Ah Receptor Pathway Intricacies; Signaling Through Diverse Protein Partners and DNA-Motifs.

The Ah receptor is a transcription factor that modulates gene expression via interactions with multiple protein partners; these are reviewed, including the novel NC-XRE pathway involving KLF6.

Hysteresis and multiple stable configurations in a magnetic fluid system.

A magnetic liquid in a horizontal Hele-Shaw cell is subjected to a vertical magnetic field. The width of the magnetic fluid finger is measured as a function of applied field and compared to a theoretical model. The theoretical model uses an energy minimization procedure and predicts a double energy minimum, hysteresis, and discontinuous transitions between a circle and a finger. The experimental data set agrees very well with the theory for a well-defined magnetic fluid finger. Near the transitions, the experiments show hysteresis and support for a double energy minimum; however, the agreement is not quite so good. The discrepancy between theory and experiment near the transition region is likely due to the simplified finger model used in the theory.

Confined ferrofluid droplet in crossed magnetic fields.

When a ferrofluid drop is trapped in a horizontal Hele-Shaw cell and subjected to a vertical magnetic field, a fingering instability results in the droplet evolving into a complex branched structure. This fingering instability depends on the magnetic field ramp rate but also depends critically on the initial state of the droplet. Small perturbations in the initial droplet can have a large influence on the resulting final pattern. By simultaneously applying a stabilizing (horizontal) azimuthal magnetic field, we gain more control over the mode selection mechanism. We perform a linear stability analysis that shows that any single mode can be selected by appropriately adjusting the strengths of the applied fields. This offers a unique and accurate mode selection mechanism for this confined magnetic fluid system. We present the results of numerical simulations that demonstrate that this mode selection mechanism is quite robust and "overpowers" any initial perturbations on the droplet. This provides a predictable way to obtain patterns with any desired number of fingers.

A phase I and II study of 2-weekly irinotecan with capecitabine in advanced gastroesophageal adenocarcinoma.

We investigated 2-weekly intravenous irinotecan combined with oral capecitabine in patients with advanced gastroesophageal adenocarcinoma. In phase I, doses were escalated in chemotherapy naïve or pretreated patients to establish maximum tolerated doses (MTD). In phase II, patients were treated at MTD as first-line therapy with the primary end point of RECIST response. Dose levels in phase I were as follows: Level 1: irinotecan 150 mg m-2 on day 1; capecitabine 850 mg m-2 12-hourly on days 1-9. Level 2: as level 1 but capecitabine 1000 mg m-2. Level 3: as level 2 but irinotecan 180 mg m-2. Level 4: as level 3 but capecitabine 1250 mg m-2. In phase I, 21 patients were entered. Maximum tolerated dose was level 3. Dose-limiting toxicities were lethargy, diarrhoea, vomiting and mucositis. In phase II, 31 patients were entered at level 3. During the first six cycles, 13 of these patients underwent dose reduction and three patients stopped treatment for toxicity. A further six patients stopped for progressive disease. The commonest grade 3-4 toxicities were lethargy (20%), diarrhoea (17%), nausea (10%) and anorexia (10%). There were no treatment-related deaths. The response rate was 32% (95% CI 16-52%). Median overall survival was 10 months. This regimen is active in gastroesophageal adenocarcinoma. However, using the MTD defined in phase I, fewer than 50% patients tolerated six cycles without modification in phase II; therefore, modification of these doses is recommended for further study.

Energetics of interacting magnetized domains.

Many of the pattern forming features of ferrofluids, lipid monolayers, type-I superconductors, and magnetic bubbles can be understood by treating them as dipolar (uniformly magnetized or polarized) domains. Here, we investigate the early stages of pattern formation in a system consisting of two quasi-two-dimensional dipolar domains. We calculate the linearized interaction energy for these domains and find that the lowest energy states are those for which each drop has an indentation directed toward the other. These theoretically preferred states compare favorably with results of experiments performed with ferrofluids.

Selective trafficking of KNOTTED1 homeodomain protein and its mRNA through plasmodesmata.

