Using computer algebra to determine rate constants in biochemistry

In earlier work we have described how computer algebra may be used to derive composite rate laws for complete systems of equations, using the mathematical technique of Gröbner Bases (Bennett, Davenport and Sauro, 1988). Such composite rate laws may then be fitted to experimental data to yield estimates of kinetic parameters. Recently we have been investigating the practical application of this methodology to the estimation of kinetic parameters for the closed two enzyme system of aspartate aminotransferase (AAT) and malate dehydrogenase (MDH) (Fisher 1990a; Fisher 1990b; Bennett and Fisher, 1990): $$\begin{gathered} aspartate + \alpha - ketoglutarate\begin{array}{*{20}c} \rightharpoonup \\ \leftharpoondown \\ \end{array} glutamate + oxaloacetate \hfill \\ {\text{oxaloacetate + NADH}}\begin{array}{*{20}c} \rightharpoonup \\ \leftharpoondown \\ \end{array} malate + NAD^ + \hfill \\ \end{gathered} $$ In this paper we present a fuller (although not yet complete) analysis of the system. We show how symbolic estimates of the error behaviour of the parameters can be made, and used to identify those which are of kinetic significance. Finally we consider how metabolic control analysis can be applied directly to such a system.     

Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay

Journal of Mathematical Biology - We investigate how to characterize the kinetic parameters of an aminotransaminase using a non-standard coupled (or auxiliary) enzyme assay, where the peculiarity...     

Using mRNA expression profiling to determine anticancer drug efficacy.

Pharmacogenomics is a fast-growing field of investigations that aims to further elucidate the inherited nature of interindividual differences in drug disposition and effects, with the ultimate goal of providing a stronger scientific basis for selecting the optimal drug therapy. Providing the right drug for the right patient is an important problem in the treatment of cancer. This is mainly due to the lack of information about the sensitivity of the tumor for a specific treatment modality, such as either chemotherapy or radiation treatment. This presentation highlights two approaches to identify responsiveness to treatment. Both approaches are based on the identification of expression profiles. The first approach concentrates on drug resistance and the second on the signaling pathways leading up to the death of the cell. Both approaches provide expression profiles; however, the more dynamic expression profiling as used to determine the signaling in damage cells promises to be a better determinant for the pharmacogenomic changes in expression profiles and, consequently, a potential better determinant for drug efficacy.     

Using real-time PCR to determine transgene copy number in wheat

Transgene copy number is usually determined by means of Southern blot analysis which can be time consuming and laborious. In this study, quantitative real-time PCR was developed to determine transgene copy number in transgenic wheat. A conserved wheat housekeeping gene,puroindoline-b, was used as an internal control to calculate transgene copy number. Estimated copy number in transgenic lines using real-time quantitative PCR was correlated with actual copy number based on Southern blot analysis. Real-time PCR can analyze hundreds of samples in a day, making it an efficient method for estimating copy number in transgenic wheat.     

Using the IUCN Red List to determine effective conservation strategies

Threatened species lists continue to grow while the world’s governments fail to meet biodiversity conservation goals. Clearly, we are failing in our attempts to conserve biodiversity. Yet 37 mammal species genuinely improved in status in the 2009 IUCN Red List, suggesting there are ways to successfully conserve biodiversity. Here, I compare the threats and conservation actions (proposed and implemented) by the expert assessors of the Red List of improving species to a further 144 declining mammal species to determine whether specific threats were more easily remedied, and whether certain conservation actions were more successful than others. Declining species were faced with different threatening processes to mammals improving in status suggesting some threats were easier to treat (e.g. hunting) than others (climate change, invasive species). Declining species had different proposed and implemented conservation actions than improving species suggesting some actions are more successful than others. Threatened species were invariably found in conservation areas, suggesting protected area creation alone is not an overly successful strategy for species at risk of extinction. Conservation actions were more frequently implemented for improving than declining species suggesting active conservation is effective in improving the status of biodiversity. There were significant differences between proposed and implemented conservation actions suggesting some actions are easier to implement than others. Reintroduction, captive breeding and hunting restriction were more effective in conserving mammals than site creation and invasive species control. These findings highlight effective conservation actions for mammals worldwide and allow the rationalisation of threat mitigation measures to ensure economically justifiable biodiversity conservation strategies.     

