Structures of inclusion complexes of halogenbenzoic acids and α-cyclodextrin based on AM1 calculations

Semi-empirical quantum mechanics calculations using AM1 (Austin Method 1) were carried out for various host-guest combinations of α-cyclodextrin and mono-halogen benzoic acids. The energetically favorable inclusion structures were identified. The AM1 results show that α-cyclodextrin complexes with mono-halogen benzoic acid acids (where the halogen is chlorine, bromide, iodine) as guest compounds are more stable in the “head first” position than in the “tail-first” position for meta and para isomers while ortho mono-halogen benzoic acids complexes with α-cyclodextrin are more stable in “tail-first” position. The calculated structures were found to be in good agreement with those obtained from crystalographic databases.      

Descriptive epidemiology of a scabies epidemic in chamois in the Dolomite Alps,Italy

In 1995, the hitherto Sarcoptes-free alpine chamois (Rupicapra rupicapra) of the Dolomite Alps (Italy) were affected by scabies for the first time after the spread of the disease from a neighbouring focus in Austria. Since then, four Agencies cooperated to warrant monitoring of the spatial and temporal progress of the outbreak and further active surveillance was carried out within an intensive study area. In ten years, 15 meta-populations numbering 10,000 chamois and 210,000 ha were encompassed with a maximum distance of 55 km from the index case. “Oil spot” advancement of the epidemic was observed together with “jumps” of 9 to 20 km followed by spreading of the infection to the intervening population units. Demographic decline of the four meta-populations so far affected for a minimum of six years ranged between 49 and 77% (), whereas similar post-epidemic densities of 1.1 to 1.7 heads/100 ha () were recorded. Contiguous resistant and sensitive herds with similar pre-epidemic density were detected on a smaller population scale, suggesting complementary mechanisms intervening besides density-dependence as determinants of the outbreak outcome. No sex or age class showed a higher sensitivity to scabies out of a sample of 1,696 infected chamois. A peak prevalence of free-ranging chamois bearing overt scabietic lesions was observed in January and February. Cases were only sporadically diagnosed in other sympatrc wild ruminants (Cervus elaphus, Capreolus capreolus and Ovis gmelini musimon), whereas all four alpine ibex (Capra ibex ibex) herds living in the surveyed area suffered from scabies-induced decline.     

Composition and distribution of internal resistance in three types of microbial fuel cells

High internal resistance is a key problem limiting the power output of the microbial fuel cell (MFC). Therefore, more knowledge about the internal resistance is essential to enhance the performance of the MFC. However, different methods are used to determine the internal resistance, which makes the comparison difficult. In this study, three different types of MFCs were constructed to study the composition and distribution of internal resistance. The internal resistance (R _i) is partitioned into anodic resistance (R _a), cathodic resistance (R _c), and ohmic resistance () according to their origin and the design of the MFCs. These three resistances were then evaluated by the “current interrupt” method and the “steady discharging” method based on the proposed equivalent circuits for MFCs. In MFC-A, MFC-B, and MFC-C, the R _i values were 3.17, 0.35, and 0.076 Ω m², the values were 2.65, 0.085, and 0.008 Ω m², the R _a values were 0.055, 0.115, and 0.034 Ω m², and the R _c values were 0.466, 0.15, and 0.033 Ω m², respectively. For MFC-B and MFC-C, the remarkable decrease in R _i compared with the two-chamber MFC was mainly ascribed to the decline in and R _c. In MFC-C, the membrane electrodes’ assembly lowered the ohmic resistance and facilitated the mass transport through the anode and cathode electrodes, resulting in the lowest R _i among the three types.     

Hologram and 3D-quantitative structure toxicity relationship studies of azo dyes

Amino azobenzenes are important dyes in the food and textile industry but their application is limited due to their mutagenicity. Computational modeling techniques were used to help understand the factors responsible for mutagenicity, and several quantitative structure toxicity relationship (QSTR) models have been derived. HQSTR (hologram QSTR) analyses indicated that different substituents at sites on both rings contribute to mutagenicity. Fragment parameters such as bond (B) and connectivity(C), as well as donor-acceptor (DA)-based model provide significant results (q² = 0.59, r² = 0.92, ) explaining these harmful effect. HQSTR results indicated that a bulky group at ring “Y” and small group at ring “X” might help to decrease mutagenicity. 3D-QSTR based on comparative molecular field analyses (CoMFA) and comparative molecular similarity index analyses (CoMSIA) are also in agreement with HQSTR. The 3D QSTR studies reveal that steric and electrostatic field effects have a strong relationship with mutagenicity (for CoMFA: q² = 0.51, r² = 0.95, and for CoMSIA: q² = 0.51, r² = 0.93 and ). In summary, negative groups and steric bulk at ring “Y” and small groups at carbon-3 of ring “X” might be helpful in reducing the mutagenicity of azo dyes.     

