Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios

Background

The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.

Methods

Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers.

Results

Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism.

Conclusion

We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.

Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth's climate warms depends in part on the persistence of soil organic carbon. Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability. Despite this, the links between microbial diversity, chemical complexity and biogeochemical nature of SOM remain missing. Here we tested the hypotheses that distinct microbial communities shape the composition of SOM, and microbial-derived SOM has distinct decomposition potential depending on its community of origin. We inoculated microbial communities of varying diversities into a model soil matrix amended with simple carbon (cellobiose) and measured the thermal stability of the resultant SOM. Using a Rock-Eval® ramped thermal analysis, we found that microbial community composition drives the chemical fingerprint of soil carbon. While diversity was not a driver of SOM composition, bacteria-only communities lead to more thermally labile soil C pools than communities with bacteria and fungi. Our results provide direct evidence for a link between microbial community structure, SOM composition, and thermal stability. This evidence demonstrates the relevance of soil microorganisms in building persistent SOM stocks.

Time-course analysis of metabolomic and microbial responses in anaerobic digesters exposed to ammonia

Omics longitudinal studies are effective experimental designs to inform on the stability and dynamics of microbial communities in response to perturbations, but time-course analytical frameworks are required to fully exploit the temporal information acquired in this context. In this study we investigate the influence of ammonia on the stability of anaerobic digestion (AD) microbiome with a new statistical framework. Ammonia can severely reduce AD performance. Understanding how it affects microbial communities development and the degradation progress is a key operational issue to propose more stable processes. Thirty batch digesters were set-up with different levels of ammonia. Microbial community structure and metabolomic profiles were monitored with 16 S-metabarcoding and GCMS (gas-chromatography-mass-spectrometry). Digesters were first grouped according to similar degradation performances. Within each group, time profiles of OTUs and metabolites were modelled, then clustered into similar time trajectories, evidencing for example a syntrophic interaction between Syntrophomonas and Methanoculleus that was maintained up to 387 mg FAN/L. Metabolites resulting from organic matter fermentation, such as dehydroabietic or phytanic acid, decreased with increasing ammonia levels. Our analytical framework enabled to fully account for time variability and integrate this parameter in data analysis.

Application of a path-modelling approach for deciphering causality relationships between microbiota, volatile organic compounds and off-odour profiles during meat spoilage

Microbiological spoilage of meat is considered as a process which involves mainly bacterial metabolism leading to degradation of meat sensory qualities. Studying spoilage requires the collection of different types of experimental data encompassing microbiological, physicochemical and sensorial measurements. Within this framework, the objective herein was to carry out a multiblock path modelling workflow to decipher causality relationships between different types of spoilage-related responses: composition of microbiota, volatilome and off-odour profiles. Analyses were performed with the Path-ComDim approach on a large-scale dataset collected on fresh turkey sausages. This approach enabled to quantify the importance of causality relationships determined a priori between each type of responses as well as to identify important responses involved in spoilage, then to validate causality assumptions. Results were very promising: the data integration confirmed and quantified the causality between data blocks, exhibiting the dynamical nature of spoilage, mainly characterized by the evolution of off-odour profiles caused by the production of volatile organic compounds such as ethanol or ethyl acetate. This production was possibly associated with several bacterial species like Lactococcus piscium, Leuconostoc gelidum, Psychrobacter sp. or Latilactobacillus fuchuensis. Likewise, the production of acetoin and diacetyl in meat spoilage was highlighted. The Path-ComDim approach illustrated here with meat spoilage can be applied to other large-scale and heterogeneous datasets associated with pathway scenarios and represents a promising key tool for deciphering causality in complex biological phenomena.

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol

Anaerobic digestion (AD) is a process that can efficiently degrade organic waste into renewable energies. AD failure is however common as the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds. Sequencing technologies enable the identification of microbial indicators of digesters inhibition, but existing studies are limited. They used different inocula, substrates, sites and types of reactors and reported different or contradictory indicators. Our aim was to identify a robust signature of microbial indicators of phenol and ammonia inhibitions across four independent AD microbial studies. To identify such signature, we applied an original multivariate integrative method on two in-house studies, then validated our approach by predicting the inhibitory status of samples from two other studies with more than 90% accuracy. Our approach shows how we can efficiently leverage on existing studies to extract reproducible microbial community patterns and predict AD inhibition to improve AD microbial management.

Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere

Data in this article provide detailed information on the diversity of bacterial communities present on 576 samples of raw pork or poultry sausages produced industrially in 2017. Bacterial growth dynamics and diversity were monitored throughout the refrigerated storage period to estimate the impact of packaging atmosphere and the use of potassium lactate as chemical preservative. The data include several types of analysis aiming at providing a comprehensive microbial ecology of spoilage during storage and how the process parameters do influence this phenomenon. The analysis includes: the gas content in packaging, pH, chromametric measurements, plate counts (total mesophilic aerobic flora and lactic acid bacteria), sensorial properties of the products, meta-metabolomic quantification of volatile organic compounds and bacterial community metagenetic analysis. Bacterial diversity was monitored using two types of amplicon sequencing (16S rRNA and GyrB encoding genes) at different time points for the different conditions (576 samples for gyrB and 436 samples for 16S rDNA). Sequencing data were generated by using Illumina MiSeq. The sequencing data have been deposited in the bioproject PRJNA522361. Samples accession numbers vary from SAMN10964863 to SAMN10965438 for gyrB amplicon and from SAMN10970131 to SAMN10970566 for 16S.

Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products

Objectives

Sequencing of 16S rDNA V3–V4 region is widely applied for food community profiling. However, two different universal forward primers (named here MUYZER-primer1 and KLINDWORTH-primer2) targeting an identical conservative sequence upstream of the V3 region of 16S rRNA gene, and only distinguished by a single mismatch are both used. This study was carried out to compare whether the accuracy of food microbiota analysis would depend on the choice of one of these two primers.

Results

Alignment of both primers with common food-borne bacteria 16S sequences revealed that the mismatch between both primers might specifically affect the amplification of Leuconostoc, Oenococcus and Fructobacillus species but not Weissella species. Food products containing either Leuconostoc and/or Weissella were selected for a detection test. As expected from our in silico analysis, our study showed that this mismatch induced a strong biased amplification specifically associated to the OTUs belonging to the genus Leuconostoc but not to the genus Weissella. In presence of Muyzer-primer1, none of the sequences expected for Leuconostoc genus was detected whereas those sequences were correctly amplified with Klindworth-primer2. Since Leuconostoc is an important genus in food, agro-environments and in digestive tract of animals, we recommend that Muyzer-primer1 should thus be abandoned for the bacterial characterization of their associated microbiota.

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.

Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics

Data in this article provide detailed information on the microbial dynamics within digesters supplemented with different support media (two types of zeolites, two types of activated carbons, one type of chitosan, one control) in presence of different inhibitory conditions (control without inhibitor, 1.3 g/L of phenol and 19 g/L of total ammonia nitrogen). Data include the operational conditions and degradation performance measurements, as well as microbial community analysis, by 16S rRNA gene sequencing, at different time points for the different conditions (samples). Sequencing data were generated by using IonTorrent PGM sequencer. This data is associated with the research articles "Improving anaerobic digestion with support media: Mitigation of ammonia inhibition and effect on microbial communities?" (Poirier et al., 2017) [1] and "Support media can steer methanogenesis in presence of phenol through biotic and abiotic effects" (Poirier et al., 2018) [2]. The sequencing data have been deposited with links to BioProject accession number PRJNA450513, in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA450513). Samples accession numbers go from SAMN08940368 to SAMN08940426.

Support media can steer methanogenesis in the presence of phenol through biotic and abiotic effects

A wide variety of inhibitors can induce anaerobic digester disruption. To avoid performance losses, support media can be used to mitigate inhibitions. However, distinguishing the physico-chemical from the biological mechanisms of such strategies remains delicate. In this framework, the impact of 10  g/L of different types of zeolites and activated carbons (AC) on microbial community dynamics during anaerobic digestion of biowaste in the presence of 1.3 g/L of phenol was evaluated with 16 S rRNA gene sequencing. In the presence of AC, methanogenesis inhibition was rapidly removed due to a decrease of phenol concentration. This abiotic effect related to the physico-chemical properties of AC led to increased final CH4 and CO2 productions by 29-31% compared to digesters incubated without support. Interestingly, although zeolite did not adsorb phenol, final CH4 and CO2 production reached comparable levels as with AC. Nevertheless, compared to digesters incubated without support, methanogenesis lag phase duration was less reduced in the presence of zeolites (5 ± 1 days) than in the presence of activated carbons (12 ± 2 days). Both types of support induced biotic effects. AC and zeolite both allowed the preservation of the major representative archaeal genus of the non-inhibited ecosystem, Methanosarcina. By contrast, they distinctly shaped bacterial populations. OTUs belonging to class W5 became dominant at the expense of OTUs assigned to orders Clostridiales, Bacteroidales and Anaerolinales in the presence of AC. Zeolite enhanced the implantation of OTUs assigned to bacterial phylum Cloacimonetes. This study highlighted that supports can induce biotic and abiotic effects within digesters inhibited with phenol, showing potentialities to enhance anaerobic digestion stability under disrupting conditions.

