Slow irreversible unfolding of Pyrococcus furiosus triosephosphate isomerase: separation and quantitation of conformers through a novel electrophoretic approach

The thermostability of hyperthermophile proteins is not easily studied because such proteins tend to be extremely recalcitrant to unfolding. Weeks of exposure to structurally destabilizing conditions are generally required to elicit any evidence of conformational change(s). The main reason for this extreme kinetic stability would appear to be the dominance of local unfolding transitions that occur within different parts of the structures of these molecules; put differently, local sub structural unfolding transitions that occur autonomously and reversibly are thought to fail to cooperate to bring about global unfolding in a facile manner, leading to a low overall observed rate of unfolding. For reasons that are not yet fully understood, unfolding is also reported to occur irreversibly in hyperthermophile proteins. Therefore, conventional experimental approaches are often unsuited to the study of their unfolding. Here, we describe a novel electrophoretic approach that facilitates separation, direct visualization, and quantitation of the folded, partially folded, and unfolded forms of the hyperthermophile protein triosephosphate isomerase from Pyrococcus furiosus, produced in the course of its irreversible structural destabilization by the combined action of heat and chemical agents. Our approach exploits (i) the irreversibility of global unfolding effected by heat and denaturants such as urea or guanidine hydrochloride, (ii) the stability of the native form of the protein to unfolding by the anionic detergent sodium dodecyl sulfate, (iii) the differential susceptibilities of various protein conformations to being bound by SDS, and (iv) the differential electrophoretic migration behavior displayed as a consequence of differential SDS binding.     

Diversity,Antimicrobial Action and Structure-Activity Relationship of Buffalo Cathelicidins

Cathelicidins are an ancient class of antimicrobial peptides (AMPs) with broad spectrum bactericidal activities. In this study, we investigated the diversity and biological activity of cathelicidins of buffalo, a species known for its disease resistance. A series of new homologs of cathelicidin4 (CATHL4), which were structurally diverse in their antimicrobial domain, was identified in buffalo. AMPs of newly identified buffalo CATHL4s (buCATHL4s) displayed potent antimicrobial activity against selected Gram positive (G+) and Gram negative (G-) bacteria. These peptides were prompt to disrupt the membrane integrity of bacteria and induced specific changes such as blebing, budding, and pore like structure formation on bacterial membrane. The peptides assumed different secondary structure conformations in aqueous and membrane-mimicking environments. Simulation studies suggested that the amphipathic design of buCATHL4 was crucial for water permeation following membrane disruption. A great diversity, broad-spectrum antimicrobial action, and ability to induce an inflammatory response indicated the pleiotropic role of cathelicidins in innate immunity of buffalo. This study suggests short buffalo cathelicidin peptides with potent bactericidal properties and low cytotoxicity have potential translational applications for the development of novel antibiotics and antimicrobial peptidomimetics.     

Computational strategies for understanding the nature of interaction in dioxin imprinted nanoporous trappers

A new computational model capable of understanding the nature of interactions in signature complexes formed between the template (2,3,7,8‐tetrachlorodibenzo‐p dioxin (TCDD)) and the functional monomers (methacrylic acid (MAA)) using density functional theory (DFT) has been designed. The polymer precursors were optimized for geometries in polymerization media, computing the interaction energies between template molecules and functional monomers of transient pre‐polymerized complexes (PPC), and structural and vibrational properties reference to theoretical infrared spectra were computed using DFT of B3LYP/6 311+G(d,p) hybrid functional method. Atom in molecule theory was used to analyze the hydrogen‐bonding characteristics of PPC of MAA–TCDD. Considering the theoretical titrations conducted in a virtual solvent box, it was found that the 1:4 molar ratio was required to form the most stable PPC in a given solvent system. The electron density plots indicate strong hydrogen bonding as shown by the 2pz dominant highest occupied molecular orbital (HOMO) character that could be the preferable sites of binding for target molecule, TCDD. Considering HOMO approach, the active adsorption sites in molecularly imprinted polymer was modeled to get insight on molecular recognition property for targeted molecule, TCDD. The proposed computational protocol is simple, accurate, and novel to design the polymer and is useful to predict the properties of polymer systems than the conventional theoretical analysis of template–monomer interactions. Copyright © 2015 John Wiley & Sons, Ltd.     

Monopolin Subunit Csm1 Associates with MIND Complex to Establish Monopolar Attachment of Sister Kinetochores at Meiosis I

Sexually reproducing organisms halve their cellular ploidy during gametogenesis by undergoing a specialized form of cell division known as meiosis. During meiosis, a single round of DNA replication is followed by two rounds of nuclear divisions (referred to as meiosis I and II). While sister kinetochores bind to microtubules emanating from opposite spindle poles during mitosis, they bind to microtubules originating from the same spindle pole during meiosis I. This phenomenon is referred to as mono-orientation and is essential for setting up the reductional mode of chromosome segregation during meiosis I. In budding yeast, mono-orientation depends on a four component protein complex referred to as monopolin which consists of two nucleolar proteins Csm1 and Lrs4, meiosis-specific protein Mam1 of unknown function and casein kinase Hrr25. Monopolin complex binds to kinetochores during meiosis I and prevents bipolar attachments. Although monopolin associates with kinetochores during meiosis I, its binding site(s) on the kinetochore is not known and its mechanism of action has not been established. By carrying out an imaging-based screen we have found that the MIND complex, a component of the central kinetochore, is required for monopolin association with kinetochores during meiosis. Furthermore, we demonstrate that interaction of monopolin subunit Csm1 with the N-terminal domain of MIND complex subunit Dsn1, is essential for both the association of monopolin with kinetochores and for monopolar attachment of sister kinetochores during meiosis I. As such this provides the first functional evidence for a monopolin-binding site at the kinetochore.     

