Ataxia-Telangiectasia Mutated Loss-of-Function Displays Variant and Tissue-Specific Differences across Tumor Types

PURPOSE

Mutations in the ATM gene are common in multiple cancers, but clinical studies of therapies targeting ATM-aberrant cancers have yielded mixed results. Refinement of ATM loss of function (LOF) as a predictive biomarker of response is urgently needed.

EXPERIMENTAL DESIGN

We present the first disclosure and preclinical development of a novel, selective ATR inhibitor, ART0380, and test its antitumor activity in multiple preclinical cancer models. To refine ATM LOF as a predictive biomarker, we performed a comprehensive pan-cancer analysis of ATM variants in patient tumors and then assessed the ATM variant-to-protein relationship. Finally, we assessed a novel ATM LOF biomarker approach in retrospective clinical data sets of patients treated with platinum-based chemotherapy or ATR inhibition.

RESULTS

ART0380 had potent, selective antitumor activity in a range of preclinical cancer models with differing degrees of ATM LOF. Pan-cancer analysis identified 10,609 ATM variants in 8,587 patient tumors. Cancer lineage-specific differences were seen in the prevalence of deleterious (Tier 1) versus unknown/benign (Tier 2) variants, selective pressure for loss of heterozygosity, and concordance between a deleterious variant and ATM loss of protein (LOP). A novel ATM LOF biomarker approach that accounts for variant classification, relationship to ATM LOP, and tissue-specific penetrance significantly enriched for patients who benefited from platinum-based chemotherapy or ATR inhibition.

CONCLUSIONS

These data help to better define ATM LOF across tumor types in order to optimize patient selection and improve molecularly targeted therapeutic approaches for patients with ATM LOF cancers.

Infectious disease modelling to inform policy

With modelling becoming increasingly important in helping to inform decisions about animal diseases, it is essential that the process be optimised to gain the maximum benefit for the decision-maker. Here, the authors set out ten steps that can improve this process for all concerned. Four steps describe initialisation to ensure that the question, answer and timescale are defined; two steps describe the modelling process and quality assurance; and four steps describe the reporting stage. The authors believe that this greater emphasis at the beginning and end of a modelling project will increase the relevance of the work and understanding of the results, and thus contribute towards better decision-making.

Small-Molecule Polθ Inhibitors Provide Safe and Effective Tumor Radiosensitization in Preclinical Models

PURPOSE

DNA polymerase theta (Polθ, encoded by the POLQ gene) is a DNA repair enzyme critical for microhomology mediated end joining (MMEJ). Polθ has limited expression in normal tissues but is frequently overexpressed in cancer cells and, therefore, represents an ideal target for tumor-specific radiosensitization. In this study we evaluate whether targeting Polθ with novel small-molecule inhibitors is a feasible strategy to improve the efficacy of radiotherapy.

EXPERIMENTAL DESIGN

We characterized the response to Polθ inhibition in combination with ionizing radiation in different cancer cell models in vitro and in vivo.

RESULTS

Here, we show that ART558 and ART899, two novel and specific allosteric inhibitors of the Polθ DNA polymerase domain, potently radiosensitize tumor cells, particularly when combined with fractionated radiation. Importantly, noncancerous cells were not radiosensitized by Polθ inhibition. Mechanistically, we show that the radiosensitization caused by Polθ inhibition is most effective in replicating cells and is due to impaired DNA damage repair. We also show that radiosensitization is still effective under hypoxia, suggesting that these inhibitors may help overcome hypoxia-induced radioresistance. In addition, we describe for the first time ART899 and characterize it as a potent and specific Polθ inhibitor with improved metabolic stability. In vivo, the combination of Polθ inhibition using ART899 with fractionated radiation is well tolerated and results in a significant reduction in tumor growth compared with radiation alone.

CONCLUSIONS

These results pave the way for future clinical trials of Polθ inhibitors in combination with radiotherapy.

