Charge self-trapping in two strand biomolecules:Adiabatic polaron approach

We investigate the properties of the excess charge(electron, hole) introduced into a two-strand biomolecule. We consider the possibility that the stable soliton excitation can be formed due to interaction of excess charge with the phonon subsystem. The influence of overlap of the molecular orbitals between adjacent structure elements of the macromolecular chain on the soliton properties is discussed. Special attention is paid to the influence of the overlapping of the molecular orbitals between structure elements placed on the different chains. Using the literature values of the basic energy parameters of the two-chain biomolecular structures, possible types of soliton solutions are discussed.

Effect of Purified Paper Wasp Ropalidia marginata Venom Toxins on Different Biomolecules in Mice Serum

This study evaluated the effects of purified paper wasp Ropalidia marginata venoms on various biomolecules in the blood serum of albino mice. Changes in the concentration of some important macromolecules, i.e., proteins, free amino acids, uric acid, cholesterol, pyruvic acid, total lipids and glucose were noted down. These alterations were measured after intraperitoneal injection of 40% and 80% 24-hour LD50 purified Ropalidia marginata venom toxin. Serum total protein levels were found to decrease to 78% after 6 hrs, while serum free amino acid levels were significantly increased to 117% 6 hrs after venom injection compared to control. It was also found that serum uric acid levels increased to 138% after 8 hrs of venom injection compared to control. The increase in serum cholesterol i.e. (101% and 106%) and pyruvic acid increased significantly to a maximum value of 106% after 6 hrs of treatment at 40% LD50. Glycogen levels in the gastrocnemius muscle were found to decrease significantly (p-0.05) to 43% and 92% at LD50 after injection of purified Ropalidia marginata venom after 8 h and 80% at LD50 compared to control. Moreover, up to 71% and 81% were obtained at 10 hrs of treatment with the same dose. In the present study, the purified toxins significantly changed the levels of biomolecules in blood serum, indicating their wider effects on cellular physiology due to toxic effects and stress on the animal. These toxins can be good antigens and stimulate immune responses in experimental mice.

Investigation of photon energy absorption properties for some biomolecules

The mass energy absorption coefficient (len=q), effective atomic number (ZPEAeff ), and electron density (NPEAeff ) of some biomolecules with potential application in radiation dosimetry were calculated for their photon energy absorption (PEA) in the energy region of 1–20 MeV. It was noticed that the values of len=q, ZPEAeff , and NPEAeff vary with the energy and composition of the biomolecules. The results for ZPEAeff were compared with effective atomic numbers (ZPIeff ) owing to the photon interaction (PI). Significant differences were noted between ZPEAeff and ZPIeff in the energy region of 10–150 keV for all of the biomolecules involved. A maximum difference of 45.36% was observed at 50 keV for creatinine hydrochloride. Moreover, the studied attenuation parameters were found to be sharply affected at the K-absorption edge of relatively high-Z elements present in the biomolecules.

Transitional metal ions induced damage to biomolecules:role of ferryl and perferryl radicals

Objective:To investigate the effect of oxidized transitional metal（ferric and cupric） ions on the amino acids.Methods:25 mmol/L hydroxyproline and 25 mmol/L histidine were incubated with 50μL Fe3+ and Cu2+ ions at pH 7.4 and 37℃for 30 mins in separate test tubes.Then 500μL of 1% thiobarbituricacid（TBA） was added to the incubated amino acids followed by addition of 500μL of glacial acetic acid.The resultant mixture was vortexed and heated at 100℃for 30 min.Absorbance readings were noted after cooling to room temperature.The experiment was repeated in the presence of various reagents,like hydroxyl radical scavengers,antioxidant enzymes,and reducing agents and metal ion chelators.Results:The pink chromogen formed with the absorbance maxima at 524 nm,AND shifted to 560 nm in alkaline pH.The absorbance was expressed as TBAadduct in MDA units.The TBA-adduct decreased in the presence of reducing agents and metal ion chelators.Antioxidant enzymes and hydroxyl radical scavengers did not show any effect. Conclusion:Transitional metal ions in their oxidized state showed significant damage to amino acids,hydroxyproline and histidine.The results indicate the possible role played by high-valent oxo-iron species,ferryl and perferry radicals in damaging biomolecules.

