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Nitric oxide (NO) is the first ubiquitous signaling molecule in the human body. The selective and sensitive detection of NO in vitro and in vivo is of high importance but remains challenging. Previous fluorescent probes for NO detection either are of poor water solubility or lack selectivity over intracellular biomolecules. Herein, we rationally designed a water-soluble, biocompatible, small molecular probe o-phenylenediamine-Phe-Phe-OH (1) for the highly selective and sensitive detection of NO in vitro and in living cells. 1 can react with NO and turn on the fluorescence emission at 367 nm via an ICT mechanism. In vitro tests indicated that 1 showed high selectivity for NO detection without interference from common anions, ROS/RNS, and intracellular biomolecules DHA, AA, or MGO. In PBS buffer, 1 was applied for detecting NO within the range of 0–12 μM with a LOD of 6 nM. Moreover, 1 was successfully applied to sense intracellularly generated NO in living cells. We anticipate that 1 could be potentially employed for studying the toxicity and bioactivity of NO in the near future. [ABSTRACT FROM AUTHOR]

Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex. [ABSTRACT FROM AUTHOR]

The present study aimed to evaluate a label-free tissue test for the detection of nasopharyngeal carcinoma (NPC) at early and advanced stages using Raman spectroscopy (RS). RS measurements were performed to acquire high quality Raman spectra on two groups of tissue samples: One group consists of 30 NPC patients at the early stages (I-II), and the other group is 46 NPC patients at the advanced stages (III-IV). Tentative assignment of Raman bands showed specific biomolecular changes associated with cancer development. Furthermore, effective diagnostic algorithms based on principal components analysis (PCA) and linear discriminant analysis (LDA) were applied for distinguishing Raman spectra of nasopharyngeal tissues from different stages, yielding a diagnostic sensitivity of 70% and a specificity of 78%. This exploratory work suggests that RS in conjunction with the PCA-LDA algorithms provides good diagnostic ability for the early and the advanced staged NPC tissues, and RS has enormous potential for the non-invasive detection of early and advanced stage NPC. [ABSTRACT FROM AUTHOR]

Primary free radicals generated under oxidative stress in cells and tissues produce a cascade of reactive secondary radicals, which attack biomolecules with efficiency determined by the reaction rate constants and target concentration. Proteins are prominent targets because they constitute the bulk of the organic content of cells and tissues and react readily with many of the secondary radicals. The reactions commonly lead to the formation of carbon-centered radicals, which generally convert in vivo to peroxyl radicals and finally to semistable hydroperoxides. All of these intermediates can initiate biological damage. This article outlines the advantages of the application of ionizing radiations to studies of radicals, with particular reference to the generation of desired radicals, studies of the kinetics of their reactions and correlating the results with events in biological systems. In one such application, formation of protein hydroperoxides in irradiated cells was inhibited by the intracellular ascorbate and glutathione. [ABSTRACT FROM AUTHOR]

The present study focuses on the green synthesis of silver nanoparticles using aqueous extract of Cardiospermum halicacabum. AgNPs were confirmed by UV-Visible spectrophotometer analysis showed SPR at 424 nm. FT-IR analysis revealed biomolecules capping of the AgNPs. XRD pattern of synthesized AgNPs was found in face-centered-cubic crystal structure and average crystal size was 23 nm. SEM analyses of the synthesized AgNPs determine the spherical shape and EDX spectra confirmed the presence of silver ions. DLS studies revealed that the synthesized AgNPs showed the average size as 74 nm and Zeta potential value of AgNPs was −34 mv. The C. halicacabum leaf extract synthesized AgNPs efficiency were tested against different bacterial pathogens MTCC-426 Proteus vulgaris, MTCC-2453 Pseudomonas aeruginosa, MTCC-96 Staphylococcus aureus, MTCC-441 Bacillus subtilis and MTCC-735 Salmonella paratyphi, and fungal pathogens Alternaria solani and Fusarium-oxysporum. The antioxidant ability of the AgNPs was tested and the results showed significant DPPH, hydroxyl and superoxide, radical scavenging activities. [ABSTRACT FROM AUTHOR]

The use of DNA as a material has opened up new possibilities in the field of nanobiotechnology. Specifically, DNA origami - a technique in which one long single-stranded DNA scaffold is folded into nanoscale shapes and structures using hundreds of short 'staple' oligonucleotides - has contributed to new innovations within this field. Nanostructures created using DNA origami have found use in applications such as biosensing, triggered drug delivery, enzyme cascades and biomolecular analysis platforms. The unmatched features of DNA nanostructures such as cell permeability, biocompatibility, and spatial positioning have contributed to DNA origami playing an important role in the development of materials for biotechnology applications. © 2015 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

The molecular characterization of the air/water interface is a key step in understanding fundamental multiphase phenomena ranging from heterogeneous chemical processes in the atmosphere to the hydration of biomolecules. The apparent simplicity of the air/water interface, however, masks an underlying complexity associated with the dynamic nature of the water hydrogen-bond network that has so far hindered an unambiguous characterization of its microscopic properties. Here, we demonstrate that the application of quantum many-body molecular dynamics, which enables spectroscopically accurate simulations of water from the gas to the condensed phase, leads to a definitive molecular-level picture of the interface region. For the first time, excellent agreement is obtained between the simulated vibrational sum-frequency generation spectrum and the most recent state-of-the-art measurements, without requiring any empirical frequency shift or ad hoc scaling of the spectral intensity. A systematic dissection of the spectral features demonstrates that a rigorous representation of nuclear quantum effects as well as of many-body energy and electrostatic contributions is necessary for a quantitative reproduction of the experimental data. The unprecedented accuracy of the simulations presented here indicates that quantum many-body molecular dynamics can enable predictive studies of aqueous interfaces, which by complementing analogous experimental measurements will provide unique molecular insights into multiphase and heterogeneous processes of relevance in chemistry, biology, materials science, and environmental research. [ABSTRACT FROM AUTHOR]

Fossil biomolecules from an endogenous source were previously identified in Cretaceous to Pleistocene fossilized bones, the evidence coming from molecular analyses. These findings, however, were called into question and an alternative hypothesis of the invasion of the bone by bacterial biofilm was proposed. Herewith we report a new finding of morphologically preserved blood-vessel-like structures enclosing organic molecules preserved in iron-oxide-mineralized vessel walls from the cortical region of nothosaurid and tanystropheid (aquatic and terrestrial diapsid reptiles) bones. These findings are from the Early/Middle Triassic boundary (Upper Roetian/Lowermost Muschelkalk) strata of Upper Silesia, Poland. Multiple spectroscopic analyses (FTIR, ToF-SIMS, and XPS) of the extracted "blood vessels" showed the presence of organic compounds, including fragments of various amino acids such as hydroxyproline and hydroxylysine as well as amides, that may suggest the presence of collagen protein residues. Because these amino acids are absent from most proteins other than collagen, we infer that the proteinaceous molecules may originate from endogenous collagen. The preservation of molecular signals of proteins within the "blood vessels" was most likely made possible through the process of early diagenetic iron oxide mineralization. This discovery provides the oldest evidence of in situ preservation of complex organic molecules in vertebrate remains in a marine environment. [ABSTRACT FROM AUTHOR]

