Molecular imprinting technology for biomedical applications

Molecularly imprinted polymers (MIPs), a type of biomimetic material, have attracted considerable interest owing to their cost-effectiveness, good physiochemical stability, favourable specificity and selectivity for target analytes, and widely used for various biological applications. It was demonstrated that MIPs with significant selectivity towards protein-based targets could be applied in medicine, diagnostics, proteomics, environmental analysis, sensors, various in vivo and/or in vitro applications, drug delivery systems, etc. This review provides an overview of MIPs dedicated to biomedical applications and insights into perspectives on the application of MIPs in newly emerging areas of biotechnology. Many different protocols applied for the synthesis of MIPs are overviewed in this review. The templates used for molecular imprinting vary from the minor glycosylated glycan-based structures, amino acids, and proteins to whole bacteria, which are also overviewed in this review. Economic, environmental, rapid preparation, stability, and reproducibility have been highlighted as significant advantages of MIPs. Particularly, some specialized MIPs, in addition to molecular recognition properties, can have high catalytic activity, which in some cases could be compared with other bio-catalytic systems. Therefore, such MIPs belong to the class of so-called 'artificial enzymes'. The discussion provided in this manuscript furnishes a comparative analysis of different approaches developed, underlining their relative advantages and disadvantages highlighting trends and possible future directions of MIP technology.

Biomolecules-Loading of 3D-Printed Alginate-Based Scaffolds for Cartilage Tissue Engineering Applications: A Review on Current Status and Future Prospective

Osteoarthritis (OA) can arise from various factor including trauma, overuse, as well as degeneration resulting from age or disease. The specific treatment options will vary based on the severity of the condition, and the affected joints. Some common treatments for OA include lifestyle modifications, medications, physical therapy, surgery and tissue engineering (TE). For cartilage tissue engineering (CTE), three-dimension (3D) scaffolds are made of biocompatible natural polymers, which allow for the regeneration of new cartilage tissue. An ideal scaffold should possess biological and mechanical properties that closely resemble those of the cartilage tissue, and lead to improved functional of knee. These scaffolds are specifically engineered to serve as replacements for damaged and provide support to the knee joint. 3D-bioprinted scaffolds are made of biocompatible materials natural polymers, which allow for the regeneration of new cartilage. The utilization of 3D bioprinting method has emerged as a novel approach for fabricating scaffolds with optimal properties for CTE applications. This method enables the creation of scaffolds that closely mimic the native cartilage in terms of mechanical characteristics and biological functionality. Alginate, that has the capability to fabricate a cartilage replacement customized for each individual patient. This polymer exhibits hydrophilicity, biocompatibility, and biodegradability, along with shear-thinning properties. These unique properties enable Alginate to be utilized as a bio-ink for 3D bioprinting method. Furthermore, chondrogenesis is the complex process through which cartilage is formed via a series of cellular and molecular signaling. Signaling pathway is as a fundamental mechanism in cartilage formation, enhanced by the incorporation of biomolecules and growth factors that induce the differentiation of stem cells. Accordingly, ongoing review is focusing to promote of 3D bioprinting scaffolds through the utilization of advanced biomolecules-loading of Alginate-based that has the capability to fabricate a cartilage replacement tailored specifically to each patient's unique needs and anatomical requirements.

Computation of topographic and three-dimensional atomic force microscopy images of biopolymers by calculating forces

Atomic force microscopy (AFM) is widely utilized to visualize the molecular motions of biomolecules. Comparison of experimentally measured AFM images with simulated AFM images based on known structures of biomolecules is often necessary to elucidate what is actually resolved in the images. Experimental AFM images are generated by force measurements; however, conventional AFM simulation has been based on geometrical considerations rather than calculating forces using molecular dynamics simulations due to limited computation time. This letter summarizes recently developed methods to simulate topographic and three-dimensional AFM (3D-AFM) images of biopolymers such as chromosomes and cytoskeleton fibers. Scanning such biomolecules in AFM measurements usually results in nonequilibrium-type work being performed. As such, the Jarzynski equality was employed to relate the nonequilibrium work to the free energy profiles, and the forces were calculated by differentiating the free energy profiles. The biomolecules and probes were approximated using a supra-coarse-grained model, allowing the simulation of force-distance curves in feasible time. It was found that there is an optimum scanning velocity and that some of polymer structures are resolved in the simulated 3D-AFM images. The theoretical background adopted to rationalize the use of small probe radius in the conventional AFM simulation of biomolecules is clarified.

