207 research outputs found
Archaea restoration raw OTU data
No full textOTU dataset of Archaea 16S ribosomal RNA from across an ecological restoration chronosequence from Mt Lofty Ranges, South Australi
Screening of DUB activity and specificity by MALDI-TOF mass spectrometry
No full textDeubiquitylases (DUBs) are key regulators of the ubiquitin system which cleave ubiquitin moieties from proteins and polyubiquitin chains. Several DUBs have been implicated in various diseases and are attractive drug targets. We have developed a sensitive and fast assay to quantify in vitro DUB enzyme activity using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Unlike other current assays, this method uses unmodified substrates, such as diubiquitin topoisomers. By analysing 42 human DUBs against all diubiquitin topoisomers we provide an extensive characterization of DUB activity and specificity. Our results confirm the high specificity of many members of the OTU and JAB/MPN/Mov34 metalloenzyme DUB families and highlight that all USPs tested display low linkage selectivity. We also demonstrate that this assay can be deployed to assess the potency and specificity of DUB inhibitors by profiling 11 compounds against a panel of 32 DUBs
DeNovo OTU Table, Phylogeny, Taxonomy Table, and Metadata
No full textDe Novo OTU table from Mothur analysi
Influence of Thermal Treatment on Kankara Kaolinite
No full textIn this work, the influence of thermal treatment on the structure of Kankara kaolinite was studied for the first time, using X-ray diffractogram (XRD), EDX, NanoSEM, FTIR-Attenuated Total Reflectance, DTA/TGA and BET surface area measurements. The treatment temperatures applied represents the peak of the transformation stages. The results show that surface area decreases with increase in temperature of treatment, while its crystal structure was transformed from the native kaolinite structure via the amorphous metakaolin to the typical mullite/crystobalite structure though with some unidentifiable peaks. The morphological studies showed that Kankara kaolinite is composed of nano-platelets of about 30nm thickness and in bundles of between 1 – 3 µm thicknesses with some marked variations/reductions as the treatment temperatures increases. The DTA/TGA result shows that the kaolinite undergoes dehydroxylation at 528.560C while been converted to metakaolin with a weight loss of about 14.4%. The presence of the characteristic OH, Al-OH, Si-OH and Si-O-Al bands were confirmed with the ATR studies which also showed the disappearance and subsequent appearance of new bands as the treatment temperature increased, this also affected the surface area and pore sizes of the transformation products
Amphibious Subjects
No full textAmphibious Subjects is an ethnographic study of a community of self-identified effeminate men— known in local parlance as sasso—residing in coastal Jamestown, a suburb of Accra, Ghana’s capital. Drawing on the Ghanaian philosopher Kwame Gyekye’s notion of “amphibious personhood,” Kwame Edwin Otu argues that sasso embody and articulate amphibious subjectivity in their self-making, creating an identity that moves beyond the homogenizing impulses of Western categories of gender and sexuality. Such subjectivity unsettles claims made by both the Christian heteronationalist state and LGBT+ human rights organizations that Ghana is predominantly heterosexual or homophobic. Weaving together personal interactions with sasso, participant observation, autoethnography, archival sources, essays from African and African-diasporic literature, and critical analyses of documentaries such as the BBC’s The World’s Worst Place to Be Gay, Amphibious Subjects is an ethnographic meditation on how Africa is configured as the “heart of homophobic darkness” in transnational LGBT+ human rights imaginaries.
“This book is a powerful synthesis of African theorization and rigorous fieldwork that presents an engaging and convincing read of a location. Kwame Edwin Otu’s work is not simply meaningful for Jamestown, Accra, Ghana, or West Africa; it has real import elsewhere while remaining committed to its locality and subjects, a rare feat.” T. J. Tallie, author of Queering Colonial Natal: Indigeneity and the Violence of Belonging in Southern Africa
“A unique project based on groundbreaking research. There is no other work that gives such elegant insight into the multifarious desires of queer life—in an African city or anywhere. Otu convincingly shows how simplistic identity categories are confounded by the fluidities and illegibilities of lived queer experience.” Jesse Weaver Shipley, Professor of African and African American Studies and Oratory, Dartmouth Colleg
Amphibious Subjects
No full textAmphibious Subjects is an ethnographic study of a community of self-identified effeminate men— known in local parlance as sasso—residing in coastal Jamestown, a suburb of Accra, Ghana’s capital. Drawing on the Ghanaian philosopher Kwame Gyekye’s notion of “amphibious personhood,” Kwame Edwin Otu argues that sasso embody and articulate amphibious subjectivity in their self-making, creating an identity that moves beyond the homogenizing impulses of Western categories of gender and sexuality. Such subjectivity unsettles claims made by both the Christian heteronationalist state and LGBT+ human rights organizations that Ghana is predominantly heterosexual or homophobic. Weaving together personal interactions with sasso, participant observation, autoethnography, archival sources, essays from African and African-diasporic literature, and critical analyses of documentaries such as the BBC’s The World’s Worst Place to Be Gay, Amphibious Subjects is an ethnographic meditation on how Africa is configured as the “heart of homophobic darkness” in transnational LGBT+ human rights imaginaries.
