DNA fingerprinting of Vibrio cholerae and Aeromonas species by pulsed-field minigel electrophoresis

DNA molecules of Vibrio cholerae and Aeromonas species were prepared by incubating immobilized cells for 4 and 2 h, respectively, with a nonenzymatic solution that contains chemical reagents only (NDSUPlus). This method gave results as reproducible as the enzymatic one that uses proteinase K, and rendered DNA molecules suitable for fingerprinting by mini-CHEF electrophoresis. As rapid DNA separations at high electric field are achieved in mini-CHEF chamber with low heat evolution, DNA restriction fragments were separated in 5 h at 10 V/cm in a single resolution window. Then, fragment separations in three resolution windows were done in 15 h. This time is shorter than the one needed by the large CHEF chamber for resolving fragments in a single resolution window. Three windows permitted to include larger numbers of restriction fragments in the calculation of isolate similarities. Both sample preparation and mini-CHEF electrophoresis may represent an alternative for performing massive epidemiological studies of V. cholerae and Aeromonas species.     

Chirality of amyloid suprastructures

Amyloids are pathological fibrillar aggregates of proteins related to more than 20 different diseases. Amyloid fibers have a characteristic cross-beta structure consisting of a series of beta-strands extended perpendicular to the fiber axis and joined by hydrogen bonds parallel to the fiber direction. Fibril aggregation results in helical suprastructures. Here we used high-resolution SEM and cryo-SEM for the study of chirality in the amyloid suprastructure. We found that amyloids of Abeta1-40 and hen lysozyme form at all hierarchical levels always and only left-handed helices. In contrast, amyloid fibers formed by the N-terminal sequence of serum amyloid A (SAA1-12) consist of right-handed helices exclusively. Consistently, the peptide enantiomer, formed of (R)-aminoacids, aggregates exclusively in left-handed helices. We conclude that the opposite handedness of the SAA1-12 amyloids is an intrinsic feature of the peptide structure. The left-handed chirality observed for the Abeta1-40 and hen lysozyme amyloid suprastructures is consistent with the conventional beta-sheet structural model. In contrast, the right-handedness observed in (all-S) SAA1-12 fibers indicates that the cross-beta structure of SAA1-12 fibers is probably not formed of beta-sheets. Whatever the answer to the dilemma of the right-handed helicity of SAA1-12 amyloid fibers is, its existence shows that the supramolecular chirality of amyloid fibers is not only dictated by the molecular chirality of the component molecules but also by their structural organization.     

Preparation and conformation of dioxocalix[4]arene derivatives

CrO(3) oxidation experiments conducted on atropisomeric forms of 2 (2(paco), 2(1,3)(-)(alt), and 2(1,2)(-)(alt)) indicate that under the reaction conditions only methylene groups located between pairs of geminal rings oriented in an anti disposition are oxidized to carbonyls. NMR data suggest that the tetrahydroxydioxocalix[4]arenes 7 and 9 adopt the partial cone and 1,2-alternate conformations, respectively. In the crystal structure of 7.2EtOAc the dioxocalixarene adopts a partial cone conformation, whereas 9 adopts in the crystal a 1,2-alternate conformation. In both conformations, pairs of geminal rings connected to a carbonyl are oriented in an anti fashion. The relative stability of the partial cone and 1,2-alternate conformations of 7 and 9 is underestimated by MM3 calculations. The topomerization barriers of 7 and 9 are 12.8 and 13.6 kcal mol(-)(1), respectively.     

Oligonucleotide loaded polypeptide‐peptide nanoparticles towards mitochondrial‐targeted delivery

Nanoparticles (NPs) consisting of biodegradable and biocompatible polymers may have the ability to deliver a cargo to specific tissue, cell type, and organelle. Various diseases, which are linked to mitochondrial genome (mtDNA) mutations and have no effective treatments, may be approached by gene therapy strategies. In this study, we adapted the recently developed mitochondria delivering polypeptide‐peptide nanoparticles (PoP‐NPs) system to carry an oligonucleotide cargo to the proximity of the mitochondria. PoP‐NPs are formulated by self‐assembly of the negatively charged polypeptide, poly gamma glutamic acid (γ‐PGA), with an amphiphilic and cationic β‐sheet peptide (PFK). Here, we show that PFK interacts favorably with oligonucleotides and thereby enables the formation of DNA‐loaded PoP‐NPs (DNA‐PoP‐NPs). DNA‐PoP‐NPs could be assembled with different peptide to oligonucleotide (N/P) ratios, and their targeting to the proximity of mitochondria in cell culture could be facilitated through NPs coating with PFK peptide.     

