Combining spore germination and heat inactivation to decontaminate materials contaminated with Bacillus anthracis spores.

AIMS: To add a spore germination step in order to reduce decontamination temperature and time requirements compared to the current hot, humid air decontamination parameters, which are 75-80°C, ≥72 h, 70-90% RH, down to ≤60°C and ≤24 h total decontamination time. METHODS AND RESULTS: Bacillus anthracis spore germination with l-alanine+inosine+calcium dipicolinate (CaDPA) was quantified at 0-40°C, several time points and spore concentrations of 5-9 log10 per ml. Germination efficiency at 0-40°C was >99% at <8 log10 spores per ml. The temperature optimum was 20°C. Germination efficiency was significantly higher but slower at 0°C compared to ≥30°C at ≥8 log10 spores per ml. A single germinant application followed by 60°C, 1-h treatment consistently inactivated >2 log10 (>99%) of spores. However, a repeat application of germinant was needed to achieve the objective of ≥6 log10 spore inactivation out of a 7 log10 challenge (≥99·9999%) for ≤24 h total decontamination time for nylon and aircraft performance coating. CONCLUSIONS: l-alanine+inosine+CaDPA stimulated germination across wide temperature and spore concentration ranges. SIGNIFICANCE AND IMPACT OF THE STUDY: Germination expands the scope of spore decontamination to include materials from any industry sector that can be sprayed with an aqueous germinant solution.

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.

BACKGROUND: In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa. RESULTS: The first metabolic reconstruction of Ca. MH11-affiliated genome bins, with a particular focus on the provisionally named "Candidatus Paraporphyromonas polyenzymogenes", illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific type IX secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrangements that are unique to Bacteroidetes species studied to date. Core metabolic proteins from Ca. P. polyenzymogenes were detected in metaproteomic data and were enriched in rumen-incubated plant biomass, indicating that active saccharification and fermentation of complex carbohydrates could be assigned to members of this novel family. Biochemical analysis of selected Ca. P. polyenzymogenes CAZymes further iterated the cellulolytic activity of this hitherto uncultured bacterium towards linear polymers, such as amorphous and crystalline cellulose as well as mixed linkage ß-glucans. CONCLUSION: We propose that Ca. P. polyenzymogene genotypes and other Ca. MH11 members actively degrade plant biomass in the rumen of cows, sheep and most likely other ruminants, utilizing singular and multi-domain catalytic CAZymes secreted through the T9SS. The discovery of a prominent role of multi-modular cellulases in the Gram-negative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria (Ruminococcus flavefaciens) and anaerobic fungi (Orpinomyces sp.), suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.

Effect of animal sera on Bacillus anthracis Sterne spore germination and vegetative cell growth.

AIMS: The aims of this work were to investigate the effects of sera on B. anthracis Sterne germination and growth. Sera examined included human, monkey and rabbit sera, as well as sera from eight other species. METHODS AND RESULTS: Standard dilution plate assay (with and without heat kill) was used as a measure of germination, and spectroscopy was used to measure growth. In addition, a Coulter Counter particle counter was used to monitor germination and growth based on bacterial size. Spores germinated best in foetal bovine and monkey sera, moderately with human sera and showed limited germination in the presence of rabbit or rat sera. Vegetative bacteria grew best in foetal bovine sera and moderately in rabbit sera. Human and monkey sera supported little growth of vegetative bacteria. CONCLUSION: The data suggested sera can have a significant impact on germination and growth of Sterne bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: These data should be considered when conducting in vitro cell culture studies and may aid in interpreting in vivo infection studies.

SU-E-T-569: A Dosimetric Comparison of Helical Tomotherapy versus Intensity Modulated Proton for Lung Cancer.

