Characterizing replication intermediates in the amplified CHO dihydrofolate reductase domain by two novel gel electrophoretic techniques

Using neutral/neutral and neutral/alkaline two-dimensional (2-D) gel techniques, we previously obtained evidence that initiation can occur at any of a large number of sites distributed throughout a broad initiation zone in the dihydrofolate reductase (DHFR) domain of Chinese hamster ovary (CHO) cells. However, other techniques have suggested a much more circumscribed mode of initiation in this locus. This dichotomy has raised the issue whether the patterns of replicating DNA on 2-D gels have been misinterpreted and, in some cases, may represent such noncanonical replication intermediates as broken bubbles or microbubbles. In an accompanying study (R. F. Kalejta and J. L. Hamlin, Mol. Cell. Biol. 16:4915-4922, 1996), we have shown that broken bubbles migrate to unique positions in three different gel systems and therefore are not likely to be confused with classic replication intermediates. Here, we have applied a broken bubble assay developed from that study to an analysis of the amplified DHFR locus in CHO cells. This assay gives information about the number and positions of initiation sites within a fragment. In addition, we have analyzed the DHFR locus by a novel stop-and-go-alkaline gel technique that measures the size of nascent strands at all positions along each arc in a neutral/neutral 2-D gel. Results of these analyses support the view that the 2-D gel patterns previously assigned to classic, intact replication bubbles and single-forked structures indeed correspond to these entities. Furthermore, potential nascent-strand start sites appear to be distributed at very frequent intervals along the template in the intergenic region in the DHFR domain.     

The Numbing Scale: psychometric properties, a preliminary report

Twenty-one antimicrobial agents were incorporated individually into Frey's agar to evaluate their inhibitory activities against 86 isolates of avian mycoplasmas recently detected in Taiwan. Among them, 45 and 37 isolates were found positive with Mycoplasma gallisepticum and Mycoplasma synoviae fluorescent antibody conjugate, respectively. Twenty-one other isolates were unable to be identified by the above 2 conjugates. All of the field isolates were highly sensitive (with MIC50 < 1 microgram/ml) to enrofloxacin, gentamicin, myplabin, tiamutin and tylosin. However, those field isolates were highly resistant (with MIC50 > 32 micrograms/ml) to apramycin, chlortetracycline (CTC), erythromycin (ER), flumequine (FI), nalidixic acid (NA), oxolinic acid (OA), oxytetracycline (OTC) and spiramycin (SP). The inhibitory activities of the antibiotics which possessed an MIC90 of 50 micrograms/ml or less against local isolates were, in decreasing order, enrofloxacin (< 0.004 microgram/ml), gentamicin (1.53 micrograms/ml), tiamutin (1.81 micrograms/ml), tylosin (3.2 micrograms/ml), streptomycin (SM; 12.0 micrograms/ml), colistin (13.1 micrograms/ml), chloramphenicol (14.0 micrograms/ml), spectinomycin (15.0 micrograms/ml), myplabin (16.0 micrograms/ml), spiramycin (30.0 micrograms/ml), minocycline (32.0 micrograms/ml). The MIC90 of OA, CTC, SM, FI, SP, OTC, ER or NA was greater than 50 micrograms/ml; which work poorly in the control of mycoplasmoses. Since the antibiotic control policy is quite loose in Taiwan, many antimicrobial agents are often freely used in clinics, with a resulting gradual decrease in the inhibitory activity to the avian mycoplasmas.     

Non-Fermi Liquid Regimes and Superconductivity in the Low Temperature Phase Diagrams of Strongly Correlated d- and f-Electron Materials

Standard models for simple metals and insulators often fail for systems based on elements with unstable d- or f-electron shells, where strong electronic correlations can generate new and unexpected states of matter. Such a scenario can often be induced when a magnetic phase transition is tuned to absolute zero temperature by an external control parameter such as chemical composition, pressure or magnetic field. At the resulting quantum critical point (QCP), emergent phenomena, such as unconventional superconductivity and novel magnetic phases are frequently observed. The temperature and energy dependences of the physical properties are also found to deviate from expectations for a simple Fermi liquid. This “non-Fermi-liquid” (NFL) behavior is commonly manifested as weak power laws and logarithmic divergences in the physical properties at low temperatures and is often found in a V-shaped region near a QCP, which has become the “classic” QCP phase diagram. However, there is also a growing number of materials where the NFL behavior either occurs far away from the QCP, within an ordered phase, or may not be associated with any putative QCP. Thus, after nearly 20 years of research, it remains unknown whether NFL physics is universal, or if a multitude of unique subclasses exist. In this article, we review research that has primarily been carried out in our laboratory on systems that exhibit NFL behavior that does not conform to the “classic” QCP scenario.     

