The identification of the transcriptional regulator CRP in Aeromonas hydrophila JMP636 and its involvement in amylase production and the 'acidic toxicity' effect

Aims: The physiological examination of amylase production by Aeromonas hydrophila JMP636 and identification of the mechanism of regulation. Methods and Results: Aeromonas hydrophila JMP636 was grown with single, then dual carbon sources; the growth cycle was followed and amylase activity throughout was monitored. The levels of cAMP, a known secondary messenger for the regulatory gene crp, were also examined. Amylase activity was regulated by catabolite repression. Physiological studies revealed that JMP636 exhibited both diauxic growth, with two carbon sources, and the 'acid toxicity' effect on glucose. The crp gene was cloned, expressed and inactivated from the JMP636 chromosome. Catabolite repression of amylase production and the 'acid toxicity' effect both require crp and were linked to cAMP levels. Conclusions: Regulation of amylase production was predicted to follow the model CRP-mediated cAMP-dependent Escherichia coli catabolite regulation system. Significance and Impact of the Study: This work provides an understanding of the physiology of the opportunistic pathogen Aer. hydrophila through identification of the mechanism of catabolite repression of amylase production and the existence of crp within this cell. It also provides a broader knowledge of global gene regulation and suggests regulatory mechanisms of other Aer. hydrophila gene/s.

Modeling and optimization of extracellular polysaccharides production by Enterobacter A47

Polysaccharides are gaining increasing attention as potential environmental friendly and sustainable building blocks in many fields of the (bio)chemical industry. The microbial production of polysaccharides is envisioned as a promising path, since higher biomass growth rates are possible and therefore higher productivities may be achieved compared to vegetable or animal polysaccharides sources. This Ph.D. thesis focuses on the modeling and optimization of a particular microbial polysaccharide, namely the production of extracellular polysaccharides (EPS) by the bacterial strain Enterobacter A47. Enterobacter A47 was found to be a metabolically versatile organism in terms of its adaptability to complex media, notably capable of achieving high growth rates in media containing glycerol byproduct from the biodiesel industry. However, the industrial implementation of this production process is still hampered due to a largely unoptimized process. Kinetic rates from the bioreactor operation are heavily dependent on operational parameters such as temperature, pH, stirring and aeration rate. The increase of culture broth viscosity is a common feature of this culture and has a major impact on the overall performance. This fact complicates the mathematical modeling of the process, limiting the possibility to understand, control and optimize productivity. In order to tackle this difficulty, data-driven mathematical methodologies such as Artificial Neural Networks can be employed to incorporate additional process data to complement the known mathematical description of the fermentation kinetics. In this Ph.D. thesis, we have adopted such an hybrid modeling framework that enabled the incorporation of temperature, pH and viscosity effects on the fermentation kinetics in order to improve the dynamical modeling and optimization of the process. A model-based optimization method was implemented that enabled to design bioreactor optimal control strategies in the sense of EPS productivity maximization. It is also critical to understand EPS synthesis at the level of the bacterial metabolism, since the production of EPS is a tightly regulated process. Methods of pathway analysis provide a means to unravel the fundamental pathways and their controls in bioprocesses. In the present Ph.D. thesis, a novel methodology called Principal Elementary Mode Analysis (PEMA) was developed and implemented that enabled to identify which cellular fluxes are activated under different conditions of temperature and pH. It is shown that differences in these two parameters affect the chemical composition of EPS, hence they are critical for the regulation of the product synthesis. In future studies, the knowledge provided by PEMA could foster the development of metabolically meaningful control strategies that target the EPS sugar content and oder product quality parameters.

Do labour mobility and networks foster geographical knowledge diffusion? The case of European regions

The goal of this paper is twofold: first, we aim to assess the role played by inventors’ cross-regional mobility and networks of collaboration in fostering knowledge diffusion across regions and subsequent innovation. Second, we intend to evaluate the feasibility of using mobility and networks information to build cross-regional interaction matrices to be used within the spatial econometrics toolbox. To do so, we depart from a knowledge production function where regional innovation intensity is a function not only of the own regional innovation inputs but also external accessible R&D gained through interregional interactions. Differently from much of the previous literature, cross-section gravity models of mobility and networks are estimated to use the fitted values to build our ‘spatial’ weights matrices, which characterize the intensity of knowledge interactions across a panel of 269 regions covering most European countries over 6 years.

