Deuterated polyunsaturated fatty acids inhibit photoirradiation-induced lipid peroxidation in lipid bilayers.

Lipid peroxidation (LPO) plays a key role in many age-related neurodegenerative conditions and other disorders. Light irradiation can initiate LPO through various mechanisms and is of importance in retinal and dermatological pathologies. The introduction of deuterated polyunsaturated fatty acids (D-PUFA) into membrane lipids is a promising approach for protection against LPO. Here, we report the protective effects of D-PUFA against the photodynamically induced LPO, using illumination in the presence of the photosensitizer trisulfonated aluminum phthalocyanine (AlPcS3) in liposomes and giant unilamellar vesicles (GUV), as assessed in four experimental models: 1) sulforhodamine B leakage from liposomes, detected with fluorescence correlation spectroscopy (FCS); 2) formation of diene conjugates in liposomal membranes, measured by absorbance at 234 nm; 3) membrane leakage in GUV assessed by optical phase-contrast intensity observations; 4) UPLC-MS/MS method to detect oxidized linoleic acid (Lin)-derived metabolites. Specifically, in liposomes or GUV containing H-PUFA (dilinoleyl-sn-glycero-3-phosphatidylcholine), light irradiation led to an extensive oxidative damage to bilayers. By contrast, no damage was observed in lipid bilayers containing 20% or more D-PUFA (D2-Lin or D10-docosahexanenoic acid). Remarkably, addition of tocopherol increased the dye leakage from liposomes in H-PUFA bilayers compared to photoirradiation alone, signifying tocopherol's pro-oxidant properties. However, in the presence of D-PUFA the opposite effect was observed, whereby adding tocopherol increased the resistance to LPO. These findings suggest a method to augment the protective effects of D-PUFA, which are currently undergoing clinical trials in several neurological and retinal diseases that involve LPO.

The skin redoxome.

Redoxome is the network of redox reactions and redox active species (ReAS) that affect the homeostasis of cells and tissues. Due to the intense and constant interaction with external agents, the human skin has a robust redox signalling framework with specific pathways and magnitudes. The establishment of the skin redoxome concept is key to expanding knowledge of skin disorders and establishing better strategies for their prevention and treatment. This review starts with its definition and progress to propose how the master redox regulators are maintained and activated in the different conditions experienced by the skin and how the lack of redox regulation is involved in the accumulation of several oxidation end products that are correlated with various skin disorders.

Progress in the photodynamic therapy treatment of Leishmaniasis.

Leishmaniasis is a serious and endemic infectious disease that has been reported in more than 90 countries and territories. The classical treatment presents a series of problems ranging from difficulty in administration, development of resistance, and a series of side effects. Photodynamic therapy (PDT) has already shown great potential for use as a treatment for leishmaniasis that is effective and non-invasive, with very minor side effects. PDT can also be inexpensive and easy to administer. In this review, we will report the most recent developments in the field, starting with the chemical diversity of photosensitizers, highlighting important mechanistic aspects, and noting information that may assist in designing and developing new and promising photosensitizer molecules.

Methylene blue-mediated Photodynamic Therapy in human retinoblastoma cell lines.

Retinoblastoma is a malignant tumor of the retinal precursor cells and one of the rarest types of pediatric tumor, often occurring in the earliest years of life. Symptoms are conditioned by tumor size and location; one of the most recurrent symptoms is a white reflex in the pupillary area, called leukocoria or cat's eye reflex. In the present work, we studied the in vitro effectiveness of Photodynamic treatment (Pdt) in two types of human retinoblastoma, Y79 and WERI-Rb cell lines, using methylene blue (MB), a photosensitizer (PS) from the phenothiazine group. The two cell lines were incubated with varying concentrations of MB (3, 7, 10, 15, 20, 25, 30, 40, and 50 µM), in the absence of light (dark cytotoxicity) and, in the presence of 664 nm laser light (phototoxicity) with fluences of 1, 1.5, 3, 5, 7, 10, and 15 J/cm2. The Y79 cell line showed higher cellular uptake values for MB than the WERI-Rb cell line. After three hours of incubation, the Y79 and WERI-Rb took up 48% and 34% of the total photosensitizer present in the medium, respectively. Using MTT assay, the results showed that the Y79 cell line was more affected by the photo treatment as demonstrated by the combination of MB concentration and light doses compared with WERI-Rb cell line. The results were correlated with the more pronounced singlet oxygen emission observed in Y79 cells. While MB does show efficacy for eradication of retinoblastoma in vitro, only studies in appropriate animal models will reveal whether the selectivity of photokilling at tolerable drug and light doses is sufficient to suggest clinical trials.

