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In situ target biomolecule analysis is of great significance for real‐time monitoring and regulation of endogenous biomarkers and elementary biomolecules in vivo. Gratifyingly, the rapid evolution of structural DNA nanotechnology during past decades has established an appealing toolbox for biological analysis and medical detection. The modulated self‐assembly and underlying canonical Watson‐Crick base‐pairing rules provide possibilities for accurate controlling of the topologies and functions of obtained nanomaterials. The probes composed of diverse DNA nanostructures and DNA‐nanoparticle complexes can create a confined space, which increases target accessibility and improves probe stability, sensitivity and specificity. In this minireview, we retrospect the research progress of in‐situ biomolecular analysis based on DNA nanostructures for intracellular and in vivo biosensors in confined space. The characteristics of distinct DNA nanomaterials are first introduced, and then the fundamentals of biosensing process of designed DNA nanostructures are emphasized. Moreover, we elucidate our perspective over the challenges of this field and discuss the potential directions of this kind of application‐oriented fabrication technique. [ABSTRACT FROM AUTHOR]

In situ target biomolecule analysis is of great significance for real‐time monitoring and regulation of endogenous biomarkers and elementary biomolecules in vivo. Gratifyingly, the rapid evolution of structural DNA nanotechnology during past decades has established an appealing toolbox for biological analysis and medical detection. The modulated self‐assembly and underlying canonical Watson‐Crick base‐pairing rules provide possibilities for accurate controlling of the topologies and functions of obtained nanomaterials. The probes composed of diverse DNA nanostructures and DNA‐nanoparticle complexes can create a confined space, which increases target accessibility and improves probe stability, sensitivity and specificity. In this minireview, we retrospect the research progress of in‐situ biomolecular analysis based on DNA nanostructures for intracellular and in vivo biosensors in confined space. The characteristics of distinct DNA nanomaterials are first introduced, and then the fundamentals of biosensing process of designed DNA nanostructures are emphasized. Moreover, we elucidate our perspective over the challenges of this field and discuss the potential directions of this kind of application‐oriented fabrication technique. [ABSTRACT FROM AUTHOR]

Reliable conformational sampling and trajectory analysis are always important to the study of the folding or binding mechanisms of biomolecules. Generally, one has to prepare many complicated parameters and follow a lot of steps to obtain the final data. The whole process is too complicated to new users. In this article, we provide a convenient and user‐friendly tool that is compatible to AMBER, called fast sampling and analysis tool (FSATOOL). FSATOOL has some useful features. First and the most important, the whole work is extremely simplified into two steps, one is the fast sampling procedure and the other is the trajectory analysis procedure. Second, it contains several powerful sampling methods for the simulation on graphics process unit, including our previous mixing replica exchange molecular dynamics method. The method combines the advantages of the biased and unbiased simulations. Finally, it extracts the dominant transition pathways automatically from the folding network by Markov state model. Users do not need to do the tedious intermediate steps by hand. To illustrate the usage of FSATOOL in practice, we perform one simulation for a RNA hairpin in explicit solvent. All the results are presented. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Axial coordination is a crucial biological process to regulate biomolecules' functions in natural enzymes. However, it is a great challenge to determine the single or dual axial interaction between the metal center of enzymes and the ligand. In this work, a controllable axial coordination system was developed based on G‐quadruplex/hemin complex by designing a series of fluorescent derivatives. The mechanism on axial coordination of G‐quadruplex/hemin with coumarin‐imidazole ligands was proposed to be single‐sided, and led to fluorescence quenching of ligands. Upon addition of nitric oxide, the fluorescence of ligands was recovered through competitive axial coordination, providing a "signal on" strategy for signal transduction. More significantly, the fluorescent imaging of intracellular nitric oxide was achieved after conjugating with gold nanoparticles. Also, the proposed protocol provided a smart strategy to monitor the relationship between nitric oxide and p53 protein activity in living cells. Single‐sided axial coordination of G‐quadruplex‐hemin complex shows significant advantages of highly reactive monomeric hemin, a single available axial site, and a strong binding capacity compared with uncomplexed hemin, which can be used as a molecular switch for in situ imaging and detection of intracellular NO through competitive axial coordination after assembly with a designed fluorescent ligand and conjugated with the nanocarrier. [ABSTRACT FROM AUTHOR]