Plasmodesmata are intercellular organelles in plants that establish cytoplasmic continuity between neighboring cells. Microinjection studies showed that plasmodesmata facilitate the cell-to-cell transport of a plant-encoded transcription factor, KNOTTED1 (KN1). KN1 can also mediate the selective plasmodesmal trafficking of kn1 sense RNA. The emerging picture of plant development suggests that cell fate is determined at least in part by supracellular controls responding to cellular position as well as lineage. One of the mechanisms that enables the necessary intercellular communication appears to involve transfer of informational molecules (proteins and RNA) through plasmodesmata.

Isolation and sequence analysis of the Pseudomonas syringae pv. tomato gene encoding a 2,3-diphosphoglycerate-independent phosphoglyceromutase.

Pseudomonas syringae pv. tomato DC3481, a Tn5-induced mutant of the tomato pathogen DC3000, cannot grow and elicit disease symptoms on tomato seedlings. It also cannot grow on minimal medium containing malate, citrate, or succinate, three of the major organic acids found in tomatoes. We report here that this mutant also cannot use, as a sole carbon and/or energy source, a wide variety of hexoses and intermediates of hexose catabolism. Uptake studies have shown that DC3481 is not deficient in transport. A 3.8-kb EcoRI fragment of DC3000 DNA, which complements the Tn5 mutation, has been cloned and sequenced. The deduced amino acid sequences of two of the three open reading frames (ORFs) present on this fragment, ORF2 and ORF3, had no significant homology with sequences in the GenBank databases. However, the 510-amino-acid sequence of ORF1, the site of the Tn5 insertion, strongly resembled the deduced amino acid sequences of the Bacillus subtilis and Zea mays genes encoding 2,3-diphosphoglycerate (DPG)-independent phosphoglyceromutase (PGM) (52% identity and 72% similarity and 37% identity and 57% similarity, respectively). PGMs not requiring the cofactor DPG are usually found in plants and algae. Enzyme assays confirmed that P. syringae PGM activity required an intact ORF1. Not only is DC3481 the first PGM-deficient pseudomonad mutant to be described, but the P. syringae pgm gene is the first gram-negative bacterial gene identified that appears to code for a DPG-independent PGM. PGM activity appears essential for the growth and pathogenicity of P. syringae pv. tomato on its host plant.

Labyrinthine pattern formation in magnetic fluids.

A quasi two-dimensional drop of a magnetic fluid (ferrofluid) in a magnetic field is one example of the many systems, including amphiphilic monolayers, thin magnetic films, and type I superconductors, that form labyrinthine patterns. The formation of the ferrofluid labyrinth was examined both experimentally and theoretically. Labyrinth formation was found to be sensitively dependent on initial conditions, indicative of a space of configurations having a vast number of local energy minima. Certain geometric characteristics of the labyrinths suggest that these multiple minima have nearly equivalent energies. Kinetic effects on pattern selection were found in studies of fingering in the presence of timedependent magnetic fields. The dynamics of this pattern formation was studied within a simple model that yields shape evolutions in qualitative agreement with experiment.

Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction.

Several DNA extraction techniques were quantitatively and qualitatively compared using both fresh and paraffin wax embedded tissue and their suitability investigated for providing DNA and RNA for the polymerase chain reaction (PCR). A one hour incubation with proteinase K was the most efficient DNA extraction procedure for fresh tissue. For paraffin wax embedded tissue a five day incubation with proteinase K was required to produce good yields of DNA. Incubation with sodium dodecyl sulphate produced very poor yields, while boiling produced 20% as much DNA as long enzyme digestion. DNA extracted by these methods was suitable for the PCR amplification of a single copy gene. Proteinase K digestion also produced considerable amounts of RNA which has previously been shown to be suitable for PCR analysis. A delay before fixation had no effect on the amount of DNA obtained while fixation in Carnoy's reagent results in a much better preservation of DNA than formalin fixation, allowing greater yields to be extracted.

Extraction of DNA from exfoliative cytology specimens and its suitability for analysis by the polymerase chain reaction.

The extraction of DNA from archival exfoliative cytology samples would allow the molecular biological analysis of this readily available material using the polymerase chain reaction (PCR). We have quantitatively and qualitatively studied the extraction of DNA from a variety of cytological preparations. For both fresh and archival cervical smears, overnight incubation with proteinase K produces high yields of high molecular weight DNA, but simply boiling the samples produces DNA suitable for PCR amplification of a single copy gene. Increasing the proteinase K incubation to several days allows the extraction of DNA from fixed and stained archival cytology slides from a variety of sites. The extracted DNA was again suitable for PCR analysis. Fresh and archival cytological material can be utilized for molecular biological study of disease processes using PCR. Archival cytological material is probably the best source of DNA and RNA after stored frozen tissue.

