Project code: KK.01.1.1.06.0002
Project title: Establishment of a laboratory for archaeogenetics at the Faculty of Agriculture, University of Zagreb.
Tender code: KK.01.1.1.06
Call title: "Developing and strengthening synergies with the horizontal activities of HORIZON 2020: Twinning and ERA Chairs".
Specific title: Increasing the capacity of the Research, Development and Innovation (IRI) sector to carry out cutting-edge research and meet the needs of industry
Project applicant:
University of Zagreb Faculty of Agriculture
prof. dr. sc. Ivica Kisić
Svetošimunska cesta 25, 10000 Zagreb, Croatia
Phone: +385 1 239 3779
Fax: +385 1 231 5300
E-mail: dekanat@agr.hr
Project manager:
University of Zagreb Faculty of Agriculture
Department of Animal Science
Prof. Ino Čurik, PhD
E-mail: icurik@agr.hr
Project team:
Assoc. Prof. Vlatka Čubrić Čurik, PhD
Assist. Prof. Maja Ferenčaković, PhD
Dinko Novosel, PhD Veterinary Pathology
Assist. Prof. Vladimir Brajković, PhD
Ivana Držaić, MSc
Summary
Archaeogenetics is a young and prestigious scientific discipline that is rapidly developing with the advent of new generation sequencing (NGS), and its research has often been published in the most prominent scientific journals. Croatia is known for its numerous archaeological sites and wealth of archaeological material of biological origin (animal and human bones), the analyses of which, a good example being the Neanderthal bones from Vindija, have enriched our knowledge of the human past. With the intention of conducting cutting-edge scientific research and establishing scientific cooperation between geneticists and scientists who study the past (archaeologists, geologists, biologists, etc.), the aim of this project is to establish a laboratory for archaeogenetics. There is no such laboratory in the wider region.
Project description
With the intention of conducting cutting-edge scientific research and establishing multidisciplinary scientific cooperation between geneticists and scientists dealing with the past (archeologists, geologists, biologists, etc.) in Croatia, the aim of this project is to establish a laboratory for archaeogenetics at the Faculty of Agriculture, University of Zagreb (LazAg). This goal is complemented by the long-term goals of the EU-funded project "MendTheGap" in the program HORIZON 2020, which focuses on the sustainability of interdisciplinary scientific cooperation. The establishment of LazAg would enable continuous analysis of archeological material of biological origin from Croatia, but also from the wider region, in our country, thus generating interest in cooperation for a longer period of time. During the two years, the project will financially ensure the physical construction and equipment of LazAg and will conduct a pilot study in the same laboratory to prove the success of the laboratory on a real example. The implementation of the project is planned in several phases: (i) preparatory actions, detailed design of LazAg and implementation of public tender (expected significant support from the Faculty of Agriculture, University of Zagreb) - estimated duration 120 days, (ii) physical construction of LazAg - planned duration 180 days, (iii) equipment of LazAg - estimated duration 90 days, (iv) testing and control of LazAg - estimated duration 60 days, (v) isolation of aDNA from animal bones (Equidae, Canidae, etc., but we reserve the right to rework) - estimated duration of 120 days, (vi) NGS analysis of the isolated aDNA fragments - estimated duration of 90 days, (vii) bioinformatics analysis of the obtained results - basic control of the results - 30 days, (viii) project promotion, and (ix) preparation and editing of the final documentation of the project - estimated duration of 40 days. Therefore, in the first (i) phase of the project, a detailed implementation plan would be prepared by LazAg and tenders would be conducted to select the best contractors and carry out the preliminary works envisaged by the project funds (civil works for space adaptation in the existing facility for the construction / installation of the clean room and equipment.) ). During this phase, all necessary permits would be obtained and architectural and technological projects would be prepared. FAZ would participate in the preparation of the space for project implementation, which is not included in the project proposal. In the second (ii) and third (iii) phases of the project, the physical construction of LazAg would be addressed, as well as the necessary equipping with the equipment detailed in the project budget. In accordance with the funds received, they would consider the quality of performance in the construction of the laboratory and meet all necessary standards as well as energy efficiency and sustainability. In the fourth phase (iv), the technical validation and verification of the LazAg functionality is foreseen so that the laboratory can meet the required quality standards (ISO 8 and ISO 7). In the next phases of the project (v-vii), a pilot archaeogenetic study would be conducted to prove the performance functionality of LazAg. This part would be carried out by bioinformatics analyzes that can test the success of molecular analyzes and quality analyzes to verify the reliability of statistical models and expected results. Of course, our pilot research in this project would end with the storage of the analyzed data in publicly available databases (e.g. in GenBank) to increase the transparency and usability of the funds spent in this project. We intend to publish the obtained results, but due to the time limit of two years, our further activities in this project are not foreseen (the publication process is lengthy), but we can expect them through an increased number of high quality scientific publications over a period of five years. Within these phases, a record of the work would be produced in a clean LazAg space. Promotion of the project is planned at the end of the second year of the project, phase (viii), through the construction of the LazAg-do inaugural website, accompanied by a media presentation of LazAg that would be accessible to the public and journalists. Furthermore, the transparency, but also the media impact of LazAg itself would be increased by the possibility to follow the work in the laboratory through a real-time presentation on the Internet. In this way, archaeogenetics would be brought closer to the general public. In the final phase (ix) of the project they would take care of the design of the project documentation and the final report.
