82 research outputs found
Computational studies of industrial hosts for improved production of the 2nd generation of biofuels
No full textIn an effort of overcoming the limited availability of fossil energy resources and moving toward a sustainable economy, the focus of the research and development in the area of biofuels has shifted towards developing the 2nd generation of fuels that should be produced via microbial fermentation. The 2nd generation biofuels should satisfy several criteria such as lower emission, higher energy density and should be less corrosive to engines. Although for many of these molecules, natural producers are known, they are not produced in the appreciated quantities. Heterologous expression of biosynthetic pathways taken from natural producers or expression of de novo synthetic pathways into microbial workhorses such as E. coli allows for production of a wide spectra of biofuels. Recently, P. putida has emerged as an amenable production hosts with a number of advantages over natural producers. P. putida is a non-pathogenic soil bacterium known for its versatile metabolism. This highly adaptive bacterium has been found to survive and grow on a wide range of substrates from pure caffeine to toxic industrial waste. Moreover, P. putida is tolerant to high toxicity compounds such as 2nd generation biofuel butanol. Counterintuitively, P. putida was seldom used as a host for the production of biofuels.
In this thesis, we performed a computational analysis of this organism to evaluate its metabolic capacities to serve as a potential 2nd generation biofuels production host. Its capacity was compared against heavily used host E. coli on the test example of production of one of the most prominent fuel candidate Methyl Ethyl Ketone (MEK).
To this end, we first performed a thermodynamic curation of the genome-scale iJN1411 model of P. putida, and we then used redGEM and lumpGEM algorithms to derive a consistently reduced large-scale stoichiometric model of P. putida. We integrated different omics data into resulting models and we proposed a novel way of constraining concentrations of the same species across different compartments while maintaining the consistency with the experimental measurements. To assess its capability to serve as a host, we evaluated and analyzed more than 3.6 millions biosynthetic pathways for production of 5 MEK precursors, in both heavily used industrial workhorse E. coli and rising P. putida. We compared their capability and performance with respect to thermodynamic feasibility and yield and we identified the most promising pathways for MEK production. Beside the discovered and evaluated pathways, we present a new way of clustering of feasible pathways and pathway precursors that allows us to classify and evaluate alternative ways for production and to better understand chemistry that leads towards the target molecule.
Identification of metabolic engineering targets for the improved biofuel production requires kinetic models. We used the ORACLE framework to generate a population of large-scale kinetic models of P. putida, and we employed these models in two studies. In the first study, for a wild-type strain of P. putida grown under aerobic conditions using glucose as a carbon source, we evaluated and validated the predictions of the generated kinetic models against a collection of experimental single-gene knockouts. In the second study, we analyzed the capacity of P. putida to adapt to increased energy demand, and we identified potential metabolic engineering targets for improved resistance of this organism to stress conditions.LCS
"Model", a Play by Milenko Paunović
No full textРад је посвећен анализи мисаоно-филозофских аспеката драме Модел Миленка Пауновића, с циљем да се у даљој перспективи детаљно истраже и протумаче елементи битни за проучавање Пауновићеве уметничке поетике коју је остварио у свом примарном, музичком стваралаштву.Composer Milenko Paunović (1889–1924) was also a librettist of his musical plays, which he created under the influence of Richard Wagner. His creative interests first developed along these lines, which resulted in synthesis in the musical plays Divina tragoedia (1910–1912) and Čengić aga (1923). However, a significant part of his dramatic oeuvre was not conditioned by the composing plans, but by the need for the literary articulation of certain thoughts and attitudes. In that context, he wrote plays Primorci (1911), Đavolova tragedija (1912), Model (1917), Dvori Srđe Zlopogleđe (1919), and a short story Dr Vrač (1919), which are important for interpreting Paunović’s worldviews and for understanding his musical works.
In most of Paunović’s plays, the themes of loneliness and the relationship between the subject and the world, free love and current morality, instinct and reason are examined. They are presented through attitudes of individual characters, aiming at confirming, refuting, or relativizing them. The thoughts to which the author constantly returns can be summarized in the following questions: Since this world, created by humans, is not good, is there a possibility for it to be improved, can a man change, reconcile with himself, and return to nature? In the search for answers, Paunović largely turns to the philosophy of Friedrich Nietzsche.
