Genetic differentiation in the urban habitat: the great tits (Parus major) of the parks of Barcelona city

The increase of urban areas has led to a fragmentation of habitats for many forest‐living species. Man‐made parks might be a solution, but they can also act as sinks that are unable to maintain themselves without immigration from natural areas. Alternatively, parks might act as true metapopulations with extinctions and colonizations. In both cases, we can expect genetic variation to be reduced in the parks compared to the natural habitat. A third alternative is that the parks have sufficient reproduction to maintain themselves. To test these hypotheses, we analysed the pattern of genetic variation in the great tit (Parus major) in 12 parks in central Barcelona, and in an adjacent forest population using microsatellites. Genetic variation was not lower in the parks compared to the forest population, but larger, and gene flow was higher from the town to the forest compared to vice versa. We found a significant genetic differentiation among the parks, with a structure that only partly reflected the geographic position of the parks. Relatedness among individuals within parks was higher than expected by chance, although we found no evidence of kin groups. Assignment tests suggest that some parks are acting as net donors of individuals to other parks. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 9–19.     

The histological structure of the calcified lung of the fossil coelacanth Axelrodichthys araripensis (Actinistia: Mawsoniidae)

Abstract: The palaeohistological study of the calcified internal organ of Axelrodichthys araripensis Maisey, 1986, a coelacanthiform from the Lower Cretaceous of Brazil (Crato (Aptian) and Santana (Albian) formations of the Araripe Basin), shows that the walls of this organ consist of osseous blades of variable thickness separated from each other by the matrix. This indicates that, in the living individuals, the walls were reinforced by ossified plates, probably separated by conjunctive tissue. This calcified sheath present in Axelrodichthys, as well as in other fossil coelacanths, lies in ventral position relative to the gut and its single anterior opening is located under the opercle, suggesting a direct connection with the pharynx or the oesophagus. The calcified organ of Axelrodichthys, like that of other fossil coelacanths, is here regarded as an ‘ossified lung’ and compared with the ‘fatty lung’ of the extant coelacanth Latimeria. The reinforcement of the pulmonary walls by the overlying osseous blades could be interpreted as a means of adapting volumetric changes in the manner of bellows, a necessary function for ventilation in pulmonary respiration. Other functional hypotheses such as hydrostatic and/or acoustic functions are also discussed.     

Human growth hormone-specific aptamer identification using improved oligonucleotide ligand evolution method

LETEG is a method developed and used for the separation and purification of proteins employing a single-step ligand (aptamers) evolution in which aptamers are eluted with an increasing temperature gradient. Using recombinant human growth hormone (rhGH) as the test purification target, and after avoiding cross reactions of aptamers with Bacillus subtilis extracellular proteins by negative SELEX, the effects of time and pH on aptamer binding to rhGH were investigated. The highest binding efficiency of aptamers on rhGH-immobilized microparticles was obtained at pH 7.0. The aptamers that interacted with rhGH were eluted by a multi-stage step-up temperature gradient in ΔT = 10 °C increments within the range T = 55–95 °C; and the strongest affinity binding was disrupted at T = 85 °C where C_Apt = 0.16 μM was eluted. The equilibrium binding data obtained was described by a Langmuir-type isotherm; where the affinity constant was K_D = 218 nM rhGH. RhGH was separated from the fermentation broth with 99.8% purity, indicating that the method developed is properly applicable even for an anionic protein.     

Parasexuality in Race 65 Colletotrichum lindemuthianum Isolates

ABSTRACT. Heterokaryosis is the initial step of the parasexual cycle, a process that provides genetic variability in filamentous fungi through the production of heterozygous diploid nuclei. To characterize the parasexual cycle in Colletotrichum lindemuthianum, we evaluated the presence of heterokaryosis, vegetative compatibility reactions, and diploid formation among isolates of Race 65 collected from different Brazilian states. Vegetative compatibility groups were identified among the isolates according to their ability to form heterokaryons. Two heterozygous diploids were selected from compatible heterokaryons, which were characterized by the segregation of the parental auxotrophic markers and by RAPD profiles.     

