particular in epidermal cells in the skin of 2-day-old zebrafish embryos. Our results demonstrate the occurrence of membrane microdomains in which the diffusion of membrane proteins in a living organism is confined. This membrane organization differed significantly from that observed in cultured cells, illustrating the relevance of performing single-molecule microscopy in living organisms.     

Toward bridging the gap between life and physics

Examination of the scale properties of living organisms and the electronic configuration of crystalline structures suggests that related modeling may be used for both. This paper comments on individual and common properties of the two systems and draws a comparison between them. Both exhibit multiple ‘scales’ separated by complex or forbidden regions and a global ‘overview’ of their scale properties. We conclude that the analogy may provide a fruitful route toward extension of the modeling of both living organisms and electronic materials, by permitting bootstrapping cross-modeling between them.     

iDRP-PseAAC: Identification of DNA Replication Proteins Using General PseAAC and Position Dependent Features

International Journal of Peptide Research and Therapeutics - DNA replication is one of the specific processes to be considered in all the living organisms, specifically eukaryotes. The prevalence...     

微生物与其他生物的共生效应、作用机制和应用前景

生物自起源开始就与其他生物建立共生体系、营共生生活、共同发挥生理生态作用,并一直协同进化至今。微生物通过与其他生物的共生,在人类健康与发展、动物健康与生长发育、植物健康与生长发育、土壤健康与土壤肥力、环境与食品安全、生物多样性保持与生态平衡、生物的遗传与进化等方面发挥众多生理生态作用。共生微生物通过直接合成激素和抗生素等次生代谢物质、调控植物相关基因表达和调节其他生物的群落结构等作用机制来发挥其功能,在医药与健康、农林牧渔业可持续生产与发展、食品加工与储藏、生态环保与生物多样性保护等方面具有十分广阔的应用前景。