Visualizing the invisible : class excursions to ignite children’s enthusiasm for microbes
McGenity, Terry J. ; Gessesse, Amare ; Hallsworth, John E. ; Garcia Cela, Esther ; Verheecke-Vaessen, Carol ; Wang, Fengping ; Chavarría, Max ; Haggblom, Max M. ; Molin, Søren ; Danchin, Antoine ; Smid, Eddy J. ; Lood, Cédric ; Cockell, Charles S. ; Whitby, Corinne ; Liu, Shuang Jiang ; Keller, Nancy P. ; Stein, Lisa Y. ; Bordenstein, Seth R. ; Lal, Rup ; Nunes, Olga C. ; Gram, Lone ; Singh, Brajesh K. ; Webster, Nicole S. ; Morris, Cindy ; Sivinski, Sharon ; Bindschedler, Saskia ; Junier, Pilar ; Antunes, André ; Baxter, Bonnie K. ; Scavone, Paola ; Timmis, Kenneth - \ 2020
Microbial Biotechnology (2020). - ISSN 1751-7907
We have recently argued that, because microbes have pervasive – often vital – influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology-literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513-1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public-health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well-being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of ‘germs’ and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination-capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision-making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology-centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre-occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.
On the merits and pitfalls of introducing a digital platform to aid conservation management : Volunteer data submission and the mediating role of volunteer coordinators
Arts, Koen ; Melero, Yolanda ; Webster, Gemma ; Sharma, Nirwan ; Tintarev, Nava ; Tait, Elizabeth ; Mellish, Christopher ; Sripada, Somayajulu ; MacMaster, Ann Marie ; Sutherland, Hollie ; Horrill, Chris ; Lambin, Xavier ; Wal, René van der - \ 2020
Journal of Environmental Management 265 (2020). - ISSN 0301-4797
Environmental citizen science - Human-computer interaction - Invasive species control - Technological innovation - Volunteer coordination - Volunteer-based management
Against a backdrop of accelerating digital innovation in nature conservation and environmental management, a real-world experiment was conducted with the research aims of assessing: 1) the effects of introducing a digital data-entry platform on volunteer data submission; and 2) the extent to which coordinators influence digital platform use by their volunteers. We focussed on a large-scale volunteer-based initiative aimed at eradicating the non-native American mink (Neovison vison) from northern Scotland. This geographically dispersed conservation initiative adopted a digital platform that allowed volunteers to submit records to a central database. We found that the platform had a direct and positive effect on volunteer data submission behaviour, increasing both the number and frequency of submissions. However, our analysis revealed striking differences in coordinator engagement with the platform, which in turn influenced the engagement of volunteers with this centrally introduced digital innovation. As a consequence, the intended organisation-wide rolling out of a digital platform translated into a diversely-implemented innovation, limiting the efficacy of the tool and revealing key challenges for digital innovation in geographically-dispersed conservation initiatives.
