Biomacromolecules Research Articles

Development and systematical evaluation of an up-converting phosphor technology based lateral flow assay for quantitative detection of Burkholderia pseudomallei

To develop an up-converting phosphor technology-based lateral-flow (UPT-LF) assay for rapid quantitative detection of Burkholderia pseudomallei on site. The strip Bps-UPT-LF strip was prepared with up-converting phosphor (UCP) particles as the bio-label using double-antibody sandwich method. Detection performance, including sensitivity, quantitative accuracy, precision, and specificity, were first evaluated using bacterial suspensions of Burkholderia pseudomallei, the related species and the strains which had similar routes of transmission with serial standard concentrations diluted by phosphate buffer, then biological and chemical reagents and simulated samples with series concentrations were employed for sample tolerance evaluation, while the operation error during on site detection was also evaluated through adjusting liquid measure. The whole detection was accomplished within 20 minutes, and the sensitivity was 10(4) CFU/ml with linear quantitative range from 10(4) CFU/ml to 10(7) CFU/ml, which covered four orders of magnitude. Bps-UPT-LF strip demonstrated high specificity with the absence of any false-positive result even at 10(7) and 10(8) CFU/ml of non-specific bacterial contamination. Not only Bps-UPT-LF strip could tolerate to high concentration of the extreme acid and basic matter (pH 1-12), saline matter (≤ 2 mol/L mixture of NaCl and KCl), viscous materials (≤ 50 g/L of PEG 20000 and ≤ 20% of glycerol) and bio-macromolecule (≥ 400 g/L of bovine serum albumin or ≥ 80 g/L of casein), but also it can directly detect animal, environmental and powder specimen, such as ≥ 400 g/L of milk powder, flour powder, fruit juice, fresh and decomposed viscera, and ≤ 200 g/L of putty powder, sucrose, gourmet powder, and soil. Operation errors of liquid measure had few effects on sensitivity and specificity, including -50%-200% of sample, -22%-44% of sample-treating buffer and -30%-30% of loading mixture. The good detection performance and tolerance performance bring the bright future for Bps-UPT-LF strip to detect Burkholderia pseudomallei on site rapidly and quantitatively for nature foci surveillance and anti-bioterrorism.

Polymeric 3D nano-architectures for transport and delivery of therapeutically relevant biomacromolecules.

A promising approach for addressing a range of diseases lies in the delivery of functional biomacromolecules such as nucleic acids or proteins to cells. Polymers, peptides and the different shapes accessible through self-assembly of polymeric and peptidic amphiphiles have been widely explored as carriers and as containers for reactions on the nanoscale. These building blocks are particularly interesting, because several essential parameters such as physical characteristics, conditions for degradation or biocompatibility can be tuned to suit specific requirements. In this review, different three-dimensional architectures ranging from dendrimers and hyperbranched molecules to micelles, vesicles and nanoparticles assembled from synthetic polymers and peptides are discussed. It is focused on their function as a carrier for biologically active macromolecules, highlighting seminal examples from the current literature and pointing out the remaining and upcoming challenges in this important area of research.

Recent advances in preparative electromigration techniques for proteins

Preparative electromigration techniques are a category of separation and preparation techniques based on differential electromigration principle. These techniques are widely applied in biomacromolecule and proteome researches. Related techniques mainly include preparative electrophoresis, preparative electrochromatography, preparative isoelectric focusing and free flow electrophoresis and so on. We review each kind of the preparative electromigration techniques on its apparatus designs, applications, advantages and disadvantages in detail. Microscale preparative electrophoresis is a hot spot in recent years. Its high resolution, high recovery and high efficiency make it a more prominent role in the biological sample analysis. In this review, we focus on some advances in microscale preparative electrophoresis and also give an outlook on preparative electromigration techniques in the future.

Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: Advances toward treatment of hepatitis B virus infections

The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV–visible and the number of binding sites were 3.33±0.2×104Lmol−1and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH=34.4kJmol−1; ΔS=184.32Jmol−1K−1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure −16.83kJmol−1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

Research progress of tissue-engineered oral mucosa

Large area defect of intra-oral or extra-oral mucosa caused by mucosa lesions need suitable graft materials for repair.Tissue engineering methods can provide effective pathway to resolve this problem.Furthermore,full thickness mucosa equivalent constructed by tissue engineering methods also can be used as a model to evaluate dental materials,drug delivery system and oral carcinogenesis.Basic issues of tissue-engineered mucosa including sources of seed cells,scaffold materials such as de-epidermised acellular dermis,collagens,fibrin glue and biomacromolecule electrostatic spinning are discussed in this review,and the application researches of tissueengineered mucosa for mucosa reconstruction and mucosa model equivalents are expounded too. Key words: Oral mucosa; Tissue engineering; Transplantation; Model; Squamous cell carcinoma

Community structure of non-coding RNA interaction network.

Rapid technological advances have shown that the ratio of non-protein coding genes rises to 98.5% in humans, suggesting that current knowledge on genetic information processing might be largely incomplete. It implies that protein-coding sequences only represent a small fraction of cellular transcriptional information. Here, we examine the community structure of the network defined by functional interactions between non-coding RNAs (ncRNAs) and proteins related bio-macromolecules (PRMs) using a two-fold approach: modularity in bipartite network and k-clique community detection. First, the high modularity scores as well as the distribution of community sizes showing a scaling-law revealed manifestly non-random features. Second, the k-clique sub-graphs and overlaps show that the identified communities of the ncRNA molecules of H. sapiens can potentially be associated with certain functions. These findings highlight the complex modular structure of ncRNA interactions and its possible regulatory roles in the cell.

Microbial Transformation of Biomacromolecules in a Membrane Bioreactor: Implications for Membrane Fouling Investigation

BackgroundThe complex characteristics and unclear biological fate of biomacromolecules (BMM), including colloidal and soluble microbial products (SMP), extracellular polymeric substances (EPS) and membrane surface foulants (MSF), are crucial factors that limit our understanding of membrane fouling in membrane bioreactors (MBRs).FindingsIn this study, the microbial transformation of BMM was investigated in a lab-scale MBR by well-controlled bioassay tests. The results of experimental measurements and mathematical modeling show that SMP, EPS, and MSF had different biodegradation behaviors and kinetic models. Based on the multi-exponential G models, SMP were mainly composed of slowly biodegradable polysaccharides (PS), proteins (PN), and non-biodegradable humic substances (HS). In contrast, EPS contained a large number of readily biodegradable PN, slowly biodegradable PS and HS. MSF were dominated by slowly biodegradable PS, which had a degradation rate constant similar to that of SMP-PS, while degradation behaviors of MSF-PN and MSF-HS were much more similar to those of EPS-PN and EPS-HS, respectively. In addition, the large-molecular weight (MW) compounds (>100 kDa) in BMM were found to have a faster microbial transformation rate compared to the small-MW compounds (<5 kDa). The parallel factor (PARAFAC) modeling of three-dimensional fluorescence excitation-emission matrix (EEM) spectra showed that the tryptophan-like PN were one of the major fractions in the BMM and they were more readily biodegradable than the HS. Besides microbial mineralization, humification and hydrolysis could be viewed as two important biotransformation mechanisms of large-MW compounds during the biodegradation process.SignificanceThe results of this work can aid in tracking the origin of membrane foulants from the perspective of the biotransformation behaviors of SMP, EPS, and MSF.