Using non-smooth models to determine thresholds for microbial pest management

Journal of Mathematical Biology - Releasing infectious pests could successfully control and eventually maintain the number of pests below a threshold level. To address this from a mathematical...     

基于PacBio Iso-Seq红棕象甲全长转录组测序分析

[目的]建立红棕象甲Rhynchophorus ferrugineus全长转录组数据库,深入挖掘红棕象甲基因数据信息.[方法]采用高通量测序平台,利用二代测序(Illumina RNA-seq)校正三代测序(PacBio Iso-Seq)的方法对红棕象甲进行全长转录组测序,并对转录组数据进行生物信息学分析.[结果]红棕象甲全长转录组平均长度为2 302 bp,N90长度为1321 bp,N50长度为2 785 bp;经CD-Hit程序去冗余,获得转录本63 801条,主要长度范围为0.5-6 k.基因功能注释表明,在NR、Swiss-Prot、KEGG、KOG、GO、NT和Pfam数据库中,分别有50 280、40 109、47 197、33 511、27 707、27 253和27 707条转录本被注释;其中,12 508条转录本均在7个数据库中有注释,54 999条转录本至少在一个数据库有注释.此外,经鉴定或预测,获得2 184个可变剪接(AS)、66 230个SSR、2 084个转录因子(TFs)和9 618条长链非编码RNA(LncRNA).CDS长度的主要分布范围为0-2 500 nt.[结论]本研究获得了红棕象甲全长转录组数据库,为红棕象甲后续分子生物学基础研究奠定基础.     

Using molecular markers to determine barleys most suitable for malt whisky distilling

Two barley quality characters of specific interest to whisky distillers are fermentability and production of the ethyl carbamate precursor, epi-heterodendrin. The former is a quantitative trait, while the latter may be determined by a single Mendelian genetic factor. Molecular markers have been used to map, to barley chromosome 5(1H), the locus responsible for epi-heterodendrin synthesis and the inheritance of this character and a closely linked microsatellite have been followed through the pedigrees of several contemporary cultivars. Six loci, which affected fermentability in random inbred lines from a barley cross, have been mapped to chromosomes 2(2H), 3(3H) and 7(5H). This would permit the use of molecular markers in a breeding programme, to select barleys best suited for distilling. In addition, one of the loci related to fermentability mapped to an area of the genome indicated, by a previous study, to affect the activity of β-amylase, a character likely to influence fermentability. Molecular markers may, therefore, be powerful tools in exploring the contribution and detecting the mode of action of the genetical components influencing malt whisky distilling. This revised version was published online in June 2006 with corrections to the Cover Date.     

Using stressor gradients to determine reference expectations for great river fish assemblages

We describe a simple empirical modeling approach for determining least-disturbed conditions for the great rivers of the Upper Mississippi River basin: Missouri, Upper Mississippi, and Ohio Rivers. We used multivariate analysis to identify reference strata (reaches for which a single reference expectation was appropriate) on each river. Strata included the Upper Missouri, Lower Missouri, impounded Upper Mississippi, unimpounded Upper Mississippi, and the Ohio River. We created a multimetric stressor gradient for each stratum using a suite of site- and landscape-scale metrics. Site-scale metrics included water chemistry, aquatic and riparian habitat, and human disturbance metrics. Landscape-scale metrics included land use, land cover, and proximity to human disturbance. The gradient was scaled from 0 (least stressed) to 1 (most stressed). Multimetric indices of condition based on fish assemblages for the Lower Missouri and Upper Mississippi River were responsive to stressor gradients based on 18–24 abiotic stressor metrics. Ohio River fish assemblages were responsive to a hand-picked three-metric gradient. We used the y-intercept of quantile regression to predict the fish index value for a stressor gradient value of 0 (the fish index value at a site with the lowest mean stressor gradient score in the reference stratum) which we designated as least-disturbed condition for the fish index for that stratum. We trisected the difference between predicted least-disturbed condition (ceiling value) and a floor value set at the 5th percentile of the sample to create thresholds for three condition classes: least-disturbed, intermediate, and most-disturbed. Based on the derived condition class thresholds for the fish index, 10% (by length) of the Lower Missouri was in least-disturbed condition, compared to 14% of the Ohio River and 19% of the impounded Upper Mississippi River. The index of condition exhibited longitudinal variation that was associated with the location of major urban areas along each river. We conclude that empirical modeling based on an abiotic stressor gradient can provide an alternative approach for deriving internal reference expectations for great rivers with few, if any, minimally disturbed sites.     

