Enhancements and modifications of primer design program Primer3

The determination of annealing temperature is a critical step in PCR design. This parameter is typically derived from the melting temperature of the PCR primers, so for successful PCR work it is important to determine the melting temperature of primer accurately. We introduced several enhancements in the widely used primer design program Primer3. The improvements include a formula for calculating melting temperature and a salt correction formula. Also, the new version can take into account the effects of divalent cations, which are included in most PCR buffers. Another modification enables using lowercase masked template sequences for primer design. Availability: Features described in this article have been implemented into the development code of Primer3 and will be available in future versions (version 1.1 and newer) of Primer3. Also, a modified version is compiled under the name of mPrimer3 which is distributed independently. The web-based version of mPrimer3 is available at http://bioinfo.ebc.ee/mprimer3/ and the binary code is freely downloadable from the URL http://bioinfo.ebc.ee/download/.     

Size-dependent predation risk in tree-feeding insects with different colouration strategies: a field experiment

1. Body size is positively correlated with fecundity in various animals, but the factors that counterbalance the resulting selection pressure towards large size are difficult to establish. Positively size-dependent predation risk has been proposed as a selective factor potentially capable of balancing the fecundity advantage of large size.
2. To construct optimality models of insect body size, realistic estimates of size-dependent predation rates are necessary. Moreover, prey traits such as colouration should be considered, as they may substantially alter the relationship between body size and mortality risk.
3. To quantify mortality patterns, we conducted field experiments in which we exposed cryptic and conspicuous artificial larvae of different sizes to bird predators, and recorded the incidence of bird attacks.
4. The average daily mortality rate was estimated to vary between 4% and 10%. In both cryptic and conspicuous larvae, predation risk increased with prey size, but the increase tended to be steeper in the conspicuous group. No main effect of colour type was found. All the quantitative relationships were reasonably consistent across replicates.
5. Our results suggest that the size dependence of mortality risk in insect prey is primarily determined by the probability of being detected by a predator rather than by a size-dependent warning effect associated with conspicuous colouration. Our results therefore imply that warningly coloured insects do not necessarily benefit more than the cryptic species from large body size, as has been previously suggested.     

Subribosomal particle analysis reveals the stages of bacterial ribosome assembly at which rRNA nucleotides are modified

Modified nucleosides of ribosomal RNA are synthesized during ribosome assembly. In bacteria, each modification is made by a specialized enzyme. In vitro studies have shown that some enzymes need the presence of ribosomal proteins while other enzymes can modify only protein-free rRNA. We have analyzed the addition of modified nucleosides to rRNA during ribosome assembly. Accumulation of incompletely assembled ribosomal particles (25S, 35S, and 45S) was induced by chloramphenicol or erythromycin in an exponentially growing Escherichia coli culture. Incompletely assembled ribosomal particles were isolated from drug-treated and free 30S and 50S subunits and mature 70S ribosomes from untreated cells. Nucleosides of 16S and 23S rRNA were prepared and analyzed by reverse-phase, high-performance liquid chromatography (HPLC). Pseudouridines were identified by the chemical modification/primer extension method. Based on the results, the rRNA modifications were divided into three major groups: early, intermediate, and late assembly specific modifications. Seven out of 11 modified nucleosides of 16S rRNA were late assembly specific. In contrast, 16 out of 25 modified nucleosides of 23S rRNA were made during early steps of ribosome assembly. Free subunits of exponentially growing bacteria contain undermodified rRNA, indicating that a specific set of modifications is synthesized during very late steps of ribosome subunit assembly.     

Material affects attack rates on dummy caterpillars in tropical forest where arthropod predators dominate: an experiment using clay and dough dummies with green colourants on various plant species

