Comparative transcriptome mining for terpenoid biosynthetic pathway genes in wild and cultivated species of Plantago

Protoplasma - Plantagos are important economical and medicinal plants that possess several bioactive secondary metabolites, such as phenolics, iridoids, triterpenes, and alkaloids. Triterpenoids...     

Research resource: Haploinsufficiency of receptor activity-modifying protein-2 (RAMP2) causes reduced fertility, hyperprolactinemia, skeletal abnormalities, and endocrine dysfunction in mice

Receptor activity-modifying protein-2 (RAMP2) is a single-pass transmembrane protein that can regulate the trafficking, ligand binding, and signaling of several G protein-coupled receptors (GPCR). The most well-characterized role of RAMP2 is in the regulation of adrenomedullin (AM) binding to calcitonin receptor-like receptor (CLR), and our previous studies using knockout mouse models support this canonical signaling paradigm. For example, Ramp2(-/-) mice die at midgestation with a precise phenocopy of the AM(-/-) and Calcrl(-/-) mice. In contrast, Ramp2(+/-) mice are viable and exhibit an expanded variety of phenotypes that are distinct from those of Calcrl(+/-) mice. Using Ramp2(+/-) female mice, we demonstrate that a modest decrease in Ramp2 expression causes severe reproductive defects characterized by fetal growth restriction, fetal demise, and postnatal lethality that is independent of the genotype and gender of the offspring. Ramp2(+/-) female mice also exhibit hyperprolactinemia during pregnancy and in basal conditions. Consistent with hyperprolactinemia, Ramp2(+/-) female mice have enlarged pituitary glands, accelerated mammary gland development, and skeletal abnormalities including delayed bone development and decreased bone mineral density. Because RAMP2 has been shown to associate with numerous GPCR, it is likely that signaling of one or more of these GPCR is compromised in Ramp2(+/-) mice, yet the precise identification of these receptors remains to be elucidated. Taken together, this work reveals an essential role for RAMP2 in endocrine physiology and provides the first in vivo evidence for a physiological role of RAMP2 beyond that of AM/CLR signaling.     

Characterization of a Drosophila Alzheimer's disease model: pharmacological rescue of cognitive defects

Transgenic models of Alzheimer's disease (AD) have made significant contributions to our understanding of AD pathogenesis, and are useful tools in the development of potential therapeutics. The fruit fly, Drosophila melanogaster, provides a genetically tractable, powerful system to study the biochemical, genetic, environmental, and behavioral aspects of complex human diseases, including AD. In an effort to model AD, we over-expressed human APP and BACE genes in the Drosophila central nervous system. Biochemical, neuroanatomical, and behavioral analyses indicate that these flies exhibit aspects of clinical AD neuropathology and symptomology. These include the generation of Aβ(40) and Aβ(42), the presence of amyloid aggregates, dramatic neuroanatomical changes, defects in motor reflex behavior, and defects in memory. In addition, these flies exhibit external morphological abnormalities. Treatment with a γ-secretase inhibitor suppressed these phenotypes. Further, all of these phenotypes are present within the first few days of adult fly life. Taken together these data demonstrate that this transgenic AD model can serve as a powerful tool for the identification of AD therapeutic interventions.     

“Free” Copper: A New Endogenous Chemical Mediator of Inflammation in Birds

For acceptance of any chemical agent as an endogenous chemical mediator of inflammation, the agent in question must fulfill some biological requirements which are (a) it should be ubiquitously present in tissues in inactive form, (b) it should be activated during process of inflammation whose increase should be identifiable, (c) it should induce or amplify some events of inflammation, (d) there must be some natural inhibitor of such active form in tissues, (e) it should be able to induce inflammatory reaction after exogenous injection, (f) such reaction should be inhibited by exogenous use of their antagonists, and (g) it should be amplified by use of agonists. Copper in its protein free or protein bound form are reported to act as pathogenic factor in inflammatory processes due to oxidative stress. But their role as endogenous chemical mediator of inflammation does not appear to be investigated thoroughly in light of abovementioned biological criterion of mediator. Present study aims at thorough exploration on role of free copper as endogenous chemical mediator of inflammation in light of above facts. It was done by estimation of total copper, protein-bound copper, and free copper along with estimation of free radical generation, increase in vascular permeability, and cellular infiltration during acute inflammatory reaction induced by carrageenan and concanavalin using chicken skin as test model. It was further evaluated by use of exogenous free copper in experimental model and their subsequent inhibition and amplification by chemical chelators of copper. Present study confirms that free copper fulfilled all the biological requirements for accepting it as an endogenous chemical mediator of inflammation.     

