Topology and life: In search of general mathematical principles in biology and sociology

Mathematical biology has hitherto emphasized the quantitative, metric aspects of the physical manifestations of life, but has neglected the relational or positional aspects, which are of paramount importance in biology. Although, for example, the processes of locomotion, ingestion, and digestion in a human are much more complex than in a protozoan, the general relations between these processes are the same in all organisms. To a set of very complicated digestive functions of a higher animal there correspond a few simple functions in a protozoan. In other words, the more complicated processes in higher organisms can be mapped on the simpler corresponding processes in the lower ones. If any scientific study of this aspect of biology is to be possible at all, there must exist some regularity in such mappings. We are, therefore, led to the following principle: If the relations between various biological functions of an organism are represented geometrically in an appropriate topological space or by an appropriate topological complex, then the spaces or complexes representing different organisms must be obtainable by a proper transformation from one or very fewprimordial spaces or complexes. The appropriate representation of the relations between the different biological functions of an organism appears to be a one-dimensional complex, or graph, which represents the “organization chart” of the organism. The problem then is to find a proper transformation which derives from this graph the graphs of all possible higher organisms. Both a primordial graph and a transformation are suggested and discussed. Theorems are derived which show that the basic principle of mapping and the transformation have a predictive value and are verifiable experimentally. These considerations are extended to relations within animal and human societies and thus indicate the reason for the similarities between some aspects of societies and organisms. It is finally suggested that the relation between physics and biology may lie on a different plane from the one hitherto considered. While physical phenomena are the manifestations of the metric properties of the four-dimensional universe, biological phenomena may perhaps reflect some local topological properties of that universe.     

A set-theoretical approach to biology

In a preceding paper (Bull. Math. Biophysics 20, 71–93, 1958) the principle of biotopological mapping was formulated in terms of a continuous mapping of an abstract space, made from the set of biological properties which characterize the organism, by an appropriate definition of neighborhoods. In this paper it is shown that we may consider directly the mappings of the different sets of properties which characterize different organisms without taking recourse to abstract spaces. All the verificable conclusions made in the preceding paper remain valid. A serious difficulty mentioned previously is, however, avoided and the possibility of more general predictions is established.     

叶际微生物研究进展

植物的叶际是一个复杂的生态系统,微生物的生存环境条件严苛。其可被利用的营养成分较少,温湿度波动大。此外,较强的紫外线辐射对于叶际微生物的生存也有很大影响。但是植物叶际却有着丰富的微生物多样性,其中还有许多有益细菌和真菌。它们通过和植物寄主的互作,改善着叶际微生物的栖居环境;其对植物病原体的拮抗亦可提高植物的抗病性。植物叶际的微生物还可以产生激素以促进植物生长,还有一些微生物可以利用农药等污染有机物作为营养物质,在污染物的环境生物修复方面显示巨大的潜力。此外,叶际微生物作为一种生态学指标在生态稳定与环境安全评价中开始发挥显著的作用。     

Molecular cross-talk between sponge host and associated microbes

Marine organisms especially those that live sessile, as sponges, are well known to have specific relationships with a great variety of microorganisms including bacteria and fungi. As most simple metazoan phylum, the Porifera, which emerged first during the transition from the non-Metazoa to the Metazoa from the common ancestor, comprise wide arrays of recognition molecules, both for Gram-negative bacteria and for Gram-positive bacteria as well as for fungi. They react specifically with effector molecules to inhibit or kill the invading microorganisms. The elicitation and the subsequent effector reactions of the sponges towards these microbes are outlined. However, besides of the elimination of bacteria and fungi, some of those taxa are kept as symbionts of the sponges, allowing them, for example, to accumulate the essential element manganese or to synthesize carotinoids. The sponges produce low-molecular-weight bioactive compounds, secondary metabolites, to eliminate the microorganisms. In addition, they are armed with cationic antimicrobial peptides allowing them to defend against invasive microorganisms and, in parallel, to kill or repel also metazoan invaders. The broad range of chemically and functionally different compounds qualifies the Porifera as the most important animal phylum to be exploited as a source for the isolation of new potential drugs. First molecular biological strategies have been outlined to obtain those compounds in a sustainable way, by producing them recombinantly.     

Marine microorganisms as an untapped source of bioactive compounds

The search for novel biologically active molecules has extended to the screening of organisms associated with less explored environments. In this sense, Oceans, which cover nearly the 67% of the globe, are interesting ecosystems characterized by a high biodiversity that is worth being explored. As such, marine microorganisms are highly interesting as promising sources of new bioactive compounds of potential value to humans. Some of these microorganisms are able to survive in extreme marine environments and, as a result, they produce complex molecules with unique biological interesting properties for a wide variety of industrial and biotechnological applications. Thus, different marine microorganisms (fungi, myxomycetes, bacteria, and microalgae) producing compounds with antioxidant, antibacterial, apoptotic, antitumoral and antiviral activities have been already isolated. This review compiles and discusses the discovery of bioactive molecules from marine microorganisms reported from 2018 onwards. Moreover, it highlights the huge potential of marine microorganisms for obtaining highly valuable bioactive compounds.     

