How an organism dies affects the fitness of its neighbors

Programmed cell death (PCD), a genetically regulated cell suicide program, is ubiquitous in the living world. In contrast to multicellular organisms, in which cells cooperate for the good of the organism, in unicells the cell is the organism and PCD presents a fundamental evolutionary problem. Why should an organism actively kill itself as opposed to dying in a nonprogrammed way? Proposed arguments vary from PCD in unicells being maladaptive to the assumption that it is an extreme form of altruism. To test whether PCD could be beneficial to nearby cells, we induced programmed and nonprogrammed death in the unicellular green alga Chlamydomonas reinhardtii. Cellular contents liberated during non-PCD are detrimental to others, while the contents released during PCD are beneficial. The number of cells in growing cultures was used to measure fitness. Thermostability studies revealed that the beneficial effect of the PCD supernatant most likely involves simple heat-stable biomolecules. Non-PCD supernatant contains heat-sensitive molecules like cellular proteases and chlorophyll. These data indicate that the mode of death affects the origin and maintenance of PCD. The way in which an organism dies can have beneficial or deleterious effects on the fitness of its neighbors.     

The center of pathological (toxic) action of metals in an people organisms and a role of galvanic currents in its induction

Chronic influence of metals on an organism differs from their sharp toxic action. In some exposed to long chronic metals influence people appear chronic inflammatory diseases, including oncological, on a background of neurologic symptoms develop. Today the overwhelming majority of the population is more 40-50 years old have metal alloys in the form of dental artificial limbs and various implantates in a body. Because of metal corrosion in organisms of these people concentration of metal ions is created. Galvanic currents induced at presence of any metals in an organism, promote corrosion, and carry of metal ions inside organism. If these currents are strong (the potential difference more 150 MB), local inflammatory pathologies development in organism due to concentration in the center of metal ions.     

A method for demonstrating genetic principles using an imaginary organism

The use of an imaginary organism to illustrate principles of genetics is described. The organism is easily drawn, and is well suited to simple printing techniques. It has been used to show independent segregation of genes, partial dominance, linkage in both sex chromosomes and in autosomes, as well as the inheritance of an autosomal gene lethal in the homozygous state. Additional exercises for students are suggested.     

Phenoptosis: programmed death of an organism

Programmed cell death (apoptosis) is well-established in many multicellular organisms. Apoptosis purifies a tissue from cells that became useless or even harmful for the organism. Similar phenomena are already described also at subcellular level (suicide of mitochondria, i.e., mitoptosis) as well as at supracellular level (degradation of some organs temporarily appearing in the course of ontogenesis and then disappearing by means of apoptosis of the organ-composing cells). Following the same logic, one may put a question about programmed death of an organism as a mechanism of purification of a kin, community of organisms, or population from individuals who became unwanted for this kin, etc. A putative mechanism of such kind is proposed to be coined "phenoptosis" by analogy with apoptosis and mitoptosis. In a unicellular organism (the bacterium Escherichia coli), three different biochemical mechanisms of programmed death are identified. All of them are actuated by the appearance of phages inside the bacterial cell. This may be regarded as a precedent of phenoptosis which prevents expansion of the phage infection among E. coli cells. Purification of a population from infected individuals looks like an evolutionary invention useful for a species. Such an invention has high chances to be also employed by multicellular organisms. Most probably, septic shock in animals and humans serves as an analog of the phage-induced bacterial phenoptosis. It is hypothesized that the stress-induced ischemic diseases of brain and heart as well as carcinogenesis if they are induced by repeated stresses also represent phenoptoses that, in contrast to sepsis, are age-dependent. There are interrelations of programmed death phenomena at various levels of complexity of the living systems. Thus, extensive mitoptosis in a cell leads to apoptotic death of this cell and extensive apoptosis in an organ of vital importance results in phenoptotic death of an individual. In line with this logic, some cases are already described when inhibition of apoptosis strongly improves the postischemic state of the organism.     

Abdominal and endometrial actinomycosis associated with an intrauterine device.

