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Vos EL, Carr RA, Hsu M, Nakauchi M, Nobel T, Russo A, Barbetta A, Tan KS, Tang L, Ilson D, Ku GY, Wu AJ, Janjigian YY, Yoon SS, Bains MS, Jones DR, Coit D, Molena D, Strong VE. Prognosis after neoadjuvant chemoradiation or chemotherapy for locally advanced gastro-oesophageal junctional adenocarcinoma. Br J Surg 2021; 108:1332-1340. [PMID: 34476473 PMCID: PMC8599637 DOI: 10.1093/bjs/znab228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Trials typically group cancers of the gastro-oesophageal junction (GOJ) with oesophageal or gastric cancer when studying neoadjuvant chemoradiation and perioperative chemotherapy, so the results may not be fully applicable to GOJ cancer. Because optimal neoadjuvant treatment for GOJ cancer remains controversial, outcomes with neoadjuvant chemoradiation versus chemotherapy for locally advanced GOJ adenocarcinoma were compared retrospectively. METHODS Data were collected from all patients who underwent neoadjuvant treatment followed by surgery for adenocarcinoma located at the GOJ at a single high-volume institution between 2002 and 2017. Postoperative major complications and mortality were compared between groups using Fisher's exact test. Overall survival (OS) and disease-free survival (DFS) were assessed by log rank test and multivariable Cox regression analyses. Cumulative incidence functions were used to estimate recurrence, and groups were compared using Gray's test. RESULTS Of 775 patients, 650 had neoadjuvant chemoradiation and 125 had chemotherapy. These groups were comparable in terms of clinical tumour and lymph node categories, although the chemoradiation group had greater proportions of white men, complete pathological response to chemotherapy, and smaller proportions of diffuse cancer, poor differentiation, and neurovascular invasion. Postoperative major complications (20.0 versus 17.6 per cent) and 30-day mortality (1.7 versus 1.6 per cent) were not significantly different between the chemoradiation and chemotherapy groups. After adjustment, type of therapy (chemoradiation versus chemotherapy) was not significantly associated with OS (hazard ratio (HR) 1.26, 95 per cent c.i. 0.96 to 1.67) or DFS (HR 1.27, 0.98 to 1.64). Type of recurrence (local, regional, or distant) did not differ after neoadjuvant chemoradiation versus chemotherapy. CONCLUSION In patients undergoing surgical resection for locally advanced adenocarcinoma of the GOJ, OS and DFS did not differ significantly between patients who had neoadjuvant chemoradiation compared with chemotherapy.
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Kirk R, Ratcliffe A, Noonan G, Uosis-Martin M, Lyth D, Bardell-Cox O, Massam J, Schofield P, Hindley S, Jones DR, Maclean J, Smith A, Savage V, Mohmed S, Charrier C, Salisbury AM, Moyo E, Metzger R, Chalam-Judge N, Cheung J, Stokes NR, Best S, Craighead M, Armer R, Huxley A. Rational design, synthesis and testing of novel tricyclic topoisomerase inhibitors for the treatment of bacterial infections part 1. RSC Med Chem 2020; 11:1366-1378. [PMID: 34095844 DOI: 10.1039/d0md00174k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
The alarming reduction in drug effectiveness against bacterial infections has created an urgent need for the development of new antibacterial agents that circumvent bacterial resistance mechanisms. We report here a series of DNA gyrase and topoisomerase IV inhibitors that demonstrate potent activity against a range of Gram-positive and selected Gram-negative organisms, including clinically-relevant and drug-resistant strains. In part 1, we present a detailed structure activity relationship (SAR) analysis that led to the discovery of our previously disclosed compound, REDX05931, which has a minimum inhibitory concentration (MIC) of 0.06 μg mL-1 against fluoroquinolone-resistant Staphylococcus aureus. Although in vitro hERG and CYP inhibition precluded further development, it validates a rational design approach to address this urgent unmet medical need and provides a scaffold for further optimisation, which is presented in part 2.
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Fincher JA, Korte AR, Dyer JE, Yadavilli S, Morris NJ, Jones DR, Shanmugam VK, Pirlo RK, Vertes A. Mass spectrometry imaging of triglycerides in biological tissues by laser desorption ionization from silicon nanopost arrays. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4443. [PMID: 31524963 DOI: 10.1002/jms.4443] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/31/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Mass spectrometry imaging (MSI) is used increasingly to simultaneously detect a broad range of biomolecules while mapping their spatial distributions within biological tissue sections. Matrix-assisted laser desorption ionization (MALDI) is recognized as the method-of-choice for MSI applications due in part to its broad molecular coverage. In spite of the remarkable advantages offered by MALDI, imaging of neutral lipids, such as triglycerides (TGs), from tissue has remained a significant challenge due to ion suppression of TGs by phospholipids, e.g. phosphatidylcholines (PCs). To help overcome this limitation, silicon nanopost array (NAPA) substrates were introduced to selectively ionize TGs from biological tissue sections. This matrix-free laser desorption ionization (LDI) platform was previously shown to provide enhanced ionization of certain lipid classes, such as hexosylceramides (HexCers) and phosphatidylethanolamines (PEs) from mouse brain tissue. In this work, we present NAPA as an MSI platform offering enhanced ionization efficiency for TGs from biological tissues relative to MALDI, allowing it to serve as a complement to MALDI-MSI. Analysis of a standard lipid mixture containing PC(18:1/18:1) and TG(16:0/16:0/16:0) by LDI from NAPA provided an ~49 and ~227-fold higher signal for TG(16:0/16:0/16:0) relative to MALDI, when analyzed without and with the addition of a sodium acetate, respectively. In contrast, MALDI provided an ~757 and ~295-fold higher signal for PC(18:1/18:1) compared with NAPA, without and with additional Na+ . Averaged signal intensities for TGs from MSI of mouse lung and human skin tissues exhibited an ~105 and ~49-fold increase, respectively, with LDI from NAPA compared with MALDI. With respect to PCs, MALDI provided an ~2 and ~19-fold increase in signal intensity for mouse lung and human skin tissues, respectively, when compared with NAPA. The complementary coverage obtained by the two platforms demonstrates the utility of using both techniques to maximize the information obtained from lipid MS or MSI experiments.
