Effects of the ruminal comminution rate and microbial contamination of particles on accuracy of in situ estimates of ruminal degradability and intestinal digestibility of feedstuffs.

Effects of considering the comminution rate -kc- and the correction of microbial contamination -using 15N techniques- of particles in the rumen on estimates of ruminally undegraded fractions and their intestinal digestibility were examined generating composite samples -from rumen-incubated residues- representative of the undegraded feed rumen outflow. The study used sunflower meal -SFM- and Italian ryegrass hay -RGH- and three rumen and duodenum cannulated wethers fed with a 40:60 RGH to concentrate diet -75 g DM/kgBW0.75-. Transit studies up to the duodenum with Yb-SFM and Eu-RGH marked samples showed higher kc values -/h- in SFM than in RGH -0.577 vs. 0.0892, p = 0.034-, whereas similar values occurred for the rumen passage rate -kp-. Estimates of ruminally undegraded and intestinal digestibility of all tested fractions decreased when kc was considered and also applying microbial correction. Thus, microbial uncorrected kp-based proportions of intestinal digested undegraded crude protein overestimated those corrected and kc-kp-based by 39% in SFM -0.146 vs. 0.105- and 761% in RGH -0.373 vs. 0.0433-. Results show that both kc and microbial contamination correction should be considered to obtain accurate in situ estimates in grasses, whereas in protein concentrates not considering kc is an important source of error.

Study of the effect of four warm mix asphalt additives on bitumen modified with 15% crumb rubber

Due to a growing concern over global warming, the bituminous mixture industry is making a constant effort to diminish its emissions by reducing manufacturing and installation temperatures without compromising the mechanical properties of the bituminous mixtures. The use of mixtures with tyre rubber has demonstrated that these mixtures can be economical and ecological and that they improve the behaviour of the pavements. However, bituminous mixtures with a high rubber content present one major drawback: they require higher mixing and installation temperatures due to the elevated viscosity caused by the high rubber content and thus they produce larger amounts of greenhouse gas emissions than conventional bituminous mixtures. This article presents a study of the effect of four viscosity-reducing additives (Sasobit®, Asphaltan A®, Asphaltan B® and Licomont BS 100®) on a bitumen modified with 15% rubber. The results of this study indicate that these additives successfully reduce viscosity, increase the softening temperature and reduce penetration. However, they do not have a clear effect on the test for elastic recovery and ductility at 25 °C.

