The electrophoretic mobility of DNA three-way junctions is affected by the sequence of overhanging single-stranded ends

The folding of three- and four-way DNA junctions is often assessed by comparing the electrophoretic mobility of restriction enzyme fragments, using the long-short arm assay. We have compared the mobility of synthetic three-way junctions that contain identical branch point sequences, but different restriction sites in the arms. We show that the mobility of fragments is affected by the sequence of the overhanging ends. In general, GC-rich overhangs produce fragments with anomalous mobilities. These anomalies can be prevented by treating the cleaved junctions with mung bean endonuclease, elevating the electrophoresis temperature or using blunt cleaving restriction endonucleases.     

A hard sphere model for order-disorder transitions in colloidal dispersions

Use of a hard sphere model and the concept of an effective hard sphere diameter of a colloidal particle with its associated double layer is reported. This method allows rapid determination of the order-disorder transition in colloidal dispersions and yields reasonable estimates of the osmotic pressures compared with “exact” Monte Carlo calculations.     

The indirect spectrophotometric determination of the sulphate ion with 2-aminoperimidine

A new spectrophotometric determination of the sulphate ion is described which uses 2-aminoperimidine hydrochloride as a precipitating reagent. The excess of the reagent is measured at 305 nm. The procedure deals with sulphate in the range 4–120 p.p.m., and relies on simple calibration. The relative standard deviation for 50 p.p.m. of sulphate is 3.7%. The interference of 100 p.p.m. of phosphate, fluoride and nitrate is only slight in the determination of 50 p.p.m. of sulphate. The method is recommended for the determination of sulphate in rain and surface waters.     

Arylthallium trifluoroacetates carbon-13 and fluorine-19 nuclear magnetic resonance: The substituent effect of the bis(trifluoroacetato)- thallium(III) group

¹³C NMR data for a series of arylthallium trifluoroacetates (ArTlX₂, X = OCOCF₃) are reported and assigned. The range of carbon—thallium couplings to be expected, the dependence on the disposition of coupled nuclei, and chemical shift effects are discussed. The Tl(OCOCF₃)₂ group is shown to be a powerful electron withdrawing group, from both the ¹³C data and ¹⁹F substituent chemical shifts of the p-fluorophenyl derivative.     

Evaluation of protocols for reproducible electrospray in-source collisionally induced dissociation on various liquid chromatography/mass spectrometry instruments and the development of spectral libraries

Mass spectral libraries provide a tool for identifying unknown compounds using both molecular weight and fragmentation information. Mass spectrometers with electrospray ionisation (ESI) and atmospheric chemical ionisation (ApCI) sources have the capability to produce data of this type using in-source collisionally induced dissociation (CID), and in-source CID libraries can be created. Due to the variation in electrospray source design from different instrument manufacturers, the production of reproducible in-source CID spectra that can be used in libraries for all instrument types is not a trivial task. To date, the evaluation of the production of in-source CID libraries has tended to focus on similar instruments from one manufacturer. The studies have also tended to focus on specific compound classes, with a limited molecular weight range.This report describes the findings from the investigation of protocols for the creation of mass spectral libraries using ESI in-source CID on six instruments from four different manufacturers. The overall goal was to create a spectral library for the identification of unknowns. The library could then be applied across all manufacturers' electrospray instruments.Two different experimental protocols were attempted. The first used a tuning compound to establish standard ESI source conditions, with fixed fragmentation potentials. The second involved the attenuation of the [M + H](+) ion to a known degree. A diverse range of compounds (pharmaceutical, photographic, pesticides) was tested to establish the reproducibility of the spectra on the six instruments. Both protocols produced spectra on the various instruments that in many cases were very similar. In other examples, the spectra differed not only in their relative ion abundances, but also in terms of the spectral content. Important observations regarding the effect of ion source design are also reported.The degree of spectral reproducibility was calculated off-line by comparing the five most abundant ions (20% for each ion that matches) from each spectrum on each instrument. This approach was adopted, as we do not possess a software package that met our requirements for spectral comparison. Match factors (% fit) were calculated by comparing each spectrum against the spectra recorded for the same compound and then for all other compounds, on each instrument. The % fit values derived by the off-line approach gave a clear view of the spectral reproducibility from instrument to instrument and also discriminated the spectra of the various compounds from each other. The applicability of this approach was tested using a blind trial in which several compounds were presented as unknowns, their in-source CID spectra recorded and the five-ion approach used for identification.     