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Cottrell TR, Thompson ED, Forde PM, Stein JE, Duffield AS, Anagnostou V, Rekhtman N, Anders RA, Cuda JD, Illei PB, Gabrielson E, Askin FB, Niknafs N, Smith KN, Velez MJ, Sauter JL, Isbell JM, Jones DR, Battafarano RJ, Yang SC, Danilova L, Wolchok JD, Topalian SL, Velculescu VE, Pardoll DM, Brahmer JR, Hellmann MD, Chaft JE, Cimino-Mathews A, Taube JM. Pathologic features of response to neoadjuvant anti-PD-1 in resected non-small-cell lung carcinoma: a proposal for quantitative immune-related pathologic response criteria (irPRC). Ann Oncol 2019; 29:1853-1860. [PMID: 29982279 DOI: 10.1093/annonc/mdy218] [Citation(s) in RCA: 348] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Neoadjuvant anti-PD-1 may improve outcomes for patients with resectable NSCLC and provides a critical window for examining pathologic features associated with response. Resections showing major pathologic response to neoadjuvant therapy, defined as ≤10% residual viable tumor (RVT), may predict improved long-term patient outcome. However, %RVT calculations were developed in the context of chemotherapy (%cRVT). An immune-related %RVT (%irRVT) has yet to be developed. Patients and methods The first trial of neoadjuvant anti-PD-1 (nivolumab, NCT02259621) was just reported. We analyzed hematoxylin and eosin-stained slides from the post-treatment resection specimens of the 20 patients with non-small-cell lung carcinoma who underwent definitive surgery. Pretreatment tumor biopsies and preresection radiographic 'tumor' measurements were also assessed. Results We found that the regression bed (the area of immune-mediated tumor clearance) accounts for the previously noted discrepancy between CT imaging and pathologic assessment of residual tumor. The regression bed is characterized by (i) immune activation-dense tumor infiltrating lymphocytes with macrophages and tertiary lymphoid structures; (ii) massive tumor cell death-cholesterol clefts; and (iii) tissue repair-neovascularization and proliferative fibrosis (each feature enriched in major pathologic responders versus nonresponders, P < 0.05). This distinct constellation of histologic findings was not identified in any pretreatment specimens. Histopathologic features of the regression bed were used to develop 'Immune-Related Pathologic Response Criteria' (irPRC), and these criteria were shown to be reproducible amongst pathologists. Specifically, %irRVT had improved interobserver consistency compared with %cRVT [median per-case %RVT variability 5% (0%-29%) versus 10% (0%-58%), P = 0.007] and a twofold decrease in median standard deviation across pathologists within a sample (4.6 versus 2.2, P = 0.002). Conclusions irPRC may be used to standardize pathologic assessment of immunotherapeutic efficacy. Long-term follow-up is needed to determine irPRC reliability as a surrogate for recurrence-free and overall survival.
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Weimer SL, Robison CI, Tempelman RJ, Jones DR, Karcher DM. Laying hen production and welfare in enriched colony cages at different stocking densities. Poult Sci 2019; 98:3578-3586. [PMID: 30938804 DOI: 10.3382/ps/pez107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/22/2019] [Indexed: 11/20/2022] Open
Abstract
Many laying hen companies in the United States are pledging to move away from intensive conventional cages to extensive housing systems. Enriched colony cages (ECC) are a practical alternative to conventional cage systems. Scientific research is limited on the effects of ECC on hen production and welfare. Therefore, the objective of this study was to evaluate the effects of stocking density on welfare and performance with the overall outcome to provide guidance on stocking density for ECC. At 16 wk, W-36 pullets were placed into 2 commercial ECC housing systems. Within each ECC enclosure, hens were allocated into 1 of 6 stocking densities: A) 465 to 484 cm2/bird, B) 581 to 606 cm2/bird, C) 652 to 677 cm2/bird, D) 754 to 780 cm2/bird, E) 799 to 832 cm2/bird, and F) 923 to 955 cm2/bird. Body weight, egg production, mortality, and Welfare Quality data were collected each 28 d period from 17 to 68 wk. The 6 ECC stocking densities had several transient effects on production measures within age periods with no difference in hen-day production (P > 0.05). Body weight was affected by stocking density (P < 0.05) where hens raised at stocking density A (465 to 484 cm2/bird) weighed at least 25 g less than hens from other stocking densities. Stocking density differences for Welfare Quality assessments were only apparent for feather coverage. Hens raised at stocking density A (465 to 484 cm2) consistently had the poorest (P < 0.05) crop, keel, belly, back, and rump feather coverage. The keel, neck, and back body regions had poorer feather coverage when hens were raised at stocking densities B (581 to 606 cm2) and C (652 to 677 cm2) compared to hens from lower stocking densities (P < 0.05). Therefore, the minimum area per hen housed in commercial ECC systems should be 754 cm2 per bird for greater feather coverage.