Using vaginal wall impedance to determine estrous cycle phase in Lewis rats

The use of Lewis rats in embryonic tissue transplantation experiments can present a challenge because of the fertility problems associated with this strain. The authors used estrous cycle phase determination to time pairings of reproductively active females and males in order to increase the likelihood that mating would occur. During a 24-month period, female rats in a production colony were evaluated for estrous phase by microscopic evaluation of vaginal smears and by vaginal impedance readings. Pairings that were arranged with females determined to be in the proestrous phase by vaginal smears resulted in a low rate of confirmed matings (14%). Serial vaginal smear sampling also produced a high incidence of pseudopregnancy. Pairings that were arranged with females determined to be in the proestrous phase by vaginal impedance readings resulted in a high rate of confirmed matings (48.1%) as well as a high rate of pregnancy (29.4%). An average of 7.2 embryos were produced per pregnancy. The vaginal impedance technique can be used to improve the breeding success rate of Lewis rats in order to maintain a stable production of embryos for experimentation.     

Using spectrophotometry to determine in vitro turnover rates of peptides in plasma

A new method for determination of first-order elimination constants for dipeptides is presented. The peptides are hydrolysed by plasma enzymes into amino acids, and ortho-phthaldialdehyde (OPA) is used to react with free primary amino groups. The concentration of free amino groups can, thus, be followed using simple spectrophotometry. A mathematical model for the concentration of free primary amino groups with time is presented through which the elimination constant, and thus the half life, can be determined by curve fitting. The method is applied to inhibitors of angiotensin-converting enzyme derived from the primary structure of milk proteins. The results show that these dipeptides have in vitro half lives ranging from 4.3-64 min, when incubated with 50% rat plasma. This explains why these casokinins in vivo only cause a very moderate and short-lasting inhibition. The model for calculation of elimination constant is limited to dipeptides that do not contain a C-terminal proline. The derivatization method can be applied to longer peptides as a crude indicator of peptide hydrolysis, but does not allow calculation of their elimination constants per se.     

Using an evolutionary algorithm to determine the parameters of a biologically inspired model of head direction cells

A biologically inspired model of head direction cells is presented and tested on a small mobile robot. Head direction cells (discovered in the brain of rats in 1984) encode the head orientation of their host irrespective of the host’s location in the environment. The head direction system thus acts as a biological compass (though not a magnetic one) for its host. Head direction cells are influenced in different ways by idiothetic (host-centred) and allothetic (not host-centred) cues. The model presented here uses the visual, vestibular and kinesthetic inputs that are simulated by robot sensors. Real robot-sensor data has been used in order to train the model’s artificial neural network connections. The main contribution of this paper lies in the use of an evolutionary algorithm in order to determine the values of parameters that determine the behaviour of the model. More importantly, the objective function of the evolutionary strategy used takes into consideration quantitative biological observations reported in the literature.     

