Design of passive methane oxidation biosystems considering their response to the presence of capillary barrier effect

La construction des biosystèmes d’oxydation passive du méthane (BOPM) est une option économique et durable pour réduire les émissions de méthane des sites d’enfouissement de déchets et des effets subséquents du réchauffement climatique. Les BOPM sont constitués de deux couches principales: la couche d'oxydation du méthane (MOL) et la couche de distribution du gaz (GDL). L'oxydation du méthane se produit dans la MOL par les réactions biochimiques des bactéries méthanotrophes, et la GDL est construite sous la MOL pour intercepter et distribuer les émissions fugitives de biogaz à la base de la MOL. Fondamentalement, l'efficacité d'un BOPM est définie en fonction de l'efficacité d'oxydation du méthane dans la MOL. Par conséquent, il est indispensable de fournir des conditions adéquates pour les activités bactériennes des méthanotrophes. En plus des paramètres environnementaux, l'intensité et la distribution du biogaz influencent l'efficacité des BOPM, et ils peuvent rendre le matériau de la MOL - avec une grande capacité d'accueillir les activités bactériennes - inutilisables en termes d'oxydation du méthane sur place. L'effet de barrière capillaire le long de l'interface entre la GDL et la MOL peut provoquer des émissions localisées de méthane, due à la restriction ou la distribution non uniforme de l’écoulement ascendant du biogaz à la base de la MOL. L'objectif principal de cette étude est d'incorporer le comportement hydraulique non saturé des BOPM dans la conception des BOPM, afin d’assurer la facilité et la distribution adéquates de l'écoulement du biogaz à la base de la MOL. Les fonctions de perméabilité à l'air des matériaux utilisés pour construire la MOL des BOPM expérimentaux au site d’enfouissement des déchets de St Nicéphore (Québec, Canada), ainsi que celles d'autres de la littérature technique, ont été étudiés pour évaluer le comportement d'écoulement non saturé du gaz dans les matériaux et pour identifier le seuil de migration sans restriction du gaz. Ce dernier seuil a été introduit en tant que un paramètre de conception avec lequel le critère de conception recommandé ici, c’est à dire la longueur de la migration sans restriction de gaz (LMSG), a été défini. La LMSG est considérée comme la longueur le long de l'interface entre la GDL et la MOL où le biogaz peut migrer à travers la MOL sans restriction. En réalisant des simulations numériques avec SEEP/W, les effets de la pente de l'interface, des paramètres définissant la courbe de rétention d'eau, de la fonction de la conductivité hydraulique du matériau de la MOL sur la valeur de la LMSG (représentant la facilité d'écoulement du biogaz à l'interface) et de la distribution de l'humidité (et par conséquent celle du biogaz) ont été évalués. Selon les résultats des simulations, la conductivité hydraulique saturée et la distribution des tailles de pores du matériau de la MOL sont les paramètres les plus importants sur la distribution de l'humidité le long de l'interface. Ce dernier paramètre influe également sur la valeur du degré de saturation et donc la facilité du biogaz à la base de la MOL. La densité sèche du matériau de MOL est un autre paramètre qui contrôle la facilité d'écoulement ascendant du biogaz. Les limitations principales de la présente étude sont associées au nombre de matériaux de MOL testés et à l'incapacité de SEEP/W de considérer l'évapotranspiration. Toutefois, compte tenu des hypothèses raisonnables dans les simulations et en utilisant les données de la littérature, on a essayé de réduire ces limitations. En utilisant les résultats des expériences et des simulations numériques, des étapes et des considérations de conception pour la sélection du matériau de MOL et de la pente d'interface ont été proposées. En effet,le comportement hydraulique non saturé des matériaux serait intégré dans les nécessités de conception pour un BOPM efficace, de sorte que la capacité maximale possible d'oxydation du méthane du matériau de la MOL soit exploitée.

