Igor Ovtchinnikov

TEACHING PORTFOLIO

University of North Dakota

FORENSIC BIOLOGY (BIOL 320)

Spring semesters, 3 credits

The objective of this course is to introduce the students to Forensic Biology, its history, methods and the application of biological evidence to a court. The ultimate goal of forensic biology is to prove the link between perpetrators and biological evidence found at crimes scenes. The concept of biological evidence, its basic types, as well as the methods of its collection and characterization are considered. The class focuses on human identification using the serological, biochemical, and genetic methods. Students intensively study 

• key concepts of molecular and population genetics and their application in forensics
• various forensic DNA markers including the CODIS STRs (short tandem repeats), mitochondrial DNA, Y chromosome SNPs (single nucleotide polymorphisms)
• interpretations of DNA profiles in crime-scene investigations
• new methods of forensic genomics based on the analysis of nuclear and mitochondrial genomes
• wildlife forensics

The course includes lectures as well as student in-class presentations, discussions of criminal cases, and the statistical evaluation of biological evidence and population databases.

This is one of the courses that the American Academy of Forensic Sciences recommends for forensic scientists and DNA analysts.

INTRODUCTION TO THE FORENSIC SCIENCES (ANTH 120 / FS 120)

Fall semesters, 3 credits

This course introduces students to science principles and the manner in which those principles are applied within various fields of the forensic sciences.  Students who complete this course will be able to

• Provide definitions of science and forensic science
• Define several fields of the forensic sciences in terms of the types of evidence processed and typical procedures conducted in the forensic lab
• To become familiar with some of the techniques used by forensic scientists to collect and examine evidence recovered from crime scenes
• To understand the importance of physical and biological evidence and the role it plays in the determination of the guilt or innocence of an individual
• Identify and describe the impact of forensic scientists to their fields

MOLECULAR BIOLOGY TECHNIQUES (BIOL 410)

4 credits

Spring semesters

Molecular biology techniques are used in many fields, ranging from basic biological research to forensic identifications. Polymerase chain reaction (PCR), one of the basic techniques that students will study in the Spring semester is routinely used for determining personal identities from crime and accident scenes, checking for pathogens, evaluating evolutionary relatedness of species, and measuring genetic variation and levels of gene expression. 

Students will gain skills needed for working in genetics, forensic, animal and plant biology laboratories that utilize molecular biology technology. They will learn how to perform basic techniques of molecular biology in three class modules: 

• Mitochondrial DNA sequencing and tracing your maternal ancestry
• Molecular cloning
• RNA manipulations

GENETICS (BIOL 315)

3 credits

This course is designed for undergraduates majoring in biology, including general biology, pre-health science, and fisheries and wildlife biology majors. The class is also suited to students in related disciplines like biochemistry, chemistry, forensic science, nursing, and psychology. The first half of the class is focused on the foundations of Mendelian and molecular genetics. In the second half, these concepts are expanded to more advanced topics. Advances in genetics and genomics touch upon virtually every aspect of our lives from our own health (i.e., birth defects, genetic diseases, and cancer) to the food we eat and the medicines we take (i.e., agriculture and biotechnology) to the environment we live in (i.e., wildlife and conservation biology). 

INTRODUCTION TO BIOLOGICAL ANTHROPOLOGY (ANTH 170)

3 credits

This course explores the basic scientific principles of the evolution and biological adaptation of our own species, Homo sapiens, and the formation of early human culture. For all of us, this is our story. Our search for what binds us together as a single species with a deep, shared history. The course takes us in several directions: beginning with an in-depth examination of evolutionary theory, through genetics and the biological diversity of modern human populations around the world, to a study of behaviors and physical traits that we share with other primates, and finally, through the fossil record of human physical evolution. The course also examines how paleoanthropologists interpret and reconstruct the biological and cultural adaptation of our earliest hominin ancestors using fossil, geological, genetic, and archaeological evidence.

