Whole‐Genome Sequencing of a Single Viral Species from a Highly Heterogeneous Sample

Metagenomic studies suggest that only a small fraction of the viruses that exist in nature have been identified and studied. Characterization of unknown viral genomes is hindered by the many genomes populating any virus sample. A new method is reported that integrates drop‐based microfluidics and computational analysis to enable the purification of any single viral species from a complex mixed virus sample and the retrieval of complete genome sequences. By using this platform, the genome sequence of a 5243 bp dsDNA virus that was spiked into wastewater was retrieved with greater than 96 % sequence coverage and more than 99.8 % sequence identity. This method holds great potential for virus discovery since it allows enrichment and sequencing of previously undescribed viruses as well as known viruses.     

Triple Emission from p‐Dimethylaminobenzonitrile–Cucurbit[8]uril Triggers the Elusive Excimer Emission

The intriguing dual‐emission behavior of p‐ dimethylaminobenzonitrile (DMABN) and the identity of the associated excited states is, arguably, the most extensively investigated and also controversially discussed molecule‐ specific phenomenon of modern photochemistry. We have now found a new, third fluorescence band when DMABN is encapsulated within the water‐soluble molecular container cucurbit[8]uril (CB8). It is centered between the previously observed emissions and assigned to the elusive excimer emission from DMABN through 1:2 CB8:DMABN complex formation. Heating of the CB8 ? (DMABN)₂ complex from 0 to 100 °C results in the dissociation of the ternary complex and restoration of the dual‐emission properties of the monomer. Alternatively, monomer emission can be obtained by selecting cucurbit[7]uril (CB7), a host homologue that is too small to accommodate two DMABN molecules, or by introducing ethyl instead of methyl groups at the amino terminus of the aminobenzonitrile guest.     

On Lipschitz extension from finite subsets

We prove that for every n ∈ ? there exists a metric space (X, d _X), an n-point subset S ? X, a Banach space (Z, \({\left\| \right\|_Z}\)) and a 1-Lipschitz function f: S → Z such that the Lipschitz constant of every function F: X → Z that extends f is at least a constant multiple of \(\sqrt {\log n} \). This improves a bound of Johnson and Lindenstrauss [JL84]. We also obtain the following quantitative counterpart to a classical extension theorem of Minty [Min70]. For every α ∈ (1/2, 1] and n ∈ ? there exists a metric space (X, d _X), an n-point subset S ? X and a function f: S → ?₂ that is α-Hölder with constant 1, yet the α-Hölder constant of any F: X → ?₂ that extends f satisfies \({\left\| F \right\|_{Lip\left( \alpha \right)}} > {\left( {\log n} \right)^{\frac{{2\alpha - 1}}{{4\alpha }}}} + {\left( {\frac{{\log n}}{{\log \log n}}} \right)^{{\alpha ^2} - \frac{1}{2}}}\). We formulate a conjecture whose positive solution would strengthen Ball’s nonlinear Maurey extension theorem [Bal92], serving as a far-reaching nonlinear version of a theorem of König, Retherford and Tomczak-Jaegermann [KRTJ80]. We explain how this conjecture would imply as special cases answers to longstanding open questions of Johnson and Lindenstrauss [JL84] and Kalton [Kal04].     

Monitoring enzyme activity using a diamagnetic chemical exchange saturation transfer magnetic resonance imaging contrast agent

Chemical exchange saturation transfer (CEST) is a new approach for generating magnetic resonance imaging (MRI) contrast that allows monitoring of protein properties in vivo. In this method, a radiofrequency pulse is used to saturate the magnetization of specific protons on a target molecule, which is then transferred to water protons via chemical exchange and detected using MRI. One advantage of CEST imaging is that the magnetizations of different protons can be specifically saturated at different resonance frequencies. This enables the detection of multiple targets simultaneously in living tissue. We present here a CEST MRI approach for detecting the activity of cytosine deaminase (CDase), an enzyme that catalyzes the deamination of cytosine to uracil. Our findings suggest that metabolism of two substrates of the enzyme, cytosine and 5-fluorocytosine (5FC), can be detected using saturation pulses targeted specifically to protons at +2 ppm and +2.4 ppm (with respect to water), respectively. Indeed, after deamination by recombinant CDase, the CEST contrast disappears. In addition, expression of the enzyme in three different cell lines exhibiting different expression levels of CDase shows good agreement with the CDase activity measured with CEST MRI. Consequently, CDase activity was imaged with high-resolution CEST MRI. These data demonstrate the ability to detect enzyme activity based on proton exchange. Consequently, CEST MRI has the potential to follow the kinetics of multiple enzymes in real time in living tissue.     

