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2.
Biophys Chem ; 312: 107281, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-38889653

RESUMEN

RNA polymerase I (Pol I) is responsible for synthesizing ribosomal RNA, which is the rate limiting step in ribosome biogenesis. We have reported wide variability in the magnitude of the rate constants defining the rate limiting step in sequential nucleotide additions catalyzed by Pol I. in this study we sought to determine if base identity impacts the rate limiting step of nucleotide addition catalyzed by Pol I. To this end, we report a transient state kinetic interrogation of AMP, CMP, GMP, and UMP incorporations catalyzed by Pol I. We found that Pol I uses one kinetic mechanism to incorporate all nucleotides. However, we found that UMP incorporation is faster than AMP, CMP, and GMP additions. Further, we found that endonucleolytic removal of a dimer from the 3' end was fastest when the 3' terminal base is a UMP. It has been previously shown that both downstream and upstream template sequence identity impacts the kinetics of nucleotide addition. The results reported here show that the incoming base identity also impacts the magnitude of the observed rate limiting step.


Asunto(s)
ARN Polimerasa I , Cinética , ARN Polimerasa I/metabolismo , ARN Polimerasa I/química , Nucleótidos/metabolismo , Nucleótidos/química
3.
J Mol Biol ; 436(12): 168606, 2024 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-38729258

RESUMEN

Eukaryotes express at least three nuclear DNA dependent RNA polymerases (Pols). Pols I, II, and III synthesize ribosomal (r) RNA, messenger (m) RNA, and transfer (t) RNA, respectively. Pol I and Pol III have intrinsic nuclease activity conferred by the A12.2 and C11 subunits, respectively. In contrast, Pol II requires the transcription factor (TF) IIS to confer robust nuclease activity. We recently reported that in the absence of the A12.2 subunit Pol I reverses bond formation by pyrophosphorolysis in the absence of added PPi, indicating slow PPi release. Thus, we hypothesized that Pol II, naturally lacking TFIIS, would reverse bond formation through pyrophosphorolysis. Here we report the results of transient-state kinetic experiments to examine the addition of nine nucleotides to a growing RNA chain catalyzed by Pol II. Our results indicate that Pol II reverses bond formation by pyrophosphorolysis in the absence of added PPi. We propose that, in the absence of endonuclease activity, this bond reversal may represent kinetic proofreading. Thus, given the hypothesis that Pol I evolved from Pol II through the incorporation of general transcription factors, pyrophosphorolysis may represent a more ancient form of proofreading that has been evolutionarily replaced with nuclease activity.


Asunto(s)
Difosfatos , ARN Polimerasa II , Saccharomyces cerevisiae , ARN Polimerasa II/metabolismo , ARN Polimerasa II/genética , Cinética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Difosfatos/metabolismo , Nucleótidos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química
4.
J Neuroimaging ; 34(4): 475-485, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38590085

RESUMEN

BACKGROUND AND PURPOSE: We aimed to test whether synthetic T1-weighted imaging derived from a post-contrast Quantitative Transient-state Imaging (QTI) acquisition enabled revealing pathological contrast enhancement in intracranial lesions. METHODS: The analysis included 141 patients who underwent a 3 Tesla-MRI brain exam with intravenous contrast media administration, with the post-contrast acquisition protocol comprising a three-dimensional fast spoiled gradient echo (FSPGR) sequence and a QTI acquisition. Synthetic T1-weighted images were generated from QTI-derived quantitative maps of relaxation times and proton density. Two neuroradiologists assessed synthetic and conventional post-contrast T1-weighted images for the presence and pattern of pathological contrast enhancement in intracranial lesions. Enhancement volumes were quantitatively compared. RESULTS: Using conventional imaging as a reference, synthetic T1-weighted imaging was 93% sensitive in revealing the presence of contrast enhancing lesions. The agreement for the presence/absence of contrast enhancement was almost perfect both between readers (k = 1 for both conventional and synthetic imaging) and between sequences (k = 0.98 for both readers). In 91% of lesions, synthetic T1-weighted imaging showed the same pattern of contrast enhancement visible in conventional imaging. Differences in enhancement pattern in the remaining lesions can be due to the lower spatial resolution and the longer acquisition delay from contrast media administration of QTI compared to FSPGR. Overall, enhancement volumes appeared larger in synthetic imaging. CONCLUSIONS: QTI-derived post-contrast synthetic T1-weighted imaging captures pathological contrast enhancement in most intracranial enhancing lesions. Further comparative studies employing quantitative imaging with higher spatial resolution is needed to support our data and explore possible future applications in clinical trials.