Real-time PCR quantification and diversity analysis of the functional genes aprA and dsrA of sulfate-reducing prokaryotes in marine sediments of the Peru continental margin and the Black Sea

Sulfate-reducing prokaryotes (SRP) are ubiquitous and quantitatively important members in many ecosystems, especially in marine sediments. However their abundance and diversity in subsurface marine sediments is poorly understood. In this study, the abundance and diversity of the functional genes for the enzymes adenosine 5'-phosphosulfate reductase (aprA) and dissimilatory sulfite reductase (dsrA) of SRP in marine sediments of the Peru continental margin and the Black Sea were analyzed, including samples from the deep biosphere (ODP site 1227). For aprA quantification a Q-PCR assay was designed and evaluated. Depth profiles of the aprA and dsrA copy numbers were almost equal for all sites. Gene copy numbers decreased concomitantly with depth from around 10(8)/g sediment close to the sediment surface to less than 10(5)/g sediment at 5 mbsf. The 16S rRNA gene copy numbers of total bacteria were much higher than those of the functional genes at all sediment depths and used to calculate the proportion of SRP to the total Bacteria. The aprA and dsrA copy numbers comprised in average 0.5-1% of the 16S rRNA gene copy numbers of total bacteria in the sediments up to a depth of ca. 40 mbsf. In the zone without detectable sulfate in the pore water from about 40-121 mbsf (Peru margin ODP site 1227), only dsrA (but not aprA) was detected with copy numbers of less than 10(4)/g sediment, comprising ca. 14% of the 16S rRNA gene copy numbers of total bacteria. In this zone, sulfate might be provided for SRP by anaerobic sulfide oxidation. Clone libraries of aprA showed that all isolated sequences originate from SRP showing a close relationship to aprA of characterized species or form a new cluster with only distant relation to aprA of isolated SRP. For dsrA a high diversity was detected, even up to 121 m sediment depth in the deep biosphere.

Information and the evolution of codon bias

The informational properties of biological systems are the subject of much debate and research. I present a general argument in favor of the existence and central importance of information in organisms, followed by a case study of the genetic code (specifically, codon bias) and the translation system from the perspective of information. The codon biases of 831 Bacteria and Archeae are analyzed and modeled as points in a 64-dimensional statistical space. The major results are that (1) codon bias evolution does not follow canonical patterns, and (2) the use of coding space in organsims is a subset of the total possible coding space. These findings imply that codon bias is a unique adaptive mechanism that owes its existence to organisms' use of information in representing genes, and that there is a particularly biological character to the resulting biased coding and information use.

Nano-silver treatments reduced bacterial colonization and biofilm formation at the stem-ends of cut gladiolus ‘Eerde’ spikes

Postharvest treatments with nano-silver (NS) alleviate bacteria-related stem blockage of some cut flowers to extend their longevity. Gladiolus (Gladiolus hybridus) is a commercially important cut flower species. For the first time, the effects of NS pulses on cut gladiolus ‘Eerde’ spikes were investigated towards reducing bacterial colonization of and biofilm formation on their stems. As compared with a deionized water (DIW) control, pulse treatments with NS at 10, 25 and 50 mg L−1 for 24 h significantly (P ≤ 0.05) prolonged the vase life of cut gladiolus spikes moved into vases containing DIW. The NS treatments enhanced floret ‘opening rate’ and ‘daily ornamental value’. Although there were no significant differences among NS treatments, a 25 mg L−1 NS pulse treatment tended to give the longest vase life and the best ‘display quality’. All NS pulse treatments significantly improved water uptake by and reduced water loss from flowering spikes, thereby delaying the loss of water balance and maintaining relative fresh weight. Fifty (50) mg L−1 NS pulse-treated cut gladiolus spikes tended to exhibit the most water uptake and highest water balance over the vase period. However, there was no significant difference between 25 and 50 mg L−1 NS pulse treatments. Observations of stem-end bacterial proliferation during the vase period on cut gladiolus spikes either with or without NS pulse treatments were performed by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). As compared to the control treatment, they revealed that the 25 mg L−1 NS pulse treatment effectively inhibited bacterial colonization and biofilm formation on the stem-end cut surface and in the xylem vessels, respectively. In vitro culture of the bacterial microflora and analysis of biofilm architecture using CLSM revealed that NS treatment restricted bacterial biofilm formation. After static culture for 24 h at 35 °C with 25 mg L−1 NS in the medium, no biofilm form or structure was evident. Rather, only limited bacterial cell number and scanty extracellular polysaccharide (EPS) material were observed. In contrast, mature bacterial biofilm architecture comprised of abundant bacteria interwoven with EPS formed in the absence of NS.