Evaluation of attraction terms in equations of state on the prediction of solubility of some biomolecules in supercritical carbon dioxide

In the present work, effect of the attraction terms of four recently modified Peng-Robinson （MPR） equations of state on the prediction of solubility of caffeine, cholesterol, uracil and erythromycin was studied. The attraction terms of two of these equations are linear relative to the acentric factor and for the other two are exponential. It is found that the later show less deviation. Also interaction parameters for the studied systems are obtained and the percentage of average absolute relative deviation （%AARD） in each calculation is displayed.

PMMA Polymer Membrane-Based Single Cylindrical Submicron Pores: Electrical Characterization and Investigation of Their Applicability in Resistive-Pulse Biomolecule Detection

Single cylindrical submicron pores in PMMA polymer membranes are micropatterned by electron beam lithography and integrated into all PMMA-based electrophoretic flow detector systems. Pore dimensions are 450 nm in diameter and 1 μm in length. The pores are electrically characterized in aqueous KCl electrolyte, exhibiting a stable time-independent ionic current through the pore with a noise level of less than 1% of the open-pore current. The current-voltage curves are linear and scale with electrolyte concentration. The negative surface charge of the membrane over-proportionally decreases pore conductance at low electrolyte concentrations (≤0.1 M) that are still beyond those typically applied in biological experiments. Pores do not exhibit rectification of current flowing through them, allowing for operation with either polarity. To allow for detection of yet much smaller particles, the described PMMA-based system also was successfully equipped with pores of 1.5 nm instead of 450 nm in diameter. This was achieved by introducing naturally occurring biological protein pores of α-hemolysin on a lipid bilayer into the prepatterned PMMA membrane of an assembled PMMA-based electrophoretic flow detector system. Characteristics of translocation events of single-stranded linear plasmid DNA molecules through the pores were recorded, and ionic current deductions during biomolecule translocation were clear and distinguished. Based on the presented submicron scale open pore ionic current transport properties, as well as the observed passage of DNA molecules through protein pores inserted into PMMA membranes, our current research proposes that all PMMA electrophoretic flow detectors exhibit an excellent potential for future use as biomedical resistive-pulse sensors, as long as pore dimensions match those of biomolecules to be detected.

Mesophilic Process and Kinetics Studies of Selected Biomolecules as Potential Enhancers of Biomethanization of Cow Dung in an Anaerobic Tubular Batch Reactor

Mesophilic biogas production and substrate decomposition is one of the significant limiting steps in biogas generation. The rate of generation and quality often affect the viability of biogas systems. This study assessed the potential for biogas process catalysis using powdered Sorghum bicolor L., Zea mays, and Pennisetum glaucum. The kinetics and biogas generation processes were studied. Experiments were conducted in 1 m3 tubular batch reactors, where batches were dosed with various organic biomolecules. Results show that the use of P. glaucum L. and S. bicolor L. reduced the biogas retention times significantly. Biogas generation commenced after the first day for digesters fed with S. bicolor L. and P. glaucum L. while one with Z. mays and control occurred on day two. The rate of biomethanation and methane content were enhanced. S. bicolor L. led to the highest methane content. Findings reveal that locally available organic biomolecules improved biogas quality and quantity.

Excess adsorption of biomolecules on soft surfaces: Adsorption of DNA, proteins and lactose on fatty surfaces

Insoluble fatty surfaces are involved in many important interactions such as in biomembranes with soluble biological macro and micromolecules. In this paper we have studied the adsorption interaction of aqueous solution of DNA, some proteins and lactose on several sparingly soluble fatty substances namely milk fat, stearic acid, palmitic acid, phosphatidyl choline and cholesterol surfaces by measuring the depletion of the adsorbates by analytical methods. Adsorption () of DNA on the soft surfaces of stearic acid, milk fat, phosphatidyl choline, palmitic acid and cholesterol was measured as a function of DNA concentration C2. In each case was found to increase with C2 until it reached the maximum value at a critical concentration . For different surfaces stands in the order: stearic acid > milk fat > phosphatidyl choline > cholesterol > palmitic acid. DNA forms multilayers on stearic acid surface. Adsorption of hemoglobin on cholesterol surface is found to be negative or zero but that of BSA on cholesterol is positive. Adsorption of gelatin on cholesterol surface is significantly higher than that of BSA. Lysozyme on cholesterol surface forms multilayers and on casein forms bilayer. The lowering of free energies ?DGo for all systems have been calculated using integrated form of the Gibbs adsorption and their values have been compared with each other. It is concluded that despite differences in the adsorption behavior of the biomolecules on various soft surfaces, free energy change expressed as Bull’s free energy change (Δ) remain nearly constant except for BSA-fatty acid interaction which may be likely due a specific interaction.

