The top-down mechanism for body-mass-abundance scaling

Scaling relationships between mean body masses and abundances of species in multitrophic communities continue to be a subject of intense research and debate. The top-down mechanism explored in this paper explains the frequently observed inverse linear relationship between body mass and abundance (i.e., constant biomass) in terms of a balancing of resource biomasses by behaviorally and evolutionarily adapting foragers, and the evolutionary response of resources to this foraging pressure. The mechanism is tested using an allometric, multitrophic community model with a complex food web structure. It is a statistical model describing the evolutionary and population dynamics of tens to hundreds of species in a uniform way. Particularities of the model are the detailed representation of the evolution and interaction of trophic traits to reproduce topological food web patterns, prey switching behavior modeled after experimental observations, and the evolutionary adaptation of attack rates. Model structure and design are discussed. For model states comparable to natural communities, we find that (1) the body-mass-abundance scaling does not depend on the allometric scaling exponent of physiological rates in the form expected from the energetic equivalence rule or other bottom-up theories; (2) the scaling exponent of abundance as a function of body mass is approximately -1, independent of the allometric exponent for physiological rates assumed; (3) removal of top-down control destroys this pattern, and energetic equivalence is recovered. We conclude that the top-down mechanism is active in the model, and that it is a viable alternative to bottom-up mechanisms for controlling body-mass-abundance relations in natural communities.

Weakly nonlinear effects associated with transverse oscillations in dusty plasma crystals

We study the amplitude modulation of transverse dust lattice waves (TDLW) propagating in a single- and double-layer dusty plasma (DP) crystal. It is shown that a modulational instability mechanism, which is related to an intrinsic nonlinearity of the sheath electric field, may occur under certain conditions. Possibility of the formation of localized excitations (envelope solitons) in the dusty plasma crystal is discussed.

FKBPL and Peptide Derivatives: Novel Biological Agents That Inhibit Angiogenesis by a CD44-Dependent Mechanism

Purpose: Antiangiogenic therapies can be an important adjunct to the management of many malignancies. Here we investigated a novel protein, FKBPL, and peptide derivative for their antiangiogenic activity and mechanism of action.

Experimental Design: Recombinant FKBPL (rFKBPL) and its peptide derivative were assessed in a range of human microvascular endothelial cell (HMEC-1) assays in vitro. Their ability to inhibit proliferation, migration, and Matrigel-dependent tubule formation was determined. They were further evaluated in an ex vivo rat model of neovascularization and in two in vivo mouse models of angiogenesis, that is, the sponge implantation and the intravital microscopy models. Antitumor efficacy was determined in two human tumor xenograft models grown in severe compromised immunodeficient (SCID) mice. Finally, the dependence of peptide on CD44 was determined using a CD44-targeted siRNA approach or in cell lines of differing CD44 status.

Results: rFKBPL inhibited endothelial cell migration, tubule formation, and microvessel formation in vitro and in vivo. The region responsible for FKBPL's antiangiogenic activity was identified, and a 24-amino acid peptide (AD-01) spanning this sequence was synthesized. It was potently antiangiogenic and inhibited growth in two human tumor xenograft models (DU145 and MDA-231) when administered systemically, either on its own or in combination with docetaxel. The antiangiogenic activity of FKBPL and AD-01 was dependent on the cell-surface receptor CD44, and signaling downstream of this receptor promoted an antimigratory phenotype.

Conclusion: FKBPL and its peptide derivative AD-01 have potent antiangiogenic activity. Thus, these agents offer the potential of an attractive new approach to antiangiogenic therapy.

