Recognition of GC base pairs by triplex forming oligonucleotides containing nucleosides derived from 2-aminopyridine.

We have attempted to alleviate the pH dependency of triplex recognition of guanine by using intermolecular triplexes containing 2-amino-5-(2-deoxy-d-ribofuranosyl)pyridine (AP) as an analogue of 2'-deoxycytidine (dC). We find that for the beta-anomer of AP, the complex between (AP)6T6and the target site G6A6*T6C6is stable, generating a clear DNase I footprint at oligonucleotide concentrations as low as 0.25 microM at pH 5.0, in contrast to 50 microM C6T6which has no effect on the cleavage pattern. This complex is still stable at pH 6.5 producing a footprint with 1 microM oligonucleotide. Oligonucleotides containing the alpha-anomer of AP are much less effective than the beta-anomer, though in some instances they are more stable than the unmodified oligonucleotides. The results of molecular dynamics studies on a range of AP-containing triplexes has rationalized the observed stability behaviour in terms of hydrogen-bonding behaviour.     

The Influence of Plant-Growth Factors on the Initiation and Growth of Crown-Gall Tumours on Primary Pinto Bean Leaves

The number of tumours developing on primary pinto bean leaves(Phaseolus vulgaris L. variety Pinto) inoculated with Agrobacteriumtumefaciens (Smith and Town.) Conn, strain B6, was increasedby as much as 100 per cent through the addition of several plant-growthfactors and antagonists of some of these factors to the freshlyinoculated leaves. Naphthylacetic acid, gibberellic acid, (2-chloroethyl)trimethylammonium chloride, and adenine gave a biphasic responsewith optimal promotions of tumour initiation at 10^-5 to 10^-4mg/ml. Tri-iodobenzoic acid and 4-chlorophenoxyisobutyric acidwere most active at 10^-1 mg/ml. Mean tumour diameter showeda direct correlation with tumour number in these experiments.The results show tumour initiation to be sensitive to growthfactor changes, possibly through a heightened traumatic responseof the wounded leaves. The growth of the tumours was unaffectedby these additions except as they altered tumour number andthis secondarily affected tumour growth.     

Identifying causal networks linking cancer processes and anti‐tumor immunity using Bayesian network inference and metagene constructs

Cancer arises from a deregulation of both intracellular and intercellular networks that maintain system homeostasis. Identifying the architecture of these networks and how they are changed in cancer is a pre‐requisite for designing drugs to restore homeostasis. Since intercellular networks only appear in intact systems, it is difficult to identify how these networks become altered in human cancer using many of the common experimental models. To overcome this, we used the diversity in normal and malignant human tissue samples from the Cancer Genome Atlas (TCGA) database of human breast cancer to identify the topology associated with intercellular networks in vivo. To improve the underlying biological signals, we constructed Bayesian networks using metagene constructs, which represented groups of genes that are concomitantly associated with different immune and cancer states. We also used bootstrap resampling to establish the significance associated with the inferred networks. In short, we found opposing relationships between cell proliferation and epithelial‐to‐mesenchymal transformation (EMT) with regards to macrophage polarization. These results were consistent across multiple carcinomas in that proliferation was associated with a type 1 cell‐mediated anti‐tumor immune response and EMT was associated with a pro‐tumor anti‐inflammatory response. To address the identifiability of these networks from other datasets, we could identify the relationship between EMT and macrophage polarization with fewer samples when the Bayesian network was generated from malignant samples alone. However, the relationship between proliferation and macrophage polarization was identified with fewer samples when the samples were taken from a combination of the normal and malignant samples. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:470–479, 2016     

A SIMPLE ALTERNATIVE TO GENERALIZED PROCRUSTES ANALYSIS: APPLICATION TO SENSORY PROFILING DATA

A statistical method for analyzing sensory profiling data obtained by means of fixed vocabulary or free choice profiling is discussed. The most interesting feature of this method is that it involves only simple statistical treatment and can therefore be performed using standard software packages. The outcomes of this method are compared to those of Generalized Procrustes Analysis on the basis of two data sets obtained, respectively, by means of fixed vocabulary and free choice profiling. A significance test is also discussed in order to assess whether the overall configuration of the products is meaningful. This significance test is based upon a simulation study involving the permutation procedure.     

A rat lung model of instilled liquid transport in the pulmonary airways.

When a liquid is instilled in the pulmonary airways during medical therapy, the method of instillation affects the liquid distribution throughout the lung. To investigate the fluid transport dynamics, exogenous surfactant (Survanta) mixed with a radiopaque tracer is instilled into tracheae of vertical, excised rat lungs (ventilation 40 breaths/min, 4 ml tidal volume). Two methods are compared: For case A, the liquid drains by gravity into the upper airways followed by inspiration; for case B, the liquid initially forms a plug in the trachea, followed by inspiration. Experiments are continuously recorded using a microfocal X-ray source and an image-intensifier, charge-coupled device image train. Video images recorded at 30 images/s are digitized and analyzed. Transport dynamics during the first few breaths are quantified statistically and follow trends for liquid plug propagation theory. A plug of liquid driven by forced air can reach alveolar regions within the first few breaths. Homogeneity of distribution measured at end inspiration for several breaths demonstrates that case B is twice as homogeneous as case A. The formation of a liquid plug in the trachea, before inspiration, is important in creating a more uniform liquid distribution throughout the lungs.     

Effects of Growth Regulators on Polyamine Content and Peroxidase Activity in Hevea brasiliensis Callus

3, 4-dichlorophenoxyacetic acid (3,4-D) and benzylaminopurine(BAP) at 9 µM (control medium) was compared with 4.5,2.25, and 0.45 µM for ability to induce callogenesis andembryogenesis from seed explants of Hevea brasiliensis. Supplyingthese growth regulators at 4.5 µM for 20 d improved embryogenicpotential compared with the control medium (El Hadrami, Carronand d'Auzac, 1991, Annals of Botany 67, 511–515), sustainedputrescine, spermidine and spermine at a higher level throughoutof much of the culture period (40–70 d), and maintainedlow levels of peroxidase activity. In the control medium, poorcallus embryogenesis is considered a consequence of rapid ageingof tissues characterized by (i) acceleration of an early buttransient production of polyamines, which promoted embryogeniccapacity, and (ii) an early peak in peroxidase activity thatwas positively correlated with callus browning, one of the factorslimiting embryogenesis. Somatic embryogenesis, polyamines, peroxidase, Hevea brasiliensis, rubber-tree