Carbon nanotubes in emulsion‐templated porous polymers: Polymer nanoparticles,sulfonation, and conductivity

Sulfonated polymers are of interest for ion exchange resins, reaction supports, and membranes for separation, filtration, fuel cells, and electrochemical devices. Sulfonic groups have been introduced into polystyrene (PS) through exposure to sulfuric acid, and carbon nanotubes (CNTs) have been added to polymers to enhance proton conductivity without creating an electronic percolation pathway. PolyHIPEs, emulsion‐templated porous polymers with highly interconnected hierarchical open‐cell porous structures, are synthesized through polymerization in the external phases of high internal phase emulsions (HIPEs). In this article, the synthesis of PS‐based CNT‐filled polyHIPEs, their structure, sulfonation, and conductivity are described. Adding CNT dispersions to the HIPEs produced polymer nanoparticle–covered polyHIPEs from polymerization within the water‐soluble surfactant micelles in the internal aqueous phase droplets. The CNTs migrated from the HIPE's aqueous phase droplets into the HIPE's organic phase and formed interconnected bundles within the polyHIPE walls, reflecting a reduction in the surfactant's ability to disperse the CNTs. The water adsorption in the hygroscopic sulfonated polyHIPEs increased the conductivity by several orders of magnitude. The conductivity of the sulfonated polyHIPE containing CNTs was more than an order of magnitude greater than that of the sulfonated polyHIPEs with no CNTs. The CNTs act as “bridges,” enhancing the connection between existing conductive pathways. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 4369–4377     

Time-varying tandem queues with blocking: modeling,analysis, and operational insights via fluid models with reflection

In this paper, we develop time-varying fluid models for tandem networks with blocking. Beyond having their own intrinsic value, these mathematical models are also limits of corresponding many-server stochastic systems. We begin by analyzing a two-station tandem network with a general time-varying arrival rate, a finite waiting room before the first station, and no waiting room between the stations. In this model, customers that are referred from the first station to the second when the latter is saturated (blocked) are forced to wait in the first station while occupying a server there. The finite waiting room before the first station causes customer loss and, therefore, requires reflection analysis. We then specialize our model to a single station (many-server fluid limit of the \(G_t/M/N/(N +H)\) queue), generalize it to k stations in tandem, and allow finite internal waiting rooms. Our models yield operational insights into network performance, specifically on the effects of line length, bottleneck location, waiting room size, and the interaction among these effects.     

Text Indexing and Dictionary Matching with One Error

The indexing problem is where a text is preprocessed and subsequent queries of the form “Find all occurrences of pattern P in the text” are answered in time proportional to the length of the query and the number of occurrences. In the dictionary matching problem a set of patterns is preprocessed and subsequent queries of the form “Find all occurrences of dictionary patterns in text T” are answered in time proportional to the length of the text and the number of occurrences.There exist efficient worst-case solutions for the indexing problem and the dictionary matching problem, but none that find approximate occurrences of the patterns, i.e., where the pattern is within a bound edit (or Hamming) distance from the appropriate text location.In this paper we present a uniform deterministic solution to both the indexing and the general dictionary matching problem with one error. We preprocess the data in time O(n log² n), where n is the text size in the indexing problem and the dictionary size in the dictionary matching problem. Our query time for the indexing problem is O(m log n log log n + tocc), where m is the query string size and tocc is the number of occurrences. Our query time for the dictionary matching problem is O(n log³ d log log d + tocc), where n is the text size and d the dictionary size. The time bounds above apply to both bounded and unbounded alphabets.     

On the asymptotic behavior of spectral functions and resolvent kernels of elliptic operators

Asymptotic formulas with remainder estimates are derived for spectral functions of general elliptic operators. The estimates are based on asymptotic expansion of resolvent kernels in the complex plane. The research of the first author reported in this document has been sponsored by the Air Force Office of Scientific Research under Grant AF EOAR 66–18, through the European Office of Aerospace Research (OAR) United States Air Force. This paper is to be part of the second author’s Ph.D. thesis written under the direction of the first author at the Hebrew University of Jerusalem.