scholarly journals Studying the Relationship between Robustness against Mutations in Metabolic Networks and Lifestyle of Organisms

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Sayed-Amir Marashi ◽  
Hawa Kouhestani ◽  
Majid Mahdavi

Robustness is the key feature of biological networks that enables living organisms to keep their homeostatic state and to survive against external and internal perturbations. Variations in environmental conditions or nutrients and intracellular changes such as genetic mutations have the potential to change stability and efficiency of an organism. Structural robustness helps biological systems to choose alternative routes of adaptation to varying conditions. In this study, in order to estimate the structural robustness in metabolic networks we presented a novel flux balance-based approach inspired by bond percolation theory. Fourteenin silicometabolic models were studied in this work in order to examine the possible relationship between the lifestyle of organisms and their metabolic robustness. The results of this study confirm that in organisms which are highly adapted to their environment robustness to mutations may decrease compared to other organisms.

Minerals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 114
Author(s):  
Kadriann Tamm ◽  
Zeinab Arab Zadeh ◽  
Rein Kuusik ◽  
Juha Kallas ◽  
Jason Yang ◽  
...  

Phosphorus is an essential and non-substitutable element for the cellular processes of all living organisms. The main source of phosphorus in the biosphere is phosphate rock. With more than 700 Mt phosphate rock, Estonia holds the largest sedimentary phosphate rock deposits in the European Union. Estonian phosphate rock is particularly outstanding due to its remarkably low content of hazardous heavy metals such as Cadmium (<5 ppm) and trace elements of Uranium (<50 ppm). It is also a reliable source of valuable elements such as rear earth elements (REEs). The aim of this study was to investigate the distribution of the main minerals (apatite and quartz) between slimes, tailings, and concentrates that formed at the froth flotation of Estonian phosphate rock with the up-to-date level of know-how and techniques. Subsequently, the relationship between the obtained grades and recovery levels in concentrates was determined based on the collector dosage and flotation duration. It was observed that the fine fraction of the tailings contains 17.9–33.49 wt% P2O5 that can be added to the final product. Moreover, it was found that, with the lower dosage of the collector, the extended flotation time does not influence the phosphate grade and a high amount of quartz remains in the concentrates. It was also shown that, by raising the collector dosage and setting the flotation time, an adequate grade (>32 wt% P2O5) and recovery (up to 98%) can be gained. The results showed that Estonian phosphate rock can be beneficiated to produce a high-quality concentrate at high recovery levels by modifying the main flotation parameters depending on the properties of the ore.


2022 ◽  
Author(s):  
Javad Zamani ◽  
Sayed-Amir Marashi ◽  
Tahmineh Lohrasebi ◽  
Mohammad-Ali Malboobi ◽  
Esmail Foroozan

Genome-scale metabolic models (GSMMs) have enabled researchers to perform systems-level studies of living organisms. As a constraint-based technique, flux balance analysis (FBA) aids computation of reaction fluxes and prediction of...


2004 ◽  
Vol 1 (1) ◽  
pp. 114-120 ◽  
Author(s):  
T. Wilhelm ◽  
J. Behre ◽  
S. Schuster

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Debolina Sarkar ◽  
Costas D. Maranas

Abstract Living organisms in analogy with chemical factories use simple molecules such as sugars to produce a variety of compounds which are necessary for sustaining life and some of which are also commercially valuable. The metabolisms of simple (such as bacteria) and higher organisms (such as plants) alike can be exploited to convert low value inputs into high value outputs. Unlike conventional chemical factories, microbial production chassis are not necessarily tuned for a single product overproduction. Despite the same end goal, metabolic and industrial engineers rely on different techniques for achieving productivity goals. Metabolic engineers cannot affect reaction rates by manipulating pressure and temperature, instead they have at their disposal a range of enzymes and transcriptional and translational processes to optimize accordingly. In this review, we first highlight how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed in systems and control engineering. Specifically, how algorithmic concepts derived in operations research can help explain the structure and organization of metabolic networks. Finally, we consider the future directions and challenges faced by the field of metabolic network modeling and the possible contributions of concepts drawn from the classical fields of chemical and control engineering. The aim of the review is to offer a current perspective of metabolic engineering and all that it entails without requiring specialized knowledge of bioinformatics or systems biology.


2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Andreas Hoppe ◽  
Sabrina Hoffmann ◽  
Andreas Gerasch ◽  
Christoph Gille ◽  
Hermann-Georg Holzhütter

2011 ◽  
Vol 26 (S2) ◽  
pp. 1936-1936
Author(s):  
X. Gonda ◽  
Z. Rihmer ◽  
K.N. Fountoulakis ◽  
M. Pompili ◽  
P. Erdös ◽  
...  

ObjectivesPeriodicity, cyclicity, and annual rhythms are inherent characteristics of living organisms, and have also been reported for diverse physiological and pathological conditions and phenomena. Season of birth was also associated with central monoamine and monoamine metabolite levels in several studies. Furthermore, several studies indicate a significant effect of season of birth on personality traits and characteristics. A relationship between birth season and novelty seeking has been described and confirmed in several studies. However, affective temperaments have not so far been studied with respect to their association with birth season.AimsThe aim of our present study was to investigate the possible association between affective temperaments and season of birth in a nonclinical sample.Methods366 university students completed the standardized Hungarian version of the TEMPS-A. Ordinary Least Squares regression was applied to explain the relationship between TEMPS-A subscales and birth season of the respondents.ResultsWe found a significant association between temperament scores and birth season in case of the Hyperthymic, Cyclothymic, Irritable and Depressive temperaments, while no significant results emerged for the Anxious temperament.ConclusionsOur results provide further evidence for an association between season of birth and personality, extending the results to affective temperaments as well. Furthermore, our results can be related to clinical observations concerning the seasonal variation of onset and hospitalization due to affective episodes, thus our results also have clinical significance.


Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1084
Author(s):  
Ekaterina N. Tolmacheva ◽  
Stanislav A. Vasilyev ◽  
Igor N. Lebedev

Genome stability is an integral feature of all living organisms. Aneuploidy is the most common cause of fetal death in humans. The timing of bursts in increased aneuploidy frequency coincides with the waves of global epigenetic reprogramming in mammals. During gametogenesis and early embryogenesis, parental genomes undergo two waves of DNA methylation reprogramming. Failure of these processes can critically affect genome stability, including chromosome segregation during cell division. Abnormal methylation due to errors in the reprogramming process can potentially lead to aneuploidy. On the other hand, the presence of an entire additional chromosome, or chromosome loss, can affect the global genome methylation level. The associations of these two phenomena are well studied in the context of carcinogenesis, but here, we consider the relationship of DNA methylation and aneuploidy in early human and mammalian ontogenesis. In this review, we link these two phenomena and highlight the critical ontogenesis periods and genome regions that play a significant role in human reproduction and in the formation of pathological phenotypes in newborns with chromosomal aneuploidy.


2013 ◽  
Vol 29 (17) ◽  
pp. 2178-2185 ◽  
Author(s):  
Yang Zhao ◽  
Takeyuki Tamura ◽  
Tatsuya Akutsu ◽  
Jean-Philippe Vert

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1743-1743 ◽  
Author(s):  
Emi Goto ◽  
Akihiro Tomita ◽  
Akihide Atsumi ◽  
Hitoshi Kiyoi ◽  
Tomoki Naoe

Abstract Abstract 1743 Poster Board I-769 Background Molecular targeting drugs, all-trans retinoic acid (ATRA)and arsenic trioxide (ATO), have major advances in the treatment of acute promyelocytic leukemia (APL). However, resistance to these drugs has been also observed in clinical practice. ATRA acts as a ligand for retinoic acid receptor alpha (RAR) and restores the aberrant transcription repression by PML-RARA fusion protein in APL cells. Previous reports demonstrate that amino-acids substitution, resulting from genetic mutations, in ligand binding domain (LBD) of RARA region of PML-RARA were closely related to drug resistance to ATRA therapy. In contrast, for ATO therapy, the molecular mechanisms of the effectiveness and also the resistance are still unclear. Here we identified a PML-RARA that holds double genetic missense mutations in RARA and PML regions, respectively, from an APL patient, who showed clinically resistance to ATRA and ATO therapy. These mutations were observed as his disease progression, and we are interested in the relationship between these mutations with drug resistance to ATRA and/or ATO. Aims Analyses of the molecular and clinical significance of the double missense mutations of PML-RARA for disease progression and resistance to ATRA and ATO therapy. Results Eight APL patients were treated with ATO in Nagoya University Hospital, Japan, during ∼5 years from Apr. 1, 2000 to Dec. 31, 2004. One out of 8 patients showed clinically ATO resistance. The patient showing ATO resistance firstly diagnosed as APL (M3 variant) from cytogenetic and chromosomal analyses, and complete remission was obtained after combination chemotherapy with ATRA. Molecular CR was confirmed by RT-PCR analysis, but after 3 month from the induction therapy, ATRA-resistant relapse was observed. After treatment with ATO therapy, response was observed, but the effectiveness was gradually decreased, resulting finally into the resistance. The patient died of disease progression. During his 7 years clinical course, leukemia cells were harvested repeatedly from his bone marrow and peripheral blood. RT-PCR using the total RNA from his tumor cells followed by DNA sequencing was performed, with the result of PML-RARA fusion gene with the bcr3 breakpoint in the intron 3 of PML. When using the tumor cells that were harvested at his terminal stage, a missense point mutation in the LBD of the RARA region of PML-RARA was confirmed. Furthermore, missense point mutation in the PML-B2 domain was also confirmed in the same cDNA clones. Interestingly, these mutations were not observed in the leukemia cells obtained at the onset. These mutations were analyzed in each sample that was obtained as his disease progressed, and some correlation between disease progression and/or the drug resistance and the timing of appearance of these two mutations were suggested. These mutated fusion transcripts were cloned into expression vectors, and we are now analyzing the function relating to the drug resistance and disease progression. Conclusions Double genetic missense mutations in the RARA-LBD and PML-B2 of PML-RARA were confirmed in ATRA and ATO resistant patient. These genetic mutations were confirmed in the leukemia cells during his disease progression, and the relationship between those mutations and drug resistances were suggested from the clinical features. Mutations in the PML-B2 domain has not been reported previously, thus, it may be important to show whether this type of mutations are related to the drug resistance, especially to ATO therapy. Disclosures Kiyoi: Novartis Pharma Co. Ltd.: Research Funding; Kyowa Hakko Kirin Co. Ltd.: Consultancy. Naoe:Kyowa Hakko Kirin Co., Ltd. : Research Funding; Chugai Pharmaceutical Co.,Ltd.: Research Funding; Wyeth K.K.: Research Funding.


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