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.

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.

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.

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.

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.

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.

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.

Dynamical estimates of chaotic systems from Poincare recurrences.

We show a function that fits well the probability density of return times between two consecutive visits of a chaotic trajectory to finite size regions in phase space. It deviates from the exponential statistics by a small power-law term, a term that represents the deterministic manifestation of the dynamics. We also show how one can quickly and easily estimate the Kolmogorov-Sinai entropy and the short-term correlation function by realizing observations of high probable returns. Our analyses are performed numerically in the Henon map and experimentally in a Chua's circuit. Finally, we discuss how our approach can be used to treat the data coming from experimental complex systems and for technological applications.

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.

Transmission of information in active networks.

Shannon's capacity theorem is the main concept behind the theory of communication. It says that if the amount of information contained in a signal is smaller than the channel capacity of a physical media of communication, it can be transmitted with arbitrarily small probability of error. This theorem is usually applicable to ideal channels of communication in which the information to be transmitted does not alter the passive characteristics of the channel that basically tries to reproduce the source of information. For an active channel, a network formed by elements that are dynamical systems (such as neurons, chaotic or periodic oscillators), it is unclear if such theorem is applicable, once an active channel can adapt to the input of a signal, altering its capacity. To shed light into this matter, we show, among other results, how to calculate the information capacity of an active channel of communication. Then, we show that the channel capacity depends on whether the active channel is self-excitable or not and that, contrary to a current belief, desynchronization can provide an environment in which large amounts of information can be transmitted in a channel that is self-excitable. An interesting case of a self-excitable active channel is a network of electrically connected Hindmarsh-Rose chaotic neurons.

Experimental observation of a complex periodic window.

The existence of a special periodic window in the two-dimensional parameter space of an experimental Chua's circuit is reported. One of the main reasons that makes such a window special is that the observation of one implies that other similar periodic windows must exist for other parameter values. However, such a window has never been experimentally observed, since its size in parameter space decreases exponentially with the period of the periodic attractor. This property imposes clear limitations for its experimental detection.

Elemental levels in tree-bark and epiphytic-lichen transplants at a mixed environment in mainland Portugal, and comparisons with an in situ lichen.

Samples of Platanus hybrida Brot. bark and Flavoparmelia caperata (L.) Hale thalli, from a clean area in northern Portugal (Baião), were transplanted into an exposure location at the south-western Atlantic coast, impacted by urban-industrial emissions (Sines), for a 10-month long experiment. Bark pieces were confined into nylon bags (2-mm mesh), and lichen thalli kept with their bark substrate (Pinus pinaster (Ait.) Sol.). Every two months, a double set of transplants (one for bark, one for lichens) was brought back into the laboratory, together with native samples of Evernia prunastri (L.) Ach. Following suitable cleansing and preparation procedures, field samples were put through INAA for elemental assessment. The results indicate that, regardless of signal magnitude, (1) concentrations in bark and lichen transplants are significantly correlated with atmospheric deposition for an appreciable number of elements; (2) there are a number of significant correlations between transplanted and native samples, and again between the latter and the deposition; and (3) the elements with biological patterns that follow the deposition in either transplanted or native samples (Co, V) are the very ones whose bioaccumulation seems to benefit from an alternation of wet-dry periods, which fits the precipitation record of the test site during the exposure term.

[On the electron stabilization within the quinone acceptor part of Rhodobacter sphaeroides photosynthetic reaction centers].

The time evolution of the photoinduced differential absorption spectrum of isolated Rhodobacter sphaeroides photosynthetic reaction centers was investigated. The measurements were carried out in the spectral region of 400-500 nm on the time scale of up to 200 microseconds. The spectral changes observed can be interpreted in terms of the effects of proton shift along hydrogen bonds between the primary quinone acceptor and the protein. A theoretical analysis of the spectrum time evolution was performed, which is based on the consideration of the kinetics of proton tunneling along the hydrogen bond. It was shown that the stabilization of the primary quinone electronic state occurs within the first several tens of microseconds after quinone reduction. It slows down upon the deuteration of reaction centers as well as after adding 90% of glycerol; on the other hand, it accelerates as temperature rises up to 40 degrees C.

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.

General framework for phase synchronization through localized sets.

We present an approach which enables one to identify phase synchronization in coupled chaotic oscillators without having to explicitly measure the phase. We show that if one defines a typical event in one oscillator and then observes another one whenever this event occurs, these observations give rise to a localized set. Our result provides a general and easy way to identify PS, which can also be used to oscillators that possess multiple time scales. We illustrate our approach in networks of chemically coupled neurons. We show that clusters of phase synchronous neurons may emerge before the onset of phase synchronization in the whole network, producing a suitable environment for information exchanging. Furthermore, we show the relation between the localized sets and the amount of information that coupled chaotic oscillator can exchange.

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.

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.

Global bifurcation destroying the experimental torus T2.

We show experimentally the scenario of a two-frequency torus T2 breakdown, in which a global bifurcation occurs due to the collision of a torus with an unstable periodic orbit, creating a heteroclinic saddle connection, followed by an intermittent behavior.

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.