Purpose and justification
The purpose of this project is to support and ensure the sustainability of multidisciplinary research (MIT ), established under the name of CrEAMA initiative and implemented within the first ranked project "Smart Integration of Genetics with Past Sciences in Croatia: Minding and Mending the Gap"- project no. 692249; acronym "MendTheGap") in the call of Horizon H2020" Enhancing Excellence and Collaboration "of the program H2020-TWINN-2015, funded by the European Union (http://mendthegap.agr.hr/). The basic idea of the "MendTheGap" project is to establish and unite the collaboration of geneticists with researchers of different profiles (archeologists, anthropologists, biologists, geologists and paleontologists) who scientifically study the distant past in different ways. The CrEAMA initiative was established with the intention of implementing an integrated approach to the sciences of the past that will lead to significant innovations and the ability to answer many important questions that the present poses to us. A significant part of the activities of the CrEAMA initiative is the development of archaeogenetics in Croatia, which we believe is a "smart" approach given the large number of archeological sites and the availability of biological material that can be genetically analyzed. While the "MendTheGap" project provides "know-how" in the field of archaeogenetics, the establishment of a physical laboratory for archaeogenetics, as one of the long-term goals of the "MendTheGap" project (http://mendthegap.agr.hr/project/objectives/strategic-long- term-goals-andsustainability/), will certainly strengthen the research potential of the CrEAMA initiative and, in the long term, promote the implementation of archaeogenetic research in Croatia. Archaeogenetics is a young discipline, the term was coined in 2001 by archeologist Andrew Colin Renfrew (https://en.wikipedia.org/wiki/Archaeogenetics) from the University of Cambridge ("Twinning" partner in the "MendTheGap" project), NGS (New Generation Sequencing) methods have developed rapidly in the last decade. Today, archaeogenetics is a scientifically respected discipline, with research results often published in the most prestigious journals (Science, Nature, PNAS, Nature Communications, etc.). The reason for this is the technical specificity and complexity of DNA isolation and molecular typing of very small amounts of highly degraded DNA, mostly found in bones. Today Croatia is not unknown in archaeogenetics, as many important materials come from our area. A good example is the resulting Neanderthal genome sequence from Vindija (http://science.sciencemag.org/content/early/2017/10/04/science.aao1887.full). However, the results related to the materials from Croatia were produced in the archaeogenetic laboratories of the developed EU countries. This is not surprising, as there are very few recognized laboratories for archaeogenetics in the world and also in the EU. For example, in a large number of Central European countries (Albania, BiH, Bulgaria, Montenegro, Czech Republic, FYROM, Croatia, Kosovo, Hungary, Slovakia, Slovenia, Serbia, Poland, etc.) there is no recognized laboratory for archaeogenetics (https://isogg.org/wiki/ List_of_forensic_and_ancient_DNA _laboratories). The construction and establishment of laboratories for archaeogenetics would create conditions for scientific excellence in the field of archaeogenetics in the region, which would make us an attractive partner in future applications for EU scientific projects, which is in line with the Strategy of Smart Specialization and Action Plan Specialization of the Republic of Croatia for the period from 2016 to 2020. (http://www.obzor2020.hr/userfiles/obzor2020/pdfs/ Strategija_pametne_specijalizacije_ RH _2016_2020.pdf). In general, training for work in archaeogenetics is a demonstration of knowledge and skill and a proof of scientific excellence that elevates training in other disciplines of applied genetics (human and veterinary medicine, agriculture and forestry, biology, etc.) to a higher level. The research to be carried out in the "proposed" laboratory would focus in particular on the study of: a) origin of domestication and genomic changes in the domestication process, b) analysis of human and animal migration in the Neolithic, c) and functional adaptations (search for lost functional variability), d) estimation of effective population size and genome mix based on high-resolution genetic information of an individual, and e) variability of deleterious mutations in extinct species (e.g. analysis of the genome of Equus hydruntinus as an extinct Pleistocene equid species). Besides scientific, archaeogenetic research is important for the knowledge and promotion of biocultural identity and the enrichment of the museum offer, which is one of the ideas of the project "MendTheGap" using the example of Cultural Center "Vela Luka", see objective 4 (http://mendthegap.agr.hr/project /objectives/target-group-specific-project-objectives/). This interaction of science and tourism with the aim of increasing the cultural offer in tourism is a declared strategic priority of the Republic of Croatia (http://www.mingo.hr/page/kategorija/programi-i-projekti-eu).
