Compensatory gene amplification restores fitness after inter‐species gene replacements

Genes introduced by gene replacements and other types of horizontal gene transfer (HGT) represent a significant presence in many archaeal and eubacterial genomes. Most alien genes are likely to be neutral or deleterious upon arrival and their long‐term persistence may require a mechanism that improves their selective contribution. To examine the fate of inter‐species gene replacements, we exchanged three native S. typhimurium genes encoding ribosomal proteins with orthologues from various other microbes. The results show that replacement of each of these three genes reduces fitness to such an extent that it would provide an effective barrier against inter‐species gene replacements in eubacterial populations. However, these fitness defects could be partially ameliorated by gene amplification that augmented the dosage of the heterologous proteins. This suggests that suboptimal expression is a common fitness constraint for inter‐species gene replacements, with fitness costs conferred by either a lower expression level of the alien protein compared with the native protein or a requirement for an increased amount of the alien protein to maintain proper function. Our findings can explain the observation that duplicated genes are over‐represented among horizontally transferred genes, and suggest a potential coupling between compensatory gene amplification after HGT and the evolution of new genes.     

Developmental changes in β-subunit composition of Na,K-ATPase in the Drosophila eye

The Drosophila genome contains at least three loci for the Na,K-ATPase β-subunit; however, only the protein products of nrv1 and nrv2 have been characterized hitherto. Here, we provide evidence that nrv3 also encodes for a functional Na,K-ATPase β-subunit, as its protein product co-precipitates with the Na,K-ATPase α-subunit. Nrv3 expression in adult flies is restricted to the nervous system in which Nrv3 is enriched in selective types of sensory cells. Because Nrv3 expression is especially prominent in the compound eye, we have analyzed the subcellular and developmental distribution of Nrv3 within the visual cells and related this distribution to those of the α-subunit and of the β-subunits Nrv1 and Nrv2. Prospective visual cells express Nrv2 in the third larval instar stage and during the first half of pupal development. During the last third of pupal life, Nrv3 gradually replaces Nrv2 as the Na,K-ATPase β-subunit in the photoreceptor cells. Adult photoreceptors express Nrv3 as their major β-subunit; the visual cells R1–R6 co-express Nrv2 at a low level, whereas R7 and R8 co-express Nrv1. Notably, β-subunits do not co-distribute exactly with the α-subunit at some developmental stages, supporting the concept that the α-subunit and β-subunit can exist in the plasma membrane without being engaged in α/β heterodimers. The non-visual cells within the compound eye express almost exclusively Nrv2, which segregates together with the α-subunit to septate junctions throughout development.     

Force spectroscopy and fluorescence microscopy of dsDNA–YOYO-1 complexes: implications for the structure of dsDNA in the overstretching region

When individual dsDNA molecules are stretched beyond their B-form contour length, they reveal a structural transition in which the molecule extends 1.7 times its contour length. The nature of this transition is still a subject of debate. In the first model, the DNA helix unwinds and combined with the tilting of the base pairs (which remain intact), results in a stretched form of DNA (also known as S-DNA). In the second model the base pairs break resulting effectively in two single-strands, which is referred to as force-induced melting. Here a combination of optical tweezers force spectroscopy with fluorescence microscopy was used to study the structure of dsDNA in the overstretching regime. When dsDNA was stretched in the presence of 10 nM YOYO-1 an initial increase in total fluorescence intensity of the dye–DNA complex was observed and at an extension where the dsDNA started to overstretch the fluorescence intensity leveled off and ultimately decreased when stretched further into the overstretching region. Simultaneous force spectroscopy and fluorescence polarization microscopy revealed that the orientation of dye molecules did not change significantly in the overstretching region (78.0°± 3.2°). These results presented here clearly suggest that, the structure of overstretched dsDNA can be explained accurately by force induced melting.     

VARIATION IN THE STRENGTH OF MALE MATE CHOICE ALLOWS LONG‐TERM COEXISTENCE OF SPERM‐DEPENDENT ASEXUALS AND THEIR SEXUAL HOSTS

In several asexual taxa, reproduction requires mating with related sexual species to stimulate egg development, even though genetic material is not incorporated from the sexuals (gynogenesis). In cases in which gynogens do not invest in male function, they can potentially have a twofold competitive advantage over sexuals because the asexuals avoid the cost of producing males. If unmitigated, however, the competitive success of the asexuals would ultimately lead to their own demise, following the extinction of the sexual species that stimulate egg development. We have studied a model of mate choice among sexual individuals and asexual gynogens, where males of the sexual species preferentially mate with sexual females over gynogenetic females, to determine if such mating preferences can stably maintain both gynogenetic and sexual individuals within a community. Our model shows that stable coexistence of gynogens and their sexual hosts can occur when there is variation among males in the degree of preference for mating with sexual females and when pickier males pay a higher cost of preference.     