Although synaptic plasticity in neural circuits is orchestrated by an ocean of genes, molecules, and proteins, the underlying mechanisms remain poorly understood. Recently, it is well acknowledged that miRNA exerts widespread regulation over the translation and degradation of target gene in nervous system. Increasing evidence suggests that quite a few specific miRNAs play important roles in various respects of synaptic plasticity including synaptogenesis, synaptic morphology alteration, and synaptic function modification. More importantly, the miRNA-mediated regulation of synaptic plasticity is not only responsible for synapse development and function but also involved in the pathophysiology of plasticity-related diseases. A review is made here on the function of miRNAs in governing synaptic plasticity, emphasizing the emerging regulatory role of individual miRNAs in synaptic morphological and functional plasticity, as well as their implications in neurological disorders. Understanding of the way in which miRNAs contribute to synaptic plasticity provides rational clues in establishing the novel therapeutic strategy for plasticity-related diseases. [ABSTRACT FROM AUTHOR]

Enzyme Linked Immunosorbent Assay (ELISA) is the gold standard assay for detecting and identifying biomolecules using antibodies as the probe. Improving ELISA is crucial for detecting disease-causing agents and facilitating diagnosis at the early stages of disease. Biotinylated antibody and streptavidin-conjugated horse radish peroxide (streptavidin-HRP) often are used with ELISA to enhance the detection of various kinds of targets. In the present study, we used a competition-based strategy in which we pre-mixed free biotin with streptavidin-HRP to generate high-performance system, as free biotin occupies some of the biotin binding sites on streptavidin, thereby providing more chances for streptavidin-HRP to bind with biotinylated antibody. ESAT-6, which is a protein secreted early during tuberculosis infection, was used as the model target. We found that 8 fM of free biotin mixed with streptavidin-HRP anchored the higher detection level of ESAT-6 by four-fold compared with detection without free biotin (only streptavidin-HRP), and the limit of detection of the new method was 250 pM. These results suggest that biotin-streptavidin competition can be used to improve the diagnosis of analytes in other types of sensors. [ABSTRACT FROM AUTHOR]

We briefly review experimental and computational studies of room temperature ionic liquids (RTILs) interacting with important classes of biomolecules, including phospholipids, peptides and proteins, nucleic acids and carbohydrates. Most of these studies have been driven by the interest for RTILs applications as solvents. Thus, available experimental data cover primarily thermodynamic properties such as the reciprocal solubility of RTILs and bio-molecules, as well as phase boundaries. Less extensive data are also available on transport properties such as diffusion and viscosity of homogeneous binary (RTILs/biomolecules) and ternary (RTIL/biomolecules/water) solutions. Most of the structural information at the atomistic level, of interest especially for biochemical, pharmaceutical and nanotechnology applications, has been made available by molecular dynamics simulations. Major exceptions to this statement are represented by the results from NMR and circular dichroism spectroscopy, by selected neutron and X-ray scattering data, and by recent neutron reflectometry measurements on lipid bilayers on surfaces, hydrated by water-RTIL solutions. A final section of our paper summarizes new developments in the field of RTILs based on amino acids, that combine in themselves the two main aspects of our discussion, i.e. ionic liquids and bio-molecules. [ABSTRACT FROM PUBLISHER]

A simple and rapid method for detection of potassium ion (K) based on a guanine chemiluminescence (CL) system is presented. In this system, one guanine-rich DNA molecule is used as the recognition element. K can cause the guanine-rich DNA to form a G-quadruplex conformation, resulting in remarkable quenching of the guanine CL intensity of guanine-rich DNA. The CL intensity of this CL system decreased with increasing K concentration, revealing a linear relationship in K concentration range from 3 × 10 to 1 × 10 M. A complete detection process can be accomplished in about 5 min. Other common cations (such as Na, NH, Mg, Ca, Zn, and Pb) did not notably interfere with K detection. The mechanism of this strategy is also discussed. The sensing strategy is low cost and simple without the requirement of complex labeling of probe DNA. The scheme is applicable to the detection of other guanine-rich aptamer-binding chemicals or biomolecules. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

14-aryl-14H-dibenzo[a,j]xanthenes are extensively used as dyes, pH-sensitive fluorescent material for visualization of biomolecules, and in laser technologies. The synthesis of aryl-14H-dibenzo[a,j]xanthene derivatives is studied using acid activated clay as reusable eco-friendly catalyst under solvent free condition. The reaction is carried out by hydrochloric acid activated clay. Clay is supplied from Kheirabad mine in Kerman province, Iran. Activation is done by 1, 2, 3, and 5 mol/L HCl. Among these catalysts, clay activated by 3 mol/L HCl was found to be a better catalyst which could be reused without any further chemical treatment eliminating the effluent disposal problems. The procedure offers advantages such as shorter reaction time, excellent yields, inexpensive catalyst, environment-friendly, and reusability of catalyst. The reaction obeys the Eley–Rideal type of mechanism. A theoretical kinetic model was developed for the evaluation of this slurry reaction. The effects of various parameters on the rate of reaction were evaluated. The reaction was found to be intrinsically controlled and there were no intraparticle as well as interaparticle mass transfer limitation on the rate of reaction. [ABSTRACT FROM PUBLISHER]

As is well-known, graphene shows a remarkable difference in affinity toward nonstructured single-stranded (ss) DNA and double-stranded (ds) DNA. This property makes it popular to prepare DNA-based optical sensors. In this work, taking this unique property of graphene in combination with the sensitive electrochemical transducer, we report a novel affinity-mediated homogeneous electrochemical aptasensor using graphene modified glassy carbon electrode (GCE) as the sensing platform. In this approach, the specific aptamer-target recognition is converted into an ultrasensitive electrochemical signal output with the aid of a novel T7 exonuclease (T7Exo)-assisted target-analog recycling amplification strategy, in which the ingeniously designed methylene blue (MB)-labeled hairpin DNA reporters are digested in the presence of target and, then, converted to numerous MB-labeled long ssDNAs. The distinct difference in differential pulse voltammetry response between the designed hairpin reporters and the generated long ssDNAs on the graphene/GCE allows ultrasensitive detection of target biomolecules. Herein, the design and working principle of this homogeneous electrochemical aptasensor were elucidated, and the working conditions were optimized. The gel electrophoresis results further demonstrate that the designed T7Exo-assisted target-analog recycling amplification strategy can work well. This electrochemical aptasensor realizes the detection of biomolecule in a homogeneous solution without immobilization of any bioprobe on electrode surface. Moreover, this versatile homogeneous electrochemical sensing system was used for the determination of biomolecules in real serum samples with satisfying results. [ABSTRACT FROM AUTHOR]