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Nobel TB, Lavery JA, Barbetta A, Gennarelli RL, Lidor AO, Jones DR, Molena D. National guidelines may reduce socioeconomic disparities in treatment selection for esophageal cancer. Dis Esophagus 2019; 32:doy111. [PMID: 30496376 PMCID: PMC6514299 DOI: 10.1093/dote/doy111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The 2011 National Comprehensive Cancer Network guidelines first incorporated the results of the landmark CROSS trial, establishing induction therapy (chemotherapy ± radiation) and surgery as the treatment standard for locoregional esophageal cancer in the United States. The effect of guideline publication on socioeconomic status (SES) inequalities in cancer treatment selection remains unknown. Patients diagnosed with Stage II/III esophageal cancer between 2004 and 2013 who underwent curative treatment with definitive chemoradiation or multimodality treatment (induction and surgery) were identified from the Surveillance, Epidemiology and End Results (SEER)-Medicare registry. Clinicopathologic characteristics were compared between the two therapies. Multivariable regression analysis was used to adjust for known factors associated with treatment selection. An interaction term with respect to guideline publication and SES was included Of the 2,148 patients included, 1,478 (68.8%) received definitive chemoradiation and 670 (31.2%) induction and surgery. Guideline publication was associated with a 16.1% increase in patients receiving induction and surgery in the low SES group (21.4% preguideline publication vs. 37.5% after). In comparison, a 4.5% increase occurred during the same period in the high SES status group (31.8% vs. 36.3%). After adjusting for factors associated with treatment selection, guideline publication was associated with a 78% increase in likelihood of receiving induction and surgery among lower SES patients (odds ratio 1.78; 95% confidence interval (CI): 1.05,3.03). Following the new guideline publication, patients living in low SES areas were more likely to receive optimal treatment. Increased dissemination of guidelines may lead to increased adherence to evidence-based treatment standards.
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Regmi P, Robison CI, Jones DR, Gast RK, Tempelman RJ, Karcher DM. Effects of different litter substrates and induced molt on production performance and welfare quality parameters of white Leghorn hens housed in multi-tiered aviary system. Poult Sci 2018; 97:3397-3404. [PMID: 29878244 DOI: 10.3382/ps/pey211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/27/2018] [Indexed: 11/20/2022] Open
Abstract
More than 90% of the commercial egg production in the United States is pledged to be in cage-free systems by 2025. Management practices like induced molting and litter area management have come under scrutiny because of the housing system change. The aim of this study was to determine the welfare and production implications of different litter substrates and also evaluate induced molting of hens in a cage-free system. Bovan White hens were housed in a multi-tier aviary system with daily access to open litter area of either Astroturf (AT), wood shavings (SH), or straw (ST) and bare concrete floor (CO) serving as control. At 68 wk of age, molt was induced in half of the hens whereas the other half continued without molting to 116 wk. Production and welfare parameters were measured periodically throughout first and second cycles. Litter substrate did not influence hen-day production and case-weight measurements. However, CO had the lowest total number of eggs produced during the first cycle (P < 0.05). Hen-day percentage was approximately 14% greater in molted hens during the second cycle with egg case weight being heavier in non-molt hens toward the end of second cycle (P < 0.05). The only welfare parameter influenced by litter substrate during the first cycle was a greater crop feather loss in AT than ST at mid-lay (P < 0.05). Keel deformations increased with age irrespective of the litter substrate with 91.5% of palpated hens having keel deformations at the end of first cycle (P < 0.05). Molting did not influence the keel palpation and footpad scores whereas frequency of moderate comb wound was greater in molt hens during molt (P < 0.05). Severe feather loss was seen in non-molt hens during the second cycle (P < 0.05). Litter substrate does not affect production and physical parameters of welfare of hens in a multi-tier aviary system. Additionally, induced molting can be successfully carried out in the multi-tier cage-free system.
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El Bakbachi O, Antoniou GA, McWilliams RG, Jones DR. Bilateral peroneal artery aneurysms. Ann R Coll Surg Engl 2017; 99:e119-e122. [PMID: 28349751 DOI: 10.1308/rcsann.2017.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
True aneurysm of the tibial arteries is a rare clinical condition. We report the case of a 67-year-old man who presented with a gradual onset of right calf swelling and pain. Imaging revealed large aneurysms arising from the proximal peroneal arteries bilaterally, measuring 7.4cm and 4cm on the right and left respectively. A detailed medical history, clinical examination and laboratory investigations did not identify evidence of an underlying cause. A surgical reconstruction with an interposition vein graft was successfully performed. To our knowledge, this is the first reported case of primary aneurysm of the peroneal artery in the English literature. We undertook a systematic literature review to identify all reported cases of primary aneurysms of the tibial arteries. The clinical presentation, modes of investigation and interventional treatments are discussed.