Formation and detection of biocoronas in the food industry and their fate in the human body

The rapid advancement of nanotechnology has opened up new avenues for applications in all stages of the food industry. Over the past decade, extensive research has emphasized that when nanoparticles (NPs) enter organisms, they spontaneously adsorbed biomolecules, leading to the formation of biocorona. This paper provided a detailed review of the process of biocorona formation in the food industry, including their classification and influencing factors. Additionally, various characterization methods to investigated the morphology and structure of biocoronas were introduced. As a real state of food industry nanoparticles in biological environments, the biocorona causes structural transformations of biomolecules bound to NPs, thus affecting their fate in the body. It can either promote or inhibit enzyme activity in the human environment, and may also positively or negatively affect the cellular uptake and toxicity of NPs. Since NPs present in the food industry will inevitably enter the human body, further investigations on biocoronas will offer valuable insights and perspectives on the safety of incorporating more NPs into the food industry.

An experimental approach to determine the gamma radiation interaction mean free path and exposure buildup factor for biomolecules

This experimental approach was designed to understand the gamma interaction parameters for the essential biomolecules, including starch soluble, cholesterol, myristic acid, glucose, oxalic acid, dextrose, salicylic acid, ethyl cellulose and sucrose. The empirical determination of gamma interaction parameters, such as interaction mean-free-path (MFP), buildup factor, and effective atomic number (Zeff) was performed by measuring mass attenuation coefficient (μ/ρ) at energies of 356 keV, 511 keV, 662 keV, 1173 keV, 1275 keV and 1332 keV. This was achieved using weak radioactive sources and a NaI(Tl) scintillation spectrometer with collimated and non-collimated transmission geometry. The experimentally determined values of gamma-ray interaction parameters were obtained non-destructively and precisely agreeing with the expected values from simulations and codes. In addition, the research findings also revealed a novel trend in gamma interaction mean free path as a function of energy and variable buildup factors for the selected biomolecules. These research findings provide valuable insight into the process of gamma radiation interaction. This approach may fulfil the increasing demand of medical, technical and academic research laboratories for a cost-effective and reliable empirical methodology to understand gamma radiation interaction with matter.

Biological and pharmacological aspects of tannins and potential biotechnological applications

Secondary metabolites are divided into three classes: phenolic, terpenoid, and nitrogenous compounds. Phenolic compounds are also known as polyphenols and include tannins, classified as hydrolysable or condensed. Herein, we explored tannins for their ROS reduction characteristics and role in homeostasis. These activities are associated with the numbers and degree of polymerisation of reactive hydroxyl groups present in the phenolic rings of tannins. These characteristics are associated with anti-inflammatory, anti-aging, and anti-proliferative health benefits. Tannins can reduce the risk of cancer and neurodegenerative diseases, such as cardiovascular diseases and Alzheimer's, respectively. These biomolecules may be used as nutraceuticals to maintain good gut microbiota. Industrial applications include providing durability to leather, anti-corrosive properties to metals, and substrates for 3D printing and in bio-based foam manufacture. This review updates regarding tannin-based research and highlights its biological and pharmacological relevance and potential applications.

Electrical biosensing system utilizing ion-producing enzymes conjugated with aptamers for the sensing of severe acute respiratory syndrome coronavirus 2

Viral outbreaks, which include the ongoing coronavirus disease 2019 (COVID-19) pandemic provoked by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are a major global crisis that enormously threaten human health and social activities worldwide. Consequently, the rapid and repeated treatment and isolation of these viruses to control their spread are crucial to address the COVID-19 pandemic and future epidemics of novel emerging viruses. The application of cost-efficient, rapid, and easy-to-operate detection devices with miniaturized footprints as a substitute for the conventional optic-based polymerase chain reaction (PCR) and immunoassay tests is critical. In this context, semiconductor-based electrical biosensors are attractive sensing platforms for signal readout. Therefore, this study aimed to examine the electrical sensing of patient-derived SARS-CoV-2 samples by harnessing the activity of DNA aptamers directed against spike proteins on viral surfaces. We obtained rapid and sensitive virus detection beyond the Debye length limitation by exploiting aptamers coupled with alkaline phosphatases, which catalytically generate free hydrogen ions which can readily be measured on pH meters or ion-sensitive field-effect transistors. Furthermore, we demonstrated the detection of the viruses of approximately 100 copies/μL in 10 min, surpassing the capability of typical immunochromatographic assays. Therefore, our newly developed technology has great potential for point-of-care testing not only for SARS-CoV-2, but also for other types of pathogens and biomolecules.

Insights into the interactions between cellulose and biological molecules

Understanding the interactions between carbohydrate polymer molecules and biomolecules is of primary significance for its application. In this paper, the interaction between cellulose and biomolecules was studied using density functional theory method, in which cellobiose, nucleobases, and aromatic amino acids were employed as the structural models of cellulose, DNA, and protein, respectively. Quantitative molecular surface electrostatic potential (ESP) results well represented how cellulose perceived by organism during the recognition. The structural and energetic studies of cellulose with biomolecules complexes show that weak interactions, such as hydrogen bonding interaction, vdW interaction, and pi-H interaction, play an important role in stabilizing these complexes. Through systematic wavefunction analysis, including reduced density gradient (RDG) and natural bond orbital (NBO) methods, the nature of these weak interactions was revealed and further graphically visualized. In-depth understanding of the interaction between cellobiose with biological model molecules may shed lights on the application of carbohydrate polymer-based materials in biological fields.