Electrochemical biosensors have played active roles at the forefront of bioanalysis because they have the potential to achieve sensitive, specific and low-cost detection of biomolecules and many others. Engineering the electrochemical sensing interface with functional nanomaterials leads to novel electrochemical biosensors with improved performances in terms of sensitivity, selectivity, stability and simplicity. Functional nanomaterials possess good conductivity, catalytic activity, biocompatibility and high surface area. Coupled with bio-recognition elements, these features can amplify signal transduction and biorecognition events, resulting in highly sensitive biosensing. Additionally, microfluidic electrochemical biosensors have attracted considerable attention on account of their miniature, portable and low-cost systems as well as high fabrication throughput and ease of scaleup. For example, electrochemical enzymetic biosensors and aptamer biosensors (aptasensors) based on the integrated microchip can be used for portable point-of-care diagnostics and environmental monitoring. This review is a summary of our recent progress in the field of electrochemical biosensors, including aptasensors, cytosensors, enzymatic biosensors and self-powered biosensors based on biofuel cells. We presented the advantages that functional nanomaterials and microfluidic chip technology bring to the electrochemical biosensors, together with future prospects and possible challenges. [ABSTRACT FROM AUTHOR]

Self-propelled nanomotors offer considerable promise for developing novel biosensing protocols involving ‘on-the-fly’ recognition events. This article reviews recent advances in using catalytic nanomotors for bioaffinity sensing and for isolating target biomolecules and cells from complex biological samples. A variety of receptors, attached to self-propelled nanoscale motors, can thus move around the sample and, along with the generated microbubbles, lead to greatly enhanced fluid transport and accelerated recognition process. Such operation addresses the challenges imposed by the slow analyte transport in designing sensitive bioaffinity assays. The recognition element can be attached onto the motor surface or embedded in the motor material itself. Receptor-functionalized nanomotors based on different biomolecular interactions have thus been shown extremely useful for rapid target isolation from complex biological samples without preparatory and washing steps. Tubular microengine microtransporters, functionalized with antibody, ss-DNA, aptamer or lectin receptors, are particularly useful for direct detection and isolation of proteins, nucleic acids, proteins or cancer cells. Micromotors with ‘built-in’ recognition, exploiting the selective binding properties of the outer layer of such micronegines, can also be used. Greatly enhanced analyte–receptor interactions can also be achieved through the increased fluid transport associated with the movement of unmodified micromotors. The attractive features of the new motion-based bioaffinity sensing and separation protocols open up new opportunities for diverse biomedical, environmental and security applications. [ABSTRACT FROM AUTHOR]

Nanomaterials constitute a class of structures that have unique physiochemical properties and are excellent scaffolds for presenting carbohydrates, important biomolecules that mediate a wide variety of important biological events. The fabrication of carbohydrate-presenting nanomaterials, glyconanomaterials , is of high interest and utility, combining the features of nanoscale objects with biomolecular recognition. The structures can also produce strong multivalent effects, where the nanomaterial scaffold greatly enhances the relatively weak affinities of single carbohydrate ligands to the corresponding receptors, and effectively amplifies the carbohydrate-mediated interactions. Glyconanomaterials are thus an appealing platform for biosensing applications. In this review, we discuss the chemistry for conjugation of carbohydrates to nanomaterials, summarize strategies, and tabulate examples of applying glyconanomaterials in in vitro and in vivo sensing applications of proteins, microbes, and cells. The limitations and future perspectives of these emerging glyconanomaterials sensing systems are furthermore discussed. [ABSTRACT FROM AUTHOR]

Sensing biomolecule interactions in living cells allows for a deeper understanding of the mechanisms governing biological processes, and has increasing significance for improvements in clinical diagnosis. It is now possible by using molecular biosensors. One method involving molecular biosensors is called molecular fluorescence complementation, usually referred to as BiFC (bimolecular fragment/fluorescence complementary/complementation) or TriFC (trimolecular fragment complementary/complementation). This complementation method is based on the principle that two non-fluorescent fragments of a fluorescent protein are brought into sufficient lyclose proximity, upon which they are reconstructed so that fluorescence is re-established. This process relies on the interaction between the two fusion partners, which normally are proteins. This method is simple, noninvasive, sensitive, and does not require specialized tools, hence being available to most standard laboratories. Here, we selectively describe three relevant examples, although many other molecular interactions have been shown to work with this method. Recent developments of this method include multicolor BiFC, which allows for simultaneous detection of multi-biomolecule interactions, RNA-protein interactions, far red and near infrared sensing systems for deep tissue imaging. Challenges in the utilization of this method are discussed. Given the current rate of technological advancements, we believe that fluorescence fragment complementing systems have the potential to be utilized across a wide range of areas, including in routine research and clinical diagnosis. [ABSTRACT FROM AUTHOR]

We designed and synthesized All-in-One (AIO) reactive azide reagents for bioorthogonal reactions with highly efficient Cu(i) ligand moieties, an azido group, and functional tags for imaging or purification. The AIO reagents displayed fast and efficient click ligation and can be applied in a wide range of in vivo systems. [ABSTRACT FROM AUTHOR]

Reactive oxygen species (ROS) are relatively simple molecules that exist within cells growing in aerobic conditions. ROS were originally associated with oxidative stress and seen as highly reactive molecules that are injurious to many cell components. More recently, however, the function of ROS as signal molecules in many plant cellular processes has become more evident. One of the most important functions of ROS is their role as a plant growth regulator. For example, ROS are key molecules in regulating plant root development, and as such, are comparable to plant hormones. In this review, the molecular mechanisms of ROS that are mainly associated with plant root growth are discussed. The molecular links between root growth regulation by ROS and other signals will also be briefly discussed. [ABSTRACT FROM AUTHOR]

