Identification of protein domains on major pilin MrkA that affects the mechanical properties of Klebsiella pneumoniae type 3 fimbriae

The Klebsiella pneumoniae type 3 fimbriae are mainly composed of MrkA pilins that assemble into a helixlike filament. This study determined the biomechanical properties of the fimbriae and analyzed 11 site-directed MrkA mutants to identify domains that are critical for the properties. Escherichia coli strains expressing type 3 fimbriae with an Ala substitution at either F34, V45, C87, G189, T196, or Y197 resulted in a significant reduction in biofilm formation. The E. coli strain expressing MrkAG189A remained capable of producing a normal number of fimbriae. Although F34A, V45A, T196A, and Y197A substitutions expressed on E. coli strains produced sparse quantities of fimbriae, no fimbriae were observed on the cells expressing MrkAC87A. Further investigations of the mechanical properties of the MrkAG189A fimbriae with optical tweezers revealed that, unlike the wild-type fimbriae, the uncoiling force for MrkAG189A fimbriae was not constant. The MrkAG189A fimbriae also exhibited a lower enthalpy in the differential scanning calorimetry analysis. Together, these findings indicate that the mutant fimbriae are less stable than the wild-type. This study has demonstrated that the C-terminal β strands of MrkA are required for the assembly and structural stability of fimbriae.     

Closed loop folding units from structural alignments: Experimental foldons revisited

Nonoverlapping closed loops of around 25–35 amino acids formed via nonlocal interactions at the loop ends have been proposed as an important unit of protein structure. This hypothesis is significant as such short loops can fold quickly and so would not be bound by the Leventhal paradox, giving insight into the possible nature of the funnel in protein folding. Previously, these closed loops have been identified either by sequence analysis (conservation and autocorrelation) or studies of the geometry of individual proteins. Given the potential significance of the closed loop hypothesis, we have explored a new strategy for determining closed loops from the insertions identified by the structural alignment of proteins sharing the same overall fold. We determined the locations of the closed loops in 37 pairs of proteins and obtained excellent agreement with previously published closed loops. The relevance of NMR structures to closed loop determination is briefly discussed. For cytochrome c, cytochrome b₅₆₂ and triosephophate isomerase, independent folding units have been determined on the basis of hydrogen exchange experiments and misincorporation proton‐alkyl exchange experiments. The correspondence between these experimentally derived foldons and the theoretically derived closed loops indicates that the closed loop hypothesis may provide a useful framework for analyzing such experimental data. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Metal-oxide-semiconductor characteristics of lanthanum cerium oxide film on Si

Metal-organic decomposed lanthanum cerium oxide (La _x Ce _y O _z ) film had been spin-coated on n-type Si substrate. Effects of post-deposition annealing temperature and time on the metal-oxide-semiconductor (MOS) properties of the film were studied. As temperature increased from 400 to 1000°C for 15 minutes dwell time, La _x Ce _y O _z demonstrated a decrease in interface trap density (D _it) and total interface trap density (D _total), which were related to the formation of SiO _x /silicates interfacial layer (IL). The lowest leakage current density and highest dielectric breakdown voltage (V _B) was obtained in 1000°C-annealed sample. When longer annealing times (30–120 minutes) were studied on the 1000°C-annealed sample, the sample annealed at 1000°C for 120 min showed the best MOS characteristics with V _B of 30 V. Reasons contributing to such observation were discussed.     

Tune-out and magic wavelengths for hydrogenlike and screened-hydrogenlike atoms

The tune-out and magic wavelengths (TMWs) for the hydrogenlike and screened-hydrogenlike atoms (Z = 1-8) are calculated using a variational method. The first three tune-out wavelengths for each of the nS (n = 1, 2, 3) states and the first three magic wavelengths for each of the 1S-nS (n = 2, 3) transitions of the hydrogenlike atoms in terms of nuclear charge Z, and the first TMWs for the above mentioned states or transitions of the screened-hydrogenlike atoms in terms of the screening parameter μ and Z are presented. All the results for the TMWs are reported for the first time in the literature except the magic wavelengths for the hydrogen atom. The magic wavelengths for hydrogen atom are in agreement with the available data. The precise estimation of the TMWs would be helpful for the design of the ion-trapping experiment of the hydrogenic systems. Our study is expected to be useful for the measurements of the hydrogenic 1S-2S and 1S-3S transitions spectroscopy for the improved accuracy.     

Inequalities for M and N0-matrices

In this paper, we study inequalities for two M or N₀-matrices A,B with A≤B. Necessary and sufficient conditions are given for positive linear combination of A and B to be an N₀-matrix.     