HUMAN MEDICAL and POPULATION GENETICS (BIOL 499 / BIOL 590)

3 credits

The genetic diversity of human populations as well as differences between individual genomes form the basis of medical and forensic genetics. In this interdisciplinary course students consider the basic laws and concepts of population genetics and their specific applications to our understanding of genetic diseases, phenotypic traits and individual identity. The course includes lectures as well as computer lab sessions and exercises, student in-class presentations and discussions of research articles. Students also perform computer analysis of human genetic diversity and make inferences about the evolutionary processes in human populations.

 University of Connecticut, Storrs, Connecticut

 ANTHROPOLOGICAL GENETICS (ANTH 305, section 20)

3 credits

Molecular genetics, bioinformatics, ancient biomolecules, forensic genetics, and cytogenetics are considered together with evidence from physical anthropology, archaeology, and linguistics to address human-ape evolutionary relations, modern human origins, and recent human population histories and dispersals.

Discussions include

• Genetics and the Making of Homo sapiens
• The Neanderthal Genome Project
• Genetics of Pacific Islanders: Was Thor Heyerdahl right?
• Genetics of Plant and Animal Domestication
• … and many other fascinating things.

HUMAN GENETICS (MCB 200)

3 credits

Conceptually the course is divided into three parts: molecular genetics, classical genetics, and human genetics.  Two 50-minute lectures each week introduce the key concepts and facilitate understanding of the basic terms.  One discussion section per week is used to review the material covered in the lectures.

HISTORY OF GENETICS (MCB 396, Section 049)

3 credits 

This interdisciplinary course explores the origins and development of the major concepts in genetics from Mendel and Darwin to the whole-genome technologies. A role of different scientific approaches, technologies, and model organisms in our understanding and transformation of the core genetic concepts is examined. The basic attention is directed to the review of the primary and most important secondary sources.

 SEQUENCING MITOCHONDRIAL DNA (MCB 327, Section 5)

1 credit

This three-day course includes the necessary techniques to isolate, amplify, sequence human mitochondrial DNA and introduces students to the comparative analysis of human mitochondrial genomes. The course is essential for students specializing in forensic, ancient, population, and medical genetics.

• Ancient genomics
• Neanderthal and modern human evolution (the Black Sea region)
• American bison genomics and ecology
• Feral and historical horses in the Great Plains
• Heritage of the Northern Plains
• Human population genetics
• Forensic DNA
• Stable isotopes in paleoecology
• Oral microbiomics

SELECTED PUBLICATIONS 

Great Plains Heritage

Ovchinnikov, I.V. & McCann, B. (2023) Mitogenomes revealed the history of bison colonization of Northern Plains after the Last Glacial Maximum. Scientific Reports (Nature), 13: 11417 (10 pages). https://doi.org/10.1038/s41598-023-37599-8. https://www.nature.com/articles/s41598-023-37599-8

Davies, G., McCann, B., Jones, L., Liccioli, S., Penedo, M.C., Ovchinnikov, I.V. (2022). Genetic Variation of the Mitochondrial DNA Control Region Across Plains Bison Herds in USA and Canada. PLoS One, 17(3): e0264823 (18 pages)

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0264823

Davies, G., McCann, B., Sturdevant, J., Swenson, F., Ovchinnikov, I.V. (2019). Isotopic Paleoecology of Northern Great Plains Bison during the Holocene. Scientific Reports (Nature), 9 (1): 16637 (11 pages); doi: 10.1038/s41598-019-52873-4.

https://www.nature.com/articles/s41598-019-52873-4

Ovchinnikov, I.V., Dahms, T., Herauf, B., McCann, B., Juras, R., Castaneda, C., Cothran, G. (2018). Genetic Diversity and Origin of the Feral Horses in Theodore Roosevelt National Park. PLoS One, 13(8), 18 pages.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0200795

Genetics of Neanderthals and Extinct Hominins

Ovchinnikov, I.V. Hominin evolution and gene flow in the Pleistocene Africa. Anthropologischer Anzeiger – Journal of Biological and Clinical Anthropology, 2013, 70(2): 221 – 227. 