Investigation of supplemental ultraviolet-B-induced changes in antioxidative defense system and leaf proteome in radish (Raphanus sativus L. cv Truthful): an insight to plant response under high oxidative stress

Impact of supplemental UV-B (sUV-B) has been investigated on photosynthetic pigments, antioxidative enzymes, metabolites, and protein profiling of radish plants under realistic field conditions. Exposure of sUV-B leads to oxidative damage in plants. However, plants possess a number of UV-protection mechanisms including a stimulation of antioxidant defense system. It caused alteration in reactive oxygen species metabolism primarily by decreasing catalase activity vis-à-vis enhanced activities of other enzymatic (superoxide dismutase, ascorbate peroxidase, and glutathione reductase) and non-enzymatic (ascorbic acid) antioxidants. Qualitative analysis of samples also showed significant reductions in photosynthetic pigments and protein content. After sUV-B exposure, protein profile showed differences mainly at eight points—126.8, 84.8, 71.9, 61.5, 47.8, 40.6, 38.9, and 17.5 kDa, whereas protein(s) of 38.9 kDa showed increment. Results of the present investigation clearly showed the adverse effect of sUV-B on total biomass at final harvest.     

Sparse sampling of water density fluctuations near liquid-vapor coexistence

Abstract

The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterisation of such free energetics is typically performed using enhanced sampling techniques such as umbrella sampling. In umbrella sampling, order parameter distributions obtained from adjacent biased simulations must overlap in order to estimate free energy differences between biased ensembles. Many biased simulations are typically required to ensure such overlap, which exacts a steep computational cost. We recently introduced a sparse sampling method, which circumvents the overlap requirement by using thermodynamic integration to estimate free energy differences between biased ensembles. Here we build upon and generalise sparse sampling for characterising the free energetics of water density fluctuations in systems near liquid-vapor coexistence. We also introduce sensible heuristics for choosing the biasing potential parameters and strategies for adaptively refining them, which facilitate the estimation of such free energetics accurately and efficiently. We illustrate the method by characterising the free energetics of cavitation in a large volume in bulk water. We also use sparse sampling to characterise the free energetics of capillary evaporation for water confined between two hydrophobic plates. In both cases, sparse sampling is nearly two orders of magnitude faster than umbrella sampling. Given its efficiency, the sparse sampling method is particularly well suited for characterising free energy landscapes for systems wherein umbrella sampling is prohibitively expensive.     

155 3D QSAR and protein–protein interaction studies on neuraminidase against Clostridium perfringens: An approach toward target identification using structure-based drug designing

