Estimation and inference of R0 of an infectious pathogen by a removal method

The basic reproductive ratio, R0, is a central quantity in the investigation and management of infectious pathogens. The standard model for describing stochastic epidemics is the continuous time epidemic birth-and-death process. The incidence data used to fit this model tend to be collected in discrete units (days, weeks, etc.), which makes model fitting, and estimation of R0 difficult. Discrete time epidemic models better match the time scale of data collection but make simplistic assumptions about the stochastic epidemic process. By investigating the nature of the assumptions of a discrete time epidemic model, we derive a bias corrected maximum likelihood estimate of R0 based on the chain binomial model. The resulting 'removal' estimators provide estimates of R0 and the initial susceptible population size from time series of infectious case counts. We illustrate the performance of the estimators on both simulated data and real epidemics. Lastly, we discuss methods to address data collected with observation error.     

Hydraulic architecture and water relations of Spartium junceum branches affected by a mycoplasm disease

Plant water relations, xylem anatomy and the hydraulic architecture of 1‐year‐old twigs of Spartium junceum, both healthy and affected by a phytoplasm disease, were studied. The disease causes twigs to be either shortened (witches broom disease, WBD) or flat (fasciate disease, FD). WBD twigs show a sevenfold increase in total leaf area, smaller and shorter xylem conduits, a higher stomatal conductance (g_l) and a decline of minimum leaf water potentials ( Ψ _l) below the turgor loss point. FD twigs had nearly twice the leaf area of the healthy controls as well as high g_l values and Ψ _l values below the turgor loss point. Moreover, significant differences between healthy and affected twigs in stem stomatal conductance (g_s) and in the total stem area were recorded. Affected twigs die back under drought stress, which is explained by a pronounced loss of hydraulic conductivity of the infected stems (40 and 60%) in FD and WBD as well as by the unfavourable ratio of weighted conduit radius ( Σ r⁴) to total surface area (A_t), so that the efficiency of the stem in supplying the whole transpiring area with water is strongly reduced.     

Multi‐Length‐Scale Morphologies in PCPDTBT/PCBM Bulk‐Heterojunction Solar Cells

Additives are known to improve the performance of organic photovoltaic devices based on mixtures of a low bandgap polymer, poly[2,6‐(4,4‐bis(2‐ethylhexyl)‐4H‐cyclopenta[2,1‐b;3,4‐b′]‐dithiophene)‐alt‐4,7‐(2,1,3‐benzothiadiazole)] (PCPDTBT) and [6,6]‐phenyl C61‐butyric acid methyl ester (PCBM). The evolution of the morphology during the evaporation of the mixed solvent, which comprises additive and chlorobenzene (CB), is investigated by in‐situ grazing incidence X‐ray scattering, providing insight into the key role the additive plays in developing a multi‐length‐scale morphology. Provided the additive has a higher vapor pressure and a selective solubility for PCBM, as the host solvent (CB) evaporates, the mixture of the primary solvent and additive becomes less favorable for the PCPDTBT, while completely solubilizing the PCBM. During this process, the PCPDTBT first crystallizes into fibrils and then the PCBM, along with the remaining PCPDTBT, is deposited, forming a phase‐separated morphology comprising domains of pure, crystalline PCPDTBT fibrils and another domain that is a PCBM‐rich mixture with amorphous PCPDTBT. X‐ray/neutron scattering and diffraction methods, in combination with UV–vis absorption spectroscopy and transmission electron microscopy, are used to determine the crystallinity and phase separation of the resultant PCPDTBT/PCBM thin films processed with or without additives. Additional thermal annealing is carried out and found to change the packing of the PCPDTBT. The two factors, degree of crystallinity and degree of phase separation, control the multi‐length‐scale morphology of the thin films and significantly influence device performance.     

In vitro chromosome doubling of nineZantedeschia cultivars

Tetraploid plants have been produced from nineZantedeschia cultivars usingin vitro colchicine treatment. Rapidly-multiplying shoot cultures were treated on a medium containing 0.05% colchicine for 1, 2 or 4 days to induce chromosome doubling. Following the treatment, most shoots were killed but the surviving shoots were multiplied for several subcultures. These shoots were then rootedin vitro and transferred to a greenhouse. Plants were screened 2 months later by measuring stomatal length, and 110 out of 565 plants were selected as putative tetraploids with a stomatal length significantly greater than in diploid control plants. Chromosome counts were carried out on root tips from 44 plants and confirmed that 38 were tetraploids, 2 were chimeras (predominantly tetraploid with a few octoploid cells), and 4 were diploids. Stomatal length has been rechecked in mature tetraploid plants of the cultivar Black Magic, demonstrating that stomatal length is a good indicator of ploidy level inZantedeschia. This study has shown that multiplying colchicine-treated shootsin vitro for several subcultures prior to transfer to soil produced very few chimeras. The stomatal length measurements are non-destructive and allow the rapid screening of a population for tetraploids.     

