A Study of Single Stage Semi‐Dry Anaerobic Digestion of Organic Fraction of Municipal Solid Waste

Solid waste generation is a natural consequence of human activity and is increasing along with population growth, urbanization and industrialization. Improper disposal of the huge amount of solid waste seriously affects the environment and contributes to climate change by the release of greenhouse gases. Practicing anaerobic digestion (AD) for the organic fraction of municipal solid waste (OFMSW) can reduce emissions to environment and thereby alleviate the environmental problems together with production of biogas, an energy source, and digestate, a soil amendment. The amenability of substrate for biogasification varies from substrate to substrate and different environmental and operating conditions such as pH, temperature, type and quality of substrate, mixing, retention time etc. Therefore, the purpose of this research work is to develop feasible semi-dry anaerobic digestion process for the treatment of OFMSW from Kerala, India for potential energy recovery and sustainable waste management. This study was carried out in three phases in order to reach the research purpose. In the first phase, batch study of anaerobic digestion of OFMSW was carried out for 100 days at 32°C (mesophilic digestion) for varying substrate concentrations. The aim of this study was to obtain the optimal conditions for biogas production using response surface methodology (RSM). The parameters studied were initial pH, substrate concentration and total organic carbon (TOC). The experimental results showed that the linear model terms of initial pH and substrate concentration and the quadratic model terms of the substrate concentration and TOC had significant individual effect (p < 0.05) on biogas yield. However, there was no interactive effect between these variables (p > 0.05). The optimum conditions for maximizing the biogas yield were a substrate concentration of 99 g/l, an initial pH of 6.5 and TOC of 20.32 g/l. AD of OFMSW with optimized substrate concentration of 99 g/l [Total Solid (TS)-10.5%] is a semi-dry digestion system .Under the optimized condition, the maximum biogas yield was 53.4 L/kg VS (volatile solid).. In the second phase, semi-dry anaerobic digestion of organic solid wastes was conducted for 45 days in a lab-scale batch experiment for substrate concentration of 100 g/l (TS-11.2%) for investigating the start-up performances under thermophilic condition (50°C). The performance of the reactor was evaluated by measuring the daily biogas production and calculating the degradation of total solids and the total volatile solids. The biogas yield at the end of the digestion was 52.9 L/kg VS for the substrate concentration of 100 g/l. About 66.7% of volatile solid degradation was obtained during the digestion. A first order model based on the availability of substrate as the limiting factor was used to perform the kinetic studies of batch anaerobic digestion system. The value of reaction rate constant, k, obtained was 0.0249 day-1. A laboratory bench scale reactor with a capacity of 36.8 litres was designed and fabricated to carry out the continuous anaerobic digestion of OFMSW in the third phase. The purpose of this study was to evaluate the performance of the digester at total solid concentration of 12% (semi-dry) under mesophlic condition (32°C). The digester was operated with different organic loading rates (OLRs) and constant retention time. The performance of the reactor was evaluated using parameters such as pH, volatile fatty acid (VFA), alkalinity, chemical oxygen demand (COD), TOC and ammonia-N as well as biogas yield. During the reactor’s start-up period, the process is stable and there is no inhibition occurred and the average biogas production was 14.7 L/day. The reactor was fed in continuous mode with different OLRs (3.1,4.2 and 5.65 kg VS/m3/d) at constant retention time of 30 days. The highest volatile solid degradation of 65.9%, with specific biogas production of 368 L/kg VS fed was achieved with OLR of 3.1 kg VS/m3/d. Modelling and simulation of anaerobic digestion of OFMSW in continuous operation is done using adapted Anaerobic Digestion Model No 1 (ADM1).The proposed model, which has 34 dynamic state variables, considers both biochemical and physicochemical processes and contains several inhibition factors including three gas components. The number of processes considered is 28. The model is implemented in Matlab® version 7.11.0.584(R2010b). The model based on adapted ADM1 was tested to simulate the behaviour of a bioreactor for the mesophilic anaerobic digestion of OFMSW at OLR of 3.1 kg VS/m3/d. ADM1 showed acceptable simulating results.

