Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin-induced nephropathy

Transcriptome analysis using microarray technology represents a powerful unbiased approach for delineating pathogenic mechanisms in disease. Here molecular mechanisms of renal tubulointerstitial fibrosis (TIF) were probed by monitoring changes in the renal transcriptome in a glomerular disease-dependent model of TIF ( adriamycin nephropathy) using Affymetrix (mu74av2) microarray coupled with sequential primary biological function-focused and secondary

Association of gene expression with sequential proliferation, differentiation and tumor formation in murine skin

Differential gene expression in two established initiation and promotion skin carcinogenesis models during promotion and tumor formation was determined by microarray technology with the purpose of distinguishing the genes more associated with neoplastic transformation from those linked with proliferation and differentiation. The first model utilized dimethylbenz[a]anthracene initiation and 12-O-tetradecanoylphorbol 13-acetate (TPA) promotion in the FVB/N mouse, and the second TPA promotion of the Tg.Ac mouse, which is endogenously initiated by virtue of an activated Ha-ras transgene. Comparison of gene expression profiles across the two models identified genes whose altered expression was associated with papilloma formation rather than TPA-induced proliferation and differentiation. DMBA suppressed TPA-induced differentiation which allowed identification of those genes associated more specifically with differentiation rather than proliferation. EASE (Expression Analysis Systemic Explorer) indicated a correlation between muscle-associated genes and skin differentiation, whereas genes involved with protein biosynthesis were strongly correlated with proliferation. For verification the altered expression of selected genes were confirmed by RT-PCR; Carbonic anhydrase 2, Thioredoxin 1 and Glutathione S-transferase omega 1 associated with papilloma formation and Enolase 3, Cystatin 6 and Filaggrin associated with TPA-induced proliferation and differentiation. In situ analysis located the papillomas Glutathione S-transferase omega 1 expression to the proliferating areas of the papillomas. Thus we have identified profiles of differential gene expression associated with the tumorigenesis and promotion stages for skin carcinogenesis in the mouse.

Cumulative or sequential assessment during hermit crab shell fights: effects of oxygen on decision rules

Agonistic interactions between animals are often settled by the use of repeated signals which advertise the resource-holding potential of the sender. According to the sequential assessment game this repetition increases the accuracy with which receivers may assess the signal, but under the cumulative assessment model the repeated performances accumulate to give a signal of stamina. These models may be distinguished by the temporal pattern of signalling they predict and by the decision rules used by the contestants. Hermit crabs engage in shell fights over possession of the gastropod shells that they inhabit. During these interactions the two roles of signaller and receiver may be examined separately because they are fixed for the duration of the encounter. Attackers rap their shell against that of the defender in a series of bouts whereas defenders remain tightly withdrawn into their shells for the duration of the contest. At the end of a fight the attacker may evict the defender from its shell or decide to give up without first effecting an eviction; the decision for defenders is either to maintain a grip on its shell or to release the shell and allow itself to be evicted. We manipulated fatigue levels separately for attackers and defenders, by varying the oxygen concentration of the water that they are held in prior to fighting, and examined the effects that this has on the likelihood of each decision and on the temporal pattern of rapping. We show that the vigour of rapping and the likelihood of eviction are reduced when the attacker is subjected to low oxygen but that this treatment has no effect on rates of eviction when applied to defenders. We conclude that defenders compare the vigour of rapping with an absolute threshold rather than with a relative threshold when making their decision. The data are compatible with the cumulative assessment model and with the idea that shell rapping signals the stamina of attackers, but do not fit the predictions of the sequential assessment game.

Radiation and the genome: from risks to opportunities for therapeutic exploitation

On 1 December 2009, the Radiation and Cancer Biology Committee of the British Institute of Radiology (BIR) held a one-day conference on the theme of radiation and the genome. Talks covered genomic instability (its importance for radiation-induced carcinogenesis and potential for exploitation in the development of novel chemoradiotherapy combinations) and the prospects of exploiting knowledge of the genome to understand how individual genetic variation can impact on a patient's likelihood of developing toxicity following radiotherapy. The meeting also provided an overview of stem cell biology and its relevance for radiotherapy in terms of both tumour (somatic) and normal tissue (germline) sensitivity to radiation. Moreover, the possibility of manipulating stem cells to reduce radiation-induced normal tissue damage was considered.

From PASS 1 to YES to AND logic: building parallel processing into molecular logic gates by sequential addition of receptors

The synthesis and photophysical characterization of a novel molecular logic gate 4, operating in water, is demonstrated based on the competition between. fluorescence and photoinduced electron transfer (PET). It is constructed according to a 'fluorophore-spacer-receptor(1)-spacer-receptor(2)' format where anthracene is the. fluorophore, receptor(1) is a tertiary amine and receptor(2) is a phenyliminodiacetate ligand. Using only protons and zinc cations as the chemical inputs and. fluorescence as the output, 4 is demonstrated to be both a two-input AND and INH logic gate. When 4 is examined in context to the YES logic gates 1 and 2, and the two-input AND logic gate 3 and three-input AND logic gate 5, each with one or more of the following receptors including a tertiary amine, phenyliminodiacetate or benzo-15-crown-5 ether, logic gate 4 is the missing link in the homologous series. Collectively, the molecular logic gates 1-5 corroborate the PET 'fluorophore-spacer-receptor' model using chemical inputs and a light-signal output and provide insight into controlling the. fluorescence quantum yield of future PET-based molecular logic gates.

Exploitation of inherited weakness in fire-damaged building sandstone: the ‘fatiguing’ of ‘shocked’ stone

The problem of the long-term impact of historical fire on masonry is not clearly understood. Much research focuses on the damage that is caused by fire in isolation, and omits to investigate the subsequent exploitation of weaknesses inherited from fire events. Fire can, for example, cause significant physical, chemical and mineralogical change to sandstone, which may then be exploited by background environmental factors such as salt and freeze–thaw weathering. To explore this experimentally, blocks of Peakmoor Sandstone were subjected to a real fire (as well as lime rendering/removal and frost cycle pre-treatments), and their subsequent response to salt weathering cycles was monitored by weight loss and visual assessment of the pattern of surface damage. Results illustrate that the post-fire deterioration of sandstone is strongly conditioned by fracture networks and soot cover inherited from the fire. The exploitation of fractures can lead to spalling during salt weathering cycles — this takes place as granular dissagregation steadily widens cracks and salts concentrate and crystallise in areas of inherited weakness. Soot cover can have a profound effect on subsequent performance. It reduces surface permeability and can be hydrophobic in character, limiting salt ingress and suppressing decay in the short term. However, as salt crystals concentrate under the soot crust, detachment of this layer can occur, exposing fire-damaged stone beneath. Understanding the subsequent exploitation of stone exposed to fire damage by background environmental factors (for example, salt weathering/ temperature cycling) is key to the post-fire management of stone decay.

Direct versus delayed pathways in strong-field non-sequential double ionization

We report full-dimensionality quantum and classical calculations of double ionization (DI) of laser-driven helium at 390 nm. Good agreement is observed. We identify the relative importance of the two main non-sequential DI pathways, the direct|with an almost simultaneous ejection of both electrons|and the delayed. We find that the delayed pathway prevails at small intensities independently of total electron energy but at high intensities the direct pathway predominates up to a certain upper-limit in total energy which increases with intensity. An explanation for this increase with intensity is provided.