Asunto(s)
Encéfalo , Medios de Contraste , Imágenes de Resonancia Magnética Multiparamétrica , Humanos , Femenino , Masculino , Persona de Mediana Edad , Adulto , Anciano , Imágenes de Resonancia Magnética Multiparamétrica/métodos , Encéfalo/diagnóstico por imagen , Neoplasias Encefálicas/diagnóstico por imagen , Sensibilidad y Especificidad , Aumento de la Imagen/métodos , Reproducibilidad de los Resultados , Anciano de 80 o más Años , Adulto Joven , Interpretación de Imagen Asistida por Computador/métodos , Adolescente , Imagen por Resonancia Magnética/métodos
5.
J Environ Sci (China) ; 138: 470-481, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38135413

RESUMEN

The close-coupled selective catalytic reduction (cc-SCR) catalyst is an effective technology to reduce tailpipe NOx emission during cold start. This paper investigated the optimal ammonia storage under steady and transient state in the cc-SCR. The study showed that a trade-off between NOx conversion efficiency and ammonia slip is observed on the pareto solutions under steady state, and the optimal ammonia storage is calculated with ammonia slip less than 10 µL/L based on the China Ⅵ emission legislation. The rapid temperature increase will lead to severe ammonia slip in the transient test cycle. A simplified 0-D calculation method on ammonia slip under transient state is proposed based on kinetic model of ammonia adsorption and desorption. In addition, the effect of ammonia storage, catalyst temperature and temperature increasing rate on ammonia slip are analyzed. The optimal ammonia storage is calculated with maximum ammonia slip less than 100 µL/L according to the oxidation efficiency of ammonia slip catalyst (ASC) downstream cc-SCR. It was found that the optimal ammonia storage under transient state is much lower than that under steady state in cc-SCR at lower temperature, and a phase diagram is established to analyze the influence of temperature and temperature increasing rate on optimal ammonia storage.


Asunto(s)
Amoníaco , Frío , Oxidación-Reducción , Temperatura , Catálisis
6.
NMR Biomed ; 37(1): e5039, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37714527

RESUMEN

In this study, we aimed to develop a fast and robust high-resolution technique for clinically feasible electrical properties tomography based on water content maps (wEPT) using Quantitative Transient-state Imaging (QTI), a multiparametric transient state-based method that is similar to MR fingerprinting. Compared with the original wEPT implementation based on standard spin-echo acquisition, QTI provides robust electrical properties quantification towards B1 + inhomogeneities and full quantitative relaxometry data. To validate the proposed approach, 3D QTI data of 12 healthy volunteers were acquired on a 1.5 T scanner. QTI-provided T1 maps were used to compute water content maps of the tissues using an empirical relationship based on literature ex-vivo measurements. Assuming that electrical properties are modulated mainly by tissue water content, the water content maps were used to derive electrical conductivity and relative permittivity maps. The proposed technique was compared with a conventional phase-only Helmholtz EPT (HH-EPT) acquisition both within whole white matter, gray matter, and cerebrospinal fluid masks, and within different white and gray matter subregions. In addition, QTI-based wEPT was retrospectively applied to four multiple sclerosis adolescent and adult patients, compared with conventional contrast-weighted imaging in terms of lesion delineation, and quantitatively assessed by measuring the variation of electrical properties in lesions. Results obtained with the proposed approach agreed well with theoretical predictions and previous in vivo findings in both white and gray matter. The reconstructed maps showed greater anatomical detail and lower variability compared with standard phase-only HH-EPT. The technique can potentially improve delineation of pathology when compared with conventional contrast-weighted imaging and was able to detect significant variations in lesions with respect to normal-appearing tissues. In conclusion, QTI can reliably measure conductivity and relative permittivity of brain tissues within a short scan time, opening the way to the study of electric properties in clinical settings.