Asphalt rubber mixtures with warm mix asphalt additives

En los últimos años, debido a la creciente preocupación por el calentamiento global y el cambio climático, uno de los retos más importantes a los que se enfrenta nuestra sociedad es el uso eficiente y económico de energía así como la necesidad correspondiente de reducir los gases de efecto invernadero (GEI). Las tecnologías de mezclas semicalientes se han convertido en un nuevo e importante tema de investigación en el campo de los materiales para pavimentos ya que ofrece una solución potencial para la reducción del consumo energético y las emisiones de GEI durante la producción y puesta en obra de las mezclas bituminosas. Por otro lado, los pavimentos que contienen polvo de caucho procedente de neumático fuera de uso, al hacer uso productos de desecho, ahorran energía y recursos naturales. Estos pavimentos ofrecen una resistencia mejorada a la formación de roderas, a la fatiga y a la fisuración térmica, reducen los costes de mantenimiento y el ruido del tráfico así como prolongan la vida útil del pavimento. Sin embargo, estas mezclas presentan un importante inconveniente: la temperatura de fabricación se debe aumentar en comparación con las mezclas asfálticas convencionales, ya que la incorporación de caucho aumenta la viscosidad del ligante y, por lo tanto, se producen mayores cantidades de emisiones de GEI. En la presente Tesis, la tecnología de mezclas semicalientes con aditivos orgánicos (Sasobit, Asphaltan A, Asphaltan B, Licomont) se incorporó a la de betunes de alta viscosidad modificados con caucho (15% y 20% de caucho) con la finalidad de dar una solución a los inconvenientes de mezclas con caucho gracias a la utilización de aditivos reductores de la viscosidad. Para este fin, se estudió si sería posible obtener una producción más sostenible de mezclas con betunes de alto contenido en caucho sin afectar significativamente su nivel de rendimiento mecánico. La metodología aplicada para evaluar y comparar las características de las mezclas consistió en la realización de una serie de ensayos de laboratorio para betunes y mezclas con caucho y con aditivos de mezclas semicalientes y de un análisis del ciclo de vida híbrido de la producción de mezclas semicalientes teniendo en cuenta la papel del aditivo en la cadena de suministro con el fin de cuantificar con precisión los beneficios de esta tecnología. Los resultados del estudio indicaron que la incorporación de los aditivos permite reducir la viscosidad de los ligantes y, en consecuencia, las temperaturas de producción y de compactación de las mezclas. Por otro lado, aunque la adición de caucho mejoró significativamente el comportamiento mecánico de los ligantes a baja temperatura reduciendo la susceptibilidad al fenómeno de fisuración térmica, la adición de las ceras aumentó ligeramente la rigidez. Los resultados del estudio reológico mostraron que la adición de porcentajes crecientes de caucho mejoraban la resistencia del pavimento con respecto a la resistencia a la deformación permanente a altas temperaturas y a la fisuración térmica a bajas temperaturas. Además, se observó que los aditivos mejoran la resistencia a roderas y la elasticidad del pavimento al aumentar el módulo complejo a altas temperaturas y al disminuir del ángulo de fase. Por otra parte, el estudio reológico confirmó que los aditivos estudiados aumentan ligeramente la rigidez a bajas temperaturas. Los ensayos de fluencia llevados a cabo con el reómetro demostraron una vez más la mejora en la elasticidad y en la resistencia a la deformación permanente dada por la adición de las ceras. El estudio de mezclas con caucho y aditivos de mezclas semicalientes llevado a cabo demostró que las temperaturas de producción/compactación se pueden disminuir, que las mezclas no experimentarían escurrimiento, que los aditivos no cambian significativamente la resistencia conservada y que cumplen la sensibilidad al agua exigida. Además, los aditivos aumentaron el módulo de rigidez en algunos casos y mejoraron significativamente la resistencia a la deformación permanente. Asimismo, a excepción de uno de los aditivos, las mezclas con ceras tenían la misma o mayor resistencia a la fatiga en comparación con la mezcla control. Los resultados del análisis de ciclo de vida híbrido mostraron que la tecnología de mezclas semicalientes es capaz de ahorrar significativamente energía y reducir las emisiones de GEI, hasta un 18% y 20% respectivamente, en comparación con las mezclas de control. Sin embargo, en algunos de los casos estudiados, debido a la presencia de la cera, la temperatura de fabricación debe reducirse en un promedio de 8 ºC antes de que los beneficios de la reducción de emisiones y el consumo de combustible puedan ser obtenidos. Los principales sectores contribuyentes a los impactos ambientales generados en la fabricación de mezclas semicalientes fueron el sector de los combustibles, el de la minería y el de la construcción. Due to growing concerns over global warming and climate change in recent years, one of the most important challenges facing our society is the efficient and economic use of energy, and with it, the corresponding need to reduce greenhouse gas (GHG) emissions. The Warm Mix Asphalt (WMA) technology has become an important new research topic in the field of pavement materials as it offers a potential solution for the reduction of energy consumption and GHG emissions during the production and placement of asphalt mixtures. On the other hand, pavements containing crumb-rubber modified (CRM) binders save energy and natural resources by making use of waste products. These pavements offer an improved resistance to rutting, fatigue and thermal cracking; reduce traffic noise and maintenance costs and prolong pavement life. These mixtures, however, present one major drawback: the manufacturing temperature is higher compared to conventional asphalt mixtures as the rubber lends greater viscosity to the binder and, therefore, larger amounts of GHG emissions are produced. In this dissertation the WMA technology with organic additives (Sasobit, Asphaltan A, Asphaltan B and Licomont) was applied to CRM binders (15% and 20% of rubber) in order to offer a solution to the drawbacks of asphalt rubber (AR) mixtures thanks to the use of fluidifying additives. For this purpose, this study sought to determine if a more sustainable production of AR mixtures could be obtained without significantly affecting their level of mechanical performance. The methodology applied in order to evaluate and compare the performance of the mixtures consisted of carrying out several laboratory tests for the CRM binders and AR mixtures with WMA additives (AR-WMA mixtures) and a hybrid input-output-based life cycle assessment (hLCA) of the production of WMA. The results of the study indicated that the incorporation of the organic additives were able to reduce the viscosity of the binders and, consequently, the production and compaction temperatures. On the other hand, although the addition of rubber significantly improved the mechanical behaviour of the binders at low temperatures reducing the susceptibility to thermal cracking phenomena, the addition of the waxes slightly increased the stiffness. Master curves showed that the addition of increasing percentages of rubber improved the resistance of the pavement regarding both resistance to permanent deformation at high temperatures and thermal cracking at low temperatures. In addition, the waxes improved the rutting resistance and the elasticity as they increased the complex modulus at high temperatures and decreased the phase angle. Moreover, master curves also attest that the WMA additives studied increase the stiffness at low temperatures. The creep tests carried out proved once again the improvement in the elasticity and in the resistance to permanent deformation given by the addition of the waxes. The AR-WMA mixtures studied have shown that the production/compaction temperatures can be decreased, that the mixtures would not experience binder drainage, that the additives did not significantly change the retained resistance and fulfilled the water sensitivity required. Furthermore, the additives increased the stiffness modulus in some cases and significantly improved the permanent deformation resistance. Except for one of the additives, the waxes had the same or higher fatigue resistance compared to the control mixture. The results of the hLCA demonstrated that the WMA technology is able to significantly save energy and reduce GHG emissions, up to 18% and 20%, respectively, compared to the control mixtures. However, in some of the case studies, due to the presence of wax, the manufacturing temperature at the asphalt plant must be reduced by an average of 8ºC before the benefits of reduced emissions and fuel usage can be obtained. The results regarding the overall impacts generated using a detailed production layer decomposition indicated that fuel, mining and construction sectors are the main contributors to the environmental impacts of manufacturing WMA mixtures.

