A biochemical mechanism for bacterial chemotaxis

Peritrichous bacteria alternately swim and tumble (thrash about with little forward progress). By selective modulation of tumbling frequency, these bacteria carry out chemotaxis, which is migration to higher concentrations of attractant or lower concentrations of repellent. A model for chemotaxis is presented in which tumbling frequency is regulated by concentration of Ca²⁺ ion at the switch that controls tumbling and swimming. Attractants cause decreased levels of free cytoplasmic Ca²⁺ ion due to binding of Ca²⁺ ion by specific proteins. This Ca²⁺ ion is released when these proteins become methylated. An alternative model. involving a cytoplasmic metabolite “compound X”, is discussed.     

The relation between hybrid vigour and genotype-environment interactions

Summary Consideration was given to the response curves and response surfaces that are obtained when genotypes are grown at various levels of environmental factors. These curves and surfaces were used to illustrate genotype-environment interactions and possible relations between two parents and their F ₁.When a hybrid had a response exactly intermediate between its parents, the metric values for the hybrid were not intermediate but varied with the environment, exhibiting different degrees of dominance including overdominance (hybrid vigour). A range in dominance for the metric also was found when the response of the hybrid was more similar to one parent than the other.A hybrid with an intermediate response has a lower phenotypic variance across environments than the mean variance of its parents. In some situations the hybrid's variance is less than that of either parent.A component of the error variation for a genotype was shown to vary with the environment having a minimal value when the environment was optimal.An algebraic treatment of response curves and surfaces was presented. In some instances the metric values for two parents and their F ₁ in a range of environments may be related in the form of a multiple regression.     

A hybrid approach for efficient and robust parameter estimation in biochemical pathways

Developing suitable dynamic models of biochemical pathways is a key issue in Systems Biology. Predictive models for cells or whole organisms could ultimately lead to model-based predictive and/or preventive medicine. Parameter estimation (i.e. model calibration) in these dynamic models is therefore a critical problem. In a recent contribution [Moles, C.G., Mendes, P., Banga, J.R., 2003b. Parameter estimation in biochemical pathways: a comparison of global optimisation methods. Genome Res. 13, 2467-2474], the challenging nature of such inverse problems was highlighted considering a benchmark problem, and concluding that only a certain type of stochastic global optimisation method, Evolution Strategies (ES), was able to solve it successfully, although at a rather large computational cost. In this new contribution, we present a new integrated optimisation methodology with a number of very significant improvements: (i) computation time is reduced by one order of magnitude by means of a hybrid method which increases efficiency while guaranteeing robustness, (ii) measurement noise (errors) and partial observations are handled adequately, (iii) automatic testing of identifiability of the model (both local and practical) is included and (iv) the information content of the experiments is evaluated via the Fisher information matrix, with subsequent application to design of new optimal experiments through dynamic optimisation.     

Biochemical basis of hybrid vigour. The genetics of grain weight of Oryza sativa

Summary Four cathodal bands (C₁, C₂, C₃ and C₄) of esterase (E₁, C₁. 3.1) were correlated with the grain weight of rice (Oryza sativa L.). Zymogram patterns indicated intensity differences among these bands infinegrain and coarse-grain varieties. Bands C₁. and C₂ were dark in fine grain varieties whereas C₃ and C₄ were dark in coarse grain varieties. These bands were specific to endosperm. Observations on fine-grain (Kalanamak), coarse grain (SR(26)B) varieties and their reciprocal hybrids indicated the presence of 4 esterase loci G₁, G₂, G₃ and G₄, corresponding to bands C₁, C₂, C₃ and C₄, respectively. A possible model for heterosis in grain weight of rice was proposed which supports the dominance theory of heterosis. In hybrid vigour the 4 esterase loci appear to be associated with grain weight and they complemented each other in an additive manner.     

The genetical basis of hybrid vigour in a highly heterotic cross of Nicotiana tabacum

The genetical control of F₁ heterosis, observed in a cross of desirable Nicotiana tabacum varieties, was investigated by analysing the data of the basic generations, triple test cross-families and random samples of doubled haploids (DH) and single-seed descent (SSD) lines. Analyses of the first-degree statistics revealed a complex control underlying the genetic variation, including the presence of epistasis, linkage, maternal effects and their interactions, in addition to the additive and dominance effects of the genes segregating in the cross. These analyses identified gene dispersion, directional dominance, and duplicate epistasis, as the main causes of heterosis. The triple test-cross analysis also confirmed the presence of non-allelic interactions and indicated that the dominance ratio, although inflated by epistasis, is consistently partial for all the traits. The extent of transgression in the recombinant inbred lines finally established unequivocally that, as in numerous other crosses, gene dispersion and unidirectional, but partial, dominance are the true causes of heterosis in this cross too.     

Biosynthesis of lasalocid A: biochemical mechanism for assembly of the carbon framework

Labeling experiments on the biosynthesis of the polyether antibiotic lasalocid A (1) using carboxylic acid precursors bearing 13C, 2H, and 3H labels at various positions established the following: (1) 2H or 3H at C-2 of propionate or 2H at C-2 of butyrate was partially retained at C-12 and C-14 of 1, respectively. (2) 2H at C-2 of propionate or at C-2 and C-3 of succinate did not label C-10. These and earlier data [Hutchinson, C. R., Sherman, M. M., Vederas, J. C., & Nakashima, T. T. (1981) J. Am. Chem. Soc. 103, 5953; Hutchinson, C. R., Sherman, M. M., McInnes, A. G., Walter, J. A., & Vederas, J. C. (1981) J. Am. Chem. Soc. 103, 5956] are consistent with a hypothesis for the stereochemical control of lasalocid A biosynthesis, whose main tenets are that the configuration of C-12 and C-14 is determined by the stereoselectivity of the carbon chain forming condensation between acyl thio ester and 2-carboxyacyl thio ester intermediates and that the configuration of C-11 and C-15 results from the reduction of 2-keto thio ester intermediates with opposing stereospecificities.     

