From mass to structure: An aromaticity index for high-resolution mass data of natural organic matter

Recent progress in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) provided extensive molecular mass data for complex natural organic matter (NOM). Structural information can be deduced solely from the molecular masses for ions with extreme molecular element ratios, in particular low H/C ratios, which are abundant in thermally altered NOM (e.g. black carbon). In this communication we propose a general aromaticity index (AI) and two threshold values as unequivocal criteria for the existence of either aromatic (AI > 0.5) or condensed aromatic structures (AI >= 0.67) in NOM. AI can be calculated from molecular formulae which are derived from exact molecular masses of naturally occurring compounds containing C, H, O, N, S and P and is especially applicable for substances with aromatic cores and few alkylations. In order to test the validity of our model index, AI is applied to FTICRMS data of a NOM deep-water sample from the Weddell Sea (Antarctica), a fulvic acid standard and an artificial dataset of all theoretically possible molecular formulae. For graphical evaluation a ternary plot is suggested for four-dimensional data representation. The proposed aromaticity index is a step towards structural identification of NOM and the molecular identification of black carbon in the environment

Evidence for a protein tether involved in somatic touch

The gating of ion channels by mechanical force underlies the sense of touch and pain. The mode of gating of mechanosensitive ion channels in vertebrate touch receptors is unknown. Here we show that the presence of a protein link is necessary for the gating of mechanosensitive currents in all low-threshold mechanoreceptors and some nociceptors of the dorsal root ganglia (DRG). Using TEM, we demonstrate that a protein filament with of length ∼100 nm is synthesized by sensory neurons and may link mechanosensitive ion channels in sensory neurons to the extracellular matrix. Brief treatment of sensory neurons with non-specific and site-specific endopeptidases destroys the protein tether and abolishes mechanosensitive currents in sensory neurons without affecting electrical excitability. Protease-sensitive tethers are also required for touch-receptor function in vivo. Thus, unlike the majority of nociceptors, cutaneous mechanoreceptors require a distinct protein tether to transduce mechanical stimuli

Accelerated search kinetics mediated by redox reactions of DNA repair enzymes

A Charge Transport (CT) mechanism has been proposed in several papers (e.g., Yavin, et al. PNAS, v102 3546 (2005)) to explain the localization of Base Excision Repair (BER) enzymes to lesions on DNA. The CT mechanism relies on redox reactions of iron-sulfur cofactors that modify the enzyme's binding affinity. These redox reactions are mediated by the DNA strand and involve the exchange of electrons between BER enzymes along DNA. We propose a mathematical model that incorporates enzyme binding/unbinding, electron transport, and enzyme diffusion along DNA. Analysis of our model within a range of parameter values suggests that the redox reactions can increase desorption of BER enzymes not already bound to their targets, allowing the enzymes to be recycled, thus accelerating the overall search process. This acceleration mechanism is most effective when enzyme copy numbers and enzyme diffusivity along the DNA are small. Under such conditions, we find that CT BER enzymes find their targets more quickly than simple "passive" enzymes that simply attach to the DNA without desorbing.Comment: 17 pages, 8 figure

Crystal protein Cry5B as a novel and powerful anthelmintic

Soil-transmitted helminths (STHs), most notably, hookworms, whipworms, and Ascaris, are nematodes that infect more than 1.5 billion of the poorest people and are amongst the leading causes of morbidity worldwide. Only two classes of de-worming drugs (anthelmintics) are available for treatment, and only one is commonly used in mass drug administrations. New anthelmintics are urgently needed to overcome emerging resistance and to produce higher cure rates. Crystal (Cry) proteins, in particular Cry5B, made by Bacillus thuringiensis (Bt) are promising new candidates. Cry5B has excellent anthelmintic properties against many free-living and parasitic nematodes, including in vivo efficacy against multiple STH infections in rodents (Heligomasmidoes polygyrus and Ancylostoma ceylanicum) and in pigs (Ascaris suum). An enormous challenge for STHs, very different from most diseases worked on in the developing world, is the requirement that therapies be very cheap (the people infected are very poor and current drugs costs pennies a dose), massively scalable (over 4 billion people are at risk from infection), and have a long shelf life in harsh environments, that have high temperature and humidity and no cold chain. We will update our progress in several key areas. We will present new data on the in vivo activity of Cry5B against a major human parasite in humans. We will also present data on the whether or not the immune system is required for Cry5B action in vivo. We will also present on our development efforts to produce a deployable version of Cry5B that is cheap, safe, scalable, and stable. These efforts are currently focused on bacterial engineering, expression, and formulation

