papa (package for the analysis of parental allocation): a computer program for simulated and real parental allocation

papa is a parental pair allocation and simulator program. The allocation method is based on the likelihood of a parental pair producing the multilocus genotype found in the offspring being tested, which will be referred to as the breeding likelihood. Estimated level and structure of allele transmission errors in offspring are parameters fed into the allocation procedure. The embodied Monte‐Carlo simulator also allows modelling of many allocation conditions, including transmission error and the estimated proportion of missing parents. Simulations may be run prior to the collection of real parents in order to define the minimal set of loci that is necessary to reach a desired level of allocation success. Post‐collection simulations aim at statistically assessing the reliability of nonsimulated allocations. Simulations output values for several random variables.     

cAMP protection of pancreatic cancer cells against apoptosis induced by ERK inhibition.

Large increases in cAMP concentration inside the cell are generally growth inhibitory for most cell lines of mesenchymal and epithelial origin. Moreover, recent data suggest a role of cAMP in survival of different cell types. Herein, the ability of forskolin (an adenylyl cyclase activator) and IBMX (3-isobutyl-1-methylxanthine) (a phosphodiesterase inhibitor) to modulate cell cycle progression and survival of human pancreatic cancer cells was evaluated. We showed that forskolin + IBMX inhibited serum-induced ERK activities, Rb hyperphosphorylation, Cdk2 activity, and p27(Kip1) downregulation and caused G1 arrest in MIA PaCa-2 cells. Furthermore, forskolin + IBMX protected pancreatic cells against apoptosis induced by prolonged inhibition of ERK activities by preventing Bcl-X(L) downregulation, activation of caspases 3, 6, 8, and 9, and PARP cleavage and by inducing Bad phosphorylation (ser112). Taken together, our data demonstrate for the first time that cAMP is an inhibitor of cell cycle progression and apoptosis in human pancreatic cancer cells.     

Influence of substitution pattern and cation binding on conformation and activity in heparin derivatives

As model compounds for the biologically important heparan sulfate, eight systematically modified heparin derivatives were studied by synchrotron radiation circular dichroism (SRCD), which is sensitive to uronic acid conformation. Substitution pattern altered uronic acid conformation, even when structural changes were made in adjacent glucosamine residues (e.g. 6-O-desulfation) and did not involve a chromophore. SRCD spectra of these derivatives following conversion to the Na+, K+, Mg2+, Ca2+, Mn2+, Cu2+ and Fe3+ cation forms revealed that almost all substitution/cation combinations resulted in unique spectra, showing that each was structurally distinct. The detailed effects that binding Na+, K+, Mg2+ and Ca2+ ions had on a 2-de-O-sulfated derivative was also studied by NMR, revealing that subtle changes in conformation (by NOE) and flexibility (by T2 measurements) resulted. Conversion to the K+ and Cu2+ ion forms also drastically modified biological activity, from inactive to active, in a cell-based assay of fibroblast growth factor-receptor (FGF2/FGFR1c) signalling and this effect was not reproduced by free cations. These observations could explain the often-contradictory data concerning structure-activity relationships for these derivatives in the literature and, furthermore, argue strongly against the established trend of considering sequence as a complete structural definition. It also provides additional means of modifying the activity of these polysaccharides and suggests a possible additional level of control in biological systems. There are also obvious potential applications for these findings in the biotechnology sphere.     

A differential phosphoproteomic analysis of retinoic acid-treated P19 cells

External stimuli trigger internal signaling events within a cell that may represent either a temporary or permanent shift in the phosphorylation state of its proteome. Numerous reports have elucidated phosphorylation sites from a variety of biological samples and more recent studies have monitored the temporal dynamics of protein phosphorylation as a given system is perturbed. Understanding which proteins are phosphorylated as well as when they are phosphorylated may indicate novel functional roles within a system and allow new therapeutic avenues to be explored. To elucidate the dynamics of protein phosphorylation within differentiating murine P19 embryonal carcinoma cells, we induced P19 cells to differentiate using all-trans-retinoic acid and developed a strategy that combines isotopically labeled methyl esterification, immobilized metal affinity chromatography, mass spectrometric analysis, and a rigorous and unique data evaluation approach. We present the largest differential phosphoproteomic analysis using isotopically labeled methyl esterification to date, identifying a total of 472 phosphorylation sites on 151 proteins; 56 of these proteins had altered abundances following treatment with retinoic acid and approximately one-third of these have been previously associated with cellular differentiation. A series of bioinformatic tools were used to extract information from the data and explore the implications of our findings. This study represents the first global gel-free analysis that elucidates protein phosphorylation dynamics during cellular differentiation.     

Impact of clear-cutting and prescribed burning on microbial diversity and community structure in a Jack pine (Pinus banksiana Lamb.) clear-cut using Biolog Gram-negative microplates

Three isolates ofFusarium avenaceum are pathogenic on spotted knapweed(Centaurea maculosa), a major weed plant of pasturelands and rangelands of the Pacific Northwestern USA. One isolate (no. 1) obtained from the European centre of origin of knapweed and isolate no. 365 native to Montana, did not significantly affect knapweed seed germination. However,F. avenaceum no. 1003, another Montana native isolate, caused a 100% decrease in seed germination and hence, no seedling emergence. When formulated, isolate no. 1003, could be recovered from treated soils after 7 days and caused a significant reduction in seedling emergence or seedling dry weight. This organism had no effect on the germination ofTriticum aestivum orMedicago sativa, but did affect the germination of other plant species.F. avenaceum appears to be a candidate for the biocontrol of spotted knapweed, however, a native isolate is potentially more effective than an isolate obtained from the centre of origin ofC. maculosa.     

Rapid extraction of plasmids from Clostridium perfringens.

Two rapid methods were evaluated for their extraction of plasmids from Clostridium perfringens. The first method involved lysis of 1 to 2 ml of C. perfringens culture by treatment with hyaluronidase, lysozyme, and sarcosyl. DNA, extracted with phenol-chloroform, was treated with RNase, boiled, and electrophoresed in a 1.2% agarose gel. The second method involved lysis of 2 ml of culture by lysozyme treatment and extraction with alkaline sodium dodecyl sulfate (SDS). Extracted DNA was treated with RNase, boiled, and electrophoresed in a 0.7% agarose gel. Of 57 strains of C. perfringens analyzed by both extraction procedures, 11 were shown to have plasmids by the alkaline SDS method which were missed by the phenol-chloroform extraction method. These new plasmids were of higher molecular mass and ranged up to 68 megadaltons. Use of the DNase inhibitor diethyl pyrocarbonate did not further improve the yield of plasmid DNA. An additional 159 isolates of C. perfringens screened by the alkaline SDS method revealed plasmids up to 80 megadaltons in mass and an overall plasmid carriage rate of 69%.