Models of Protocells Undergoing Asymmetrical Division.

The conditions that allow for the sustained growth of a protocell population are investigated in the case of asymmetrical division. The results are compared to those of previous studies concerning models of symmetrical division, where synchronization (between duplication of the genetic material and fission of the lipid container) was found under a variety of different assumptions about the kinetic equations and about the place where molecular replication takes place. Such synchronization allows a sustained proliferation of the protocell population. In the asymmetrical case, there can be no true synchronization, since the time to duplication may depend upon the initial size, but we introduce a notion of homogeneous growth that actually allows for the sustained reproduction of a population of protocells. We first analyze Surface Reaction Models, defined in the text, and we show that in many cases they undergo homogeneous growth under the same kinetic laws that lead to synchronization in the symmetrical case. This is the case also for Internal Reaction Models (IRMs), which, however, require a deeper understanding of what homogeneous growth actually means, as discussed below.

Comparison of effect of CdS QD and ZnS QD and their corresponding salts on growth, chlorophyll content and antioxidative capacity of tomato.

When applied in the same concentration to tomato plants, cadmium sulfate (CdSO4) and zinc sulfate (ZnSO4) were transported from soil to roots and from roots to shoots more readily than their nano counterparts: cadmium sulfide quantum dots (CdS QD) and zinc sulfide quantum dots (ZnS QD). Compared to the CdS QD, he higher rate of transport of CdSO4 resulted in a greater negative effect on growth, chlorophyll content, antioxidant properties, lipid peroxidation and activation of antioxidant defence systems. Although ZnSO4 was transported more rapidly than ZnS QD, the overall effect of Zn addition was positive (increase in total plant mass, stem length, antioxidant content and decrease in lipid peroxidation). However, these effects were more pronounced in the case of ZnS QD, suggesting that the mechanisms underpinning the activity of ZnS QD and ZnSO4 were different. Thus, the risk of phytotoxicity and food chain transfer of the two elements depended on their form (salt or nanoform), and consequently their effects on plants' growth and physiology were different.

This work elucidates the mechanisms underlying the responses of CdS QD and ZnS QD in contrast to those of their corresponding salts on tomato plants. Our results showed that faster transport from roots to leaves in the case of salts in respect to the nanoform augment their detrimental impact on tomato's antioxidant properties and growth and make the nanoform of both a better alternative for crop application either as fertilizers or as pesticides.

Cadmium Sulfide Quantum Dots, Mitochondrial Function and Environmental Stress: A Mechanistic Reconstruction through In Vivo Cellular Approaches in Saccharomyces cerevisiae.

Research on the effects of engineered nanomaterials (ENMs) on mitochondria, which represent one of the main actors in cell function, highlighted effects on ROS production, gametogenesis and organellar genome replication. Specifically, the mitochondrial effects of cadmium sulfide quantum dots (CdS QDs) exposure can be observed through the variation in enzymatic kinetics at the level of the respiratory chain and also by analyzing modifications of reagent and products in term of the bonds created and disrupted during the reactions through Fourier-transform infrared spectroscopy (FTIR). This study investigated both in intact cells and in isolated mitochondria to observe the response to CdS QDs treatment at the level of electron transport chain in the wild-type yeast Saccharomyces cerevisiae and in the deletion mutant Δtom5, whose function is implicated in nucleo-mitochondrial protein trafficking. The changes observed in wild type and Δtom5 strains in terms of an increase or decrease in enzymatic activity (ranging between 1 and 2 folds) also differed according to the genetic background of the strains and the respiratory chain functionality during the CdS QDs treatment performed. Results were confirmed by FTIR, where a clear difference between the QD effects in the wild type and in the mutant strain, Δtom5, was observed. The utilization of these genetic and biochemical approaches is instrumental to clarify the mitochondrial mechanisms implicated in response to these types of ENMs and to the stress response that follows the exposure.

Serum Mass Spectrometry Proteomics and Protein Set Identification in Response to FOLFOX-4 in Drug-Resistant Ovarian Carcinoma.

