Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific

Length changes in human mitochondrial DNA (mtDNA) are potentially useful markers for inferring the evolutionary history of populations. One such length change is a nine base pair (9-bp) deletion that is located in the intergenic region between the COII gene and the Lysine tRNA gene (COII/tRNALys intergenic region). This deletion has been used as a genetic marker to trace descent from peoples of East Asian origin. A geographic cline of the deletion frequency across modern Pacific Islander populations suggests that the deletion may be useful for tracing prehistoric Polynesian origins and affinities. Mitochondrial DNA sequence variation within two variable segments of the control region (CR) permits a number of inferences regarding the evolutionary history of the 9-bp deletion that cannot be determined from frequency data alone. We obtained CR sequences from 74 mtDNAs with the 9-bp deletion from Indonesia, coastal Papua New Guinea (PNG), and American Samoa. Phylogenetic and pairwise distribution analysis of these CR sequences pooled with previously published CR sequences reveals that the deletion arose independently in Africa and Asia and suggests possible multiple origins of the deletion in Asia. A clinal increase of the frequency of the 9-bp deletion across the three Pacific populations is associated with a decrease in CR sequence diversity, consistent with founder events. Furthermore, analysis of pairwise difference distributions indicates an expansion time of proto-Polynesians that began 5,500 yr ago from Southeast Asia. These results are consistent with the express train model of Polynesian origins.      

Effect of PGR5 impairment on photosynthesis and growth in Arabidopsis thaliana

PGR5 has been reported as an important factor for the activity of the ferredoxin-dependent cyclic electron transport around PSI. To elucidate the role of PGR5 in C(3) photosynthesis, we characterized the photosynthetic electron transport rate (ETR), CO(2) assimilation and growth in the Arabidopsis thaliana pgr5 mutant at various irradiances and with CO(2) regimes. In low-light-grown pgr5, the CO(2) assimilation rate and ETR were similar to the those of the wild type at low irradiance, but decreased at saturating irradiance under photorespiratory conditions as well as non-photorespiratory conditions. Although non-photochemical quenching of chlorophyll fluorescence (NPQ) was not induced in the pgr5 mutant under steady-state photosynthesis, we show that it was induced under dark to light transition at low CO(2) concentration. Under low light conditions in air, pgr5 showed the same growth as the wild type, but a significant growth reduction compared with the wild type at >150 mumol photons m(-2) s(-1). This growth impairment was largely suppressed under high CO(2) concentrations. Based on the intercellular CO(2) concentration dependency of CO(2) assimilation, ETR and P700 oxidation measurements, we conclude that reduction of photosynthesis and growth result from (i) ATP deficiency and (ii) inactivation of PSI. We discuss these data in relation to the role of PGR5-dependent regulatory mechanisms in tuning the ATP/NADPH ratio and preventing inactivation of PSI, especially under conditions of high irradiance or enhanced photorespiration.     

Long-chain fatty acyl-coenzyme A-induced inhibition of glucokinase in pancreatic islets from rats depleted in long-chain polyunsaturated omega3 fatty acids

The metabolism of D-glucose was recently reported to be impaired in pancreatic islets from second generation rats depleted in long-chain polyunsaturated omega3 fatty acids. Considering the increased clearance of circulating non-esterified fatty acids prevailing in these rats, a possible inhibition of glucokinase in insulin-producing cells by endogenous long-chain fatty acyl-CoA was considered. The present study was mainly aimed at assessing the validity of the latter proposal. The activity of glucokinase in islet homogenates, as judged from the increase in D-glucose phosphorylation rate in response to a rise in the concentration of the hexose represented, in the omega3-depleted rats, was only 81.8 +/- 4.8% (n = 11; p < 0.005) of the paired value recorded in control animals. This coincided with the fact that the inclusion of D-glucose 6-phosphate (3.0 mM) and D-fructose 1-phosphate (1.0 mM) in the assay medium resulted in a lesser fractional decrease of D-glucose phosphorylation in omega3-depleted rats than in control animals. Moreover, whereas palmitoyl-CoA (50 microM) decreased the activity of glucokinase by 38.0 +/- 6.0% (n = 4; p < 0.01) in islet homogenates from normal rats, the CoA ester failed to affect significantly the activity of glucokinase in islet homogenates from omega3-depleted rats. These findings afford direct support for the view that glucokinase is indeed inhibited by endogenous long-chain fatty acyl-CoA in islets from omega3-depleted rats, such an inhibition probably participating to the alteration of D-glucose catabolism prevailing in these islets.     