Regulation of cyclin D1 by the BRCA1-BARD1 complex

Background BRCA1 and cyclin D₁ are both essential for normal breast development and mutation or aberration of their expression is associated with breast cancer [1,2]. Cyclin D₁ is best known as a G₁ cyclin where it regulates the G₁ to S phase transition by acting as a rate-limiting subunit of CDK4/6 kinase activity. More recently, however, Stacey has demonstrated that cyclin D₁ levels in G₂/M determine whether a cell continues to proliferate or exits the cell cycle [3]. The majority of BRCA1 in the cell is bound to BARD1 through their N-terminal RING domains. Heterodimerization is essential for the stability and correct localization of the complex and confers ubiquitin ligase activity to BRCA1. The importance of the ligase activity of BRCA1 to breast cancer development is inferred from the fact that N-terminal diseaseassociated mutations are proposed to reduce ligase activity [4]. Methods Protein–protein interactions were demonstrated using yeast-two-hybrid and coimmunoprecipitation. Protein levels were altered through overexpression, siRNA and antisense technology. The effect of proteasome inhibitors and cycloheximide treatment was also examined. Results We initially identified cyclin D₁ as a binding partner of BARD1 in a yeast-two-hybrid screen and defined the minimal binding region as the N-terminus of BARD1. This interaction was confirmed in vivo by coimmunoprecipitation. The N-terminus of BARD1 also binds BRCA1 and imparts ubiquitin ligase activity to the complex. Covalent modification of proteins with ubiquitin is a common regulatory mechanism in eukaryotic cells. Traditionally polyubiquitin chains linked through lysine 48 target proteins for degradation by the 26 S proteasome. We have demonstrated that cyclin D₁ protein levels are inversely related to BRCA1 and BARD1 levels in several model systems. Furthermore, regulation of cyclin D1 levels occurs through a post-transcriptional mechanism and requires the ligase activity of BRCA1. Interestingly, this phenomenon is cell-cycle regulated, occurring in G₂/M. Conclusion We propose that cyclin D₁ is a potential substrate for BRCA1 ubiquitination and that this targets cyclin D₁ for proteasomal-mediated degradation. Future work will focus on ascertaining the functional consequence of cyclin D₁ regulation by the BRCA1–BARD1 complex; in particular, the impact of BRCA1, mediated through regulation of cyclin D₁, on the proliferation versus differentiation decision.

T-box 2 represses NDRG1 through an EGR1-dependent mechanism to drive the proliferation of breast cancer cells

T-box 2 (TBX2) is a transcription factor involved in mammary development and is known to be overexpressed in a subset of aggressive breast cancers. TBX2 has previously been shown to repress growth control genes such as p14(ARF) and p21(WAF1/cip1). In this study we show that TBX2 drives proliferation in breast cancer cells and this is abrogated after TBX2 small interfering RNA (siRNA) knockdown or after the expression of a dominant-negative TBX2 protein. Using microarray analysis we identified a large cohort of novel TBX2-repressed target genes including the breast tumour suppressor NDRG1 (N-myc downregulated gene 1). We show that TBX2 targets NDRG1 through a previously undescribed mechanism involving the recruitment of early growth response 1 (EGR1). We show EGR1 is required for the ability of TBX2 to repress NDRG1 and drive cell proliferation. We show that TBX2 interacts with EGR1 and that TBX2 requires EGR1 to target the NDRG1 proximal promoter. Abrogation of either TBX2 or EGR1 expression is accompanied by the upregulation of cell senescence and apoptotic markers. NDRG1 can recapitulate these effects when transfected into TBX2-expressing cells. Together, these data identify a novel mechanism for TBX2-driven oncogenesis and highlight the importance of NDRG1 as a growth control gene in breast tissue. Oncogene (2010) 29, 3252-3262; doi: 10.1038/onc.2010.84; published online 29 March 2010

Structural Defects in Ion Chains by Quenching the External Potential: The Inhomogeneous Kibble-Zurek Mechanism

The nonequilibrium dynamics of an ion chain in a highly anisotropic trap is studied when the transverse trap frequency is quenched across the value at which the chain undergoes a continuous phase transition from a linear to a zigzag structure. Within Landau theory, an equation for the order parameter, corresponding to the transverse size of the zigzag structure, is determined when the vibrational motion is damped via laser cooling. The number of structural defects produced during a linear quench of the transverse trapping frequency is predicted and verified numerically. It is shown to obey the scaling predicted by the Kibble-Zurek mechanism, when extended to take into account the spatial inhomogeneities of the ion chain in a linear Paul trap.

