ETHYLENE RESPONSE FACTOR 115 integrates jasmonate and cytokinin signaling machineries to repress adventitious rooting in Arabidopsis

Adventitious root initiation (ARI) is ade novoorganogenesis program and a key adaptive trait in plants. Several hormones regulate ARI but the underlying genetic architecture that integrates the hormonal crosstalk governing this process remains largely elusive. In this study, we use genetics, genome editing, transcriptomics, hormone profiling and cell biological approaches to demonstrate a crucial role played by the APETALA2/ETHYLENE RESPONSE FACTOR 115 transcription factor. We demonstrate that ERF115 functions as a repressor of ARI by activating the cytokinin (CK) signaling machinery. We also demonstrate thatERF115is transcriptionally activated by jasmonate (JA), an oxylipin-derived phytohormone, which represses ARI in NINJA-dependent and independent manners. Our data indicate that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Altogether, our results reveal a previously unreported molecular network involving cooperative crosstalk between JA and CK machineries that represses ARI

Thresholds in deep-seabed mining: A primer for their development

The establishment of thresholds is integral to environmental management. This paper introduces the use of thresholds in the context of deep-seabed mining, a nascent industry for which an exploitation regime of regulations, standards and guidelines is still in the process of being developed, and for which the roles and values of thresholds have yet to be finalised. There are several options for integrating thresholds into the International Seabed Authority’s regulatory regime, from being stipulated in regulations to being part of a mining contract, each option having its own advantages and disadvantages. Here we explore the range of ways that thresholds can be derived, set out the challenges in translating ecological and management data into thresholds, highlight factors for acceptance and operationalisation of thresholds in deep-seabed mining, and explain the necessity of refining thresholds as knowledge on impacts to features improves. Some comparable marine industries already use thresholds and these could potentially be used as starting points for the development of thresholds for deep-seabed mining. In order to be acceptable to the wide range of deep-seabed mining stakeholders, thresholds need to strike a balance among levels of harm acceptable by society, levels of environmental precaution justifiable by governments, scientific robustness, and operational practicality

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which are poorly characterized or unknown. New algorithms are needed to estimate these parameters and enable researchers to build increasingly comprehensive models. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new parameter estimation algorithms for whole-cell models. We asked participants to identify a subset of parameters of a whole-cell model given the model’s structure and in silico “experimental” data. Here we describe the challenge, the best performing methods, and new insights into the identifiability of whole-cell models. We also describe several valuable lessons we learned toward improving future challenges. Going forward, we believe that collaborative efforts supported by inexpensive cloud computing have the potential to solve whole-cell model parameter estimation

Probing core polarization around 78Ni: intermediate energy Coulomb excitation of 74Ni

The study of the evolution of nuclear shells far from stability provides fundamental information about the shape and symmetry of the nuclear mean field. Nuclei with large neutron/proton ratio allow to probe the density dependence of the effective interaction. Indeed, it was recently shown that tensor and three-body forces play an important role in breaking and creating magic numbers. Of particular interest is the region of 78Ni where the large neutron excess coincides with a double shell closure. We have recently measured the B(E2; 0+ → 2+) of the 74Ni nucleus in an intermediate-energy Coulomb excitation experiment performed at the National Superconducting Cyclotron Laboratory of the Michigan State University. The 74Ni secondary beam has been produced by fragmentation of 86Kr at 140 AMeV on a thick Be target. Selected radioactive fragments impinged on a secondary 197Au target where the measurement of the emitted γ-rays allows to extract the Coulomb excitation cross section and related structure information. Preliminary B(E2) values do not point towards an enhancement of the transition matrix element and the comparison to what was already measured by Aoi and co-workers in [1] opens new scenarios in the interpretation of the shell evolution of the Z=28 isotopes

A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem

Oil pollution in the North Sea: the impact of governance measures on oil pollution over several decades

Oil pollution entering the marine environment has been an issue of concern for many decades. It can come from riverine or land-based sources, accidental and intentional discharges from ships, or as a by-product of offshore oil extraction. Growing awareness of the impact of oil pollution on the marine environment has led, since the late 1960s, to the introduction of measures to reduce or eliminate pollution from shipping and the offshore oil industry. A framework for environmental protection of the North Sea has developed over many decades through international agreements, regional cooperation, and national measures, while education has also played an important role with modern-day sailors being given due training to understand that dumping waste at sea is illegal in many areas, and is harmful to the marine environment. This paper presents data on trends in pollution from ships and oil installations. While significant reductions in oil pollution have been identified over more than two decades, there remain some areas where action is needed to reduce inputs still further, especially from oil and gas platforms

High-spin structures in Xe 132 and Xe 133 and evidence for isomers along the N=79 isotones

