Ocean of sound: underwater gliders observing the oceanic environment

Ocean gliders play an increasingly important role in the Global Ocean Observing System. They are now routinely used to monitor the ocean, along repeated transect lines from the coast to the open ocean, in remote locations and during severe weather events. They offer persistent presence at sea, collecting high-resolution scientific measurements during months- to year-long missions and over thousands of kilometres. The ocean glider com-munity continuously develops new sensors, new navigation capabilities and new usage for underwater gliders, increasing their observation range. This thesis investigates the opportunity offered by addition of passive acoustic monitoring (PAM) capability on ocean gliders and the associated technical challenges. Ocean gliders’ specificities, such as quiet propulsion, low speed and vertical profiling make them highly suitable for PAM applications. Ocean gliders were equipped with PAM systems during 12 missions in different conditions, in polar regions, in open ocean remote lo-cations and along routine coastal transect lines. This thesis reviews the currently avail-able PAM glider solutions, identifies technical challenges and desirable developments and presents pathways to improved scientific PAM glider observations. Intense ocean glider presence in the northwestern Mediterranean basin provided an experimental framework to demonstrate the ability to collect valuable scientific information from PAM glider surveys. Wind speed measurements obtained from glider-borne acoustic recordings, up to 20m s−1, colocated with collection of oceanographic profiles, can improve air-sea interaction studies. Sperm whale acoustic activity detected on PAM glider recordings provides information on population distribution and behaviour along the glider tracks. Wide addition of PAM systems on the ocean glider fleet would benefit for its global time and space coverage, enabling long-term observations in key areas, critical for conservation, monitoring of anthropogenic pressure and assessment of ecosystems health

Wellington : a novel method for the accurate identification of digital genomic footprints from DNase-seq data

The expression of eukaryotic genes is regulated by cis-regulatory elements such as promoters and enhancers, which bind sequence-specific DNA-binding proteins. One of the great challenges in the gene regulation field is to characterise these elements. This involves the identification of transcription factor (TF) binding sites within regulatory elements that are occupied in a defined regulatory context. Digestion with DNase and the subsequent analysis of regions protected from cleavage (DNase footprinting) has for many years been used to identify specific binding sites occupied by TFs at individual cis-elements with high resolution. This methodology has recently been adapted for high-throughput sequencing (DNase-seq). In this study, we describe an imbalance in the DNA strand-specific alignment information of DNase-seq data surrounding protein–DNA interactions that allows accurate prediction of occupied TF binding sites. Our study introduces a novel algorithm, Wellington, which considers the imbalance in this strand-specific information to efficiently identify DNA footprints. This algorithm significantly enhances specificity by reducing the proportion of false positives and requires significantly fewer predictions than previously reported methods to recapitulate an equal amount of ChIP-seq data. We also provide an open-source software package, pyDNase, which implements the Wellington algorithm to interface with DNase-seq data and expedite analyses

Sperm whale presence observed using passive acoustic monitoring from gliders of opportunity

Habitat use by the endangered Mediterranean sperm whale subpopulation remains poorly understood, especially in winter. The sustained presence of oceanographic autonomous underwater vehicles in the area presents an opportunity to improve observation effort, enabling collection of valuable sperm whale distribution data, which may be crucial to their conservation. Passive acoustic monitoring loggers were deployed on vertically profiling oceanographic gliders surveying the north-western Mediterranean Sea during winter 2012-2013 and June 2014. Sperm whale echolocation 'usual click' trains, characteristic of foraging activity, were detected and classified from the recordings, providing information about the presence of sperm whales along the glider tracks. Widespread presence of sperm whales in the north-western Mediterranean Sea was confirmed. Winter observations suggest different foraging strategies between the Ligurian Sea, where mobile and scattered individuals forage at all times of day, and the Gulf of Lion, where larger aggregations target intense oceanographic features in the open ocean such as fronts and mixing events, with reduced acoustic presence at dawn. This study demonstrates the ability to successfully observe sperm whale behaviour from passive acoustic monitoring gliders. We identified possible mission design changes to optimize data collected from passive acoustic monitoring glider surveys and significantly improve sperm whale population monitoring and habitat use

Guidance on acoustic monitoring from marine autonomous vehicles

A feasibility study presenting results from acoustic monitoring from marine autonomous vehicles in typical coastal ocean conditions (i.e. 50-­100m depth) to investigate current capability in measuring marine noise levels and detection of vocalisation of marine mammals and to provide guidance on future us

Glider and satellite monitoring of the variability of the suspended particle distribution and size in the Rhône ROFI

An experiment was carried out in the Gulf of Lions (NW Mediterranean) in February 2014 to assess the temporal and spatial variability of the distribution and size of suspended particulate matter (SPM) in the Rhône Region of Freshwater Influence (ROFI). A set of observations from an autonomous underwater glider, satellite ocean color data, and meteorological and hydrological time-series data highlighted the high variability of the Rhône River surface turbid plume and presence of a bottom nepheloid layer (BNL) that depended on wind and river discharge conditions. While continental winds pushed the surface plume offshore, marine winds pressed the plume at the coast and favored the sedimentation of as well as nourishment of the BNL. Moderate storm events favored breakage of the plume stratification and along-shelf transport of Rhône River particles. The spectral slopes of glider and satellite-derived light backscattering coefficients, γ, were used as a proxies of the SPM size distribution. The results clearly showed that the change of the SPM size in the nepheloid layers was induced by the flocculation of fine sediments, which became finer seaward throughout the ROFI, as well as the effect of rough weather in the breakup of flocs

