Enzyme Kinetics: Systematic Generation of Valid King-Altman Patterns

One of the most generally applicable algorithms for the derivation of steady-state rate equations for complex enzyme reaction mechanisms is that of King and Altman. Several modifications of this algorithm have been suggested; however, each requires the generation of numerous valid and invalid patterns and the subsequent elimination of those that are invalid. A method is presented, employing topological theory of linear graphs, for the systematic generation of only those patterns which are valid. This method is readily adaptable to use on a digital computer. An independent method for the calculation of the number of valid patterns is also presented. This calculation can be used to substantiate the accuracy of the patterns obtained. This calculation is also adaptable to computerization. Examples are included to demonstrate both the generation of patterns and the calculation of their number for specific enzyme mechanisms.     

An automatic method for deriving steady-state rate equations.

A method is described for systematically deriving steady-state rate equations. It is based on the schematic method of King & Altman [J. Phys. Chem. (1956) 60, 1375-1378], but is expressed in purely algebraic terms. It is suitable for implementation as a computer program, and a program has been written in FORTRAN IV and deposited as Supplementary Publication SUP 50078 (12 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1977) 161, 1-2.     

Derivation of a velocity equation for a reaction model witwh two binding sites for acetylcholinesterase

The authors suggest a kinetic model with two binding sites for acetylcholinesterase; it is suitable to study particular enzyme forms that show a kinetic pattern which cannot be explained by the model with a single binding site of Krupka and Laidler. The velocity equation was obtained using the algorithm of King and Altman and carrying out elementary calculations.     

Schematic methods for probabilistic enzyme kinetics.

The theory of steady-state enzyme processes which avoids using the mass action law of chemical kinetics and consistently describes catalytic mechanisms by probabilistic concepts has recently been proposed (Mazur, 1991, J. theor. Biol. 148, 229-242). To facilitate the analysis of complex reaction graphs by this theory the possibility of constructing schematic rules similar to those used in classical kinetics is studied. It is found that due to the similarity of algebraic procedures the popular method of King & Altman can be applied in probabilistic kinetics in addition to the earlier proposed rule based on enumeration of cycles of the reaction graph. This similarity also allows one to adapt many other shortcut methods of classical kinetics for probabilistic reaction graphs. The paper considers separately the possibility of transforming reaction mechanisms so that the initial graph is replaced by a simpler but equivalent one. It is shown that there are few cases when a group of states can be replaced by one united state, with earlier known rules such as the rule of Cha for equilibrium stages being particular cases of a more general procedure. In addition a novel method is proposed which performs step-by-step reduction of any reaction graph. All the new methods can be adapted for traditional kinetics as well. The results obtained demonstrate that many schematic rules of classical kinetics are of probabilistic origin.     

A smart device inertial-sensing method for gait analysis

The purpose of this study was to establish and cross-validate a method for analyzing gait patterns determined by the center of mass (COM) through inertial sensors embedded in smart devices. The method employed an extended Kalman filter in conjunction with a quaternion rotation matrix approach to transform accelerations from the object onto the global frame. Derived by double integration, peak-to-trough changes in vertical COM position captured by a motion capture system, inertial measurement unit, and smart device were compared in terms of averaged and individual steps. The inter-rater reliability and levels of agreement for systems were discerned through intraclass correlation coefficients (ICC) and Bland–Altman plots. ICCs corresponding to inter-rater reliability were good-to-excellent for position data (ICCs,.80–.95) and acceleration data (ICCs,.54–.81). Levels of agreements were moderate for position data (LOA, 3.1–19.3%) and poor for acceleration data (LOA, 6.8%–17.8%). The Bland–Altman plots, however, revealed a small systematic error, in which peak-to-trough changes in vertical COM position were underestimated by 2.2 mm; the Kalman filter?s accuracy requires further investigation to minimize this oversight. More importantly, however, the study?s preliminary results indicate that the smart device allows for reliable COM measurements, opening up a cost-effective, user-friendly, and popular solution for remotely monitoring movement. The long-term impact of the smart device method on patient rehabilitation and therapy cannot be underestimated: not only could healthcare expenditures be curbed (smart devices being more affordable than today‘s motion sensors), but a more refined grasp of individual functioning, activity, and participation within everyday life could be attained.     

