Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study

2D gel electrophoresis is a tool for measuring protein regulation, involving image analysis by dedicated software (PDQuest, Melanie, etc.). Here, partial least squares discriminant analysis was applied to improve the results obtained by classic image analysis and to identify the significant spots responsible for the differences between two datasets. A human colon cancer HCT116 cell line was analyzed, treated and not treated with a new histone deacetylase inhibitor, RC307. The proteins regulated by RC307 were detected by analyzing the total lysates and nuclear proteome profiles. Some of the regulated spots were identified by tandem mass spectrometry. The preliminary data are encouraging and the protein modulation reported is consistent with the antitumoral effect of RC307 on the HCT116 cell line. Partial least squares discriminant analysis coupled with backward elimination variable selection allowed the identification of a larger number of spots than classic PDQuest analysis. Moreover, it allows the achievement of the best performances of the model in terms of prediction and provides therefore more robust and reliable results. From this point of view, the multivariate procedure applied can be considered a good alternative to standard differential analysis, also taking into account the interdependencies existing among the variables.     

Ground and low-lying excited states of propadienylidene (H2C=C=C:) obtained by negative ion photoelectron spectroscopy

A joint experimental-theoretical study has been carried out on electronic states of propadienylidene (H(2)CCC), using results from negative-ion photoelectron spectroscopy. In addition to the previously characterized X(1)A(1) electronic state, spectroscopic features are observed that belong to five additional states: the low-lying ?(3)B(1) and b(3)A(2) states, as well as two excited singlets, ?(1)A(2) and B(1)B(1), and a higher-lying triplet, c(3)A(1). Term energies (T(0), in cm(-1)) for the excited states obtained from the data are: 10,354±11 (?(3)B(1)); 11,950±30 (b(3)A(2)); 20,943±11 (c(3)A(1)); and 13,677±11 (?(1)A(2)). Strong vibronic coupling affects the ?(1)A(2) and B(1)B(1) states as well as ?(3)B(1) and b(3)A(2) and has profound effects on the spectrum. As a result, only a weak, broadened band is observed in the energy region where the origin of the B(1)B(1) state is expected. The assignments here are supported by high-level coupled-cluster calculations and spectral simulations based on a vibronic coupling Hamiltonian. A result of astrophysical interest is that the present study supports the idea that a broad absorption band found at 5450 ? by cavity ringdown spectroscopy (and coincident with a diffuse interstellar band) is carried by the B(1)B(1) state of H(2)CCC.     

Dynamic mapping of CN rotation following photoexcitation of ICN-

In a spin: the dynamics of photoexcited ICN(-) (Ar)(0-5) are presented. Photodetachment produces quasi-thermal electron emission that leaves ICN with up to 2.85 eV of internal energy. Photodissociation at 2.5 eV leads to one-atom caging and highly solvated anion products. Calculations indicate efficient energy transfer into CN rotation upon excitation to the (2)Π(1/2) excited state. CN rotation is vital to explain the unique dynamics observed.     

Intramolecular cyclization of alkoxyaminosugars: access to novel glycosidase inhibitor families

We report the synthesis of two novel families of iminosugars as glycosidase inhibitors involving an intramolecular cyclization between an N-alkoxyamino group and a latent aldehyde of a reducing sugar as the key step. Using this methodology we have prepared the hitherto unknown bicyclic polyhydroxylated N-(methoxy, benzyloxy)anhydroazepanes and N-benzyloxy-d-xylonojirimycin; all these novel compounds turned out to be moderate β-glucosidase inhibitors in a pH-dependent manner.     

Micropatterning topology on soft substrates affects myoblast proliferation and differentiation

Micropatterning techniques and substrate engineering are becoming useful tools to investigate several aspects of cell-cell interaction biology. In this work, we rationally study how different micropatterning geometries can affect myoblast behavior in the early stage of in vitro myogenesis. Soft hydrogels with physiological elastic modulus (E = 15 kPa) were micropatterned in parallel lanes (100, 300, and 500 μm width) resulting in different local and global myoblast densities. Proliferation and differentiation into multinucleated myotubes were evaluated for murine and human myoblasts. Wider lanes showed a decrease in murine myoblast proliferation: (69 ± 8)% in 100 μm wide lanes compared to (39 ± 7)% in 500 μm lanes. Conversely, fusion index increased in wider lanes: from (46 ± 7)% to (66 ± 7)% for murine myoblasts, and from (15 ± 3)% to (36 ± 2)% for human primary myoblasts, using a patterning width of 100 and 500 μm, respectively. These results are consistent with both computational modeling data and conditioned medium experiments, which demonstrated that wider lanes favor the accumulation of endogenous secreted factors. Interestingly, human primary myoblast proliferation is not affected by patterning width, which may be because the high serum content of their culture medium overrides the effect of secreted factors. These data highlight the role of micropatterning in shaping the cellular niche through secreted factor accumulation, and are of paramount importance in rationally understanding myogenesis in vitro for the correct design of in vitro skeletal muscle models.     

