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.

Evidence for H2O2 as the product of reduction of oxygen by alternative oxidase in mitochondria from potato tubers

Oxygen Consumption by alternative oxidase (AOX), present in mitochondria of many angiosperms, is known to be cyanide-resistant in contrast to cytochrome oxidase. Its activity in potato tuber (Solarium tuberosum L.) was induced following chilling treatment at 4 degrees C.About half of the total O-2 consumption of succinate oxidation in such mitochondria was found to be sensitive to SHAM, a known inhibitor of AOX activity. Addition of catalase to the reaction mixture of AOX during the reaction decreased the rate of SHAM-sensitive oxygen consumption by nearly half, and addition at the end of the reaction released nearly half of the consumed oxygen by AOX, both typical of catalase action on H2O2. These findings with catalase suggest that the product of reduction of AOX is H2O2 and not H2O, as previously Surmised. In potatoes Subjected to chill stress (4 degrees C) for periods of 3, 5 and >= 8 days the activity of AOX in mitochondria increased progressively with a corresponding increase in the AOX protein detected by immunoblot of the protein.

Tree-ring based hydroclimate reconstruction over northern Vietnam from Fokienia hodginsii: eighteenth century mega-drought and tropical Pacific influence

We present here the first statistically calibrated and verified tree-ring reconstruction of climate from continental Southeast Asia.The reconstructed variable is March-May (MAM) Palmer Drought Severity Index (PDSI) based on ring widths from 22 trees (42 radial cores) of rare and long-lived conifer, Fokienia hodginsii (Po Mu as locally called) from northern Vietnam. This is the first published tree ring chronology from Vietnam as well as the first for this species. Spanning 535 years, this is the longest cross-dated tree-ring series yet produced from continental Southeast Asia. Response analysis revealed that the annual growth of Fokienia at this site was mostly governed by soil moisture in the pre-monsoon season. The reconstruction passed the calibration-verification tests commonly used in dendroclimatology, and revealed two prominent periods of drought in the mid-eighteenth and late-nineteenth enturies. The former lasted nearly 30 years and was concurrent with a similar drought over northwestern Thailand inferred from teak rings, suggesting a ``mega-drought'' extending across Indochina in the eighteenth century. Both of our reconstructed droughts are consistent with the periods of warm sea surface temperature (SST)anomalies in the tropical Pacific. Spatial correlation analyses with global SST indicated that ENSO-like anomalies might play a role in modulating droughts over the region, with El Nio (warm) phases resulting in reduced rainfall. However, significant correlation was also seen with SST over the Indian Ocean and the north Pacific,suggesting that ENSO is not the only factor affecting the climate of the area. Spectral analyses revealed significant peaks in the range of 53.9-78.8 years as well as in the ENSO-variability range of 2.0 to 3.2 years.

Synthesis, characterization and photocatalytic activity of MxCe1-xVO4 (M = Li, Ca and Fe)

Non-stoichiometric substituted cerium vanadates, MxCe1-xVO4 (M = Li, Ca and Fe), were synthesized by solid-state reactions. The crystal structure was analyzed by powder X-ray diffraction and it exhibits a tetragonal zircon Structure, crystallizing in the space group I4(1)/amd with a = 7.3733(4) and c = 6.4909(4) angstrom and Z = 4. Particle sizes were in the range of 600-800 nm, as observed by scanning electron microscopy. The thermal analysis of the compounds showed phase stability up to 1100 degrees C. The UV diffuse reflectance spectra indicated that the compounds have band gaps in the range of 2.6-2.9 eV. The photocatalytic activity of these Compounds was investigated for the first time for the degradation of different dyes, and organics, the oxidation of cyclohexane and the hydroxylation of benzene. The degradation of dyes was modeled using the Langmuir-Hinshelwood kinetics, while the oxidation of cyclohexane and hydroxylation of benzene were modeled using a free radical mechanism and a series reaction mechanism, respectively.

