title: Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

authors: Pochon, Xavier

subjects: Science & Technology

abstract: High-throughput sequencing metabarcoding studies in marine biosecurity have largely focused on targeting environmental DNA (eDNA). DNA can persist extracellularly in the environment, making discrimination of living organisms difficult. In this study, bilge water samples (i.e., water accumulating on-board a vessel during transit) were collected from 15 small recreational and commercial vessels. eDNA and eRNA molecules were co-extracted and the V4 region of the 18S ribosomal RNA gene targeted for metabarcoding. In total, 62.7% of the Operational Taxonomic Units (OTUs) were identified at least once in the corresponding eDNA and eRNA reads, with 19.5% unique to eDNA and 17.7% to eRNA. There were substantial differences in diversity between molecular compartments; 57% of sequences from eDNA-only OTUs belonged to fungi, likely originating from legacy DNA. In contrast, there was a higher percentage of metazoan (50.2%) and ciliate (31.7%) sequences in the eRNA-only OTUs. Our data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps. The proportions of eDNA/eRNA shared and unshared OTUs were highly heterogeneous within individual bilge water samples. Multiple factors including boat type and the activities performed on-board, such as washing of scientific equipment, may play a major role in contributing to this variability. For some marine biosecurity applications analysis, eDNA-only data may be sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential. For these circumstances, we suggest only including OTUs that are present in both eDNA and eRNA data. OTUs found only in the eRNA data need to be interpreted with caution until further research provides conclusive evidence for their origin.

text: Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications High-throughput sequencing metabarcoding studies in marine biosecurity have largely focused on targeting environmental DNA (eDNA). DNA can persist extracellularly in the environment, making discrimination of living organisms difficult. In this study, bilge water samples (i.e., water accumulating on-board a vessel during transit) were collected from 15 small recreational and commercial vessels. eDNA and eRNA molecules were co-extracted and the V4 region of the 18S ribosomal RNA gene targeted for metabarcoding. In total, 62.7% of the Operational Taxonomic Units (OTUs) were identified at least once in the corresponding eDNA and eRNA reads, with 19.5% unique to eDNA and 17.7% to eRNA. There were substantial differences in diversity between molecular compartments; 57% of sequences from eDNA-only OTUs belonged to fungi, likely originating from legacy DNA. In contrast, there was a higher percentage of metazoan (50.2%) and ciliate (31.7%) sequences in the eRNA-only OTUs. Our data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps. The proportions of eDNA/eRNA shared and unshared OTUs were highly heterogeneous within individual bilge water samples. Multiple factors including boat type and the activities performed on-board, such as washing of scientific equipment, may play a major role in contributing to this variability. For some marine biosecurity applications analysis, eDNA-only data may be sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential. For these circumstances, we suggest only including OTUs that are present in both eDNA and eRNA data. OTUs found only in the eRNA data need to be interpreted with caution until further research provides conclusive evidence for their origin.

year: 2017

title: The impact of background and context on car distance estimation

authors: Zhang, Fan

subjects: Distance Estimation

abstract: It is well established that people underestimate the distance to objects depicted in virtual environments and two-dimensional (2D) displays. The reasons for the underestimation are still not fully understood. It is becoming more common to use virtual environment displays for driver training and testing and so understanding the distortion of perceived space that occurs in these displays is vital. We need to know what aspects of the display cause the observer to misperceive the distance to objects in the simulated environments. The research reported in this thesis investigated how people estimate distance between themselves and a car in front of them, within a number of differing environmental contexts.  Four experiments were run using virtual environment displays of various kinds and a fifth experiment was run in a real-world setting.
It was found that distance underestimation when viewing 2D displays is very common, even when familiar objects such as cars are used as the targets. The experiments also verified that people have a greater underestimation of distance in a virtual environment compared to a real-world setting. A surprising and somewhat counterintuitive result was that people underestimate distance more when the scene depicts forward motion of the observer compared to a static view.  The research also identified a number of visual features in the display (e.g., texture information) and aspects of the display (e.g., field of view) that affected the perception of distance or that had no effect. The findings should help the designers of driver-training simulators and testing equipment to better understand the types of errors that can potentially occur when humans view two-dimensional virtual environment displays.

text: The impact of background and context on car distance estimation It is well established that people underestimate the distance to objects depicted in virtual environments and two-dimensional (2D) displays. The reasons for the underestimation are still not fully understood. It is becoming more common to use virtual environment displays for driver training and testing and so understanding the distortion of perceived space that occurs in these displays is vital. We need to know what aspects of the display cause the observer to misperceive the distance to objects in the simulated environments. The research reported in this thesis investigated how people estimate distance between themselves and a car in front of them, within a number of differing environmental contexts.  Four experiments were run using virtual environment displays of various kinds and a fifth experiment was run in a real-world setting.
It was found that distance underestimation when viewing 2D displays is very common, even when familiar objects such as cars are used as the targets. The experiments also verified that people have a greater underestimation of distance in a virtual environment compared to a real-world setting. A surprising and somewhat counterintuitive result was that people underestimate distance more when the scene depicts forward motion of the observer compared to a static view.  The research also identified a number of visual features in the display (e.g., texture information) and aspects of the display (e.g., field of view) that affected the perception of distance or that had no effect. The findings should help the designers of driver-training simulators and testing equipment to better understand the types of errors that can potentially occur when humans view two-dimensional virtual environment displays.

year: 2014

title: Moonwalking "Backwards into the Future": 'Poi E,' Music Video, and Documentary

authors: Perrott, Lisa

subjects: Art

abstract: Explores how contemporary music videos travel across, shape, and transform various media, online platforms, art institutions, and cultural industries

text: Moonwalking "Backwards into the Future": 'Poi E,' Music Video, and Documentary Explores how contemporary music videos travel across, shape, and transform various media, online platforms, art institutions, and cultural industries

year: 2023-11-02