A Soft Copper(II) Porous Coordination Polymer with Unprecedented Aqua Bridge and Selective Adsorption Properties

Herein, the synthesis, crystal structure, and full characterization of a new soft porous coordination polymer (PCP) of ([Cu₂(dmcapz)₂(OH₂)]DMF_1.5)_n ( 1 ) formulation, which is easily obtained in the reaction of CuX₂ (X=Cl, NO₃) salts with 3,5‐dimethyl‐4‐carboxypyrazole (H₂dmcapz) is present. Compound 1 shows a copper(II) dinuclear secondary building unit (SBU), which is supported by two pyrazolate bridges and an unprecedented H₂O bridge. The dinuclear SBUs are further bridged by the carboxylate ligands to build a diamondoid porous network. The structural transformations taking place in 1 framework upon guest removal/uptake has been studied in detail. Indeed, the removal of the bridging water molecules gives rise to a metastable evacuated phase ( 1 b ) that transforms into an extremely stable porous material ( 1 c ) after freezing at liquid‐nitrogen temperature. The soaking of 1 c into water allows the complete and instantaneous recover of the water‐exchanged material ( 1 a′ ). Remarkably, 1 b and 1 c materials possess structural bistability, which results in the switchable adsorptive functions. Therefore, the gas‐adsorption properties of both materials have been studied by means of single‐component gas adsorption isotherms as well as by variable‐temperature pulse‐gas chromatography. Both materials present permanent porosity and selective gas‐adsorption properties towards a variety of gases and vapors of environmental and industrial interest. Moreover, the flexible nature of the coordination network and the presence of highly active convergent open metal sites confer on these materials intriguing gas‐adsorption properties with guest‐triggered framework‐breathing phenomena being observed. The plasticity of Cu^II metal center and its ability to form stable complexes with different coordination numbers is at the origin of the structural transformations and the selective‐adsorption properties of the studied materials.     

Staying alive: new perspectives on cell immobilization for biosensing purposes

Intact living cells, because of their simplicity of use and their ability to provide highly valuable functional information, are well suited to biosensing applications. Cells can be genetically engineered by introduction of reporter proteins, modified to achieve analyte selectivity for their sensing capabilities, and connected to a transducer to obtain whole-cell biosensors. These bioanalytical features are increasingly attracting attention in the pharmaceutical, environmental, medical, and industrial fields. Whole-cell biosensors based on different recognition elements and transduction mechanisms have been also incorporated into portable devices and, with recent advances in micro and nanofabrication and microfluidics technology, miniaturized to achieve single-cell level analysis. Cell immobilization, widely used in, for example, microbial biofermentors or bioremediation systems, is now emerging as an appealing way of integrating whole-cell biosensors into devices, to maintain long-term cell viability, to increase the reproducibility of the cell’s response, and to avoid the spread of genetically modified cells into the environment, the latter being very important when devices are used for analysis in the field. A plethora of materials and functionalized surfaces have been proposed for immobilization of microbial or mammalian cells, each one having peculiar advantages and limitations. This critical review highlights and discusses recent trends, together with selected bioanalytical applications of immobilized viable cells. In particular the review focuses on some aspects that seem to hold great promise for future applications of immobilized cells, spanning from microbial biosensors to microbial biofilms, cell microarrays, and single-cell analysis.     

Chemical Identification of Specialized Metabolites from Sulla (Hedysarum coronarium L.) Collected in Southern Italy

Sulla (Hedysarum coronarium L.) is a biennal forage legume originated from the Mediterranean basin and used for animal feeding due to its high forage quality and palatability. Several species of Hedysarum have been considered for their nutritional, pharmaceutical, and biological properties, and different applications have been reported, both for human consumption and animal nutrition. Although a systematic investigation of the chemical constituents of Hedysarum spp. has been performed in order to provide chemotaxonomic evidences for the genus and to support the pharmacological application of several species within the genus, few data are available on the chemical constituents of H. coronarium, and only the content of condensed tannins and flavonoids in leaves has been previously reported. In the present paper, results from a detailed chemical analysis of the extracts from the leaves and flowers of H. coronarium grown wild in southern Italy are presented. Identification of the main specialized metabolites within the chemical classes of flavonoids, proanthocyanidins and saponins, is described, including considerations on their content in the two plant organs. Information acquired from this study expands the knowledge on H. coronarium as a source of valuable phytochemicals for different applications in human and animal health and nutrition.     

Stepwise dansyl grafting on the kaolinite interlayer surface

A block copolymer (PS-b-poly(l-Glu)) composed of polystyrene and poly(l-glutamic acid) was used as a stabilizer for dispersion polymerization of styrene. When dispersion polymerization of styrene was conducted at 70 °C in 80% dimethylformamide-water with 0.5 wt% PS-b-poly(l-Glu), spherical polystyrene particles with D_n = 0.72 μm and narrow size distribution were obtained. Whereas AIBN concentration did not have any effects on particle size, molecular weight of the polystyrene particles was strongly dependent on the initiator concentration. As concentration of the PS-b-poly(l-Glu) increased from 0.2 to 1.0 wt%, particle size decreased from D_n = 0.91 to 0.69 μm with keeping surface area occupied by one poly(l-glutamic acid) chain about S = 50 nm². On the other hand, an increase in initial concentration of styrene from 2 to 20 wt% caused an increase in particle size from D_n = 0.48 to 1.36 μm and a decrease in surface area per poly(l-glutamic acid) block from S = 91 to 45 nm². Colloidal stability of the polystyrene particles in aqueous solution was responsive to pH due to the surface-grafted poly(l-glutamic acid). For dispersion polymerization of styrene, the PS-b-poly(l-Glu) functions as both a stabilizer and a surface modifier.