Download Leila Mamirova

CURRICULUM VITAE
Konstantin Yur’evich Popadin
DATE OF BIRTH: 28 May 1979
CITIZENSHIP: Russia
PROFESSIONAL ADDRESS: Institute for information transmission problems of the Russian
Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Moscow, 127994, Russia
PHONE: 7(903)0107415 (mobile); 7(495)9329325 (home);
E-MAIL: [email protected]
EDUCATION AND QUALIFICATIONS:
2007-Present. Post-doc in Bioinformatics. : Institute for information transmission problems of the Russian
Academy of Sciences (Kharkevich Institute)
2004-2007. Post-doc in Bioinformatics. Department of Genetics, Biological Faculty of M.V.
Lomonosov Moscow State University (MSU):
2001-2004. PhD in Biology. “Evolution of genes and genomes in the absence of homologous
recombination” Department of General Ecology, Biological Faculty of MSU
2001-2004. 10 mathematical courses on the Department of Applied Mathematics and Cybernetics of
MSU
1996-2001. MSc in Biology. Department of Vertebrate Zoology, Biological Faculty of MSU
1993-1996. High School Diploma. Biology and Chemistry
MY INTERESTS INCLUDE:
Broad aspects of Evolution, evolutionary genetics, evolution of sex, purifying selection, life-history
evolution,
TEACHING:
September 2006 - December 2006. Department of Genetics of MSU
“Selective chapters in evolutionary genetics”:
Evolution of mutability: mutational rate, selection coefficients, purifying selection;
Population dynamics of mobile elements – influence of recombination level;
Mutation-selection equilibrium and how to decrease mutational load;
Evolution of genes in the absence of homologous recombination;
Pluses and minuses of sexual reproduction;
Effectively-neutral evolution and potential consequences of accumulation of slightlydeleterious mutations: case of mitochondrial genome.
February 2006 – Mart 2006. Department of Genetics of MSU
Computer seminars “Searching of positive and negative selection using molecular data”.
January 2004 – June 2004, Faculty of Foreign Languages, MSU. Lecture course in English:
“Basic Biology”.
PROFESSIONAL SKILLS:
Bioinformatics:
Extraction of genome-data from public databases in WWW (by hand or using Perl’s robots);
Treatment of sequences using Perl scripts and number of special programs;
Statistical analysis: descriptive statistics, estimation and hypothesis testing, analysis of
variance (nested, multiway), different types of regression analyses (linear/nonlinear regressions with
one/many variables, influence of qualitative variables using Dummy variables or logistic regression,
accounting of effect of nonindependence of data (linear/nonlinear mixed-effects regresion models)),
correlation analyses (rank correlation, principal axes method).
Investigation of evolution process using mathematical models:
theory of games;
methods of optimization;
COMPUTER SKILLS:
Scientific Softwares: R, S-PLUS, MatLab, SAS;
Programming Languages: PERL, using Perl & LWP module to automate WWW-routines, C++,
HTML;
Graphical packages: Corel Draw, Adobe PhotoShop;
LANGUAGES: Russian (native), English (fluent).
PUBLICATIONS:
Nikolaev SI, Montoya-Burgos JI, Popadin K, Parand L, Margulies EH. Life-history traits drive the
evolutionary rates of mammalian coding and noncoding genomic elements. Proc Natl Acad Sci
U S A. 2007, 104(51):20443-8.
Popadin KY, Mamirova LA, Kondrashov FA. A manually curated database of tetrapod
mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 2007,
8(1):441
Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K. Accumulation of slightly deleterious
mutations in mitochondrial protein-coding genes of large versus small mammals. Proc Natl
Acad Sci USA. 2007, 104(33):13390-5.
Mamirova L, Popadin K, Gelfand MS. Purifying selection in mitochondria, free-living and obligate
intracellular proteobacteria. BMC Evol Biol. 2007, 7(1):17.
Popadin K. and Mamirova L. 2004. The history of a single chromosome. Priroda 9, 11-16, (in
Russian).
