Parasites in hybridizing communities: the Red Queen again?

Over the past two decades, infection levels in hybrids have frequently been compared with those in their progenitor species to find out whether parasites favour or penalize hybridization. Four static infection scenarios are possible, depending on whether hybrid resistance differs from that of one or both parental species. All four alternatives have been supported by some empirical data, but any potential dynamics might have been overlooked because of limited sampling or experimental designs. However, coevolutionary oscillations generated by frequency-dependent selection might provide a better explanation for the observed results than does a static genetic perspective of host resistance.     

Try Tri again? Resolving species boundaries in the Lomatium triternatum (Apiaceae) complex

Species boundaries have traditionally been delimited by applying phenotypic characters to a morphological species concept. With an increased understanding of the complexities of speciation as a process, species concepts have proliferated while at the same time, the ability to gather greater numbers and types of molecular characters has expanded the means by which species can be delimited. Phylogenetic studies of molecular data provide an opportunity to identify reciprocally monophyletic groupsand have led to the identification of cryptic or nearly cryptic species in which subtle differences in phenotypes or ecological niches can be uncovered only after monophyletic groups have been identified. Here, we investigate evolutionary relationships among a group of species in the Lomatium triternatum complex using molecular phylogenetic analyses for all samples, and ecological parameters for two of the 38 species included in this study. The results indicate that there are more reciprocally monophyletic groups in this complex than had been estimated using phenotypic data alone. The ecological data show a clear differentiation for the one pair of sister species where ecological sampling was available, implying that divergence within this group may have resulted from environmental selection for soil preferences that have been strong enough to result in speciation.     

Dissecting the role of the ?29 terminal protein DNA binding residues in viral DNA replication

Phage ϕ29 DNA replication takes place by a protein-priming mechanism in which the viral DNA polymerase catalyses the covalent linkage of the initiating nucleotide to a specific serine residue of the terminal protein (TP). The N-terminal domain of the ϕ29 TP has been shown to bind to the host DNA in a sequence-independent manner and this binding is essential for the TP nucleoid localisation and for an efficient viral DNA replication in vivo. In the present work we have studied the involvement of the TP N-terminal domain residues responsible for DNA binding in the different stages of viral DNA replication by assaying the in vitro activity of purified TP N-terminal mutant proteins. The results show that mutation of TP residues involved in DNA binding affects the catalytic activity of the DNA polymerase in initiation, as the K_m for the initiating nucleotide is increased when these mutant proteins are used as primers. Importantly, this initiation defect was relieved by using the ϕ29 double-stranded DNA binding protein p6 in the reaction, which decreased the K_m of the DNA polymerase for dATP about 130–190 fold. Furthermore, the TP N-terminal domain was shown to be required both for a proper interaction with the DNA polymerase and for an efficient viral DNA amplification.     

Antarctic DNA barcoding; a drop in the ocean?

Coordinated, circum-Antarctic sampling expeditions during International Polar Year 2008/09 have given access to comprehensive collections suitable for DNA barcoding. Collaborations between the Census of Antarctic Marine Life (CAML), the Marine Barcode of Life project and the Canadian Centre for DNA Barcoding have enabled the Antarctic scientific community to initiate large-scale DNA barcoding projects to record the genetic diversity of Antarctic marine fauna, coordinated by the CAML Barcoding Campaign. A total of 20,355 marine specimens from more than 2,000 morphospecies covering 18 phyla are in the processing pipeline, and to date, 11,530 sequences have been processed with the remainder due by the end of 2010. Here, we present results on the current geographic and taxonomic coverage of DNA barcode data in the Southern Ocean and identify the remaining gaps. We show how DNA barcoding in the Antarctic is answering important questions regarding marine genetic diversity and challenging current assumptions of species distribution at the poles.     

"Resonances" in the dielectric absorption of DNA?

An attempt was made to confirm previous reports of resonant-like dielectric absorption of plasmid DNA in aqueous solutions at 1-10 GHz. The dielectric properties of the sample were measured using an automatic network analyzer with two different techniques. One technique used an open-ended coaxial probe immersed in the sample; the other employed a coaxial transmission line. No resonances were observed that could be attributed to the sample; however, resonance-type artifacts were prominent in the probe measurements. The coaxial line technique appears to be less susceptible to such artifacts. We note two important sources of error in the calibration of the automatic network analyzer using the probe technique.     