Goodwin, W., Ovchinnikov, I. Neanderthal mitochondrial DNA. In: eLS (Encyclopedia of Life Sciences). John Wiley & Sons, Ltd: Chichester, 2013. http://onlinelibrary.wiley.com 

Ovchinnikov, I.V. Reconstructing the mitochondrial genomes of extinct hominins using a bioinformatics approach. In: Genomics I: Humans, Animals and Plants. iConcept Press, Hong Kong – Brisbane, 2012 (15 pages). https://www.iconceptpress.com/books/genomics-i-humans--animals-and-plants/ 

Ovchinnikov, I.V. & Kholina, O.I. Genome digging: Insight into the mitochondrial genome of Homo. PLoS One 2010, 5: e14278 (11 pages).

Ovchinnikov, I., Goodwin, W. Neanderthal DNA. An invited article for the McGraw-Hill Yearbook of Science and Technology 2008, New York.

Goodwin, W., Ovchinnikov I. Ancient DNA and the Neanderthals. In: Bandelt, H.-J., Macaulay, V., and Richards, M. (Eds.) Human Mitochondrial DNA and the Evolution of Homo sapiens. Nucleic Acids and Molecular Biology, Vol. 18. Berlin – Heidelberg: Springer-Verlag, 2006: 199 – 222.

Goodwin W, Ovchinnikov I.  Neanderthal DNA. In: Cooper, D.N. (ed.) Nature Encyclopedia of the Human Genome. London: Nature Publishing Group, 2003, Vol. 4:  282-286.

Ovchinnikov I, Goodwin W. The isolation and identification of Neanderthal mitochondrial DNA. Profiles in DNA 2001, 4, 2: 7-9.

Ovchinnikov I, Lidén K, Goodwin W. Neanderthal DNA in the Caucasus and population genetics of archaic humans. Athena Review: Journal of Archaeology, History, and Exploration 2001, 2: 53-58.

Ovchinnikov I.V., Götherstöm A, Romanova GP, Kharitonov VM, Lidén K, Goodwin W. Reply: Neanderthal DNA: Not just old but old and cold? Nature 2001, 410: 772.

Ovchinnikov I.V., Götherstöm A, Romanova GP, Kharitonov VM, Lidén K, Goodwin W. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 2000, 404: 490-493. 

LINE-1 Retrotransposons 

Mathews, L.M., Chi, S.Y., Greenberg, N., Ovchinnikov, I., Swergold, G.D. Large differences between LINE-1 amplification rates in the human and chimpanzee lineages. American Journal of Human Genetics 2003, 72: 739-748.

Ovchinnikov, I., Rubin, A., Swergold, G. Tracing the LINEs of Human Evolution. Proceedings of the National Academy of Sciences of the United States of America 2002, 99: 10522-10527.

Ovchinnikov, I., Troxel, A., Swergold, G. Genomic characterization of recent human LINE-1 insertions: Evidence supporting random transposition. Genome Research 2001, 11: 2050-2058. 

Forensic and Ancient DNA 

Ovchinnikov, I.V., Malek, M.J., Kjelland, K., Drees, K. (2016). Whole human mitochondrial DNA sequencing. In John Walker, William Goodwin (Ed.), Forensic DNA Typing Protocols. Methods in Molecular Biology, Vol. 1420, pp. 157 - 172. New York: Springer Humana Press. http://www.springer.com/series/7651. 

Ovchinnikov, I.V., Malek, M.J., Drees, K., Kholina, O.I. Mitochondrial DNA variation in Tajiks living in Tajikistan. Legal Medicine, 2014, 16: 390 – 395.

Ovchinnikov, I.V., Goodwin, W. Ancient human DNA from Sungir? Journal of Human Evolution 2003, 44: 389-392.