Role of microorganism growth phase in the accumulation and characteristics of biomacromolecules (BMM) in a membrane bioreactor

The objective of this study was to highlight the significance of microorganism growth on the production of biomacromolecules (BMM) in a membrane bioreactor (MBR). During the MBR operation, both polysaccharides and proteins in the sludge supernatant were found to increase steadily in exponential growth phase (EGP) due to higher organic loading rates and microbial primary metabolism. Subsequently, both increased continuously and then decreased sharply in the following deceleration growth phase (DGP). Finally, the BMM maintained a low and steady level as the sludge reached stationary growth phase (SGP). The results of batch experiments showed that the sludge under DGP was prone to produce much more BMM than that under SGP as a result of a nutrients decrease and higher microbial secondary metabolism activities. Furthermore, large-molecular weight (MW) compounds (>100 kDa) made up the majority of BMM in the EGP and DGP. In contrast, the small-MW compounds (<5 kDa) became a more and more important BMM fraction as the microorganism growth shifted to the SGP. The characterization by three-dimensional excitation-emission matrix (EEM) fluorescence spectroscopy indicated that the fluorescence compounds in the BMM pool were mainly comprised of aromatic and tryptophan protein-like substances, and humic substances. The protein-like substances were related with microorganism growth more greatly than the humic substances. Generally, the microorganism physiological stages (i.e.growth/decay) play a crucial role in the formation of BMM in the MBRs.

Characterization of the size-fractionated biomacromolecules: Tracking their role and fate in a membrane bioreactor

This article presents a study aimed at the fractionation and characterization of what is thought to be one of the most complex organic mixtures produced by activated sludge: biomacromolecules (BMM). Photometric quantification combined with excitation–emission matrix (EEM) fluorescence spectroscopy and nuclear magnetic resonance (NMR) measurements were used to characterize BMM in a membrane bioreactor (MBR) from a chemical perspective. Overall, the BMM in sludge supernatant were mainly present in three fractions: colloidal BMM (BMMc, >0.45 μm), biopolymeric BMM (BMMb, 0.45 μm–100 kDa) and low molecular weight (MW) fraction (<5 kDa). The analysis of fluorescence regional integration (FRI) showed that the organics in membrane permeate and those in the low-MW fraction of sludge supernatant were of similar chemical composition. The characterization by NMR suggested that the BMMc fraction had similar carbon content of proteins and polysaccharides. In contrast, the BMMb and the low-MW BMM were proved to be carbonaceous and aromatics, respectively. Moreover, because of the high MW and gelling property, polysaccharides were found to have a high potential to accumulate on the membranes. In addition, the lipids present in the BMMb of the sludge supernatant were demonstrated to be another important foulant due to their large size. Our results also indicated that aromatic proteins had a higher fouling propensity than tryptophan proteins though they were of similar size nature. This work could be useful for better understanding of the chemical nature of BMMs in MBRs.

Novel nanoplatform for oral delivery of anti-cancer biomacromolecules

Oral administration of bio–macromolecules is an uphill task and the challenges from varying pH and enzymatic activity are difficult to overcome. In this regard, nanotechnology promises the new hope and offers advantages such as controlled release, target specific delivery, combinatorial therapy and many more. In this study, we demonstrate the formulation of a novel alginate enclosed, chitosan coated ceramic, anti cancer nano carrier (ACSC NC). These NC were loaded with multi functional anti cancer bovine lactoferrin (Lf), a natural milk based protein, for improvement of intestinal absorption, in order to develop a novel platform to carry anti cancer protein and/or peptides for oral therapy. Here we demonstrate the size, morphology, internalisation and release profiles of the nanoparticles (NC) under varying pH as perceived in human digestive system. We further determine the uptake of these particles by colon cancer cell lines by measuring the endocytosis and transcytosis of the NC. These NC can be used for future targeted protein/peptide or nucleic acid based drug delivery to treat difficult diseases including cancer.

Application of scanning probe microscopes to nanostructures of biomacromolecules in food systems.

Application of scanning probe microscopes to nanostructures of biomacromolecules in food systems.

Biomacromolecules: Introduction to structure, Function and Informatics. By C. Stan Tsai

Biomacromolecules: Introduction to structure, Function and Informatics. By C. Stan Tsai

Dissolution of biomacromolecules in organic solvents by nano-complexing with poly(ethylene glycol)

Various biomacromolecules (BMs) such as proteins, DNA, and carbohydrates are extremely difficult to be dissolved in a single organic solvent phase for sustained release or targeted delivery formulation. In this study, three different BMs could be solubilized in selected organic solvents by forming poly(ethylene glycol) (PEG)-assisted nano-complexes while maintaining their structural integrity. Dynamic light scattering (DLS) and atomic force microscopy (AFM) analysis revealed that proteins, DNA, and carbohydrate polymers could be nano-complexed with PEG in various organic solvents. The diameter of nano-complexes decreased roughly from ∼600 nm to ∼100 nm with increasing weight ratio of PEG/BM. The present solubilization technique could be potentially applied for sustained release formulations of various therapeutic biological drugs.

