Long‐term allelopathic control of phytoplankton by the submerged macrophyte Elodea nuttallii

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Characteristics of site variation among clones of the 340-base pair,tandemly repeated EcoR1 family of human DNA

Twenty-four clones of EcoR1-restricted, 340-base pair (bp) DNA derived from human DNA have been sequenced and compared to a published consensus sequence for this family. No two clones were found to have identical sequences; the clones studied differed from the consensus sequence in as few as 1 or as many as 41 sites. On the average in these clones, a 5.2% divergence from exact homology was found, with 1 of 10 of the site variations being nonrandom, i.e., cases in which five or more clones had the same nucleotide substitution at that site (viz., 53, 124, 126, 138, 152, and 157). At site 157, for example, 16 of the 24 clones differed from the reference sequence. Positions and their respective changes, as compared to the consensus sequence, are summarized. Variations are discussed with relation to possible functions for these sequences.This research was supported in part by Center for Disease Control Grant 1 K01 OH 0035-01, and K.M. was awarded a fellowship from NIOSH Educational Resource Center Grant 5-T15-OH07085.     

Influence of nutrients, submerged macrophytes and zooplankton grazing on phytoplankton biomass and diversity along a latitudinal gradient in Europe

In order to evaluate latitudinal differences in the relationship of phytoplankton biomass and diversity with environmental conditions in shallow lakes, we sampled 98 shallow lakes from three European regions: Denmark (DK), Belgium/The Netherlands (BNL) and southern Spain (SP). Phytoplankton biomass increased with total phosphorus (TP) concentrations and decreased with submerged macrophyte cover across the three regions. Generic richness was significantly negatively related to submerged macrophyte cover and related environmental variables. Zooplankton:phytoplankton biomass ratios were positively related to submerged macrophyte cover and negatively to phytoplankton generic richness in DK and BNL, suggesting that the low generic richness in lakes with submerged macrophytes was due to a higher zooplankton grazing pressure in these regions. In SP, phytoplankton generic richness was not influenced by zooplankton grazing pressure but related to conductivity. We observed no relationship between phytoplankton generic richness and TP concentration in any of the three regions. The three regions differed significantly with respect to mean local and regional generic richness, with BNL being more diverse than the other two regions. Our observations suggest that phytoplankton diversity in European shallow lakes is influenced by submerged macrophyte cover indirectly by modulating zooplankton grazing. This influence of submerged macrophytes and zooplankton grazing on phytoplankton diversity decreases from north to south.     

The influence of plant-associated filter feeders on phytoplankton biomass: a mesocosm study

Low phytoplankton biomass usually occurs in the presence of submerged macrophytes, possibly because submerged macrophytes enhance top-down control of phytoplankton by offering a refuge for efficient grazers like Daphnia against fish predation. However, other field studies also suggest that submerged macrophytes suppress phytoplankton in the absence of Daphnia. In order to investigate these mechanisms further, we conducted an outdoor mesocosm experiment to study the effect of submerged macrophytes (Elodea nuttallii) on phytoplankton and zooplankton biomass. The experiment combined four nutrient addition levels (0, 10, 100, and 1000 μg P l⁻¹; N/P ratio: 16) with three macrophyte levels (no macrophytes, artificial macrophytes, and real macrophytes). We inoculated the tanks with species-rich inocula of phytoplankton and zooplankton but excluded fish or macro-invertebrates. Probably due to the lack of predators in the mesocosms, potential grazing rates of pelagic zooplankton (estimated from zooplankton biomass) did not differ between the macrophyte treatment combinations. Compared to the treatment combinations without macrophytes, lower phytoplankton biomass occurred in the treatment combinations with real macrophytes at all the nutrient addition levels and in those with artificial macrophytes at all the nutrient levels except the highest. Significantly, higher abundances of plant-associated filter feeders (Simocephalus vetulus and Ceriodaphnia spp.) occurred in the treatment combinations with real and artificial macrophytes. The estimated potential grazing rate of these plant-associated filter feeders indicated that these filter feeders could be responsible for the lower phytoplankton biomass in the presence of real and artificial macrophytes. Our results suggest that the plant-associated filter feeders may be significant grazers in vegetated shallow lakes.     

Tree diversity mitigates defoliation after a drought‐induced tipping point

Understanding the processes that underlie drought‐related tree vitality loss is essential for anticipating future forest dynamics, and for developing management plans aiming at increasing the resilience of forests to climate change. Forest vitality has been continuously monitored in Europe since the acid rain alert in the 1980s, and the intensive monitoring plots of ICP Forests offer the opportunity to investigate the effects of air pollution and climate change on forest condition. By making use of over 100 long‐term monitoring plots, where crown defoliation has been assessed extensively since 1990, we discovered a progressive shift from a negative to a positive effect of species richness on forest health. The observed tipping point in the balance of net interactions, from competition to facilitation, has never been reported from real ecosystems outside experimental conditions; and the strong temporal consistency of our observations with increasing drought stress emphasizes its climate change relevance. Furthermore, we show that higher species diversity has reduced the severity of defoliation in the long term. Our results confirm the greater resilience of diverse forests to future climate change‐induced stress. More generally, they add to an accumulating body of evidence on the large potential of tree species mixtures to face manifold disturbances in a changing world.     