The experimentally pathogenesis of Aeromonas hydrophila in Astacus leptodactylus with emphasis on temperature in bacterial pathogenesis

In this study, four hundred freshwater Crayfish (A. leptodactylus) with average weight of 25-40g were purchased from Aras dam reservoirs in west Azerbayjan province and transported to Iranian Artemia Research Center of Uromya province in September 2010. (One hundred crayfish extra purchased for probably mortality). Before implement of experiment the Crayfish were acclimated for ten days. These experiments was designed in four group treatments (Number, 1,2,3,4) and one control group (Number 5) in triplicate with 20 Crayfish in each repetition prepared of glass aquarium with size (50x40x30cm). Many of infected Crayfish were used for isolation of bacteria. Haemolymph sample had been gathered from infected Crayfish with cutting their antennules and transferred to TSA medium (tryptic soy agar) and then A. hydrophila were determined in order to biochemical test. The treatments and repetitions has exposed to A. hydrophila. The concentrations of the bacteria in 4 treatments were respectively 3 x 108 (T=10-15°C), 3x106 (T=25°C), 3 x 106 and 3 x 104 Cfu mL-1 (T=10- i5oc) (4, 2, 3 and 1) that were prepared in individual containers for exposure of treatments. The control (5) prepared without any bacteria and disinfected by oxytetracycline antibiotic with concentration 100 ppm for 24 hours. The hemolymph samples were withdrawn from abdominal second segments of Crayfish for measuring of THC and TPC in interval hours (2, 6, 12, 24, 48, 96, 144, 240 and 336). For histopatological studies the crayfish samples fixed in Davidson fixative. The results indicated that interval 2 hours after experiment the difference of THC value between treatment 4 with control and treatments 1,2, and 3 was significant (P< 0.05). After 48 hours of experiment the difference of THC value between control group with treatment 1 ,2 and 3 was significant (P< 0.05). The interval 336 hours after experiment also the difference of THC value between treatment 2 with treatments 1, 3 and 4 was significant (P< 0.05). The finding of TPP value showed that the last time after challenge (336 h) there was significant difference between treatment 2 with treatment 4 and control group (P< 0.05). In histopathology studying, in hepatopancreas observed hemocyte aggregated and necrosis withof peknosis nucleus that with increased concentration of bacteria and temperature, The value of hemocyte has increased. Gill revealed necrosis and cell death especially with increased concentration of bacteria and temperature. In lower concentration of bacteria in heart no difference observed, but with increased concentration of bacteria (3 x 108) the low aggregation of hemocyte observed in heart. In treatment 3 x 106 with high temperature also distributed of high hemocyte in heart was observed. In digestive system didn't appear any difference in treatments land 3 but in concentration of 3 x 108 Cfu m1-1 and 3 x 106 (T=25°C) in digestive system was revealed the low aggregation of hemocyte.

Normative conflicts in international investment law: the case of environmental law

This dissertation investigates the relationship between investment and environmental obligations from the perspective of international investment law. In order to do so, the dissertation will consider how these obligations might enter into conflicts and what tools are available to investment tribunals to solve these normative conflicts. The dissertation analyses in order interpretative techniques, conflict resolution tools available in general international law, as expressed in the Vienna Convention on the Law of Treaties, and finally express clauses in international investment agreements. The dissertation includes the review of some relevant case law arising from investment agreements in investment treaty tribunals, to discover how in practice these conflict resolution tools are applied and to assess their effectiveness. This dissertation places itself squarely within the debate between the unity and the fragmentation of international law; therefore it tackles the issue of normative conflicts resolution in a dispute settlement environment with the view of gauging their value in maintaining the unity of international law and defuse the risk of fragmentation. The dissertation can only conclude that much work remains to be done, including by providing a more comprehensive taxonomy of possible interventions, both on the legal and political sphere.