Biomarker assessment of organic matter sources and degradation in Canadian High Arctic littoral sediments

This paper presents an uncomplicated approach to improve estimates of groundwater nutrient load to a marine embayment. A two-dimensional chemical profile of shallow groundwater was analysed in a sandy beach in three seasons (early summer, late summer and mid winter) and an adjusted estimate of groundwater nutrient discharge was derived that accounts for a complex biogeochemical environment and non-conservative behaviour of nutrients in the pre-discharge beach groundwater. The study was conducted at Cockburn Sound, Western Australia, where there has been significant groundwater contamination and associated marine ecological degradation. Losses in nitrogen and increases in phosphorus were observed along the discharge pathway beyond that expected from mixing with marine water, and the changes were attributed to chemically and biologically mediated reactions. A slow groundwater velocity (0.14–0.18 m day^?1), high organic carbon (TOC = 0.35–4.9 mmol l^?1, DOC = 0.28–4.6 mmol l^?1) and low to sub-oxic conditions (DO = 0.4–24% saturation) were deemed suitable for chemically and biologically mediated reactions to occur and subsequently alter regional estimates of groundwater nutrient concentration. Accounting for this environment, groundwater loads were calculated that were 1–2 orders of magnitude less than previous regional-based estimates: 0.4–13 kg NO _x ^?  day^?1, 0.2–24 kg NH₄ ⁺ day^?1 and 0.004–0.8 kg FRP day^?1. This paper applies knowledge of recent research and presents scope to marine managers or modellers to account for groundwater inputs to the marine environment.     

Do anthropogenic corridors homogenize plant communities at a local scale? A case studied in Tenerife (Canary Islands)

Biological homogenization is defined as a process that occurs when native species are replaced by common and dominant exotic species or due to depletion and expansion of native species, reducing the beta diversity between areas or habitats. Islands are particularly vulnerable to plant invasion, and as a consequence, homogenization is a process that can become faster and more intense in islands than in continental areas. We recorded vascular plant species composition in roadside communities along a strong altitudinal gradient using plots beside the road and at two distances from the road (0–50 and 50–100 m). We analyzed the results separately for each group of plots with a Detrended Correspondence Analysis (DCA) including and excluding exotic species. The results revealed that where exotic species were most abundant, i.e., at the road edge, they can create an effect of floristic homogenization where three similar roads are compared. At a distance of >50 m from the road, where exotic species are less frequent, this effect has already disappeared, indicating that it is a local phenomenon, closely related to the highly disturbed roadside environment. Furthermore, floristic homogenization seems to be more important at higher altitudes (>1000 m), probably related to higher diversity in native plant communities and lower levels of human disturbances. Roads allow humans to reach relatively remote and sometimes well-conserved areas, and, at the same time, facilitate the spread of exotic plants and the most common native species which can locally create floristic homogenization in roadside communities on this oceanic island. A deeper understanding of the effects of these anthropogenic corridors at the local and regional scales is therefore required to integrate road planning and management with the aim of conserving the value of the natural areas.     

A global comparison of plant invasions on oceanic islands

Oceanic islands have long been considered to be particularly vulnerable to biotic invasions, and much research has focused on invasive plants on oceanic islands. However, findings from individual islands have rarely been compared between islands within or between biogeographic regions. We present in this study the most comprehensive, standardized dataset to date on the global distribution of invasive plant species in natural areas of oceanic islands. We compiled lists of moderate (5–25% cover) and dominant (>25% cover) invasive plant species for 30 island groups from four oceanic regions (Atlantic, Caribbean, Pacific, and Western Indian Ocean). To assess consistency of plant behaviour across island groups, we also recorded present but not invasive species in each island group.We tested the importance of different factors discussed in the literature in predicting the number of invasive plant species per island group, including island area and isolation, habitat diversity, native species diversity, and human development. Further we investigated whether particular invasive species are consistently and predictably invasive across island archipelagos or whether island-specific factors are more important than species traits in explaining the invasion success of particular species.We found in total 383 non-native spermatophyte plants that were invasive in natural areas on at least one of the 30 studied island groups, with between 3 and 74 invaders per island group. Of these invaders about 50% (181 species) were dominants or co-dominants of a habitat in at least one island group. An extrapolation from species accumulation curves across the 30 island groups indicates that the total current flora of invasive plants on oceanic islands at latitudes between c. 35°N and 35°S may eventually consist of 500–800 spermatophyte species, with 250–350 of these being dominant invaders in at least one island group. The number of invaders per island group was well predicted by a combination of human development (measured by the gross domestic product (GDP) per capita), habitat diversity (number of habitat types), island age, and oceanic region (87% of variation explained). Island area, latitude, isolation from continents, number of present, non-native species with a known invasion history, and native species richness were not retained as significant factors in the multivariate models.Among 259 invaders present in at least five island groups, only 9 species were dominant invaders in at least 50% of island groups where they were present. Most species were invasive only in one to a few island groups although they were typically present in many more island groups. Consequently, similarity between island groups was low for invader floras but considerably higher for introduced (but not necessarily invasive) species – especially in pairs of island groups that are spatially close or similar in latitude. Hence, for invasive plants of natural areas, biotic homogenization among oceanic islands may be driven by the recurrent deliberate human introduction of the same species to different islands, while post-introduction processes during establishment and spread in natural areas tend to reduce similarity in invader composition between oceanic islands. We discuss a number of possible mechanisms, including time lags, propagule pressure, local biotic and abiotic factors, invader community assembly history, and genotypic differences that may explain the inconsistent performance of particular invasive species in different island groups.     

