Role Of Biomolecules Research Articles

Fluorescent Compounds Having the Spaced and Integrated Type Receptors

Fluorescent receptors have gained much attention because of their usefulness in analysis and clarification of the roles of biomolecules in living systems. Molecular structures of the integrated type including that the receptor itself is fluorescent, and play an important role in having the functionality or selectivity of the fluorescent compounds. These spaced type fluorescent receptors are required to have special molecular design in order to transmit the information of molecular recognition to the fluorescent unit through the spacer unit. Compared with the spaced type fluorescent receptors, number of the integrated type receptors is limited due to the difficult molecular design and synthesis. Modification of alteration of the fluorophore frequently caused deterioration of the fluorescent property. Various spaced type and integrated type fluorescent receptors including switch on-off receptors are introduced in this article.

Biomimetic Synthesis of Silver Nanoparticles Using Endosymbiotic Bacterium InhabitingEuphorbia hirtaL. and Their Bactericidal Potential

The present investigation aims to evaluate biomimetic synthesis of silver nanoparticles using endophytic bacterium EH 419 inhabiting Euphorbia hirta L. The synthesized nanoparticles were initially confirmed with change in color from the reaction mixture to brown indicating the synthesis of nanoparticles. Further confirmation was achieved with the characteristic absorption peak at 440 nm using UV-Visible spectroscopy. The synthesized silver nanoparticles were subjected to biophysical characterization using hyphenated techniques. The possible role of biomolecules in mediating the synthesis was depicted with FTIR analysis. Further crystalline nature of synthesized nanoparticles was confirmed using X-ray diffraction (XRD) with prominent diffraction peaks at 2θ which can be indexed to the (111), (200), (220), and (311) reflections of face centered cubic structure (fcc) of metallic silver. Transmission electron microscopy (TEM) revealed morphological characteristics of synthesized silver nanoparticles to be polydisperse in nature with size ranging from 10 to 60 nm and different morphological characteristics such as spherical, oval, hexagonal, and cubic shapes. Further silver nanoparticles exhibited bactericidal activity against panel of significant pathogenic bacteria among which Pseudomonas aeruginosa was most sensitive compared to other pathogens. To the best of our knowledge, present study forms first report of bacterial endophyte inhabiting Euphorbia hirta L. in mediating synthesizing silver nanoparticles.

Extracellular synthesis of silver nanoparticles by novel Pseudomonas veronii AS41G inhabiting Annona squamosa L. and their bactericidal activity

In present investigation extracellular synthesis of silver nanoparticles were synthesized using cell free supernatant of Pseudomonas veronii AS41G isolated from Annona squamosa L. The bacterium significantly reduced silver nitrate to generate silver nanoparticles which was characterized with hyphenated techniques. Synthesis of silver nanoparticles preliminary confirmed by UV–Visible spectrophotometry with the intense peak at 410nm, Further FTIR analysis revealed the possible role of biomolecules in the supernatant responsible for mediating the nanoparticles formation. The XRD spectra exhibited the characteristic Bragg peaks of 100, 111, 200, and 220 facets of the face centred cubic symmetry of nanoparticles suggesting that these nanoparticles were crystalline in nature. TEM microgram showed polydispersity of nanoparticles with size ranging from 5 to 50nm. Synthesized silver nanoparticles showed antibacterial activity against human and environmental pathogens including MRSA. The study enlightens the role of biosynthesized silver nanoparticles as an emerging alternative for drug resistant microorganisms. The obtained results are promising enough to pave the environmentally benign nanoparticle synthesis processes without use of any toxic chemicals and also envision the emerging role of endophytes towards synthesis of nanoparticles. With scanty reports available on P.veronii species, a new role has been reported in this study which will be very valuable for future researchers working on it.

Role of biomolecules on annulus fibrosus micromechanics: Effect of enzymatic digestion on elastic and failure properties

Uniaxial tension was applied to selectively digested single lamellar human cadaveric annulus fibrosus specimens to investigate the role of different biomolecules in annular biomechanics. Single layered and inter-lamellar annulus fibrosus samples were obtained from 10 isolated cadaveric lumbar intervertebral discs in one of four orientations: longitudinal, transverse, radial, and circumferential. Within each orientation the samples were subjected to a selective enzymatic digestion protocol with collagenase, elastase, chondroitinase ABC, or 1× Phosphate Buffered Saline. Uniaxial tensile tests were performed to failure at a strain rate of 0.005s−1. Failure stress and strain, and elastic moduli were compared among the digested conditions. The collagenase- and elastase-treated groups had the most significant effect on the mechanical properties among the orientation groups, decreasing the failure stress for both interlaminar and intralaminar groups. Collagenase-treated groups showed an increase in the failure strain following enzymatic digestion for the intralaminar groups and one interlaminar testing direction (circumferential). The chondroitinase ABC-treated group only had a significant impact on the single layer orientations, decreasing the failure stress and strain (intralaminar group). The digested properties described provide insights into the laminar mechanical behavior and the role of the molecular components to the annular mechanical behavior. Understanding annular mechanics may prove insightful in diagnosis, prevention and repair of debilitating intervertebral disc disorders and manufacturing of tissue-engineered annulus.