Fluorescent probes for biomolecule detection under environmental stress

The use of fluorescent probes in visible detection has been developed over the last several decades. Biomolecules are essential in the biological processes of organisms, and their distribution and concentration are largely influenced by environmental factors. Significant advances have occurred in the applications of fluorescent probes for the detection of the dynamic localization and quantity of biomolecules during various environmental stress-induced physiological and pathological processes. Herein, we summarize representative examples of small molecule-based fluorescent probes that provide bimolecular information when the organism is under environmental stress. The discussion includes strategies for the design of smart small-molecule fluorescent probes, in addition to their applications in biomolecule imaging under environmental stresses, such as hypoxia, ischemia-reperfusion, hyperthermia/hypothermia, organic/inorganic chemical exposure, oxidative/reductive stress, high glucose stimulation, and drug treatment-induced toxicity. We believe that comprehensive insight into the beneficial applications of fluorescent probes in biomolecule detection under environmental stress should enable the further development and effective application of fluorescent probes in the biochemical and biomedical fields.

Suppression of Energy Metabolism in Cancer Cells with Nutrient-Sensing Nanodrugs

Uncontrolled growth of tumor cells is highly dependent on the energy metabolism. Fasting-mimicking diet (FMD) is a low-calorie, low-protein, low-sugar diet representing a promising strategy for cancer treatment. However, triglyceride stored in adipose tissue is hydrolyzed into free fatty acids and glycerol for energy supply during FMD treatment. Herein, we design a nutrient-sensing nanodrug, VFETX, which is self-assembled with vitamin B1 (VB1), ferrous ions, and etomoxir (ETX). FMD treatment upregulate the expression of VB1 transporters on tumor cells, thereby increasing cellular uptake and tumor accumulation of VFETX. Importantly, treatments of VFETX and FMD synergistically inhibit the energy metabolism in tumor cells and subsequently markedly enhance cytotoxicity of ETX. As a result, VFETX nanodrugs efficiently inhibit the growth of two tumor models in vivo without obvious side effects. This study demonstrates the potential of FMD-assisted nutrient-sensing nanodrugs for cancer therapy.

Biomolecules Production from Greenhouse Gases by Methanotrophs

Harmful effects on living organisms and the environment are on the rise due to a significant increase in greenhouse gas (GHG) emissions through human activities. Therefore, various research initiatives have been carried out in several directions in relation to the utilization of GHGs via physicochemical or biological routes. An environmentally friendly approach to reduce the burden of significant emissions and their harmful effects is the bioconversion of GHGs, including methane (CH4) and carbon dioxide (CO2), into value-added products. Methanotrophs have enormous potential for the efficient biotransformation of CH4 to various bioactive molecules, including biofuels, polyhydroxyalkanoates, and fatty acids. This review highlights the recent developments in methanotroph-based systems for methanol production from GHGs and proposes future perspectives to improve process sustainability via biorefinery approaches.

Transistor-Based Biomolecule Sensors: Recent Technological Advancements and Future Prospects

Transistor-based sensors have been widely recognized to be highly sensitive and reliable for point-of-care/bed-side diagnosis. In this line, a range of cutting-edge technologies has been generated to elevate the role of transistors for biomolecule detection. Detection of a wide range of clinical biomarkers has been reported using various configurations of transistors. The inordinate sensitivity of transistors to the field-effect imparts high sensitivity toward wide range of biomolecules. This overview has gleaned the present achievements with the technological advancements using high performance transistor-based sensors. This review encloses transistors incorporated with a variety of functional nanomaterials and organic elements for their excellence in selectivity and sensitivity. In addition, the technological advancements in fabrication of these microdevices or nanodevices and functionalization of the sensing elements have also been discussed. The technological gap in the realization of sensors in transistor platforms and the resulted scope for research has been discussed. Finally, foreseen technological advancements and future research perspectives are described.

