A process-based control for evolvable production systems

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Rational manipulation of mRNA folding free energy allows rheostat control of pneumolysin production by Streptococcus pneumoniae

Rational manipulation of mRNA folding free energy allows rheostat control of pneumolysin production by Streptococcus pneumoniae

Design and control of combined chemical processes for the production of pure enantiomers

Magdeburg, Univ., Fak. für Elektrotechnik und Informationstechnik, Diss., 2013

Positive control of swarming, rhamnolipid synthesis, and lipase production by the posttranscriptional RsmA/RsmZ system in Pseudomonas aeruginosa PAO1.

In Pseudomonas aeruginosa, the small RNA-binding, regulatory protein RsmA is a negative control element in the formation of several extracellular products (e.g., pyocyanin, hydrogen cyanide, PA-IL lectin) as well as in the production of N-acylhomoserine lactone quorum-sensing signal molecules. RsmA was found to control positively the ability to swarm and to produce extracellular rhamnolipids and lipase, i.e., functions contributing to niche colonization by P. aeruginosa. An rsmA null mutant was entirely devoid of swarming but produced detectable amounts of rhamnolipids, suggesting that factors in addition to rhamnolipids influence the swarming ability of P. aeruginosa. A small regulatory RNA, rsmZ, which antagonized the effects of RsmA, was identified in P. aeruginosa. Expression of the rsmZ gene was dependent on both the global regulator GacA and RsmA, increased with cell density, and was subject to negative autoregulation. Overexpression of rsmZ and a null mutation in rsmA resulted in quantitatively similar, negative or positive effects on target genes, in agreement with a model that postulates titration of RsmA protein by RsmZ RNA.

Control of brood male production in the Argentine ant Iridomyrmex humilis (Mayr)

The influence of various social factors on the production of males was investigated in the Argentine ant, Iridomyrmex humilis. In this polygynous species, the workers which are monomorphic are unable to lay reproductive eggs, so all the males are the progeny of the queens. Although male eggs appear to be laid by mated queens throughout the year, in large stock colonies males are reared periodically (every 3 or 4 months); males develop from brood taken from these colonies at any point in the cycle and given queenless or queenright (1 to 5 queens) units. This is in striking contrast to many other species of ants where it is generally assumed that male eggs are laid seasonnally. Comparative experiments suggest that several related factors influence the rearing of males as far as the pupal stage. Worker/larva ratio: The proportion of male larvae developing in standardized units in which the worker/larva ratio was varied from 0.25 to 25 demonstrated that low ratios inhibit male production. Queen influence: In standardized units where the worker/larva ratio was high the presence of queens did not inhibit the rearing of males suggesting that there is no queen inhibitory pheromone controlling male experimental production. Data suggest evidence that queens prevent male production by means of appropriation of food. Diet: Male larvae failed to pupate in experimental societies deprived of protein. Thus, the production of males appears to be controlled by the amount of food available to larvae. This depends on foraging activity, the quantity of brood in relation to the number of workers and the number of queens in the society.

Global GacA-steered control of cyanide and exoprotease production in Pseudomonas fluorescens involves specific ribosome binding sites.

The conserved two-component regulatory system GacS/GacA determines the expression of extracellular products and virulence factors in a variety of Gram-negative bacteria. In the biocontrol strain CHA0 of Pseudomonas fluorescens, the response regulator GacA is essential for the synthesis of extracellular protease (AprA) and secondary metabolites including hydrogen cyanide. GacA was found to exert its control on the hydrogen cyanide biosynthetic genes (hcnABC) and on the aprA gene indirectly via a posttranscriptional mechanism. Expression of a translational hcnA'-'lacZ fusion was GacA-dependent whereas a transcriptional hcnA-lacZ fusion was not. A distinct recognition site overlapping with the ribosome binding site appears to be primordial for GacA-steered regulation. GacA-dependence could be conferred to the Escherichia coli lacZ mRNA by a 3-bp substitution in the ribosome binding site. The gene coding for the global translational repressor RsmA of P. fluorescens was cloned. RsmA overexpression mimicked partial loss of GacA function and involved the same recognition site, suggesting that RsmA is a downstream regulatory element of the GacA control cascade. Mutational inactivation of the chromosomal rsmA gene partially suppressed a gacS defect. Thus, a central, GacA-dependent switch from primary to secondary metabolism may operate at the level of translation.

