Recent advances in the development of tissue transglutaminase (TG2) inhibitors

Tissue transglutaminase (TG2) is a Ca2+-dependent enzyme and probably the most ubiquitously expressed member of the mammalian transglutaminase family. TG2 plays a number of important roles in a variety of biological processes. Via its transamidating function, it is responsible for the cross-linking of proteins by forming isopeptide bonds between glutamine and lysine residues. Intracellularly, Ca2+ activation of the enzyme is normally tightly regulated by the binding of GTP. However, upregulated levels of TG2 are associated with many disease states like celiac sprue, certain types of cancer, fibrosis, cystic fibrosis, multiple sclerosis, Alzheimer's, Huntington's and Parkinson's disease. Selective inhibitors for TG2 both cell penetrating and non-cell penetrating would therefore serve as novel therapeutic tools for the treatment of these disease states. Moreover, they would provide useful tools to fully elucidate the cellular mechanisms TG2 is involved in and help comprehend how the enzyme is regulated at the cellular level. The current paper is intended to give an update on the recently discovered classes of TG2 inhibitors along with their structure-activity relationships. The biological properties of these derivatives, in terms of both activity and selectivity, will also be reported in order to translate their potential for future therapeutic developments. © 2011 Springer-Verlag.

Tissue transglutaminase in tumour progression:Friend or foe?

Basic biological processes in which tissue transglutaminase (TG2, tTG) is thought to be important including apoptosis, cell adhesion and migration, ECM homeostasis and angiogenesis are key stages in the multistage tumour progression cascade. Studies undertaken with primary tumours and experimental models suggest that TG2 expression and activity in the tumour body and surrounding matrix generally decreases with tumour progression, favouring matrix destabilisation, but supporting angiogenesis and tumour invasion. In contrast, in the secondary metastatic tumour TG2 is often highly expressed whereby its potential roles in cell survival both at the intra- and extracellular level become important. In the following review the underlying molecular basis for the selection of these different phenotypes in tumour types and the anomaly for the requirement of TG2 is discussed in relation to the complex events of tumour progression. © 2007 Springer-Verlag.

Studies on the mechanism of action on antitumour imidazotetrazinones

The imidazotetrazinones are clinically active antitumour agents, temozolomide currently proving successful in the treatment of melanomas and gliomas. The exact nature of the biological processes underlying response are as yet unclear.This thesis attempts to identify the cellular targets important to the cytotoxicity of imidazotetrazinones, to elucidate the pathways by which this damage leads to cell death, and to identify mechanisms by which tumour cells may circumvent this action. The levels of the DNA repair enzymes O6-alkylguanine-DNA-alkyltransferase (O6-AGAT) and 3-methyladenine-DNA-glycosylase (3MAG) have been examined in a range of murine and human cell lines with differential sensitivity to temozolomide. All the cell lines were proficient in 3MAG despite there being 40-fold difference in sensitivity to temozolomide. This suggests that while 3-methyladenine is a major product of temozolomide alkylation of DNA it is unlikely to be a cytotoxic lesion. In contrast, there was a 20-fold variation in O6-AGAT levels and the concentration of this repair enzyme correlated with variations in cytotoxicity. Furthermore, depletion of this enzyme in a resistant, O6-AGAT proficient cell line (Raji), by pre-treatment with the free base O6-methylguanine resulted in 54% sensitisation to the effects of temozolomide. These observations have been extended to 3 glioma cell lines; results that support the view that the cytotoxicity of temozolomide is related to alkylation at the O6-position of guanine and that resistance to this drug is determined by efficient repair of this lesion. It is clear, however, the other factors may influence tumour response since temozolomide showed little differential activity towards 3 established solid murine tumours in vivo, despite different tumour O6-AGAT levels. Unlike mitozolomide, temozolomide is incapable of cross-linking DNA and a mechanism by which O6-methylguanine may exert lethality is unclear. The cytotoxicity of the methyl group may be due to its disruption of DNA-protein interactions, or alternatively cell death may not be a direct result of the alkyl group itself, but manifested by DNA single-strand breaks. Enhanced alkaline elution rates were found for the DNA of Raji cells treated with temozolomide following alkyltransferase depletion, suggesting a relationship between O6-methylguanine and the induction single-strand breaks. Such breaks can activate poly(ADP-ribose) synthetase (ADPRT) an enzyme capable of rapid and lethal depletion of cellular NAD levels. However, at concentrations of temozolomlde relevant in vivo little change in adenine nucleotides was detected in cell lines, although this enzyme would appear important in modulating DNA repair since inhibition of ADPRT potentiated temozolomide cytotoxicity in Raji cells but not O6-AGAT deficient GM892A cells. Cell lines have been reported that are O6-AGAT deficient yet resistant to methylating agents. Thus, resistance to temozolomide may arise not only by removal of the methyl group from the O6-position of guanine, but also from another mechanism involving caffeine-sensitive post-replication repair or mismatch repair activity. A modification of the standard Maxam Gilbert sequencing technique was used to determine the sequence specificity of guanine-N7 alkylation. Temozolomide preferentially alkylated runs of guanines with the intensity of reaction increasing with the number of adjacent guanines in the DNA sequence. Comparable results were obtained with a polymerase-stop assay, although neither technique elucidates the sequence specificity of O6-guanine alkylation. The importance of such specificity to cytotoxicity is uncertain, although guanine-rich sequences are common to the promoter regions of oncogenes. Expression of a plasmid reporter gene under the control of the Ha-ras proto~oncogene promoter was inhibited by alkylation with temozolomide when transfected into cancer cell lines, However, this inhibition did not appear to be related to O6~guanine alkylation and therefore would seem unimportant to the chemotherapeutic activity of temozolomide.