Extracellular vesicles (EVs) actively participate in intercellular communication and pathological processes. Studying the molecular signatures of EVs is key to reveal their biological functions and clinical values, which, however, is greatly hindered by their sub‐100 nm dimensions, the low quantities of biomolecules each EV carries, and the large population heterogeneity. Now, single‐EV flow cytometry analysis is introduced to realize single EV counting and phenotyping in a conventional flow cytometer for the first time, enabled by target‐initiated engineering (TIE) of DNA nanostructures on each EV. By illuminating multiple markers on single EVs, statistically significant differences are revealed among the molecular signatures of EVs originating from several breast cancer cell lines, and the cancer cell‐derived EVs among the heterogeneous EV populations are successfully recognized. Thus, our approach holds great potential for various biological and biomedical applications. Single extracellular vesicle (EV) flow cytometry analysis enabled by target‐initiated engineering (TIE) of DNA nanostructures reveals unique molecular signatures of individual vesicles and differentiates EV sub‐populations. [ABSTRACT FROM AUTHOR]

Recent advances in cellular analysis revealed that the seemingly identical cells are heterogeneous in term of functionality, compositions, and genetic performance. These differences cause difficulty in the diagnostic for a specific model of disease. Detection of biomolecules such as DNA, RNA, and protein or analysis of cell(s), detection of cell surface molecules, and secreted protein, can help us to improve the understanding of a targeted disease and development of new diagnostic and therapeutic approaches. A single‐cell includes the minute quantity of these target molecules. Microfluidic devices have the ability to capture a single‐cell and its lysate into a pico or femtoliter volumes droplet, or micro‐well thus preventing dilution and limiting diffusion. In this review we described the advancement and limitations in microfluidic techniques used toward single‐cells analysis. In systematic life sciences, in order to obtain mammalian tissue and then crushing it to a single‐cell for analysis using microfluidic platform five major levels can be categorized. The isolated single‐cells are prone to on‐chip or off‐chip analysis for the targeted biomolecules. [ABSTRACT FROM AUTHOR]

Abstract: Reporter strains have proven to be powerful tools to study Mycobacterium tuberculosis (Mtb) physiology. Transcriptional and translational reporter strains are engineered by fusing a readout gene, encoding a fluorescent, luminescent or enzymatic protein, downstream of a promoter or in‐frame with a gene of interest. When the reporter is expressed, it generates a signal that acts as a synthetic phenotype, enabling the study of physiologies that might have otherwise been hidden. This review will discuss approaches for generating reporter strains in Mtb and how they can be used as tools for high‐throughput genetic and small molecule screening and as biomarkers for examining Mtb responses to drug or immune stresses during animal infections. Fluorescent reporter strains have an added benefit in that they can be used for single‐cell studies both in vitro and in vivo, thus enabling the study of mechanisms underlying phenotypic heterogeneity. Recent examples of the use of Mtb reporter strains will be presented with a focus on how they can be used as tools for drug discovery and development. © 2018 IUBMB Life, 70(9):818–825, 2018 [ABSTRACT FROM AUTHOR]

Carbon monoxide (CO) has long been known as the “silent killer” owing to its ability to form carboxyhemoglobin—the main cause of CO poisoning in humans. Its role as an endogenous neurotransmitter, however, was suggested in the early 1990s. Since then, the biological activity of CO has been widely examined via both the direct administration of CO and in the form of so-called “carbon monoxide releasing molecules (CORMs).” This overview will explore the general physiological effects and potential therapeutic applications of CO when delivered in the form of CORMs. [ABSTRACT FROM AUTHOR]

Abstract: Emerging applications in the field of chemical biology are currently limited by the lack of bioorthogonal reactions allowing both removal and linkage of chemical entities on complex biomolecules. We recently discovered a novel reaction between iminosydnones and strained alkynes leading to two products resulting from ligation and fragmentation of iminosydnones under physiological conditions. We now report the synthesis of a panel of substituted iminosydnones and the structure reactivity relationship between these compounds and strained alkyne partners. This study identified the most relevant substituents, which allow to increase the rate of the transformation and to develop a bifunctional cleavable linker with improved kinetics. [ABSTRACT FROM AUTHOR]

Abstract: Weak ligand–receptor recognition events are often amplified by recruiting multiple regulatory biomolecules to the action site in biological systems. However, signal amplification in in vitro biomimetic systems generally lack the spatiotemporal regulation in vivo. Herein we report a framework nucleic acid (FNA)‐programmed strategy to develop valence‐controlled signal amplifiers with high modularity for ultrasensitive biosensing. We demonstrated that the FNA‐programmed signal amplifiers could recruit nucleic acids, proteins, and inorganic nanoparticles in a stoichiometric manner. The valence‐controlled signal amplifier enhanced the quantification ability of electrochemical biosensors, and enabled ultrasensitive detection of tumor‐relevant circulating free DNA (cfDNA) with sensitivity enhancement of 3–5 orders of magnitude and improved dynamic range. [ABSTRACT FROM AUTHOR]

