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.     

Proximal regioselectivity of the O,O'-dialkylation of tetrahydroxyketocalix[4]arene

The only dialkylated products obtained in the reaction of tetrahydroxyketocalixarene 2a with MeI/K(2)CO(3) or PhCH(2)Br/K(2)CO(3) are the corresponding proximal (i.e., 1,2) O,O'-dialkyl ethers, in contrast to the parent tetrahydroxycalix[4]arene 1a which affords the distal (1,3) dialkyl ether derivatives. Pairs of geminally alkylated phenoxy groups in the conformationally rigid dibenzylated and tetrabenzylated derivatives are oriented in an anti fashion. These results can be rationalized assuming that the 1,3-alternate arrangement of the rings preferred by 2a is adopted during all the intermediate stages of the alkylation. The NMR spectra (in CDCl(3)) of the monomethyl, dimethyl, trimethyl, and tetramethyl ether derivatives of 2a are in agreement with a 1,3-alternate conformation.     

Liquid chromatographic determination of multiple sulfonamides, nitrofurans, and chloramphenicol residues in pasteurized milk

A rapid and selective liquid chromatographic method was developed to detect 6 sulfonamides, 3 nitrofurans, and chloramphenicol residues in pasteurized milk. The 10 drugs were extracted with chloroform-acetone and the organic phase was evaporated; the residues were dissolved in an aqueous sodium acetate buffer solution 0.02M (pH = 4.8), and the fat was removed by washing with hexane. The aqueous layer was collected, filtered, and injected. The 6 sulfonamides and chloramphenicol were detected at 275 nm ultraviolet (UV) using a gradient system starting with sodium acetate buffer solution-acetonitrile (95 + 5) and finishing with sodium acetate buffer solution-acetonitrile (80 + 20). Nitrofurans were detected at 375 nm (UV) isocratically with sodium acetate buffer solution-acetonitrile (80 + 20). For 50 ppb fortified milk, the average recoveries were (sulfathiazole) 65.52%; (sulfamerazine) 75.36%; (sulfamethazine) 93.94%; (sulfachlorpyridazine) 75.94%; (sulfamethoxazole) 85.18%; (sulfamonomethoxine) 83.45%; (chloramphenicol) 104.17%; (nitrofurazone) 91.81%; (furazolidone) 100.76%; and (furaltadone) 72.38%. Method detection limits ranged from 4 ppb (nitrofurazone) to 16 ppb (sulfamethazine). Some matrix interferences (3-7 ppb) were observed only with sulfonamides.     

Ozonolysis of 1,4-cyclohexadienes in the presence of methanol and acid. Mechanism and intermediates in the conversion of 1,4-cyclohexadiene derivatives to beta-keto esters

Conditions for the preparation of beta-keto esters directly from 1,4-cyclohexadiene derivatives are described. This procedure is a further step in the application of the synthetic methodology, which consists of the combination of Birch reduction of available benzene derivatives followed by ozonolysis. In this work, the syntheses of derivatives of dimethyl gamma-keto-alpha-aminoadipate and dimethyl beta-keto glutamate from the corresponding 1,4-cyclohexadiene derivatives are described. The latter compounds are prepared from phenylalanine and phenylglycine, respectively. The study of the ozonolysis of simple alkyl derivatives of 1,4-cyclohexadiene in the presence of methanol, both in the presence and absence of acid, helped to establish the mechanism of this reaction. The proximity of the two double bonds, which are cleaved, leads to the intermediate formation of 1,2-dioxolane derivatives that could be identified by NMR spectroscopy. It is shown that regardless of the regioselectivity of the cleavage of the primary ozonide, which is formed, all 1,2-dioxolane derivatives can lead to beta-keto esters. This is due to the equilibrium between these dioxolanes in the presence of methanol and acid.     

Temperature-dependent and friction-controlled electrochemically induced shuttling along molecular strings associated with electrodes.

