Quantifying impacts of plastic debris on marine wildlife identifies ecological breakpoints

Quantifying sublethal effects of plastics ingestion on marine wildlife is difficult, but key to understanding the ontogeny and population dynamics of affected species. We developed a method that overcomes the difficulties by modelling individual ontogeny under reduced energy intake and expenditure caused by debris ingestion. The predicted ontogeny is combined with a population dynamics model to identify ecological breakpoints: cessation of reproduction or negative population growth. Exemplifying this approach on loggerhead turtles, we find that between 3% and 25% of plastics in digestive contents causes a 2.5–20% reduction in perceived food abundance and total available energy, resulting in a 10–15% lower condition index and 10% to 88% lower total seasonal reproductive output compared to unaffected turtles. The reported plastics ingestion is insufficient to impede sexual maturation, but population declines are possible. The method is readily applicable to other species impacted by debris ingestion.     

Systematic biases in DNA copy number originate from isolation procedures

Background

The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.

Results

While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.

Conclusion

These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.     

Unraveling the Nexus: Exploring the Pathways to Combined Resource Use

In response to the unprecedented decline in global natural resource endowments, the so‐called nexus framework is gaining increasing influence on resource management practices. In this research, we approach the resource nexus through the concept of nexus pathways. Nexus pathways are configurations that resource flows follow along supply chains leading to the combined use of two or more resources. Three general types of pathways are identified: direct (on‐site use), dependent (one‐way supply chains), and interdependent (supply‐chain feedbacks). We quantify and compare each pathway by means of multiregional input‐output analysis and structural path analysis, and apply this approach to a comparative case study on the water‐energy nexus (WEN) in the United States and China. Interdependencies or feedbacks are generally thought to be relevant for the WEN, especially between water and energy sectors. Our economy‐wide analysis for both countries indicates, however, that feedbacks neither play an important role in the WEN nor substantially take place between water and energy sectors. The most important feedbacks contribute to less than 1% of total resource use, and these take place mostly between manufacturing sectors. Overall, the studied WEN is mostly driven by dependent pathways and, to a lesser degree, direct resource use. Comparative differences between the two countries are largely explained by differences in economic structure, technology, and resource endowments. Our findings call into question current research and policy focus and suggest greater attention to less complex, but more determining, pathways leading to absolute resource use.     

Limited seed retention during winter inhibits vegetation establishment in spring,affecting lateral marsh expansion capacity

Coastal systems worldwide deliver vital ecosystem services, such as biodiversity, carbon sequestration, and coastal protection. Effectivity of these ecosystem services increases when vegetation is present. Understanding the mechanisms behind vegetation establishment in bio‐geomorphic systems is necessary to understand their ability to recover after erosive events and potential adaptations to climate change. In this study, we examined how seed availability affects vegetation establishment in the salt marsh–intertidal flat transition zone: the area with capacity for lateral marsh expansion. This requires vegetation establishment; therefore, seed availability is essential. In a 6‐month field experiment, we simulated a before and after winter seed dispersal at two locations, the salt‐marsh vegetation edge and the intertidal flat, and studied seed retention, the seed bank, and the seed viability of three pioneer marsh species: Salicornia procumbens, Aster tripolium, and Spartina anglica. During winter storm conditions, all supplied seeds eroded away with the sediment surface layer. After winter, supplied seeds from all three species were retained, mostly at the surface while 9% was bioturbated downwards. In the natural seed bank, A. tripolium and S. anglica were practically absent while S. procumbens occurred more frequently. The viability of S. procumbens seeds was highest at the surface, between 80% and 90%. The viability quickly decreased with depth, although viable S. procumbens seeds occurred up to 15 cm depth. Only when seeds were supplied after winter, many S. procumbens and some S. anglica individuals did establish successfully in the transition zone. Viable seed availability formed a vegetation establishment threshold, even with a local seed source. Our results suggest that, although boundary conditions such as elevation, inundation, and weather conditions were appropriate for vegetation establishment in spring, the soil surface in winter can be so dynamic that it limits lateral marsh expansion. These insights can be used for designing effective nature‐based coastal protection.     

The short 5′ untranslated region of the βA3/A1-crystallin mRNA is responsible for leaky ribosomal scanning

Leaky ribosomal scanning allows the expression of multiple proteins from a single mRNA by occasionally skipping the first start codon, and initiating translation at a subsequent one. A3- and A1-crystallin, two members of the -crystallin family of vertebrate eye lens proteins, are produced via this mechanism, of which, until now, only very few examples have been found in eukaryotic genes. Since the two start codons on the A3/A1 messenger lie in the same reading frame, the two translated proteins are identical, except for the 17 residues shorter N-terminal extension of A1-crystallin. It has been suggested that the very short leader (5–7 nucleotides) of the A3/A1 messenger might cause slippage at the first start codon, although the unfavorable context of this start codon might also be responsible. Using transient transfections, we now demonstrate that increasing the length of the leader sequence to 67 nucleotides indeed completely abolishes translation initiation at the second start codon, and thus expression of the A1-crystallin protein. Messengers having a leader of 5, 7 or 14 nucleotides all express both A3- and A1-crystallin at very similar relative levels.