Asunto(s)
Imagen por Resonancia Magnética , Agua , Adulto , Humanos , Adolescente , Estudios Retrospectivos , Imagen por Resonancia Magnética/métodos , Tomografía , Tomografía Computarizada por Rayos X , Conductividad Eléctrica , Fantasmas de Imagen , Procesamiento de Imagen Asistido por Computador/métodos , Encéfalo
7.
Front Mol Biosci ; 10: 1258333, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37780207

RESUMEN

Thioredoxin/glutathione reductase (TGR) from the platyhelminthic parasitic worms has recently been identified as a drug target for the treatment of schistosomiasis. Schistosomes lack catalase, and so are heavily reliant on the regeneration of reduced thioredoxin (Trx) and glutathione (GSH) to reduce peroxiredoxins that ameliorate oxidative damage from hydrogen peroxide generated by the host immune response. This study focuses on the characterization of the catalytic mechanism of Schistosoma mansoni TGR (SmTGR). Variant forms of SmTGR were studied to assign the function of residues that participate in the electron distribution chain within the enzyme. Using anaerobic transient state spectrophotometric methods, redox changes for the FAD and NADPH were observed and the function of specific residues was defined from observation of charge transfer absorption transitions that are indicative of specific complexations and redox states. The C159S variant prevented distribution of electrons beyond the flavin and as such did not accumulate thiolate-FAD charge transfer absorption. The lack of this absorption facilitated observation of a new charge transfer absorption consistent with proximity of NADPH and FAD. The C159S variant was used to confine electrons from NADPH at the flavin, and it was shown that NADPH and FAD exchange hydride in both directions and come to an equilibrium that yields only fractional FAD reduction, suggesting that both have similar reduction potentials. Mutation of U597 to serine resulted in sustained thiolate-FAD charge transfer absorption and loss of the ability to reduce Trx, indicating that the C596-U597 disulfide functions in the catalytic sequence to receive electrons from the C154 C159 pair and distribute them to Trx. No kinetic evidence for a loss or change in function associated with the distal C28-C31 disulfide was observed when the C31S variant reductive half-reaction was observed. The Y296A variant was shown to slow the rate of but increase extent of reduction of the flavin, and the dissociation of NADP+. The H571 residue was confirmed to be the residue responsible for the deprotonation of the C159 thiol, increasing its reactivity and generating the prominent thiolate-FAD charge transfer absorption that accumulates with oxidation of the flavin.