Regulation of antibiotic production in root-colonizing Peudomonas spp. and relevance for biological control of plant disease.

Certain strains of fluorescent pseudomonads are important biological components of agricultural soils that are suppressive to diseases caused by pathogenic fungi on crop plants. The biocontrol abilities of such strains depend essentially on aggressive root colonization, induction of systemic resistance in the plant, and the production of diffusible or volatile antifungal antibiotics. Evidence that these compounds are produced in situ is based on their chemical extraction from the rhizosphere and on the expression of antibiotic biosynthetic genes in the producer strains colonizing plant roots. Well-characterized antibiotics with biocontrol properties include phenazines, 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, lipopeptides, and hydrogen cyanide. In vitro, optimal production of these compounds occurs at high cell densities and during conditions of restricted growth, involving (i) a number of transcriptional regulators, which are mostly pathway-specific, and (ii) the GacS/GacA two-component system, which globally exerts a positive effect on the production of extracellular metabolites at a posttranscriptional level. Small untranslated RNAs have important roles in the GacS/GacA signal transduction pathway. One challenge in future biocontrol research involves development of new strategies to overcome the broad toxicity and lack of antifungal specificity displayed by most biocontrol antibiotics studied so far.

The early IL-4 response to Leishmania major responsible for progressive disease in BALB/c mice is subject to the control of autocrine IL-2 production and regulatory CD4+C25+ T cells