Weak rectifying behaviour of p-SnS/n-ITO heterojunctions

This work explores the electrical properties of p-SnS/n-ITO heterojunction at different temperatures. The p-type SnS film was deposited on n-type ITO substrate using the thermal evaporation technique and its junction properties were studied using two probe method. The as-grown p-n junction exhibited weak rectifying behaviour with a low Saturation current of the order of similar to 10(-6) A. While increasing temperature, the saturation current of the junction is increased and however, its series resistance decreased. At all temperatures the junction exhibited three types of transport mechanisms depending on applied bias-voltage. At lower voltages the junction showed nearly ideal diode characteristics. The junction behaviour with respect to bias-voltage and temperature is discussed with the help of existing theories and energy band diagram.

An elegant direct route for the preparation of pyridinium, ammonium and alkali metal hexafluorotitanates (IV)

Pyridinium hexafluorotitanate (IV) has been prepared by a one step procedure. Addition of titanium tetrachloride to pyridinium poly(hydrogen fluoride) yields nearly quantitative amounts of pyridinium hexafluorotitanate(IV). Making use of pyridinium hexafluorotitanate as precursor, ammonium and alkali metal (Na, K, Rb, and Cs) hexafluorotitanates have been prepared in good yields. These salts have been characterised by IR, N.M.R. (1H, 13C and 19F), X-ray powder diffraction data and chemical analysis.

Crystal and molecular structure of the quinoxaline antibiotic analog TANDEM (des-N-tetramethyltriostin A)

The crystal structure of TANDEM (des-N-tetramethyltriostin A), a synthetic analogue of the quinoxaline antibiotic triostin A, has been determined independently at -135 and 7 'C and refined to R values of 0.088 and 0.147, respectively. The molecule has approximate 2-fold symmetry, with the quinoxaline chromophores and the disulfide cross-bridge projecting from opposite sides of the peptide ring. The quinoxaline groups are nearly parallel to each other and separated by about 6.5 A. The peptide backbone resembles a distorted antiparallel 13 ribbon joined by intramolecular hydrogen bonds N-H(LVal)--O(L-Ala). At low temperatures, the TANDEM molecule is surrounded by a regular first- and second-order hydration sphere containing 14 independent water molecules. At room temperature, only the first-order hydration shell is maintained. Calculations of the interplanar separation of the quinoxaline groups as a function of their orientation with respect to the peptide ring support the viability of TANDEM to intercalate bifunctionally into DNA.

Structure of a peptide oxazolone: 2-(1'-benzyloxycarbonylamino-1'-methylethyl)-4,4-dimethyl-5-oxazolone

C16H20N204, monoclinic, P21, a = 6.270 (1),b= 11.119(3),c= ll.640(4)A, fl= 100.7 (2)°,Dm = 1-27 (flotation), Dc = 1-26 Mg m -3, Z = 2. The structure has been refined to a final R value of 0.041 for 1584 independent counter-measured reflections. The oxazolone ring in the molecule is nearly planar. The exocyclic O atom is 0.065 A out of the plane defined by the other four atoms in the ring belonging to the lactone group. The difference in length between the two adjacent C-O bonds in the ring is small, but significant. The crystal structure is stabilized by van der Waals interactions and a N--H... N hydrogen bond.

Interrogating an insect society

Insect societies such as those of ants, bees, and wasps consist of 1 or a small number of fertile queens and a large number of sterile or nearly sterile workers. While the queens engage in laying eggs, workers perform all other tasks such as nest building, acquisition and processing of food, and brood care. How do such societies function in a coordinated and efficient manner? What are the rules that individuals follow? How are these rules made and enforced? These questions are of obvious interest to us as fellow social animals but how do we interrogate an insect society and seek answers to these questions? In this article I will describe my research that was designed to see answers from an insect society to a series of questions of obvious interest to us. I have chosen the Indian paper wasp Ropalidia marginata for this purpose, a species that is abundantly distributed in peninsular India and serves as an excellent model system. An important feature of this species is that queens and workers are morphologically identical and physiologically nearly so. How then does an individual become a queen? How does the queen suppress worker reproduction? How does the queen regulate the nonreproductive activities of the workers? What is the function of aggression shown by different individuals? How and when is the queen's heir decided? I will show how such questions can indeed be investigated and will emphasize the need for a whole range of different techniques of observation and experimentation.

