The genealogy of a sequence subject to purifying selection at multiple sites

We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely unchanged. This result is relevant to the large number of coalescent estimation procedures, which generally assume neutrality for segregating polymorphisms--applying these estimators to evolutionarily constrained sequences could lead to a significant degree of bias. We also estimate the statistical power of several neutrality tests in detecting weak to moderate purifying selection and find that the power is quite good for some parameter combinations. This result contrasts with previous studies, which predicted low statistical power because of the minor effect that weak purifying selection has on the shape of a genealogy. Finally, we investigate the effect of Hill-Robertson interference among linked deleterious mutations on patterns of molecular variation. We find that dependence among selected loci can substantially reduce the efficacy of even fairly strong purifying selection.     

Podocyte Expression of Membrane Transporters Involved in Puromycin Aminonucleoside-Mediated Injury

Several complex mechanisms contribute to the maintenance of the intricate ramified morphology of glomerular podocytes and to interactions with neighboring cells and the underlying basement membrane. Recently, components of small molecule transporter families have been found in the podocyte membrane, but expression and function of membrane transporters in podocytes is largely unexplored. To investigate this complex field of investigation, we used two molecules which are known substrates of membrane transporters, namely Penicillin G and Puromycin Aminonucleoside (PA).We observed that Penicillin G pre-administration prevented both in vitro and in vivo podocyte damage caused by PA, suggesting the engagement of the same membrane transporters by the two molecules. Indeed, we found that podocytes express a series of transporters which are known to be used by Penicillin G, such as members of the Organic Anion Transporter Polypeptides (OATP/Oatp) family of influx transporters, and P-glycoprotein, a member of the MultiDrug Resistance (MDR) efflux transporter family.Expression of OATP/Oatp transporters was modified by PA treatment. Similarly, in vitro PA treatment increased mRNA and protein expression of P-glycoprotein, as well as its activity, confirming the engagement of the molecule upon PA administration.In summary, we have characterized some of the small molecule transporters present at the podocyte membrane, focusing on those used by PA to enter and exit the cell. Further investigation will be needed to understand precisely the role of these transporter families in maintaining podocyte homeostasis and in the pathogenesis of podocyte injury.     

IL-21 induces tumor rejection by specific CTL and IFN-gamma-dependent CXC chemokines in syngeneic mice

IL-21 is an immune-stimulatory four alpha helix cytokine produced by activated T cells. To study the in vivo antitumor activities of IL-21, TS/A murine mammary adenocarcinoma cells were genetically modified to secrete IL-21 (TS/A-IL-21). These cells developed small tumors that were subsequently rejected by 90% of s.c. injected syngeneic mice. Five days after injection, TS/A-IL-21 tumors showed numerous infiltrating granulocytes, NK cells, and to a lesser extent CD8(+) T cells, along with the expression of TNF-alpha, IFN-gamma, and endothelial adhesion molecules ICAM-1 and VCAM-1. At day 7, CD8(+) and CD4(+) T cells increased together with IFN-gamma, and the CXC chemokines IFN-gamma-inducible protein 10, monokine induced by IFN-gamma, and IFN-inducible T cell alpha-chemoattractant. The TS/A-IL-21 tumor displayed a disrupted vascular network with abortive sprouting and signs of endothelial cell damage. In vivo depletion experiments by specific Abs showed that rejection of TS/A-IL-21 cells required CD8(+) T lymphocytes and granulocytes. When injected in IFN-gamma-deficient mice, TS/A-IL-21 cells formed tumors that regressed in only 29% of animals, indicating a role for IFN-gamma in IL-21-mediated antitumor response, but also the existence of IFN-gamma-independent effects. Most immunocompetent mice rejecting TS/A-IL-21 cells developed protective immunity against TS/A-pc (75%) and against the antigenically related C26 colon carcinoma cells (61%), as indicated by rechallenge experiments. A specific CTL response against the gp70-env protein of an endogenous murine retrovirus coexpressed by TS/A and C26 cells was detected in mice rejecting TS/A-IL-21 cells. These data suggest that IL-21 represents a suitable adjuvant in inducing specific CTL responses.     