Popadin K. 2003. The Evolution of Sex: Role of Deleterious Mutations and Mobile Elements (a
review). Zhyrnal Obshei Biologii 64: 463-478. [In Russian with English summary]
Popadin K. 2002. Вody size of Holopedium gibberum under the influence of fish predation in small
subarctic lakes. Verh. Internat. Verein. Limnol. 28 (1): 204-209.
CONFERENCES, WORKSHOPS, SEMINARS:
Popadin K, 2008. Nucleotide repeats in mitochondrial genome determine Chordata and human
lifespan. Gordon Research Conference “Mitochondria & Chloroplasts”, Biddeford ME USA.
Popadin K, 2008. Life-history Traits Drive the Rates of Accumulation of Slightly-deleterious
Mutations in Mammalian Coding Elements. XX International Congress of Genetics to be held in
Berlin, Germany.
Popadin K. 2008. TRNA’S FREE ENERGY AND EVOLUTION OF MITOCHONDRIAL
GENOME. Sixth International Conference on Bioinformatics of Genome Regulation and
Structure (BGRS 2008)
Popadin K, 2007. Evolution of tRNA molecules in mitochondrial genomes of tetrapodes. Proceedings
of the International Moscow Conference on Computational Molecular Biology. Moscow,
Russia.
Popadin K, Mamirova L, Polishchuk L, Knorre D, Kondrashov F. 2005. Effectively-neutral evolution
of mitochondrial genes of mammals. Proceedings of the International Moscow Conference on
Computational Molecular Biology. P. 307-308. July 18-21. Moscow, Russia.
Popadin K. 2005. Evolution of genes in absence of homologous recombination. Proceedings of the
International Novosibirsk Workshop on Biosphere Origin and Evolution. P. 285-286. 26-29
June, Novosibirsk, Russia.
Popadin K. 2004. Origin and evolution of sexual reproduction. 23 November, MOIP. Moscow,
Russia.
Popadin K. 2004. How long is it possible to exist without sex? Seminar of Department of General
Ecology, Biological Faculty of Lomonosov Moscow State University. Russia
“http://www.sevin.ru/fundecology/archive/8_04_2004.html"
Popadin K. 2003. Ancient asexuals and the maintenance of sex. PARTNER Workshop –1. Ancient
asexuals and time-scales. 20-23 November, Wageningen, The Netherlands.
Popadin K. 4 –9 February 2001. "Вody size of Holopedium gibberum under the influence of fish
predation in small subarctic lakes. 28 Congress of Society International Limnology (SIL),
Melbourne (Australia).
Popadin. K. 2000. Body size and fitness of Holopedium gibberum. Fifth conference of biological
station at White Sea of M.V. Lomonosov Moscow State University (Russia).
Galimov Ya.R. and Popadin K. 2000. Hatching of Daphnia ephippial eggs: intrapopulation and
interpopulation variance of diapause’s timing. International conference ‘The problems of
hydroecology’, Sankt-Peterburg (Russia).
GRANTS AND AWARDS:
Russian Foundation of Basic Research (RFBR) – initiative grant. 2008-2010.
Russian Science Support Foundation Grant. 2008-2009.
Grant of President of the Russian Federation. 2008-2009.
Russian Foundation of Basic Research (RFBR) – travel grant for participation in the PARTNER
workshop -1, Wageningen (The Netherlands), 20-23 November 2003, № 03-04-58921-z.
Russian Foundation of Basic Research (RFBR) 2003 № 03-04-06830-mas.
Russian Foundation of Basic Research (RFBR) 2002 № 02-04-06380-mas.
Russian Foundation of Basic Research (RFBR) - travel grant for participation in the 28 Congress of
Society International Limnology (SIL), Melbourne (Australia), 4-9 February 2001, № 01-04-58507-z.
International Soros Scientific Educational Program (ISSEP), 1997.
