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.     

Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test

We report here a test of the Semi-Explicit Assembly (SEA) model in the solvation free energy category of the SAMPL3 blind prediction event (summer 2011). We tested how dependent the SEA results are on the chosen force field by performing calculations with both the General Amber and OPLS force fields. We compared our SEA results with full molecular dynamics simulations in explicit solvent. Of the 20 submissions, our SEA/OPLS results gave the second smallest RMS errors in free energies compared to experiments. SEA gives results that are very similar to those of its underlying force field and explicit solvent model. Hence, while the SEA water modeling approach is much faster than explicit solvent simulations, its predictions appear to be just as accurate.     

Minors in large almost‐5‐connected non‐planar graphs

It is shown that every sufficiently large almost‐5‐connected non‐planar graph contains a minor isomorphic to an arbitrarily large graph from one of six families of graphs. The graphs in these families are also almost‐5‐connected, by which we mean that they are 4‐connected and all 4‐separations contain a “small” side. As a corollary, every sufficiently large almost‐5‐connected non‐planar graph contains both a K_{3, 4}‐minor and a ‐minor. The connectivity condition cannot be reduced to 4‐connectivity, as there are known infinite families of 4‐connected non‐planar graphs that do not contain a K_{3, 4}‐minor. Similarly, there are known infinite families of 4‐connected non‐planar graphs that do not contain a ‐minor.     

Fabricating electrodes for amperometric detection in hybrid paper/polymer lab-on-a-chip devices

We present a novel, low-resource fabrication and assembly method for creating disposable amperometric detectors in hybrid paper-polymer devices. Currently, mere paper-based microfluidics is far from being able to achieve the same level of process control and integration as state-of-the-art microfluidic devices made of polymers. To overcome this limitation, in this work both substrate types are synergistically combined through a hybrid, multi-component/multi-material system assembly. Using established inkjet wax printing, we transform the paper into a profoundly hydrophobic substrate in order to create carbon electrodes which are simply patterned from carbon inks via custom made adhesive stencils. By virtue of the compressibility of the paper substrate, the resulting electrode-on-paper hybrids can be directly embedded in conventional, 3D polymeric devices by bonding through an adhesive layer. This manufacturing scheme can be easily recreated with readily available off-the-shelf equipment, and is extremely cost-efficient and rapid with turn-around times of only a few hours.     

Denaturation mapping of Saccharomyces cerevisiae

Optical mapping of DNA provides large-scale genomic information that can be used to assemble contigs from next-generation sequencing, and to detect rearrangements between single cells. A recent optical mapping technique called denaturation mapping has the advantage of using physical principles rather than the action of enzymes to probe genomic structure. Denaturation mapping uses fluorescence microscopy to image the pattern of partial melting along a DNA molecule extended in a channel of cross-section 120 nm at the heart of a nanofluidic device. We used denaturation mapping to locate single DNA molecules on the yeast genome (12.1 Mbp) by comparing images to a computationally predicted map for the entire genome sequence. By locating 84 molecules we assembled an optical map of the yeast genome with > 50% coverage.     

Synthesis of manzacidin A and C: efficient construction of quaternary carbon stereocenters bearing nitrogen substituents

An efficient synthetic method for stereoselective construction of asymmetric quaternary carbon stereocenters, bearing nitrogen in the form of Boc-protected allyl amines, has been developed. This methodology is employed in the synthesis of marine alkaloids, manzacidin A and C.     

Synthesis, crystal structure, spectroscopic and electrochemical properties, and H2-evolving activity of a new [PtCl(terpyridine)]+ derivative with viologen-like redox properties

A new Pt(II)-based metalloviologen analog, [PtCl(Mepytpy)](2+) (abbreviated as PV(2+); Mepytpy(+) = 4'-(4-methyl-pyridinio)-2,2':6',2'-terpyridine), was synthesized and its spectroscopic and electrochemical properties were investigated. The structures of Mepytpy(+) and PV(2+) were solved by single-crystal X-ray diffraction analysis. Electrochemical studies in DMF (N,N-dimethylformamide) revealed that both the first and second reduction potentials of PV(2+) (E = -0.87 V vs. Fc/Fc(+) for PV(2+)/PV(+)˙; E = -1.31 V vs. Fc/Fc(+) for PV(+)˙/PV(0)) are nearly consistent with those of methylviologen (N,N'-dimetyl-4,4'-bipyridinium, MV(2+)) (E = -0.90 V vs. Fc/Fc(+) for MV(2+)/MV(+)˙; E = -1.28 V vs. Fc/Fc(+) for MV(+)˙/MV(0)), where the first reduction of PV(2+) is assigned as the reduction at the Mepytpy(+) ligand bound to the Pt(ii) ion. Upon the addition of a reducing agent Na(2)S(2)O(4) into an aqueous acetate buffer solution (pH = 5.0) of PV(2+), the generation of one-electron-reduced radical species (PV(+)˙) was spectrophotometrically observed and was assigned based on the time-dependent density functional theory (TD-DFT) calculations. The H(2)-evolving activity of PV(2+) was evaluated in the presence of a sacrificial electron donor (EDTA) in an aqueous acetate buffer solution (pH = 5.0). It was found that the stability of the metalloviologen PV(2+) during the photolysis is much higher than that of the parent compound [PtCl(tpy)](+).     

Rhodium-catalyzed linear cross-trimerization of two different alkynes with an alkene and two different alkenes with an alkyne

Crossing paths with rhodium: A cationic Rh(I)/H(8)-BINAP complex has been found to catalyze the linear cross-trimerization of terminal alkynes, acetylenedicarboxylates, and acrylamides to give substituted trienes. The asymmetric linear cross-trimerization, giving substituted chiral dienes, has also been achieved by using monosubstituted alkenes and (R)-BINAP instead of terminal alkynes and H(8)-BINAP (see scheme; H(8)-BINAP = 2,2'-bis(diphenylphosphino)-5,5',6,6',7,7',8,8'-octahydro-1,1'-binaphthyl; BINAP = 2,2'-bis(diphenylphosphino)-1,1'-binaphthyl]).     

Rhodium-catalyzed C-H bond activation/[4 + 2] annulation/aromatization cascade to produce phenol, naphthol, phenanthrenol, and triphenylenol derivatives

It has been established that a cationic rhodium(I)/dppp complex catalyzes the aldehyde C-H bond activation/[4 + 2] annulation/aromatization cascade to produce phenol, naphthol, phenanthrenol, and triphenylenol derivatives from readily available conjugated alkynyl aldehydes and alkynes.