Functional and genetic analysis of the colon cancer network

Cancer is a complex disease that has proven to be difficult to understand on the single-gene level. For this reason a functional elucidation needs to take interactions among genes on a systems-level into account. In this study, we infer a colon cancer network from a large-scale gene expression data set by using the method BC3Net. We provide a structural and a functional analysis of this network and also connect its molecular interaction structure with the chromosomal locations of the genes enabling the definition of cis- and trans-interactions. Furthermore, we investigate the interaction of genes that can be found in close neighborhoods on the chromosomes to gain insight into regulatory mechanisms. To our knowledge this is the first study analyzing the genome-scale colon cancer network.

Interactions of a non-thermal atmospheric pressure plasma effluent with PC-3 prostate cancer cells

The effect of a radio-frequency driven, microscale non thermal atmospheric pressure plasma jet operated in helium with vol. 0.3% molecular oxygen gas admixture, on PC-3 prostate cancer cells has been investigated. The viability of cells exposed to the plasma was found to decrease with increasing plasma exposure time, with apoptosis through caspase and PARP cleavage being observed. High concentrations of nitrite and nitrate were detected in growth media exposed to the plasma and were found to increase in a time dependent manner post exposure. This indicates a slow release of reactive nitrogen species into the growth media, which is likely to influence cellular response to plasma exposure.

PALLADIUM CATALYZED TANDEM CYCLIZATION-ANION CAPTURE PROCESSES .1. BACKGROUND AND HYDRIDE ION CAPTURE BY ALKYL-PALLADIUM AND PI-ALLYL-PALLADIUM SPECIES

A new, wide ranging, synthetically powerful, catalytic tandem cyclisation-anion capture process is proposed which depends on the rate of cyclisation of an organopalladium specifies (RPdX) onto a proximate alkene or diene being significantly faster than anion exchange and reductive elimination in the sequence RPdX --> RPdY --> RY + Pd(0). The catalytic cyclisation - anion capture sequence is illustrated for hydride capture by a wide variety of substrates giving rise to fused- and spiro-, carbo- and hetero-cyclic systems, regio- and stereo-specifically.

THE SYNTHESIS OF BRIDGED-RING CARBOCYCLES AND HETEROCYCLES VIA PALLADIUM CATALYZED REGIOSPECIFIC CYCLIZATION REACTIONS

A catalyst system comprising 10 mol % (Pd(OAc) and 20 mol % PPh3 effects the cyclisation of aryl halides onto proximate alkenes via 5-, 6-, and 7-exo-trig, and 7-endo-trig processes giving a variety of bridged-ring carbo- and hetero-cycles in excellent yield. Double bond isomerisation in the product is rarely encountered and may be suppressed by the addition of Tl(1) salts. One example of diastereospecific bis-cyclisation is given and the crystal structure of 1-aza-2-sulphonyl-3,4-benzobicyclo[3.2.1]nona-6-ene is reported.

Effects of peer network interactions on adolescent cannabis use

Purpose
This study capitalises on three waves of longitudinal data from a cohort of 4351 secondary school pupils to examine the effects on individuals’ cannabis use uptake of both peer cannabis use and position within a peer network.

Design/methodology/approach
Both cross-sectional and individual fixed effects models are used to estimate the effect on cannabis use of nominated friends’ cannabis use, of reciprocity and transitivity of nominations across the friendship cluster, and of interactions between these nominated friends. Post hoc analyses parsed the behaviour of reciprocating and non-reciprocating friends.

Findings
Cannabis use varied depending on the stability of friendship network and the degree of reciprocity and interconnectedness within the group. Behavioural influence was strong, but interaction effects were observed between the prevalence of cannabis use among friends, the structure of the friendship group and ego’s proximity to group members. These interactions demonstrate that behavioural influence is more salient in more cohesive groups. When reciprocating and non-reciprocating friends’ mean cannabis use were separated, influence from reciprocating friends was estimated at twice the magnitude of other friends.

Originality/value
While preventing any one individual from using cannabis is likely to have a multiplier effect on classmates, the bonds and interactions between classmates will determine which classmates are affected by this multiplier and the salience of that effect.

Contested urbanism: Access and control issues in Tundikhel, Kathmandu

Contested Open Spaces?: Access and control issues in Tundikhel, Kathmandu

Public spaces play a role of political, economic and cultural transformation of cities and the impact of these transformations on the nature of public space.