Glider-based active acoustic monitoring of currents and turbidity in the coastal zone

The recent integration of Acoustic Doppler Current Profilers (ADCPs) onto underwater gliders changes the way current and sediment dynamics in the coastal zone can be monitored. Their endurance and ability to measure in all weather conditions increases the probability of capturing sporadic meteorological events, such as storms and floods, which are key elements of sediment dynamics. We used a Slocum glider equipped with a CTD (Conductivity, Temperature, Depth), an optical payload, and an RDI 600 kHz phased array ADCP. Two deployments were carried out during two contrasting periods of the year in the Rhone River region of freshwater influence (ROFI). Coastal absolute currents were reconstructed using the shear method and bottom tracking measurements, and generally appear to be in geostrophic balance. The responses of the acoustic backscatter index and optical turbidity signals appear to be linked to changes of the particle size distribution in the water column. Significantly, this study shows the interest of using a glider-ADCP for coastal zone monitoring. However, the comparison between suspended particulate matter dynamics from satellites and gliders also suggests that a synoptic view of the processes involved requires a multiplatform approach, especially in systems with high spatial and temporal variability, such as the Rhone ROFI area

Glider and satellite monitoring of the variability of the suspended particle distribution and size in the Rhône ROFI

An experiment was carried out in the Gulf of Lions (NW Mediterranean) in February 2014 to assess the temporal and spatial variability of the distribution and size of suspended particulate matter (SPM) in the Rhône Region of Freshwater Influence (ROFI). A set of observations from an autonomous underwater glider, satellite ocean color data, and meteorological and hydrological time-series data highlighted the high variability of the Rhône River surface turbid plume and presence of a bottom nepheloid layer (BNL) that depended on wind and river discharge conditions. While continental winds pushed the surface plume offshore, marine winds pressed the plume at the coast and favored the sedimentation of as well as nourishment of the BNL. Moderate storm events favored breakage of the plume stratification and along-shelf transport of Rhône River particles. The spectral slopes of glider and satellite-derived light backscattering coefficients, γ, were used as a proxies of the SPM size distribution. The results clearly showed that the change of the SPM size in the nepheloid layers was induced by the flocculation of fine sediments, which became finer seaward throughout the ROFI, as well as the effect of rough weather in the breakup of flocs

LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage

LMO2 is a bridging factor within a DNA binding complex and is required for definitive haematopoiesis to occur. The developmental stage of the block in haematopoietic specification is not known. We show that Lmo2-/- mouse embryonic stem cells differentiated to Flk-1+ haemangioblasts, but less efficiently to haemogenic endothelium, which only produced primitive haematopoietic progenitors. Genome-wide approaches indicated that LMO2 is required at the haemangioblast stage to position the TAL1/LMO2/LDB1 complex to regulatory elements that are important for the establishment of the haematopoietic developmental program. In the absence of LMO2, the target site recognition of TAL1 is impaired. The lack of LMO2 resulted in altered gene expression levels already at the haemangioblast stage, with transcription factor genes accounting for ∼15% of affected genes. Comparison of Lmo2-/- with Tal1-/- Flk-1+ cells further showed that TAL1 was required to initiate or sustain Lmo2 expression

Gliders for passive acoustic monitoring of the oceanic environment

Ocean gliders are quiet, buoyancy-driven, long-endurance, profiling autonomous platforms. Gliders therefore possess unique advantages as platforms for Passive Acoustic Monitoring (PAM) of the marine environment. In this paper, we review available glider platforms and passive acoustic monitoring systems, and explore current and potential uses of passive acoustic monitoring-equipped gliders for the study of physical oceanography, biology, ecology and for regulatory purposes. We evaluate limiting factors for passive acoustic monitoring glider surveys, such as platform-generated and flow noise, weight, size and energy constraints, profiling ability and slow movement. Based on data from 34 passive acoustic monitoring glider missions, it was found that <13% of the time spent at sea was unsuitable for passive acoustic monitoring measurements, either because of surface communications or glider manoeuvre, leaving the remainder available for subsequent analysis. To facilitate the broader use of passive acoustic monitoring gliders, we document best practices and include workarounds for the typical challenges of a passive acoustic monitoring glider mission. Three research priorities are also identified to improve future passive acoustic monitoring glider observations: 1) Technological developments to improve sensor integration and preserve glider endurance; 2) improved sampling methods and statistical analysis techniques to perform population density estimation from passive acoustic monitoring glider observations; and 3) calibration of the passive acoustic monitoring glider to record absolute noise levels, for anthropogenic noise monitoring. It is hoped this methodological review will assist glider users to broaden the observational capability of their instruments, and help researchers in related fields to deploy passive acoustic monitoring gliders in their studies