Expression of the proteolysis-inducing factor core peptide mRNA is upregulated in both tumour and adjacent normal tissue in gastro-oesophageal malignancy

Gastro-oesophageal cancer is associated with a high incidence of cachexia. Proteolysis-inducing factor (PIF) has been identified as a possible cachectic factor and studies suggest that PIF is produced exclusively by tumour cells. We investigated PIF core peptide (PIF-CP) mRNA expression in tumour and benign tissue from patients with gastro-oesophageal cancer and in gastro-oesophageal biopsies for healthy volunteers. Tumour tissue and adjacent benign tissue were collected from patients with gastric and oesophageal cancer (n = 46) and from benign tissue only in healthy controls (n = 11). Expression of PIF-CP mRNA was quantified by real-time PCR. Clinical and pathological information along with nutritional status was collected prospectively. In the cancer patients, PIF-CP mRNA was detected in 27 (59%) tumour samples and 31 (67%) adjacent benign tissue samples. Four (36%) gastro-oesophageal biopsies from healthy controls also expressed PIF-CP mRNA. Expression was higher in tumour tissue (P = 0.031) and benign tissue (P = 0.022) from cancer patients compared with healthy controls. In the cancer patients, tumour and adjacent benign tissue PIF-CP mRNA concentrations were correlated with each other (P<0.0001, r = 0.73) but did not correlate with weight loss or prognosis. Although PIF-CP mRNA expression is upregulated in both tumour and adjacent normal tissue in gastro-oesophageal malignancy, expression does not relate to prognosis or cachexia. Post-translational modification of PIF may be a key step in determining the biological role of PIF in the patient with advanced cancer and cachexia. © 2006 Cancer Research.

Technology valuation within the context of transfer collaborations with Chinese machine tool companies

The point of departure for this study was a recognition of the differences in suppliers' and acquirers' judgements of the value of technology when transferred between the two, and the significant impacts of technology valuation on the establishment of technology partnerships and effectiveness of technology collaborations. The perceptions, transfer strategies and objectives, perceived benefits and assessed technology contributions as well as associated costs and risks of both suppliers and acquirers were seen to be the core to these differences. This study hypothesised that the capability embodied in technology to yield future returns makes technology valuation distinct from the process of valuing manufacturing products. The study hence has gone beyond the dimensions of cost calculation and price determination that have been discussed in the existing literature, by taking a broader view of how to achieve and share future added value from transferred technology. The core of technology valuation was argued as the evaluation of the 'quality' of the capability (technology) in generating future value and the effectiveness of the transfer arrangement for best use of such a capability. A dynamic approach comprising future value generation and realisation within the context of specific forms of collaboration was therefore adopted. The research investigations focused on the UK and China machine tool industries, where there are many technology transfer activities and the value issue has already been recognised in practice. Data were gathered from three groups: machine tool manufacturing technology suppliers in the UK and acquirers in China, and machine tool users in China. Data collecting methods included questionnaire surveys and case studies within all the three groups. The study has focused on identifying and examining the major factors affecting value as well as their interactive effects on technology valuation from both the supplier's and acquirer's point of view. The survey results showed the perceptions and the assessments of the owner's value and transfer value from the supplier's and acquirer's point of view respectively. Benefits, costs and risks related to the technology transfer were the major factors affecting the value of technology. The impacts of transfer payment on the value of technology by the sharing of financial benefits, costs and risks between partners were assessed. The close relationship between technology valuation and transfer arrangements was established by which technical requirements and strategic implications were considered. The case studies reflected the research propositions and revealed that benefits, costs and risks in the financial, technical and strategic dimensions interacted in the process of technology valuation within the context of technology collaboration. Further to the assessment of factors affecting value, a technology valuation framework was developed which suggests that technology attributes for the enhancement of contributory factors and their contributions to the realisation of transfer objectives need to be measured and compared with the associated costs and risks. The study concluded that technology valuation is a dynamic process including the generation and sharing of future value and the interactions between financial, technical and strategic achievements.

Peptide binding prediction for the human class II MHC allele HLA-DP2:a molecular docking approach

MHC class II proteins bind oligopeptide fragments derived from proteolysis of pathogen antigens, presenting them at the cell surface for recognition by CD4+ T cells. Human MHC class II alleles are grouped into three loci: HLA-DP, HLA-DQ and HLA-DR. In contrast to HLA-DR and HLA-DQ, HLA-DP proteins have not been studied extensively, as they have been viewed as less important in immune responses than DRs and DQs. However, it is now known that HLA-DP alleles are associated with many autoimmune diseases. Quite recently, the X-ray structure of the HLA-DP2 molecule (DPA*0103, DPB1*0201) in complex with a self-peptide derived from the HLA-DR a-chain has been determined. In the present study, we applied a validated molecular docking protocol to a library of 247 modelled peptide-DP2 complexes, seeking to assess the contribution made by each of the 20 naturally occurred amino acids at each of the nine binding core peptide positions and the four flanking residues (two on both sides).