Roles of Biomolecules in the Biosynthesis of Silver Nanoparticles: Case of Gardenia jasminoides Extract

Rapid development of biosynthesis of metal nanoparticles using plants has attracted extensive interests to further investigate this novel and eco-friendly method. In the biosynthesis process, the plant may act as reducing agent, capping agent or shape directing agent. However, identifying specific roles of various components in the plant is challenging. In this study, we use biosynthesis of silver nanoparticles with Gardenia jasminoides Ellis extract to address this issue. The formation process of silver nanoparticles is investigated and the nanoparticles are characterized with the ultraviolet-visible spectroscopy, Fourier transform infrared spectra and scanning electron microscopy. The results indicate that the Gardenia jasminoides Ellis extract can reduce silver ions to form silver nanoparticles, stabilize the nanoparticles, and affect the growth of silver nanocrystal to form silver nanowires. Only geniposide in the extract exhibits good shape-directing ability for silver nanowires. It is found that bovine albumin is a potential capping agent, whereas rutin, gallic acid and chlorogenic acid possess reducing and capping ability.

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π-π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained.

Biomimetically Triggered Inorganic Crystal Transformation by Biomolecules: A New Understanding of Biomineralization

Phase transformation is an important strategy in biomineralization. However, the role of biomolecules in the mineral transition is poorly understood despite the fact that the biomineralization society greatly highlights the organic controls in the formation of the inorganic phase. Here, we report an induced biomimetic phase transformation from brushite (a widely used calcium phosphate precursor in biological cement) to hydroxyapatite (main inorganic composition of skeletal mineral) by citrate (a rich organic component in bone tissue). The transformation in the absence of the organic additive cannot be spontaneously initiated in an aqueous solution with a pH of 8.45 (no phase transition is detected in 4 days), which is explained by a high interfacial energy barrier between brushite-solution and hydroxyapatite-solution interfaces. Citrate can oppositely regulate these two interfaces, which decreases and increases the stabilities of brushite and hydroxyapatite surfaces in the solution, respectively. Thus, the interfacial energy barrier can be greatly reduced in the presence of citrate and the reaction is triggered; e.g., at 1 mM citrate, the total transformation from brushite to hydroxyapatite can be completed within 3 days. The relationship between the transition kinetics and citrate concentration is also studied. The work reveals how the organic components direct solid-solid phase transformation, which can be understood by an energetic control of the interfacial barrier. It is emphasized that the terms of interfacial energy must be taken into account in the studies of phase transformation. We suggest that this biomimetic approach may provide an in-depth understanding of biomineralization.

Analysis of Sulfur Metasecretome in Mixed Cultures of Acidithiobacillus Thiooxidans and Acidithiobacillus Ferrooxidans

The role of biomolecules in bioleaching of copper sulphide minerals carried out by bacterial consortia with predominating acidithiobacilli species is of outmost interest. The proteomic analysis on bioleaching bacterial strains have been focused up to date on full Acidithiobacillus ferrooxidans proteome, allowing the identification of proteins belonging to the general stress response, phosphate limiting conditions and the ones linked to the periplasmic fraction. Our study shows for the first time the differential expression of secreted proteins by means of standard proteomics between pure cultures of Acidithiobacillus thiooxidans and in mixture with A. ferroxidans (metasecretome) grown in sulfur, where a set of proteins is de novo synthesized in the mixed culture, identifying an Omp40-like protein possibly related to bacterial adhesion, an hypothetical protein PSEEN2944 with unknown function and up-regulation of a cytochrome c biogenesis protein, findings that give an insight into the role of proteins at the sulfur – bacteria interface, highlighting the outputs of bacterial interactions in biomining environments at the protein secretion level.