“This book is a powerful synthesis of African theorization and rigorous fieldwork that presents an engaging and convincing read of a location. Kwame Edwin Otu’s work is not simply meaningful for Jamestown, Accra, Ghana, or West Africa; it has real import elsewhere while remaining committed to its locality and subjects, a rare feat.” T. J. Tallie, author of Queering Colonial Natal: Indigeneity and the Violence of Belonging in Southern Africa
“A unique project based on groundbreaking research. There is no other work that gives such elegant insight into the multifarious desires of queer life—in an African city or anywhere. Otu convincingly shows how simplistic identity categories are confounded by the fluidities and illegibilities of lived queer experience.” Jesse Weaver Shipley, Professor of African and African American Studies and Oratory, Dartmouth Colleg
High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration: OTU raw data matrix
No full texteDNA metabarcoding: Three 25 m x 25 m quadrats were randomly selected per site, giving a total of 24 quadrats across the 8 sites. Soil was sampled from the 0-10 cm and 20-30 cm soil horizons at each quadrat. A representative 50 g sample of soil was collected at each of these 24 quadrats by pooling nine soil samples from each soil depth, including soil from open areas and under plants. These nine soil samples were pooled into a sterile plastic bag, and homogenized using a sterilized trowel. All soil samples (n = 48) were frozen on site in sterile 50 mL falcon tubes until DNA extraction hereafter referred to as technical replicates.<p><b>Credit</b><br/>We at TERN acknowledge the Traditional Owners and Custodians throughout Australia, New Zealand and all nations. We honour their profound connections to land, water, biodiversity and culture and pay our respects to their Elders past, present and emerging.<br/>We thank A. Bissett, S. Kennedy, Z. Baruch, S. Caddy-Retalic, L. Clarke, S. Kennedy, I. Fox, M. Laws, K. McCallum, and J. McDonald for technical and field assistance. We are grateful for support from the BASE project, Australian Genome Research Facility, BioPlatforms Australia, and SA Water. This work was supported by Australian Research Council funding to AJL and MFB (DE150100542; DP150103414), and China Scholarship Council funding to DY (201408410176). We would also like to acknowledge the contribution of the BASE project partners DOI 10.4227/71/ 561c9bc670099, an initiative supported by Bioplatforms Australia with funds provided by the Australian Commonwealth Government through the National Collaborative Research Infrastructure Strategy.<b>Purpose</b><br/>This project was conducted during the author's PhD. The OTU data was generated for the manuscript titled "High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration" that uses eDNA assessment to provide a significant extension to current restoration monitoring practice.Progress Code: completedMaintenance and Update Frequency: notPlannedWe present a High-throughput eDNA dataset of fungi to track functional recovery in ecological restoration in the form of an OTU raw data matrix. We generated a total of 4,993,144 ITS fungal raw reads (118,884 ± 42,210 SD per replicate) across the 42 replicates. A total of 4,955,680 fungal sequences (117,430 ± 42,164 SD per replicate) remained for further analysis after quality filtering. The OTU data provide information on fungal flux at this restoration site through a stagger of years and can be used accordingly
Archaeal community responses to a decade of ecological restoration: OTU raw data matrix
No full texteDNA metabarcoding : Three 25 m x 25 m quadrats were randomly selected per site, giving a total of 24 quadrats across the 8 sites. Soil was sampled from the 0-10 cm and 20-30 cm soil horizons at each quadrat. A representative 50 g sample of soil was collected at each of these 24 quadrats by pooling nine soil samples from each soil depth, including soil from open areas and under plants. These nine soil samples were pooled into a sterile plastic bag, and homogenized using a sterilized trowel. All soil samples (n = 48) were frozen on site in sterile 50 mL falcon tubes until DNA extraction, hereafter referred to as technical replicates.