The use of short time-on-stream in situ spectroscopic transient kinetic isotope techniques to investigate the mechanism of hydrocarbon selective catalytic reduction (HC-SCR) of NOx at low temperatures

The problem of differentiating between active and spectator species that have similar infrared spectra has been addressed by developing short time-on-stream in situ spectroscopic transient isotope experimental techniques (STOS-SSITKA). The techniques have been used to investigate the reaction mechanism for the reduction of nitrogen oxides (NOx) by hydrocarbons under lean-burn (excess oxygen) conditions on a silver catalyst. Although a nitrate-type species tracks the formation of isotopically labeled dinitrogen, the results show that this is misleading because a nitrate-type species has the same response to an isotopic switch even under conditions where no dinitrogen is produced. In the case of cyanide and isocyanate species, the results show that it is possible to differentiate between slowly reacting spectator isocyanate species, probably adsorbed on the oxide support, and reactive isocyanate species, possibly on or close to the active silver phase. The reactive isocyanate species responds to an isotope switch at a rate that matches that of the rate of formation of the main product, dinitrogen. It is concluded that these reactive isocyanates could potentially be involved in the reduction of NOx whereas there is no evidence to support the involvement of nitrate-type species that are observable by infrared spectroscopy.

Investigating the mechanism of the H 2-assisted selective catalytic reduction (SCR) of NOx with octane using fast cycling transient in situ DRIFTS-MS analysis

A mechanistic study of the H-2-assisted Selective Catalytic Reduction (SCR) of NOx with octane as reductant over a Ag/Al2O3 catalyst was carried out using a modified DRIFTS cell coupled to a mass spectrometer Using fast transient cycling switching of H-2 with a time resolution of a few seconds It was possible to differentiate potential reaction intermediates from other moieties that are clearly spectator species Using such a periodic operation mode effects were uncovered that are normally hidden in conventional transient studies which typically consist of a single transient In experiments based on a single transient addition of H-2 to or removal of H-2 from the SCR feed it was found that the changes in the concentrations of gaseous species (products and reactants) were not matched by changes at comparable timescales of the concentration of surface species observed by IR This observation indicates that the majority of sur face species observed by DRIFTS under steady-state reaction conditions are spectators In contrast under fast cycling experimental conditions It was found that a surface isocyanate species had a temporal response that matched that of N-15(2) This suggests that some of the isocyanate species observed by infrared spectroscopy could be important intermediates in the hydrogen-assisted SCR reaction although it is emphasised that this may be dependent on the way in which the infrared spectra are obtained It is concluded that the use of fast transient cycling switching techniques may provide useful mechanistic information under certain circumstances.

BRCA1 transcriptionally regulates genes associated with the basal breast cancer phenotype

Background Ten to twenty per cent of breast tumours exhibit a basallike genetic profile and these tumours carry a poor prognosis. Breast tumours which contain germline mutations for BRCA1 commonly exhibit a molecular profile similar to basal breast tumours. BRCA1 is a tumour suppressor gene which is mutated in up to 5–10% of breast cancer cases and is involved in multiple cellular processes including DNA damage control, cell cycle checkpoint control, apoptosis, ubiquitination and transcriptional regulation.

Methods Microarray-based profiling was carried out using the HCC1937EV and HCC1937BR breast cancer cell lines. Basal gene and protein expression levels were analysed by qRT-PCR and western blotting. ChIP analyses were performed and demonstrated that BRCA1 regulates basal gene expression through a transcriptional mechanism involving c-myc.

Results We have previously carried out microarray-based expression profiling to examine differences in gene expression when BRCA1 is reconstituted in BRCA1 mutated HCC1937 breast cancer cells. We observed that p-cadherin and the cytokeratin 5 and cytokeratin 17 genes, which are strongly correlated with the basal phenotype, are differentially expressed when BRCA1 is reconstituted. In addition, qRT-PCR and ChIP analysis of BRCA1 reconstituted cells show that BRCA1 represses the expression of these basal genes by a transcriptional mechanism. Furthermore, abrogation of endogenous BRCA1 protein in the T47D cell line using siRNA results in reexpression of these basal genes, suggesting that BRCA1 expression levels may be important in basal gene expression. We have also demonstrated that BRCA1 is physically associated with the promoter regions of basal genes through an association with c-myc. Consequently, we have confirmed that siRNA inhibition of c-myc in T47D cells results in re-expression of these genes.

