The phage‐driven microbial loop in petroleum bioremediation

During the drilling process and transport of crude oil, water mixes with the petroleum. At oil terminals, the water settles to the bottom of storage tanks. This drainage water is contaminated with emulsified oil and water-soluble hydrocarbons and must be treated before it can be released into the environment. In this study, we tested the efficiency of a continuous flow, two-stage bioreactor for treating drainage water from an Israeli oil terminal. The bioreactor removed all of the ammonia, 93% of the sulfide and converted 90% of the total organic carbon (TOC) into carbon dioxide. SYBR Gold staining indicated that reactor 1 contained 1.7 × 10⁸ bacteria and 3.7 × 10⁸ phages per millilitre, and reactor 2 contained 1.3 × 10⁸ bacteria and 1.7 × 10⁹ phages per millilitre. The unexpectedly high mineralization of TOC and high concentration of phage in reactor 2 support the concept of a phage-driven microbial loop in the bioremediation of the drainage water. In general, application of this concept in bioremediation of contaminated water has the potential to increase the efficiency of processes.     

Modulation of Glucose Metabolism by Balanced Deep-Sea Water Ameliorates Hyperglycemia and Pancreatic Function in Streptozotocin-Induced Diabetic Mice

The aim of this study was to determine the effects of balanced deep-sea water (BDSW) on hyperglycemia and glucose intolerance in streptozotocin (STZ)-induced diabetic mice. BDSW was prepared by mixing DSW mineral extracts and desalinated water to yield a final hardness of 1000–4000 ppm. Male ICR mice were assigned to 6 groups; mice in each group were given tap water (normal and STZ diabetic groups) or STZ with BDSW of varying hardness (0, 1000, 2000, and 4000 ppm) for 4 weeks. The STZ with BDSW group exhibited lowered fasting plasma glucose levels than the STZ-induced diabetic group. Oral glucose tolerance tests showed that BDSW improves impaired glucose tolerance in STZ-induced diabetic mice. Histopathological evaluation of the pancreas showed that BDSW restores the morphology of the pancreatic islets of Langerhans and increases the secretion of insulin in STZ-induced diabetic mice. Quantitative real-time PCR assay revealed that the expression of hepatic genes involved in gluconeogenesis, glucose oxidation, and glycogenolysis was suppressed, while the expression of the genes involved in glucose uptake, β-oxidation, and glucose oxidation in muscle were increased in the STZ with BDSW group. BDSW stimulated PI3-K, AMPK, and mTOR pathway-mediated glucose uptake in C₂C₁₂ myotubes. BDSW increased AMPK phosphorylation in C₂C₁₂ myotubes and improved impaired AMPK phosphorylation in the muscles of STZ-induced diabetic mice. Taken together, these results suggest that BDSW is a potential anti-diabetic agent, owing to its ability to suppress hyperglycemia and improve glucose intolerance by modulating glucose metabolism, recovering pancreatic islets of Langerhans and increasing glucose uptake.     

Effects of land use and environment on alien and native macrophytes: lessons from a large‐scale survey of Australian rivers

Aim We sampled riverine macrophyte communities and environmental conditions to compare drivers of alien and native abundance and to provide a general set of environmental correlates of invasion by aquatic macrophytes. Location Streams adjacent to three land‐use types (intensive, agricultural and natural) across a large latitudinal gradient (approximately 27° S–43° S) in Australia. Sites were located near Brisbane (Queensland), Sydney (New South Wales), Canberra (Australian Capital Territory), Melbourne (Victoria) and Hobart (Tasmania). Methods Alien and native aquatic plant species cover, water quality, forest canopy and adjacent land use were measured in three catchment locations (low‐, mid‐ and upper‐catchment) in all cities. Mean richness and cover of native and alien macrophytes were compared in the five cities, three catchment locations, and three land‐use types. Correlation tests examined relationships between alien and native richness at transect, site and city scales. Canonical correspondence analysis (CCA) determined the effects of environment on cover and richness of native and alien plant groups (emergents, floating, forbs/other, graminoids and submerged). Results Variation existed in the aquatic plant community at all scales, but strong patterns emerged with respect to land use and environmental gradients. Alien abundance was more responsive to anthropogenic disturbance (e.g. greater in intensive and agricultural land‐use types, and greater where dissolved nutrients and conductivity were high) than natives, which were unaffected by land‐use type and less responsive overall to environmental gradients. Native and alien richness were uncorrelated at all scales. Main conclusions Natives and aliens of the same life form did not respond similarly to the environment, suggesting inherent differences in their ability to capitalize on anthropogenic disturbance. Our results suggest invasion‐susceptible habitats are those that receive nutrient pollutants and that occur in urban and agricultural areas low in the catchment. Our confidence in these patterns is strengthened by their consistency across a large latitudinal gradient.     

