Periodic Reporting for period 2 - PUSHH (Palaeoproteomics to Unleash Studies on Human History)
Okres sprawozdawczy: 2022-03-01 do 2024-08-31
Between 2020 and 2024 the Marie Skłodowska-Curie European Training Network (ETN) "PUSHH - Palaeoproteomics to Unleash Studies on Human History" provided international doctoral training on palaeoproteomics applied to palaeontology, palaeoanthropology and archaeology. Sequencing ancient proteins is currently the only effective method for obtaining the genetic data needed to determine the evolutionary relationships of vertebrate species that vanished millions of years ago. The momentum within ancient biomolecules research is outstripping the ability to deliver comprehensive training programmes at the national level. Today, individual research units within Europe are mainly recognised for their specific strengths either in proteomic research in the biopharma sector, or in (micro)morphometrical observation of fossils and ancient artefacts. As a consequence, students are being forced to specialise at too early a stage, often without a full understanding of the impressive growth of the discipline and its intersecting elements. The PUSHH ETN started to fill these advanced training gaps in palaeoproteomics, by preparing a cohort of specialists in analysis of ancient protein residues from paleontological, palaeoanthropological and archaeological materials. PUSHH also guided the ESRs to develop the advanced interdisciplinary knowledge required to achieve seamless integration of palaeoproteomics with the established principles and practices of cultural heritage restoration and conservation. Finally, PUSHH defined a coherent training environment where interdisciplinary knowledge, as well as specific research-related and transferable skills, contributed to scaffold the ESRs’ professional thinking. The mind-set (or “forma mentis”) the PUSHH alumni acquired during their early-stage training experience will strongly affect their future professional practice.
Since its launch, the PUSHH ETN has made stable progress in delivering its activities with contributions from the entire consortium.
PUSHH provided international and intersectoral training to improve the ESRs’ knowledge, and prevention of unethical research practices of the past and present, including “helicopter research” and marginalisation of local researchers, in palaeontology, paleoanthropology and archaeology. To fulfil the PUSHH objectives, all the ESRs have received training in state-of-the-art analytical and bioinformatic technologies for the investigation of ancient proteins. The training programme also included workshops focusing on transferable skills, research management, entrepreneurship, ethics in palaeontology and palaeoanthropology, and scientific communication for the broad audience. The network-wide planned training activities have been specifically designed to enhance the expertise of the ESRs, and the collaborations in the network have given the ESRs the possibility to achieve a better and broader understanding of proteomics studies in the academic, industrial, and museum environment. The rich secondment plan gave all the fellows the possibility to see a different work environment within and outside the academic system. Since the very beginning of the project, the PUSHH consortium was characterised by a strong sense of community and collaboration. Starting from the very first few months of the ESRs’ projects, and culminating in the network of secondments, multiple opportunities were created for network-wide interaction and exposure to many different work environments, methodologies and professional mindsets. The involvement of partners in the private sector exposed the fellows to the mindset and the culture of the corporate environment. The interaction with colleagues from academic and cultural institutions from the countries of origin of the fossil material studied exposed the PUSHH fellows to the ethical requirements necessary to responsibly study cultural and biological heritage material originating from outside the EU and educated them to be aware and considerate about the needs and expectations of local museums and about their mission aiming at preserving cultural heritage for everybody. Some of the fellows had their secondments in the private sector and they had the opportunity to experience in person how research is structured and managed there.