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Jones DR, Guard J, Gast RK, Buhr RJ, Fedorka-Cray PJ, Abdo Z, Plumblee JR, Bourassa DV, Cox NA, Rigsby LL, Robison CI, Regmi P, Karcher DM. Influence of commercial laying hen housing systems on the incidence and identification of Salmonella and Campylobacter. Poult Sci 2016; 95:1116-24. [PMID: 26976901 PMCID: PMC4876611 DOI: 10.3382/ps/pew036] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/05/2016] [Indexed: 11/30/2022] Open
Abstract
The housing of laying hens is important for social, industrial, and regulatory aspects. Many studies have compared hen housing systems on the research farm, but few have fully examined commercial housing systems and management strategies. The current study compared hens housed in commercial cage-free aviary, conventional cage, and enriched colony cage systems. Environmental and eggshell pool samples were collected from selected cages/segments of the housing systems throughout the production cycle and monitored for Salmonella and Campylobacter prevalence. At 77 wk of age, 120 hens per housing system were examined for Salmonella and Campylobacter colonization in the: adrenal glands, spleen, ceca, follicles, and upper reproductive tract. All isolates detected from environmental swabs, eggshell pools, and tissues were identified for serotype. Two predominant Salmonella were detected in all samples: S. Braenderup and S. Kentucky. Campylobacter coli and C. jejuni were the only Campylobacter detected in the flocks. Across all housing systems, approximately 7% of hens were colonized with Salmonella, whereas > 90% were colonized with Campylobacter. Salmonella Braenderup was the isolate most frequently detected in environmental swabs (P < 0.0001) and housing system impacted Salmonella spp. shedding (P < 0.0001). Campylobacter jejuni was the isolate most frequently found in environmental swabs (P < 0.01), while housing system impacted the prevalence of C. coli and jejuni in ceca (P < 0.0001). The results of this study provide a greater understanding of the impact of hen housing systems on hen health and product safety. Additionally, producers and academia can utilize the findings to make informed decisions on hen housing and management strategies to enhance hen health and food safety.
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Fulkerson CM, Dhawan D, Jones DR, Marquez VE, Jones PA, Wang Z, Wu Q, Klaunig JE, Fourez LM, Bonney PL, Knapp DW. Pharmacokinetics and toxicity of the novel oral demethylating agent zebularine in laboratory and tumor bearing dogs. Vet Comp Oncol 2015; 15:226-236. [PMID: 26178438 DOI: 10.1111/vco.12159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/07/2015] [Accepted: 05/07/2015] [Indexed: 12/31/2022]
Abstract
The purpose of this study was to determine the plasma pharmacokinetics (PK) and toxicity of zebularine, an oral cytidine analog with demethylating activity, in dogs. Plasma zebularine concentrations were determined by HPLC-MS/MS following an oral zebularine dose of 8 or 4 mg kg-1 . Plasma zebularine clearance was constant. Mean maximum concentration (Cmax ) was 23 ± 4.8 and 8.6 ± 1.4 µM following 8 and 4 mg kg-1 , respectively. Mean half-life was 5.7 ± 0.84 and 7.1 ± 2.1 following 8 and 4 mg kg-1 , respectively. A single 8 mg kg-1 dose was well tolerated. Daily 4 mg kg-1 treatment in three laboratory dogs resulted in grade 4 neutropenia (n = 3), grade 1 anorexia (n = 2) and grade 1 or 2 dermatologic changes (n = 2). All adverse events resolved with supportive care. A 4 mg kg-1 dose every 21 days was well tolerated. A follow-up dose escalation study is in progress with a lower starting dose.
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Karcher DM, Jones DR, Abdo Z, Zhao Y, Shepherd TA, Xin H. Impact of commercial housing systems and nutrient and energy intake on laying hen performance and egg quality parameters. Poult Sci 2015; 94:485-501. [PMID: 25630672 PMCID: PMC4990894 DOI: 10.3382/ps/peu078] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/23/2014] [Accepted: 10/25/2014] [Indexed: 11/20/2022] Open
Abstract
The US egg industry is exploring alternative housing systems for laying hens. However, limited published research related to cage-free aviary systems and enriched colony cages exists related to production, egg quality, and hen nutrition. The laying hen's nutritional requirements and resulting productivity are well established with the conventional cage system, but diminutive research is available in regards to alternative housing systems. The restrictions exist with limited availability of alternative housing systems in research settings and the considerable expense for increased bird numbers in a replicate due to alternative housing system design. Therefore, the objective of the current study was to evaluate the impact of nutrient and energy intake on production and egg quality parameters from laying hens housed at a commercial facility. Lohmann LSL laying hens were housed in three systems: enriched colony cage, cage-free aviary, and conventional cage at a single commercial facility. Daily production records were collected along with dietary changes during 15 production periods (28-d each). Eggs were analyzed for shell strength, shell thickness, Haugh unit, vitelline membrane properties, and egg solids each period. An analysis of covariance (ANCOVA) coupled with a principal components analysis (PCA) approach was utilized to assess the impact of nutritional changes on production parameters and monitored egg quality factors. The traits of hen-day production and mortality had a response only in the PCA 2 direction. This finds that as house temperature and Met intake increases, there is an inflection point at which hen-day egg production is negatively effected. Dietary changes more directly influenced shell parameters, vitelline membrane parameters, and egg total solids as opposed to laying hen housing system. Therefore, further research needs to be conducted in controlled research settings on laying hen nutrient and energy intake in the alternative housing systems and resulting impact on egg quality measures.