2395LGE CMR predicts sudden death and VT in adults with repaired tetralogy of Fallot - a prospective study with 3500 patient follow up years

Background

Adults with repaired tetralogy of Fallot (rtoF) are at risk of ventricular arrhythmia and sudden cardiac death (SCD). Cross-sectional data suggest association of late gadolinium enhancement (LGE) cardiovascular magnetic resonance imaging (CMR) with adverse clinical risk factors

Purpose

We sought to determine prognosis related to LGE CMR.

Methods

In this prospective cohort study the primary composite outcome comprised the first of cardiovascular death (SCD or heart failure-related), aborted SCD (successfully resuscitated cardiac arrest or appropriate AICD shock for ventricular fibrillation), and clinical sustained ventricular tachycardia (VT>30 seconds duration).

Results

In 531 rtoF patients (median age 32; 23–42, 296 (56%) male, NYHA≥II 17%) followed up after LGE CMR for median 5 (1.7–8.9) years, there were 39 primary composite outcomes: 10 SCD, 11 heart failure related deaths (2 perioperative RV failure), 2 aborted SCD and 16 clinical sustained VT events. At study end, there were 28 ventricular arrhythmic events in 28 rtoF patients (10 SCD, 16 clinical sustained VT, 2 aborted VF) that were significantly predicted by RV LGE extent (HR 1.45 CI: 1.3–1.6; P<0.001).

Univariable predictors of the primary outcome were RV LGE score; HR: 1.44 (1.31–1.57; p<0.001), (Figure) together with older age; HR: 1.05 (1.02–1.07; P<0.001), late repair; HR: 1.04 (1.02–1.07; p<0.001), lower RV ejection fraction; HR: 0.92 (0.89–0.95; p<0.001), larger RVOT akinetic length; HR: 1.04 (1.02–1.06; p<0.001) larger right atrial area; HR: 1.2 (1.12–1.29; p<0.001); higher BNP levels; HR: 1.01 (1–1.02; p<0.001), lower peak VO2; HR: 0.89 (0.83–0.96; p=0.001), prior atrial arrhythmia; HR: 5.3 (2.8–10.07; p<0.001), and non-sustained VT; HR: 4.1 (2.1–7.7; p<0.001). Inducible VT did not predict the primary outcome; HR: 2.1 (0.57–8; p=0.25)

In multivariable analysis both RV LGE score and indexed right atrial area (RAAi) only, remained predictive of the primary outcome (HR 1.29 CI: 1.12–1.49; p<0.001 and HR 1.1 CI: 1.02–1.12; p=0.01, respectively). Patients could accordingly be stratified such that supramedian RV LGE score (≥5) and RAAi ≥16cm2/m2 had 5-year event free survival 84% vs 94% for supramedian RV LGE score (≥5) and RAAi <16cm2/m2 or 98% for inframedian RV LGE score with RAAI<16cm2/m2. Figure.

Conclusions

For every unit increase in CMR defined RV fibrosis score there is a 44% increased risk of sudden cardiac death and VT. LGE CMR and maximal right atrial area should therefore be incorporated into risk stratification for sudden death in adults with rTOF.

Acknowledgement/Funding

British heart foundation

Correction: High performing AgNW transparent conducting electrodes with a sheet resistance of 2.5 Ω Sq-1 based upon a roll-to-roll compatible post-processing technique

Correction for 'High performing AgNW transparent conducting electrodes with a sheet resistance of 2.5 Ω Sq-1 based upon a roll-to-roll compatible post-processing technique' by D. Kumar et al., Nanoscale, 2019, DOI: 10.1039/c8nr07974a.

High performing AgNW transparent conducting electrodes with a sheet resistance of 2.5 Ω Sq-1 based upon a roll-to-roll compatible post-processing technique

A report of transparent and conducting silver nanowires (AgNWs) that produce remarkable electrical performance, surface planarity and environmental stability is given. This research presents an innovative process that relies on three sequential steps, which are roll-to-roll (R2R) compatible: thermal embossing, infrared sintering and plasma treatment. This process leads to the demonstration of a conductive film with a sheet resistance of 2.5 Ω sq-1 and high transmittance, thus demonstrating the highest reported figure-of-merit in AgNWs to date (FoM = 933). A further benefit of the process is that the surface roughness is substantially reduced compared to traditional AgNW processing techniques. The consideration of the long-term stability is given by developing an accelerated life test process that simultaneously stresses the applied bias and temperature. Regression line fitting shows that a ∼150-times improvement in stability is achieved under 'normal operational conditions' when compared to traditionally deposited AgNW films. X-ray photoelectron spectroscopy (XPS) is used to understand the root cause of the improvement in long-term stability, which is related to reduced chemical changes in the AgNWs.