Are there insertions in the ribosomal DNA of vertebrates?

We have analysed the Eco RI restriction pattern of rDNA of the newt Triturus vulgaris and of some other amphibian species by Southern blotting and hybridization with nick-translated Xenopus rDNA prepared from the recombinant plasmids pXlr11 and pXlr12 (21). After hybridization with r11, the 28S coding fragments become visible in two bands, a prominent one of 5.3 kb and a weak band of 5.9 kb representing about 8% of the 28S genes. The evidence obtained so far by additional digestions with Bam HI and Bgl II indicates that in this species and in Triturus helveticus the coding regions of the 5.9 kb fragments are interrupted by an insertion 0.6 kb in length located in a 1.6 kb Bgl II fragment at the 3' end of the Eco RI fragment, which we believe to be the first described in a vertebrate.     

How does the suppression of energy supplementation affect herbage intake,performance and parasitism in lactating saddle mares?

Agroecology opens up new perspectives for the design of sustainable farming systems by using the stimulation of natural processes to reduce the inputs needed for production. In horse farming systems, the challenge is to maximize the proportion of forages in the diet, and to develop alternatives to synthetic chemical drugs for controlling gastrointestinal nematodes. Lactating saddle mares, with high nutritional requirements, are commonly supplemented with concentrates at pasture, although the influence of energy supplementation on voluntary intake, performance and immune response against parasites has not yet been quantified. In a 4-month study, 16 lactating mares experimentally infected with cyathostome larvae either received a daily supplement of barley (60% of energy requirements for lactation) or were non-supplemented. The mares were rotationally grazed on permanent pastures over three vegetation cycles. All the mares met their energy requirements and maintained their body condition score higher than 3. In both treatments, they produced foals with a satisfying growth rate (cycle 1: 1293 g/day; cycle 2: 1029 g/day; cycle 3: 559 g/day) and conformation (according to measurements of height at withers and cannon bone width at 11 months). Parasite egg excretion by mares increased in both groups during the grazing season (from 150 to 2011 epg), independently of whether they were supplemented or not. This suggests that energy supplementation did not improve mare ability to regulate parasite burden. Under unlimited herbage conditions, grass dry matter intake by supplemented mares remained stable around 22.6 g DM/kg LW per day (i.e. 13.5 kg DM/al per day), whereas non-supplemented mares increased voluntary intake from 22.6 to 28.0 g DM/kg LW per day (13.5 to 17.2 kg DM/al per day) between mid-June and the end of August. Hence total digestible dry matter intake and net energy intake did not significantly differ between supplemented and non-supplemented mares during the second and third cycles. In conclusion, supplementing lactating mares at pasture should not be systematic because their adaptive capacities enable to increase herbage intake and ensure foal growth. Further research is needed to determine the herbage allowance threshold below which supplementation is required.     

Is the nuclear matrix the site of DNA replication in eukaryotic cells?

Four types of experiment were carried out to test the recently proposed model of matrix-bound replication in eukaryotic cells. In experiments with pulse-labelling we found preferential association of newly replicated DNA with the matrix only when the procedure for isolation includes first high-salt treatment of isolated nuclei and then digestion with nucleases, or when prior to digestion the nuclei have been stored for a prolonged time. In both cases, however, evidence was found that this preferential association is due to a secondary, artifactual binding of the newly replicated chromatin region to the matrix elements. Pulse-chase experiments and experiments with continuous labelling were carried out to answer the question whether during replication the DNA is reeled through the replication complexes, i.e., whether newly replicated DNA is temporarily or permanently associated with the matrix. The results showed that at that time the matrix DNA does not move from its site of attachment. Since, according to the model of matrix-bound replication, the forks are assumed to be firmly anchored to high-salt resistant proteinaceous matrix structures, the chromatin fragments isolated with endonuclease not recognizing newly replicated DNA and purified by sucrose gradient centrifugation should be free of replication intermediates. The electronmicroscopic analysis of such fragments revealed the existence of intact replication micro-bubbles. Moreover, the fragments with replication configurations appeared as smooth chromatin fibres not attached to elements characteristic for the matrix. All these experiments suggest that the nuclear skeleton is not a native site of DNA replication in eukaryotic cells.     

