Efficient reversal of phiC31 integrase recombination in mammalian cells

Over the past decade, the integrase enzyme from phage phiC31 has proven to be a useful genome engineering tool in a wide variety of species, including mammalian cells. The enzyme efficiently mediates recombination between two distinct sequences, attP and attB, producing recombinant product sites, attL and attR. The reaction proceeds exclusively in a unidirectional manner, because integrase is unable to synapse attL and attR. To date, use of phiC31 integrase has been limited to attP × attB recombination. The factor needed for the reverse reaction – the excisionase or recombination directionality factor (RDF) – was identified recently and shown to function in vitro and in bacterial cells. To determine whether the phiC31 RDF could also function in mammalian cells, we cloned and tested several vectors that permit assessment of phiC31 RDF activity in mammalian environments. In the human and mouse cell lines tested (HeLa, HEK293, and NIH3T3), we observed robust RDF activity, using plasmid and/or genomic assays. This work is the first to demonstrate attL–attR serine integrase activity in mammalian cells and validates phiC31 RDF as a new tool that will enable future studies to take advantage of phiC31 integrase recombination in the forward or reverse direction.     

Restoration of native vegetation following exclosure establishment on communal grazing lands in Tigray,Ethiopia

Questions: Is plant species richness, diversity and above‐ground standing biomass enhanced after establishing exclosures on communal grazing lands? What factors influence the effectiveness of exclosures to restore degraded native vegetation in Tigray, Ethiopia? Location: Northern Ethiopia. Methods: We used a space‐for‐time substitution approach to detect changes in plant species richness, diversity and above‐ground standing biomass after conversion of communal grazing lands to exclosures. We selected replicated (n=3) 5‐, 10‐, 15‐ and 20‐year‐old exclosures and paired each exclosure with an adjacent communal grazing land to ensure that soil and terrain conditions were as similar as possible among each pair. Results: All exclosures displayed higher plant species richness, diversity and biomass than the communal grazing lands. Differences in plant species richness and biomass between an exclosure age and adjacent communal grazing land were higher in oldest than in youngest exclosures. In exclosures, much of the variability in plant species composition and biomass was explained by a combination of edaphic (total nitrogen, phosphorus, texture and soil pH) and site (precipitation and altitude) variables (R²=0.72–0.82). Edaphic and site variables also explained much of the variability in plant species composition in communal grazing lands (R²=0.76–0.82). Our study shows that all exclosures are at an early stage of succession. The increase in economically important indigenous shrub and tree species with exclosure age suggests that, with time, a valuable afromontane forest may develop. Conclusions: Establishment of exclosures on communal grazing lands is a viable option to restore degraded native vegetation. However, before expanding exclosures, the ecological consequences of additional exclosures should be investigated as further expansion of exclosures could increase grazing pressure on remaining grazing areas. Furthermore, consideration of edaphic and site variables will help optimize selection of areas for establishment of exclosures and enhance natural regeneration in exclosures in the future.     

Analysing the effect of movement on local survival: a new method with an application to a spatially structured population of the arboreal gecko Gehyra variegata

Mortality during movement between habitat patches is the most obvious cost of dispersal, but rarely it has been demonstrated empirically. An approach is presented, which uses capture–mark–recapture data of an arboreal gecko species to determine the effect of individual movement on local survival in a spatially structured population. Because capture–mark–recapture data are widely available for a range of animal species, it should be possible to extend their application to other species. The method is based on the assumption that the tendency to be a territorial animal or to be a floating animal is fixed during the study period. The advantage of our approach is that only one additional parameter has to be estimated for describing movement risks. We further tested the power of our approach to detect an association of movement and mortality with simulated capture histories. The study revealed a strong negative effect of movement on local survival. Hence, animals that moved more often between trees had a lower survival rate. Interestingly, the mean movement rate for males was significantly higher than for females, which should lead to a biased sex ratio towards females in the population. As there was an even sex ratio in the population, we discuss not mutually exclusive explanations for this finding like differences in emigration rates between sexes, differences in survival rates between sexes, or a skewed sex ratio in offspring.     

