Mycobacterium tuberculosis lineage: a naming of the parts

There have been many reports of groups of related Mycobacterium tuberculosis strains described variously as lineages, families or clades. There is no objective definition of these groupings making it impossible to define relationships between those groups with biological advantages. Here we describe two groups of related strains obtained from an epidemiological study in Tanzania which we define as the Kilimanjaro and Meru lineages on the basis of IS6110 restriction fragment length polymorphism (RFLP), polymorphic GC rich sequence (PGRS) RFLP and mycobacterial interspersed repeat unit (MIRU) typing. We investigated the concordance between each of the typing techniques and the dispersal of the typing profiles from a core pattern. The Meru lineage is more dispersed than the Kilimanjaro lineage and we speculate that the Meru lineage is older. We suggest that this approach provides an objective definition that proves robust in this epidemiological study. Such a framework will permit associations between a lineage and clinical or bacterial phenomenon to be tested objectively. This definition will also enable new putative lineages to be objectively tested

Growth and yield of 3 hybrid papayas (Carica papaya L.) under mulched and bare ground conditions

At Yarwun (151.3˚E, 23.75˚S), Australia, papaya Hybrid 29 yielded twice as much fruit as Hybrid 11 and 30% more than Hybrid 13. The plots mulched with coarse grass hay yielded 50% more fruit than the plots with bare ground. The highest yielding treatment, Hybrid 29 + mulch, averaged the equivalent of 81 t/ha.year over the 16.5-month harvest period. The yields were achieved in spite of inadequate water supply due to drought and the loss of 877 plants from 1441 plant positions (4 plants per position) due to the 3 phytoplasma diseases; dieback, yellow crinkle and mosaic. Hybrid 29 produced higher yields than the other hybrids by flowering early on shorter plants with thicker stems and setting more fruit that commenced lower down on the stem. Hybrid 13 was intermediate in size and the amount of fruit setting between Hybrid 29 and Hybrid 11 but was the slowest to flower and set fruit. Hybrid 11 had the thinnest and tallest stems, flowered at an intermediate time between the other 2 hybrids and produced fewer flowers and fruit resulting in the lowest yield. Mulching increased stem height and thickness, promoted earlier flowering and increased fruit set, yield and average fruit weigh

Post-ratoon growth and yield of three hybrid papayas (Carica papaya L.) under mulched and bare-ground conditions

At Yarwun (151.3°E, 23.75°S), a trial was conducted to compare 3 papaya hybrids (Hybrid 29, Hybrid 11 and Hybrid 13) under mulching with grass hay or in bare ground. The viability of ratooning a papaya crop was also investigated. After a 16-month cropping season plants were cut to a 750-mm stump (ratooned) about monthly over a 3.5-month period and, following a 4.5-month regrowth period, were harvested for a period of 11 months (post-ratoon). Hybrid 29 yielded (by weight) 54% more than Hybrid 11 and 92% more than Hybrid 13 during the 3.5-month ratooning period. At the commencement of ratooning, Hybrid 29 plants were 41–58 cm shorter than Hybrid 11 and 13 plants, allowing the Hybrid 29 plants to be retained for longer before being ratooned. Hybrid 29 also returned to fruiting more quickly with a greater proportion of plants (97%) with fruit at the first post-ratoon harvest compared with Hybrid 11 (87%). Following regrowth (post-ratoon) the 3 hybrids produced similar yields. All 3 hybrids were equally susceptible to the 3 phytoplasma diseases and to nematodes. The plots mulched with coarse grass hay yielded 70% more during the ratooning period and 116% more post-ratoon than the plots with bare ground. This difference was attributed in part to fewer root-knot nematodes, the roots being more heavily infected with vesicular arbuscular mycorrhiza, the use of the complete upper soil profile by the roots, reduced rainfall run off and less soil loss in the mulched treatment. The highest yielding treatment, mulched Hybrid 29, averaged the equivalent of 55 t/ha.year during ratooning, 43 t/ha.year over the 11-month post-ratoon harvest period and 65 t/ha.year over the entire plant–ratoon cycle. These yields were achieved in spite of drought conditions and quite severe outbreaks of the phytoplasma diseases, dieback, yellow crinkle and mosaic, with 60% of plant positions infected with dieback during the post-ratoon period. Theoretical yield estimations using the data from the plant and post-ratoon crops indicated that ratooning may give superior average monthly yields compared with 2 successive plant crops because of the reduced time required for the ratooned crop to return to production. The study demonstrated the benefits of mulching, the superiority of Hybrid 29 and that ratooning may be successfully used in papaya. In environments similar to Yarwun, Hybrid 29, or similar hybrids, with mulching is recommended for commercial production. If land, time or finances are limiting, consideration should be given to ratooning the plant crop based on monthly cut outs over a 3–4-month ratooning period with vacant plant positions replanted during ratooning

Growth, yield and phenology of 2 hybrid papayas (Carica papaya L.) as influenced by method of water application