产油微生物油脂生物合成与代谢调控研究进展

自然界中少量微生物在适宜条件下产生并贮存质量超过其细胞干重 2 0 %的油脂 ,具有这种表型的菌种称为产油微生物。产油微生物利用可再生资源 ,得到的微生物油脂与植物油脂具有相似的脂肪酸组成 ,有的还含有丰富的多不饱和脂肪酸 ,具有广阔开发应用前景。简要介绍了产油微生物的种类和代谢特点 ,较详细地阐述了微生物产油机制和代谢调控途径的最新研究进展 ,并对微生物油脂研究的未来发展方向提出了初步见解     

Organismic sets: Outline of a general theory of biological and social organisms

The discussion as to whether societies are organisms andvice versa has been going on for a long time. The question is meaningless unless a clear definition of the term “organism” is made. Once such a definition is made, the question may be answered by studying whether there exists any relational isomorphism between what the biologist calls an organism and what the sociologist calls society. Such a study should also include animal societies studied by ecologists. Both human and animal societies are sets of individuals together with certain other objects which are the products of their activities. A multicellular organism is a set of cells together with some products of their activities. A cell itself may be regarded as a set of genes together with the products of their activities because every component of the cell is either directly or indirectly the result of the activities of the genes. Thus it is natural to define both biological and social organisms as special kinds of sets. A number of definitions are given in this paper which define what we call here organismic sets. Postulates are introduced which characterize such sets, and a number of conclusions are drawn. It is shown that an organismic set, as defined here, does represent some basic relational aspects of both biological organisms and societies. In particular a clarification and a sharpening of the Postulate of Relational Forces given previously (Bull. Math. Biophysics,28, 283–308, 1966) is presented. It is shown that from the basic definitions and postulates of the theory of organismic sets, it folows that only such elements of those sets will aggregate spontaneously, which are not completely “specialized” in the performance of only one activity. It is further shown that such “non-specialized” elements undergo a process of specialization, and as a result of it their spontaneous aggregation into organismic sets becomes impossible. This throws light on the problem of the origin of life on Earth and the present absence of the appearance of life by spontaneous generation. Some applications to problems of ontogenesis and philogenesis are made. Finally the relation between physics, biology, and sociology is discussed in the light of the theory of organismic sets.     

Microbial interactions in the vaginal ecosystem, with emphasis on the pathogenesis of bacterial vaginosis

During bacterial vaginosis (BV), populations of lactobacilli which are generally dominant in the vagina of overtly healthy women are replaced by other facultative and anaerobic microorganisms. Some Lactobacillus strains produce hydrogen peroxide and all produce lactic acid; however, the antagonistic role of these metabolites in vivo remains controversial. Positive interactions among BV-associated organisms may contribute to the pathogenesis of BV and its sequelae.     

Microorganism lipid droplets and biofuel development

Lipid droplet (LD) is a cellular organelle that stores neutral lipids as a source of energy and carbon. However, recent research has emerged that the organelle is involved in lipid synthesis, transportation, and metabolism, as well as mediating cellular protein storage and degradation. With the exception of multi-cellular organisms, some unicellular microorganisms have been observed to contain LDs. The organelle has been isolated and characterized from numerous organisms. Triacylglycerol (TAG) accumulation in LDs can be in excess of 50% of the dry weight in some microorganisms, and a maximum of 87% in some instances. These microorganisms include eukaryotes such as yeast and green algae as well as prokaryotes such as bacteria. Some organisms obtain carbon from CO2 via photosynthesis, while the majority utilizes carbon from various types of biomass. Therefore, high TAG content generated by utilizing waste or cheap biomass, coupled with an efficient conversion rate, present these organisms as bio-tech ‘factories’ to produce biodiesel. This review summarizes LD research in these organisms and provides useful information for further LD biological research and microorganism biodiesel development. [BMB Reports 2013; 46(12): 575-581]     

Thermostable enzymes

In general, enzyme thermostability is an intrinsic property, determined by the primary structure of the protein. However, external environmental factors including cations, substrates, co-enzymes, modulators, polyols and proteins often increase enzyme thermostability. With some exceptions, enzymes present in thermophiles are more stable than their mesophilic counterparts. Some organisms produce enzymes with different thermal stability properties when grown at lower and higher temperatures. There are commercial advantages in carrying out enzymic reactions at higher temperatures. Some industrial enzymes exhibit high thermostability. More stable forms of other industrial enzymes are eagerly being sought.     