Free radical generation occurs continuously within cells as a consequence of common metabolic processes. However, in high concentrations, whether from endogenous or exogenous sources, free radicals can lead to oxidative stress; a harmful process that cause serious damages to all biomolecules in our body hence impairs cell functions and even results in cell death and diseased states. Oxidative injuries accumulate over time and participate in cancer development, cardiovascular and neurodegenerative disorders as well as aging. Nature has bestowed the human body with a complex web of antioxidant defense system including enzymatic antioxidants like glutathione peroxidase and glutathione reductase, catalase and superoxide dismutase as well as non-enzymatic antioxidants such as thiol antioxidants, melatonin, coenzyme Q, and metal chelating proteins, which are efficient enough to fight against excessive free radicals. Also, nutrient antioxidants such as vitamin C, vitamin E, carotenoids, polyphenols, and trace elements are known to have high antioxidant potency to assist in minimizing harmful effects of reactive species. The immune system is also extremely vulnerable to oxidant and antioxidant balance as uncontrolled free radical production can impair its function and defense mechanism. The present paper reviews the ways by which free radicals form in the body and promote tissue damage, as well as the role of the antioxidants defense mechanisms. Finally, we will have a brief glance at oxidants and antioxidants relevance to the immune system. [ABSTRACT FROM AUTHOR]

Myceliophthora thermophilasyn.Sporotrichum thermophileis a ubiquitous thermophilic mould with a strong ability to degrade organic matter during optimal growth at 45 °C. Both genome analysis and experimental data have suggested that the mould is capable of hydrolyzing all major polysaccharides found in biomass. The mould is able to secrete a large number of hydrolytic enzymes (cellulases, laccases, xylanases, pectinases, lipases, phytases and some other miscellaneous enzymes) employed in various biotechnological applications. Characterization of the biomass-hydrolyzing activity of wild and recombinant enzymes suggests that this mould is highly efficient in biomass decomposition at both moderate and high temperatures. The native enzymes produced by the mould are more efficient in activity than their mesophilic counterparts beside their low enzyme titers. The mould is able to synthesize various biomolecules, which are used in multifarious applications. Genome sequence data ofM. thermophilaalso supported the physiological data. This review describes the biotechnological potential of thermophilic mould,M. thermophilasupported by genomic and experimental evidences. [ABSTRACT FROM PUBLISHER]

Nitric oxide (NO) is a ubiquitous biological messenger molecule, and plays the active roles in the regulation of various physiological processes. Although numerous NO fluorescent probes have also been successfully developed in the past ten years, it still remains challenging to increase the response rate for NO while having the high selectivity and sensitivity. In this work, a simple N -nitrosation reaction of the electron-rich aromatic secondary amine with NO under aerobic condition has been utilized for the first time to construct fluorescent probe for NO. The resulting probe 1 , containing a N -benzyl-4-hydroxyaniline moiety as reaction group and a BODIPY dye as fluorescence reporter, could detect NO with the fast fluorescence off-on response (within seconds), high sensitivity (nM level), and excellent selectivity over various reactive oxygen species (ROS) as well as dehydroascorbic acid (DHA), ascorbic acid (AA), and methylglyoxal (MGO). Even in the presence of glutathione (GSH, a high reactive biothiol for NO), the probe still works well for NO. Further, a mitochondria-targetable probe 2 was exploited by introducing a targeted triphenylphosphonium cation into probe 1 scaffold. It's excellent NO sensing performance as well as its ability to specifically target mitochondria and image NO there have been nicely demonstrated. With the two probes, the basal and stimulation-induced NO in RAW264.7 murine macrophages as well as the endogenous NO in endothelial cells after oxygen–glucose deprivation (OGD) have been successfully visualized. [ABSTRACT FROM AUTHOR]

The science of Geomicrobiology , which deals with mineral- microbe interaction in nature contributes effectively to three important processes namely- mineral and metal bioremediation, biomining and soil mineral formation by microbes. Bioremediation one of the important process of the above, degrades or transforms hazardous contaminants to less toxic compounds. Several groups of fungi have proved highly efficient in this aspect, with asbestos being one such toxic entity in the environment on which their activity was studied. The present investigation uses the same tool as a device for detoxifying asbestos, a potent carcinogenic entity; with fungal isolates native to the asbestos mines of Rajasthan, India, being investigated for the first time. The cellular mechanism of asbestos toxicity is mainly attributed to the presence of iron in its chemical composition which catalyzes generation of free radicals leading to oxidation of biomolecules. The two dominant novel species found therein, identified as Aspergillus tubingenesis and Coemansia reversa have proved capable of actively removing iron from asbestos fibers as studied by scanning electron microscopy- electron diffraction X-ray (SEM–EDX) analysis. This probably could lead to a reduction in toxicity of asbestos, due to reduced iron concentration as reported in related studies. Many fungi are known to release iron chelating compounds, siderophores, which could be instrumental in the study. The findings related to two new fungal species being added to the list of earlier identified fungal bioremediators of asbestos, widens the prospect of using bioremediation as an effective tool for asbestos detoxification [ABSTRACT FROM AUTHOR]

An ideal bioanalytical method would allow carrying out sensitive, selective, reproducible, fast, and in situ chemical measurements of the composition, structure and function of complex biological systems. Physical chemistry possesses advanced structure analyzing techniques which are suitable to solve, at a sub-molecular level, the structure of biomolecules. However, the prerequisite of the presence of the electrolyte solution limits the number of applicable structure analyzing techniques. Infrared spectroscopy is one of the most powerful analytical techniques used to identify the structure of biomolecules, monitor structural changes under various experimental environments and physical states. In addition, infrared reflection absorption spectroscopy (IRRAS) has been successfully applied to study supramolecular films at the solid|liquid interface. Assemblies of biomolecules belong to a particularly demanding because they bring specific for the maintenance of their functions experimental requirements which have to be taken into account planning in situ spectroelectrochemical experiments. In this paper potnential of in situ IRRAS under electrochemical control for studies of structural changes in assemblies of biomolecules such as lipid bilayers and protein films is described. Studies of different classes of biomolecules bring certain experimetnal conditions concerning the electrolyte composition, pH value, temperature or chemical nature of the solid support, which have to be fulfilled. Obviously, these conditons may significantly restrict the applicability of the in situ PM IRRAS. The selection of the solid substrate with required optical and electrical properties, the optical window and the electrolyte composition have to be adapted to the needs of biomolecules. Adjustement of experimetnal conditions as well as possibilites of the enlargement of the in situ PM IRRAS for studies of biomimetic assemblies is reviewed in this paper. Furthermore, experimetnal resutls reporting potenial driven changes in models of cell membranes and protein films are reviewed. Pioneering studies aiminig at the determination of structural changes in lipid membranes exposed to physiological electric fields and interacting simultaneously with protiens are described. [ABSTRACT FROM AUTHOR]