Small‐angle X‐ray scattering (SAXS) analysis of biomolecules is increasingly common with a constantly high demand for comprehensive and efficient sample quality control prior to SAXS experiments. As monodisperse sample suspensions are desirable for SAXS experiments, latest dynamic light scattering (DLS) techniques are most suited to obtain non‐invasive and rapid information about the particle size distribution of molecules in solution. A multi‐receiver four‐channel DLS system was designed and adapted at the BioSAXS endstation of the EMBL beamline P12 at PETRA III (DESY, Hamburg, Germany). The system allows the collection of DLS data within round‐shaped sample capillaries used at beamline P12. Data obtained provide information about the hydrodynamic radius of biological particles in solution and dispersity of the solution. DLS data can be collected directly prior to and during an X‐ray exposure. To match the short X‐ray exposure times of around 1 s for 20 exposures at P12, the DLS data collection periods that have been used up to now of 20 s or commonly more were substantially reduced, using a novel multi‐channel approach collecting DLS data sets in the SAXS sample capillary at four different neighbouring sample volume positions in parallel. The setup allows online scoring of sample solutions applied for SAXS experiments, supports SAXS data evaluation and for example indicates local inhomogeneities in a sample solution in a time‐efficient manner. Biological macromolecules with different molecular weights were applied to test the system and obtain information about the performance. All measured hydrodynamic radii are in good agreement with DLS results obtained by employing a standard cuvette instrument. Moreover, applying the new multi‐channel DLS setup, a reliable radius determination of sample solutions in flow, at flow rates normally used for size‐exclusion chromatography–SAXS experiments, and at higher flow rates, was verified as well. This study also shows and confirms that the newly designed sample compartment with attached DLS instrumentation does not disturb SAXS measurements. [ABSTRACT FROM AUTHOR]

Abstract: Scalable methods currently are lacking for isolation of long ssDNA, an important material for numerous biotechnological applications. Conventional biomolecule purification strategies achieve target capture using solid supports, which are limited in scale and susceptible to contamination owing to nonspecific adsorption and desorption on the substrate surface. We herein disclose selective nascent polymer catch and release (SNAPCAR), a method that utilizes the reactivity of growing poly(acrylamide‐co‐acrylate) chains to capture acrylamide‐labeled molecules in free solution. The copolymer acts as a stimuli‐responsive anchor that can be precipitated on demand to pull down the target from solution. SNAPCAR enabled scalable isolation of multi‐kilobase ssDNA with high purity and 50–70 % yield. The ssDNA products were used to fold various DNA origami. SNAPCAR‐produced ssDNA will expand the scope of applications in nanotechnology, gene editing, and DNA library construction. [ABSTRACT FROM AUTHOR]

Soft and deformable liquid metals (LMs) are building components in various systems related to uncertain and dynamic task environments. Herein we describe the development of a biomolecule-triggered external-manipulation method involving LM conjugates for the construction of future innovative soft robotics operating in physiological environments. Functional soft hybrids composed of a liquid-metal droplet, a thiolated ligand, and proteins were synthesized for the expression of diverse macroscopic commands, such as attachment to cells, binary fusion, and self-propelled movement through molecular recognition and enzymatic reactions. Our technology could be used to create new state-of-the-art soft robots for chemical and biomedical engineering applications. [ABSTRACT FROM AUTHOR]

For many proteins, phosphorylation regulates their interaction with other biomolecules. Herein, we describe an unexpected phenomenon whereby phosphate groups are transferred non-enzymatically from one interaction partner to the other within a binding interface upon activation in the gas phase. Providing that a high affinity exists between the donor and acceptor sites, this phosphate transfer is very efficient and the phosphate groups only ligate to sites in proximity to the binding region. Consequently, such phosphate-transfer reactions may define with high precision the binding site between a phosphoprotein and its binding partner, as well as reveal that the binding site in this system is retained in the phase transfer from solution to the gas phase. [ABSTRACT FROM AUTHOR]

Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. [ABSTRACT FROM AUTHOR]

Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis. Computational analysis of HDXMS requires several steps. A typical workflow for proteins consists of identification of (non-)deuterated peptides or fragments of the protein under study (local analysis), or identification of the deuterated protein as a whole (global analysis); determination of the deuteration level; estimation of the protection extent or exchange rates of the labile backbone amide hydrogen atoms; and a statistically sound interpretation of the estimated protection extent or exchange rates. Several algorithms, specifically designed for HDX analysis, have been proposed. They range from procedures that focus on one specific step in the analysis of HDX data to complete HDX workflow analysis tools. In this review, we provide an overview of the computational methods and discuss outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:649-667, 2017 [ABSTRACT FROM AUTHOR]

Microfluidic systems have emerged as a new class of perfusable in vitro culture models that have helped advance and refine our understanding of microvascular function. Cutting-edge microfluidic models have successfully integrated principles from quantitative analysis of vascular function, in vitro flow chambers, microfabrication techniques, and 3D tissue scaffolds. Here, we review the evolution of microfluidic systems, namely their progression from 2D planar microchannel arrays to 3D microtissue analogs, and highlight their recent contributions in elucidating the role of biomolecular transport and fluid mechanical stimuli in controlling angiogenesis. Further advancement of microfluidic systems in recapitulating tissue-level phenomena in vitro, controlling important physiochemical and biological parameters, and integrating cellular and molecular analysis will help further enhance their application within the microcirculation research community. [ABSTRACT FROM AUTHOR]

Biomolecular regulatory networks are organised around hubs, which can interact with a large number of targets. These targets compete with each other for access to their common hubs, but whether the effect of this competition would be significant in magnitude and in function is not clear. In this review, the authors discuss recent in vivo studies that analysed the system level retroactive effects induced by target competition in microRNA and mitogen-activated protein kinase regulatory networks. The results of these studies suggest that downstream targets can regulate the overall state of their upstream regulators, and thus cannot be ignored in analysing biomolecular networks. [ABSTRACT FROM AUTHOR]

Anthropogenic activities resulted in major shifts in nutrient inputs to coastal seas, which may have altered the biomolecule composition of phytoplankton because of different C : N : P requirements for biosynthesis. In order to understand the effects of N- and P-limitation on the allocation of photosynthetically fixed C, we directly measured seasonal and spatial dynamics of amino acid, fatty acid and carbohydrate concentrations and biosynthesis rates in the phytoplankton of the North Sea using a novel 13C-tracer approach. Nutrient limitation and season had large effects on composition and biosynthesis rates of all biochemical classes, for instance the contribution of protein derived amino acids varied up to fourfold in concentration and up to eightfold in biosynthesis rates. Nutrient specific effects and the prevailing nutrient limitations were identified by short-term (24-72 h) nutrient addition experiments. Addition of the growth-limiting nutrient increased amino acid synthesis while storage compound synthesis decreased concurrently. The strongest effect was detected in N-limited flagellates, where amino acid synthesis increased up to fivefold within 24 h upon relief of nutrient limitation. P-limitation was only detected in diatom-dominated near-coast stations, and amino acid synthesis responded much slower, likely because of the necessary preceding synthesis of ribosomes. This metabolic elasticity of phytoplankton in response to nutrient availability will have major consequences for their nutritional value within the food web and subsequently the carrying capacity of coastal ecosystems. [ABSTRACT FROM AUTHOR]

Efficient incorporation of modified nucleotides by DNA polymerases is essential for many cutting-edge biomolecular technologies. The present study compares the acceptance of either alkene- or alkyne-modified nucleotides by KlenTaq DNA polymerase and provides structural insights into how 7-deaza-adenosine and deoxyuridine with attached alkene-modifications are incorporated into the growing DNA strand. Thereby, we identified modified nucleotides that prove to be superior substrates for KlenTaq DNA polymerase compared with their natural analogues. The knowledge can be used to guide future design of functionalized nucleotide building blocks. [ABSTRACT FROM AUTHOR]

Protein aggregation is a hallmark of the major neurodegenerative diseases including Alzheimer's, Parkinson's, Huntington's and motor neuron and is a symptom of a breakdown in the management of proteome foldedness. Indeed, it is remarkable that under normal conditions cells can keep their proteome in a highly crowded and confined space without uncontrollable aggregation. Proteins pose a particular challenge relative to other classes of biomolecules because upon synthesis they must typically follow a complex folding pathway to reach their functional conformation (native state). Non-native conformations, including the unfolded nascent chain, are highly prone to aberrant interactions, leading to aggregation. Here we review recent advances in knowledge of proteostasis, approaches to monitor proteostasis and the impact that protein aggregation has on biology. We also include discussion of the outstanding challenges. © 2017 IUBMB Life, 69(2):49-54, 2017 [ABSTRACT FROM AUTHOR]