Direct use values and passive use values: implications for conservation of large carnivores

We made a quantitative analysis of the responses of urban and rural residents in Sweden to arguments supporting and opposing conservation of large carnivores. The most important arguments in favour of conservation were: “I want them [the large carnivores] to exist in Sweden, even if I will never see any of them”, “Sweden should share the responsibility of conserving the large carnivores” and “We owe it [conservation of large carnivores] to future generations”. We found only small differences between rural and urban residents. For arguments opposing conservation, the difference between rural and urban areas was slightly greater. The most important arguments opposing conservation of large carnivores were: “They may have serious negative impact on livestock farming”, “They may have serious negative impact on reindeer husbandry” and “May inflict suffering on injured livestock”. We conclude that there seems to be less support for direct use values such as hunting, ecotourism or just experiencing large carnivores, this may imply that the minimum viable population size can be used as a long-term management goal for large carnivore populations, possibly with an exception for bears. We also conclude that a separate conservation or management plan is needed for each species, since the conflicts with human interests vary greatly between the different carnivore species.     

On the biotopology of protein biosynthesis

The present paper is an attempt to outline a possible approach to the study of concrete cellular systems in terms of relational biology as developed by Rashevsky and Rosen. The basic ideas and the formalism of Rosen’s (M,R)-systems, proposed as a model of abstract biological systems, are used in order to represent the cellular protein biosynthesis. A diagram corresponding to the activation of amino acids and synthesis of amino-acyl-transfer RNA, the attachment of _t RNA to a specific codon of messenger RNA and peptide bond synthesis with the release of a protein molecule, is constructed. The systemM thus obtained for the synthesis of a proteinp _k receives a set of environmental inputs, that is, the twently naturally occurring amino acids and emits a single output, thep _k protein. The problem of noncontractibility of inputs in the system is then analyzed. In our context, it is found that the noncontractibility is not associated with the whole amino acid setS _pk but with an “essential amino acid set” , so that and represent the set of amino acids which can be replaced or absent. According to our considerations, the biochemical concept of “essential amino acid” acquires a new significance, that is, what seems “essential” is linked with the ability to form a giventRNA _t ∼a _i complex in a suitable augmented dependent set essential for the biosynthesis of a functional protein. Eventually the discussion of re-establishability leads to some important biological implications concerning the existence of ambiguous codons and the degeneracy phenomenon in the genetic code, as anecessary biochemical tool involved in adaptive processes.     

Spatially distributed stochasticity and the constancy of ecosystems

Ifconstancy is a measure of an ecosystem's (in) variability through time andstability is a measure of the system's ability to damp and recover from environmental perturbations, then constancy depends not only on stability but also on the frequency and amplitude of perturbations—theenvironmental “noise level”. The stability of an ecosystem reflects its texture, extent, and viscosity (fine-scale structure); the noise level experienced by the system (“effective” noise level) reflects the level at any point (“ambient” noise level), the spectrum of stochastic scale (regional distribution of stochasticity), and the system's spatial extent (size, or number of patches included). The coefficient of variation of a limiting stochastic variate is a measure of the effective noise level. Ifp is the total number of patches in the system (its extent) andn is the number of contiguous patches with noise signals correlated through time (its stochastic scale), then the coefficient of variation is directly proportional to whenevern<p. Thus ecosystems of small stochastic scalen or large sizep damp out environmental noise by “spreading the risk” in space, thereby reducing their variability in time.     

