We describe PCR primers and amplification protocols developed to obtain introns from conserved nuclear genes in deep-sea protobranch bivalves. Because almost no sequence data for protobranchs are publically available, mollusk and other protostome sequences from GenBank were used to design degenerate primers, making these loci potentially useful in other invertebrate taxa. Amplification and sequ...

Using a comparative approach, the web program PriFi (http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main) designs pairs of primers useful for PCR amplification of genomic DNA in species where prior sequence information is not available. The program works with an alignment of DNA sequences from phylogenetically related species and outputs a list of possibly degenerate primer pairs fulfilling a numbe...

Eurosta solidaginis, the goldenrod gall fly, becomes freeze tolerant in early autumn. Many physiological changes occur to confer freeze tolerance, including the syntheses of cryoprotectant carbohydrates, changes in membrane lipid composition, increases in larval mass, and induction of ice nucleation (Morrissye and Baust 1976). Little is known about genes involved in the freeze tolerance capacit...

It is well known that in operations research‎, ‎degeneracy can cause a cycle in a network‎ ‎simplex algorithm which can be prevented by maintaining strong‎ ‎feasible bases in each pivot‎. ‎Also‎, ‎in a network consists of n arcs‎ ‎and m nodes‎, ‎not considering any new conditions on the entering‎ ‎variable‎, ‎the upper bound of consecutive degenerate pivots is equal‎ $left( ‎begin{array}{c}‎ ‎n...

white-rot basidiomycetes are one of the most important lignolytic microorganisms. these fungi have been reported to secrete three main classes of lignin degrading enzymes: lignin peroxidases (lips), manganese peroxidases (mnps) and laccases. in this study, for the first time the lignin degrading capability of two plant pathogens i.e. hyphodermella rosae and h. corrugata was evaluated using both...

Evaluating the specificity of polymerase chain reaction (PCR) primers is an essential step in PCR primer design. The MFEprimer-2.0 server allows users to check primer specificity against genomic DNA and messenger RNA/complementary DNA sequence databases quickly and easily. MFEprimer-2.0 uses a k-mer index algorithm to accelerate the search process for primer binding sites and uses thermodynamic...

Genes of the major histocompatibility complex (Mhc) are the most polymorphic functional loci in mammalian populations, but little is known of Mhc variability in natural populations of nonmammalian vertebrates. To help extend such studies to birds and relatives, we present a pair of degenerate primers that amplify polymorphic segments of one chain (the beta chain) of the class II genes from the ...

The use of molecular diagnostic techniques for bioprospecting and microbial diversity study purposes has gained more attention thanks to their functionality, low cost and quick results. In this context, ten degenerate primers were designed for the amplification of polyhydroxyalkanoate synthase (phaC) gene, which is involved in the production of polyhydroxyalkanoate (PHA)-a biodegradable, renewa...