Global patterns and drivers of ecosystem functioning in rivers and riparian zones
Tiegs, Scott D. ; Costello, David M. ; Isken, Mark W. ; Woodward, Guy ; McIntyre, Peter B. ; Gessner, Mark O. ; Chauvet, Eric ; Griffiths, Natalie A. ; Flecker, Alex S. ; Acuña, Vicenç ; Albariño, Ricardo ; Allen, Daniel C. ; Alonso, Cecilia ; Andino, Patricio ; Arango, Clay ; Aroviita, Jukka ; Barbosa, Marcus V.M. ; Barmuta, Leon A. ; Baxter, Colden V. ; Bell, Thomas D.C. ; Bellinger, Brent ; Boyero, Luz ; Brown, Lee E. ; Bruder, Andreas ; Bruesewitz, Denise A. ; Burdon, Francis J. ; Callisto, Marcos ; Canhoto, Cristina ; Capps, Krista A. ; Castillo, María M. ; Clapcott, Joanne ; Colas, Fanny ; Colón-Gaud, Checo ; Cornut, Julien ; Crespo-Pérez, Verónica ; Cross, Wyatt F. ; Culp, Joseph M. ; Danger, Michael ; Dangles, Olivier ; Eyto, Elvira De; Derry, Alison M. ; Villanueva, Veronica Díaz ; Douglas, Michael M. ; Elosegi, Arturo ; Encalada, Andrea C. ; Entrekin, Sally ; Espinosa, Rodrigo ; Ethaiya, Diana ; Ferreira, Verónica ; Ferriol, Carmen ; Flanagan, Kyla M. ; Fleituch, Tadeusz ; Follstad Shah, Jennifer J. ; Barbosa, André Frainer ; Friberg, Nikolai ; Frost, Paul C. ; Garcia, Erica A. ; Lago, Liliana García ; Soto, Pavel Ernesto García ; Ghate, Sudeep ; Giling, Darren P. ; Gilmer, Alan ; Gonçalves, José Francisco ; Gonzales, Rosario Karina ; Graça, Manuel A.S. ; Grace, Mike ; Grossart, Hans Peter ; Guérold, François ; Gulis, Vlad ; Hepp, Luiz U. ; Higgins, Scott ; Hishi, Takuo ; Huddart, Joseph ; Hudson, John ; Imberger, Samantha ; Iñiguez-Armijos, Carlos ; Iwata, Tomoya ; Janetski, David J. ; Jennings, Eleanor ; Kirkwood, Andrea E. ; Koning, Aaron A. ; Kosten, Sarian ; Kuehn, Kevin A. ; Laudon, Hjalmar ; Leavitt, Peter R. ; Lemes Da Silva, Aurea L. ; Leroux, Shawn J. ; LeRoy, Carri J. ; Lisi, Peter J. ; MacKenzie, Richard ; Marcarelli, Amy M. ; Masese, Frank O. ; McKie, Brendan G. ; Medeiros, Adriana Oliveira ; Meissner, Kristian ; Miliša, Marko ; Mishra, Shailendra ; Miyake, Yo ; Moerke, Ashley ; Mombrikotb, Shorok ; Mooney, Rob ; Moulton, Tim ; Muotka, Timo ; Negishi, Junjiro N. ; Neres-Lima, Vinicius ; Nieminen, Mika L. ; Nimptsch, Jorge ; Ondruch, Jakub ; Paavola, Riku ; Pardo, Isabel ; Patrick, Christopher J. ; Peeters, Edwin T.H.M. ; Pozo, Jesus ; Pringle, Catherine ; Prussian, Aaron ; Quenta, Estefania ; Quesada, Antonio ; Reid, Brian ; Richardson, John S. ; Rigosi, Anna ; Rincón, José ; Rîşnoveanu, Geta ; Robinson, Christopher T. ; Rodríguez-Gallego, Lorena ; Royer, Todd V. ; Rusak, James A. ; Santamans, Anna C. ; Selmeczy, Géza B. ; Simiyu, Gelas ; Skuja, Agnija ; Smykla, Jerzy ; Sridhar, Kandikere R. ; Sponseller, Ryan ; Stoler, Aaron ; Swan, Christopher M. ; Szlag, David ; Teixeira-De Mello, Franco ; Tonkin, Jonathan D. ; Uusheimo, Sari ; Veach, Allison M. ; Vilbaste, Sirje ; Vought, Lena B.M. ; Wang, Chiao Ping ; Webster, Jackson R. ; Wilson, Paul B. ; Woelfl, Stefan ; Xenopoulos, Marguerite A. ; Yates, Adam G. ; Yoshimura, Chihiro ; Yule, Catherine M. ; Zhang, Yixin X. ; Zwart, Jacob A. - \ 2019
Science Advances 5 (2019)1. - ISSN 2375-2548 - p. 14966 - 14973.
River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.
Improved Pastures Support Early Indicators of Soil Restoration in Low-input Agroecosystems of Nicaragua
Webster, Emily ; Gaudin, Amélie C.M. ; Pulleman, Mirjam ; Siles, Pablo ; Fonte, Steven J. - \ 2019
Environmental Management 64 (2019)2. - ISSN 0364-152X - p. 201 - 212.