Population genetics of <Emphasis Type="Italic">Collisella subrugosa</Emphasis> (Patellogastropoda: Acmaeidae): evidence of two scales of population structure

Marine invertebrate populations usually show high levels of genetic variability that has frequently been associated with spatial and temporal environmental heterogeneity. One of the most heterogeneous marine environments is the intertidal zone, the habitat of Collisella subrugosa, the most widespread and abundant Brazilian limpet. C. subrugosa has planktonic larvae that can disperse over long distances, what can promote gene flow among shores, working against interpopulational differentiation. In this study we investigated the genetic variability and populational substructure of C. subrugosa through analysis of 24 allozyme loci in 14 samples (590 individuals) collected along 2,700 km of the Brazilian coast. The genetic variability was high ( and ), as expected for intertidal species. Genetic differentiation among samples was low (F _ST = 0.03) what may reflect intensive gene flow associated with larval dispersal. However, we detected an isolation-by-distance pattern of population substructure in one sampled region. High levels of heterozygote deficiency were also observed for many loci in each sample. Alternative hypothesis are discussed, and the “breeding groups” is suggested to explain these pattern, indicating the main cause as environmental heterogeneity.     

Importance of adult survival, local recruitment and immigration in a declining boreal forest passerine, the willow tit Parus montanus

Population growth rate (λ) and its components (adult survival, local recruitment, immigration and their relative contributions to λ) were studied in the declining willow tit Parus montanus in Northern Finland. Capture–recapture models for open populations were used to estimate the population parameters and their process variation. Adult survival was fairly high with low variation (0.593, CV=0.067). As expected, local recruitment was lower and more variable (0.063, CV=0.610). During the 12-year study, the population growth rate averaged to one (0.988, CV=0.197; calculated as However, if the present processes continue, population projections show that the population is likely to decline. There was considerable temporal variation in the relative contributions of demographic parameters to λ. In all years, adult survival had the highest relative contribution (mean 64%) to the population growth rate and it was the least variable trait. Immigration had a higher relative contribution (22%) to λ than local recruitment (14%). Based on the results for the contributions to λ, the main conservation concern for willow tits is adult survival. Due to low variation, adult survival may be difficult to enhance, but at least it should be prevented from declining. High stochasticity in local recruitment and immigration is probably an inherent characteristic of highly seasonal environments, making these traits difficult to address for conservation practices.     

On the stock estimation for some fishery systems

In this work we address the stock estimation problem for two fishery models. We show that a tool from nonlinear control theory called “observer” can be helpful to deal with the resource stock estimation in the field of renewable resource management. It is often difficult or expensive to measure all the state variables characterising the evolution of a given population system, therefore the question arises whether from the observation of certain indicators of the considered system, the whole state of the population system can be recovered or at least estimated. The goal of this paper is to show how some techniques of control theory can be applied for the approximate estimation of the unmeasurable state variables using only the observed data together with the dynamical model describing the evolution of the system. More precisely we shall consider two fishery models and we shall show how to built for each model an auxiliary dynamical system (the observer) that uses the available data (the total of caught fish) and which produces a dynamical estimation of the unmeasurable stock state x(t). Moreover the convergence speed of towards x(t) can be chosen.     

A quantum model for controlled enzymic reactions

A quantum model for the general enzymic reaction,E+S ⇌ ES → P, is presented, starting with the assumptions that any chemical substanceS, which may be a substrate for a particularE _(S)-enzyme is a microphysical system and any enzymeE-molecule, capable of interacting with anS-substrate is a “measuring system” which will “measure” one or more of theS-observables. According to the above assumptions a stochastic model of the reaction is constructed and a computer simulation of the steady state performed. The results thus obtained predicted fluctuations in the enzymic reaction rate, function of the substrate “perturbation”. On an experimental basis it is demonstrated that the irradiation of an enzymic substrate with low energies results in the inducement of a dose-dependent oscillatory behavior in the corresponding enzymic reaction rate. In the reaction type, the oscillations thus induced in theE-activity by the corresponding substrates are out-of-phase, realizing a biochemical discriminating net. Likewise, in an reaction type, the oscillations induced by the irradiatedS-substrate in the activities of the respective enzyme, realize a biochemical switching net.     

