Genotyping of pantophysin I (Pan I) of Atlantic cod (Gadus morhua L.) by allele‐specific PCR

The two main allelic variants of the Atlantic cod (Gadus morhua L.) pantophysin I (Pan I) locus have different frequencies within different cod stocks. The Dra I polymorphism which distinguishes the two alleles can thus be used for discrimination of coastal and offshore cod populations. We present a new method for Pan I genotyping using fluorescent allele‐specific duplex polymerase chain reaction (PCR). This method is more rapid, reliable and cost‐effective than the previously published method and it is not affected by DNA source and quality. This improvement is important for studies demanding high throughput and accuracy of Pan I genotyping     

Widespread hybridization between the Greater Spotted Eagle Aquila clanga and the Lesser Spotted Eagle Aquila pomarina (Aves: Accipitriformes) in Europe

Hybridization is a significant threat for endangered species and could potentially even lead to their extinction. This concern applies to the globally vulnerable Greater Spotted Eagle Aquila clanga, a species that co‐occurs, and potentially interbreeds, with the more common Lesser Spotted Eagle Aquila pomarina in a vast area of Eastern Europe. We applied single nucleotide polymorphism (SNP) and microsatellite markers in order to study hybridization and introgression in 14 European spotted eagle populations. We detected hybridization and/or introgression in all studied sympatric populations. In most regions, hybridization took place prevalently between A. pomarina males and A. clanga females, with introgression to the more common A. pomarina. However, such a pattern was not as obvious in regions where A. clanga is still numerous. In the course of 16 years of genetic monitoring of a mixed population in Estonia, we observed the abandonment of A. clanga breeding territories and the replacement of A. clanga pairs by A. pomarina, whereby on several occasions hybridization was an intermediate step before the disappearance of A. clanga. Although the total number of Estonian A. clanga × A. pomarina pairs was twice as high as that of A. clanga pairs, the number of pairs recorded yearly were approximately equal, which suggests a higher turnover rate in interbreeding pairs. This study shows that interspecific introgressive hybridization occurs rather frequently in a hybrid zone at least 1700‐km wide: it poses an additional threat for the vulnerable A. clanga, and may contribute to the extinction of its populations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 725–736.     

Symbiosome-like intracellular colonization of cereals and other crop plants by nitrogen-fixing bacteria for reduced inputs of synthetic nitrogen fertilizers

It has been forecast that the challenge of meeting increased food demand and protecting environmental quality will be won or lost in maize, rice and wheat cropping systems, and that the problem of environmental nitrogen enrichment is most likely to be solved by substituting synthetic nitrogen fertilizers by the creation of cereal crops that are able to fix nitrogen symbiotically as legumes do. In legumes, rhizobia present intracellularly in membrane-bound vesicular compartments in the cytoplasm of nodule cells fix nitrogen endosymbiotically. Within these symbiosomes, membrane-bound vesicular compartments, rhizobia are supplied with energy derived from plant photosynthates and in return supply the plant with biologically fixed nitrogen, usually as ammonia. This minimizes or eliminates the need for inputs of synthetic nitrogen fertilizers. Recently we have demonstrated, using novel inoculation conditions with very low numbers of bacteria, that cells of root meristems of maize, rice, wheat and other major non-legume crops, such as oilseed rape and tomato, can be intracellularly colonized by the non-rhizobial, non-nodulating, nitrogen fixing bacterium, Gluconacetobacter diazotrophicus that naturally occurs in sugarcane. G. diazotrophicus expressing nitrogen fixing (nifH) genes is present in symbiosome-like compartments in the cytoplasm of cells of the root meristems of the target cereals and non-legume crop species, somewhat similar to the intracellular symbiosome colonization of legume nodule cells by rhizobia. To obtain an indication of the likelihood of adequate growth and yield, of maize for example, with reduced inputs of synthetic nitrogen fertilizers, we are currently determining the extent to which nitrogen fixation, as assessed using various methods, is correlated with the extent of systemic intracellular colonization by G. diazotrophicus, with minimal or zero inputs.     