Artemisinin–(Iso)quinoline Hybrids by C−H Activation and Click Chemistry: Combating Multidrug‐Resistant Malaria

A substantial challenge worldwide is emergent drug resistance in malaria parasites against approved drugs, such as chloroquine (CQ). To address these unsolved CQ resistance issues, only rare examples of artemisinin (ART)‐based hybrids have been reported. Moreover, protein targets of such hybrids have not been identified yet, and the reason for the superior efficacy of these hybrids is still not known. Herein, we report the synthesis of novel ART–isoquinoline and ART–quinoline hybrids showing highly improved potencies against CQ‐resistant and multidrug‐resistant P. falciparum strains (EC₅₀ (Dd2) down to 1.0 nm ; EC₅₀ (K1) down to 0.78 nm ) compared to CQ (EC₅₀ (Dd2)=165.3 nm ; EC₅₀ (K1)=302.8 nm ) and strongly suppressing parasitemia in experimental malaria. These new compounds are easily accessible by step‐economic C?H activation and copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC) click reactions. Through chemical proteomics, putatively hybrid‐binding protein targets of the ART‐quinolines were successfully identified in addition to known targets of quinoline and artemisinin alone, suggesting that the hybrids act through multiple modes of action to overcome resistance.     

Applying Ant System for solving Unequal Area Facility Layout Problems

Ant Colony Optimization (ACO) is a young metaheuristic algorithm which has shown promising results in solving many optimization problems. To date, a formal ACO-based metaheuristic has not been applied for solving Unequal Area Facility Layout Problems (UA-FLPs). This paper proposes an Ant System (AS) (one of the ACO variants) to solve them. As a discrete optimization algorithm, the proposed algorithm uses slicing tree representation to easily represent the problems without too restricting the solution space. It uses several types of local search to improve its search performance. It is then tested using several case problems with different size and setting. Overall, the proposed algorithm shows encouraging results in solving UA-FLPs.     

Benchmark calculations of Rényi,Tsallis entropies,and Onicescu information energy for ground state helium using correlated Hylleraas wave functions

Accurate values of physical quantities serve as the stepping stone for further researches. Consequently, we provide benchmark values of Shannon, Rényi, Tsallis entropies, and Onicescu information energy for ground state helium. With the highly correlated Hylleraas wave functions, our calculations fully considered the effect of electron correlation. Presented numerical results converge with increasing size of basis set, fulfill analytic relations between the quantities, and satisfactorily agree with those in the literature. In particular, we present these information-theoretic quantities with high accuracy, and it is believed that the reported data would be a valuable reference for further research on information-theoretic quantities of atomic and molecular systems.     

Fractional Gouy phase

In general, the total Gouy phase shift has the form n pi, where n need not be an integer. As a result of the Fourier transforming property of a lens, the Gouy phase is found to be related to the types of discontinuities at the upper or lower range of the pupil function Q(c) resulting from the asymptotic order of the Fourier transform. The sign of the Gouy phase is also related to the slope of the pupil function. The oscillations of the Gouy phase shift arise from the strength of the nondominant discontinuity.     

Use of ultraviolet-light irradiated multiple myeloma cells as immunogens to generate tumor-specific cytolytic T lymphocytes

Background

As the eradication of tumor cells in vivo is most efficiently performed by cytolytic T lymphocytes (CTL), various methods for priming tumor-reactive lymphocytes have been developed. In this study, a method of priming CTLs with ultraviolet (UV)-irradiated tumor cells, which results in termination of tumor cell proliferation, apoptosis, as well as upregulation of heat shock proteins (HSP) expression is described.

Methods

Peripheral blood mononuclear cells (PBMC) were primed weekly with UV-irradiated or mitomycin-treated RPMI 8226 multiple myeloma cells. Following three rounds of stimulation over 21 days, the lymphocytes from the mixed culture conditions were analyzed for anti-MM cell reactivity.

Results

By day 10 of cultures, PBMCs primed using UV-irradiated tumor cells demonstrated a higher percentage of activated CD8+/CD4- T lymphocytes than non-primed PBMCs or PBMCs primed using mitomycin-treated MM cells. Cytotoxicity assays revealed that primed PBMCs were markedly more effective (p < 0.01) than non-primed PBMCs in killing RPMI 8226 MM cells. Surface expression of glucose regulated protein 94 (Grp94/Gp96) and Grp78 were both found to be induced in UV-treated MM cells.

Conclusion

Since, HSP-associated peptides are known to mediate tumor rejection; these data suggest that immune-mediated eradication of MM cells could be elicited via a UV-induced HSP process. The finding that the addition of 17-allylamide-17-demethoxygeldanamycin (17AAG, an inhibitor of HSP 90-peptide interactions) resulted in decreased CTL-induced cytotoxicity supported this hypothesis. Our study, therefore, provides the framework for the development of anti-tumor CTL cellular vaccines for treating MM using UV-irradiated tumor cells as immunogens.