Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways

<p>Abstract</p> <p>Background</p> <p>In the present article, we propose a method for determining optimal metabolic pathways in terms of the level of concentration of the enzymes catalyzing various reactions in the entire metabolic network. The method, first of all, generates data on reaction fluxes in a pathway based on steady state condition. A set of constraints is formulated incorporating weighting coefficients corresponding to concentration of enzymes catalyzing reactions in the pathway. Finally, the rate of yield of the target metabolite, starting with a given substrate, is maximized in order to identify an optimal pathway through these weighting coefficients.</p> <p>Results</p> <p>The effectiveness of the present method is demonstrated on two synthetic systems existing in the literature, two pentose phosphate, two glycolytic pathways, core carbon metabolism and a large network of carotenoid biosynthesis pathway of various organisms belonging to different phylogeny. A comparative study with the existing extreme pathway analysis also forms a part of this investigation. Biological relevance and validation of the results are provided. Finally, the impact of the method on metabolic engineering is explained with a few examples.</p> <p>Conclusions</p> <p>The method may be viewed as determining an optimal set of enzymes that is required to get an optimal metabolic pathway. Although it is a simple one, it has been able to identify a carotenoid biosynthesis pathway and the optimal pathway of core carbon metabolic network that is closer to some earlier investigations than that obtained by the extreme pathway analysis. Moreover, the present method has identified correctly optimal pathways for pentose phosphate and glycolytic pathways. It has been mentioned using some examples how the method can suitably be used in the context of metabolic engineering.</p

Apoptosis and the activity of ceramide, Bax and Bcl-2 in the lungs of neonatal rats exposed to limited and prolonged hyperoxia

BACKGROUND: The aim of the study is to examine the effect of limited and prolonged hyperoxia on neonatal rat lung. This is done by examining the morphologic changes of apoptosis, the expression of ceramide, an important mediator of apoptosis, the expression of inflammatory mediators represented by IL-1β and the expression of 2 proto-oncogenes that appear to modulate apoptosis (Bax and Bcl-2). METHODS: Newborn rats were placed in chambers containing room air or oxygen above 90% for 7 days. The rats were sacrificed at 3, 7 or 14 days and their lungs removed. Sections were fixed, subjected to TUNEL, Hoechst, and E-Cadherin Staining. Sections were also incubated with anti-Bcl-2 and anti-Bax antisera. Bcl-2 and Bax were quantitated by immunohistochemistry. Lipids were extracted, and ceramide measured through a modified diacylglycerol kinase assay. RT-PCR was utilized to assess IL-1β expression. RESULTS: TUNEL staining showed significant apoptosis in the hyperoxia-exposed lungs at 3 days only. Co-staining of the apoptotic cells with Hoechst, and E-Cadherin indicated that apoptotic cells were mainly epithelial cells. The expression of Bax and ceramide was significantly higher in the hyperoxia-exposed lungs at 3 and 14 days of age, but not at 7 days. Bcl-2 was significantly elevated in the hyperoxia-exposed lungs at 3 and 14 days. IL-1β expression was significantly increased at 14 days. CONCLUSION: Exposure of neonatal rat lung to hyperoxia results in early apoptosis documented by TUNEL assay. The early rise in Bax and ceramide appears to overcome the anti-apoptotic activity of Bcl-2. Further exposure did not result in late apoptotic changes. This suggests that apoptotic response to hyperoxia is time sensitive. Prolonged hyperoxia results in acute lung injury and the shifting balance of ceramide, Bax and Bcl-2 may be related to the evolution of the inflammatory process

Utilizing heat regeneration within hydraulic pressure accumulator

Tekniikan kehittyessä toimilaitteiden ja järjestelmien suunnittelussa ja toteutuksessa laitteiden ja koneiden energia- ja kustannustehokkuus nousevat jatkuvasti tärkeämpään rooliin. Hydraulisilla toimilaitteilla saavutetaan korkea tehotiheys, mutta järjestelmien kokonaishyötysuhde on usein heikko. Hyötysuhdetta voidaan nostaa lisäämällä järjestelmiin energian talteenotto, jolloin työkierroista voidaan normaalisti hukkaan menevää energiaa varastoida ja käyttää uudelleen seuraavassa työkierrossa. Hydraulisissa energian talteenottojärjestelmissä energiaa varastoidaan tyypillisesti hydraulipaineakkuihin. Paineakuissa energia varastoituu puristamalla paineakun kaasutilavuudessa olevaa kaasua. Puristusvaiheen aikana kaasun lämpötila nousee ja lämpö alkaa virrata paineakusta ympäristöön. Tämä energian virtaaminen ympäristöön muodostaa merkittävimmän yksittäisen paineakun hyötysuhdetta laskevan tekijän. Tämän työn tavoitteena oli nostaa mäntäpaineakun hyötysuhdetta hyödyntämällä lämmön regenerointia. Lämmön regeneroinnilla pyritään varastoimaan kaasussa puristusvaiheessa syntyvä lämpöenergia lämpöregeneraattoriin ja luovuttamaan energia takaisin kaasuun paineakun purkusyklin aikana. Työssä suunniteltu lämpöregeneraattori perustui faasimuutosmateriaalien hyödyntämiseen energiavarastona. Faasimuutosmateriaalit soveltuvat erinomaisesti lämpövarastoiksi, sillä ne kykenevät sitomaan suuren määrän energiaa faasimuutoksen aikana, jolloin työssä suunniteltu lämpöregeneraattori saatiin mahdutettua mäntäpaineakun sisälle. Työssä saatujen mittaustuloksien perusteella pääteltiin, että lämpöregeneraattorin dynamiikan merkitys nousi merkittävämmäksi kuin lämpöregeneraattorin kyky varastoida lämpöenergiaa. Lämpöregeneraattorin hidas dynamiikka ei mahdollista tehokasta energian talteenottoa nopeista puristus- tai purkusykleistä, ja tämän takia lämpöregeneraattorista saatava hyöty jäi pieneksi. Työssä toteutetulla lämpöregeneraattorilla saavutettiin parhaimmillaan 3 prosenttiyksikön hyötysuhteen nousu verrattaessa samaan mäntäpaineakkuun ilman lämmön regenerointia.As new technological advances are made the importance of energy efficiency and cost effective solutions are even more important when designing and producing new machine systems. Hydraulic systems offer great performance in different actuators, but the general efficiency of the whole hydraulic systems is usually low. Energy efficiency can be improved by utilizing energy recovery systems. With energy recovery some of the normally wasted energy can be recovered and used in the next work cycle. Hydraulic energy recovery systems usually store energy in hydraulic pressure accumulators. Within the hydraulic pressure accumulator, energy is stored by compressing gas inside the accumulator’s gas volume. When compressing gas, heat builds up within the gas and temperature difference between the gas and its surroundings causes heat energy to flow out of the gas. This energy flow is the single most significant factor lowering energy efficiency of the accumulator. The goal of this study was to increase the efficiency of piston type hydraulic pressure accumulator by utilizing heat regeneration. With heat regeneration, heat energy that is generated in the gas during compression cycle is stored in the heat regenerator to be released during the following decompression cycle. Heat regenerator designed in this study utilizes phase change materials to store heat energy. Phase change materials absorb a lot of energy during phase change and thus they are commonly used as heat storages. The results obtained in this study indicate that the dynamic properties of the heat regenerator are more important than the capability to store heat energy. Low dynamic properties prevent the heat regenerator from storing and releasing energy effectively during fast compression and decompression cycles. With the heat regenerator designed in this study the energy efficiency of the accumulator increased by maximum of 3 percentage units when compared to the same accumulator without heat regeneration