Role of Aeromonas hydrophila in bacterial septicemia of cultured carps in Khouzestan Province and investigation on protectivity of bacterin (s) prepared from acute isolate(s) of it

Motile Aeromonas are the most common bacteria of freshwater in the world that cause disease in fish and other cold-blooded and warm-blooded hosts. Among this group of bacteria, Aeromonas hydrophila is important in causing complications such as fin rot, skin ulcers and lethal hemorrhagic septicemia in fish. Several virulence factors involved in the pathogenesis of Aeromonas hydrophila, including extracellular enzymes (protease, lipase, elastase, gelatinase and nuclease) and toxins. From the exotoxins, hemolysin, aerolysin and cytolytic enterotoxin play an important role in pathogenesis. Detection of virulence markers by PCR as a key component of determining the pathogenesis of the bacteria and using indigenous vaccines for better immunization against this disease is important. In this study, a total of 200 fanned carps (126 common carp. 39 silver carp and 35 of grass carp) with symptoms suspected aeromonas septicemia were isolated from Khouzestan province farms. 125 bacteria belong to Aeromonas genus detected by biochemical and PCR methods. 31 of all isolates recognized as Aeromonas hydrophila with biochemical methods, I6srRNA detection and Lipase genes. Results showed that the role of Aeromonas sp. and Aeromonas hydrophila in fish with disease symptoms were 62.5% and 15.5% respectively. By using specific primers, three virulence genes including hemolysin, aerolysine and cytolytic enterotoxin were detected in these confirmed isolates, that 18 isolates (58/06%) hemolysin positive (hlyA +), 16 isolates (51/61%) aerolysine positive (aerA+) and 23 isolates (74/19%) for cytolytic enterotoxin gene (act+) were positive. The result of present study showed that most of the confirmed isolates genotype was hlyA+ act- with frequency equal to 51/61%. For investigating the protection effect of acut strain of bacteria, UV inactivated bacterin was used.

Phenolic profile and antimicrobial activity of dietary supplements based on Cochlospermum angolensis Welw.

Cochlospermum angolensis Welw. (borututu) is a widespread tree in Angola that belongs to the Cochlospermaceae family. Its bark infusion is used in the traditional medicine of Angola for the treatment of jaundice, hepatic diseases and for the prophylaxis of malaria [1]. In the present work, three formulations based on this plant (infusion, pills, and syrup) were characterized by HPLC-DAD-ESI/MS regarding phenolic composition, and evaluated by their in vitro antimicrobial activity against isolates of multiresistant bacteria (Escherichia coli, Escherichia coli spectrum extended producer of β-lactamases (ESBL), Proteus mirabilis, methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa). The infusion and pills revealed the highest variety of phenolic compounds, with eleven compounds identified. Protocatechuic acid was only present in infusions, being the most abundant compound, while (epi)gallocatechin-O-gallate and eucaglobulin/globulusin were the main molecules identified in pills and syrup, respectively. Methyl ellagic acids, eucaglobulin/globulusin B (Fig. 1) and (epi)gallocatechin-O-gallate were found in all the formulations. The infusion revealed antimicrobial activity against all the studied bacteria with the exception of P. mirabilis whereas the pills revealed activity in E. coli ESBL and MRSA. No significant antimicrobial activity was detected in the syrup, in agreement with its low concentrations of phenolic compounds. None of the tested formulations inhibited P. mirabilis. Considering the obtained results, C. angolensis infusion can be considered a good source of phenolic compounds as well as a good antimicrobial agent.