Improved analysis of bacterial CGH data beyond the log-ratio paradigm

Background

While the theory of enzyme kinetics is fundamental to analyzing and simulating biochemical systems, the derivation of rate equations for complex mechanisms for enzyme-catalyzed reactions is cumbersome and error prone. Therefore, a number of algorithms and related computer programs have been developed to assist in such derivations. Yet although a number of algorithms, programs, and software packages are reported in the literature, one or more significant limitation is associated with each of these tools. Furthermore, none is freely available for download and use by the community.

Results

We have implemented an algorithm based on the schematic method of King and Altman (KA) that employs the topological theory of linear graphs for systematic generation of valid reaction patterns in a GUI-based stand-alone computer program called KAPattern. The underlying algorithm allows for the assumption steady-state, rapid equilibrium-binding, and/or irreversibility for individual steps in catalytic mechanisms. The program can automatically generate MathML and MATLAB output files that users can easily incorporate into simulation programs.

Conclusion

A computer program, called KAPattern, for generating rate equations for complex enzyme system is a freely available and can be accessed at http://www.biocoda.org.     

Krill-feeding behaviour of gentoo penguins as shown by animal-borne camera loggers

Animal-borne camera loggers were used to examine the patterns of prey encounter and feeding behaviour of gentoo penguins at King George Island, Antarctica. The still images from the camera loggers showed that the penguins encountered the swarms of krill for 25.5% (range: 8–38%) of their dives (>5 m) on average, during their foraging trips (mean duration of 5.4 h, n = 7 trips). They encountered krill swarms during the dives to 10–70 m depth, in pelagic as well as benthic habitats. In the benthic habitat, the penguins swam just above the sea floor and headed downward over a krill swarm, probably using the sea floor to assist them to feed on mobile swarms. The shallow coastal waters would be the important foraging habitat of gentoo penguins breeding in King George Island.     

Determination of internal diffusion limitation and its macroscopic kinetics of the transesterification of CPB alcohol catalyzed by immobilized lipase in organic media

Optically active cyanohydrin esters such as (S)-α-cyano-3-phenoxybenzyl (CPB) acetate can be obtained with enzymatic transesterification of racemic cyanohydrins in organic media. The influence of internal diffusion limitation on transesterification of CPB alcohol with vinyl acetate catalyzed by immobilized lipase was studied. Internal diffusion limitation could not be ignored since the immobilized lipase granule was not small enough. In order to express the effect of internal diffusion limitation quantitatively, a method was proposed which calculates the effective diffusion coefficient (D_e) first and then calculates apparent Thiele modulus (Φ) and finally obtains internal diffusion effectiveness factor, η value (0.55). D_e was calculated to be 3.1 × 10⁻¹⁰ m² s⁻¹ by supposing that the immobilized lipase was a sphere granule and the diffusion only existed in one dimension. Φ was calculated to be 2.2 by presuming that transport of substrate through the catalyst could be described by Fick's law. Using King–Altman method, a kinetic model of the transesterification of CPB alcohol with vinyl acetate in organic media in the presence of internal diffusion limitation was proposed based on ping-pong bi–bi mechanism. The relative error of the model was 11.18%. A practicable method to evaluate η value and relatively simple model for such kind of reaction system was proposed in this paper.     

Ultrasound does not provide reliable results for the measurement of the patellar tendon cross sectional area

PurposeThis study examined the reliability of patellar tendon cross sectional area (CSA) measurement using brightness mode ultrasonography.MethodsThe patellar tendon CSA of fourteen participants was examined on two different days and at three different positions (proximal, median and distal). Five trials per day were conducted in each position, replacing the ultrasound probe on every trial. The images were examined by three different and equally experienced observers. We compared the mean of the five trials in each position to examine the day, observer and position effect. Further, Bland and Altman plots, root mean square (RMS) differences and intraclass correlation coefficients (ICC) were calculated.ResultsThere was a significant (p < 0.05) day, observer and position effect on the CSA, while the average ICC was 0.592. The Bland and Altman plots showed that differences between conditions or groups, should be in average lower than 37% or higher than 55% of the patellar tendon CSA to be important for clinical or intervention studies.ConclusionOur findings show low reliability of the method, which resulted from the low clarity and unclear visibility of tissue boundaries in the ultrasound images. Therefore, the measurement of the CSA of the patellar tendon using ultrasound does not provide accurate and reliable results.     