Résumé : La majorité des souches de souris de laboratoire sont résistantes à l'infection par le parasite Leishmania major (L. major). A l'opposé, les souris de la souche BALB développent une maladie évolutive. La résistance et la sensibilité sont corrélées avec l'apparition de lymphocytes T CD4+ spécifiques du parasite, Th1 (de l'anglais T helper) ou Th2 respectivement. La réponse aberrante Th2 chez les souris de la souche BALB/c dépend, au moins en partie, de façon critique de la production rapide d'IL-4 suite à l'infection. Ce pic précoce d'IL-4 est produit par une population de lymphocytes T CD4+ restreinte aux molécules du MHC de classe II, exprimant les chaînes du récepteur des cellules T Vß4-Va8. Ces lymphocytes sont spécifiques d'un épitope de l'homologue Leishmania de la molécule RACK1 des mammifères, appelée LACK. Il a été clairement démontré que l'IL-4 rapidement produite par ces cellules T CD4+ Vß4-Va8 induit la maturation Th2 responsable de la sensibilité vis-à-vis de L. major. Des expériences ont été entreprises pour étudier la régulation de cette réponse précoce d'IL-4. Dans ce travail, nous avons documenté, dans les cellules provenant des ganglions de souris sensibles infectées par L. major, une augmentation de la transcription de l'ARNm de l'IL-2 qui précède la réponse précoce d'IL-4. La neutralisation de l'IL-2 durant les premiers jours d'infection induit la maturation des cellules Thl et la résistance vis-à-vis de L. major. Ces effets de l'anticorps anti-IL-2 neutralisant sont liés à sa capacité d'interférer avec la transcription rapide d'IL-4 des cellules CD4+ réactives à l'antigène LACK. Une augmentation similaire d'IL-2 survient chez les souris résistantes C57BL/6 qui sont incapables de générer la réponse précoce d'IL-4. Cependant, la protéiné LACK induit une transcription précoce d'IL-2 uniquement chez les souris sensibles. Des expériences de reconstitution utilisant des souris C.B.-17 SCID et des cellules T CD4+ réactives à LACK provenant de souris BALB/c IL-2-~démontrent un mode d'action autocrine de l'IL-2 sur la régulation de la réponse précoce d'IL4. Par conséquent, chez les souris C57BL/6, l'absence du pic précoce d'ARNm de l'IL-4 important pour la progression de la maladie paraît liée à l'incapacité des cellules T CD4+ réactives à LACK de produire de l'IL-2. Un rôle dans le contrôle de la production précoce d'IL-4 par les cellules T régulatrices CD4+CD25+ a été investigué en déplétant in vivo cette population de cellules. La déplétion induit une élévation du pic précoce de l'ARNm de l'IL-4 dans les ganglions drainant de souris BALB/c, ainsi qu'une exacerbation du cours de la maladie avec des taux augmentés d'IL-4 dans les ganglions. La réponse rapide d'IL-2 vis-à-vis de L. major est aussi significativement augmentée chez les souris BALB/c déplétées en cellules CD4+CD25+. De plus, nous avons démontré que le transfert de 10puissance(7) cellules provenant de la rate de souris BALB/c déplétées en cellules T régulatrices CD4+CD25+ rend les souris SCID sensibles à l'infection et permet la différentiation Th2. Au contraire, les souris SCID reconstituées avec 10' cellules de la rate de souris BALB/c contrôle sont résistantes à infection par L. major et développent une réponse Thl. Chez les souris SCID reconstituées avec des cellules de rate déplétées en cellules exprimant le marqueur CD25, le traitement avec un anticorps neutralisant l'IL-4 au moment de l'infection par L. major prévient le développement de la réponse Th2 et rend ces souris résistantes à l'infection. Ces résultats démontrent que les cellules T régulatrices CD4+CD25+ jouent un rôle dans la régulation du pic précoce d'IL-4 responsable du développement cellulaire Th2 dans ce modèle d'infection. Summary Mice from most strains are resistant to infection with Leishmania major (L. major). In contrast, BALB mice develop progressive disease. Resistance and susceptibility result from parasite-specific CD4+ Thl or Th2 cells, respectively. The aberrant Th2 response in BALB/c mice depends, at least in part, upon the production of IL-4 early after infection. The CD4+ T cells responsible for this early IL-4 response to L. major express a restricted TCR repertoire (Vß4-Va8) and respond to an I-Ad-restricted epitope of the Leishmania homologue of mammalian RACK1, designated LACK. The role of these cells and the IL-4 they produce for subsequent Th2 cell development and disease progression in BALB/c mice was demonstrated. Experiments have been undertaken to study the regulation of the rapid IL-4 production to L. major. In this report, we document an IL-2 mRNA burst, preceding the reported early IL-4 response, in draining lymph nodes of susceptible mice infected with L. major. Neutralization of IL-2 during the first days of infection redirected Thl cell maturation and resistance to L. major, through interference with the rapid IL-4 transcription in LACKreactive CD4+ cells. A burst of IL-2 transcripts also occurred in infected C57BL/6 mice that do not mount an early IL-4 response. However, although the LACK protein induced IL-2 transcripts in susceptible mice, it failed to trigger this response in resistant C57BL/6 mice. Reconstitution experiments using C.B.-17 SCID mice and LACK-reactive CD4+ T cells from IL-2-/- BALB/c mice showed that triggering of the early IL-4 response required autocrine IL2. Thus, in C57BL/6 mice, the inability of LACK-reactive CD4+ T cells to express early IL-4 mRNA transcription, important for disease progression, appears due to an incapacity of these cells to produce IL-2. A role for CD4+CD25+ regulatory T cells in the control of this early IL-4 production was investigated by depleting in vivo this regulatory T cell population. Depletion induced an increase in the early burst of IL-4 mRNA in the draining lymph nodes of BALB/c mice, and exacerbated the course of disease with higher levels of IL-4 mRNA and protein in their lymph nodes. The rapid IL-2 response to L. major is also significantly enhanced in BALB/c mice depleted of CD4+CD25+ cells. We further showed that transfer of 10~ BALB/c spleen cells that were depleted of CD4+CD25+ regulatory T cells rendered SCID mice susceptible to infection and allowed Th2 differentiation while SCID mice reconstituted with 10 control BALB/c spleen cells were resistant to infection with L. major and developed a Thl response. Treatment with a mAb against IL-4 upon infection with L. major in SCID mice reconstituted with CD25-depleted spleen cells prevented the development of Th2 polarization and rendered them resistant to infection. These results demonstrate that CD4+CD25+ regulatory T cells play a role in regulating the early IL-4 mRNA and the subsequent development of a Th2 response in this model of infection.

