Adult heart transplantation under tacrolimus (FK506) immunosuppression: Histopathologic observations and comparison to a cyclosporine-based regimen with lympholytic (ATG) induction

Background: Tacrolimus (FK506) is an effective immunosuppressant for human heart transplantation, but information about its effects on cardiac allograft and nonallograft kidney and liver histopathologic study is limited. Methods: We therefore reviewed 1145 endomyocardial biopsy specimens and eight autopsy results from 80 heart transplant recipients who received tacrolimus as baseline immunosuppression. These were compared with 619 endomyocardial biopsy specimens and four autopsy results from 51 patients treated with cyclosporine-based immunosuppression with lympholytic induction (CLI) by use of rabbit anti-thymocyte globulin. Twenty-one histologic features including the International Society for Heart and Lung Transplantation histopathologic grade were retrospectively assessed without knowledge of the treatment regimen. The lymphocyte growth index on biopsy specimens obtained from these patients was also compared. Results: In general, there were no qualitative differences in the histopathologic appearance of various allograft syndromes between tacrolimus- and CLI-treated patients. Thus histopathologic criteria used to diagnose various graft syndromes are applicable under tacrolimus immunosuppression. However, early (between 10 and 30 days) after transplantation, biopsy specimens from patients treated with tacrolimus showed a significantly higher percentage of inflamed fragments (p = 0.02), the inflammation tended to be more severe (p = 0.09), and the rejection grade tended to be slightly higher (p = 0.08). In contrast, during the late transplantation period (275 to 548 days), biopsy specimens from patients treated with CLI showed a significantly higher percentage of inflamed fragments (p = 0.03), more severe inflammation (p = 0.03), higher rejection grades (p = 0.01), and a higher frequency of Quilty lesions (p = 0.05). Although overall freedom from any grade 3A or higher rejection was greater in the CLI-treated arm, tacrolimus was successfully used to treat refractory rejection in three patients from the CLI-treated arm. Concern has been raised in the literature about the possibility of tacrolimus being a direct hepatotoxin and an accelerant of allograft obliterative arteriopathy. However, no evidence to support either of these contentions was detected in this patient population. In contrast, tacrolimus is clearly nephrotoxic, although similar to cyclosporine in this regard. Conclusions: Tacrolimus is an effective immunosuppressive drug for heart transplantation. The cardiac allograft histopathologic study of patients treated with tacrolimus immunosuppression does not significantly differ from those given conventional, cyclosporine-based triple therapy with lympholytic induction

Electrochemical synthesis of peroxomonophosphate using boron-doped diamond anodes

A new method for the synthesis of peroxomonophosphate, based on the use of boron-doped diamond electrodes, is described. The amount of oxidant electrogenerated depends on the characteristics of the supporting media (pH and solute concentration) and on the operating conditions (temperature and current density). Results show that the pH, between values of 1 and 5, does not influence either the electrosynthesis of peroxomonophosphate or the chemical stability of the oxidant generated. Conversely, low temperatures are required during the electrosynthesis process to minimize the thermal decomposition of peroxomonophosphate and to guarantee significant oxidant concentration. In addition, a marked influence of both the current density and the initial substrate is observed. This observation can be explained in terms of the contribution of hydroxyl radicals in the oxidation mechanisms that occur on diamond surfaces. In the assays carried out below the water oxidation potential, the generation of hydroxyl radicals did not take place. In these cases, peroxomonophosphate generation occurs through a direct electron transfer and, therefore, at these low current densities lower concentrations are obtained. On the other hand, at higher potentials both direct and hydroxyl radical-mediated mechanisms contribute to the oxidant generation and the process is more efficient. In the same way, the contribution of hydroxyl radicals may also help to explain the significant influence of the substrate concentration. Thus, the coexistence of both phosphate and hydroxyl radicals is required to ensure the generation of significant amounts of peroxomonophosphoric acid

Different Behavior of Enteric Bacteria and Viruses in Clay and Sandy Soils after Biofertilization with Swine Digestate

Enteric pathogens from biofertilizer can accumulate in the soil, subsequently contaminating water and crops. We evaluated the survival, percolation and leaching of model enteric pathogens in clay and sandy soils after biofertilization with swine digestate: PhiX-174, mengovirus (vMC0), Salmonella enterica Typhimurium and Escherichia coli O157:H7 were used as biomarkers. The survival of vMC0 and PhiX-174 in clay soil was significantly lower than in sandy soil (ıPT90 values of 10.520 0.600 vs. 21.270 1.100 and 12.040 0.010 vs. 43.470 1.300, respectively) and PhiX- 174 showed faster percolation and leaching in sandy soil than clay soil (ıPT90 values of 0.46 and 2.43, respectively). S. enterica Typhimurium was percolated and inactivated more slowly than E. coli O157:H7 (ıPT90 values of 9.340 0.200 vs. 6.620 0.500 and 11.900 0.900 vs. 10.750 0.900 in clay and sandy soils, respectively), such that E. coli O157:H7 was transferred more quickly to the deeper layers of both soils evaluated (percolation). Our findings suggest that E. coli O157:H7 may serve as a useful microbial biomarker of depth contamination and leaching in clay and sandy soil and that bacteriophage could be used as an indicator of enteric pathogen persistence. Our study contributes to development of predictive models for enteric pathogen behavior in soils, and for potential water and food contamination associated with biofertilization, useful for risk management and mitigation in swine digestate recycling.RTA2014-00024-C04-01 from the Spanish Ministry of Economy and Innovation and the Brazilian CNPq Project number 472804/2013-8, an dby CAPES/PNPD and CAPES/PDSE