Mixture generalized linear models for multiple interval mapping of quantitative trait Loci in experimental crosses

Summary .  Quantitative trait loci mapping in experimental organisms is of great scientific and economic importance. There has been a rapid advancement in statistical methods for quantitative trait loci mapping. Various methods for normally distributed traits have been well established. Some of them have also been adapted for other types of traits such as binary, count, and categorical traits. In this article, we consider a unified mixture generalized linear model (GLIM) for multiple interval mapping in experimental crosses. The multiple interval mapping approach was proposed by Kao, Zeng, and Teasdale (1999, Genetics 152, 1203–1216) for normally distributed traits. However, its application to nonnormally distributed traits has been hindered largely by the lack of an efficient computation algorithm and an appropriate mapping procedure. In this article, an effective expectation–maximization algorithm for the computation of the mixture GLIM and an epistasis-effect-adjusted multiple interval mapping procedure is developed. A real data set, Radiata Pine data, is analyzed and the data structure is used in simulation studies to demonstrate the desirable features of the developed method.     

Biological functions of carotenoids--diversity and evolution

Carotenoids first emerged in archaebacteria as lipids reinforcing cell membranes. To serve this function their long molecules have extremely rigid backbone due to the linear chain of usually 10 to 11 conjugated C=C bonds in transconfiguration--the length corresponding the thickness of hydrophobic zone of membrane which they penetrate as "molecular rivets". Carotenoids retain their membrane-reinforcing function in some fungi and animals. The general structure of carotenoid molecule, originally having evolved for mechanical functions in membranes, possess a number of other properties that were later used for independent functions. The most striking fact is that these properties proved to fit some new functions to perfection. The polyene chain of 9-11 double bonds absorbs light precisely in the gap of chlorophyll absorption--function as accessory light-harvesting pigments in all plants; Unique arrangement of electronic levels owing to the by polyene chain structure makes carotenoids the only natural compounds capable of excitation energy transfer both (i) from carotenoid excited state to chlorophyll in the light-harvesting complex and (ii) from triplet chlorophyll or singlet oxygen to carotenoid in photosynthetic reaction centers--protection of RC from photodamage. The linear system of conjugated C=C bonds provides high reducing potential of carotenoid molecules making them potent antioxidants in lipid formations. Still, there is a lack of evidence of the chemical antioxidant function of carotenoids, especially in higher organisms; most data demonstrate an antioxidant ability rather than a function. Carotenoids have many other independent biological functions, including: specific coloration patterns in plants and animals, screening from excessive light and spectral filtering, defense of egg proteins from proteases in some invertebrates; the direct carotenoid derivative--retinal--acts as visual pigment in all animals and as chromophore in bacteriorhodopsin photosynthesis, retinoic acid in animals and abscisic acid in plants serve as hormones. All these functions utilize various properties (mechanical, electronic, stereospecific) of a single structure evolved in bacteria for a single membrane-reinforcing function, thus demonstrating an example of pure evolutionary preadaptation. One of the practical conclusions that can be reached by reviewing uniquely diverse properties and functions of carotenoids is that, when considering possible mechanisms of their effects in organisms (e.g., anticarcinogenic action), all their functional traits should be taken into account.     

单萜类化合物的微生物合成

单萜类化合物是萜类化合物的一种,一般具有挥发性和较强的香气,部分单萜还具有抗氧化、抗菌、抗炎等生理活性,是医药、食品和化妆品工业的重要原料.近年来,利用微生物异源合成单萜类化合物的研究引起了科研人员的广泛关注,但因产量低、生产成本高等限制了其大规模应用.合成生物学的迅猛发展为微生物生产单萜类化合物提供了新的手段,通过改...     

Some results and prospects of studies in the area of marine biochemistry and biotechnology]

Recent studies on bioactive metabolites from marine macro- and microorganisms are reviewed with 83 refs. Structures of new sulphated and glycosylated secondary metabolites, which have been reported to have antifungal, immunomodulatory, and cytotoxic properties, are given. Some peculiarities of biosynthesis of natural compounds in marine organisms are revealed. It was shown that some natural products, isolated earlier from sponges, are produced by microbial symbionts. Different physiological activities associated with 8000 marine microbial (mainly symbiotic) strains are discussed as well as some prospects of marine biochemistry and biotechnology development.     