Ovarian cancer is a highly lethal gynecological malignancy. Drug resistance rapidly occurs, and different therapeutic approaches are needed. So far, no biomarkers have been discovered to predict early response to therapies in the case of multi-treated ovarian cancer patients. The aim of our investigation was to identify a protein panel and the molecular pathways involved in chemotherapy response through a combination of studying proteomics and network enrichment analysis by considering a subset of samples from a clinical setting. Differential mass spectrometry studies were performed on 14 serum samples from patients with heavily pretreated platinum-resistant ovarian cancer who received the FOLFOX-4 regimen as a salvage therapy. The serum was analyzed at baseline time (T0) before FOLFOX-4 treatment, and before the second cycle of treatment (T1), with the aim of understanding if it was possible, after a first treatment cycle, to detect significant proteome changes that could be associated with patients responses to therapy. A total of 291 shared expressed proteins was identified and 12 proteins were finally selected between patients who attained partial response or no-response to chemotherapy when both response to therapy and time dependence (T0, T1) were considered in the statistical analysis. The protein panel included APOL1, GSN, GFI1, LCATL, MNA, LYVE1, ROR1, SHBG, SOD3, TEC, VPS18, and ZNF573. Using a bioinformatics network enrichment approach and metanalysis study, relationships between serum and cellular proteins were identified. An analysis of protein networks was conducted and identified at least three biological processes with functional and therapeutic significance in ovarian cancer, including lipoproteins metabolic process, structural component modulation in relation to cellular apoptosis and autophagy, and cellular oxidative stress response. Five proteins were almost independent from the network (LYVE1, ROR1, TEC, GFI1, and ZNF573). All proteins were associated with response to drug-resistant ovarian cancer resistant and were mechanistically connected to the pathways associated with cancer arrest. These results can be the basis for extending a biomarker discovery process to a clinical trial, as an early predictive tool of chemo-response to FOLFOX-4 of heavily treated ovarian cancer patients and for supporting the oncologist to continue or to interrupt the therapy.

Super-Exponential Growth in Models of a Binary String World.

The Theory of the Adjacent Possible (TAP) equation has been proposed as an appropriate description of super-exponential growth phenomena, where a phase of slow growth is followed by a rapid increase, leading to a "hockey stick" curve. This equation, initially conceived to describe the growth in time of the number of new types of artifacts, has also been applied to several natural phenomena. A possible drawback is that it may overestimate the number of new artifact types, since it does not take into account the fact that interactions, among existing types, may produce types which have already been previously discovered. We introduce here a Binary String World (BSW) where new string types can be generated by interactions among (at most two) already existing types. We introduce a continuous limit of the TAP equation for the BSW; we solve it analytically and show that it leads to divergence in finite time. We also introduce a criterion to distinguish this type of behavior from the familiar exponential growth, which diverges only as t → ∝. In the BSW, it is possible to directly model the generation of new types, and to check whether the newborns are actually novel types, thus discarding the rediscoveries of already existing types. We show that the type of growth is still TAP-like, rather than exponential, although of course in simulations one never can observes true divergence. We also show that this property is robust with respect to some changes in the model, as long as it deals with types (and not with individuals).

Protein Analysis of A. halleri and N. caerulescens Hyperaccumulators When Exposed to Nano and Ionic Forms of Cd and Zn.

Hyperaccumulator plant species growing on metal-rich soils can accumulate high quantity of metals and metalloids in aerial tissues, and several proteomic studies on the molecular mechanisms at the basis of metals resistance and hyperaccumulation have been published. Hyperaccumulator are also at the basis of the phytoremediation strategy to remove metals more efficiently from polluted soils or water. Arabidopsis halleri and Noccea caerulescens are both hyperaccumulators of metals and nano-metals. In this study, the change in some proteins in A. halleri and N. caerulescens was assessed after the growth in soil with cadmium and zinc, provided as sulphate salts (CdSO4 and ZnSO4) or sulfide quantum dots (CdS QDs and ZnS QDs). The protein extracts obtained from plants after 30 days of growth were analyzed by 2D-gel electrophoresis (2D SDS-PAGE) and identified by MALDI-TOF/TOF mass spectrometry. A bioinformatics analysis was carried out on quantitative protein differences between control and treated plants. In total, 43 proteins resulted in being significatively modulated in A. halleri, while 61 resulted in being modulated in N. caerulescens. Although these two plants are hyperaccumulator of both metals and nano-metals, at protein levels the mechanisms involved do not proceed in the same way, but at the end bring a similar physiological result.