8.
Neuroimage Clin ; 40: 103509, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37717382

RESUMEN

OBJECTIVES: The disruption of the blood-brain barrier (BBB) is a key and early feature in the pathogenesis of demyelinating multiple sclerosis (MS) lesions and has been neuropathologically demonstrated in both active and chronic plaques. The local overt BBB disruption in acute demyelinating lesions is captured as signal hyperintensity in post-contrast T1-weighted images because of the contrast-related shortening of the T1 relaxation time. On the contrary, the subtle BBB disruption in chronic lesions is not visible at conventional radiological evaluation but it might be of clinical relevance. Indeed, persistent, subtle BBB leakage might be linked to low-grade inflammation and plaque evolution. Here we hypothesised that 3D Quantitative Transient-state Imaging (QTI) was able to reveal and measure T1 shortening (ΔT1) reflecting small amounts of contrast media leakage in apparently non-enhancing lesions (ANELs). MATERIALS AND METHODS: Thirty-four patients with relapsing remitting MS were included in the study. All patients underwent a 3 T MRI exam of the brain including conventional sequences and QTI acquisitions (1.1 mm isotropic voxel) performed both before and after contrast media administration. For each patient, a ΔT1 map was obtained via voxel-wise subtraction of pre- and post- contrast QTI-derived T1 maps. ΔT1 values measured in ANELs were compared with those recorded in enhancing lesions and in the normal appearing white matter. A reference distribution of ΔT1 in the white matter was obtained from datasets acquired in 10 non-MS patients with unrevealing MR imaging. RESULTS: Mean ΔT1 in ANELs (57.45 ± 48.27 ms) was significantly lower than in enhancing lesions (297.71 ± 177.52 ms; p < 0. 0001) and higher than in the normal appearing white matter (36.57 ± 10.53 ms; p < 0.005). Fifty-two percent of ANELs exhibited ΔT1 higher than those observed in the white matter of non-MS patients. CONCLUSIONS: QTI-derived quantitative ΔT1 mapping enabled to measure contrast-related T1 shortening in ANELs. ANELs exhibiting ΔT1 values that deviate from the reference distribution in non-MS patients may indicate persistent, subtle, BBB disruption. Access to this information may be proved useful to better characterise pathology and objectively monitor disease activity and response to therapy.


Asunto(s)
Esclerosis Múltiple Recurrente-Remitente , Esclerosis Múltiple , Humanos , Barrera Hematoencefálica/diagnóstico por imagen , Barrera Hematoencefálica/metabolismo , Esclerosis Múltiple/patología , Medios de Contraste/metabolismo , Encéfalo/patología , Esclerosis Múltiple Recurrente-Remitente/patología , Imagen por Resonancia Magnética/métodos
9.
ACS Synth Biol ; 12(9): 2707-2714, 2023 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-37561998

RESUMEN

13C metabolic flux analysis is a powerful tool for metabolism characterization in metabolic engineering and synthetic biology. However, the widespread adoption of this tool is hindered by limited software availability and computational efficiency. Currently, the most widely accepted 13C-flux tools, such as INCA and 13CFLUX2, are developed in a closed-source environment. While several open-source packages or software are available, they are either computationally inefficient or only suitable for flux estimation at isotopic steady state. To address the need for a time-efficient computational tool for the more complicated flux analysis at an isotopically nonstationary state, especially for understanding the single-carbon substrate metabolism, we present FreeFlux. FreeFlux is an open-source Python package that performs labeling pattern simulation and flux analysis at both isotopic steady state and transient state, enabling a more comprehensive analysis of cellular metabolism. FreeFlux provides a set of interfaces to manipulate the objects abstracted from a labeling experiment and computational process, making it easy to integrate into other programs or pipelines. The flux estimation by FreeFlux is fast and reliable, and its validity has been confirmed by comparison with results from other computational tools using both synthetic and experimental data. FreeFlux is freely available at https://github.com/Chaowu88/freeflux with a detailed online tutorial and documentation provided at https://freeflux.readthedocs.io/en/latest/index.html.


Asunto(s)
Análisis de Flujos Metabólicos , Programas Informáticos , Análisis de Flujos Metabólicos/métodos , Isótopos de Carbono/química , Simulación por Computador , Ingeniería Metabólica
10.
Entropy (Basel) ; 25(6)2023 May 30.
Artículo en Inglés | MEDLINE | ID: mdl-37372220

RESUMEN

This paper considers the active fault isolation problem for a class of uncertain multimode fault systems with a high-dimensional state-space model. It has been observed that the existing approaches in the literature based on a steady-state active fault isolation method are often accompanied by a large delay in making the correct isolation decision. To reduce such fault isolation latency significantly, this paper proposes a fast online active fault isolation method based on the construction of residual transient-state reachable set and transient-state separating hyperplane. The novelty and benefit of this strategy lies in the embedding of a new component called the set separation indicator, which is designed offline to distinguish the residual transient-state reachable sets of different system configurations at any given moment. Based on the results delivered by the set separation indicator, one can determine the specific moments at which the deterministic isolation is to be implemented during online diagnostics. Meanwhile, some alternative constant inputs can also be evaluated for isolation effects to determine better auxiliary excitation signals with smaller amplitudes and more differentiated separating hyperplanes. The validity of these results is verified by both a numerical comparison and an FPGA-in-loop experiment.

