A new facultatively autotrophic hydrogen- and sulfur-oxidizing bacterium from an alkaline environment

An alkaliphilic bacterium, strain AHO 1, was isolated from an enrichment culture with hydrogen at pH 10 inoculated with a composite sample of sediments from five highly alkaline soda lakes (Kenya). This bacterium is a gram-negative, nonmotile, rod-shaped, obligately aerobic, and facultatively autotrophic hydrogen-oxidizing organism. It was able to oxidize reduced sulfur compounds to sulfate during heterotrophic growth. It utilized a wide range of organic compounds as carbon and energy sources and grew mixotrophically with hydrogen and acetate. With sulfur compounds, mixotrophic growth was observed only in acetate-limited continuous culture. The normal pH range for autotrophic growth with hydrogen was pH 8.0–10.25, with a pH optimum at 9–9.5. Growth at pH values lower than 8.0 was extremely slow. Heterotrophic growth with acetate was optimal at pH 10.0. The hydrogen-oxidizing activity of whole cells was maximal at pH 9.0 and still substantial up to pH 11. NAD-dependent hydrogenase activity was found in the soluble fraction of the cell-free extract, but no methylene blue-dependent activity in either the soluble or membrane fractions was observed. On the basis of its pH profile, the soluble hydrogenase of strain AHO 1 was a typical pH-neutral enzyme. Phylogenetic analysis revealed that strain AHO 1 belongs to the α-3 subgroup of the Proteobacteria with a closest relation to a recently described alkaliphilic aerobic bacteriochlorophyll a-containing bacterium "Roseinatronobacter thiooxidans." Received: February 29, 2000 / Accepted: April 3, 2000     

Feeding rate as valuable information in primate feeding ecology

In this review I outline studies on wild non-human primates using information on feeding rate, which is defined as the food intake per minute on a dry-weight basis; further, I summarize the significance of feeding rate in primate feeding ecology. The optimal foraging theory has addressed three aspects of animal feeding: (1) optimal food patch choice, (2) optimal time allocation to different patches, and (3) optimal food choice. In order to gain a better understanding of these three aspects, the feeding rate itself or its relevance indices (e.g., rates of calorie and protein intake) could be appropriate measures to assess the quality of food and food patches. Moreover, the feeding rate plays an essential role in estimation of total food intake, because it varies greatly for different food items and the feeding time is not a precise measure. The feeding rate could also vary across individuals who simultaneously feed on the same food items in the same food patch. Body size-dependent and rank-dependent differences in the feeding rate sometimes cause individuals to take strategic behavioral options. In the closing remarks, I discuss the usefulness of even limited data on feeding rate obtained under adverse observational conditions in understanding primate feeding ecology.     

A new shell-bearing organism from the Cambrian Spence Shale of Utah

A new shell-bearing organism with preserved soft tissue, Armilimax pauljamisoni n. gen. n. sp., is reported from the middle Cambrian (Miaolingian: Wuliuan) Miners Hollow locality of the Spence Shale of northern Utah. The described organism is known from a single articulated specimen and preserves a prominent shell, a slug-like body, as well as a U-shaped digestive tract. Its overall appearance is similar to halkieriids, but it does not preserve sclerites. The possible affinities of the new taxon and potential reasons for the presence of a U-shaped gut are discussed. Armilimax pauljamisoni is the first shell-bearing animal of its kind from the Great Basin and extends the diversity of body plans in the Spence Shale Fossil-Lagerstätte.     

Mechanism of antioxidant protection of an organism from oxidative stress

The analysis of the literature and authors' data concerning the mechanism of antioxidant protection of the organism under conditions of "oxygen stress" is submitted. Possible mechanisms of initiation of free radical reactions with participation of oxygen and the role of hydroxyl radicals, being one of the basic factors, determining toxic action of oxygen, are considered. The methods of estimation of antiradical activity of biologically active compounds are characterized.     