Urban open space(s) in Kathmandu have been an important part of the city’s urbanism. Historically they have played an important role in the city as spaces for religious, cultural, social and political and military activities during the 300 years of unified monarchy. Throughout the civil war period (Maoist insurgency between 1996 and 2006) they became material locations for political activities, and a site for protests and dharnas. In post-conflict Kathmandu, especially since the abolition of Monarchy in May 28, 2008, these spaces are increasingly seen being claimed by street hawkers, informal sellers and individuals reflecting a new set of users and functions, whereas a significant part of Tundikhel still remains under the military occupation posing important questions around access, identity and control of an important space.


Public spaces are broadly defined as crossroads where different paths and trajectories meet, sometimes overlapping and other times colliding (Madanipour, 2003). Using Tudikhel in Kathmandu, this research examines the increasing collision and contestations witnessed through social, political and neoliberal interactions. It explores how spaces are constantly
contested, negotiated and as a result reshaped through these interactions. It is observed that multiple forces are at play to gain control and access of this important open space, leading to increasing fragmentation of the space, and erosion of its historic significance both as cultural venue and a symbol of democracy in modern Nepal. It is argued that increasing disconnection of Tudikhel from wider urban setting has contributed to exacerbation of these contestations

Membrane fission is promoted by insertion of amphipathic helices and is restricted by crescent BAR domains

Shallow hydrophobic insertions and crescent-shaped BAR scaffolds promote membrane curvature. Here, we investigate membrane fission by shallow hydrophobic insertions quantitatively and mechanistically. We provide evidence that membrane insertion of the ENTH domain of epsin leads to liposome vesiculation, and that epsin is required for clathrin-coated vesicle budding in cells. We also show that BAR-domain scaffolds from endophilin, amphiphysin, GRAF, and β2-centaurin limit membrane fission driven by hydrophobic insertions. A quantitative assay for vesiculation reveals an antagonistic relationship between amphipathic helices and scaffolds of N-BAR domains in fission. The extent of vesiculation by these proteins and vesicle size depend on the number and length of amphipathic helices per BAR domain, in accord with theoretical considerations. This fission mechanism gives a new framework for understanding membrane scission in the absence of mechanoenzymes such as dynamin and suggests how Arf and Sar proteins work in vesicle scission.

Integrating personality research and animal contest theory:Aggressiveness in the green swordtail xiphophorus helleri

Aggression occurs when individuals compete over limiting resources. While theoretical studies have long placed a strong emphasis on context-specificity of aggression, there is increasing recognition that consistent behavioural differences exist among individuals, and that aggressiveness may be an important component of individual personality. Though empirical studies tend to focus on one aspect or the other, we suggest there is merit in modelling both within- and among-individual variation in agonistic behaviour simultaneously. Here, we demonstrate how this can be achieved using multivariate linear mixed effect models. Using data from repeated mirror trials and dyadic interactions of male green swordtails, Xiphophorus helleri, we show repeatable components of (co)variation in a suite of agonistic behaviour that is broadly consistent with a major axis of variation in aggressiveness. We also show that observed focal behaviour is dependent on opponent effects, which can themselves be repeatable but were more generally found to be context specific. In particular, our models show that within-individual variation in agonistic behaviour is explained, at least in part, by the relative size of a live opponent as predicted by contest theory. Finally, we suggest several additional applications of the multivariate models demonstrated here. These include testing the recently queried functional equivalence of alternative experimental approaches, (e.g., mirror trials, dyadic interaction tests) for assaying individual aggressiveness. © 2011 Wilson et al.

Gold nanoparticle surface functionalization: mixed monolayer versus hetero bifunctional peg linker

To create a clinically relevant gold nanoparticle (AuNP) treatment, the surface must be functionalized with multiple ligands such as drugs, antifouling agents and targeting moieties. However, attaching several ligands of differing chemistries and lengths, while ensuring they all retain their biological functionality remains a challenge. This review compares the two most widely employed methods of surface co-functionalization, namely mixed monolayers and hetero-bifunctional linkers. While there are numerous in vitro studies successfully utilizing both surface arrangements, there is little consensus regarding their relative merits. Animal and preclinical studies have demonstrated the effectiveness of mixed monolayer functionalization and while some promising in vitro results have been reported for PEG linker capped AuNPs, any potential benefits of the approach are not yet fully understood.