This paper is dedicated to the analysis of the reflective and philosophical aspects of the play Model, to further explore and interpret in detail the elements important for the study of Paunović’s artistic poetics, which he achieved in his primary, musical works. Within this framework, different understandings of life, the world, creativity as sublimation, and the art as a sphere that promotes the pursuit of truth and self-knowledge, represented in this play by its main protagonists, are considered
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
No full textBackground: Pseudomonas putida is a promising candidate for the industrial production of biofuels and biochemicals because of its high tolerance to toxic compounds and its ability to grow on a wide variety of substrates. Engineering this organism for improved performances and predicting metabolic responses upon genetic perturbations requires reliable descriptions of its metabolism in the form of stoichiometric and kinetic models. Results: In this work, we developed kinetic models of P. putida to predict the metabolic phenotypes and design metabolic engineering interventions for the production of biochemicals. The developed kinetic models contain 775 reactions and 245 metabolites. Furthermore, we introduce here a novel set of constraints within thermodynamics-based flux analysis that allow for considering concentrations of metabolites that exist in several compartments as separate entities. We started by a gap-filling and thermodynamic curation of iJN1411, the genome-scale model of P. putida KT2440. We then systematically reduced the curated iJN1411 model, and we created three core stoichiometric models of different complexity that describe the central carbon metabolism of P. putida. Using the medium complex-ity core model as a scaffold, we generated populations of large-scale kinetic models for two studies. In the first study, the developed kinetic models successfully captured the experimentally observed metabolic responses to several single-gene knockouts of a wild-type strain of P. putida KT2440 growing on glucose. In the second study, we used the developed models to propose metabolic engineering interventions for improved robustness of this organism to the stress condition of increased ATP demand. Conclusions: The study demonstrates the potential and predictive capabilities of the kinetic models that allow for rational design and optimization of recombinant P. putida strains for improved production of biofuels and biochemi-cals. The curated genome-scale model of P. putida together with the developed large-scale stoichiometric and kinetic models represents a significant resource for researchers in industry and academia.LCS
Computational analysis of Pseudomonas Putida metabolism Using Large-scale Kinetic Models
No full textP. putida is a highly adaptive, non-pathogenic, soil bacterium that can grow on a wide range of substrates, and it is tolerant to high toxicity compounds. For these reasons, it emerged recently as one of the most promising production hosts for a wide range of chemicals. In this work, we performed a computational analysis of this organism to evaluate its metabolic capacities and design metabolic engineering strategies to improve its robustness to stress conditions. To this end, we first performed a thermodynamic curation of the genome-scale iJN1411 model of P. putida KT2440, and we then used redGEM and lumpGEM algorithms to derive a consistently reduced large-scale stoichiometric model of P. putida. We integrated experimental data into the resulting core stoichiometric model, and we computed the thermodynamically-consistent steady state of metabolic fluxes. We then used the ORACLE framework to generate a population of large-scale kinetic models around the computed steady state, and we employed these models in two studies. In the first study, for wild-type strain of P. putida KT2440 grown under aerobic conditions using glucose as a carbon source, we evaluated and validated the predictions of the generated kinetic models against a collection of experimental single-gene knockouts. In the second study, we analyzed the capacity of P. putida to adapt to increased energy demand and we identified potential metabolic engineering targets for improved resistance of this organism to stress conditions. This work demonstrates the potential and usefulness of kinetic models in rational metabolic engineering strategies for (i) understanding the physiology of production hosts, (ii) optimizing production pathways, and (iii) improving the metabolic responses of organisms to environmental stresses.LCS
Predicted responses of a large-scale Pseudomonas putida KT2440 kinetic metabolic model to several single-gene knockouts are consistent with experimental observations
No full textP. putida emerged as one of the most promising production hosts for a wide range of chemicals, due to its fast growth with a low nutrient and cellular energy demand, considerable metabolic versatility, ability to grow in wide range of chemicals, suitability for genetic manipulations and its robustness and high flexibility to adapt and counteract different stresses. One of the main advantages of P. putida compared to commonly used industrial hosts such as E. coli is its superior tolerance to toxic compounds such as benzene, toluene, ethylbenzene, xylene and other hydrocarbons. In this work, we developed a large-scale kinetic model of P.putida to predict the metabolic phenotypes and design metabolic engineering interventions for the production of biochemicals. We first performed a gap-filling and thermodynamic curation of the genome-scale iJN1411 model of P. putida KT2440. The redGEM and lumpGEM algorithms for the systematic reduction of stoichiometric genome-scale models are then applied to the curated iJN1411 to derive a consistently reduced large-scale stoichiometric model of P. putida. Using this model as a scaffold, we next employed the ORACLE framework to generate a population of large-scale kinetic models around the experimentally observed steady state. To illustrate the predictive capabilities of these models, we performed two studies. First, for a wild-type strain of P. putida KT2440 growing on glucose under aerobic conditions, we computed metabolic responses to several single-gene knockouts, and the developed kinetic models successfully captured the experimentally observed phenotypes. In the second study, we proposed metabolic engineering interventions for improved robustness of this organism to stress conditions. Overall, the results from these studies suggest that the developed models of P. putida metabolism can successfully be used for metabolic engineering design.LCS
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
No full textDalmatian etymologies of Constantine Porphyrogenitus
No full textCilj je rada bio okupiti dalmatinske etimologije na jednom mjestu, promotriti
njihov odnos prema ostalim etimologijama u De administrando imperio kao i
njihov međusobni odnos, njihova zajednička i posebna obilježja. Pokazalo se
da su tumačenja imena u dalmatinskim poglavljima izrazito brojnija u odnosu
na ostatak spisa. Isto tako da su ta tumačenja obuhvatila svih pet kopnenih romanskih
gradova i svih sedam slavenskih zajednica u njihovu zaleđu. To je
sustavnost kakva se ne sreće u drugim dijelovima spisa. Premda se Porfirogenetu
često pripisuje strast za etimologiziranjem, čini se da je podrijetlo
velike većine, a možda i svih tumačenja imena lokalno, dalmatinsko. To se
zaključuje na temelju mjesne inspiracije u tumačenju i na temelju jezika kojim
se tumače etimoni. Riječ je redovito o latinskom ili slavenskom. Za razliku od
prijedloga I. Đurića, da bi "romejski" uključivao oba klasična jezika, ukazuje
se na razloge po kojima se "romejski” može i, zacijelo, treba uvijek razumjeti
samo kao latinski. Osobitost je dalmatinskih etimologija učestala poraba riječi
5 i 0cA,bktoIn De administrando imperio there are over 50 etymologies, of which in
Dalmatian chapters (29-36) there are 23 etymologies, almost half, even though
those chapters take less than one sixth of the texst of De administrando imperio.