Fabrication of metal-organic frameworks (MOFs) with large apertures triggers a brand-new research area for selective encapsulation of biomolecules within MOF nanopores. The underlying inclusion mechanism is yet to be clarified however. Here we report a molecular dynamics study on the mechanism of protein encapsulation in MOFs. Evaluation for the binding of amino acid side chain analogues reveals that van der Waals interaction is the main driving force for the binding and that guest size acts as a key factor predicting protein binding with MOFs. Analysis on the conformation and thermodynamic stability of the miniprotein Trp-cage encapsulated in a series of MOFs with varying pore apertures and surface chemistries indicates that protein encapsulation can be achieved via maintaining a polar/nonpolar balance in the MOF surface through tunable modification of organic linkers and Mg-O chelating moieties. Such modifications endow MOFs with a more biocompatible confinement. This work provides guidelines for selective inclusion of biomolecules within MOFs and facilitates MOF functions as a new class of host materials and molecular chaperones. [ABSTRACT FROM AUTHOR]

Most of the protein-based diseases are caused by anomalies in the functionality and stability of these molecules. Experimental and theoretical studies of the conformational dynamics of proteins are becoming in this respect essential to understand the origin of these anomalies. However, a description of the conformational dynamics of proteins based on mechano-energetic principles still remains elusive because of the intrinsic high flexibility of the peptide chains, the participation of weak noncovalent interactions, and the role of the ubiquitous water solvent. In this work, the conformational dynamics of trialanine dissolved in water (D2O) is investigated through Molecular Dynamics (MD) simulations combined with instantaneous normal modes (INMs) analysis both at equilibrium and after the vibrational excitation of the C-terminal amide I mode. The conformational equilibrium between a and pPII conformers is found to be altered by the intramolecular relaxation of the amide I mode as a consequence of the different relaxation pathways of each conformer which modify the amount of vibrational energy stored in the torsional motions of the tripeptide, so the a ? pPII and pPII ? a conversion rates are increased differently. The selectivity of the process comes from the shifts of the vibrational frequencies with the conformational changes that modify the resonance conditions driving the intramolecular energy flows. [ABSTRACT FROM AUTHOR]

A series of diseases, ranging from cholera via travelers' diarrhea to hamburger disease, are caused by bacterially produced toxic proteins. In particular, a toxic protein unit is brought into the host cell upon binding to specific membrane-bound oligosaccharides on the host cell membrane. For example, the protein that causes cholera, cholera toxin (CT), has five identical, symmetrically placed binding pockets (B proteins), on top of which the toxic A protein resides. A promising strategy to counteract the devastating biological effects of this AB5 protein involves the development of inhibitors that can act as mimics of membrane-bound GM1 molecules, i.e., that can bind CT strongly and selectively. To reach this goal, two features are essential: First of all, the inhibitor should display oligosaccharides that resemble as much as possible the naturally occurring cell-surface pentasaccharide onto which CT normally binds, the so-called GM1 sugar (the oligosaccharide part of which is then labeled GM1os). Second, the inhibitor should be able to bind CT via multivalent interactions so as to bind CT as strongly as possible to allow for a real competition with the cell-membrane-bound GM1 molecules. In this Account, we present elements of the path that leads to strong CT inhibition by outlining the roles of multivalency and the development and use of GM1 mimics. First, multivalency effects were investigated using "sugar-coated" platforms, ranging from dendritic structures with up to eight oligosaccharides to platforms that mimicked the fivefold symmetry of CT itself. The latter goal was reached either via synthetic scaffolds like corannulene or calix[5]arene or via the development of a neolectin CT mimic that itself carries five GM1os groups. Second, the effect of the nature of the oligosaccharide appended to this platform was investigated via the use of oligosaccharides of increasing complexity, from galactose and lactose to the tetrasaccharide GM2os and eventually to GM1os itself. The combination of these threads gives rise to a series of inhibitors that can strongly bind CT, with IC50 values below 100 pM, and in some cases can even bind one-on-one. [ABSTRACT FROM AUTHOR]

A novel platinum(ii) organometallic complex, [Pt(pbi)(Me)(DMSO)], bearing the 2-(2′-pyridyl)-benzimidazole (pbiH) ligand, was synthesized and fully characterized. Interestingly, the reaction of this organometallic platinum(ii) complex with two distinct gold(i) phosphane compounds afforded the corresponding heterobimetallic derivatives with the pbi ligand bridging the two metal centers. The antiproliferative properties in vitro of [Pt(pbi)(Me)(DMSO)] and its gold(i) derivatives as well as those of the known coordination platinum(ii) and palladium(ii) complexes with the same ligand, of the general formula [MCl2(pbiH)], were comparatively evaluated against A2780 cancer cells, either sensitive or resistant to cisplatin. A superior biological activity of the organometallic compound clearly emerged compared to the corresponding platinum(ii) complex; the antiproliferative effects are further enhanced upon attaching the gold(i) triphenylphosphine moiety to the organometallic Pt compound. Remarkably, these novel metal species are able to overcome nearly complete resistance to cisplatin. Significant mechanistic insight into the study compounds was gained after investigating their reactions with a few representative biomolecules by electrospray mass spectrometry and X-ray crystallography. The obtained results are comprehensively discussed. [ABSTRACT FROM AUTHOR]

Background: Engineered nanomaterials (ENMs) interact with different biomolecules as soon as they are in contact, resulting in the formation of a biomolecule 'corona'. Hence, the 'corona' defines the biological identity of the ENMs and could affect the response of the immune system to ENM exposure. With up to 40 % of the world population suffering from type I allergy, a possible modulation of allergen effects by binding to ENMs is highly relevant with respect to work place and consumer safety. Therefore, the aim of this present study was to gain an insight into the interactions of gold nanoparticles with different seasonally and perennially occurring outdoor and indoor allergens. Methods: Gold nanoparticles (AuNPs) were conjugated with the major allergens of birch pollen (Bet v 1), timothy grass pollen (Phl p 5) and house dust mite (Der p 1). The AuNP-allergen conjugates were characterized by means of TEM negative staining, dynamic light scattering (DLS), z-potential measurements and hyperspectral imaging. Furthermore, 3D models were constructed, based on the characterization data, to visualize the interaction between the allergens and the AuNPs surface. Differences in the activation of human basophil cells derived from birch/grass pollen- and house dust mite-allergic patients in response to free allergen and AuNP-allergen conjugates were determined using the basophil activation assay (BAT). Potential allergen corona replacement during BAT was controlled for using Western blotting. The protease activity of AuNP-Der p 1 conjugates compared to free Der p 1 was assessed, by an enzymatic activity assay and a cellular assay pertaining to lung type II alveolar epithelial cell tight junction integrity. Results: The formation of a stable corona was found for all three allergens used. Our data suggest, that depending on the allergen, different effects are observed after binding to ENMs, including enhanced allergic responses against Der p 1 and also, for some patients, against Bet v 1. Moreover elevated protease activity of AuNP-Der p 1 conjugates compared to free Der p 1 was found. Conclusion: In summary, this study presents that conjugation of allergens to ENMs can modulate the human allergic response, and that protease activity can be increased. [ABSTRACT FROM AUTHOR]