Improving anaerobic digestion with support media: Mitigation of ammonia inhibition and effect on microbial communities

This study aimed at providing a better understanding of the influence of support media (10g/L of zeolites, 10g/L of activated carbons, and 1g/L of chitosan) on key phylotypes steering anaerobic digestion (AD) performance in presence of 19g/L of Total Ammonia Nitrogen (TAN) within batch digesters. Support media did not influence TAN concentration. However, both zeolites and activated carbon 1 reduced methanization lag phase by 47% and 25%, respectively. By contrast, activated carbon 2 and chitosan led to an increase of methanization lag phase by 51% and 32%, respectively. 16S rRNA gene sequencing revealed that zeolites preserved Methanosarcina and enhanced Methanobacterium. In presence of activated carbon 1, Methanoculleus, became predominant earlier than without support while chitosan and activated carbon 2 limited its implantation. This study highlighted potentialities to use supports to enhance AD stability under extreme TAN concentration and evidenced their specific influence on the microbiota composition.

Cationic switchable lipids: pH-triggered molecular switch for siRNA delivery

A pH-sensitive molecular switch able to change its conformation upon protonation at endosomal pH values is embedded into the structure of cationic lipidoid materials, thus conferring endosomal escape properties. Involvement of the conformational switch in the endosomal escape process was confirmed and leading material identified was able to induce efficient gene knockdown both in vitro and in vivo. The lipid nanoparticles reported here are promising for therapeutic applications and this work could serve as a template for future design of stimulus-responsive (ionic, redox, light) molecular switch for drug and gene delivery.

Acclimation strategy to increase phenol tolerance of an anaerobic microbiota

A wide variety of inhibitory substances can induce anaerobic digester upset or failure. In this work the possibility to improve the resistance of an anaerobic microbiota to a common pollutant, the phenol, was evaluated in a lab-scale semi-continuous bioreactor. An acclimation strategy, consisting in a regular step-wise adaptation of the microbiota to stressful condition was employed. Degradation performances were monitored and molecular tools (16S sequencing and ARISA fingerprinting technique) were used to track changes in the microbial community. The acclimation strategy progressively minimized the effect of phenol on degradation performances. After 3 successive disturbance episodes, microbiota resistance was considerably developed and total inhibition threshold increased from 895 to 1942mg/L of phenol. Microbiota adaptation was characterized by the selection of the most resistant Archaea OTU from Methanobacterium genus and an important elasticity of Bacteria, especially within Clostridiales and Bacteroidales orders, that probably enabled the adaptation to more and more stressful conditions.

Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators?

Performance stability is a key operational issue for anaerobic digestion (AD) and phenolic compounds are regularly mentioned as a major cause of digester failures. To get more insights into AD microbiota response to a wide range of inhibition levels, anaerobic batch toxicity assays were conducted with ten phenol concentrations up to 5.00 g/L. Final AD performance was not impaired up to 1.00 g/L. However, progressive shifts in microbial community structure were detected from 0.50 g/L. The methanogenic function was maintained along with increasing initial phenol concentrations up to 2.00 g/L thanks to the emergence of genus Methanoculleus at the expense of Methanosarcina. Within syntrophic populations, family Syntrophomonadaceae proportion was gradually reduced by phenol while Synergistaceae gained in importance in the microbiome. Moreover, at 2.00 g/L, the relative abundance of families belonging to order Clostridiales dropped, leading to the predominance of populations assigned to order Bacteroidales even though it did not prevent final AD performance deterioration. It illustrates the high level of adaptability of archaeal and bacterial communities and suggests the possibility of determining early warning microbial indicators associated with phenol inhibition.

Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes

Ammonia inhibition represents a major operational issue for anaerobic digestion (AD). In order to get more insights into AD microbiota resistance, anaerobic batch reactors performances were investigated under a wide range of Total Ammonia Nitrogen (TAN) concentrations up to 50.0g/L at 35°C. The half maximal inhibitory concentration (IC50) value was determined to be 19.0g/L. Microbial community dynamics revealed that above a TAN concentration of 10.0g/L, remarkable modifications within archaeal and bacterial communities occurred. 16S rRNA gene sequencing analysis showed a gradual methanogenic shift between two OTUs from genus Methanosarcina when TAN concentration increased up to 25.0g/L. Proportion of potential syntrophic microorganisms such as Methanoculleus and Treponema progressively raised with increasing TAN up to 10.0 and 25.0g/L respectively, while Syntrophomonas and Ruminococcus groups declined. In 25.0g/L assays, Caldicoprobacter were dominant. This study highlights the emergence of AD key phylotypes at extreme ammonia concentrations.

