Fruit and Seed Volatiles: Multiple Stage Settings, Actors and Props in an Evolutionary Play

Plants emit volatile organic compounds (VOCs) from most parts of their anatomy. Conventionally, the volatiles of leaves, flowers, fruits and seeds have been investigated separately. This review presents an integrated perspective of volatiles produced by fruits and seeds in the context of selection on the whole plant. It suggests that fruit and seed volatiles may only be understood in the light of the chemistry of the whole plant. Fleshy fruit may be viewed as an ecological arena within which several evolutionary games are being played involving fruit VOCs. Fruit odour and colour may be correlated and interact via multimodal signalling in influencing visits by frugivores. The hypothesis of volatile crypsis in the evolution of hard seeds as protection against volatile diffusion and perception by seed predators is reviewed. Current views on the role of volatiles in ant dispersal of seeds or myrmecochory are summarised, especially the suggestion that ants are being manipulated by plants in the form of a sensory trap while providing this service. Plant VOC production is presented as an emergent phenotype that could result from multiple selection pressures acting on various plant parts; the ``plant'' phenotype and VOC profile may receive significant contributions from symbionts within the plant. Viewing the plant as a holobiont would benefit an understanding of the emergent plant phenotype.

Sources of major ions and processes affecting the geochemical and isotopic signatures of subsurface waters along a tropical river, Southwestern India

Systematic monitoring of subsurface hydrogeochemistry has been carried out for a period of one year in a humid tropical region along the Nethravati-Gurupur River. The major ion and stable isotope (delta O-18 and delta H-2) compositions are used to understand the hydrogeochemistry of groundwater and its interaction with surface water. In the study, it is observed that intense weathering of source rocks is the major source of chemical elements to the surface and subsurface waters. In addition, agricultural activities and atmospheric contributions also control the major ion chemistry of water in the study area. There is a clear seasonality in the groundwater chemistry, which is related to the recharge and discharge of the hydrological system. On a temporal scale, there is a decrease in major cation concentrations during the monsoon which is a result of dilution of sources from the weathering of rock minerals, and an increase in anion concentrations which is contributed by the atmosphere, accompanied by an increase in water level during the monsoon. The stable isotope composition indicates that groundwater in the basin is of meteoric origin and recharged directly from the local precipitation during the monsoonal season. Soon after the monsoon, groundwater and surface water mix in the subsurface region. The groundwater feeds the surface water during the lean river flow season.

One-Carbon Metabolic Pathway Rewiring in Escherichia coli Reveals an Evolutionary Advantage of 10-Formyltetrahydrofolate Synthetase (Fhs) in Survival under Hypoxia

In cells, N-10-formyltetrahydrofolate (N-10-fTHF) is required for formylation of eubacterial/organellar initiator tRNA and purine nucleotide biosynthesis. Biosynthesis of N-10-fTHF is catalyzed by 5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). All eubacteria possess FolD, but some possess both FolD and Fhs. However, the reasons for possessing Fhs in addition to FolD have remained unclear. We used Escherichia coli, which naturally lacks fhs, as our model. We show that in E. coli, the essential function of folD could be replaced by Clostridium perfringens fhs when it was provided on a medium-copy-number plasmid or integrated as a single-copy gene in the chromosome. The fhs-supported folD deletion (Delta folD) strains grow well in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N-10-fTHF in the Delta folD strain (supported by plasmid-borne fhs) were limiting despite the high capacity of the available Fhs to synthesize N-10-fTHF in vitro. Auxotrophy for purines could be alleviated by supplementing formate to the medium, and that for glycine was alleviated by engineering THF import into the cells. The Delta folD strain (harboring fhs on the chromosome) showed a high NADP(+)-to-NADPH ratio and hypersensitivity to trimethoprim. The presence of fhs in E. coli was disadvantageous for its aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. The computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria.

