Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

Background: Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. These include recently discovered prokaryotic polymorphic toxin systems implicated in intra-specific conflicts. They are characterized by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. Prior analysis revealed a striking diversity of nuclease and deaminase domains among the toxin modules. We systematically investigated polymorphic toxin systems using comparative genomics, sequence and structure analysis. Results: Polymorphic toxin systems are distributed across all major bacterial lineages and are delivered by at least eight distinct secretory systems. In addition to type-II, these include type-V, VI, VII (ESX), and the poorly characterized "Photorhabdus virulence cassettes (PVC)", PrsW-dependent and MuF phage-capsid-like systems. We present evidence that trafficking of these toxins is often accompanied by autoproteolytic processing catalyzed by HINT, ZU5, PrsW, caspase-like, papain-like, and a novel metallopeptidase associated with the PVC system. We identified over 150 distinct toxin domains in these systems. These span an extraordinary catalytic spectrum to include 23 distinct clades of peptidases, numerous previously unrecognized versions of nucleases and deaminases, ADP-ribosyltransferases, ADP ribosyl cyclases, RelA/SpoT-like nucleotidyltransferases, glycosyltranferases and other enzymes predicted to modify lipids and carbohydrates, and a pore-forming toxin domain. Several of these toxin domains are shared with host-directed effectors of pathogenic bacteria. Over 90 families of immunity proteins might neutralize anywhere between a single to at least 27 distinct types of toxin domains. In some organisms multiple tandem immunity genes or immunity protein domains are organized into polyimmunity loci or polyimmunity proteins. Gene-neighborhood-analysis of polymorphic toxin systems predicts the presence of novel trafficking-related components, and also the organizational logic that allows toxin diversification through recombination. Domain architecture and protein-length analysis revealed that these toxins might be deployed as secreted factors, through directed injection, or via inter-cellular contact facilitated by filamentous structures formed by RHS/YD, filamentous hemagglutinin and other repeats. Phyletic pattern and life-style analysis indicate that polymorphic toxins and polyimmunity loci participate in cooperative behavior and facultative 'cheating' in several ecosystems such as the human oral cavity and soil. Multiple domains from these systems have also been repeatedly transferred to eukaryotes and their viruses, such as the nucleo-cytoplasmic large DNA viruses. Conclusions: Along with a comprehensive inventory of toxins and immunity proteins, we present several testable predictions regarding active sites and catalytic mechanisms of toxins, their processing and trafficking and their role in intra-specific and inter-specific interactions between bacteria. These systems provide insights regarding the emergence of key systems at different points in eukaryotic evolution, such as ADP ribosylation, interaction of myosin VI with cargo proteins, mediation of apoptosis, hyphal heteroincompatibility, hedgehog signaling, arthropod toxins, cell-cell interaction molecules like teneurins and different signaling messengers.

Growth standards of patients with Noonan and Noonan-like syndromes with mutations in the RAS/MAPK pathway

Noonan syndrome (NS) and Noonan-like syndromes (NLS) are autosomal dominant disorders caused by heterozygous mutations in genes of the RAS/MAPK pathway. The aim of the study was to construct specific growth charts for patients with NS and NLS. Anthropometric measurements (mean of 4.3 measurements per patient) were obtained in a mixed cross-sectional and longitudinal mode from 127 NS and 10 NLS patients with mutations identified in PTPN11 (n?=?90), SOS1 (n?=?14), RAF1 (n?=?10), KRAS (n?=?8), BRAF (n?=?11), and SHOC2 (n?=?4) genes. Height, weight, and body mass index (BMI) references were constructed using the lambda, mu, sigma (LMS) method. Patients had birth weight and length within normal ranges for gestational age although a higher preterm frequency (16%) was observed. Mean final heights were 157.4?cm [-2.4 standard deviation score (SDS)] and 148.4?cm (-2.2?SDS) for adult males and females, respectively. BMI SDS was lower when compared to Brazilian standards (BMI SDS of -0.9 and -0.5 SDS for males and females, respectively). Patients harboring mutations in RAF1 and SHOC2 gene were shorter than other genotypes, whereas patients with SOS1 and BRAF mutations had more preserved postnatal growth. In addition, patients with RAF1 and BRAF had the highest BMI whereas patients with SHOC2 and KRAS mutations had the lowest BMI. The present study established the first height, weight, and BMI reference curves for NS and NLS patients, based only on patients with a proven molecular cause. These charts can be useful for the clinical follow-up of patients with NS and NLS. (c) 2012 Wiley Periodicals, Inc.