Patterns of morphological traits shaping the feeding guilds in the intertidal mudflat fishes of the Indian Sundarbans

Broad-scale patterns of resource utilization and the corresponding morphological evolution is a result of an integral relationship among form and function. In addition, there is also an inherent role of the latter in determining species co-interaction and assemblage pattern that forms an integral aspect of ecological research. The present study aimed to evaluate the ecomorphological relationship among 37 fish species inhabiting the intertidal mudflats of the Indian Sundarbans by outlining the following objectives: (i) identifying and characterizing feeding guilds/groups and (ii) understanding the inter-relationship between morphometry with (a) the established feeding guild classifications and (b) observed prey taxa (that characterizes these feeding groups) for determining the role of morphometry in prey acquisition followed by (iii) the evaluation of their potential phylogenetic convergence among the species. For the first objective, two approaches for feeding guild classification were made (3-Guild and 8-Guild) for assessing the prediction accuracy of morphological characters in identifying the different guilds. While the former was based on troph values, the latter classification mode relied on the similarities in diet composition among the different fish species. For addressing the second objective, we employed two different models namely, linear discriminant (LDA) and redundancy analysis (RDA). While the LDA model tested the prediction accuracy of morphological traits in classifying the different feeding guilds, RDA was applied to model the correlation between the morphological traits and the prey categories. In the LDA model, morphological characters showed higher accuracy (78.4%) in classifying three feeding groups rather than eight feeding groups (73%). Following this, the RDA model (explaining 79.78% of constrained variance) showed gill raker intensity, protrusion length, head depth, caudal peduncle, eye diameter and inter-orbital distance to be highly associated with selection of specific prey types by species, thereby characterizing a particular feeding guild. However, generalized linear models testing for correlation between troph value and feeding groups showed substantial variation (90.35%) in the dietary index being explained by the 8-Guild classification. Hence, our study maintains the assumption that broad morphological differentiation acts as one of the underlying processes resulting in dietary variations that results in the varying modes of resource utilization by the coexisting species, thereby determining the structure of a trophic guild. Furthermore, it also suggests that in terms of prey abundance or selectivity, the 8-Guild model is much more conducive in representing the feeding habits of the species while the morphological traits reflected a relatively broader scheme of classification, (i.e., 3-Guild model) with certain traits being phylogenetically conserved within these groups.     

Light signaling and UV‐B‐mediated plant growth regulation

Light plays an important role in plants’ growth and development throughout their life cycle. Plants alter their morphological features in response to light cues of varying intensity and quality. Dedicated photoreceptors help plants to perceive light signals of different wavelengths. Activated photoreceptors stimulate the downstream signaling cascades that lead to extensive gene expression changes responsible for physiological and developmental responses. Proteins such as ELONGATED HYPOCOTYL5 (HY5) and CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) act as important factors which modulate light‐regulated gene expression, especially during seedling development. These factors function as central regulatory intermediates not only in red, far‐red, and blue light pathways but also in the UV‐B signaling pathway. UV‐B radiation makes up only a minor fraction of sunlight, yet it imparts many positive and negative effects on plant growth. Studies on UV‐B perception, signaling, and response in plants has considerably surged in recent times. Plants have developed different strategies to use UV‐B as a developmental cue as well as to withstand high doses of UV‐B radiation. Plants’ responses to UV‐B are an integration of its cross‐talks with both environmental factors and phytohormones. This review outlines the current developments in light signaling with a major focus on UV‐B‐mediated plant growth regulation.     

Antivascular therapy for multidrug-resistant ovarian tumors by macitentan, a dual endothelin receptor antagonist

Endothelin receptors (ETRs) are often overexpressed in ovarian tumors, which can be resistant to conventional therapies. Thus, we investigated whether blockage of the ETR pathways using the dual ETR antagonist macitentan combined with taxol or cisplatinum can produce therapy for orthotopically growing multidrug-resistant (MDR) human ovarian carcinoma. In several studies, nude mice were injected in the peritoneal cavity with HeyA8-MDR human ovarian cancer cells. Ten days later, mice were randomized to receive vehicle (saline), macitentan (oral, daily), taxol (intraperitoneal, weekly), cisplatinum (intraperitoneal, weekly), macitentan plus taxol, or macitentan plus cisplatinum. Moribund mice were killed, and tumors were collected, weighed, and prepared for immunohistochemical analysis. The HeyA8-MDR tumors did not respond to taxol, cisplatinum, or macitentan administered as single agents. In contrast, combination therapy with macitentan and taxol or macitentan and cisplatinum significantly decreased the tumor incidence and weight and significantly increased the survival of mice and their general condition. Multiple immunohistochemical analyses revealed that treatment with macitentan and macitentan plus taxol or cisplatinum inhibited the phosphorylation of ETRs, decreased the levels of pVEGFR2, pAkt, and pMAPK in tumor cells after 2 weeks of treatment and induced a first wave of apoptosis in tumor-associated endothelial cells followed by apoptosis in surrounding tumor cells. Our study shows that ovarian cancer cells, which express the endothelin axis and are multidrug resistant, are exquisitely sensitive to treatment with a dual ET antagonist and can be resensitized to both taxol and cisplatinum. This combined therapy led to a significant reduction in tumor weight.