Environmental niche patterns of native and non-native fishes within an invaded African river system

To test ecological niche theory, this study investigated the spatial patterns and the environmental niches of native and non-native fishes within the invaded Great Fish River system, South Africa. For the native fishes, there were contrasting environmental niche breadths that varied from being small to being large and overlapped for most species, except minnows that were restricted to headwater tributaries. In addition, there was high niche overlap in habitat association among fishes with similar distribution. It was therefore inferred that habitat filtering-driven spatial organisation was important in explaining native species distribution patterns. In comparison, most non-native fishes were found to have broad environmental niches and these fishes showed high tolerance to environmental conditions, which generally supported the niche opportunity hypothesis. The proliferation of multiple non-native fishes in the mainstem section suggest that they form a functional assemblage that is probably facilitated by the anthropogenic modification of flow regimes through inter-basin water transfer. Based on the distribution patterns observed in the study, it was inferred that there was a likelihood of negative interactions between native and non-native fishes. Such effects are likely to be exacerbated by altered flow regime that was likely to have negative implications for native ichthyofauna.     

Lack of adequate seed supply is a major bottleneck for effective ecosystem restoration in Chile: friendly amendment to Bannister et al. (2018)

We argue that the need for a quality seed supply chain is a major bottleneck for the restoration of Chile's native ecosystems, thus supplementing the list of bottlenecks proposed by Bannister et al. in 2018. Specifically, there is a need for defining seed transfer zones, developing standards and capacities for properly collecting and storing seeds, reducing information gaps on seed physiology and longevity, and implementing an efficient seed supply chain with certification of seed origin and quality. Without such capacities, countries are unlikely to meet their restoration commitments. Although we focus on bottlenecks in Chile, the issues we raise are relevant to other countries and thus the global agenda for ecological restoration.     

Endemic freshwater finfish of Asia: distribution and conservation status

Freshwater finfish species richness and level of endemism in East, and South and South‐East Asia that included 17 nations were studied using available databases, and included nation‐wise distribution, habitat types, and conservation status. The number of endemic finfish species in the region was 559, belonging to 47 families. Families Cyprinidae and Balitoridae accounted for 43.5% and 16.2% of the total number of endemic species in the region, respectively, followed by Sisoridae (25), Gobiidae (20), Melanotaeniidae (19), and Bagridae (16), and the other 41 families had at least one endemic species. Nation‐wise the most number of endemic freshwater finfish species occur in India (191), followed by China (88), Indonesia (84), and Myanmar (60). In India, the endemic species accounted for 26.4% of the native freshwater fish fauna, followed by South Korea (16.9%), the Philippines, (16.3%) and Myanmar (15.7%). Statistically significant relationships discerned between the number of indigenous and endemic species richness to land area (X_la in 10³ km²) of the nations in the region were, Y_in = 218.961 Ln(X_la) – 843.1 (R² = 0.735; P < 0.001) and Y_e = 28.445 Ln X_la?134.47 (R² = 0.534; P < 0.01), respectively, and between indigenous and endemic species richness was Y_e = 0.079X_n? 1.558 (R² = 0.235; P < 0.05). The overall conservation status of endemic finfish in Asia was satisfactory in that only 92 species were in some state of vulnerability, of which 37 species (6.6%) are endangered or critically endangered. However, the bulk of these species (83.7%) were cave‐ and or lake‐dwelling fish. However, nation‐wise, the endemic freshwater finfish fauna of the Philippines and Sri Lanka, based on the imperilment index, were found to be in a highly vulnerable state. Among river basins, the Mekong Basin had the highest number of endemic species (31.3%). The discrepancies between databases are highlighted and the need to consolidate information among databases is discussed. It is suggested that the Mekong Basin be considered as a biodiversity hotspot, and appropriate management strategies be introduced in this regard.     

