Miniaturized bead-beating device to automate full DNA sample preparation processes for gram-positive bacteria

We have developed a miniaturized bead-beating device to automate nucleic acids extraction from Gram-positive bacteria for molecular diagnostics. The microfluidic device was fabricated by sandwiching a monolithic flexible polydimethylsiloxane (PDMS) membrane between two glass wafers (i.e., glass-PDMS-glass), which acted as an actuator for bead collision via its pneumatic vibration without additional lysis equipment. The Gram-positive bacteria, S. aureus and methicillin-resistant S. aureus, were captured on surface-modified glass beads from 1 mL of initial sample solution and in situ lyzed by bead-beating operation. Then, 10 μL or 20 μL of bacterial DNA solution was eluted and amplified successfully by real-time PCR. It was found that liquid volume fraction played a crucial role in determining the cell lysis efficiency in a confined chamber by facilitating membrane deflection and bead motion. The miniaturized bead-beating operation disrupted most of S. aureus within 3 min, which turned out to be as efficient as the conventional benchtop vortexing machine or the enzyme-based lysis technique. The effective cell concentration was significantly enhanced with the reduction of initial sample volume by 50 or 100 times. Combination of such analyte enrichment and in situ bead-beating lysis provided an excellent PCR detection sensitivity amounting to ca. 46 CFU even for the Gram-positive bacteria. The proposed bead-beating microdevice is potentially useful as a nucleic acid extraction method toward a PCR-based sample-to-answer system.     

Inhibition of NF-κB prevents high glucose-induced proliferation and plasminogen activator inhibitor-1 expression in vascular smooth muscle cells

Recent epidemiologic studies clearly showed that early intensive glucose control has a legacy effect for preventing diabetic macrovascular complications. However, the cellular and molecular processes by which high glucose leads to macrovascular complications are poorly understood. Vascular smooth muscle cell (VSMC) dysfunction due to high glucose is a characteristic of diabetic vascular complications. Activation of nuclear factor-κB (NF-κB) may play a key role in the regulation of inflammation and proliferation of VSMCs. We examined whether VSMC proliferation and plasminogen activator inhibitor-1 (PAI-1) expression induced by high glucose were mediated by NF-κB activation. Also, we determined whether selective inhibition of NF-κB would inhibit proliferation and PAI-1 expression in VSMCs. VSMCs of the aorta of male SD rats were treated with various concentrations of glucose (5.6, 11.1, 16.7, and 22.2 mM) with or without an inhibitor of NF-κB or expression of a recombinant adenovirus vector encoding an IκB-α mutant (Ad-IκBαM). VSMC proliferation was examined using an MTT assay. PAI-1 expression was assayed by real-time PCR and PAI-1 protein in the media was measured by ELISA. NF-κB activation was determined by immunohistochemical staining, NF-κB reporter assay, and immunoblotting. We found that glucose stimulated VSMC proliferation and PAI-1 expression in a dose-dependent manner up to 22.2 mM. High glucose (22.2 mM) alone induced an increase in NF-κB activity. Treatment with inhibitors of NF-κB such as MG132, PDTC or expression of Ad-IκB-αM in VSMCs prevented VSMC proliferation and PAI-1 expression induced by high glucose. In conclusion, inhibition of NF-κB activity prevented high glucose-induced VSMC proliferation and PAI-1 expression.     

Simvastatin inhibits osteoclast differentiation by scavenging reactive oxygen species

