In goldfish the discriminative ability for odours persists after reduction of the olfactory epithelium, and rapidly returns after olfactory nerve axotomy and crossing bulbs

Goldfish are ideal vertebrates for the study of regeneration within the peripheral and the central olfactory system. The present behavioural investigations studied the effects of bilateral lesions on the animals' ability to qualitatively discriminate two amino acids (10(-6) M) and their performance in two more difficult tasks: (i) rewarded amino acid applied in a lower concentration, and (ii) rewarded stimulus contaminated. A 50 and 85% reduction of the olfactory epithelium resulted in no recordable behavioural deficit. After axotomy of olfactory nerves and lateral olfactory tractotomy, fishes were anosmic for seven to ten days. Following replacement of sensory cells in the epithelium, and after regeneration of olfactory tract fibres a full functional recovery i.e. a highly specific regeneration, was recorded. After three surgical modifications of the olfactory bulbs' position, (i) crossing olfactory tracts and bulbs, (ii) crossing tracts and turning bulbs, and (iii) turning bulbs upside down, a full functional recovery was recorded for amino-acid discrimination in a similar concentration. A permanent, and similar slight deficit was, however, found during application of different concentrations, and of contaminated stimuli when medial lateral halves of the bulb were in 'incorrect' position (i) and (ii), or olfactory bulbs were positioned in the vicinity of the contralateral epithelium (i) and (ii).     

Combined use of spectroscopic and energy calculation methods for the determination of peptide conformation in solution

This paper describes the combined use of energy calculations and spectroscopic data for the determination of peptide conformations in solution. The approach involves (i) experimental measurements of spectroscopic parameters for a molecule, (ii) calculation of these parameters for low-energy conformers previously determined with regard to local fluctuations in conformation and (iii) a random search for statistically weighted combinations of conformers which provide a good agreement between the calculated and experimental data. The above approach was used to study the conformation of a spin-labelled angiotensin molecule (SL-AT). It appears that the C-terminal hexapeptide of SL-AT possesses two geometrically different spatial forms of the backbone in aqueous solution, with mean values for the statistical weight of 0.78 and 0.22, respectively. In contrast, the N-terminal part of the molecule is conformationally labile. The data obtained can be used to describe the conformation of angiotensin in solution.     

Dimensional analysis of nerve models

General equations for (i) a uniform patch of nerve membrane, (ii) a continuous (unmyelinated) axon and (iii) a noded (myelinated) axon are analyzed using dimensional analysis. The original dimensioned equations are transformed to dimensionless equations. These equations contain dimensionless constants called similarity parameters which are functions of the physical constants or parameters of the system. (The similarity parameters are analogous to such quantities as the Reynolds number and Mach number used in fluid dynamics.) There is one similarity parameter for each of cases (i) and (ii), and four for case (iii). All dimensioned systems having the same values of all the similarity parameters form a similarity class.Once a quantity such as threshold stimulus or conduction velocity is computed for one member of any similarity class, the same quantity can be easily computed for any other member of the same class, by a simple formula containing the physical constants of the system, called a generating equation, or by an even simpler expression of proportionality, called a scaling relation.     

Conformational analysis of two novel cytotoxic C2-substituted pyrrolo[2,3-f]quinolines in aqueous media,organic solvents,membrane bilayers and at the putative active site

We have performed: (i) conformational analysis of two novel cytotoxic C2-substituted pyrrolo[2,3-f]quinolines 5e and 5g in deuterated dimethylsulfoxide (DMSO-d₆) utilizing NOE results from NMR spectroscopy; (ii) molecular dynamics (MD) calculations in water, DMSO and dimyristoyl phosphatidylcholine bilayers and (iii) molecular docking and MD calculations on DNA nucleotide sequences. The obtained results for the two similar in structure molecules showed differences in: (i) their conformational properties in silico and in media that reasonably simulate the biological environment; (ii) the way they are incorporated into the lipid bilayers and therefore their diffusion ability and (iii) molecular docking capacity as it is depicted from their different binding scores.     

A theoretical framework for biological control of soil-borne plant pathogens: Identifying effective strategies

We develop and analyse a flexible compartmental model of the interaction between a plant host, a soil-borne pathogen and a microbial antagonist, for use in optimising biological control. By extracting invasion and persistence thresholds of host, pathogen and biological control agent, performing an equilibrium analysis, and numerical investigation of sensitivity to parameters and initial conditions, we determine criteria for successful biological control. We identify conditions for biological control (i) to prevent a pathogen entering a system, (ii) to eradicate a pathogen that is already present and, if that is not possible, (iii) to reduce the density of the pathogen. Control depends upon the epidemiology of the pathogen and how efficiently the antagonist can colonise particular habitats (i.e. healthy tissue, infected tissue and/or soil-borne inoculum). A sharp transition between totally effective control (i.e. eradication of the pathogen) and totally ineffective control can follow slight changes in biologically interpretable parameters or to the initial amounts of pathogen and biological control agent present. Effective biological control requires careful matching of antagonists to pathosystems. For preventative/eradicative control, antagonists must colonise susceptible hosts. However, for reduction in disease prevalence, the range of habitat is less important than the antagonist's bulking-up efficiency.     

