Force-induced melting of DNA—evidence for peeling and internal melting from force spectra on short synthetic duplex sequences

Overstretching of DNA occurs at about 60–70 pN when a torsionally unconstrained double-stranded DNA molecule is stretched by its ends. During the transition, the contour length increases by up to 70% without complete strand dissociation. Three mechanisms are thought to be involved: force-induced melting into single-stranded DNA where either one or both strands carry the tension, or a B-to-S transition into a longer, still base-paired conformation. We stretch sequence-designed oligonucleotides in an effort to isolate the three processes, focusing on force-induced melting. By introducing site-specific inter-strand cross-links in one or both ends of a 64 bp AT-rich duplex we could repeatedly follow the two melting processes at 5 mM and 1 M monovalent salt. We find that when one end is sealed the AT-rich sequence undergoes peeling exhibiting hysteresis at low and high salt. When both ends are sealed the AT sequence instead undergoes internal melting. Thirdly, the peeling melting is studied in a composite oligonucleotide where the same AT-rich sequence is concatenated to a GC-rich sequence known to undergo a B-to-S transition rather than melting. The construct then first melts in the AT-rich part followed at higher forces by a B-to-S transition in the GC-part, indicating that DNA overstretching modes are additive.     

The Customer Isn't Always Right—Conservation and Animal Welfare Implications of the Increasing Demand for Wildlife Tourism

Tourism accounts for 9% of global GDP and comprises 1.1 billion tourist arrivals per annum. Visits to wildlife tourist attractions (WTAs) may account for 20–40% of global tourism, but no studies have audited the diversity of WTAs and their impacts on the conservation status and welfare of subject animals. We scored these impacts for 24 types of WTA, visited by 3.6–6 million tourists per year, and compared our scores to tourists’ feedback on TripAdvisor. Six WTA types (impacting 1,500–13,000 individual animals) had net positive conservation/welfare impacts, but 14 (120,000–340,000 individuals) had negative conservation impacts and 18 (230,000–550,000 individuals) had negative welfare impacts. Despite these figures only 7.8% of all tourist feedback on these WTAs was negative due to conservation/welfare concerns. We demonstrate that WTAs have substantial negative effects that are unrecognised by the majority of tourists, suggesting an urgent need for tourist education and regulation of WTAs worldwide.     

On the cultivation of free-living marine and estuarine nematodes

Although a large body of literature exists on the systematics and ecology of free-living marine and brackish-water nematodes, key questions on the nature and magnitude of interactions between nematodes and other organisms in the benthos remain unanswered. Relatively few authors have investigated live nematodes in food web studies or in experiments dealing with the nematodes’ response to a varying environment. It is mainly for the latter purpose that attempts have been made to maintain, rear and cultivate selected species. This paper describes the methodology used for the maintenance, rearing, and eventual permanent agnotobiotic cultivation of a variety of estuarine nematodes. Spot plates, where small samples of sediment or macrophyte material are inoculated on a sloppy agar layer, have been used for the purpose of maintenance and initial cultivation. Those species that reproduce on spot plates are then selected for monospecific cultivation on agar layers with different nutrient enrichments and with micro-organisms cotransferred from the spot plates as food. Mixtures of bacto and nutrient agar prepared in artificial seawater were specifically suitable for the xenic cultivation of nine bacterivorous and, when supplied with Erdschreiber nutrients, two algivorous/bacterivorous nematode species. Up to three generations of five other nematode species have been reared under laboratory conditions, and several more were kept alive and active for variable periods of time on agar. Generation times observed on spot plates forAdoncholaimus fuscus andOncholaimus oxyuris were substantially shorter than previously published estimates and suggest a correspondingly higher predatory and scavenging potency for these and related enoplids. A procedure for the long-term storage of nematodes at −80°C with glycerol as a cryoprotectant was successfully used forDiplolaimella dievengatensis, Panagrolaimus sp. 1, andPellioditis marina, but not forDiplolaimelloides meyli. The authors have also summarized the existing literature on the cultivation of marine and brackish-water nematodes. Continuous cultivation appears to have been successful mainly for Aufwuchs and epiphytic nematodes; only few sediment-dwellers have been established in permanent culture. Of only just over 30 species that have ever been cultivated, more than half belong to one family (Monhysteridae) and three are Rhabditida, an order poorly represented in the marine environment. Four species have been grown in monoxenic and one in axenic culture, the latter though with limited success. It is concluded that our understanding of the basic nutritional requirements of marine nematodes is as yet insufficient, and that the culture techniques which have so far mainly deployed agar or liquid substrates, while being suitable for the cultivation of Aufwuchs and epiphytic nematodes, do not accurately enough mimic gradients specific of the natural habitat of many sediment-dwellers.     