Osteoclasts, together with osteoblasts, control the amount of bone tissue and regulate bone remodeling. Osteoclast differentiation is an important factor related to the pathogenesis of bone-loss related diseases. Reactive oxygen species (ROS) acts as a signal mediator in osteoclast differentiation. Simvastatin, which inhibits 3-hydroxy-3-methylglutaryl coenzyme A, is a hypolipidemic drug which is known to affect bone metabolism and suppresses osteoclastogenesis induced by receptor activator of nuclear factor-κB ligand (RANKL). In this study, we analyzed whether simvastatin can inhibit RANKL-induced osteoclastogenesis through suppression of the subsequently formed ROS and investigated whether simvastatin can inhibit H2O2-induced signaling pathways in osteoclast differentiation. We found that simvastatin decreased expression of tartrate-resistant acid phosphatase (TRAP), a genetic marker of osteoclast differentiation, and inhibited intracellular ROS generation in RAW 264.7 cell lines. ROS generation activated NF-κB, protein kinases B (AKT), mitogen-activated protein kinases signaling pathways such as c-JUN N-terminal kinases, p38 MAP kinases as well as extracellular signal- regulated kinase. Simvastatin was found to suppress these H2O2-induced signaling pathways in osteoclastogenesis. Together, these results indicate that simvastatin acts as an osteoclastogenesis inhibitor through suppression of ROS-mediated signaling pathways. This indicates that simvastatin has potential usefulness for osteoporosis and pathological bone resorption.     

Versatile grafting approaches to star-shaped POSS-containing hybrid polymers using RAFT polymerization and click chemistry

An alkyne-bearing polyhedral oligomeric silsesquioxane (POSS) core was used to prepare POSS-containing polymer hybrids using 'grafting to' or 'grafting from' strategies in combination with reversible chain transfer and click chemistry.     

On the relationship between catalytic residues and their protein contact number

Due to advances in structural biology, an increasing number of protein structures of unknown function have been deposited in Protein Data Bank (PDB). These proteins are usually characterized by novel structures and sequences. Conventional comparative methodology (such as sequence alignment, structure comparison, or template search) is unable to determine their function. Thus, it is important to identify protein's function directly from its structure, but this is not an easy task. One of the strategies used is to analyze whether there are distinctive structure-derived features associated with functional residues. If so, one may be able to identify the functional residues directly from a single structure. Recently, we have shown that protein weighted contact number is related to atomic thermal fluctuations and can be used to derive motional correlations in proteins. In this report, we analyze the weighted contact-number profiles of both catalytic residues and non-catalytic residues for a dataset of 760 structures. We found that catalytic residues have distinct distributions of weighted contact numbers from those of non-catalytic residues. Using this feature, we are able to effectively differentiate catalytic residues from other residues with a single optimized threshold value. Our method is simple to implement and compares favourably with other more sophisticated methods. In addition, we discuss the physics behind the relationship between catalytic residues and their contact numbers as well as other features (such as residue centrality or B-factors) associated with catalytic residues.     

Anti-inflammatory and antioxidant components from Hygroryza aristata

Twenty-six known compounds and two new compounds, including a new lignan, (7S*,8R*,7'R*,8'S*)-icariol A?-9-O-β-xylopyranoside (1), and a new indole alkaloid, hygarine (2), were isolated from the extracts of Hygroryza aristata (Gramineae). The structures of all compounds were elucidated on the basis of NMR spectral analysis. The compounds (-)-epigallocatechin-3-O-gallate (4) and (-)-epicatechin-3-O-gallate (5) possess free radical scavenging activities and compound 1 could inhibit superoxide anion generation and elastase release by fMLP/CB-induced human neutrophils with IC?? values of 19.33 ± 0.86 and 24.14 ± 1.59 μM, respectively.     

High throughput label-free platform for statistical bio-molecular sensing

Sensors are crucial in many daily operations including security, environmental control, human diagnostics and patient monitoring. Screening and online monitoring require reliable and high-throughput sensing. We report on the demonstration of a high-throughput label-free sensor platform utilizing cantilever based sensors. These sensors have often been acclaimed to facilitate highly parallelized operation. Unfortunately, so far no concept has been presented which offers large datasets as well as easy liquid sample handling. We use optics and mechanics from a DVD player to handle liquid samples and to read-out cantilever deflection and resonant frequency. Also, surface roughness is measured. When combined with cantilever deflection the roughness is discovered to hold valuable additional information on specific and unspecific binding events. In a few minutes, 30 liquid samples can be analyzed in parallel, each by 24 cantilever-based sensors. The approach was used to detect the binding of streptavidin and antibodies.     

