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https://www.readbyqxmd.com/read/29353021/phosphoproteomics-unveils-stable-energy-supply-as-key-to-flooding-tolerance-in-kandelia-candel
#1
Dezhuo Pan, Lingxia Wang, Fanglin Tan, Si Lu, Xiaojie Lv, Madiha Zaynab, Chi-Lien Cheng, Yakubu Saddeeq Abubakar, Shipin Chen, Wei Chen
The mangrove Kandelia candel (L.) Druce experiences daily flooding cycles. To explore the molecular mechanism underlying the physiological adaptation of K. candel to flooding, the potential role of protein phosphorylation in flooding responses was investigated by a large-scale quantitative phosphoproteomic analysis using isobaric tag for relative and absolute quantitation. Total 2141 unique phosphopeptides and 2603 non-redundant phosphorylation sites were identified from 1516 phosphoproteins in K. candel leaves...
January 15, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29349465/exploring-candidate-biomarkers-for-lung-and-prostate-cancers-using-gene-expression-and-flux-variability-analysis
#2
Yazdan Asgari, Pegah Khosravi, Zahra Zabihinpour, Mahnaz Habibi
Genome-scale metabolic models have provided valuable resources for exploring changes in metabolism under normal and cancer conditions. However, metabolism itself is strongly linked to gene expression, so integration of gene expression data into metabolic models might improve the detection of genes involved in the control of tumor progression. Herein, we considered gene expression data as extra constraints to enhance the predictive powers of metabolic models. We reconstructed genome-scale metabolic models for lung and prostate, under normal and cancer conditions to detect the major genes associated with critical subsystems during tumor development...
January 19, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29347780/stochastic-thermodynamics-for-a-periodically-driven-single-particle-pump
#3
Alexandre Rosas, Christian Van den Broeck, Katja Lindenberg
We present the stochastic thermodynamic analysis of a time-periodic single-particle pump, including explicit results for flux, thermodynamic force, entropy production, work, heat, and efficiency. These results are valid far from equilibrium. The deviations from the linear (Onsager) regime are discussed.
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347531/local-stability-analysis-of-a-low-dissipation-heat-engine-working-at-maximum-power-output
#4
I Reyes-Ramírez, J Gonzalez-Ayala, A Calvo Hernández, M Santillán
In this paper we address the stability of a low-dissipation (LD) heat engine (HE) under maximum power conditions. The LD system dynamics are analyzed in terms of the contact times between the engine and the external heat reservoirs, which determine the amount of heat exchanged by the system. We study two different scenarios that secure the existence of a single stable steady state. In these scenarios, contact times dynamics are governed by restitutive forces that are linear functions of either the heat amounts exchanged per cycle, or the corresponding heat fluxes...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347495/momentum-transport-and-nonlocality-in-heat-flux-driven-magnetic-reconnection-in-high-energy-density-plasmas
#5
Chang Liu, William Fox, Amitava Bhattacharjee, Alexander G R Thomas, Archis S Joglekar
Recent theory has demonstrated a novel physics regime for magnetic reconnection in high-energy-density plasmas where the magnetic field is advected by heat flux via the Nernst effect. Here we elucidate the physics of the electron dissipation layer in this regime. Through fully kinetic simulation and a generalized Ohm's law derived from first principles, we show that momentum transport due to a nonlocal effect, the heat-flux-viscosity, provides the dissipation mechanism for magnetic reconnection. Scaling analysis, and simulations show that the reconnection process comprises a magnetic field compression stage and quasisteady reconnection stage, and the characteristic width of the current sheet in this regime is several electron mean-free paths...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347381/maximum-entropy-modeling-of-metabolic-networks-by-constraining-growth-rate-moments-predicts-coexistence-of-phenotypes
#6
Daniele De Martino
In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347088/effect-of-polymer-additives-on-heat-transport-and-large-scale-circulation-in-turbulent-rayleigh-b%C3%A3-nard-convection
#7
Jian-Ping Cheng, Hong-Na Zhang, Wei-Hua Cai, Si-Ning Li, Feng-Chen Li
The present paper presents direct numerical simulations of Rayleigh-Bénard convection (RBC) in an enclosed cell filled with the polymer solution in order to investigate the viscoelastic effect on the characteristics of heat transport and large-scale circulation (LSC) of RBC. To overcome the difficulties in numerically solving a high Weissenberg number (Wi) problem of viscoelastic fluid flow with strong elastic effect, the log-conformation reformulation method was implemented. Numerical results showed that the addition of polymers reduced the heat flux and the amount of heat transfer reduction (HTR) behaves nonmonotonically, which firstly increases but then decreases with Wi...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347080/derivation-of-stable-burnett-equations-for-rarefied-gas-flows
#8
Narendra Singh, Ravi Sudam Jadhav, Amit Agrawal
A set of constitutive relations for the stress tensor and heat flux vector for the hydrodynamic description of rarefied gas flows is derived in this work. A phase density function consistent with Onsager's reciprocity principle and H theorem is utilized to capture nonequilibrium thermodynamics effects. The phase density function satisfies the linearized Boltzmann equation and the collision invariance property. Our formulation provides the correct value of the Prandtl number as it involves two different relaxation times for momentum and energy transport by diffusion...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346979/variational-formulation-of-a-quantitative-phase-field-model-for-nonisothermal-solidification-in-a-multicomponent-alloy