Comparison of intervertebral disc displacements measured under applied loading with MRI at 3.0 T and 9.4 T

The purpose of this study was to compare displacement behavior of cyclically loaded cadaveric human intervertebral discs as measured noninvasively on a clinical 3.0 T and a research 9.4 T MRI system. Intervertebral discs were cyclically compressed at physiologically relevant levels with the same MRI-compatible loading device in the clinical and research systems. Displacement-encoded imaging was synchronized to cyclic loading to measure displacements under applied loading with MRI (dualMRI). Displacements from the two systems were compared individually using linear regression and, across all specimens, using Bland–Altman analysis. In-plane displacement patterns measured at 3.0 T and 9.4 T were qualitatively comparable and well correlated. Bland–Altman analyses showed that over 90% of displacement values within the intervertebral disc regions of interest lay within the limits of agreement. Measurement of displacement using dualMRI using a 3.0 T clinical system is comparable to that of a 9.4 T research system. Additional refinements of software, technique implementation, and image processing have potential to improve agreement between different MRI systems. Despite differences in MRI systems in this initial implementation, this work demonstrates that dualMRI can be reliably implemented at multiple magnetic field strengths, permitting translation of dualMRI for a variety of applications in the study of tissue and biomaterial biomechanics.     

Body temperature in premature infants during the first week of life: Exploration using infrared thermal imaging

BackgroundHypothermia is a problem for very premature infants after birth and leads to increased morbidity and mortality. Previously we found very premature infants exhibit abnormal thermal patterns, keeping foot temperatures warmer than abdominal temperatures for their first 12 h of life.PurposeWe explored the utility of infrared thermography as a non-invasive method for measuring body temperature in premature infants in an attempt to regionally examine differential temperatures.ResultsOur use of infrared imaging to measure abdominal and foot temperature for extremely premature infants in heated, humid incubators was successful and in close agreement using Bland and Altman technique with temperatures measured by skin thermistors.ConclusionsOur study methods demonstrated that it was feasible to capture full body temperatures of extremely premature infants while they were resting in a heated, humid incubator using a Flir SC640 infrared camera. This technology offers researchers and clinicians a method to examine acute changes in perfusion differentials in premature infants which may lead to morbidity.     

Identification of Pseudomonas aeruginosa in water-bottling plants on the basis of procedures included in ISO 16266:2006

ISO 16266:2006 provides a standardized procedure for the isolation and identification of Pseudomonas aeruginosa in waters. In some cases the method described in this ISO is not conclusive enough to confirm or discard the presence of this opportunistic human pathogen. In this study the capacity of the procedure described in ISO 16266:2006 to identify presumptive P. aeruginosa isolates was evaluated.Forty-one presumptive P. aeruginosa strains, previously isolated from water-bottling plants following ISO 16266:2006, were submitted to all the tests recommended by ISO 16266:2006 (Cetrimide agar with nalidixic acid, King B agar, Acetamide broth and Oxidase test). Additional tests that have been widely used for the identification of P. aeruginosa were also performed (Asparagine broth and King A agar). Furthermore, we also conducted the non-compulsory ISO 16266:2006 assay to study the capacity of the strains to grow at 4 °C and 42 °C. Finally, all the strains were biochemically phenotyped with PhP-48 plates (Bactus AB, Sweden) and API 20NE galleries (Biomérieux, France), and their 16 rRNA gene was sequenced.ISO 16266:2006 correctly identified 27 out of 29 genotypically confirmed P. aeruginosa isolates, although two false negative identifications were obtained.Growth in Asparagine broth should be discarded as a confirmative test as it showed false negatives and false positives. In contrast, API 20NE galleries correctly identified all the confirmed isolates.King A medium and growth tests at 4 °C and 42 °C correctly discriminated all the studied strains, even the two that were not identified with the basic ISO 16266:2006 tests.Given that King A medium and growth tests at 4 °C and 42 °C are straightforward, rapid, and inexpensive, it is strongly recommended that they be used for routine confirmation of P. aeruginosa when applying ISO 16266:2006.     

