DNA sequencing

Determination of the sequence of DNA is one of the most important aspects of modern molecular biology. New sequencing methods currently being developed enable DNA sequence to be determined increasingly faster and more efficiently. One of the major advances in sequencing technology is the development of automated DNA sequencers. These utilize fluorescent rather than radioactive labels. A laser beam excites the fluorescent dyes, the emitted fluorescence is collected by detectors, and the information analyzed by computer. Robotic work stations are being developed to perform template preparation and purification, and the sequencing reactions themselves. Research is currently in progress to develop the technology of mass spectrometry for DNA sequencing. Success in this endeavor would mean that the gel electrophoresis step in DNA sequencing could be eliminated. A major innovation has been the application of polymerase chain reaction (PCR) technology to DNA sequence determination, which has led to the development of linear amplification sequencing (cycle sequencing). This very powerful yet technically simple method of sequencing has many advantages over conventional techniques, and may be used in manual or automated methods. Other recent innovations proposed recently to increase speed and efficiency include multiplex sequencing. This consists of pooling a number of samples and processing them as pools. After electrophoresis, the DNA is transferred to a membrane, and sequence images of the individual samples are obtained by sequential hybridizations with specific labeled oligonucleotides. Multiplex DNA sequencing has been used in conjunction with direct blotting electrophoresis to facilitate transfer of the DNA to a membrane. Chemiluminescent detection can also be used in conjunction with multiplex DNA sequencing to visualize the image on the membrane.     

Electrostatically stabilized metal oxide particle dispersions in carbon dioxide

We report electrostatic stabilization of micrometer-sized TiO(2) particles at long range (several micrometers) in liquid and supercritical CO(2) despite the ultralow dielectric constant, as low as 1.5. The counterions were solubilized in dry reverse micelles, formed with a low-molecular weight cationic perfluoropolyether trimethylammonium acetate surfactant, to prevent ion pairing with the particle surface. Dynamic light scattering and settling velocities indicate a particle diameter of 620-740 nm. The electrophoretic mobility of -2.3 x 10(-8) m(2)/V s indicated a particle charge on the order of -1.7 x 10(-17) C, or 105 elementary negative charges per particle. The balance of particle compression by an electric field versus electrostatic repulsion generated an amorphous arrangement of particles with 5-9 mum spacing, indicating Debye lengths greater than 1 mum. Scattering patterns also indicate that chains of particles may be achieved in CO(2) by dielectrophoresis with alternating fields. The electrostatic stabilization has been achieved by solubilizing a small concentration of counterions in only a small fraction of the reverse micelles in the double layer. Whereas many low-molecular weight surfactants have been shown to form reverse micelles in CO(2), very few polymers are able to stabilize micrometer-sized colloids sterically. Thus, electrostatic stabilization has the potential to expand markedly the domain of colloid science in apolar supercritical fluids.     

Guided ion beam studies of the reactions of O+, O 2 + , N+ and N 2 + with silane

Guided ion beam mass spectrometry is used to measure the cross sections as a function of kinetic energy for reaction of SiH₄ with O⁺(⁴S), O ₂ ⁺ (²Π_g,v=0), N⁺(³P), and N ₂ ⁺ (²Σ _g ⁺ ,v=0). All four ions react with silane by dissociative charge-transfer to form SiH _m ⁺ (m=0?3), and all but N ₂ ⁺ also form SiXH _m ⁺ products where (m=0?3) andX=O, O₂ or N. The overall reactivity of the O⁺, O ₂ ⁺ , and N⁺ systems show little dependence on kinetic energy, but for the case of N ₂ ⁺ , the reaction probability and product distribution relies heavily on the kinetic energy of the system. The present results are compared with those previously reported for reactions of the rare gas ions with silane [13] and are discussed in terms of vertical ionization from the 1t ₂ and 3a ₁ bands of SiH₄. Thermal reaction rates are also provided and dicussed.     

Role of sphingomyelin-MAPKs pathway in heat-induced apoptosis

The role of sphingomyelinase (SMase) activation and mitogen activated protein kinases (MAPKs) activation in cellular apoptosis was investigated during the hyperthermic treatment of HL-60 human leukemia cells. Treating the cells for 1 h at 43(o)C caused more than 50% of cellular apoptosis within several hours. The neutral-SMase activity in the cells treated for 1 h at 42(o)C was slightly increased but decreased in the cells treated at 43(o)C or 44(o)C for the same period whereas the acid SMase activity was slightly increased after heating the cells at 42(o)C and 43(o)C and markedly increased at 44(o)C for 1 h. Treatment of cells with inhibitors of SMase activation and ceramide formation significantly reduced the heat-induced apoptosis. Three major families of mitogen-activated protein kinases (MAPKs), i.e. ERK1/2, p38 and JNK, were activated by the hyperthermic treatment of cells. Inhibition of ERK1/2 with PD98059 exerted little effect on the heat-induced apoptosis and p38 inhibition with SB203580 slightly lessened apoptosis whereas, inhibition of JNK with SP600125 markedly suppressed the heat-induced apoptosis. These results indicate that heat-shock induced the activation of SMase, particularly acid-SMase, thereby causing apoptosis and that JNK played a pivotal role in heat-induced apoptosis in HL-60 leukemia cells.     

Time Window Expansion for HDX Analysis of an Intrinsically Disordered Protein

Application of typical HDX methods to examine intrinsically disordered proteins (IDP), proteins that are natively unstructured and highly dynamic at physiological pH, is limited because of the rapid exchange of unprotected amide hydrogens with solvent. The exchange rates of these fast exchanging amides are usually faster than the shortest time scale (10 s) employed in typical automated HDX-MS experiments. Considering the functional importance of IDPs and their association with many diseases, it is valuable to develop methods that allow the study of solution dynamics of these proteins as well as the ability to probe the interaction of IDPs with their wide range of binding partners. Here, we report the application of time window expansion to the millisecond range by altering the on-exchange pH of the HDX experiment to study a well-characterized IDP; the activation domain of the nuclear receptor coactivator, peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α). This method enabled mapping the regions of PGC-1α that are stabilized upon binding the ligand binding domain (LBD) of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ). We further demonstrate the method’s applicability to other binding partners of the IDP PGC-1α and pave the way for characterizing many other biologically important ID proteins.

Novel nonperipheral octa-3-hydroxypropylthio substituted metallo-phthalocyanines: synthesis,characterization, and investigation of their electrochemical,photochemical and computational properties

The current study describes the synthesis, electrochemical, computational, and photochemical properties of octa (3-hydroxypropylthio) substituted cobalt (II) ( 4 ), copper (II) ( 5 ), nickel (II) ( 6 ) and zinc(II) ( 7 ) phthalocyanine derivatives. These novel compounds were characterized by elemental analysis,¹H,¹³C NMR, FT-IR, UV-Vis, and MS. The redox behaviors of these metallo-phthalocyanines were investigated by the cyclic voltammetric method. The optimized molecular structure and gauge-including atomic orbital (GIAO)¹H and¹³C NMR chemical shift values of these phthalocyanines in the ground state had been calculated by using B3LYP/6–31G(d,p) basis set. The outcomes of the optimized molecular structure were given and compared with the experimental NMR values. The photochemical properties including photodegradation and singlet oxygen generation of zinc(II) phthalocyanine were studied in DMSO solution for the determination of its photosensitizer behaviors.