Progress 10/01/13 to 09/30/18
Outputs
Target Audience:The target of this project is international and covers the range from producers, through commercializers to consumers, as it aims at providing tools and concepts for detection of DNA-carrying microscopic particles, such as microbial cells, fragments of larger organism, pollen grains, etc. The successful development offield-based, inexpensive and distributive (as previously defined in REE reports) microbe-detection methods opens the possibility of wider applications in medical and industrial fields, environmental (non-agricultural) situations and beyond, although these last were not direct targets of the project. Changes/Problems:Two major changes/problems emerged during the development of this project: 1. The distribution of the method and device was slower than expected, due to lack of sufficient funding. Part of the problem relates the fact that a distributive and inexpensive method/device aimed at a population without ample financing makes it very difficult to raise sufficient funds to arrive at a mass-produced device, distribute it and make use of the information collected from the devices. This is a conundrum that will continue to be a focus of attention in the PI's laboratory. 2. There was an irregular and very unfortunate development when the graduate student who was instrumental in the development of the device decided to publish an article as a single author, without the PI's authorization. Further to this, the same individual is now working in an industrial context, where he might be seeking patent protection to some (not all) of the aspects of development leading to the successful device. The PI is in the process of following up and pursuing redress for these problems. What opportunities for training and professional development has the project provided?Hundreds of people among stakeholders in the field of international agriculture were exposed to the concepts and the specific applications of the method developed here. How have the results been disseminated to communities of interest?Direct presentations by the PI, web-based presentations. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The following goal was fully accomplished: "Methods and devices for the simple, inexpensive and massive identification of air-, insect-, and sediment-borne particles containing DNA, such as cells." The method was demonstrated and performed in participative manner in Spain, Switzerland, South Africa, Mexico and the US. Technical discussions and participation in community-based scientific meetingsPublic presentations and grassroots popularization efforts were started, but not developed to a high-profile. No mapping-level capacity was achieved.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Bektas, A. A Multiplex, Fluorescent, and Isothermal Method for Detecting Genetically Modified Maize. Food Anal. Methods (2018) 11: 686. https://doi.org/10.1007/s12161-017-1041-9
|
Progress 10/01/16 to 09/30/17
Outputs
Target Audience:This report period covers the roll-out of the methods and devices produced under this project at an international level. At this level, the audience was the field-based communities of farmers, social and governmental organizations and academic institutions and individuals concerned about the development of field-based, inexpensive and distributive (as previously defined in REE reports) microbe-detection methods. In particular, the method at this point is demonstrated by the detection of DNA sequences that characterize genetically modified crops, which are a source of interest for large sectors of society. For this reporting period, the locales of demonstration were Spain, Switzerland, South Africa and Mexico. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The last PhD student associated with the project continued on for an extra year as a postdoc, and is now fully employed, thanks to this method, in the detection/diagnostics agricultural industry. Two undergraduates received training in the general concepts and methods. How have the results been disseminated to communities of interest?This has been the main focus of the reporting period. Farmers, farmer organizations, governmental and non-governmental organizations, as well as academic players in the field were invited to purpose-designed field seminars/demonstrations. With this, knowledge and anticipation about the methods was made available from the ground-up to those most directly involved with the question of introgression of DNA materials from genetically modified crops into fields where these materials were not expected. Once this necessary step of dissemination has been achieved, the next step will be to produce more traditional journal publications. What do you plan to do during the next reporting period to accomplish the goals?I am now dedicated to the completion of publications, including detailed descriptions and more general considerations of the benefits and values, as well as the pitfalls, of the methods developed through this REES project.
Impacts
What was accomplished under these goals?
