Iron/iron oxide nanoparticles: advances in microbial fabrication, mechanism study, biomedical, and environmental applications.

Microbially synthesized iron oxide nanoparticles (FeONPs) hold great potential for biomedical, clinical, and environmental applications owing to their several unique features. Biomineralization, a process that exists in almost every living organism playing a significant role in the fabrication of FeONPs through the involvement of 5-100 nm sized protein compartments such as dodecameric (Dps), ferritin, and encapsulin with their diameters 9, 12, and ∼32 nm, respectively. This contribution provides a detailed overview of the green synthesis of FeONPs by microbes and their applications in biomedical and environmental fields. The first part describes our understanding in the biological fabrication of zero-valent FeONPs with special emphasis on ferroxidase (FO) mediated series of steps involving in the translocation, oxidation, nucleation, and storage of iron in Dps, ferritin, and encapsulin protein nano-compartments. Secondly, this review elaborates the significance of biologically synthesized FeONPs in biomedical science for the detection, treatment, and prevention of various diseases. Thirdly, we tried to provide the recent advances of using FeONPs in the environmental process, e.g. detection, degradation, remediation and treatment of toxic pesticides, dyes, metals, and wastewater.

Biological synthesis of metallic nanoparticles (MNPs) by plants and microbes: their cellular uptake, biocompatibility, and biomedical applications.

Metallic nanoparticles (MNPs) with their diverse physical and chemical properties have been applied in various biomedical domains. The increasing demand for MNPs has attracted researchers to develop straightforward, inexpensive, simple, and eco-friendly processes for the enhanced production of MNPs. To discover new biomedical applications first requires knowledge of the interactions of MNPs with target cells. This review focuses on plant and microbial synthesis of biological MNPs, their cellular uptake, biocompatibility, any biological consequences such as cytotoxicity, and biomedical applications. We highlighted the involvement of biomolecules in capping and stabilization of MNPs and the effect of physicochemical parameters particularly the pH on the synthesis of MNPs. Recently achieved milestones to understand the role of synthetic biology (SynBiol) in the synthesis of tailored MNPs are also discussed.

Enhanced remediation of bispyribac sodium by wheat (Triticum aestivum) and a bispyribac sodium degrading bacterial consortium (BDAM).

The use of plant-bacterial association is a promising approach for the enhanced remediation of pesticides. Generally, both rhizo- and endosphere bacteria assist their host plants to survive in the contaminated environment. In this work, we have studied the individual and combined effects of wheat (Triticum aestivum) and a previously optimized bispyribac sodium (BS) degrading bacterial consortium (BDAM) on the degradation of BS and plant biomass production. Results showed that the bacterial strains of the BDAM have successfully survived in the plant rhizo-as well as endosphere and enhanced degradation of BS and plant biomass. In soil spiked with 2 mg/kg and 5 mg/kg of BS and was planted and inoculated with BDAM (P_I) showed 100% degradation of BS both in rhizosphere soil and endosphere of the plant. However, during the same period (45 days) the degradation of BS was 96 and 90%, and 93 and 84% in inoculated but un-planted (I_UP) and planted but un-inoculated (P_UI) soils spiked with 2 and 5 mg/kg, respectively. Liquid chromatography-mass spectrometry (LC-MS) analysis of the treated samples showed novel degradation products of BS. Based on the results, we concluded that plant-bacterial association is an efficient tool for enhanced remediation of BS contaminated soil and herbicide free crop production.

Effects of large gradient high magnetic field (LG-HMF) on the long-term culture of aquatic organisms: Planarians example.