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Jones DR, Marchant RE, von Recum H, Sen Gupta A, Kottke-Marchant K. Photoinitiator-free synthesis of endothelial cell-adhesive and enzymatically degradable hydrogels. Acta Biomater 2015; 13:52-60. [PMID: 25462848 PMCID: PMC4416228 DOI: 10.1016/j.actbio.2014.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/07/2014] [Accepted: 11/05/2014] [Indexed: 12/13/2022]
Abstract
We report on a photoinitiator-free synthetic method of incorporating bioactivity into poly(ethylene glycol) (PEG) hydrogels in order to control physical properties, enzymatic biodegradability and cell-specific adhesiveness of the polymer network, while eliminating the need for UV-mediated photopolymerization. To accomplish this, hydrogel networks were polymerized using Michael addition with four-arm PEG acrylate (10 kDa), using a collagenase-sensitive peptide (CSP) as a crosslinker, and introducing an endothelial cell-adhesive peptide either terminally (RGD) or attached to the crosslinking peptide sequence (CSP-RGD). The efficiency of the Michael addition reactions were determined by nuclear magnetic resonance and Ellman's assay. Successful decoupling of cell adhesivity and physical properties was demonstrated by quantifying and comparing the swelling ratios and Young's moduli of various hydrogel formulations. Degradation profiles were established by incubating functionalized hydrogels in collagenase solutions (0.0-1.0 μg ml(-1)), demonstrating that functionalized hydrogels degraded at a rate dependent upon collagenase concentration. Moreover, it was shown that the degradation rate was independent of CSP-RGD concentration. Cell attachment and proliferation on functionalized hydrogels were compared for various RGD concentrations, providing evidence that cell attachment and proliferation were directly related to relative amounts of the CSP-RGD combination peptide. An increase in cell viability was achieved using Michael addition techniques when compared to UV polymerization, and was assessed by a LIVE/DEAD fluorescence assay. This photoinitiator-free method shows promise in creating hydrogel-based tissue engineering scaffolds allow for decoupled cell adhesivity and physical properties and that render greater cell viability.
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Jones DR. Measuring midkine: the utility of midkine as a biomarker in cancer and other diseases. Br J Pharmacol 2015; 171:2925-39. [PMID: 24460734 DOI: 10.1111/bph.12601] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/15/2013] [Accepted: 01/17/2014] [Indexed: 01/05/2023] Open
Abstract
Midkine (MK) is a pleiotropic growth factor prominently expressed during embryogenesis but down-regulated to neglible levels in healthy adults. Many published studies have demonstrated striking MK overexpression compared with healthy controls in various pathologies, including ischaemia, inflammation, autoimmunity and, most notably, in many cancers. MK expression is detectable in biopsies of diseased, but not healthy, tissues. Significantly, because it is a soluble cytokine, elevated MK is readily apparent in the blood and other body fluids such as urine and CSF, making MK a relatively convenient, accessible, non-invasive and inexpensive biomarker for population screening and early disease detection. The first diagnostic tests that quantify MK are just now receiving regulatory clearance and entering the clinic. This review examines the current state of knowledge pertaining to MK as a biomarker and highlights promising indications and clinical settings where measuring MK could make a difference to patient treatment. I also raise outstanding questions about reported variants of MK as well as MK's bio-distribution in vivo. Answering these questions in future studies will enhance our understanding of the significance of measured MK levels in both patients and healthy subjects, and may reveal further opportunities for measuring MK to diagnose disease. MK has already proven to be a biomarker that can significantly improve detection, management and treatment of cancer, and there is significant promise for developing further MK-based diagnostics in the future.
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Jones DR, Cox NA, Guard J, Fedorka-Cray PJ, Buhr RJ, Gast RK, Abdo Z, Rigsby LL, Plumblee JR, Karcher DM, Robison CI, Blatchford RA, Makagon MM. Microbiological impact of three commercial laying hen housing systems. Poult Sci 2014; 94:544-51. [PMID: 25480737 PMCID: PMC4990896 DOI: 10.3382/ps/peu010] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Hen housing for commercial egg production continues to be a societal and regulatory concern. Controlled studies have examined various aspects of egg safety, but a comprehensive assessment of commercial hen housing systems in the US has not been conducted. The current study is part of a holistic, multidisciplinary comparison of the diverse aspects of commercial conventional cage, enriched colony cage, and cage-free aviary housing systems and focuses on environmental and egg microbiology. Environmental swabs and eggshell pools were collected from all housing systems during 4 production periods. Total aerobes and coliforms were enumerated, and the prevalence of Salmonella and Campylobacter spp. was determined. Environmental aerobic and coliform counts were highest for aviary drag swabs (7.5 and 4.0 log cfu/mL, respectively) and enriched colony cage scratch pad swabs (6.8 and 3.8 log cfu/mL, respectively). Aviary floor and system wire shell pools had the greatest levels of aerobic contamination for all eggshell pools (4.9 and 4.1 log cfu/mL, respectively). Hens from all housing systems were shedding Salmonella spp. (89–100% of manure belt scraper blade swabs). The dry belt litter removal processes for all housing systems appear to affect Campylobacter spp. detection (0–41% of manure belt scraper blade swabs) considering detection of Campylobacter spp. was much higher for other environmental samples. Aviary forage area drag swabs were 100% contaminated with Campylobacter spp., whereas enriched colony cage scratch pads had a 93% positive rate. There were no differences in pathogen detection in the shell pools from the 3 housing systems. Results indicate egg safety is enhanced when hens in alternative housing systems use nest boxes. Additionally, current outcomes indicate the use of scratch pads in hen housing systems needs to be more thoroughly investigated for effects on hen health and egg safety.