The rapid onset of resistance to new drugs and emergence of antibiotic resistant bacteria has led to resurgence in life-threatening bacterial infections. These problems have revitalized interest in antibiotics and lead to new research. To gain further insight between structural and biological activity of Clostridium perfringens, a gram-positive anaerobe responsible for food poisoning, mynecrosis in wound infections, and enterotoxemia in humans. We have considered various in silico approaches for developing new drug leads, based on small ligand structure. The importance of neuraminidases in the virulence of C. perfringens makes it a potent target for the studies of drug designing against this microbe. Natural products or their direct derivatives play crucial roles in many diseases. In the present study, 3D QSAR analysis using kNN-MFA method was performed on a series of pterocarpan derivatives as Clostridial neuraminidase inhibitors. Twenty-five compounds using random selection and sphere exclusion method for the division of dataset into training and test set were chosen. kNN-MFA methodology with stepwise, simulated annealing and genetic algorithm was used for model building and four predictive models have been generated. The most significant model has a high internal predictivity of 64.80% (q ²?=?0.6480) and an external predictivity of 95.46% (r ²?=?0.9546). Model showed that electrostatic and steric interactions play important role in determining neuraminidase inhibitory activity. The kNN-MFA plots provide further understanding of the relationship between structural features of substituted pterocarpan derivatives and their activities which were applied for designing new compounds as inhibitors. The drug likeliness of these compounds was checked through ADME property prediction and their interaction with the neuraminidase was checked by molecular docking studies. Moreover, analysis of protein–protein interaction network of NanI in C. perfringens was done.     

Mycobacterial STAND adenylyl cyclases: The HTH domain binds DNA to form biocrystallized nucleoids

Mycobacteria harbor a unique class of adenylyl cyclases with a complex domain organization consisting of an N-terminal putative adenylyl cyclase domain fused to a nucleotide-binding adaptor shared by apoptotic protease-activating factor-1, plant resistance proteins, and CED-4 (NB-ARC) domain, a tetratricopeptide repeat (TPR) domain, and a C-terminal helix-turn-helix (HTH) domain. The products of the rv0891c-rv0890c genes represent a split gene pair, where Rv0891c has sequence similarity to adenylyl cyclases, and Rv0890c harbors the NB-ARC-TPR-HTH domains. Rv0891c had very low adenylyl cyclase activity so it could represent a pseudoenzyme. By analyzing the genomic locus, we could express and purify Rv0890c and find that the NB-ARC domain binds ATP and ADP, but does not hydrolyze these nucleotides. Using systematic evolution of ligands by exponential enrichment (SELEX), we identified DNA sequences that bound to the HTH domain of Rv0890c. Uniquely, the HTH domain could also bind RNA. Atomic force microscopy revealed that binding of Rv0890c to DNA was sequence independent, and binding of adenine nucleotides to the protein induced the formation of higher order structures that may represent biocrystalline nucleoids. This represents the first characterization of this group of proteins and their unusual biochemical properties warrant further studies into their physiological roles in future.     

Impact of ambient and supplemental ultraviolet-B stress on kidney bean plants: an insight into oxidative stress management

In the present study, the response of kidney bean (Phaseolus vulgaris L. cv. Pusa Komal) plants was evaluated under three different levels of ultraviolet-B (UV-B), i.e., excluded UV-B (eUV-B), ambient UV-B (aUV-B; 5.8 kJ m^?2 day^?1), and supplemental UV-B (sUV-B; 280–315 nm; ambient?+?7.2 kJ m^?2 day^?1), under near-natural conditions. eUV-B treatment clearly demonstrated that both aUV-B and sUV-B are capable of causing significant changes in the plant’s growth, metabolism, economic yield, genome template stability, total protein, and antioxidative enzyme profiles. The experimental findings showed maximum plant height at eUV-B, but biomass accumulation was minimum. Significant reductions in quantum yield (Fv/Fm) were observed under both aUV-B and sUV-B, as compared to eUV-B. UV-B-absorbing flavonoids increased under higher UV-B exposures with consequent increments in phenylalanine ammonia lyase (PAL) activities. The final yield was significantly higher in plants grown under eUV-B, compared to those under aUV-B and sUV-B. Total protein profile through sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and analysis of isoenzymes, like superoxide dismutase (SOD), peroxidase (POX), catalase (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (GPX), and glutathione reductase (GR), through native PAGE revealed major changes in the leaf proteome under aUV-B and sUV-B, depicting induction of some major stress-related proteins. The random amplified polymorphic DNA (RAPD) profile of genomic DNA also indicated a significant reduction of genome template stability under UV-B exposure. Thus, it can be inferred that more energy is diverted for inducing protection mechanisms rather than utilizing it for growth under high UV-B level.