Ovchinnikov, I., Buzhilova, A., Mednikova, M., Goodwin, W., Curry, G. Ethnic affinities of the ancient human Jety-Asar population by mitochondrial DNA analysis. Electrophoresis 1999, 20: 1729-1732.

Ovchinnikov, I.V., Ovtchinnikova, O.I., Druzina, E.B., Buzhilova, A.P., Makarov, N.A. Molecular genetic sex determination of Medieval human remains from North Russia: Comparison with archaeological and anthropological criteria. Anthropologischer Anzeiger 1998, 56: 7-15.

Rogaev, E., Ovchinnikov, I.V., George-Hyslop, P., Rogaeva, E. Comparison of mitochondrial DNA sequences of T.N. Kulikovskii-Romanov, the nephew of Tsar Nikolai II Romanov, with those of DNA obtained from the putative remains of the Tsar. Russian Journal of Genetics 1996, 32: 1472-1474. 

Ovchinnikov IV, Chystiakov DA, Nosikov VV, Ovtchinnikova OI, Chizhov VV. PCR-based determination of  HLA-DQA1 and some VNTR  allele  frequency  profiles  in  East Slavonic populations for identity testing.  In:  Advances in Forensic Sciences. Ed. by B.Jacob, W.Bonte. Berlin, 1995, V.6: 97-106. 

Ovtchinnikova OI, Chelnokova MV, Ovchinnikov IV. High degraded DNA typing for discrimination of decomposed human remains after explosion. In: Advances in Forensic Sciences. Ed. by B.Jacob, W.Bonte. Berlin, 1995, V.6: 137-139. 

Ovchinnikov IV, Gavrilov DK, Nosikov VV, Debabov VG. Use of the polymerase chain reaction for typing allelic variants of the human HLA-DQA1 gene by hybridization with oligonucleotide probes specific for particular alleles. Molecular Biology (Moscow) 1991, 25: 1266-1272. 

Ovchinnikov IV, Gavrilov DK, Nosikov VV, Debabov VG. The use of polymerase chain reaction to analyze allelic variations of HLA-DQ alpha and beta genes. In: Metabolism and Enzymology of Nucleic Acids Including Gene and Protein Engineering. Ed. by J.Balan. Bratislava, 1991: 227-235. 

Medical Genetics 

Illarioshkin SN, Bagieva GKh, Klyushnikov SA, Ovchinnikov IV, Markova ED, Ivanova-Smolenskaya IA. Different phenotypes of Friedreich’s ataxia within one “pseudo-dominant” genealogy: relationships between trinucleotide (GAA) repeat lengths and clinical features. European Journal of Neurology 2000, 7: 535-540. 

Anokhina, I.P., Veretinskaia, A.G., Vasileva, G.N. & Ovchinnikov, I,V. Biological mechanisms of individual predisposition to psychoactive drug abuse. Human Physiology (Moscow) 2000, 26, 6: 74-81. 

Ivanova-Smolenskaya IA, Ovchinnikov IV, Karabanov AV, Deineko NL, Poleshchuk VV, Markova ED, Illarioshkin SN. A major mutation in the ATP7B gene in Russian families with Wilson’s disease. Journal of Medical Genetics 1999, 36: 174. 

Ovchinnikov IV, Druzina E, Ovtchinnikova O, Zagorovskaya T, Nebarakova T, Anokhina IP. Polymorphism of dopamine receptor D2 and D4 genes among alcohol-dependent subjects with Slavic surnames. Addiction Biology 1999, 4: 399-404. 

Illarioshkin, S.N., Druzina, E.B., Bagieva, G., Markova, E.D., Miklina, N.I., Ovchinnikov, I.V. & Ivanova-Smolenskaya, I.A. Friedreich’s disease: a real spectrum of clinical manifestations and direct DNA-diagnostics. Korsakov Journal of Neurology and Psychiatry (Moscow) 1999, 99, 8: 15-19. 