11.
J Mol Biol ; 435(15): 168186, 2023 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-37355033

RESUMEN

RNA polymerase I (Pol I) synthesizes ribosomal RNA (rRNA), which is the first and rate-limiting step in ribosome biosynthesis. A12.2 (A12) is a critical subunit of Pol I that is responsible for activating Pol I's exonuclease activity. We previously reported a kinetic mechanism for single-nucleotide incorporation catalyzed by Pol I lacking the A12 subunit (ΔA12 Pol I) purified from S. cerevisae and revealed that ΔA12 Pol I exhibited much slower incorporation compared to Pol I. However, it is unknown if A12 influences each nucleotide incorporation in the context of transcription elongation. Here, we show that A12 contributes to every repeating cycle of nucleotide addition and that deletion of A12 results in an entirely different kinetic mechanism compared to WT Pol I. We found that instead of one irreversible step between each nucleotide addition cycle, as reported for wild type (WT) Pol I, the ΔA12 variant requires one reversible step to describe each nucleotide addition. Reversibility fundamentally requires slow PPi release. Consistently, we show that Pol I is more pyrophosphate (PPi) concentration dependent than ΔA12 Pol I. This observation supports the model that PPi is retained in the active site of ΔA12 Pol I longer than WT Pol I. These results suggest that A12 promotes PPi release, revealing a larger role for the A12.2 subunit in the nucleotide addition cycle beyond merely activating exonuclease activity.


Asunto(s)
Difosfatos , ARN Polimerasa I , Difosfatos/metabolismo , Exonucleasas , Nucleótidos/metabolismo , ARN Polimerasa I/química , ARN Polimerasa I/genética , ARN Polimerasa I/metabolismo
12.
Methods Enzymol ; 685: 373-403, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37245908

RESUMEN

Dihydropyrimidine dehydrogenase (DPD) catalyzes the reduction of the 5,6-vinylic bond of uracil and thymine with electrons from NADPH. The complexity of the enzyme belies the simplicity of the reaction catalyzed. To accomplish this chemistry DPD has two active sites that are ∼60Šapart, both of which house flavin cofactors, FAD and FMN. The FAD site interacts with NADPH, while the FMN site with pyrimidines. The distance between the flavins is spanned by four Fe4S4 centers. Though DPD has been studied for nearly 50years, it is only recently that the novel apects of its mechanism have been described. The primary reason for this is that the chemistry of DPD is not portrayed adequately by known descriptive steady-state mechanism categories. The highly chromophoric nature of the enzyme has recently been exploited in transient-state to document unexpected reaction sequences. Specifically, DPD undergoes reductive activation prior to catalytic turnover. Two electrons are taken up from NADPH and transmitted via the FAD and Fe4S4 centers to form the FAD•4(Fe4S4)•FMNH2 form of the enzyme. This form of the enzyme will only reduce pyrimidine substrates in the presence NADPH, establishing that hydride transfer to the pyrimidine precedes reductive reactivation that reinstates the active form of the enzyme. DPD is therefore the first flavoprotein dehydrogenase known to complete the oxidative half-reaction prior to the reductive half-reaction. Here we describe the methods and deduction that led to this mechanistic assignment.