#9
Munekazu Ohno, Tomohiro Takaki, Yasushi Shibuta
A variational formulation of a quantitative phase-field model is presented for nonisothermal solidification in a multicomponent alloy with two-sided asymmetric diffusion. The essential ingredient of this formulation is that the diffusion fluxes for conserved variables in both the liquid and solid are separately derived from functional derivatives of the total entropy and then these fluxes are related to each other on the basis of the local equilibrium conditions. In the present formulation, the cross-coupling terms between the phase-field and conserved variables naturally arise in the phase-field equation and diffusion equations, one of which corresponds to the antitrapping current, the phenomenological correction term in early nonvariational models...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29340863/effects-of-urease-and-nitrification-inhibitors-on-the-soil-mineral-nitrogen-dynamics-and-nitrous-oxide-n2o-emissions-on-calcareous-soil
#10
Rui Tao, Jun Li, Yu Guan, Yongchao Liang, Baowei Hu, Jun Lv, Guixin Chu
Urease inhibitors and nitrification inhibitors can reduce nitrogen (N) loss in agriculture soil. However, the effect of inhibitors on soil N2O emissions under the drip irrigation system remains unclear. A pot and a field experiment with two inhibitors were conducted to explore how inhibitors regulate soil nitrogen transformation and N2O emissions. In the pot experiment, three treatments included control, urea, and urea + N-(n-butyl)thiophosphoric triamide (NBPT, urease inhibitor). In the field experiment, three treatments included control, urea, and urea + NBPT + 2-chloro-6-(trichloromethyl)pyridine (nitrapyrin, nitrification inhibitor)...
January 17, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29338005/inferring-cell-state-by-quantitative-motility-analysis-reveals-a-dynamic-state-system-and-broken-detailed-balance
#11
Jacob C Kimmel, Amy Y Chang, Andrew S Brack, Wallace F Marshall
Cell populations display heterogeneous and dynamic phenotypic states at multiple scales. Similar to molecular features commonly used to explore cell heterogeneity, cell behavior is a rich phenotypic space that may allow for identification of relevant cell states. Inference of cell state from cell behavior across a time course may enable the investigation of dynamics of transitions between heterogeneous cell states, a task difficult to perform with destructive molecular observations. Cell motility is one such easily observed cell behavior with known biomedical relevance...
January 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29336468/increased-expression-of-sterol-regulatory-element-binding-protein%C3%A2-2-alleviates-autophagic-dysfunction-in-nafld
#12
Chunwei Cheng, Xiaoling Deng, Keshu Xu
Sterol regulatory element binding protein‑2 (SREBP‑2) is an important transcription factor in lipid homeostasis. A previous study showed that SREBP‑2 also activated autophagic genes during cell‑sterol depletion. Alterations in autophagy are reported to be involved in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). However, whether the regulation of SREBP‑2 restores dysfunctional autophagy in hepatocytes during NAFLD remains to be elucidated. In the present study, a steatosis model was established with palmitic acid (PA) treatment at the indicated times and concentrations...
January 16, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29335637/expression-profiling-of-host-and-virus-during-a-coccolithophore-bloom-provides-insights-into-the-role-of-viral-infection-in-promoting-carbon-export
#13
Uri Sheyn, Shilo Rosenwasser, Yoav Lehahn, Noa Barak-Gavish, Ron Rotkopf, Kay D Bidle, Ilan Koren, Daniella Schatz, Assaf Vardi
The cosmopolitan coccolithophore Emiliania huxleyi is a unicellular eukaryotic alga that forms vast blooms in the oceans impacting large biogeochemical cycles. These blooms are often terminated due to infection by the large dsDNA virus, E. huxleyi virus (EhV). It was recently established that EhV-induced modulation of E. huxleyi metabolism is a key factor for optimal viral infection cycle. Despite the huge ecological importance of this host-virus interaction, the ability to assess its spatial and temporal dynamics and its possible impact on nutrient fluxes is limited by current approaches that focus on quantification of viral abundance and biodiversity...
January 15, 2018: ISME Journal
https://www.readbyqxmd.com/read/29335445/trophic-ecology-of-glass-sponge-reefs-in-the-strait-of-georgia-british-columbia
#14
Amanda S Kahn, Jackson W F Chu, Sally P Leys
Sponges link the microbial loop with benthic communities by feeding on bacteria. Glass sponge reefs on the continental shelf of western Canada have extremely high grazing rates, consuming seven times more particulate carbon than can be supplied by vertical flux alone. Unlike many sponges, the reef building species Aphrocallistes vastus has no microbial symbionts and removes little dissolved organic carbon. To determine how reef sponges therefore get enough food to sustain such substantial grazing we measured stable carbon and nitrogen isotope signatures of water, sediment and sponge tissues...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29333574/unique-metabolic-activation-of-adipose-tissue-macrophages-in-obesity-promotes-inflammatory-responses
#15
Lily Boutens, Guido J Hooiveld, Sourabh Dhingra, Robert A Cramer, Mihai G Netea, Rinke Stienstra
AIMS/HYPOTHESIS: Recent studies have identified intracellular metabolism as a fundamental determinant of macrophage function. In obesity, proinflammatory macrophages accumulate in adipose tissue and trigger chronic low-grade inflammation, that promotes the development of systemic insulin resistance, yet changes in their intracellular energy metabolism are currently unknown. We therefore set out to study metabolic signatures of adipose tissue macrophages (ATMs) in lean and obese conditions...