Investigation on two magnon scattering processes in pulsed laser deposited epitaxial nickel zinc ferrite thin film

Ferromagnetic resonance (FMR) measurements are employed to evaluate the presence of the two magnon scattering contribution in the magnetic relaxation processes of the epitaxial nickel zinc ferrite thin films deposited using pulsed laser deposition (PLD) on the (0 0 1) MgAl2O4 substrate. Furthermore, the reciprocal space mapping reveals the presence of microstructural defects which acts as an origin for the two magnon scattering process in this thin film. The relevance of this scattering process is further discussed for understanding the higher FMR linewidth in the in-plane configuration compared to the out-of-plane configuration. FMR measurements also reveal the presence of competing uniaxial and cubic anisotropy in the studied films.

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

Background: In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contains 3,786 families corresponding to ``Domains of Unknown Function'' (DUF) or ``Uncharacterized Protein Family'' (UPF), of which 3,087 families have no reported three-dimensional structure, constituting almost one-fourth of the known protein families in search for both structure and function. Results: We applied a `computational structural genomics' approach using five state-of-the-art remote similarity detection methods to detect the relationship between uncharacterized DUFs and domain families of known structures. The association with a structural domain family could serve as a start point in elucidating the function of a DUF. Amongst these five methods, searches in SCOP-NrichD database have been applied for the first time. Predictions were classified into high, medium and low-confidence based on the consensus of results from various approaches and also annotated with enzyme and Gene ontology terms. 614 uncharacterized DUFs could be associated with a known structural domain, of which high confidence predictions, involving at least four methods, were made for 54 families. These structure-function relationships for the 614 DUF families can be accessed on-line at http://proline.biochem.iisc.ernet.in/RHD_DUFS/. For potential enzymes in this set, we assessed their compatibility with the associated fold and performed detailed structural and functional annotation by examining alignments and extent of conservation of functional residues. Detailed discussion is provided for interesting assignments for DUF3050, DUF1636, DUF1572, DUF2092 and DUF659. Conclusions: This study provides insights into the structure and potential function for nearly 20 % of the DUFs. Use of different computational approaches enables us to reliably recognize distant relationships, especially when they converge to a common assignment because the methods are often complementary. We observe that while pointers to the structural domain can offer the right clues to the function of a protein, recognition of its precise functional role is still `non-trivial' with many DUF domains conserving only some of the critical residues. It is not clear whether these are functional vestiges or instances involving alternate substrates and interacting partners. Reviewers: This article was reviewed by Drs Eugene Koonin, Frank Eisenhaber and Srikrishna Subramanian.

Risk-Sensitive Ergodic Control of Continuous Time Markov Processes With Denumerable State Space

In this article, we study risk-sensitive control problem with controlled continuous time Markov chain state dynamics. Using multiplicative dynamic programming principle along with the atomic structure of the state dynamics, we prove the existence and a characterization of optimal risk-sensitive control under geometric ergodicity of the state dynamics along with a smallness condition on the running cost.

The electronic, chemical and electrocatalytic processes and intermediates on iron oxide surfaces during photoelectrochemical water splitting

We re-assess experimental soft X-ray absorption spectra of the oxygen K-shell which we recorded operando from iron oxide during photoelectrochemical water splitting in KOH electrolyte. In particular, we refer to recently reported transitional electron hole states which originate within the charge carrier depletion layer of the iron oxide and on the iron oxide surface. For the latter we find that an intermediate oxy-peroxo species is formed on the iron oxide with increasing bias potential, which disappears upon further polarization of the electrode, concomitantly with the evolution and disappearance of the aforementioned surface state. The oxygen spectra contain also the spectroscopic signatures of the electrolyte water, the position of which changes with increasing bias potential towards lower X-ray energies, revealing the breaking and formation of hydrogen bonds in the water during the experiment. Combined with potential dependent impedance spectroscopy data we are able to sketch the molecular structure of chemical intermediates and their charge carrier dynamics. (C) 2015 Elsevier B.V. All rights reserved.

Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv

Drug repurposing to explore target space has been gaining pace over the past decade with the upsurge in the use of systematic approaches for computational drug discovery. Such a cost and time-saving approach gains immense importance for pathogens of special interest, such as Mycobacterium tuberculosis H37Rv. We report a comprehensive approach to repurpose drugs, based on the exploration of evolutionary relationships inferred from the comparative sequence and structural analyses between targets of FDA-approved drugs and the proteins of M. tuberculosis. This approach has facilitated the identification of several polypharmacological drugs that could potentially target unexploited M. tuberculosis proteins. A total of 130 FDA-approved drugs, originally intended against other diseases, could be repurposed against 78 potential targets in M. tuberculosis. Additionally, we have also made an attempt to augment the chemical space by recognizing compounds structurally similar to FDA-approved drugs. For three of the attractive cases we have investigated the probable binding modes of the drugs in their corresponding M. tuberculosis targets by means of structural modelling. Such prospective targets and small molecules could be prioritized for experimental endeavours, and could significantly influence drug-discovery and drug-development programmes for tuberculosis.

An evolutionary formalism for weak quantum measurements

Unitary evolution and projective measurement are fundamental axioms of quantum mechanics. Even though projective measurement yields one of the eigenstates of the measured operator as the outcome, there is no theory that predicts which eigenstate will be observed in which experimental run. There exists only an ensemble description, which predicts probabilities of various outcomes over many experimental runs. We propose a dynamical evolution equation for the projective collapse of the quantum state in individual experimental runs, which is consistent with the well-established framework of quantum mechanics. In case of gradual weak measurements, its predictions for ensemble evolution are different from those of the Born rule. It is an open question whether or not suitably designed experiments can observe this alternate evolution.

Use of Sr isotopes as a tool to decipher the soil weathering processes in a tropical river catchment, southwestern India

River water composition (major ion and Sr-87/Sr-86 ratio) was monitored on a monthly basis over a period of three years from a mountainous river (Nethravati River) of southwestern India. The total dissolved solid (TDS) concentration is relatively low (46 mg L-1) with silica being the dominant contributor. The basin is characterised by lower dissolved Sr concentration (avg. 150 nmol L-1), with radiogenic Sr-87/Sr-86 isotopic ratios (avg. 0.72041 at outlet). The composition of Sr and Sr-87/Sr-86 and their correlation with silicate derived cations in the river basin reveal that their dominant source is from the radiogenic silicate rock minerals. Their composition in the stream is controlled by a combination of physical and chemical weathering occurring in the basin. The molar ratio of SiO2/Ca and Sr-87/Sr-86 isotopic ratio show strong seasonal variation in the river water, i.e., low SiO2/Ca ratio with radiogenic isotopes during non-monsoon and higher SiO2/Ca with less radiogenic isotopes during monsoon season. Whereas, the seasonal variation of Rb/Sr ratio in the stream water is not significant suggesting that change in the mineral phase being involved in the weathering reaction could be unlikely for the observed molar SiO2/Ca and Sr-87/Sr-86 isotope variation in river water. Therefore, the shift in the stream water chemical composition could be attributed to contribution of ground water which is in contact with the bedrock (weathering front) during non-monsoon and weathering of secondary soil minerals in the regolith layer during monsoon. The secondary soil mineral weathering leads to limited silicate cation and enhanced silica fluxes in the Nethravati river basin. (C) 2015 Elsevier Ltd. All rights reserved.

Determinantal point processes in the plane from products of random matrices

We show that the density of eigenvalues for three classes of random matrix ensembles is determinantal. First we derive the density of eigenvalues of product of k independent n x n matrices with i.i.d. complex Gaussian entries with a few of matrices being inverted. In second example we calculate the same for (compatible) product of rectangular matrices with i.i.d. Gaussian entries and in last example we calculate for product of independent truncated unitary random matrices. We derive exact expressions for limiting expected empirical spectral distributions of above mentioned ensembles.