Only α1 and α2 domains of the α-chain of the major histocompatibility complex (MHC) directly bind peptide antigens (Ag-s) and the T-cell receptor (TCR). Significant plasticity was found in the TCR but only minor in (α1 + α2). The α3-domain position variation was noted only in connection to its binding the coreceptor CD8. We apply our methods for identifying functional conformational changes in proteins to a systematic study of similarities between 43 X-ray structures of the entire α chains of MHC-I HLA-A2. Out of 903 different αHLA-A2 pairs 203 show similarities within the earlier determined uncertainty threshold and unexpectedly form three similarity clusters (SCs) with all/most structures in a cluster similar within the uncertainty threshold. Pairs from different SCs always differ above the threshold, mainly due to variations in the α3 position/structure. All structures in SC3 cannot bind the CD8 coreceptor. Strong hydrogen bonds between (α1 + α2) and α3 differ between SC1 and SC2 but are nearly invariant within each SC. Small conformational changes in the (α1 + α2), caused by Ag-s differences, act as an α3 "allosteric switch" between SC2 and SC1. Binding of CD8 to SC2-HLA-A2 (Tax-type Ag-s) changes it to SC1-HLA-A2 (HuD-type Ag-s). HuD binding to HLA-A2 is much less stable than Tax binding. CD8-liganded HLA-A2 preference for binding HuD suggests that CD8-HLA-A2 may present a weakly binding peptide for TCR recognition, supporting the hypothesis that CD8 increases TCR avidity to weak Ag-s. Other HLA-A2 functions may involve α3. TCR-A6-liganded-Tax-type-HLA-A2s form two small clusters, similar to either A6-liganded-HuD or A6-liganded-native-Tax HLA-A2s. [ABSTRACT FROM AUTHOR]

A novel bio-organic molecule, 3-(3-chloro-4-methoxy-phenyl)-1-(4,5-dimethoxy-2-methyl phenyl) prop-2-en-1-one (I), has been synthesized and characterized by FTIR,1H, and13C NMR. To understand the role of solvents, UV-vis absorption, and fluorescence study has been carried out using different solvents. The single-crystal X-ray diffraction technique has been studied to confirm the three dimensional structure of the compound and the hydrogen bond interactions involved in the stability of the structure. The ab-initio and density functional theory (DFT) are used to optimize the molecular structure. The calculated results show that the predicted geometry can well reproduce structural parameters. In addition, frontier molecular orbitals and Mullikan charge distributions are carried out by using RHF and B3LYP methods. The synthesized compound has been screened for its antimicrobial and antifungal activities against different panel of organisms. [ABSTRACT FROM AUTHOR]

l -Carnitine, a biomolecule able to cross the blood–brain barrier exploiting specific transporters, behaves as mono or bidentate anionic ligand for Pt(II) in the new amino complexes cis -[Pt( l -carnitine-O) 2 (NH 3 ) 2 ](BF 4 ) 2 ( 1 ), cis -[PtCl( l -carnitina-O)(NH 3 ) 2 ]BF 4 ( 2 ), [Pt( l -carnitine-O,O′)(1,2-DACH)]BF 4 ( 3 ), [Pt( l -carnitine-O) 2 (1,2-DACH)](BF 4 ) 2 ( 4 ), and [PtCl( l -carnitine-O)(1,2-DACH)](BF 4 ) ( 5 ). Four complexes with DMSO have been also prepared and characterized: the synthetic intermediate [Pt(CO 3 )(DMSO) 2 ] ( 6 ), [Pt( l -carnitine-O,O′)(DMSO) 2 ]BF 4 ( 7 ), cis -[Pt( l -carnitine-O) 2 (DMSO) 2 ](BF 4 ) 2 ( 8 ) and cis -[PtCl( l -carnitine-O)(DMSO) 2 ]BF 4 , ( 9 ). The antiproliferative activity of three representative complexes 1 , 5 and 7 has been assayed against three human cancer cell lines A2780, K562 and SKOV3, and it was found comparable to that of the parent active compounds cis -[PtCl 2 (1,2-DACH)] and cisplatin. [ABSTRACT FROM AUTHOR]

Background: Rauwolfia vomitoria is a plant with sedative properties found useful in the management of psychotic disorders, with adverse effects being reported on its use in different brain areas. Aims and Objectives: To investigate the acute effect of combination of Rauwolfia vomitoria with either Gongronema latifolium or Vernonia amygdalina on spatial learning and memory, and some bio-molecules in rats. Materials and Methods: 24 adult male Wistar rats weighing between 220 g - 300 g were equally divided into four groups (1-4). Group 1 animals were the control treated with 0.5 ml of Tween 20. Groups 2, 3 and 4 animals were administered respectively; 150 mg/kg of R. vomitoria, a combination of 150 mg/kg of R. vomitoria and 200 mg/kg of G. latifolium, and a combination of 150 mg/kg of R. vomitoria and 200 mg/kg of V. amygdalina for seven days. On days 4-7 concurrent with treatment, spatial learning and memory test was carried out using the Morris water maze, and the animals were sacrificed twelve hours after the last treatment. Their sera were used for enzyme and other bio-molecules analysis. Results: There was no difference in spatial learning and memory. The activities of aspartate aminotransferase, alanine aminotransferase and alkaline phosphatase, and the serum cholesterol and triglycerides levels were also not different compared to the control group. Conclusion: The dose and duration of administration of the extract of R. vomitoria either alone, or in combination with G. latifolium or V. amygdalina may not affect spatial learning or memory, or alter serum biomolecules. [ABSTRACT FROM AUTHOR]

