Problems of joint display of species and site scores in correspondence analysis

Joint plots of species and site scores in correspondence analysis can be interpreted so that points which are in the same direction from the origin are closely associated. Species and site scores can thus be compared. Within each set of scores the location of points is also meaningful. Owing to the unimodal species response model which can be recovered by the correspondence analysis, the location of the species points in respect to the site points indicates the location of the optimum when direct weighted averages are used. However, when the eigenvalue of the solution is low, very different joint plots are derived when the set which is used for computing the weighted averages for the other set is changed. This makes the interpretation of the between-set proximities in the joint plot vague. Generally, it is not possible to deduce the species composition of a site or sites where a species occurs from the joint plot, although for some pairs of species and sites this is justified. Although the proximity interpretation is not possible in every case, a joint plot display can greatly enhance the interpretation of results.     

Offspring Defence in Relation to Litter Size and Age: Experiment in the Bank vole Clethrionomys glareolus

According to parental investment theory, nest defence activity should be related to the reproductive value of the offspring. Alternative hypotheses suggest that defence activity may, for example, depend upon the conspicuousness of the young. Studies concerning this topic have been carried out almost exclusively on birds and experimental data on the diversity of organisms is lacking. Bank voles Clethrionomys glareolus were used to study the effects of the number and age of offspring upon the pup defence activity of mothers. Male bank voles are infanticidal and thus an adult male was used as a predator. Defence trials were conducted in the laboratory and filmed for subsequent analysis. Litter sizes were divided into three treatment groups: reduced (−2 pups), control (±0 pups) and enlarged (+2 pups). In order to study the effect of offspring age upon maternal defence activity the trials were conducted twice: when the pups were 3 and 8 days old. Defence activity increased with the number of offspring and enlarged litters were most actively defended. This result supports parental investment theory and conclusions drawn by earlier studies of birds. However, in contrast to the conclusions of earlier studies, older offspring were defended less than the younger ones. Whilst new-born pups are totally defenceless against predators their vulnerability decreases as they age. Therefore, we suggest that maternal aggression in female bank voles is related to the value as well as to the vulnerability of the offspring. The validity of this explanation and the determinants of parental investment decisions in small mammals in general deserve further study. This revised version was published online in July 2006 with corrections to the Cover Date.     

The Structure of the NTPase That Powers DNA Packaging into Sulfolobus Turreted Icosahedral Virus 2

Biochemical reactions powered by ATP hydrolysis are fundamental for the movement of molecules and cellular structures. One such reaction is the encapsidation of the double-stranded DNA (dsDNA) genome of an icosahedrally symmetric virus into a preformed procapsid with the help of a genome-translocating NTPase. Such NTPases have been characterized in detail from both RNA and tailed DNA viruses. We present four crystal structures and the biochemical activity of a thermophilic NTPase, B204, from the nontailed, membrane-containing, hyperthermoacidophilic archaeal dsDNA virus Sulfolobus turreted icosahedral virus 2. These are the first structures of a genome-packaging NTPase from a nontailed, dsDNA virus with an archaeal host. The four structures highlight the catalytic cycle of B204, pinpointing the molecular movement between substrate-bound (open) and empty (closed) active sites. The protein is shown to bind both single-stranded and double-stranded nucleic acids and to have an optimum activity at 80°C and pH 4.5. The overall fold of B204 places it in the FtsK-HerA superfamily of P-loop ATPases, whose cellular and viral members have been suggested to share a DNA-translocating mechanism.