Partioning of dietary energy of chickens fed maize or wheat-based diets with and without a commercial blend of phytogenic feed additives

The aim of the study was to investigate the effects of a standardized mixture of a commercial blend of phytogenic feed additives containing 5% carvacrol, 3% cinnamaldehyde, and 2% capsicum on utilization of dietary energy and performance in broiler chickens. Four experimental diets were offered to the birds from 7 to 21 d of age. These included 2 basal control diets based on either wheat or maize that contained 215 g CP/kg and 12.13 MJ/kg ME and another 2 diets using the basal control diets supplemented with the plant extracts combination at 100 mg/kg diet. Each diet was fed to 16 individually penned birds following randomization. Dietary plant extracts improved feed intake and weight gain (P < 0.05) and slightly (P < 0.1) improved feed efficiency of birds fed the maize-based diet. Supplementary plant extracts did not change dietary ME (P > 0.05) but improved (P < 0.05) dietary NE by reducing the heat increment (P < 0.05) per kilogram feed intake. Feeding phytogenics improved (P < 0.05) total carcass energy retention and the efficiency of dietary ME for carcass energy retention. The number of interactions between type of diet and supplementary phytogenic feed additive suggest that the chemical composition and the energy to protein ratio of the diet may influence the efficiency of phytogenics when fed to chickens. The experiment showed that although supplementary phytogenic additives did not affect dietary ME, they caused a significant improvement in the utilization of dietary energy for carcass energy retention but this did not always relate to growth performance.

Use of tomato and cucumber horticulture by-products in goat diets: effects o nrumen fermentation and microbial communities in batch and continuous cultures

