Response of the ArcCHECK® device at 6 MV and 15 MV for VMAT and IMRT quality control

PurposeTo study the response of the ArcCHECK® device as VMAT and IMRT verification system.MethodsVarious tests analyzing the linearity, the repeatability and the angular dependence of the device response, its dependence with the pulse repetition rate and the leakage losses were performed. The long-term response in dose measurements and the uniformity of the detectors conforming the system were controlled using a statistical process control program. The Elekta Infinity™ 6 and 15 MV photon beams were used.ResultsThe device showed excellent repeatability and linearity. The differences between the responses obtained for any pair of angular incidences were less than 2%. The absorbed dose increased by 3% when the pulse repetition rate varied from 50 to 600 MU/min. Results are in overall agreement with those found in previous works for the ArcCHECK®, in which a reduced number of the device diodes were analyzed, and for the MapCheck®, an older 2D device that used the same diodes. Charge losses were found to be negligible except for some of the diodes of the device. The statistical process control program is a very useful tool to control the correct functioning of the device in the long term.ConclusionsThe results of the analysis carried out indicate that the working and stability conditions of the ArcCHECK® device are adequate for its purpose. The dependence with the pulse repetition rate should be considered when VMAT or similar treatments are evaluated. A control program for the statistical monitoring of the device would be desirable and useful.     

Interactions between a commercial preparation of Bacillus thuringiensis and β-exotoxin in the fall armyworm,Spodoptera frugiperda

A commercial preparation of Bacillus thuringiensis (Dipel) and its β-exotoxin were assayed alone and in combination against neonate (3- to 6-hr-old) fall armyworm, Spodoptera frugiperda, larvae using a microdroplet technique. Positive dosage-mortality response curves were determined for each agent. Combination bioassays were then conducted using dosages based on these curves. Presence or absence of interactions was determined by comparing mortality levels from the combination assays with expected mortality levels using single degree of freedom χ² tests. Synergism occurred in 14 of 18 combinations of B. thuringiensis and β-exotoxin tested. Four combinations, all of which contained low individual dosages, exhibited additivity of effects. Maximum deviation of observed from expected mortality occurred at the combination of LC₃₀ for B. thuringiensis plus LC₃₀ for β-exotoxin (observed = 100%, expected = 51%). The data suggested that both agents were contributing to the synergism in this system, but that B. thuringiensis was a slightly stronger synergist than β-exotoxin.     

Optimisation of the transmit beam parameters for generation of subharmonic signals in native and altered populations of a commercial microbubble contrast agent SonoVue®

The aim of this work was to establish the optimum acoustic characterisation approach and insonation transmit beam parameters for subharmonic signal generation with ‘native’ and ‘altered’ populations of a commonly-used microbubble contrast agent. Dynamic contrast-enhanced (DCE) ultrasound is a non-invasive method of imaging the microvasculature, typically implemented using harmonic imaging. Subharmonic imaging, in which echoes at half the fundamental frequency are detected, detects signals which are generated by the ultrasound contrast agents (UCAs) but not by tissue. However, optimal transmission parameters and furthermore, the optimum acoustic characterisation method have not been established. The subharmonic response of ‘native’ and ‘altered’ UCA, altered through decantation, was investigated at transmit centre frequencies 1.8–5 MHz and pulse lengths 1–8 cycles. The ‘altered’ UCA had reduced polydispersity (1–4 µm: 82% bubble volume), compared to ‘native’ (4–10 µm: 57% bubble volume). A custom-built narrow-band acoustic characterisation system was found to be more appropriate for acoustic characterisation compared to the commonly used broadband pulse-echo approach. Both UCA generated the highest subharmonic signal at pulse length of 3-cycles. The maximum ‘native’ subharmonic signal was generated at a transmit centre frequency of 1.9 MHz, corresponding to a subharmonic at 0.95 MHz. This optimal frequency increased in the ‘altered’ population to 2.3–2.5 MHz, bringing the subharmonic above 1 MHz and hence into a range amenable to clinical abdominal imaging transducers. The use of subharmonic signal detection coupled with a modified UCA size distribution has potential to significantly improve the quantification sensitivity and accuracy of DCE ultrasound imaging.     