Natural Object Categorization

This thesis addresses the problem of categorizing natural objects. To provide a criteria for categorization we propose that the purpose of a categorization is to support the inference of unobserved properties of objects from the observed properties. Because no such set of categories can be constructed in an arbitrary world, we present the Principle of Natural Modes as a claim about the structure of the world. We first define an evaluation function that measures how well a set of categories supports the inference goals of the observer. Entropy measures for property uncertainty and category uncertainty are combined through a free parameter that reflects the goals of the observer. Natural categorizations are shown to be those that are stable with respect to this free parameter. The evaluation function is tested in the domain of leaves and is found to be sensitive to the structure of the natural categories corresponding to the different species. We next develop a categorization paradigm that utilizes the categorization evaluation function in recovering natural categories. A statistical hypothesis generation algorithm is presented that is shown to be an effective categorization procedure. Examples drawn from several natural domains are presented, including data known to be a difficult test case for numerical categorization techniques. We next extend the categorization paradigm such that multiple levels of natural categories are recovered; by means of recursively invoking the categorization procedure both the genera and species are recovered in a population of anaerobic bacteria. Finally, a method is presented for evaluating the utility of features in recovering natural categories. This method also provides a mechanism for determining which features are constrained by the different processes present in a multiple modal world.

Software for identifying bacteria - PIBWin

The PIBWin programme provides probabilistic identification of unknown bacterial isolates against identification matrices of known strains. Bryant TN. PIBWin - software for probabilistic identification. Journal of Applied Microbiololgy. 2004;97(6):1326-7.

Infecciones urinarias en gestantes y adherencia a guía de manejo en primer nivel – Colmedica. Bogotá D.C., 2007

Las Infecciones Urinarias son causa de frecuente morbilidad, afecta a amplios sectores de la población, conllevan la utilización de antibióticos, afectan más a las mujeres, siendo un significativo problema de salud debido a su incidencia durante el embarazo que es del l0%1, diagnosticándose en la primera visita del control prenatal. Aproximadamente el 15% de las mujeres, tendrán una infección urinaria en alguna época durante su vida, con riesgos a largo plazo y calidad de vida. Amerita la detección temprana, el tratamiento oportuno y eficaz, el estudio y seguimiento posteriores.

A study on the phylogeny and the ecology of ammonia-oxidizing bacteria using a new molecular marker based on the gene amoB