Sheep production as a Senecio spp. control tool

Since poisoning by Senecio spp. is one of the main causes of cattle death in southern Brazil, control of these plants is a priority for the local livestock production. After the pasture has been mowed, grazing by 16 sheep was efficient for controlling Senecio brasiliensis and Senecio madagascariensis populations in a 5.5-hectare area that had long been severely infested with these species. A total of 28,629 plants among S. brasiliensis (flower-of-souls, 10,122) and S.madagascariensis (fireweed, 18,507) were almost completely eliminated in a two-year period. The number of sheep was kept at 3.0 stock units/ha, but a variable number of cattle were temporarily stocked according to pasture availability. The major sanitary practice applied to the sheep was anthelmintic administration. Liver biopsies taken from sheep and cattle before and after experimental period didn't reveal any change associable with seneciosis. The performance levels of the sheep were comparable to those observed in flocks managed under traditional extensive grazing systems in southern Brazil.

Effect of Lactobacillus sp. isolates supernatant on Escherichia coli O157:H7 enhances the role of organic acids production as a factor for pathogen control

Many attempts have been made to establish the control of foodborne pathogens through Lactobacillus isolates and their metabolism products with success being obtained in several situations. The aim of this study was to investigate the antagonistic effect of eight Lactobacillusisolates, including L. caseisubsp. pseudoplantarum,L. plantarum, L. reuteri and L. delbrueckii subsp. delbrueckii, on the pathogenic Escherichia colistrain O157:H7. The inhibitory effect of pure cultures and two pooled cultures supernatants of Lactobacillus on the growth of pathogenic bacteria was evaluated by the spot agar method and by monitoring turbidity. Antimicrobial activity was confirmed for L. reuteri and L. delbrueckii subsp. delbrueckii and for a pool of lactic acid bacteria. The neutralized supernatant of the pool exerted a higher antimicrobial activity than that of the individual strains. Furthermore, D-lactic acid and acetic acid were produced during growth of the Lactobacillus isolates studied.

Weed control under integrated nutrient management systems in faba bean (Vicia faba) production in Egypt

Two field experiments were conducted in two successive seasons, 2005/2006 and 2006/2007, to determine whether management can improve faba bean competitiveness with weeds, thus helping to achieve its yield potential. The experiment included five treatments, composed of organic and mineral fertilizers, alone and mixed at different rates, along with a control and six weed control treatments, including oxadiargyl, prometryn, hand hoeing treatments alone or mixed with the herbicides, and a nonweeded treatment (control).The herbicide treatments were not superior to the two hand-hoeing treatments. Using compost favored growth and yield of faba bean more than of weeds. Adding fertilizer also improved most yield parameters. Application of compost alone or combined with 50 or 100% of the recommended NPK rate improved faba bean growth in terms of net assimilation rate, specific leaf area, and leaf weight ratio as components of relative growth rate. This improvement in growth resulted in increase of seed yield, yield components and protein of faba bean. Faba bean yield performance improved under interactive fertilizer effects and weed control treatments as growth improved, as a result of nutrient release from fertilizers and weed control.