Cadmium Sulfide Quantum Dots Adversely Affect Gametogenesis in Saccharomyces cerevisiae.

In the last decades, nanotechnology-based tools have attracted attention in the scientific community, due to their potential applications in different areas from medicine to engineering, but several toxicological effects mediated by these advanced materials have been shown on the environment and human health. At present, the effects of engineered nanomaterials on gametogenesis have not yet been well understood. In the present study, we addressed this issue using the yeast Saccharomyces cerevisiae as a model eukaryote to evaluate the effects of cadmium sulfide quantum dots (CdS QDs) on sporulation, a process equivalent to gametogenesis in higher organisms. We have observed that CdS QDs cause a strong inhibition of spore development with the formation of aberrant, multinucleated cells. In line with these observations, treatment with CdS QDs down-regulates genes encoding crucial regulators of sporulation process, in particular, the transcription factor Ndt80 that coordinates different genes involved in progression through the meiosis and spore morphogenesis. Down-regulation of NDT80 mediated by CdS QDs causes a block of the meiotic cell cycle and a return to mitosis, leading to the formation of aberrant, multinucleated cells. These results indicate that CdS QDs inhibit gametogenesis in an irreversible manner, with adverse effects on cell-cycle progression.

Attractor-Specific and Common Expression Values in Random Boolean Network Models (with a Preliminary Look at Single-Cell Data).

Random Boolean Networks (RBNs for short) are strongly simplified models of gene regulatory networks (GRNs), which have also been widely studied as abstract models of complex systems and have been used to simulate different phenomena. We define the "common sea" (CS) as the set of nodes that take the same value in all the attractors of a given network realization, and the "specific part" (SP) as the set of all the other nodes, and we study their properties in different ensembles, generated with different parameter values. Both the CS and of the SP can be composed of one or more weakly connected components, which are emergent intermediate-level structures. We show that the study of these sets provides very important information about the behavior of the model. The distribution of distances between attractors is also examined. Moreover, we show how the notion of a "common sea" of genes can be used to analyze data from single-cell experiments.

Engineered Nanomaterial Exposure Affects Organelle Genetic Material Replication in Arabidopsis thaliana.

Mitochondria and chloroplasts not only are cellular energy sources but also have important regulatory and developmental roles in cell function. CeO2, FeOx ENMs, ZnS, CdS QDs, and relative metal salts were utilized in Murashige-Skoog (MS) synthetic growth medium at different concentrations (80-500 mg L-1) and times of exposures (0-20 days). Analysis of physiological and molecular response of A. thaliana chloroplasts and mitochondrion demonstrates that ENMs increase or decrease functionality and organelle genome replication. Exposure to nanoscale CeO2 and FeOx causes an 81-105% increase in biomass, whereas ZnS and CdS QDs yielded neutral or a 59% decrease in growth, respectively. Differential effects between ENMs and their corresponding metal salts highlight nanoscale-specific response pathways, which include energy production and oxidative stress response. Differences may be ascribed to ENM and the metal salt dissolution rate and the toxicity of the metal ion, which suggests eventual biotransformation processes occurring within the plant. With regard to specific effects on plastid (pt) and mitochondrial (mt) DNA, CdS QD exposure triggered potential variations at the substoichiometric level in the two organellar genomes, while nanoscale FeOx and ZnS QDs caused a 1- to 3-fold increase in ptDNA and mtDNA copy numbers. Nanoparticle CeO2 exposure did not affect ptDNA and mtDNA stoichiometry. These findings suggest that modification in stoichiometry is a potential morpho-functional adaptive response to ENM exposure, triggered by modifications of bioenergetic redox balance, which leads to reducing the photosynthesis or cellular respiration rate.

Asymptotic Information-Theoretic Detection of Dynamical Organization in Complex Systems.

The identification of emergent structures in complex dynamical systems is a formidable challenge. We propose a computationally efficient methodology to address such a challenge, based on modeling the state of the system as a set of random variables. Specifically, we present a sieving algorithm to navigate the huge space of all subsets of variables and compare them in terms of a simple index that can be computed without resorting to simulations. We obtain such a simple index by studying the asymptotic distribution of an information-theoretic measure of coordination among variables, when there is no coordination at all, which allows us to fairly compare subsets of variables having different cardinalities. We show that increasing the number of observations allows the identification of larger and larger subsets. As an example of relevant application, we make use of a paradigmatic case regarding the identification of groups in autocatalytic sets of reactions, a chemical situation related to the origin of life problem.

