Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

Background Fruit abscission depends on cell separation that occurs within specialized cell layers that constitute an abscission zone (AZ). To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Results Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. Conclusions The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process

Capacity management by global shipping alliances : findings from a game experiment

The present article uses game experiments to understand the dynamics of oligopolistic competition in liner shipping markets. We show how a limited number of carriers, interacting over time, acting independently or grouped into global shipping alliances, are able to effectively and jointly reduce excess capacity. A serious game (called TRALIN) has been designed to this end, mimicking the global liner shipping market where four to five global shipping alliances compete on a set of 12 routes, connecting four ports of call for a few sequential voyages. Carriers are initially subject to low profits due to over-capacity and have to anticipate competitor capacity decisions and vessel deployment simultaneously. Results from 18 experimental games with 4644 decisions were collected and statistically analysed to confirm the main tenets of oligopoly theory and to highlight the existence of a learning effect from successive interactions (rounds in games). Our results suggest that a 'coordinated' reduction in capacity is more likely to occur when the number of competitors is limited, but even more when excessive capacity is high, urging the need for cooperation; a learning effect amongst market participants is detected over time. Serious games are flexible tools for improving our understanding of competition, the organization of liner shipping networks, and the role played by global shipping alliances. This tool may help practitioners to understand how over-capacity is evolving within the competitive process, and what factors may influence it. Although voluntarily made simplistic for the purpose of experiments, our design allows one to focus on the main tenets of oligopoly theory as applied to shipping markets

Protecting the downstream migration of salmon smolts from hydroelectric power plants with inclined racks and optimized bypass water discharge

The sustained development of hydropower energy in the last century has caused important ecological impacts, promoting recent advances in efficient mitigation measures to be implemented in existing and future hydropower plants. Although upstream fish migration has been largely addressed with the development of fish-pass infrastructures, downstream passage solutions are often missing or inefficient, strengthening the need for their improvement and efficiency assessment. The efficiency of horizontally inclined (26 degrees) low bar spacing racks associated to a bypass was assessed using salmon smolts radiotelemetry along three successive hydropower plants (HPP) in the Ariege River (southern France). In average, nearly 90% of the smolts were successfully protected by the racks and rapidly guided to the bypass, within few minutes in most cases. Furthermore, we detected a significant positive influence of the bypass discharge (Q(bp%) expressed as the proportion of concurrent HPP discharge) on the probability of successful bypass passage, reaching 85% of successful passage with a Q(bp%) of only 3%, and more than 92% when the Q(bp%) exceeded 5%. The probability of bypass passage without hesitation (e.g. passage within the first 5 min) also increased with Q(bp%), and reached 90% with 5% of Q(bp%). Passage without hesitation was especially detected on the site having larger bypass entrances and transversal currents, providing better guidance into the bypass. High-efficiency results of inclined racks yielded with reduced Q(bp%) confirmed their relevance to mitigate some of the HPP ecological impacts, re-establishing safe downstream salmon migration with lower impact on energy production than older less efficient solutions

RibBX of Bradyrhizobium ORS285 plays an important role in intracellular persistence in various Aeschynomene host plants

Bradyrhizobium ORS285 forms a nitrogen-fixating symbiosis with both Nod factor (NF)-dependent and NF-independent Aeschynomene spp. The Bradyrhizobium ORS285 ribBA gene encodes for a putative bifunctional enzyme with 3,4-dihydroxybutanone phosphate (3,4-DHBP) synthase and guanosine triphosphate (GTP) cyclohydrolase II activities, catalyzing the initial steps in the riboflavin biosynthesis pathway. In this study, we show that inactivating the ribBA gene does not cause riboflavin auxotrophy under free-living conditions and that, as shown for RibBAs from other bacteria, the GTP cyclohydrolase II domain has no enzymatic activity. For this reason, we have renamed the annotated ribBA as ribBX. Because we were unable to identify other ribBA or ribA and ribB homologs in the genome of Bradyrhizobium ORS285, we hypothesize that the ORS285 strain can use unconventional enzymes or an alternative pathway for the initial steps of riboflavin biosynthesis. Inactivating ribBX has a drastic impact on the interaction of Bradyrhizobium ORS285 with many of the tested Aeschynomene spp. In these Aeschynomene spp., the ORS285 ribBX mutant is able to infect the plant host cells but the intracellular infection is not maintained and the nodules senesce early. This phenotype can be complemented by reintroduction of the 3,4-DHBP synthase domain alone. Our results indicate that, in Bradyrhizobium ORS285, the RibBX protein is not essential for riboflavin biosynthesis under free-living conditions and we hypothesize that its activity is needed to sustain riboflavin biosynthesis under certain symbiotic conditions

Ship- and island-based atmospheric soundings from the 2020 EUREC(4)A field campaign [Data paper]

To advance the understanding of the interplay among clouds, convection, and circulation, and its role in climate change, the Elucidating the role of clouds-circulation coupling in climate campaign (EUREC(4)A) and Atlantic Tradewind Ocean-Atmosphere Mesoscale Interaction Campaign (ATOMIC) collected measurements in the western tropical Atlantic during January and February 2020. Upper-air radiosondes were launched regularly (usually 4-hourly) from a network consisting of the Barbados Cloud Observatory (BCO) and four ships within 6-16 degrees N, 51-60 degrees W. From 8 January to 19 February, a total of 811 radiosondes measured wind, temperature, and relative humidity. In addition to the ascent, the descent was recorded for 82% of the soundings. The soundings sampled changes in atmospheric pressure, winds, lifting condensation level, boundary layer depth, and vertical distribution of moisture associated with different ocean surface conditions, synoptic variability, and mesoscale convective organization. Raw (Level 0), quality-controlled 1 s (Level 1), and vertically gridded (Level 2) data in NetCDF format (Stephan et al., 2020) are available to the public at AERIS (https://doi.org/10.25326/137). The methods of data collection and post-processing for the radiosonde data set are described here