We examined the 68Ga labeling of the α-helical peptide, DOTA-FAMP, and evaluated conformational changes during radiolabeling. 68Ga-DOTA-FAMP is a positron emission tomography probe candidate for atherosclerotic plaques. The labeling yield achieved by Zhernosekov's method (using acetone for 68Ga purification) was compared with that achieved by the original and 2 modified Mueller's methods (using NaCl solution). Modified method I involves desalting the 68Ga prior to labeling, and modified method II involves the inclusion of ethanol in the labeling solution. The labeling yield using Zhernosekov's method was 62% ± 5.4%. In comparison, Mueller's original method gave 8.9% ± 1.7%. Modified method I gave a slight improvement of 32% ± 2.1%. Modified method II further increased the yield to 66% ± 3.4%. Conformational changes were determined by circular dichroism spectroscopy, revealing that these differences could be attributed to conformational changes. Heat treatment affects peptide conformation, which leads to aggregation and decreases the labeling yield. Mueller's method is simpler, but harsh conditions preclude its application to biomolecules. To suppress aggregation, we included a desalting process and added ethanol in the labeling solution. These changes significantly improved the labeling yield. Before use for imaging, conformational changes of biomolecules during radiolabeling should be evaluated by circular dichroism spectroscopy to ensure the homogeneity of the labeled product. [ABSTRACT FROM AUTHOR]

Polyvinylidene fluoride (PVDF) membrane surfaces were ad hoc functionalized chemically to make them suitable for enzymatic immobilization. The process was performed by grafting the membrane surface with 1,4-diaminobutane and subsequently by activating it with glutarhaldehyde. The chemico-physical properties of the original PVDF membrane and of the modified membranes were studied by infrared spectroscopy, scanning electron microscopy, and static contact angle measurements. The activated membranes were used as a support for covalent immobilization of tyrosinase. The activity of free and immobilized enzyme was studied and compared. The experimental data showing the specific activity of the immobilized enzyme are similar to the value obtained with the free one. This means that the immobilization procedure did not alter the catalytic properties of the tyrosinase. In addition, the surface modification of the PVDF made it a promising material to use in enzyme or biomolecule immobilization processes. [ABSTRACT FROM AUTHOR]

Surface material functionalization including layer-by-layer (LbL) polyelectrolyte films with incorporated nanoparticles is a growing field with a wide range of biomedical applications: drug reservoirs, medical devices, or tissue engineering. In parallel, gold nanoparticles (AuNPs) can be grafted by drugs and sensitive molecules using simple protocols. This study shows that AuNP behavior is modified when they are entrapped into three partner LbL films in comparison to the colloidal solution. A polycationic (polyallylamine hydrochloride (PAH)) and a polyanionic (polyacrylic acid (PAA)) polymer is used to build films based on three cycles ((PAH/AuNP/PAA)3). To investigate the interaction with biomolecules and cells, three different films are developed changing the outer layer (either PAH or AuNP or PAA) with the same number of AuNP deposit. The best biocompatibility is observed with a polyacrylic acid outer layer. Due to the high capacity of drug grafting on gold nanoparticles, the results seem promising for the development of nanostructured biomedical devices. [ABSTRACT FROM AUTHOR]

During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Qexp of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Qexp, 2) inaccuracies in the function [ABSTRACT FROM AUTHOR]

Magnetic nanoparticles (MNPs) have been drawing much technological interests in medical diagnostics and therapy. However, it remains a challenge reducing false signal arising from non-specific interactions. Here, we coated MNPs with polyelectrolyte multilayer (PEM) films by layer-by-layer deposition with poly(allylamine hydrochloride) and poly(acrylic acid). The polyelectrolytes multilayers film prevented irreversible coagulation of MNPs and could be used for conjugation of biomolecules on the MNPs. Furthermore, we also demonstrated a potential application of the PEM-coated MNPS into a microfluidic system. [ABSTRACT FROM AUTHOR]

