flux analysis
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2022 ◽  
Author(s):  
Paul Dijkstra ◽  
Weichao Wu ◽  
Michaela Dippold ◽  
Egbert Schwartz ◽  
Bruce Hungate ◽  
...  

Abstract Biochemistry is an essential yet often undervalued aspect of soil ecology, especially in soil C cycling. We assume based on tradition, intuition or hope that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic biochemical processes that permeate the world of ecosystem processes. From these patterns, we can estimate activities of the biochemical reactions of the central C metabolic network and gain insights into the ecophysiology of microbial biosynthesis and growth and maintenance energy requirements; important components of Carbon Use Efficiency (CUE).The biochemical pathways used to metabolize glucose vary from soil to soil, with mostly glycolysis in some soils, and pentose phosphate or Entner-Doudoroff pathways in others. However, notwithstanding this metabolic diversity, glucose use efficiency is high and thus substrate use for maintenance energy and overflow respiration is low in these three soils. These results contradict current dogma based on four decades of research in soil ecology. We identify three main shortcomings in our current understanding of substrate use efficiency: 1) in numeric and conceptual models, we lack appreciation of the strategies that microbes employ to quickly reduce energy needs in response to starvation; 2) production of exudates and microbial turnover affect whole-soil CUE more than variation in maintenance energy demand; and 3) whether tracer experiments can be used to measure the long-term substrate use efficiency of soil microbial communities depends critically on the ability of non-growing cells to take up tracer substrates, how biosynthesis responds to these substrates, as well as on how cellular activities scale to the community level.To move the field of soil ecology forward, future research must consider the details of microbial ecophysiology and develop new tools that enable direct measurement of microbial functioning in intact soils. We submit that 13C metabolic flux analysis is one of those new tools.


2022 ◽  
pp. 100011
Author(s):  
Lucas Gerken-Starepravo ◽  
Xianfeng Zhu ◽  
Bovinille Anye Cho ◽  
Fernando Vega-Ramon ◽  
Oliver Pennington ◽  
...  

Author(s):  
Wei Chen ◽  
Bo Peng ◽  
Huanfang Huang ◽  
Ye Kuang ◽  
Zhe Qian ◽  
...  

To investigate the concentrations, spatial distribution, potential sources and mass fluxes of organochlorine pesticides (OCPs) and polycyclic aromatic hydrocarbons (PAHs) in waters from the Danshui River Basin, a total of 20 water samples were collected and analyzed from a karstic river in Western Hubei of Central China. The average concentrations of total OCPs and PAHs in the river water were 4719 pg·L−1 and 26.2 ng·L−1, respectively. The characteristic ratios of different isomers and the composition analysis of individual OCPs and PAHs revealed that HCHs originated from a mixed input of technical HCHs and Lindane, DDTs were mainly from technical DDTs, and PAHs mainly originated from biomass and coal combustion. The mass flux analysis showed that PAHs had a higher emission and heavier burden than OCPs in the Danshui River Basin. OCPs and PAHs emitted from agricultural or other human activities could enter the groundwater and then be transported to the surface/river water in the karst area. The adsorption of OCPs and PAHs by particles and the sedimentation of particles could be the primary processes to intercept these pollutants in the water of the karstic river system.


Nutrients ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 80
Author(s):  
Thunnicha Ondee ◽  
Krit Pongpirul ◽  
Kantima Janchot ◽  
Suthicha Kanacharoen ◽  
Thanapat Lertmongkolaksorn ◽  
...  