Five Roman cities and seven Slav communities are described in Dalmatian
chapters. The names of all of them are explained. Such comprehensive approach
can not be found in any other part of De administrando imperio. Appart from
them there is only the etymology of mountain pass Kleisa and river Bona.
Constantine Porphyrogenitus is often considered as the author of those
etymologies. But, judging by local inspiration and languages in which the names
are interpreted, regularly Latin or Slavic, author concludes that the majority of
the ethnologies, perhaps even all of them, are of local origin. Therefor the author
disagrees with Yugoslav byzantologist Duric, who suggests that Constantine's
Romaic language includes both - Latin and Greek. The author is convinced that
it is always Latin.
The word 8mXeKxoq meaning ‘language’ can be found 14 times in De
administrando imperio, of which 11 times in Dalmatian etymologies. Obviously
it has to be the manner of Constantine's assistant expressing who rote Dalmatian
chapters. The same can be said for the verb épprjvebeuai ‘it means’, which
usually appears in Dalmatian etymologies, unlike other etymologies, where other
synonimic expressions appear as well
THE RUGOVSKA CHARTER — EXAMPLE OF SELF-MANAGEMENT CONTROL OF VENDETTA IN A KOSOVO VILLAGE
No full textThis work reviews the wide use and nature of vendetta in Kosovo The
author gives particular attention to possibilities for controlling the blood-feud in
modern day.
According to tradition, the quarrelling parties were reconciliated by the
so-called plećnija (Council of wise Men), whereas in more recent times the
state government undertook this task. This articles however discusses the character
of the peace councils which, within the frame of the Socialist Federation,
work to prevent blood-feuds. As example of a document which helps prevent
blood-feuds in a controlled manner is the Rugovska Charter. All inhabitants of the
mentioned area in Kosovo have accepted the charter, promising they will not take
revenge among themselves in the future. The results achieved from this charter
have surpassed all optimistic expectations. After its adoption, not one murder as
a result of vendetta took place in this area. The peace council, using this charter
as its basis, gained recognition in controlling vendetta.
The author emphasizes the advantage of using such prevention methods,
which are based on traditional law, yet adopted to the modern selFmanagcment
system principles
The res judicata rule in jurisdictional decisions of the international Court of justice
No full textThe author discusses the effects of the res judicata rule as regards jurisdictional decisions of the International Court of Justice. He finds that there exists a special position of a judgment on preliminary objection in respect to both aspects of the res judicata rule - its binding force and finality. A perception of distinct relativity of a jurisdictional decision of the Court, expressing its interlocatory character pervades, in his opinion, the body of law regulating the Court's activity. Preliminary objections as such do not exhaust objections to the jurisdiction of the Court, as evidenced by non-preliminary objections to the jurisdiction of the Court giving rise to the application of the principle compétence de la compétence understood in the narrow sense. With regard to the binding force of a judgment on preliminary objections, it does not create legal obligations stricto sensu. The author finds that the relative character of jurisdictional decisions of the Court as compared with a judgment on the merits is justified on a number of grounds
Relationship between the International Court of Justice and the International Criminal Tribunal for the former Yugoslavia in respect of the adjudication of genocide
No full textBy opting for the approach based on the dichotomy of individual criminal responsibility for the act of genocide and the responsibility of the State in both the Bosnian and Croatian Genocide cases, the International Court of Justice enabled the establishment of a jurisprudential connection with the judgments of the International Criminal Tribunal for the Former Yugoslavia. After outlining the reasons for adopting such an approach, which are classified as both positive and negative, the author offers an extensive analysis of the differences between the ICJ and ICTY, stressing the necessity to take these differences into account when considering the interconnection between the 'World Court' and the ICTY as a specialized tribunal. The paper focuses on the need for a balanced and critical approach to the jurisprudence of the ICTY as regards genocide, by differentiating between the Tribunal s factual and legal findings. The author insists that a substantive criterion, not a formal one, must be applied with a view to the proper assessment of the factual findings of the Tribunal in accordance with the standards of judicial reasoning of the ICJ. As regards the treatment of the ICTY's legal findings which relate to genocide, it is stressed that their uncritical acceptance would compromise the determination of the relevant rules of the Genocide Convention by the Court. Namely, the law applied by the ICTY as regards the crime of genocide is not equivalent to the relevant law established by the Convention and may be understood as its progressive development rather than its application
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