Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes
- Authors: Sloan, Shelly , Jenvey, C. J. , Piedrafita, David , Preston, Sarah , Stear, Michael
- Date: 2021
- Type: Text , Journal article
- Relation: Bmc Biotechnology Vol. 21, no. 1 (May 17 2021), p.
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Blood and saliva-derived exomes from healthy Caucasian subjects do not display overt evidence of somatic mosaicism
- Authors: Hall, Nathan , Mamrot, Jared , Frampton, Chris , Read, Prue , Steele, Edward , Bischoff, Robert , Lindley, Robyn
- Date: 2020
- Type: Text , Journal article
- Relation: Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis Vol. 821, no. (2020), p.
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- Description: Somatic mosaicism is a normal occurrence during development in the tissues and organs. As part of establishing a “healthy population “(HP) background or base-line, we investigated whether such mosaicism can be routinely detected in the circulating DNA secured from a rigorously designed healthy human liquid biopsy clinical trial (saliva, blood). We deployed next generation (NG) whole exome sequencing (WES) at median exome coverage rates of 97.2 % (-to-30x) and 70.0 % (-to-100x). We found that somatic mosaicism is not detectable by such standard bulk WES sequencing assays in saliva and blood DNA in 24 normal healthy Caucasians of both sexes from 18 to 60 years of age. We conclude that for circulating DNA using standard WES no novel somatic mutational variants can be detected in protein-coding regions of normal healthy subjects. This implies that the extent within normal tissues of somatic mosaicism must be at a lower level, below the detection threshold, for these circulating DNA WES read depths. © 2020 The Author(s)
Rainforest, woodland or swampland? Integrating time, space and culture to manage an endangered ecosystem complex in the Australian wet tropics
- Authors: Lynch, A. , Ferrier, Asa , Ford, A. J. , Haberle, Simon , Rule, Stephen , Schneider, Larissa , Zawadzki, A. , Metcalfe, Daniel
- Date: 2020
- Type: Text , Journal article
- Relation: Landscape Ecology Vol. 35, no. 1 (2020), p. 83-99
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- Description: Context: Transdisciplinary research is important where information from multiple fields is required to develop ecologically and culturally appropriate environmental planning that protects local conservation and socio-cultural values. Objectives: Here, we describe research to inform ecosystem restoration and conservation of Chumbrumba Swamp within the Wet Tropics World Heritage Area, Australia. Many such open wetlands in the region have been degraded through agriculture and pastoral production, but there has been little research into their status, history and conservation needs. Methods: The recent to pre-European settlement history of the site was explored, along with spatial variation of vegetation communities at the site, and these data integrated with historical and ethnographical information on the site and its cultural values. Results: The botanical and palaeoecological analyses showed that Chumbrumba Swamp comprises a unique and highly sensitive ecosystem mosaic with high biodiversity. An endangered ecosystem complex, 82 vascular plant species, several disjunct or endemic taxa, and species at new northern range limits were recorded within its 20 ha area. The site comprises a stable swamp site with fringing woodland and rainforest that has persisted for around 5000 years. European settlement overlaid changes in the vegetation from disturbance (e.g. fire, clearing, grazing). However, fire also affected the swamp site during pre-European times. Conclusions: Historical and ethnographic information contextualised the biophysical data and confirmed the cultural importance of the site and the dynamic interactions between ‘people and nature’. These results have been used to inform environmental restoration and validate the importance of a transdisciplinary and precautionary approach to planning wetland restoration and conservation. © 2019, Springer Nature B.V.
A roadmap to generate renewable protein binders to the human proteome
- Authors: Colwill, Karen , Persson, Helena , Jarvik, Nicholas , Wyrzucki, Arkadiusz , Wojcik, John , Koide, Akiko , Kossiakoff, Anthony , Koide, Shohei , Sidhu, Sachdev , Dyson, Michael , Pershad, Kritika , Pavlovic, John , Karatt-Vellatt, Aneesh , Schofield, Darren , Kay, Brian , McCafferty, John , Mersmann, Michael , Meier, Doris , Mersmann, Jana , Helmsing, Saskia , Hust, Michael , Dubel, Stefan , Berkowicz, Susan , Freemantle, Alexia , Spiegel, Michael , Sawyer, Alan , Layton, Daniel , Nice, Edouard , Dai, Anna , Rocks, Oliver , Williton, Kelly , Fellouse, Frederic , Hersi, Kadija , Pawson, Tony , Nilsson, Peter , Sundberg, Marten , Sjoberg, Ronald , Sivertsson, Asa , Schwenk, Jochen , Takanen, Jenny , Hober, Sophia , Uhlen, Mathias , Dahlgren, Lars-Goran , Flores, Alex , Johansson, Ida , Weigelt, Johan , Crombet, Lissette , Loppnau, Peter , Kozieradzki, Ivona , Cossar, Doug , Arrowsmith, C. , Edwards, Aled , Graslund, Susanne
- Date: 2011
- Type: Text , Journal article
- Relation: Nature Methods Vol. 8, no. 7 (2011), p. 551-558
- Full Text: false
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- Description: Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders.
Activation of proteases in an anaerobic sulphidogenic bioreactor
- Authors: Whiteley, Chris , Pletschke, Brett , Rose, Peter , Tshivhunge, Sylvia , Watson, Shaun , Whittington-Jones, Kevin
- Date: 2004
- Type: Text , Journal article
- Relation: Biotechnology Letters Vol. 26, no. 1 (2004), p. 55-59
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- Description: Activities of proteases were stimulated by specific sulphur metabolites during the enhanced hydrolysis of complex polymeric organic carbon in an anaerobic sulphidogenic environment. While sulphate at 1000 mg l(-1) inhibited proteases by 50%, there was a 2.5-fold increase in activity of proteases by added sulphite and a 3.6-fold increase from added sulphide. Two hypothetical models are proposed. First the sulphur species, sulphite (HSO3-) and sulphide (HS-), liberated at different times during the sulphate reduction process, directly activate the proteases, which are associated with the organic particulate matter, leading to a subsequent enhancement of hydrolysis of polymeric material. Second, they indirectly activate the proteases by neutralising the cations on the floc surface disrupting the integrity of the organic particulate floc therebye releasing further entrapped enzymes from the organic particulate matter.