Nitrogen doses and weed control via intercropping with gliricidia for corn production

Many studies have demonstrated the beneficial influence of nitrogen doses on corn dry grain yield and green ear yield. Due to a growing concern with environmental degradation, many agricultural practices, adopted in the past, are being reexamined. With regard to weed control, strategies that employ mechanical control, including intercrops, are being the object of renewed interest. The purpose of this study was to evaluate the effects of the application of nitrogen doses (0, 40, 80, and 120 kg N ha-1; as ammonium sulfate) and weed control on the growth, green ear yield, and grain yield of the AG 1051 corn cultivar. A randomized block experimental design with split-plots and nine replications was adopted. In addition to nitrogen rates, the AG 1051 cultivar was submitted to the following treatments, applied to subplots: no weeding, two hoeings (at 20 and 40 days after sowing), and intercropping with gliricídia (Gliricidia sepium). Gliricidia was sowed at corn planting, between the corn rows, using two seedlings per pit, in pits spaced 0.30 m apart. Gliricidia did not provide weed control, and gave plant growth, green ear yield and grain yield values similar to the no weeding treatment. However, regarding the number of mature ears got, intercropping with gliricidia did not differ from the two-hoeing treatment. Weed control did not have an effect on plant height and number of marketable, husked green ears, with the application of 120 kg N ha-1; indicating that nitrogen improved the corn's competitive ability. The two-hoeing treatment provided the best means for total green ears weight, number of marketable husked ears, both unhusked and husked marketable ear weight, grain yield and its components than the other treatments. Nitrogen application increased corn growth, green ear yield, and grain yield, as well as weed green biomass, but reduced the stand and growth of gliricidia.

Oxalic acid and calcium oxalate in production of wood-containing paper : formation, analysis, and control