A novel preference for an invasive plant as a mechanism for animal hybrid speciation

Homoploid hybrid speciation--speciation via hybridization without a change in chromosome number--is rarely documented and poorly understood in animals. In particular, the mechanisms by which animal homoploid hybrid species become ecologically and reproductively isolated from their parents are hypothetical and remain largely untested by experiments. For the many host-specific parasites that mate on their host, choosing the right host is the most important ecological and reproductive barrier between these species. One example of a host-specific parasite is the Lonicera fly, a population of tephritid fruit flies that evolved within the last 250 years likely by hybridization between two native Rhagoletis species following a host shift to invasive honeysuckle. We studied the host preference of the Lonicera fly and its putative parent species in laboratory experiments. The Lonicera fly prefers its new host, introduced honeysuckle, over the hosts of both parental species, demonstrating the rapid acquisition of preference for a new host as a means of behavioral isolation from the parent species. The parent taxa discriminate against each other's native hosts, but both accept honeysuckle fruit, leaving the potential for asymmetric gene flow from the parent species. Importantly, this pattern allows us to formulate hypotheses about the initial formation of the Lonicera fly. As mating partners from the two parent taxa are more likely to meet on invasive honeysuckle than on their respective native hosts, independent acceptance of honeysuckle by both parents likely preceded hybridization. We propose that invasive honeysuckle served as a catalyst for the local breakdown of reproductive isolation between the native parent species, a novel consequence of the introduction of an exotic weed. We describe behavioral mechanisms that explain the initial hybridization and subsequent reproductive isolation of the hybrid Lonicera fly. These results provide experimental support for a combination of host shift and hybridization as a model for hybrid speciation in parasitic animals.     

A biochemical hypothesis to explain the mechanism of luteal regression

It seems likely that luteal regression may involve a direct biochemical action of prostaglandin F₂α (PGF₂α) on the luteal cell since there are now several reports that PGF₂α can directly inhibit steroidogenesis . However, the mechanism of such an action of PGF₂α remains obscure.This article initially reviews the central role of adenosine 3,^I5^I-mono-phosphate (c-AMP) in initiating and maintaining the structural and functional changes occurring on luteinisation. A mechanism is suggested, supported by results obtained using granulosa cells in tissue culture, in which PGF₂α initiates functional luteolysis by inhibiting further synthesis of c-AMP. This mechanism is then used in conjunction with further observations to provide a possible explanation for the inability of PGF₂α to regress newly formed corpora lutea. Finally, the possible mechanisms of structural regression are discussed.     

Switching mechanism for branched biochemical fluxes: graph-theoretical analysis

A graph-theoretical method is applied to characterize the structure of a simplest switching mechanism of common biochemical importance. This mechanism is based on competition of two coupled substrate-binding pathways for a single substrate. No other regulatory interactions are shown to be needed for the switching phenomenon to be observed. It is shown that switch in branch effluxes is observed as bistability or reciprocal oscillations, depending on the value of steady influx. Frequency of reciprocal efflux oscillations in branches is regulated by steady influx. Therefore, the switching mechanism can function as the coding mechanism in the manner of "influx steady level-efflux frequency". The calculated kinetic equations for the switching mechanism demonstrate very steep transitions in the branch fluxes without using high non-linearity of these equations.     

The phytochromes: A biochemical mechanism of signaling in sight?

The biochemical mechanism by which the phytochrome family of plant sensory photoreceptors transmit perceived informational light signals downstream to transduction pathway components is undetermined. The recent sequencing of the entire genome of the cyanobacterium Synechocystis, however, has revealed a protein that has an NH₂-terminal domain with striking sequence similarity to the photosensory NH₂-terminal domain of the phytochromes, and a COOH-terminal domain strongly related to the transmitter histidine kinase module of bacterial two-component sensors. The Synechocystis protein is capable of autocatalytic chromophore ligation and exhibits photoreversible light-absorption changes analogous to the phytochromes, indicating its capacity to function as an informational photoreceptor. Together with earlier observations that the COOH-terminal domains of the plant phytochromes also have sequence similarity to the histidine kinases, these data suggest that the cyanobacteria utilize photoregulated histidine kinases as a sensory system and that the plant phytochromes may be evolutionary descendants of these photoreceptors.     

A biochemical hypothesis to explain the mechanism of luteal regression.

It seems likely that luteal regression may involve a direct biochemical action of prostaglandin F2alpha (PGF2alpha) on the luteal cell since there are now several reports that PGF2alpha can directly inhibit steroidogenesis in vitro. However, the mechanism of such an action of PGF2alpha remains obscure. This article initially reviews the central role of adenosine 3,I5I-mono-phosphate (c-AMP) in initiating and maintaining the structural and functional changes occurring on luteinisation. A mechanism is suggested, supported by results obtained using granulosa cells in tissue culture, in which PGF2alpha initiates functional luteolysis by inhibiting further synthesis of c-AMP. This mechanism is then used in conjunction with further in vitro observations to provide a possible explanation for the inability of PGF2alpha to regress newly formed corpora lutea. Finally, the possible mechanisms of structural regression are discussed.