Projects Proposed by Faculty of Science for the 7th call
Endocrine disrupters in wastewater treatment sludge and their removal during composting process – “Compost-ED”
The “Compost-ED” project will focus on the microbial degradation of “Endocrine Disruptors” (EDs) during bioremediation trials. EDs encompass a wide variety of chemical substances, mainly of anthropogenic origin, which represent a serious threat for humans and, mostly, aquatic environment. Such chemicals are responsible for the disruption of the hormonal homeostasis in both humans and wildlife orgaisms, since they can mimic or antagonize endogenous hormones, altering their synthesis and metabolism. Modern analytical techniques have allowed the detection and quantification of EDs in various environmental compartments, disclosing the hormonal load to which we are exposed. On the one hand, wastewater treatment plants (WWTP) are considered as “sink” of EDs, since they receive sewage and process waters from urban and industrial districts, and on the other hand as “source” of ED contamination of the environment, due to the proven inefficiency in removing such contaminants. Therefore, WWTP effluents and sludges (biosolids) contain significant amount of ED (up to the high mg/kg range), which are disposed of in surface waters and agricultural soils, respectively.
As for WWTP biosolids, co-composting of sludge with “green waste” has been proposed as treatment to stabilize and sanitize such matrices before use as soil fertilizer. However, the microbial processes occurring during such composting treatments, as well as the fate of EDs and other micropollutants, have not been fully elucidated yet. Therefore, the aim of this project is to employ cutting-edge techniques and tools of microbial ecology, high-throughput sequencing and bioinformatics (metagenomic), advanced analytical chemistry and biochemistry to unravel many of such, yet unanswered, questions.
The major goals are to (i) identify and describe microbial pathways involved in the metabolism of selected EDs, (ii) detect key intermediates of the EDs degradation pathways and study their toxicity and metabolization rates (chromatography-mass spectrometry), (iii) study of microbial community structure and dynamics during contaminant breakdown (metagenomics, phospholipids fatty acid analysis), (iv) identify and characterize the most effective ED degraders among fungi and bacteria (using Stable Isotope Probing and labeled contaminants), and (v) test the effectiveness of co-composting treatments also by means of bioassays (recombinant yeast assays, human cell lines – ELISA) and ecotoxicological analyses (using test organisms according to standard protocols).
The “Compost-ED” project is highly interdisciplinary and falls into Assoc. Prof. Tomaš Cajthaml’s areas of expertise, as it is witnessed by his publication record. Therefore, the whole work will be carried out and completed under his supervision and in collaboration with his research team.
Contact person: Doc. RNDr. Tomáš Cajthaml, Ph.D.
Cajthaml@biomed.cas.cz; tel.: 777090128
Significance of free-living metamonads for understanding of the early evolution of eukaryotes
The eukaryotic phylum Metamonada includes mainly endobiotic lineages (symbionts, commensals and parasites like Giardia and Trichomonas) and a few free-living species (e.g. genera Carpediemonas, Pseudotrichomonas, Trimastix). The common feature of all metamonads is the possession of reduced forms of mitochondria, such as hydrogenosomes and mitosomes. The Metamonada is especially interesting group to study the evolution of parasitism, adaptation to anaerobic habitats, and reductive evolution of mitochondrion by means of comparative morphology, transcriptomics/genomics, and molecular phylogeny. This inference generally centers on two medicinally most important lineages of parasitic metamonads: trichomonads (e.g. Trichomonas vaginalis) and diplomonads (e.g. Giardia intestinalis), which represent combination of unique morphological characteristics, reduced forms of mitochondria, and controversial phylogenetic positions within eukaryotes. Yet, the ancestor of metamonads was almost certainly free-living, as almost all lineages identified so far include free-living members. The free-living representatives possess more conserved cellular traits and less divergent gene sequences than parasitic lineages. Therefore, free-living metamonad lineages are crucial for reconstruction of evolution and phylogeny of this phylum as well as the position of Metamonada in the eukaryotic phylogeny.
The research project will center on the characterization of free-living metamonads and endobiotic relatives in order to understand the evolutionary history of the Metamonada and eukaryotes as whole. Some evidence suggests that a metamonad organism, Monocercomonoides, is the first example of a eukaryote, which lost mitochondria completely. Sophisticated transmission electron microscopy with serial sectioning of this organism is inevitable to provide explicit data of cellular characteristics. The project will consist of tree main parts: (1) Characterizing Monocercomonoides, its free-living relatives, Trimastix, and novel free-living relatives of parasitic trichomonads and diplomonads at ultrastructural levels with a particular focus at the comparative analysis of cytoskeleton and thorough investigation of their organellar complement. (2) Transcriptomic investigation to understand the major transition to endobiotic life style and the reductive evolution of mitochondria related organelles. (3) Multigene phylogenetic analyses of those metamonads with inclusion of data from free-living species in order to recover a robust tree of metamonads and the position of metamonads within eukaryotes. New ultrastructural and molecular data will shed more light onto biological questions like transition between free-living and parasitic way of life, evolutionary history and reductive evolution of mitochondria in this group, and the origin and subsequent radiation of the microtubular cytoskeleton systems in metamonads.