Effect of the hinge protein on the heme iron site of cytochrome c1

X-ray absorption spectroscopic (XAS) studies on cytochrome C1 from beef heart mitochondria were conducted to identify the effect of the hinge protein [Kim, C.H., & King, T.E. (1983) J. Biol. Chem. 258, 13543-13551] on the structure of the heme site in cytochrome c1. A comparison of XAS data of highly purified "one-band" and "two-band" cytochrome c1 [Kim, C.H., & King, T.E. (1987) Biochemistry 26, 1955-1961] demonstrates that the hinge protein exerts a rather pronounced effect on the heme environment of the cytochrome c1: a conformational change occurs within a radius of approximately 5 A from the heme iron in cytochrome c1 when the hinge protein is bound to cytochrome c1. This result may be correlated with the previous observations that the structure and reactivity of cytochrome c1 are affected by the hinge protein [Kim, C.H., & King, T.E. (1987) Biochemistry 26, 1955-1961; Kim, C.H., Balny, C., & King, T.E. (1987) J. Biol. Chem. 262, 8103-8108].     

Soil properties and distributions of invertebrates and bacteria from King George Island (Arctowski Station), maritime Antarctic

Soils of the Admiralty Bay region at King George Island, maritime Antarctic are described and analysed for invertebrates and microorganisms. Results showed a great variety of soils: cambisols, umbrisols, regosols, podzols, leptosols, gleysols and relic ornithogenic soils were found. Surface layers, especially of cambisols, umbrisols and podzols, showed a diverse fauna, governed by nematodes, collemboles and mites. The bacterial flora is analysed for total counts and biomass distribution in different layers using epifluorescence microscopy. Influences of soil organic matter can be described by different patterns of mean bacterial cell volumes related to soil cover and depth distributions. Received: 21 February 1997 / Accepted: 28 April 1997     

<Emphasis Type="Italic">Drepanocladus longifolius</Emphasis> (Amblystegiaceae), an addition to the moss flora of King George Island,South Shetland Islands,with a review of Antarctic benthic mosses

Drepanocladus longifolius (Mitt.) Paris is recorded for the first time from King George Island, South Shetland Islands, in the maritime Antarctic. It was collected in West Lake during the 23rd Chinese National Antarctic Research Expedition in 2006–2007. The moss was found at a depth of 5–6 m attached to the bed of the lake. The stems of the moss are about 1–1.5 m in length. The moss exhibits seasonal growth patterns, with shorter branch internodes, more widely spaced leaves and more branches in summer than in winter. Most of the branches are initiated in summer. The annual shoot extension is about 3–6 cm, which implies that the plants must be at least 15 years of age. The distribution of aquatic moss species and records in Antarctica is outlined and discussed and the nomenclature of previous reports clarified.     

Sex identification in King Penguins Aptenodytes patagonicus through morphological and acoustic cues

In the context of sexual selection, animals have developed a variety of cues conveying information about the sex of an individual to conspecifics. In many colonial seabird species, where females and males are monomorphic and do not show obvious differences in external morphology, acoustic cues are an important signal for individual and sex recognition. Here, we study the vocal and morphological sex dimorphism in the King Penguin Aptenodytes patagonicus, a colonial, monomorphic seabird for which our knowledge about the role of vocalizations and morphology in mate choice is very limited. Data were collected at Possession Island, Crozet Archipelago, in a breeding colony consisting of about 16 000 breeding pairs. Using measurements of six morphological features and analysing acoustic parameters of call recordings of adult individuals, we show that King Penguins can be sexed based on a single morphological measurement of the beak with an accuracy of 79%. We found a sex‐specific syntax in adult King Penguin calls that provided a 100% accurate method to distinguish between the sexes in our study population. To confirm the method at the species level, we analysed calls recorded from King Penguin adults in Kerguelen Island, 1300 km away from our study population and found the same accuracy of the sex‐specific syntax. This sex‐specific syllable arrangement is rare in non‐passerines and is a first step in understanding the mate choice process in this species. Furthermore, it offers a cost‐effective, non‐invasive technique for researchers to sex King Penguins in the field.     

Comparative analysis of three methods from dried blood spots for expeditious DNA extraction from mosquitoes; suitable for PCR based techniques