A quantitative system of age analysis for the dog-whelk, Nucella lapillus

Past attempts to age classify dog-whelks are revised briefly. The most satisfactory method is a system which relies upon familarity of morphological characteristics with which to separate population samples into five different classes. An attempt has been made to quantitate this system. Definite standards have been suggested as the criteria with which to separate the five age classes, and a series of simple methods have been demonstrated which, when followed give finite values for each of these standards. The standards suggested are: (i) the lower limits for shell-length in mature individuals; (ii) the lip-thickness coinciding with maturity; (iii) the upper limits for shell-length in juvenile crevice dwellers. The methods of estimate for values for these standards are illustrated in practice with population samples from Blackrock, Sussex. The values thus obtained and the methods used in each estimation are discussed with view to their validity. It is reasonable to suspect that the quantitative age classification system can be used to classify dog-whelks from any shore provided large enough population samples are collected to estimate the values for each standard. Use of the system is further demonstrated by classification of animals from the shore at Martin's Haven, Pembrokeshire.     

A simple method for differential isolation of freely dispersed and particle-associated peat microorganisms

Differential isolation of physiologically and ecologically diverse microbial groups facilitates evaluation of their activities in the environment. Here we describe a new method for differential isolation of freely dispersed and particle-associated peat microorganisms. The method is based on sequential elution of peat. Two types of natural peat, "young" sphagnum peat and "old" reed-based peat that have significantly different molecular composition as revealed by solid-state 13C NMR, were used for the method development. Various combinations of elution parameters (pH values, surfactant concentration, and sonication) were tested. Protein yield, CFU counts, 16S rDNA gene sequence, and T-RFLP analyses were used as criteria for evaluating the effectiveness of the elution protocols. The optimal method consisted of sequential elutions with (i) pH 6.2, 0.1 M potassium phosphate buffer, (ii) the same buffer amended with 0.01% of Tween 80, and (iii) treatment (ii) amended with sonication for 2 min. This method allowed differential isolation of freely dispersed and particle-associated microorganisms with (i) highest yield, (ii) highest diversity within the each microbial fraction, and (iii) best discrimination between the freely dispersed and particle-associated microbial communities. The method was applied for characterization of peat microbial communities and revealed different taxonomic composition and similar spatial organization of sphagnum and reed-sage peat microorganisms.     

Olfactory acuity in theropods: palaeobiological and evolutionary implications

This research presents the first quantitative evaluation of the olfactory acuity in extinct theropod dinosaurs. Olfactory ratios (i.e. the ratio of the greatest diameter of the olfactory bulb to the greatest diameter of the cerebral hemisphere) are analysed in order to infer the olfactory acuity and behavioural traits in theropods, as well as to identify phylogenetic trends in olfaction within Theropoda. A phylogenetically corrected regression of olfactory ratio to body mass reveals that, relative to predicted values, the olfactory bulbs of (i) tyrannosaurids and dromaeosaurids are significantly larger, (ii) ornithomimosaurs and oviraptorids are significantly smaller, and (iii) ceratosaurians, allosauroids, basal tyrannosauroids, troodontids and basal birds are within the 95% CI. Relative to other theropods, olfactory acuity was high in tyrannosaurids and dromaeosaurids and therefore olfaction would have played an important role in their ecology, possibly for activities in low-light conditions, locating food, or for navigation within large home ranges. Olfactory acuity was the lowest in ornithomimosaurs and oviraptorids, suggesting a reduced reliance on olfaction and perhaps an omnivorous diet in these theropods. Phylogenetic trends in olfaction among theropods reveal that olfactory acuity did not decrease in the ancestry of birds, as troodontids, dromaeosaurids and primitive birds possessed typical or high olfactory acuity. Thus, the sense of smell must have remained important in primitive birds and its presumed decrease associated with the increased importance of sight did not occur until later among more derived birds.     

