Cognitive landscape and information: new perspectives to investigate the ecological complexity

Landscape ecology deals with ecological processes in their spatial context. It shares with ecosystem ecology the primate of emergent ecological disciplines. The aim of this contribution is to approach the definition of landscapes using cognitive paradigms. Neutral-based landscape (NbL), individual-based landscape (IbL) and observed-based landscape (ObL) are defined to explore the cognitive mechanisms. NbL represents the undecoded component of the cognitive matrix. The IbL is the portion of landscape perceived by the biological sensors. ObL is the part of the cognitive matrix perceived using the cultural background of the observer. The perceived landscape (PL) is composed by the sum of these three approaches of landscape perception. Two further types of information (sensu Stonier) are recognized in this process of perception: the compressed information, as it is present inside the cognitive matrix, and the decompressed information that will structure the PL when a semiotic relationship operates between the organisms and the cognitive matrix. Scaling properties of these three PL components are recognized in space and time. In NbL scale seems irrelevant, in IbL the perception is filtered by organismic scaling and in ObL the spatio-temporal scale seems of major importance. Definitively, perception is scale-dependent. A combination of the cognitive approach with information paradigms to study landscapes opens new perspectives in the interpretation of ecological complexity.     

Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor

Edema factor (EF), a key anthrax exotoxin, has an anthrax protective antigen-binding domain (PABD) and a calmodulin (CaM)-activated adenylyl cyclase domain. Here, we report the crystal structures of CaM-bound EF, revealing the architecture of EF PABD. CaM has N- and C-terminal domains and each domain can bind two calcium ions. Calcium binding induces the conformational change of CaM from closed to open. Structures of the EF-CaM complex show how EF locks the N-terminal domain of CaM into a closed conformation regardless of its calcium-loading state. This represents a mechanism of how CaM effector alters the calcium affinity of CaM and uncouples the conformational change of CaM from calcium loading. Furthermore, structures of EF-CaM complexed with nucleotides show that EF uses two-metal-ion catalysis, a prevalent mechanism in DNA and RNA polymerases. A histidine (H351) further facilitates the catalysis of EF by activating a water to deprotonate 3'OH of ATP. Mammalian adenylyl cyclases share no structural similarity with EF and they also use two-metal-ion catalysis, suggesting the catalytic mechanism-driven convergent evolution of two structurally diverse adenylyl cyclases.     

Molecular analysis of the avirulence gene avr9 of the fungal tomato pathogen Cladosporium fulvum fully supports the gene-for-gene hypothesis

The interaction between the fungal pathogen Cladosporium fulvum and tomato is supposed to have a gene-for-gene basis. Races of C. fulvum which have 'overcome' the resistance gene Cf9 of tomato, lack the avirulence gene avr9 which encodes a race-specific peptide elicitor. Races avirulent on tomato genotypes carrying the resistance gene Cf9 produce the race-specific peptide elicitor, which induces the hypersensitive response (HR) on those genotypes. The causal relationship between the presence of a functional avr9 gene and avirulence on tomato genotype Cf9 was demonstrated by cloning of the avr9 gene and subsequent transformation of C. fulvum. A race virulent on tomato genotype Cf9 was shown to become avirulent by transformation with the cloned avr9 gene. These results clearly demonstrate that the avr9 gene is responsible for cultivar specificity on tomato genotype Cf9 and fully support the gene-for-gene hypothesis. The avr9 gene is the first fungal avirulence gene to be cloned.     

