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Metabolic Pathway - DOAJ

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Last Updated: 23 April 2022

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PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search.

The microbial pathway design of a metabolic pathway is a significant step in the process of designing an effective microbial cell factory to produce high value-added chemicals. However, there has been a lack of cost-effective ways to automatically perform metabolic network reduction. Here, we introduce a novel uniformity to calculate the main substrate-product pairs of known biochemical reactions and design further an effective metabolic pathway design software named PyMiner. We know that the nodes involved in the extraction metabolic network's creation are large in size, but that distribution is uneven, so we devise a conditional search strategy that reduces search time in 90 percent of cases.

Source link: https://doi.org/10.1371/journal.pone.0266783


Losartan ameliorates renal interstitial fibrosis through metabolic pathway and Smurfs-TGF-β/Smad

The epithelial-mesenchymal transdifferentiation of renal tubular epithelial cells is thought to be the key to renal fibrosis. TGF-/Smad and metabolomics were measured in this research. Male C57BL/6 J mice were injected with the UUO model and given losartan for 28 days in a row. Losartan also reduced UUO-induced abnormal serum chemical profile and renal function, according to the study. These results, in summary, showed that losartan could influence the TGF-/Smad and metabolic pathways in UUO model mice by ubiquitination to reduce renal fibrosis.

Source link: https://doi.org/10.1016/j.biopha.2022.112931


Metabolic Pathway of Cardiospecific Troponins: From Fundamental Aspects to Diagnostic Role (Comprehensive Review)

Since the introduction of new detection techniques, cardiovascular sensitivity and diagnostic capabilities of cardiospecific Tns have increased drastically. Prognostic markers have also been introduced for the use of cardiospecific Tns as diagnostic markers both at the early stages of cardiovascular disease pathology and in non-ischemic extra-cardiac pathologies that can adversely influence CMC. Cardiospecific Tns are also present in blood serum, but also in other biological fluids, according to new studies. However, the key aspects of cardiospecific Tns' metabolic pathway are not fully understood, in particular, specific mechanisms of absorption and removal of Tns from the human body, catheters, and elimination of Tns from CMC, while Tns' circulation and elimination of Tns from CMC, organ transplantation and elimination of Tns from CMC, Tns from the human body, transport of Tns from CMC are not known, while other physiological fluids and triggers.

Source link: https://doi.org/10.3389/fmolb.2022.841277


PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search

A vital step in the process of establishing a cost-effective microbial cell factory to produce high value-added chemicals is a Metabolic pathway map. However, there have been a lack of effective ways to achieve metabolic network reduction automatically. Given that the nodes in this research's extracted metabolic network are large in number but poorly distributed in distribution, we propose a conditional search algorithm that reduces search time in 90 percent of cases. Consequently, PyMiner is a convenient and cost-effective device for metabolic pathway design.

Source link: https://doaj.org/article/3fd3adeac9ca45719710499cdc2fcee8


Predicted expression of genes involved in the thiopurine metabolic pathway and azathioprine discontinuation due to myelotoxicity

We hypothesized that among TPMT and NUDT15 normal metabolizers, a score combining the genetically predicted expression of other proteins in the thiopurine pathway could place a higher risk of azathioprine discontinuation due to myelotoxicity. We conducted a retrospective cohort study of new azathioprine users who had normal TPMT and NUDT15 metabolizers. We used flexible Least Absolute Shrinkage and Selection Operator regression to select genes that were responsible for discontinuing azathioprine due to myelotoxicity in 1201 White patients receiving azathioprine for an inflammatory disease. Patients in the highest scoring group had a greater risk of discontinuing azathioprine than those in the lowest tertile. In conclusion, a score combining the predicted expression of AOX1 and NUDT15 normal metabolizers was attributed to an elevated risk of discontinuing azathioprine due to myelotoxicity.