Brachiaria brizantha - Earthworms - Pasture degradation - Permanganate oxidizable carbon - Silvopastoral systems - Soil health
Pasture degradation hinders livestock production and ecosystem services that support rural smallholder communities throughout Latin America. Silvopastoral systems, with improved pasture cultivars (especially Brachiaria spp.) and multipurpose trees, offer a promising strategy to restore soils and improve livelihoods in the region. However, studies evaluating the impact of such systems on pasture productivity and soil health under realistic smallholder constraints are lacking. We evaluated the impact of improved pasture grass and tree establishment on a suite of soil health indicators in actively grazed, low-input, farmer-managed silvopastoral systems. In August 2013, paired pasture treatments (improved grass with trees vs. traditional pastures) were established on nine farms with similar land-use histories near Matagalpa, Nicaragua. On each farm, one treatment was left as traditional pasture with naturalized grass (Hyparrhenia rufa), while the adjacent treatment was sown with the improved grass (Brachiaria brizantha cv. Marandu) and planted with tree saplings without fertilizer. In August 2015, we measured standing biomass and a suite of chemical, biological, and physical soil health variables. Improved silvopastoral systems with B. brizantha produced more standing grass biomass and supported higher levels of earthworm populations and permanganate oxidizable carbon (POXC) compared to the traditional control. Correlations suggest that earthworms and POXC were associated with incipient improvements to soil aggregate stability and water holding capacity. We report measurable improvements to soil health just two years following the establishment of improved pasture systems under common smallholder management practices and suggest that these systems, even with minimal fertility inputs, have the potential to enhance regional sustainability.
Burgess, T.M. & Webster, R. 1980. Optimal interpolation and isarithmic mapping of soil properties. I. The semi-variogram and punctual kriging. Journal of Soil Science, 31, 315–331. : Commentary on the impact of Burgess & Webster (1980a) by R.M. Lark, G.B.M. Heuvelink and T.F.A. Bishop
Lark, R.M. ; Heuvelink, G.B.M. ; Bishop, T.F.A. - \ 2019
European Journal of Soil Science 70 (2019)1. - ISSN 1351-0754 - p. 7 - 10.
Erratum to: The sponge microbiome project
Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
GigaScience 7 (2018)12. - ISSN 2047-217X
The sponge microbiome project
Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
GigaScience 6 (2017)10. - ISSN 2047-217X
16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
Genetic selection for dairy cow welfare and resilience to climate change
Pryce, J. ; Haas, Y. de - \ 2017
In: Achieving sustainable production of milk / Webster, John, Burleigh Dodds Science Publishing Limited - ISBN 9781786760524
Rates of genetic gain in dairy cows are impressive, especially for milk production traits that drive profitability (VanRaden 2004). However, narrow breeding goals focused on milk production traits are detrimental to reproductive performance and health of cows (Rauw et al. 1998), and consequently there has been pressure to develop breeding values to enable selection that balances both production and non-production traits. Although, the rationale to extend breeding goals initially focused entirely on the impact of the new breeding value to farmer profitability, breeding goals are now becoming more complex in order to meet challenges set by consumers and society (Boichard and Brochard 2012; Martin-Collado et al. 2015). For example, the growing human population places more pressure on the available limited resources; global changes may mean hotter drier conditions to manage livestock and there is also increased consumer awareness about animal welfare and farming conditions. To accommodate this requirement, over recent decades there has been a rapid expansion of the number of breeding values that are available for farmers to select on. Almost without exception these breeding values rely on large amounts of field data that are freely available through current recording systems, such as milk production, calving records, insemination dates, pregnancy test outcomes, health records and culling dates.
Predicting the HMA-LMA status in marine sponges by machine learning
Moitinho-Silva, Lucas ; Steinert, Georg ; Nielsen, Shaun ; Hardoim, Cristiane C.P. ; Wu, Yu Chen ; McCormack, Grace P. ; López-Legentil, Susanna ; Marchant, Roman ; Webster, Nicole ; Thomas, Torsten ; Hentschel, Ute - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 14 p.
16S rRNA gene - Marine sponges - Microbial diversity - Microbiome - Random forest - Symbiosis
The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered "HMA indicators" and "LMA indicators." Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n = 44) and LMA (n = 74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities.
|Engineers at the Patient’s Bedside: : The Case of Silence in Inter-institutional Educational Innovation
Verouden, Nick ; Sanden, M.C.A. van der; Aarts, M.N.C. - \ 2016
In: The Silences of Science / Mellor, Felicity, Webster, Stephen, London : Routledge - ISBN 9781472459978 - p. 89 - 112.
Innovation in science and technology is increasingly linked with interdisciplinarity. Encouraging this trend depends in part on cutting-edge educational programmes that revise, reinvent and redesign curricula as interdisciplinary vehicles, establishing and re-establishing relations between traditional ﬁelds and areas of expertise (Stone et al., 1999; Casey, 1994). Such programmes are valuable because they can overcome ‘silo’ mentalities and equip prospective students with the skills and knowledge necessary for understanding and solving complex societal problems (Stone et al.,1999; McFadden et al., 2010). Although these programmes are very promising, their development and
implementation also brings challenges. The literature on curriculum development shows that many programmes have struggled to achieve true integration (McFadden et al., 2010; Stone et al., 1999). Dam-Mieras et al. (2008), in their study of an international master’s programme in sustainable development and management developed collaboratively by nine universities, observed that universities have their own experts and own programmes and that the ‘not invented here’ argument inﬂuences how details about new programme are discussed. Focussing on innovative online instruction courses, Xu and Morris (2007) found that the absence of group cohesiveness between faculty and project coordinators can hinder the collaborative course development process and aﬀect the quality of the end product. Stone et al. (1999) emphasize that faculty members and administrators work at cross-purposes and view each other’s initiatives with suspicion. Given the importance that scientists, academic institutions and policy makers ascribe to innovation, along with their assumption that such innovation is a sure result of interdisciplinarity, it is essential to gain a better understanding of how curriculum development in academic education actually works. For this chapter, we consider how processes of connecting and inter-
relating could add to our understanding of the problems and dilemmas that arise in developing and implementing such programmes. Scholars of innovation, in science and technology and beyond, have explained that innovation is not some abstract algorithm: it relies on interaction and collaboration between
multiple actors with diﬀerent expertises, visions, priorities and investment (Van Bommel et al., 2011; Leeuwis and Aarts, 2011; Akrich et al., 2002; Fonseca, 2002). This process of interacting is very diﬃcult, however, and creates many tensions. This is revealed by studies that show the lurking problems of connecting previously unconnected people around new ideas and technologies. These studies show how innovation processes become deﬁned by competition for scarce resources, protracted negotiations over priorities and interests, and dynamics of inclusion and exclusion (Leeuwis andAarts, 2011; Pretty, 1995; Van Bommel et al., 2011). Fonseca (2002) hence explains that innovation always creates a paradoxical situation, in which organizations, in their search to accelerate change and adapt to and ﬁnd solutions for external challenges and demands, unavoidably create new and unpredictable interactional patterns. Given that interacting is a complicated matter in innovation processes, a
key question within the management of innovation literature is how we can account for the way relevant actors connect, or fail to connect (Akrich et al., 2002). In this respect, verbal communication is often cited as an essential mechanism for eﬀectively connecting important actors and social groups around innovative ideas, products, or technologies (Van Bommel et al., 2011). In turn, the markers of eﬀective verbal communication as a frame for innovation are seen to be openness, dialogue, and the ability to cooperate and be reﬂective on one’s thoughts and actions (Stilgoe et al., 2013). Thorp and Goldstein (2010), writing about university innovation, describe conversations as the fertile ground from which innovation grows and urge us to make time and space for those conversations. Dialogue and openness are seen as indicators of the quality of interaction, and process transparency as a decisive component of academic innovation. By being open or transparent in discussing issues and problems, actors build conﬁdence that negotiation is ‘real’ and not a cover-up for private backroom deals (de Bruijn and ten Heuvelhof, 2008). Although there is a wealth of research on communication for innovation,
most scholarly work focuses on what is exchanged verbally, on how actors collate all the relevant evidence, put it on the table and discuss it openly. As of yet, silence is absent from these studies of communication for innovation. Building on recent organizational and strategy scholarship, in which silence is approached as an intricate concept with powerful functions and meanings in social interaction (Van Assche and Costaglioli, 2012; Carter et al., 2008; Henriksen and Dayton, 2006; Panteli and Fineman, 2005; Tucker and Edmondson, 2003; Jaworski, 2005; Morrison and Milliken, 2000), we suggest that silence merits much more attention in analyses of academic innovation. This chapter therefore explores the role of moments of silence during interactions within networks developing and implementing educational innovation. The structure of this chapter is as follows. We start by looking at the litera-
ture on dynamic innovation networks and communication and complement these insights with scholarship on silence within organization studies. After brieﬂy introducing our approach, we present the ﬁndings of a study of an inter-institutional and interdisciplinary joint bachelor’s programme that was
implemented at the interface of health and technology. The purpose of the study was to better understand the signiﬁcance of moments of silence in developing and implementing this programme. We end with the implications of our ﬁndings for steering in the context of interdisciplinary innovation.
High C3 photosynthetic capacity and high intrinsic water use efficiency underlies the high productivity of the bioenergy grass Arundo donax
Webster, R.J. ; Driever, S.M. ; Kromdijk, Johannes ; McGrath, Justin ; Leakey, A.D.B. ; Siebke, Katharina ; Demetriades-Shah, Tanvir ; Bonnage, Steve ; Peloe, Tony ; Lawson, Tracy ; Long, S.P. - \ 2016
Scientific Reports 6 (2016). - ISSN 2045-2322
Arundo donax has attracted interest as a potential bioenergy crop due to a high apparent productivity. It uses C3 photosynthesis yet appears competitive with C4 grass biomass feedstock's and grows in warm conditions where C4 species might be expected to be that productive. Despite this there has been no systematic study of leaf photosynthetic properties. This study determines photosynthetic and photorespiratory parameters for leaves in a natural stand of A. donax growing in southern Portugal. We hypothesise that A. donax has a high photosynthetic potential in high and low light, stomatal limitation to be small and intrinsic water use efficiency unusually low. High photosynthetic rates in A. donax resulted from a high capacity for both maximum Rubisco (Vc,max 117 μ1/4mol CO2 m-2 s-1) and ribulose-1:5-bisphosphate limited carboxylation rate (Jmax 213 μ1/4mol CO2 m-2 s-1) under light-saturated conditions. Maximum quantum yield for light-limited CO2 assimilation was also high relative to other C3 species. Photorespiratory losses were similar to other C3 species under the conditions of measurement (25%), while stomatal limitation was high (0.25) resulting in a high intrinsic water use efficiency. Overall the photosynthetic capacity of A. donax is high compared to other C3 species, and comparable to C4 bioenergy grasses.
Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa
Bassil, N.V. ; Davis, T.M. ; Zhang, Hailong ; Ficklin, Stephen ; Mittmann, Mike ; Webster, Teresa ; Mahoney, Lise ; Wood, David ; Alperin, E.S. ; Rosyara, U.R. ; Koehorst-vanc Putten, Herma ; Monfort, Amparo ; Sargent, D.J. ; Amaya, Iraida ; Denoyes, Beatrice ; Bianco, Luca ; Dijk, Thijs van; Pirani, Ali ; Iezzoni, Amy ; Main, Dorrie ; Peace, Cameron ; Yang, Yilong ; Whitaker, Vance ; Verma, Sujeet ; Bellon, Laurent ; Brew, Fiona ; Herrera, Raul ; Weg, Eric van de - \ 2015
BMC Genomics 16 (2015)1. - ISSN 1471-2164
Fragaria - Genotyping array - Plant breeding - Polyploidy - Reduced ploidy - Single nucleotide polymorphism - Strawberry
A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. Results: About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. Conclusions: The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
Development of the WagRhSNP AXIOM SNP Array Based on Sequences from Tetraploid Cut Roses and Garden Roses
Smulders, M.J.M. ; Voorrips, R.E. ; Esselink, G. ; Santos Leonardo, T.M. ; Westende, W.P.C. van 't; Vukosavljev, M. ; Koning-Boucoiran, C.F.S. ; Weg, W.E. van de; Arens, P.F.P. ; Schulz, D. ; Debener, T. ; Bellon, L. ; Mittmann, M. ; Pirani, A. ; Webster, T. ; Brew, F. ; Cox, P. ; Maliepaard, C.A. - \ 2015
In: Proceedings VIth International Symposiul on Rose Research and Cultivation. - ISHS - ISBN 9789462610552 - p. 177 - 184.