The role of modelling in predicting rabies and understanding the impact of control measures

Rabies is probably the most commonly modelled disease as both its epidemiology and host dynamics are well understood. Models are simplifications of reality and there are different approaches to achieving these representations. Over time, modelling has moved from simple mathematical methods towards more realistic biological models that incorporate spatial and individual variation. In this article, the author reviews models that have increased our understanding of actions taken to manage disease. The most developed of these focus on fox (Vulpes vulpes) rabies in Europe, where a suite of models has helped researchers to explore fox management options and the complications caused by other potential hosts, such as raccoon dogs (Nyctereutes procyonoides). Models of dog (Canis familiaris) rabies support the idea of a 70% vaccine threshold for disease elimination and are now being used to explore and optimise management methods, combining vaccination with either surgical sterilisation or the use of chemical sterilisation. Future challenges are also identified, such as the need to develop practical management models in other hosts, and to explore different Lyssavirus strains in bats.

In-depth synthetic, physicochemical and in vitro biological investigation of a new ternary V(IV) antioxidant material based on curcumin

Curcumin is a natural product with a broad spectrum of beneficial properties relating to pharmaceutical applications, extending from traditional remedies to modern cosmetics. The biological activity of such pigments, however, is limited by their solubility and bioavailability, thereby necessitating new ways of achieving optimal tissue cellular response and efficacy as drugs. Metal ion complexation provides a significant route toward improvement of curcumin stability and biological activity, with vanadium being a representative such metal ion, amply encountered in biological systems and exhibiting exogenous bioactivity through potential pharmaceuticals. Driven by the need to optimally increase curcumin bioavailability and bioactivity through complexation, synthetic efforts were launched to seek out stable species, ultimately leading to the synthesis and isolation of a new ternary V(IV)-curcumin-(2,2'-bipyridine) complex. Physicochemical characterization (elemental analysis, FT-IR, Thermogravimetry (TGA), UV-Visible, NMR, ESI-MS, Fluorescence, X-rays) portrayed the solid-state and solution properties of the ternary complex. Pulsed-EPR spectroscopy, in frozen solutions, suggested the presence of two species, cis- and trans-conformers. Density Functional Theory (DFT) calculations revealed the salient features and energetics of the two conformers, thereby complementing EPR spectroscopy. The well-described profile of the vanadium species led to its in vitro biological investigation involving toxicity, cell metabolism inhibition in S. cerevisiae cultures, Reactive Oxygen Species (ROS)-suppressing capacity, lipid peroxidation, and plasmid DNA degradation. A multitude of bio-assays and methodologies, in comparison to free curcumin, showed that it exhibits its antioxidant potential in a concentration-dependent fashion, thereby formulating a bioreactivity profile supporting development of new efficient vanado-pharmaceuticals, targeting (extra)intra-cellular processes under (patho)physiological conditions.

In vitro mesenchymal stem cell response to a CO2 laser modified polymeric material

With an ageing world population it is becoming significantly apparent that there is a need to produce implants and platforms to manipulate stem cell growth on a pharmaceutical scale. This is needed to meet the socio-economic demands of many countries worldwide. This paper details one of the first ever studies in to the manipulation of stem cell growth on CO2 laser surface treated nylon 6,6 highlighting its potential as an inexpensive platform to manipulate stem cell growth on a pharmaceutical scale. Through CO2 laser surface treatment discrete changes to the surfaces were made. That is, the surface roughness of the nylon 6,6 was increased by up to 4.3μm, the contact angle was modulated by up to 5° and the surface oxygen content increased by up to 1atom %. Following mesenchymal stem cell growth on the laser treated samples, it was identified that CO2 laser surface treatment gave rise to an enhanced response with an increase in viable cell count of up to 60,000cells/ml when compared to the as-received sample. The effect of surface parameters modified by the CO2 laser surface treatment on the mesenchymal stem cell response is also discussed along with potential trends that could be identified to govern the mesenchymal stem cell response.