On the origin and scope of the second language speech production disadvatage

Los hablantes bilingües tienen un acceso al léxico más lento y menos robusto que los monolingües, incluso cuando hablan en su lengua materna y dominante. Este fenómeno, comúnmente llamado “la desventaja bilingüe” también se observa en hablantes de una segunda lengua en comparación con hablantes de una primera lengua. Una causa que posiblemente contribuya a estas desventajas es el uso de control inhibitorio durante la producción del lenguaje: la inhibición de palabras coactivadas de la lengua actualmente no en uso puede prevenir intrusiones de dicha lengua, pero al mismo tiempo ralentizar la producción del lenguaje. El primer objetivo de los estudios descritos en este informe era testear esta hipótesis mediante diferentes predicciones generadas por teorías de control inhibitorio del lenguaje. Un segundo objetivo era investigar la extensión de la desventaja bilingüe dentro y fuera de la producción de palabras aisladas, así como avanzar en el conocimiento de las variables que la modulan. En lo atingente al primer objetivo, la evidencia obtenida es incompatible con un control inhibitorio global, desafiando la idea de mecanismos específicos en el hablante bilingüe utilizados para la selección léxica. Esto implica que una explicación común para el control de lenguaje y la desventaja bilingüe en el acceso al léxico es poco plausible. En cuanto al segundo objetivo, los resultados muestran que (a) la desventaja bilingüe no tiene un impacto al acceso a la memoria; (b) la desventaja bilingüe extiende a la producción del habla conectada; y (c) similitudes entre lenguas a diferentes niveles de representación así como la frecuencia de uso son factores que modulan la desventaja bilingüe.   

The tension between academic knowledge production and online peer production

Peer-reviewed

Growth and demise of Permian biogenic chert along northwest Pangea: evidence for end-Permian collapse of thermohaline circulation

The Permian Chert Event (PCE) was a 30 Ma long episode of unusual chert accumulation along the northwest margin of Pangea, and possibly worldwide. The onset of the PCE occurred at about the Sakmarian-Artinskian boundary in the Sverdrup Basin, Canadian Arctic, where it coincides with a maximum flooding event, the ending of high-frequency/high-amplitude shelf cyclicity, the onset of massive biogenic chert deposition in deep-water distal areas, and a long-term shift from warm- to cool-water carbonate sedimentation in shallow-water proximal areas. A similar and coeval shift is observed from the Barents Sea to the northwestern USA. A landward and southward expansion of silica factories occurred during the Middle and Late Permian at which time warm-water carbonate producers disappeared completely from the northwest margin of Pangea. Biotically impoverished and increasingly narrow cold-water carbonate factories (characterised by non-cemented bioclasts of sponges, bryozoans, echinoderms and brachiopods) were then progressively replaced by silica factories. By Late Permian time, little carbonate sediments accumulated in the Barents Sea and in the Sverdrup Basin. where the deep- to shallow-water sedimentary spectrum was occupied by siliceous sponge spicules. By that time, biogenic silica sedimentation was common throughout the world. Silica factories collapsed in the Late Permian, abruptly bringing the PCE to an end. In northwest Pangea, the end- Permian collapse of the PCE was associated with a major transgression and with a return to much warmer oceanic and continental climatic conditions. Chert deposition resumed in the distal oceanic areas during the early Middle Triassic (Anisian) after a 8-10 Ma interruption (Early Triassic Chert Gap). The conditions necessary for the onset, expansion and zenith of the PCE were provided by the thermohaline circulation of nutrient-rich cold waters along the northwestern and western margin of Pangea, and possibly throughout the world oceans. These conditions provided an efficient transportation mechanism that constantly replenished the supply of silica in the area, created a nutrient- and oxygen-rich environment favouring siliceous biogenic productivity. established cold sea-floor conditions, hindering silica dissolution, while increasing calcium carbonate solubility, and provided conditions adverse to organic and inorganic carbonate production, The northwest margin of Pangea was, for nearly 30 Ma. bathed by cold waters presumably derived from the seasonal melting of northern sea ice, the assumed engine for thermohaline circulation. This process started near the Sakmarian-Artinskian boundary. intensified throughout Middle and Late Permian time and ceased suddenly in latest Permian time, It led to oceanic conditions much colder than normally expected from the palaeolatitudes. and the influence of cold northerly-derived water was felt as far south southern Nevada. The demise of silica factories was caused by the rapid breakdown of these conditions and the establishment of a much warmer marine environment accompanied by sluggish circulation and perhaps a reduced input of dissolved silica to the ocean. Complete thawing of northern sea ice would have ended thermohaline circulation and led to warm and sluggish oceanic conditions inimical to the production. accumulation and preservation of biogenic silica.