Implication of gut microbiota in nonalcoholic fatty liver disease

International audience

A Visual Analytics Approach to Comparing Cohorts of Event Sequences

Sequences of timestamped events are currently being generated across nearly every domain of data analytics, from e-commerce web logging to electronic health records used by doctors and medical researchers. Every day, this data type is reviewed by humans who apply statistical tests, hoping to learn everything they can about how these processes work, why they break, and how they can be improved upon. To further uncover how these processes work the way they do, researchers often compare two groups, or cohorts, of event sequences to find the differences and similarities between outcomes and processes. With temporal event sequence data, this task is complex because of the variety of ways single events and sequences of events can differ between the two cohorts of records: the structure of the event sequences (e.g., event order, co-occurring events, or frequencies of events), the attributes about the events and records (e.g., gender of a patient), or metrics about the timestamps themselves (e.g., duration of an event). Running statistical tests to cover all these cases and determining which results are significant becomes cumbersome. Current visual analytics tools for comparing groups of event sequences emphasize a purely statistical or purely visual approach for comparison. Visual analytics tools leverage humans' ability to easily see patterns and anomalies that they were not expecting, but is limited by uncertainty in findings. Statistical tools emphasize finding significant differences in the data, but often requires researchers have a concrete question and doesn't facilitate more general exploration of the data. Combining visual analytics tools with statistical methods leverages the benefits of both approaches for quicker and easier insight discovery. Integrating statistics into a visualization tool presents many challenges on the frontend (e.g., displaying the results of many different metrics concisely) and in the backend (e.g., scalability challenges with running various metrics on multi-dimensional data at once). I begin by exploring the problem of comparing cohorts of event sequences and understanding the questions that analysts commonly ask in this task. From there, I demonstrate that combining automated statistics with an interactive user interface amplifies the benefits of both types of tools, thereby enabling analysts to conduct quicker and easier data exploration, hypothesis generation, and insight discovery. The direct contributions of this dissertation are: (1) a taxonomy of metrics for comparing cohorts of temporal event sequences, (2) a statistical framework for exploratory data analysis with a method I refer to as high-volume hypothesis testing (HVHT), (3) a family of visualizations and guidelines for interaction techniques that are useful for understanding and parsing the results, and (4) a user study, five long-term case studies, and five short-term case studies which demonstrate the utility and impact of these methods in various domains: four in the medical domain, one in web log analysis, two in education, and one each in social networks, sports analytics, and security. My dissertation contributes an understanding of how cohorts of temporal event sequences are commonly compared and the difficulties associated with applying and parsing the results of these metrics. It also contributes a set of visualizations, algorithms, and design guidelines for balancing automated statistics with user-driven analysis to guide users to significant, distinguishing features between cohorts. This work opens avenues for future research in comparing two or more groups of temporal event sequences, opening traditional machine learning and data mining techniques to user interaction, and extending the principles found in this dissertation to data types beyond temporal event sequences.

Physicochemical properties of water quality of Imeh, Edegelem and Chokocho communities located along Otamiri-oche River in Etche Ethnic Nationality of Rivers State, Nigeria

Some physiochemical properties of water quality of Otamiri-oche River which runs through Imeh, Edegelem and Chokocho Communities in Etche ethnic nationality of Rivers State, Nigeria were investigated. Samples were collected in triplicate from the three different locations along the river in both rainy and dry seasons. Each sampling points is located 500m away from the successive one, and the samples were taken from the open river at the zone extending beyond the shoreline. Samples were stored in ice packs and immediately taken to the laboratory to investigate some selected physico-chemical characteristics. Also, bacteriological study was carried out on the samples. The laboratory results of the selected physico-chemical parameters when compared with the world health organization (WHO) standard showed that all the selected physico-chemical parameters were within the world health organization (WHO) permissible in both rainy and dry season except pH. For rainy season, the pH values were 5.00±0.00, 5.40 ±0.40, and 5.40± 0.30 for Imeh, Edegelem and Chokocho respectively. For the dry season, the pH values were 5.83± 0.01, 5.56±0.01, 5.90±0.01 for Imeh, Edegelem and Chokocho respectively. Also magnesium hardness exceeded the World Health Organization (WHO) permissible limit in rainy season only. The results of bacteriological study showed that all the sampling locations contained high numbers of coliform bacteria in both rainy and dry seasons. The number of coliform bacteria during rainy season was 25.00±0.00, 25.00±0.00, and 35.00±0.00 for Imeh, Edegelem and Chokocho respectively. Those of dry season were 93.00±3.55, 56.66±4.49, and 35.60±4.17 for Imeh, Edegelem and Chokocho respectively. The difference between the rainy and dry season was tested statistically using the t-test. The results of the statistical analyses showed a significant difference (p<0.05) between the rainy and dry seasons.