Mitochondrial DNA clonality in the dock: can surveillance swing the case?

Mitochondrial DNA (mtDNA) is a favoured tool of evolutionary biologists because its high mutation rate generates enough signal to make inferences about population history over short time frames. Furthermore, mtDNA inheritance is clonal, being transmitted only through the maternal line. This enables evolutionary histories to be assembled without the complexities introduced by biparental recombination. Recently, a single case of human biparental inheritance has been reported. Given this, and the role supposed clonal inheritance has had in shaping our knowledge of human population history, it is essential to establish a method for identifying any recombinant mtDNA molecules in our population. A reliable surveillance mechanism would either maintain our confidence in clonal inheritance or indicate the inaccuracy of our inferences.     

Is there an error correcting code in the base sequence in DNA?

Modern methods of encoding information into digital form include error check digits that are functions of the other information digits. When digital information is transmitted, the values of the error check digits can be computed from the information digits to determine whether the information has been received accurately. These error correcting codes make it possible to detect and correct common errors in transmission. The sequence of bases in DNA is also a digital code consisting of four symbols: A, C, G, and T. Does DNA also contain an error correcting code? Such a code would allow repair enzymes to protect the fidelity of nonreplicating DNA and increase the accuracy of replication. If a linear block error correcting code is present in DNA then some bases would be a linear function of the other bases in each set of bases. We developed an efficient procedure to determine whether such an error correcting code is present in the base sequence. We illustrate the use of this procedure by using it to analyze the lac operon and the gene for cytochrome c. These genes do not appear to contain such a simple error correcting code.     

Who's on first in the cellular response to DNA damage?

Cellular DNA-repair pathways involve proteins that have roles in other DNA-metabolic processes, as well as those that are dedicated to damage removal. Several proteins, which have diverse functions and are not known to have roles in DNA repair, also associate with damaged DNA. These newly discovered interactions could either facilitate or hinder the recognition of DNA damage, and so they could have important effects on DNA repair and genetic integrity. The outcome for the cell, and ultimately for the organism, might depend on which proteins arrive first at sites of DNA damage.     

Tools to study DNA repair: what's in the box?

Our understanding of the DNA repair mechanisms that preserve genome integrity has increased greatly in recent years. To follow the DNA repair process, researchers have developed sophisticated techniques including live cell imaging, local damage induction and refined biochemical assays. These techniques have helped to elucidate the 'orchestration' of DNA repair mechanisms (i.e. the order of factor assembly around the lesion, the identification of new functions of known factors and the discovery of novel key regulators involved in DNA repair). We will discuss the uses and the limitations of these methods and their applications in the study of DNA repair.     

Involvement of the Yeast DNA Polymerase δ in DNA Repair in Vivo

The POL3 encoded catalytic subunit of DNA polymerase δ possesses a highly conserved C-terminal cysteine-rich domain in Saccharomyces cerevisiae. Mutations in some of its cysteine codons display a lethal phenotype, which demonstrates an essential function of this domain. The thermosensitive mutant pol3-13, in which a serine replaces a cysteine of this domain, exhibits a range of defects in DNA repair, such as hypersensitivity to different DNA-damaging agents and deficiency for induced mutagenesis and for recombination. These phenotypes are observed at 24°, a temperature at which DNA replication is almost normal; this differentiates the functions of POL3 in DNA repair and DNA replication. Since spontaneous mutagenesis and spontaneous recombination are efficient in pol3-13, we propose that POL3 plays an important role in DNA repair after irradiation, particularly in the error-prone and recombinational pathways. Extragenic suppressors of pol3-13 are allelic to sdp5-1, previously identified as an extragenic suppressor of pol3-11. SDP5, which is identical to HYS2, encodes a protein homologous to the p50 subunit of bovine and human DNA polymerase δ. SDP5 is most probably the p55 subunit of Polδ of S. cerevisiae and seems to be associated with the catalytic subunit for both DNA replication and DNA repair.