Anokhina, I.P., Vertinskaia, A.G., Vekshina, N.L., Nebarakova, T.P., Ovchinnikov, I.V., Druzina, E.B. & Ovchinnikova, O.I. Hereditary alcoholism: some neuro-chemical and genetic mechanisms. Proceedings of the Russian Academy of Medical Sciences 1999, 6: 43-47. 

Illarioshkin SN, Slominsky PA, Ovchinnikov  IV,  Markova ED, Miklina NI, Klyushnikov SA, Shadrina M, Vereshchagin NV, Limborskaya  SA, Ivanova-Smolenskaya IA. Spinocerebellar ataxia type 1 in Russia.  Journal of Neurology 1996, 243: 506-510. 

Gavrilov DK, Ovchinnikov IV, Chelnokova MV, Nosikov VV. The use of synthetic oligonucleotide primers for prenatal diagnosis of sex in chorionic villi via the polymerase chain reaction. Nucleic Acids Research 1991, 19 (Suppl.): 257. 

Gavrilov DK, Ovchinnikov IV, Nosikov VV. The use of PCR technique and sequence specific oligonucleotides for HLA-DQA1 and DQB1 gene typing in a group of insulin-dependent diabetes mellitus patients in the Russian population of Moscow. Nucleic Acids Research 1991, 19 (Suppl.): 258. 

Gavrilov DK, Ovchinnikov IV, Vassilev VB, Mosikov VV. The use of polymerase chain reaction for amplification of DNA from paraffin-embedded tissues in patients with hepatitis B virus infection. Path. Res. Pract. 1991, 187: 692-693.

Wildlife Genomics, Microbiomics, Paleoecology and Environmental DNA.

The Laboratory of Evolutionary and Forensic Genetics at the University of North Dakota (www.und.edu) is inviting applications from highly motivated students who pursue a PhD degree. MS candidates will be also considered.

Students will be engaged in a project on the historic, current and future status of bison herds from biological, archaeological, and cultural perspectives. This cross-disciplinary project represents an opportunity to get intensive training in the methods of ancient and modern DNA analyses including high-throughput genome sequencing, stable isotope profiling, computational analysis and statistical modelling. The examples of our recent publications: Ovchinnikov et al. Diversity and Origin of the Feral Horses in Theodore Roosevelt National Park. PLoS One, 2018, 13(8); Davies et al. Isotopic Paleoecology of Northern Great Plains Bison during the Holocene. Scientific Reports, 2019, 9(1): 16637; Davies et al. Genetic Variation of the Mitochondrial DNA Control Region Across Plains Bison Herds in USA and Canada. PLoS One, 2022, 17(3). Although the wildlife project is focused on bison genetics and paleoecology, we have opportunities to develop new projects on computational analysis of big oral and environmental microbiome data as well as on genomics and microbiome study of human migrations and evolution with the focus on the Great Plains and Eurasia.   

Candidates should demonstrate motivation for hard laboratory work and strong interest in genomics and computational biology. Preference will be given to candidates with a proven record of computational analysis and bioinformatics skills. Additional experience in sequencing technologies is a plus.

If you are interested, you need to apply to the University of North Dakota Biology Graduate Program using the regular procedure. Requirements and How to Apply procedure can be found in the UND Biology Graduate School websites:

https://und.edu/programs/biology-phd/requirements.html

How To Apply to UND Graduate School | University of North Dakota

The additional information can be also found in the Biology Department website:

https://arts-sciences.und.edu/academics/biology/

The position starts in January or August 2023. To receive full consideration for the January kickoff, the Biology Graduate Program needs to receive applications and required materials by September 15, 2022. 

Potential graduate students are also encouraged to make contact with Dr. Igor Ovchinnikov.

Contact information:

Dr. Igor Ovchinnikov
Associate Professor
Lab. of Evolutionary and Forensic Genetics
Department of Biology
Forensic Science Program
University of North Dakota

Email: igor.ovtchinnikov@und.edu

The Lab constantly consider undergrad applications from students who want to get research credits working in genetics, genomics, computational analysis, image analysis, palynology and microscopy.