Biomacromolecules: Introduction to structure, function, and informatics by C. S. Tsai

Biomacromolecules: Introduction to structure, function, and informatics by C. S. Tsai

Biomacromolecules: Intrduction to structure, Function and Informatics. By C. Stan Tsai

Biomacromolecules: Intrduction to structure, Function and Informatics. By C. Stan Tsai

Biomacromolecules: Introduction to structure, Function and Informatics. By C. Stan Tsai

Biomacromolecules: Introduction to structure, Function and Informatics. By C. Stan Tsai

Biomacromolecules of Algae and Plants and their Fossil Analogues

Biomacromolecules of Algae and Plants and their Fossil Analogues

Immobilization of biomacromolecules on poly-L-lactide surface via a layer-by-layer method for the improving of its cytocompatibility to bone marrow stromal cells

Hyaluronic acid (HA) and chitosan (CS) were immobilized on the surface of poly-L-lactide (PLLA) by the following procedure: Firstly, PLLA was aminolyzed with 1, 6-hexanediamine, and part of the PLLA surface ester groups were converted to free amino groups. Then negatively charged hyaluronic acid and positively charged chitosan were deposited onto the surface of aminolyzed PLLA film in a layer-by-layer assembly manner. The effect of the layer-by-layer deposition was evaluated by ATR-FTIR spectroscopy, Raman spectroscopy and static contact angle measurements. The cytocompatibility of PLLA sample to bone marrow stromal cells (BMSCs) was improved after modification with chitosan and HA. The cell attachment, activity, and proliferation on CS/HA modified PLLA films were enhanced comparing with the control. The cells cultured on the modified PLLA samples excreted abundant cytoplasm and can differentiate to vascular smooth muscle (SM)-like (SM-like) cells. A macroporous three-dimensional PLLA scaffold was prepared by integrating both the technique of freeze-drying and particle leaching. Layer-by-layer modification by HA/CS and cell culture was also applied on this scaffold. The scaffold cultured with BMSCs for 2 weeks has been tested successfully in vivo as a patch for repairing the artificial incision on canine pulmonary artery.

3SA05 生体水素水和水データベース(生物情報データベースの高度化・標準化)

3SA05 生体水素水和水データベース(生物情報データベースの高度化・標準化)

Silicification and biosilicification - Part 7: Poly-L-arginine mediated bioinspired synthesis of silica

Precipitated silica is synthesized commercially by neutralizing sodium silicate solution under harsh conditions of pH and temperature. In contrast, the formation of ornate silica structures in biological systems (biosilicification) occurs at (or close to) pH 7 under ambient conditions and is thought to be mediated by proteins. Determination of the primary sequences of these proteins has led to the identification of various amino acids that have been proposed to be important in biosilicification. The corresponding synthetic polyamino acids are now being successfully used in bioinspired materials chemistry for developing new materials and processes. Here we report the formation of well-defined silica in vitro as facilitated by poly-L-arginine (PLAr) under ambient conditions and at neutral pH. Two different silica precursors were used in this investigation; tetramethoxysilane (TMOS) and water glass. Scanning Electron Microscopy (SEM) was used for studying the silica morphology and it was revealed that the silica spheres had typical diameters in the range 300–500nm. The PLAr is a cationically charged macromolecule at neutral pH and is believed to act as a catalyst/template/scaffold for the formation of silica in vitro in analogous fashion to certain biomacromolecules that are able to facilitate silicification/biosilicification. These results are discussed here in the context of the role(s) of (bio)macromolecules that facilitate (bio)mineralization.