Mathisson's helical motions demystified

The motion of spinning test particles in general relativity is described by Mathisson-Papapetrou-Dixon equations, which are undetermined up to a spin supplementary condition, the latter being today still an open question. The Mathisson-Pirani (MP) condition is known to lead to rather mysterious helical motions which have been deemed unphysical, and for this reason discarded. We show that these assessments are unfounded and originate from a subtle (but crucial) misconception. We discuss the kinematical explanation of the helical motions, and dynamically interpret them through the concept of hidden momentum, which has an electromagnetic analogue. We also show that, contrary to previous claims, the frequency of the helical motions coincides exactly with the zitterbewegung frequency of the Dirac equation for the electron.Comment: To appear in the Proceedings of the Spanish Relativity Meeting 2011 (ERE2011), "Towards new paradigms", Madrid 29 August - 2 September 201

Reference Frames and the Physical Gravito-Electromagnetic Analogy

The similarities between linearized gravity and electromagnetism are known since the early days of General Relativity. Using an exact approach based on tidal tensors, we show that such analogy holds only on very special conditions and depends crucially on the reference frame. This places restrictions on the validity of the "gravito-electromagnetic" equations commonly found in the literature.Comment: 9 Pages, 1 figure. To appear in the Proceedings of the IAU Symposium 261 "Relativity in Fundamental Astronomy: Dynamics, Reference Frames, and Data Analysis", Virginia Beach, USA, 27 April - 1 May 200

Stepwise implementation of high-throughput sequencing metabarcoding to estuarine macrobenthic communities

This work was supported by FEDER through POFC-COMPETE by national funds from ‘Fundação para a Ciência e a Tecnologia (FCT)’ in the scope of the grant FCOMP-01-0124-FEDER-015429 and also by the strategic programme UID/BIA/04050/2013 (POCI-01- 0145-FEDER-007569) also funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI). Jorge Lobo was supported by a PhD fellowship (SFRH/BD/69750/2010) from FCT.info:eu-repo/semantics/publishedVersio

DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

Morphology-based profling of benthic communities has been extensively applied to aquatic ecosystems’ health assessment. However, it remains a low-throughput, and sometimes ambiguous, procedure. Despite DNA metabarcoding has been applied to marine benthos, a comprehensive approach providing species-level identifcations for estuarine macrobenthos is still lacking. Here we report a combination of experimental and feld studies to assess the aptitude of COI metabarcoding to provide robust species-level identifcations for high-throughput monitoring of estuarine macrobenthos. To investigate the ability of metabarcoding to detect all species present in bulk DNA extracts, we contrived three phylogenetically diverse communities, and applied four diferent primer pairs to generate PCR products within the COI barcode region. Between 78–83% of the species in the contrived communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct estuarine sites. Our results indicate that species richness would be considerably underestimated if only morphological methods were used: globally 27 species identifed through morphology versus 61 detected by metabarcoding. Although further refnement is required to improve efciency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifcations in estuarine macrobenthos monitoring.This study has been funded by the project “Te NextSea: Next generation monitoring of coastal ecosystems in a scenario of global change” (operação NORTE-01-0145-FEDER-000032), supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). JL was supported by a PhD fellowship (SFRH/BD/69750/2010) from FCT. Tis study had the fnancial support of Fundação para a Ciência e Tecnologia (FCT), through the strategic project UID/MAR/04292/2013 granted to MARE. Te authors would like to thank Stephanie Boilard (Biodiversity Institute of Ontario) for her support in the lab work.info:eu-repo/semantics/publishedVersio

Electromagnetic and Gravitational Invariants

The curvature invariants have been subject of recent interest in the context of the experimental detection of the gravitomagnetic field, namely due to the debate concerning the notions of "extrinsic" and "intrinsic" gravitomagnetism. In this work we explore the physical meaning of the curvature invariants, dissecting their relationship with the gravitomagnetic effects

Species gap analysis in DNA barcode reference libraries of marine non-indigenous species in the Azores archipelago