The transitional nuclei Xe132 and Xe133 are investigated after multinucleon-transfer (MNT) and fusion-evaporation reactions. Both nuclei are populated (i) in Xe136+Pb208 MNT reactions employing the high-resolution Advanced GAmma Tracking Array (AGATA) coupled to the magnetic spectrometer PRISMA, (ii) in the Xe136+Pt198 MNT reaction employing the GAMMASPHERE spectrometer in combination with the gas-detector array CHICO, and (iii) as an evaporation residue after a Te130(α,xn)Xe134-xn fusion-evaporation reaction employing the HORUS γ-ray array at the University of Cologne. The high-spin level schemes are considerably extended above the Jπ=(7-) and (10+) isomers in Xe132 and above the 11/2- isomer in Xe133. The results are compared to the high-spin systematics of the Z=54 as well as the N=78 and N=79 chains. Furthermore, evidence is found for a long-lived (T1/2â‰1μs) isomer in Xe133 which closes a gap along the N=79 isotones. Shell-model calculations employing the SN100PN and PQM130 effective interactions reproduce the experimental findings and provide guidance to the interpretation of the observed high-spin features

Towards the lowest-energy limit for light ions identification with silicon pixel-type detectors

An in-beam test of two pixel-type silicon detectors of the TRACE detector project has been performed at Laboratori Nazionali di Legnaro (Italy). The aim was to investigate the lowest kinetic energy values at which isotopic identification of heavy-ion reactions products with mass A 3c 10 is possible, by using a single-layer silicon detector. Two separate read-out chains, analog and digital, were used, and the Pulse Shape Analysis technique was employed to obtain the particle identification matrices for the digitally processed data. The results confirmed the high capability of the Pulse Shape Analysis method which can be used for light ion identification, with performances similar to the analog approach. Separation in both charge and mass was obtained for Li and Be isotopes, however, the presence of a significant background from alpha particles severely limited the data analysis in the lower energy region. Due to this effect, the identification of the light products ( 7,6 Li isotopes) could be possible down to 3c 24.5 MeV only, while the 9,7 Be isotopes were separable down to 3c 29 MeV. This gives the value of < 4 MeV/nucleon as the lowest kinetic energy for light products identification by using the pixel-type detectors of the TRACE project, in the present experimental conditions

Semi-Automated Image Analysis for the Assessment of Megafaunal Densities at the Arctic Deep-Sea Observatory HAUSGARTEN

Megafauna play an important role in benthic ecosystem function and are sensitive indicators of environmental change. Non-invasive monitoring of benthic communities can be accomplished by seafloor imaging. However, manual quantification of megafauna in images is labor-intensive and therefore, this organism size class is often neglected in ecosystem studies. Automated image analysis has been proposed as a possible approach to such analysis, but the heterogeneity of megafaunal communities poses a non-trivial challenge for such automated techniques. Here, the potential of a generalized object detection architecture, referred to as iSIS (intelligent Screening of underwater Image Sequences), for the quantification of a heterogenous group of megafauna taxa is investigated. The iSIS system is tuned for a particular image sequence (i.e. a transect) using a small subset of the images, in which megafauna taxa positions were previously marked by an expert. To investigate the potential of iSIS and compare its results with those obtained from human experts, a group of eight different taxa from one camera transect of seafloor images taken at the Arctic deep-sea observatory HAUSGARTEN is used. The results show that inter- and intra-observer agreements of human experts exhibit considerable variation between the species, with a similar degree of variation apparent in the automatically derived results obtained by iSIS. Whilst some taxa (e. g. Bathycrinus stalks, Kolga hyalina, small white sea anemone) were well detected by iSIS (i. e. overall Sensitivity: 87%, overall Positive Predictive Value: 67%), some taxa such as the small sea cucumber Elpidia heckeri remain challenging, for both human observers and iSIS

Semi-Automated Image Analysis for the Assessment of Megafaunal Densities at the Arctic Deep-Sea Observatory HAUSGARTEN

Megafauna play an important role in benthic ecosystem function and are sensitive indicators of environmental change. Non-invasive monitoring of benthic communities can be accomplished by seafloor imaging. However, manual quantification of megafauna in images is labor-intensive and therefore, this organism size class is often neglected in ecosystem studies. Automated image analysis has been proposed as a possible approach to such analysis, but the heterogeneity of megafaunal communities poses a non-trivial challenge for such automated techniques. Here, the potential of a generalized object detection architecture, referred to as iSIS (intelligent Screening of underwater Image Sequences), for the quantification of a heterogenous group of megafauna taxa is investigated. The iSIS system is tuned for a particular image sequence (i.e. a transect) using a small subset of the images, in which megafauna taxa positions were previously marked by an expert. To investigate the potential of iSIS and compare its results with those obtained from human experts, a group of eight different taxa from one camera transect of seafloor images taken at the Arctic deep-sea observatory HAUSGARTEN is used. The results show that inter- and intra-observer agreements of human experts exhibit considerable variation between the species, with a similar degree of variation apparent in the automatically derived results obtained by iSIS. Whilst some taxa (e. g. Bathycrinus stalks, Kolga hyalina, small white sea anemone) were well detected by iSIS (i. e. overall Sensitivity: 87%, overall Positive Predictive Value: 67%), some taxa such as the small sea cucumber Elpidia heckeri remain challenging, for both human observers and iSIS