A spatial stochastic model for rumor transmission

We consider an interacting particle system representing the spread of a rumor by agents on the d-dimensional integer lattice. Each agent may be in any of the three states belonging to the set {0,1,2}. Here 0 stands for ignorants, 1 for spreaders and 2 for stiflers. A spreader tells the rumor to any of its (nearest) ignorant neighbors at rate lambda. At rate alpha a spreader becomes a stifler due to the action of other (nearest neighbor) spreaders. Finally, spreaders and stiflers forget the rumor at rate one. We study sufficient conditions under which the rumor either becomes extinct or survives with positive probability.

MULTIPLICITY OF NONRADIAL SOLUTIONS FOR A CLASS OF QUASILINEAR EQUATIONS ON ANNULUS WITH EXPONENTIAL CRITICAL GROWTH

In this paper, we establish the existence of many rotationally non-equivalent and nonradial solutions for the following class of quasilinear problems (p) {-Delta(N)u = lambda f(vertical bar x vertical bar, u) x is an element of Omega(r), u > 0 x is an element of Omega(r), u = 0 x is an element of Omega(r), where Omega(r) = {x is an element of R-N : r < vertical bar x vertical bar < r + 1}, N >= 2, N not equal 3, r >0, lambda > 0, Delta(N)u = div(vertical bar del u vertical bar(N-2)del u) is the N-Laplacian operator and f is a continuous function with exponential critical growth.

Production of Human Antibody Fragments Binding to Melittin and Phospholipase A2 in Africanised Bee Venom: Minimising Venom Toxicity

The hybrid created from the crossbreeding of European and African bees, known as the Africanised bee, has provided numerous advantages for current beekeeping. However, this new species exhibits undesirable behaviours, such as colony defence instinct and a propensity to attack en masse, which can result in serious accidents. To date, there is no effective treatment for cases of Africanised bee envenomation. One promising technique for developing an efficient antivenom is the use of phage display technology, which enables the production of human antibodies, thus avoiding the complications of serum therapy, such as anaphylaxis and serum sickness. The aim of this study was to produce human monoclonal single-chain Fv (scFv) antibody fragments capable of inhibiting the toxic effects of Africanised bee venom. We conducted four rounds of selection of antibodies against the venom and three rounds of selection of antibodies against purified melittin. Three clones were selected and tested by enzyme-linked immunosorbent assay to verify their specificity for melittin and phospholipase A2. Two clones (C5 and C12) were specific for melittin, and one (A7) was specific for phospholipase A2. In a kinetic haemolytic assay, these clones were evaluated individually and in pairs. The A7-C12 combination had the best synergistic effect and was chosen to be used in the assays of myotoxicity inhibition and lethality. The A7-C12 combination inhibited the in vivo myotoxic effect of the venom and increased the survival of treated animals.

Microtensile bond strength of resin composite to dentin treated with Er:YAG laser of bleached teeth

The objective of this study was to evaluate the influence of Er:YAG laser (lambda = 2.94 mu m) on microtensile bond strength (mu TBS) and superficial morphology of bovine dentin bleached with 16% carbamide peroxide. Forty bovine teeth blocks (7 x 3 x 3 mm(3)) were randomly assigned to four groups: G1- bleaching and Er:YAG irradiation with energy density of 25.56 J/cm(2) (focused mode); G2 - bleaching; G3 - no-bleaching and Er:YAG irradiation (25.56 J/cm(2)); G4 - control, non-treated. G1 and G2 were bleached with 16% carbamide peroxide for 6 h during 21 days. Afterwards, all blocks were abraded with 320 to 600-grit abrasive papers to obtain flat standardized dentin surfaces. G1 and G3 were Er:YAG irradiated. Blocks were immediately restored with 4-mm-high composite resin (Adper Single Bond 2, Z-250-3 M/ESPE). After 24 h, the restored blocks (n = 9) were serially sectioned and trimmed to an hour-glass shape of approximately 1 mm(2) at the bonded interface area, and tested in tension in a universal testing machine (1 mm/ min). Failure mode was determined at a magnification of 100x using a stereomicroscope. One block of each group was selected for scanning electron microscope (SEM) analysis. mu TBS data was analyzed by two-way ANOVA and Tukey test (alpha = 0.05). Mean bond strengths (SD) in MPa were: G1- 32.7 (5.9)(A); G2- 31.1 (6.3)(A); G3- 25.2 (8.3)(B); G4- 36.7 (9.9).(A) Groups with different uppercase letters were significantly different from each other (p < .05). Enamel bleaching procedure did not affect mu TBS values for dentin adhesion. Er:YAG laser irradiation with 25.56 J/cm(2) prior to adhesive procedure of bleached teeth did not affect mu TBS at dentin and promoted a dentin surface with no smear layer and opened dentin tubules observed under SEM. On the other hand, Er:YAG laser irradiation prior to adhesive procedure of non-bleached surface impaired mu TBS compared to the control group.