Taxonomic and functional homogenization of an endemic desert fish fauna

Aim The highly endemic fishes of the arid Southwest USA have been heavily impacted by human activities resulting in one of the most threatened fish faunas in the world. The aim of this study was to examine the patterns and drivers of taxonomic and functional beta diversity of freshwater fish in the Lower Colorado River Basin across the 20th century. Location Lower Colorado River Basin (LCRB). Methods The taxonomic and functional similarities of watersheds were quantified to identify patterns of biotic homogenization or differentiation over the period 1900–1999. Path analysis was used to identify the relative influence of dam density, urban land use, precipitation regimes and non‐native species richness on observed changes in fish faunal composition. Results The fish fauna of the LCRB has become increasingly homogenized, both taxonomically (1.1% based on β_sim index) and functionally (6.2% based on Bray–Curtis index), over the 20th century. The rate of homogenization varied substantially; range declines of native species initially caused taxonomic differentiation (?7.9% in the 1960s), followed by marginal homogenization (observed in the 1990s) in response to an influx of non‐native species introductions. By contrast, functional homogenization of the basin was evident considerably earlier (in the 1950s) because of the widespread introduction of non‐native species sharing similar suites of biological traits. Path analysis revealed that both taxonomic and functional homogenization were positively related to the direct and indirect (facilitation by dams and urbanization) effects of non‐native species richness. Main conclusions Our study simultaneously examines rates of change in multiple dimensions of the homogenization process. For the endemic fish fauna of the LCRB, we found that the processes of taxonomic and functional homogenization are highly dynamic over time, varying both in terms of the magnitude and rate of change over the 20th century.     

Developing Native Multispecies Sod: An Alternative Rehabilitation Method for Disturbed Lands

Natural and anthropogenic disturbance provides a mechanism for resetting the species assemblage within natural communities. Following anthropogenic disturbance particularly, there are generally more weedy species. Restoration of ecosystem structure and function in disturbed areas could aid in the control of these undesirable species. Attempts to re‐establish vegetation via direct sowing, hydroseeding, drill seeding, imprinting or plugging of either native or non‐native species can be effective, but can result in increased erosion and weed proliferation prior to desirable cover of the intended species. The use of native species for rehabilitation can be preferable because non‐native species are often less suited to the local environment and can pose a threat to the integrity of adjacent ecosystems. Native multispecies sod could become a useful rehabilitation tool, but research is needed to determine which species to use and the appropriate number of species to include. Mixtures of 4–7 native species were grown for 7 months, and clipped dry biomass, species percent abundance, and total ground cover were assessed over time in order to determine the suitability of 20 native species for sod production. Despite differences between mixtures at some harvests, all mixtures established and produced similar biomass by the end of the study. Final percent cover varied widely among species; 16 of the 20 species increased significantly over the course of production. Differences in total ground cover between mixtures were explained by the growth of the particular species rather than any synergistic effect of species diversity.     

A novel approach for adding smart functionalities to cellulosic fabrics

A water soluble nanocomposite, based on Ag-nanoparticles (Ag-NPs) loaded on hyperbranched poly (amide-amine, HBPAA) was prepared, characterized and utilized in functional finishing as well as in combined reactive dyeing/and functional finishing of linen, cotton and viscose fabrics. Incorporation of the nanocomposite alone and in combination with reactive dyes in easy care finishing formulations brought about an outstanding antibacterial functionality of the finished and the dyed/finished fabrics even after 15 laundering cycles along with a slight negative impact on other performance properties. Improvement or decrement in the functional, comfort, and dyeing properties is governed by the type of cellulosic substrate.     

How different from random are docking predictions when ranked by scoring functions?

