Unravelling metal speciation in the microenvironment surrounding phytoplankton cells to improve predictions of metal bioavailability.

A lack of knowledge on metal speciation in the microenvironment surrounding phytoplankton cells (i.e., the phycosphere) represents an impediment to accurately predicting metal bioavailability. Phycosphere pH and O2 concentrations from a diversity of algae species were compiled. For marine algae in the light, the average increases were 0.32 pH units and 0.17 mM O2 in the phycosphere, whereas in the dark the average decreases were 0.10 pH units and 0.03 mM O2, in comparison to bulk seawater. In freshwater algae, the phycosphere pH increased by 1.28 units, whereas O2 increased by 0.38 mM in the light. Equilibrium modeling showed that the pH alteration influenced the chemical species distribution (i.e., free ion, inorganic complexes, and organic complexes) of Al, Cd, Co, Cu, Fe, Hg, Mn, Ni, Pb, Sc, Sm, and Zn in the phycosphere, and the O2 fluctuation increased oxidation rates of Cu(I), Fe(II) and Mn(II) from 2 to 938-fold. The pH/O2-induced changes in phycosphere metal chemistry were larger for freshwater algae than for marine species. Reanalyses of algal metal uptake data in the literature showed that uptake of the trivalent metals (Sc, Sm and Fe), in addition to divalent metals, can be better predicted after considering the phycosphere chemistry

HI-NESS:a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.Genome Instability and Cance

Unique establishment of procephalic head segments is supported by the identification of cis-regulatory elements driving segment-specific segment polarity gene expression in Drosophila

Anterior head segmentation is governed by different regulatory mechanisms than those that control trunk segmentation in Drosophila. For segment polarity genes, both initial mode of activation as well as cross-regulatory interactions among them differ from the typical genetic circuitry in the trunk and are unique for each of the procephalic segments. In order to better understand the segment-specific gene network responsible for the procephalic expression of the earliest active segment polarity genes wingless and hedgehog, we started to identify and analyze cis-regulatory DNA elements of these genes. For hedgehog, we could identify a cis-regulatory element, ic-CRE, that mediates expression specifically in the posterior part of the intercalary segment and requires promoter-specific interaction for its function. The intercalary stripe is the last part of the metameric hedgehog expression pattern that appears during embryonic development, which probably reflects the late and distinct establishment of this segment. The identification of a cis-regulatory element that is specific for one head segment supports the mutant-based observation that the expression of segment polarity genes is governed by a unique gene network in each of the procephalic segments. This provides further indication that the anterior-most head segments represent primary segments, which are set up independently, in contrast to the secondary segments of the trunk, which resemble true repetitive units

Understanding Principles of the Dynamic Biochemical Networks of Life Through Systems Biology

Systems Biology brings the potential to discover fundamental principles of Life that cannot be discovered by considering individual molecules. This chapter discusses a number of early, more recent, and upcoming discoveries of such network principles. These range from the balancing of fluxes through metabolic networks, the potential of those networks for truly individualized medicine, the time dependent control of fluxes and concentrations in metabolism and signal transduction, the ways in which organisms appear to regulate metabolic processes vis-à-vis limitations therein, tradeoffs in robustness and fragility, and a relation between robustness and time dependences in the cell cycle. The robustness considerations will lead to the issue whether and how evolution has been able to put in place design principles of control engineering such as infinite robustness and perfect adaptation in the hierarchical biochemical networks of cell biology © 2014 Elsevier Inc. All rights reserved

Understanding Principles of the Dynamic Biochemical Networks of Life Through Systems Biology

Systems Biology brings the potential to discover fundamental principles of Life that cannot be discovered by considering individual molecules. This chapter discusses a number of early, more recent, and upcoming discoveries of such network principles. These range from the balancing of fluxes through metabolic networks, the potential of those networks for truly individualized medicine, the time dependent control of fluxes and concentrations in metabolism and signal transduction, the ways in which organisms appear to regulate metabolic processes vis-à-vis limitations therein, tradeoffs in robustness and fragility, and a relation between robustness and time dependences in the cell cycle. The robustness considerations will lead to the issue whether and how evolution has been able to put in place design principles of control engineering such as infinite robustness and perfect adaptation in the hierarchical biochemical networks of cell biology © 2014 Elsevier Inc. All rights reserved

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise.

Transcriptional stochasticity can be measured by counting the number of mRNA molecules per cell. Cell-to-cell variability is best captured in terms of concentration rather than molecule counts, because reaction rates depend on concentrations. We combined single-molecule mRNA counting with single-cell volume measurements to quantify the statistics of both transcript numbers and concentrations in human cells. We compared three cell clones that differ only in the genomic integration site of an identical constitutively expressed reporter gene. The transcript number per cell varied proportionally with cell volume in all three clones, indicating concentration homeostasis. We found that the cell-to-cell variability in the mRNA concentration is almost exclusively due to cell-to-cell variation in gene expression activity, whereas the cell-to-cell variation in mRNA number is larger, due to a significant contribution of cell volume variability. We concluded that the precise relationship between transcript number and cell volume sets the biological stochasticity of living cells. This study highlights the importance of the quantitative measurement of transcript concentrations in studies of cell-to-cell variability in biology

Mechanisms of toxic action of copper and copper nanoparticles in two Amazon fish species: Dwarf cichlid ( Apistogramma agassizii ) and cardinal tetra ( Paracheirodon axelrodi )

Made available in DSpace on 2018-12-11T16:52:13Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-07-15Fundação de Amparo à Pesquisa do Estado do AmazonasConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Copper oxide nanoparticles (nCuO) are widely used in boat antifouling paints and are released into the environment, potentially inducing toxicity to aquatic organisms. The present study aimed to understand the effects of nCuO and dissolved copper (Cu) on two ornamental Amazon fish species: dwarf cichlid (Apistogramma agassizii) and cardinal tetra (Paracheirodon axelrodi). Fish were exposed to 50% of the LC50 for nCuO (dwarf cichlid 58.31 μg L−1 and cardinal tetra 69.6 μg L−1) and Cu (dwarf cichlid 20 μg L−1 and cardinal tetra 22.9 μg L−1) for 24, 48, 72 and 96 h. Following exposure, aerobic metabolic rate (ṀO2), gill osmoregulatory physiology and mitochondrial function, oxidative stress markers, and morphological damage were evaluated. Our results revealed species specificity in metabolic stress responses. An increase of ṀO2 was noted in cardinal tetra exposed to Cu, but not nCuO, whereas ṀO2 in dwarf cichlid showed little change with either treatment. In contrast, mitochondria from dwarf cichlid exhibited increased proton leak and a resulting decrease in respiratory control ratios in response to nCuO and Cu exposure. This uncoupling was directly related to an increase in reactive oxygen species (ROS) levels. Our findings reveal different metabolic responses between these two species in response to nCuO and Cu, which are probably caused by the differences between species natural histories, indicating that different mechanisms of toxic action of the contaminants are associated to differential osmoregulatory strategies among species.Brazilian National Institute for Research of the Amazon Laboratory of Ecophysiology and Molecular Evolution, Ave André Araújo, 2936 AleixoMount Allison University Dept. of Chemistry and Biochemistry, 63C York St.São Paulo State University (UNESP) Institute of BiosciencesSão Paulo State University (UNESP) Institute of BiosciencesFundação de Amparo à Pesquisa do Estado do Amazonas: N° 3159/08CNPq: N° 573976/2008-