The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review)

Biological processes are subject to the influence of numerous factors and their interactions, which may be non-linear in nature. In a recombinant protein production experiment, understanding the relative importance of these factors, and their influence on the yield and quality of the recombinant protein being produced, is an essential part of its optimisation. In many cases, implementing a design of experiments (DoE) approach has delivered this understanding. This chapter aims to provide the reader with useful pointers in applying a DoE strategy to improve the yields of recombinant yeast cultures.

Characterization of Transglutaminase 2 in macrophage clearance of apoptotic cells

Removal of dead or diseased cells is crucial feature of apoptosis for managing many biological processes such as tissue remodelling, tissue homeostasis and resolution and control of immune responses throughout life. Tissue transglutaminase (TG2) is a protein crosslinking enzyme that has been implicated in apoptotic cell clearance but also mediates many important cell functions including cell adhesion, migration and monocyte-macrophage differentiation. Cell surface-associated TG2 regulates cell adhesion and migration, via its association with receptors such as syndecan-4, ß1 and ß3 integrin. Whilst defective apoptotic cell clearance has been described in TG2-deficient mice, the precise extracellular role of TG2 in apoptotic cell clearance remains ill-defined. This thesis addresses macrophage TG2 in cell corpse clearance. TG2 expression (cytosolic and cell surface) in human macrophages was revealed and data demonstrate that loss of TG2 activity through the use of inhibitors of function, including cellimpermeable inhibitors significantly inhibit the ability of macrophages to clear apoptotic cells (AC). This includes reduced macrophage recruitment to and binding of apoptotic cells. Association studies reveal TG2-syndecan-4 interaction through heparan sulphate side chains, and knockdown of syndecan-4 reduces cell surface TG2 activity and apoptotic cell clearance. Furthermore, inhibition of TG2 activity reduces crosslinking of CD44, reported to augment AC clearance. Thus it defines for the first time a role for TG2 activity at the cell surface of human macrophages in multiple stages of AC clearance and proposed that TG2, in association with heparan sulphates, may exert its effect on AC clearance via crosslinking of CD44.

Magnetite-doped polydimethylsiloxane (PDMS) for phosphopeptide enrichment

Reversible phosphorylation plays a key role in numerous biological processes. Mass spectrometry-based approaches are commonly used to analyze protein phosphorylation, but such analysis is challenging, largely due to the low phosphorylation stoichiometry. Hence, a number of phosphopeptide enrichment strategies have been developed, including metal oxide affinity chromatography (MOAC). Here, we describe a new material for performing MOAC that employs a magnetite-doped polydimethylsiloxane (PDMS), that is suitable for the creation of microwell array and microfluidic systems to enable low volume, high throughput analysis. Incubation time and sample loading were explored and optimized and demonstrate that the embedded magnetite is able to enrich phosphopeptides. This substrate-based approach is rapid, straightforward and suitable for simultaneously performing multiple, low volume enrichments. © the Partner Organisations 2014.

The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review)

Biological processes are subject to the influence of numerous factors and their interactions, which may be non-linear in nature. In a recombinant protein production experiment, understanding the relative importance of these factors, and their influence on the yield and quality of the recombinant protein being produced, is an essential part of its optimisation. In many cases, implementing a design of experiments (DoE) approach has delivered this understanding. This chapter aims to provide the reader with useful pointers in applying a DoE strategy to improve the yields of recombinant yeast cultures.

PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community.

Binocular summation, binocular fusion and the transition to diplopia

The visual system combines spatial signals from the two eyes to achieve single vision. But if binocular disparity is too large, this perceptual fusion gives way to diplopia. We studied and modelled the processes underlying fusion and the transition to diplopia. The likely basis for fusion is linear summation of inputs onto binocular cortical cells. Previous studies of perceived position, contrast matching and contrast discrimination imply the computation of a dynamicallyweighted sum, where the weights vary with relative contrast. For gratings, perceived contrast was almost constant across all disparities, and this can be modelled by allowing the ocular weights to increase with disparity (Zhou, Georgeson & Hess, 2014). However, when a single Gaussian-blurred edge was shown to each eye perceived blur was invariant with disparity (Georgeson & Wallis, ECVP 2012) – not consistent with linear summation (which predicts that perceived blur increases with disparity). This blur constancy is consistent with a multiplicative form of combination (the contrast-weighted geometric mean) but that is hard to reconcile with the evidence favouring linear combination. We describe a 2-stage spatial filtering model with linear binocular combination and suggest that nonlinear output transduction (eg. ‘half-squaring’) at each stage may account for the blur constancy.

A methodology for evaluating and selecting processes for natural gas conditioning

The aim of this work was to develop a generic methodology for evaluating and selecting, at the conceptual design phase of a project, the best process technology for Natural Gas conditioning. A generic approach would be simple and require less time and would give a better understanding of why one process is to be preferred over another. This will lead to a better understanding of the problem. Such a methodology would be useful in evaluating existing, novel and hybrid technologies. However, to date no information is available in the published literature on such a generic approach to gas processing. It is believed that the generic methodology presented here is the first available for choosing the best or cheapest method of separation for natural gas dew-point control. Process cost data are derived from evaluations carried out by the vendors. These evaluations are then modelled using a steady-state simulation package. From the results of the modelling the cost data received are correlated and defined with respect to the design or sizing parameters. This allows comparisons between different process systems to be made in terms of the overall process. The generic methodology is based on the concept of a Comparative Separation Cost. This takes into account the efficiency of each process, the value of its products, and the associated costs. To illustrate the general applicability of the methodology, three different cases suggested by BP Exploration are evaluated. This work has shown that it is possible to identify the most competitive process operations at the conceptual design phase and illustrate why one process has an advantage over another. Furthermore, the same methodology has been used to identify and evaluate hybrid processes. It has been determined here that in some cases they offer substantial advantages over the separate process techniques.

Lipoidal species in ocular spoilation processes

Tear component deposition onto contact lenses is termed `spoilation' and occurs due to the interaction of synthetic polymers with their biological fluid environment. Spoilation phenomena alter the physico-chemical properties of hydrophilic contact lenses, diminishing the optical properties of the lens; causing discomfort and complications for the wearer. Eventually these alterations render the lens unwearable. The primary aim of this interdisciplinary study was to develop analytical techniques capable of analysing the minute quantities of biological deposition involved, in particular the lipid fraction. Prior to this work such techniques were unavailable for single contact lenses. It is envisaged that these investigations will further the understanding of this biological interfacial conversion. Two main analytical techniques were developed: a high performance liquid chromatography (HPLC) technique and fluorescence spectrofluorimetry. The HPLC method allows analysis of a single contact lens and provided previously unavailable valuable information about variations in the lipid profiles of deposited contact lenses and patient tear films. Fluorescence spectrophotofluorimetry is a sensitive non-destructive technique for observing changes in the fluorescence intensity of biological components on contact lenses. The progression and deposition of tear materials can be monitored and assessed for both in vivo and in vitro spoiled lenses using this technique. An improved in vitro model which is comparable to tears and chemically mimics ocular spoilation was also developed. This model allows the controlled study of extrinsic factors and hydrogel compositions. These studies show that unsaturated tear lipids, probably unsaturated fatty acids, are involved in the interfacial conversion of hydrogel lenses, rendering them incompatible with the ocular microenvironment. Lipid interaction with the lens surface then facilitates secondary deposition of other tear components. Interaction, exchange and immobilisation (by polymerisation) of the lipid layer appears to occur before the final and rapid growth of more complex, insoluble discrete deposits, sometimes called `white spots'.