Forced convection during feedback approach curve measurements in scanning electrochemical microscopy: maximal displacement velocity with a microdisk

In scanning electrochemical microscopy (SECM), an approach curve performed in feedback mode involves the downward displacement of a microelectrode toward a substrate while applying a bias to detect dissolved electroactive species at a diffusion-limited rate. The resulting measured current is said to be at steady state. In order to reduce the required measurement time, the approach velocity can be increased. In this paper, we investigate experimentally and theoretically the combination of diffusion and convection processes related to a moving microdisk electrode during feedback approaches. Transient modeling and numerical simulations with moving boundaries are performed, and the results are compared to the experimental approach curves obtained in aqueous solution. The geometry and misalignment of the microelectrode influence the experimental approach curves recorded at high approach velocities. The effects are discussed through the decomposition of the current into transient diffusional, radial convectional, and axial convectional contributions. Finally a ready-to-use expression is provided to rapidly evaluate the maximal approach velocity for steady state measurements as a function of the microelectrode geometry and the physical properties of the media. This expression holds for the more restrictive case of negative feedback as well as other modes, such as SECM approach curves performed at substrates displaying first order kinetics.

Schizophrenia patients with polydipsia and water intoxication are characterized by greater severity of psychotic illness and a more frequent history of alcohol abuse

Polydipsia and water intoxication (PWI) are relatively frequent among schizophrenic subjects, particularly in institutional settings and may lead to severe complications. However, little is known on their association with other characteristics of psychosis. Hence, we took advantage of a cohort of 114 subjects extensively assessed on natural history and clinical variables to examine the correlates of PWI in chronic schizophrenia. We randomly sampled DSM-IV schizophrenic subjects from: i) a lower functioning subgroup, i.e., long-term psychiatric wards or highly structured group housing facilities; and ii) a higher functioning subgroup, i.e., patients living in the community without supervision. Subjects were assessed from multiple sources for lifetime severity of positive, disorganisation, negative and depressive symptoms, premorbid adjustment, age of onset, level of functioning, comorbid diagnoses of substance abuse and lifetime history of PWI. Twelve subjects (10.5%) met our PWI criteria. We observed more severe psychotic symptoms, earlier onset, poorer current adjustment and more frequent prior alcohol use disorder in PWI subjects. When restricting comparisons to patients living in institutional setting, differences on clinical and natural history variables vanished but the association between PWI and prior alcohol abuse persisted (72.7% in PWI vs. 21.4% in non-PWI subjects, p<0.01). Onset of alcohol abuse predated the onset of PWI by a mean of 12.8 years. PWI schizophrenic subjects are characterized by a non-specific greater severity on a broad array of clinical and natural history variables and by a specific association with prior alcohol abuse. Thus, our data suggest that a greater severity of illness and a prior history of alcohol use disorders interact in increasing the risk of developing PWI in chronic schizophrenic patients.

Grinding up wheat: a massive loss of nucleotide diversity since domestication

Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analyzed nucleotide diversity at 21 loci in a sample of 101 individuals representing 4 taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum, and bread wheats) to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify 2 genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms--by 69% in bread wheat and 84% in durum wheat--with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3--giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness--an important trait for end-use quality in wheat.

A factor analysis of the Strauss and Carpenter revised outcome criteria scale: a validation of the French translation

This article seeks to validate the French translation of the Strauss and Carpenter revised outcome criteria scale (SCOCS-R) through the study of its interrater reliability, its convergent validity, and its factor structure. Using a sample of 113 DSM-IV schizophrenic subjects, we assessed the interrater reliability of the SCOCS-R and its convergent validity with an already validated scale (Social and Occupational Functioning Assessment Scale). The factor structure of the SCOCS-R was assessed using a principal components analysis. Interrater reliability was excellent (ri > or = 0.88 for each of the individual items), and the convergent validity with the Social and Occupational Functioning Assessment Scale proved to be highly satisfactory (r = 0.89; p < .0001). Factor analyses yielded two factors corresponding to social functioning and professional functioning. These factors accounted for 78% of the variance of outcome. These results demonstrate the reliability and the validity of the French translation of the SCOCS-R. Moreover, the two dimensions yielded by our factor analysis add to the evidence of the multidimensional structure of outcome. This article supports the relevance of the SCOCS-R to assess the dimensions of outcome in schizophrenic subjects.

Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data

Estimation of long-term effective population size (N(e)) from polymorphism data alone requires an independent knowledge of mutation rate. Microsatellites provide the opportunity to estimate N(e) because their high mutation rate can be estimated from observed mutations. We used this property to estimate N(e) in allotetraploid wheat Triticum turgidum at four stages of its history since its domestication. We estimated the mutation rate of 30 microsatellite loci. Allele-specific mutation rates mu were predicted from the number of repeats of the alleles. Effective population sizes were calculated from the diversity parameter theta = 4N(e)mu. We demonstrated from simulations that the unbiased estimator of theta based on Nei's heterozygosity is the most appropriate for estimating N(e) because of a small variance and a relative robustness to variations in the mutation model compared to other estimators. We found a N(e) of 32,500 individuals with a 95% confidence interval of [20,739; 45,991] in the wild ancestor of wheat, 12,000 ([5790; 19,300]) in the domesticated form, 6000 ([2831; 9556]) in landraces, and 1300 ([689; 2031]) in recent improved varieties. This decrease illustrates the successive bottlenecks in durum wheat. No selective effect was detected on our loci, despite a complete loss of polymorphism for two of them.

Self-calibration of biplanar radiographs for a retrospective comparative study of the 3D correction of adolescent idiopathic scoliosis

A novel technique for the 3D reconstruction of the spine from X-ray images is presented. The algorithm is based on the self-calibration of biplanar radiographs. It allows the 3D reconstruction of spines from old uncalibrated preoperative and postoperative radiographs. The reliability of the new self-calibration technique was investigated by validating its results against those of the Direct Linear Transform (DLT) on real images. An accuracy experiment was also performed using a dry spine specimen under controlled conditions. The results indicate that self-calibration is a viable technique, accurate enough to extract meaningful 3D clinical data for retrospective studies.

Optimizing adherence to pharmaceutical care plans

Adherence to pharmacotherapy is essential to optimal therapeutic outcomes. The pivotal role of the pharmacist in optimizing adherence encompasses many actions: assessing the adherence problem, identifying predisposing factors, providing comprehensive counseling, and recommending specific adherence strategies targeted to the patient's needs. Patients who have chronic conditions, physical or cognitive impairments, or cultural backgrounds outside the mainstream may have special needs that should be addressed in the adherence plan. Pharmaceutical care plans also should take into account the patient's age, stage of life, and literacy level. Although a wide range of adherence aids and strategies are available, the key to success is to tailor the intervention to the individual patient and, when necessary, to combine interventions to optimize adherence.

A Krüppel-like zinc finger protein is involved in nitrogen-fixing root nodule organogenesis

Mechanisms regulating plant host differentiation of the nitrogen-fixing root nodules remain mostly unknown. Sinorhizobium meliloti induces this process in Medicago sativa in which the Mszpt2-1 gene is expressed in vascular bundles of roots and nodules. This gene codes for a Krüppel-like zinc finger protein, a class of transcription factors involved in many animal developmental processes. Expression of Mszpt2-1 in yeast cells conferred osmotic tolerance. Antisense plants grew normally but developed nonfunctional nodules, in which differentiation of the nitrogen-fixing zone and bacterial invasion were arrested. Hence, a vascular bundle-associated Krüppel-like gene is required for the formation of the central nitrogen-fixing zone of the root nodule.

General and self-consistent method for the calibration of polarization modulators, polarimeters, and mueller-matrix ellipsometers

Calibration of polarization-state generators (PSG's), polarimeters, and Mueller-matrix ellipsometers (MME's) is an important factor in the practical use of these instruments. A new general procedure, the eigenvalue calibration method (ECM), is presented. It can calibrate any complete MME consisting of a PSG and a polarimeter that generate and measure, respectively, all the states of polarization of light. In the ECM, the PSG and the polarimeter are described by two 4 x 4 matrices W and A, and their 32 coefficients are determined from three or four measurements performed on reference samples. Those references are smooth isotropic samples and perfect linear polarizers. Their optical characteristics are unambiguously determined during the calibration from the eigenvalues of the measured matrices. The ECM does not require accurate alignment of the various optical elements and does not involve any first-order approximation. The ECM also displays an efficient error control capability that can be used to improve the MME behavior. The ECM is illustrated by an experimental calibration, at two wavelengths (458 and 633 nm), of a MME consisting of a coupled phase modulator associated with a prism division-of-amplitude polarimeter.