The objective of this work was to compare the quality, purity and quantity of DNA isolated from dried blood spots (DBS) by three methods (Chelex-100, QIAamp DNA mini kit, and TE (Tris EDTA)-Buffer). Sample collection was performed in six districts in Odisha, India and screened for cases of clinical malaria and dengue and vector density. Mosquito abdomens were spotted on Whatman 3MM (MERCK) Filter paper and dried for 10 min at room temperature. DNA was isolated from DBS using three methods (Chelex-100, QIAamp DNA mini kit, and TE-Buffer), and PCR was used to determine the feeding behaviours of vector mosquitoes. DNA was quantified using a UV-spectrophotometer, and q-PCR was used to determine the target gene copy number to compare the methods. The QIAamp DNA mini kit method was used as the reference method. The yield and purity of DNA extracted with Chelex-100 and TE were 14–72 ng/µl and 1.51–1.85 and 9–50 ng/µl and 1.68–2.1, respectively. DNA extracted using the Chelex-100 method was stored for over 1 month at ? 20 °C and was suitable for later use. The Chelex-100 method had a sensitivity of 99.5% and specificity of 78%. A Bland–Altman plot suggested that the Chelex-100 method was similar to the QIAamp DNA mini kit method for determining the feeding behaviours of vector mosquitoes. The Chelex-100 method is simple, cost-effective, and safe and requires minimal time for DNA extraction from dried blood spots. In malaria and dengue research, detecting the feeding behaviours from mosquito DNA from dried blood spots on filter paper by PCR is an easy, minimally invasive and inexpensive molecular technique that can be performed in remote areas.

     

Preparation and properties of cardiac cytochrome c1

A method for the large-scale isolation of beef heart mitochondrial cytochrome c1 in high purity was developed. This method gave higher yield of "one-band" cytochrome c1 than previously reported [Kim, C. H., & King, T. E. (1981) Biochem. Biophys. Res. Commun. 102, 607-614]. In addition, the present method was effective in the preparation of "two-band" cytochrome c1 which was used to prepare the hinge protein according to the principle of sequential resolution [Kim, C. H., & King, T. E. (1983) J. Biol. Chem. 258, 13543-13551]. The isolation of one-band and two-band cytochrome c1 by this procedure could be completed within 3 or 4 days starting with succinate-cytochrome c reductase. One-band cytochrome c1 showed a molecular weight of 44,000 by sedimentation equilibrium and 29,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The disparities in these data from the actual value of 27,924 by amino acid sequence analysis, as previously reported [Wakabayashi, S., Matsubara, H., Kim, C. H., & King, T. E. (1982) J. Biol. Chem. 257, 9335-9344], are most probably due to the formation of detergent or detergent-phosphate complex. A comparison of some properties of one-band cytochrome c1 with those of two-band cytochrome c1 clearly showed significant differences between the two preparations. These results suggest the hypothesis that one of the possible roles of the hinge protein in the mitochondrial respiratory chain is to stabilize the conformation of cytochrome c1.     

A new analysis method for the comparison of 2 temporal patterns,with indices of association

A new method for evaluating the degree of association between the behavioural patterns of 2 individuals is described and illustrated. It is proposed discrimination should be made between the unit for sampling (sample interval) and the unit for analysis. The length of the sample interval affects analysis accuracy, while the length of the analysis unit affects the analysis scale. A new “moving analysis unit (MAU) method” is proposed to divide an observation period into analysis units. The MAU method, with various lengths of analysis units, allows for various aspects of interaction between 2 individuals. As a similarity coefficient between the 2 temporal patterns, Iwao's ω (Iwao 1977) is proposed. Investigation of nonparametric confidence intervals of ω is performed with the bootstrap (Efron 1979), which is also applied for obtaining the null hypothesis distribution of ω. The MAU method, ω and the bootstrap are applied to the analysis of both insect and human communication.     

Hybridisation between South polar skua (Catharacta maccormicki) and Brown skua (C. antarctica lonnbergi) in the Antarctic Peninsula region

Hybridisation between South polar skua (C. maccormicki) and Brown skua (C. antarctica lonnbergi) in the area of the Antarctic Peninsula is known at least since the beginning of the last century but no survey has been done so far. This paper reviews information on the species composition of skua colonies of more than 10 pairs in the Antarctic Peninsula region, and the incidence of mixed pairs. Morphometrics, population size and breeding success were examined in detail at King George Island. The northward distribution of South polar skuas extended to King George Island (62°11′ S 59°00′ W), with a small outlying population on Signy Island (60°45′ S 45°36′ W), whereas Brown skuas did not breed further south than Anvers Island archipelago (64°46′ S 64°03′ W). The proportion of mixed pairs was highest at the northern end of the ∼500-km-wide hybrid zone. Body size distribution of sympatric skuas from King George Island is clearly bimodal but overlaps considerably and hybrids cannot be identified. Skua population sizes at Potter Peninsula/King George Island remained stable between 1994 and 2004. Numbers of mixed breeding pairs fluctuated more strongly than those of pure species pairs. Breeding success of Brown skuas varied the least.