Population genetic structure of serotine bats (Eptesicus serotinus) across Europe and implications for the potential spread of bat rabies (European bat lyssavirus EBLV-1)

Understanding of the movements of species at multiple scales is essential to appreciate patterns of population connectivity and in some cases, the potential for pathogen transmission. The serotine bat (Eptesicus serotinus) is a common and widely distributed species in Europe where it frequently harbours European bat lyssavirus type 1 (EBLV-1), a virus causing rabies and transmissible to humans. In the United Kingdom, it is rare, with a distribution restricted to south of the country and so far the virus has never been found there. We investigated the genetic structure and gene flow of E. serotinus across the England and continental Europe. Greater genetic structuring was found in England compared with continental Europe. Nuclear data suggest a single population on the continent, although further work with more intensive sampling is required to confirm this, while mitochondrial sequences indicate an east-west substructure. In contrast, three distinct populations were found in England using microsatellite markers, and mitochondrial diversity was very low. Evidence of nuclear admixture indicated strong male-mediated gene flow among populations. Differences in connectivity could contribute to the high viral prevalence on the continent in contrast with the United Kingdom. Although the English Channel was previously thought to restrict gene flow, our data indicate relatively frequent movement from the continent to England highlighting the potential for movement of EBLV-1 into the United Kingdom.

A comparative study on the presence of C-type viral particles in placentas from primates and other animals

C-type particles are found in human, baboon, marmoset, rhesus, patas, and cynomolgus monkeys. A cebus monkey and two chimpanzee placentas have failed thus far to show the presence of these particles. Of the nonprimate tissues examined one mouse and one guinea pig placenta were positive whereas a rabbit placenta was negative. Variations in number of particles present in tissues as well as number of animals of a given species containing particles are noted. The isolation of foamyviruses from placenta cultures makes critical evaluation and interpretation of findings imperative. Several considerations suggest that the presence of foamyviruses is coincidental.

The activation of the Akt/PKB signalling pathway in the brains of clozapine-exposed rats is linked to hyperinsulinemia and not a direct drug effect

The second generation antipsychotic drug clozapine is a much more effective therapy for schizophrenia than first generation compounds, but the reasons for this are poorly understood. We have previously shown that one distinguishing feature of clozapine is its ability to raise glucagon levels in animal models and thus causes prolonged hyperinsulinemia without inducing hypoglycaemia. Previous studies have provided evidence that defects in Akt/PKB and GSK3 signalling can contribute to development of psychiatric diseases. Clozapine is known to activate Akt/PKB in the brain, and some studies have indicated that this is due to a direct effect of the drug on the neurons. However, we provide strong evidence that elevated insulin levels induced by clozapine are in fact the real cause of the drug's effects on Akt/PKB and GSK3 in the brain. This suggests that the elevated levels of insulin induced by clozapine may contribute to this drug's therapeutic efficacy.

Clozapine directly increases insulin and glucagon secretion from islets: implications for impairment of glucose tolerance