Synergistic integration of metal nanoclusters and biomolecules as hybrid systems for therapeutic applications

Therapeutic nanoparticles are designed to enhance efficacy, real-time monitoring, targeting accuracy, biocompatibility, biodegradability, safety, and the synergy of diagnosis and treatment of diseases by leveraging the unique physicochemical and biological properties of well-developed bio-nanomaterials. Recently, bio-inspired metal nanoclusters (NCs) consisting of several to roughly dozens of atoms (<2 nm) have attracted increasing research interest, owing to their ultrafine size, tunable fluorescent capability, good biocompatibility, variable metallic composition, and extensive surface bio-functionalization. Hybrid core-shell nanostructures that effectively incorporate unique fluorescent inorganic moieties with various biomolecules, such as proteins (enzymes, antigens, and antibodies), DNA, and specific cells, create fluorescently visualized molecular nanoparticle. The resultant nanoparticles possess combinatorial properties and synergistic efficacy, such as simplicity, active bio-responsiveness, improved applicability, and low cost, for combination therapy, such as accurate targeting, bioimaging, and enhanced therapeutic and biocatalytic effects. In contrast to larger nanoparticles, bio-inspired metal NCs allow rapid renal clearance and better pharmacokinetics in biological systems. Notably, advances in nanoscience, interfacial chemistry, and biotechnologies have further spurred researchers to explore bio-inspired metal NCs for therapeutic purposes. The current review presents a comprehensive and timely overview of various metal NCs for various therapeutic applications, with a special emphasis on the design rationale behind the use of biomolecules/cells as the main scaffolds. In the different hybrid platform, we summarize the current challenges and emerging perspectives, which are expected to offer in-depth insight into the rational design of bio-inspired metal NCs for personalized treatment and clinical translation.

Innovative hydrogel containing polymeric nanocapsules loaded with phloretin: Enhanced skin penetration and adhesion

Dermatological applications of phloretin are restricted by its poor aqueous solubility. Nanotechnology has been proposed as strategy to increase the apparent drug solubility in aqueous media. This study aimed to develop, characterize, and evaluate the antitumoral effects and safety of polymeric nanocapsules containing phloretin (NCPhl). Further, to incorporate NC-Phl in an innovative semi-solid formulation (HG-NCPhl) to evaluate its performance using porcine skin model. NC-Phl was prepared and the effects in MRC5, HACAT, and SK-mel28 cells were evaluated. Hydrogels were prepared with Lecigel ® and characterized for their nanotechnological properties, adhesion (in vitro washability), and penetration/permeation studies in porcine skin. NC-Phl had a cytotoxic effect against Sk-Mel-28 cells and the population doubling time was increased upon treatment with NC-Phl for longer culture periods; notably when cells were treated for 72 h and then followed for 7 days after the treatment was removed (p < 0.05). HG-NC-Phl was considered adhesive and had a higher capacity to penetrate all skin layers compared with HG-Phl (p < 0.05). The innovative hydrogel HGNC-Phl promoted a drug-reservoir in the stratum corneum and higher penetration of the flavonoid into the epidermis. Therefore, this approach can be considered as a platform to establish versatile dermatological solutions for both cosmeceutics and melanoma therapy.

Accurate and rapid calculation of hydration free energy and its physical implication for biomolecular functions

Here we review a new method for calculating a hydration free energy (HFE) of a solute and discuss its physical implication for biomolecular functions in aqueous environments. The solute hydration is decomposed into processes 1 and 2. A cavity matching the geometric characteristics of the solute at the atomic level is created in process 1. Solute-water van der Waals and electrostatic interaction potentials are incorporated in process 2. The angle-dependent integral equation theory combined with our morphometric approach is applied to process 1, and the three-dimensional reference interaction site model theory is employed for process 2. Molecular models are adopted for water. The new method is characterized by the following. Solutes with various sizes including proteins can be treated in the same manner. It is almost as accurate as the molecular dynamics simulation despite its far smaller computational burden. It enables us to handle a solute possessing a significantly large total charge without difficulty. The HFE can be decomposed into a variety of physically insightful, energetic, and entropic components. It is best suited to the elucidation of mechanisms of protein folding, pressure and cold denaturation of a protein, and different types of molecular recognition.

Implementation of adaptive integration method for free energy calculations in molecular systems

Estimating free energy differences by computer simulation is useful for a wide variety of applications such as virtual screening for drug design and for understanding how amino acid mutations modify protein interactions. However, calculating free energy differences remains challenging and often requires extensive trial and error and very long simulation times in order to achieve converged results. Here, we present an implementation of the adaptive integration method (AIM). We tested our implementation on two molecular systems and compared results from AIM to those from a suite of other methods. The model systems tested here include calculating the solvation free energy of methane, and the free energy of mutating the peptide GAG to GVG. We show that AIM is more efficient than other tested methods for these systems, that is, AIM results converge to a higher level of accuracy and precision for a given simulation time.