Identification of Turning Points in the Research on Titanium Dioxide Production and Application

This dissertation "Identification of turning points in the research on titanium dioxide production and application" aims at detecting in scientific literatures emerging trends and sudden changes in titanium dioxide production and application. These key changes are then studied to determine its transient patterns and its effect on the research on titanium dioxide production and application The source of information is from bibliographic data which discussed titanium dioxide production and application. These bibliographic data where obtained from ISI Web of Knowledge and then formed into a network of clusters by applying software called Citespace.

Enhancing Customer Knowledge and Its Sharing At a Paper Production Line

This study has been made for specific paper production line at an international forest industry company in Finland. The main purpose for the study was a need to examine the current situation of the customer knowledge and its’ sharing at case production line, recognize the problems in it and finally, find out the improvement actions. The study is composed of theoretical and empirical parts. In theoretical part, knowledge management and information sharing in addition to customer knowledge management are presented. Empirical data from case production line was collected by using survey questionnaires. The results are analyzed in discussion and conclusions and finally, study ends with summary which includes recommendations. Based on the study, the amount and quality of customer knowledge and gaining and transferring the customer knowledge were found as the main challenges. The proposed solutions were discovered from moving towards more dynamic operating environment and in the area of customer knowledge management, especially from the communities of creation.

Etiology and epidemiology of Pythium root rot in hydroponic crops: current knowledge and perspectives

The etiology and epidemiology of Pythium root rot in hydroponically-grown crops are reviewed with emphasis on knowledge and concepts considered important for managing the disease in commercial greenhouses. Pythium root rot continually threatens the productivity of numerous kinds of crops in hydroponic systems around the world including cucumber, tomato, sweet pepper, spinach, lettuce, nasturtium, arugula, rose, and chrysanthemum. Principal causal agents include Pythium aphanidermatum, Pythium dissotocum, members of Pythium group F, and Pythium ultimum var. ultimum. Perspectives are given of sources of initial inoculum of Pythium spp. in hydroponic systems, of infection and colonization of roots by the pathogens, symptom development and inoculum production in host roots, and inoculum dispersal in nutrient solutions. Recent findings that a specific elicitor produced by P. aphanidermatum may trigger necrosis (browning) of the roots and the transition from biotrophic to necrotrophic infection are considered. Effects on root rot epidemics of host factors (disease susceptibility, phenological growth stage, root exudates and phenolic substances), the root environment (rooting media, concentrations of dissolved oxygen and phenolic substances in the nutrient solution, microbial communities and temperature) and human interferences (cropping practices and control measures) are reviewed. Recent findings on predisposition of roots to Pythium attack by environmental stress factors are highlighted. The commonly minor impact on epidemics of measures to disinfest nutrient solution as it recirculates outside the crop is contrasted with the impact of treatments that suppress Pythium in the roots and root zone of the crop. New discoveries that infection of roots by P. aphanidermatum markedly slows the increase in leaf area and whole-plant carbon gain without significant effect on the efficiency of photosynthesis per unit area of leaf are noted. The platform of knowledge and understanding of the etiology and epidemiology of root rot, and its effects on the physiology of the whole plant, are discussed in relation to new research directions and development of better practices to manage the disease in hydroponic crops. Focus is on methods and technologies for tracking Pythium and root rot, and on developing, integrating, and optimizing treatments to suppress the pathogen in the root zone and progress of root rot.