Assessment of future trends
The explosive development of NGS methodology, together with the development of computer capabilities, has greatly accelerated the indexing and analytical capacity of archeological material. At the same time, archaeogenetic analyzes, as the most complex discipline in NGS application, have become the subject of interest and prestige in the publications of the most prominent scientific journals. Thus, there are rumors that without archaeogenetic analyzes, it is now difficult to publish the results of archeological research in journals such as Science and Nature. In some ways, the ability to perform archaeogenetic analyzes correlates with publication in journals with high scientific impact (impact factor), but the criteria and complexity of the analyzes performed are constantly increasing. Whereas fifteen years ago the analysis of an mtDNA fragment (a sample older than 2000 years) was sufficient for a "high quality" publication, five years ago the analysis of the entire mitogen was necessary for an "equivalent" publication, today we are witnessing publications of the entire sequenced whole genome for individuals older than 7000 years (examples are analyzes of the human and bovine genomes). Also, in the past it was only possible to isolate aDNA from cold regions, but today this is also possible from archeological material found in places with warm climates. A major influence on the discovery of aDNA isolation was also the realization that the efficiency of the analysis can be improved many times over if the analysis is performed from rock bones (http://journals.plos.org/plosone/article?id=10.1371/journal.pone. 0170940). Encouragingly, a considerable number of rock bones were found in the faunal archeological material in Croatia, indicating a good archaeogenetic potential of our sites. Of course, we expect standards to rise, but it is always better to be there from the beginning of a significant development in a particular research. The Faculty of Agriculture at the University of Zagreb is a scientific institution which, although financed by the state, operates on the market, where its reputation is evaluated by several parameters, of which the quality and quantity of scientific publications are the basic indicators of success. Thus, rankings are published annually, on the basis of which each university, but also individual components of the university are evaluated. For example, according to Shanghai Ranking List (ARWU), the University of Split is ranked 501 to 600, while the University of Zagreb is in the last group between 800 and 1000. The ARWU lists are indicators of academic and research success, such as: a) the number of students and professors who have won the Nobel Prize or Fields Medal, b) the number of researchers whose work is regularly cited in other scientific publications, c) the number of articles published in prestigious scientific journals such as Nature and Science, and d) the number of articles in major scientific databases and academic success in relation to the number of full-time professors. Also according to the well-known QS World University Ranking list (https://www.topuniversities.com/university-rankings/university-subject-rankings/2017/agriculture-forestry), in the field of agriculture and forestry, the University of Zagreb is among the first 150 universities. Also according to the quality and quantity of scientific publications in agricultural sciences, the University of Zagreb is the 148th university after NTU Ranking List (http://nturanking.lis.ntu.edu.tw/DataPage/TOP300.aspx?query= Agriculture & y = 2017) . In the FAZ evaluation process, it is often emphasized that a greater number of publications in high quality journals is necessary, as opposed to a satisfactory quantity. Thus, publications in high quality journals as well as citations are a major factor influencing the rank of the university and thus FAZ. In general, it is not common in agricultural sciences to publish research results in top scientific journals. The establishment of a laboratory for archaeogenetics would therefore have a multiple effect on the frequency of publication in "top journals" and thus on success in world rankings. Ranking, of course, also increases the prestige of the university and FAZ as its component, and thus, in addition to national prestige, affects the attractiveness to a larger number of students interested in this study. Furthermore, the interaction of genetics with archeologists would also impact on a number of publications in the social sciences, specifically archeology. In addition to the above, we believe that archaeogenetics in itself is an attractive and fascinating discipline for the media and that the existence and visibility of LazAg would have a positive impact on public perceptions of agriculture and FAZ. Similarly, the existence of LazAg would be a strategic feature of FAZ through which it could become known in the field of archaeogenetics in the region and thus attract other researchers in the region to collaborate in this field.