Large gradient high magnetic field (LG-HMF) is a powerful tool to study the effects of altered gravity on organisms. In our study, a platform for the long-term culture of aquatic organisms was designed based on a special superconducting magnet with an LG-HMF, which can provide three apparent gravity levels (µ g, 1 g, and 2 g), along with a control condition on the ground. Planarians, Dugesia japonica, were head-amputated and cultured for 5 days in a platform for head reconstruction. After planarian head regeneration, all samples were taken out from the superconducting magnet for a behavioral test under geomagnetic field and normal gravity conditions. To analyze differences among the four groups, four aspects of the planarians were considered, including head regeneration rate, phototaxis response, locomotor velocity, and righting behavior. Data showed that there was no significant difference in the planarian head regeneration rate under simulated altered gravity. According to statistical analysis of the behavioral test, all of the groups had normal functioning of the phototaxis response, while the planarians that underwent head reconstruction under the microgravity environment had significantly slower locomotor velocity and spent more time in righting behavior. Furthermore, histological staining and immunohistochemistry results helped us reveal that the locomotor system of planarians was affected by the simulated microgravity environment. We further demonstrated that the circular muscle of the planarians was weakened (hematoxylin and eosin staining), and the epithelial cilia of the planarians were reduced (anti-acetylated tubulin staining) under the simulated microgravity environment. Bioelectromagnetics. 2018;39:428-440. © 2018 Wiley Periodicals, Inc.

High-efficiency antibacterial calcium alginate/lysozyme/AgNPs composite sponge for wound healing.

Infection poses a significant barrier to effective wound repair, leading to increased inflammatory responses that ultimately result in incomplete and prolonged wound healing. To address this challenge, numerous antibacterial ingredients have been incorporated into dressings to inhibit wound infection. Our previous work demonstrated that lysozyme/silver nanoparticles (LYZ/AgNPs) complexes, prepared using an eco-friendly one-step aqueous method, exhibited excellent antibacterial efficacy with favorable biosafety. To further explore its potential application in advancing wound healing, calcium alginate (CA) with good porosity, water absorption, and water retention capacities was formulated with LYZ/AgNPs to prepare composite sponge (CA/LYZ/AgNPs). As expected, in vivo experiments involving full-thickness skin wound and scald wound healing experiments demonstrated that CA-LYZ-AgNPs composite sponges with excellent biocompatibility exhibited remarkable antibacterial activity against gram-positive bacteria, gram-negative bacteria and fungi, and outperformed the wound healing process efficacy of other commercially available AgNPs-loaded wound dressings. In summary, this work introduces a CA/LYZ/AgNPs sponge featuring exceptional antibacterial efficacy and biocompatibility, thus holding promising potential in wound care applications.

A strategy for selecting the pH of protein solutions to enhance crystallization.

The pH of a solution is an important parameter in crystallization that needs to be controlled in order to ensure success. The actual pH of the crystallization droplet is determined by the combined contribution of the buffers in the screening and protein solutions, although the contribution of the latter to the pH is often ignored. In this study, the effects of the buffer and protein solution pH values on the results of screening are systematically investigated. It was found that these parameters significantly affected the results and thus the following strategy for the selection of appropriate pH values is proposed: (i) when screening with only one protein solution, the pH should be as low, as high or as divergent from the pI as possible for a basic, acidic or neutral protein, respectively, within its stable pH range; (ii) when screening with two protein solutions, the pH values should be well separated from one another; and (iii) when multiple pH values are utilized, an even distribution of pH values is the best approach to increase the success rate of crystallization.

Correlation between protein sequence similarity and crystallization reagents in the biological macromolecule crystallization database.

The protein structural entries grew far slower than the sequence entries. This is partly due to the bottleneck in obtaining diffraction quality protein crystals for structural determination using X-ray crystallography. The first step to achieve protein crystallization is to find out suitable chemical reagents. However, it is not an easy task. Exhausting trial and error tests of numerous combinations of different reagents mixed with the protein solution are usually necessary to screen out the pursuing crystallization conditions. Therefore, any attempts to help find suitable reagents for protein crystallization are helpful. In this paper, an analysis of the relationship between the protein sequence similarity and the crystallization reagents according to the information from the existing databases is presented. We extracted information of reagents and sequences from the Biological Macromolecule Crystallization Database (BMCD) and the Protein Data Bank (PDB) database, classified the proteins into different clusters according to the sequence similarity, and statistically analyzed the relationship between the sequence similarity and the crystallization reagents. The results showed that there is a pronounced positive correlation between them. Therefore, according to the correlation, prediction of feasible chemical reagents that are suitable to be used in crystallization screens for a specific protein is possible.

[Viral pathogens of acute lower respiratory tract infection in hospitalized children from East Guangdong of China].