The temperature and solvent composition dependence of the electrochemically stimulated rate of shuttling of the redox-active cyclophane, cyclobis(paraquat-p-phenylene), on a molecular string has been studied. The molecular string includes a pi-donor diiminebenzene-site that is associated on one side with an electrode, and stoppered on the other side with an adamantane unit. The cyclophane rests on the pi-donor site, owing to stabilizing pi-donor-acceptor interactions. Electrochemical reduction of the cyclophane units, to the bis-radical cation cyclophane, results in the shuttling of the reduced cyclophane towards the electrode, a process that is driven by the removal of the stabilizing donor-acceptor interactions, and the electrostatic attraction of the reduced product by the electrode. The latter process is energetically downhill, and is temperature-independent. Upon oxidation of the reduced cyclophane that is associated with the electrode, the energetically uphill shuttling of the oxidized cyclophane to the pi-donor site proceeds. The rate of this translocation process has been found to be temperature-dependent, and controlled by the solvent composition. The experimental results have been theoretically analyzed in terms of Kramers' molecular friction model. The theoretical fitting of the experimental results, using solutions of variable composition, reveals that the rate-constants for the uphill reaction in a pure aqueous solution follow the temperature-dependence of the viscosity of water. The results demonstrate the significance of friction phenomena in shuttling processes within molecular machines.     

Stability of sulfonamides,nitrofurans, and chloramphenicol residues in preserved raw milk samples measured by liquid chromatography

A stability study was made of 10 antimicrobials: 6 sulfonamides, 3 nitrofurans, and chloramphenicol residues in raw milk samples preserved with 0.1 % potassium dichromate (K2Cr2O7) and 0.05% mercuric bichloride (HgCl2) during cold storage for 7 days. Preserved milk samples fortified with 50 ppb of each antimicrobial were analyzed by liquid chromatography (modified AOAC Method 993.32). Drugs were extracted with chloroform-acetone after solvent evaporation residues were dissolved with aqueous sodium acetate buffer solution (0.02M, pH 4.8), and fat was removed with hexane. Sulfonamides and chloramphenicol were detected at 275 nm (UV) by using a gradient system of sodium acetate buffer solution-acetonitrile starting at 95 + 5 (v/v) and finishing at 80 + 20 (v/v). Nitrofurans were detected at 375 nm (UV) isocratically with sodium acetate buffer solution-acetonitrile (80 + 20, v/v). Residues stability was measured through recovery data. Sulfamethoxazole, sulfachloropyridazine, nitrofurazone, furazolidone, and furaltadone residues remained stable in the presence of either preservative for 7 days. Sulfamethazine and chloramphenicol were not affected by K2Cr2O7, but had significant losses (p <0.05) when HgCl2 was used: 26.2 and 13.4%, respectively. Average recoveries of sulfamonomethoxine, sulfamerazine, and sulfathiazole significantly decreased by Day 7, with losses of 17.1, 17.2, and 23.2% for K2Cr2O7, and 23.3, 20.7, and 48.0% for HgCl2, respectively. During 5 days of cold storage all antimicrobials tested, except sulfathiazole, remained stable in milk samples preserved with 0.1 % K2Cr2O7 or 0.05% HgCl2.     

Electronic structure of copper phthalocyanine: a comparative density functional theory study

We present a systematic density functional theory study of the electronic structure of copper phthalocyanine (CuPc) using several different (semi)local and hybrid functionals and compare the results to experimental photoemission data. We show that semilocal functionals fail qualitatively for CuPc primarily because of underbinding of localized orbitals due to self-interaction errors. We discuss an appropriate choice of functional for studies of CuPc/metal interfaces and suggest the Heyd-Scuseria-Ernzerhof screened hybrid functional as a suitable compromise functional.     

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.     

A Locust-Inspired Model of Collective Marching on Rings

We study the collective motion of autonomous mobile agents in a ringlike environment. The agents’ dynamics are inspired by known laboratory experiments on the dynamics of locust swarms. In these experiments, locusts placed at arbitrary locations and initial orientations on a ring-shaped arena are observed to eventually all march in the same direction. In this work we ask whether, and how fast, a similar phenomenon occurs in a stochastic swarm of simple locust-inspired agents. The agents are randomly initiated as marching either clockwise or counterclockwise on a discretized, wide ring-shaped region, which we subdivide into k concentric tracks of length n. Collisions cause agents to change their direction of motion. To avoid this, agents may decide to switch tracks to merge with platoons of agents marching in their direction. We prove that such agents must eventually converge to a local consensus about their direction of motion, meaning that all agents on each narrow track must eventually march in the same direction. We give asymptotic bounds for the expected time it takes for such convergence or “stabilization” to occur, which depends on the number of agents, the length of the tracks, and the number of tracks. We show that when agents also have a small probability of “erratic”, random track-jumping behavior, a global consensus on the direction of motion across all tracks will eventually be reached. Finally, we verify our theoretical findings in numerical simulations.