Site-directed (gene) mutagenesis has been the most useful method available for the conversion of one amino acid residue of a given protein into another. Until relatively recently, this strategy was limited to the twenty standard amino acids. The ongoing maturation of stop codon suppression and related technologies for unnatural amino acid incorporation has greatly expanded access to nonstandard amino acids by expanding the scope of the translational apparatus. However, the necessity for translation of genetic changes restricts the diversity of residues that may be incorporated. Herein we highlight an alternative approach, termed post-expression mutagenesis, which operates at the level of the very functional biomolecules themselves. Using the lens of retrosynthesis, we highlight prospects for new strategies in protein modification, alteration, and construction which will enable protein science to move beyond the constraints of the 'translational filter' and lead to a true synthetic biology. [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]

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]

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]

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]

In this study, dummy imprinting technology was employed for the preparation of l-phenylalanine-imprinted microspheres. Ionic liquids were utilized as both a 'dummy' template and functional monomer, and 4-vinylpyridine and ethylene glycol dimethacrylate were used as the assistant monomer and cross-linker, respectively, for preparing a surface-imprinted polymer on poly(divinylbenzene) microspheres. By the results obtained by theoretical investigation, the interaction between the template and monomer complex was improved as compared with that between the template and the traditional l-phenylalanine-imprinted polymer. The batch experiments indicated that the imprinting factor reached 2.5. Scatchard analysis demonstrated that the obtained 'dummy' molecularly imprinted microspheres exhibited an affinity of 77.4 M·10−4, significantly higher that of a traditional polymer directly prepared by l-phenylalanine, which is in agreement with theoretical results. Competitive adsorption experiments also showed that the molecularly imprinted polymer with the dummy template effectively isolated l-phenylalanine from l-histidine and l-tryptophan with separation factors of 5.68 and 2.68, respectively. All these results demonstrated that the polymerizable ionic liquid as the dummy template could enhance the affinity and selectivity of molecularly imprinted polymer, thereby promoting the development of imprinting technology for biomolecules. [ABSTRACT FROM AUTHOR]

The toxic gas H2S has recently emerged as one of the important signaling molecules in biological systems. Thus understanding the production, distribution, and mode of action of H2S in biological system is important, but the fleeting and reactive nature of H2S makes it a daunting task. Herein we report a biocompatible, nitro-functionalized metal-organic framework as reaction-based fluorescence turn-on probe for fast and selective H2S detection. The selective turn-on performance of MOF remains unaffected even in presence of competing biomolecules. [ABSTRACT FROM AUTHOR]

Metal ions play an important role in the catalysis and folding of proteins and oligonucleotides. Their localization within the three-dimensional fold of such biomolecules is therefore an important goal in understanding structure-function relationships. A trilateration approach for the localization of metal ions by means of long-range distance measurements based on electron paramagnetic resonance (EPR) is introduced. The approach is tested on the Cu2+ center of azurin, and factors affecting the precision of the method are discussed. [ABSTRACT FROM AUTHOR]

BACKGROUND:Arbuscularmycorrhizal fungi (AMF) are soil organisms that associatewith plant roots and promote plant growth, increasing theconcentrationof secondary metabolites, which aremolecules of interest to thepharmaceutical industry. Passiflora alata is a Brazilian medicinalplant that is used as a rawmaterial for anxiolyticphytotherapeutic agents. The anxiolyticproperties are related to the presence of biomolecules in the plant material, principally flavonoids. The objective of this study was to evaluate the effect of inoculation with AMF and organic fertilization on the production of soluble carbohydrates and total foliar proteins, phenols and flavonoids in P. alata seedlings. RESULTS: There was an effect of the tested treatments on the analyzed variables. Seedlings inoculated and cultivated in soil to which 0.15 kg vermicompost kg-1 had been added showed increased growth and production of primary and secondary metabolites comparedwith treatmentswith lower levels of manure, which did not differ fromthose cultivated in soilwith 0.2 kg vermicompost kg-1. CONCLUSION: The inoculation of P. alata seedlings with Gigaspora albida is an alternative to maximize the production of pharmacologically important foliar biomolecules, especially flavonoids, with benefits that vary in accordance with the fertility of the soil. [ABSTRACT FROM AUTHOR]

In contrast to proteins, much less attention has been focused on the development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force fields are not accurate enough to capture the properties of even simple nucleic acid constructs. In this article, we review our efforts to develop coarse-grained (CG) models that capture the underlying physics for the particular length scale of interest. Two models are discussed. One of them is the three interaction site (TIS) model, in which each nucleotide is represented by three beads corresponding to sugar, phosphate, and base. The other is the self-organized polymer (SOP) model, in which each nucleotide is represented as a single interaction center. Applications of the TIS model to study the complexity of hairpin formation and the effects of crowding in a shifting equilibrium between two conformations in human telomerase pseudoknot are described. The work on crowding illustrates a direct link to the activity of telomerase. We use the SOP model to describe the response of the Tetrahymena ribozyme to force. The simulated unfolding pathways agree well with single molecule pulling experiments. We also review predictions for the unfolding pathways for the Azoarcus ribozyme. The success of the CG applications to describe dynamics in RNA gives hope that more complex processes involving RNA-protein interactions can be tackled using variants of the proposed models. [ABSTRACT FROM AUTHOR]