<p><b>Credit</b><br/>We at TERN acknowledge the Traditional Owners and Custodians throughout Australia, New Zealand and all nations. We honour their profound connections to land, water, biodiversity and culture and pay our respects to their Elders past, present and emerging.<br/>We thank A. Bissett, S. Kennedy, Z. Baruch, S. Caddy-Retalic, L. Clarke, S. Kennedy, I. Fox, M. Laws, K. McCallum, and J. McDonald for technical and field assistance. We are grateful for support from the BASE project, Australian Genome Research Facility, BioPlatforms Australia, and SA Water. This work was supported by Australian Research Council funding to AJL and MFB (DE150100542; DP150103414), and China Scholarship Council funding to DY (201408410176). We would also like to acknowledge the contribution of the BASE project partners DOI 10.4227/71/ 561c9bc670099, an initiative supported by Bioplatforms Australia with funds provided by the Australian Commonwealth Government through the National Collaborative Research Infrastructure Strategy.<b>Purpose</b><br/>This project was conducted as a part of the author's PhD. The OTU data was generated for the manuscript titled "Archaeal community responses to a decade of ecological restoration" that uses eDNA assessment to provide a significant extension to current restoration monitoring practice.Progress Code: completedMaintenance and Update Frequency: notPlannedWe generated a total of 2,313,977 16S archaeal raw reads across the 36 replicates (64,277 ± 23,335 SD per replicate). A total of 2,299,955 archaeal sequences (63,888 ± 23,473 SD per replicate) and 1,937 archaeal OTUs (54 ± 20 SD per replicate) remained for further analysis after quality filtering. The OTU data provide information on archaeal flux at an active restoration site at Mt Bold, a water catchment reserve of the Mt Lofty Ranges in South Australia, through a stagger of years and can be used accordingly
Revegetation rewilds the soil bacterial microbiome of an old field- Part 1: OTU raw data matrix
No full textEDNA metabarcoding: Three 25 m x 25 m quadrats were randomly selected per site, giving a total of 24 quadrats across the 8 sites. Soil was sampled from the 0-10 cm and 20-30 cm soil horizons at each quadrat. A representative 50 g sample of soil was collected at each of these 24 quadrats by pooling nine soil samples from each soil depth, including soil from open areas and under plants. These nine soil samples were pooled into a sterile plastic bag, and homogenised using a sterilised trowel. All soil samples (n = 48) were frozen on site in sterile 50 mL falcon tubes until DNA extraction- hereafter referred to as technical replicates.<p><b>Credit</b><br/>We at TERN acknowledge the Traditional Owners and Custodians throughout Australia, New Zealand and all nations. We honour their profound connections to land, water, biodiversity and culture and pay our respects to their Elders past, present and emerging.<br/>The authors thank A. Bissett, A. Fitzgerald, A. Young, Z. Baruch, S. Caddy-Retalic, L. Clarke, S. Kennedy, I. Fox, M. Laws, K. McCallum, and J. McDonald for technical and field assistance. We are grateful for technical, field and site access support from the Australian Genome Research Facility, BioPlatforms Australia, SA Water and the Terrestrial Ecosystem Research Network. This work was supported by Australian Research Council funding to AJL and MFB (DE150100542; DP150103414).<b>Purpose</b><br/>This project forms part of the authors PhD. The OTU data was generated for a manuscript in Molecular Ecology "Revegetation rewilds the soil bacterial microbiome of an old field" https://doi.org/10.1111/mec.14081 that uses eDNA assessment to provide a significant extension to current restoration monitoring practice.Progress Code: completedMaintenance and Update Frequency: notPlannedThe authors analyzed a total of 3,002,411 quality-filtered bacterial 16S rRNA gene sequences in the 48 technical replicates across 8 revegetation chronosequence sites, consisting of 3,316 OTUs. Nine bacterial phyla dominated this dataset, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia.The OTU data provide information on bacterial flux at this restoration site through a stagger of years and can be used accordingly
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