A hydrogen-bonded polar network in the core of the glucagon-like peptide-1 receptor is a fulcrum for biased agonism:lessons from class B crystal structuress

The glucagon-like peptide 1 (GLP-1) receptor is a class B G protein-coupled receptor (GPCR) that is a key target for treatments for type II diabetes and obesity. This receptor, like other class B GPCRs, displays biased agonism, though the physiologic significance of this is yet to be elucidated. Previous work has implicated R2.60190 , N3.43240 , Q7.49394 , and H6.52363 as key residues involved in peptide-mediated biased agonism, with R2.60190 , N3.43240 , and Q7.49394 predicted to form a polar interaction network. In this study, we used novel insight gained from recent crystal structures of the transmembrane domains of the glucagon and corticotropin releasing factor 1 (CRF1) receptors to develop improved models of the GLP-1 receptor that predict additional key molecular interactions with these amino acids. We have introduced E6.53364 A, N3.43240 Q, Q7.49493N, and N3.43240 Q/Q7.49 Q/Q7.49493N mutations to probe the role of predicted H-bonding and charge-charge interactions in driving cAMP, calcium, or extracellular signal-regulated kinase (ERK) signaling. A polar interaction between E6.53364 and R2.60190 was predicted to be important for GLP-1- and exendin-4-, but not oxyntomodulin-mediated cAMP formation and also ERK1/2 phosphorylation. In contrast, Q7.49394 , but not R2.60190 /E6.53364 was critical for calcium mobilization for all three peptides. Mutation of N3.43240 and Q7.49394 had differential effects on individual peptides, providing evidence for molecular differences in activation transition. Collectively, this work expands our understanding of peptide-mediated signaling from the GLP-1 receptor and the key role that the central polar network plays in these events.

Technology transfer to China:a study of strategy in 20 EU industrial companies

Foreign direct investment has been important in China's economic development since the early 1980s. In recent years, the volume of inward FDI into China, according to some estimates, has been second only to that into the USA. The Chinese government has emphasised the need for FDI to be coupled with the transfer of more advanced technologies to China. For foreign companies, technology transfer raises the risk of losing their technology based competitive advantage to potential competitor firms. This risk may be exacerbated by insufficient legal protection of intellectual property rights in China. After briefly reviewing the development of Chinese official policy on technology transfer, this paper considers the strategy adopted by EU companies regarding the transfer of technology; in particular in advanced technology sectors. The research on which the paper is based included an analysis of information gathered from 20 leading EU companies with investments in China and operating in high-technology sectors. Information was gathered from senior company managers based in both China and Europe during the second half of 1998. The main findings include a measure of reluctance on the part of EU companies to transfer their core technologies to China and to base R&D capability there. At the same time, the companies appear aware that this policy may be unsustainable in the longer-term in the face of Chinese official policy and a desire to expand their operations in China. While they attempt to protect their existing technological knowledge, most of them accept that there will be technology "leakage" and therefore the most effective strategy is to maintain their technological lead through R&D.

Highly sensitive bend sensor based on Bragg grating in eccentric core polymer fiber

We report on an optical bend sensor based on a Bragg grating inscribed in an eccentric core polymer optical fiber. The device exhibits the strong fiber orientation dependence, the wide bend curvature range of ± 22.7 m-1 and high bend sensitivity of 63 pm/m-1.

State intervention in technology in the post war years: case studies in technology policy

This thesis is concerned with the means by which the state in Britain has attempted to influence the technological development of private industry in the period 1945-1979. Particular emphasis is laid on assessing the abilities of technology policy measures to promote innovation. With that objective, the innovation literature is selectively reviewed to draw up an analytical framework to evaluate the innovation content of policy (Chapter 2). Technology policy is taken to consist of the specific measures utilised by government and its agents that affect the technological behaviour of firms. The broad sweep of policy during the period under consideration is described in Chapter 3 which concentrates on elucidating its institutional structure and the activities of the bodies involved. The empirical core of the thesis consists of three parallel case studies of policy toward the computer, machine tool and textile machinery industries (Chapters 4-6). The studies provide detailed historical accounts of the development and composition of policy, relating it to its specific institutional and industrial contexts. Each reveals a different pattern and level of state intervention. The thesis concludes with a comparative review of the findings of the case studies within a discussion centred on the arguments presented in Chapter 2. Topics arising include the state's differential support for the range of activities involved in innovation, the location of state-funded R&D, the encouragement of supplier-user contact, and the difficulties raised in adoption and diffusion.

