Trophic Level Stability-Inducing Effects of Predaceous Early Juvenile Fish in an Estuarine Mesocosm Study

Background

Classically, estuarine planktonic research has focussed largely on the physico-chemical drivers of community assemblages leaving a paucity of information on important biological interactions.

Methodology/Principal Findings

Within the context of trophic cascades, various treatments using in situ mesocosms were established in a closed estuary to highlight the importance of predation in stabilizing estuarine plankton abundances. Through either the removal (filtration) or addition of certain planktonic groups, five different trophic systems were established. These treatments contained varied numbers of trophic levels and thus different “predators” at the top of the food chain. The abundances of zooplankton (copepod and polychaete), ciliate, micro-flagellate, nano-flagellate and bacteria were investigated in each treatment, over time. The reference treatment containing apex zooplanktivores (early juvenile mullet) and plankton at natural densities mimicked a natural, stable state of an estuary. Proportional variability (PV) and coefficient of variation (CV) of temporal abundances were calculated for each taxon and showed that apex predators in this experimental ecosystem, when compared to the other systems, induced stability. The presence of these predators therefore had consequences for multiple trophic levels, consistent with trophic cascade theory.

Conclusions/Significance

PV and CV proved useful indices for comparing stability. Apex predators exerted a stabilizing pressure through feeding on copepods and polychaetes which cascaded through the ciliates, micro-flagellates, nano-flagellates and bacteria. When compared with treatments without apex predators, the role of predation in structuring planktonic communities in closed estuaries was highlighted.     

Telomere stability and development of ctc1 mutants are rescued by inhibition of EJ recombination pathways in a telomerase-dependent manner

The telomeres of linear eukaryotic chromosomes are protected by caps consisting of evolutionarily conserved nucleoprotein complexes. Telomere dysfunction leads to recombination of chromosome ends and this can result in fusions which initiate chromosomal breakage–fusion–bridge cycles, causing genomic instability and potentially cell death or cancer. We hypothesize that in the absence of the recombination pathways implicated in these fusions, deprotected chromosome ends will instead be eroded by nucleases, also leading to the loss of genes and cell death. In this work, we set out to specifically test this hypothesis in the plant, Arabidopsis. Telomere protection in Arabidopsis implicates KU and CST and their absence leads to chromosome fusions, severe genomic instability and dramatic developmental defects. We have analysed the involvement of end-joining recombination pathways in telomere fusions and the consequences of this on genomic instability and growth. Strikingly, the absence of the multiple end-joining pathways eliminates chromosome fusion and restores normal growth and development to cst ku80 mutant plants. It is thus the chromosomal fusions, per se, which are the underlying cause of the severe developmental defects. This rescue is mediated by telomerase-dependent telomere extension, revealing a competition between telomerase and end-joining recombination proteins for access to deprotected telomeres.     

The need for broader ecological and socioeconomic tools to evaluate the effectiveness of coral restoration programs

Coral reef restoration initiatives are burgeoning in response to the need for novel management strategies to address dramatic global declines in coral cover. However, coral restoration programs typically lack rigor and critical evaluation of their effectiveness. A review of 83 peer‐reviewed papers that used coral transplantation for reef restoration reveals that growth and survival of coral fragments were the most widely used indicators of restoration success, with 88% of studies using these two indicators either solely (55%) or in combination with a limited number of other ecological factors (33%). In 53% of studies, reef condition was monitored for 1 year or less, while only 5% of reefs were monitored for more than 5 years post‐transplantation. These results highlight that coral reef restoration science has focused primarily on short‐term experiments to evaluate the feasibility of techniques for ecological restoration and the initial establishment phase post‐transplantation, rather than on longer‐term outcomes for coral reef communities. Here, we outline 10 socioecological indicators that comprehensively evaluate the effectiveness of coral reef restoration across the four pillars of sustainability (i.e. environmental, sociocultural, governance, and economic contributions to sustainable communities). We recommend that evaluations of the effectiveness of coral restoration programs integrate ecological indicators with sociocultural, economic, and governance considerations. Assessing the efficacy of coral restoration as a tool to support reef resilience will help to guide future efforts and ensure the sustainable maintenance of reef ecosystem goods and services.     

Heterologous expression of naturally evolved putative de novo proteins with chaperones

Over the past decade, evidence has accumulated that new protein‐coding genes can emerge de novo from previously non‐coding DNA. Most studies have focused on large scale computational predictions of de novo protein‐coding genes across a wide range of organisms. In contrast, experimental data concerning the folding and function of de novo proteins are scarce. This might be due to difficulties in handling de novo proteins in vitro, as most are short and predicted to be disordered. Here, we propose a guideline for the effective expression of eukaryotic de novo proteins in Escherichia coli. We used 11 sequences from Drosophila melanogaster and 10 from Homo sapiens, that are predicted de novo proteins from former studies, for heterologous expression. The candidate de novo proteins have varying secondary structure and disorder content. Using multiple combinations of purification tags, E. coli expression strains, and chaperone systems, we were able to increase the number of solubly expressed putative de novo proteins from 30% to 62%. Our findings indicate that the best combination for expressing putative de novo proteins in E. coli is a GST‐tag with T7 Express cells and co‐expressed chaperones. We found that, overall, proteins with higher predicted disorder were easier to express.StatementToday, we know that proteins do not only evolve by duplication and divergence of existing proteins but also arise from previously non‐coding DNA. These proteins are called de novo proteins. Their properties are still poorly understood and their experimental analysis faces major obstacles. Here, we aim to present a starting point for soluble expression of de novo proteins with the help of chaperones and thereby enable further characterization.     

Combined effect of the Saccharomyces cerevisiae lag phase and the non-Saccharomyces consortium to enhance wine fruitiness and complexity

Applied Microbiology and Biotechnology - Non-Saccharomyces (NS) species that are either naturally present in grape must or added in mixed fermentation with S. cerevisiae may impact the wine’s...