Supervisor: doc. RNDr. Ivan Čepička, Ph.D., Dept. of Zoology, Faculty of Science, Charles University in Prague
Co-supervisor: Mgr. Vladimír Hampl, Ph.D., Dept. of Parasitology, Faculty of Science, Charles University in Prague
Contact: firstname.lastname@example.org; tel.: +420 2 21951072
Evolution of brain complexity and processing capacity in non-mammalian vertebrates
Neurons are the basic computational units of the brain. Their number is therefore believed to be the best available approximation of the brain's computational capacity. However, until recently the predominant surrogate measure of brain capacity was brain size – often relative brain size derived from brain-body allometry. The notion that higher encephalization correlates with improved cognitive abilities has recently been disputed in favor of the absolute number of cortical neurons and connections, or simply the total number of brain/forebrain neurons. Moreover, the instrumentalization of the isotropic fractionator technique has led to the discovery that starkly different neuronal scaling rules apply to different mammalian orders. Consequently, brain size cannot be used as a reliable measure of brain functional capacity, at least not in broad comparative analyses. Currently, total brain neuron counts are available only for a limited array of mammals; data for non-mammalian vertebrates are not available. This project has two aims. The primary goal is to analyze the brain cellular scaling rules in birds, which constitute an important model group to study cognitive capacities. Using the isotropic fractionator method combined with flow cytometry cell counting, the total numbers of neuronal and glial cells and glia/neuron ratios in whole brains and parts thereof will be estimated in representatives of six monophyletic groups of birds representing major avian clades. This unique dataset comprising ~ 70 avian species will allow comparisons of the revealed scaling rules between basal and advanced avian taxa, which differ in the level of encephalization and cognitive abilities, and between taxa that feature different developmental patterns, migratory strategies and social systems, as well as comparison of the cellular scaling rules revealed in birds with those revealed in mammals. The secondary goal is to optimize homogenization, immunostaining and cell counting protocols for reptilian, amphibian and fish brain tissue. The prospective candidate should have a good knowledge of comparative neuroanatomy, experience with the isotropic fractionator, flow cytometry and laser microdissection, and communication/organization skills (co-supervision of master and doctoral theses is expected).
1. Herculano-Houzel S. 2012 The remarkable, yet not extraordinary, human brain as a scaled-up primate brain and its associated cost. Proc Natl Acad Sci U S A 109, 10661-10668. (doi:10.1073/pnas.1201895109).
2. Herculano-Houzel S. 2011 Not All Brains Are Made the Same: New Views on Brain Scaling in Evolution. Brain Behav Evol 78(1), 22-36. (doi:10.1159/000327318).
3. Herculano-Houzel S., Collins C.E., Wong P.Y., Kaas J.H. 2007 Cellular scaling rules for primate brains. Proc Natl Acad Sci U S A 104(9), 3562-3567. (doi:10.1073/pnas.0611396104).
4. Herculano-Houzel S., Mota B., Lent R. 2006 Cellular scaling rules for rodent brains. Proc Natl Acad Sci U S A 103(32), 12138-12143. (doi:10.1073/pnas.0604911103).
Mgr. Pavel Němec, PhD.
email@example.com, phone: ++420 2 2195 1855
Migration of low-fraction melts and fluids in seismically active regions:
numerical simulation and mechanical consequences of reactive flow
Magma-derived fluids are possible triggers of earthquake sequences. Various geodynamic settings are characterized by recurrent seismic activity that occurs simultaneously with abundant fluid degassing. This also applies to West Bohemia/Vogtland earthquake swarms, which suggest spatial and temporal links to the formation and movement of high-pressure fluids in the lithosphere. The causal relationships involving pressure-volume changes or fluid-phase transformations such as boiling or immiscibility, capable of the largest mechanical energy release and its focusing, however, are not yet understood.
The postdoctoral project will concentrate on the seismogenic effect of low-fraction intergranular partial melts or aqueous-carbonic fluids, which represent the main factors responsible for hydraulic weakening of high permeability zones in the continental lithosphere. It will address rheological links between the fluid and melt migration, their mechanical consequences for initiation and propagation of slip instabilities, that is, the seismic activity. The postdoctoral fellow will be responsible for developing numerical models and evaluating experimental results, which relate reactive fluid flow, porosity formation and destruction, and mechanical response of fluid expansion and separation: (1) implementation of pressure-volume-temperature equations of state for aqueous-carbonic fluids applicable to high temperatures and pressures, and algorithm development for equilibrium partitioning in two-phase mixtures, pressure changes, and tension effects, (2) development of the two-dimensional hydrodynamic model for porous and fractured media, and (3) application of the model to the seismicity of West Bohemia/Vogtland earthquake swarms. This project is expected to contribute to our understanding of seismicity triggering in the presence of two-phase fluids in the fractured lithosphere, with application to diverse geodynamic settings. The successful applicant will become part of a vibrant scientific team bridging two areas of geosciences at the Faculty of Science, Charles University in Prague and involving additional international collaborators.
doc. RNDr. Tomáš Fischer, Ph.D.
Institute of Hydrogeology, Engineering Geology and Applied Geophysics
doc. David Dolejš, Ph.D.
Institute of Petrology and Structural geology