Cosmological measure with volume averaging and the vacuum energy problem

In this paper, we give a possible solution to the cosmological constant problem. It is shown that the traditional approach, based on volume weighting of probabilities, leads to an incoherent conclusion: the probability that a randomly chosen observer measures Lambda = 0 is exactly equal to 1. Using an alternative, volume averaging measure, instead of volume weighting can explain why the cosmological constant is non-zero.

Ionic Transport and Water Vapor Uptake of Ammonium Exchanged Perfluorosulfonic Acid Membranes

Nafion membranes series N117 doped with ammonium, at different cation fractions (H+/NH4+), were investigated for ionic transport and water vapor uptake, for several water activities and temperatures. Ammonium cations change both properties of the polymer in a similar manner. Membrane ionic conductivity and water vapor uptake (lambda) decrease as the ammonium concentration increases in the polymer. Ionic transport activation energies are calculated and the transport mechanism of ammonium ions in Nafion is discussed. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.040203jes] All rights reserved.

Generalized non-commutative inflation

Non-commutative geometry indicates a deformation of the energy-momentum dispersion relation f (E) = E/pc (not equal 1) for massless particles. This distorted energy-momentum relation can affect the radiation-dominated phase of the universe at sufficiently high temperature. This prompted the idea of non-commutative inflation by Alexander et al (2003 Phys. Rev. D 67 081301) and Koh and Brandenberger (2007 JCAP06(2007) 021 and JCAP11(2007) 013). These authors studied a one-parameter family of a non-relativistic dispersion relation that leads to inflation: the a family of curves f (E) = 1 + (lambda E)(alpha). We show here how the conceptually different structure of symmetries of non-commutative spaces can lead, in a mathematically consistent way, to the fundamental equations of non-commutative inflation driven by radiation. We describe how this structure can be considered independently of (but including) the idea of non-commutative spaces as a starting point of the general inflationary deformation of SL(2, C). We analyze the conditions on the dispersion relation that leads to inflation as a set of inequalities which plays the same role as the slow-roll conditions on the potential of a scalar field. We study conditions for a possible numerical approach to obtain a general one-parameter family of dispersion relations that lead to successful inflation.

Up-conversion properties of lanthanide-organic frameworks and how to track ammunitions using these materials

This manuscript reports the first example of up-conversion properties involving Yb3+ and Tb3+ ions in five isostructural Lanthanide-Organic Frameworks (LnOFs), herein designated as UCMarker-1 to UCMarker-5, respectively, and their application as optical probes for the identification of gunshot residues (GSRs) and the ammunition encryption procedure. The excitation of the Yb3+2 F-7/2 <-> F-2(5/2) transition (980 nm) at room temperature leads to visible up-conversion (UC) emission of Tb3+ D-5(4) -> F-7(J). The GSR and lead-free primer residues are easily identified upon UV radiation (lambda = 254 nm). These results prove that the exploration of LnOFs to identify GSR is attractive for the identification of ammunition origins or caliber recognition.

Elemental abundances and classification of carbon-enhanced metal-poor stars

We present a detailed study of carbon-enhanced metal-poor (CEMP) stars, based on high-resolution spectroscopic observations of a sample of 18 stars. The stellar spectra for this sample were obtained at the 4.2 m William Herschel Telescope in 2001 and 2002, using the Utrecht Echelle Spectrograph, at a resolving power R similar to 52 000 and S/N similar to 40, covering the wavelength range lambda lambda 3700-5700 angstrom. The atmospheric parameters determined for this sample indicate temperatures ranging from 4750 K to 7100 K, log g from 1.5 to 4.3, and metallicities -3.0 <= [Fe/H]<=-1.7. Elemental abundances for C, Na, Mg, Sc, Ti, Cr, Cu, Zn, Sr, Y, Zr, Ba, La, Ce, Nd, Sm, Eu, Gd, Dy are determined. Abundances for an additional 109 stars were taken from the literature and combined with the data of our sample. The literature sample reveals a lack of reliable abundance estimates for species that might be associated with the r-process elements for about 67% of CEMP stars, preventing a complete understanding of this class of stars, since [Ba/Eu] ratios are used to classify them. Although eight stars in our observed sample are also found in the literature sample, Eu abundances or limits are determined for four of these stars for the first time. From the observed correlations between C, Ba, and Eu, we argue that the CEMP-r/s class has the same astronomical origin as CEMP-s stars, highlighting the need for a more complete understanding of Eu production.