Limits of life in MgCl2‐containing environments: chaotropicity defines the window

The biosphere of planet Earth is delineated by physico-chemical conditions that are too harsh for, or inconsistent with, life processes and maintenance of the structure and function of biomolecules. To define the window of life on Earth (and perhaps gain insights into the limits that life could tolerate elsewhere), and hence understand some of the most unusual biological activities that operate at such extremes, it is necessary to understand the causes and cellular basis of systems failure beyond these windows. Because water plays such a central role in biomolecules and bioprocesses, its availability, properties and behaviour are among the key life-limiting parameters. Saline waters dominate the Earth, with the oceans holding 96.5% of the planet's water. Saline groundwater, inland seas or saltwater lakes hold another 1%, a quantity that exceeds the world's available freshwater. About one quarter of Earth's land mass is underlain by salt, often more than 100 m thick. Evaporite deposits contain hypersaline waters within and between their salt crystals, and even contain large subterranean salt lakes, and therefore represent significant microbial habitats. Salts have a major impact on the nature and extent of the biosphere, because solutes radically influence water's availability (water activity) and exert other activities that also affect biological systems (e.g. ionic, kosmotropic, chaotropic and those that affect cell turgor), and as a consequence can be major stressors of cellular systems. Despite the stressor effects of salts, hypersaline environments can be heavily populated with salt-tolerant or -dependent microbes, the halophiles. The most common salt in hypersaline environments is NaCl, but many evaporite deposits and brines are also rich in other salts, including MgCl(2) (several hundred million tonnes of bischofite, MgCl(2).6H(2)O, occur in one formation alone). Magnesium (Mg) is the third most abundant element dissolved in seawater and is ubiquitous in the Earth's crust, and throughout the Solar System, where it exists in association with a variety of anions. Magnesium chloride is exceptionally soluble in water, so can achieve high concentrations (> 5 M) in brines. However, while NaCl-dominated hypersaline environments are habitats for a rich variety of salt-adapted microbes, there are contradictory indications of life in MgCl(2)-rich environments. In this work, we have sought to obtain new insights into how MgCl(2) affects cellular systems, to assess whether MgCl(2) can determine the window of life, and, if so, to derive a value for this window. We have dissected two relevant cellular stress-related activities of MgCl(2) solutions, namely water activity reduction and chaotropicity, and analysed signatures of life at different concentrations of MgCl(2) in a natural environment, namely the 0.05-5.05 M MgCl(2) gradient of the seawater : hypersaline brine interface of Discovery Basin - a large, stable brine lake almost saturated with MgCl(2), located on the Mediterranean Sea floor. We document here the exceptional chaotropicity of MgCl(2), and show that this property, rather than water activity reduction, inhibits life by denaturing biological macromolecules. In vitro, a test enzyme was totally inhibited by MgCl(2) at concentrations below 1 M; and culture medium with MgCl(2) concentrations above 1.26 M inhibited the growth of microbes in samples taken from all parts of the Discovery interface. Although DNA and rRNA from key microbial groups (sulfate reducers and methanogens) were detected along the entire MgCl(2) gradient of the seawater : Discovery brine interface, mRNA, a highly labile indicator of active microbes, was recovered only from the upper part of the chemocline at MgCl(2) concentrations of less than 2.3 M. We also show that the extreme chaotropicity of MgCl(2) at high concentrations not only denatures macromolecules, but also preserves the more stable ones: such indicator molecules, hitherto regarded as evidence of life, may thus be misleading signatures in chaotropic environments. Thus, the chaotropicity of MgCl(2) would appear to be a window-of-life-determining parameter, and the results obtained here suggest that the upper MgCl(2) concentration for life, in the absence of compensating (e.g. kosmotropic) solutes, is about 2.3 M.

Role of biomolecules from human renal stone matrix on COM crystal growth.

Human renal calculi surgically removed from kidney stone patients were obtained and chemically analysed. Stones with CaOx (calcium oxalate) as the major component were washed in 0.15 M NaCl with gentle stirring for 48 h and then pulverised to a fine powder. The powder was extracted with 0.05 M EGTA, 1 mM PMSF and 1% beta-mercaptoethanol for 4 days at 4 degrees C, the suspensions and the supernatants obtained were filtered through an Amicon Model 200 apparatus (mol. wt. cut off of 10,000 daltons) under nitrogen at 40 p.s.i. and concentrated to a known volume. The method of Nakagawa et al. [7] was employed to study the ability of > 10 kDa fractions to influence COM growth using metastable solution of CaCl2 and Na2C2O4 containing traces of 14C-oxalic acid. Potent biomolecules having the ability to influence CaOx precipitation were subjected to isolation, purification and characterization. Standard biochemical procedures, e.g. ultracentrifugation, ion-exchange chromatography, molecular sieve chromatography and SDS-PAGE, etc., were employed. Results revealed that human renal calculi extract contains biomolecules that can inhibit as well as stimulate the growth of preformed COM (calcium oxalate monohydrate) crystals. Most potent stimulator of CaOx growth was found to have a molecular weight of 66 kDa.