Asunto(s)
Dihidrouracilo Deshidrogenasa (NADP) , Uracilo , Animales , Dihidrouracilo Deshidrogenasa (NADP)/genética , Dihidrouracilo Deshidrogenasa (NADP)/metabolismo , NADP/química , Oxidación-Reducción , Dominio Catalítico , Flavina-Adenina Dinucleótido/metabolismo , Cinética , Mamíferos/metabolismo
13.
Arch Biochem Biophys ; 736: 109517, 2023 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-36681231

RESUMEN

Dihydropyrimidine dehydrogenase (DPD) is a flavin dependent enzyme that catalyzes the reduction of the 5,6-vinylic bond of pyrimidines uracil and thymine with electrons from NADPH. DPD has two active sites that are separated by ∼60 Å. At one site NADPH binds adjacent to an FAD cofactor and at the other pyrimidine binds proximal to an FMN. Four Fe4S4 centers span the distance between these active sites. It has recently been established that the enzyme undergoes reductive activation prior to reducing the pyrimidine. In this initial process NADPH is oxidized at the FAD site and electrons are transmitted to the FMN via the Fe4S4 centers to yield the active state with a cofactor set of FAD•4(Fe4S4)•FMNH2. The catalytic chemistry of DPD can be studied in transient-state by observation of either NADPH consumption or charge transfer absorption associated with complexation of NADPH adjacent to the FAD. Here we have utilized both sets of absorption transitions to find evidence for specific additional aspects of the DPD mechanism. Competition for binding with NADP+ indicates that the two charge transfer species observed in activation/single turnover reactions arise from NADPH populating the FAD site before and after reductive activation. An additional charge transfer species is observed to accumulate at longer times when high NADPH concentrations are mixed with the enzyme•pyrimidine complex and this data can be modelled based on asymmetry in the homodimer. It was also shown that, like pyrimidines, dihydropyrimidines induce rapid reductive activation indicating that the reduced pyrimidine formed in turnover can stimulate the reinstatement of the active state of the enzyme. Investigation of the reverse reaction revealed that dihydropyrimidines alone can reductively activate the enzyme, albeit inefficiently. In the presence of dihydropyrimidine and NADP+ DPD will form NADPH but apparently without measurable reductive activation. Pyrimidines that have 5-substituent halogens were utilized to probe both reductive activation and turnover. The linearity of the Hammett plot based on the rate of hydride transfer to the pyrimidine establishes that, at least to the radius of an iodo-group, the 5-substituent volume does not have influence on the observed kinetics of pyrimidine reduction.


Asunto(s)
Dihidrouracilo Deshidrogenasa (NADP) , Pirimidinas , Animales , Oxidación-Reducción , Dihidrouracilo Deshidrogenasa (NADP)/química , NADP/metabolismo , Espectrofotometría , Pirimidinas/metabolismo , Cinética , Flavina-Adenina Dinucleótido/química , Mamíferos/metabolismo
14.
Environ Res ; 217: 114788, 2023 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-36403652

RESUMEN

Biofilter (BF) has been regarded as a versatile gas treatment technology for removing volatile organic compounds (VOCs) from contaminated gas streams. In order for BF to be utilized in the industrial setting, it is essential to conduct research aimed at removing VOC mixtures under different inlet loading conditions, i.e. as a function of the gas flow rate and inlet VOC concentrations. The main aim of this study was to apply artificial neural networks (ANN) and determine the relationship between flow rate (FR), pressure drop (PD), inlet concentration (C), and removal efficiency (RE) in the BF treating gas-phase benzene and xylene mixtures. The ANN model was trained and tested to assess the removal efficiency of benzene (REB) and xylene (REX) under the influence of different FR, PD and C. The model's performance was assessed using a cross-validation method. The REb varied from 20% to >60%, while the REx varied from 10% to 70% during the different experimental phases of BF operation. The causal index (CI) technique was used to determine the sensitivity of the input parameters on the output variables. The ANN model with a topology of 4-4-2 performed the best in terms of predicting the RE profiles of both the pollutants. Furthermore, the effect was more pronounced for xylene because an increase in the benzene concentration reduced xylene removal (CI = -25.7170) more severely than benzene removal. An increase in the xylene concentration had a marginally positive effect on the benzene removal (CI = +0.1178).