Rose, as many other important ornamental, vegetable and field crops, is polyploid. This poses constraints in genetic analyses due to the occurrence of multiple alleles at marker and trait loci and the existence of multiple allele dosages. Developments in marker discovery (next generation sequencing), detection (SNP arrays) and analysis (software for dosage scoring) now make it feasible to develop high-density molecular marker maps for the homologous chromosomes in tetraploids separately, and thus perform QTL analysis in tetraploids. We developed a SNP array for rose to develop genetic maps in tetraploid garden roses and cut roses, which are to be used for inheritance studies and genetic mapping. Here we have indicated the general strategy followed for developing a SNP array and for scoring and using the SNP data generated, and elaborated on the activities undertaken to use the WagRhSNP Axiom array in rose. The array design is not proprietary but can be used by all researchers working in rose
Fungal Planet description sheets: 107-127
Crous, P.W. ; Summerell, B.A. ; Shivas, R.G. ; Burgess, T.I. ; Decock, C.A. ; Dreyer, L.L. ; Granke, L.L. ; Guest, D.I. ; Hardy, G.E.St.J. ; Hausbeck, M.K. ; Hüberli, D. ; Jung, T. ; Koukol, O. ; Lennox, C.L. ; Liew, E.C.Y. ; Lombard, L. ; McTaggart, A.R. ; Pryke, J.S. ; Roets, F. ; Saude, C. ; Shuttleworth, L.A. ; Stukely, M.J.C. ; Vánky, K. ; Webster, B.J. ; Windstam, S.T. ; Groenewald, J.Z. - \ 2012
Persoonia 28 (2012). - ISSN 0031-5850 - p. 138 - 182.
sp-nov - allied genera - south-africa - diaporthales - eucalyptus - genus - cryphonectriaceae - gnomoniaceae - reevaluation - evolutionary
Novel species of microfungi described in the present study include the following from Australia: Phytophthora amnicola from still water, Gnomoniopsis smithogilvyi from Castanea sp., Pseudoplagiostoma corymbiae from Corymbia sp., Diaporthe eucalyptorum from Eucalyptus sp., Sporisorium andrewmitchellii from Enneapogon aff. lindleyanus, Myrmecridium banksiae from Banksia, and Pilidiella wangiensis from Eucalyptus sp. Several species are also described from South Africa, namely: Gondwanamyces wingfieldii from Protea caffra, Montagnula aloes from Aloe sp., Diaporthe canthii from Canthium inerne, Phyllosticta ericarum from Erica gracilis, Coleophoma proteae from Protea caffra, Toxicocladosporium strelitziae from Strelitzia reginae, and Devriesia agapanthi from Agapanthus africanus. Other species include Phytophthora asparagi from Asparagus officinalis (USA), and Diaporthe passiflorae from Passiflora edulis (South America). Furthermore, novel genera of coelomycetes include Chrysocrypta corymbiae from Corymbia sp. (Australia), Trinosporium guianense, isolated as a contaminant (French Guiana), and Xenosonderhenia syzygii, from Syzygium cordatum (South Africa). Pseudopenidiella piceae from Picea abies (Czech Republic), and Phaeocercospora colophospermi from Colophospermum mopane (South Africa) represent novel genera of hyphomycetes. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Effects of human handling during early rearing on the behaviour of dairy calves
Schütz, K.E. ; Hawke, M.L. ; Waas, J.R. ; McLeay, L.M. ; Bokkers, E.A.M. ; Reenen, C.G. van; Webster, J.R. ; Stewart, M. - \ 2012
Animal Welfare 21 (2012)1. - ISSN 0962-7286 - p. 19 - 26.