Oxidative Consumption of Oral Biomolecules by Therapeutically-Relevant Doses of Ozone

In view of its potent microbicidal actions, ozone (O3) offers much potential for application as a therapeutic agent in oral health, e.g. in the treatment of dental caries. This oxidant is extremely reactive towards biomolecules present in the oral environment, and in this study we have employed high-resolution proton (1H) nuclear magnetic resonance (NMR) spectroscopy to determine the nature and extent of the oxidation of biomolecules known to be present in carious dentin, plaque and saliva. Phosphate-buffered (pH 7.00) aqueous solutions containing sodium pyruvate, α-D-glucose, L-cys teine and L-methionine (5.00 mM) were treated with gaseous O3 (4.48 mmol.) delivered by a therapeutic O3 generating device. Attack of O3 on methionine and cysteine generated the corresponding primary oxidation products of these substrates, specifically methionine sulphoxide [98% ± 4% (mean ± SEM) yield] and cystine (95% ± 6% yield) respectively, and treatment of pyruvate with this oxidant produced acetate and CO2 via an oxidative decarboxylation process (93% ± 4% yield). Reaction of O3 with α-D-glucose gave rise to formate as a major product (24% ± 2% yield). In conclusion, multicomponent 1H NMR analysis of appropriate chemical model systems provides valuable molecular information regarding the reactivity of O3 towards biomolecules present in the oral environment, information which is of much relevance to its therapeutic mechanisms of action. Moreover, in view of the much higher concentrations of these O3-scavenging biomolecules in oral fluid and/or soft tissue environments than that of O3 applied, they may also serve to offer protection against putative adverse effects inducible by any of this oxidant which escapes from its site of therapeutic application (e.g., at primary root carious lesions).

Living Matter in Crash Test:How Biomolecules Respond to Mecha nical Forces

The Group on Protein Mechanics and Evolution at the CAS-MPG Partner Institute for Computational Biology,Shanghai,was established in January 2007 and headed by Dr.Frauke Gr?ter.The Klaus Tschira Lab has continued the eff orts of this former Independent Junior Research Group,since Dr.Gr?ter took up a position at the Heidelberg Institute of Theoretical Studies(HITS)in Heidelberg,Germany。

Real-Time and Spatial Electroanalysis of Biomolecules in One Living Cell Using Liquid-Phase Modified Nanopipette

The well-developed solid-phase modified strategy at the electrode has enabled the preparation of biosensors for the detection of multiple analytes,even in single living cells.However,limited assay elements can be modified at the solid surface,restricting the types of molecules that can be analyzed and the sensitivity of detection.Here,a novel liquid-phase modified strategy at the tip of a nanopipette is designed to realize real-time and local analysis of biomolecules inside the cell that are barely detectable using solid-phase modified nanoelectrodes.This design utilizes the nanotip structure at a platinized carbon open nanopipette to stably retain a nanodroplet that contains the required reagents with high reactivity for the assay of the target analyte.The generated hydrogen peroxide is electrochemically quantified at the Pt layer to carry out the real-time measurement in a living cell with a spatial resolution of 70 nm.Taking advantage of highly spatial and real-time detection,uneven distribution of sphingomyelinase(SMase)in the living CT26 cell is unprecedentedly shown to exhibit the significance in the establishment of liquid-phase modified nanopipette.This new modification strategy opens up a new direction for sensor design and consequently advances the development of biosensors in the chemical and biological research.