3D printing of bone tissue engineering scaffolds

Tissue engineering is promising in realizing successful treatments of human body tissue loss that current methods cannot treat well or achieve satisfactory clinical outcomes. In scaffold-based bone tissue engineering, a high performance scaffold underpins the success of a bone tissue engineering strategy and a major direction in the field is to produce bone tissue engineering scaffolds with desirable shape, structural, physical, chemical and biological features for enhanced biological performance and for regenerating complex bone tissues. Three-dimensional (3D) printing can produce customized scaffolds that are highly desirable for bone tissue engineering. The enormous interest in 3D printing and 3D printed objects by the science, engineering and medical communities has led to various developments of the 3D printing technology and wide investigations of 3D printed products in many industries, including biomedical engineering, over the past decade. It is now possible to create novel bone tissue engineering scaffolds with customized shape, architecture, favorable macro-micro structure, wettability, mechanical strength and cellular responses. This article provides a concise review of recent advances in the R & D of 3D printing of bone tissue engineering scaffolds. It also presents our philosophy and research in the designing and fabrication of bone tissue engineering scaffolds through 3D printing.

Aptamer-gold nanoparticle doped covalent organic framework followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for selective enrichment and detection of human insulin

In this work, we introduced an aptamer modified Au nanoparticles doped covalent organic frameworks composite (IBAs-AuNPs/COF) to improve the property of selective enrichment of insulin from serum samples. The Au nanoparticles were immobilized on imine-based COF by in-situ reduction reaction via mussel inspired polydopamine coating, and then sulfhydryl-containing aptamers were bonded to the surface of AuNPs through an Au-S linkage. Due to the excellent adsorption property of COF and specific recognition between insulin and IBAs, the IBAs-AuNPs/COF composites show selective and satisfactory extraction property to insulin in serum samples. Excellent specifity was obtained for insulin in the presence of 50-fold interfering substances including human immunoglobulin, lysozyme and biotin. The concentrations of insulin in the range of 1.0 to 50.0 μg L^-1 show good linear relationship (R² = 0.9917) with limit of detection and limit of quantitation of 0.28 μg L^-1 and 0.93 μg L^-1, respectively. Then, the IBAs-AuNPs/COF composites were applied to enrich insulin in serum samples followed by analysis with matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS). After the recovery experiment, the developed method shows good recoveries in range of 91.6%-112.4% with low RSD value (2.4%-9.4%, n = 3) for diabetic and healthy serum samples. The developed IBAs-AuNPs/COF composites propose a new perspective for selective and efficient enrichment of biomarkers in serum samples by functionalized COF.

Covalent immobilization of biomolecules on stent materials through mussel adhesive protein coating to form biofunctional films

It is widely accepted that surface biofunctional modification may be an effective approach to improve biocompatibility and confer new bioactive properties on biomaterials. In this work, mussel adhesive protein (MAP) was applied as a coating on 316 L stainless steel substrates (316 L SS) and stents, and then either immobilized VEGF or CD34 antibody were added to create biofunctional films. The properties of the MAP coating were characterized by scanning electron microscope (SEM), atomic force microscope (AFM) and a water contact angle test. Universal tensile testing showed that the MAP coating has adequate adhesion strength on a 316 L stainless steel material surface. Subsequent cytotoxicity and hemolysis rate tests showed that the MAP coatings have good biocompatibility. Moreover, using N-(3-Dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride and N-hydroxysulfosussinimide (EDC/NHS) chemistry, VEGF and CD34 antibody were immobilized on the MAP coatings. The amount and immobilized yield of VEGF on the MAP coatings were analyzed by enzyme-linked immuno-assays (ELISA). Finally, an endothelial cells culture showed that the VEGF biofunctional film can promote the viability and proliferation of endothelial cells. An in vitro CD34⁺ cells capturing test also verified the bioactive properties of the CD34 antibody coated stents. These results showed that the MAP coatings allowed effective biomolecule immobilization, providing a promising platform for vascular device modification.

Enzymatically Catalyzed Radiofluorination of Biomolecules

There has been significant and rapid growth in the development of amino acid-based molecular imaging agents (e.g., peptides, proteins, and antibody constructs) largely due to facile library preparation and high throughput screening. Positron-emitting fluorine-18 (half-life = 109.7 min) has a unique set of properties that match well with the pharmacokinetics of smaller sized constructs. Several indirect fluorine-18 labeling approaches have been developed yet only a few have advanced to human trials. Enzymatically catalyzed radiofluorination utilizing lipoic acid ligase shows promise as a mild site-specific method for coupling fluorine-18-labeled carboxylate substrates with biomolecules. Methods for preparation of two [¹⁸F]fluorocarboxylates and their ligation to a specific peptide sequence (LAP peptide) are presented herein.