Billing third party payers for pharmaceutical care services

OBJECTIVE

To describe the steps pharmacists must complete when seeking compensation from third party payers for pharmaceutical care services.

DATA SOURCES

Government publications; professional publications, including manuals and newsletters; authors' personal experience.

DATA SYNTHESIS

Pharmacists in increasing numbers are meeting with success in getting reimbursed by third party payers for patient care activities. However, many pharmacists remain reluctant to seek compensation because they do not understand the steps involved. Preparatory steps include obtaining a provider/supplier number, procuring appropriate claim forms, developing data collection and documentation systems, establishing professional fees, creating a marketing plan, and developing an accounting system. To bill for specific patient care services, pharmacists need to collect the patient's insurance information, obtain a statement of medical necessity from the patient's physician, complete the appropriate claim form accurately, and submit the claim with supporting documentation to the insurer. Although many claims from pharmacists are rejected initially, pharmacists who work with third party payers to understand the reasons for denial of payment often receive compensation when claims are resubmitted.

CONCLUSION

Pharmacists who follow these guidelines for billing third party payers for pharmaceutical care services should notice an increase in the number of paid claims.

Songs of innocence and experience: student's poems about their medical education

Personal creative writing is increasingly used in medical schools to foster self-reflection. This article looks particularly at poetry as a vehicle for expressing personal experiences of professional development. The authors present a series of poems written by students at their medical school. In them, the students reflect on embryology, gross anatomy, telling (or not telling) bad news to trusting patients (and family members), encountering death, and encountering their own anger and frustration with the demands of medicine. These poems not only capture individual students' feelings and imaginations but also demonstrate the students' constant struggle to sustain their idealism about medicine throughout the four years of their education.

Endings, secrets, and silences: overreading in narrative inquiry

Qualitative researchers seek to understand the words of the people they interview and may use narrative inquiry to find meaning in the stories told by research participants. Narrative inquiry entails "overreading," a sensitivity to unspoken or indirect statement, which is central to interpretation. Some of the tools of the literary overreader are applied to two research interviews, particularly as they direct readers to attend to inconsistencies, endings, repetitions, and silence. Because overreading is also intrusive, we conclude with some considerations about how far the overreader of the research may legitimately go.

Phenotypic variation and persistence of Histoplasma capsulatum yeasts in host cells

Many Histoplasma capsulatum strains spontaneously give rise to variants during broth culture or subsequent to ingestion by epithelial cells. Unlike their parents, these variants are defective in killing macrophages and lack a major cell wall constituent, alpha-(1,3)-glucan. Inside macrophages, where the variants can persist for several weeks, they adopted an unusual morphology strikingly similar to that reported in the tissues of persistently infected humans or animals. These yeasts were often enlarged or misshapen (allomorphic), but were viable. Decreased cytotoxicity for macrophages was more strongly associated with allomorph formation than was the absence of cell wall alpha-(1,3)-glucan. Allomorphs were also formed in rat and mouse resident macrophages, but not in hamster trachea epithelial cells, indicating that host cell type influences the morphology of these yeasts. We propose that during H. capsulatum infection of mammalian hosts, spontaneous variants arise which can be recognized by their unusual morphologies. In contrast with their virulent parents, such variants "peacefully coexist" within macrophages, potentially contributing to the establishment of latency in vivo.

Virtual text and the growth of meaning in qualitative analysis

Qualitative researchers frequently analyze data in the form of narrative, such as responses to open-ended interview questions. Researchers acknowledge the validity of more than one interpretation of the same narrative but, to date, have offered little justification for multiple valid interpretations. A concept for literary theory, "the virtual text" is presented to help explain the mechanism of multiple interpretations and provide a justification for their validity. An example from the first author's research is provided.

Efficacy of nonsteroidal anti-inflammatory drugs in the treatment of acute renal colic. A meta-analysis

OBJECTIVE

To evaluate the efficacy of nonsteroidal anti-inflammatory drugs (NSAIDs) compared with placebo or analgesic agents in the treatment of acute renal colic.

DATA SOURCES

The MEDLINE and EMBASE databases were searched using the following terms: anti-inflammatory agent, colic, kidney diseases, and ureteral diseases. The Family Medicine Library Index, references of retrieved articles, and documentation centers of pharmaceutical companies were also consulted.

STUDY SELECTION

Among 60 retrieved articles, 19 were selected by consensus of a group of four physicians, based on the following criteria: randomized controlled trials, NSAID compared with placebo or analgesic agent in the treatment of acute renal colic, and articles written in either French or English.