L'agricultura i la industrialització han causat un augment significatiu del nombre d'ambients rics en amoni. La presència de compostos nitrogenats redueix la qualitat de l'aigua, causant problemes de toxicitat, deteriorant el medi ambient i fins i tot afectant la salut humana. En conseqüència, la nitrificació s'ha convertit en un procés global que afecta al cicle del nitrogen a la biosfera. Els bacteris oxidadors d'amoni (AOB) són els responsables de l'oxidació de l'amoni a nitrit, i juguen un paper essencial en el cicle del nitrogen. Els primers oxidadors d'amoni foren aïllats a finals del segle XIX, però la lentitud del seu creixement i les dificultats per cultivar-los feren que fins als anys 80, amb els primers estudis emprant el gen 16SrDNA, no s'assolís un coneixement complert d'aquest grup bacterià. Actualment les bases de dades contenen multitud d'entrades amb seqüències corresponents a AOB. L'objectiu d'aquest treball era trobar, desenvolupar i avaluar eines útils i fiables per a l'estudi dels AOB en mostres ambientals. En aquest treball primer descrivim la utilització de la hibridació in situ amb fluorescència (FISH), mitjançant l'aplicació de sondes amb diana en el 16SrRNA dels AOB. La FISH ens va permetre detectar i recomptar aquest grup bacterià; no obstant, aquest mètode no permetia la detecció de noves seqüències, pel que es necessitava una nova eina. Amb aquesta intenció vam aplicar la seqüència de la sonda Nso1225 en una PCR. El fet d'amplificar específicament un fragment del 16SrDNA dels AOB va suposar el desenvolupament d'una nova eina molecular que permetia detectar la presència i diversitat d'aquests bacteris en ambients naturals. Malgrat tot, algunes seqüències pertanyents a bacteris no oxidadors d'amoni del subgrup β dels proteobacteris, eren també obtingudes amb aquesta tècnica. Així mateix, un dels inconvenients de l'ús del 16SrDNA com a marcador és la impossibilitat de detectar simultàniament els AOB que pertanyen als subgrups β i γ dels proteobacteris. El gen amoA, que codifica per la subunitat A de l'enzim amoni monooxigenasa (AMO), era aleshores àmpliament utilitzat com a marcador per a la detecció dels AOB. En aquest treball també descrivim la utilització d'aquest marcador en mostres procedents d'un reactor SBR. Aquest marcador ens va permetre identificar seqüències de AOB en la mostra, però la necessitat de detectar amoA mitjançant clonatge fa que l'ús d'aquest marcador requereixi massa temps per a la seva utilització com a eina en estudis d'ecologia microbiana amb moltes mostres. Per altra banda, alguns autors han assenyalat l'obtenció de seqüències de no AOB en utilitzar amoA en un protocol de PCR-DGGE. Amb la finalitat d'obtenir una eina ràpida i rigorosa per detectar i identificar els AOB, vam desenvolupar un joc nou d'oligonucleòtids amb diana en el gen amoB, que codifica per a la subunitat transmembrana de l'enzim AMO. Aquest gen ha demostrat ser un bon marcador molecular pels AOB, oferint, sense tenir en compte afiliacions filogenètiques, una elevada especificitat, sensibilitat i fiabilitat. En aquest treball també presentem una anàlisi de RT-PCR basada en la detecció del gen amoB per a la quantificació del gènere Nitrosococcus. El nou joc d'oligonucleòtids dissenyat permet una enumeració altament específica i sensible de tots els γ-Nitrosococcus coneguts. Finalment, vam realitzar un estudi poligènic, comparant i avaluant els marcadors amoA, amoB i 16SrDNA, i vàrem construir un arbre filogenètic combinat. Com a resultat concloem que amoB és un marcador adequat per a la detecció i identificació dels AOB en mostres ambientals, proporcionant alhora agrupacions consistents en fer inferències filogenètiques. Per altra banda, la seqüència sencera del gen 16S rDNA és indicada com a marcador en estudis amb finalitats taxonòmiques i filogenètiques en treballar amb cultius purs de AOB.

The role of fungi and bacteria on the organic matter decomposition process in streams: interaction and relevance in biofilms

L'objectiu d'aquest estudi és el d'investigar sobre l'ús de matèria orgànica per part dels fongs i bacteris que colonitzen diferents substrats bentònics en rius Mediterranis i analitzar l'efecte dels factors ambientals i antròpics sobre l'estabilitat estructural i funcional de les comunitats del biofilm. La metodologia emprada en aquest estudi consisteix en: i) anàlisi de la biomassa bacteriana i fúngica, ii) anàlisi de la composició de les comunitats bentòniques (identificació d'hifomicets aquàtics i anàlisi del 16S rDNA bacterià), i iii) anàlisi de l'activitat enzimàtica extracel·lular relacionada amb el reciclatge de matèria orgànica en rius.

Lactic acid bacteria as bioprotective agents against foodborne pathogens and spoilage microorganisms in fresh fruits and vegetables

La present tesi doctoral es centra en l'aplicació dels bacteris de l'àcid lactic (BAL) com a agents bioprotectors davant microorganismes patògens i deteriorants.Es van aïllar i seleccionar BAL de fruites i hortalisses fresques i es van assajar in vitro davant 5 microorganismes fitopatògens i 5 patògens humans.Es van realitzar assajos d'eficàcia en pomes Golden Delicious amb tots els aïllats enfront les infeccions causades pel fong Penicillium expansum. La soca més eficaç era Weissella cibaria TM128, que reduïa el diàmetre de les infeccions en un 50%.Les soques seleccionades es van assajar enfront els patògens Salmonella typhimurium, Escherichia coli i Listeria monocytogenes en enciams Iceberg i pomes Golden Delicious.Els BAL interferien eficientment amb el creixemet de S. typhimurium, and L. monocytogenes, però van mostrar poc efecte enfront E. coli.Finalment, es van realitzar assajos dosi-resposta amb les soques Leuconostoc mesenteroides CM135, CM160 and PM249 enfront L. monocytogenes. De totes les soques assajades, la soca CM160 va ser la més efectiva.