PURPOSE: To evaluate the dosimetric difference between helical tomotherapy (HT) and intensity modulated proton therapy (IMPT) treatment for lung cancer patients. METHODS: Five patients treated by HT at University of Wisconsin Carbone Cancer Center were selected. HT plans were generated on TomoTherapy treatment planning station (TomoTherapy Inc., USA). The field widths were set to 2.5 cm for all patients in this study. The IMPT plans were generated using the same planning CT and contours with our in-house treatment planning system. Three to five field spot scanning IMPT were used to deliver uniform doses to the targets while minimizing the irradiated lung volume. The proton spots used has a Gaussian sigma of 6mm and are placed on a rectangular grid. The dose distribution of each proton spot is calculated using a pencil beam algorithm with tissue heterogeneity corrections. All the dosimetric analyses are performed using normalized total dose. Alpha/beta ratios were set to 3 for normal tissues and 10 for tumors. RESULTS: IMPT plans showed improvement of critical structure avoidance and target dose uniformity for all patients. Reductions in mean lung doses of between 81% to 27% were observed in the IMPT plans relative to the HT. The equivalent uniform dose of the target improved from 49.2 Gy in HT plan to 60.04 Gy in IMPT for patient #2, and equivalent for other cases. The maximum doses to cord were reduced by 20.5 Gy on average using IMPT. In two patient cases, the normal tissue complication probabilities were reduced by 53% and 14% with IMPT. CONCLUSION: IMPT provides improved dose homogeneity on the target and normal structure sparing compared with HT in the treatment of non-small cell carcinoma in lung. Significant reduction of mean lung dose was demonstrated, as well as toxicity to organs at risk adjacent to the target.

Development of a signature probe targeting the 16S-23S rRNA internal transcribed spacer of a ruminal Ruminococcus flavefaciens isolate from reindeer.

The cellulolytic Ruminococcus flavefaciens has previously been introduced into the ruminant rumen to increase microbial degradation of plant cell wall carbohydrates. The functional effect of an introduced bacterium depends on its ability to establish in the digestive tract, and signature probes can be used as a tool to track and quantify introduced strains. The purpose of this current study was to develop an oligonucleotide signature probe targeting the 16S-23S rRNA internal transcribed spacer (ITS) of a putative probiotic cellulolytic isolate (R. flavefaciens strain 8/94-32) from the rumen of reindeer (Rangifer tarandus tarandus). The 16S-23S rRNA gene ITS of three Ruminococcus strains; R. flavefaciens strain 8/94-32, R. flavefaciens FD-1 and Ruminococcus albus Ra-8, was investigated. The ITS region has been reported to vary more between closely related bacteria compared to the widely used 16S rRNA gene, and a high degree of sequence polymorphism was indeed detected between the three Ruminococcus strains studied. Based on observed sequence differences, two oligonucloetide probes, ITSRumi1 and ITSRumi2, targeting the ITS region of the R. flavefaciens isolate 8/94-32 were developed. Probe specificity was evaluated in dot blot hybridisations with R. flavefaciens isolate 8/94-32 and four other Ruminococcus-strains tested. The probe ITSRumi1 gave positive signals for the R. flavefaciens isolate 8/94-32 only, while probe ITSRumi2 gave positive signals for R. flavefaciens isolate 8/94-32 as well as for R. albus Ra-8. The result of hybridisations with the probe ITSRumi1 indicates that the probe is specific for the R. flavefaciens strain 8/94-32 amongst the four Ruminococcus-strains tested, and is promising for further studies using it as a signature probe for tracking this strain when re-introduced to the reindeer rumen.

Preliminary evidence for involvement of the tumour suppressor gene CHD5 in a family with cutaneous melanoma.

BACKGROUND: Cutaneous melanoma is rapidly increasing in incidence worldwide and approximately 5% of melanomas are hereditary. Deletions in chromosome 1p36 have been detected in melanoma but no candidate melanoma tumour suppressor gene has yet been found in this area. Recently, strong evidence has been reported that CHD5 is a tumour suppressor gene in this region. OBJECTIVES: To investigate CHD5 involvement in familial melanoma. METHODS: Peripheral blood DNA from 47 melanoma families who do not carry mutations in any of the three currently recognized melanoma genes, 398 patients with sporadic melanoma and 398 geographically matched nonmelanoma-bearing controls were studied. Linkage investigation, single nucleotide polymorphism (SNP) genotyping and mutation screening studies were carried out on the CHD5 locus. RESULTS: The CHD5 gene was not excluded by linkage analysis in any of the families. On SNP genotyping, the CHD5 rs7513548 SNP was found to be significantly associated with sporadic melanoma (odds ratio 1·53, 95% confidence interval 1·13-2·06). The AG genotype was found in 208 cases and 169 controls (cf. 141 and 175 cases and controls, respectively, for the AA genotype). On CHD5 mutation screening, a total of 50 single-base substitutions were detected. Of these, 39 were intronic and 11 were exonic. While 32 were previously recognized variants, 18 were newly identified. Three, in exons 4, 31 and 32, led to nonsynonymous substitutions. A p.Met1576Ile substitution was identified in a mother and daughter, both with invasive cutaneous melanoma. CONCLUSIONS: This study appears to be the first report of CHD5 variants in familial cutaneous melanoma. Such CHD5 variants could block or alter the ability of CHD5 to regulate the cell cycle pathway and to effect cellular control. As only one of the 47 families studied has this variant, it appears to be a rare event and further screening of melanoma families is required to confirm whether or not CHD5 is involved in melanoma pathogenesis.