Nitrogen-dependent metabolic regulation of lipid production in microalga Scenedesmus vacuolatus

Microalga Scenedesmus vacuolatus exhibited maximum growth, protein and carbohydrate contents at 10.0 mM concentration of nitrate, 1.0 mM of glutamate nitrogen and at C/N ratio (12 mM acetate+10 mM nitrate). However, these cell constituents showed the highest values in the C+N grown cells, but the lipid content was found to be the highest glutamate grown cells. FTIR analysis of Lipid/Carbohydrate and Lipid/Protein ratio and flow cytometric analysis of neutral lipids revealed higher lipid content in the glutamate grown cells than in the nitrogen starved, nitrate and C+N grown cells. The nitrate reductase activity was the highest in the C+ N grown cells and the lowest activity was found in the glutamate grown cells. A corollary of these results suggested that suppression of nitrogen assimilatory system, whether by glutamate or by nitrogen deprivation, was the most suitable physiological condition for enhanced lipid synthesis and biofuel production in microalgal cells.

Abiotic phosphorus recycling from adsorbed ribonucleotides on a ferrihydrite-type mineral: Probing solution and surface species

Iron (Fe) (oxyhydr)oxide minerals, which are amongst most reactive minerals in soils and sediments, are known to exhibit strong adsorption of inorganic phosphate (P_i) and organophosphate (P_o) compounds. Beyond synthetic P_o compounds, much still remains unknown about the reactivity of these minerals to transform naturally-occurring P_o compounds to P_i, particularly with respect to solution versus surface speciation of P_o hydrolysis. To investigate this reactivity with a ferrihydrite-type mineral and ribonucleotides, we employed high-resolution liquid chromatography-mass spectrometry (LC-MS), X-ray absorption near-edge structure (XANES), Fourier-transform infrared (FTIR) spectroscopy, and molecular modeling. Kinetic experiments were conducted with the mineral (1 g L^-1) reacted with adenosine monophosphate, diphosphate, or triphosphate (respectively AMP, ADP, ATP; 50 µM). Analysis of solution organic species by LC-MS implied that only adsorption occurred with AMP and ADP but both adsorption and dephosphorylation of ATP were evident. Maximum adsorption capacities per gram of mineral were 40.6 ± 0.8 µmol AMP, 35.7 ± 1.6 µmol ADP, and 10.9 ± 1.0 µmol ATP; solution dephosphorylated by-products accounted for 15% of initial ATP. Subsequent XANES analysis of the surface species revealed that 16% of adsorbed AMP and 30% of adsorbed ATP were subjected to dephosphorylation, which was not fully quantifiable from the solution measurements. Molecular simulations predicted that ADP and ATP were complexed mainly via the phosphate groups whereas AMP binding also involved multiple hydrogen bonds with the adenosine moiety; our FTIR data confirmed these binding confirmations. Our findings thus imply that specific adsorption mechanisms dictate the recycling and subsequent trapping of P_i from ribonucleotide-like biomolecules reacted with Fe (oxyhydr)oxide minerals.

Computational solvation analysis of biomolecules in aqueous ionic liquid mixtures : From large flexible proteins to small rigid drugs

Based on their tunable properties, ionic liquids attracted significant interest to replace conventional, organic solvents in biomolecular applications. Following a Gartner cycle, the expectations on this new class of solvents dropped after the initial hype due to the high viscosity, hydrolysis, and toxicity problems as well as their high cost. Since not all possible combinations of cations and anions can be tested experimentally, fundamental knowledge on the interaction of the ionic liquid ions with water and with biomolecules is mandatory to optimize the solvation behavior, the biodegradability, and the costs of the ionic liquid. Here, we report on current computational approaches to characterize the impact of the ionic liquid ions on the structure and dynamics of the biomolecule and its solvation layer to explore the full potential of ionic liquids.

G-quadruplex aptamer selection using capillary electrophoresis-LED-induced fluorescence and Illumina sequencing

One of the major difficulties that arises when selecting aptamers containing a G-quadruplex is the correct amplification of the ssDNA sequence. Can aptamers containing a G-quadruplex be selected from a degenerate library using non-equilibrium capillary electrophoresis (CE) of equilibrium mixtures (NECEEM) along with high-throughput Illumina sequencing? In this article, we present some mismatches of the G-quadruplex T29 aptamer specific to thrombin, which was PCR amplified and sequenced by Illumina sequencing. Then, we show the proportionality between the number of sequenced molecules of T29 added to the library and the number of sequences obtained in Illumina sequencing, and we find that T29 sequences from this aptamer can be detected in a random library of ssDNA after the sample is fractionated by NECEEM, amplified by PCR, and sequenced. Treatment of the data by the counting of double-stranded DNA T29 sequences containing a maximum of two mismatches reveals a good correlation with the enrichment factor (f_E). This factor is the ratio of the number of aptamer sequences found in the collected complex sample divided by the total number of sequencing reads (aptamer and non-aptamer) plus the quantity of T29 molecules (spiked into a DNA library) injected into CE.