Second generation antipsychotics cause derangements in glucose metabolism that are often interpreted as insulin resistance. In previous studies we have shown that this is not classical insulin resistance but the drugs were actually inducing a hyperglycaemic state associated with elevated hepatic glucose output (HGO) and increased levels of glucagon and insulin. However, it remains unclear whether these effects are directly elicited by drug actions in the liver and pancreas, or whether they are indirectly mediated. Here we investigated if clozapine is capable of inducing insulin resistance in the liver or enhancing insulin and glucagon secretion from the pancreas. It was observed that insulin signalling was elevated in livers from animals treated with clozapine indicating there was no insulin resistance in the early steps of insulin signalling. To explore whether the defects arise at later stages of insulin action we used an isolated perfused liver system. In this model, clozapine had no direct effect on insulin's counter regulatory effect on epinephrine-induced HGO. In isolated mouse islets clozapine significantly increased glucose-stimulated insulin secretion while simultaneously blocking glucose-induced reductions in glucagon secretion. We also show that the non-peptidic glucagon receptor like peptide-1 (GLP-1) receptor agonist Boc5 was able to overcome the inhibitory effects of clozapine on glucose metabolism. Taken together these results suggest that clozapine does not have any direct effect on glucose metabolism in the liver but it simultaneously stimulates insulin and glucagon secretion, a situation that would allow for the concurrent presence of high glucose and high insulin levels in treated animals.

Traceability from a US perspective

Traceability of a food consists of development of "an information trail that follows the food product's physical trail". Internationally, the US is lagging behind many countries in developing traceability systems for food in general and especially for livestock, poultry and their products. The US food industry is developing, implementing and maintaining traceability systems designed to improve food supply management, facilitate traceback for food safety and quality, and differentiate and market foods with subtle or undetectable quality attributes. Traceability, for livestock, poultry and meat, in its broadest context, can, could, or will eventually be used: (1) to ascertain origin and ownership, and to deter theft and misrepresentation, of animals and meat; (2) for surveillance, control and eradication of foreign animal diseases; (3) for biosecurity protection of the national livestock population; (4) for compliance with requirements of international customers; (5) for compliance with country-of-origin labeling requirements; (6) for improvement of supply-side management, distribution/delivery systems and inventory controls; (7) to facilitate value-based marketing; (8) to facilitate value-added marketing; (9) to isolate the source and extent of quality-control and food-safety problems; and (10) to minimize product recalls and make crisis management protocols more effective. Domestically and internationally, it has now become essential that producers, packers, processors, wholesalers, exporters and retailers assure that livestock, poultry and meat are identified, that record-keeping assures traceability through all or parts of the complete life-cycle, and that, in some cases, the source, the production-practices and/or the process of generating final products, can be verified. At issue, as the US develops traceback capabilities, will be the breadth, depth and precision of its specific traceability systems.

A diagnostic study of Echinococcus multilocularis in red foxes (Vulpes vulpes) from Great Britain

Alveolar echinococcosis is caused by a parasitic tapeworm Echinococcus multilocularis and is a serious disease with high fatality in humans. The definitive primary host is the red fox (Vulpes vulpes) but domestic animals (dogs and to a lesser extent cats) as well as several genera of rodents can also be infected with the parasite. There is, to date, no evidence of indigenous cases of E. multilocularis in Great Britain (GB) but in most of continental Europe the parasite is considered to be endemic and/or slowly spreading. All pet dogs entering the United Kingdom (UK) under the pet travel scheme (PETS) are therefore currently treated with an anthelmintic effective against Echinococcus spp. Surveillance of red foxes is required to demonstrate disease freedom and maintain this regulation to prevent further geographical spread of the parasite to free areas within the EU. A study of 588 wild red foxes collected from across Great Britain (GB) between October 1999 and November 2000 found no Echinococcus spp. This report describes a further study of GB foxes collected predominately during 2005 and 2006. Fox faecal samples (n=384) were examined for both E. multilocularis and Echinococcus granulosus using an egg isolation procedure followed by PCR method, based on published primer sets. A non-specific primer set that amplifies Taenia spp. as well as Mesocestoides, Dipylidium and Diphyllobothrium was also included in the assay to validate the test procedure as these parasites are expected to be more common in wild fox populations. All faecal samples tested negative for both E. multilocularis and E. granulosus but results for approximately 35% of the samples indicated the presence of Taenia spp. or other closely related cestodes. This data contributes to the evidence that suggests that E. multilocularis is not present in mainland Britain and justifies the requirement for ongoing surveillance to demonstrate disease freedom.

High-throughput small molecule screening reveals structurally diverse compounds that inhibit the growth of Escherichia coli O157:H7 in vitro

Escherichia coli O157:H7 colonizes the gastrointestinal tract of ruminants asymptomatically and may enter the human food supply through fecal contamination. A fraction of individuals infected by E. coli O157:H7 develop hemolytic uremic syndrome, a life-threatening condition. When individuals infected by E. coli O157:H7 are treated with certain antibiotics, an increased incidence of hemolytic uremic syndrome may result. This finding supports the need to identify novel compounds that can either reduce the load of E. coli O157:H7 entering the human food supply or serve as alternative therapeutic treatments for infected individuals. We developed a high-throughput turbidometric assay to identify novel compounds that inhibit E. coli O157:H7 growth. Pin transfers were performed to introduce small molecule libraries into 384-well plates, where each well contained approximately 5.0 log CFU of E. coli O157:H7. Plates were incubated at 37°C for 18 h, and the optical density was measured to determine the effect of each small molecule. A total of 64,562 compounds were screened in duplicate, and 43 unique compounds inhibited E. coli O157:H7 growth. Thirty-eight of the 43 inhibitory compounds belonged to known bioactive libraries, and the other 5 compounds were from commercial libraries derived from splitting and pooling. Inhibitory compounds from known bioactive libraries were most frequently therapeutic antibiotics (n = 34) but also included an antiviral compound, a compound that disrupts the citric acid cycle, and two biguanide compounds, which have been used for various nonclinical applications. We identified two novel compounds (i.e., biguanides) that should be studied further for their ability to reduce pathogen populations in foods.

Olanzapine effects on body composition, food preference, glucose metabolism and insulin sensitivity in the rat

The atypical antipsychotic drug olanzapine induces weight gain and defects in glucose metabolism in patients. Using a rat model we investigated the effects of acute and long term olanzapine treatment on weight gain, food preference and glucose metabolism. Olanzapine treated rats fed a chow diet grew more slowly than vehicle controls but olanzapine treated animals fed a high fat/sugar diet grew faster than control animals on the same diet. These changes in weight were paralleled by changes in fat mass. Olanzapine also induced a strong preference for a high fat/high sugar diet. Acute exposure to olanzapine rapidly induced severe impairments of glucose tolerance and increased insulin secretion but did not impair insulin tolerance. These results indicate the defect in glucose metabolism induced by acute olanzapine treatment was most likely due to increased hepatic glucose output associated with a reduction in active GLP-1 levels and correspondingly high glucagon levels.

Towards a standardised surveillance for Trichinella in the European Union

Each year, more than 167 million pigs in the European Union (EU) are tested for Trichinella spp. under the current meat hygiene regulations. This imposes large economic costs on countries, yet the vast majority of these pigs test negative and the public health risk in many countries is therefore considered very low. This work reviewed the current Trichinella status across the EU as well as the national level of monitoring and reporting. It also reviewed which animal species were affected by Trichinella and in which species it should be surveyed. This information was used to design a cost-effective surveillance programme that enables a standardised monitoring approach within the EU. The proposed surveillance programme relies on identifying sub-populations of animals with a distinct risk. Low-risk pigs are finisher pigs that originate from so-called controlled housing. All other pigs are considered high-risk pigs. Controlled housing is identified by the application of a specific list of management and husbandry practices. We suggest that member states (MS) be categorised into three classes based on the confidence that Trichinella can be considered absent, in the specified sub-population of pigs above a specified design prevalence which we set to 1 per million pigs. A simple and transparent method is proposed to estimate this confidence, based on the sensitivity of the surveillance system, taking into account the sensitivity of testing and the design prevalence. The probability of detecting a positive case, if present, must be high (>95 or >99%) to ensure that there is a low or negligible risk of transmission to humans through the food chain. In MS where the probability of a positive pig is demonstrated to be negligible, testing of fattening pigs from a sub-population consisting of pigs from controlled housing can be considered unnecessary. Furthermore, reduced testing of finishers from the sub-population consisting of pigs from non-controlled housing might even be considered, if conducted in conjunction with a proportionate sampling scheme and a risk-based wildlife surveillance programme where applicable. The proposed surveillance programme specifies the required number of samples to be taken and found negative, in a MS. A MS with no data or positive findings will initially be allocated to class 1, in which all pigs should be tested. When a MS is able to demonstrate a 95% or 99% confidence that Trichinella is absent, the MS will be allocated to class 2 or 3, in which the testing requirement is lower than in class 1.