The role a botanical institute can play in the conservation of the terrestrial biodiversity in a developing country

The need to integratein situ conservation into the planning process is outlined, and the importance of vegetation survey to determine conservation priorities and to identify areas suitable forin situ conservation is stressed. A case is presented, drawing on experience gained in Zimbabwe, of how a botanical institute can become an integral part of biological conservation. The institute should consist of a herbarium, a botanical garden, a gene bank and a vegetation survey unit. The function of each section, how they interlink, and how they can be integrated are discussed.     

Detection of a C-insertion polymorphism within the human tumor necrosis factor alpha (TNFA) gene

We have identified a C-insertion polymorphism in the 5'UTR of the first exon of the human tumor necrosis factor alpha (TNFA) gene. TNFA is a cytokine that plays an important role in the inflammatory response.     

Experiments with artificial nests provide evidence for ant community stratification and nest site limitation in a tropical forest

Ants are dominant in tropical forests and many species nest in hollow cavities. The manner in which species are vertically stratified in these complex habitats is not known, with lack of nest sites being proposed to limit ant populations. Here, we assess ant community stratification and nest site limitation in a lowland rainforest in New Guinea using experimental addition of artificial bamboo nests of two cavity sizes (small: ~12 mm large: ~32 mm diameter) placed at ground level, in the understorey, and in the canopy. We also conducted a pilot experiment to test the utility of nest translocation. Nests were checked for occupancy after 10 weeks and half of the occupied nests were then translocated between forest plots, while keeping same vertical position. Occupancy of small nests was much higher in the understorey and canopy than at ground level (~75% vs. ~25%). Translocation was successful, as a majority of nests was inhabited by the same species before and after translocation and there was no impact of translocation to a different plot compared to the control, except for a reduction in colony size at ground level. Our experiment demonstrates a vertical stratification in community composition of ants nesting in hollow dead cavities and shows that these ants are more nest site limited in the higher strata than at ground level. Use of small artificial cavities has great potential for future experimental studies, especially for those focused on arboreal ants, as occupancy is high and translocation does not negatively affect their colony size. Abstract in Tok Pisin is available with online material.     

Retrograde Traffic Out of the Yeast Vacuole to the TGN Occurs via the Prevacuolar/Endosomal Compartment

A large number of trafficking steps occur between the last compartment of the Golgi apparatus (TGN) and the vacuole of the yeast Saccharomyces cerevisiae. To date, two intracellular routes from the TGN to the vacuole have been identified. Carboxypeptidase Y (CPY) travels through a prevacuolar/endosomal compartment (PVC), and subsequently on to the vacuole, while alkaline phosphatase (ALP) bypasses this compartment to reach the same organelle. Proteins resident to the TGN achieve their localization despite a continuous flux of traffic by continually being retrieved from the distal PVC by virtue of an aromatic amino acid–containing sorting motif. In this study we report that a hybrid protein based on ALP and containing this retrieval motif reaches the PVC not by following the CPY sorting pathway, but instead by signal-dependent retrograde transport from the vacuole, an organelle previously thought of as a terminal compartment. In addition, we show that a mutation in VAC7, a gene previously identified as being required for vacuolar inheritance, blocks this trafficking step. Finally we show that Vti1p, a v-SNARE required for the delivery of both CPY and ALP to the vacuole, uses retrograde transport out of the vacuole as part of its normal cellular itinerary.