DISSERTATION
EVOLUTION IN THE ABSENCE OF HOMOLOGOUS RECOMBINATION: ECOLOGICAL
AND GENETIC MECHANISMS OF ORIGIN AND EXISTENCE
03.00.16 ecology & 03.00.15 genetics
Majority of works on evolution have been written for sexual organisms, and thus some
important evolutionary conceptions could not be applied to asexual lines directly (for example,
conception of species). If we define evolution as a process of accumulation of favorable mutations
and elimination of deleterious ones it is necessary to understand the peculiarities of the process in
asexual species and non-recombining regions of DNA: what is the mutational rate in asexual lines as
compared to sexual, is there effective elimination of deleterious mutations and how frequently do
favorable mutations can be combined with each other? Answers on these questions will help us to
solve the main evolution puzzle – why does majority of organisms have sexual reproduction?
The main goal of the work is to determine specific traits of ancient asexual species and nonrecombinant regions of DNA and to discuss their possible adaptive sense. There three specific tasks:
1. To analyze distribution of deleterious mutations in asexual populations which were originated from
sexual populations with various mutational parameters (mutational rate, coefficient of selection
against mutations, interaction of mutations with each other);
2. To reveal ecological and genetic traits, specific for ancient asexual species such as rotifera Bdelloidea and freshwater crustacea -Darwinulidae;
3. To reveal specific traits of structure and molecular evolution of Y chromosome of mammals and
mitochondrial genome of mammals as examples of non-recombinant genes.
In the work I have constructed mathematical model of origin and maintenance of asexual
species from sexual ones and consider possible ways of further evolution. I have obtained the first
evidences of rather effective elimination of slightly-deleterious mutations in mitochondrial genes as
compared to bacterial orthologous. Also, comparing mitochondrial genes of mammals on I have
found out the more effective purifying selection in small-bodied species as compared to large-bodied
ones.
SUMMARY OF KONSTANTIN POPADIN’S WORKS –
EVOLUTIONARY GENETICS OF MITOCHONDRIA
My main scientific interest is searching of relationships between genetic and ecological traits
of vertebrate animals using tools of bioinformatic. Genetic traits of each species (such as rate of
accumulation of neutral or slightly deleterious mutations, abundance of nucleotide repeats, Gibbs
Energy of transfer RNA’s molecules, physical-chemical traits of proteins) I estimate from complete
sequences of mitochondrial genomes. Among ecological – physiological traits I consider body mass,
trophic level, generation time, body temperature and basal metabolic rate. For each revealed trend, I
suggest evolutionary model with potential functional explanation of the correlation. Investigation of
such models helps to understand the basic rules of molecular evolution.
The main topic of my work is investigation of evolutionary dynamic of slightly deleterious
mutations in mitochondrial genome of vertebrate species and human. Recently, we have analyzed the
rate of accumulation of slightly deleterious mutations in mitochondrial genomes of 110 mammalian
species. We have revealed that rate of accumulation of these mutations is higher in large-bodied
mammals as compared to small-bodied ones. We interpret this correlation in the light of the
effectively neutral theory of molecular evolution – the probability of fixation of slightly deleterious
mutation due to random genetic drift is higher in populations with low size (i.e. in large-bodied
mammals), while majority of slightly deleterious mutations is effectively eliminated in populations
with high size (i.e. in small bodied mammals). In other words, the selection is more effective in
populations of high size as compared to populations with low size, and body mass is just an
approximation of population size of the species (the larger the body size the smaller the population
size). The work was published as two separate articles in Proceedings of the National Academy of
Science USA (Popadin et al. 2007 PNAS, 104: 13390-5; Nikolaev et al, 2007. PNAS, 104: 2044320448).
Additionally we have compared power of purifying selection in mitochondrial and
proteobacterial genes and we have revealed, that mitochondria despite the absence of recombination
and strong genetic drift due to low effective size possess more effective elimination of slightly
deleterious mutations as compared with bacteria (Mamirova et al. 2007. BMC Evol Biol. 7(1):17.).
Also we constructed manually curated database of secondary structures of tRNAs from mtDNA of
tetrapodes (Popadin et al. 2007, BMC Bioinformatics. 8(1):441), which we plan to use in evolutionary
aspects.
Since deleterious mutations might determine predisposition of humans to various diseases and
even constrain their lifespan, now I investigate dynamic of deleterious mutations in mitochondrial
genomes of human populations.