The combination of smart hydrogels and fibre optic sensor technology for analyte detection

The subject of investigation of the present research is the use of smart hydrogels with fibre optic sensor technology. The aim was to develop a costeffective sensor platform for the detection of water in hydrocarbon media, and of dissolved inorganic analytes, namely potassium, calcium and aluminium. The fibre optic sensors in this work depend upon the use of hydrogels to either entrap chemotropic agents or to respond to external environmental changes, by changing their inherent properties, such as refractive index (RI). A review of current fibre optic technology for sensing outlined that the main principles utilised are either the measurement of signal loss or a change in wavelength of the light transmitted through the system. The signal loss principle relies on changing the conditions required for total internal reflection to occur. Hydrogels are cross-linked polymer networks that swell but do not dissolve in aqueous environments. Smart hydrogels are synthetic materials that exhibit additional properties to those inherent in their structure. In order to control the non-inherent properties, the hydrogels were fabricated with the addition of chemotropic agents. For the detection of water, hydrogels of low refractive index were synthesized using fluorinated monomers. Sulfonated monomers were used for their extreme hydrophilicity as a means of water sensing through an RI change. To enhance the sensing capability of the hydrogel, chemotropic agents, such as pH indicators and cobalt salts, were used. The system comprises of the smart hydrogel coated onto an exposed section of the fibre optic core, connected to the interrogation system measuring the difference in the signal. Information obtained was analysed using a purpose designed software. The developed sensor platform showed that an increase in the target species caused an increase in the signal lost from the sensor system, allowing for a detection of the target species. The system has potential applications in areas such as clinical point of care, water detection in fuels and the detection of dissolved ions in the water industry.

Peptide length significantly influences in vitro affinity for MHC class II molecules

Class II Major Histocompatibility Complex (MHC) molecules have an open-ended binding groove which can accommodate peptides of varying lengths. Several studies have demonstrated that peptide flanking residues (PFRs) which lie outside the core binding groove can influence peptide binding and T cell recognition. By using data from the AntiJen database we were able to characterise systematically the influence of PFRs on peptide affinity for MHC class II molecules.

Integration of a 3D hydrogel matrix within a hollow core photonic crystal fibre for DNA probe immobilization

In this paper, we demonstrate the integration of a 3D hydrogel matrix within a hollow core photonic crystal fibre (HC-PCF). In addition, we also show the fluorescence of Cy5-labelled DNA molecules immobilized within the hydrogel formed in two different types of HC-PCF. The 3D hydrogel matrix is designed to bind with the amino groups of biomolecules using an appropriate cross-linker, providing higher sensitivity and selectivity than the standard 2D coverage, enabling a greater number of probe molecules to be available per unit area. The HC-PCFs, on the other hand, can be designed to maximize the capture of fluorescence to improve sensitivity and provide longer interaction lengths. This could enable the development of fibre-based point-of-care and remote systems, where the enhanced sensitivity would relax the constraints placed on sources and detectors. In this paper, we will discuss the formation of such polyethylene glycol diacrylate (PEGDA) hydrogels within a HC-PCF, including their optical properties such as light propagation and auto-fluorescence.

ProxiMAX Randomisation:a new technology for non-degenerate saturation mutagenesis of contiguous codons

ProxiMAX randomisation achieves saturation mutagenesis of contiguous codons without degeneracy or bias. Offering an alternative to trinucleotide phosphoramidite chemistry, it uses nothing more sophisticated than unmodified oligonucleotides and standard molecular biology reagents and as such, requires no specialised chemistry, reagents nor equipment. When particular residues are known to affect protein activity/specificity, their combinatorial replacement with all 20 amino acids, or a subset thereof, can provide a rapid route to generating proteins with desirable characteristics. Conventionally, saturation mutagenesis replaced key codons with degenerate ones. Although simple to perform, that procedure resulted in unnecessarily large libraries, termination codons and inherent uneven amino acid representation. ProxiMAX randomisation is an enzyme-based technique that can encode unbiased representation of all or selected amino acids or else can provide required codons in pre-defined ratios. Each saturated position can be defined independently of the others. ProxiMAX randomisation is achieved via saturation cycling: an iterative process comprising blunt end ligation, amplification and digestion with a Type IIS restriction enzyme. We demonstrate both unbiased saturation of a short 6-mer peptide and saturation of a hypervariable region of a scfv antibody fragment, where 11 contiguous codons are saturated with selected codons, in pre-defined ratios. As such, ProxiMAX randomisation is particularly relevant to antibody engineering. The development of ProxiMAX randomisation from concept to reality is described.