The use of scientometric parameters for the evaluation of scientific contributions

This paper deals with the application of scientometric parameters in the evaluation of scientists, either as individuals or in small formal groups. The parameters are divided into two groups: parameters of scientific productivity and citation parameters. The scientific productivity was further subdivided into three types of parameters: (i) total productivity, (ii) partial productivity, and (iii) productivity in scientific fields and subfields. These citation parameters were considered: (i) impact factors of journals, (ii) impact factors of scientific fields and subfields, (iii) citations of individual papers, (iv) citations of individual authors, (v) expected citation rates and relative citation rates, and (vi) self-citations, independent citations and negative citations. Particular attention was payed to the time-dependence of the scientometric parameters. If available, numeric values of the world parameters were given and compared with the data about the scientific output of Croatian scientists.     

A discrete model of bacterial metabolism

This paper describes a computer model of the intermediary metabolismof bacteria during steady-state growth and during adaptations,e g. to new carbon sources. Metabolic regulation is representedas a process of optimisation, in which the trend is towardsimproved metabolic performance. The model uses linear programmingtechniques for the optimisation The implementation falls intofour phases: (i) assembly of model parameters; (ii) calculations;(iii) storage of solutions and (iv) projection of solutions.The use of a commercial database and a commercial spreadsheethas proved to be of great assistance in the first and thirdphases. A metabolic map format, with the optional addition ofconversion values, names of enzymes or co-factors has been usedto project the results in a form convenient for inspection. Received on August 22, 1985; accepted on January 3, 1985     

Spatially and temporally regulated expression of specific heparan sulfate epitopes in the developing mouse olfactory system

Heparan sulfate (HS) comprises a structurally diverse group of glycosaminoglycans present ubiquitously on cell surfaces and in the extracellular matrix. The spatially and temporally regulated expression of specific HS structures is essential for various developmental processes in the nervous system but their distributions in the mouse olfactory system have not been explored. Here, we examined the spatiotemporal distribution of particular HS species in the developing mouse olfactory system using three structure‐specific monoclonal antibodies (HepSS‐1, JM403 and NAH46). The major findings were as follows. (i) During olfactory bulb morphogenesis, the HepSS‐1 epitope was strongly expressed in anterior telencephalic cells and coexpressed with fibroblast growth factor receptor 1. (ii) In early postnatal glomeruli, the JM403 epitope was expressed at different levels among individual glomeruli. The expression pattern and levels of the JM403 epitope were both associated with those of ephrin‐A3. (iii) In the vomeronasal system, the JM403 epitope was expressed in all vomeronasal axons but became increasingly restricted to vomeronasal axons terminating in the anterior region of the accessory olfactory bulb by 3 weeks of age. Our results demonstrate that each HS epitope exhibits a unique expression pattern during the development of the mouse olfactory system. Thus, each HS epitope is closely associated with particular developmental processes of the olfactory system and might have a particular role in developmental events.     

Heme-linked ionization and ligand binding produce identical changes of proximal heme stereochemistry in reduced horseradish peroxidase. Evidence for existence of two protein conformations

The visible and near infrared magnetic circular dichroism spectra of chemically reduced horseradish peroxidase at neutral and alkaline pH values and 5-coordinate protoheme-(2-methylimidazole) at pH 9.1 were compared at 4.2 K with those of photolysis products of their carbon monoxide complexes. From the results obtained we concluded that: (i) there are two protein conformations of HRP which determine the geometry of the Fe-N(His) bond; (ii) the transition from one conformation (heme stereochemistry) to another can be induced by either heme-linked ionization or ligand binding; (iii) a trigger mechanism for switching between two conformations has to exist.     

Inferring the causes of the three waves of the 1918 influenza pandemic in England and Wales

Past influenza pandemics appear to be characterized by multiple waves of incidence, but the mechanisms that account for this phenomenon remain unclear. We propose a simple epidemic model, which incorporates three factors that might contribute to the generation of multiple waves: (i) schools opening and closing, (ii) temperature changes during the outbreak, and (iii) changes in human behaviour in response to the outbreak. We fit this model to the reported influenza mortality during the 1918 pandemic in 334 UK administrative units and estimate the epidemiological parameters. We then use information criteria to evaluate how well these three factors explain the observed patterns of mortality. Our results indicate that all three factors are important but that behavioural responses had the largest effect. The parameter values that produce the best fit are biologically reasonable and yield epidemiological dynamics that match the observed data well.     

Design of substrate label for steady state flux measurements in plant systems using the metabolic network of Brassica napus embryos

Steady state metabolic flux analysis using (13)C labeled substrates is of growing importance in plant physiology and metabolic engineering. The quality of the flux estimates in (13)C metabolic flux analysis depend on the: (i) network structure; (ii) flux values; (iii) design of the labeling substrate; and (iv) label measurements performed. Whereas the first two parameters are facts of nature, the latter two are to some extent controlled by the experimenter, yet they have received little attention in most plant studies. Using the metabolic flux map of developing Brassica napus (Rapeseed) embryos, this study explores the value of optimal substrate label designs obtained with different statistical criteria and addresses the applicability of different optimal designs to biological questions. The results demonstrate the value of optimizing the choice of labeled substrates and show that substrate combinations commonly used in bacterial studies can be far from optimal for mapping fluxes in plant systems. The value of performing additional experiments and the inclusion of measurements is also evaluated.     

