95725 - ARCHEOLOGIA BIOMOLECOLARE

Learning outcomes

At the end of the course the student has basic and applicative technical-scientific skills concerning the use of biomolecular technologies for the study and conservation of biological materials from archaeological contexts, in particular with regard to the analysis of DNA extracted from human, animal and plant remains, aimed at their characterization and genetic identification and related scientific problems.

Course contents

The course focuses on the study of the main biomolecules (DNA, proteins, lipids, carbohydrates) and stable isotopes, which are often preserved in paleontological, archaeological and historical remains (human, animal and plant remains, food residues, artifacts, etc.), aimed at contributing to the reconstruction of different aspects of human biocultural history: the evolutionary origins, biodiversity and migratory dynamics of the genus Homo; adaptation processes and responses to climate and environmental change and cultural and technological innovations; the demographic and social structure, mobility, patterns of life and subsistence as well as the health conditions and diseases of past populations. In this perspective, the course, while finding its privileged field of interest in the historical-archaeological and anthropological fields, offers significant repercussions also for the natural, environmental and biomedical sciences.

The program of the course is divided into three parts. The first part aims to provide the basic scientific and technical-applicative knowledge on biomolecules and stable isotopes as well as on the analytical methodologies used for their study of ancient remains, synthetically organized in the points below.

• Overview of the potential and responses that the analysis of the main biomolecules and stable isotopes, which remain in ancient samples, can provide in the field of historical-archaeological and anthropological research, and related problems.

• Preliminary notions of chemistry and biology of biomolecules (nucleic acids, proteins, lipids and carbohydrates).

• Residual biomolecules in ancient remains: sampling criteria and methods; problems of preservation, degradation and contamination; extraction techniques; next-generation methods for analysis and sequencing; Mass spectrometry; meanings and application limits.

• Notions of chemistry, geochemistry and biology of stable isotopes; methods of analysis of stable isotopes of carbon, nitrogen, strontium and oxygen; isotopic ratios in collagen and other ancient proteins and in the mineral phase of skeletal findings.

The second part of the program is dedicated to illustrating the most relevant applications of biomolecular and isotopic analyses to archaeological, bioarchaeological, paleoanthropological and paleopathological investigations related to the following points:

• contribution to the reconstruction of the phylogeny and evolutionary history of humans, as well as the migratory dynamics and dispersion of human populations;

• reconstruction of the individual biological profile (sex, age of death, phenotypic characters), determination of diet and inferences on human mobility; identification of genes potentially involved in genetic or multifactorial diseases, for the purposes of paleopathological diagnostics, in human remains of archaeological origin;

• determination of family relationships and contribute to the reconstruction of the biodemographic and social structure of ancient human groups represented by human remains;

• personal identification and verification of the authenticity of human remains attributed to famous individuals of the past;

• reconstruction of the origins and epidemiological history of infectious diseases, identification of pathogens and study of their evolution and spread; analysis of microbiomes;

• taxonomic diagnosis of faunal and plant remains and study of their evolutionary processes, also in relation to climate change and bio-cultural processes, such as domestication, agriculture and breeding.

The third part of the program has a practical-applicative character and consists in carrying out practical experiences in the laboratory concerning the sampling of remains, sample preparation, extraction and analysis techniques, as well as biostatistical treatment (including hints of applied bioinformatics) and the critical interpretation of the data obtained.

Specifically, the student will thus be able to acquire skills and practical experience:

• in the techniques of collecting and preparing samples to be subjected to analysis of ancient DNA, proteins and isotopes;

• in the practical application in the laboratory of extraction, quantification and processing protocols of the samples under examination;

• in statistical processing, including basic notions of applied bioinformatics, as well as in the interpretation of the generated data.

This course is linked to the course of "Laboratory of Archaeogenetics", lasting 50 hours and which usually takes place during the month of June, in which the interested student will be able to deepen the theoretical and practical aspects of genetics and genomics related to the analysis of DNA extracted from ancient finds (for information contact Prof. Elisabetta Cilli).

Readings/Bibliography

- Brown T., Brown K.- Biomolecular archaeology. An introduction. Wiley-Blackwell, 2011.

- Richards M.P., Britton K. - Archaeological Science. An introduction. Cambridge University Press 2020.

- Caramelli D. - Antropologia molecolare: manuale di base. Firenze University Press, 2009.

- Donati C., Stefani M., Taddei N. - Biologia & Genetica, Zanichelli 2019.

- Cilli E. (2022) Archaeogenetics. Encyclopedia of Archaeology. 2nd ed.

- Orlando, L., Allaby, R., Skoglund, P. et al. (2021) Ancient DNA analysis. Nat Rev Methods Primers 1, 14.

- Cappellini E., Prohaska A., Racimo F. et al. (2018) Ancient Biomolecules and Evolutionary Inference. Annual Review of Biochemistry, 87:1, 1029-1060.

- Warinner C., Korzow Richter K., Collins M.J. (2022) Paleoproteomics. Chemical Reviews Article DOI: 10.1021/acs.chemrev.1c00703

In Virtuale the list of pages of the texts to be studied for the exam, the scientific articles covered in class and the slides of the lessons will be uploaded.

Suggested reading

-Paabo S. - L'uomo di Neanderthal. Alla ricerca dei genomi perduti. Einaudi, 2014.

-Reich D. - Chi siamo e come siamo arrivati fin qui. Raffaello Cortina, 2019.

-Barbujani G. - Sillabario di genetica. Bompiani, 2019.

Teaching methods

The course will be carried out through lectures related to the topics of the program that can be supplemented by seminar activities on specific topics. Students will be asked to take an active part in the lessons through interventions, questions, requests for clarification and / or insights. During the lessons will be projected slides organized through PowerPoint, which will be made available to students.

Assessment methods

The assessment of learning consists of an oral exam. The first part will consist of an exposition of a case study, preferably through a PowerPoint presentation, in which the student will illustrate a scientific article, which can be chosen among the various case studies presented in class or among others that have captured the student's interest. The topic must be agreed with Prof. Cilli and the presentation must be sent at least one week before the exam. The second part of the exam will concern the verification of the preparation on the topics of the program.

In order to pass the exam, the student must prove to have acquired adequate knowledge, both general and systematic, on the various topics in the program and to have mastered the scientific and methodological tools of the discipline. For the purposes of the final grade of the test will be evaluated:

• the degree of scientific and methodological depth of the topics covered;

• the ability to support a critical and reasoned discussion on the topics in the program and to perform the necessary logical-deductive links;

• the ability to make interdisciplinary connections;

• the property of language and the quality of the exhibition.

Evaluation of the exam

The exam includes an assessment of the level of learning of the topics in the program with a grade expressed in thirtieths.

Graduation of the final grade:

• Very in-depth knowledge of the topics together with high critical analysis skills, connection and safe mastery of specific terminology: grade 30-30L;

• In-depth knowledge of the topics together with good analytical and critical skills and possession of an adequate mastery of specific terminology: grade 27-29;

• Technically adequate preparation and sufficient analytical skills, even if not particularly articulated, expressed in a correct language: grade 23-26;

• Sufficient preparation and analytical skills, expressed in a barely formally correct language: grade 18-22.

Non-attending students.

The program of the course is the same for both attending and non-attending students. The attendance of the lessons is strongly recommended for the achievement of a good profit, however, students who for valid reasons cannot attend are invited to contact the teacher, during the reception hours, for the suggestion of the necessary supplementary texts.

Teaching tools

The teaching material consisting of the slides used during the lessons and the scientific articles presented during classses can be found in Virtuale

Office hours

See the website of Elisabetta Cilli