Flux balance analysis of biological systems: applications and challenges

Systems level modelling and simulations of biological processes are proving to be invaluable in obtaining a quantitative and dynamic perspective of various aspects of cellular function. In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used. Unlike mechanistic simulations that depend on accurate kinetic data, which are scarcely available, FBA is based on the principle of conservation of mass in a network, which utilizes the stoichiometric matrix and a biologically relevant objective function to identify optimal reaction flux distributions. FBA has been used to analyse genome-scale reconstructions of several organisms; it has also been used to analyse the effect of perturbations, such as gene deletions or drug inhibitions in silico. This article reviews the usefulness of FBA as a tool for gaining biological insights, advances in methodology enabling integration of regulatory information and thermodynamic constraints, and finally addresses the challenges that lie ahead. Various use scenarios and biological insights obtained from FBA, and applications in fields such metabolic engineering and drug target identification, are also discussed. Genome-scale constraint-based models have an immense potential for building and testing hypotheses, as well as to guide experimentation.

Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA: Additional role of RuvB-binding domain and inter species variability

RuvA, along with RuvB, is involved in branch migration of heteroduplex DNA in homologous recombination. The structures of three new crystal forms of RuvA from Mycobacterium tuberculosis (MtRuvA) have been determined. The RuvB-binding domain is cleaved off in one of them. Detailed models of the complexes of octameric RuvA from different species with the Holliday junction have also been constructed. A thorough examination of the structures presented here and those reported earlier brings to light the hitherto unappreciated role of the RuvB-binding domain in determining inter-domain orientation and oligomerization. These structures also permit an exploration of the interspecies variability of structural features such as oligomerization and the conformation of the loop that carries the acidic pin, in terms of amino acid substitutions. These models emphasize the additional role of the RuvB-binding domain in Holliday junction binding. This role along with its role in oligomerization could have important biological implications.

A sensitive immunochemical method for detecting 5mC in DNA fragments

Abstract is not available.

Mathematics, programming, and STEM

Learning mathematics is a complex and dynamic process. In this paper, the authors adopt a semiotic framework (Yeh & Nason, 2004) and highlight programming as one of the main aspects of the semiosis or meaning-making for the learning of mathematics. During a 10-week teaching experiment, mathematical meaning-making was enriched when primary students wrote Logo programs to create 3D virtual worlds. The analysis of results found deep learning in mathematics, as well as in technology and engineering areas. This prompted a rethinking about the nature of learning mathematics and a need to employ and examine a more holistic learning approach for the learning in science, technology, engineering, and mathematics (STEM) areas.

Non-bonded interactions in 2,2,4,4-tetramethyl-1,3-cyclobutanedithione and 2,2,4,4-tetramethyl-3-thio-1,3-cyclobutanedione

Electronic absorption and emission spectra as well as He(I) photoelectron spectra of 2,2,4,4-tetramethyl-,3-cyclobutanedithione and 2,2,4,4-tetramethyl-1-3-thio-1,3-cyclobutanedione have been interpreted on the basis of molecular orbital calculations. The results show that the non-bonded orbital of the dithione is split owing to through-bond interaction, the magnitude of splitting being 0.4 eV. The π* orbital of the dithione appears to be split by about 0.2 eV. Electronic absorption spectra show evidence for the existence of four n—π* transitions, arising out of the splitting of the orbitals referred to above, just as in the case of 2,2,4,4-tetramethyl-1,3-cyclobutanedione. Electronic and photoelectron spectra of the thio-dione show evidence for weak interaction between the C=S and C&.zdbnd;O groups, probably via π* orbitals. Infrared spectra of both the dithione and the thio-dione are consistent with the planar cyclobutane ring; the ring-puckering frequency responsible for non-bonded interactions is around 67 cm−1 in both the dithione and the thio-dione, the value not being very different from that in the dione. The 1,3-transannular distance is also similar in the three molecules.

SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases

Cultivated groundnut (Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust (Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ≥0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal-Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits.

Laboratory information management software for genotyping workflows: Applications in high throughput crop genotyping

Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow Results: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. Conclusions: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/bt-software-d-lims.htm

The Alpha-Method Direct Transcription In Path Constrained Dynamic Optimization

Numerically discretized dynamic optimization problems having active inequality and equality path constraints that along with the dynamics induce locally high index differential algebraic equations often cause the optimizer to fail in convergence or to produce degraded control solutions. In many applications, regularization of the numerically discretized problem in direct transcription schemes by perturbing the high index path constraints helps the optimizer to converge to usefulm control solutions. For complex engineering problems with many constraints it is often difficult to find effective nondegenerat perturbations that produce useful solutions in some neighborhood of the correct solution. In this paper we describe a numerical discretization that regularizes the numerically consistent discretized dynamics and does not perturb the path constraints. For all values of the regularization parameter the discretization remains numerically consistent with the dynamics and the path constraints specified in the, original problem. The regularization is quanti. able in terms of time step size in the mesh and the regularization parameter. For full regularized systems the scheme converges linearly in time step size.The method is illustrated with examples.