Influence of Lantana camara and its removal on tree dynamics in a recently burnt wet Sclerophyll forest in Northern NSW

Lantana (Lantana camara) has adverse effects on plant communities across Australia. Fire, sometimes recommended as a management strategy for Lantana, is likely to have both beneficial and detrimental effects on Lantana and native trees. It is therefore important to evaluate the regeneration of Lantana‐invaded woody plant communities postfire. We examined the effect of Lantana removal by herbicide spray on both Lantana density and small tree (<5 cm diameter at breast height; DBH) attributes (abundance, height, DBH and diversity) in an area previously burnt. On a subset of the data, which was not sprayed, we also examined small tree attributes along a gradient of Lantana density. The herbicide treatment of postfire Lantana regrowth significantly reduced Lantana density compared to the areas left unmanaged by herbicide and increased the stem diameter of Celery Wood (Polyscias elegans). We found that, as Lantana stem density increased in no‐spray plots, the abundance of Poison Peach (Trema tomentosa), Celery Wood, and Eucalyptus and allied genera (Angophora and Corymbia) decreased. In addition, height of wattles (Acacia irrorata and A. maidenii) increased with increasing Lantana density. As postfire regeneration of Lantana reduced abundance of some species, additional control of Lantana was required to assist community regeneration.     

Genome wide SNP discovery,analysis and evaluation in mallard (<Emphasis Type="Italic">Anas platyrhynchos</Emphasis>)

Background

Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl.

Results

More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72.

Conclusion

We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.

     

Evolution and connectivity in the world-wide migration system of the mallard: Inferences from mitochondrial DNA

Background

Yami and Ivatan islanders are Austronesian speakers from Orchid Island and the Batanes archipelago that are located between Taiwan and the Philippines. The paternal genealogies of the Yami tribe from 1962 monograph of Wei and Liu were compared with our dataset of non-recombining Y (NRY) chromosomes from the corresponding families. Then mitochondrial DNA polymorphism was also analyzed to determine the matrilineal relationships between Yami, Ivatan, and other East Asian populations.

Results

The family relationships inferred from the NRY Phylogeny suggested a low number of paternal founders and agreed with the genealogy of Wei and Liu (P < 0.01). Except for one Y short tandem repeat lineage (Y-STR), seen in two unrelated Yami families, no other Y-STR lineages were shared between villages, whereas mtDNA haplotypes were indiscriminately distributed throughout Orchid Island. The genetic affinity seen between Yami and Taiwanese aborigines or between Ivatan and the Philippine people was closer than that between Yami and Ivatan, suggesting that the Orchid islanders were colonized separately by their nearest neighbors and bred in isolation. However a northward gene flow to Orchid Island from the Philippines was suspected as Yami and Ivatan peoples both speak Western Malayo-Polynesian languages which are not spoken in Taiwan. Actually, only very little gene flow was observed between Yami and Ivatan or between Yami and the Philippines as indicated by the sharing of mtDNA haplogroup B4a1a4 and one O1a1* Y-STR lineage.

Conclusions

The NRY and mtDNA genetic information among Yami tribe peoples fitted well the patrilocal society model proposed by Wei and Liu. In this proposal, there were likely few genetic exchanges among Yami and the Philippine people. Trading activities may have contributed to the diffusion of Malayo-Polynesian languages among them. Finally, artifacts dating 4,000 YBP, found on Orchid Island and indicating association with the Out of Taiwan hypothesis might be related to a pioneering stage of settlement, as most dating estimates inferred from DNA variation in our data set ranged between 100-3,000 YBP.     

Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures

Zinc-finger nucleases (ZFNs) drive efficient genome editing by introducing a double-strand break into the targeted gene. Cleavage is induced when two custom-designed ZFNs heterodimerize upon binding DNA to form a catalytically active nuclease complex. The importance of this dimerization event for subsequent cleavage activity has stimulated efforts to engineer the nuclease interface to prevent undesired homodimerization. Here we report the development and application of a yeast-based selection system designed to functionally interrogate the ZFN dimer interface. We identified critical residues involved in dimerization through the isolation of cold-sensitive nuclease domains. We used these residues to engineer ZFNs that have superior cleavage activity while suppressing homodimerization. The improvements were portable to orthogonal domains, allowing the concomitant and independent cleavage of two loci using two different ZFN pairs. These ZFN architectures provide a general means for obtaining highly efficient and specific genome modification.     

Biological control as an invasion process: disturbance and propagule pressure affect the invasion success of Lythrum salicaria biological control agents

Understanding the mechanisms behind the successful colonization and establishment of introduced species is important for both preventing the invasion of unwanted species and improving release programs for biological control agents. However, it is often not possible to determine important introduction details, such as date, number of organisms, and introduction location when examining factors affecting invasion success. Here we use biological control introduction data to assess the role of propagule pressure, disturbance, and residence time on invasion success of four herbivorous insect species introduced for the control of the invasive wetland plant, Lythrum salicaria, in the Columbia River Estuary. Two sets of field surveys determined persistence at prior release sites, colonization of new sites, and abundance within colonized sites. We quantified propagule pressure in four ways to examine the effect of different measurements. These included three measurements of introduction size (proximity to introduction site, introduction size at a local scale, and introduction size at a regional scale) and one measure of introduction number (number of introduction events in a region). Disturbance was examined along a tidal inundation gradient (distance from river mouth) and as habitat (island or mainland). Statistical models and model averaging were used to determine which factors were driving invasion success. In this study we found: (1) sparse evidence for the positive influence of propagule pressure on invasion success; (2) disturbance can negatively affect the invasion success of herbivorous insects; (3) the effects of disturbance and propagule pressure are species specific and vary among invasion stages, and (4) not all measures of propagule pressure show the same results, therefore single measures and proxies should be used cautiously.     

Differential influence of clonal integration on morphological and growth responses to light in two invasive herbs

Background and aims

In contrast to seeds, high sensitivity of vegetative fragments to unfavourable environments may limit the expansion of clonal invasive plants. However, clonal integration promotes the establishment of propagules in less suitable habitats and may facilitate the expansion of clonal invaders into intact native communities. Here, we examine the influence of clonal integration on the morphology and growth of ramets in two invasive plants, Alternanthera philoxeroides and Phyla canescens, under varying light conditions.

Methods

In a greenhouse experiment, branches, connected ramets and severed ramets of the same mother plant were exposed under full sun and 85% shade and their morphological and growth responses were assessed.

Key results

The influence of clonal integration on the light reaction norm (connection×light interaction) of daughter ramets was species-specific. For A. philoxeroides, clonal integration evened out the light response (total biomass, leaf mass per area, and stem number, diameter and length) displayed in severed ramets, but these connection×light interactions were largely absent for P. canescens. Nevertheless, for both species, clonal integration overwhelmed light effect in promoting the growth of juvenile ramets during early development. Also, vertical growth, as an apparent shade acclimation response, was more prevalent in severed ramets than in connected ramets. Finally, unrooted branches displayed smaller organ size and slower growth than connected ramets, but the pattern of light reaction was similar, suggesting mother plants invest in daughter ramets prior to their own branches.

Conclusions

Clonal integration modifies light reaction norms of morphological and growth traits in a species-specific manner for A. philoxeroides and P. canescens, but it improves the establishment of juvenile ramets of both species in light-limiting environments by promoting their growth during early development. This factor may be partially responsible for their ability to successfully colonize native plant communities.     

Coordination of calcium signalling by endothelial-derived nitric oxide in the intact liver

Calcium ions (Ca2+) and nitric oxide (NO) are key signalling molecules that are implicated in the regulation of numerous cellular processes. Here we show that, in the intact liver, stimulation of endothelial cells by bradykinin coordinates the propagation of vasopressin-dependent intercellular Ca2+ waves across hepatic plates, and markedly increases the frequency of Ca2+ oscillations in individual hepatocytes. Modulation of Ca2+ oscillations by bradykinin is lost following isolation of hepatocytes, but restored in co-cultures of hepatocytes and endothelial cells. The sensitizing effects of bradykinin are mimicked by NO donors and abrogated by NO inhibitors. Thus, crosstalk between NO and Ca2+ signalling pathways through the microvasculature is probably an important mechanism for the coordination of liver function and may have a function in other organs.