Terpenes as ‘resistance-busting” anthelmintic drug

There is an urgent need for new therapies for parasitic helminthic diseases affecting 1.5-2 billion people worldwide due to the threat of wide-spread resistance development to existing treatments and due to problems of incomplete efficacies. Terpenes are plant secondary metabolites and major essential oil constituents. Historically, the terpene thymol was successfully used to cure hookworm infections in the 1900’s. Although effective, large doses were needed and thymol treatment had significant side effects. Because free terpenes are absorbed in the stomach, less than 10% of oral terpenes entered the site where the parasites live. To overcome these problems we have developed microparticle encapsulated terpenes and enteric coated terpene capsules. We screened 20 terpenes for anthelmintic activity in vitro against adult stages of the hookworm and whipworm parasitic nematodes Ancylostoma ceylanicum and Trichuris muris. Here we will present results of this work, which shows the promising potential for some terpenes as pan-nematode anthelmintics. This work has allowed us to classify terpenes into at least two groups based on their in vitro killing kinetics. We have also shown that some terpenes are effective against an albendazole-resistant Caenorhabditis elegans strain suggesting that terpenes may play an important role in overcoming helminthic drug resistance. We will also present our work on optimizing lead terpene formulations in vitro and in vivo in animal models of parasitic nematode infection in order to overcome the challenges and realize the potential of “resistance-busting” terpene-based anthelmintic therapies

Theoretical Spectra of Terrestrial Exoplanet Surfaces

We investigate spectra of airless rocky exoplanets with a theoretical framework that self-consistently treats reflection and thermal emission. We find that a silicate surface on an exoplanet is spectroscopically detectable via prominent Si-O features in the thermal emission bands of 7 - 13 \mu m and 15 - 25 \mu m. The variation of brightness temperature due to the silicate features can be up to 20 K for an airless Earth analog, and the silicate features are wide enough to be distinguished from atmospheric features with relatively high-resolution spectra. The surface characterization thus provides a method to unambiguously identify a rocky exoplanet. Furthermore, identification of specific rocky surface types is possible with the planet's reflectance spectrum in near-infrared broad bands. A key parameter to observe is the difference between K band and J band geometric albedos (A_g (K)-A_g (J)): A_g (K)-A_g (J) > 0.2 indicates that more than half of the planet's surface has abundant mafic minerals, such as olivine and pyroxene, in other words primary crust from a magma ocean or high-temperature lavas; A_g (K)-A_g (J) < -0.09 indicates that more than half of the planet's surface is covered or partially covered by water ice or hydrated silicates, implying extant or past water on its surface. Also, surface water ice can be specifically distinguished by an H-band geometric albedo lower than the J-band geometric albedo. The surface features can be distinguished from possible atmospheric features with molecule identification of atmospheric species by transmission spectroscopy. We therefore propose that mid-infrared spectroscopy of exoplanets may detect rocky surfaces, and near-infrared spectrophotometry may identify ultramafic surfaces, hydrated surfaces and water ice.Comment: Accepted for publication on the Ap

First Kepler results on compact pulsators II: KIC 010139564, a new pulsating subdwarf B (V361 Hya) star with an additional low-frequency mode

We present the discovery of nonradial pulsations in a hot subdwarf B star based on 30.5 days of nearly continuous time-series photometry using the \emph{Kepler} spacecraft. KIC 010139564 is found to be a short-period pulsator of the V361 Hya (EC 14026) class with more than 10 independent pulsation modes whose periods range from 130 to 190 seconds. It also shows one periodicity at a period of 3165 seconds. If this periodicity is a high order g-mode, then this star may be the hottest member of the hybrid DW Lyn stars. In addition to the resolved pulsation frequencies, additional periodic variations in the light curve suggest that a significant number of additional pulsation frequencies may be present. The long duration of the run, the extremely high duty cycle, and the well-behaved noise properties allow us to explore the stability of the periodic variations, and to place strong constraints on how many of them are independent stellar oscillation modes. We find that most of the identified periodicities are indeed stable in phase and amplitude, suggesting a rotation period of 2-3 weeks for this star, but further observations are needed to confirm this suspicion.Comment: 10 pages, accepted for publication in MNRA