Identification and expression analysis of cold-regulated genes from the cold-hardy Citrus relative Poncirus trifoliata (L.) Raf.

Citrus is a cold-sensitive genus and most commercially important varieties of citrus are susceptible to freezes. On the other hand, Poncirus trifoliata (L.) Raf. is an interfertile Citrus relative that can tolerate temperatures as low as −26°C when fully cold acclimated. Therefore, it has been used for improving cold tolerance in cold-sensitive commercial citrus rootstock varieties and in attempts to improve scion varieties. In this study, cDNA libraries were constructed from both 2-day cold-acclimated and from non-acclimated Poncirus seedlings using a subtractive hybridization method with the objective of identifying cold-regulated genes. A total of 192 randomly picked clones, 136 from the cold-induced library and 56 from the cold-repressed library, were sequenced. The majority of these clones showed sequence homology to previously identified cold-induced and/or environmental stress-regulated genes in Arabidopsis. In addition, some of them shared homology with cold and/or environmental stress-induced genes previously identified in other herbaceous and woody perennial plants and some showed no homology with sequences in GenBank. When these 192 cDNAs were analyzed by reverse northern blot with cold-acclimated and non-acclimated probes, 92 of the cDNAs displayed significantly increased expression, ranging from 2 to 49-fold, during cold acclimation; all 92 were from the cold-induced library. Surprisingly no clones displayed significantly repressed expression in response to cold. Analysis of a number of selected genes individually in northern blots of mRNA from cold-acclimated and non-acclimated plants largely confirmed the reverse northern analysis, verifying induction of expression of selected cDNAs in response to cold. The results showed that subtractive hybridization is an efficient method for identification of cold-induced genes in plants with limited sequence information available. This study also revealed that genes induced during cold acclimation of the cold-hardy citrus relative P. trifoliata are similar to those in Arabidopsis, indicating that similar pathways may be present and activated during cold acclimation in woody perennial plants.     

Contents of metals in some wild mushrooms

The concentrations of 7 metals (lead, cadmium, manganese, copper, nickel, silver, and chromium) were determined in 32 different species of wild mushrooms. The mushroom samples, which have been using for food and some medical purposes, were collected from Konya, an Inner Anatolian region of Turkey. The highest metal concentrations were determined as 39 mg/kg Pb and 3.72 mg/kg Cd in Trichaptum abietinum, 467 mg/kg Mn in Panaeolus sphinctrinus, 326 mg/kg Cu in Trametes versicolor, 69.4 mg/kg Ni in Helvella spadicea, 6.97 mg/kg Ag in Agaricus campestris, and 84.5 mg/kg Cr in Phellinus igniarius. The maximum contents are 1.52, 2.22, and 60.2 mg/kg in Pleurotus eryngii (for Pb), Amanita vaginata (for Cd), and Helvella leucomelana (for Cu), respectively. These results were compared according to the WHO/FAO standard.     

Production, properties and application to biocatalysis of a novel extracellular alkaline phenol oxidase from the thermophilic fungus Scytalidium thermophilum