Case studies on the formation of chalcogenide self-assembled monolayers on surfaces and dissociative processes

This report examines the assembly of chalcogenide organic molecules on various surfaces, focusing on cases when chemisorption is accompanied by carbon-chalcogen atom-bond scission. In the case of alkane and benzyl chalcogenides, this induces formation of a chalcogenized interface layer. This process can occur during the initial stages of adsorption and then, after passivation of the surface, molecular adsorption can proceed. The characteristics of the chalcogenized interface layer can be significantly different from the metal layer and can affect various properties such as electron conduction. For chalcogenophenes, the carbon-chalcogen atombond breaking can lead to opening of the ring and adsorption of an alkene chalcogenide. Such a disruption of the pi-electron system affects charge transport along the chains. Awareness about these effects is of importance from the point of view of molecular electronics. We discuss some recent studies based on X-ray photoelectron spectroscopy that shed light on these aspects for a series of such organic molecules.

Electron transfer amongst flavo- and hemo-proteins: diffusible species effect the relay processes, not protein-protein binding

Hitherto, electron transfer (ET) between redox proteins has been deemed to occur via donor-acceptor binding, and diffusible reactive species are considered as deleterious side-products in such systems. Herein, ET from cytochrome P450 reductase (CPR, an animal membrane flavoprotein) and horseradish peroxidase (HRP, a plant hemoprotein) to cytochrome c (Cyt c, a soluble animal hemoprotein) was probed under diverse conditions, using standard assays. ET in the CPR-Cyt c system was critically inhibited by cyanide and sub-equivalent levels of polar one-electron cyclers like copper ions, vitamin C/Trolox and superoxide dismutase. In the presence of lipids, inhibition was also afforded by amphipathic molecules vitamin E, palmitoyl-vitamin C and the membrane hemoprotein, cytochrome b(5). Such nonspecific inhibition (by diverse agents in both aqueous and lipid phases) indicated that electron transfer/relay was effected by small diffusible agents, whose lifetimes are shortened by the diverse radical scavengers. When CPR was retained in a dialysis membrane and Cyt c presented outside in free solution, ET was still observed. Further, HRP (taken at nM levels) catalyzed oxidation of a phenolic substrate was significantly inhibited upon the incorporation of sub-nM levels of Cyt c. The findings imply that CPR-Cyt c or HRP-Cyt c binding is not crucial for ET. Further, fundamental quantitative arguments (based on diffusion/collision) challenge the erstwhile protein-protein binding-assisted ET hypothesis. It is proven beyond reasonable doubt that mobile and diffusible electron carriers (ions and radicals) serve as ``redox-relay agents'' in the biological ET models/setup studied.

Characteristic Dimensionless Numbers in Multi-Scale and Rate-Dependent Processes

For this sake, the macroscopic equations of mechanics and the kinetic equations of the microstructural transformations should form a unified set that be solved simultaneously. As a case study of coupling length and time scales, the trans-scale formulation

Effects of heat-treatment processes on the electroless Ni-B coating and its natural aging mechanism

A Ni-B coating was prepared with EN using potassium borohydride reducing agent. The as-plated micro-structure of the coating was confirmed from XRD to be a mixture of amorphous and supersaturated solid solution. Three kinds of phase transformation were observed from the DSC curve. Different from the previous works, the formation of Ni4B3 and Ni2B was found during some transformation processes. The key factors which influence the variation of micro-hardness and micro-structure in deposits are the formation, the size and amount of Ni3B, Ni4B3 and Ni2B. Aging of the deposits treated under some heat treatment conditions occurred at room temperature. Changes of the micro-hardness indicated aging phenomena evidently. the natural aging phenomena are concerned with various kinds of decomposition of borides, especially with Ni4B3 phase. The extent of natural aging depends on the formation and the quantity of Ni(4)B3 and Ni2B.