Linkage Mapping of DNA Markers Generated with Specific and Non-Specific Gene Primers in Soybean

Polymerase chain reaction (PCR) has been used extensively in the construction of linkage maps for many cultivated crops including soybean, [Glycine max (L.) Merr]. In this study, four sets of oligonucleotide primer pairs of known genes (pearl millet Adh 1, nodule specific proline-rich protein, Drosophila homeobox, heat shock protein), several different combinations from kits A, D, E, and J of arbitrary primers and five primer pairs of soybean simple sequence repeats of varying length (Satt 9, Satt 20, Satt 42, Satt 64, and Satt 30) were utilized in PCR to identify molecular markers which were then used to construct a genetic linkage map. DNA for the PCR reactions was isolated from 65 recombinant inbred soybean lines resulting from crossing PI 290,136 and BARC-2 (Rj ₄ ), followed by self-pollination for seven generations without selection. Mapmaker 3.0, a computer package, was used for construction of the linkage map. A total of 43 polymorphic markers were identified; 30 markers were linked and distributed among 5 linkage groups while 13 markers were unlinked. Arbitrary primers revealed more polymorphisms than specific primers. A combination of arbitrary primers A5 and A18 revealed the maximum number of polymorphic bands. Five observed linkage groups can be expanded in future soybean research by using additional markers.     

The use of DNA markers to estimate the extent and nature of genetic variability in Solatium tuberosum cultivars

High levels of DNA polymorphism were detected in 27 Solanum tuberosum cultivars examined. Combinations of at least two c-DNA clones have been identified which in conjunction with EcoRI allow important UK potato cultivars to be characterised by their molecular profiles. The widely grown North American cultivar Russett Burbank was also successfully fingerprinted. Estimates of genetic diversity based on restriction fragment length polymorphism (RFLP) data indicate the important role that wild potato species and exotic germplasm have played in the development of the cultivars studied. A graphical method for simultaneously highlighting similarities and differences between genotypes for individual hybridising fragments is presented. This approach is particularly useful in identifying and recording fragments which are unique to certain genotypes. Two potato cultivars: Fiona and Morag produce unique RFLP profiles when digested with EcoRI and EcoRV and probed with a flax ribosomal DNA sequence. Both Fiona and Morag possess incomplete or partial (quantitative) type resistance to G. pallida which was transferred from S. vernei. The preferential transmission of the r-DN A fragments from S. vernei may indicate that this locus is associated with genetic factors controlling resistance to G. pallida.     

Comparison of geographically distant populations of Rhizobium isolated from root nodules of Phaseolus vulgaris

Seventy-two rhizobial strains were isolated from the root nodules of french beans ( Phaseolus vulgaris ). They were sampled from two geographically distant field populations and 18 additional different sites in France. They were characterized by a) plasmid profiles, (b) RFLP analysis of total cellular DNA using various chromosomal and symbiotic gene probes (including nif H from Rhizobium etli bv. phaseoli ) and c) their ability to nodulate a potential alternative host, L. leucocephala. Over half of the isolates were ascribed to Rhizobium leguminosarum bv. phaseoli on the basis of the hybridization analysis, the possession of multiple copies of nif H and their inability to nodulate L. leucocephala. The remaining isolates belonged to 2 groups which were shown to be genomically distinct from R. leguminosarum bv. phaseoli, R. etli bv. phaseoli and R. tropici. Most members of these two groups shared with R. tropici the ability to nodulate L. leucocephala and, for isolates of only one of these groups, the presence of one copy of nif H. Members of each of the 3 taxa were widely distributed in France and circumstantial evidence of pSym transfer between them was shown. R. leguminosarum bv. phaseoli and one of the two novel groups co-occurred within the two geographically distant populations. Individual genotypes were conserved between them. The finding of a third taxon at various other locations indicated additional diversity among rhizobia nodulating beans.     

Structure of the intergenic spacer region from the ribosomal RNA gene family of white spruce (Picea glauca)

Five genomic clones containing ribosomal DNA repeats from the gymnosperm white spruce (Picea glauca) have been isolated and characterized by restriction enzyme analysis. No nucleotide variation or length variation was detected within the region encoding the ribosomal RNAs. Four clones which contained the intergenic spacer (IGS) region from different rDNA repeats were further characterized to reveal the sub-repeat structure within the IGS. The sub-repeats were unusually long, ranging from 540 to 990 bp but in all other respects the structure of the IGS was very similar to the organization of the IGS from wheat, Drosophila and Xenopus.     

Rest length and compliance of non-immobilised and immobilised rabbit soleus muscle and tendon

The first aim of this study was to measure the contributions of muscle and tendon to the total compliance of resting muscle-tendon units. A second aim was to determine whether the decrease in muscle-tendon unit rest length produced by prolonged immobilisation in a shortened position is mediated primarily by adaptations of the muscle or tendon. One ankle joint from each of five rabbits was immobilised in a plantarflexed position for 14 days. The passive length-tension properties of soleus muscle fascicles and tendons from both hindlimbs were measured using a video-based tensile-testing system. In non-immobilised muscles, muscle fascicle strains exceeded tendon strains by up to four times. However, because the rest length of tendon was much greater than that of muscle fascicles, changes in tendon length accounted for nearly half of the total change in muscle-tendon unit length. The rest length of immobilised muscle-tendon units was less than that of non-immobilised muscle-tendon units from contralateral limbs. Most of this difference was attributable to a change in the rest length of the tendon; there was little change in the rest length of muscle fascicles. It is concluded that the tendon is responsible for a large part of the compliance of rabbit soleus muscle-tendon units at physiological resting tensions, and that adaptation of tendon rest length is the primary mechanism by which the rabbit soleus shortens in response to immobilisation at short lengths. Accepted: 7 May 1997