Mutual Gains and Distributive Ideologies in South Africa: Theorizing Negotiations between Communities and Protected Areas

With the rise of joint management of protected areas, community representatives are increasingly involved in formal negotiations with state officials, nongovernmental organizations (NGOs) and other actors. Policy recommendations have commonly idealized “win-win” scenarios. Theoretical work on negotiation from psychology and management studies, however, points to identifiable circumstances under which the goal of a mutually beneficial “win-win” situation may limit the strategies, and ultimately the benefits, available to communities. Instead, an antagonistic, “distributive” approach to negotiations may be more compatible with the pressures on and strategies available to community representatives. The tensions between a “mutual gains” and “distributive” approach to negotiations are evident in two land claims on protected areas in South Africa: the Dwesa-Cwebe Nature Reserves, and the Pafuri Triangle, a portion of Kruger National Park. In each, NGOs that operated with a “mutual gains” strategy, espousing a “win-win” scenario, came to be perceived as collaborating with conservation agencies. Meanwhile, as negotiation theory would suggest, community representatives inclined towards a “distributive” strategy and allied with a second set of explicitly advocatory NGOs. Expecting that communities should embrace a “win-win” scenario from the outset is unrealistic and likely to reduce communities’ power in negotiations.

The Poetics of Purpose

Hackles have been raised in biosemiotic circles by T. L. Short’s assertion that semiosis, as defined by Peirce, entails “acting for purposes” and therefore is not found below the level of the organism (2007a:174–177). This paper examines Short’s teleology and theory of purposeful behavior and offers a remedy to the disagreement. Remediation becomes possible when the issue is reframed in the terms of the complexity sciences, which allows intentionality to be understood as the interplay between local and global aspects of a system within a system. What is called “acting for purposes” is not itself a type of behavior so much as a relationship between a dynamic system that “exists for a purpose” and its microprocesses that “serve purposes.” The “intentional object” of philosophy is recast here as the holistic self-organized dynamics of a system, which exists for the purpose of self-maintenance, and that constrains the parts’ behaviors, which serve the purpose of forming the system. (A “system” can be any emergent, e.g. an abiotic form, an adapted species, a self, a conditioned response, thought, or a set of ideas.) The self-organized whole, which is represented to the parts in their own constrained behaviors, assumes the guiding function so long attributed to the mysterious “intentional object.” If emergent self-causation is not disallowed, creative originality, as well as directionality, becomes part of the definition of purposeful behavior. Thus, key tools used here, required for understanding emergence, come from poetics rather than semoitics. In the microprocesses of self-organization, I find what I call “accidental” indices and icons — which are poetic in the sense that they involve mere metonymic contiguity and metaphoric similarity — and which are preferentially selected under constrained conditions allowing radically new connections to habituate into an “intentional” self-organized system that, not coincidentally, has some of the emergent characteristics of a conventional symbolic system.

A relational theory of the structural changes induced in biological systems by alterations in environment

It is shown that a wide variety of structural alterations in both the “metabolic” and “genetic” apparatus of ( , ℜ)-systems can result from specific changes in the environment of such systems. A number of specific examples are investigated in order to demonstrate the scope of these alterations. Certain biological applications of this discussion are suggested, including a suggestion for a possible interpretation of the mitotic cycle. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Contract #AF 49 (638)-917.     

Sources of variability in spotted owl population growth rate: testing predictions using long-term mark–recapture data

For long-lived iteroparous vertebrates that annually produce few young, life history theory predicts that reproductive output (R) and juvenile survival should influence temporal variation in population growth rate (λ) more than adult survival does. We examined this general prediction using 15 years of mark–recapture data from a population of California spotted owls (Strix occidentalis occidentalis). We found that survival of individuals ≥1 year old (ϕ) exhibited much less temporal variability , where CV is coefficient of variation, than R and that R was strongly influenced by environmental stochasticity. Although λ was most sensitive ( ; log-transformed sensitivity) to ϕ and much less sensitive to either R or juvenile survival (survival rate of owls from fledging to 1 year old; ), we estimated that R contributed as much as ϕ to the observed annual variability in λ. The contribution of juvenile survival to variability in λ was proportional to its These results are consistent with the hypothesis that natural selection may have favored the evolution of longevity in spotted owls as a strategy to increase the probability of experiencing favorable years for reproduction. Our finding that annual weather patterns that most affected R (temperature and precipitation during incubation) and ϕ (conditions during winter related to the Southern Oscillation Index) were equally good at explaining temporal variability in λ supports the conclusion that R and ϕ were equally responsible for variability in λ. Although currently accepted conservation measures for spotted owl populations attempt to enhance survival, our results indicated that conservation measures that target R may be as successful, as long as actions do not reduce ϕ.     