Progress in the photodynamic therapy treatment of Leishmaniasis

Leishmaniasis is a serious and endemic infectious disease that has been reported in more than 90 countries and territories. The classical treatment presents a series of problems ranging from difficulty in administration, development of resistance, and a series of side effects. Photodynamic therapy (PDT) has already shown great potential for use as a treatment for leishmaniasis that is effective and non-invasive, with very minor side effects. PDT can also be inexpensive and easy to administer. In this review, we will report the most recent developments in the field, starting with the chemical diversity of photosensitizers, highlighting important mechanistic aspects, and noting information that may assist in designing and developing new and promising photosensitizer molecules.

Inactivation of milk-borne pathogens by blue light exposure.

Food safety and quality management play a pivotal role in the dairy industry. Milk is a highly nutritious food that also provides an excellent medium for growth of pathogenic microorganisms. Thus, dairy industry focuses most of their processes and costs on keeping contamination levels as low as possible. Thermal processes for microbial decontamination may be effective; however, they cannot provide excellent organoleptic, nutritional, and decontamination properties simultaneously. In this scenario, microbial inactivation by exposure to blue light is a promising alternative method in the food industry due to its intrinsic antimicrobial properties free of any thermal effect. Therefore, this study aimed to determine the inactivation kinetics induced by blue light (λ = 413 nm) against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Salmonella Typhimurium, and Mycobacterium fortuitum cells suspended in whole milk or saline solution. We also performed a series of optic spectroscopies to investigate possible degradation of milk components. All species were sensitive to photoinactivation suspended either in saline solution or milk. Inactivation kinetics differs significantly depending on the suspension medium and each species is differently affected. All bacterial species tested presented more than 5 log10 of inactivation within less than 2 h of irradiation (720 J/cm2). Infrared spectroscopy did not reveal any significant alteration in any of the milk constituents (e.g., sugars, proteins, and lipids). Riboflavin (vitamin B2) was the only significantly degraded constituent found. Therefore, we conclude that microbial inactivation performed by blue light presents extraordinary potential for processes in the dairy industry.

Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology.

The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology

The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

Spectroscopy as a tool to evaluate hair damage and protection.

OBJECTIVE: Methods that can be used to analyse hair damage and to support a claim of hair protection are important for the cosmetic industry. There are many approaches available, but they are usually laborious and expensive. The researchers propose a simple fluorescence method that is based upon the emissive properties of damaged hair. METHODS: Hair fluorescence was observed when using both fluorimetry and microscopic procedures. The method was developed by comparing native hair with hair that was damaged by UVA and visible light. RESULTS: Spectroscopic properties (absorption and emission) of hair in the visible range are presented. The changes in the emissive properties of hair during irradiation were characterized and they were correlated with photobleaching, which is due to the generation of singlet oxygen. Emissions were also obtained in the hair shafts that had been previously treated with chamomile extract and this treatment was able to avoid hair bleaching. CONCLUSION: The emissive properties of hair in the visible range can be used as a tool for the evaluation of hair damage and protection. This method can be useful as a tool in order to claim substantiation.

Riddling: Chimera's dilemma.

We investigate the basin of attraction properties and its boundaries for chimera states in a circulant network of Hénon maps. It is known that coexisting basins of attraction lead to a hysteretic behaviour in the diagrams of the density of states as a function of a varying parameter. Chimera states, for which coherent and incoherent domains occur simultaneously, emerge as a consequence of the coexistence of basin of attractions for each state. Consequently, the distribution of chimera states can remain invariant by a parameter change, and it can also suffer subtle changes when one of the basins ceases to exist. A similar phenomenon is observed when perturbations are applied in the initial conditions. By means of the uncertainty exponent, we characterise the basin boundaries between the coherent and chimera states, and between the incoherent and chimera states. This way, we show that the density of chimera states can be not only moderately sensitive but also highly sensitive to initial conditions. This chimera's dilemma is a consequence of the fractal and riddled nature of the basin boundaries.

Inference of topology and the nature of synapses, and the flow of information in neuronal networks.

The characterization of neuronal connectivity is one of the most important matters in neuroscience. In this work, we show that a recently proposed informational quantity, the causal mutual information, employed with an appropriate methodology, can be used not only to correctly infer the direction of the underlying physical synapses, but also to identify their excitatory or inhibitory nature, considering easy to handle and measure bivariate time series. The success of our approach relies on a surprising property found in neuronal networks by which nonadjacent neurons do "understand" each other (positive mutual information), however, this exchange of information is not capable of causing effect (zero transfer entropy). Remarkably, inhibitory connections, responsible for enhancing synchronization, transfer more information than excitatory connections, known to enhance entropy in the network. We also demonstrate that our methodology can be used to correctly infer directionality of synapses even in the presence of dynamic and observational Gaussian noise, and is also successful in providing the effective directionality of intermodular connectivity, when only mean fields can be measured.