Association of MC1R variants and host phenotypes with melanoma risk in CDKN2A mutation carriers: a GenoMEL study.

BACKGROUND: Carrying the cyclin-dependent kinase inhibitor 2A (CDKN2A) germline mutations is associated with a high risk for melanoma. Penetrance of CDKN2A mutations is modified by pigmentation characteristics, nevus phenotypes, and some variants of the melanocortin-1 receptor gene (MC1R), which is known to have a role in the pigmentation process. However, investigation of the associations of both MC1R variants and host phenotypes with melanoma risk has been limited. METHODS: We included 815 CDKN2A mutation carriers (473 affected, and 342 unaffected, with melanoma) from 186 families from 15 centers in Europe, North America, and Australia who participated in the Melanoma Genetics Consortium. In this family-based study, we assessed the associations of the four most frequent MC1R variants (V60L, V92M, R151C, and R160W) and the number of variants (1, ≥2 variants), alone or jointly with the host phenotypes (hair color, propensity to sunburn, and number of nevi), with melanoma risk in CDKN2A mutation carriers. These associations were estimated and tested using generalized estimating equations. All statistical tests were two-sided. RESULTS: Carrying any one of the four most frequent MC1R variants (V60L, V92M, R151C, R160W) in CDKN2A mutation carriers was associated with a statistically significantly increased risk for melanoma across all continents (1.24 × 10(-6) ≤ P ≤ .0007). A consistent pattern of increase in melanoma risk was also associated with increase in number of MC1R variants. The risk of melanoma associated with at least two MC1R variants was 2.6-fold higher than the risk associated with only one variant (odds ratio = 5.83 [95% confidence interval = 3.60 to 9.46] vs 2.25 [95% confidence interval = 1.44 to 3.52]; P(trend) = 1.86 × 10(-8)). The joint analysis of MC1R variants and host phenotypes showed statistically significant associations of melanoma risk, together with MC1R variants (.0001 ≤ P ≤ .04), hair color (.006 ≤ P ≤ .06), and number of nevi (6.9 × 10(-6) ≤ P ≤ .02). CONCLUSION: Results show that MC1R variants, hair color, and number of nevi were jointly associated with melanoma risk in CDKN2A mutation carriers. This joint association may have important consequences for risk assessments in familial settings.

Revised UK guidelines for the management of cutaneous melanoma 2010.

These guidelines for the management of cutaneous melanoma present an evidence-based guidance for treatment, with identification of the strength of evidence available at the time of preparation of the guidelines, and a brief overview of epidemiology, diagnosis, investigation, and follow-up.

Digestive challenges for vertebrate animals: microbial diversity, cardiorespiratory coupling, and dietary specialization.

The digestive system is the interface between the supply of food for an animal and the demand for energy and nutrients to maintain the body, to grow, and to reproduce. Digestive systems are not morphologically static but rather dynamically respond to changes in the physical and chemical characteristics of the diet and the level of food intake. In this article, we discuss three themes that affect the ability of an animal to alter digestive function in relation to novel substrates and changing food supply: (1) the fermentative digestion in herbivores, (2) the integration of cardiopulmonary and digestive functions, and (3) the evolution of dietary specialization. Herbivores consume, digest, and detoxify complex diets by using a wide variety of enzymes expressed by bacteria, predominantly in the phyla Firmicutes and Bacteroidetes. Carnivores, such as snakes that feed intermittently, sometimes process very large meals that require compensatory adjustments in blood flow, acid secretion, and regulation of acid-base homeostasis. Snakes and birds that specialize in simple diets of prey or nectar retain their ability to digest a wider selection of prey. The digestive system continues to be of interest to comparative physiologists because of its plasticity, both phenotypic and evolutionary, and because of its widespread integration with other physiological systems, including thermoregulation, circulation, ventilation, homeostasis, immunity, and reproduction.

Fate and transport of zoonotic, bacterial, viral, and parasitic pathogens during swine manure treatment, storage, and land application.

