Hidden degrees of freedom in aperiodic materials

Numerous crystalline materials, including those of bioorganic origin, comprise incommensurate sublattices whose mutual arrangement is described in a superspace framework exceeding three dimensions. We report direct observation by neutron diffraction of superspace symmetry breaking in a solid-solid phase transition of an incommensurate host-guest system: the channel inclusion compound of nonadecane/urea. Strikingly, this phase transition generates a unit cell doubling that concerns only the modulation of one substructure by the other-an internal variable available only in superspace. This unanticipated pathway for degrees of freedom to rearrange leads to a second phase transition, which again is controlled by the higher dimensionality of superspace. These results reveal nature's capacity to explore the increased number of phases allowed in aperiodic crystals.     

Recombination and the nature of bacterial speciation

Genetic surveys reveal the diversity of bacteria and lead to the questioning of species concepts used to categorize bacteria. One difficulty in defining bacterial species arises from the high rates of recombination that results in the transfer of DNA between relatively distantly related bacteria. Barriers to this process, which could be used to define species naturally, are not apparent. Here, we review conceptual models of bacterial speciation and describe our computer simulations of speciation. Our findings suggest that the rate of recombination and its relation to genetic divergence have a strong influence on outcomes. We propose that a distinction be made between clonal divergence and sexual speciation. Hence, to make sense of bacterial diversity, we need data not only from genetic surveys but also from experimental determination of selection pressures and recombination rates and from theoretical models.     

Are ricefields a good alternative to natural marshes for waterbird communities in the Camargue, southern France?

Rice cultivation has frequently been suggested to provide an important wetland habitat for waterbirds. However, in contrast to most other regions of the Mediterranean, the Camargue still has a substantial amount of surface area of natural marshes. Thus, we compared the abundance, species richness, and community composition of waterbirds in ricefields and natural marshes of the Camargue, during a one-year study. Based on surveys conducted at 4–7 day intervals in 1997–1998, our results suggest that natural marshes had substantially greater abundance of waterbirds, with ca. 99% of the individuals having been observed in natural marshes. Estimates of species richness and associated parameters further indicated that ricefields were clearly less rich than natural marshes. Although our results were rather striking for the Camargue, they may not be applicable to other regions because of the relatively high availability of natural marshes and differences in management of ricefields.     

Changes in physicochemical characteristics and volatile constituents of yellow- and white-fleshed nectarines during maturation and artificial ripening

Changes in the volatile composition during maturation and artificial ripening of yellow-fleshed nectarines were investigated by means of GC-FID and GC-MS over three years (1999-2001). Unripe and commercially ripe fruits were placed in ripening chambers until complete ripening and compared to tree-ripe nectarines. Firmness, weight, soluble solids (SS), titratable acidity (TA), SS/TA ratio, organic acids, and sugars were also determined. Furthermore, the tree-ripe and artificially ripened yellow-fleshed nectarines were subjected to sensory analysis by a taste panel. In 2001, a similar experiment on white-fleshed nectarines (cv. Vermeil) was performed to compare with the results obtained on yellow-fleshed nectarines. Levels of volatiles compounds, in particular, lactones and C(13) norisoprenoids, were found to be the same or higher in the artificially ripened nectarines compared with the tree-ripe nectarines. In addition, no significant difference was observed for sweetness, sourness, and the intensities of "peach odors" or "peach aroma" in the sensory analysis between the tree-ripe samples and the artificially ripened nectarines. However, in the latter the levels of SS and the SS/TA ratio were very close to those observed in the initial unripe samples and significantly lower than those observed in tree-ripe nectarines.     

A high-throughput DNA extraction method for barley seed

A non-destructive, quick DNA extraction method for barley seed is described. The method is simple and consists of drilling out a sample from the seed, adding sodium hydroxide, heating in a microwave oven and neutralizing with Tris-HCl. The seed DNA extract can be used directly for PCR with extra cycles added to the PCR programme compared to PCR programmes used for leaf extracts. This protocol was developed in particular for a micro satellite marker genetically linked to barley yellow mosaic virus resistance, but it can be applied toother markers of interest for barley breeding. The quick seed extraction protocol makes it possible to handle thousands of samples per day. Extraction of DNA from seed also facilitates transfer of plant material compared to the long-distance transfer of leaf samples. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evaluation of the in vivo anthelmintic properties of Mitragyna inermis (Willd.) as a livestock dewormer against parasitic hematophagous worm Haemonchus contortus infections in different breeds of lambs

Tropical Animal Health and Production - Gastrointestinal (GI) nematodes remain a major constraint on livestock production throughout the world. This study assessed the in vivo efficacy of the...     