January 14, 2018: Diabetologia
https://www.readbyqxmd.com/read/29328652/trade-induced-atmospheric-mercury-deposition-over-china-and-implications-for-demand-side-controls
#16
Long Chen, Jing Meng, Sai Liang, Haoran Zhang, Wei Zhang, Maodian Liu, Yindong Tong, Huanhuan Wang, Wei Wang, Xuejun Wang, Jiong Shu
Mercury (Hg) is of global concern because of its adverse effects on humans and the environment. In addition to long-range atmospheric transport, Hg emissions can be geographically relocated through economic trade. Here, we investigate the effect of China's interregional trade on atmospheric Hg deposition over China, using an atmospheric transport model and multiregional input-output analysis. In general, total atmospheric Hg deposition over China is 408.8 Mg yr-1, and 32% of this is embodied in China's interregional trade, with the hotspots occurring over Gansu, Henan, Hebei, and Yunnan provinces...
January 12, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29328444/sp1-reduces-autophagic-flux-through-activating-p62-in-gastric-cancer-cells
#17
Xiao-Wu Xu, Chen-Wei Pan, Xiao-Min Yang, Lei Zhou, Zhi-Qiang Zheng, De-Chun Li
Gastric cancer is the most common type of gastrointestinal cancer, causing mortality worldwide. However, the underlying molecular mechanism in gastric cancer progression remains unclear. The autophagic flux was determined in gastric cancer cells overexpressing or inhibiting Sp1 transcription factor (SP1) using western blotting, reverse transcription‑polymerase chain reaction and immunofluorescence staining. Luciferase and ChIP assays were performed to detect the potential underlying mechanism of SP1 in gastric cancer cells...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29327288/expression-of-pfkfb3-and-ki67-in-lung-adenocarcinomas-and-targeting-pfkfb3-as-a-therapeutic-strategy
#18
Xiaoli Li, Jian Liu, Li Qian, Honggang Ke, Chan Yao, Wei Tian, Yifei Liu, Jianguo Zhang
Phosphofructokinase-2/fructose-2, 6-bisphosphatase 3 (PFKFB3) catalyzes the synthesis of F2,6BP, which is an allosteric activator of 6-phosphofructo-1-kinase (PFK-1): the rate-limiting enzyme of glycolysis. During tumorigenesis, PFKFB3 increases glycolysis, angiogenesis, and tumor progression. In this study, our aim was to investigate the significance of PFKFB3 and Ki67 in human lung adenocarcinomas and to target PFKFB3 as a therapeutic strategy. In this study, we determined the expression levels of PFKFB3 mRNA and proteins in cancerous and normal lung adenocarcinomas by quantitative reverse transcription PCR (qRT-PCR), Western blot analysis, and tissue microarray immunohistochemistry analysis, respectively...
January 11, 2018: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29323411/demographic-quantification-of-carbon-and-nitrogen-dynamics-associated-with-root-turnover-in-white-clover
#19
Gavin D Scott, John A Baddeley, Christine A Watson, David Robinson
As well as capturing resources, roots lose resources during their lives. We quantified carbon (C) and nitrogen (N) losses associated with root turnover in white clover (Trifolium repens L.). We grew contrasting cultivars for 18 weeks in soil microcosms. Using repeated in situ observations, destructive sampling, and demographic analysis, we measured changes in C and N concentrations in dry matter of 1st - or 2nd -order (terminal) roots to derive C and N fluxes into and out of root cohorts. C and N fluxes from roots during turnover depended on cohort age and order...
January 11, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29321807/different-modulation-of-panax-notoginseng-on-the-absorption-profiling-of-triptolide-and-tripterine-from-tripterygium-wilfordii-in-rat-intestine
#20
Yiqun Li, Huiting Cao, Mengzhu Liu, Benyong Zhang, Xinlong Zhang, Donglei Shi, Liwei Guo, Jinao Duan, Xueping Zhou, Huaxu Zhu, Qichun Zhang
Background: Compatibility with Panax notoginseng (PN) reduced the plasma concentration of triptolide and delayed the Tmax of Tripterygium wilfordii (TW), the sovereign medicine of Qing-Luo Tong-Bi decoction, which hinted the absorption process of triptolide might be involved in decreasing the toxicity in liver and kidney. Methods: The absorption of triptolide, triptonide, wilforlide and tripterine from monomer, TW, TW-PN, TW-Caulis Sinomenii (TW-CS) and Qing-Luo Tong-Bi were analyzed in duodenum, jejunum, ileum and colon of rat via single-pass intestinal perfusion model...
2018: Chinese Medicine
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