Starch determination in Chlorella vulgaris—a comparison between acid and enzymatic methods

Different methods for estimating starch in Chlorella vulgaris were compared with the view of establishing a procedure suitable for rapid and accurate determination of starch content in this microalgal species. A close agreement was observed between methods that use perchloric acid and enzymatic methods that use α-amylase and amyloglucosidase to hydrolyze the starch of microalgae grown under different nitrogen culture conditions. Starch values obtained by these methods were significantly higher than those estimated by using hydrochloric acid as solubilizing and hydrolyzing agent. The enzymatic method (EM1) proved to be the most rapid and precise method for microalgal starch quantification. Furthermore, the evaluation of resistant starch by enzymatic methods assayed in nitrogen-sufficient and nitrogen-starved cells showed that no formation of this type of starch occurred in microalgae, meaning that this should not interfere with starch content determinations.     

Evaluation of two commercial methods for the susceptibility testing of Candida species: Vitek 2® and Sensititre YeastOne®

Background

An increased incidence of fungal infections caused by Candida species, especially Candida glabrata and Candida krusei, which are less susceptible to azoles, has been observed. Standardized susceptibility testing is essential for clinical management and for monitoring the epidemiology of resistance.

Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTLs across tomato species

Quantitative trait loci (QTLs) for several fruit traits in tomato were mapped and characterized in a backcross population of an interspecific cross between Lycopersicon esculentum fresh-marker breeding line NC84173 and L. pimpinellifolium accession LA722. A molecular linkage map of this cross that was previously constructed based on 119 BC1 individuals and 151 RFLP markers was used for the QTL mapping. The parental lines and 119 BC1S1 families (self-pollinated progeny of BC1 individuals) were grown under field conditions at two locations, Rock Spring, PA, and Davis, CA, and fruits were scored for weight (FW), polar (PD) and equatorial diameters (ED), shape (FS), total soluble solids content (SSC), pH and lycopene content (LYC). For each trait, between 4 and 10 QTLs were identified with individual effects ranging between 4.4% and 32.9% and multilocus QTL effects ranging between 39% and 75% of the total phenotypic variation. Most QTL effects were predictable from the parental phenotypes, and several QTLs were identified that affected more than one trait. A few pairwise epistatic interactions were detected between QTL-linked and QTL-unlinked markers. Despite great differences between PA and CA growing conditions, the majority of FW QTLs (78%) and SSC QTLs (75%) in the two locations shared similar genomic positions. Almost all of the QTLs that were identified in the present study for FW and SSC were previously identified in six other studies that used different interspecific crosses of tomato; this indicates conservation of QTLs for fruit traits across tomato species. Altogether, the seven studies identified at least 28 QTLs for FW and 32 QTLs for SSC on the 12 tomato chromosomes. However, for each trait a few major QTLs were commonly identified in 4 or more studies; such ‘popular’ QTLs should be of considerable interest for breeding purposes as well as basic research towards cloning of QTLs. Notably, a majority of QTLs for increased SSC also contributed to decreased fruit size. Therefore, to significantly increase SSC of the cultivated tomato, some compromise in fruit size may be unavoidable. This revised version was published online in June 2006 with corrections to the Cover Date.     