From Molecules to Life: Quantifying the Complexity of Chemical and Biological Systems in the Universe

Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms. Entities with a certain level of information complexity directly require a functionally complex mechanism for their production or replication and are hence indicative for life-like systems. In order to describe entities combining molecular and information complexity, the term biogenic unit was introduced. Exemplified biogenic unit complexities were calculated for ribozymes, protein enzymes, multimeric protein complexes, and even an entire virus particle. Complexities of prokaryotic and eukaryotic cells, as well as multicellular organisms, were estimated. Thereby distinct evolutionary stages in complexity space were identified. The here developed approach to compare the complexity of biogenic units allows for the first time to address the gradual characteristics of prebiotic and life-like systems without the need for a definition of life. This operational concept may guide our search for life in the Universe, and it may direct the investigations of prebiotic trajectories that lead towards the evolution of complexity at the origins of life.

Effects of florfenicol on the antioxidant status, detoxification system and biomolecule damage in the swimming crab (Portunus trituberculatus)

Florfenicol (FLR) is the most commonly used antibacterial agent in aquaculture because of its wide spectrum of activity and few side-effects. We characterized the toxicokinetics of FLR in the swimming crab (Portunus trituberculatus) after intravenous (IV) dosing (20, 40 and 80mg/kg). The results showed that FLR significantly suppressed the antioxidant system of the hepatopancreas. FLR induced transcriptional expression of phase I and phase II detoxification genes (CYP3 and GST, respectively) in a dose- and clearance time-dependent manner and altered the expression of their corresponding enzymes (erythromycin N-demethylase and glutathione S-transferase, respectively). Moreover, FLR induced the transcription of ATP-binding cassette (ABC) transporter subfamily B (ABCB) and subfamily G (ABCG), although ABCG transcription was not induced by FLR at 20mg/kg. Additionally, higher FLR doses caused significant biomolecule damage during the first 48h after delivery. This study will provide an improved understanding of the exact mechanism underlying toxicity in aquatic organisms.

Molecular dynamics simulations and applications in computational toxicology and nanotoxicology

Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations.

NOESY-WaterControl: a new NOESY sequence for the observation of under-water protein resonances

Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω₂). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω₂. The 2D NOESY maps obtained using the new sequence thus provide more information than the maps obtained with conventional water suppression, thereby lessening the number of experiments needed to complete resonance assignments of biomolecules. The 2D NOESY-WaterControl map of BPTI showed strong bound water and exchangeable proton signals in ω₁ but these signals were absent in ω₂, indicating the possibility of using the new sequence to discriminate bound water and exchangeable proton resonances from non-labile proton resonances with similar chemical shifts to water.

Poly(lactic acid) for delivery of bioactive macromolecules

Therapeutic biomolecules often require frequent administration and supramolecular dosing to achieve therapeutic efficiencies and direct infusion into treatment or defect sites results in inadequate physiological response and at times severe side effects or mis-targeting. Delivery systems serve several purposes such as increased circulatory time, increased biomolecule half-life, and incorporation of new innovations can enable highly specific cell targeting and improved cell and nucleus permeability. Poly(lactic acid) (PLA) has become a "material of choice" due to wide availability, reproducible synthetic route, customization, versatility, biodegradability and biocompatibility. Furthermore, PLA is amenable to a variety of fabrication methodologies and chemistries allowing an expansive library correlating physio-chemical properties, characteristics, and applications. This article discusses challenges to biomolecule delivery, and classical approaches of PLA based biomolecule delivery and targeting strategies under development and in trials.

Biosensors based on graphene oxide and its biomedical application

Graphene oxide (GO) is one of the most attributed materials for opening new possibilities in the development of next generation biosensors. Due to the coexistence of hydrophobic domain from pristine graphite structure and hydrophilic oxygen containing functional groups, GO exhibits good water dispersibility, biocompatibility, and high affinity for specific biomolecules as well as properties of graphene itself partly depending on preparation methods. These properties of GO provided a lot of opportunities for the development of novel biological sensing platforms, including biosensors based on fluorescence resonance energy transfer (FRET), laser desorption/ionization mass spectrometry (LDI-MS), surface-enhanced Raman spectroscopy (SERS), and electrochemical detection. In this review, we classify GO-based biological sensors developed so far by their signal generation strategy and provide the comprehensive overview of them. In addition, we offer insights into how the GO attributed in each sensor system and how they improved the sensing performance.