Dosimetric characterization of an 192Ir brachytherapy source with the Monte Carlo code PENELOPE

Monte Carlo calculations are highly spread and settled practice to calculate brachytherapy sources dosimetric parameters. In this study, recommendations of the AAPM TG-43U1 report have been followed to characterize the Varisource VS2000 ¹⁹²Ir high dose rate source, provided by Varian Oncology Systems.In order to obtain dosimetric parameters for this source, Monte Carlo calculations with PENELOPE code have been carried out. TG-43 formalism parameters have been presented, i.e., air kerma strength, dose rate constant, radial dose function and anisotropy function. Besides, a 2D Cartesian coordinates dose rate in water table has been calculated. These quantities are compared to this source reference data, finding results in good agreement with them.The data in the present study complement published data in the next aspects: (i) TG-43U1 recommendations are followed regarding to phantom ambient conditions and to uncertainty analysis, including statistical (type A) and systematic (type B) contributions; (ii) PENELOPE code is benchmarked for this source; (iii) Monte Carlo calculation methodology differs from that usually published in the way to estimate absorbed dose, leaving out the track-length estimator; (iv) the results of the present work comply with the most recent AAPM and ESTRO physics committee recommendations about Monte Carlo techniques, in regards to dose rate uncertainty values and established differences between our results and reference data.The results stated in this paper provide a complete parameter collection, which can be used for dosimetric calculations as well as a means of comparison with other datasets from this source.     

An energetic correlation of ab initio and NMR studies of the 3'-gauche effect in 3'-substituted thymidines

A straightforward correlation of our experimental NMR findings on 3'-substituted thymidine derivatives with that of the ab initio calculations shows that (i) the delta Go298kNRM of N reversible S equilibrium in nucleoside can be predicted from the ab initio calculated delta ES-N obtained from 6-311++G** level of theory; (ii) the substituent-dependent steric and stereoelectronic effects on the bias of the two-state N reversible S equilibrium in nucleosides can also be predicted from the ab initio calculations with sufficiently large basis functions, and (iii) the necessity of mimicking the solvation behaviour of the experimental NMR measurement condition in the ab initio calculations of biomolecules is also emphasized.     

Calculations of protein volumes: sensitivity analysis and parameter database

MOTIVATION: The precise sizes of protein atoms in terms of occupied packing volume are of great importance. We have previously presented standard volumes for protein residues based on calculations with Voronoi-like polyhedra. To understand the applicability and limitations of our set, we investigated, in detail, the sensitivity of the volume calculations to a number of factors: (i) the van der Waals radii set, (ii) the criteria for including buried atoms in the calculations or atom selection, (iii) the method of positioning the dividing plane in polyhedra construction, and (iv) the set of structures used in the averaging. RESULTS: We find that different radii sets have only moderate affects to the distribution and mean of volumes. Atom selection and dividing plane methods cause larger changes in protein atoms volumes. More significantly, we show how the variation in volumes appears to be clearly related to the quality of the structures analyzed, with higher quality structures giving consistently smaller average volumes with less variance.     

Imaging dose-dependent pharmacokinetics of an RGD-fluorescent dye conjugate targeted to alpha v beta 3 receptor expressed in Kaposi's sarcoma

Dynamic fluorescence images were obtained from xenografts bearing a subcutaneous human Kaposi's sarcoma (KS1767) immediately following the intravenous injection of an integrin-receptor targeting Cy5.5-c(KRGDf) at a dose ranging from 0.75 to 6 nmol/mouse. The fluorescence images were acquired using an intensified charge-coupled device system and were analyzed with a three-compartment pharmacokinetic (PK) model to determine uptake parameters in the tumor and normal tissue regions of interest as a function of administered dose. Our results show that the uptake of Cy5.5-c(KRGDf) in tumor regions were: (i) significantly greater than the contralateral normal tissue regions; (ii) linearly increased with dose of Cy5.5-c(KRGDf) up to 1.5 nmol/mouse; and (iii) blocked by preinjection of c(KRGDf). Above doses of 1.5 nmol/mouse, the uptake no longer increased with dose, suggesting integrin receptor saturation. In normal tissues, the PK uptake parameters were not influenced by Cy5.5-c(KRGDf) dose nor by the preadministration of c(KRGDf).