Kinetic behaviour of α-galactosidase produced by Absidia griseola: a comparison between free and immobilized forms of the enzyme

In this research the characteristics of free (partially purified) and immobilized (mould pellets of Absidia griseola) -galactosidase have been investigated. Inhibition studies of the enzyme showed that p-nitrophenol and sucrose do not have any inhibitory effect on the enzyme, but that galactose is a competitive inhibitor. In the immobilized form, inhibition was lower than in the free enzyme and the level of inhibition decreased as the temperature increased. The activity and stability of free and immobilized enzyme were investigated with respect to temperature, and the results showed that the optimal temperature range of the free enzyme was 45–50 °C, while the immobilized enzyme had an optimum at 55–60 °C. The optimum pH for the free enzyme was 6.0 and the value was decreased to 5.0 by immobilizing. The experimental effectiveness factors were found to be represented as a single function of the modified Thiele modulus, including parameters such as pellet size, enzyme concentration in the pellets and substrate concentration. Both experimental and theoretical data concerning effectiveness factors are nearly the same.     

Quantitative proteomic analysis by iTRAQ<Superscript>®</Superscript> for the identification of candidate biomarkers in ovarian cancer serum

Background

Ovarian cancer is the most lethal gynecologic malignancy, with the majority of cases diagnosed at an advanced stage when treatments are less successful. Novel serum protein markers are needed to detect ovarian cancer in its earliest stage; when detected early, survival rates are over 90%. The identification of new serum biomarkers is hindered by the presence of a small number of highly abundant proteins that comprise approximately 95% of serum total protein. In this study, we used pooled serum depleted of the most highly abundant proteins to reduce the dynamic range of proteins, and thereby enhance the identification of serum biomarkers using the quantitative proteomic method iTRAQ^®.

Results

Medium and low abundance proteins from 6 serum pools of 10 patients each from women with serous ovarian carcinoma, and 6 non-cancer control pools were labeled with isobaric tags using iTRAQ^® to determine the relative abundance of serum proteins identified by MS. A total of 220 unique proteins were identified and fourteen proteins were elevated in ovarian cancer compared to control serum pools, including several novel candidate ovarian cancer biomarkers: extracellular matrix protein-1, leucine-rich alpha-2 glycoprotein-1, lipopolysaccharide binding protein-1, and proteoglycan-4. Western immunoblotting validated the relative increases in serum protein levels for several of the proteins identified.

Conclusions

This study provides the first analysis of immunodepleted serum in combination with iTRAQ^® to measure relative protein expression in ovarian cancer patients for the pursuit of serum biomarkers. Several candidate biomarkers were identified which warrant further development.

     

Design and development of a new ambr250® bioreactor vessel for improved cell and gene therapy applications

The emergence of cell and gene therapies has generated significant interest in their clinical and commercial potential. However, these therapies are prohibitively expensive to manufacture and can require extensive time for development due to our limited process knowledge and understanding. The automated ambr250® stirred-tank bioreactor platform provides an effective platform for high-throughput process development. However, the original dual pitched-blade 20 mm impeller and baffles proved sub-optimal for cell therapy candidates that require suspension of microcarriers (e.g. for the culture of adherent human mesenchymal stem cells) or other particles such as activating Dynabeads® (e.g. for the culture of human T-cells). We demonstrate the development of a new ambr250® stirred-tank bioreactor vessel which has been designed specifically to improve the suspension of microcarriers/beads and thereby improve the culture of such cellular systems. The new design is unbaffled and has a single, larger elephant ear impeller. We undertook a range of engineering and physical characterizations to determine which vessel and impeller configuration would be most suitable for suspension based on the minimum agitation speed (N_JS) and associated specific power input (P/V)_JS. A vessel (diameter, T, = 60 mm) without baffles and incorporating a single elephant ear impeller (diameter 30 mm and 45° pitch-blade angle) was selected as it had the lowest (P/V)_JS and therefore potentially, based on Kolmogorov concepts, was the most flexible system. These experimentally-based conclusions were further validated firstly with computational fluid dynamic (CFD) simulations and secondly experimental studies involving the culture of both T-cells with Dynabeads® and hMSCs on microcarriers. The new ambr250® stirred-tank bioreactor successfully supported the culture of both cell types, with the T-cell culture demonstrating significant improvements compared to the original ambr250® and the hMSC-microcarrier culture gave significantly higher yields compared with spinner flask cultures. The new ambr250® bioreactor vessel design is an effective process development tool for cell and gene therapy candidates and potentially for autologous manufacture too.