Water relations under root chilling in a sensitive and tolerant tomato species

The shoots of cultivated tomato (Lycopersicon esculentum cv. T5) wilt if their roots are exposed to chilling temperatures of around 5 °C. Under the same treatment, a chilling‐tolerant congener (Lycopersicon hirsutum LA 1778) maintains shoot turgor. To determine the physiological basis of this differential response, the effect of chilling on both excised roots and roots of intact plants in pressure chambers were investigated. In excised roots and intact plants, root hydraulic conductance declined with temperature to nearly twice the extent expected from the temperature dependence of the viscosity of water, but the response was similar in both species. The species differed markedly, however, in stomatal behaviour: in L. hirsutum, stomatal conductance declined as root temperatures were lowered, whereas the stomata of L. esculentum remained open until the roots reached 5 °C, and the plants became flaccid and suffered damage. Grafted plants with the shoots of one genotype and roots of another indicated that the differential stomatal behaviour during root chilling has distinct shoot and root components.     

Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot

According to the history of the cultivated carrot, root colour can be considered as a structural factor of carrot germplasm. Therefore, molecular variations of carotenoid biosynthesis genes, these being involved in colour traits, represent a good putative source of polymorphism related to diversity structure. Seven candidate genes involved in the carotenoid biosynthesis pathway have been analysed from a sample of 48 individual plants, each one from a different cultivar of carrot (Daucus carota L. ssp. sativus). The cultivars were chosen to represent a large diversity and a wide range of root colour. A high single nucleotide polymorphism (SNP) frequency of 1 SNP per 22 bp (mean π _sil = 0.020) was found on average within these genes. The analysis of genetic structure from carotenoid biosynthesis gene sequences and 17 putatively neutral microsatellites showed moderate genetic differentiation between cultivars originating from the West and the East (F _ST = 0.072), this being consistent with breeding history, but not previously evidenced by molecular tools. Surprisingly, carotenoid biosynthesis genes did not exhibit decay of LD (mean r ²  = 0.635) within the 700–1,000 bp analysed, even though a fast decay level of LD is expected in outcrossing species. The high level of intralocus LD found for carotenoid biosynthesis genes implies that candidate-gene association mapping for carrot root colour should be useful to validate gene function, but may be unable to identify precisely the causative variations involved in trait determinism. Finally this study affords the first molecular evidence of a genetic structure in cultivated carrot germplasm related to phylogeography.     

Applications of direct detection device in transmission electron microscopy

A prototype direct detection device (DDD) camera system has shown great promise in improving both the spatial resolution and the signal to noise ratio for electron microscopy at 120–400 keV beam energies (Xuong et al., 2007. Methods in Cell Biology, 79, 721–739). Without the need for a resolution-limiting scintillation screen as in the charge coupled device (CCD), the DDD camera can outperform CCD based systems in terms of spatial resolution, due to its small pixel size (5 μm). In this paper, the modulation transfer function (MTF) of the DDD prototype is measured and compared with the specifications of commercial scientific CCD camera systems. Combining the fast speed of the DDD with image mosaic techniques, fast wide-area imaging is now possible. In this paper, the first large area mosaic image and the first tomography dataset from the DDD camera are presented, along with an image processing algorithm to correct the specimen drift utilizing the fast readout of the DDD system.     

Impact of past and present land‐management on the C‐balance of a grassland in the Swiss Alps

