A bioluminescence method for direct measurement of phosphodiesterase activity

We have adapted bioluminescence methods to be able to measure phosphodiesterase (PDE) activity in a one-step technique. The method employs a four-enzyme system (PDE, adenylate kinase (AK) using excess CTP instead of ATP as substrate, pyruvate kinase (PK), and firefly luciferase) to generate ATP, with measurement of the concomitant luciferase-light emission. Since AK, PK, and luciferase reactions are coupled to recur in a cyclic manner, AMP recycling maintains a constant rate of ATP formation, proportional to the steady-state AMP concentration. The cycle can be initiated by the PDE reaction that yields AMP. As long as the PDE reaction is rate limiting, the system is effectively at steady state and the bioluminescence kinetics progresses at a constant rate proportional to the PDE activity. In the absence of cAMP and PDE, low concentrations of AMP trigger the AMP cycling, which allows standardizing the system. The sensitivity of the method enables detection of <1 μU (pmol/min) of PDE activity in cell extracts containing 0.25–10 μg protein. Assays utilizing pure enzyme showed that 0.2 mM IBMX completely inhibited PDE activity. This single-step enzyme- and substrate-coupled cyclic-reaction system yields a simplified, sensitive, reproducible, and accurate method for quantifying PDE activities in small biological samples.     

Climate‐driven shifts in the distribution of koala‐browse species from the Last Interglacial to the near future

The koala's Phascolarctos cinereus distribution is currently restricted to eastern and south‐eastern Australia. However, fossil records dating from 70 ± 4 ka (ka = 10³ yr) from south‐western Australia and the Nullarbor Plain are evidence of subpopulation extinctions in the southwest at least after the Last Interglacial (~128–116 ka). We hypothesize that koala sub‐population extinctions resulted from the eastward retraction of the koala's main browse species in response to unsuitable climatic conditions. We further posit a general reduction in the distribution of main koala‐browse trees in the near future in response climate change. We modelled 60 koala‐browse species and constructed a set of correlative species distribution models for five time periods: Last Interglacial (~128–116 ka), Last Glacial Maximum (~23–19 ka), Mid‐Holocene (~7–5 ka), present (interpolations of observed data, representative of 1960–1990), and 2070. We based our projections on five hindcasts and one forecast of climatic variables extracted from WorldClim based on two general circulation models (considering the most pessimistic scenario of high greenhouse‐gas emissions) and topsoil clay fraction. We used 17 dates of koala fossil specimens identified as reliable from 70 (± 4) to 535 (± 49) ka, with the last appearance of koalas at 70 ka in the southwest. The main simulated koala‐browse species were at their greatest modelled extent of suitability during the Last Glacial Maximum, with the greatest loss of koala habitat occurring between the Mid‐Holocene and the present. We predict a similar habitat loss between the present and 2070. The spatial patterns of habitat change support our hypothesis that koala extinctions in the southwest, Nullarbor Plain and central South Australia resulted from the eastward retraction of the dominant koala‐browse species in response to long‐term climate changes. Future climate patterns will likely increase the extinction risk of koalas in their remaining eastern ranges.     

Stereoselective Covalent Binding of Anti-benzo(a)pyrene Diol Epoxide to DNA Conformation of Enantiomer Adducts