Effects of genetic markers and implant strategy on longissimus and gluteus muscle tenderness of calf-fed steers and heifers

Effects of genotype (GEN) and implant program (IMP) on LM and gluteus muscle (GM) tenderization were investigated using crossbred steer (n = 185) and heifer (n = 158) calves. The 3-marker GeneSTAR Tenderness panel [CAST (calpastatin), CAPN1 316 (µ-calpain), and CAPN1 4751 (µ-calpain)] was used to determine the GEN of each animal (reported as total number of favorable alleles, 0 through 6). Calves were randomly assigned to 1 of 2 IMP, conventional (CNV) or delayed. Cattle in the CNV group were implanted at the beginning of the finishing period with Revalor-IS or Revalor-IH (Intervet Inc., Millsboro, DE), and then reimplanted 59 d later with Revalor-S or Revalor-H (Intervet Inc.). Calves in the delayed group received a single terminal implant (Revalor-S or Revalor-H) administered 45 d after initiation of the finishing period. Warner-Bratzler shear force (WBSF) was measured on LM and GM steaks at 3, 7, 14, 21, and 28 d postmortem. No interactions between the main effects of sex, IMP, or GEN were detected (P > 0.05) for WBSF. An IMP × postmortem aging (age) interaction was detected (P < 0.05) for LM and GM WBSF. For both muscles, steaks from CNV cattle had WBSF values that were approximately 0.2 kg greater (P < 0.05) than the values for steaks from delayed animals, but only during the early postmortem period (3 to 7 d). A linear effect of GEN on WBSF was detected (P < 0.05) for LM and GM steaks. Within each muscle, steaks from cattle with 6 favorable alleles had WBSF values 0.33 kg less than the values for steaks from cattle with 1 favorable allele. The GEN × age interaction was not significant for LM (P = 0.14) or GM (P = 0.20), but a numerical trend was observed for the effect of GEN on WBSF to diminish as age increased. To investigate how genetic markers could be interfaced with current beef carcass quality grading, cattle were sorted into 2 gene marker groups (GMG), ≤3 vs. ≥4 favorable alleles. For both muscles, GMG was effective only at identifying tenderness differences within the Select grade. When aged ≤14 d, Select LM steaks from cattle with ≥4 alleles had smaller (P < 0.05) WBSF values than did LM steaks from animals with ≤3 alleles. Preslaughter factors (sex, IMP, and GMG) controlled in the present study each accounted for less than 7% of the explained variation in tenderness of the test population. Results from this study suggest that the 3 GeneSTAR Tenderness markers were associated with small differences (0.33 kg) in WBSF and may be useful for increasing the consistency of Select beef, but these specific markers accounted for only a minor amount of variation in beef tenderness.

Establishing an appropriate mode of comparison for measuring the performance of marbling score output from video image analysis beef carcass grading systems