The reporting period covers the initiation and development of the last part of my general goals described above. Map-making remains a long-term goal that will continue to be developed, but the methods and devices were completed to field-abled stage. It must be stressed that these are completely novel methods and devices, designed and developed from the ground-up, to the point where detection of specific DNA sequences in the field was achieved in the absence of usual needs implied by other methods such as PCR. In the reporting period of 2017, we were able to perfom what I believe to be the world's first sequence-specific amplification and detection of DNA in the field, in the absence of electricity, electronics, refrigeration, any sort of precise measurement (such as pipetting), and in the hands of untrained operators. Although there were a couple of journal publications to report, the main achievement in this period was the successful perfomance of the detection in a relevant ecological and social context.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Miluse Trtikova, Andre Lohn, Rosa Binimelis, Ignacio Chapela, Bernadette Oehen, Niklaus Zemp, Alex Widmer & Angelika Hilbeck. Scientific Reports. Volume 7, Article number: 1560 (2017)
Bektas, A. A Multiplex, Fluorescent, and Isothermal Method
for Detecting Genetically Modified Maize. Food Anal. Methods
DOI 10.1007/s12161-017-1041-9
doi:10.1038/s41598-017-01478-w
|
Progress 10/01/15 to 09/30/16
Outputs
Target Audience:The target audience includes, but is not limited to, the scientific and technical community. Most importantly, the key target audience is end users of the methods developed. Specifically, these are small-scale and widespread producers, consumers, policy-makers and citizens in general, who are receiving a novel, inexpensive and robust method to allow for detailed detection, monitoring and mapping of DNA sequences carried by microbiological particles. For the period of report, the application being promoted is the detection of transgenic DNA sequences (Genetically Modified Organisms, or GMO), because of the steadily growing interest in this field in commerce, environment, as well as academic ecology, conservation, medicine, and other fields. The audience is also not limited to California or the United States, but rather encompasses wide audiences at an international level. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?In each of the nodes of our growing network of participant cooperators, at least one Principal Investigator was trained on the methods, but several other workshop participants were exposed for the first time to the concepts and specifics of the methods. In total, perhaps 30-50 academic and producer-based actors were trained. How have the results been disseminated to communities of interest?Although formal scientific publications are being produced with the specific descriptions of the methods, the main medium of dissemination has been the performance of workshops with field-based demonstrations supported by laboratory- and classroom sessions. What do you plan to do during the next reporting period to accomplish the goals?I will continue to perform two clearly delimited tasks: First, to bring up the prototype-level at which the method and devices have been produced to pilot level. This implies the development of semi-mass production of key elements of the method, such as freeze-dried reagents of consistent quality and reliability, wax-embedded reagents, and simple visualization devices. Second, I will continue to perform workshops based on the growing interest on the methods. Specifically, new workshops are planned in Spain and Switzerland, and I will spend the Summer further developing capacities in the UNAM-based collaboration, the COllege of the Southern Border facility, and under the auspices of the Ethnobotanical Garden in the City of Oaxaca.
Impacts
What was accomplished under these goals?
The year 2016 saw the first public demonstration of the methods and devices developed under this project. The demonstrations were implemented using the network of collaboration that we developed also as part of this project. In February, two workshops were performed in academic institutions in Mexico City and San Cristobal Las Casas. The hosting institutions were the National Autonomous Unviersity of Mexico, and the College of the Southern Border. The specific audience was academic biologists, as well as selected practitioners in the apiculture community, where the device was used to detect specific DNA sequences (CaMV, Zein, among others) in pollen grains in honey. In May, workshops and presentations were performed under the auspices of our Swiss collaborators, the Eidgenössische Technische Hochschule Zürich (ETH-Z), from where a new collaboration and workshops were further carried out in South Africa (University of South Africa, Potchefstroom). Here, the method was used on maize flour samples with the same DNA sequences as used in Mexico.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Marchand, Philippe, Alexandra N. Harmon-Threatt, and Ignacio Chapela. "Testing models of bee foraging behavior through the analysis of pollen loads and floral density data." Ecological Modelling 313 (2015): 41-49.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Bekta?, Ali, and Ignacio Chapela. "Efficiency of a fluorescent, non-extraction LAMP DNA amplification method: toward a field-based specific detection of maize pollen grains." Aerobiologia 32.3 (2016): 481-488.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2015
Citation:
Tonak, Ali Bekta?. "Loop-Mediated Isothermal Amplification for the Mapping of Microbes: An Anti-Capitalist Approach." (2015).