Abstract

The conformation of adducts derived from the reactions and covalent binding of the (+) and (-) enantiomers of 7β, 8α-dihydroxy-9α, 10α-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (anti-BaPDE) with double-stranded calf thymus DNA in vitro were investigated utilizing the electric linear dichroism technique. The linear dichroism and absorption spectra of the covalent DNA complexes are interpreted in terms of a superposition of two types of binding sites. One of these conformations (site I) is a complex in which the plane of the pyrene residue is close to parallel (within 30°) to the planes of the DNA bases (quasi-intercalation), while the other (site II) is an external binding site; this latter type of adduct is attributed to the covalent binding of anti-BaPDE to the exocyclic amino group of deoxyguanine (N2-dG), while site I adducts are attributed to the 06-deoxyguanine and N6-deoxyadenine adducts identified in the product analysis of P. Brookes and M.R. Osborne (Carcinogenesis (1982) 3, 1223–1226). Site II adducts are dominant (~90% in the covalent complexes derived from the (+) enantiomer), but account for only 50±5% of the adducts in the case of the (—)-enantiomer. The orientation of site II complexes is different by 20±10° in the adducts derived from the binding of the (+) and the (—) enantiomers to DNA, the long axis of the pyrene chromophore being oriented more parallel to the axis of the DNA helix in the case of the (+) enantiomer. These findings support the proposals by Brookes and Osborne that the difference in spatial orientation of the N2-dG adducts of (-)-anti-BaPDE together with their lower abundance may account for the lower biological activity of the (—) enantiomer. The external site II adducts, rather than site I adducts, appear to be correlated with the biological activity of these comoounds.     

Ecological change in the lower Omo Valley around 2.8 Ma

Late Pliocene climate changes have long been implicated in environmental changes and mammalian evolution in Africa, but high-resolution examinations of the fossil and climatic records have been hampered by poor sampling. By using fossils from the well-dated Shungura Formation (lower Omo Valley, northern Turkana Basin, southern Ethiopia), we investigate palaeodietary changes in one bovid and in one suid lineage from 3 to 2 Ma using stable isotope analysis of tooth enamel. Results show unexpectedly large increases in C₄ dietary intake around 2.8 Ma in both the bovid and suid, and possibly in a previously reported hippopotamid species. Enamel δ¹³C values after 2.8 Ma in the bovid (Tragelaphus nakuae) are higher than recorded for any living tragelaphin, and are not expected given its conservative dental morphology. A shift towards increased C₄ feeding at 2.8 Ma in the suid (Kolpochoerus limnetes) appears similarly decoupled from a well-documented record of dental evolution indicating gradual and progressive dietary change. The fact that two, perhaps three, disparate Pliocene herbivore lineages exhibit similar, and contemporaneous changes in dietary behaviour suggests a common environmental driver. Local and regional pollen, palaeosol and faunal records indicate increased aridity but no corresponding large and rapid expansion of grasslands in the Turkana Basin at 2.8 Ma. Our results provide new evidence supporting ecological change in the eastern African record around 2.8 Ma, but raise questions about the resolution at which different ecological proxies may be comparable, the correlation of vegetation and faunal change, and the interpretation of low δ¹³C values in the African Pliocene.     

Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider

Mediterranean mountain ranges harbour highly endemic biota in islandlike habitats. Their topographic diversity offered the opportunity for mountain species to persist in refugial areas during episodes of major climatic change. We investigate the role of Quaternary climatic oscillations in shaping the demographic history and distribution ranges in the spider Harpactocrates ravastellus, endemic to the Pyrenees. Gene trees and multispecies coalescent analyses on mitochondrial and nuclear DNA sequences unveiled two distinct lineages with a hybrid zone around the northwestern area of the Catalan Pyrenees. The lineages were further supported by morphological differences. Climatic niche‐based species distribution models (SDMs) identified two lowland refugia at the western and eastern extremes of the mountain range, which would suggest secondary contact following postglacial expansion of populations from both refugia. Neutrality test and approximate Bayesian computation (ABC) analyses indicated that several local populations underwent severe bottlenecks followed by population expansions, which in combination with the deep population differentiation provided evidence for population survival during glacial periods in microrefugia across the mountain range, in addition to the main Atlantic and Mediterranean (western and eastern) refugia. This study sheds light on the complexities of Quaternary climatic oscillations in building up genetic diversity and local endemicity in the southern Europe mountain ranges.     

The secE gene of Helicobacter pylori

Despite extensive annotation by two independent teams, the Helicobacter pylori genome appeared to lack a complete secretion machinery. The use of clinical isolates to substantiate in silico annotation is used here to identify the missing secE component of the major secretion machinery of Helicobacter pylori.