Fat reduction and anti-inflammation are commonly claimed properties of probiotics. Lactiplantibacillus plantarum and Enterococcus faecium were tested in high fat-induced obesity mice and in vitro experiments. After 16 weeks of probiotics, L. plantarum dfa1 outperforms E. faecium dfa1 on the anti-obesity property as indicated by body weight, regional fat accumulation, serum cholesterol, inflammatory cytokines (in blood and colon tissue), and gut barrier defect (FITC-dextran assay). With fecal microbiome analysis, L. plantarum dfa1 but not E. faecium dfa1 reduced fecal abundance of pathogenic Proteobacteria without an alteration in total Gram-negative bacteria when compared with non-probiotics obese mice. With palmitic acid induction, the condition media from both probiotics similarly attenuated supernatant IL-8, improved enterocyte integrity and down-regulated cholesterol absorption-associated genes in Caco-2 cell (an enterocyte cell line) and reduced supernatant cytokines (TNF-α and IL-6) with normalization of cell energy status (extracellular flux analysis) in bone-marrow-derived macrophages. Due to the anti-inflammatory effect of the condition media of both probiotics on palmitic acid-activated enterocytes was neutralized by amylase, the active anti-inflammatory molecules might, partly, be exopolysaccharides. As L. plantarum dfa1 out-performed E. faecium dfa1 in anti-obesity property, possibly through the reduced fecal Proteobacteria, with a similar anti-inflammatory exopolysaccharide; L. plantarum is a potentially better option for anti-obesity than E. faecium.


Biomedicines ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 28
Author(s):  
Gerardo Della Sala ◽  
Consiglia Pacelli ◽  
Francesca Agriesti ◽  
Ilaria Laurenzana ◽  
Francesco Tucci ◽  
...  

Defining the metabolic phenotypes of cancer-initiating cells or cancer stem cells and of their differentiated counterparts might provide fundamental knowledge for improving or developing more effective therapies. In this context we extensively characterized the metabolic profiles of two osteosarcoma-derived cell lines, the 3AB-OS cancer stem cells and the parental MG-63 cells. To this aim Seahorse methodology-based metabolic flux analysis under a variety of conditions complemented with real time monitoring of cell growth by impedentiometric technique and confocal imaging were carried out. The results attained by selective substrate deprivation or metabolic pathway inhibition clearly show reliance of 3AB-OS on glycolysis and of MG-63 on glutamine oxidation. Treatment of the osteosarcoma cell lines with cisplatin resulted in additive inhibitory effects in MG-63 cells depleted of glutamine whereas it antagonized under selective withdrawal of glucose in 3AB-OS cells thereby manifesting a paradoxical pro-survival, cell-cycle arrest in S phase and antioxidant outcome. All together the results of this study highlight that the efficacy of specific metabolite starvation combined with chemotherapeutic drugs depends on the cancer compartment and suggest cautions in using it as a generalizable curative strategy.


2021 ◽  
Author(s):  
Jeffrey J Czajka ◽  
Deepanwita Banerjee ◽  
Thomas T Eng ◽  
Javier Menasalvas ◽  
Chunsheng Yan ◽  
...  

Microbial cell factory development often faces bottlenecks after initial rounds of design-build-test-learn (DBTL) cycles as engineered producers respond unpredictably to further genetic modifications. Thus, deciphering metabolic flux and correcting bottlenecks are key components of DBTL cycles. Here, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using both 13C-metabolic flux analysis (13C-MFA) and metabolite measurements. The results indicated the conservation of the cyclic Entner-Doudoroff (ED)-EMP pathway flux, downregulation of the TCA cycle and pyruvate shunt, and glyoxylate shunt activation. At the metabolite level, the CRISPR/dCpf1-interference mediated multiplex repression decreased gluconate/2-ketogluconate secretion and altered several intracellular TCA metabolite concentrations, leading to succinate overflow. Further strain engineering based on the metabolic knowledge first employed an optimal ribosome binding site (RBS) to achieve stronger product-substrate growth coupling (1.6-fold increase). Then, deletion strains were constructed using ssDNA recombineering. Of the five strains tested, deletion of the PHA operon (ΔphaAZC-IID) resulted in a 2.2-fold increase in growth phase production compared to the optimal RBS construct. After 72 h of batch cultivation, the ΔphaAZC-IID strain had 1.5-fold and 1.8-fold increases of indigoidine titer compared to the improved RBS construct and the original strain, respectively. Overall, the findings provided actionable DBTL targets as well as insights into physiological responses and flux buffering when new recombineering tools were used for engineering P. putida KT2440.


