Rate of recombinational deletion among human endogenous retroviruses

The fate of most human endogenous retroviruses (HERVs) has been to undergo recombinational deletion. This process involves homologous recombination between the flanking long terminal repeats (LTRs) of a full-length element, leaving a relic structure in the genome termed a solo LTR. We examined loci in one family, HERV-K(HML2), and found that the deletion rate decreased markedly with age: the rate among recently integrated loci was almost 200-fold higher than that among loci whose insertion predated the divergence of humans and chimpanzees (8 x 10(-5) and 4 x 10(-7) recombinational deletion events per locus per generation, respectively). One hypothesis for this finding is that increasing mutational divergence between the flanking LTRs reduces the probability of homologous recombination and thus the rate of solo LTR formation. Consistent with this idea, we were able to replicate the observed rates by a simulation in which the probability of recombinational deletion was reduced 10-fold by a single mutation and 100-fold by any additional mutations. We also discuss the evidence for other factors that may influence the relationship between locus age and the rate of deletion, for example, host recombination rates and selection, and highlight the consequences of recombinational deletion for dating recent HERV integrations.     

Correcting errors in synthetic DNA through consensus shuffling

Although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1–3 random errors/kb of DNA. Here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic DNA. In this method, errors are revealed as mismatches by re-hybridization of the population. The DNA is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding protein (MutS). PCR assembly of the remaining fragments yields a new population of full-length sequences enriched for the consensus sequence of the input population. We show that two iterations of consensus shuffling improved a population of synthetic green fluorescent protein (GFPuv) clones from ~60 to >90% fluorescent, and decreased errors 3.5- to 4.3-fold to final values of ~1 error per 3500 bp. In addition, two iterations of consensus shuffling corrected a population of GFPuv clones where all members were non-functional, to a population where 82% of clones were fluorescent. Consensus shuffling should facilitate the rapid and accurate synthesis of long DNA sequences.     

The effect of cadaverine on the formation of anabasine from lysine in hairy root cultures of Nicotiana hesperis

Unlabelled cadaverine did not diminish the incorporation into anabasine of ¹⁴C from L-[U-¹⁴C] lysine supplied to hairy root cultures of Nicotiana nesperis, despite causing a stimulation of anabasine production. The finding is discussed in the context of previous observations indicating that free cadaverine is not an intermediate in the biosynthesis of anabasine from lysine.     

The cytogenetics of thelytoky in a predominantly asexual parasitoid wasp with covert sex.

Asexual lineages in the parasitoid wasp Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae) have previously been shown to have occasionally undergone sexual reproduction and recombination with males from related sexual populations. In the present study, the cytogenetic system of asexual females in this species is shown by 4',6-diamidino-2-phenylindole dihydrochloride (DAPI) staining to be central fusion automixis. This system has the potential to allow occasional sex and recombination without leading to an elevation of ploidy and with the maintenance of at least some heterozygosity. No evidence of the bacterial symbiont Wolbachia was found, and the observed system was compared with that in parasitoid wasps where asexuality is the result of Wolbachia infection.     

Preservation of hymenopteran specimens for subsequent molecular and morphological study

Some guidelines are presented for long-term preservation of insects for non-traditional systematic studies such as DNA sequencing and internal anatomical research. The main criteria for good DNA preservation appear to be the rapidity with which the DNA is protected from enzymatic and chemical breakdown, and subsequent storage conditions. The immediate post mortem treatment of specimens appears particularly important to the preservation of amplifiable DNA. For storage we recommend 70–100% ethanol at low temperature, deep freezing, and critical point or chemical drying direct from alcohol. For internal anatomy, traditional fixatives, 70% ethanol in a refrigerator, critical point drying or chemical drying are recommended. Cold-storage in 70% ethanol with or without subsequent critical point drying or chemical drying using hexamethyldisilazane allow both molecular and morphological study.     

The effect of forest disturbance on the leaf litter ant fauna in Ghana

In order to observe the effect of forest loss on the leaf litter ant fauna in Ghana, West Africa, samples were taken in primary forest, secondary forest and in cocoa plots. Ants were extracted from the leaf litter by sieving followed by suspension in Winkler bags. The species composition and species richness in the three different habitats were compared and no significant difference was found between them. It was concluded that most primary forest leaf litter ant species continue to survive in parts of the agricultural landscape which has largely replaced their original habitat.     

A Molecular Phylogeny of the Aphidiinae (Hymenoptera: Braconidae)

Phylogenetic relationships within the Aphidiinae, and between this and other subfamilies of Braconidae (Hymenoptera), were investigated using sequence data from three genes: elongation factor-1α, cytochrome b, and the second expansion segment of the 28S ribosomal subunit. Variation in both protein-coding genes was characterized by a high level of homoplasy, but analysis of the expansion segment—robust over a range of alignment methods and parameters—resolved some of the older divergences. Parsimony analysis of the combined data suggests the following tribal relationships: (Ephedrini + (Praini + (Aphidiini + Trioxini))). In addition, the cyclostome subfamilies were found to form a clade separate from the Aphidiinae, but relationships between the Aphidiinae and the noncyclostome braconids could not be resolved. The inferred phylogeny also supported a secondary loss of internal pupation within the Praini and a polyphyletic origin of endoparasitism within the Braconidae.