The effect of electric field on callus induction with rape hypocotyls

The influence of electric field treatment on dedifferentiation and calli formation on rape hypocotyls was investigated. Segments, 10 mm long, of the upper part of rape (Brassica napus L., cv. Góczański) hypocotyls were stimulated by different combinations of voltage/time (1.5 V/120 h, 3 V/3 h, 10 V/15 min and 30 V/30 s) under in vitro conditions. With all electric field treatments, segments oriented with their apical part towards the cathode produced more calli as compared to control (non-treated with electric field). Under opposite orientation slight inhibition of callus growth was observed. As the strongest effect on callus growth was observed after treatment with 30 V/30 s, this electric field treatment was selected for following analyses: the incorporation of [14C]-2,4-D (2,4-dichlorophenoxyacetic acid) and [14C]-BAP (benzylaminopurine) from the culture medium, changes in ACC (1-aminocyclopropane-1-carboxylic acid) level and the redox activity in apical and bottom parts of hypocotyls during 18 d of culture. In contrast to changes in fresh weight, electric field treatment (30 V/30 s) stimulated a higher accumulation of 2,4-D and BAP in basal parts of hypocotyls than in apical ones. Moreover, orienting the apical part towards the cathode resulted in lower uptake of hormones as compared with the opposite orientation. The ACC concentration increased, especially in the basal parts of hypocotyls, independently on electric field application. However, the highest level was observed after electric field treatment with orientation of the apical part towards the anode. The distribution of oxidative substances (measured as the amount of ferric ions) between the apical and bottom part of hypocotyls was not changed when the apical parts were oriented towards the cathode. Under these conditions a decrease in apical and an increase in basal parts was observed during culture. Opposite orientation influenced the redistribution of oxidative substances from the first day of electric field treatment. Based on these results we suggest that electric field action can be connected with its influence on specific concentration of oxidative substances and hormone distribution in cells.     

Effects of Porosity and Mixed Convection on MHD Two Phase Fluid Flow in an Inclined Channel

The present study deals with the flow and heat transfer analysis of two immiscible fluids in an inclined channel embedded in a porous medium. The channel is divided in two phases such that a third grade fluid occupies the phase I and a viscous fluid occupies the phase II. Both viscous and third grade fluids are electrically conducting. A constant magnetic field is imposed perpendicular to the channel walls. The mathematical model is developed by using Darcy''s and modified Darcy''s laws for viscous and third grade fluids respectively. The transformed ordinary differential equations are solved numerically using a shooting method. The obtained results are presented graphically and influence of emerging parameters is discussed in detail.     

On-line parameter and state estimation of continuous cultivation by extended Kalman filter

Summary The on-line estimation of biomass concentration and of three variable parameters of the non-linear model of continuous cultivation by an extended Kalman filter is demonstrated. Yeast growth in aerobic conditions on an ethanol substrate is represented by an unstructured non-linear stochastic t-variant dynamic model. The filter algorithm uses easily accessible data concerning the input substrate concentration, its concentration in the fermentor and dilution rate, and estimates the biomass concentration, maximum specific growth rate, saturation constant and substrate yield coefficient. The microorganismCandida utilis, strain Vratimov, was cultivated on the ethanol substrate. The filter results obtained with the real data from one cultivation experiment are presented. The practical possibility of using this method for on-line estimation of biomass concentration, which is difficult to measure, is discussed.Nomenclature D dilution rate (h^-1) - DO₂ dissolved oxygen concentration (%) - E identity matrix - F Jacobi matrix of the deterministic part of the system equations g - g continuousn-vector non-linear real function - h m-vector non-linear real function - K Kalman filter gain matrix - K _S saturation constant (kgm^-3) - K_S expectation of the saturation constant estimate - M Jacobi matrix of the deterministic part of the measurement equations h - P(t₀) co-variance matrix of the initial values of the state - P(t_k/t_k) c-variance matrix of the error in (t _k|t _k) - P(t_k+1/t_k) co-variance matrix of the error in (t _k+1|t _k - Q co-variance matrix of the state noise - R co-variance matrix of the output noise - S substrate concentration (kgm^-3) - S _i input substrate concentration - t time - t _k discrete time instant with indexk=0, 1, 2,... - u(t) input vector - v(t_k) measurement (output) noise sequence - w(t) n-vector white Gaussian random process - x(t₀) initial state of the system - (t₀) expectation of the initial state values - x(t) n-dimensional state vector - x(t_k) state vector at the time instantt _k - (t_k|t_k) expectation of the state estimate at timet _k when measurements are known to the timet _k - (t_k+1|t_k) expectation of the state prediction - X biomass concentration (kgm^-3) - expectation of the biomass concentration estimate - y(t_k) m-dimensional output vector at the time instantt _k - Y _XIS substrate yield coefficient - _X|S expectation of the substrate yield coefficient estimate - specific growth rate (h^-1) - _M maximum specific growth rate (h^-1) - expectation of the maximum specific growth rate estimate - state transition matrix     