Effect of Metronidazole on Halitosis of 2 to 10 Years Old Children

Background: Regarding the fact that halitosis has social and personal aspects which can lead to social embarrassment and consequently low self-esteem and self-confidence in subjects suffering from the problem, especially children, its proper treatment is an important issue. Objectives: The aim of this study was to evaluate the effect of metronidazole as a nonspecific antimicrobial agent in the treatment of halitosis in children. Materials and Methods: In this study, 2-10 years old children with oral halitosis were enrolled. Children without H. pylori infection and parasitic infection were randomized in two interventional and control groups. Metronidazole was given 5mg/kg/day for one week. Information regarding the demographic characteristics of studied population and halitosis (duration and time of day with more halitosis and its severity) before and after intervention was recorded using a questionnaire Results: 77 children with halitosis were studied in two interventional (40 children) and control (37 children) groups. There was no significant difference between two groups before intervention. After intervention, halitosis improvement rate - according to the reports of mothers of studied children - was higher significantly in intervention group (P < 0.05). Conclusions: The results support the effectiveness of metronidazole in the treatment of halitosis. Moreover, it supports recent findings regarding the participation of specific bacteria specially unculturable ones in the pathogenesis of the disease.

Assessing the safety of Pseudomonas putida introduction in the environment: an overview of ecotoxicological tests.

Risk assessment guidelines for the environmental release of microbial agents are performed in a tiered sequence which includes evaluation of exposure effects on non target organisms. However, it becomes important to verify whether environmental risk assessment from temperate studies is applicable to tropical countries, as Brazil. Pseudomonas putida is a bacteria showing potential to be used for environmental applications as bioremediation and plant disease control. This study investigates the effects of this bacteria exposure on rodents and aquatic organisms (Daphnia similes) that are recommended to be used as non-target organism in environmental risk assessments. Also, the microbial activity in three different soils under P. putida exposure was evaluated. Rats did not show clinical alterations, although the agent was recovered 16 h after the exposure in lung homogenates. The bacteria did not reduce significantly the reproduction and survival of D. similis. The soil enzymatic activities presented fluctuating values after inoculation with bacteria. The measurement of perturbations in soil biochemical characteristics is presented as an alternative way of monitoring the overall effects of the microbial agent to be introduced even in first stage (Tier I) of the risk assessment in tropical ecosystems.

Escherichia coli : host interactions in the pathogenesis of canine pyometra

Tese de Doutoramento em Ciências Veterinárias na Especialidade de Ciências Biológicas e Biomédicas

The Early Intestinal Microbiota of Healthy Korean Newborns

Background: The microflora hypothesis may be the underlying explanation for the growth of inflammatory disease. In addition to many known affecting factors, knowing the gut microbiota of healthy newborns can help to understand the gut immunity and modulate it. Objectives: This study examined the microbiota of healthy newborns from urban regions. Patients and Methods: We enrolled 128 full-term newborns, born at Seoul St. Mary and St. Paul hospital from January 2009 to February 2010. All 143 samples of feces were cultivated in six culture plates to determine the amounts of total bacteria, anaerobes, gram-positive bacteria, coliforms, lactobacilli, and bifidobacteria. The samples were evaluated with a bivariate correlation between coliforms and lactobacilli. Terminal restriction fragment length polymorphism (T-RFLP) analysis with HhaI and MspI and a clustering analysis were performed for determination of diversity. Results: Bacteria were cultured in 61.5% of feces in the following order: anaerobes, gram-positive bacteria, lactobacilli, coliform, and bifidobacteria. The growth of total bacteria and lactobacilli increased in feces defecated after 24 hours of birth (P < 0.001, P = 0.008) and anaerobes decreased (P = 0.003). A negative correlation between the growth of lactobacilli and coliforms was found (r = -463, P < 0.001). Conclusions: This study confirms that bacterial colonization of healthy newborns born in cities is non-sterile, but has early diversification and inter-individuality.