Synchronised firing patterns in a random network of adaptive exponential integrate-and-fire neuron model.

We have studied neuronal synchronisation in a random network of adaptive exponential integrate-and-fire neurons. We study how spiking or bursting synchronous behaviour appears as a function of the coupling strength and the probability of connections, by constructing parameter spaces that identify these synchronous behaviours from measurements of the inter-spike interval and the calculation of the order parameter. Moreover, we verify the robustness of synchronisation by applying an external perturbation to each neuron. The simulations show that bursting synchronisation is more robust than spike synchronisation.

Spike timing-dependent plasticity induces non-trivial topology in the brain.

We study the capacity of Hodgkin-Huxley neuron in a network to change temporarily or permanently their connections and behavior, the so called spike timing-dependent plasticity (STDP), as a function of their synchronous behavior. We consider STDP of excitatory and inhibitory synapses driven by Hebbian rules. We show that the final state of networks evolved by a STDP depend on the initial network configuration. Specifically, an initial all-to-all topology evolves to a complex topology. Moreover, external perturbations can induce co-existence of clusters, those whose neurons are synchronous and those whose neurons are desynchronous. This work reveals that STDP based on Hebbian rules leads to a change in the direction of the synapses between high and low frequency neurons, and therefore, Hebbian learning can be explained in terms of preferential attachment between these two diverse communities of neurons, those with low-frequency spiking neurons, and those with higher-frequency spiking neurons.

Tilted excitation implies odd periodic resonances.

Our aim is to unveil how resonances of parametric systems are affected when symmetry is broken. We showed numerically and experimentally that odd resonances indeed come about when the pendulum is excited along a tilted direction. Applying the Melnikov subharmonic function, we not only determined analytically the loci of saddle-node bifurcations delimiting resonance regions in parameter space but also explained these observations by demonstrating that, under the Melnikov method point of view, odd resonances arise due to an extra torque that appears in the asymmetric case.

Successful network inference from time-series data using mutual information rate.

This work uses an information-based methodology to infer the connectivity of complex systems from observed time-series data. We first derive analytically an expression for the Mutual Information Rate (MIR), namely, the amount of information exchanged per unit of time, that can be used to estimate the MIR between two finite-length low-resolution noisy time-series, and then apply it after a proper normalization for the identification of the connectivity structure of small networks of interacting dynamical systems. In particular, we show that our methodology successfully infers the connectivity for heterogeneous networks, different time-series lengths or coupling strengths, and even in the presence of additive noise. Finally, we show that our methodology based on MIR successfully infers the connectivity of networks composed of nodes with different time-scale dynamics, where inference based on Mutual Information fails.

Chaotic, informational and synchronous behaviour of multiplex networks.

The understanding of the relationship between topology and behaviour in interconnected networks would allow to charac- terise and predict behaviour in many real complex networks since both are usually not simultaneously known. Most previous studies have focused on the relationship between topology and synchronisation. In this work, we provide analytical formulas that shows how topology drives complex behaviour: chaos, information, and weak or strong synchronisation; in multiplex net- works with constant Jacobian. We also study this relationship numerically in multiplex networks of Hindmarsh-Rose neurons. Whereas behaviour in the analytically tractable network is a direct but not trivial consequence of the spectra of eigenvalues of the Laplacian matrix, where behaviour may strongly depend on the break of symmetry in the topology of interconnections, in Hindmarsh-Rose neural networks the nonlinear nature of the chemical synapses breaks the elegant mathematical connec- tion between the spectra of eigenvalues of the Laplacian matrix and the behaviour of the network, creating networks whose behaviour strongly depends on the nature (chemical or electrical) of the inter synapses.

Markovian language model of the DNA and its information content.

This work proposes a Markovian memoryless model for the DNA that simplifies enormously the complexity of it. We encode nucleotide sequences into symbolic sequences, called words, from which we establish meaningful length of words and groups of words that share symbolic similarities. Interpreting a node to represent a group of similar words and edges to represent their functional connectivity allows us to construct a network of the grammatical rules governing the appearance of groups of words in the DNA. Our model allows us to predict the transition between groups of words in the DNA with unprecedented accuracy, and to easily calculate many informational quantities to better characterize the DNA. In addition, we reduce the DNA of known bacteria to a network of only tens of nodes, show how our model can be used to detect similar (or dissimilar) genes in different organisms, and which sequences of symbols are responsible for most of the information content of the DNA. Therefore, the DNA can indeed be treated as a language, a Markovian language, where a 'word' is an element of a group, and its grammar represents the rules behind the probability of transitions between any two groups.