Comparative Analysis of Proteins Regulated during Cadmium Sulfide Quantum Dots Response in Arabidopsis thaliana Wild Type and Tolerant Mutants.

In previous work, two independent Arabidopsis thaliana Ac/Ds transposon insertional mutant lines, atnp01 and atnp02, were identified that showed a higher level of tolerance than the wild type (wt) line to cadmium sulfide quantum dots (CdS QDs). The tolerance response was characterized at physiological, genetic and transcriptomic levels. In this work, a comparative analysis was performed on protein extracts from plantlets of the two mutants and of wt, each treated with 80 mg L-1 CdS QDs. A comparative protein analysis was performed by 2D-PAGE, and proteins were characterized by MALDI-TOF/TOF mass spectrometry. Of 250 proteins identified from all three lines, 98 showed significant changes in relative abundance between control and CdS QD-treated plantlets. The wt, atnp01, and atnp02 control-treated pairs respectively showed 61, 31, and 31 proteins with differential expression. The two mutants had a different response to treatment in terms of type and quantity of up- and downregulated proteins. This difference became more striking when compared to wt. A network analysis of the proteins differentially expressed in atnp01 and atnp02 included several of those encoded by putative genes accommodating the transposons, which were responsible for regulation of some proteins identified in this study. These included nifu-like protein 3 (Nfu3), involved in chloroplast assembly, elongator complex 3 (Elo3), involved in transcriptional elongation, magnesium-chelate subunit-2 (Chli2), involved in chlorophyll biosynthesis, and protein phosphatase 2C (PP2C) which mediates abiotic stress response.

Improved electroless platinum contacts on CdZnTe X- and γ-rays detectors.

Platinum is a promising candidate for the realization of blocking electrical contacts on cadmium-zinc-telluride (CdZnTe or CZT) radiation detectors. However, the poor mechanical adhesion of this metal often shortens the lifetime of the final device. In this work, a simple and effective procedure to obtain robust platinum contacts by electroless deposition is presented. Microscopical analysis revealed the final thickness and composition of the contact layer and its adhesion to the bulk crystal. The blocking nature of the Pt-CdZnTe junction, essential to obtain low noise devices, was confirmed by current-voltage measurements. The planar Pt-CdZnTe-Pt detectors showed good room temperature spectroscopic performance with energy resolution of 4% (2.4 keV) and 3% (3.7 keV) FWHM at 59.5 and 122.1 keV, respectively. Finally, we showed, for the first time, that platinum contacts allow the estimation of the carrier lifetime and mobility of both holes and electrons by using current transient measurements. This demonstrated the optimal hole extraction capability of such contacts.

Proteomic Analysis Identifies Markers of Exposure to Cadmium Sulphide Quantum Dots (CdS QDs).

The use of cadmium sulphide quantum dot (CdS QD)-enabled products has become increasingly widespread. The prospect of their release in the environment is raising concerns. Here we have used the yeast model Saccharomyces cerevisiae to determine the potential impact of CdS QD nanoparticles on living organisms. Proteomic analyses and cell viability assays performed after 9 h exposure revealed expression of proteins involved in oxidative stress and reduced lethality, respectively, whereas oxidative stress declined, and lethality increased after 24 h incubation in the presence of CdS QDs. Quantitative proteomics using the iTRAQ approach (isobaric tags for relative and absolute quantitation) revealed that key proteins involved in essential biological pathways were differentially regulated over the time course of the experiment. At 9 h, most of the glycolytic functions increased, and the abundance of the number of heat shock proteins increased. This contrasts with the situation at 24 h where glycolytic functions, some heat shock proteins as well as oxidative phosphorylation and ATP synthesis were down-regulated. It can be concluded from our data that cell exposure to CdS QDs provokes a metabolic shift from respiration to fermentation, comparable to the situation reported in some cancer cell lines.

Data on miRNome changes in human cells exposed to nano- or ionic- forms of Cadmium.