Structure and dynamics of two-dimensional sheared granular flows

The structure and dynamics of the two-dimensional linear shear flow of inelastic disks at high area fractions are analyzed. The event-driven simulation technique is used in the hard-particle limit, where the particles interact through instantaneous collisions. The structure (relative arrangement of particles) is analyzed using the bond-orientational order parameter. It is found that the shear flow reduces the order in the system, and the order parameter in a shear flow is lower than that in a collection of elastic hard disks at equilibrium. The distribution of relative velocities between colliding particles is analyzed. The relative velocity distribution undergoes a transition from a Gaussian distribution for nearly elastic particles, to an exponential distribution at low coefficients of restitution. However, the single-particle distribution function is close to a Gaussian in the dense limit, indicating that correlations between colliding particles have a strong influence on the relative velocity distribution. This results in a much lower dissipation rate than that predicted using the molecular chaos assumption, where the velocities of colliding particles are considered to be uncorrelated.

Direct estimation of an element of order matrix from H-1 NMR spectra of strongly dipolar coupled spins

NMR spectra of molecules oriented in thermotropic liquid crystalline media provide information on the molecular structure and order. The spins are generally strongly dipolar coupled and the spectral analyse require the tedious and time consuming numerical iterative calculations. The present study demonstrates the application of multiple quantum spin state selective detection of single quantum transitions for mimicking the homonuclear decoupling and the direct estimation of an element of ordering matrix. This information is utilized to estimate the nearly accurate starting dipolar couplings for iterative calculations. The studies on the spectra of strongly dipolar coupled five and six interacting spin systems are reported.

Structure of the disodium salt of glucose 1-phosphate hydrate, 2Na+.C6H11O9P2-.3.5H2O

Mr= 367.2, monoclinic, C2, a = 8.429 (1),b= 10.184(2), c= 16.570(2)A, /~= 99.18 (1) °, U= 1404.2 A 3, z = 4, D m = 1.73, D x = 1.74 Mg m -3,Cu K~, 2 = 1.5418 A, g = 2.99 mm -1, F(000) = 764,T= 300K, final R for 1524 observed reflections is0.069. The endocyclic C-O bonds in the glucose ring are nearly equal with C(5)-O(5)= 1.445 (10) and C(1)-O(5)= 1.424(10). The pyranose sugar ring adopts a 4C 1 chair conformation. The conformation about the exocyclic C(5)-C(6) bond is gauche-gauche, in contrast to gauche-trans observed in the structure of the dipotassium salt of glucose 1-phosphate. The phosphate ester bond, P-O(1), is 1.641 (6)A, slightly longer than the 'high-energy' P-,.O bond in the monopotassium salt of phosphoenolpyruvate [1.612 (6)A]. Two sodium ions are six coordinated while the third has only five neighbours.

L-Arginine L-aspartate

C6HxsN40 +.C4H6NO~-, monoclinic, P2,,a = 5.511 (3), b = 8.438 (4), c = 15.265 (9) A, fl = 97.9 (I) °, D,, -- 1.467 (8) (flotation), D c = 1.452 Mg m -a, Z = 2. The structure has been refined to a final R value of 0.044 for 1226 independent counter-measured reflections. The conformation of the arginine molecule is different from those previously observed, whereas the conformation of the aspartate ion is similar to that found in L-aspartic acid, DL-aspartic acid and L-lysine L-aspartate. The unlike molecules aggregate into separate alternating layers and the a-amino and acarboxylate groups in the arginine layer are periodically brought into close proximity in a 'headto-tail' arrangement. There exist a specific ion-pair interaction involving electrostatic attraction and two nearly parallel N-H...O hydrogen bonds between the guanidyl group and the a-carboxylate group of the aspartate ion.

