Sequence-specific long range networks in PSD-95/discs large/ZO-1 (PDZ) domains tune their binding selectivity.

Protein-protein interactions mediated by modular protein domains are critical for cell scaffolding, differentiation, signaling, and ultimately, evolution. Given the vast number of ligands competing for binding to a limited number of domain families, it is often puzzling how specificity can be achieved. Selectivity may be modulated by intradomain allostery, whereby a remote residue is energetically connected to the functional binding site via side chain or backbone interactions. Whereas several energetic pathways, which could mediate intradomain allostery, have been predicted in modular protein domains, there is a paucity of experimental data to validate their existence and roles. Here, we have identified such functional energetic networks in one of the most common protein-protein interaction modules, the PDZ domain. We used double mutant cycles involving site-directed mutagenesis of both the PDZ domain and the peptide ligand, in conjunction with kinetics to capture the fine energetic details of the networks involved in peptide recognition. We performed the analysis on two homologous PDZ-ligand complexes and found that the energetically coupled residues differ for these two complexes. This result demonstrates that amino acid sequence rather than topology dictates the allosteric pathways. Furthermore, our data support a mechanism whereby the whole domain and not only the binding pocket is optimized for a specific ligand. Such cross-talk between binding sites and remote residues may be used to fine tune target selectivity

Plasma levels of the proprotein convertase furin and incidence of diabetes and mortality

Background. Diabetes mellitus is linked to premature mortality of virtually all causes. Furin is a proprotein convertase broadly involved in the maintenance of cellular homeostasis; however, little is known about its role in the development of diabetes mellitus and risk of premature mortality. Objectives. To test if fasting plasma concentration of furin is associated with the development of diabetes mellitus and mortality. Methods. Overnight fasted plasma furin levels were measured at baseline examination in 4678 individuals from the population-based prospective Malmo Diet and Cancer Study. We studied the relation of plasma furin levels with metabolic and hemodynamic traits. We used multivariable Cox proportional hazards models to investigate the association between baseline plasma furin levels and incidence of diabetes mellitus and mortality during 21.3-21.7 years follow-up. Results. An association was observed between quartiles of furin concentration at baseline and body mass index, blood pressure and plasma concentration of glucose, insulin, LDL and HDL cholesterol (vertical bar 0.11 vertical bar Conclusion. Individuals with high plasma furin concentration have a pronounced dysmetabolic phenotype and elevated risk of diabetes mellitus and premature mortality.Peer reviewe

Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner

Epigenetic changes are frequently observed in cancer. However, their role in establishing or sustaining the malignant state has been difficult to determine due to the lack of experimental tools that enable resetting of epigenetic abnormalities. To address this, we applied induced pluripotent stem cell (iPSC) reprogramming techniques to invoke widespread epigenetic resetting of glioblastoma (GBM)-derived neural stem (GNS) cells. GBM iPSCs (GiPSCs) were subsequently redifferentiated to the neural lineage to assess the impact of cancer-specific epigenetic abnormalities on tumorigenicity. GiPSCs and their differentiating derivatives display widespread resetting of common GBM-associated changes, such as DNA hypermethylation of promoter regions of the cell motility regulator TES (testis-derived transcript), the tumor suppressor cyclin-dependent kinase inhibitor 1C (CDKN1C; p57KIP2), and many polycomb-repressive complex 2 (PRC2) target genes (e.g., SFRP2). Surprisingly, despite such global epigenetic reconfiguration, GiPSC-derived neural progenitors remained highly malignant upon xenotransplantation. Only when GiPSCs were directed to nonneural cell types did we observe sustained expression of reactivated tumor suppressors and reduced infiltrative behavior. These data suggest that imposing an epigenome associated with an alternative developmental lineage can suppress malignant behavior. However, in the context of the neural lineage, widespread resetting of GBM-associated epigenetic abnormalities is not sufficient to override the cancer genome