As a consequence of the restrictions implemented to mitigate the spread of the COVID19 pandemics, most of the planned activities were deployed with minor delays. Despite these changes though, none of the PUSHH activities had to be completely cancelled and all the PUSHH project’s intended learning objectives were maintained. All the network-wide training activities were delivered:
Workshop 1: “Start-up phase of the doctorate”; host: UCPH and UCT
- module 1: “Start-up phase of the doctorate”
- module 2: “Academic writing”
- module 3: “[Social] media & public relations for science”
- module 4: “Ethics In Research”
Workshop 2: “Palaeoproteomics hands-on practical courses”; hosts: UBx and UCPH
- module 1: “Advanced mass spectrometry applied to cultural heritage Summer School”
- module 2: “Practical Palaeoproteomics Summer School”
Workshop 3: “MaxQuant Summer School”; host: MPG
Workshop 4: “Paleoanthropological and paleontological excavation and fieldwork”; host: CENIEH
Workshop 5: “Grant writing, peer-review and advanced project management skills”; host: UNIFI
Workshop 6: “Entrepreneurial skills”; host: UCPH
Workshop 7: “Introduction to University Pedagogy”; host: UCPH
PUSHH provided international and intersectoral training to improve the ESRs’ knowledge, and prevention of unethical research practices of the past and present, including “helicopter research” and marginalisation of local researchers, in palaeontology, paleoanthropology and archaeology. To fulfil the PUSHH objectives, all the ESRs have received training in state-of-the-art analytical and bioinformatic technologies for the investigation of ancient proteins. The training programme also included workshops focusing on transferable skills, research management, entrepreneurship, ethics in palaeontology and palaeoanthropology, and scientific communication for the broad audience. The network-wide planned training activities have been specifically designed to enhance the expertise of the ESRs, and the collaborations in the network have given the ESRs the possibility to achieve a better and broader understanding of proteomics studies in the academic, industrial, and museum environment. The rich secondment plan gave all the fellows the possibility to see a different work environment within and outside the academic system. Since the very beginning of the project, the PUSHH consortium was characterised by a strong sense of community and collaboration. Starting from the very first few months of the ESRs’ projects, and culminating in the network of secondments, multiple opportunities were created for network-wide interaction and exposure to many different work environments, methodologies and professional mindsets. The involvement of partners in the private sector exposed the fellows to the mindset and the culture of the corporate environment. The interaction with colleagues from academic and cultural institutions from the countries of origin of the fossil material studied exposed the PUSHH fellows to the ethical requirements necessary to responsibly study cultural and biological heritage material originating from outside the EU and educated them to be aware and considerate about the needs and expectations of local museums and about their mission aiming at preserving cultural heritage for everybody. Some of the fellows had their secondments in the private sector and they had the opportunity to experience in person how research is structured and managed there.
As a consequence of the restrictions implemented to mitigate the spread of the COVID19 pandemics, most of the planned activities were deployed with minor delays. Despite these changes though, none of the PUSHH activities had to be completely cancelled and all the PUSHH project’s intended learning objectives were maintained. All the network-wide training activities were delivered:
Workshop 1: “Start-up phase of the doctorate”; host: UCPH and UCT
- module 1: “Start-up phase of the doctorate”
- module 2: “Academic writing”
- module 3: “[Social] media & public relations for science”
- module 4: “Ethics In Research”
Workshop 2: “Palaeoproteomics hands-on practical courses”; hosts: UBx and UCPH
- module 1: “Advanced mass spectrometry applied to cultural heritage Summer School”
- module 2: “Practical Palaeoproteomics Summer School”
Workshop 3: “MaxQuant Summer School”; host: MPG
Workshop 4: “Paleoanthropological and paleontological excavation and fieldwork”; host: CENIEH
Workshop 5: “Grant writing, peer-review and advanced project management skills”; host: UNIFI
Workshop 6: “Entrepreneurial skills”; host: UCPH
Workshop 7: “Introduction to University Pedagogy”; host: UCPH
The scientific results generated within the PUSHH consortium appeared as pre-prints and on the most prestigious peer-reviewed scientific journals (PMID: 38297117, 38277452 and DOI https://doi.org/10.1038/s41580-024-00803-2(odnośnik otworzy się w nowym oknie)). Some of them have been assigned a significative innovative potential (PMID: 39324540). The results generated within the PUSHH consortium represented the scientific and methodological foundations (PMID: 38671208, 38777088 and 38302753) of other prestigious grants awarded to some of the PUSHH consortium members. PUSHH enabled addressing major unsettled debates about African and Asian extinct hominid phylogeny, by developing and deploying a new generation of palaeoproteomic workflows, relying on the most advanced mass spectrometry and bioinformatic solutions currently available. The technologies developed in PUSHH will be used to recover genetic information beyond the limits of ancient DNA preservation. PUSHH has demonstrated that ancient protein sequence variation is large enough to allow confident phylogenetic placement of extinct species otherwise recalcitrant to ancient DNA analysis. Furthermore, it has recently demonstrated that an almost complete set of ancient proteins, i.e. a palaeoproteome, can be consistently retrieved from dental enamel specimens ~20 millions of years old, from sub-polar areas (BiorXiv preprint: doi: https://doi.org/10.1101/2024.06.07.597871(odnośnik otworzy się w nowym oknie)). Finally, before some of the workflows developed in the PUSHH ETN were developed and deployed, there was no economically viable way to perform large-scale sex and species identification on morphologically non-informative bone and tooth specimens from paleontological, palaeoanthropological and archaeological contexts. By developing and deploying these new high-resolution mass spectrometry-based approaches, in the near future it will be possible to open service platforms to democratise species and sex identification from ancient materials.