Dental Pulp Vascular Permeability Changes Induced by Dental Bleaching

Aiming to compare the effect of different light sources for dental bleaching on vascular permeability of dental pulps, forty-eight incisors were used. The bleaching agent (35% hydrogen peroxide) was activated by halogen light; LED (Light Emitting Diode) or LED, followed by laser phototherapy (LPT) (lambda = 780 nm; 3 J/cm(2)). After the bleaching procedures, the animals received an intra-arterial dye injection and one hour later were sacrificed. The teeth were diaphanized and photographed. The amount of blue stain content of each dental pulp was quantified using a computer imaging program. The data was statistically compared (p <= 0.05). The results showed a significant higher (p <= 0.01) dye content in the groups bleached with halogen light, compared with the control, LED and LED plus LPT groups. Thus, tooth bleaching activated by LED or LED plus LPT induces lesser resulted in increased vascular permeability than halogen light.

STRUCTURE AND BIFURCATION OF PULLBACK ATTRACTORS IN A NON-AUTONOMOUS CHAFEE-INFANTE EQUATION

The Chafee-Infante equation is one of the canonical infinite-dimensional dynamical systems for which a complete description of the global attractor is available. In this paper we study the structure of the pullback attractor for a non-autonomous version of this equation, u(t) = u(xx) + lambda(xx) - lambda u beta(t)u(3), and investigate the bifurcations that this attractor undergoes as A is varied. We are able to describe these in some detail, despite the fact that our model is truly non-autonomous; i.e., we do not restrict to 'small perturbations' of the autonomous case.

Serrumab: A human monoclonal antibody that counters the biochemical and immunological effects of Tityus serrulatus venom

In Brazil, the species Tityus serrulatus is responsible for the most severe cases of scorpion envenomation. There is currently a need for new scorpion anti-venoms that are more effective and less harmful. This study attempted to produce human monoclonal antibodies capable of inhibiting the activity of T. serrulatus venom (TsV), using the Griffin.1 library of human single-chain fragment-variable (scFv) phage antibodies. Four rounds of phage antibody selection were performed, and the round with the highest phage antibody titer was chosen for the production of monoclonal phage antibodies and for further analysis. The scFv 2A, designated serrumab, was selected for the production and purification of soluble antibody fragments. In a murine peritoneal macrophage cell line (J774.1), in vitro assays of the cytokines interleukin (IL)-6, tumor necrosis factor (TNF)-alpha, and IL-10 were performed. In male BALB/c mice, in vivo assays of plasma urea, creatinine, aspartate transaminase, and glucose were performed, as well as of neutrophil recruitment and leukocyte counts. It was found that serrumab inhibited the TsV-induced increases in the production of IL-6, TNF alpha, and IL-10 in J774.1 cells. The in vivo inhibition assay showed that serrumab also prevented TsV-induced increases in the plasma levels of urea, creatinine, aspartate transaminase, and glucose, as well as preventing the TsV-induced increase in neutrophil recruitment. The results indicate that the human monoclonal antibody serrumab is a candidate for inclusion in a mixture of specific antibodies to the various toxins present in TsV. Therefore, serrumab shows promise for use in the production of new anti-venom.

An experimental study of low-level laser therapy in rat Achilles tendon injury

The aim of this controlled animal study was to investigate the effect of low-level laser therapy (LLLT) administered 30 min after injury to the Achilles tendon. The study animals comprised 16 Sprague Dawley male rats divided in two groups. The right Achilles tendons were injured by blunt trauma using a mini guillotine, and were treated with LLLT or placebo LLLT 30 min later. The injury and LLLT procedures were then repeated 15 hours later on the same tendon. One group received active LLLT (lambda = 904 nm, 60 mW mean output power, 0.158 W/cm(2) for 50 s, energy 3 J) and the other group received placebo LLLT 23 hours after LLLT. Ultrasonographic images were taken to measure the thickness of the right and left Achilles tendons. Animals were then killed, and all Achilles tendons were tested for ultimate tensile strength (UTS). All analyses were performed by blinded observers. There was a significant increase in tendon thickness in the active LLLT group when compared with the placebo group (p < 0.05) and there were no significant differences between the placebo and uninjured left tendons. There were no significant differences in UTS between laser-treated, placebo-treated and uninjured tendons. Laser irradiation of the Achilles tendon at 0.158 W/cm(2) for 50 s (3 J) administered within the first 30 min after blunt trauma, and repeated after 15 h, appears to lead to edema of the tendon measured 23 hours after LLLT. The guillotine blunt trauma model seems suitable for inflicting tendon injury and measuring the effects of treatment on edema by ultrasonography and UTS. More studies are needed to further refine this model.