RNA interference: from an ancient mechanism to a state of the art therapeutic application?

Now that the sequencing of many genomes has been completed, the basic challenges are finding the genes and predicting their functions. Up until now, a large information gap has existed between the knowledge of genome sequence and our knowledge of protein function. The assessment of gene function may be performed using the tools of reverse genetics, including knock-out mice, antisense oligomers, aptamers, and ribozymes. These approaches have been superseded by RNA interference (RNAi), which exhibits much more potency for the investigation of protein function than the techniques listed above. As already known some years ago, RNAi is based on an ancient anti-viral defense mechanism in lower eukaryotes. It is induced by double-stranded RNA and its processing to 21–23 nt small interfering RNAs (siRNAs), which cause the degradation of homologous endogenous mRNA. The way RNAi works has still to be determined, but it already serves as a first-choice approach to generate loss-of-function phenotypes among a broad variety of eukaryotic species, such as nematodes, flies, plants, fungi and mammals. RNAi also represents an extremely powerful tool, becoming a therapeutic approach to curing infectious diseases originated by viral or parasitic invasion. In this review we present the current view of how RNAi works in different eukaryotic species and its high potential for functional genomics and in rational drug design.     

'Molecular farming' of antibodies in plants

'Molecular farming' is the production of valuable recombinant proteins in transgenic organisms on an agricultural scale. While plants have long been used as a source of medicinal compounds, molecular farming represents a novel source of molecular medicines, such as plasma proteins, enzymes, growth factors, vaccines and recombinant antibodies, whose medical benefits are understood at a molecular level. Until recently, the broad use of molecular medicines was limited because of the difficulty in producing these proteins outside animals or animal cell culture. The application of molecular biology and plant biotechnology in the 1990s showed that many molecular medicines or vaccines could be synthesised in plants and this technology is termed 'molecular farming'. It results in pharmaceuticals that are safer, easier to produce and less expensive than those produced in animals or microbial culture. An advantage of molecular farming lies in the ability to perform protein production on a massive scale using hectares of cultivated plants. These plants can then be harvested and transported using the agricultural infrastructure. Thus, molecular farming allows rapid progress from genetic engineering to crop production, and new cash crops producing recombinant proteins are already being commercially exploited. We speculate that as functional genomics teaches us more about the nature of disease, molecular farming will produce many of the protein therapeutics that can remedy it.     

Mark-recapture estimators for dual frame population size of prominent nesting structures: the effect of uncertain detection probability

The combined mark-recapture and line transect sampling methodology proposed by Alpizar-Jara and Pollock [Journal of Environmental and Ecological Statistics, 3(4), 311–327, 1996; In Marine Mammal Survey and Assessment Methods Symposium. G.W. Garner, S.C. Amstrup, J.L. Laake, B.F.J. Manly, L.L. McDonald, and D.C. Robertson (Eds.), A.A. Balkema, Rotterdam, Netherlands, pp. 99–114, 1999] is used to illustrate the estimation of population size for populations with prominent nesting structures (i.e., bald eagle nests). In the context of a bald eagle population, the number of nests in a list frame corresponds to a pre-marked sample of nests, and an area frame corresponds to a set of transect strips that could be regularly monitored. Unlike previous methods based on dual frame methodology using the screening estimator [Haines and Pollock (Journal of Environmental and Ecological Statistics, 5, 245–256, 1998a; Survey Methodology, 24(1), 79–88, 1998b)], we no longer need to assume that the area frame is complete (i.e., all the nests in the sampled sites do not need to be seen). One may use line transect sampling to estimate the probability of detection in a sampled area. Combining information from list and area frames provides more efficient estimators than those obtained by using data from only one frame. We derive an estimator for detection probability and generalize the screening estimator. A simulation study is carried out to compare the performance of the Chapman modification of the Lincoln–Petersen estimator to the screening estimator. Simulation results show that although the Chapman estimator is generally less precise than the screening estimator, the latter can be severely biased in presence of uncertain detection. The screening estimator outperforms the Chapman estimator in terms of mean squared error when detection probability is near 1 wheareas the Chapman estimator outperforms the screening estimator when detection probability is lower than a certain threshold value depending on particular scenarios.     

Gastroliths in<Emphasis Type="Italic"> Yanornis</Emphasis>: an indication of the earliest radical diet-switching and gizzard plasticity in the lineage leading to living birds?

Yanornis martini is an Early Cretaceous basal ornithurine bird. Its fish-eating diet was previously recognized from a discrete mass of disarticulated fish remains discovered in its abdominal region. A new complete and articulated specimen of Yanornis martini preserves abundant in-situ gastroliths such as have been associated with a herbivorous diet. We suggest that the occurrence of gastroliths in this specimen, fish remains in a second, and the lack of gastroliths in three others, is consistent with diet-switching in Yanornis martini. Incompatibility of the preserved data with explanations of the grit as an artifact of preservation or result of accidental ingestion is discussed. This discovery indicates the earliest presence of intermittent diet change (and associated gizzard plasticity) observed in extant birds seasonally and in response to changes in available food sources.     