Model for tumour growth with treatment by continuous and pulsed chemotherapy.

In this work we investigate a mathematical model describing tumour growth under a treatment by chemotherapy that incorporates time-delay related to the conversion from resting to hunting cells. We study the model using values for the parameters according to experimental results and vary some parameters relevant to the treatment of cancer. We find that our model exhibits a dynamical behaviour associated with the suppression of cancer cells, when either continuous or pulsed chemotherapy is applied according to clinical protocols, for a large range of relevant parameters. When the chemotherapy is successful, the predation coefficient of the chemotherapic agent acting on cancer cells varies with the infusion rate of chemotherapy according to an inverse relation. Finally, our model was able to reproduce the experimental results obtained by Michor and collaborators [Nature 435 (2005) 1267] about the exponential decline of cancer cells when patients are treated with the drug glivec.

Spatiotemporal resolution of BDNF neuroprotection against glutamate excitotoxicity in cultured hippocampal neurons.

Brain-derived neurotrophic factor (BDNF) protects hippocampal neurons from glutamate excitotoxicity as determined by analysis of chromatin condensation, through activation of extracellular signal-regulated kinase (ERK) and phosphatidylinositol 3-kinase (PI3-K) signaling pathways. However, it is still unknown whether BDNF also prevents the degeneration of axons and dendrites, and the functional demise of synapses, which would be required to preserve neuronal activity. Herein, we have studied the time-dependent changes in several neurobiological markers, and the regulation of proteolytic mechanisms in cultured rat hippocampal neurons, through quantitative western blot and immunocytochemistry. Calpain activation peaked immediately after the neurodegenerative input, followed by a transient increase in ubiquitin-conjugated proteins and increased abundance of cleaved-caspase-3. Proteasome and calpain inhibition did not reproduce the protective effect of BDNF and caspase inhibition in preventing chromatin condensation. However, proteasome and calpain inhibition did protect the neuronal markers for dendrites (MAP-2), axons (Neurofilament-H) and the vesicular glutamate transporters (VGLUT1-2), whereas caspase inhibition was unable to mimic the protective effect of BDNF on neurites and synaptic markers. BDNF partially prevented the downregulation of synaptic activity measured by the KCl-evoked glutamate release using a Förster (Fluorescence) resonance energy transfer (FRET) glutamate nanosensor. These results translate a time-dependent activation of proteases and spatial segregation of these mechanisms, where calpain activation is followed by proteasome deregulation, from neuronal processes to the soma, and finally by caspase activation in the cell body. Moreover, PI3-K and PLCγ small molecule inhibitors significantly blocked the protective action of BDNF, suggesting an activity-dependent mechanism of neuroprotection. Ultimately, we hypothesize that neuronal repair after a degenerative insult is initiated at the synaptic level.

Reversed-phase HPLC/FD method for the quantitative analysis of the neurotoxin BMAA (ß-N-methylamino-L-alanine) in cyanobacteria.

A method has been developed and optimized in order to detect and quantify the non-protein amino acid ß-N-methylamino-L-alanine(BMAA) in cyanobacteria. The novelty of the method is that we have used methanol instead of acetonitrile as the eluent. The method includes extraction with 0.1 M trichloroacetic acid (free BMAA) or protein hydrolysis with 6 M hydrochloric acid (total BMAA), derivatization with AQC (6-aminoquinolyl-N-hydroxysuccinimidyl carbamate) and reversed-phase high-performance liquid chromatography analysis with fluorescence detection (HPLC/FD). Detection limits ranged from 0.35 to 0.75 pg injected, while quantification limits ranged from 1.10 to 2.55 pg injected for total and free BMAA hydrolysis, respectively. The linear response range was up to 850 pmol in both methods, embracing three orders of magnitude. The method was successfully applied to a lyophilized estuarine species of Nostoc (LEGE 06077). All previous published methods for BMAA quantification, using HPLC/FD, have reported the usage of acetonitrile. This is the first report using methanol as the mobile phase. Although the elution strength differs with both solvents, the final method proved efficient for the quantification of BMAA in this complex sample. The method resulted effective, low-priced, and simple, being suitable for routine monitoring of BMAA in cyanobacteria.