Molecular Biosciences Research Experience at the Czech Academy of Sciences Biology Centre

The Molecular Biosciences Research Experience (MBRE) at the Czech Academy of Sciences Biology Centre in Ceske Budejovice, Czech, is designed to introduce rising juniors and sophomores who are members of groups underrepresented in science (ethnic minority students and economically disadvantaged students) to the research involving the use of molecular techniques.  Participating laboratories at the Biology Centre are drawn from the Institutes of Parasitology, Plant Sciences, and Entomology.  This 10-week summer research experience is preceded by six weeks of preparatory meetings (2 hours per week starting in April) on the University of Arizona campus.  The program is contingent upon funding from the National Science Foundation to the University of Arizona.

Program Benefits

Participants will receive

  • Round trip airfare (and ground transportation in Czech) from Tucson to Ceske Budejovice
  • Room and board (participants housed in University of South Bohemia dormitories in a room with a same gender roommate)
  • A stipend for time abroad doing research
  • Scientific training and cultural experiences

MBRE Eligibility

To be eligible to apply for MBRE, students must:

  • Be an enrolled student at the University of Arizona or Pima Community College during the Spring of 2019 and planning to register for the Fall 2019 Semester (PCC students who are enrolled in at least one credit hour at UA for the spring 2019 semester are particularly encouraged to apply)
  • Have an interest in biosciences research and have completed at least one college level biology course and one college level mathematics course
  • Be in good academic standing and have a 3.0 GPA in college level math and science courses
  • Be an American citizen or permanent resident of the United States
  • Be a member of a group underrepresented in STEM disciplines (e.g. ethnic minority students, economically disadvantaged students, etc.)
  • Be emotionally mature (as reflected in the personal statement and letters of reference)
  • Be willing and able to attend all of the preparatory sessions in the spring semester and to work full time in a Czech laboratory for 10 weeks in the summer (dates of the program are predetermined).

Application Process

The application process includes a complete 2019 MBRE Application and, for finalists, an interview. The application consists of:

  • A 600-word personal statement in which the applicant introduces him/herself to the committee, discusses his/her educational and career goals, and how an international research experience in Czech will advance these goals.
  • A description of the applicant’s previous research or laboratory experience (if any).
  • A letter of recommendation from a university or college science or math instructor and one from another reference. If the applicant has previous research or laboratory experience one letter should come from the head of the laboratory. Letters should be sent directly from references to the address below and should arrive by the deadline.
  • Official transcripts from all colleges or universities attended; these should be sent directly to the address below.
  • Review the list of potential mentors and rank order the three of most interest to you. See below for list of participating mentors.

Submit all application materials to:

Carol Bender
c/o Undergraduate Biology Research Program
Life Sciences South #348
P.O. Box 210106
Tucson, AZ 85721-0106

The deadline for applications is:  February 15, 2019.

Program Benefits

Participants will receive

  • Round trip airfare (and ground transportation in Czech) from Tucson to Ceske Budejovice
  • Room and board (participants housed in University of South Bohemia dormitories in a room with a same gender roommate)
  • A stipend for time abroad doing research
  • Scientific training and cultural experiences

MBRE Mentors:

Institute of Entomology

Dr. David Dolezel. Organisms living in temperate regions, such as Europe or North America, have to cope with seasonal weather changes. It is a great advantage to prepare for seasonal adversities in advance, to anticipate them. The day-to-night length ratio (so called photoperiod) is the most stable and reliable signal. Although the photoperiod measurement is essential adaptation for thousands of insect species, the actual mechanism is unclear. The goal of our group is to shed some light on the architecture of insect photoperiodic timer at genetic level and to explore any possible connection with circadian clock genes. To achieve that, we use the linden bug, Pyrrhocoris apterus, an insect species with robust seasonal phenotype and recently established genetic tools. From research on Drosophila we know certain circadian clock genes participating in regulation of periodic activity in flies. The key question is whether the role of these genes is conserved across taxa. The linden bug is an ideal model to test it: (i) it is phylogenetically far from fly and some of its genes are even more similar to mammals. (ii) We have efficient tools to do the experiment. The work consists of gene identification from our transcriptome database (finding the homolog of known Drosophila gene), PCR, cloning PCR product, preparation of dsRNA, injection of dsRNA into bugs and analysis of locomotor activity (which is automatically recorded). The student will have opportunity to cover complete experimental procedure and learn large number of molecular biology techniques in relatively short training period.