Advances in probing single biomolecules: From DNA bases to glycans

Imaging biomolecules in real space is crucial for gaining a comprehensive understanding of the properties and functions of biological systems at the most fundamental level.Among the various imaging techniques available for biomolecules and their assembled nanostructures,scanning probe microscopy(SPM)provides a powerful and nondestructive imaging option.SPM is unique in visualizing intrinsically disordered biomolecules at the nanometer scale(e.g.,glycans).This review highlights recent achievements in studying biomolecules using SPM technique,focusing on DNA bases,amino acids,proteins,and glycans.The atomic-level analysis of biomolecules made possible by SPM allows for a more accurate definition of the local structure–property relationship.High-resolution SPM imaging of single biomolecules offers a new way to study basic processes of life at the molecular level.

Biomolecule capturing and sensing on 2D transition metal dichalcogenide canvas

Since the isolation of graphene in 2004,two-dimensional(2D)materials such as transition metal dichalcogenide(TMD)have attracted numerous interests due to their unique van der Waals structure,atomically thin body,and thickness-dependent properties.In recent years,the applications of TMD in public health have emerged due to their large surface area and high surface sensitivities,as well as their unique electrical,optical,and electrochemical properties.In this review,we focus on state-of-the-art methods to modulate the properties of 2D TMD and their applications in biosensing.Particularly,this review provides methods for designing and modulating 2D TMD via defect engineering and morphology control to achieve multi-functional surfaces for molecule capturing and sensing.Furthermore,we compare the 2D TMD-based biosensors with the traditional sensing systems,deepening our understanding of their action mechanism.Finally,we point out the challenges and opportunities of 2D TMD in this emerging area.

Manipulation and detection of single nanoparticles and biomolecules by a photonic nanojet

Optical methods to manipulate and detect nanoscale objects are highly desired in both nanomaterials and molecular biology fields.Optical tweezers have been used to manipulate objects that range in size from a few hundred nanometres to several micrometres.The emergence of near-field methods that overcome the diffraction limit has enabled the manipulation of objects below 100 nm.A highly free manipulation with signal-enhanced real-time detection,however,remains a challenge for single sub-100-nm nanoparticles or biomolecules.Here we show an approach that uses a photonic nanojet to perform the manipulation and detection of single sub-100-nm objects.With the photonic nanojet generated by a dielectric microlens bound to an optical fibre probe,three-dimensional manipulations were achieved for a single 85-nm fluorescent polystyrene nanoparticle as well as for a plasmid DNA molecule.Backscattering and fluorescent signals were detected with the enhancement factors up to~103 and~30,respectively.The demonstrated approach provides a potentially powerful tool for nanostructure assembly,biosensing and single-biomolecule studies.

From surface to bulk modification: Plasma polymerization of amine-bearing coating by synergic strategy of biomolecule grafting and nitric oxide loading

Integration of two or more biomolecules with synergetic and complementary effects on a material surface can help to obtain multi-functions for various biomedical applications.However,the amounts of biomolecules integrated and their physiological functions are compromised due to the limited surface anchoring sites.Herein,we propose a novel concept of film engineering strategy“from surface to bulk synergetic modification”.This new concept is realized by employing the surface amine groups of plasma polymerized allylamine(PPAm)film for grafting a molecule e.g.,thrombin inhibitor,bivalirudin(BVLD),meanwhile its bulk amine groups is used as a universal depot for storing and releasing therapeutic nitric oxide(NO)gas as supplement to the functions of BVLD.It is demonstrated that such a“from surface to bulk synergetic modification”film engineering can impart the modified-substrates with anti-platelet and anti-coagulant dual functions,giving rise to a highly endotheliummimetic thromboresistant property.We believe that our research provides a very promising strategy to deliver multifunctional surface versatilely that require NO release in combination with other properties,which will find broad biomedical applications in blood-contacting devices,and et al.Moreover,it also provides a brand-new film engineering strategy for tailoring surface multi-functionalities of a wide range of materials.

Overcome Debye Length Limitations for Biomolecule Sensing Based on Field Effective Transistors

Biosensors based on field effective transistor(FET)have aroused tremendous attention in the past few years owning to their huge application in drug discovery,disease diagnosis and environmental monitoring.The FET biosensors possess small volume,high sensitivity at ultra-low concentration,considerable mechanical strength,as well as excellent stability in solution,which plays a vital role in the point of care testing(POCT)systems.Recent advances have summarized some progress involved in the improvement of morphology and structure of channel materials,the functionalization of organic molecule,the influence of device operation and sensing environment on the detecting performance.However,for FET biosensors,the charge screening phenomena were inevitable in the solution,which seriously degrade the device performance.In this article,we summarize recent advances to overcome debye length limitations for biomolecule sensing based on FET.We will firstly describe the charge screening mechanism,then focous on the strategy to overcome charge screening,including synthesizing special channel materials with crumpled morphology,designing aptamer binding mode,and modulating device measurement.Finally,we discuss the major challenges and perspectives about overcoming debye length limitations of FET biosensors.These summaries provide further insights to realize real-time,lable-free,high-sensitivity FET sensors for medical healthcare.