“Studies on extracellular enzyme production during growth of Pleurotus sp. on lignocellulosic agriwaste and the utilization of spent mushroom substrate”

Commercially, Pleurotus spp. of mushroom are cultivated in bags. After mushroom cultivation, spent substrate remains as residual material. Proper recycling of spent substrate is beneficial for our economy. Spent substrate can be utilized for various other value added purposes through the proper knowledge of its components. Composition of various components depends on the activity of extracellular enzymes in the spent substrate. The present study was conducted to know the enzyme profile of some major extracellular enzymes - cellulase, hemicellulase (xylanase), pectinase and ligninase (lignin peroxidase and laccase) and to estimate cellulose, hemicellulose, pectin and lignin in the substrate. The use of spent substrate as a source of fibre and ethanol, and in the biodegradation of phenol by Pleurotus spp. was also investigated

Modelling of global crop production and resulting N2O emissions

Landwirtschaft spielt eine zentrale Rolle im Erdsystem. Sie trägt durch die Emission von CO2, CH4 und N2O zum Treibhauseffekt bei, kann Bodendegradation und Eutrophierung verursachen, regionale Wasserkreisläufe verändern und wird außerdem stark vom Klimawandel betroffen sein. Da all diese Prozesse durch die zugrunde liegenden Nährstoff- und Wasserflüsse eng miteinander verknüpft sind, sollten sie in einem konsistenten Modellansatz betrachtet werden. Dennoch haben Datenmangel und ungenügendes Prozessverständnis dies bis vor kurzem auf der globalen Skala verhindert. In dieser Arbeit wird die erste Version eines solchen konsistenten globalen Modellansatzes präsentiert, wobei der Schwerpunkt auf der Simulation landwirtschaftlicher Erträge und den resultierenden N2O-Emissionen liegt. Der Grund für diese Schwerpunktsetzung liegt darin, dass die korrekte Abbildung des Pflanzenwachstums eine essentielle Voraussetzung für die Simulation aller anderen Prozesse ist. Des weiteren sind aktuelle und potentielle landwirtschaftliche Erträge wichtige treibende Kräfte für Landnutzungsänderungen und werden stark vom Klimawandel betroffen sein. Den zweiten Schwerpunkt bildet die Abschätzung landwirtschaftlicher N2O-Emissionen, da bislang kein prozessbasiertes N2O-Modell auf der globalen Skala eingesetzt wurde. Als Grundlage für die globale Modellierung wurde das bestehende Agrarökosystemmodell Daycent gewählt. Neben der Schaffung der Simulationsumgebung wurden zunächst die benötigten globalen Datensätze für Bodenparameter, Klima und landwirtschaftliche Bewirtschaftung zusammengestellt. Da für Pflanzzeitpunkte bislang keine globale Datenbasis zur Verfügung steht, und diese sich mit dem Klimawandel ändern werden, wurde eine Routine zur Berechnung von Pflanzzeitpunkten entwickelt. Die Ergebnisse zeigen eine gute Übereinstimmung mit Anbaukalendern der FAO, die für einige Feldfrüchte und Länder verfügbar sind. Danach wurde das Daycent-Modell für die Ertragsberechnung von