OBJECTIVE: To investigate the viral pathogens of acute lower respiratory tract infection (ALRTI) in hospitalized children from East Guangdong Province of China and the relationship of the pathogens with age and seasons. METHODS: The nasopharyngeal aspirates samples obtained from 345 hospitalized children with ALRTI were investigated for respiratory syncytial virus (RSV), human bocavirus (HBoV), human metapneumovirus (hMPV), influenza virus types A and B, rhinovirus, parainfluenza virus types 1 and 3 and adenovirus by PCR. RESULTS: Viral pathogens were detected in 178 patients (51.6%). RSV was the most frequent (19.3%). Novel viruses hMPV (3.2%) and HBoV (3.2%) were found. A highest detection rate (61.9%) of virus was found between January to March. The infants aged 1 to 6 months showed a higher detection rate (71.3%) of virus than the other age groups. The detection rate of viral pathogens was 72.6% in children with bronchiolitis, followed by asthmatic bronchitis (70.0%) and bronchial pneumonia (44.6%). CONCLUSIONS: RSV remained the leading viral pathogens in children with ALRTI in East Guangdong of China. Novel viruses HBoV and hMPV were also important pathogens. The detection rate of viral pathogens was associated with seasonal changes and age. Different respiratory infectious diseases had different viral detection rates, with highest detection rate in bronchiolitis cases.

Optimization for silver remediation from aqueous solution by novel bacterial isolates using response surface methodology: Recovery and characterization of biogenic AgNPs.

Silver is a toxic but precious heavy metal that has been implemented in diverse biomedical and environmental sectors. Extensive use of this metal has provoked severe environmental concerns. Hence there is an increasing demand for the development of a simple, inexpensive and eco-friendly approach for the remediation and recovery of silver. In this study, novel bacterial strains Enterobacter cloacae SMP1, Cupriavidus necator SMP2, and Bacillus megaterium SMP3 were isolated from silver mining site for the sake of silver remediation. Various experimental factors including temperature, pH and inoculum size (I_S) were optimized for silver remediation by SMP1 using central composite design (CCD) based on response surface methodology (RSM). For maximum 100% removal of silver the optimized values of temperature, pH and I_S were 23.5 °C, 7.5 and 2% (v/v) respectively in less than 10 h of incubation. Simultaneously, silver nanoparticles (AgNPs) were harvested through centrifugation (M1) and by applying voltage (M2) to the crude remediation mixture. The AgNPs, characterized by UV-vis spectroscopy, dynamic light scattering (DLS), and cryo-scanning transmission electron microscopy (Cryo-SETM), were spherical shaped and 1.75-8.7 nm in diameter. The average zeta potentials (ZP) of AgNPs isolated by M1, and M2 were -35.8 mV and -45.2 mV respectively.

RNA binding motif protein 3: a potential biomarker in cancer and therapeutic target in neuroprotection.

RNA binding motif 3 (RBM3) is a highly conserved cold-induced RNA binding protein that is transcriptionally up-regulated in response to harsh stresses. Featured as RNA binding protein, RBM3 is involved in mRNA biogenesis as well as stimulating protein synthesis, promoting proliferation and exerting anti-apoptotic functions. Nowadays, accumulating immunohistochemically studies have suggested RBM3 function as a proto-oncogene that is associated with tumor progression and metastasis in various cancers. Moreover, emerging evidences have also indicated that RBM3 is equally effective in neuroprotection. In the present review, we provide an overview of current knowledge concerning the role of RBM3 in various cancers and neuroprotection. Additionally, its potential roles as a promising diagnostic marker for cancer and a possible therapeutic target for neuro-related diseases are discussed.

Ligand-binding characterization of simulated ß-adrenergic-like octopamine receptor in Schistocerca gregaria via progressive structure simulation.