Members of the public are always somewhat aware of foodborne and other zoonotic pathogens; however, recent illnesses traced to produce and the emergence of pandemic H1N1 influenza virus have increased the scrutiny on all areas of food production. The Council for Agricultural Science and Technology has recently published a comprehensive review of the fate and transport of zoonotic pathogens that can be associated with swine manure. The majority of microbes in swine manure are not zoonotic, but several bacterial, viral, and parasitic pathogens have been detected. Awareness of the potential zoonotic pathogens in swine manure and how treatment, storage, and handling affect their survival and their potential to persist in the environment is critical to ensure that producers and consumers are not at risk. This review discusses the primary zoonotic pathogens associated with swine manure, including bacteria, viruses, and parasites, as well as their fate and transport. Because the ecology of microbes in swine waste is still poorly described, several recommendations for future research are made to better understand and reduce human health risks. These recommendations include examination of environmental and ecological conditions that contribute to off-farm transport and development of quantitative risk assessments.

Identification of A- and B-site cation vacancy defects in perovskite oxide thin films.

Cation vacancies on both sublattices (V(Ti), V(Sr)) have been identified in homoepitaxial pulsed laser deposited SrTiO3 films using high intensity variable energy positron annihilation lifetime spectroscopy (PALS) measurements. Film nonstoichiometry was varied by varying laser fluence. PALS showed that on increasing the fluence above the Ti/Sr∼1 value, the concentration ratio [V(Sr)]/[V(Ti)] systematically increased. Reducing the fluence into the Ti-poor region below resulted in additional vacancy cluster defect formation. Vacancy concentrations greater than ∼50 ppm were observed in all films.

Epidemiology of invasive cutaneous melanoma.

Data are presented on the current incidence of melanoma with recent and predicted future trends illustrating a likely continuing increase in incidence. Risk factors for developing melanoma are discussed, including current known melanoma susceptibility genes. Phenotypic markers of high-risk subjects include high counts of benign melanocytic naevi. Other risk factors considered include exposure to natural and artificial ultraviolet radiation, the effect of female sex hormones, socioeconomic status, occupation, exposure to pesticides and ingestion of therapeutic drugs including immunosuppressives and non-steroidal anti-inflammatory drugs. Aids to earlier diagnosis are considered, including public education, screening and use of equipment such as the dermatoscope. Finally, the current pattern of survival and mortality is described.

Utility of adjuvant systemic therapy in melanoma.

The lack of effective drugs in stage IV melanoma has impacted the effectiveness of adjuvant therapies in stage II/III disease. To date, chemotherapy, immunostimulants and vaccines have been used with minimal success. Interferon (IFN) has shown an effect on relapse-free survival (RFS) in several clinical trials; however, without a clinically significant effect on overall survival (OS). A recently conducted meta-analysis demonstrated prolongation of disease-free survival (DFS) in 7% and OS benefit in 3% of IFN-treated patients when compared with observation-only patients. There were no clear differences for the dose and duration of treatment observed. Observation is still an appropriate control arm in adjuvant clinical trials. Regional differences exist in Europe in the adjuvant use of IFN. In Northwest Europe, IFN is infrequently prescribed. In Central and Mediterranean Europe, dermatologists commonly prescribe low-dose IFN therapy for AJCC stage II and III disease. High-dose IFN regimens are not commonly used. The population of patients that may benefit from IFN needs to be further characterised, potentially by finding biomarkers that can predict response. Such studies are ongoing.

An evidence base for reconsidering current follow-up guidelines for patients with cutaneous melanoma less than 0.5 mm thick at diagnosis.

BACKGROUND: Despite current guidelines, there is uncertainty about the required duration and frequency of follow-up visits for patients with invasive primary cutaneous melanoma < 0.5 mm thick. OBJECTIVES: To review patients with invasive melanoma thinner than 0.5 mm followed for at least 5 years to provide an evidence base for considering modification of guidelines. METHODS: A retrospective review of 430 patients diagnosed in the west of Scotland during 1992-2001 with melanoma < 0.5 mm was carried out. Recurrence, deaths from melanoma and second primary melanomas were all identified. RESULTS: From 1992 to 2001, 430 melanomas < 0.5 mm thick at diagnosis were diagnosed out of a total of 3036 primary cutaneous melanomas. To date there have been 593 deaths from melanoma (19%) in the whole group. Five of these deaths were reported in patients with melanomas < 0.5 mm, but on pathological review two were thicker than 0.5 mm at diagnosis (1.5 and > 3 mm), and the remaining three patients all developed thicker second primary melanomas (2.7, 12.0 and 19.0 mm) with a recurrence pattern and timing indicating that these thicker primaries were the cause of death. Fourteen further patients developed a second primary melanoma, and 13 are currently alive and disease free, one dying of other causes. CONCLUSIONS: Our data indicate that recurrence and subsequent death from melanomas < 0.5 mm is a very rare event, and that quarterly follow-up for 3 years will yield very few events. Modification of current guideline recommendations are suggested to include a period of patient education concentrating on recognition of second primary tumours followed by rapid access to an expert opinion if required.