Soft topographic map for clustering and classification of bacteria

In this work a new method for clustering and building a topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification or erroneous annotations in the database.

Iron Uptake and Homeostasis in Microorganisms

Preface. Iron is considered to be a minor element employed, in a variety of forms, by nearly all living organisms. In some cases, it is utilised in large quantities, for instance for the formation of magnetosomes within magnetotactic bacteria or during use of iron as a respiratory donor or acceptor by iron oxidising or reducing bacteria. However, in most cases the role of iron is restricted to its use as a cofactor or prosthetic group assisting the biological activity of many different types of protein. The key metabolic processes that are dependent on iron as a cofactor are numerous; they include respiration, light harvesting, nitrogen fixation, the Krebs cycle, redox stress resistance, amino acid synthesis and oxygen transport. Indeed, it is clear that Life in its current form would be impossible in the absence of iron. One of the main reasons for the reliance of Life upon this metal is the ability of iron to exist in multiple redox states, in particular the relatively stable ferrous (Fe2+) and ferric (Fe3+) forms. The availability of these stable oxidation states allows iron to engage in redox reactions over a wide range of midpoint potentials, depending on the coordination environment, making it an extremely adaptable mediator of electron exchange processes. Iron is also one of the most common elements within the Earth’s crust (5% abundance) and thus is considered to have been readily available when Life evolved on our early, anaerobic planet. However, as oxygen accumulated (the ‘Great oxidation event’) within the atmosphere some 2.4 billion years ago, and as the oceans became less acidic, the iron within primordial oceans was converted from its soluble reduced form to its weakly-soluble oxidised ferric form, which precipitated (~1.8 billion years ago) to form the ‘banded iron formations’ (BIFs) observed today in Precambrian sedimentary rocks around the world. These BIFs provide a geological record marking a transition point away from the ancient anaerobic world towards modern aerobic Earth. They also indicate a period over which the bio-availability of iron shifted from abundance to limitation, a condition that extends to the modern day. Thus, it is considered likely that the vast majority of extant organisms face the common problem of securing sufficient iron from their environment – a problem that Life on Earth has had to cope with for some 2 billion years. This struggle for iron is exemplified by the competition for this metal amongst co-habiting microorganisms who resort to stealing (pirating) each others iron supplies! The reliance of micro-organisms upon iron can be disadvantageous to them, and to our innate immune system it represents a chink in the microbial armour, offering an opportunity that can be exploited to ward off pathogenic invaders. In order to infect body tissues and cause disease, pathogens must secure all their iron from the host. To fight such infections, the host specifically withdraws available iron through the action of various iron depleting processes (e.g. the release of lactoferrin and lipocalin-2) – this represents an important strategy in our defence against disease. However, pathogens are frequently able to deploy iron acquisition systems that target host iron sources such as transferrin, lactoferrin and hemoproteins, and thus counteract the iron-withdrawal approaches of the host. Inactivation of such host-targeting iron-uptake systems often attenuates the pathogenicity of the invading microbe, illustrating the importance of ‘the battle for iron’ in the infection process. The role of iron sequestration systems in facilitating microbial infections has been a major driving force in research aimed at unravelling the complexities of microbial iron transport processes. But also, the intricacy of such systems offers a challenge that stimulates the curiosity. One such challenge is to understand how balanced levels of free iron within the cytosol are achieved in a way that avoids toxicity whilst providing sufficient levels for metabolic purposes – this is a requirement that all organisms have to meet. Although the systems involved in achieving this balance can be highly variable amongst different microorganisms, the overall strategy is common. On a coarse level, the homeostatic control of cellular iron is maintained through strict control of the uptake, storage and utilisation of available iron, and is co-ordinated by integrated iron-regulatory networks. However, much yet remains to be discovered concerning the fine details of these different iron regulatory processes. As already indicated, perhaps the most difficult task in maintaining iron homeostasis is simply the procurement of sufficient iron from external sources. The importance of this problem is demonstrated by the plethora of distinct iron transporters often found within a single bacterium, each targeting different forms (complex or redox state) of iron or a different environmental condition. Thus, microbes devote considerable cellular resource to securing iron from their surroundings, reflecting how successful acquisition of iron can be crucial in the competition for survival. The aim of this book is provide the reader with an overview of iron transport processes within a range of microorganisms and to provide an indication of how microbial iron levels are controlled. This aim is promoted through the inclusion of expert reviews on several well studied examples that illustrate the current state of play concerning our comprehension of how iron is translocated into the bacterial (or fungal) cell and how iron homeostasis is controlled within microbes. The first two chapters (1-2) consider the general properties of microbial iron-chelating compounds (known as ‘siderophores’), and the mechanisms used by bacteria to acquire haem and utilise it as an iron source. The following twelve chapters (3-14) focus on specific types of microorganism that are of key interest, covering both an array of pathogens for humans, animals and plants (e.g. species of Bordetella, Shigella, , Erwinia, Vibrio, Aeromonas, Francisella, Campylobacter and Staphylococci, and EHEC) as well as a number of prominent non-pathogens (e.g. the rhizobia, E. coli K-12, Bacteroides spp., cyanobacteria, Bacillus spp. and yeasts). The chapters relay the common themes in microbial iron uptake approaches (e.g. the use of siderophores, TonB-dependent transporters, and ABC transport systems), but also highlight many distinctions (such as use of different types iron regulator and the impact of the presence/absence of a cell wall) in the strategies employed. We hope that those both within and outside the field will find this book useful, stimulating and interesting. We intend that it will provide a source for reference that will assist relevant researchers and provide an entry point for those initiating their studies within this subject. Finally, it is important that we acknowledge and thank wholeheartedly the many contributors who have provided the 14 excellent chapters from which this book is composed. Without their considerable efforts, this book, and the understanding that it relays, would not have been possible. Simon C Andrews and Pierre Cornelis