Discovery of a Novel Function for Human Rad51: MAINTENANCE OF THE MITOCHONDRIAL GENOME*

Homologous recombination (HR) plays a critical role in facilitating replication fork progression when the polymerase complex encounters a blocking DNA lesion, and it also serves as the primary mechanism for error-free repair of DNA double strand breaks. Rad51 is the central catalyst of HR in all eukaryotes, and to this point studies of human Rad51 have focused exclusively on events occurring within the nucleus. However, substantial amounts of HR proteins exist in the cytoplasm, yet the function of these protein pools has not been addressed. Here, we provide the first demonstration that Rad51 and the related HR proteins Rad51C and Xrcc3 exist in human mitochondria. We show stress-induced increases in both the mitochondrial levels of each protein and, importantly, the physical interaction between Rad51 and mitochondrial DNA (mtDNA). Depletion of Rad51, Rad51C, or Xrcc3 results in a dramatic decrease in mtDNA copy number as well as the complete suppression of a characteristic oxidative stress-induced copy number increase. Our results identify human mtDNA as a novel Rad51 substrate and reveal an important role for HR proteins in the maintenance of the human mitochondrial genome.     

Rapid T cell receptor delineation reveals clonal expansion limitation of the magnitude of the HIV-1-specific CD8+ T cell response

TCRs mediate CTL specificity, but TCRs recognizing the same epitope often differ between persons due to their stochastic derivation. The role of this variability in the pathogenesis of virus infections and malignancies has been technically difficult to study. We apply an adaptation of TCR spectratyping to study HIV-specific CTLs, defining the clonal breadth and sequences of epitope-specific TCRs from PBMCs without cellular sorting or molecular cloning. Examining 48 CTL responses in 12 persons reveals a mean of 4.5 ± 2.7 clones per response, of both public and private clonotypes. The number of identified epitope-specific TCRs correlates with CTL frequency across epitopes, suggesting that clonal breadth limits the magnitude of the CTL response against HIV-1 in vivo. HLA A- and B-restricted CTLs are similar in their TCR breadth in this small cohort, preliminarily suggesting that qualitative differences may account for their disparate impacts on pathogenesis. Overall, these findings demonstrate that the magnitude of the CTL response in chronic HIV-1 infection is constrained by TCR clonal breadth, suggesting maximal expansion of CTLs in response to chronic antigenic stimulation.     

Aging in a Long-Lived Clonal Tree

From bacteria to multicellular animals, most organisms exhibit declines in survivorship or reproductive performance with increasing age (“senescence”) [1],[2]. Evidence for senescence in clonal plants, however, is scant [3],[4]. During asexual growth, we expect that somatic mutations, which negatively impact sexual fitness, should accumulate and contribute to senescence, especially among long-lived clonal plants [5],[6]. We tested whether older clones of Populus tremuloides (trembling aspen) from natural stands in British Columbia exhibited significantly reduced reproductive performance. Coupling molecular-based estimates of clone age with male fertility data, we observed a significant decline in the average number of viable pollen grains per catkin per ramet with increasing clone age in trembling aspen. We found that mutations reduced relative male fertility in clonal aspen populations by about 5.8×10⁻⁵ to 1.6×10⁻³ per year, leading to an 8% reduction in the number of viable pollen grains, on average, among the clones studied. The probability that an aspen lineage ultimately goes extinct rises as its male sexual fitness declines, suggesting that even long-lived clonal organisms are vulnerable to senescence.