Papperstillverkningen störs ofta av oönskade föreningar som kan bilda avsättningar på processytor, vilket i sin tur kan ge upphov till störningar i pappersproduktionen samt försämring av papperskvaliteten. Förutom avsättningar av vedharts är stenliknande avlagringar av svårlösliga salter vanliga. I vårt dagliga liv är kalkavlagringar i kaffe- och vattenkokare exempel på liknande problem. I massa- och pappersindustrin är en av de mest problematiska föreningarna kalciumoxalat; detta salt är nästan olösligt i vatten och avlagringarna är mycket svåra att avlägsna. Kalciumoxalat är också känt som en av orsakerna till njurstenar hos människor. Veden och speciellt barken innehåller alltid en viss mängd oxalat men en större källa är oxalsyra som bildas när massan bleks med oxiderande kemikalier, t.ex. väteperoxid. Kalciumoxalat bildas när oxalsyran reagerar med kalcium som kommer in i processen med råvattnet, veden eller olika tillsatsmedel. I denna avhandling undersöktes faktorer som påverkar bildningen av oxalsyra och utfällningen av kalciumoxalat, med hjälp av bleknings- och utfällningsexperiment. Forskningens fokus låg speciellt på olika sätt att förebygga uppkomsten av avlagringar vid tillverkning av trähaltigt papper. Resultaten i denna avhandling visar att bildningen av oxalsyra samt utfällning av kalciumoxalat kan påverkas genom processtekniska och våtändskemiska metoder. Noggrann avbarkning av veden, kontrollerade förhållanden under den alkaliska peroxidblekningen, noggrann hantering och kontroll av andra lösta och kolloidala substanser, samt utnyttjande av skräddarsydd kemi för kontroll av avlagringar är nyckelfaktorer. Resultaten kan utnyttjas då man planerar blekningssekvenser för olika massor samt för att lösa problem orsakade av kalciumoxalat. Forskningsmetoderna som användes i utfällningsstudierna samt för utvärdering av tillsatsmedel kan också utnyttjas inom andra områden, t.ex. bryggeri- och sockerindustrin, där kalciumoxalatproblem är vanligt förekommande. -------------------------------------------- Paperinvalmistusta häiritsevät usein erilaiset epäpuhtaudet, jotka kiinnittyvät prosessipinnoille ja haittaavat tuotantoa sekä paperin laatua. Puun pihkan lisäksi eräs yleinen ongelma on niukkaliukoisten suolojen aiheuttamat kivettymät. Kalkkisaostuma kahvinkeittimessä on esimerkki vastaavasta ongelmasta arkielämässä. Massa- ja paperiteollisuudessa yksi hankalimmista kivettymien muodostajista on kalsiumoksalaatti, koska se on lähes liukenematonta ja sen aiheuttamat saostumat ovat erittäin vaikeasti poistettavia. Kalsiumoksalaatti on yleisesti tunnettu myös munuaiskivien aiheuttajana ihmisillä. Puu ja varsinkin sen kuori sisältää aina jonkin verran oksalaattia, mutta suurempi lähde on kuitenkin oksaalihappo jota muodostuu valkaistaessa massaa hapettavilla kemikaaleilla, kuten vetyperoksidilla. Kalsiumoksalaattia syntyy kun veden, puun ja lisäaineiden mukana prosessiin tuleva kalsium reagoi oksalaatin kanssa. Tässä väitöskirjatyössä tutkittiin oksaalihapon muodostumiseen ja kalsiumoksalaatin saostumiseen vaikuttavia tekijöitä valkaisu- ja saostumiskokeiden avulla. Tutkimuksen painopiste oli saostumien ehkäisemisessä puupitoisten painopaperien valmistuksessa. Työssä saadut tulokset osoittavat että oksaalihapon muodostumiseen ja kalsiumoksalaatin saostumiseen voidaan vaikuttaa sekä prosessiteknisten että märänpään kemian keinojen avulla. Tehokas puun kuorinta, optimoidut olosuhteet peroksidivalkaisussa, muiden liuenneiden ja kolloidisten aineiden hallinta sekä räätälöidyn kemian hyödyntäminen kalsiumoksalaattisaostumien torjunnassa ovat keskeisissä rooleissa ongelmien välttämiseksi. Väitöskirjatyön tuloksia voidaan hyödyntää massan valkaisulinjoja suunniteltaessa sekä kalsiumoksalaatin aiheuttamien ongelmien ratkaisemisessa. Tutkimusmenetelmiä, joita käytettiin saostumiskokeissa ja eri lisäaineiden vaikutusten arvioinnissa, voidaan hyödyntää massa- ja paperiteollisuuden lisäksi myös muilla alueilla, kuten sokeri- ja panimoteollisuudessa, joissa ongelma on myös yleinen.

Effect of metabolic control on interferon-gamma and interleukin-10 production by peripheral blood mononuclear cells from type 1 and type 2 diabetic patients

The objective of the present study was to evaluate the production of cytokines, interferon-g (INF-g) and interleukin-10 (IL-10), in cultures of peripheral blood mononuclear cells (PBMC) from type 1 and type 2 diabetic patients and to correlate it with inadequate and adequate metabolic control. We studied 11 type 1 and 13 type 2 diabetic patients and 21 healthy individuals divided into two groups (N = 11 and 10) paired by sex and age with type 1 and type 2 diabetic patients. The PBMC cultures were stimulated with concanavalin-A to measure INF-g and IL-10 supernatant concentration by ELISA. For patients with inadequate metabolic control, the cultures were performed on the first day of hospitalization and again after intensive treatment to achieve adequate control. INF-g levels in the supernatants of type 1 diabetic patient cultures were higher compared to type 2 diabetic patients with adequate metabolic control (P < 0.001). Additionally, INF-g and IL-10 tended to increase the liberation of PBMC from type 1 and 2 diabetic patients with adequate metabolic control (P = 0.009 and 0.09, respectively). The increased levels of INF-g and IL-10 released from PBMC of type 1 and 2 diabetic patients with adequate metabolic control suggest that diabetic control improves the capacity of activation and maintenance of the immune response, reducing the susceptibility to infections.