Actinomycotic endometrial infection associated with an intrauterine device (IUD) complicated chronic abdominal inflammatory disease in a 28-year-old woman. Colonies of organisms with morphologic resemblance to and staining reactions of Actinomyces israelii were observed in tissue adherent to the IUD and in inflamed omental and pericolic tissues. However, the organism could not be cultured. Because intact tissues are resistant to actinomyces it is likely that the IUD created an environment favouring the establishment and growth of the organism.     

Level of microelements-metals in animal blood as an informative indicator of response to low-intensity short duration electromagnetic irradiation

The comparison (juxtaposition) of the rats and the rabbits organism reactions on the electromagnetic irradiation (1.5 GHz, 300 microW/cm2, non-stop mode, 30 min) by the index of the physiological status indicators and of the blood microelements (ME)--metals concentration is presented. This physiological status indicators display that the mentioned irradiation is an underthreshold effect for central nerve system, which doesn't cause the essential changes on the organism level. In the same time, the reliable blood microelements-metals concentration shifts are established. And this let us suppose the ME-indicator as the most informative value of an organism reaction on the electromagnetic irradiations corresponding to the underthreshold effects for the central nerve system.     

Preparedness for an anthrax attack

Bacillus anthracis is a long-known bacterial organism with a uniquely stable spore stage. Its stability and the lethal disease which results when the spore is inhaled made it a favorite of state-sponsored biological weapons programs throughout the Cold War era. It is also believed to be high on the list of candidate microbial agents which could be used by terrorist groups or lone actors. Its unique characteristics make protection of humans, especially civilians, from an intentional biological attack very difficult. The author argues that an all-hazards/public health approach – which would also be needed for any natural or deliberate outbreak, no matter the agent – should serve as a foundation of preparation for the specific anthrax countermeasures. Because B. anthracis is a unique organism, specific countermeasures for anthrax detection, diagnostics, prophylaxis and therapy, should be developed in nations or regions where the threat of biological attack is believed to warrant such preparation. Other considerations for a nation interested in anthrax preparedness are discussed.     

Can an organism select new valuable information from environment

The process of selecting new information by the organism ("learning") was studied. To take a decision, key patterns have to be set a priori, and so knowledge accumulation (learning) based on pattern recognition is impossible. It was shown that the only physical process that, takes place during the emergence of an external signal is the triggering of a priori programmes. An equivalent biophysical scheme of pattern recognition and taking the decisions by the organism was developed in which a signal received by the receptor leads to the synthesis of one of possible catalysts. The catalyst starts up the corresponding thermodynamic process. The information contained in the organism does not change during this process.     

A new mathematical model of the dynamics of an age cohort population

A new generalized conception of an organism is given. Based on this conception, a new mathematical model of ontogenesis of an individual and the survival of the age cohort of population was proposed. By using real data on the dynamics of the survival of the age cohort of population, the model enables one to determine the parameters characterizing the relationship man-environment in the context of survival and calculate the dynamics (from birth to death) of the model variables of the state of the organism.     

The microbial metabolism of acetophenone. Metabolism of acetophenone and some chloroacetophenones by an Arthrobacter species

1. An organism that utilizes acetophenone as sole source of carbon and energy was isolated in pure culture and tentatively identified as an Arthrobacter sp. 2. Cell-free extracts of the acetophenone-grown organism contained an enzyme, acetophenone oxygenase, that catalysed an NADPH-dependent consumption of O(2) in the presence of the growth substrate; approx. 1mol of O(2) and 1mol of NADPH were consumed per mol of acetophenone oxidized. 3. Cell-free extracts also contained an enzyme capable of the hydrolysis of phenyl acetate to phenol and acetate. The amount of this esterase was increased markedly by growth on acetophenone. 4. The observed products of the acetophenone oxygenase reaction by crude cell-free extracts were phenol and acetate. However, inhibition of the phenyl acetate esterase by paraoxon resulted in the formation of phenyl acetate from acetophenone. 5. A degradative sequence is proposed in which acetophenone is metabolized by an oxygen-insertion reaction to form phenyl acetate. Further metabolism occurs by hydrolysis of this ester. 6. The organism and extracts were shown to metabolize chlorinated acetophenones. The environmental implications of this observation are discussed.     