A fast and reliable detection and identification of microorganisms is crucial in environmental science, for food quality as well as medical diagnosis. In these fields, all types of Raman spectroscopy are gaining more and more importance during the last years. The review provides an extensive overview of recent research, technical expertise, and scientific findings based on Raman spectroscopic detection and identification of microorganisms within the years 2010 and 2015, demonstrating the diverse capability of Raman spectroscopy as a modern analytical tool. Raman spectroscopy distinguishes itself from other currently applied techniques by its easy application at low cost, its high speed of analysis, and its broad information content on both the chemical composition and the structure of biomolecules within the microorganisms. Slight chances in the chemical composition of microorganisms can be monitored by means of Raman spectroscopy and used to differentiate genera, species, or even strains. Detection of pathogens is possible from complex matrices, such as soil, food, and body fluids. Further, spectroscopic studies of host-pathogen interactions are addressed as well as the effect of antibiotics on bacteria. Copyright © 2015 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Model-based techniques were used to resolve fluorescence datasets related to the interactions of two complementary oligonucleotides (which were tagged by fluorescein and Texas red respectively) in the presence of 13 nm gold nanoparticles (AuNPs). This system was selected as an example to demonstrate the advantages of model-based techniques in studying interactions of nanoparticles and biomolecules, and providing better insight to such nano-bio systems which is in turn helpful for designing more efficient sensor/delivery systems. The adsorption isotherms were analyzed by model-based Scatchard and Langmuir methods and the results were the adsorption constants of the oligonucleotides on AuNPs and the number of binding sites on AuNPs. This is the first reported application of Scatchard method where DNA is the adsorbate. The main part of the study is focused on the application of more sophisticated model-based techniques to analyze complex three-way excitation–emission fluorescence data sets recorded through the adsorption/hybridization process. A novel model-based restricted Tucker3 method is also proposed to estimate the hybridization constant. An advantage of this technique is the estimation of the concentration profiles of all involving chemical components, even those without a fluorescence signal. [ABSTRACT FROM AUTHOR]

Background: Budding yeast, S. cerevisiae, has been used extensively as a model organism for studying cellular processes in evolutionarily distant species, including humans. However, different human tissues, while inheriting a similar genetic code, exhibit distinct anatomical and physiological properties. Specific biochemical processes and associated biomolecules that differentiate various tissues are not completely understood, neither is the extent to which a unicellular organism, such as yeast, can be used to model these processes within each tissue. Results: We present a novel framework to systematically quantify the suitability of yeast as a model organism for different human tissues. To this end, we develop a computational method for dissecting the global human interactome into tissue-specific cellular networks. By individually aligning these networks with the yeast interactome, we simultaneously partition the functional space of human genes, and their corresponding pathways, based on their conservation both across species and among different tissues. Finally, we couple our framework with a novel statistical model to assess the conservation of tissue-specific pathways and infer the overall similarity of each tissue with yeast. We further study each of these subspaces in detail, and shed light on their unique biological roles in the human tissues. Conclusions: Our framework provides a novel tool that can be used to assess the suitability of the yeast model for studying tissue-specific physiology and pathophysiology in humans. Many complex disorders are driven by a coupling of housekeeping (universally expressed in all tissues) and tissue-selective (expressed only in specific tissues) dysregulated pathways. While tissue-selective genes are significantly associated with the onset and development of a number of tissue-specific pathologies, we show that the human-specific subset has even higher association. Consequently, they provide excellent candidates as drug targets for therapeutic interventions. [ABSTRACT FROM AUTHOR]

The amidation reaction between C60 with an activated ester group (1) and acetylated Glc (AcGlc) with an amino group (2) was performed to yield the target AcGlc-pendant C60 compound (3). The water soluble deacetylated compound, Glc-pendant C60 compound (4), exhibited high photocytotoxicity against HeLa cells due to the more efficient singlet oxygen generation as compared with that of Glc-pendant azafulleroids. [ABSTRACT FROM AUTHOR]

In the present paper, the double role of one of the squarylium dyes is presented. First it was shown the role of 1,3-bis( N -ethyl-2-methylenebenzoxazole)squarine as a spectroscopic probe for bovine serum albumin determination. Next the photoinitiating ability of squarylium dye incorporated in two- and three-component systems for free radical polymerization of trimethylolpropane triacrylate has been investigated. In such system squarylium dyes act as sensitizer (primary light absorber). The radical photopolymerization of an acrylate was observed upon irradiation with ion-argon laser. [ABSTRACT FROM AUTHOR]

Interaction of bovine serum albumin (BSA) and DNA base (adenine) with sulfapyridine (SP) and sulfadiazine (SD) was investigated by UV–visible, fluorescence, cyclic voltammetry and molecular docking methods. In isolated adenine, multiple emission maxima appear at 430, 330 and 288 nm where as single emission is observed (338 nm) in the BSA molecule. Absorbance and fluorescence intensities of BSA and adenine were decreased as the concentrations of SP and SD increased. The binding constant and binding site value of sulfa drugs with adenine is lower than that of sulfa with BSA. SP is strongly interacting with BSA/adenine than that of SD. Pyridine moiety (in SP) is strongly interact with BSA/adenine than that of pyrimidine moiety (in SD). The oxidative peak currents of sulfa drugs are decreased with BSA/adenine solution and the peak potential was shifted positively. Molecular docking results revealed that the secondary structure of protein was affected upon interaction with the drug. [ABSTRACT FROM AUTHOR]

Cytokines, lymphocytes, platelets and several biomolecules have long been implicated in the pathology of rheumatoid arthritis (RA), and the influences of antibody production and tagging, and cytokine, chemokine and enzyme production at specific rheumatoid joints were thought to be exclusive to the advancement of disease parameters. Another role player in RA is red blood cells (RBCs) which, of late, have been found to be involved in RA pathobiology, as there is a positive correlation between RBC counts and joint pathology, as well as with inflammatory biomarkers in the disease. There is also an association between RBC distribution width and the incidence of myocardial infarction amongst RA patients, and there is a change in the lipid distribution within RBC membranes. Of late, certain RBC-associated factors with previously obscure roles and cell-derived particles thought to be inconsequential to the other constituents of plasma were found to be active biomolecular players. Several of these have been discovered to be present in or originating from RBCs. Their influences have been shown to involve in membrane dynamics that cause structural and functional changes in both platelets and RBCs. RBC-derived microparticles are emerging entities found to play direct roles in immunomodulation via interactions with other plasma cells. These correlations highlight the direct influences of RBCs on exacerbating RA pathology. This review will attempt to shed more light on how RBCs, in the true inflammatory milieu of RA, are playing an even greater role than previously assumed. [ABSTRACT FROM AUTHOR]

Time-resolved structural information is key to understand the mechanism of biological processes, such as catalysis and signalling. Recent developments in X-ray sources as well as data collection and analysis methods are making routine time-resolved X-ray crystallography and solution scattering experiments a real possibility for structural biologists. Here we review the information that can be obtained from these techniques and discuss the considerations that must be taken into account when designing a time-resolved experiment. [ABSTRACT FROM AUTHOR]

Most of the reports in literature dedicated to the use of glycosyl hydrolases for the preparation of glycosides are about gluco- (α- and β-form) and galacto-sidase (β-form), reflecting the high-availability of both anomers of glucosides and of β-galactosides and their wide-ranging applications. Hence, the idea of this review was to analyze the literature focusing on hardly-mentioned natural and engineered glycosyl hydrolases. Their performances in the synthetic mode and natural hydrolytic potential are examined. Both the choice of articles and their discussion are from a biomolecular and a biotechnological perspective of the biocatalytic process, shedding light on new applicative ideas and on the assortment of biomolecular diversity. The hope is to elicit new interest for the development of biocatalysis and to gather attention of biocatalyst practitioners for glycosynthesis. [ABSTRACT FROM AUTHOR]

