Gel-based proteomics reveals potential novel protein markers of ozone stress in leaves of cultivated bean and maize species of Panama

We examined responses of cultivated bean (Phaseolus vulgaris L. cv. IDIAP R-3) and maize (Zea mays L. cv. Guarare 8128) plants exposed to ozone (O(3)) using a leaf injury assessment and proteomics approach. Plants grown for 16 days in greenhouse were transferred to an O(3) chamber and exposed continuously to 0.2 ppm O(3) or filtered pollutant-free air for up to 72 h. CBB-stained gels revealed changes in ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) protein. By Western analysis changes in marker proteins for O(3) damage in leaves by 1-DE were checked. In bean leaves, two superoxide dismutase (SOD) protein (19 and 20 kDa) were dramatically decreased, while ascorbate peroxidase (APX, 25 kDa), small heat shock protein (HSP, 33 kDa), and a naringenin-7-O-methyltransferase (NOMT, 42 kDa) were increased by O(3). In maize leaves, expression levels of catalase (increased), SOD (decreased), and APX (increased) were drastically changed by O(3) depending on the leaf stage, whereas crossreacting HSPs (24 and 30 kDa) and NOMT (41 kDa) proteins were strongly increased in O(3)-stressed younger leaves. These results indicated a clear modulation of oxidative stress-, heat shock-, and secondary metabolism-related proteins by O(3). Finally, 2-DE at 72 h after O(3) exposure revealed changes (induction/suppression) in expression levels of 25 and 12 protein spots in bean and maize leaves, respectively. Out of these, ten and nine nonredundant proteins in bean and maize, respectively, were identified by MS. A novel pathogenesis-related protein 2 may serve as a potential marker for O(3) stress in bean.     

Ultrahigh-pressure dual online solid phase extraction/capillary reverse-phase liquid chromatography/tandem mass spectrometry (DO-SPE/cRPLC/MS/MS): a versatile separation platform for high-throughput and highly sensitive proteomic analyses

Capillary RPLC/ESI-MS (cRPLC/ESI-MS) is one of the most powerful analytical tools for current proteomic research. The development of cRPLC techniques coupled online to a mass spectrometer has focused on increasing the separation efficiency, detection sensitivity, and throughput. Recently, the use of high-pressure (over 10,000 psi) LC systems that utilize long, small inner diameter capillary columns has gained much attention for proteomic analyses. In this study, we developed an ultrahigh-pressure dual online SPE/capillary RPLC (DO-SPE/cRPLC) system. This LC system employs two online SPE columns and two capillary columns (75 microm inner diameter x 1 m length) in a single separation system, and has a maximum operating pressure of 10,000 psi. This DO-SPE/cRPLC system is capable of providing high-resolution separation in addition to several other advantageous features, such as high reproducibility in terms of the LC retention time, rapid sample injection, online desalting, online sample enrichment of dilute samples, and increased throughput as a result of essentially removing the column equilibration time between successive experiments. We coupled the DO-SPE/cRPLC system online to a tandem mass spectrometer to allow high-throughput proteomic analyses. In this paper, we demonstrate the efficiency of this DO-SPE/cRPLC/MS/MS system by its use in the analyses of proteomic samples exhibiting different levels of complexity.     

Synthesis,X-ray crystal structure,and electrochemistry of trans-bis(ferrocenecarboxylato)(tetraphenylporphyrinato)tin(IV)

trans-Bis(ferrocenecarboxylato)(5,10,15,20-tetraphenylporphyrinato)tin(IV) complex Sn(TPP)(FcCOO)₂ has been synthesized and fully characterized. The X-ray structural analysis of Sn(TPP)(FcCOO)₂ reveals that the tin(IV) center is octahedrally coordinated by the porphyrin occupying the square base and axial coordination of two ferrocenecarboxylato ligands in an anti orientation with respect to each other. The Fe(II) center of the ferrocenecarboxylato ligand lies 5.7 Å from the tin(IV) center of the porphyrin ring. The cyclic voltammogram of Sn(TPP)(FcCOO)₂ exhibits three distinctive redox couples consisting of one oxidative wave and two reductive waves due to the ferrocenecarboxylato ligands and the porphyrin ring, respectively.     

Thermally cross-linked superparamagnetic iron oxide nanoparticles: synthesis and application as a dual imaging probe for cancer in vivo

We report the fabrication and characterization of thermally cross-linked superparamagnetic iron oxide nanoparticles (TCL-SPION) and their application to the dual imaging of cancer in vivo. Unlike dextran-coated cross-linked iron oxide nanoparticles, which are prepared by a chemical cross-linking method, TCL-SPION are prepared by a simple, thermal cross-linking method using a Si-OH-containing copolymer. The copolymer, poly(3-(trimethoxysilyl)propyl methacrylate-r-PEG methyl ether methacrylate-r-N-acryloxysuccinimide), was synthesized by radical polymerization and used as a coating material for as-synthesized magnetite (Fe3O4) SPION. The polymer-coated SPION was further heated at 80 degrees C to induce cross-linking between the -Si(OH)3 groups in the polymer chains, which finally generated TCL-SPION bearing a carboxyl group as a surface functional group. The particle size, surface charge, presence of polymer-coating layers, and the extent of thermal cross-linking were characterized and confirmed by various measurements, including dynamic light scattering, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The carboxyl TCL-SPION was converted to amine-modified TCL-SPION and then finally to Cy5.5 dye-conjugated TCL-SPION for use in dual (magnetic resonance/optical) in vivo cancer imaging. When the Cy5.5 TCL-SPION was administered to Lewis lung carcinoma tumor allograft mice by intravenous injection, the tumor was unambiguously detected in T2-weighted magnetic resonance images as a 68% signal drop as well as in optical fluorescence images within 4 h, indicating a high level of accumulation of the nanomagnets within the tumor site. In addition, ex vivo fluorescence images of the harvested tumor and other major organs further confirmed the highest accumulation of the Cy5.5 TCL-SPION within the tumor. It is noteworthy that, despite the fact that TCL-SPION does not bear any targeting ligands on its surface, it was highly effective for tumor detection in vivo by dual imaging.     