Two in vitro experiments were conducted to analyse the effects of replacing dietary barley grain with wastes of tomato and cucumber fruits and a 1 : 1 tomato : cucumber mixture on rumen fermentation characteristics and microbial abundance. The control (CON) substrate contained 250 g/kg of barley grain on a dry matter (DM) basis, and another 15 substrates were formulated by replacing 50, 100, 150, 200 or 250 g of barley grain/kg with the same amount (DM basis) of tomato or cucumber fruits or 1 : 1 tomato : cucumber mixture. In Expt 1, all substrates were incubated in batch cultures with rumen micro-organisms from goats for 24 h. Increasing amounts of tomato, cucumber and the mixture of both fruits in the substrate increased final pH and gas production, without changes in final ammonia-nitrogen (NH3-N) concentrations, substrate degradability and total volatile fatty acid (VFA) production, indicating that there were no detrimental effects of any waste fruits on rumen fermentation. Therefore, in Expt 2 the substrates including 250 g of waste fruits (T250, C250 and M250 for tomato, cucumber and the mixture of both fruits, respectively) and the CON substrate were incubated in single-flow continuous-culture fermenters for 8 days. Total VFA production did not differ among substrates, but there were differences in VFA profile. Molar proportions of propionate, isobutyrate and isovalerate were lower and acetate : propionate ratio was greater for T250 compared with CON substrate. Fermentation of substrates containing cucumber (C250 and M250) resulted in lower proportions of acetate, isobutyrate and isovalerate and acetate : propionate ratio, but greater butyrate proportions than the CON substrate. Carbohydrate degradability and microbial N synthesis tended to be lower for substrates containing cucumber than for the CON substrate, but there were no differences between CON and T250 substrates. Abundance of total bacteria, Fibrobacter succinogenes and Ruminococcus flavefaciens, fungi, methanogenic archaea and protozoa were similar in fermenters fed T250 and CON substrates, but fermenters fed C250 and M250 substrates had lower abundances of R. flavefaciens, fungi and protozoa than those fed the CON substrate. Results indicated that tomato fruits could replace dietary barley grain up to 250 g/kg of substrate DM without noticeable effects on rumen fermentation and microbial populations, but the inclusion of cucumber fruits at 250 g/kg of substrate DM negatively affected some microbial populations as it tended to reduce microbial N synthesis and changed the VFA profile. More studies are needed to identify the dietary inclusion level of cucumber which produces no detrimental effects on rumen fermentation and microbial growth.

Analysis of microbial populations in Rusitec fermenters fed diets of variable composition

Fermenters are widely used to study ruminal fermentation, but information on microbial populations developing in fermenters over the incubation period is limited. Four Rusitec fermenters were fed 2 diets representative of those administered to dairy sheep(DAI; 50:50 alfalfa hay:concentrate) and fattening lambs (FAT; 15:85 barley straw:concentrate) in a crossover design with 2 14-d incubation periods to assess the evolution of the microbial populations. There were 4 fermenters per diet.

Evolution of microbial diversity during prolonged starvation

Models of evolutionary processes postulate that new alleles appear in populations through random spontaneous mutation. Alleles that confer a competitive advantage in particular environments are selected and populations can be taken over by individuals expressing these advantageous mutations. We have studied the evolutionary process by using Escherichia coli cultures incubated for prolonged periods of time in stationary phase. The populations of surviving cells were shown to be highly dynamic, even after many months of incubation. Evolution proceeded along different paths even when the initial conditions were identical. As cultures aged, the takeovers by fitter mutants were incomplete, resulting in the coexistence of multiple mutant forms and increased microbial diversity. Thus, the study of bacterial populations in stationary phase provides a model system for understanding the evolution of diversity in natural populations.

Effects of hydrocarbon contamination on soil microbial community and enzyme activity

Acknowledgment I would like to gratefully acknowledge the government of Saudi Arabia for the scholarship and financial support.

Signalling through MyD88 drives surface expression of the mycobacterial receptors MCL (Clecsf8, Clec4d) and Mincle (Clec4e) following microbial stimulation

Acknowledgements We would like to thank the staff of the animal facility for their support and care for our animals. Funding was provided by the Wellcome Trust (102705) and Medical Research Council (UK) (MR/J004820/1) and a University of Aberdeen Studentship to BK.

Separate jasmonate-dependent and salicylate-dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens

The endogenous plant hormones salicylic acid (SA) and jasmonic acid (JA), whose levels increase on pathogen infection, activate separate sets of genes encoding antimicrobial proteins in Arabidopsis thaliana. The pathogen-inducible genes PR-1, PR-2, and PR-5 require SA signaling for activation, whereas the plant defensin gene PDF1.2, along with a PR-3 and PR-4 gene, are induced by pathogens via an SA-independent and JA-dependent pathway. An Arabidopsis mutant, coi1, that is affected in the JA-response pathway shows enhanced susceptibility to infection by the fungal pathogens Alternaria brassicicola and Botrytis cinerea but not to Peronospora parasitica, and vice versa for two Arabidopsis genotypes (npr1 and NahG) with a defect in their SA response. Resistance to P. parasitica was boosted by external application of the SA-mimicking compound 2,6-dichloroisonicotinic acid [Delaney, T., et al. (1994) Science 266, 1247–1250] but not by methyl jasmonate (MeJA), whereas treatment with MeJA but not 2,6-dichloroisonicotinic acid elevated resistance to Alternaria brassicicola. The protective effect of MeJA against A. brassicicola was the result of an endogenous defense response activated in planta and not a direct effect of MeJA on the pathogen, as no protection to A. brassicicola was observed in the coi1 mutant treated with MeJA. These data point to the existence of at least two separate hormone-dependent defense pathways in Arabidopsis that contribute to resistance against distinct microbial pathogens.