Highly variable, outcrossed papaya lines irrigated with overhead sprinklers were grown at Yarwun (151.3˚E, 23.75˚S) in Queensland, Australia. The inherent variability made scientifically based comparative studies impractical. The advent of uniform hybrid papaya lines allowed the testing of 2 of these hybrids under 3 irrigation methods, 2 of which had the potential to greatly reduce water use compared with overhead sprinklers. Yields of 92 t/ha.year were achieved by both papaya Hybrids 29 and 1E. Water application method did not influence yield. About 26% of plants were lost due to the phytoplasma diseases dieback, yellow crinkle and mosaic over the life of the trial. Downward yield fluctuations were related to poor fruit set in winter when pollinators (Family Sphingidae) were not present and growth was slow due to hot dry periods affecting fruit set. The resultant fruit (about 6 months later) were small and reduced in number. Irrigation with overhead sprinklers using saline water (1400–4000 S/cm) damaged leaves and reduced growth of plants. Winter spot was most severe in July, August and September, in Hybrid 29 with overhead irrigation. Height of plants 13 weeks after planting was greater under trickle irrigation due to less damage from the saline water supply than in the overhead sprinkler treatment. Hybrid 29 set fruit at 94.3 cm above ground compared with 117.6 cm for Hybrid 1E

Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations

Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between transcription factors and the operators of genes and that between ligands and binding sites of allosteric enzymes are typical examples of such molecular interactions. In order to obtain the general mathematical framework of biological regulations, we formulate these interactions as finite Markov processes and establish a computational theory of regulatory activities of macromolecules based mainly on graphical analysis of their state transition diagrams. The contribution is summarized as follows: (1) Stochastic interpretation of Michaelis-Menten equation is given. (2) Notion of \textit{probability flow} is introduced in relation to detailed balance. (3) A stochastic analogy of \textit{Wegscheider condition} is given in relation to loops in the state transition diagram. (4) A simple graphical method of computing the regulatory activity in terms of ligands' concentrations is obtained for Wegscheider cases.Comment: 20 pages, 13 figure

Transient behavior in Single-File Systems

We have used Monte-Carlo methods and analytical techniques to investigate the influence of the characteristics, such as pipe length, diffusion, adsorption, desorption and reaction rates on the transient properties of Single-File Systems. The transient or the relaxation regime is the period in which the system is evolving to equilibrium. We have studied the system when all the sites are reactive and when only some of them are reactive. Comparisons between Mean-Field predictions, Cluster Approximation predictions, and Monte Carlo simulations for the relaxation time of the system are shown. We outline the cases where Mean-Field analysis gives good results compared to Dynamic Monte-Carlo results. For some specific cases we can analytically derive the relaxation time. Occupancy profiles for different distribution of the sites both for Mean-Field and simulations are compared. Different results for slow and fast reaction systems and different distribution of reactive sites are discussed.Comment: 18 pages, 19 figure

Thixotropy in macroscopic suspensions of spheres

An experimental study of the viscosity of a macroscopic suspension, i.e. a suspension for which Brownian motion can be neglected, under steady shear is presented. The suspension is prepared with a high packing fraction and is density-matched in a Newtonian carrier fluid. The viscosity of the suspension depends on the shear rate and the time of shearing. It is shown for the first time that a macroscopic suspension shows thixotropic viscosity, i.e. shear-thinning with a long relaxation time as a unique function of shear. The relaxation times show a systematic decrease with increasing shear rate. These relaxation times are larger when decreasing the shear rates, compared to those observed after increasing the shear. The time scales involved are about 10000 times larger than the viscous time scale and about 1000 times smaller than the thermodynamic time scale. The structure of the suspension at the outer cylinder of a viscometer is monitored with a camera, showing the formation of a hexagonal structure. The temporal decrease of the viscosity under shear coincides with the formation of this hexagonal pattern

A population Monte Carlo scheme with transformed weights and its application to stochastic kinetic models

This paper addresses the problem of Monte Carlo approximation of posterior probability distributions. In particular, we have considered a recently proposed technique known as population Monte Carlo (PMC), which is based on an iterative importance sampling approach. An important drawback of this methodology is the degeneracy of the importance weights when the dimension of either the observations or the variables of interest is high. To alleviate this difficulty, we propose a novel method that performs a nonlinear transformation on the importance weights. This operation reduces the weight variation, hence it avoids their degeneracy and increases the efficiency of the importance sampling scheme, specially when drawing from a proposal functions which are poorly adapted to the true posterior. For the sake of illustration, we have applied the proposed algorithm to the estimation of the parameters of a Gaussian mixture model. This is a very simple problem that enables us to clearly show and discuss the main features of the proposed technique. As a practical application, we have also considered the popular (and challenging) problem of estimating the rate parameters of stochastic kinetic models (SKM). SKMs are highly multivariate systems that model molecular interactions in biological and chemical problems. We introduce a particularization of the proposed algorithm to SKMs and present numerical results.Comment: 35 pages, 8 figure