human-animal interactions - play-behavior - veal calves - cattle - welfare - cows - reactivity - responses - contact - heifers
We examined the effects of daily positive or negative human handling on the behaviour of Holstein-Friesian dairy calves (n = 20 calves per treatment, five calves per group). The response to humans and indicators of positive emotions were examined at four weeks of age. Calves that received positive handling approached a familiar handler within 1 min in 50% of the handling sessions compared to 17% of the sessions for negatively handled calves but showed no difference when approaching an unfamiliar person. Calves that received positive handling showed less avoidance behaviour in their home pen to an approaching unfamiliar person (score, positive: 3.7, negative: 2.8) but there was no treatment effect on flight distance when tested outside the home pen. Both treatment groups responded similarly to a novel object and performed the same amount of play behaviour. Calves that received positive handling interacted more with cow brushes than calves that received negative handling (positive: 9.9%, negative: 7.9% of the total time). At three months of age, avoidance behaviour was re-tested, this time including 20 control animals of the same breed and age, reared routinely on-farm. Controls showed more avoidance behaviour (positive: 1.5, negative: 1.0, control: 0.3) and had a greater flight distance (positive: 3.3 m, negative: 3.7 m, control: 4.9 m). The results confirm existing literature demonstrating that the quantity and quality of handling influence the response towards humans. Little evidence was found that the type of early handling influences behaviours indicative of positive emotions.
Epidemiology and effective control of Altenaria altenata, causal agent of dead (dormant) flower bud disease of pear
Wenneker, M. ; Joosten, N.N. ; Anbergen, R.H.N. ; Vink, P. ; Bruggen, A.S. van - \ 2011
In: ISHS Acta Horticulturae 909. - ISHS - ISBN 9789066055049 - p. 485 - 490.
Dead flower buds are a common phenomenon in pear culture in The Netherlands, Belgium and Mediterranean countries. Disease cases are also reported from South America. The disease is characterized by a partial or complete necrosis of flower buds during tree dormancy. The disease progresses during winter and spring, eventually resulting in the death of most flowers and decay of buds at flowering. In The Netherlands the problem is mostly found in the main pear cultivar ‘Conference’, but cultivars such as ‘Doyenne du Comice’ and ‘Gieser Wildeman’ are also affected. Disease incidence may be as high as 80-90%. Possible causes mentioned are abiotic stresses, incompatibility between scion and cultivar, and plant pathogens and pests. Research in recent years revealed that pear growth regulation does not prevent the occurrence of dead flower buds. Also, the bacterium Pseudomonas syringae pv. syringae (P.s.s.) was commonly regarded as the causal agent of dead flower buds in pear, although the relation between P.s.s. and dead flower buds in orchards has never been proven in The Netherlands. However, the fungus Alternaria alternata was found in diseased flower buds and also often in symptomless flower buds. A linear relationship between infection rate and dead flower bud disease incidence was found. Pathogenicity tests and Koch’s postulates were carried out. It was concluded that A. alternata is the causal agent of dead (dormant) flower bud disease. A. alternata is known to cause late blight in pistachio and several diseases in fruit crops such as moldy-core in apple and brown rot in citrus. By identifying the causal agent of dead flower bud disease, an effective control strategy could be developed. In field trials it was proven that fungicide treatments can reduce disease incidence significantly.
Crop load regulation in 'Conference' pears
Maas, F.M. ; Steeg, P.A.H. van der - \ 2011
In: XI International Pear Symposium, General Roca(Rio Negro), Argentina, 16 - 19 November, 2010. - ISHS - ISBN 9789066055049 - p. 367 - 379.