Scale-dependent habitat selection in migratory frugivorous passerines

Frugivorous migrants may select fruit-rich habitats en route to attain high food rewards, yet their stopover behavior may also be shaped by other considerations, such as predation risk. During 1996–2001 we investigated autumn stopover habitat use of three Sylvia warblers (sylviids; S. hortensis, S. atricapilla and S. curruca) and three Turdidae chats (turdids; Cercotrichas galactotes, Oenanthe hispanica and Phoenicurus phoenicurus) in planted groves of the fruiting tree Pistacia atlantica in Lahav Forest, Israel, which is located at the edge of a desert. We used fecal analysis, a constant-effort trapping scheme and field observations to estimate the extent of frugivory, and bird habitat and microhabitat selection with regard to natural fruit and foliage densities. We also measured bird microhabitat selection in a set of fruit-manipulated trees. We trapped a total of 2,357 birds during the course of the study. Although sylviids exhibited higher frugivory level than turdids, both species groups exhibited a similar significantly positive correlation between bird and fruit densities at the habitat scale. However, at the microhabitat scale, sylviids selected densely foliated trees, whilst turdids were randomly distributed among trees. Our findings suggest that both species groups selected fruit-rich stopover habitats to take advantage of the high food availability before the demanding migration journey. No other mechanism except predation avoidance can explain the sylviids microhabitat selection; the migrants used foliage cover to reduce bird detectability by raptors. We conclude that en route passerines may use staging habitats in a sophisticated manner, by adopting scale-related behavior with regard to the availability of food and refuge cover.     

Genetic variation in natural honeybee populations,<Emphasis Type="Italic"> Apis mellifera capensis</Emphasis>

Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.     

Factors inducing the intense burrowing activity of the red-swamp crayfish,<Emphasis Type="Italic"> Procambarus clarkii</Emphasis>, an invasive species

The burrowing activity of the invasive red-swamp crayfish, Procambarus clarkii, was studied along a 25-m-long transect in an irrigation ditch system in Italy. Our objective was to understand the factors inducing this species intense digging, which can result in bank collapse and consequently in severe damage to both agricultural fields and natural ecosystems. Burrow morphology and position, together with their occupancy by crayfish and digging, were recorded once every 6 h for 10 consecutive days. The majority of burrows were simple, although a few had a chimney and were constructed at a farther distance from the water surface than simple burrows. Burrow occupancy and digging, together with their plugged/unplugged status, were constant throughout a 24-h cycle and were not related to any abiotic parameter of the habitat. Crayfish occupied and dug a burrow for a relatively short time (6 h on average). Once abandoned, old burrows were rarely reoccupied and often collapsed, while crayfish excavated new ones. As a result, the overall number of burrows increased. This massive use of banks by P. clarkii seems to be related to soil composition and humidity, which favour crayfish digging but also cause the easy collapse of burrows.     

Early maps as stepping stones for the reconstruction of historic ecological conditions and biota

We reconstructed the flora of a European region at a historical point in time from historical topographical maps that contain rather precise information about the condition and composition of habitats. The ecological information obtained from these maps can be enriched through the potential of broadly diversified archival information. This study is confined to grassland communities. Considerations in terms of phytosociology make historical lists of plant species a good starting point for the reconstruction of grassland communities. The combination of historical and scientific methods proves suitable for reconstructing specific historical environmental conditions. Taking into account the frequency of relevant historical sources in European archives as well as in archives abroad, this approach claims for far-reaching application to ecosystem restoration matters, especially if ecological information from natural sources is missing.     

Silvery mole-rats (<Emphasis Type="Italic">Heliophobius argenteocinereus</Emphasis>, Bathyergidae) change their burrow architecture seasonally

Little is known about seasonal changes in burrowing activity and burrow architecture in subterranean African mole-rats (Bathyergidae, Rodentia). The solitary genus Heliophobius is the least known genus of this family. We examined burrow systems of the silvery mole-rat ( Heliophobius argenteocinereus) in Malawi in two periods of the dry season. Burrow pattern was influenced by the time of the year, becoming more reticulated at the peak of the dry season when soil was dry and hard. Overall digging activity did not cease during the dry season; yet burrowing strategy changed and the soil was deposited in tunnels rather than transported to mounds. The length of burrow systems was correlated with the body mass of the respective occupants. In spite of their solitary habits – and contrary to the prediction of the aridity food-distribution hypothesis – silvery mole-rats are able to occupy poor habitats with low food supply.     

Assessment of global industrial-age anthropogenic arsenic contamination

Arsenic, a carcinogenic trace element, threatens not only the health of millions of humans and other living organisms, but also global sustainability. We present here, for the first time, the global industrial-age cumulative anthropogenic arsenic production and its potential accumulation and risks in the environment. In 2000, the world cumulative industrial-age anthropogenic arsenic production was 4.53 million tonnes. The world-wide coal and petroleum industries accounted for 46% of global annual gross arsenic production, and their overall contribution to industrial-age gross arsenic production was 27% in 2000. Global industrial-age anthropogenic As sources (as As cumulative production) follow the order: As mining production >As generated from coal >As generated from petroleum. The potential industrial-age anthropogenic arsenic input in world arable surface in 2000 was 2.18 mg arsenic kg^–1, which is 1.2 times that in the lithosphere. The development of substitute materials for arsenic applications in the agricultural and forestry industries and controls of arsenic emissions from the coal industry may be possible strategies to significantly decrease arsenic pollution sources and dissipation rates into the environment.