Mitotic chromosomes of species in the subgenusDrosophila (Diptera:Drosophilidae)

The karyotypes of 17 species in the subgenusDrosophila are compared according to their taxonomical relationships. Although closely related species often possess similar karyotypes, the karyotypes diverge considerably within the subgenus. Thus extensive chromosome rearrangements did occur during the speciation. Species with higher chromosome numbers do not necessarily have higher average of total chromosome length per cell.     

Acceptance and perceived barriers of implementing a guideline for managing low back in general practice

Background

There is considerable interest today in shared decision-making (SDM), defined as a decision-making process jointly shared by patients and their health care provider. However, the data show that SDM has not been broadly adopted yet. Consequently, the main goal of this proposal is to bring together the resources and the expertise needed to develop an interdisciplinary and international research team on the implementation of SDM in clinical practice using a theory-based dyadic perspective.

Methods

Participants include researchers from Canada, US, UK, and Netherlands, representing medicine, nursing, psychology, community health and epidemiology. In order to develop a collaborative research network that takes advantage of the expertise of the team members, the following research activities are planned: 1) establish networking and on-going communication through internet-based forum, conference calls, and a bi-weekly e-bulletin; 2) hold a two-day workshop with two key experts (one in theoretical underpinnings of behavioral change, and a second in dyadic data analysis), and invite all investigators to present their views on the challenges related to the implementation of SDM in clinical practices; 3) conduct a secondary analyses of existing dyadic datasets to ensure that discussion among team members is grounded in empirical data; 4) build capacity with involvement of graduate students in the workshop and online forum; and 5) elaborate a position paper and an international multi-site study protocol.

Discussion

This study protocol aims to inform researchers, educators, and clinicians interested in improving their understanding of effective strategies to implement shared decision-making in clinical practice using a theory-based dyadic perspective.     

Characterization of truncated forms of abnormal prion protein in Creutzfeldt-Jakob disease

In prion disease, the abnormal conformer of the cellular prion protein, PrP(Sc), deposits in fibrillar protein aggregates in brain and other organs. Limited exposure of PrP(Sc) to proteolytic digestion in vitro generates a core fragment of 19-21 kDa, named PrP27-30, which is also found in vivo. Recent evidence indicates that abnormal truncated fragments other than PrP27-30 may form in prion disease either in vivo or in vitro. We characterized a novel protease-resistant PrP fragment migrating 2-3 kDa faster than PrP27-30 in Creutzfeldt-Jakob disease (CJD) brains. The fragment has a size of about 18.5 kDa when associated with PrP27-30 type 1 (21 kDa) and of 17 kDa when associated with type 2 (19 kDa). Molecular mass and epitope mapping showed that the two fragments share the primary N-terminal sequence with PrP27-30 types 1 and 2, respectively, but lack a few amino acids at the very end of C terminus together with the glycosylphosphatidylinositol anchor. The amounts of the 18.5- or 17-kDa fragments and the previously described 13-kDa PrP(Sc) C-terminal fragment relatively to the PrP27-30 signal significantly differed among CJD subtypes. Furthermore, protease digestion of PrP(Sc) or PrP27-30 in partially denaturing conditions generated an additional truncated fragment of about 16 kDa only in typical sporadic CJD (i.e. MM1). These results show that the physicochemical heterogeneity of PrP(Sc) in CJD extends to abnormal truncated forms of the protein. The findings support the notion of distinct structural "conformers" of PrP(Sc) and indicate that the characterization of truncated PrP(Sc) forms may further improve molecular typing in CJD.