Medicinally important secondary metabolites in recombinant microorganisms or plants: Progress in alkaloid biosynthesis

Plants produce a high diversity of natural products or secondary metabolites which are important for the communication of plants with other organisms. A prominent function is the protection against herbivores and/or microbial pathogens. Some natural products are also involved in defence against abiotic stress, e.g. UV-B exposure. Many of the secondary metabolites have interesting biological properties and quite a number are of medicinal importance. Because the production of the valuable natural products, such as the anticancer drugs paclitaxel, vinblastine or camptothecin in plants is a costly process, biotechnological alternatives to produce these alkaloids more economically become increasingly important. This review provides an overview of the state of art to produce alkaloids in recombinant microorganisms, such as bacteria or yeast. Some progress has been made in metabolic engineering usually employing a single recombinant alkaloid gene. More importantly, for benzylisoquinoline, monoterpene indole and diterpene alkaloids (taxanes) as well as some terpenoids and phenolics the proof of concept for production of complex alkaloids in recombinant Escherichia coli and yeast has already been achieved. In a long-term perspective, it will probably be possible to generate gene cassettes for complete pathways, which could then be used for production of valuable natural products in bioreactors or for metabolic engineering of crop plants. This will improve their resistance against herbivores and/or microbial pathogens.     

What has happened to the “aquatic phycomycetes” (sensu Sparrow)? Part II: Shared properties of zoosporic true fungi and fungus-like microorganisms

Many species of zoosporic heterotrophic parasites, saprotrophs and mutualists in the Phyla Perkinsozoa (dinoflagellates), Oomycota, Hyphochytriomycota, Labyrinthulomycota and Phyomyxea share morphological characteristics with zoosporic true fungi especially with some of the Chytridiomycota and with fungus-like organisms in the Phyla Mesomycetozoea, Chytridiomycota and Aphelidae. These characteristics include chemotactic motile zoospores, zoosporangia which produce zoospores, thick walled resistant cysts, rhizoid-like structures, hyphal-like structures and cell walls surrounding the cells in several phases of their life cycle. These assemblages also inhabit both marine and freshwater ecosystems in which aquatic fungi and fungus-like organisms are found, have similar life cycles, grow on similar substrates, use similar infection strategies and infect some of the same host plants and animals. Many of these species were once included in the aquatic phycomycetes, an ecological assemblage of microorganisms but not a valid taxonomic group. Some of the shared characteristics are discussed in this review.     

Marine microorganisms as biocontrol agents against fungal phytopathogens and mycotoxins

Mycotoxins are a serious food safety concern for human and animal health. Much attention should be paid to the dietary exposure to mycotoxins in order to minimise the risk of mycotoxin contamination in the food chain. Among the reported strategies to manage the mycotoxin contamination into food and feed, biological control seems a promising approach, depending on their biological origins, and on the use of living organisms or their derivatives. Marine microorganisms have developed unique metabolic and physiological capabilities to thrive in extreme habitats and produce novel metabolites which are not often present in microbes of terrestrial origin. Some marine bacteria and fungi have a good potential for the control of fungal phytopathogens and mycotoxins. Biologists and chemists are needed to work together to explore the storehouse of marine microorganisms and marine active metabolites, because marine bacteria and fungi have a huge potential for practical application in biocontrol of fungal phytopathogens and preventing mycotoxin contamination.     

Ultraviolet irradiation and repair--possible factors determining the evolution of DNA structure

It is suggested that DNA in first organisms on the Earth was enriched by GC-pairs due to intensive solar UV-irradiation. In the course of progressive evolution, nucleotide composition of DNA shifted to the favour of AT-pairs. This shift to higher photosensitivity became possible because of the development of reparation systems and screening of DNA in cells. The latter phenomenon is better revealed in higher organisms, accounting their stable TA-type of DNA. In lower forms, peculiarities of their habitats provided some conditions for variability of nucleotide composition. High content of GC-pairs remained in those of them which are subjected to the influence of solar irradiation. Parasitic microorganisms and those safely protected from solar radiation developed towards the AT-type of DNA. Both in higher and lower organisms, AT-pairs are richer in those zoms of DNA which are presented by several copies and in which mutations are less significant for the organism therefore being permissible. Structural genes exhibit heterogeneous nucleotide composition which provides for higher variability of the synthesized proteins.     

Biocatalytic ketone reduction—a powerful tool for the production of chiral alcohols—part I: processes with isolated enzymes

Traditional cultivation-based methods to quantify microbial abundance are not suitable for analyses of microbial communities in environmental or medical samples, which consist mainly of uncultured microorganisms. Recently, different cultivation-independent quantification approaches have been developed to overcome this problem. Some of these techniques use specific fluorescence markers, for example ribosomal ribonucleic acid targeted oligonucleotide probes, to label the respective target organisms. Subsequently, the detected cells are visualized by fluorescence microscopy and are quantified by direct visual cell counting or by digital image analysis. This article provides an overview of these methods and some of their applications with emphasis on (semi-)automated image analysis solutions.