Dr. Jan Hrcek. This laboratory uses molecular techniques and laboratory experiments to describe complex natural food webs and to understand how they are composed and how they function. We use wild fruit flies and their parasitic wasps from the Australian rainforest. A genetics model system is used to answer questions in community and evolutionary ecology, including: i) How do the predicted effects of climate change including changes in abiotic conditions and species composition impact food web structure and stability? ii) How will host immunity and parasitoid attack mechanisms respond to climate change? iii) What is the role of endosymbiotic bacteria and microbiome in shaping food webs? The student will learn to reconstruct host – parasitoid or host – symbiont interaction networks using DNA metabarcoding (both lab work and bioinformatics), detect symbionts and parasites using PCR, cure Drosophila from symbionts and establish the symbiont phenotype.

Institute of Plant Molecular Biology

Dr. Jiri Macas. The lab aims to uncover molecular mechanisms of centromere determination and evolution, using two groups of closely-related organisms, where each group includes species with different types of centromere organization. Using these models, it is possible to investigate the transition between different centromere types on a relatively uniform genetic background of related genomes. The first model group, Cuscuta, is the only plant genus known to contain both species with monocentric and holocentric chromosomes. The second model group, the legume tribe Fabeae, was selected due to the occurrence of meta-polycentric chromosomes which might represent an intermediate state between regional and dispersed centromeres. Experiments employ sequencing, bioinformatics, and cytogenetic techniques to perform identification, sequence characterization and comparative analysis of centromeric repeats from different species, identification and characterization of genes coding for CenH3 and additional kinetochore proteins, microscopic study of centromeric chromatin and analysis of transcriptional activity of centromeric regions.

Dr. Radek Litvin. Influence of pH on energy transfer and photoprotective capabilities in purified membranes from photosynthetic algae and plants. Photosynthesis is the source of organic carbon which powers our bodies and a large part of our economy. Photosynthesis requires a delicate balance between harvesting light to power light-driven enzymes and protecting against harmful effects of unquenched excited molecules when there is too much light energy. Light- dependent reactions of photosynthesis take place in a system of membranes containing pigment-binding protein complexes. One of the key mechanisms of photoprotection depends on low pH in the medium surrounding these membranes. During photosynthesis, protons are translocated across the membrane and in overexcitation, the low pH generated triggers protective mechanisms. The specific molecular mechanisms have been studied but they are not precisely understood. This project will investigate these mechanisms on the membrane level. The project will involve preparation of photosynthetic membranes and analysis of their properties in different pH levels via time-resolved and steady-state absorption and fluorescence optical spectroscopy methods. The project requires basic wet lab skills and interest in understanding biophysical methods.

Dr. Igor Koloniuk. The student will be involved in research related to plant viruses infecting strawberries, including their detection and molecular characterization. It will include preparation of RNA extracts from strawberry plants and associated aphids. Using two step reverse transcription real time quantitative polymerase chain reaction, estimation of a viral replication will be performed and compared in both groups of samples.