Human activities and biodiversity opportunities in pre-industrial cultural landscapes: relevance to conservation

1. Conservation practices in Europe frequently attempt to perpetuate or mimic the ‘traditional’ forms of management of semi-natural habitats, but with a limited understanding of what these entailed. 2. We review the emerging understanding of ecological processes, structures and management interventions that enhance biodiversity (wildlife) at diverse scales. These are then examined in the context of pre-industrial (c. 1200-1750) land management systems in lowland England, in order to identify historic practices which are likely to have provided important wildlife resources, but which are relatively neglected in current conservation management. 3. Principles enhancing alpha and beta diversity and the conservation status of threatened species, include: structural complexity and heterogeneity at nested spatial scales; physical disturbance and exposure of mineral substrate; nutrient removal; lengthened successional rotations; and spatial variation in grazing regimes. 4. The available evidence suggests that pre-industrial management was generally characterised by: intense resource exploitation and significant levels of biomass harvest; complex nested structural heterogeneity both between and within landscape elements; overlaying of multiple land-uses; and spatial and temporal variability in management, rendering the concept of long-lived ‘traditional’ practice problematic. Grazing patterns are poorly understood but intensive grazing was probably the norm in most contexts, potentially resulting in simplified sward structures and suppressed ecotonal vegetation. 5. In much of the pre-industrial period, early-successional and disturbed microhabitats were widespread but ungrazed or lightly grazed herb-rich vegetation may have been limited, the converse of current conservation management. The key change since then has been homogenisation at multiple scales, coupled with reduction of specific niches and conditions. 6. Synthesis and applications: In adopting perceived ‘traditional’ management practices, modern conservation rarely achieves the range and complexity of conditions that were present in the past. A better understanding of past practices allows more favourable management of those surviving semi-natural habitats where historic assemblages persist – with greater emphasis on physical disturbance and variability in prescriptions both temporally and spatially. When creating or restoring habitats, after interruption of management sufficiently long for dependent assemblages to be lost, better appreciation of historic management encourages novel forms of intervention to enhance biodiversity, with emphasis on complex structural and spatial heterogeneity at nested scales, biomass removal and nutrient reduction. These two distinct but overlapping approaches are complementary to the use of large herbivores to create and maintain dynamic ecotonal mosaics in the manner advocated by some proponents of ‘rewilding’

Estimating the prevalence of food risk increasing behaviours in UK kitchens

© 2017 Jones et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Foodborne disease poses a serious threat to public health. In the UK, half a million cases are linked to known pathogens and more than half of all outbreaks are associated with catering establishments. The UK Food Standards Agency (FSA) has initiated the UK Food Hygiene Rating Scheme in which commercial food establishments are inspected and scored with the results made public. In this study we investigate the prevalence of food risk increasing behaviours among chefs, catering students and the public. Given the incentive for respondents to misreport when asked about illegal or illicit behaviours we employed a Randomised Response Technique designed to elicit more accurate prevalence rates of such behaviours. We found 14% of the public not always hand-washing immediately after handling raw meat, poultry or fish; 32% of chefs and catering students had worked within 48 hours of suffering from diarrhoea or vomiting. 22% of the public admitted having served meat “on the turn” and 33% of chefs and catering students admitted working in kitchens where such meat was served; 12% of the public and 16% of chefs and catering students admitted having served chicken at a barbeque when not totally sure it was fully cooked. Chefs in fine-dining establishment were less likely to wash their hands after handling meat and fish and those who worked in award winning restaurants were more likely to have returned to work within 48 hours of suffering from diarrhoea and vomiting. We found no correlation between the price of a meal in an establishment, nor its Food Hygiene Rating Score, and the likelihood of any of the food malpractices occurring