Methanogenesis in an Upflow Anaerobic Sludge Blanket Reactor at pH 6 on an Acetate-Propionate Mixture

High-rate anaerobic digestion can be applied in upflow anaerobic sludge blanket reactors for the treatment of various wastewaters. In upflow anaerobic sludge blanket reactors, sludge retention time is increased by a natural immobilization mechanism (viz. the formation of a granular type of sludge). When this sludge is cultivated on acid-containing wastewater, the granules mainly consist of an acetoclastic methanogen resembling Methanothrix soehngenii. This organism grows either in rods or in long filaments. Attempts to cultivate a stable sludge consisting predominantly of Methanosarcina sp. on an acetate-propionate mixture as substrate by lowering the pH from 7.5 during the start-up to approximately 6 failed. After 140 days of continuous operation of the reactor a filamentous organism resembling Methanothrix soehngenii prevailed in the sludge. The specific methanogenic activity of this sludge on acetate-propionate was optimal at pH 6.6 to 6.8 and 7.0 to 7.2, respectively.     

General equilibrium of an ecosystem

Ecosystems and economies are inextricably linked: ecosystem models and economic models are not linked. Consequently, using either type of model to design policies for preserving ecosystems or improving economic performance omits important information. Improved policies would follow from a model that links the systems and accounts for the mutual feedbacks by recognizing how key ecosystem variables influence key economic variables, and vice versa. Because general equilibrium economic models already are widely used for policy making, the approach used here is to develop a general equilibrium ecosystem model which captures salient biological functions and which can be integrated with extant economic models. In the ecosystem model, each organism is assumed to be a net energy maximizer that must exert energy to capture biomass from other organisms. The exerted energies are the "prices" that are paid to biomass, and each organism takes the prices as signals over which it has no control. The maximization problem yields the organism's demand for and supply of biomass to other organisms as functions of the prices. The demands and supplies for each biomass are aggregated over all organisms in each species which establishes biomass markets wherein biomass prices are determined. A short-run equilibrium is established when all organisms are maximizing and demand equals supply in every biomass market. If a species exhibits positive (negative) net energy in equilibrium, its population increases (decreases) and a new equilibrium follows. The demand and supply forces in the biomass markets drive each species toward zero stored energy and a long-run equilibrium. Population adjustments are not based on typical Lotka-Volterra differential equations in which one entire population adjusts to another entire population thereby masking organism behavior; instead, individual organism behavior is central to population adjustments. Numerical simulations use a marine food web in Alaska to illustrate the model and to show several simultaneous predator/prey relationships, prey switching by the top predator, and energy flows through the web.     

Phenylobacterium falsum sp. nov., an Alphaproteobacterium isolated from a nonsaline alkaline groundwater, and emended description of the genus Phenylobacterium

A Gram-negative bacterium designated AC-49T was isolated from an alkaline groundwater with a pH 11.4. This organism formed rod-shaped cells, was strictly aerobic, catalase and oxidase positive, with an optimum growth temperature of 35 degrees C and an optimum pH value of 8.0. Strain AC-49T assimilated primarily amino acids and some Krebs cycle metabolites, did not use sugars for growth. The organism did not grow on L-phenylalanine or antipyrin. The G+ C content of DNA was 66.9 mol%. The phylogenetic analyses based on the 16S rRNA sequencing showed that the closest relatives of strain AC-49T were Phenylobacterium lituiforme and Phenylobacterium immobile, indicating that the organism is a member of the order Caulobacterales of the Alphaproteobacteria. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain AC-49T, represents a novel species of the genus Phenylobacterium for which we propose the name Phenylobacterium falsum sp. nov.     