Evaluation of integration technology approaches in the healthcare supply chain

Healthcare organisations are increasingly being challenged to look at their operations and find opportunities to improve the quality, efficiency and effectiveness of their supply chain services. In light of this situation, there is an apparent need for healthcare organisations to invest in integration technologies and to achieve the integration of supply chain processes, in order to break up the historical structure characterised by numerous interfaces and the segregation of responsibilities. The aim of this paper is to take an independent look at the healthcare supply chain and identify at different levels the core entities, processes, information flows, and system integration challenges which impede supply chain quality improvements to be realised. Moreover, this paper proposes, from an information systems perspective, a framework for the evaluation of different integration technology approaches, which can be used as a potential guideline tool for assessing integration technology alternatives, in order to add value to a healthcare-supply-chain management system. Copyright © 2007 Inderscience Enterprises Ltd.

Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity:in silico bioinformatic step-by-step guide using quantitative structure-activity relationships

Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide-major histocompatibility complex (MHC)-binding affinity based on QSAR technology have now become important components of modern computational immunovaccinology. Historically, such approaches have been built around semiqualitative, classification methods, but these are now giving way to quantitative regression methods. We review three methods--a 2D-QSAR additive-partial least squares (PLS) and a 3D-QSAR comparative molecular similarity index analysis (CoMSIA) method--which can identify the sequence dependence of peptide-binding specificity for various class I MHC alleles from the reported binding affinities (IC50) of peptide sets. The third method is an iterative self-consistent (ISC) PLS-based additive method, which is a recently developed extension to the additive method for the affinity prediction of class II peptides. The QSAR methods presented here have established themselves as immunoinformatic techniques complementary to existing methodology, useful in the quantitative prediction of binding affinity: current methods for the in silico identification of T-cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate computational prediction of peptide-MHC affinity. We have reviewed various human and mouse class I and class II allele models. Studied alleles comprise HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3101, HLA-A*6801, HLA-A*6802, HLA-B*3501, H2-K(k), H2-K(b), H2-D(b) HLA-DRB1*0101, HLA-DRB1*0401, HLA-DRB1*0701, I-A(b), I-A(d), I-A(k), I-A(S), I-E(d), and I-E(k). In this chapter we show a step-by-step guide into predicting the reliability and the resulting models to represent an advance on existing methods. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred.

Microarray-formatted clinical biomarker assay development using peptide aptamers to anterior gradient-2

Anterior gradient-2 protein was identified using proteomic technologies as a p53 inhibitor which is overexpressed in human cancers, and this protein presents a novel pro-oncogenic target with which to develop diagnostic assays for biomarker detection in clinical tissue. Combinatorial phage-peptide libraries were used to select 12 amino acid polypeptide aptamers toward anterior gradient-2 to determine whether methods can be developed to affinity purify the protein from clinical biopsies. Selecting phage aptamers through four rounds of screening on recombinant human anterior gradient-2 protein identified two classes of peptide ligand that bind to distinct epitopes on anterior gradient-2 protein in an immunoblot. Synthetic biotinylated peptide aptamers bound in an ELISA format to anterior gradient-2, and substitution mutagenesis further minimized one polypeptide aptamer to a hexapeptide core. Aptamers containing this latter consensus sequence could be used to affinity purify to homogeneity human anterior gradient-2 protein from a single clinical biopsy. The spotting of a panel of peptide aptamers onto a protein microarray matrix could be used to quantify anterior gradient-2 protein from crude clinical biopsy lysates, providing a format for quantitative screening. These data highlight the utility of peptide combinatorial libraries to acquire rapidly a high-affinity ligand that can selectively bind a target protein from a clinical biopsy and provide a technological approach for clinical biomarker assay development in an aptamer microarray format.

The spectral sensitivity of long period gratings fabricated in elliptical core D-shaped optical fiber

Long period gratings (LPGs) were written into a D-shaped optical fibre, which has an elliptical core with a W-shaped refractive index profile. The LPG's attenuation bands were found to be sensitive to the polarisation of the interrogating light with a spectral separation of about 15nm between the two orthogonal polarisation states. In addition, two spectrally overlapping attenuation bands corresponding to orthogonal polarisation states were observed; modelling successfully reproduced this spectral feature. The spectral sensitivity of both orthogonal states was experimentally measured with respect to temperature, surrounding refractive index, and directional bending. These LPG devices produced blue and red wavelength shifts of the stop-bands due to bending in different directions. The measured spectral sensitivities to curvatures, d?/dR , ranged from -3.56nm m to +6.51nm m. The results obtained with these LPGs suggest that this type of fibre may be useful as a shape/bend sensor. It was also demonstrated that the neighbouring bands could be used to discriminate between temperature and bending and that overlapping orthogonal polarisation attenuation bands can be used to minimise error associated with polarisation.