The synthesis of short- and medium-chain-length poly(hydroxyalkanoate) mixtures from glucose- or alkanoic acid-grown <Emphasis Type="Italic">Pseudomonas oleovorans</Emphasis>

Pseudomonas oleovorans NRRL B-778 accumulated mixtures of poly-3-hydroxybutyrate (PHB) and medium-chain-length poly(hydroxyalkanoates) (mcl-PHAs) when grown on glucose, octanoic acid or oleic acid, whereas growth on nonanoic acid or undecanoic acid resulted in copolymers of poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHB-co-HV). Acetone fractionation verified the presence of PHB/mcl-PHA mixtures. The acetone-insoluble (AIS) fractions of the polymers derived from glucose (PHA-glucose), octanoic acid (PHA-octanoic) and oleic acid (PHA-oleic) were exclusively PHB while the acetone-soluble (AS) fractions contained mcl-PHA composed of differing ratios of 3-hydroxy-acid monomer units, which ranged in chain length from 6 to 14 carbon atoms. In contrast, both the AIS and AS fractions from the polymers derived from nonanoic acid (PHA-nonanoic) and undecanoic acid (PHA-undecanoic) were composed of comparable ratios of 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV). The unfractionated PHA-glucose, PHA-octanoic and PHA-oleic polymers had melting temperatures (T _m) between 177 and 179°C, enthalpies of fusion (ΔH _f) of 20 cal/g and glass transition temperatures (T _g) of 3–4°C. This was due to the large PHB content in the polymer mixtures. On the other hand, the PHA-nonanoic and PHA-undecanoic polymers had thermal properties that supported their copolymer nature. In both cases, the T _m values were 161°C, ΔH _f values were 7cal/g and T _g values were −3°C. Journal of Industrial Microbiology & Biotechnology (2002) 28, 147–153 DOI: 10.1038/sj/jim/7000231 Received 30 July 2001/ Accepted in revised form 04 November 2001     

Cytosolic isocitrate dehydrogenase in humans, mice, and voles and phylogenetic analysis of the enzyme family

In this study, we report cDNA sequences of the cytosolic NADP-dependent isocitrate dehydrogenase for humans, mice, and two species of voles (Microtus mexicanus and Microtus ochrogaster). Inferred amino acid sequences from these taxa display a high level of amino acid sequence conservation, comparable to that of myosin beta heavy chain, and share known structural features. A Caenorhabditis elegans enzyme that was previously identified as a protein similar to isocitrate dehydrogenase is most likely the NADP-dependent cytosolic isocitrate dehydrogenase enzyme equivalent, based on amino acid similarity to mammalian enzymes and phylogenetic analysis. We also suggest that NADP-dependent isocitrate dehydrogenases characterized from alfalfa, soybean, and eucalyptus are most likely cytosolic enzymes. The phylogenetic tree of various isocitrate dehydrogenases from eukaryotic sources revealed that independent gene duplications may have given rise to the cytosolic and mitochondrial forms of NADP-dependent isocitrate dehydrogenase in animals and fungi. There appears to be no statistical support for a hypothesis that the mitochondrial and cytosolic forms of the enzyme are orthologous in these groups. A possible scenario of the evolution of NADP-dependent isocitrate dehydrogenases is proposed.      

Microtubule assembly and disassembly at alkaline pH

Although it is now apparent that the intracellular pH may rise considerably above neutrality under physiological conditions, information on the effect of alkaline pH on microtubule assembly and disassembly is still quite fragmentay. We have studied the assembly/disassembly of bovine brain microtubule protein at alkaline pH in vitro. When microtubules are assembled to a new steady state at pH less than 7 and pH is then made more alkaline, they undergo a rapid disassembly to a new steady state. This disassembly is reversed by acidification. The degree of disassembly is determined largely by the pH- dependence of the critical concentration, which increases five to eight times, from pH 7 to 8. A fraction of assembly-incompetent tubulin is identified that increases with pH, but its incompetency is largely reversed with acidification. Measurements of microtubule lengths are used to indicate that disassembly occurs by uniform shortening of microtubules. A comparison of shortening by alkalinization with dilution suggests that the intrinsic rate of disassembly is accelerated by increasing pH. The capacity for initiating assembly is progressively lost with incubation at alkaline pH (although some protection is afforded by sulfhydryl-reducing agents). However, direct assembly from depolymerized mixtures is possible at least up to pH 8.3, and the steady state achieved at these alkaline pH values is stable. Such preparations are readily disassembled by cold and podophyllotoxin (PLN). Disassembly induced by PLN is also markedly enhanced at alkaline pH, suggesting a corresponding enhancement of “treadmilling.” The implications of physiological events leading to alkaline shifts of pH for microtubule assembly/disassembly are discussed, particularly in the light of recent hypotheses regarding treadmilling and its role in controlling the distribution of microtubules in vivo.     