Care of the old—A matter of ethics, organization and relationships

The world stands on the threshold of a demographic revolution called global ageing. According to the World Health Organization (WHO), the population aged 60 and over is expected to increase from today's 650 million to an estimated 2 billion by 2050. Alongside demographic changes, dramatic changes can also be observed in older people's services. The shift has resulted in reduced government spending on caring for ill and frail older people in health care. Today, many governments have developed strategies to keep older people living well in their private home for as long as possible and have replaced long-term care institutions with residential homes. The aim of this study was to illuminate the meaning of caring for older people as experienced by health care students and professionals working in this field. Interviews were carried out with 17 women and one man, aged 21–65 years; six were Registered Nurses (RN), six were Enrolled Nurses (EN) and six were nursing students. The interviews were analyzed with a phenomenological hermeneutical approach and provided three themes and eight sub-themes: Ethical moral self with sub-themes “meeting the needs of the old”, “pliability towards the old”, and “difficulties in meeting aggressiveness”; Organizational and co-workers ethical moral actions with sub-themes, “co-workers who are offensive”, and “supportive and non-supportive leaders”: The relation with the old persons and their relatives with sub-themes “fellowship and closeness in the relation”, “uncertainty and fear in the relation”, and, “demands from the older persons’ close relatives”

Charge-Fluctuation-Induced Non-analytic Bending Rigidity

In this Letter, we consider a neutral system of mobile positive and negative charges confined on the surface of curved films. This may be an appropriate model for: i) a highly charged membrane whose counterions are confined to a sheath near its surface; ii) a membrane composed of an equimolar mixture of anionic and cationic surfactants in aqueous solution. We find that the charge fluctuations contribute a non-analytic term to the bending rigidity that varies logarithmically with the radius of curvature. This may lead to spontaneous vesicle formation, which is indeed observed in similar systems.Comment: Revtex, 9 pages, no figures, submitted to PR

The Method of Images in Cosmology

31 pages, 18 figures31 pages, 18 figuresWe apply the method of images to the exact initial data for cosmological models that contain a number of regularly arranged discrete masses. This allows us to join cosmological regions together by throats, and to construct wormholes in the initial data. These wormholes allow for the removal of the asymptotically flat "flange" regions that would otherwise exist on the far side of black holes. The method of images also provides us with a way to investigate the definition of mass is cosmology, and the cosmological consequences of the gravitational interaction energies between massive objects. We find evidence that the interaction energies within clusters of massive objects do indeed appear to contribute to the total energy budget in the cosmological regions of the space-time

Differential expression analysis for sequence count data

*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq

A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1

Glioblastoma multiforme (GBM) is the most common primary brain cancer in adults and there are few effective treatments. GBMs contain cells with molecular and cellular characteristics of neural stem cells that drive tumour growth. Here we compare responses of human glioblastoma-derived neural stem (GNS) cells and genetically normal neural stem (NS) cells to a panel of 160 small molecule kinase inhibitors. We used live-cell imaging and high content image analysis tools and identified JNJ-10198409 (J101) as an agent that induces mitotic arrest at prometaphase in GNS cells but not NS cells. Antibody microarrays and kinase profiling suggested that J101 responses are triggered by suppression of the active phosphorylated form of polo-like kinase 1 (Plk1) (phospho T210), with resultant spindle defects and arrest at prometaphase. We found that potent and specific Plk1 inhibitors already in clinical development (BI 2536, BI 6727 and GSK 461364) phenocopied J101 and were selective against GNS cells. Using a porcine brain endothelial cell blood-brain barrier model we also observed that these compounds exhibited greater blood-brain barrier permeability in vitro than J101. Our analysis of mouse mutant NS cells (INK4a/ARF(-/-), or p53(-/-)), as well as the acute genetic deletion of p53 from a conditional p53 floxed NS cell line, suggests that the sensitivity of GNS cells to BI 2536 or J101 may be explained by the lack of a p53-mediated compensatory pathway. Together these data indicate that GBM stem cells are acutely susceptible to proliferative disruption by Plk1 inhibitors and that such agents may have immediate therapeutic value

Applying Occam\u27s razor to global agricultural land use change

We present a parsimonious agricultural land-use model that is designed to replicate global land-use change while allowing the exploration of uncertainties in input parameters. At the global scale, the modelled uncertainty range of agricultural land-use change covers observed land-use change. Spatial patterns of cropland change at the country level are simulated less satisfactorily, but temporal trends of cropland change in large agricultural nations were replicated by the model. A variance-based global sensitivity analysis showed that uncertainties in the input parameters representing to consumption preferences are important for changes in global agricultural areas. However, uncertainties in technological change had the largest effect on cereal yields and changes in global agricultural area. Uncertainties related to technological change in developing countries were most important for modelling the extent of cropland. The performance of the model suggests that highly generalised representations of socio- economic processes can be used to replicate global land-use change