Using latent effects to determine the ecological importance of dissolved organic matter to marine invertebrates

The uptake and utilization of dissolved organic matter (DOM)by marine invertebrates is a field that has received significantattention over the past 100 years. Although it is well establishedthat DOM is taken up by marine invertebrates, the extent towhich it contributes to an animal's survival, growth, and reproduction(that is, the ecological benefits) remains largely unknown.Previous work seeking to demonstrate the putative ecologicalbenefits of DOM uptake have examined them within a single lifestage of an animal. Moreover, most of the benefits are demonstratedthrough indirect approaches by examining (1) mass balance, or(2) making comparisons of oxyenthalpic conversions of transportrates to metabolic rate as judged by oxygen consumption. Wesuggest that directly examining delayed metamorphosis or thelatent effects associated with nutritional stress of larvaeis a better model for investigating the ecological importanceof DOM to marine invertebrates. We also provide direct evidencethat availability of DOM enhances survival and growth of thebryozoan Bugula neritina. That DOM offsets latent effects inB. neritina suggests that the underlying mechanisms are at leastin part energetic.     

Using attainment of the designated aquatic life use to determine adverse environmental impact

Section 316(b) of the Clean Water Act requires that cooling-water intake structures (CWIS) use Best Technology Available (BTA) to minimize adverse environmental impacts (AEI). The U.S. EPA has not defined AEI, and there is no clear consensus regarding its definition. Nonetheless, operational definitions are necessary to evaluate design alternatives and to measure the success of mitigative measures. Rather than having to develop measures of aquatic health that are highly site-specific, controversial, and often unlikely to elicit agreement from all sides of the environmental fence, it may be more productive to use existing ecological assessment tools. Aquatic Life Uses (ALU) already provide a regulatory framework to assess the quality (health) of the aquatic community in various habitats (e.g., warmwater habitat, exceptional warmwater habitat). Attainment of the ALU indicates that further point source controls are unnecessary, whereas nonattainment indicates that those pollutants or stressors causing the nonattainment must be reduced. A similar approach for existing water intakes is recommended. That is, attainment of the designated ALU will be taken as an indication that there is no AEI. Although attainment of the ALU may not be a foolproof indicator of a lack of AEI, this approach seems more reasonable that using scarce monetary resources to fix problems that likely do not exist, or having both regulators and the regulated community expend their resources debating whether various observed biological responses do or do not constitute AEI.     

Using carapace measurements to determine the sex of Antarctic krill, Euphausia superba

Krill (Euphausia superba) carapace measurements (length and width; mm) collected from plankton tows in the South Shetland Islands (SSI), Antarctica are used to test the generality of a common discriminant function developed to reconstruct krill length frequencies in Antarctic fur seal diets for the area surrounding South Georgia (SG). Total length and sex ratio of krill in the SSI were overestimated by 5.6 and 154%, respectively, when the SG allometric equations were applied to 3 years (2003–2005) of data. These errors arise and increase as a result of krill population dynamics, specifically recruitment that contributes large proportions of immature krill, misclassified as males by the SG discriminant function. We develop sex-specific regression models based on separate discriminant functions that provide significantly better discriminatory power. However, our analysis indicates that reconstructions of krill sex ratio and length composition in the ocean environment are less reliable in years when the ratio of immature to mature krill is high. For the SSI area, five out of 14 years (35.7%) surveyed (1992–2005) had proportions of immature to mature adult krill ≥ 0.50.     

Using surface plasmon resonance to directly determine binding affinities of combinatorially selected cyclopeptides and their linear analogs to a streptavidin chip

In our recent report, several HPQ-containing streptavidin ligands were identified from a structurally constrained combinatorial library, and the relative affinities in IC(50) of these tight-binding ligands were revealed by a captured enzyme-linked immunosorbent assay. In the present work, surface plasmon resonance was employed to directly evaluate the binding affinities between immobilized streptavidin and combinatorially selected ligands. The equilibrium dissociation constants and kinetic on/off rates of a previously identified N-to-side chain and newly synthesized N-to-C cyclopeptides were readily deduced using Scatchard analysis and computational simulation. It was found that both cyclopeptides bound streptavidin far more tightly than its linear counterpart ( approximately 1000-fold), while the reversed (QPH) linear and cyclic peptidyl ligands were hardly recognized by streptavidin. Consequently, not only was the binding specificity of synthetic ligands distinguished qualitatively but also the entropic advantage of conformationally constrained cyclopeptides over their linear forms was demonstrated quantitatively by surface plasmon resonance.