Controlled synthesis of CdSe quantum dots by a microwave-enhanced process: a green approach for mass production

A method that does not employ hot-injection techniques has been developed for the size-tunable synthesis of high-quality CdSe quantum dots (QDs) with zinc blende structure. In this environmentally benign synthetic route, which uses less toxic precursors, solvents, and capping ligands, CdSe QDs that absorb visible light are obtained. The size of the as-prepared CdSe QDs and thus their optical properties can be manipulated by changing the microwave reaction conditions. The QDs were characterized by XRD, TEM, UV/Vis, FTIR, time-resolved fluorescence spectroscopy, and fluorescence spectrophotometry. In this approach, the reaction is conducted in open air and at a much lower temperature than in hot-injection techniques. The use of microwaves in this process allows for a highly reproducible and effective synthesis protocol that is fully adaptable for mass production and can be easily employed to synthesize a variety of semiconductor QDs with the desired properties. Possible applications of the CdSe QDs were assessed by deposition on TiO(2) films.     

Preparation of airborne Ag/CNT hybrid nanoparticles using an aerosol process and their application to antimicrobial air filtration

Carbon nanotubes (CNTs) have been widely used in a variety of applications because of their unique structure and excellent mechanical and electrical properties. Additionally, silver (Ag) nanoparticles exhibit broad-spectrum biocidal activity toward many different bacteria, fungi, and viruses. In this study, we prepared Ag-coated CNT hybrid nanoparticles (Ag/CNTs) using aerosol nebulization and thermal evaporation/condensation processes and tested their usefulness for antimicrobial air filtration. Droplets were generated from a CNT suspension using a six-jet collison nebulizer, passed through a diffusion dryer to remove moisture, and entered a thermal tube furnace where silver nanoparticles were generated by thermal evaporation/condensation at ～980 °C in a nitrogen atmosphere. The CNT and Ag nanoparticle aerosols mixed together and attached to each other, forming Ag/CNTs. For physicochemical characterization, the Ag/CNTs were introduced into a scanning mobility particle sizer (SMPS) for size distribution measurements and were sampled by the nanoparticle sampler for morphological and elemental analyses. For antimicrobial air filtration applications, the airborne Ag/CNT particles generated were deposited continuously onto an air filter medium. Physical characteristics (fiber morphology, pressure drop, and filtration efficiency) and biological characteristics (antimicrobial tests against Staphylococcus epidermidis and Escherichia coli bioaerosols) were evaluated. Real-time SMPS and transmission electron microscopy (TEM) data showed that Ag nanoparticles that were <20 nm in diameter were homogeneously dispersed and adhered strongly to the CNT surfaces. Because of the attachment of Ag nanoparticles onto the CNT surfaces, the total particle surface area concentration measured by a nanoparticle surface area monitor (NSAM) was lower than the summation of each Ag nanoparticle and CNT generated. When Ag/CNTs were deposited on the surface of an air filter medium, the antimicrobial activity against test bacterial bioaerosols was enhanced, compared with the deposition of CNTs or Ag nanoparticles alone, whereas the filter pressure drop and bioaerosol filtration efficiency were similar to those of CNT deposition only. At a residence time of 2 h, the relative microbial viabilities of gram-positive S. epidermidis were ～32, 13, 5, and 0.9% on the control, CNT-, Ag nanoparticle-, and Ag/CNT-deposited filters, respectively, and those of gram-negative E. coli were 13, 2.1, 0.4, and 0.1% on the control, CNTs, Ag nanoparticles, and Ag/CNTs, respectively. These Ag/CNT hybrid nanoparticles may be useful for applications in biomedical devices and antibacterial control systems.     

Complete NMR data of methoxylated cis- and trans-stilbenes as well as 1,2-diphenylethanes

Resveratrol is a polyphenol isolated from many natural sources including grapes, mulberries, eucalyptus, spruce, lilies, and peanuts. The hydroxyl groups in polyphenols can be substituted with various functional groups, allowing production of multiple derivatives. NMR spectroscopy is used to identify new derivatives. Since the complete NMR data of the known derivatives can be useful for identification of the newly isolated derivatives, here, we report the synthesis of 14 methoxylated stilbenes and four 1,2-diphenylethanes and their NMR data.