Predation can be one of the key factors that determine abundance in insect herbivore communities, and drive evolution of body size, and anti‐predator traits, including crypsis. Population dynamics and selection pressures will depend on the identity of dominant predators in the system, and these may vary substantially among habitats. Arthropods emerge as chief predators on caterpillars in the understorey of non‐montane tropical forest, whereas birds dominate elsewhere. In a tropical forest in Uganda, Africa, we evaluated marks on dummy caterpillars that differed in size, material (clay vs. dough), colourant, and plant species on which dummy caterpillars were exposed. We included live caterpillars to estimate the extent to which studies using artificial caterpillars reflect actual levels of predation. Ants and wasps were the most important damagers of dummy caterpillars, whereas bug and beetle damage was very rare, and no bird or small mammal damage was observed. Daily attack rates did not differ significantly from apparent mortality of live caterpillars (daily mortality = 12.1%), but dummy caterpillars made from dough were attacked more frequently (daily attack rate = 18.4%) than those from clay (daily attack rate = 6.9%). Caterpillars of different colour and size, and caterpillars exposed on different plant species had the same chances to be predated. This is in contrast to results from temperate area studies where birds dominate and are not affected by dummy caterpillar material, but prefer larger caterpillars. Our results are consistent with dominant predators on tropical forest caterpillars being invertebrates that are more chemically than visually oriented, so that: (1) material used for dummy caterpillars is important, (2) background matching is relatively unimportant, and (3) being large may have less of a cost. These patterns in predation might facilitate polyphagy and evolution of large body size in tropical Lepidoptera.     

Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins

Tah18-Dre2 is a recently identified yeast protein complex, which is highly conserved in human and has been implicated in the regulation of oxidative stress induced cell death and in cytosolic Fe-S proteins synthesis. Tah18 is a diflavin oxido-reductase with binding sites for flavin mononucleotide, flavin adenine dinucleotide and nicotinamide adenine dinucleotide phosphate, which is able to transfer electrons to Dre2 Fe-S clusters. In this work we characterized in details the interaction between Tah18 and Dre2, and analysed how it conditions yeast viability. We show that Dre2 C-terminus interacts in vivo and in vitro with the flavin mononucleotide- and flavin adenine dinucleotide-binding sites of Tah18. Neither the absence of the electron donor nicotinamide adenine dinucleotide phosphate-binding domain in purified Tah18 nor the absence of Fe-S in aerobically purified Dre2 prevents the binding in vitro. In vivo, when this interaction is affected in a dre2 mutant, yeast viability is reduced. Conversely, enhancing artificially the interaction between mutated Dre2 and Tah18 restores cellular viability despite still reduced cytosolic Fe-S cluster biosynthesis. We conclude that Tah18-Dre2 interaction in vivo is essential for yeast viability. Our study may provide new insight into the survival/death switch involving this complex in yeast and in human cells.     

Characterization of species-specific repeats in 613 prokaryotic species

Prokaryotes are in general believed to possess small, compactly organized genomes, with repetitive sequences forming only a small part of them. Nonetheless, many prokaryotic genomes in fact contain species-specific repeats (>85 bp long genomic sequences with less than 60% identity to other species) as we have previously demonstrated. However, it is not known at present how frequent such species-specific repeats are and what their functional roles in bacterial genomes may be. Therefore, we have conducted a comprehensive survey of prokaryotic species-specific repeats and characterized them to examine as to whether there are functional classes among different repeats or not and how they are mutually related to each other. Of the 613 distinct prokaryotic species analyzed, 97% were found to contain at least one species-specific repeats. It seems interesting to note that the species-specific repeats thus identified appear to be functionally variable in different genomes: in some genomes, they are mostly associated with duplicated protein-coding genes, whereas in some other genomes with rRNA and tRNA genes. Contrary to what may be expected, only one-fourth of the species-specific repeats were found to be associated with mobile genetic elements.     

Levan Enhances Associated Growth of Bacteroides,Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota

The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry. Eleven fecal samples from healthy donors were incubated in phosphate-buffered defined medium with or without levan supplementation and varying presence of amino acids. The generation of heat, changes in pH and microbiota composition, concentrations of produced and consumed metabolites during the growth were determined. The composition of fecal microbiota and profile of metabolites changed in response to substrate (levan and amino acids) availability. The main products of levan metabolism were acetic, lactic, butyric, propionic and succinic acids and carbon dioxide. Associated growth of levan-degrading (e.g. Bacteroides) and butyric acid-producing (e.g. Faecalibacterium) taxa was observed in levan-supplemented media. The study shows that the capacity of levan and possibly also other dietary fibers/prebiotics to modulate the composition and function of colon microbiota can be predicted by using isothermal microcalorimetry of fecal samples linked to metabolite and consortia analyses.