Genetic comparison of experimental farmed strains and wild Icelandic populations of Atlantic cod (Gadus morhua L.)

Microsatellite DNA loci and the Pantophysin locus (Pan I) were used to investigate levels of genetic diversity within farmed strains of Atlantic cod Gadus morhua and to compare them with the wild source population. A total of 282 farmed samples originating from a spawning ground off the south-west coast of Iceland were sampled in the years 2002 and 2003, and 258 wild cod were collected at the same spawning ground in the same years. The farmed strains exhibited a lower mean number of alleles and allelic diversity than the wild samples at the microsatellite loci. Significant differences were observed between wild and farmed samples both in allele and genotype frequencies at the Pan I locus. We argue that the genetic divergence of wild and farmed samples of Atlantic cod may be due to a small number of effective founding breeders contributing to the genetic variation of the farmed strains, inducing a reduction in allelic diversity. We discuss the potential effect of breeding practices on the genetic diversity of Atlantic cod.     

Hemocyte characteristics in families of oysters, Crassostrea gigas, selected for differential survival during summer and reared in three sites

High variability among individuals is often encountered when hemocyte characteristics are measured in bivalves. Such variability is suspected to result partly from genetic factors. In this study, hemocyte characteristics of six families of Crassostrea gigas were compared by flow cytometry at one sampling date in October 2001. These families were obtained from a nested, half-sibling cross design, and reared from July to October 2001 at three sites distributed along the French Atlantic coast from north to south: Baie des Veys (Normandy), Rivière d'Auray (Brittany) and Ronce (Marennes-oléron Basin, Poitou Charentes).

Among the 15 measured hemocyte characteristics, production of reactive oxygen species (ROS) of untreated hemocytes (maintained in filtered sterile seawater) and treated hemocytes (zymosan at 20 particles per hemocyte, and with Vibrio sp. S322 at 50 bacteria per hemocyte) was the most notable differences between families. This supports the existence of a genetic basis, at least partly, for the hemocyte characteristics of oysters, and especially for ROS production.

Among the six families analyzed, three have shown high survival during summer (named as “resistant”, mean mortality 5.2%) and three experienced high mortality during summer (named as “susceptible”, 30.6% mean mortality). Families showing high or low survival to summer mortality had similar hemocyte characteristics, regardless of the environmental conditions or reproductive state. Resistant families were observed to have higher total hemocyte counts and lower production of ROS than susceptible families. Moreover, ROS production of hemocytes from susceptible families was diminished significantly more by pathogenic Vibrio than that of resistant families. However, this study demonstrates also that rearing site strongly affected the hemocyte characteristics of all families of oysters, most notably hemocyte concentration and morphology (size and granularity), production of reactive oxygen species (ROS), and susceptibility to the cytotoxic activity of the pathogenic Vibrio sp. S322 (50 bacteria/hemocyte). Food availability and reproductive state are the most probable explanations for the site differences observed. Finally, it appeared difficult to link oyster survival during summer mortality to hemocyte profiles evaluated at one sampling date; other relevant indicators would probably help explaining oyster survival during summer mortality events.     

Exploring the “last biotic frontier”: Are temperate forest canopies special for saproxylic beetles?

Conserving saproxylic beetles in temperate forests will require a better understanding of habitat requirements. So far, quantitative community studies have rarely considered their vertical requirements. In comparison with the tropical forest canopy, it remains to be seen whether a comparably high level of beetle diversity exists in the temperate forest canopy.We compared saproxylic beetle assemblages at two vertical levels in three temperate French forests. Two datasets originated from emergence traps of pine and oak deadwood substrates (mid-canopy and forest floor branches) in lowland forests. The third compared flying beetle fauna at mid-canopy and understory levels using pairs of flight interception traps in beech-fir mountain forests.Our study provided contrasting results regarding the contribution of each stratum to biodiversity. Whereas higher abundance and species richness were apparent in understory samples in beech-fir stands and in oak branches, no difference for richness - or even the opposite pattern for abundance - was observed in pine branches. A significant inter-strata dissimilarity was revealed in all datasets. Each stratum harbored specialist taxa. Exclusive canopy species accounted for 20-40% of all species. In accordance with dissimilarity partitioning, arboreal saproxylic beetle communities were not just nested subsets of ground assemblages.It is likely that microhabitat requirements, food availability and other non-resource-based factors (microclimate preference, species interactions) drive the stratification of beetle assemblages.Our results lend support (i) to the recommendation of a multi-strata sampling strategy for forest insects and (ii) to management practices in favour of valuable canopy micro-habitats.