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101.
One strategy for estimating total catch is to employ two separate surveys that independently estimate total fishing effort and catch rate with the estimator for total catch formed by their product. Survey designs for estimating catch rate often involve interviewing the fishermen during their fishing episodes. Such roving designs result in incomplete episode data and characteristically have employed a model in which the catch rate is assumed to be constant over time. This article extends the problem to that of estimating total catch in the presence of a declining catch rate due, e.g., to gear saturation. Using a gill net fishery as an example, a mean-of-ratios type of estimator for the catch rate together with its variance estimator are developed. Their performance is examined using simulations, with special attention given to effects of restrictions on the roving survey window. Finally, data from a Fraser River gill net fishery are used to illustrate the use of the proposed estimator and to compare results with those from an estimator based on a constant catch rate. 相似文献
102.
In this paper, the dynamical behavior of an SIRS epidemic model with birth pulse, pulse vaccination, and saturation incidence is studied. By using a discrete map, the existence and stability of the infection-free periodic solution and the endemic periodic solution are investigated. The conditions required for the existence of supercritical bifurcation are derived. A threshold for a disease to be extinct or endemic is established. The Poincaré map and center manifold theorem are used to discuss flip bifurcation of the endemic periodic solution. Moreover, numerical simulations for bifurcation diagrams, phase portraits and periodic solutions, which are illustrated with an example, are in good agreement with the theoretical analysis. 相似文献
103.
Anirikh Chakrabarti Ljubisa Miskovic Keng Cher Soh Prof. Vassily Hatzimanikatis 《Biotechnology journal》2013,8(9):1043-1057
Mathematical modeling is an essential tool for the comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the construction and analysis of stoichiometric models made it possible to define limits on steady-state metabolic behavior using flux balance analysis. However, detailed information on enzyme kinetics and enzyme regulation is needed to formulate kinetic models that can accurately capture the dynamic metabolic responses. The use of mechanistic enzyme kinetics is a difficult task due to uncertainty in the kinetic properties of enzymes. Therefore, the majority of recent works considered only mass action kinetics for reactions in metabolic networks. Herein, we applied the optimization and risk analysis of complex living entities (ORACLE) framework and constructed a large-scale mechanistic kinetic model of optimally grown Escherichia coli. We investigated the complex interplay between stoichiometry, thermodynamics, and kinetics in determining the flexibility and capabilities of metabolism. Our results indicate that enzyme saturation is a necessary consideration in modeling metabolic networks and it extends the feasible ranges of metabolic fluxes and metabolite concentrations. Our results further suggest that enzymes in metabolic networks have evolved to function at different saturation states to ensure greater flexibility and robustness of cellular metabolism. 相似文献
104.
Lipopolysaccharide (LPS), the major constituent of the outer membrane of Gram-negative bacteria, is the very first site of interactions with the antimicrobial peptides. In this work, we have determined a solution conformation of melittin, a well-known membrane active amphiphilic peptide from honey bee venom, by transferred nuclear Overhauser effect (Tr-NOE) spectroscopy in its bound state with lipopolysaccharide. The LPS bound conformation of melittin is characterized by a helical structure restricted only to the C-terminus region (residues A15-R24) of the molecule. Saturation transfer difference (STD) NMR studies reveal that several C-terminal residues of melittin including Trp19 are in close proximity with LPS. Isothermal titration calorimetry (ITC) data demonstrates that melittin binding to LPS or lipid A is an endothermic process. The interaction between melittin and lipid A is further characterized by an equilibrium association constant (Ka) of 2.85 × 106 M− 1 and a stoichiometry of 0.80, melittin/lipid A. The estimated free energy of binding (ΔG0), − 8.8 kcal mol− 1, obtained from ITC experiments correlates well with a partial helical structure of melittin in complex with LPS. Moreover, a synthetic peptide fragment, residues L13-Q26 or mel-C, derived from the C-terminus of melittin has been found to contain comparable outer membrane permeabilizing activity against Escherichia coli cells. Intrinsic tryptophan fluorescence experiments of melittin and mel-C demonstrate very similar emission maxima and quenching in presence of LPS micelles. The Red Edge Excitation Shift (REES) studies of tryptophan residue indicate that both peptides are located in very similar environment in complex with LPS. Collectively, these results suggest that a helical conformation of melittin, at its C-terminus, could be an important element in recognition of LPS in the outer membrane. 相似文献
105.