The data included in this paper are associated with a research article entitled 'Differences in toxicity, mitochondrial function and miRNome in human cells exposed in vitro to Cd as CdS quantum dots or ionic Cd' [1]. The article concerns the use of miRNAs as biomarkers for engineered nanomaterials (ENMs) risk assessment. Two different type of human cells, HepG2 and THP-1, were exposed to different forms of Cadmium: nanoscale, as CdS quantum dots (CdS QDs), and ionic, as CdSO4 8/3 -hydrate (Cd(II)). The cells were treated with sub-toxic doses of CdS QDs; 3 µg ml-1 in HepG2 and 6.4 µg ml-1 and 50 µg ml-1 in THP-1, as well as equivalent cadmium doses as Cd(II). In this dataset, changes in expression levels of miRNAs are reported. In addition, GO enrichment analyses of target genes of miRNAs modulated by Cd stress, network analysis of the microRNome and an in silico pathway analysis are also reported. These data enhance and also summarize much of the data independently presented in the research article and therefore, must be considered as supplementary.

Evolving Always-Critical Networks.

Living beings share several common features at the molecular level, but there are very few large-scale "operating principles" which hold for all (or almost all) organisms. However, biology is subject to a deluge of data, and as such, general concepts such as this would be extremely valuable. One interesting candidate is the "criticality" principle, which claims that biological evolution favors those dynamical regimes that are intermediaries between ordered and disordered states (i.e., "at the edge of chaos"). The reasons why this should be the case and experimental evidence are briefly discussed, observing that gene regulatory networks are indeed often found on, or close to, the critical boundaries. Therefore, assuming that criticality provides an edge, it is important to ascertain whether systems that are critical can further evolve while remaining critical. In order to explore the possibility of achieving such "always-critical" evolution, we resort to simulated evolution, by suitably modifying a genetic algorithm in such a way that the newly-generated individuals are constrained to be critical. It is then shown that these modified genetic algorithms can actually develop critical gene regulatory networks with two interesting (and quite different) features of biological significance, involving, in one case, the average gene activation values and, in the other case, the response to perturbations. These two cases suggest that it is often possible to evolve networks with interesting properties without losing the advantages of criticality. The evolved networks also show some interesting features which are discussed.

Differences in toxicity, mitochondrial function and miRNome in human cells exposed in vitro to Cd as CdS quantum dots or ionic Cd.

Cadmium is toxic to humans, although Cd-based quantum dots exerts less toxicity. Human hepatocellular carcinoma cells (HepG2) and macrophages (THP-1) were exposed to ionic Cd, Cd(II), and cadmium sulfide quantum dots (CdS QDs), and cell viability, cell integrity, Cd accumulation, mitochondrial function and miRNome profile were evaluated. Cell-type and Cd form-specific responses were found: CdS QDs affected cell viability more in HepG2 than in THP-1; respective IC20 values were ∼3 and ∼50 µg ml-1. In both cell types, Cd(II) exerted greater effects on viability. Mitochondrial membrane function in HepG2 cells was reduced 70 % with 40 µg ml-1 CdS QDs but was totally inhibited by Cd(II) at corresponding amounts. In THP-1 cells, CdS QDs has less effect on mitochondrial function; 50 µg ml-1 CdS QDs or equivalent Cd(II) caused 30 % reduction or total inhibition, respectively. The different in vitro effects of CdS QDs were unrelated to Cd uptake, which was greater in THP-1 cells. For both cell types, changes in the expression of miRNAs (miR-222, miR-181a, miR-142-3p, miR-15) were found with CdS QDs, which may be used as biomarkers of hazard nanomaterial exposure. The cell-specific miRNome profiles were indicative of a more conservative autophagic response in THP-1 and as apoptosis as in HepG2.

Cadmium sulfide quantum dots impact Arabidopsis thaliana physiology and morphology.