Flow over a cylinder with a hinged-splitter plate

Previous work on rigid splitter plates in the wake of a bluff body has shown that the primary vortex shedding can be suppressed for sufficiently long splitter plates. In the present work, we study the problem of a hinged-splitter plate in the wake of a circular cylinder. The splitter plate can rotate about the hinge at the base of the cylinder due to the unsteady fluid forces acting on it, and hence the communication between the two sides of the wake is not totally disrupted as in the rigid splitter plate case. In our study, we investigate this problem in the limit where the stiffness and internal damping associated with the hinge are negligible, and the mass ratio of the splitter plate is small. The experiments show that the splitter plate oscillations increase with Reynolds numbers at low values of Re, and are found to reach a saturation amplitude level at higher Re, Re>4000. This type of saturation amplitude level that appears to continue indefinitely with Re, appears to be related to the fact that there is no structural restoring force, and has been observed previously for transversely oscillating cylinders with no restorin force. In the present case, the saturation tip amplitude level can be tip to 0.45D, where D is the cylinder diameter. For this hinged-rigid splitter plate case, it is found that the splitter plate length to cylinder diameter ratio (L/D) is crucial in determining the character and magnitude of the oscillations. For small splitter plate length (L/D <= 3.0), the oscillations appear to be nearly periodic with tip amplitudes of about 0.45D nearly independent of L/D. The nondiinensional oscillation frequencies (fD/U) on the other hand are found to continuously vary with L/D from fD/U approximate to 0.2 at L/D = 1 to fD/U approximate to 0.1 at L/D = 3. As the splitter plate length is further increased beyond L/D >= 4.0, the character of the splitter plate oscillations suddenly changes. The oscillations become aperiodic with much smaller amplitudes. In this long splitter plate regime, the spectra of the oscillations become broadband, and are reminiscent of the change in character of the wake oscillations seen in the earlier fixed-rigid splitter plate case for L/D >= 5.0. In the present case of the hinged-splitter plate, the sudden transition seen as the splitter plate length (L/D) is increased from 3 to 4 may be attributed to the fact that the wake vortices are no longer able to synchronize with the plate motions for larger splitter plate lengths. Hence, as observed in other vortex-induced vibration problems, the oscillations becomeaperiodic and the amplitude reduces dramatically.

Coalescence of rigid droplets in a stirred dispersion-II. Band-limited force fluctuations

The coalescence of nearly rigid liquid droplets in a turbulent flow field is viewed as the drainage of a thin film of liquid under the action of a stochastic force representing the effect of turbulence. The force squeezing the drop pair is modelled as a correlated random function of time. The drops are assumed to coalesce once the film thickness becomes smaller than a critical thickness while they are regarded as separated if their distance of separation is larger than a prescribed distance. A semi-analytical solution is derived to determine the coalescence efficiency. The veracity of the solution procedure is established via a Monte-Carlo solution scheme. The model predicts a reversing trend of the dependence of the coalescence efficiency on the drop radii, the film liquid viscosity and the turbulence energy dissipation per unit mass, as the relative fluctuation increases. However, the dependence on physical parameters is weak (especially at high relative fluctuation) so that for the smallest droplets (which are nearly rigid) the coalescence efficiency may be treated as an empirical constant. The predictions of this model are compared with those of a white-noise force model. The results of this paper and those in Muralidhar and Ramkrishna (1986, Ind. Engng Chem. Fundam. 25, 554-56) suggest that dynamic drop deformation is the key factor that influences the coalescence efficiency.