Novel characteristics of the biological properties of the yeast Saccharomyces cerevisiae eukaryotic initiation factor 2A

Eukaryotic initiation factor 2A (eIF2A) has been shown to direct binding of the initiator methionyl-tRNA (Met-tRNA(i)) to 40 S ribosomal subunits in a codon-dependent manner, in contrast to eIF2, which requires GTP but not the AUG codon to bind initiator tRNA to 40 S subunits. We show here that yeast eIF2A genetically interacts with initiation factor eIF4E, suggesting that both proteins function in the same pathway. The double eIF2A/eIF4E-ts mutant strain displays a severe slow growth phenotype, which correlated with the accumulation of 85% of the double mutant cells arrested at the G(2)/M border. These cells also exhibited a disorganized actin cytoskeleton and elevated actin levels, suggesting that eIF2A might be involved in controlling the expression of genes involved in morphogenic processes. Further insights into eIF2A function were gained from the studies of eIF2A distribution in ribosomal fractions obtained from either an eIF5BDelta (fun12Delta) strain or a eIF3b-ts (prt1-1) strain. It was found that the binding of eIF2A to 40 and 80 S ribosomes was not impaired in either strain. We also found that eIF2A functions as a suppressor of Ure2p internal ribosome entry site-mediated translation in yeast cells. The regulation of expression from the URE2 internal ribosome entry site appears to be through the levels of eIF2A protein, which has been found to be inherently unstable with a half-life of approximately 17 min. It was hypothesized that this instability allows for translational control through the level of eIF2A protein in yeast cells.

Mapping the yeast host cell response to recombinant membrane protein production:relieving the biological bottlenecks

Understanding the structures and functions of membrane proteins is an active area of research within bioscience. Membrane proteins are key players in essential cellular processes such as the uptake of nutrients, the export of waste products, and the way in which cells communicate with their environment. It is therefore not surprising that membrane proteins are targeted by over half of all prescription drugs. Since most membrane proteins are not abundant in their native membranes, it is necessary to produce them in recombinant host cells to enable further structural and functional studies. Unfortunately, achieving the required yields of functional recombinant membrane proteins is still a bottleneck in contemporary bioscience. This has highlighted the need for defined and rational optimization strategies based upon experimental observation rather than relying on trial and error. We have published a transcriptome and subsequent genetic analysis that has identified genes implicated in high-yielding yeast cells. These results have highlighted a role for alterations to a cell's protein synthetic capacity in the production of high yields of recombinant membrane protein: paradoxically, reduced protein synthesis favors higher yields. These results highlight a potential bottleneck at the protein folding or translocation stage of protein production.

Signal processing for molecular and cellular biological physics:an emerging field

Recent advances in our ability to watch the molecular and cellular processes of life in action-such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer-raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied.

Techno-economic assessment and uncertainty analysis of thermochemical processes for second generation biofuels

Biomass-To-Liquid (BTL) is one of the most promising low carbon processes available to support the expanding transportation sector. This multi-step process produces hydrocarbon fuels from biomass, the so-called “second generation biofuels” that, unlike first generation biofuels, have the ability to make use of a wider range of biomass feedstock than just plant oils and sugar/starch components. A BTL process based on gasification has yet to be commercialized. This work focuses on the techno-economic feasibility of nine BTL plants. The scope was limited to hydrocarbon products as these can be readily incorporated and integrated into conventional markets and supply chains. The evaluated BTL systems were based on pressurised oxygen gasification of wood biomass or bio-oil and they were characterised by different fuel synthesis processes including: Fischer-Tropsch synthesis, the Methanol to Gasoline (MTG) process and the Topsoe Integrated Gasoline (TIGAS) synthesis. This was the first time that these three fuel synthesis technologies were compared in a single, consistent evaluation. The selected process concepts were modelled using the process simulation software IPSEpro to determine mass balances, energy balances and product distributions. For each BTL concept, a cost model was developed in MS Excel to estimate capital, operating and production costs. An uncertainty analysis based on the Monte Carlo statistical method, was also carried out to examine how the uncertainty in the input parameters of the cost model could affect the output (i.e. production cost) of the model. This was the first time that an uncertainty analysis was included in a published techno-economic assessment study of BTL systems. It was found that bio-oil gasification cannot currently compete with solid biomass gasification due to the lower efficiencies and higher costs associated with the additional thermal conversion step of fast pyrolysis. Fischer-Tropsch synthesis was the most promising fuel synthesis technology for commercial production of liquid hydrocarbon fuels since it achieved higher efficiencies and lower costs than TIGAS and MTG. None of the BTL systems were competitive with conventional fossil fuel plants. However, if government tax take was reduced by approximately 33% or a subsidy of £55/t dry biomass was available, transport biofuels could be competitive with conventional fuels. Large scale biofuel production may be possible in the long term through subsidies, fuels price rises and legislation.