Although the main features of the protein folding problem are coming into clearer focus, the microscopic viewpoint of nucleic acid folding mechanisms is only just beginning to be addressed. Experiments, theory, and simulations are pointing to complex thermodynamic and kinetic mechanisms. As is the case for proteins, molecular dynamics (MD) simulations continue to be indispensable tools for providing a molecular basis for nucleic acid folding mechanisms. In this review, we provide an overview of biomolecular folding mechanisms focusing on nucleic acids. We outline the important interactions that are likely to be the main determinants of nucleic acid folding energy landscapes. We discuss recent MD simulation studies of empirical force field and Go-type MD simulations of RNA and DNA folding mechanisms to outline recent successes and the theoretical and computational challenges that lie ahead. [ABSTRACT FROM AUTHOR]

We are the first to investigate the relationship between protein handedness and the rate of protein folding. Our findings demonstrate that small three-helix, left-handed proteins are less densely packed and should result in faster folding than that of right-handed, three-helix proteins. At the same time, right-handed, three-helix proteins have higher mechanical stability than the left-handed proteins. Moreover, from our analysis we have revealed that bacterial three-helix proteins have some advantages in packing over eukaryotic right-handed, three-helix proteins, which should result in faster folding. [ABSTRACT FROM AUTHOR]

Intracellular signaling inside living cells is controlled by the specific localization of biomolecules, including proteins, with timescales ranging from milliseconds to several hours. To elucidate the related spatial and temporal signal processes, development of optical probes for cellular events is a challenging task in present studies. Herein, we describe recent advances in the basic design of the optical probes, which have been inspired by luminescent creatures, and their practical application to visualize intracellular events in living cells and animals. A discussion of different probe designs reveals their benefits and shortcomings. [ABSTRACT FROM AUTHOR]

The efficacy of drugs and biomolecules relies on their ability to pass through the bilayer. The development of methods to directly and sensitively monitor these membrane transport processes has remained an experimental challenge. A macrocyclic host ( p-sulfonatocalix[4]arene or cucurbit[7]uril) and a fluorescent dye (lucigenin or berberine) are encapsulated as a chemosensing ensemble inside liposomes, which allows for a direct, real-time fluorescence monitoring of the passage of unlabeled bioorganic analytes. This in vitro assay is transferable to different channel proteins and analytes, has potential for fluorescence-based screening, e.g., of channel modulators, and yields the absolute kinetics of translocation. Using this new biophysical method, we observed for the first time direct rapid translocation of protamine, an antimicrobial peptide, through the bacterial transmembrane protein OmpF. [ABSTRACT FROM AUTHOR]

The article explores the important role played by computer scientists in modern biology. It examines the relevance of bioinformatics to the advancement of the molecular life sciences due to its ability to analyze and inspect huge amounts of data. Information is also presented on structural bioinformatics which can be used for the prediction and analysis of the structures of biomolecules.

A novel biomaterial based on polyurethane (PU) was prepared through physical incorporation of lysine-containing copolymer to improve its hemocompatibility and surface recognition of plasminogen. The lysine-containing copolymer was synthesized via the copolymerization of 2-ethylhexyl methacrylate (EHMA), oligo (ethylene glycol) methyl ether methacrylate (OEGMA) and 6- tert-butoxycarbonyl amino-2-(2-methyl-acryloylamino)-hexanoic acid tert-butyl ester (Lys(P)MA), followed by the deprotection of COOH and ε-NH2 groups on lysine residues in the copolymer. The composition of the copolymer can be adjusted by varying the monomer feed ratio. The three components contribute to improving the compatibility with PU, resistance to nonspecific protein adsorption and specific binding of plasminogen, respectively. The binding capacity towards plasminogen increased with the lysine content in the copolymer. This approach illustrates a simple way for the generation of novel biomaterials with improved hemocompatibility and surface recognition of specific biomolecules. [ABSTRACT FROM AUTHOR]