Asunto(s)
Contaminantes Atmosféricos , Compostaje , Compuestos Orgánicos Volátiles , Benceno , Xilenos , Contaminantes Atmosféricos/análisis , Filtración , Compuestos Orgánicos Volátiles/análisis , Gases , Biodegradación Ambiental
15.
Sensors (Basel) ; 22(23)2022 Nov 29.
Artículo en Inglés | MEDLINE | ID: mdl-36501986

RESUMEN

This article proposes a queueing model of the operation of a wireless sensor network node, in which a threshold strategy for starting the node after a period of no transmission is used. In this model, transmission of packets is resumed when the number of packets in the accumulation buffer reaches a predefined level. In the literature, most of the results for models with limited access to the service station are obtained in equilibrium. In this paper, a formula for the Laplace transform of the transient queue-size distribution is obtained and written using the key input parameters of the system. The analytical apparatus uses the concept of the embedded Markov chain, the formula for total probability, renewal theory and some supporting algebraic results. Numerical examples are attached as well.

16.
Front Genet ; 13: 815476, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35281848

RESUMEN

Motivation: The increasing availability of metabolomic data and their analysis are improving the understanding of cellular mechanisms and how biological systems respond to different perturbations. Currently, there is a need for novel computational methods that facilitate the analysis and integration of increasing volume of available data. Results: In this paper, we present Totoro a new constraint-based approach that integrates quantitative non-targeted metabolomic data of two different metabolic states into genome-wide metabolic models and predicts reactions that were most likely active during the transient state. We applied Totoro to real data of three different growth experiments (pulses of glucose, pyruvate, succinate) from Escherichia coli and we were able to predict known active pathways and gather new insights on the different metabolisms related to each substrate. We used both the E. coli core and the iJO1366 models to demonstrate that our approach is applicable to both smaller and larger networks. Availability: Totoro is an open source method (available at https://gitlab.inria.fr/erable/totoro) suitable for any organism with an available metabolic model. It is implemented in C++ and depends on IBM CPLEX which is freely available for academic purposes.

17.
Glob Chang Biol ; 28(9): 2930-2939, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35100483

RESUMEN

Forest and savanna ecosystems naturally exist as alternative stable states. The maximum capacity of these ecosystems to absorb perturbations without transitioning to the other alternative stable state is referred to as 'resilience'. Previous studies have determined the resilience of terrestrial ecosystems to hydroclimatic changes predominantly based on space-for-time substitution. This substitution assumes that the contemporary spatial frequency distribution of ecosystems' tree cover structure holds across time. However, this assumption is problematic since ecosystem adaptation over time is ignored. Here we empirically study tropical forests' stability and hydroclimatic adaptation dynamics by examining remotely sensed tree cover change (ΔTC; aboveground ecosystem structural change) and root zone storage capacity (Sr ; buffer capacity towards water-stress) over the last two decades. We find that ecosystems at high (>75%) and low (<10%) tree cover adapt by instigating considerable subsoil investment, and therefore experience limited ΔTC-signifying stability. In contrast, unstable ecosystems at intermediate (30%-60%) tree cover are unable to exploit the same level of adaptation as stable ecosystems, thus showing considerable ΔTC. Ignoring this adaptive mechanism can underestimate the resilience of the forest ecosystems, which we find is largely underestimated in the case of the Congo rainforests. The results from this study emphasise the importance of the ecosystem's temporal dynamics and adaptation in inferring and assessing the risk of forest-savannah transitions under rapid hydroclimatic change.