The differential mechanisms of CdS QDs (Quantum Dots) and Cd ion toxicity to Arabidopsis thaliana (L.) Heynh were investigated. Plants were exposed to 40 and 60 mg L-1 for CdS QDs and 76.9 and 115.2 mg L-1 CdSO4·7H2O and toxicity was evaluated at 5, 20, 35 (T5, T20, T35) days after exposure. Oxidative stress upon exposure was evaluated by biochemical essays targeting non-enzymatic oxidative stress physiological parameters, including respiration efficiency, total chlorophylls, carotenoids, ABTS and DPPH radicals reduction, total phenolics, GSH redox state, lipid peroxidation. Total Cd in plants was measured with AAS. Root and leaf morphology and element content were assessed in vivo utilizing low-vacuum Environmental Scanning Electron Microscopy (ESEM) with X-ray microanalysis (EDX). This integrated approach allowed identification of unique nanoscale CdS QDs toxicity to the plants that was distinct from CdSO4 exposure. The analyses highlighted that CdS QDs and Cd ions effects are modulated by the developmental stage of the plant, starting from T20 till T35 the plant development was modulated by the treatments, in particular CdS QDs induced early flowering. Both treatments induced Fe accumulation in roots, but at different intensities, while CdS QDs was associated with Mn increase into plant leaf. CdSO4 elicited higher levels of oxidative stress compared with QDs, especially the former treatment caused more intense respiration damages and reduction in chlorophyll and carotenoids than the latter. The two types of treatments impact differently on root and leaf morphology.

Kinetic Rate Constants of Gold Nanoparticle Deposition on Silicon.

We fabricated gold nanoparticles on nanoporous silicon microparticles using electroless deposition in a hydrofluoric acid solution containing gold chloride. The reaction was followed by UV spectrometer analysis of the absorbance of the solution (proportional to the nanoparticle concentration) for two temperatures (20 and 50 °C). The results indicate that the process is autocatalytic, described by a pseudo-first-order reaction, the apparent rate constant kobs of which was determined by utilizing UV spectrometer data. We found that the reaction rate constant at 20 °C is 7 × 10-3 s-1 and that at 50 °C is 2.9 × 10-2 s-1. Scanning electron microscope (SEM) analysis of samples and diffusion-limited aggregation (DLA) simulations were used to validate the results. This study aims to resolve the kinetics of the electroless deposition of gold on silicon at the nanoscale, in the present state of art missing a quantitative characterization, for certain conditions of growth and given values of temperature and concentration of the reagents. Results may have applications to the synthesis of gold nanoparticles and their use as nanosensors, drug delivery systems, or metal nanometamaterials with advanced optical properties.

Sustainable Growth and Synchronization in Protocell Models.

The growth of a population of protocells requires that the two key processes of replication of the protogenetic material and reproduction of the whole protocell take place at the same rate. While in many ODE-based models such synchronization spontaneously develops, this does not happen in the important case of quadratic growth terms. Here we show that spontaneous synchronization can be recovered (i) by requiring that the transmembrane diffusion of precursors takes place at a finite rate, or (ii) by introducing a finite lifetime of the molecular complexes. We then consider reaction networks that grow by the addition of newly synthesized chemicals in a binary polymer model, and analyze their behaviors in growing and dividing protocells, thereby confirming the importance of (i) and (ii) for synchronization. We describe some interesting phenomena (like long-term oscillations of duplication times) and show that the presence of food-generated autocatalytic cycles is not sufficient to guarantee synchronization: in the case of cycles with a complex structure, it is often observed that only some subcycles survive and synchronize, while others die out. This shows the importance of truly dynamic models that can uncover effects that cannot be detected by static graph theoretical analyses.

In Vivo-In Vitro Comparative Toxicology of Cadmium Sulphide Quantum Dots in the Model Organism Saccharomyces cerevisiae.

The aim of this work was to use the yeast Saccharomyces cerevisiae as a tool for toxicogenomic studies of Engineered Nanomaterials (ENMs) risk assessment, in particular focusing on cadmium based quantum dots (CdS QDs). This model has been exploited for its peculiar features: a short replication time, growth on both fermentable and oxidizable carbon sources, and for the contextual availability of genome wide information in the form of genetic maps, DNA microarray, and collections of barcoded mutants. The comparison of the whole genome analysis with the microarray experiments (99.9% coverage) and with the phenotypic analysis of 4688 barcoded haploid mutants (80.2% coverage), shed light on the genes involved in the response to CdS QDs, both in vivo and in vitro. The results have clarified the mechanisms involved in the exposure to CdS QDs, and whether these ENMs and Cd2+ exploited different pathways of response, in particular related to oxidative stress and to the maintenance of mitochondrial integrity and function. Saccharomyces cerevisiae remains a versatile and robust alternative for organismal toxicological studies, with a high level of heuristic insights into the toxicology of more complex eukaryotes, including mammals.