Ocean currents shape the microbiome of Arctic marine sediments

Prokaryote communities were investigated on the seasonally stratified Alaska Beaufort Shelf (ABS). Water and sediment directly underlying water with origin in the Arctic, Pacific or Atlantic oceans were analyzed by pyrosequencing and length heterogeneity-PCR in conjunction with physicochemical and geographic distance data to determine what features structure ABS microbiomes. Distinct bacterial communities were evident in all water masses. Alphaproteobacteria explained similarity in Arctic surface water and Pacific derived water. Deltaproteobacteria were abundant in Atlantic origin water and drove similarity among samples. Most archaeal sequences in water were related to unclassified marine Euryarchaeota. Sediment communities influenced by Pacific and Atlantic water were distinct from each other and pelagic communities. Firmicutes and Chloroflexi were abundant in sediment, although their distribution varied in Atlantic and Pacific influenced sites. Thermoprotei dominated archaea in Pacific influenced sediments and Methanomicrobia dominated in methane-containing Atlantic influenced sediments. Length heterogeneity-PCR data from this study were analyzed with data from methane-containing sediments in other regions. Pacific influenced ABS sediments clustered with Pacific sites from New Zealand and Chilean coastal margins. Atlantic influenced ABS sediments formed another distinct cluster. Density and salinity were significant structuring features on pelagic communities. Porosity co-varied with benthic community structure across sites and methane did not. This study indicates that the origin of water overlying sediments shapes benthic communities locally and globally and that hydrography exerts greater influence on microbial community structure than the availability of methane

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility. © 2014 Hogg et al

RsmW, Pseudomonas aeruginosa small non-coding RsmA-binding RNA upregulated in biofilm versus planktonic growth conditions

BACKGROUND: Biofilm development, specifically the fundamentally adaptive switch from acute to chronic infection phenotypes, requires global regulators and small non-coding regulatory RNAs (sRNAs). This work utilized RNA-sequencing (RNA-seq) to detect sRNAs differentially expressed in Pseudomonas aeruginosa biofilm versus planktonic state. RESULTS: A computational algorithm was devised to detect and categorize sRNAs into 5 types: intergenic, intragenic, 5′-UTR, 3′-UTR, and antisense. Here we report a novel RsmY/RsmZ-type sRNA, termed RsmW, in P. aeruginosa up-transcribed in biofilm versus planktonic growth. RNA-Seq, 5’-RACE and Mfold predictions suggest RsmW has a secondary structure with 3 of 7 GGA motifs located on outer stem loops. Northern blot revealed two RsmW binding bands of 400 and 120 bases, suggesting RsmW is derived from the 3’-UTR of the upstream hypothetical gene, PA4570. RsmW expression is elevated in late stationary versus logarithmic growth phase in PB minimal media, at higher temperatures (37°C versus 28°C), and in both gacA and rhlR transposon mutants versus wild-type. RsmW specifically binds to RsmA protein in vitro and restores biofilm production and reduces swarming in an rsmY/rsmZ double mutant. PA4570 weakly resembles an RsmA/RsmN homolog having 49% and 51% similarity, and 16% and 17% identity to RsmA and RsmN amino acid sequences, respectively. PA4570 was unable to restore biofilm and swarming phenotypes in ΔrsmA deficient strains. CONCLUSION: Collectively, our study reveals an interesting theme regarding another sRNA regulator of the Rsm system and further unravels the complexities regulating adaptive responses for Pseudomonas species

SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation

Salmonella enterica is a prominent bacterial pathogen with implications on human and animal health. Salmonella serovars could be classified as gastro-intestinal or extra-intestinal. Genome-wide comparisons revealed that extra-intestinal strains are closer relatives of gastro-intestinal strains than to each other indicating a parallel evolution of this trait. Given the complexity of the differences, a systems-level comparison could reveal key mechanisms enabling extra-intestinal serovars to cause systemic infections. Accordingly, in this work, we introduce a unique resource, SalmoNet, which combines manual curation, high-throughput data and computational predictions to provide an integrated network for Salmonella at the metabolic, transcriptional regulatory and protein-protein interaction levels. SalmoNet provides the networks separately for five gastro-intestinal and five extra-intestinal strains. As a multi-layered, multi-strain database containing experimental data, SalmoNet is the first dedicated network resource for Salmonella. It comprehensively contains interactions between proteins encoded in Salmonella pathogenicity islands, as well as regulatory mechanisms of metabolic processes with the option to zoom-in and analyze the interactions at specific loci in more detail. Application of SalmoNet is not limited to strain comparisons as it also provides a Salmonella resource for biochemical network modeling, host-pathogen interaction studies, drug discovery, experimental validation of novel interactions, uncovering new pathological mechanisms from emergent properties and epidemiological studies. SalmoNet is available at http://salmonet.org

Recommendations for the diagnosis of pediatric tuberculosis

Tuberculosis (TB) is still the world's second most frequent cause of death due to infectious diseases after HIV infection, and this has aroused greater interest in identifying and managing exposed subjects, whether they are simply infected or have developed one of the clinical variants of the disease. Unfortunately, not even the latest laboratory techniques are always successful in identifying affected children because they are more likely to have negative cultures and tuberculin skin test results, equivocal chest X-ray findings, and atypical clinical manifestations than adults. Furthermore, they are at greater risk of progressing from infection to active disease, particularly if they are very young. Consequently, pediatricians have to use different diagnostic strategies that specifically address the needs of children. This document describes the recommendations of a group of scientific societies concerning the signs and symptoms suggesting pediatric TB, and the diagnostic approach towards children with suspected disease