Grasslands cover about 40% of the ice‐free global terrestrial surface, but their quantitative importance in global carbon exchange with the atmosphere is still highly uncertain, and thus their potential for carbon sequestration remains speculative. Here, we report on CO₂ exchange of an extensively used mountain hay meadow and pasture in the Swiss pre‐Alps on high‐organic soils (7–45% C by mass) over a 3‐year period (18 May 2002–20 September 2005), including the European summer 2003 heat‐wave period. During all 3 years, the ecosystem was a net source of CO₂ (116–256 g C m^?2 yr^?1). Harvests and grazing cows (mostly via C export in milk) further increased these C losses, which were estimated at 355 g C m^?2 yr^?1 during 2003 (95% confidence interval 257–454 g C m^?2 yr^?1). Although annual carbon losses varied considerably among years, the CO₂ budget during summer 2003 was not very different from the other two summers. However, and much more importantly, the winter that followed the warm summer of 2003 observed a significantly higher carbon loss when there was snow (133±6 g C m^?2) than under comparable conditions during the other two winters (73±5 and 70±4 g C m^?2, respectively). The continued annual C losses can most likely be attributed to the long‐term effects of drainage and peat exploitation that began 119 years ago, with the last significant drainage activities during the Second World War around 1940. The most realistic estimate based on depth profiles of ash content after combustion suggests that there is an 500–910 g C m^?2 yr^?1 loss associated with the decomposition of organic matter. Our results clearly suggest that putting efforts into preserving still existing carbon stocks may be more successful than attempts to increase sequestration rates in such high‐organic mountain grassland soils.     

New subunits NDH-M, -N, and -O, encoded by nuclear genes, are essential for plastid Ndh complex functioning in higher plants

In higher plants, the Ndh complex reduces plastoquinones and is involved in cyclic electron flow around photosystem I, supplying extra-ATP for photosynthesis, particularly under environmental stress conditions. Based on plastid genome sequences, the Ndh complex would contain 11 subunits (NDH-A to -K), but homologies with bacterial complex indicate the probable existence of additional subunits. To identify missing subunits, tobacco (Nicotiana tabacum) NDH-H was His tagged at its N terminus using plastid transformation. A functional Ndh subcomplex was purified by Ni(2+) affinity chromatography and its subunit composition analyzed by mass spectrometry. Five plastid encoded subunits (NDH-A, -H, -I, -J, and -K) were identified as well as three new subunits (NDH-M, -N, and -O) homologous to cyanobacterial and higher plant proteins. Arabidopsis thaliana mutants missing one of these new subunits lack a functional Ndh complex, and NDH-M and NDH-N are not detected in a tobacco transformant lacking the Ndh complex. We discuss the involvement of these three nuclear-encoded subunits in the functional integrity of the plastidial complex.     

European mink-polecat hybridization events: hazards from natural process?

Determining the significance of hybridization events raises essential issues both in conservation and in evolutionary biology. Here, we report a genetic investigation of sympatric polecat and endangered European mink populations. Although the two species were morphologically very similar, the European mink and the polecat were easily discriminated from allozymes and microsatellites and showed a high level of private alleles (effective number of alleles: mink=1.45 and polecat=3.09). Nevertheless, the allozymic polymorphism remained lower in the European mink (4 loci, 10.5%) than in polecat (9 loci, 23.7%). Similarly, from microsatellite data, the polymorphism only reached 36% at 0.99 in the European mink; whereas in the polecat, the polymorphism reached 82% at 0.99. Natural hybridization events between two native species were detected. Because of the low fertility of hybrids, interbreeding could be regarded as producing "hybrid sink" that leads to a progressive assimilation of mink by polecat. Nonetheless, pure mink populations inhabited streams in western France, and hybridization events were only detected in areas where mink were rare and now presumed disappeared. Rather than revealing the poor efficiency of the specific recognition system, our results suggest that hybridization is associated with the scarcity of mating partners.     

Genetic neighbourhood and effective population size in the endangered European mink <Emphasis Type="Italic">Mustela lutreola</Emphasis>

Genetic neighbourhood and effective population size (N _e) are critical factors when determining the potential survival of threatened species. Carnivores have intrinsically small effective numbers, because, as top predators, they show low densities. The European mink, Mustela lutreola, is one of the most endangered carnivores in the world and has suffered continual decline and local extinctions. The genetic neighbourhood, area within which adults could randomly mate, averaged N _a = 31.7 km diameter, allowing that population size within the neighbourhood area only ranged from N _b = 6.1 to 22.8 animals. Although the population size was assessed in one of the main mink populations in the world, this neighbourhood size is far below the values regarded as critical in literature. However, in contrast with recent propositions, the ratio N _e /N only ranged between 0.09 and 0.19, estimates close to the average recognised by Frankham [(1995) Genetic Research 66: 95–107] for wildlife populations. In the context of the challenge to conserve this endangered carnivore, the studied neighbourhood provided crucial information suggesting both a low neighbourhood size and severe disturbance of breeding exchanges, emphasising the dramatically threatened status of the European mink.