Coastal regions are widely recognised for their ecologic and socio-economic importance. The spread of invasive species, along with global climate change, overexploitation, pollution and habitat destruction, is a major threat to coastal ecosystems (Solan et al. 2004). Some of these species, in particular macroalgae and invertebrates, can spread quickly and become invasive, causing severe ecologic and economic impacts. When prevention fails, the early detection and surveillance of NIS could be essential for coordinating a timely and effective response to invasions. Marine ecosystems on oceanic islands, such as Azores, can be especially prone to invasions by non-indigenous species since they are characterized by a small number of native species and by a high availability of empty niches, and thus, the list of NIS is relatively long (Micael et al. 2014). There are no doubts that traditional morphology-based methods have highly contributed to the current knowledge about NIS communities inhabiting Portuguese coastal waters, including the Portuguese oceanic islands (Micael et al. 2014, Chainho et al. 2015). However, the hurdles associated with morphological methods may compromise the early detection and monitoring of the most risky species. On the other hand, DNA-based tools promise advantages over traditional ones, particularly the identification of individuals and life stages that cannot be recognized by using morphological approaches (Darling and Mahon 2011). Plus, most surveys typically target specific species or taxonomic groups, which may neither accurately represent overall ecosystems’ condition nor allow an early detection of NIS. Due to the above-mentioned reasons, it becomes a priority to develop and optimize novel detection methods capable to overcome some of these challenges and that would allow an early detection and ease the monitoring of NIS in coastal ecosystems. Particularly, the combination of DNA barcoding with high-throughput sequencing (HTS) renders metabarcoding the capacity to bolster current biodiversity assessments techniques (Cristescu 2014). Within this approach, genetic information can be obtained through the use of standardized DNA barcode markers targeting a wide taxonomic range of organisms in mixed specimens or environmental samples (Cristescu 2014). DNA-based tools promise a number of potential benefits over traditional methods, including increased sensitivity and specificity as well as greater throughput and cost effectiveness. However, the success of DNA-based methods is greatly dependent on the availability, taxonomic coverage and reliability of reference sequence databases, whose deficiencies can potentially compromise species identifications through HTS (Briski et al. 2016). In this study we conducted a species-gap analysis of DNA barcode sequences available for marine NIS occurring in the Azores archipelago in the Barcode of Life Data System V4 (BOLD V4) (Ratnasingham and Hebert 2007) and in the GenBank (https://www.ncbi.nlm.nih.gov/genbank/). The list of NIS occurring in Azores was compiled from a wide variety of sources, mainly from literature searches through scientific papers and reports, including recent field and taxonomic studies, and supplemented with existing databases and this is the list that was submitted to the 2019 interim ICES WGITMO report (International Council for the Exploration of the Sea; Working Group on Introductions and Transfers of Marine Organisms). The taxonomic classification of the compiled NIS followed the AlgaeBase and World Register of Marine Species (WoRMS) databases. A checklist of 80 marine NIS occurring in Azores archipelago was compiled and the species in the list were checked for the presence of public sequences on both BOLD v4 and GenBank databases. The species in the list were distributed by three kingdoms: i) Animalia (48 species), ii) Plantae (30 species) and iii) Chromista (2 species), comprehending 10 phyla. The most well represented phyla with NIS were Chordata (15 species), Mollusca and Bryozoa (both with 8 species) within Animalia, and Rhodophyta within Plantae (26 species); while the only represented phyla within Chromista was Ochrophyta with 2 species. In total, 3,884 sequences belonging to 25 different markers were found for the 80 species, published in BOLD and GenBank. Among these published sequences, the COI-5P is the most well represented loci, with 3,224 records belonging to 44 species. However, from the total species in the list, 25 were still missing a DNA sequence, which corresponded to ca. 31% of the total NIS. In addition, within sequenced species ca. 14% were singletons (i.e. only one sequence available). Animalia NIS were the most well represented with sequences, missing only for ca. 27% of the species, while for Chromista and Plantae the gap of missing species was higher than 35%. The current study allowed us to characterize the gaps in available sequences in public repositories for marine NIS occurring in the Azores archipelago. Actions developing DNA-based tools should be a priority for detection and effective management of biological invasions. DNA-based tools would allow the detection of early developmental stages or smaller organisms, reducing the time from introduction to discovery and increasing the success of NIS control and/or eradication (Holman et al. 2018). However, the gaps found in reference libraries can have strong implications for an accurate species identification through DNA-based tools. Prioritization efforts should be conducted in order to fulfil these gapsFCT – Fundação para a Ciência e a Tecnologia, I.P., in the scope of the project PTDC/BIA-BMA/29754/2017 and by FEDER funds through the Operational Programme for Competitiveness Factors - COMPETE and by National Funds through FCT - Foundation for Science and Technology under the UID/BIA/50027/2013 and POCI-01-0145-FEDER-00682

Integration of DNA-based approaches in aquatic ecological assessment using benthic macroinvertebrates

Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.This work was supported by the "Contrato-Programa" UIDB/04050/2020 and the project NIS-DNA (PTDC/BIA-BMA/29754/2017) funded by national funds through the FCT I.P (Foundation for Science and Technology). Financial support granted by the FCT to S.D. (CEECIND/00667/2017) and B.R.L. (PD/BD/127994/2016) is also acknowledged. A.F.F. was supported by the project FRESHING founded by the FCT and COMPETE (PTDC/AAGMAA/2261/2014-POCI-01-0145-FEDER356016824). M.J.F. was supported by FCT through MARE strategic project UIDB/04292/2020 and Norma Transitoria-DL57/2016