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Jones DR, Bachawala P, Mack J. Incorporation of balls, tubes, and bowls in nanotechnology. Top Curr Chem (Cham) 2014; 348:37-52. [PMID: 24760613 DOI: 10.1007/128_2013_519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The development of nanotechnology has been spearheaded by the development and discovery of new materials. The earliest materials theorized to be used in nanotechnology were fullerenes and nanotubes. Although fullerenes and nanotubes have a rich history in the area of nanotechnology, fullerene fragments, which share some the same properties as fullerenes and nanotubes, show potential in the field of nanotechnology as well. Fullerene fragments were synthesized close to 20 years prior to the discovery of fullerenes; however due to their complex synthesis they remained in relative obscurity in the field of nanotechnology. More recently, improved syntheses of corannulene and other fullerene fragments on an industrial scale have led to their potential in industrial applications. With the mass production of corannulene finally being realized, many new structures and exciting properties are making its way into the chemical literature.
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van Dam RA, Humphrey CL, Harford AJ, Sinclair A, Jones DR, Davies S, Storey AW. Site-specific water quality guidelines: 1. Derivation approaches based on physicochemical, ecotoxicological and ecological data. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:118-130. [PMID: 23846952 DOI: 10.1007/s11356-013-1780-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/26/2013] [Indexed: 06/02/2023]
Abstract
Generic water quality guidelines (WQGs) are developed by countries/regions as broad scale tools to assist with the protection of aquatic ecosystems from the impacts of toxicants. However, since generic WQGs cannot adequately account for the many environmental factors that may affect toxicity at a particular site, site-specific WQGs are often needed, especially for high environmental value ecosystems. The Australian and New Zealand Guidelines for Fresh and Marine Water Quality provide comprehensive guidance on methods for refining or deriving WQGs for site-specific purposes. This paper describes three such methods for deriving site-specific WQGs, namely: (1) using local reference water quality data, (2) using biological effects data from laboratory-based toxicity testing, and (3) using biological effects data from field surveys. Two case studies related to the assessment of impacts arising from mining operations in northern Australia are used to illustrate the application of these methods. Finally, the potential of several emerging methods designed to assess thresholds of ecological change from field data for deriving site-specific WQGs is discussed. Ideally, multiple lines of evidence approaches, integrating both laboratory and field data, are recommended for deriving site-specific WQGs.
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Nangalia J, Massie CE, Baxter EJ, Nice FL, Gundem G, Wedge DC, Avezov E, Li J, Kollmann K, Kent DG, Aziz A, Godfrey AL, Hinton J, Martincorena I, Van Loo P, Jones AV, Guglielmelli P, Tarpey P, Harding HP, Fitzpatrick JD, Goudie CT, Ortmann CA, Loughran SJ, Raine K, Jones DR, Butler AP, Teague JW, O'Meara S, McLaren S, Bianchi M, Silber Y, Dimitropoulou D, Bloxham D, Mudie L, Maddison M, Robinson B, Keohane C, Maclean C, Hill K, Orchard K, Tauro S, Du MQ, Greaves M, Bowen D, Huntly BJP, Harrison CN, Cross NCP, Ron D, Vannucchi AM, Papaemmanuil E, Campbell PJ, Green AR. Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2. N Engl J Med 2013; 369:2391-2405. [PMID: 24325359 PMCID: PMC3966280 DOI: 10.1056/nejmoa1312542] [Citation(s) in RCA: 1376] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Somatic mutations in the Janus kinase 2 gene (JAK2) occur in many myeloproliferative neoplasms, but the molecular pathogenesis of myeloproliferative neoplasms with nonmutated JAK2 is obscure, and the diagnosis of these neoplasms remains a challenge. METHODS We performed exome sequencing of samples obtained from 151 patients with myeloproliferative neoplasms. The mutation status of the gene encoding calreticulin (CALR) was assessed in an additional 1345 hematologic cancers, 1517 other cancers, and 550 controls. We established phylogenetic trees using hematopoietic colonies. We assessed calreticulin subcellular localization using immunofluorescence and flow cytometry. RESULTS Exome sequencing identified 1498 mutations in 151 patients, with medians of 6.5, 6.5, and 13.0 mutations per patient in samples of polycythemia vera, essential thrombocythemia, and myelofibrosis, respectively. Somatic CALR mutations were found in 70 to 84% of samples of myeloproliferative neoplasms with nonmutated JAK2, in 8% of myelodysplasia samples, in occasional samples of other myeloid cancers, and in none of the other cancers. A total of 148 CALR mutations were identified with 19 distinct variants. Mutations were located in exon 9 and generated a +1 base-pair frameshift, which would result in a mutant protein with a novel C-terminal. Mutant calreticulin was observed in the endoplasmic reticulum without increased cell-surface or Golgi accumulation. Patients with myeloproliferative neoplasms carrying CALR mutations presented with higher platelet counts and lower hemoglobin levels than patients with mutated JAK2. Mutation of CALR was detected in hematopoietic stem and progenitor cells. Clonal analyses showed CALR mutations in the earliest phylogenetic node, a finding consistent with its role as an initiating mutation in some patients. CONCLUSIONS Somatic mutations in the endoplasmic reticulum chaperone CALR were found in a majority of patients with myeloproliferative neoplasms with nonmutated JAK2. (Funded by the Kay Kendall Leukaemia Fund and others.).