|
Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Farmers, consumers of agricultural products. Beekeepers, honey marketing individuals, companies and institutions. Regulatory agencies. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One graduate student was graduated after training in the statistical and mathematical aspects of the project. Another graduate student reached the point of writing his dissertation on the biochemical aspects of the method. How have the results been disseminated to communities of interest?Yes. Peer reviewed publications have been targetted first, but we have prepared the ground for the next step in the project, which will be the socialization of the method with a "pilot scale" population: beekeepers. What do you plan to do during the next reporting period to accomplish the goals?Most of the work left to do in the period of the project includes a certain amount of laboratory work, and field testing for optimization and quality control, but most importantly we will focus now on the socialization of the method and devices, making them available widely. Workshops with pilot-level groups (academics, beekeepers) are already planned for the next period. As a pilot group we have chosen beekeepers because of their relatively high level of technical capacity, their well-organized communities, and the contacts we have developed as part of this project. Neverhteless, many other user groups will become more and more relevant to the socialization program as the next period proceeds.
Impacts
What was accomplished under these goals?
A new method and devices for the detection and monitoring of any DNA sequence in the field was finally accomplished after years of development. Although initially this project was focused on pollen and air-borne particles, the method developed is not limited to these samples, and is instead of very wide application wherever DNA detection is called for in an environmental situation. The inexpensive and vastly simplified method is compatible with ground-operators who are not deeply knowledgeable or trained in laboratory methods, thus the method is open for many applications driven horizontally (distributed monitoring, citizen science), as well as any situation where access to a laboratory is not immediately available,
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Bektas A, Chapela I (2014) Loop-mediated isothermal amplification of single pollen grains. J Integr Plant Biol 56: 741748. doi: 10.1111/jipb.12191
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Bektas A, Chapela I (2015). Efficiency of a fluorescent, non-extraction LAMP DNA amplification method: toward a field-based specific detection of maize pollen grains. Aerobiologia
pp 1-8. doi: 10.1007/s10453-016-9420-z
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Marchand P, Harmon-Threatt AN, Chapela I (2015).
Testing models of bee foraging behavior through the analysis of pollen loads and floral density data. Ecological Modelling 313: 4149. doi:10.1016/j.ecolmodel.2015.06.019
|
Progress 10/01/13 to 09/30/14
Outputs
Target Audience: Although the target audience in this project encompasses a large variety of social and economic actors, this reporting period was characterized by the completion of methods and devices at proof-of-concept and prototype levels. For this reason, the actual people reached during this period was limited to institutions and individuals at decision-making level in foundations (Christensen, Lea, Persephone Rising foundations) and educational institutions. In the next period, as publications are finalized, the device and methods developed will serve a large group of actors in the agricultural and environmental communities. In preparation for that period, we have actively developed a wide network of links with our first target community: beekeepers and honey-producers/commercializers. This includes the whole chain of stewardship for the honey and pollen markets, specifically in the sector of the market identified as "sustainable", "fair trade", and "organic". In this preparatory effort, presentations and multiple contacts were developed with honey-producing associations and their academic and commercial links in Southern Mexico (through the Ecosur, an academic branch of the Colegio de la Frontera Sur, in CHiapas, Mexico) and for various countries through the most important commercializer of fair-trade and sustainable honey in Europe, the company GEPA. in Wuppertal, Germany. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Formal training of two PhD-level students (Ali Tonak, Philippe Marchand) and one undergraduate student (Michelle Katuna). How have the results been disseminated to communities of interest? For the reporting period, during which no publications were yet completed, the only dissemination was achieved through small, ad-hocseminars with potential funders and also with groups of honey producers and commercializers. What do you plan to do during the next reporting period to accomplish the goals? The next reporting period will be dominated by the public dissemniation of our results and the initiation of application of our methods at the pilot-scale level. We have identified the specific group of honey- and pollen producers as a target group for this purpose, and we have established the relationships necessary to facilitate the pilot-scale goal. Publications will take place both through the traditional scientific literature, but also through seminars and participation in other formal and semi-formal fora of academic and non-academic actors.
Impacts
What was accomplished under these goals?
The reporting period comprises the final achievement of the main goal of this project: the DNA-sequence specific detection of single particles (pollen grains) in air- and honey-samples. The method accomplishes the goals of field-enabled capacity, extremely-low cost and extremely-low requirement of expertise in its operation. These are the elements, demonstrated at the concept-level and prototype-level during this period, for the desired high-throughput, distributive mapping goal of the project overall.
Publications
|
|