title: MIR task and evaluation techniques

authors: McEnnis, Daniel

subjects: computer science

abstract: Existing tasks in MIREX have traditionally focused on low-level MIR tasks working with flat (usually DSP-only) ground-truth. These evaluation techniques, however, can not evaluate the increasing number of algorithms that utilize relational data and are not currently utilizing the state of the art in evaluating ranked or ordered output. This paper summarizes the state of the art in evaluating relational ground-truth. These components are then synthesized into novel evaluation techniques that are then applied to 14 concrete music document retrieval tasks, demonstrating how these evaluation techniques can be applied in a practical context.

text: MIR task and evaluation techniques Existing tasks in MIREX have traditionally focused on low-level MIR tasks working with flat (usually DSP-only) ground-truth. These evaluation techniques, however, can not evaluate the increasing number of algorithms that utilize relational data and are not currently utilizing the state of the art in evaluating ranked or ordered output. This paper summarizes the state of the art in evaluating relational ground-truth. These components are then synthesized into novel evaluation techniques that are then applied to 14 concrete music document retrieval tasks, demonstrating how these evaluation techniques can be applied in a practical context.

year: 2009-08-12

title: Cultivating microbial dark matter - A combination of traditional and molecular techniques

authors: King, Charlotte

abstract: The services bacteria offer the world are immense and impact people's lives daily. They were first described by Antoni van Leeuwenhoek in 1676, but bacteria have been utilised in the medical, agricultural, and food and beverage industries even before they were formally identified. Microbes’ roles in the environment for cycling of nutrients, climate regulation and pollution are becoming more well understood, and they are also utilised to answer a wide variety of research questions in disparate fields. Traditional cultivation techniques were initially developed to study bacteria and understand their functions as isolates. Such cultivation techniques have become rarer as new molecular and bioinformatic tools have been developed. These cultivation- independent techniques have allowed the study of microbial life genetic data which led to the finding that 99% of all microbial species were yet to be cultured and studied in a laboratory. The applications of these unstudied organisms could be unprecedented, though their cultivation remains challenging due to the requirement of specific nutrients that are hard to identify, very slow growth rates, environmental conditions that are difficult to replicate in a laboratory setting, live in symbiosis with other organisms, or live in extreme climates. Therefore, much of the information may be overlooked and hidden in this microbial dark matter. Methods such as metagenomics, metagenome-assembled genomes (MAGs), and single amplified genomes (SAGs) have provided us with genomic data for previously uncharacterised microbes from diverse environments. However, such data is still limited. Omics tools can provide insights into what is living there and what it can potentially do. However, this data is regularly incomplete due to the processes involved in sequencing, and conclusions are often drawn from associations relating to cultured organisms. This can lead to potentially spurious conclusions as a gene may behave differently in different species, and the absence of genes may depend on how the data was analysed. Therefore, cultured isolates of the organism are vital. To combat this issue of an uncultivated majority, it is important to have a targeted approach to culture, what is wanted, not just what is easy.

This thesis aimed to provide an easy-to-follow, straightforward workflow to cultivate target environmental organisms using standard molecular tools and methods readily accessible in any standard microbiological laboratory. The idea is to isolate and culture what is specifically wanted or needed, not just what is easy. Specifically, it combined classical cultivation and molecular techniques to target a sulphur-reducing, obligate anaerobe from an environmental sample— namely a Desulfurella sp. from a geothermal pool in Rotorua, New Zealand.
In order to provide the desired targeted approach, specific primers needed to be designed and assessed to first find the right sampling site for the initial inoculum and second to ensure the target is not lost throughout the culturing process. I designed and evaluated primers for targeting specific taxa at different stringency levels. Initially, I tested published primers (EPS_F/EPS_R, Gittel et al., 2012) aimed at Epsilonproteobacteria, which were reclassified into the Campylobacterota phylum (including Desulfurella sp.). These primers did not target Desulfurella sp., so I modified them (EPS_FM/EPS_RL) to produce a longer amplicon for broader Campylobacterota detection. However, these also amplified non-target species (e.g., Desulfobacterota). Finally, I designed a third set of primers (DS_F/DS_R) specific to Desulfurella sp., confirmed by in silico testing. These primers allow assessment of Desulfurella sp. and broader Campylobacterota before sequencing.
The second experimental chapter focuses on enriching the target using the previously described primers, classical cultivation techniques, and molecular tools. Site selection was based on the 1000 Springs Project (Power et al., 2018). Culturing was performed originally with DSMZ Desulfurella medium and later modified, investigating pH (4 and 6) and temperature (50°C and 30°C) variations and adapting it for solid media by replacing elemental sulphur with sodium polysulfide. I used a vacuum food sealer to cultivate anaerobes, an accessible and portable alternative to expensive anaerobic chambers. Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to assess axenicity before sending samples for 16S rRNA gene and whole genome sequencing. Desulfurella was detected in each culture using species-specific primers (DS_F/DS_R), enabling its phylogenetic placement. However, despite Desulfurella presence in the 16S rRNA gene amplicon sequencing, a metagenome-assembled genome (MAG) could not be produced. This thesis discusses lessons learned and suggests improvements for future studies.