Chiroptical properties of n-nitrosopyrrolidines and n-nitrosamino acids : Implications for the nitrosamine sector rule

CD data for a variety of N-nitrosamino acids and N-nitrosopyrrolidines are presented. The effects of nitrosamino group conformation, pyrrolidine ring geometry, different perturbing substituents, and especially intramolecular H-bonding upon the n → π^* CD band are discussed. Stereochemical conclusions can be made with confidence in many cases, although no sector diagram, as yet published, successfully correlates all the available chiroptical data in this series of compounds. However, a negative CD band due to the π → π* transition was observed tor all N-nitrosamines having the L-proline configuration at C-2, regardless of nitroso group conformation; it is suggested that this band be used whenever possible for stereochemical correlations.     

The210Pb and137Cs profiles in sediment cores from Bay of Quinte,Lake Ontario

²¹⁰Pb,²²⁶Ra and¹³⁷Cs profiles have been measured for sediment cores from three locations in Bay of Quinte, Lake Ontario, Canada. Compaction of the sediment with depth of burial is taken into account in calculating recent sedimentation rates and age profiles at these locations from the excess²¹⁰Pb profiles. The rates are 1.803+0.592 cm·y^–1 (0.254±0.083 g·cm^–2·y^–1), 0.101±0.017 cm·y^–1 (0.036+0.006 g·cm^–2·y^–1), and 0.795±0.218 cm·y^–1 (0.076±0.021 g·cm^–2·y^–1). The corresponding fluxes of excess²¹⁰Pb to sediment/water interface are determined to be 1.652, 0.253, and 1.123 pCi·cm^–2·y^–1, respectively. The anomalies observed in the radionuclide concentration profiles are attributed to physical mixing. It is postulated that the significantly higher flux of²¹⁰Pb observed at one of the locations is due to inputs from Trent River which joins the Bay near this location.     

Internalization and processing of the EGF receptor in the induction of DNA synthesis in cultured fibroblasts: the endocytic activation hypothesis.

The addition of EGF to cultured murine 3T3 cells produces a decrease in EGF binding activity with concomitant internalization and degradation of the initially bound EGF. When the EGF receptor on cultured 3T3 cells is affinity labeled with high specific activity 125I-EGF, and the fate of the affinity labeled EGF-receptor complex determined, the loss in binding activity was accounted for by receptor internalization and subsequent proteolytic processing of the EGF receptor molecules in the lysosomes. Studies of the effects of EGF concentration on EGF binding by cells, EGF-induced receptor internalization and EGF-induced stimulation of 3H-thymidine uptake into cellular DNA show that there is a direct correlation between EGF-induced receptor internalization and EGF-induced stimulation of DNA synthesis, but not between EGF binding and EGF-induced stimulation of DNA synthesis. This correlation is lost at high EGF concentrations, where stimulation of DNA synthesis is suboptimal. Optimal stimulation of DNA synthesis requires a minimum of 6 h of incubation of EGF with cells, and the suboptimal stimulation of DNA synthesis at high EGF concentration is intensified when the period of incubation of EGF with cells is less than 6 h. These data are consistent with a model of hormone signal transmission by Endocytic Activation, wherein the activation of EGF-induced processes requires constant EGF-induced internalization of receptor for a requisite 6-8 h period as an obligatory step in production of "second messenger" in the action of this hormone.     

Detection of a biomarker for Alzheimer's disease from synthetic and clinical samples using a nanoscale optical biosensor

A nanoscale optical biosensor based on localized surface plasmon resonance (LSPR) spectroscopy has been developed to monitor the interaction between the antigen, amyloid-beta derived diffusible ligands (ADDLs), and specific anti-ADDL antibodies. Using the sandwich assay format, this nanosensor provides quantitative binding information for both antigen and second antibody detection that permits the determination of ADDL concentration and offers the unique analysis of the aggregation mechanisms of this putative Alzheimer's disease pathogen at physiologically relevant monomer concentrations. Monitoring the LSPR-induced shifts from both ADDLs and a second polyclonal anti-ADDL antibody as a function of ADDL concentration reveals two ADDL epitopes that have binding constants to the specific anti-ADDL antibodies of 7.3 x 10(12) M(-1) and 9.5 x 10(8) M(-1). The analysis of human brain extract and cerebrospinal fluid samples from control and Alzheimer's disease patients reveals that the LSPR nanosensor provides new information relevant to the understanding and possible diagnosis of Alzheimer's disease.     

The PLAC1-homology region of the ZP domain is sufficient for protein polymerisation

Background  

Hundreds of extracellular proteins polymerise into filaments and matrices by using zona pellucida (ZP) domains. ZP domain proteins perform highly diverse functions, ranging from structural to receptorial, and mutations in their genes are responsible for a number of severe human diseases. Recently, PLAC1, Oosp1-3, Papillote and CG16798 proteins were identified that share sequence homology with the N-terminal half of the ZP domain (ZP-N), but not with its C-terminal half (ZP-C). The functional significance of this partial conservation is unknown.