Coccidia-induced mucogenesis promotes the onset of necrotic enteritis by supporting Clostridium perfringens growth.

This study tested the hypothesis that a host mucogenic response to an intestinal coccidial infection promotes the onset of necrotic enteritis (NE). A chick NE model was used in which birds were inoculated with Eimeria acervulina and E. maxima and subsequently with Clostridium perfringens (EAM/CP). A second group of EAM/CP-infected birds was treated with the ionophore narasin (NAR/EAM/CP). These groups were compared to birds that were either non-infected (NIF), or infected only with E. acervulina and E. maxima (EAM), or C. perfringens (CP). The impact of intestinal coccidial infection and anti-coccidial treatment on host immune responses and microbial community structure were evaluated with histochemical-, cultivation- and molecular-based techniques. Barrier function was compromised in EAM/CP-infected birds as indicated by elevated CFUs for anaerobic bacteria and C. perfringens in the spleen when compared to NIF controls at day 20, with a subsequent increase in intestinal NE lesions and mortality at day 22. These results correlate positively with a host inflammatory response as evidenced by increased ileal interleukin (IL)-4, IL-10 and IFN-gamma RNA expression. Concurrent increases in chicken intestinal mucin RNA expression, and goblet cell number and theca size indicate that EAM/CP induced an intestinal mucogenic response. Correspondingly, the growth of mucolytic bacteria and C. perfringens as well as alpha toxin production was greatest in EAM/CP-infected birds. The ionophore narasin, which directly eliminates coccidia, reduced goblet cell theca size, IL-10 and IFN-gamma expression, the growth of mucolytic bacteria including C. perfringens, coccidial and NE lesions and mortality in birds that were co-infected with coccidia and C. perfringens. Collectively the data support the hypothesis that coccidial infection induces a host mucogenic response providing a growth advantage to C. perfringens, the causative agent of NE.

Effect of insertional mutations in the pueA and pueB genes encoding two polyurethanases in Pseudomonas chlororaphis contained within a gene cluster.

AIMS: To better understand the role of PueA and PueB from Pseudomonas chlororaphis in polyurethane degradation, the present study was conducted to create insertional mutants in their respective genes. METHODS AND RESULTS: Growth kinetic studies showed that the pueA knockout mutant had a greater effect than the pueB knockout mutant. The pueA mutant had an 80% decrease in cell density from that of the wild type, while the pueB mutant had an 18% decrease in cell density. Polyurethane utilization followed Michaelis-Menten kinetics. The pueA and pueB mutants exhibited a 17% and 10% decrease respectively in growth rate using polyurethane when compared with the wild type. CONCLUSIONS: In this present study, pueA and pueB, are shown to be part of an ABC transporter gene cluster that consists of seven open reading frames. Mutational analysis results suggest that PueA may play a more major role in polyurethane degradation than PueB based on cell density and growth rates. SIGNIFICANCE AND IMPACT OF THE STUDY: The results from this study provide a starting point for the eventual enhancement and bioremediation of polyurethane waste. Understanding the role of polyurethane-degrading enzymes is useful for the creation of strains for this purpose.

A visual skills inventory for children with neurological impairments.

Children with neurological impairments often have visual deficits that are difficult to quantify. We have compared visual skills evaluated by carers with results of a comprehensive visual assessment. Participants were 76 children with mild to profound intellectual and/or motor impairment (33 males, 43 females; age range 7mo-16y; mean age 5y 1mo [SD 4y 2mo]) who completed a visual skills inventory before attending a special vision clinic. The inventory included 16 questions about visual skills and responses to familiar situations. Responses were augmented by taking a structured clinical history, compared with visual evoked potential (VEP) and/or acuity card measures of visual acuity, and examined using exploratory factor analysis. Acuity ranged from normal to no light perception, and was positively associated with responses to individual questions. After excluding four uninformative questions, an association between the remaining questions and two significant independent factors was found. Factor 1 was associated with questions about visual recognition (e.g. 'Does your child see a small silent toy?') and these items were correlated with both the VEP and acuity card thresholds. Factor 2 was associated primarily with questions about visually mediated social interactions (e.g. 'Does he/she return your silent smile?'). Evaluation of visual skills in children with neurological impairment can provide valid information about the quality of children's vision. Questions with the highest validity for predicting vision are identified.