Weizen, Reis, Mais, Soja, Hirse, Hülsenfrüchten, Kartoffel, Cassava und Baumwolle parametrisiert und kalibriert. Die Simulationsergebnisse zeigen, dass Daycent die wichtigsten Klima-, Boden- und Bewirtschaftungseffekte auf die Ertragsbildung korrekt abbildet. Berechnete Länderdurchschnitte stimmen gut mit Daten der FAO überein (R2 = 0.66 für Weizen, Reis und Mais; R2 = 0.32 für Soja), und räumliche Ertragsmuster entsprechen weitgehend der beobachteten Verteilung von Feldfrüchten und subnationalen Statistiken. Vor der Modellierung landwirtschaftlicher N2O-Emissionen mit dem Daycent-Modell stand eine statistische Analyse von N2O-und NO-Emissionsmessungen aus natürlichen und landwirtschaftlichen Ökosystemen. Die als signifikant identifizierten Parameter für N2O (Düngemenge, Bodenkohlenstoffgehalt, Boden-pH, Textur, Feldfrucht, Düngersorte) und NO (Düngemenge, Bodenstickstoffgehalt, Klima) entsprechen weitgehend den Ergebnissen einer früheren Analyse. Für Emissionen aus Böden unter natürlicher Vegetation, für die es bislang keine solche statistische Untersuchung gab, haben Bodenkohlenstoffgehalt, Boden-pH, Lagerungsdichte, Drainierung und Vegetationstyp einen signifikanten Einfluss auf die N2O-Emissionen, während NO-Emissionen signifikant von Bodenkohlenstoffgehalt und Vegetationstyp abhängen. Basierend auf den daraus entwickelten statistischen Modellen betragen die globalen Emissionen aus Ackerböden 3.3 Tg N/y für N2O, und 1.4 Tg N/y für NO. Solche statistischen Modelle sind nützlich, um Abschätzungen und Unsicherheitsbereiche von N2O- und NO-Emissionen basierend auf einer Vielzahl von Messungen zu berechnen. Die Dynamik des Bodenstickstoffs, insbesondere beeinflusst durch Pflanzenwachstum, Klimawandel und Landnutzungsänderung, kann allerdings nur durch die Anwendung von prozessorientierten Modellen berücksichtigt werden. Zur Modellierung von N2O-Emissionen mit dem Daycent-Modell wurde zunächst dessen Spurengasmodul durch eine detailliertere Berechnung von Nitrifikation und Denitrifikation und die Berücksichtigung von Frost-Auftau-Emissionen weiterentwickelt. Diese überarbeitete Modellversion wurde dann an N2O-Emissionsmessungen unter verschiedenen Klimaten und Feldfrüchten getestet. Sowohl die Dynamik als auch die Gesamtsummen der N2O-Emissionen werden befriedigend abgebildet, wobei die Modelleffizienz für monatliche Mittelwerte zwischen 0.1 und 0.66 für die meisten Standorte liegt. Basierend auf der überarbeiteten Modellversion wurden die N2O-Emissionen für die zuvor parametrisierten Feldfrüchte berechnet. Emissionsraten und feldfruchtspezifische Unterschiede stimmen weitgehend mit Literaturangaben überein. Düngemittelinduzierte Emissionen, die momentan vom IPCC mit 1.25 +/- 1% der eingesetzten Düngemenge abgeschätzt werden, reichen von 0.77% (Reis) bis 2.76% (Mais). Die Summe der berechneten Emissionen aus landwirtschaftlichen Böden beträgt für die Mitte der 1990er Jahre 2.1 Tg N2O-N/y, was mit den Abschätzungen aus anderen Studien übereinstimmt.

Assessment of the strategies of organic fruit production and fruit drying in Uganda