It is important to design insecticides having both low drug resistance and less undesirable toxicity for desert locust control. Specific GPCRs of Schistocerca gregaria, especially ß-adrenergic-like octopamine receptor (SgOctßR), can be considered as its potential effective insecticide targets. However, either the unavailability of SgOctßR's structure or the inadequate capability of its sequence lead the development of insecticide for Schistocerca gregaria meets its plateau. To relax this difficulty, this paper develops a promising progressive structure simulation from SgOctßR's sequence, to its predicted structure of SgOctßR in vacuum, to its conformation as well as its complex with endogenous ligand octopamine in a solvent-membrane system. The combined approach of multiple sequence alignment, static structural characterization, and dynamic process of conformational change during binding octopamine reveal three important aspects. The first one is the characterization of SgOctßR's active pocket, including the attending secondary structure elements, its hydrophobic residues and nonpolar surface. The second one is the interaction with octopamine, especially the involved hydrogen bonds and an aromatic stacking of pi-pi interactions. The third one is the potential binding sites, including six highly conserved residues and one highly variable residue for locust insecticide design. This work is definitely helpful for the further structure-based drug design for efficient and eco-friendly insecticides, as well as site-directed mutagenesis biochemical research of SgOctßR.

Myocyte enhancer factor 2C and its directly-interacting proteins: A review.

Myocyte enhancer factor 2C (MEF2C) is a transcription factor of MADS box family involved in the early development of several human cells including muscle (i.e., skeletal, cardiac, and smooth), neural, chondroid, immune, and endothelial cells. Dysfunction of MEF2C leads to embryo hypoplasia, disorganized myofibers and perinatal lethality. The main role of MEF2C is its regulation of muscle development. It has been reported that MEF2C-knockout mice die on embryonic day 9.5 from unnatural development of cardiovascular. The effects of MEF2C are mediated by its directly-interacting proteins; therefore, the investigation of these interactions is critical in order to clarify MEF2C's biological function. In this study, we review twenty-five proteins that directly interact with MEF2C, including nineteen proteins related to muscle development, four proteins related to neural cell development, one protein related to chondroid cell development, four proteins related to immune cell development, and two proteins related to endothelial cell development. Among these proteins, the interaction of MEF2C with MRFs is important for differentiation of developing muscle cells. MEF2C interacts with Sox18 for endothelial vessel morphogenesis. The interaction of MEF2C with Cabin1 is important for maintaining T-cell inactivation. Investigating the interactions of MEF2C and its directly-interacting proteins is not only helpful to understand of the physiological function of MEF2C, but also provides a target for future rational drug design.

Preparation of cross-linked hen-egg white lysozyme crystals free of cracks.

Cross-linked protein crystals (CLPCs) are very useful materials in applications such as biosensors, catalysis, and X-ray crystallography. Hence, preparation of CLPCs is an important research direction. During the preparation of CLPCs, an often encountered problem is that cracks may appear in the crystals, which may finally lead to shattering of the crystals into small pieces and cause problem in practical applications. To avoid cross-link induced cracking, it is necessary to study the cracking phenomenon in the preparation process. In this paper, we present an investigation on how to avoid cracking during preparation of CLPCs. An orthogonal experiment was designed to study the phenomenon of cross-link induced cracking of hen-egg white lysozyme (HEWL) crystals against five parameters (temperature, solution pH, crystal growth time, glutaraldehyde concentration, and cross-linking time). The experimental results showed that, the solution pH and crystal growth time can significantly affect cross-link induced cracking. The possible mechanism was studied, and optimized conditions for obtaining crack-free CLPCs were obtained and experimentally verified.

A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive.

Recombinant expression of proteins has become an indispensable tool in modern day research. The large yields of recombinantly expressed proteins accelerate the structural and functional characterization of proteins. Nevertheless, there are literature reported that the recombinant proteins show some differences in structure and function as compared with the native ones. Now there have been more than 100,000 structures (from both recombinant and native sources) publicly available in the Protein Data Bank (PDB) archive, which makes it possible to investigate if there exist any proteins in the RCSB PDB archive that have identical sequence but have some difference in structures. In this paper, we present the results of a systematic comparative study of the 3D structures of identical naturally purified versus recombinantly expressed proteins. The structural data and sequence information of the proteins were mined from the RCSB PDB archive. The combinatorial extension (CE), FATCAT-flexible and TM-Align methods were employed to align the protein structures. The root-mean-square distance (RMSD), TM-score, P-value, Z-score, secondary structural elements and hydrogen bonds were used to assess the structure similarity. A thorough analysis of the PDB archive generated five-hundred-seventeen pairs of native and recombinant proteins that have identical sequence. There were no pairs of proteins that had the same sequence and significantly different structural fold, which support the hypothesis that expression in a heterologous host usually could fold correctly into their native forms.