Activation of int-1 and int-2 loci in GRf mammary tumors.

The Mtv-2 locus is known to be associated with a high mammary tumor incidence (97%) and early development of mammary tumors (3-13 months) in GR mice. However, it was not previously known whether the provirus which resides at the Mtv-2 locus is tumorigenic in and of itself or whether reintegration of proviruses generated from Mtv-2 is required for tumorigenesis. Foster-nursing GR mice on C57/BL mice eliminates the milk-borne source of GR virus, and allows the study of Mtv-2 derived proviruses alone. Using this approach, we have tested predictions which follow from the "positional" versus "reintegrational" models of tumorigenesis. Specifically, we have examined tumors from primary foster-nursed (GRf) mice to determine if MMTV proviruses derived from Mtv-2 were scattered randomly throughout the genome or were clustered in the vicinity of the int-1 and int-2 loci, which are thought to be associated with mammary tumorigenesis. It was found that the majority of spontaneous GRf mammary tumors that were tested have MMTV proviral integrations in either or both of the int-1 and int-2 loci and have transcription of either or both of the int loci. Tumors induced by Mtv-2, therefore, appear to have arisen via a mechanism similar to the activation of the int loci by exogenous (milk-borne) MMTV proviruses.

Analysis of JHM central nervous system infections in rats.

Intracerebral inoculation of murine coronavirus JHM into 2- to 3-day-old Wistar Furth rats causes an acute encephalomyelitis, while inoculations at 10 days of age usually result in hind leg paralysis. To examine the distribution of viral antigens within this infected central nervous system (CNS) tissue, we used the avidin-biotin-peroxidase method to detect monoclonal and polyclonal antibodies bound to JHM structural proteins; in addition we used the Western blot technique to detect viral proteins. Our study demonstrated the following characteristics: Infected neuronal and glial cells produced viral nucleocapsid and E2 glycoprotein. The synthesis of these viral structural proteins was not restricted to cells in any particular part of the central nervous system. While JHM E2 proteins could be detected in individual cells of JHM-infected CNS tissue, the relative level of detectable E2 protein in the total CNS tissue of infected rats was reduced by more than 13-fold compared with JHM-infected tissue culture cells. Hippocampus neuronal cells provided a sensitive indication of JHM infection. These cells invariably contained antigens in both acutely and chronically infected animals. The distribution of cells containing viral antigens differed markedly for JHM-induced acute encephalitis and chronic demyelinating disease. Acutely infected brains had large lesions containing low levels of viral antigen scattered throughout the brain. One percent to ten percent of histologically normal cells in many parts of the brain contained viral antigens; in addition, more neuronal cells than glial cells were observed to be antigen-positive. The hippocampus appeared normal with hematoxylin-eosin staining; however, a scattered infection of neuronal cells was apparent.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization of murine hepatitis virus (JHM) RNA from rats with experimental encephalomyelitis.

When Wistar Furth rats are inoculated intracerebrally with the murine hepatitis virus JHM they often develop a demyelinating disease with resulting hind leg paralysis. Using an RNA transfer procedure and hybridization kinetic analysis, the virus-specific RNA in these rats was characterized. The pattern of JHM-specific RNA varied with individual infections of Wistar Furth rats. However, two species of JHM-specific RNA, the nucleocapsid and a 2.1-2.4 X 10(6)-Da RNA species were generally present. A general decrease in JHM-specific RNA in brains and spinal cord samples taken later than 20 days postinoculation was observed; however, JHM-specific RNA persisted in the spinal cord longer than in the brain of these rats.

An in vitro test of platelet viability.

The survival of transfused platelets is inversely related to the time of storage of platelets in vitro. The effects of storage on the ability of platelets to produce retraction of clots and on the morphologic alterations of platelets within the clots has been studied. The results suggest that clot retraction, using low concentrations of platelets, may be useful as an in vitro method for evaluating the viability of platelets.