Movements of wintering surf scoters: predator responses to different prey landscapes

The distribution of predators is widely recognized to be intimately linked to the distribution of their prey. Foraging theory suggests that predators will modify their behaviors, including movements, to optimize net energy intake when faced with variation in prey attributes or abundance. While many studies have documented changes in movement patterns of animals in response to temporal changes in food, very few have contrasted movements of a single predator species naturally occurring in dramatically different prey landscapes. We documented variation in the winter movements, foraging range size, site fidelity, and distribution patterns of a molluscivorous sea duck, the surf scoter (Melanitta perspicillata), in two areas of coastal British Columbia with very different shellfish prey features. Baynes Sound has extensive tidal flats with abundant clams, which are high-quality and temporally stable prey for scoters. Malaspina Inlet is a rocky fjord-like inlet where scoters consume mussels that are superabundant and easily accessible in some patches but are heavily depleted over the course of winter. We used radio telemetry to track surf scoter movements in both areas and found that in the clam habitats of Baynes Sound, surf scoters exhibited limited movement, small winter ranges, strong foraging site fidelity, and very consistent distribution patterns. By contrast, in mussel habitats in the Malaspina Inlet, surf scoters displayed more movement, larger ranges, little fidelity to specific foraging sites, and more variable distribution patterns. We conclude that features associated with the different prey types, particularly the higher depletion rates of mussels, strongly influenced seasonal space use patterns. These findings are consistent with foraging theory and confirm that predator behavior, specifically movements, is environmentally mediated.     

Molecular identification and properties of a light-insensitive rice catalase-B expressed in E. coli

Catalase plays a central role in plant stress responses but is highly susceptible to photoinhibition. A rice catalase-B protein avoiding photoinhibition was developed by mutagenesis of specific amino acids: Leu-189 to Trp-189 and His-225 to Thr-225 and then recombinantly expressed in E. coli. In addition, the site specific mutation also induced 2–2.5-fold increase in enzyme velocity with high affinity for its substrate and showed nearly a 3-fold lower K _m than the wild protein. These characteristic of mutated rice catalase-B is highly promising in transgenic research to increase plant productivity under stress conditions.     

Rodent foraging is affected by indirect, but not by direct, cues of predation risk

We used foraging trays to determine whether oldfield mice, Peromyscuspolionotus, altered foraging in response to direct cues of predationrisk (urine of native and nonnative predators) and indirectcues of predation risk (foraging microhabitat, precipitation,and moon illumination). The proportion of seeds remaining ineach tray (a measure of the giving-up density [GUD]) was usedto measure risk perceived by mice. Mice did not alter theirGUD when presented with cues of native predators (bobcats, Lynxrufus, and red foxes, Vulpes vulpes), recently introduced predators(coyotes, Canis latrans), nonnative predators (ocelots, Leoparduspardalis), a native herbivore (white-tailed deer, Odocoileusvirginianus), or a water control. Rather, GUD was related tomicrohabitat: rodents removed more seeds from foraging trayssheltered beneath vegetative cover compared with exposed traysoutside of cover. Rodents also removed more seeds during nightswith precipitation and when moon illumination was low. Our resultssuggest that P. polionotus used indirect cues rather than directcues to assess risk of vertebrate predation. Indirect cues maybe more reliable than are direct scent cues for estimating riskfrom multiple vertebrate predators that present the most riskin open environments.     

Barogali et l’Oued Doure. Deux gisements représentatifs du Paléolithique ancien en République de Djibouti