text: Cultivating microbial dark matter - A combination of traditional and molecular techniques The services bacteria offer the world are immense and impact people's lives daily. They were first described by Antoni van Leeuwenhoek in 1676, but bacteria have been utilised in the medical, agricultural, and food and beverage industries even before they were formally identified. Microbes’ roles in the environment for cycling of nutrients, climate regulation and pollution are becoming more well understood, and they are also utilised to answer a wide variety of research questions in disparate fields. Traditional cultivation techniques were initially developed to study bacteria and understand their functions as isolates. Such cultivation techniques have become rarer as new molecular and bioinformatic tools have been developed. These cultivation- independent techniques have allowed the study of microbial life genetic data which led to the finding that 99% of all microbial species were yet to be cultured and studied in a laboratory. The applications of these unstudied organisms could be unprecedented, though their cultivation remains challenging due to the requirement of specific nutrients that are hard to identify, very slow growth rates, environmental conditions that are difficult to replicate in a laboratory setting, live in symbiosis with other organisms, or live in extreme climates. Therefore, much of the information may be overlooked and hidden in this microbial dark matter. Methods such as metagenomics, metagenome-assembled genomes (MAGs), and single amplified genomes (SAGs) have provided us with genomic data for previously uncharacterised microbes from diverse environments. However, such data is still limited. Omics tools can provide insights into what is living there and what it can potentially do. However, this data is regularly incomplete due to the processes involved in sequencing, and conclusions are often drawn from associations relating to cultured organisms. This can lead to potentially spurious conclusions as a gene may behave differently in different species, and the absence of genes may depend on how the data was analysed. Therefore, cultured isolates of the organism are vital. To combat this issue of an uncultivated majority, it is important to have a targeted approach to culture, what is wanted, not just what is easy.

This thesis aimed to provide an easy-to-follow, straightforward workflow to cultivate target environmental organisms using standard molecular tools and methods readily accessible in any standard microbiological laboratory. The idea is to isolate and culture what is specifically wanted or needed, not just what is easy. Specifically, it combined classical cultivation and molecular techniques to target a sulphur-reducing, obligate anaerobe from an environmental sample— namely a Desulfurella sp. from a geothermal pool in Rotorua, New Zealand.
In order to provide the desired targeted approach, specific primers needed to be designed and assessed to first find the right sampling site for the initial inoculum and second to ensure the target is not lost throughout the culturing process. I designed and evaluated primers for targeting specific taxa at different stringency levels. Initially, I tested published primers (EPS_F/EPS_R, Gittel et al., 2012) aimed at Epsilonproteobacteria, which were reclassified into the Campylobacterota phylum (including Desulfurella sp.). These primers did not target Desulfurella sp., so I modified them (EPS_FM/EPS_RL) to produce a longer amplicon for broader Campylobacterota detection. However, these also amplified non-target species (e.g., Desulfobacterota). Finally, I designed a third set of primers (DS_F/DS_R) specific to Desulfurella sp., confirmed by in silico testing. These primers allow assessment of Desulfurella sp. and broader Campylobacterota before sequencing.
The second experimental chapter focuses on enriching the target using the previously described primers, classical cultivation techniques, and molecular tools. Site selection was based on the 1000 Springs Project (Power et al., 2018). Culturing was performed originally with DSMZ Desulfurella medium and later modified, investigating pH (4 and 6) and temperature (50°C and 30°C) variations and adapting it for solid media by replacing elemental sulphur with sodium polysulfide. I used a vacuum food sealer to cultivate anaerobes, an accessible and portable alternative to expensive anaerobic chambers. Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to assess axenicity before sending samples for 16S rRNA gene and whole genome sequencing. Desulfurella was detected in each culture using species-specific primers (DS_F/DS_R), enabling its phylogenetic placement. However, despite Desulfurella presence in the 16S rRNA gene amplicon sequencing, a metagenome-assembled genome (MAG) could not be produced. This thesis discusses lessons learned and suggests improvements for future studies.

year: 2024

title: Between the borders

authors: Apiata, Hāwea

abstract: Ekphrasis in response to the artwork 'Taniko Border 6' by Ngāti Raukawa artist, John Bevan Ford.

text: Between the borders Ekphrasis in response to the artwork 'Taniko Border 6' by Ngāti Raukawa artist, John Bevan Ford.

year: 2023-11-30