Recent advances in molecular fluorescent probes for organic phosphate biomolecules recognition

Organic phosphate biomolecules(OPBs) are indispensable components of eukaryotes and prokaryotes,such as acting as the fundamental components of cell membranes and important substrates for nucleic acids. They play pivotal roles in various biological processes, such as energy conservation, metabolism,and signal modulation. Due to the difficulty of detection caused by variety OPBs, investigation of their respective physiological effects in organisms has been restrained by the lack of efficient tools. Many small fluorescent probes have been employed for selective detection and monitoring of OPBs in vitro or in vivo due to the advantages of tailored properties, biodegradability and in situ high temporal and spatial resolution imaging. In this review, we summarize the recent advances in fluorescent probes for OPBs,such as nucleotides, NAD(P)H, FAD/FMN and PS. Importantly, we describe their identification mechanisms in detail and discuss the general strategies for these OPBs probe designs, which provide new insights and ideas for the future probe designs.

Biomolecule-templated photochemical synthesis of silver nanoparticles： Multiple readouts of localized surface plasmon resonance for pattern recognition

Silver nanoparticles （AgNPs） with distinct localized surface plasmon resonance （LSPR） absorption spectra can be synthesized using different proteins as templates upon irradiation by light. We utilized the multiple readouts of LSPR signals of AgNPs to construct sensor arrays for pattern recognition of proteins. Room temperature, aqueous solutions, and lack of harsh reducing reagents make the whole process inherently ＂green＂. Meanwhile, the strategy efficiently simplified the process of array-receptor preparation and data acquisition, leading to lower time consumption, sample use, and cost. Furthermore, the system can differentiate proteins using flexible and alterable sensor elements by choosing different combinations of LSPR signals at different wavelengths. The principle of the sensor design can also be further extended to differentiate other biomolecules. The study provides a new method to construct feasible, economical, and general nanoparficle-based sensing arrays for pattern recognition.

Glassy dynamics of water at interface with biomolecules: A Mode Coupling Theory test

We study the slow dynamics of hydration water upon cooling in two different biological aqueous solutions,one containing a molecule of lysozyme and another with trehalose molecules.In particular we test if the glassy behaviour of these solutions fulfils the predictions of the popular Mode Coupling Theory of glassy dynamics.In particular we test the Time Temperature Superposition Principle and the matching of the exponents of the theory.Our results confirm that this theory is able to describe the dynamical behaviour of supercooled water also in non ideal cases as the ones under investigation in the region of mild supercooling.

Advances in the pathogenesis and clinical application prospects of tumor biomolecules in keloid

Keloid scarring is a kind of pathological healing manifestation after skin injury and possesses various tumor properties,such as the Warburg effect,epithelial-mesenchymal transition(EMT),expression imbalances of apoptosis-related genes and the presence of stem cells.Abnormal expression of tumor signatures is critical to the initiation and operation of these effects.Although previous experimental studies have recognized the potential value of a single or several tumor biomolecules in keloids,a comprehensive evaluation system for multiple tumor signatures in keloid scarring is still lacking.This paper aims to summarize tumor biomolecules in keloids from the perspectives of liquid biopsy,genetics,proteomics and epigenetics and to investigate their mechanisms of action and feasibility from bench to bedside.Liquid biopsy is suitable for the early screening of people with keloids due to its noninvasive and accurate performance.Epigenetic biomarkers do not require changes in the gene sequence and their reversibility and tissue specificity make them ideal therapeutic targets.Nonetheless,given the ethnic specificity and genetic predisposition of keloids,more large-sample multicenter studies are indispensable for determining the prevalence of these signatures and for establishing diagnostic criteria and therapeutic efficacy estimations based on these molecules.