Microbial iron transport via a siderophore shuttle: A membrane ion transport paradigm

A mechanism of ion transport across membranes is reported. Microbial transport of Fe3+ generally delivers iron, a growth-limiting nutrient, to cells via highly specific siderophore-mediated transport systems. In contrast, iron transport in the fresh water bacterium Aeromonas hydrophila is found to occur by means of an indiscriminant siderophore transport system composed of a single multifunctional receptor. It is shown that (i) the siderophore and Fe3+ enter the bacterium together, (ii) a ligand exchange step occurs in the course of the transport, and (iii) a redox process is not involved in iron exchange. To the best of our knowledge, there have been no other reports of a ligand exchange mechanism in bacterial iron transport. The ligand exchange step occurs at the cell surface and involves the exchange of iron from a ferric siderophore to an iron-free siderophore already bound to the receptor. This ligand exchange mechanism is also found in Escherichia coli and seems likely to be widely distributed among microorganisms.

A phylogenomic approach to microbial evolution

To study the origin and evolution of biochemical pathways in microorganisms, we have developed methods and software for automatic, large-scale reconstructions of phylogenetic relationships. We define the complete set of phylogenetic trees derived from the proteome of an organism as the phylome and introduce the term phylogenetic connection as a concept that describes the relative relationships between taxa in a tree. A query system has been incorporated into the system so as to allow searches for defined categories of trees within the phylome. As a complement, we have developed the pyphy system for visualising the results of complex queries on phylogenetic connections, genomic locations and functional assignments in a graphical format. Our phylogenomics approach, which links phylogenetic information to the flow of biochemical pathways within and among microbial species, has been used to examine more than 8000 phylogenetic trees from seven microbial genomes. The results have revealed a rich web of phylogenetic connections. However, the separation of Bacteria and Archaea into two separate domains remains robust.

Prediction of operons in microbial genomes

Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P ≥ 0.98) to belong to the same operon. The sensitivity of our method is 30–50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site http://www.tigr.org/tigr-scripts/operons/operons.cgi.

The Comprehensive Microbial Resource

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.

A novel microbial habitat in the mid-ocean ridge subseafloor

The subseafloor at the mid-ocean ridge is predicted to be an excellent microbial habitat, because there is abundant space, fluid flow, and geochemical energy in the porous, hydrothermally influenced oceanic crust. These characteristics also make it a good analog for potential subsurface extraterrestrial habitats. Subseafloor environments created by the mixing of hot hydrothermal fluids and seawater are predicted to be particularly energy-rich, and hyperthermophilic microorganisms that broadly reflect such predictions are ejected from these systems in low-temperature (≈15°C), basalt-hosted diffuse effluents. Seven hyperthermophilic heterotrophs isolated from low-temperature diffuse fluids exiting the basaltic crust in and near two hydrothermal vent fields on the Endeavour Segment, Juan de Fuca Ridge, were compared phylogenetically and physiologically to six similarly enriched hyperthermophiles from samples associated with seafloor metal sulfide structures. The 13 organisms fell into four distinct groups: one group of two organisms corresponding to the genus Pyrococcus and three groups corresponding to the genus Thermococcus. Of these three groups, one was composed solely of sulfide-derived organisms, and the other two related groups were composed of subseafloor organisms. There was no evidence of restricted exchange of organisms between sulfide and subseafloor habitats, and therefore this phylogenetic distinction indicates a selective force operating between the two habitats. Hypotheses regarding the habitat differences were generated through comparison of the physiology of the two groups of hyperthermophiles; some potential differences between these habitats include fluid flow stability, metal ion concentrations, and sources of complex organic matter.