Probabilistic Approach to Determining Unbiased Random-coil Carbon-13 Chemical Shift Values from the Protein Chemical Shift Database

We describe a probabilistic model for deriving, from the database of assigned chemical shifts, a set of random coil chemical shift values that are “unbiased” insofar as contributions from detectable secondary structure have been minimized (RCCS_u). We have used this approach to derive a set of RCCS_u values for ¹³C^α and ¹³C^β for 17 of the 20 standard amino acid residue types by taking advantage of the known opposite conformational dependence of these parameters. We present a second probabilistic approach that utilizes the maximum entropy principle to analyze the database of ¹³C^α and ¹³C^β chemical shifts considered separately; this approach yielded a second set of random coil chemical shifts (RCCS). Both new approaches analyze the chemical shift database without reference to known structure. Prior approaches have used either the chemical shifts of small peptides assumed to model the random coil state (RCCS_peptide) or statistical analysis of chemical shifts associated with structure not in helical or strand conformation (RCCS). We show that the RCCS values are strikingly similar to published RCCS_peptide and RCCS values. By contrast, the RCCS_u values differ significantly from both published types of random coil chemical shift values. The differences (RCCS_peptide−RCCS_u) for individual residue types show a correlation with known intrinsic conformational propensities. These results suggest that random coil chemical shift values from both prior approaches are biased by conformational preferences. RCCS_u values appear to be consistent with the current concept of the “random coil” as the state in which the geometry of the polypeptide ensemble samples the allowed region of (ϕ,ψ)-space in the absence of any dominant stabilizing interactions and thus represent an improved basis for the detection of secondary structure. Coupled with the growing database of chemical shifts, this probabilistic approach makes it possible to refine relationships among chemical shifts, their conformational propensities, and their dependence on pH, temperature, or neighboring residue type.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Biological functions of antioxidants in plant transformation

Browning and necrosis of transformed cells/tissues, and difficulty to regenerate transgenic plants from the transformed cells/tissues (recalcitrance) are common in Agrobacterium-mediated transformation process in many plant species. In addition, most crop transformation methods that use NPTII selection produce a significant number of nontransgenic shoots, called “shoot escapes” even under stringent selection conditions. These common problems of plant transformation, (browning and necrosis of transformed cells/tissues, recalcitrance, and the occurrence of shoot escapes) severely reduces transformation efficiency. Recent research indicates that reactive oxygen species (ROS) such as superoxide radical , the hydrogen peroxide (H₂O₂), the hydroxyl radical (OH′), and the peroxyl radical () may be playing an important role in tissue browning and necrosis during transformation. This review examines the role of ROS in in vitro recalcitrance and genetic transformation and the opportunities to improve transformation efficiency using antioxidants.     

Identification of conservation units in the European Mergus merganser based on nuclear and mitochondrial DNA markers

The conservation status of small breeding areas of the Goosander (Mergus merganser merganser) in Central Europe is unclear. Geographic isolation of these areas suggests restricted gene flow to and from large North-European populations. On the other hand, migrating Goosanders from northern Europe join the Central European breeding population for wintering. To evaluate the conservation status of the small breeding areas we assessed the genetic structure of M. merganser populations in Europe by examining two nuclear marker systems (microsatellites and Single Nucleotide Polymorphisms, SNP) and mitochondrial (mtDNA) control region sequence variation for Goosanders in 11 sampling areas representing three of five distinct breeding areas and two subspecies (M. m. merganser and M. m. americanus). Overall population differentiation estimates including both subspecies were high, both based on mtDNA () and nuclear markers (θ _ST = 0.219; 95% CI 0.088–0.398, SNP and microsatellites combined). Within Europe, mtDNA revealed a strong overall () and significant pairwise population differentiation between almost all comparisons. In contrast, both nuclear marker systems combined revealed only a small overall genetic differentiation (θ _ST = 0.022; 95% CI 0.003–0.041). The strong genetic differentiation based on female-inherited mtDNA but not on biparentally inherited nuclear markers can be explained by sex-biased dispersal and strong female philopatry. Therefore, small breeding areas in Europe are endangered despite large male-mediated gene-flow, because when these populations decline, only males—but due to strong philopatry not females—can be efficiently supplemented by migration from the large North European populations. We therefore propose to manage the small breeding areas independently and to strengthen conservation efforts for this species in Central Europe.