Jonathan M. O’Brien Walter K. Dodds Kymberly C. Wilson Justin N. Murdock Jessica Eichmiller 《Biogeochemistry》2007,84(1):31-49
We conducted 15NO3− stable isotope tracer releases in nine streams with varied intensities and types of human impacts in the upstream watershed
to measure nitrate (NO3−) cycling dynamics. Mean ambient NO3− concentrations of the streams ranged from 0.9 to 21,000 μg l−1 NO3−–N. Major N-transforming processes, including uptake, nitrification, and denitrification, all increased approximately two
to three orders of magnitude along the same gradient. Despite increases in transformation rates, the efficiency with which
stream biota utilized available NO3−-decreased along the gradient of increasing NO3−. Observed functional relationships of biological N transformations (uptake and nitrification) with NO3− concentration did not support a 1st order model and did not show signs of Michaelis–Menten type saturation. The empirical
relationship was best described by a Efficiency Loss model, in which log-transformed rates (uptake and nitrification) increase
with log-transformed nitrate concentration with a slope less than one. Denitrification increased linearly across the gradient
of NO3− concentrations, but only accounted for ∼1% of total NO3− uptake. On average, 20% of stream water NO3− was lost to denitrification per km, but the percentage removed in most streams was <5% km−1. Although the rate of cycling was greater in streams with larger NO3− concentrations, the relative proportion of NO3− retained per unit length of stream decreased as NO3− concentration increased. Due to the rapid rate of NO3− turnover, these streams have a great potential for short-term retention of N from the landscape, but the ability to remove
N through denitrification is highly variable. 相似文献
106.
Bastien Bissaro Olivier Saurel Faten Arab-Jaziri Luc Saulnier Alain Milon Maija Tenkanen Pierre Monsan Michael J. O'Donohue Régis Fauré 《Biochimica et Biophysica Acta (BBA)/General Subjects》2014
Background
The development of enzyme-mediated glycosynthesis using glycoside hydrolases is still an inexact science, because the underlying molecular determinants of transglycosylation are not well understood. In the framework of this challenge, this study focused on the family GH51 α-l-arabinofuranosidase from Thermobacillus xylanilyticus, with the aim to understand why the mutation of position 344 provokes a significant modification of the transglycosylation/hydrolysis partition.Methods
Detailed kinetic analysis (kcat, KM, pKa determination and time-course NMR kinetics) and saturation transfer difference nuclear magnetic resonance spectroscopy was employed to determine the synthetic and hydrolytic ability modification induced by the redundant N344 mutation disclosed in libraries from directed evolution.Results
The mutants N344P and N344Y displayed crippled hydrolytic abilities, and thus procured improved transglycosylation yields. This behavior was correlated with an increased pKa of the catalytic nucleophile (E298), the pKa of the acid/base catalyst remaining unaffected. Finally, mutations at position 344 provoked a pH-dependent product inhibition phenomenon, which is likely to be the result of a significant modification of the proton sharing network in the mutants.Conclusions and general significance
Using a combination of biochemical and biophysical methods, we have studied TxAbf-N344 mutants, thus revealing some fundamental details concerning pH modulation. Although these results concern a GH51 α-l-arabinofuranosidase, it is likely that the general lessons that can be drawn from them will be applicable to other glycoside hydrolases. Moreover, the effects of mutations at position 344 on the transglycosylation/hydrolysis partition provide clues as to how TxAbf can be further engineered to obtain an efficient transfuranosidase. 相似文献107.