Contact time- and pH-dependent adhesion and cohesion of low molecular weight chitosan coated surfaces

Low molecular weight chitosan (LMW chitosan, ∼5 kDa) potentially has many desirable biomedical applications such as anti-microbial, anti-tumor, and anti-diabetes. Unlike high molecular weight chitosan, LMW chitosan is easily dissolvable in aqueous solutions even at neutral and basic pH, but its dissolution mechanism is not well understood. Here, we measured adhesion and cohesion of molecularly thin LMW chitosan films in aqueous solutions in different buffer pHs (from 3.0 to 8.5) using a surface forces apparatus (SFA). Interestingly, significantly lower adhesion force was measured for LMW chitosan films compared to the high molecular weight chitosan (∼150 kDa) films. Not only the strength of adhesion is lower, but also the critical contact time where adhesion starts to increase with contact time is longer. The results from both the SFA and atomic force microscopy (AFM) indicate that, in physiological and basic conditions, the low cohesion of LMW chitosan due to the stiffness of the chain which cause strong electrostatic correlation energy penalty when they are aggregated. Here, we propose the reduction in cohesion for shorter chitosan (LMW chitosan) as an explanation of its high solubility of LMW chitosan in physiological pHs.

Highly sensitive, selective and rapid LC-MS method for simultaneous quantification of diadenosine polyphosphates in human plasma

BACKGROUND

Diadenosine polyphosphates (ApnAs) are endogenous mediators involved in large number of physiologic and pathophysiologic processes. The quantification of diadenosine polyphosphates in plasma and biological matrices is still challenging. Therefore, there is an urgent need for a simple and reliable quantification method suitable for clinical studies. The classical quantification of diadenosine polyphosphates is based on chromatographic separation and UV adsorption of the resulting fractions. These procedures are associated with low selectivity due to co-eluting plasma components. Therefore, we developed and validated a highly sensitive, selective and rapid LC-ESI-MS method for simultaneous quantification of ApnAs (with n=3-6) in human plasma within this study. The identities of the endogenous ApnAs (with n=3-6) were revealed by comparison of ESI-MS/MS fragment spectra of isolated endogenous compounds with those of authentic ApnAs.

METHODS

Diadenosine polyphosphates were extracted from 100μl human plasma using weak anion-exchange extraction cartridges. The separation of ApnAs was achieved using capillary C18 columns. ESI-HCT mass spectrometer (Bruker Daltonik, Germany) operated in negative ion mode was used for detection and quantification of ApnAs.

RESULTS

A calibration curve was established for diadenosine polyphosphate free plasma in the concentration range 1.9-125nM (r(2)>0.998) for all analytes. The intra- and inter-day accuracies were in the range of 91.4% and 110.9%. The intra- and inter-day precisions were determines as 0.1% and 11.4%, respectively. The mean plasma concentrations of ApnAs were quantified as 31.9±5.9nM for Ap3A, 40.4±6.6nM for Ap4A, 10.7±1.5nM for Ap5A and 10.0±18.9nM for Ap6A.

DISCUSSION

The developed and validated ESI MS-based method for quantification of diadenosine polyphosphates in human plasma was successfully evaluated within the study. Conclusion Since the quantification is based on a volume of 100μl plasma, this method is highly applicable for clinical applications aiming at the validation of the impact of highly physiological and pathophysiological active diadenosine polyphosphates.

Protein and water confined in nanometer-scale reverse micelles studied by near infrared, terahertz, and ultrafast visible spectroscopies

Protein-containing reverse (PCR) micelles are suitable systems to study the properties of proteins and waters in a cell-like environment. A model for determining the structural parameters of PCR micelles, such as the aqueous cavity size and molecule number of water within the reverse micelle, is presented. The model is based on an important hypothesis that the structural parameters of the protein-unfilled reverse micelle do not change after solubilization of protein. I describe a procedure using near infrared spectroscopy of OH stretching vibration band of water to verify the hypothesis. Further, the terahertz (THz) absorption spectrum of myoglobin is derived from THz time-domain spectroscopy of the PCR micellar solution, and the states of waters in reverse micelles with and without protein are discussed on the basis of the structural parameters. The last topic is on internal dynamics of PCR micelles on timescales from femtoseconds to nanoseconds studied by femtosecond time-resolved fluorescence spectroscopy.

A highly sensitive and label free biosensing platform for wireless sensor node system

In this paper, we propose a radio-frequency (RF) biosensor platform based on oscillation frequency deviation at 2.4 GHz. Its feasibility is experimentally demonstrated with the well-known biomolecular binding systems such as biotin-streptavidin and deoxyribonucleic acid (DNA) hybridization. For a basic principle of our biosensing system, the impedance of a resonator with the biomolecular immobilization is at first varied so that the corresponding change results in frequency change of an oscillator. Especially, to enhance the sensitivity of the proposed system, a surface acoustic wave (SAW) filter having a high-Q factor (~2000) is utilized. From the resulting component, even a small change of oscillation frequency can be transformed into a large output amplitude variation. According to the experimental results, it is found that our system shows the low detectable limit (~1 ng/ml) and fast response time (~real-time) for different target biomolecules, i.e. streptavidin and complementary DNA (cDNA). As a result, we find that our device is an effective biosensing system that can be used for a label-free and real-time measurement of the biomolecular binding events.