Scytalidium thermophilum produces an extracellular phenol oxidase on glucose-containing medium. Certain phenolic acids, specifically gallic acid and tannic acid, induce the expression of the enzyme. Production at 45°C in batch cultures is growth-associated and is enhanced in the presence of 160 μM CuSO₄.5 H₂O and 3 mM gallic acid. The highest enzyme activity is observed at pH 7.5 and 65°C, on catechol. When incubated for 1 h at pH 7 and pH 8, 95% and 86% of the activity is retained. Thermostability decreases gradually from 40°C to 80°C. Estimated molecular mass is c. 83 kDa, and pI is acidic at c. 5.4. Substrate specificity and inhibition analysis in culture supernatants suggest that the enzyme has unique properties showing activity towards catechol; 3,4-dihydroxy-l-phenylalanine (l-DOPA); 4-amino-N, N-diethylaniline (ADA); p-hydroquinone; gallic acid; tannic acid and caffeic acid, and no activity towards l-tyrosine, guaiacol, 2,2′-azino-bis(3-ethyl-benzthiazoline-6-sulphonic acid) (ABTS) and syringaldazine. Inhibition is observed in the presence of salicyl hydroxamic acid (SHAM) and p-coumaric acid. Enzyme activity is enhanced by cetyltrimethylammonium bromide (CTAB) and polyvinylpyrrolidone (PVP), and the organic solvents dimethyl sulfoxide (DMSO) and ethanol. No inhibition is observed in the presence of carbon monoxide. Benzoin, benzoyl benzoin and hydrobenzoin are converted into benzil, and stereoselective oxidation is observed on hydrobenzoin. The reported enzyme is novel due to its catalytic properties resembling mainly catechol oxidases, but displaying some features of laccases at the same time.     

A Generic Shallow Lake Ecosystem Model Based on Collective Expert Knowledge

We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake ecosystem model by augmenting the individual cognitive maps drawn by 8 scientists working in the area of shallow lake ecology. We calculated graph theoretical indices of the individual cognitive maps and the collective cognitive map produced by augmentation. There were a total of 32 variables with 113 connections in the collective cognitive map. The graph theoretical indices revealed internal cycles showing non-linear dynamics in the shallow lake ecosystem. The ecological processes were organized democratically without a top-down hierarchical structure. The most central variable in the collective map was submerged plants. The strongest connections were suspended solids concentration decreasing water clarity, phosphorus concentration increasing the phytoplankton biomass, higher water clarity increasing submerged plants, benthivorous fish biomass reducing submerged plants and increasing suspended solids concentration, and submerged plants decreasing suspended solids. The steady state condition of the generic model was a characteristic turbid shallow lake ecosystem. The generic shallow lake ecosystem model had the tendency to go into a turbid state since there were no dynamic environmental changes that could cause shifts between a turbid and a clearwater state, and the generic model indicated that only a dynamic disturbance regime could maintain the clearwater state. The model developed herein captured the empirical behavior of shallow lakes, and contained the basic model of the Alternative Stable States Theory. In addition, our model expanded the basic model by quantifying the relative effects of connections and by extending it with 22 more variables and 99 more weighted causal connections. Using our expanded model we ran 4 simulations: harvesting submerged plants, nutrient reduction, fish removal without nutrient reduction, and biomanipulation. Only biomanipulation, which included fish removal and nutrient reduction, had the potential to shift the turbid state into clearwater state. The structure and relationships in the generic model as well as the outcomes of the management simulations were supported by actual field studies in shallow lake ecosystems. Thus, fuzzy cognitive mapping methodology enabled us to understand the complex structure of shallow lake ecosystems as a whole and obtain a valid generic model based on tacit knowledge of experts in the field.     

Age-related Patterns of Upper Arm Muscle and Fat Area in Turkish Children and Assessment of Nutritional Status

Anthropometric estimation of midarm muscularity and fatness was employed as a general index of nutritional status in developing countries. The present study attempts to evaluate the sex- and age-related pattern of regional muscle and fat area characteristics in Turkish children. A cross-sectional study was carried out on 1,068 10- to 14-year-old children (583 boys and 485 girls) from junior high schools in Ankara, the capital city of Turkey. According to general anthropometric protocols, weight, height, triceps skinfold thickness, and midarm circumference measurements were taken and socioeconomic data were collected. Arm muscle area (AMA) and arm fat area (AFA) were calculated and centile curves were evaluated using least median squares method. Results showed significant sexual dimorphism in muscle and fat patterning. AFA was found to be higher among girls and AMA among boys. The present findings suggest that the different levels of socioeconomic status (SES) appeared to be more prevalent on muscularity among boys (p < 0.05) and adiposity among girls (p < 0.001).