8-Chloroadenosine Sensitivity in Renal Cell Carcinoma Is Associated with AMPK Activation and mTOR Pathway Inhibition

The adenosine analog 8-chloroadenosine has been shown to deplete ATP and inhibit tumor growth in hematological malignancies as well as in lung and breast cancer cell lines. We investigated effects of 8-chloroadenosine on clear cell (cc) renal cell carcinoma (RCC) cell lines. 8-chloroadenosine was effective against ccRCC cell viability in vitro, with IC₅₀ ranging from 2 μM in the most sensitive CAKI-1 to 36 μM in the most resistant RXF-393. Proteomic analysis by reverse-phase protein array revealed that 8-chloroadenosine treatment leads to inhibition of the mTOR pathway. In time-course experiments, 8-chloroadenosine treatment rapidly activated AMPK, measured by AMPK and ACC phosphorylation, and subsequently caused dephosphorylation of p70S6K and ribosomal protein RPS6 in the sensitive cell lines. However, in the resistant cell lines, AMPK activity and the mTOR pathway were unaffected by the treatment. We also noted that the resistant cell lines had elevated basal levels of phospho RPS6 and AKT. Inhibition of PI3K pathway enhanced the efficacy of 8-chloroadenosine across all cell lines. Our observations indicate that 8-chloroadenosine activity is associated with inhibition of the mTOR pathway, and that phospho RPS6 and PI3K pathway activation status may determine resistance. Among solid tumors, RCC is one of the few susceptible to mTOR inhibition. We thus infer that 8-chloroadenosine may be effective in RCC by activating AMPK and inhibiting the mTOR pathway.     

SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees

Background  

Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT). By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft (RSPR) operation and the number of RSPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of RSPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of RSPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees.     

Synergistic anti‐proliferative and pro‐apoptotic activity of combined therapy with bortezomib,a proteasome inhibitor,with anti‐epidermal growth factor receptor (EGFR) drugs in human cancer cells

The article to which this erratum refers was published in J Cell Physiol (2008) 216: 698–707. © 2008 Wiley‐Liss, Inc. DOI: 10.1002/jcp.21444     

Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin

Background  

Membrane proteins form key nodes in mediating the cell's interaction with the surroundings, which is one of the main reasons why the majority of drug targets are membrane proteins.     

Two conserved domains in the NGF propeptide are necessary and sufficient for the biosynthesis of correctly processed and biologically active NGF.

The three members of the neurotrophin family (NGF, BDNF and NT-3) are synthesized as large precursor proteins which undergo proteolytic processing to yield biologically active, mature neurotrophic factors. We have used in vitro mutagenesis to examine the pro-region in the NGF precursor protein as a first step towards a general understanding of the role of propeptides in the biosynthesis of neurotrophins. Our results demonstrate that only two small domains within the NGF propeptide are required for the expression and secretion of properly processed and biologically active, recombinant mouse NGF in COS-7 cells. Domain I plays an important role in the expression of active NGF while domain II is involved in proteolytic processing. Both domains are partially conserved between the propeptides of NGF proteins isolated from different species as well as BDNF and NT-3.     

Regional Eradication of Mycoplasma hyopneumoniae From Pig Herds and Documentation of Freedom of the Disease

The objectives of this study were to 1) screen all sow herds in a region for M. hyopneumoniae, 2) to effectuate an eradication programme in all those herds which were shown to be infected with M. hyopneumoniae, and 3) to follow the success of the screening and the eradication programmes. The ultimate goal was to eradicate M. hyopneumoniae from all member herds of a cooperative slaughterhouse (153 farrowing herds + 85 farrowing-to-finishing herds + 150 specialised finishing herds) before year 2000. During 1998 and 1999, a total of 5067 colostral whey and 755 serum samples (mean, 25 samples/herd) were collected from sow herds and analysed for antibodies to M. hyopneumoniae by ELISA. Antibodies were detected in 208 (3.6%) samples. Two farrowing herds (1.3%) and 20 farrowing-to-finishing herds (23.5%) were shown to be infected with M. hyopneumoniae. A programme to eradicate the infection from these herds was undertaken. During March 2000, a survey was made to prove the success of the screening and the eradication programmes. In total, 509 serum samples were collected randomly from slaughtered finishing pigs. Antibodies to M. hyopneumoniae were not detected in 506 of the samples, whereas 3 samples were considered suspicious or positive. Accordingly, 3 herds were shown to be infected. One of the herds was previously falsely classified as non-infected. Two of the herds were finishing herds practising continuous flow system (CF). Unlike finishing herds which practice all-in/all-out management routines on herd level, CF herds do not get rid of transmissible diseases spontaneously between batches, for which reason a screening was made in the rest of the CF herds (total n = 7). Consequently, 2 more infected herds were detected. In addition to the results of the survey, a decreasing prevalence of lung lesions at slaughter (from 5.2% to 0.1%) and lack of clinical breakdowns indicated that all member herds were finally free from M. hyopneumoniae in the end of year 2000.     

User guide for mapping-by-sequencing in Arabidopsis

Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.