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Jones DR, Anderson KE, Guard JY. Prevalence of coliforms, Salmonella, Listeria, and Campylobacter associated with eggs and the environment of conventional cage and free-range egg production. Poult Sci 2012; 91:1195-202. [PMID: 22499879 DOI: 10.3382/ps.2011-01795] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is a desire by US consumers for eggs produced by hens in alternative production systems. As the retail shell-egg market offers these products to accommodate consumer demands, additional information is needed to ensure processing methodologies result in safe eggs from all egg sources. A study was conducted to determine if there were differences in the prevalence of coliforms, Salmonella, Listeria, and Campylobacter on and within eggs and in the environment of a sister flock of conventional cage and free-range laying hens. Microbial sampling occurred approximately every 6 wk between 20 and 79 wk of age. A random sampling of typical coliform colonies produced 371 viable isolates for biochemical identification. Twenty-nine genera or species of bacteria were identified. There was a significantly greater (P < 0.0001) prevalence of Campylobacter in the free-range nest box swabs compared with that in the free-range grass and conventional cage swab samples (number of positives: 8 nest box, 1 grass, 0 cage). Seven isolates of Listeria innocua were detected with no significant difference in prevalence between the treatments. Isolates were associated with eggshells (2 free-range floor, 1 cage) and the free-range environment (2 nest box, 2 grass). There were 21 Salmonella isolates detected between all sample locations, with no significant difference in the prevalence of Salmonella detection between the treatments. Additional studies are needed to fully understand the effect of alternative production methods on the prevalence of pathogens and coliforms associated with nest-run eggs and the production environment.
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Zhu J, He P, Lin L, Jones DR, Marchant RE. Biomimetic poly(ethylene glycol)-based hydrogels as scaffolds for inducing endothelial adhesion and capillary-like network formation. Biomacromolecules 2012; 13:706-13. [PMID: 22296572 PMCID: PMC3310151 DOI: 10.1021/bm201596w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The extracellular matrix (ECM) is an attractive model for designing synthetic scaffolds with a desirable environment for tissue engineering. Here, we report on the synthesis of ECM-mimetic poly(ethylene glycol) (PEG) hydrogels for inducing endothelial cell (EC) adhesion and capillary-like network formation. A collagen type I-derived peptide GPQGIAGQ (GIA)-containing PEGDA (GIA-PEGDA) was synthesized with the collagenase-sensitive GIA sequence attached in the middle of the PEGDA chain, which was then copolymerized with RGD capped-PEG monoacrylate (RGD-PEGMA) to form biomimetic hydrogels. The hydrogels degraded in vitro with the rate dependent on the concentration of collagenase and also supported the adhesion of human umbilical vein ECs (HUVECs). Biomimetic RGD/GIA-PEGDA hydrogels with incorporation of 1% RGD-PEGDA into GIA-PEGDA hydrogels induced capillary-like organization when HUVECs were seeded on the hydrogel surface, while RGD/PEGDA and GIA-PEGDA hydrogels did not. These results indicate that both cell adhesion and biodegradability of scaffolds play important roles in the formation of capillary-like networks.
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Anderson KE, Jones DR. Effect of genetic selection on growth parameters and tonic immobility in Leghorn pullets. Poult Sci 2012; 91:765-70. [PMID: 22334754 DOI: 10.3382/ps.2011-01799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four genetic stocks of Leghorn pullets were used to evaluate the effects of genetic selection on growth and fearfulness behavior. Three of the stocks were the Ottawa randombred control stocks from 1950 (CS5), 1959 (CS7), and 1972 (CS10). The fourth stock was a 1993 commercial laying stock (CCS) whose ancestors were involved in the formation of the randombred control stocks. Pullets were reared in a brood and grow poultry house with flat deck cages. Each stock was comprised of 840 birds with 21 replicates per strain. Body weight and feed consumption were monitored biweekly. At 16 wk of age, a 20-hen sample from each strain was analyzed for BW, body composition, and tonic immobility. There were significant (P < 0.05) differences among the stocks for BW of 1,403; 1,333; 1,332; and 1,428 g for the CS5, CS7, CS10, and CCS stocks, respectively. Furthermore, significant differences occurred with regard to feed consumption, livability, and frame size. There were no differences among the stocks in tonic immobility. Measurement of circulating corticosterone levels were shown to be significantly (P < 0.05) higher in the CCS stock (7.64 ng/mL) than for both the CS5 (4.50 ng/mL) and CS7 (4.61 ng/mL) stocks, whereas the CS10 stock was intermediate with 6.45 ng/mL. Genetic selection has affected growth parameters, although there appears to be no change in fearfulness behavior but an increase in corticosterone levels in stocks from later years.
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Wiggins SM, Reijnders MP, Abuazoum S, Hart K, Welsh GH, Issac RC, Jones DR, Jaroszynski DA. Note: femtosecond laser micromachining of straight and linearly tapered capillary discharge waveguides. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:096104. [PMID: 21974631 DOI: 10.1063/1.3640410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Gas-filled capillary discharge waveguides are important structures in laser-plasma interaction applications, such as the laser wakefield accelerator. We present the methodology for applying femtosecond laser micromachining in the production of capillary channels (typically 200-300 μm in diameter and 30-40 mm in length), including the formalism for capillaries with a linearly tapered diameter. The latter is demonstrated to possess a smooth variation in diameter along the length of the capillary (tunable with the micromachining trajectories). This would lead to a longitudinal plasma density gradient in the waveguide that may dramatically improve the laser-plasma interaction efficiency in applications.