Expression and regulation of the metalloproteinase ADAM-8 during human neutrophil pathophysiological activation and its catalytic activity on L-selectin shedding

A disintegrin and metalloproteinase domain (ADAM) proteins are a family of transmembrane glycoproteins with heterogeneous expression profiles and proteolytic, cell-adhesion, -fusion, and -signaling properties. One of its members, ADAM-8, is expressed by several cell types including neurons, osteoclasts, and leukocytes and, although it has been implicated in osteoclastogenesis and neurodegenerative processes, little is known about its role in immune cells. In this study, we show that ADAM-8 is constitutively present both on the cell surface and in intracellular granules of human neutrophils. Upon in vitro neutrophil activation, ADAM-8 was mobilized from the granules to the plasma membrane, where it was released through a metalloproteinase-dependent shedding mechanism. Adhesion of resting neutrophils to human endothelial cells also led to up-regulation of ADAM-8 surface expression. Neutrophils isolated from the synovial fluid of patients with active rheumatoid arthritis expressed higher amounts of ADAM-8 than neutrophils isolated from peripheral blood and the concentration of soluble ADAM-8 in synovial fluid directly correlated with the degree of joint inflammation. Remarkably, the presence of ADAM-8 both on the cell surface and in suspension increased the ectodomain shedding of membrane-bound L-selectin in mammalian cells. All these data support a potential relevant role for ADAM-8 in the function of neutrophils during inflammatory response.     

Factors that influence the radiofrequency power output of GSM mobile phones

Epidemiological studies of mobile phone use and risk of brain cancer have relied on self-reported use, years as a subscriber, and billing records as exposure surrogates without addressing the level of radiofrequency (RF) power output. The objective of this study was to measure environmental, behavioral and engineering factors affecting the RF power output of GSM mobile phones during operation. We estimated the RF-field exposure of volunteer subjects who made mobile phone calls using software-modified phones (SMPs) that recorded output power settings. Subjects recruited from three geographic areas in the U.S. were instructed to log information (place, time, etc.) for each call made and received during a 5-day period. The largest factor affecting energy output was study area, followed by user movement and location (inside or outside), use of a hands-free device, and urbanicity, although the two latter factors accounted for trivial parts of overall variance. Although some highly statistically significant differences were identified, the effects on average energy output rate were usually less than 50% and were generally comparable to the standard deviation. These results provide information applicable to improving the precision of exposure metrics for epidemiological studies of GSM mobile phones and may have broader application for other mobile phone systems and geographic locations.     

Novel water-soluble photosensitizers from dextrans

Novel water-soluble polymeric photosensitizers based on the natural polymer dextran were synthesized and studied. The modified dextran contained photoactive anthracene (An) chromophores. They were soluble in water with the solubility decreasing with an increase in the number of An moieties bound to the polymeric chain. In aqueous solutions, the macromolecules adopted a compact conformation which resulted in the formation of hydrophobic microdomains. The properties of these domains were characterized with molecular probes such as perylene and pyrazolo-quinoline derivative. The polymer absorbed in the UV/vis region and photosensitized reactions mediated by energy and/or electron transfer from electronically excited An to the molecules of organic compounds solubilized in polymeric microdomains or resided in water.     

A Protein Deep Sequencing Evaluation of Metastatic Melanoma Tissues

Malignant melanoma has the highest increase of incidence of malignancies in the western world. In early stages, front line therapy is surgical excision of the primary tumor. Metastatic disease has very limited possibilities for cure. Recently, several protein kinase inhibitors and immune modifiers have shown promising clinical results but drug resistance in metastasized melanoma remains a major problem. The need for routine clinical biomarkers to follow disease progression and treatment efficacy is high. The aim of the present study was to build a protein sequence database in metastatic melanoma, searching for novel, relevant biomarkers. Ten lymph node metastases (South-Swedish Malignant Melanoma Biobank) were subjected to global protein expression analysis using two proteomics approaches (with/without orthogonal fractionation). Fractionation produced higher numbers of protein identifications (4284). Combining both methods, 5326 unique proteins were identified (2641 proteins overlapping). Deep mining proteomics may contribute to the discovery of novel biomarkers for metastatic melanoma, for example dividing the samples into two metastatic melanoma “genomic subtypes”, (“pigmentation” and “high immune”) revealed several proteins showing differential levels of expression. In conclusion, the present study provides an initial version of a metastatic melanoma protein sequence database producing a total of more than 5000 unique protein identifications. The raw data have been deposited to the ProteomeXchange with identifiers PXD001724 and PXD001725.