DATA EXTRACTION

Independent data extraction by four evaluators using a 20-item checklist. Final assessment was by group consensus.

DATA SYNTHESIS

The 19 articles presented 20 studies, most comparing parenteral diclofenac or indomethacin (18 of 20) with placebo (n = 4) or analgesic agents (n = 16), most of which were narcotic agents. The results of pain relief 20 to 30 minutes after drug administration were pooled using the Mantel-Haenszel method for three distinct groups of studies: (1) NSAIDs vs placebo (n = 4): relative risk (RR), 2.34 (95% confidence interval [CI], 1.79 to 3.07); (2) NSAIDs vs analgesic agents, partial pain relief (n = 9): RR, 1.07 (95% CI, 1.02 to 1.12); and (3) NSAIDs vs analgesic agents, complete pain relief (n = 9): RR, 1.19 (95% CI, 1.03 to 1.37).

CONCLUSIONS

Parenteral NSAIDs are more effective than placebo and as effective as analgesic agents in the treatment of acute renal colic.

Application of biotyping and DNA typing of Candida albicans to the epidemiology of recurrent vulvovaginal candidiasis

One-hundred and five Candida albicans isolates from various anatomic sites of 28 patients, obtained at the onset of two consecutive episodes of well-documented recurrent vulvovaginitis, were typed by methods relying on physiologic or genomic markers. The isolates represented a wide variety of types, and neither a single biotype nor genotype was associated with recurrent vaginitis or a particular body site. Patients generally carried similar strains at various anatomic sites that persisted over time. Genomic methods indicated an 86% rate of relapse, which suggested that most recurrent vaginal infections are of endogenous origin. A similar evaluation with biotyping methods was inconclusive because of a lack of reproducibility, resulting from clonal variation or switching, and difficulties in establishing the number of phenotypic tests necessary to distinguish between identical and different strains. Therefore, Southern hybridization was considered the ideal reference method to study the epidemiology of C. albicans infections.

Isolation and partial characterization of a transformation-associated sequence from human nasopharyngeal carcinoma

A transforming activity associated with Chinese nasopharyngeal carcinoma (NPC) cell line CNE2 DNA has been identified by transfer into nontransformed promotion-sensitive mouse JB6(P+) C141 cells. To clone this transformation-associated sequence, we carried out three cycles of transfection, followed by cloning of anchorage-independent transformants in soft agar. A tertiary CNE/JB6 clonal transfectant cell line 625 whose DNA showed transforming activity, as indicated in both soft-agar assay and nude-mice implantation, was used to make a genomic library in the vector lambda dash. Using the human repeated sequence Blur 8 to screen the library, we obtained 10 human Alu-positive clones. A cloned Alu-positive insert of 16 kbp, CNE 323, was characterized in detail. CNE 323 transferred moderate transforming activity when introduced into JB6 P+ cells and showed no homology to Ha-, Ki-, or N-ras genes; human promotion sensitivity genes; src, myb, jun, myc, fos, raf, or int-2 oncogenes; or epidermal growth factor receptor. The isolated CNE 323 DNA sequence appeared to preserve the genomic structure of the original sequence found in CNE2 cells and in nude mouse tumors induced by CNE2 cells or by CNE/JB6 transfectant cells, indicating that the cloned NPC sequence was activated during NPC carcinogenesis and not during transfection or construction of the library, and that the cloned sequence or a larger sequence of which it was part played a role in tumor formation. Finally, we identified a 1.3-kb mRNA that hybridizes to a subclone of the 16-kb NPC sequence in CNE2 cell poly (A)+ RNA.

The voices of the medical record

The medical record, as a managerial, historic, and legal document, serves many purposes. Although its form may be well established and many of the cases documented in it 'routine' in medical experience, what is written in the medical record nevertheless records decisions and actions of individuals. Viewed as an interpretive 'text', it can itself become the object of interpretation. This essay applies literary theory and methodology to the structure, content, and writing style(s) of an actual medical record for the purpose of exploring the relationship between the forms and language of medical discourse and the daily decisions surrounding medical treatment. The medical record is shown to document not only the absence of a consistent treatment plan for the patient studied but also a breakdown in communication between different health professionals caring for that patient. The paper raises questions about the kind of education being given to house staff in this instance. The essay concludes with a consideration of how such situations might be more generally avoided.