A beef carcass instrument grading system that improves accuracy and consistency of marbling score (MS) evaluation would have the potential to advance value-based marketing efforts and reduce disparity in quality grading among USDA graders, shifts, and plants. The objectives of this study were to use output data from the Video Image Analysis-Computer Vision System (VIA-CVS, Research Management Systems Inc., Fort Collins, CO) to develop an appropriate method by which performance of video image analysis MS output could be evaluated for accuracy, precision, and repeatability for purposes of seeking official USDA approval for using an instrument in commerce to augment assessment of quality grade, and to use the developed standards to gain approval for VIA-CVS to assist USDA personnel in assigning official beef carcass MS. An initial MS output algorithm was developed (phase I) for the VIA-CVS before 2 separate preliminary instrument evaluation trials (phases II and III) were conducted. During phases II and III, a 3-member panel of USDA expert graders independently assigned MS to 1,068 and 1,242 stationary carcasses, respectively. Mean expert MS was calculated for each carcass. Additionally, a separate 3-member USDA expert panel developed a consensus MS for each carcass in phase III. In phase II, VIA-CVS stationary triple-placement and triple-trigger instrument repeatability values (n = 262 and 260, respectively), measured as the percentage of total variance explained by carcasses, were 99.9 and 99.8%, respectively. In phases II and III, 95% of carcasses were assigned expert MS for which differences between individual expert MS, and for which the consensus MS in phase III only, was < or = 96 MS units. Two differing approaches to simple regression analysis, as well as a separate method-comparability analysis that accommodates error in both dependent and independent variables, were used to assess accuracy and precision of instrument MS predictions vs. mean expert MS. Method-comparability analysis was more appropriate in assessing the bias and precision of instrument MS predictions. Ether-extractable fat percentages (n = 257; phase II) differed among MS (P < 0.05) but were not suitable to predict or validate assigned MS. The performance and reproducibility of expert MS assignment in future evaluations was considered, and an official USDA performance standard was established, to which an instrument must conform to be approved for official on-line MS assessment. The VIA-CVS subsequently was approved to assign MS to carcasses on-line after completion of a 2006 USDA instrument approval trial conducted according to methods developed during completion of this study.

Fate of Listeria monocytogenes during freezing, thawing and home storage of frankfurters

Little information is available regarding the fate of Listeria monocytogenes during freezing, thawing and home storage of frankfurters even though recent surveys show that consumers regularly store unopened packages in home freezers. This study examined the effects of antimicrobials, refrigerated storage, freezing, thawing method, and post-thawing storage (7 degrees C) on L. monocytogenes on frankfurters. Inoculated (2.1 log CFU/cm(2)) frankfurters formulated without (control) or with antimicrobials (1.5% potassium lactate plus 0.1% sodium diacetate) were vacuum-packaged, stored at 4 degrees C for 6 or 30 d and then frozen (-15 degrees C) for 10, 30, or 50 d. Packages were thawed under refrigeration (7 degrees C, 24 h), on a countertop (23 +/- 2 degrees C, 8 h), or in a microwave oven (2450 MHz, 1100 watts, 220 s followed by 120 s holding), and then stored aerobically (7 degrees C) for 14 d. Bacterial populations were enumerated on PALCAM agar and tryptic soy agar plus 0.6% yeast extract. Antimicrobials completely inhibited (p < 0.05) growth of L. monocytogenes at 4 degrees C for 30 d under vacuum-packaged conditions, and during post-thawing aerobic storage at 7 degrees C for 14 d. Different intervals between inoculation and freezing (6 or 30 d) resulted in different pathogen levels on control frankfurters (2.1 or 3.9 log CFU/cm(2), respectively), while freezing reduced counts by <1.0 log CFU/cm(2). Thawing treatments had little effect on L. monocytogenes populations (<0.5 log CFU/cm(2)), and post-thawing fate of L. monocytogenes was not influenced by freezing or by thawing method. Pathogen counts on control samples increased by 1.5 log CFU/cm(2) at d-7 of aerobic storage, and reached 5.6 log CFU/cm(2) at d-14. As indicated by these results, consumers should freeze frankfurters immediately after purchase, and discard frankfurters formulated without antimicrobials within 3 d of thawing and/or opening.

Running climate models on grids using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them also involves complicated workflows implemented as shell scripts. A new grid middleware system that is well suited to climate modelling applications is presented in this paper. Grid Remote Execution (G-Rex) allows climate models to be deployed as Web services on remote computer systems and then launched and controlled as if they were running on the user's own computer. Output from the model is transferred back to the user while the run is in progress, to prevent it from accumulating on the remote system and to allow the user to monitor the model. G-Rex has a representational state transfer (REST) architectural style, featuring a Java client program that can easily be incorporated into existing scientific workflow scripts. Some technical details of G-Rex are presented, with examples of its use by climate modellers.