Effects of predatory risk and resource renewal on the timing of foraging activity in a gerbil community

The foraging decisions of animals are often influenced by risk of predation and by the renewal of resources. For example, seed-eating gerbils on sand dunes in the Negev Desert of Israel prefer to forage in the bush microhabitat and during darker hours due to risk of predation. Also, daily renewal of seed resource patches and timing of nightly foraging activity in a depleting environment play important roles in species coexistence. We examined how these factors influence the timing of gerbil foraging by quantifying foraging activity in seed resource patches that we experimentally renewed hourly during the night. As in previous work, gerbils showed strong preference for the safe bush microhabitat and foraged less in response to high levels of illumination from natural moon light and from artificial sources. We demonstrate here for the first time that gerbils also responded to temporal and spatial heterogeneity in predatory risk through their timing of activity over the course of each night. Typically, gerbils concentrated their activity early in the night, but this changed with moon phase and in response to added illumination. These results can be understood in terms of the nature of patch exploitation by gerbils and the role played by the marginal value of energy in determining the cost of predation. They further show the dynamic nature of gerbil foraging decisions, with animals altering foraging efforts in response to time, microhabital, moon phase, illumination, and resource availability.     

The stereochemistry of benzo[a]pyrene-2'-deoxyguanosine adducts affects DNA methylation by SssI and HhaI DNA methyltransferases

The biologically most significant genotoxic metabolite of the environmental pollutant benzo[a]pyrene (B[a]P), (+)-7R,8S-diol 9S,10R-epoxide, reacts chemically with guanine in DNA, resulting in the predominant formation of (+)-trans-B[a]P-N(2)-dG and, to a lesser extent, (+)-cis-B[a]P-N(2)-dG adducts. Here, we compare the effects of the adduct stereochemistry and conformation on the methylation of cytosine catalyzed by two purified prokaryotic DNA methyltransferases (MTases), SssI and HhaI, with the lesions positioned within or adjacent to their CG and GCGC recognition sites, respectively. The fluorescence properties of the pyrenyl residues of the (+)-cis-B[a]P-N(2)-dG and (+)-trans-B[a]P-N(2)-dG adducts in complexes with MTases are enhanced, but to different extents, indicating that aromatic B[a]P residues are positioned in different microenvironments in the DNA-protein complexes. We have previously shown that the (+)-trans-isomeric adduct inhibits both the binding and methylating efficiencies (k(cat)) of both MTases [Subach OM, Baskunov VB, Darii MV, Maltseva DV, Alexandrov DA, Kirsanova OV, Kolbanovskiy A, Kolbanovskiy M, Johnson F, Bonala R, et al. (2006) Biochemistry45, 6142-6159]. Here we show that the stereoisomeric (+)-cis-B[a]P-N(2)-dG lesion has only a minimal effect on the binding of these MTases and on k(cat). The minor-groove (+)-trans adduct interferes with the formation of the normal DNA minor-groove contacts with the catalytic loop of the MTases. However, the intercalated base-displaced (+)-cis adduct does not interfere with the minor-groove DNA-catalytic loop contacts, allowing near-normal binding of the MTases and undiminished k(cat) values.     

Rapid directed molecular evolution of fluorescent proteins in mammalian cells

In vivo imaging of model organisms is heavily reliant on fluorescent proteins with high intracellular brightness. Here we describe a practical method for rapid optimization of fluorescent proteins via directed molecular evolution in cultured mammalian cells. Using this method, we were able to perform screening of large gene libraries containing up to 2 × 10⁷ independent random genes of fluorescent proteins expressed in HEK cells, completing one iteration of directed evolution in a course of 8 days. We employed this approach to develop a set of green and near‐infrared fluorescent proteins with enhanced intracellular brightness. The developed near‐infrared fluorescent proteins demonstrated high performance for fluorescent labeling of neurons in culture and in vivo in model organisms such as Caenorhabditis elegans, Drosophila, zebrafish, and mice. Spectral properties of the optimized near‐infrared fluorescent proteins enabled crosstalk‐free multicolor imaging in combination with common green and red fluorescent proteins, as well as dual‐color near‐infrared fluorescence imaging. The described method has a great potential to be adopted by protein engineers due to its simplicity and practicality. We also believe that the new enhanced fluorescent proteins will find wide application for in vivo multicolor imaging of small model organisms.     

Preparation of DNA-duplexes, containing internucleotide thiophosphate groups in various positions of the recognition site for the EcoRII restriction endonuclease

Twenty-four 12-mer DNA duplexes, each containing a chiral phosphorothioate group successively replacing one of the internucleotide phosphate groups either in the EcoRII recognition site (5'CCA/TGG) or near to it, were obtained for studying the interaction of the restriction endonuclease EcoRII with internucleotide DNA phosphates. Twelve of the 12-mer oligonucleotides were synthesized as Rp and Sp diastereomeric mixtures. Six of them were separated by reversed-phase HPLC using various buffers. Homogeneous diastereomers of the other oligonucleotides were obtained by enzymatic ligation of the Rp and Sp diastereomers of 5- to 7-mer oligonucleotides preliminarily separated by HPLC with the corresponding short oligonucleotides on a complementary DNA template. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2003, vol. 29, no. 6; see also http://www.maik.ru.     

Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling

To determine the molecular mechanism of DNA recognition and catalysis by EcoRII DNA-methyltransferase (M.EcoRII) binding and methylation by the enzyme of 14-mer substrate analogs containing 2-aminopurine or 1',2'-dideoxy-D-ribofuranose in the M.EcoRII recognition site have been studied. Efficiencies of methylation and DNA binding affinities depend on the location of modified nucleoside residues within the M.EcoRII recognition site. A structural model of M.EcoRII in complex with substrate DNA and cofactor analog S-adenosyl-L-homocysteine (AdoHcy) was built using the previously solved structures of Hhal and HaeIII DNA-methyltransferases as templates. The model was constructed according to the recently developed "Frankenstein's monster" approach. Based on the model, amino acid residues taking part in interactions with DNA were predicted. Besides, based on both theoretical and experimental data obtained the groups of atoms of the heterocyclic bases within the M.EcoRII recognition site presumably involved in interaction with the enzyme were proposed.     

Probing of contacts between <Emphasis Type="Italic">Eco</Emphasis>RII DNA methyltransferase and DNA with the use of substrate analogs and molecular modeling

The molecular mechanisms of DNA recognition and modification by EcoRII DNA methyltransferase (M.EcoRII) were studied using 14-mer substrate analogs containing 2-aminopurine or 1′,2′-dideoxy-D-ribofuranose in the M.EcoRII recognition site. The efficiency of DNA binding and methylation depended on the position of a modified nucleoside residue in the recognition site. A structural model of M.EcoRII in complex with substrate DNA and the cofactor analog S-adenosyl-L-homocysteine (AdoHcy) was constructed using the available crystal structures of M.Hha and M.HaeIII and the recent Frankenstein’s monster approach. The amino acid residues interacting with DNA were predicted based on the model. In addition, theoretical and experimental findings made it possible to predict the groups of atoms of the heterocyclic bases of the M.EcoRII recognition site that are presumably involved in the interactions with the enzyme.     

pH-dependent binding of the Epsin ENTH domain and the AP180 ANTH domain to PI(4,5)P2-containing bilayers

Epsin and AP180 are essential components of the endocytotic machinery, which controls internalization of protein receptors and other macromolecules at the cell surface. Epsin and AP180 are recruited to the plasma membrane by their structurally and functionally related N-terminal ENTH and ANTH domains that specifically recognize PtdIns(4,5)P₂. Here, we show that membrane anchoring of the ENTH and ANTH domains is regulated by the acidic environment. Lowering the pH enhances PtdIns(4,5)P₂ affinity of the ENTH and ANTH domains reinforcing their association with lipid vesicles and monolayers. The pH dependency is due to the conserved histidine residues of the ENTH and ANTH domains, protonation of which is necessary for the strong PtdIns(4,5)P₂ recognition, as revealed by liposome binding, surface plasmon resonance, NMR, monolayer surface tension and mutagenesis experiments. The pH sensitivity of the ENTH and ANTH domains is reminiscent to the pH dependency of the FYVE domain suggesting a common regulatory mechanism of membrane anchoring by a subset of the PI-binding domains.     

An enhanced monomeric blue fluorescent protein with the high chemical stability of the chromophore

Commonly used monomeric blue fluorescent proteins suffer from moderate brightness. The brightest of them, mTagBFP, has a notably low chemical stability over time. Prolonged incubation of mTagBFP leads to its transition from a blue fluorescent state with absorbance at 401 nm to a non-fluorescent state with absorbance at 330 nm. Here, we have determined the chemical structure of the degraded product of the blue mTagBFP-like chromophore. On the basis of mTagBFP we have developed an improved variant, named mTagBFP2. mTagBFP2 exhibits 2-fold greater chemical stability and substantially higher brightness in live cells than mTagBFP. mTagBFP2 is also 1.2-fold and 1.7-fold more photostable than mTagBFP in widefield and confocal microscopy setups, respectively. mTagBFP2 maintains all other beneficial properties of the parental mTagBFP including the high pH stability and fast chromophore formation. The enhanced photostability and chromophore chemical stability of mTagBFP2 make it a superior protein tag. mTagBFP2 performs well in the numerous protein fusions and surpasses mTagBFP as a donor in Förster resonance energy transfer with several green fluorescent protein acceptors.     

Measuring the benefit of habitat selection

We used a behavioral bioassay to estimate the advantages thattwo species of gerbils (Gerbillus allenbyi and G. pyramidum)experienced by preferring a semistabilized dune habitat overa stabilized sand habitat. We used the magnitude of foragingeffort by the gerbils to signal the difference between thetwo habitats. When they were foraging as much in stabilizedsand as in semistabilized dune, we inferred that these habitatswere providing equivalent rewards. We performed a series ofexperiments in two 1-ha field enclosures, each containing similarproportions of stabilized sand and semistabilized dune. Eachenclosure contained a population of only one of the species.By varying the amount of seeds added (either 0.5, 1, 2, or 3g of seeds in 18 seed trays) to each habitat and monitoringthe behavior of the gerbils, we were able to fit a curve thatreflected the change in habitat preference as a function ofseed addition rate. We were also able to show how much seedaddition had to be added to bring the two habitats into equaluse. Each species required only 13 g/ha/night to entirely offsetthe advantage of the semistabilized dune.