Gene Transfer and the Reconstruction of Life’s Early History from Genomic Data

The metaphor of the unique and strictly bifurcating tree of life, suggested by Charles Darwin, needs to be replaced (or at least amended) to reflect and include processes that lead to the merging of and communication between independent lines of descent. Gene histories include and reflect processes such as gene transfer, symbioses and lineage fusion. No single molecule can serve as a proxy for the tree of life. Individual gene histories can be reconstructed from the growing molecular databases containing sequence and structural information. With some simplifications these gene histories can be represented by furcating trees; however, merging these gene histories into web-like organismal histories, including the transfer of metabolic pathways and cell biological innovations from now-extinct lineages, has yet to be accomplished. Because of these difficulties in interpreting the record retained in molecular sequences, correlations with biochemical fossils and with the geological record need to be interpreted with caution. Advances to detect and pinpoint transfer events promise to untangle at least a few of the intertwined histories of individual genes within organisms and trace them to the organismal ancestors. Furthermore, analysis of the shape of molecular phylogenetic trees may point towards organismal radiations that might reflect early mass extinction events that occurred on a planetary scale.     

Survival and alteration of the plasmid-containing microorganism Escherichia coli Z905/pPHL7 introduced into manmade closed aquatic microcosms.

It has been demonstrated that the transgenic microorganism Escherichia coli Z905/pPHL7 (AprLux+) can exist for a long time at an elevated concentration of mineral salts. The microorganism was introduced into microcosms with sterile brackish water (salinity variable from 21 to 22 g l-1) taken from Lake Shira (Khakasia, Russia). The survival of the microorganism was estimated both by measuring the growth of the colonies on solid nutrient media and by the bioluminescence exhibited by the transgenic strain in samples from the microcosms and in the enrichment culture with the added selective factor-ampicillin (50 micrograms/ml). In the enrichment culture, the bioluminescent signal was registered through the 160-day experiment. It has been shown that in the closed microcosms with brackish water the E. coli strain becomes heterogeneous in its ampicillin resistance. The populations of the transgenic strain were mainly represented by isolates able to persist in the medium containing 50 micrograms/ml, but there were also the cells (about 10%) with the threshold of ampicillin resistance not more than 0.05 micrograms/ml. Thus, it was shown that in the microcosms with brackish water and in the absence of the selective factor the transgenic strain survives and retails the recombinant plasmid.     

Population dynamics of transgenic microorganisms in the different microecosystem conditions.

The role of key environmental factors in adaptation of spore-forming and non-spore-forming transgenic microorganisms (TM) have been studied in model ecosystems. Model TM Escherichia coli Z905 (bearing plasmid genes of bacterial luminescence Ap (r) Lux+) has been found to have a higher adaptation potential than TM Bacillus subtilis 2335/105 (bearing genes of human alpha 2-interferon Km (r) Inf+), planned for employment as a living vaccine under varying environmental conditions. Effects of abiotic factors on migration of natural and recombinant plasmids between microorganisms under model ecosystem conditions has been estimated. The transgenic microorganisms with low copy number survived better under introduction conditions in the microcosms studied. This trend has been shown to be independent of the microcosm type and its complexity. Grant numbers: 99-04-96017, 25, 00-07-9011.     

Expression of cloned genes of transgenic microorganisms introduced into man-made ecosystems.

Modeling of transgenic microorganism introduction into small man-made ecosystems can help forecast changes in expression of cloned genes under different conditions of existence. Introduction of the E. coli Z905/pPHL7 strain containing a plasmid with luminescent system genes of luminous bacteria led to changes in cell and colony morphology, reduction in metabolic activity of cells, and, as a result, a lower level of expression of cloned gene. A low concentration of nutrients has been shown to favor greatly the phenotypic change of cells of the recombinant strain. Expression of cloned genes changed due to: a lower concentration of plasmid DNA, a change in regulation of cloned genes, and a change in cells of biosynthesis of substrates needed for expression of luminescent genes. The conducted investigations can provide a basis for the use of marker transgenic microorganisms in closed ecosystems of different types. Grant numbers: 99-04-96017, 00-07-9011.     