A degradable hyperbranched poly(ester amine) based on poloxamer diacrylate and polyethylenimine as a gene carrier

Polyethylenimine (PEI) is a well-known cationic polymer which has high transfection efficiency due to its buffering effect. However, nondegradability, cytotoxicity, aggregation, and short-circulation time in vivo still need to be overcome for a successful gene delivery. Degradable, hyperbranched poly(ester amine)s (PEAs) based on poloxamer diacrylate and low molecular weight branched PEI, were successfully synthesized and evaluated as a nonviral gene carrier. The PEAs were obtained in significant yields through Michael type addition reaction of diacrylate monomers and low molecular weight branched PEI. Analysis of degradation products by the reduction in molecular weight demonstrated that PEAs degrade in a controlled fashion. The PEA showed good DNA binding ability and the sizes of complexes under physiological condition were below 150 nm, implicating its potential for intracellular delivery. It showed lower cytotoxicity in three different cell lines (A549, 293T, and HepG2) compared with PEI 25K. PEAs showed much higher transfection efficiencies in three cell lines compared with PEI 25K and PEI 1.8K, and revealed little serum dependency in A549 cell line when the content of poloxamer in the PEA was increased up to 30%.     

In situ micro-sized gel-forming injectable implant using biodegradable amphiphilic graft copolymer

A synthesized graft polymer is used as a biodegradable polymer for an in situ gel-forming injectable implant system. The amphiphilic character of the polymer in the graft structure lowered the viscosity of the polymer solution, which enabled easy injection. A micro-sized gel can be obtained with this system, which has not been found for previous in situ gel-forming systems with poly[(D,L-lactide)-co-glycolide] copolymer. In addition, a protein particle embedded gel exhibits good in vitro drug release performance as a result of the enhanced stability and shorter diffusion length.     

Efficient and reliable calculation of rice-ramsperger—kassel-marcus unimolecular reaction rate constants for biopolymers: Modification of beyer-swinehart algorithm for degenerate vibrations

The Beyer-Swinehart (BS) algorithm, which calculates vibrational state density and sum, was modified for simultaneous treatment of degenerate vibrations. The modified algorithm was used in the grouped-frequency mode of the Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular reaction rate constant calculation for proteins with relative molecular mass as large as 100,000. Compared to the original BS method, reduction in computation time by a factor of around 3000 was achieved. Even though large systematic errors arising from frequency grouping were observed for state densities and sums, they more or less canceled each other, thus enabling reliable rate constant calculation. The present method is thought to be adequate for efficient and reliable RRKM calculations for any macromolecule in the gas phase such as the molecular ions of proteins, nucleic acids, and carbohydrates generated inside a mass spectrometer. The algorithm can also be used to calculate the internal energy distribution of a macromolecule at thermal equilibrium.     

A hexagonal prismatic porphyrin array: synthesis, STM detection, and efficient energy hopping in near-infrared region

A belt-shaped hexagonal cyclic porphyrin array 2 that comprises of six meso-meso, beta-beta, beta-beta triply linked diporphyrins 3 bridged by 1,3-phenylene spacers is prepared by oxidation from cyclic dodecameric array 1 consisting of six meso-meso directly linked diporphyrins 4 with DDQ and Sc(OTf)3. The absorption spectrum of 2 is similar to that of the constituent subunit 3 but shows a slight red-shift for the Q-bands in near-infrared (NIR) region, indicating the exciton coupling between the neighboring diporphyrin chromophores. Observed total exciton coupling energies in the absorption spectra were largely matched with the calculated values based on point-dipole exciton coupling approximation. It was found that the experimental exciton coupling strength (292 cm(-1)) of the Q-band in 2 is slightly larger than the calculated one (99 cm(-1)), indicating that the electronic communications are enhanced through 1,3-phenylene linkers in hexameric macromolecule. A rate of the excitation energy hopping (EEH) that occurs in 2 at the lowest excited singlet state in the near-infrared region has been determined to be (1.8 ps)(-1) on the basis of the pump-power dependent femtosecond transient absorption (TA) and the transient absorption anisotropy (TAA) decay measurements. The 2 times faster EEH rate of 2 than that of 1 (4.0 ps)(-1) mainly comes from involving through-bond energy transfer among diporphyrin subunits via 1,3-phenylene bridges as well as F?rster-type through-space EEH processes. STM measurement of 2 in the Cu(100) surface revealed that it takes several discrete conformations with respect to the relative orientation of neighboring diporphyrins. Collectively, an effective EEH in the NIR region is realized in 2 due largely to the intensified oscillator strength in the S(1) state (Q-band) and the close proximity held by 1,3-phenylene spacers.