Author(s):  
Panit Kamma ◽  
CHAKRIT SUVANJUMRAT

The partially premixed flame was modelled using an open-source software based on finite volume method (FVM) of computational fluid dynamics (CFD), called OpenFOAM. The assessment of the tabulation dynamics adaptive chemistry (TDAC) algorithms for facilitating the computation was of interest. A total of seven models were performed, consisting of six models of the TDAC framework application and a direct computation model without TDAC. Simulation results were validated by comparing against the thermal flame height (HT) of Irandoost et al. [28]. The heat released rate was established from simulation results to identify the flame front and HT. This is a novel technique to illustrate the flame front, which agreed well with the experiment. Subsequently, it was found that all but one of the reduced mechanism methods agreed well in predicting the HT. The exception was DRGEP. Particularly, the CFD results were optimal. It was discovered that the TDAC based on the mechanism reduction called element flux analysis (EFA) was the second-fastest but optimal choice to solve the partially premixed flame model.


Sensors ◽  
2021 ◽  
Vol 21 (24) ◽  
pp. 8474
Author(s):  
Mubarak Alotaibi ◽  
Barmak Honarvar Shakibaei Asli ◽  
Muhammad Khan

Non-Invasive Inspection (NII) has become a fundamental tool in modern industrial maintenance strategies. Remote and online inspection features keep operators fully aware of the health of industrial assets whilst saving money, lives, production and the environment. This paper conducted crucial research to identify suitable sensing techniques for machine health diagnosis in an NII manner, mainly to detect machine shaft misalignment and gearbox tooth damage for different types of machines, even those installed in a hostile environment, using literature on several sensing tools and techniques. The researched tools are critically reviewed based on the published literature. However, in the absence of a formal definition of NII in the existing literature, we have categorised NII tools and methods into two distinct categories. Later, we describe the use of these tools as contact-based, such as vibration, alternative current (AC), voltage and flux analysis, and non-contact-based, such as laser, imaging, acoustic, thermographic and radar, under each category in detail. The unaddressed issues and challenges are discussed at the end of the paper. The conclusions suggest that one cannot single out an NII technique or method to perform health diagnostics for every machine efficiently. There are limitations with all of the reviewed tools and methods, but good results possible if the machine operational requirements and maintenance needs are considered. It has been noted that the sensors based on radar principles are particularly effective when monitoring assets, but further comprehensive research is required to explore the full potential of these sensors in the context of the NII of machine health. Hence it was identified that the radar sensing technique has excellent features, although it has not been comprehensively employed in machine health diagnosis.


2021 ◽  
Author(s):  
Alena Gschwind ◽  
Christian Marx ◽  
Marie D. Just ◽  
Paula Severin ◽  
Hannah Behring ◽  
...  

Abstract BackgroundAutophagy plays an essential role in maintaining cellular homeostasis and in the response to cellular stress. Autophagy is also involved in cell cycle progression, yet the relationship between these processes is not clearly defined.ResultsIn exploring this relationship, we observed that the inhibition of autophagy impaired the G2/M phase-arresting activity of etoposide but enhanced the G1 phase-arresting activity of palbociclib. We further investigated the connection of basal autophagy and cell cycle by utilizing the autophagosome tracer dye Cyto-ID in two ways. First, we established a double-labeling flow-cytometric procedure with Cyto-ID and the DNA probe DRAQ5, permitting the cell cycle phase-specific determination of autophagy in live cells. This approach demonstrated that different cell cycle phases were associated with different autophagy levels: G1 phase cells had the lowest one and G2/M phase cells had the highest one. Second, we developed a flow-cytometric cell sorting procedure based on Cyto-ID that separates cell populations into fractions with low, medium and high autophagy. Cell cycle analysis of Cyto-ID-sorted cells confirmed that the high autophagy fraction contained a much higher percentage of G2/M phase cells than the low autophagy fraction. Beyond that, Cyto-ID-based cell sorting proved also to be useful for assessing other autophagy-related processes: extracellular flux analysis revealed metabolic differences between the cell populations, with higher autophagy being associated with higher respiration, higher mitochondrial ATP production and higher glycolysis.ConclusionThis work sheds new light on the interrelation of autophagy and cell cycle by establishing a novel cell sorting technique based on Cyto-ID.


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