Accelerating NLTE radiative transfer by means of the Forth-and-Back Implicit Lambda Iteration: A two-level atom line formation in 2D Cartesian coordinates

State-of-the-art methods in multidimensional NLTE radiative transfer are based on the use of local approximate lambda operator within either Jacobi or Gauss–Seidel iterative schemes. Here we propose another approach to the solution of 2D NLTE RT problems, Forth-and-Back Implicit Lambda Iteration (FBILI), developed earlier for 1D geometry. In order to present the method and examine its convergence properties we use the well-known instance of the two-level atom line formation with complete frequency redistribution. In the formal solution of the RT equation we employ short characteristics with two-point algorithm. Using an implicit representation of the source function in the computation of the specific intensities, we compute and store the coefficients of the linear relations J=a+bS$J=a+\mathit{bS}$ between the mean intensity J and the corresponding source function S. The use of iteration factors in the ‘local’ coefficients of these implicit relations in two ‘inward’ sweeps of 2D grid, along with the update of the source function in other two ‘outward’ sweeps leads to four times faster solution than the Jacobi’s one. Moreover, the update made in all four consecutive sweeps of the grid leads to an acceleration by a factor of 6–7 compared to the Jacobi iterative scheme.     

Potential of salt-accumulating and salt-secreting halophytic plants for recycling sodium chloride in human urine in bioregenerative life support systems

This study addresses the possibility of growing different halophytic plants on mineralized human urine as a way to recycle NaCl from human wastes in a bioregenerative life support system (BLSS). Two halophytic plant species were studied: the salt-accumulating Salicornia europaea and the salt-secreting Limonium gmelinii. During the first two weeks, plants were grown on Knop’s solution, then an average daily amount of urine produced by one human, which had been preliminarily mineralized, was gradually added to the experimental solutions. Nutrient solutions simulating urine mineral composition were gradually added to control solutions. NaCl concentrations in the stock solutions added to the experimental and control solutions were 9 g/L in the first treatment and 20 g/L in the second treatment. The mineralized human urine showed some inhibitory effects on S. europaea and L. gmelinii. The biomass yield of experimental plants was lower than that of control ones. If calculated for the same time period (120 d) and area (1 m²), the amount of sodium chloride taken up by S. europaea plants would be 11.7 times larger than the amount taken up by L. gmelinii plants (486 g/m² vs. 41 g/m²). Thus, S. europaea is the better choice of halophyte for recycling sodium chloride from human wastes in BLSS.     

Some ecological mechanisms to generate habitability in planetary subsurface areas by chemolithotrophic communities: the Río Tinto subsurface ecosystem as a model system

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Río Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Río Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.     

Spectral properties of backscattered solar Ly-α radiation in the heliosphere: A search for heliospheric boundary effects

We explore the imprints of the solar wind interaction with the local interstellar medium on spectral properties of backscattered solar Ly-α radiation. We employ a newly developed effective model for the interstellar H atom velocity distribution function in the heliosphere ( Katushkina and Izmodenov, 2011). The model takes into account both global effects of H atom perturbations at the heliospheric boundaries and local (i.e. within 10–20 AU from the Sun) effects of the solar ionization, charge exchange, solar gravitation and radiation pressure.     

Bursts of geomagnetic pulsations in the frequency range 0.2-5 Hz excited by large changes of the solar wind pressure

We present the results of studying the magnetospheres’s response to sharp changes of the solar wind flow (pressure) based on observations of variations of the ions flux of the solar wind onboard the Inreball-1 satellite and of geomagnetic pulsations (the data of two mid-latitude observatories and one auroral observatory are used). It is demonstrated that, when changes of flow runs into the magnetosphere, in some cases short (duration ~ < 5 min) bursts of geomagnetic pulsations are excited in the frequency range Δf~ 0.2–5 Hz. The bursts of two types are observed: noise bursts without frequency changes and wide-band ones with changing frequency during the burst. A comparison is made of various properties of these bursts generated by pressure changes at constant velocity of the solar wind and by pressure changes on the fronts of interplanetary shock waves at different directions of the vertical component of the interplanetary magnetic field.