Bioflocculation as an innovative harvesting strategy for microalgae

Microalgae are a promising new source of biomass for the production of third generation biofuels but, so far, the majority of microalgal biomass has been used for high-value applications. New low-cost technologies are needed to make the production and processing of microalgae economically feasible for low-value applications. A major challenge lies in the harvesting of microalgae, which requires a cost-efficient separation technology. Flocculation, especially bioflocculation, is an attractive low-cost separation technology. Various new bioflocculation strategies have been claimed to generate major advances in cost-efficient harvesting. Here, we review the recent advances in bioflocculation based on algal–bacterial, algal–fungal, or algal–algal interactions within the framework of microalgae biomass harvesting for biofuel production. We also discuss recent advances using infochemicals and genetic engineering for the induction of bioflocculation.     

Knockdown of DNA ligase IV/XRCC4 by RNA interference inhibits herpes simplex virus type I DNA replication

Herpes simplex virus has a linear double-stranded DNA genome with directly repeated terminal sequences needed for cleavage and packaging of replicated DNA. In infected cells, linear genomes rapidly become endless. It is currently a matter of discussion whether the endless genomes are circles supporting rolling circle replication or arise by recombination of linear genomes forming concatemers. Here, we have examined the role of mammalian DNA ligases in the herpes simplex virus, type I (HSV-1) life cycle by employing RNA interference (RNAi) in human 1BR.3.N fibroblasts. We find that RNAi-mediated knockdown of DNA ligase IV and its co-factor XRCC4 causes a hundred-fold reduction of virus yield, a small plaque phenotype, and reduced DNA synthesis. The effect is specific because RNAi against DNA ligase I or DNA ligase III fail to reduce HSV-1 replication. Furthermore, RNAi against DNA ligase IV and XRCC4 does not affect replication of adenovirus. In addition, high multiplicity infections of HSV-1 in human DNA ligase IV-deficient cells reveal a pronounced delay of production of infectious virus. Finally, we demonstrate that formation of endless genomes is inhibited by RNAi-mediated depletion of DNA ligase IV and XRCC4. Our results suggests that DNA ligase IV/XRCC4 serves an important role in the replication cycle of herpes viruses and is likely to be required for the formation of the endless genomes early during productive infection.     

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

Background

Bisulfite sequencing using next generation sequencers yields genome-wide measurements of DNA methylation at single nucleotide resolution. Traditional aligners are not designed for mapping bisulfite-treated reads, where the unmethylated Cs are converted to Ts. We have developed BS Seeker, an approach that converts the genome to a three-letter alphabet and uses Bowtie to align bisulfite-treated reads to a reference genome. It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes non-unique and low-quality mappings.

Results

We tested our aligner on synthetic data, a bisulfite-converted Arabidopsis library, and human libraries generated from two different experimental protocols. We evaluated the performance of our approach and compared it to other bisulfite aligners. The results demonstrate that among the aligners tested, BS Seeker is more versatile and faster. When mapping to the human genome, BS Seeker generates alignments significantly faster than RMAP and BSMAP. Furthermore, BS Seeker is the only alignment tool that can explicitly account for tags which are generated by certain library construction protocols.

Conclusions

BS Seeker provides fast and accurate mapping of bisulfite-converted reads. It can work with BS reads generated from the two different experimental protocols, and is able to efficiently map reads to large mammalian genomes. The Python program is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html.     

GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter

The bacterial genus Clavibacter has only one species, Clavibacter michiganensis, containing five subspecies. All five are plant pathogens, among which three are recognized as quarantine pests (mentioned on the EPPO A2 list). Prevention of their introduction and epidemic outbreaks requires a reliable and accurate identification. Currently, identification of these bacteria is time consuming and often problematic, mainly because of cross-reactions with other plant-associated bacteria in immunological tests and false-negative results in PCR detection methods. Furthermore, distinguishing closely related subspecies is not straightforward. This study aimed at evaluating the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fragment of the gyrB sequence for the reliable and fast identification of the Clavibacter subspecies. Amplification and sequencing of gyrB using a single primer set had sufficient resolution and specificity to identify each subspecies based on both sequence similarities in cluster analyses and specific signatures within the sequences. All five subspecies also generated distinct and reproducible MALDI-TOF MS profiles, with unique and specific ion peaks for each subspecies, which could be used as biomarkers for identification. Results from both methods were in agreement and were able to distinguish the five Clavibacter subspecies from each other and from representatives of closely related Rathayibacter, Leifsonia or Curtobacterium species. Our study suggests that proteomic analysis using MALDI-TOF MS and gyrB sequence are powerful diagnostic tools for the accurate identification of Clavibacter plant pathogens.