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Halsey LG, White CR, Enstipp MR, Wilson RP, Butler PJ, Martin GR, Grémillet D, Jones DR. Assessing the validity of the accelerometry technique for estimating the energy expenditure of diving double-crested cormorants Phalacrocorax auritus. Physiol Biochem Zool 2011; 84:230-7. [PMID: 21460533 DOI: 10.1086/658636] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Over the past few years, acceleration-data loggers have been used to provide calibrated proxies of energy expenditure: the accelerometry technique. Relationships between rate of oxygen consumption and a derivation of acceleration data termed "overall dynamic body acceleration" (ODBA) have now been generated for a range of species, including birds, mammals, and amphibians. In this study, we examine the utility of the accelerometry technique for estimating the energy expended by double-crested cormorants Phalacrocorax auritus to undertake a dive cycle (i.e., a dive and the subsequent pause at the surface before another dive). The results show that ODBA does not calibrate with energy expenditure in diving cormorants, where energy expenditure is calculated from measures of oxygen uptake during surface periods between dives. The possible explanations include reasons why energy expenditure may not relate to ODBA but also reasons why oxygen uptake between dives may not accurately represent energy expenditure during a dive cycle.
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Liu Y, Mayo MW, Nagji AS, Smith PW, Ramsey CS, Li D, Jones DR. Phosphorylation of RelA/p65 promotes DNMT-1 recruitment to chromatin and represses transcription of the tumor metastasis suppressor gene BRMS1. Oncogene 2011; 31:1143-54. [PMID: 21765477 PMCID: PMC3219802 DOI: 10.1038/onc.2011.308] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The majority of patients with lung cancer present with metastatic disease. Chronic inflammation and subsequent activation of NF-κB have been associated the development of cancers. The RelA/p65 subunit of NF-κB is typically associated with transcriptional activation. In this report we show that RelA/p65 can function as an active transcriptional repressor through enhanced methylation of the BRMS1 metastasis suppressor gene promoter via direct recruitment of DNMT-1 to chromatin in response to TNF. TNF-mediated phosphorylation of S276 on RelA/p65 is required for RelA/p65-DNMT-1 interactions, chromatin loading of DNMT-1, and subsequent BRMS1 promoter methylation and transcriptional repression. The ability of RelA/65 to function as an active transcriptional repressor is promoter specific as the NF-κB-regulated gene cIAP2 is transcriptionally activated while BRMS1 is repressed under identical conditions. Small molecule inhibition of either of the minimal interacting domains between RelA/p65-DNMT-1 and RelA/p65-BRMS1 promoter abrogates BRMS1 methylation and its transcriptional repression. The ability of RelA/p65 to directly recruit DNMT-1 to chromatin resulting in promoter-specific methylation and transcriptional repression of tumor metastasis suppressor gene BRMS1 highlights a new mechanism through which NF-κB can regulate metastatic disease, and offers a potential target for newer generation epigenetic oncopharmaceuticals.
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Jones DR, Lawrence KC, Yoon SC, Heitschmidt GW. Salmonella contamination in shell eggs exposed to modified-pressure imaging for microcrack detection. Poult Sci 2011; 90:1616-9. [PMID: 21673180 DOI: 10.3382/ps.2010-01155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcracks in egg shells are a food safety risk and are difficult for professional human graders to detect. Modified-pressure imaging technology with 99.6% accuracy has been developed to detect microcracks. This study was conducted to determine whether the microcrack detection system would increase penetration of Salmonella into egg contents or lead to cross-contamination within the system. Thirty dozen grade A large white retail eggs were used for each of 3 replicates. Cracked eggs were removed and 72 eggs/replicate were dip inoculated in buffered peptone water containing 10(5) cfu/mL of nalidixic acid-resistant Salmonella Typhimurium (ST), whereas 144 eggs were dipped in sterile buffered peptone water. All eggs were incubated overnight at 25°C before imaging. Forty-five eggs of each treatment were imaged in the following order: control, inoculated, control. Imaged and nonimaged eggs from each treatment were used for cultural analysis of a shell rinse, shell emulsion, and contents sample for each egg. The ST levels were monitored on brilliant green sulfa agar with 200 mg/L of nalidixic acid. Egg contents were also enriched to determine the prevalence of ST in low levels. Salmonella Typhimurium was not detected on or in any of the control eggs, including the eggs imaged after the inoculated eggs. The highest level of ST was detected in inoculated shell emulsions (4.79 log cfu/mL). No differences in ST levels were found for any sample location between imaged and nonimaged inoculated eggs. Therefore, the modified-pressure imaging system for microcrack detection did not result in microbial cross-contamination or increase the level of microbial penetration in inoculated eggs. The imaging system can be used to assess eggs for cracks without negative food safety implications.
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Holt PS, Davies RH, Dewulf J, Gast RK, Huwe JK, Jones DR, Waltman D, Willian KR. The impact of different housing systems on egg safety and quality. Poult Sci 2011; 90:251-62. [PMID: 21177467 DOI: 10.3382/ps.2010-00794] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A move from conventional cages to either an enriched cage or a noncage system may affect the safety or quality, or both, of the eggs laid by hens raised in this new environment. The safety of the eggs may be altered either microbiologically through contamination of internal contents with Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) or other pathogens, or both, or chemically due to contamination of internal contents with dioxins, pesticides, or heavy metals. Quality may be affected through changes in the integrity of the shell, yolk, or albumen along with changes in function, composition, or nutrition. Season, hen breed, flock age, and flock disease-vaccination status also interact to affect egg safety and quality and must be taken into account. An understanding of these different effects is prudent before any large-scale move to an alternative housing system is undertaken.
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