In the Republic of Djibouti, surveys and excavations, carried out from 1985 to 1992, confirmed the presence of the pre-Acheulean (Oldowan) and Acheulean sites in the country. Three seasons of excavations (1985-1987 in the Gobaad Basin, have unearthed in a hardened compact clay strata of an ancient marshland dating to the Lower Pleistocene, the fossilized skeletal remains of an Elephas recki ileretensis. Numerous stone tools have been gathered with the bones. The E.S.R. dating the elephant’s lower third molar gave a date between 1,.6 and 1,.3 MY that would confirm its paleontological grouping and the membership of this butchery site to the Oldowan period. The animal appeared to have been lying on its left side. The cranial roof had been separated from the calvarium, perhaps to get at the brain; but the skull remains in anatomic connection with the tusks. The jaw (mandible) seems to have been broken to extract the tongue. Hominids, perhaps Homo ergaster, knapped tools from a nearly outcrop of poor quality lava. The tools were specifically adapted to their needs, such as scraping, chopping and scattering the bones. The site has yielded 569 artifacts: utilized material and hammerstones (121); pebble tools (32); cores (14); “debitage” products (366); retouched flakes (36). Artifacts are rarely retouched and often broken. Five different types of choppers have been classified. The polyedrons and one bola make up 22% of the pebble tools. The cores are divided into unipolar, centripetal and polyhedrical types. In another site, Haïdalo, an almost complete skeleton of an Elephas recki recki in anatomical connection and without any sign of predation, has been found at eight kilometers from Barogali. During surveys in the Ali Sabîh region (1990-1992) seven sectors have been discovered and prospected in the Oued Doure Basin. On the surface area and also in situ into some little pits, 345 rhiolitic Acheulean artifacts have been found, near rhyolitic outcrop. These artifacts are generally large. The choppers (18) can be dividended into 2 sets : side choppers (55%) and end choppers (27%), often with a bifacial cutting edge. There is only one polyedron, but we have found eight heavy scrapers. The Acheulean group is important (43 tools). The bifaces are varied and there are also a few cleavers and picks. Cores are numerous (92) and Levallois cores are preponderant (45%). We find also centripetal cores (27%) and so unipolar, bipolar and polyhedral cores. Tools made of flakes (118) are numerous: scrapers are typologically diversified. Some of them have a double utilization. Notch tools, denticulate tools are presents but also end scrapers, burin, borer, back knifes and scantily retouched flakes. The characters of this lithic material, large cores and big flakes, large bifaces of various types, cleavers and retouched flakes, indicates that they are Acheulean products. So, the Doure Site can be placed in the Middle / Upper Acheulean transition.     

An extension of presence/absence coefficients to abundance data: a new look at absence

Abstract. Alternative community analyses, based on quantitative and presence/absence data, are comparable logically if the data type is the only factor responsible for differences among results. For presence/absence indices that consider mutual absences, no quantitative alternatives are known. To facilitate such comparisons, a new family of similarity coefficients is proposed for abundance data. Formally, this extension is achieved by generalizing the four cells of the usual 2 × 2 contingency table to the quantitative case. This implies an expanded meaning of absence: for a given species at a given site it is understood as the difference between the actual value and the maximum detected in the entire study. The correspondence between 10 presence/absence coefficients and their quantitative counterparts is evaluated by graphical comparisons based on artificial data. The behaviour of the new functions is also examined using field data representing post‐fire regeneration processes in grasslands and a chronosequence pertaining to forest regeneration after clear‐cut. The examples suggest that the new coefficients are most informative for data sets with low beta‐diversity and temporal background changes.     

Tracing the invasion characteristics of the yellow-legged hornet,Vespa velutina nigrithorax (Hymenoptera: Vespidae), in Korea using newly detected variable mitochondrial DNA sequences

The yellow-legged hornet, Vespa velutina nigrithorax (Hymenoptera: Vespidae), invaded South Korea in 2003 through Busan metropolitan city, which is located in the southeast region of the country. Previous studies aiming to trace the origin of V. velutina in Korea used a portion of mitochondrial (mt) COI and detected a single haplotype common to the site of origin. However, no subsequent study on invasive dynamics such as additional entry and/or another site of entry has been performed. In this study, segments of mt COI, CytB, and lrRNA were sequenced from 238 individuals collected in 11 Korean and two Japanese localities, but no variation in each gene was observed. Thus, we developed two intergenic spacer (IGS) sequences from the publicly available mt genome of V. velutina, which provided substantially increased variability (i.e., 19 haplotypes with 1.74% maximum sequence divergence in 1,129–1,146-bp-long concatenated sequences). Population genetic analyses using the concatenated sequences unexpectedly provided higher genetic diversity estimates in the northwest and southwest regions, both of which also harbor international cargo ports, than in the southeast region, in which Busan is located. Furthermore, this genetic result was roughly concordant with our questionnaire survey demonstrating that V. velutina was observed in apiaries located in the northwest and southwest regions up to 2012, when there was no reported prevalent distribution of the hornet beyond the southeast region. These results collectively suggest that the northwest and southwest regions of Korea are additional sites of V. velutina entry to the country, independent from the southeast region origin.