Asunto(s)
Ecosistema , Bosques , Aclimatación , Adaptación Fisiológica , Árboles
18.
Entropy (Basel) ; 23(11)2021 Oct 27.
Artículo en Inglés | MEDLINE | ID: mdl-34828108

RESUMEN

The transient behavior of the finite-buffer queueing model with batch arrivals and generally distributed repeated vacations is analyzed. Such a system has potential applications in modeling the functioning of production systems, computer and telecommunication networks with energy saving mechanism based on cyclic monitoring the queue state (Internet of Things, wireless sensors networks, etc.). Identifying renewal moments in the evolution of the system and applying continuous total probability law, a system of Volterra-type integral equations for the time-dependent queue-size distribution, conditioned by the initial buffer state, is derived. A compact-form solution for the corresponding system written for Laplace transforms is obtained using an algebraic approach based on Korolyuk's potential method. An illustrative numerical example presenting the impact of the service rate, arrival rate, initial buffer state and single vacation duration on the queue-size distribution is attached as well.

19.
Antioxidants (Basel) ; 10(9)2021 Sep 12.
Artículo en Inglés | MEDLINE | ID: mdl-34573078

RESUMEN

Lignin biodegradation has been extensively studied in white-rot fungi, which largely belong to order Polyporales. Among the enzymes that wood-rotting polypores secrete, lignin peroxidases (LiPs) have been labeled as the most efficient. Here, we characterize a similar enzyme (ApeLiP) from a fungus of the order Agaricales (with ~13,000 described species), the soil-inhabiting mushroom Agrocybe pediades. X-ray crystallography revealed that ApeLiP is structurally related to Polyporales LiPs, with a conserved heme-pocket and a solvent-exposed tryptophan. Its biochemical characterization shows that ApeLiP can oxidize both phenolic and non-phenolic lignin model-compounds, as well as different dyes. Moreover, using stopped-flow rapid spectrophotometry and 2D-NMR, we demonstrate that ApeLiP can also act on real lignin. Characterization of a variant lacking the above tryptophan residue shows that this is the oxidation site for lignin and other high redox-potential substrates, and also plays a role in phenolic substrate oxidation. The reduction potentials of the catalytic-cycle intermediates were estimated by stopped-flow in equilibrium reactions, showing similar activation by H2O2, but a lower potential for the rate-limiting step (compound-II reduction) compared to other LiPs. Unexpectedly, ApeLiP was stable from acidic to basic pH, a relevant feature for application considering its different optima for oxidation of phenolic and nonphenolic compounds.

20.
Nanomaterials (Basel) ; 11(8)2021 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-34443752

RESUMEN

As the stress-strain curve of standardized metal samples provides the basic details about mechanical properties of structural materials, the polarization curve or current-voltage characteristics of fuel cells are vitally important to explore the scientific mechanism of various solid oxide cells aiming at low operational temperatures (below 600 °C), ranging from protonic conductor ceramic cells (PCFC) to emerging Semiconductor ionic fuel cell (SIFC)/Semiconductor membrane fuel cells (SMFC). Thus far, worldwide efforts to achieve higher nominal peak power density (PPD) at a low operational temperature of over 0.1 s/cm ionic conductivity of electrolyte and super catalyst electrode is the key challenge for SIFCs. Thus, we illustrate an alternative approach to the present PPD concept and current-voltage characteristic. Case studies reveal that the holy grail of 1 W/cm2 from journal publications is expected to be reconsidered and normalized, since partial cells may still remain in a transient state (TS) to some extent, which means that they are unable to fulfill the prerequisite of a steady state (SS) characteristic of polarization curve measurement. Depending on the testing parameters, the reported PPD value can arbitrarily exist between higher transient power density (TPD) and lower stable power density (SPD). Herein, a standardized procedure has been proposed by modifying a quasi-steady state (QSS) characterization based on stabilized cell and time-prolonged measurements of common I-V plots. The present study indicates, when compared with steady state value, that QSS power density itself still provides a better approximation for the real performance of fuel cells, and concurrently recalls a novel paradigm transformation from a transient to steady state perspective in the oxide solid fuel cell community.

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