On organism: environment buffers and their ecological significance

We consider, from a physical perspective, the case where the interface between an organism and its environment becomes large enough that it acts as a buffer regulating their matter and energy exchanges. We illustrate the physiological and evolutionary role of buffers through the example of lungfish estivation. Then we ponder the relevance of buffers of this kind to the quest for a general definition of concepts like niche construction, the extended phenotype, and related ones, whose meaning is conveyed at present mostly through particular examples. Finally, we comment on the potential significance of buffers to organism—environment codetermination in the sense originally suggested by Lewontin.     

Acetobacter methanolicus--a new organism for genetic studies

A new bacterial strain is described belonging to Acetobacter methanolicus species. It is of industrial value as a producer of protein and methanol products. The strain is acidophile and this feature comprises a conspicuous technological advantage. The results of bacteriophage and cell interactions are reported. They might be potentially useful for elaboration of the transduction technique for the strain. The collection of mutants was obtained including those utilizing methanol, having auxotrophic markers as well as streptomycin and rifampicin resistances. The transfer of plasmids RSF1010 and R68 to Acetobacter methanolicus from other bacteria has been demonstrated.     

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

NetSeed is a web tool and Perl module for analyzing the topology of metabolic networks and calculating the set of exogenously acquired compounds. NetSeed is based on the seed detection algorithm, developed and validated in previous studies. AVAILABILITY: The NetSeed web-based tool, open-source Perl module, examples and documentation are freely available online at: http://depts.washington.edu/elbogs/NetSeed.     

Conditioning from an information processing perspective

The framework provided by Claude Shannon's [Bell Syst. Technol. J. 27 (1948) 623] theory of information leads to a quantitatively oriented reconceptualization of the processes that mediate conditioning. The focus shifts from processes set in motion by individual events to processes sensitive to the information carried by the flow of events. The conception of what properties of the conditioned and unconditioned stimuli are important shifts from the tangible properties to the intangible properties of number, duration, frequency and contingency. In this view, a stimulus becomes a CS if its onset substantially reduces the subject's uncertainty about the time of occurrence of the next US. One way to represent the subject's knowledge of that time of occurrence is by the cumulative probability function, which has two limiting forms: (1) The state of maximal uncertainty (minimal knowledge) is represented by the inverse exponential function for the random rate condition, in which the US is equally likely at any moment. (2) The limit to the subject's attainable certainty is represented by the cumulative normal function, whose momentary expectation is the CS-US latency minus the time elapsed since CS onset. Its standard deviation is the Weber fraction times the CS-US latency.     

Population genetics from an information perspective

Some basic effects of population genetics are derived governing the occurrences of alleles A(i)and genotypes A(i)A(j)among its members. A principle of extreme physical information (EPI) is used. These effects are (1) the equation of genetic change, (2) Fisher's theorem of partial change, (3) a new uncertainty principle, and (4) the monotonic decrease of Fisher information with time, indicating increased disorder for the population. General conditions of population change are allowed: fitness coefficients w(ij)generally changing with time [except in effect (2)], population randomly or non-randomly mating, and a general number of loci present within each chromosome. EPI is a practical tool for deriving probability laws. It is an outgrowth of a physical process that occurs during any act of measurement. Here the measurement is the random observation of a genotype A(i)A(j). This observation is to be used to estimate the time of the observation, called "evolutionary time". The measurement activity incurs errors in the estimated observation time and fitness value of the observed genotype. By the Cramer-Rao inequality, the product of the two uncertainties must exceed unity [effect (3)]. The Fisher information I in data space is postulated to originate in the space of the genotype where it had some generally larger value J. The EPI principle extremizes the loss of information (I--J) with I=1/2 J. The solution gives rise to effects (1) and (2). Finally, it is shown that effect (4) holds when the population approaches an equilibrium state, e.g. for time values greater than a threshold if fitness coefficients w(ij)are constant. EPI provides a common framework for deriving physical laws and laws of population genetics. The new effects (3) and (4) are confirmed through computer simulation.