Radiation down-regulates replication origin activity throughout the S phase in mammalian cells

An asynchronous culture of mammalian cells responds acutely to ionizing radiation by inhibiting the overall rate of DNA replication by approximately 50% for a period of several hours, presumably to allow time to repair DNA damage. At low and moderate doses, this S phase damage-sensing (SDS) pathway appears to function primarily at the level of individual origins of replication, with only a modest inhibition of chain elongation per se. We have shown previously that the majority of the inhibition observed in an asynchronous culture can be accounted for by late G1cells that were within 2-3 h of entering the S period at the time of irradiation and which then fail to do so. A much smaller effect was observed on the overall rate of replication in cells that had already entered the S phase. This raised the question whether origins of replication that are activated within S phase per se are inhibited in response to ionizing radiation. Here we have used a two-dimensional gel replicon mapping strategy to show that cells with an intact SDS pathway completely down-regulate initiation in both early- and late-firing rDNA origins in human cells. We also show that initiation in mid- or late-firing rDNA origins is not inhibited in cells from patients with ataxia telangiectasia, confirming the suggestion that these individuals lack the SDS pathway.     

Mechanisms of cement hydration

The current state of knowledge of cement hydration mechanisms is reviewed, including the origin of the period of slow reaction in alite and cement, the nature of the acceleration period, the role of calcium sulfate in modifying the reaction rate of tricalcium aluminate, the interactions of silicates and aluminates, and the kinetics of the deceleration period. In addition, several remaining controversies or gaps in understanding are identified, such as the nature and influence on kinetics of an early surface hydrate, the mechanistic origin of the beginning of the acceleration period, the manner in which microscopic growth processes lead to the characteristic morphologies of hydration products at larger length scales, and the role played by diffusion in the deceleration period. The review concludes with some perspectives on research needs for the future.     

Effect of the Interfacial Transition Zone on the Conductivity of Portland Cement Mortars

The electrical conductivity of portland cement mortars was determined experimentally as a function of the volume fraction of sand and the degree of hydration. The results were analyzed using theoretical models that represent the mortars as three-phase, interactive composites. The three phases are the matrix paste, the aggregate, and the thin interfacial transition zone between the two. The microstructure and properties of the conductive phases (the transition zone and the matrix paste) were determined by a micrometer-scale microstructural model, and were used in conjunction with random-walk algorithms and differential-effective medium theory to determine the overall mortar conductivities. The presence of the transition zone was not found to significantly affect the global electrical conductivity of the mortar. However, there were significant differences in conductivity between the transition zone and matrix pastes when examined on a local level. These differences were found to vary with hydration and were most significant when the degree of hydration was between 0.5 and 0.8.     

The Zymark BenchMatetrade mark. A compact, fully-automated solution-phase reaction work-up facility for multiple parallel synthesis

The rapid growth of multiple parallel synthesis in our laboratories has created a demand for a robust, easily accessed automated system for solution-phase reaction work-up, since the manual work-up of large numbers of small-scale reactions is both time-consuming and tedious, and is a rate limiting step in the generation of large numbers of compounds for test. Work-up in chemical organic synthesis consists of a series of post-reaction operations designed using differential chemical properties to remove excess reagent or starting material, reagent products and, where possible reaction by-products. Careful consideration of post-reaction operations as a clean-up step can obviate the requirement for purification. Generally, work-up can be resolved into four operations: filtration, solvent addition (dilution, trituration), washing and separation (partition) and it is the selection and ordering of these four basic operations that constitutes a chemical work-up. Following the proven success of centralized Zymate robotic systems in the compilation, execution and work-up of complex reaction sequences, a centralized chemical work-up service has been in operation for over 12 months. It now seemed prudent that the needs of multiple parallel synthesis would be better served by the development of a compact, automated system, capable of operating in a standard chemistry laboratory fume-hood. A Zymark BenchMate platform has been configured to perform the four basic operations of chemical solution work-up. A custom-built filtration station, incorporating an integrated tipping facility for the sample tube has also been developed. Compilation of each work-up is through a set of Visual Basic procedure screens, each dedicated to a particular work-up scenario. Methods are compiled at the chemist's own PC and transferred to the BenchMate via a diskette.