     

Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip®arrays

Background

The availability of both mouse and human draft genomes has marked the beginning of a new era of comparative mammalian genomics. The two available mouse genome assemblies, from the public mouse genome sequencing consortium and Celera Genomics, were obtained using different clone libraries and different assembly methods.

Results

We present here a critical comparison of the two latest mouse genome assemblies. The utility of the combined genomes is further demonstrated by comparing them with the human 'golden path' and through a subsequent analysis of a resulting conserved sequence element (CSE) database, which allows us to identify over 6,000 potential novel genes and to derive independent estimates of the number of human protein-coding genes.

Conclusion

The Celera and public mouse assemblies differ in about 10% of the mouse genome. Each assembly has advantages over the other: Celera has higher accuracy in base-pairs and overall higher coverage of the genome; the public assembly, however, has higher sequence quality in some newly finished bacterial artifical chromosome clone (BAC) regions and the data are freely accessible. Perhaps most important, by combining both assemblies, we can get a better annotation of the human genome; in particular, we can obtain the most complete set of CSEs, one third of which are related to known genes and some others are related to other functional genomic regions. More than half the CSEs are of unknown function. From the CSEs, we estimate the total number of human protein-coding genes to be about 40,000. This searchable publicly available online CSEdb will expedite new discoveries through comparative genomics.     

Analysis of the interactions between Eudragit® L100 and porcine pancreatic trypsin by calorimetric techniques

Flexible-chain polymers with charge (polyelectrolytes) can interact with globular proteins with a net charge opposite to the charge of the polymers forming insoluble complexes polymer-protein. In this work, the interaction between the basic protein trypsin and the anionic polyelectrolyte Eudragit^® L100 was studied by using isothermal calorimetric titrations and differential scanning calorimetry. Turbidimetric assays allowed determining that protein-polymer complex was insoluble at pH below 5 and the trypsin and Eudragit^® L100 concentrations required forming the insoluble complex. DSC measurements showed that the T_m and denaturalization heat of trypsin increased in the polymer presence and the complex unfolded according to a two-state model. ΔH° and ΔS° binding parameters obtained by ITC were positives agree with hydrophobic interaction between trypsin and polymer. However, ionic strength of 1.0 M modified the insoluble complex formation. We propose a mechanism of interaction between Eudragit^® L100 and trypsin molecules that involves both hydrophobic and electrostatic interactions. Kinetic studies of complex formation showed that the interaction requires less than 1 min achieving the maximum quantity of complex. Finally, a high percentage of active trypsin was precipitated (approximately 76% of the total mass of protein). These findings could be useful in different protocols such as a protein isolation strategy, immobilization or purification of a target protein.     

Interactions between hare and brent goose in a salt marsh system; evidence for food competition?

In this study we accumulate evidence that brown hare competes with brent goose for food resources in a temperate salt marsh. We show that both species overlap in habitat use and share food plants. The two herbivores mainly used the common habitat at different times of the day, with hares active in the dark and geese during the daylight. During the morning and evening, however, the habitat was exploited simultaneously. Food availability was manipulated by excluding brent geese on both small-scale (30 m²) and large-scale (0.96 ha) plots, while hares had free access everywhere. Exclusion of brent geese enhanced the level of utilisation by hares in both Festuca and Puccinellia dominated marshes, which are among the most intensively grazed parts of the salt marsh. The increase in hare grazing pressure following goose exclusion was stronger, when the adjacent control plots had attracted more goose visitation. When geese were excluded, the decrease in Festuca consumption by geese was completely matched by increased hare grazing, while for Puccinellia only part of the `surplus' was harvested. Enhanced levels of hare utilisation were not due to geese interfering directly with hare, nor due to hares avoiding goose droppings. Considering the interaction from the other perspective, hares were observed to disturb geese effectively in every spring. This might have reduced exploitation by geese of the shared resources. On the basis of our experimental results, we conclude that in this salt- marsh system competition for food with brent geese plays a role in the habitat use of hares, and that hares can reduce goose exploitation of shared habitats. Received: 30 March 1998 / Accepted: 6 July 1998     