Proteins in living organisms express various important functions by interacting with other proteins and molecules. Therefore, many efforts have been made to investigate and predict protein-protein interactions (PPIs). Analysis of strengths of PPIs is also important because such strengths are involved in functionality of proteins. In this paper, we propose several feature space mappings from protein pairs using protein domain information to predict strengths of PPIs. Moreover, we perform computational experiments employing two machine learning methods, support vector regression (SVR) and relevance vector machine (RVM), for dataset obtained from biological experiments. The prediction results showed that both SVR and RVM with our proposed features outperformed the best existing method. [ABSTRACT FROM AUTHOR]

Rotlichtschalter: Tetra ‐ ortho ‐ methoxysubstituierte Aminoazobenzole bilden bei neutralem pH ‐ Wert Azoniumionen, isomerisieren bei Bestrahlung mit rotem Licht (635 nm) zur cis ‐ Form und kehren thermisch innerhalb von Sekunden zur trans ‐ Form zurück. [ABSTRACT FROM AUTHOR]

Nanoporentechniken, die die Funktionen natürlicher Ionenkanäle nachahmen, sind nützliche Methoden für den Einzelmolekülnachweis. Das Verfahren erlaubt die selektive Analyse von Nukleinsäuren in Echtzeit und im Hochdurchsatz. Zwei Arten von Nanoporen finden Anwendung: biologische Nanoporen und Festkörpernanoporen. Dieser Kurzaufsatz beleuchtet die Grundlagen und jüngsten Fortschritte bei der nanoporenbasierten Sequenzierung und Detektion von Nukleinsäuren. Außerdem wird eine neuartige, erst kürzlich eingeführte Nanoporentechnik für die Analyse von Biomolekülen vorgestellt. Nach dem Vorbild der Natur: Die Funktionen natürlicher Ionenkanäle werden von künstlichen biologischen und Festkörpernanoporen nachgeahmt, die große Perspektiven für den Nachweis und die Sequenzierung von DNA bieten. Die Grundlagen und jüngsten Fortschritte werden hier zusammengefasst, und ein neues System für die nanoporenbasierte Analyse wird diskutiert. [ABSTRACT FROM AUTHOR]

Magnetische Nanopartikel (MNPs), die mit einem Magnetfeld ausgerichtet werden können, werden genutzt, um großflächige Anordnungen aus biologischen Nanofasern zu erzeugen, deren Orientierung durch das angelegte Magnetfeld vorgegeben ist. Wenn diese Nanofasern mit MNPs bedeckt sind, können sie durch das externe Magnetfeld horizontal oder vertikal ausgerichtet werden. [ABSTRACT FROM AUTHOR]

Bioadhesives are high molecular weight, biocompatible, biodegradable polymers used to join two surfaces where at least one of them is a living tissue. Bioadhesives are used for two main purposes, first as a replacement for surgical sutures and second as a substitute for traditional drug dosage systems. There are several considerations and issues associated with the use of biopolymers in suture-less surgery as well as in drug delivery systems. Herein is presented a review of bioadhesives; the focus being on the adhesive properties. Bioadhesives for tissue joining are considered first, along with their main characteristics and advantages. That is followed by a discussion on the use of bioadhesives as drug carriers for efficient drug delivery. [ABSTRACT FROM AUTHOR]

Biomolecule-ion interactions that occur during changes in pH value are a crucial but poorly investigated area that underlies the aggregation of inorganic nanocrystals. Meanwhile, the disorderly growth of calcium phosphate (CaP) nanocrystals is an obstacle that limits its practical applications. Herein, we have demonstrated for the first time that a simple two-step pH-adjustment process for a gelatin hydrosol reaction medium can modulate the ordered self-assembly of trace-element-doped CaP nanocrystals into porous beads. Two methods are used to adjust the initial pH value of gelatin hydrosol: One is to firstly adjust the pH value to 3.0 and then to 4.0 with acid/base solutions, whilst the other is to directly adjust the pH value to 4.0 with acid. Spherical CaP porous beads are rapidly produced through the two-step pH-adjustment process, whereas the one-step pathway results in disorderly CaP aggregates. We believe that the introduction of additives for pH adjustment is the dominant factor in disturbing the electrokinetic parameters and for driving the self-assembly of nanocrystals, whereas the nucleation of CaP nanocrystals prior to assembly is caused by the relaxation/condensation of the polypeptide network, owing to the increase in pH value on the introduction of the basic calcium salt. This method is facile and rapid and these highly bioactive porous beads are particularly promising for use in hard-tissue repair, , and drug delivery. [ABSTRACT FROM AUTHOR]