Interest of biotyping Candida albicans in chronic vulvovaginitis

Chronic vulvovaginitis due to Candida albicans is a major clinical problem for the physician. Although new antifungal drugs are now available, the therapeutic approach of this disease remains disappointing. The aims of this study were two-fold. First, we wanted to evaluate the reliability of a single sampling performed by most clinicians in verifying if the yeast infects the entire genital mucosa or a preferential site and, second, to biotype the strains recovered in order to see if more than one strain are responsible for the infection. We found, in 18 patients suffering from vaginal candidosis, that the entire genital mucosa was infected by the yeast and the strain recovered from the different genital sites in a single patient was the same in 100% of the cases. Only 1.4% of the samples were negative. In addition, we biotyped the strains obtained from the gastrointestinal tract of these patients to evaluate this site as a potential source of infection. We obtained gastrointestinal tract samples for 15 of the 18 patients and we could identify C. albicans in 100% of the cases. Furthermore, 73.3% of the patients harboured the same strains of C. albicans in the gastrointestinal tract as in the vagina.

Volatile nitrosamine levels and genotoxicity of food samples from high-risk areas for nasopharyngeal carcinoma before and after nitrosation

Traditional life-style, especially food habits, infection by Epstein-Barr virus (EBV) and genetic factors, have been associated with an increased risk of nasopharyngeal carcinoma (NPC). N-Nitroso compounds and other carcinogens either present in food or formed endogenously, as well as food constituents that activate EBV, have been suspected as etiological factors in NPC pathogenesis. For their characterization preserved food items, frequently consumed in NPC endemic areas in Tunisia, South China and Greenland, were sampled and screened for the presence of mutagens and volatile nitrosamines before and after nitrosation. Aqueous extracts as well as 2 organic extracts of the samples were assayed for genotoxicity in 2 Salmonella typhimurium strains and the SOS chromotest. The same extracts had previously been analyzed for volatile nitrosamines and for EBV-activating substances in Raji cells. In our study, 13 out of 16 food samples showed a weak, directly-acting genotoxicity in the SOS chromotest in at least one of the extracts, but only one sample from Greenland was found to be weakly mutagenic in Salmonella TA 98. Chemical nitrosation for 9 out of 15 samples of aqueous food extracts increased the genotoxic effect in the SOS chromotest. Levels of volatile nitrosamines were also elevated for 12 out of 15 samples; highest levels of N-nitrosodimethylamine were found in hard salted and dried fish from China (1,200 micrograms/kg) and highest N-nitrosopyrrolidine levels in a Tunisian spice (3,840 micrograms/kg). In non-nitrosated aqueous food extracts, the level of volatile nitrosamines and genotoxic activities were not correlated with the EBV-inducing activity of the same samples. After chemical nitrosation, EBV-inducing activity was decreased or showed no change and was not correlated with increases in either the genotoxicity or the nitrosamine levels. Our results suggest that EBV-activating compounds belong to a different class of substances. However, there was an association between the changes in genotoxicity and nitrosamine levels due to nitrosation.

Treatment of cutaneous candidosis in guinea pigs: effect of zinc oxide on the antifungal efficacy of nystatin

This article describes the in vivo evaluation of a new topical preparation (Zincostatin) indicated for Candida albicans infected diaper rash. In order to study the influence of the 20% zinc oxide (W/W) (a protectant) on the anti-candidal efficacy of the 100,000 U/g of nystatin found in the ointment, groups of guinea pigs received different treatments with or without local occlusion. Zinc oxide, nystatin, or the combination of both were applied, in the ointment base, on the backs of the animals inoculated with a fresh strain of Candida albicans. Macroscopic and microbiological evaluation of the skin lesions were assessed at regular intervals during 21 days. While the two treatments containing nystatin were more effective than zinc oxide alone, the latter agent did not decrease the efficacy of the antifungal drug in combination therapy. Also, zinc oxide seemed to afford some protection against local maceration induced by occlusion, which increased the severity of the infection.

Epstein-Barr virus activation in Raji cells by extracts of preserved food from high risk areas for nasopharyngeal carcinoma

Epstein-Barr virus (EBV) activation of latent infection and traditional life styles, especially food habits, have been strongly associated with an increased risk of nasopharyngeal carcinoma (NPC) in humans. On the basis of anthropological studies in Tunisia, southern China and Greenland, extracts of representative preserved food items consumed frequently by the high-risk populations for NPC were assayed for the presence of EBV activators in Raji cells. A strong EBV activation activity was observed in aqueous extracts of some Cantonese salted dried fish from China, harissa (a spice mixture) and to a lesser extent qaddid (dry mutton preserved in olive oil) from Tunisia. These new data may support epidemiological evidence for the importance of Cantonese salted and dried fish and other food items in the etiology of NPC.