Luciana Cardoso Bonadia Fernando Augusto de Lima Marson Jose Dirceu Ribeiro Ilma Aparecida Paschoal Monica Corso Pereira Antonio Fernando Ribeiro Carmen Silvia Bertuzzo 《Gene》2014
Background
There are nearly 2000 cystic fibrosis transmembrane regulator (CFTR) mutations that cause cystic fibrosis (CF). These mutations are classified into six classes; on the one hand, the first three classes cause severe disease involvement in early childhood, on the other hand, the Class IV, V and VI mutations cause minor severe disease in the same age. Nowadays, with therapeutic advances in CF management and competence of pediatricians, physicians of adults have to deal with two groups of CF patients: (i) adults diagnosed in childhood with severe mutations and (ii) adults who initiated symptoms in adulthood and with Class IV, V and VI mutations. The aim of this study was to analyze adults from a clinical center, treated as CF disease, screening the CFTR genotype and evaluating the clinical characteristics.Methods
Thirty patients followed as CF disease at the University Hospital were enrolled. After a complete molecular CFTR negative screening and sweat test levels between 40 and 59 mEq/L, five patients were characterized as non-CF disease and were excluded. Molecular screening was performed by CFTR gene sequencing/MLPA or by specific mutation screening. Clinical data was obtained from medical records. The patients were divided into three groups: (1) patients with Class I, II and III mutations in two CFTR alleles; (2) genotype with at least one allele of Class IV, V or VI CFTR mutations and, (3) non-identified CFTR mutation + one patient with one allele with CFTR mutation screened (Class I).Results
There was an association of CFTR class mutation and sodium/chloride concentration in the sweat test (sodium: p = 0.040; chloride: p = 0.016), onset of digestive symptoms (p = 0.012), lung function parameter (SpO2 — p = 0.016), Bhalla score (p = 0.021), age at diagnosis (p = 0.008) and CF-related diabetes (p = 0.029). There was an association between Pseudomonas aeruginosa chronic colonization (as clinical marker for the lung disease status) and lung impairment (FEV1% — p = 0.027; Bhalla score — p = 0.021), CF-related diabetes (p = 0.040), chloride concentration in the sweat test (p = 0.040) and chronic infection by microorganisms (Staphylococcus aureus — p = 0.039; mucoid P. aeruginosa — p = 0.001). There is no positive association with the status of other clinical markers and the CFTR genotype groups. For clinical association with pancreatic insufficiency (as clinical marker for digestive symptoms), no association was related.Conclusion
The adults with CF diagnosed by sweat test have specific clinical and genotypic characteristics, being a population that should be studied to cause better future management. Some patients treated as CF disease by clinical symptoms, showed no disease, taking into account the sweat test and complete exon sequencing/MLPA screening. 相似文献108.
Krista Chamberlain Mya Johnson Terry-Elinor Reid Tzvia I. Springer 《Biochemistry and Biophysics Reports》2022
Multi-drug resistant infections caused by the opportunistic pathogen, Pseudomonas aeruginosa (P. aeruginosa), are a continuing problem that contribute to morbidity and mortality in immunocompromised hosts such as cystic fibrosis (CF), wound and burn patients. The bacterial toxin ExoU is one of four potent toxins that P. aeruginosa secretes into the epithelial cells of hosts. In this study, NMR Saturation Transfer Difference (STD) and in silico Schrödinger Computational Modeling were used to identify a possible binding site of a novel ligand methoctramine targeting ExoU. Future project goals will be to design a structure activity relationship (SAR) study of methoctramine and ExoU and lead to a new drug solving ExoU toxicity P. aeruginosa exerts in the clinical environment. 相似文献
109.
Kevin Brindle Susan Krikler 《Biochimica et Biophysica Acta (BBA)/Molecular Cell Research》1985,847(3)
31P-NMR measurements of saturation transfer have been used to measure phosphate consumption in respiratory competent cells of the yeast Saccharomyces cerevisiae. Measurements of oxygen consumption and maintenance of the cells in a metabolic steady state during the NMR experiments were facilitated by immobilisation of the cells in an agarose gel matrix which could be perfused in the NMR spectrometer. The contribution of glycolysis to the observed rate of phosphate consumption was estimated by simultaneously measuring glucose consumption and ethanol production in the perfusion buffer. The remaining phosphate consumption, which was attributed to flux through the reaction catalysed by the mitochondrial ATP synthase, combined with measurements of oxygen consumption allowed estimation of a P:O ratio (mol ATP synthesised:atoms oxygen consumed) which was close to 3. 相似文献
110.
Mammals are able to perceive and differentiate a great number of structurally diverse odorants through the odorant's interaction with odorant receptors (ORs), proteins found within the cell membrane of olfactory sensory neurons. The natural gas industry has used human olfactory sensitivity to sulfur compounds (thiols, sulfides, etc.) to increase the safety of fuel gas transport, storage, and use through the odorization of this product. In the United States, mixtures of sulfur compounds are used, but the major constituent of odorant packages is 2-methylpropane-2-thiol, also known as tert-butyl mercaptan. It has been fundamentally challenging to understand olfaction and odorization due to the low affinity of odorous ligands to the ORs and the difficulty in expressing a sufficient number of OR proteins. Here, we directly observed the binding of tert-butyl mercaptan and another odiferous compound, cis-cyclooctene, to mouse OR MOR244-3 on living cells by saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy. This effort lays the groundwork for resolving molecular mechanisms responsible for ligand binding and resulting signaling, which in turn will lead to a clearer understanding of odorant recognition and competition. 相似文献