Conclusions Our results suggest that BRCA1 is involved in the transcriptional regulation of genes associated with the basal phenotype and that BRCA1 controls basal gene expression through a transcriptional mechanism involving c-myc. Further work is now concentrating on defining the relationship between BRCA1 and basal gene expression and how this may affect clinical responses to breast cancer chemotherapy.

Biosorption of toxic chromium from aqueous phase by lignin: mechanism, effect of other metal ions and salts

Surface reaction methodology was implicated in the optimization of hexavalent chromium removal onto lignin with respect to the process parameters. The influence of altering the conditions for removal of chromium(VI), for instance; solution pH, ionic strength, initial concentration, the dose of biosorbent, presence of other metals (Zn and Cu), presence of salts and biosorption-desorption studies, were investigated. It was found that the biosorption capacity of lignin depends on solution pH, with a maximum biosorption capacity for chromium at pH 2. Experimental equilibrium data were fitted to five different isotherm models by non-linear regression method, however, the biosorption equilibrium data were well interpreted by the Freundlich isotherm. The maximum biosorption capacities (q(max)) obtained using Dubinin-Radushkevich and Khan isotherms for Cr(VI) biosorption are 31.6 and 29.1 mg/g. respectively. Biosorption showed pseudo second order rate kinetics at different initial concentrations of Cr(VI). The intraparticle diffusion study indicated that film diffusion may be involved in the current study. The percentage removal of chromium on lignin decreased significantly in the presence of NaHCO3 and K2P2O7 salts. Desorption data revealed that nearly 70% of the Cr(VI) adsorbed on lignin could be desorbed using 0.1 M NaOH. It was evident that the biosorption mechanism involves the attraction of both hexavalent chromium (anionic) and trivalent chromium (cationic) onto the surface of lignin. (C) 2011 Elsevier B.V. All rights reserved.

Apo J/clusterin expression and secretion: Evidence for 15-deoxy-Δ12,14-PGJ2-dependent mechanism

Cyclooxygenase-2 (Cox-2) and Apo J/clusterin are involved in inflammatory resolution and have each been reported to inhibit NF-?B signalling. Using a well-validated rat pheochromocytoma (PC12) cell culture model of Cox-2 over-expression the current study investigated inter-dependence between Cox-2 and clusterin with respect to induction of expression and impact on NF-?B signalling. Both gene expression and immunoblot analysis confirmed that intracellular and secreted levels of clusterin were elevated in Cox-2 over-expressing cells (PCXII). Clusterin expression was increased in control (PCMT) cells in a time- and dose-dependent manner by 15-deoxy-? 12,14-prostaglandin J 2 (15d-PGJ 2), but not PGE 2, and inhibited in PCXII cells by pharmacological Cox inhibition. In PCXII cells, inhibition of two transcription factors known to be activated by 15d-PGJ 2, heat shock factor 1 (HSF-1) and peroxisome proliferator activated receptor (PPAR)?, by transcription factor oligonucleotide decoy and antagonist (GW9662) treatment, respectively, reduced clusterin expression. While PCXII cells exhibited reduced TNF-a-induced cell surface ICAM-1 expression, IkB phosphorylation and degradation were similar to control cells. With respect to the impact of Cox-2-dependent clusterin upregulation on NF-?B signalling, basal levels of I?B were similar in control and PCXII cells, and no evidence for a physical association between clusterin and phospho-I?B was obtained. Moreover, while PCXII cells exhibited reduced NF-?B transcriptional activity, this was not restored by clusterin knock-down. These results indicate that Cox-2 induces clusterin in a 15d-PGJ 2-dependent manner, and via activation of HSF-1 and PPAR?. However, the results do not support a model whereby Cox-2/15d-PGJ 2-dependent inhibition of NF-?B signalling involves clusterin.