Institute of Parasitology

Dr. Ryan Rego. Borrelia are a unique set of bacteria belonging to the Spirochete family. They have a segmented genome made up of a chromosome as well as many linear and circular plasmids. More than 70% of the genes that are encoded within their genome belong only to the Borrelia family with no homologues in other bacteria. They are not free-living but are usually part of a tick-mammal zoonotic cycle. They undergo a variety of genetic rearrangements within their plasmid content leading to strains lacking plasmids or to strains with more than one copy of the plasmid. The lab is looking at the Restriction-Modification (R-M) genes of the various genospecies Borrelia present in Europe. There are more than 14 separate genospecies within Europe that very clearly have their own ecological niches and the lab seeks to understand if the R-M machinery to recognize foreign DNA is common for all of them or is unique to each particular Borrelia species and how this may impact the role in genetic exchange within the spircohetes of Europe. This would also help provide an understanding in how to overcome the R-M system of these Borrelia when trying to knockout and complement genes of interest. Lab projects look at the transformation efficiency of using a shuttle vector modified in vivo by one species of Borrelia and how acceptable is it for another species compared to shuttle vector DNA generated in vivo in E. coli. The project would also look at using an in vivo method of modifying genetic exchange constructs using Borrelia proteins important for sequence methylation before transformation in Borrelia. This would help us look at improving transformation of this highly recalcitrant bacterium.

Dr. Zdenek Paris. It has been reported in yeast that nuclear tRNA export serves as a quality control mechanism for properly processed and modified tRNAs. This lab focuses on whether the unique members of the Trypanosoma brucei tRNA retrograde export pathway TbMex67- TbMtr2 serve as a quality control mechanism, prior the export of tRNAs into cytosol. RNAi knock downs of the newly identified tRNA exporters will be tested for the levels of a nucleus specific tRNA modification, base methylation at position 37 (m1G37) in both nucleus and cytosol. The lab has demonstrated that TbTRM5 is responsible for m1G formation of several tRNAs in trypanosomes, with its predominant localization in the nucleus (38). Detection of this modification will take advantage of methylation preventing the annealing of a specific fluorescently labeled probe versus a probe designed upstream or downstream of the modified position G37. Levels of the modified and un-modified tRNA will be quantified by fluorescent microscopy.

Dr. Alena Zikova. Trypanosoma brucei has a complex life cycle that alternates between a mammalian host and the tsetse fly. Depending on the carbon sources available in these varied environments, this protist switches between glycolysis and oxidative phosphorylation to produce ATP. This results in the dramatic structural and metabolic remodeling of the single mitochondrion. Each of the insect vector developmental cell types can be created in vitro by overexpressing a single RNA binding protein. Preliminary data with this cell line suggests that the molecular mechanisms responsible for the metabolic rewiring may be similar to what is described in cancer cells. We observe increased expression of TbIF1, the T. brucei inhibitory factor of the FoF1-ATPase, and the subsequent increase in ROS production that potentially signals a switch to aerobic glycolysis. The student will use the in vitro T. brucei differentiating cell line to characterize the role of TbIF1 in the structural and metabolic remodeling of the mitochondrion by combining genetic and biochemical tools.

Dr. Dan Sojka. Cysteine and aspartic peptidases and their inhibitors play an important role in the nutrition of insects that rely on metabolizing hemoglobin. The “omics” era enables the identification of these enzymes and their isoenzyme forms but in silico analyses do not confirm their exact roles. Current contributions indicate some highly specific and/or essential roles for these isoenzymes in physiology. This lab functionally and biochemically characterizes these enzymes. A short-term summer project fits in to this large mosaic concept as one small yet very important stone. The student will learn PCR, clone and express recombinant enzymes, purify them, prepare antibodies and verify activity in assays with fluorogenic protease substrates and inhibitors using the 96-plate fluorescence reader. If successful, the student will learn multiplex Western blotting (including chemiluminiscence, fluorescence and stain-free technologies) and perform immuno-light and confocal microscopy using the affinity purified antibodies against recombinant enzymes. S/he will perform functional characterization and phenotyping using RNA interference of selected enzymes or inhibitors and standardized phenotype monitoring and evaluation. The outcomes are a great training in the basal molecular biology techniques usable over various biology fields.