Organic agriculture in Uganda is developing at a fast pace and despite this trend Uganda is still unable to produce enough fresh and dry organic fruits mainly pineapple to meet the exporters demand. This current research investigated the strategies of farmers at production level by assessing the pros and cons of fruit growing, organic agriculture and fruit drying in order to understand the underlying causal factor for the low production of organic dry fruits in a major fruit producing district of Uganda. The study was carried out in two separate and distinctive areas; one which only produces and export fresh organic pineapple and the other which exports dried fruits (mainly pineapple and papaya). About 10% of the farmers in the two study areas were surveyed using questionnaires which were further followed by semi-structured interviews and participatory rural appraisals activities with various types of farmers in order to understand the different decisions and strategies of farmers. 82% and 74% of farmers in the two study areas grew fruits as it gave better economic returns and for 77% and 90% respectively in the two study areas, the reasons for growing fruit was the ease of selling compared to other crops. All the farmers were relying on coffee husk for growing organic pineapples. However, 50% of the farmers want to grow pineapples (either organic or conventional) but couldn't afford to buy coffee husk. Fruit drying was mainly a strategy to utilize cheap fruits during harvesting seasons for value addition. 71% and 42% of farmers in the two study areas wanted to dry fruits but it was beyond their economic capacity to buy the driers. Decision of the farmers whether to grow fruits or cereals, organic or conventional agriculture and selling the fruits as fresh or dry were dependent mainly on the economic, knowledge and resource availability of each type of practices. It is concluded that the main barrier for an increase in the production of organic dried fruits is at the processing level, and the limited capacity for investments in drying facilities.

The role of NGO in informal seed production and dissemination: The case of eastern Ethiopia

Seed is the basic input to crop production. Farmer-based seed production as an alternative agricultural technology transfer is increasingly given especial attention in developing countries where food insecurity is critical. This paper aims to assess the seed production and dissemination strategy among smallholder farmers in eastern Ethiopia that has been introduced by Hararghe Catholic Secretariat (a Non-GovernmentalOrganization). A survey of 160 households in four administrative districts and focus group discussions were used to collect data. While narratives helped understand the process, logistic regressionwas used to identify determinants of land allocation to seed production. Results indicate the crucial role of informal networks and social capital as facilitators of access to production inputs, information and knowledge. The informal seed supply system initiated by the NGO has a huge potential to benefit smallholder farmers by improving their access to higher-yielding varieties of various crops, thereby contributing to an increase in their wellbeing. However, the traditional practice of seed exchange, influenced by social relations, will remain uneconomical to seed producers. Thus, the paper suggests that this potential can be further exploited if some preconditions such as establishment of seed banks, investment in human capital, removal of the underlying constraints and creation of reliable seed markets are given emphasis.

Farmers’ knowledge and perceptions of potato pests and their management in Uganda

As we initiate entomological research on potato (Solanum tuberosum L.) in Uganda, there is need to understand farmers’ knowledge of existing insect pest problems and their management practices. Such information is important for designing a suitable intervention and successful integrated pest management (IPM) strategy. A farm household survey using a structured questionnaire was conducted among 204 potato farmers in six districts of Uganda (i.e., Kabale, Kisoro, Mbale, Kapchorwa, Mubende, and Kyegegwa) during August and September 2013. Diseases, insect pests, price fluctuations, and low market prices were the four highest ranked constraints in potato production, in order of decreasing importance. Cutworms (Agrotis spp.), aphids (Myzus persicae (Sulzer)), and potato tuber moth (Phthorimaea operculella (Zeller)) were the three most severe insect pests. Ants (Dorylis orantalis Westwood), whiteflies (Bemisia tabaci (Gennadius)), and leafminer flies (Liriomyza huidobrensis (Blanchard)) were pests of moderate importance. Major yield losses are predominantly due to late blight (Phytophthora infestans (Mont.) de Bary) and reached 100% without chemical control in the districts of Kabale, Kisoro, Mbale, and Kapchorwa. On average, farmers had little to moderate knowledge about pest characteristics. The predominant control methods were use of fungicides (72% of respondents) and insecticides (62% of respondents). On average, only 5% of the 204 farmers knew about insect pests and their natural enemies. This lack of knowledge calls for training of both farmers and extension workers in insect pest identification, their biology, and control. Empowering farmers with knowledge about insect pests is essential for the reduction of pesticide misuse and uptake of more environmentally friendly approaches like IPM. Field surveys would need follow-up in order to assess the actual field infestation rates and intensities of each insect pest and compare the results with the responses received from farmers.