Sea state from single optical images : a methodology to derive wind-generated ocean waves from cameras, drones and satellites

Sea state is a key variable in ocean and coastal dynamics. The sea state is either sparsely measured by wave buoys and satellites or modelled over large scales. Only a few attempts have been devoted to sea state measurements covering a large domain; in particular its estimation from optical images. With optical technologies becoming omnipresent, optical images offer incomparable spatial resolution from diverse sensors such as shore-based cameras, airborne drones (unmanned aerial vehicles/UAVs), or satellites. Here, we present a standalone methodology to derive the water surface elevation anomaly induced by wind-generated ocean waves from optical imagery. The methodology was tested on drone and satellite images and compared against ground truth. The results show a clear dependence on the relative azimuth view angle in relation to the wave crest. A simple correction is proposed to overcome this bias. Overall, the presented methodology offers a practical way of estimating ocean waves for a wide range of applications

Automatic water detection from multidimensional hierarchical clustering for Sentinel-2 images and a comparison with Level 2A processors

Continuous monitoring of water surfaces is essential for water resource management. This study presents a nonparametric unsupervised automatic algorithm for the identification of inland water pixels from multispectral satellite data using multidimensional clustering and a high-performance subsampling approach for large scenes. Clustering analysis is a technique that is used to identify similar samples in a multidimensional data space. The spectral information and derived indices were used to characterize each scene pixel individually. A machine learning approach with random subsampling and generalization through a Na ve Bayes classifier was also proposed to make the application of complex algorithms to large scenes feasible. Accuracy was evaluated using an independent dataset that provides water bodies in 15 Sentinel-2 images over France acquired in different seasons and that covers a large range of water bodies and water colour types. The validation dataset covers a water surface of more than 1200 km(2) (approximately 12 million pixels) including over 80,000 water bodies outlined using a semiautomatic active learning method, which were manually revised. The classification results were compared to the water pixel classification using three of the major Level 2A processors (MAJA, Sen2Cor and FMask) and two of the most common thresholding techniques: Otsu and Canny-edge. An input mask was used to remove coastal waters, clouds, shadows and snow pixels. Water pixels were identified automatically from the clustering process without the need for ancillary or pretrained data. Combinations using up to three water indices (Modified Normalized Difference Water Index-MNDWI, Normalized Difference Water Index-NDWI and Multiband Water Index-MBWI) and two reflectance bands (B8 and B12) were tested in the algorithm, and the best combination was NDWI-B12. Of all the methods, our method achieved the highest mean kappa score, 0.874, across all tested scenes, with a per-scene kappa ranging from 0.608 to 0.980, and the lowest mean standard deviation of 0.091. Standard Otsu's thresholding had the worst performance due to the lack of a bimodal histogram, and the Canny-edge variation achieved an overall kappa of 0.718 when used with the MNDWI. For water masks provided by generic processors, FMask outperformed MAJA and Sen2Cor and obtained an overall kappa of 0.764. In-depth analysis shows a quick drop in performance for all of the methods in identifying water bodies with a surface area below 0.5 ha, but the proposed approach outperformed the second best method by 34% in this size class

Dire wolves were the last of an ancient New World canid lineage

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America(1), yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae(2,3), there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently. Dire wolves split from living canids around 5.7 million years ago and originated in the New World isolated from the ancestors of grey wolves and coyotes, which evolved in Eurasia and colonized North America only relatively recently

Historical and future contributions of inland waters to the Congo Basin carbon balance

As the second largest area of contiguous tropical rainforest and second largest river basin in the world, the Congo Basin has a significant role to play in the global carbon (C) cycle. For the present day, it has been shown that a significant proportion of global terrestrial net primary productivity (NPP) is transferred laterally to the land-ocean aquatic continuum (LOAC) as dissolved CO2, dissolved organic carbon (DOC), and particulate organic carbon (POC). Whilst the importance of LOAC fluxes in the Congo Basin has been demonstrated for the present day, it is not known to what extent these fluxes have been perturbed historically, how they are likely to change under future climate change and land use scenarios, and in turn what impact these changes might have on the overall C cycle of the basin. Here we apply the ORCHILEAK model to the Congo Basin and estimate that 4 % of terrestrial NPP (NPP = 5800 +/- 166 Tg C yr(-1)) is currently exported from soils and vegetation to inland waters. Further, our results suggest that aquatic C fluxes may have undergone considerable perturbation since 1861 to the present day, with aquatic CO2 evasion and C export to the coast increasing by 26 % (186 +/- 41 to 235 +/- 54 Tg C yr(-1)) and 25 % (12 +/- 3 to 15 +/- 4 Tg C yr(-1)), respectively, largely because of rising atmospheric CO2 concentrations. Moreover, under climate scenario RCP6.0 we predict that this perturbation could continue; over the full simulation period (1861-2099), we estimate that aquatic CO2 evasion and C export to the coast could increase by 79 % and 67 %, respectively. Finally, we show that the proportion of terrestrial NPP lost to the LOAC could increase from approximately 3 % to 5 % from 1861-2099 as a result of increasing atmospheric CO2 concentrations and climate change. However, our future projections of the Congo Basin C fluxes in particular need to be interpreted with some caution due to model limitations. We discuss these limitations, including the wider challenges associated with applying the current generation of land surface models which ignore nutrient dynamics to make future projections of the tropical C cycle, along with potential next steps