Estimativa do Índice de Área Foliar (IAF) e Biomassa em pastagem no estado de Rondônia, Brasil
Zanchi, F.B. ; Waterloo, M.J. ; Randow, C. von; Kruijt, B. ; Cardoso, F.L. ; Manzi, A.O. - \ 2009
Acta Amazonica 39 (2009)2. - ISSN 0044-5967 - p. 335 - 348.
Medidas mensais da altura da pastagem, biomassa total, variações de biomassa viva e morta, a área específica foliar (SLA) e o Índice de Área de Folha (IAF) de fevereiro de 1999 a janeiro de 2005 na Fazenda Nossa Senhora (FNS) e em Rolim de Moura (RDM) entre Fevereiro a Março de 1999, Rondônia, Brasil. A pastagem predominante é Urochloa brizantha (Hochst. ex A. Rich) R. D. Webster (99% na FNS e 76% em RDM), com pequenas manchas de Urochloa humidicula (Rendle). A altura média anual da grama foi de ~0,16 m. Com o pastejo, o mínimo mensal foi de 0,09 m (estação seca) e máximo de 0,3 m sem pastejo (estação úmida). O IAF, biomassa total, material morto, vivo e SLA tiveram valores médios de 2,5 m2 m-2 , 2202 kg ha-1, 2916 kg ha-1 e 19 m2 kg-1 respectivamente. A média mensal da biomassa foi 4224 kg ha-1 em 2002 e 6667 kg ha-1 em 2003. Grande variação sazonal do material vivo e morto, sendo mais alto o vivo durante a estação úmida (3229 contra 2529 kg ha-1), sendo o morto maior durante a seca (2542 contra 1894 kg ha-1). O nível de água no solo variou de -3,1 a -6,5 m durante as estações. Em médias anuais os IAF foram de 1,4 em 2000 a 2,8 em 2003 e o SLA entre 16,3 m2 kg-1 em 1999 e 20,4 m2 kg-1 em 2001. As observações do Albedo variaram de 0,18 para 0,16 em relação aos altos valores de IAF.
Book review: R. Webster, M.A. Oliver: Geostatistics for Environmental Scientists, 2nd ed.
Heuvelink, G.B.M. - \ 2009
Mathematical Geosciences 41 (2009). - ISSN 1874-8961 - p. 487 - 489.
|Effects of previous handling on calf responses towards humans
Schütz, K.E. ; Stewart, M. ; Hawke, M.L. ; Bokkers, E.A.M. ; Reenen, C.G. van; Webster, J.R. - \ 2009
- p. 170 - 170.
Human-animal relationships affect the production and welfare of animals. We investigated whether the type of handling of dairy calves influences their response towards humans. Forty, group-housed, Holstein-Friesian calves were exposed to either positive (e.g. soft voices, slow movements, patting) or negative (e.g. rough voices, rapid movements, pushing) handling (n=20 calves/treatment, 5 calves/group), twice daily (7 min/session) from 4 days to 5 weeks of age. Reactions towards humans were investigated around 4 weeks of age in a 'calf escape test' in their home pens, and by measuring the flight distance in a raceway. In the calf escape test, each calf was given a score between 0 and 4 depending on whether the observer could (1) make eye contact, (2) take 1, or (3) 2 steps towards the calf, or (4) touch the calf before it moved away (defined as moving both forelegs). Data were analysed using ANOVA. Calves that received positive handling showed less avoidance behaviour (mean score; positive:3.7, negative:2.8, sd:0.66, p=0.039) but there was no difference between the treatment groups in flight distance (positive:0.6m, negative:0.7m, sed:0.24m, p=0.526). Calves that received positive handling were 3 times more likely to voluntarily approach a human within 1min, compared to negatively handled calves (50% vs 17% of the calves approached the human, sed: 9.8%, p=0.015). When the calves were 3 months old, we repeated the flight distance and calf escape tests and added a control group (n=20) of the same age that had been reared under normal farm management (minimal handling). Controls showed more avoidance behaviour in the calf escape test (mean score; positive:1.5, negative:1.0, control:0.3, sd:0.21, p