Source link: https://doi.org/10.1111/cts.13243


Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae

Abstract Background The introduction of novel yeast strains with increased tolerance toward inhibitors in lignocellulosic hydrolysates is highly desirable for bio-ethanol production. However, genetic engineering methods addressing yeast tolerance to weak organic acids have been difficult, considering the mechanism of toxicity is unclear. Result Data In this research, the effect of acetic acid on xylose fermentation in a recombinant xylose-fermenting strain of Saccharomyces cerevisiae was determined by investigating metabolite profiles. Conclusions Our metabolomic approach prompted one of the chemical reactions related to acetic acid's release of acetic acid, and the focus now shifts attention on non-oxidative PPP as a target for metabolic engineering. The identification of gene targets with material significance is an important challenge for metabolic engineering. This research has found that metabolomics is a useful tool to design logical strategies to breed tolerance to stress by genetic engineering.

Source link: https://doi.org/10.1186/1475-2859-10-2


Synthetic metabolic engineering-a novel, simple technology for designing a chimeric metabolic pathway

Abstract Background The incorporation of biotechnology in chemical manufacturing has been lauded as a key component of a sustainable society. However, biocatalytic chemical conversions' practical uses are often limited due to their complexities, including the unpredictability of product yield and the difficult tolerable control of fermentation processes. Artificial synthetic pathways tailored for chemical manufacturing could be developed and installed by rationally combining those modules together, providing the modules with a unified style. Results of nine recombinant E. coli strains overproducing either one of Pyrococcus horikoshii's cofactor-independence phosphate dehydrogenase or the non-phosphorylating phosphate dehydrogenase of Thermococcus kodakarensis' non-phosphorylating glycerates dehydrogenase phosphate dehydrogenase of the non-phosphate phosphate Embden-t E. phosphate dehydrogenase dehydrogena phosphate dehydrogena dehydrating phosphate dehydrogenase dehydrating phosphate dehydrating phosphate dehydrating phosphate dehydrogenase dehydratas A stoichiometric amount of lactate was generated from glucose with a total ATP turnover number of 31.

Source link: https://doi.org/10.1186/1475-2859-11-120


Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway

Colorectal cancer appears to be more refractory to checkpoint blockers than in the case of a patient with mismatch repair deficiencies. Therefore, new advancements in the care of the majority of mismatch repair proficiency type of CRC patients are considered a significant clinical problem linked to programmed death 1 inhibitors. In the present study, we investigated the effects of gut microbiome of MSS-type CRC tumor-bearing mice treated with different antibiotics on PD-1 antibody immunotherapy responses. Our findings revealed that the gut microbiome played a major role in the PD-1 antibody-treated treatment of CT26 tumor-bearing mice. Compared to the Control group, the injection of antibiotics counteracted the efficacy of PD-1 antibody in inhibiting tumor formation. Our results show that changes in the gut microbiome influence the glycerophospholipid metabolic pathway, thereby regulating the therapeutic activity of PD-1 antibody in MSS-type CRC tumor-bearing mice.

Source link: https://doi.org/10.3389/fmicb.2020.00814


Peretinoin, an Acyclic Retinoid, Inhibits Hepatitis B Virus Replication by Suppressing Sphingosine Metabolic Pathway In Vitro

Hepatitis C virus and hepatitis B virus infection are both common causes of hepatocellular carcinoma. At a dose that did not cause cytotoxicity, Peretinoin dramatically reduced the amounts of intracellular HBV-DNA, nuclear ccDNA, and HBV transcript at a rate that did not cause cytotoxicity. Peretinoin improved the binding of histone deacetylase 1 to ccDNA in the nucleus and negatively reduced HBV transcription, according to Mechanistically, although peretinoin raised the expression of HBV-related transcription factors, as seen for other retinoids. Peretinoin stimulates HDAC1 and subsequently reduces HBV replication by blocking the sphingosine metabolic pathway, which ultimately leads to HBV replication. Peretinoin, therefore, may be a novel therapeutic agent for HBV replication and chemoprevention of HCC.

Source link: https://doi.org/10.3390/ijms19020108

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions