The effect of drought on the large mammal populations of Zambezi riverine woodlands

Large mammals were counted in Zambezi alluvial woodlands and on the adjacent ecotone in the north of Mana Pools National Park, Zimbabwe, from April 1981 until October 1989. Densities of all large herbivores on the alluvium in the daytime increased during the dry season. Year-to-year variation was studied by comparing end-of-dry-season densities. Flooding of the Zambezi River, controlled by Kariba Dam 100 km upstream, ceased in 1981 and the densities of all species on the alluvium declined in 1982. Rainfall was low in 1982 and very low in 1983 and 1984. The density of buffalo in the study area declined, owing to high mortality and a change in habitat utilization (buffalo herds spent more time in the south of the park). Densities of other species were high during the drought, but the densities of waterbuck, kudu, eland, bushbuck and warthog declined in 1985. Zebra density declined on the ecotone, but not on the alluvium. The densities of eland and kudu increased in 1986 and 1988, respectively, but the densities of the other species were still low in 1989. Impala density on the alluvium in October was related to rainfall during the preceding wet season and was high in drought years. Elephant density declined after a management cull. Rhinoceros density decreased by > 90% during the 1985/6 wet season, as a result of poaching and captures. The long-term decline in the densities of grazers was probably due primarily to the cessation of flooding by the Zambezi River, rather than to low local rainfall in some years. During the drought, the large grazers (e.g. buffalo) died before the smaller grazers (e.g. warthog). Waterbuck density declined less than the density of other grazers, because waterbuck could cross to vegetated sandbanks in the Zambezi River.     

Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel

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High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

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Design, expression, and characterization of a synthetic human cannabinoid receptor and cannabinoid receptor/ G-protein fusion protein.

We report here the synthesis and characterization of two gene constructs designed to facilitate structure/function studies of the human neuronal cannabinoid receptor, CB1. The first gene, which we call shCB1, is a synthetic gene containing unique restriction sites spaced roughly 50-100 bases apart to facilitate rapid mutagenesis and cloning. A nine amino acid epitope tag (from the rhodopsin C-terminus) is also present in the shCB1 C-terminal tail to enable detection and purification using the monoclonal antibody 1D4. We find that that the shCB1 gene can be transiently expressed in COS cells with yield of approximately 10-15 micro g receptor per 15 cm plate and is wild type like in its ability to bind cannabinoid ligands. Our confocal microscopy studies indicate shCB1 targets to the membrane of HEK293 cells and is internalized in response to agonist. To facilitate functional studies, we also made a chimera in which the C-terminus of shCB1 was fused with the N-terminus of a G-protein alpha subunit, Galphai. The shCB1/Galphai chimera shows agonist stimulated GTPgammaS binding, and thus provides a simplified way to measure agonist induced CB1 activation. Taken together, the shCB1 and shCB1/Galphai gene constructs provide useful tools for biochemical and biophysical examinations of CB1 structure, activation and attenuation.     

Historical demography of common carp estimated from individuals collected from various parts of the world using the pairwise sequentially markovian coalescent approach

The inference of historical demography of a species is helpful for understanding species’ differentiation and its population dynamics. However, such inference has been previously difficult due to the lack of proper analytical methods and availability of genetic data. A recently developed method called Pairwise Sequentially Markovian Coalescent (PSMC) offers the capability for estimation of the trajectories of historical populations over considerable time periods using genomic sequences. In this study, we applied this approach to infer the historical demography of the common carp using samples collected from Europe, Asia and the Americas. Comparison between Asian and European common carp populations showed that the last glacial period starting 100 ka BP likely caused a significant decline in population size of the wild common carp in Europe, while it did not have much of an impact on its counterparts in Asia. This was probably caused by differences in glacial activities in East Asia and Europe, and suggesting a separation of the European and Asian clades before the last glacial maximum. The North American clade which is an invasive population shared a similar demographic history as those from Europe, consistent with the idea that the North American common carp probably had European ancestral origins. Our analysis represents the first reconstruction of the historical population demography of the common carp, which is important to elucidate the separation of European and Asian common carp clades during the Quaternary glaciation, as well as the dispersal of common carp across the world.     

Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNA^Phe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNA^Phe, despite these oxidized residues not being directly implicated in PheRS activity. Here, we solve a 3.6 Å cryo-electron microscopy structure of oxidized S. Typhimurium PheRS. We find that oxidation results in widespread structural rearrangements in the β-subunit editing domain and enlargement of its editing domain. Oxidization also enlarges the phenylalanyl-adenylate binding pocket but to a lesser extent. Together, these changes likely explain why oxidation leads to hyperaccurate editing and decreased misincorporation of tyrosine. Taken together, these results help increase our understanding of the survival of S. Typhimurium during human infection.