Phylogeny of the pecan scab fungus <Emphasis Type="Italic">Fusicladium effusum</Emphasis> G. Winter based on the cytochrome b gene sequence

Pecan scab, caused by the fungus Fusicladium effusum, is the most devastating disease of pecan (Carya illinoinensis) trees and is responsible for the majority of disease management efforts applied to that crop. The taxonomy of the fungus changed several times in the last decade and most recently, using ITS nrDNA data and conventional taxonomic methods, the organism was renamed F. effusum. In our study, a conserved region of the mitochondrial cytochrome b gene was sequenced from three isolates of F. effusum. The obtained sequences showed 95% nucleic acid and 100% amino acid homology (201–266 amino acids on exon 5 of the cytochrome b gene) with Venturia inaequalis (NCBI GenBank accession number AF047029). And in the maximum parsimony tree based on nucleotide sequences, F. effusum and V. inaequalis were clustered, with a 92% bootstrap value. The taxonomic classification of the pecan scab fungus was supported based on the cytochrome b region.     

Evaluation of measurement uncertainties of an analytical method for the determination of aflatoxin M<Subscript>1</Subscript> in milk and milk powder

The mycotoxin aflatoxin M₁ (AfM₁) is a serious food safety hazard for which the European Commission has already established a maximum permissible level of 0.05 μg/kg AfM₁ in milk and products thereof. For control analysis laboratories are increasingly asked to submit full uncertainties of their analytical results.The evaluation of measurement uncertainties of an analytical method for the determination of AfM₁ in milk and milk powder on the basis of ‘in-house’ validation data in compliance with the ‘Guide to the Expression of Uncertainty in Measurement (GUM)’ [1] and the ‘EURACHEM Guide’ [2] is described. A similar approach will be used to assess the performance of methods employed by laboratories participating in the certification of reference materials for AfM₁ in milk powder.     

An invasive crayfish affects egg survival and the potential recovery of an endangered population of Arctic charr

1. Many fish stocks have declined, because of overharvesting, habitat destruction and introduced species. Despite efforts to rehabilitate some of these stocks, not all are responding or are recovering only slowly. 2. In freshwater systems, introduced crayfish are often problematic, and it has been suggested that their egg predation could reduce recruitment in depleted stocks of native fish. 3. Here, we report the results of a field experiment, using experimental cages, on the extent of predation on eggs of great Arctic charr (Salvelinus umbla) in Lake Vättern, Europe’s fifth largest lake. Here, the great Arctic charr has declined dramatically and is listed as critically endangered. 4. We were able to partition the total loss rate of eggs into background mortality, predation by introduced signal crayfish (Pacifastacus leniusculus) and predation by native fish. The mortality rate of charr eggs because of crayfish was estimated at more than five times that because of native fish. Of the total loss of eggs, 80% is believed to be caused by crayfish and 14% by fish, with 6% being natural background mortality. 5. In a worst case scenario, our data infer that only 25% of the original number of eggs would survive, compared with 75% in the absence of crayfish. This could impair recovery of the stock of the endangered great Arctic charr in Lake Vättern. 6. Contrary to earlier claims that crayfish predation on eggs of great Arctic charr is insignificant, our results indicate that crayfish predation may exceed fish predation and suggest that the abundance of signal crayfish on the spawning sites of great Arctic charr should be managed.