Dimethylsulfide is an energy source for the heterotrophic marine bacterium Sagittula stellata

Dimethylsulfide (DMS) is a volatile organosulfur compound, ubiquitous in the oceans, that has been credited with various roles in biogeochemical cycling and in climate control. Various oceanic sinks of DMS are known - both chemical and biological - although they are poorly understood. In addition to the utilization of DMS as a carbon or a sulfur source, some Bacteria are known to oxidize it to dimethylsulfoxide (DMSO). Sagittula stellata is a heterotrophic member of the Alphaproteobacteria found in marine environments. It has been shown to oxidize DMS during heterotrophic growth on sugars, but the reasons for and the mechanisms of this oxidation have not been investigated. Here, we show that the oxidation of DMS to DMSO is coupled to ATP synthesis in S. stellata and that DMS acts as an energy source during chemoorganoheterotrophic growth of the organism on fructose and on succinate. DMS dehydrogenase (which is responsible for the oxidation of DMS to DMSO in other marine Bacteria) and DMSO reductase activities were absent from cells grown in the presence of DMS, indicating an alternative route of DMS oxidation in this organism.     

Use of Dogs as an Assay for Clostridium perfringens Enterotoxin

Three techniques for using the dog as an assay organism for Clostridium perfringens enterotoxin are described. These are believed to be more convenient than ligated ileal-loop procedures.     

Cancer as a Programmed Death of an Organism

The hypothesis introduces the idea that there is a critical level of mutagenesis that triggers a program of organism death by means of proliferation of killer cells. Similarly to apoptosis, which is an altruistic suicidal act of a faulty cell threatening the stability of a multicellular organism, a malignant tumor is an altruistic suicide of an individual carrier of harmful alleles threatening genetic stability of the population.     

Microbial metabolism as an evolutionary response: the cybernetic approach to modeling

The growth and metabolic capabilities of microorganisms depend on their interactions with the culture medium. Many media contain two or more key substrates, and an organism may have different preferences for the components. Microorganisms adjust their preferences according to the prevailing conditions so as to favor their own survival. Cybernetic modeling describes this evolutionary strategy by defining a goal that an organism tries to attain optimally at all times. The goal is often, but not always, maximization of growth, and it may require the cells to manipulate their metabolic processes in response to changing environmental conditions. The cybernetic approach overcomes some of the limitations of metabolic control analysis (MCA), but it does not substitute MCA. Here we review the development of the cybernetic modeling of microbial metabolism, how it may be combined with MCA, and what improvements are needed to make it a viable technique for industrial fermentation processes.     

Measurement of the rate of hydrogen production by Clostridium butyricum using an amperometric method

Abstract The rate of production of hydrogen by Clostridium butyricum was measured using a modified oxygraph equipment. As an example of the application of the method, some results of the investigations on the effect of short-chain volatile fatty acids on the metabolism of the organism are shown.     

Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model

Predicting the phenotype of an organism from its genotype is a central question in genetics. Most importantly, we would like to find out if the perturbation of a single gene may be the cause of a disease. However, our current ability to predict the phenotypic effects of perturbations of individual genes is limited. Network models of genes are one tool for tackling this problem. In a recent study, (Lee et al.) it has been shown that network models covering the majority of genes of an organism can be used for accurately predicting phenotypic effects of gene perturbations in multicellular organisms. .     

Genomic variability within an organism exposes its cell lineage tree

What is the lineage relation among the cells of an organism? The answer is sought by developmental biology, immunology, stem cell research, brain research, and cancer research, yet complete cell lineage trees have been reconstructed only for simple organisms such as Caenorhabditis elegans. We discovered that somatic mutations accumulated during normal development of a higher organism implicitly encode its entire cell lineage tree with very high precision. Our mathematical analysis of known mutation rates in microsatellites (MSs) shows that the entire cell lineage tree of a human embryo, or a mouse, in which no cell is a descendent of more than 40 divisions, can be reconstructed from information on somatic MS mutations alone with no errors, with probability greater than 99.95%. Analyzing all approximately 1.5 million MSs of each cell of an organism may not be practical at present, but we also show that in a genetically unstable organism, analyzing only a few hundred MSs may suffice to reconstruct portions of its cell lineage tree. We demonstrate the utility of the approach by reconstructing cell lineage trees from DNA samples of a human cell line displaying MS instability. Our discovery and its associated procedure, which we have automated, may point the way to a future "Human Cell Lineage Project" that would aim to resolve fundamental open questions in biology and medicine by reconstructing ever larger portions of the human cell lineage tree.