The recent synthetic development of a variety of nanoparticles has led to their widespread application in diagnostics and therapeutics. In particular, the controlled size and shape of nanoparticles precisely determine their unique chemical and physical properties, which is highly attractive for accurate analysis of given systems. In addition to efforts toward controlling the synthesis and properties of nanoparticles, the surface functionalization of nanoparticles with biomolecules has been intensively investigated since the mid-1990s. The complicated yet programmable properties of biomolecules have proved to substantially enhance and enrich the novel functions of nanoparticles to achieve 'smart' nanoparticle materials. In this review, the advances in chemical functionalization of four types of representative nanoparticle with DNA and protein molecules in the past five years are critically reviewed, and their future trends are predicted. [ABSTRACT FROM AUTHOR]

Boronate affinity materials, as unique sorbents, have emerged as important media for the selective separation and molecular recognition of cis-diol-containing compounds. With the introduction of boronic acid functionality, boronate affinity materials exhibit several significant advantages, including broad-spectrum selectivity, reversible covalent binding, pH-controlled capture/release, fast association/desorption kinetics, and good compatibility with mass spectrometry. Because cis-diol-containing biomolecules, including nucleosides, saccharides, glycans, glycoproteins and so on, are the important targets in current research frontiers such as metabolomics, glycomics and proteomics, boronate affinity materials have gained rapid development and found increasing applications in the last decade. In this review, we critically survey recent advances in boronate affinity materials. We focus on fundamental considerations as well as important progress and new boronate affinity materials reported in the last decade. We particularly discuss on the effects of the structure of boronate ligands and supporting materials on the properties of boronate affinity materials, such as binding pH, affinity, selectivity, binding capacity, tolerance for interference and so on. A variety of promising applications, including affinity separation, proteomics, metabolomics, disease diagnostics and aptamer selection, are introduced with main emphasis on how boronate affinity materials can solve the issues in the applications and what merits boronate affinity materials can provide. [ABSTRACT FROM AUTHOR]

The specific targeting of either tumor cells or immune cells in vivo by carefully designed and appropriately surface-functionalized nanocarriers may become an effective therapeutic treatment for a variety of diseases. Carbohydrates, which are prominent biomolecules, have shown their outstanding ability in balancing the biocompatibility, stability, biodegradability, and functionality of nanocarriers. The recent applications of sugar (mono/oligosaccharides and/or polysaccharides) for the development of nanomedicines are summarized in this review, including the application of carbohydrates for the surface-functionalization of various nanocarriers and for the construction of the nanocarrier itself. Current problems and challenges are also addressed. [ABSTRACT FROM AUTHOR]

Nanostructured porous silicon (PSi) is a promising material for the label-free detection of biomolecules, but it currently suffers from limited applicability due to poor sensitivity, typically in micromolar range. This work presents the design, operation concept, and characterization of a novel microfluidic device and assay that integrates an oxidized PSi optical biosensor with electrokinetic focusing for a highly sensitive label-free detection of nucleic acids. Under proper oxidation conditions, the delicate nanostructure of PSi can be preserved, while providing sufficient dielectric insulation for application of high voltages. This enables the use of signal enhancement techniques, which are based on electric fields. Here, the DNA target molecules are focused using an electric field within a finite and confined zone, and this highly concentrated analyte is delivered to an on-chip PSi Fabry–Pérot optical transducer, pre-functionalized with capture probes. Using reflective interferometric Fourier transform spectroscopy real-time monitoring, a 1000-fold improvement in limit of detection is demonstrated compared to a standard assay, using the same biosensor. Thus, a measured limit of detection of 1 × 10−9 M is achieved without compromising specificity. The concepts presented herein can be readily applied to other ionic targets, paving way for the development of other highly sensitive chemical and biochemical assays. [ABSTRACT FROM AUTHOR]

Rationale The search for the conditions which must have prevailed in the long-distant past during the conversion of inanimate matter into animate matter is a fascinating area of research and it continues to draw the attention of the scientific community. The initiation of life on this planet must have been preceded by the development of biomolecules, amongst which amino acids have unique importance. Formation of amino acids under a certain set of conditions is shown in the present experiments. Methods Solutions of ammonium carboxylates or the mixture of two such salts were prepared in 3:6.9:0.1 (v/v/v) acetonitrile/water/formic acid at a concentration of 50 μM. The studies were performed using a quadrupole time-of-flight (QqTOF) mass spectrometer. The formation of different amino acids was detected with high-resolution mass spectrometry. Results Here, we show the formation of amino acids when a solution of ammonium salts was injected into an electrospray ionization (ESI)-QqTOF-MS instrument. The ammonium salts were the source of NH3 and CO2 and H2O was available in the medium. It seems that the combination of NH3, CO2, and H2O leads to the formation of amino acids. Conclusions Further to the literature reports of formation of amino acids under the reduced atmosphere represented by gases such as NH3, CH4, H2 and H2O, here we demonstrate the formation of amino acids by the combination of NH3/NO2, CO2 and water vapours in the ESI source of the mass spectrometer. Copyright © 2015 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Immunoassays exploit the highly selective interaction between antibodies and antigens to provide a vital method for biomolecule detection at low concentrations. Developers and practitioners of immunoassays have long known that non-specific binding often restricts immunoassay limits of quantification (LOQs). Aside from non-specific binding, most efforts by analytical chemists to reduce the LOQ for these techniques have focused on improving the signal amplification methods and minimizing the limitations of the detection system. However, with detection technology now capable of sensing single-fluorescence molecules, this approach is unlikely to lead to dramatic improvements in the future. Here, fundamental interactions based on the law of mass action are analytically connected to signal generation, replacing the four- and five-parameter fittings commercially used to approximate sigmoidal immunoassay curves and allowing quantitative consideration of non-specific binding and statistical limitations in order to understand the ultimate detection capabilities of immunoassays. The restrictions imposed on limits of quantification by instrumental noise, non-specific binding, and counting statistics are discussed based on equilibrium relations for a sandwich immunoassay. Understanding the maximal capabilities of immunoassays for each of these regimes can greatly assist in the development and evaluation of immunoassay platforms. While many studies suggest that single molecule detection is possible through immunoassay techniques, here, it is demonstrated that the fundamental limit of quantification (precision of 10 % or better) for an immunoassay is approximately 131 molecules and this limit is based on fundamental and unavoidable statistical limitations. [ABSTRACT FROM AUTHOR]

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at ; a full web server is available at , including source code and ancillary programs. [ABSTRACT FROM AUTHOR]