Thermoelectric Properties of Co4Sb12 Skutterudite Materials with Partial In Filling and Excess In Additions

The properties of Co4Sb12 with various In additions were studied. X-ray diffraction revealed the presence of the pure δ-phase of In0.16Co4Sb12, whereas impurity phases (γ-CoSb2 and InSb) appeared for x = 0.25, 0.40, 0.80, and 1.20. The homogeneity and morphology of the samples were observed by Seebeck microprobe and scanning electron microscopy, respectively. All the quenched ingots from which the studied samples were cut were inhomogeneous in the axial direction. The temperature dependence of the Seebeck coefficient (S), electrical conductivity (σ), and thermal conductivity (κ) was measured from room temperature up to 673 K. The Seebeck coefficient of all In-added Co4Sb12 materials was negative. When the filler concentration increases, the Seebeck coefficient decreases. The samples with In additions above the filling limit (x = 0.22) show an even lower Seebeck coefficient due to the formation of secondary phases: InSb and CoSb2. The temperature variation of the electrical conductivity is semiconductor-like. The thermal conductivity of all the samples decreases with temperature. The central region of the In0.4Co4Sb12 ingot shows the lowest thermal conductivity, probably due to the combined effect of (a) rattling due to maximum filling and (b) the presence of a small amount of fine-dispersed secondary phases at the grain boundaries. Thus, regardless of the non-single-phase morphology, a promising ZT (S 2 σT/κ) value of 0.96 at 673 K has been obtained with an In addition above the filling limit.

Size dependence and dispersion behavior of the first hyperpolarizability of copper nanoparticles

We have probed the size dependency of the first hyperpolarizability (b) of copper nanoparticles by hyper-Rayleigh scattering (HRS). Our results indicate that second harmonic generation (SHG) originates predominantly at the surface of the nanoparticles as long as the size (d) remains small compared to the wavelength (k). However, volume contribution to the SH response due to the retardation effect becomes important when particle size grows beyond the `small particle limit'. There is a significant dispersion in the b values of copper nanoparticles owing tothe presence of the strong surface plasmon resonance (SPR) band.

Origin of the activation barrier in the process of hydrogen abstraction: the perturbation treatment

The perturbation treatment previously given is extended to explain the process of hydrogen abstraction from the various hydrogen donor molecules by the triplet nπ* state of ketones or the ground state of the alkyl or alkoxy radical. The results suggest that, as the ionization energy of the donor bonds is decreased, the reaction is accelerated and it is not influenced by the bond strength of the donor bonds. The activation barrier in such reactions arises from a weakening of the charge resonance term as the ionization energy of the donor bond increases.

Nucleosome core protein: Asymmetric dissociation of the octamer

The octameric nucleosomal core-histone complex, (H2A)2-(H2B)2-(H3)2-(H4)2, isolated from rat liver, undergoes dissociation during gel exclusion chromatography as a result of dilution occurring in the columns. The elution pattern at pH 7.0 and 4°C showed a sharp leading peak containing all four histones but predominantly H3 and H4, and a trailing peak containing equal amounts of histones H2A and H2B. As column length was increased the area under the leading peak decreased and that under the trailing peak increased. In addition the relative positions of the two peaks varied with column length. From an analysis of the data on increase in elution volume of the leading peak in relation to column length an apparent molecular weight of 86 000 was calculated for the undissociated molecule. Its apparent molecular weight, histone composition and pattern of further dissociation in relation to column length suggest that this species is the hexamer, (H2A-H2B)-(H3)2-(H4)2. At pH 7.0 and 4°C the dissociation of the core complex appears to be as follows: (H2A)2-(H2B)2-(H3)2-(H4)2 → (H2A-H2B) + (H2A-H2B)-(H3)2-(H4)2 → 2(H2A-H2B) + (H3)2-(H4)2 This dissociation was accelerated by an increase in temperature or decrease in pH and was accompanied by marked conformational changes as judged by circular dichroism measurements.

A hydrodynamical study of the flow in renal tubules

The hydrodynamical problem of flow in proximal renal tubule is investigated by considering axisymmetric flow of a viscous, incompressible fluid through a long narrow tube of varying cross-section with reabsorption at the wall. Two cases for reabsorption have been studied (i) when the bulk flow,Q, decays exponentially with the axial distancex, and (ii) whenQ is an arbitrary function ofx such thatQ-Q 0 can be expressed as a Fourier integral (whereQ 0 is the flux atx=0). The analytic expressions for flow variables have been obtained by applying perturbation method in terms of wall parameter ε. The effects of ε on pressure drop across the tube, radial velocity and wall shear have been studied in the case of exponentially decaying bulk flow and it has been found that the results are in agreement with the existing ones for the renal tubules.

A comparative study of the photochemical hydrogen-abstraction reactions of a ketone and a thione

A perturbation treatment was developed for the comparative study of the abstraction of hydrogen from methane by formaldehyde and thioformaldehyde in their nπ* and ππ* states. Both in-plane and perpendicularplane reactions are considered. Results are qualitative but reveal clearly the prominent distinguishing features of these two photochemical processes in agreement with the experimental observations.

Sex Determination - A Hypothesis Based On Noncoding Dna

Certain recent models of sex determination in mammals, Drosophila melanogaster, Caenorhabditis elegans, and snakes are examined in the light of the hypothesis that the relevant genetic regulatory mechanisms are similar and interrelated. The proposed key element in each of these instances is a noncoding DNA sequence, which serves as a high-affinity binding site for a repressor-like molecule regulating the activity of a major "sex-determining" gene. On this basis it is argued that, in several eukaryotes, (i) certain DNA sequences that are sex-determining are noncoding, in the sense that they are not the structural genes of a sex-determining protein; (ii) in some species these noncoding sequences are present in one sex and absent in the other, while in others their copy number or accessibility to regulatory molecules is significantly unequal between the two sexes; and (iii) this inequality determines whether the embryo develops into a male or a female.