Docking algorithms predict the structure of protein–protein interactions. They sample the orientation of two unbound proteins to produce various predictions about their interactions, followed by a scoring step to rank the predictions. We present a statistical assessment of scoring functions used to rank near‐native orientations, applying our statistical analysis to a benchmark dataset of decoys of protein–protein complexes and assessing the statistical significance of the outcome in the Critical Assessment of PRedicted Interactions (CAPRI) scoring experiment. A P value was assigned that depended on the number of near‐native structures in the sampling. We studied the effect of filtering out redundant structures and tested the use of pair‐potentials derived using ZDock and ZRank. Our results show that for many targets, it is not possible to determine when a successful reranking performed by scoring functions results merely from random choice. This analysis reveals that changes should be made in the design of the CAPRI scoring experiment. We propose including the statistical assessment in this experiment either at the preprocessing or the evaluation step. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

The yeast Ski complex is a hetero-tetramer

The yeast Ski complex assists the exosome in the degradation of mRNA. The Ski complex consists of three components; Ski2, Ski3, and Ski8, believed to be present in a 1:1:1 stoichiometry. Measuring the mass of intact isolated endogenously expressed Ski complexes by native mass spectrometry we unambiguously demonstrate that the Ski complex has a hetero-tetrameric stoichiometry consisting of one copy of Ski2 and Ski3 and two copies of Ski8. To validate the stoichiometry of the Ski complex, we performed tandem mass spectrometry. In these experiments one Ski8 subunit was ejected concomitant with the formation of a Ski2/Ski3/Ski8 fragment, confirming the proposed stoichiometry. To probe the topology of the Ski complex we disrupted the complex and mass analyzed the thus formed subcomplexes, detecting Ski8-Ski8, Ski2-Ski3, Ski8-Ski2, and Ski8-Ski8-Ski2. Combining all data we construct an improved structural model of the Ski complex.     

A new hypothesis on the simultaneous direct and indirect proton pump mechanisms in NADH-quinone oxidoreductase (complex I)

Recently, Sazanov’s group reported the X-ray structure of whole complex I [Nature, 465, 441 (2010)], which presented a strong clue for a “piston-like” structure as a key element in an “indirect” proton pump. We have studied the NuoL subunit which has a high sequence similarity to Na⁺/H⁺ antiporters, as do the NuoM and N subunits. We constructed 27 site-directed NuoL mutants. Our data suggest that the H⁺/e⁻ stoichiometry seems to have decreased from (4H⁺/2e⁻) in the wild-type to approximately (3H⁺/2e⁻) in NuoL mutants. We propose a revised hypothesis that each of the “direct” and the “indirect” proton pumps transports 2H⁺ per 2e⁻.     

Production of fully assembled and active Aquifex aeolicus F1FO ATP synthase in Escherichia coli

Background

F₁F_O ATP synthases catalyze the synthesis of ATP from ADP and inorganic phosphate driven by ion motive forces across the membrane. A number of ATP synthases have been characterized to date. The one from the hyperthermophilic bacterium Aquifex aeolicus presents unique features, i.e. a putative heterodimeric stalk. To complement previous work on the native form of this enzyme, we produced it heterologously in Escherichia coli.

Methods

We designed an artificial operon combining the nine genes of A. aeolicus ATP synthase, which are split into four clusters in the A. aeolicus genome. We expressed the genes and purified the enzyme complex by affinity and size-exclusion chromatography. We characterized the complex by native gel electrophoresis, Western blot, and mass spectrometry. We studied its activity by enzymatic assays and we visualized its structure by single-particle electron microscopy.

Results

We show that the heterologously produced complex has the same enzymatic activity and the same structure as the native ATP synthase complex extracted from A. aeolicus cells. We used our expression system to confirm that A. aeolicus ATP synthase possesses a heterodimeric peripheral stalk unique among non-photosynthetic bacterial F₁F_O ATP synthases.

Conclusions

Our system now allows performing previously impossible structural and functional studies on A. aeolicus F₁F_O ATP synthase.

General significance

More broadly, our work provides a valuable platform to characterize many other membrane protein complexes with complicated stoichiometry, i.e. other respiratory complexes, the nuclear pore complex, or transporter systems.