Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.We thank Tom Schiøtte and Martin Vinther Sørensen at the Zoological Museum of Copenhagen for providing historical shell samples from the Invertebrate Collection. We thank Adeline Bidault for Vibrio DNA extraction, Kristian Hanghøj for technical assistance, Mikkel Schubert and Gabriel Renaud for fruitful discussions, the PALEOMIX group and the staff of the Danish National High-Throughput DNA Sequencing Centre for support. This work was supported by the Danish Council for Independent Research, Natural Sciences (FNU, 4002-00152B); the Danish National Research Foundation (DNRF94); the EPT PROXACHEOBIO from Université Européenne de Bretagne (2010–2012); the APEGE initiative PaleoCOO of the Centre National de la Recherche Scientifique; the cluster of excellence LabexMER (ANR-10-LABX-19; METHOMOL) under the program “Investissements d'Avenir”; the UK Natural Environment Research Council (NE/H023356/1); the EU Marie Curie ARAMACC Initial Training Network (FP7-PEOPLE-2013-ITN 604802); the “Chaires d'Attractivité 2014” IDEX, University of Toulouse, France (OURASI)

0.3-4.3 GHz frequency-accurate fractional-N frequency synthesizer with integrated VCO and nested mixed-radix digital Δ-Σ Modulator-based divider controller

If the modulus of the digital delta-sigma modulator (DΔΣM) in a fractional-N frequency synthesizer is a power of two, then the output frequency is constrained to be a rational multiple of the phase detector frequency (fPD), where the denominator of the rational multiplier is a power of two. If the required output frequency is not related to f\rm PD in this way, one is forced to approximate the ratio by using a small programmable modulus DΔΣM or a very large power-of-two modulus. Both of these solutions involve additional hardware. Furthermore, the programmable modulus solution can suffer from spurs, while the large power of two lacks accuracy. This paper presents a new solution, based on mixed-radix algebra, where the required ratio is formed by combining two different moduli. The programmable modulus solves the accuracy problem, while the large power-of-two modulus minimizes the spur content. In addition, the phase detector can be clocked at high speed. This paper explains the theoretical foundations of the method, elaborates a design methodology, and presents measured results for an 0.18 μm SiGe BiCMOS prototype. © 2014 IEEE

The tubercular badger and the uncertain curve:- The need for a multiple stressor approach in environmental radiation protection.

This article presents the results of a workshop held in Stirling, Scotland in June 2018, called to examine critically the effects of low-dose ionising radiation on the ecosphere. The meeting brought together participants from the fields of low- and high-dose radiobiology and those working in radioecology to discuss the effects that low doses of radiation have on non-human biota. In particular, the shape of the low-dose response relationship and the extent to which the effects of low-dose and chronic exposure may be predicted from high dose rate exposures were discussed. It was concluded that high dose effects were not predictive of low dose effects. It followed that the tools presently available were deemed insufficient to reliably predict risk of low dose exposures in ecosystems. The workshop participants agreed on three major recommendations for a path forward. First, as treating radiation as a single or unique stressor was considered insufficient, the development of a multidisciplinary approach is suggested to address key concerns about multiple stressors in the ecosphere. Second, agreed definitions are needed to deal with the multiplicity of factors determining outcome to low dose exposures as a term can have different meanings in different disciplines. Third, appropriate tools need to be developed to deal with the different time, space and organisation level scales. These recommendations permit a more accurate picture of prospective risks.International Union of Radioecolog