Optimal protection of stabilised dry live bacteria from bile toxicity in oral dosage forms by bile acid adsorbent resins

We previously found that dried live bacteria of a vaccine strain can be temporarily sensitive to bile acids and suggested that Bile Adsorbing Resins (BAR) can be used in oral vaccine tablets to protect dried bacteria from intestinal bile. Here, we report a quantitative analysis of the ability of BAR to exclude the dye bromophenol blue from penetrating into matrix tablets and also sections of hard capsule shells. Based on this quantitative analysis, we made a fully optimised formulation, comprising 25% w/w of cholestyramine in Vcaps™ HPMC capsules. This gave effectively 100% protection of viability from 4% bile, with 4200-fold more live bacteria recovered from this formulation compared to unprotected dry bacteria. From the image analysis, we found that the filler material or compaction force used had no measurable effect on dye exclusion but did affect the rate of tablet hydration. Increasing the mass fraction of BAR gave more exclusion of dye up to 25% w/w, after which a plateau was reached and no further dye exclusion was seen. More effective dye exclusion was seen with smaller particle sizes (i.e. cholestyramine) and when the BAR was thoroughly dried and disaggregated. Similar results were found when imaging dye penetration into capsule sections or tablets. The predictions of the dye penetration study were tested using capsules filled with dried attenuated Salmonella vaccine plus different BAR types, and the expected protection from bile was found, validating the imaging study. Surprisingly, depending on the capsule shell material, some protection was given by the capsule alone without adding BAR, with Vcaps™ HPMC capsules providing up to 174-fold protection against 1% bile; faster releasing Vcaps Plus™ HPMC capsules and Coni Snap™ gelatin capsules gave less protection.