Mesoporous silica-coated hollow manganese oxide nanoparticles as positive T1 contrast agents for labeling and MRI tracking of adipose-derived mesenchymal stem cells

Mesoporous silica-coated hollow manganese oxide (HMnO@mSiO(2)) nanoparticles were developed as a novel T(1) magnetic resonance imaging (MRI) contrast agent. We hypothesized that the mesoporous structure of the nanoparticle shell enables optimal access of water molecules to the magnetic core, and consequently, an effective longitudinal (R(1)) relaxation enhancement of water protons, which value was measured to be 0.99 (mM(-1)s(-1)) at 11.7 T. Adipose-derived mesenchymal stem cells (MSCs) were efficiently labeled using electroporation, with much shorter T(1) values as compared to direct incubation without electroporation, which was also evidenced by signal enhancement on T(1)-weighted MR images in vitro. Intracranial grafting of HMnO@mSiO(2)-labeled MSCs enabled serial MR monitoring of cell transplants over 14 days. These novel nanoparticles may extend the arsenal of currently available nanoparticle MR contrast agents by providing positive contrast on T(1)-weighted images at high magnetic field strengths.     

Theoretical investigation into competing unimolecular reactions encountered in the pyrolysis of acetamide

Motivated by the necessity to understand the pyrolysis of alkylated amines, unimolecular decomposition of acetamide is investigated herein as a model compound. Standard heats of formation, entropies, and heat capacities, are calculated for all products and transition structures using several accurate theoretical levels. The potential energy surface is mapped out for all possible channels encountered in the pyrolysis of acetamide. The formation of acetamedic acid and 1-aminoethenol and their subsequent decomposition pathways are found to afford the two most energetically favored pathways. However, RRKM analysis shows that the fate of acetamedic acid and 1-aminoethenol at all temperatures and pressures is to reisomerize to the parent acetamide. 1-Aminoethenol, in particular, is predicted to be a long-lived species enabling its participation in bimolecular reactions that lead to the formation of the major experimental products. Results presented herein reflect the importance of bimolecular reactions involving acetamide and 1-aminoethenol in building a robust model for the pyrolysis of N-alkylated amides.     

Syntheses, crystal structures, transport properties and first-principles electronic structure study of the (tTTF)2X (X=Br, I) low-dimensional antiferromagnets

An efficient synthetic procedure for the preparation of unsymmetrically substituted tetrathiafulvalene (TTF) donors has been used to obtain the trimethylene-tetrathiafulvalene (tTTF) donor with high purity. Good quality crystals of the two (tTTF)(2)X (X = Br, I) salts have been obtained by electrocrystallization. The two salts are isomorphous and contain tTTF layers which are built from (tTTF)(2) dimeric units. Both systems are low-dimensional antiferromagnets with the highest Ne?el temperatures for TTF based radical cation salts: ≈ 35 K (Br salt) and ≈43 K (I salt). The resistivity is found to substantially decrease with pressure although both salts still have activated conductivity at 25 kbar. First-principles Density Functional Theory (DFT) calculations have been used to investigate the relative strength of the three different types of magnetic interactions in the tTTF layers as well as the potential magnetic ground states. These calculations successfully predict the nature of the ground state and suggest a possible correlation between structural details and Ne?el temperatures for the bromine and iodine salts. Remarkably, the calculated antiferromagnetic ground state can be predicted from the nesting properties of the Fermi surface for the hypothetical Pauli paramagnetic metallic state.     

Quasisymmetric embeddings, the observable diameter, and expansion properties of graphs

It is shown that the edges of any n-point vertex expander can be replaced by new edges so that the resulting graph is an edge expander, and such that any two vertices that are joined by a new edge are at distance in the original graph. This result is optimal, and is shown to have various geometric consequences. In particular, it is used to obtain an alternative perspective on the recent algorithm of Arora et al. [Proceedings of the 36th Annual ACM Symposium on the Theory of Computing, 2004, pp. 222-231.] for approximating the edge expansion of a graph, and to give a nearly optimal lower bound on the ratio between the observable diameter and the diameter of doubling metric measure spaces which are quasisymmetrically embeddable in Hilbert space.     

Spectral theory of metastability and extinction in birth-death systems

We suggest a general spectral method for calculating the statistics of multistep birth-death processes and chemical reactions of the type mA-->nA (m and n are positive integers) which possess an absorbing state. The method employs the generating function formalism in conjunction with the Sturm-Liouville theory of linear differential operators. It yields accurate results for the extinction statistics and for the quasistationary probability distribution, including large deviations, of the metastable state. The power of the method is demonstrated on the example of binary annihilation and triple branching 2A--> ?, A-->3A, representative of the rather general class of dissociation-recombination reactions.