Biomarker response and therapy prediction in renal denervation therapy – the role of MR-proadrenomedullin in a multicenter approach

Background: Renal denervation has been proposed as a therapeutic option in patients with resistant hypertension. Circulating blood borne biomarkers might be helpful to identify individuals responding to RDN therapy. MR-proADM is a strong prognostic marker in patients with cardiovascular disease. The aim of this multicenter study was to evaluate the effect of RDN on MR-proADM concentrations.

Methods and results: We measured MR-proADM, BNP, and MR-proANP in 110 patients before and after RDN in a multicenter setting. All patients were followed up after 1 and 6 months by office and ambulatory blood pressure (BP) measurements. The mean office BP decreased from 165/89 to 152/87?mmHg 6 months after RDN (systolic: p?<?0.001; diastolic: ns), the responder-rate was 74%. Intriguingly MR-proADM concentrations increased from 0.66 to 0.69?nmol/L (p?<?0.001) and were significantly associated with reduction of systolic office BP after 6 months in multivariate analyses (coefficient ?0.0018, p?<?0.001). In therapy-responders MR-proADM concentrations showed a significantly higher increase over time (coefficient 0.0105, p?<?0.05), as compared to non-responders. There were no significant differences in BP change for individuals with low and high baseline MR-proADM (BP-Delta low MR-proADM ?23/?4?mmHg vs. high MR-proADM ?24/?5?mmHg). The natriuretic biomarkers BNP and MR-proANP did not change significantly after 6 months. Biomarkers at baseline were not able to predict for therapy-responder.

Conclusion: In patients undergoing RDN, baseline measurements of various biomarkers had no prognostic use for therapy success in this short time follow-up period in a multicenter approach. Intriguingly, MR-proADM showed a significant association with BP reduction after 6 months.     

High yield purification of JNK1β1 and activation by in vitro reconstitution of the MEKK1 → MKK4 → JNK MAPK phosphorylation cascade

The c-Jun N-terminal kinase (JNK) pathway forms part of the mitogen-activated protein kinase (MAPK) signaling pathways comprising a sequential three-tiered kinase cascade. Here, an upstream MAP3K (MEKK1) phosphorylates and activates a MAP2K (MKK4 and MKK7), which in turn phosphorylates and activates the MAPK, JNK. The C-terminal kinase domain of MEKK1 (MEKK-C) is constitutively active, while MKK4/7 and JNK are both activated by dual phosphorylation of S/Y, and T/Y residues within their activation loops, respectively. While improvements in the purification of large quantities of active JNKs have recently been made, inadequacies in their yield, purity, and the efficiency of their phosphorylation still exist. We describe a novel and robust method that further improves upon the purification of large yields of highly pure, phosphorylated JNK1β1, which is most suitable for biochemical and biophysical characterization. Codon harmonization of the JNK1β1 gene was used as a precautionary measure toward increasing the soluble overexpression of the kinase. While JNK1β1 and its substrate ATF2 were both purified to >99% purity as GST fusion proteins using GSH-agarose affinity chromatography and each cleaved from GST using thrombin, constitutively-active MEKK-C and inactive MKK4 were separately expressed in E. coli as thioredoxin-His₆-tagged proteins and purified using urea refolding and Ni²⁺-IMAC, respectively. Activation of JNK1β1 was then achieved by successfully reconstituting the JNK MAPK activation cascade in vitro; MEKK-C was used to activate MKK4, which in turn was used to efficiently phosphorylate and activate large quantities of JNK1β1. Activated JNK1β1 was thereafter able to phosphorylate ATF2 with high catalytic efficiency.