Discrimination Amongst Leishmania by Polymerase Chain Reaction and Hybridization with Small Subunit Ribosomal DNA Derived Oligonucleotides

ABSTRACT. A method for discriminating among Leishmania is described, based upon small subunit ribosomal DNA sequence differences. The method was to amplify the entire 2.2 kb small subunit rDNA by polymerase chain reaction using conserved primers specific for the 5' and 3' termini of the small subunit ribosomal RNA, and then hybridize the product dotted onto nylon membranes with labeled oligonucleotides. The design of the hybridization probes was based upon complete small subunit rDNA sequences from L. amazonensis, L. major and L. guyanensis and partial sequences of L. mexicana, L. braziliensis, L. tropica and L. chagasi. A high degree of sequence similarity (> 99%) among species was found. However, sufficient sequence divergence occurred to permit the design of internal oligonucleotide probes specific for species complexes. This procedure successfully discriminated amongst a wide range of Leishmania isolates. The method detected as few as 10 cultured organisms and detected parasites in tissue samples from experimentally infected animals. Non-radioactive labeling showed the same specificity and sensitivity as radioactive probes.     

Shaking a leg and hot to trot: the effects of body size and temperature on running speed in ants

Abstract.  1. Data were compiled from the literature and our own studies on 24 ant species to characterise the effects of body size and temperature on forager running speed.
2. Running speed increases with temperature in a manner consistent with the effects of temperature on metabolic rate and the kinetic properties of muscles.
3. The exponent of the body mass-running speed allometry ranged from 0.14 to 0.34 with a central tendency of approximately 0.25. This body mass scaling is consistent with both the model of elastic similarity, and a model combining dynamic similarity with available metabolic power.
4. Even after controlling for body size or temperature, a substantial amount of inter-specific variation in running speed remains. Species with certain lifestyles [e.g. nomadic group predators, species which forage at extreme (>60 °C) temperatures] may have been selected for faster running speeds.
5. Although ants have a similar scaling exponent to mammals for the running speed allometry, they run slower than predicted compared with a hypothetical mammal of similar size. This may in part reflect physiological differences between invertebrates and vertebrates.     

Misprescription and misuse of one‐tailed tests

One‐tailed statistical tests are often used in ecology, animal behaviour and in most other fields in the biological and social sciences. Here we review the frequency of their use in the 1989 and 2005 volumes of two journals (Animal Behaviour and Oecologia), their advantages and disadvantages, the extensive erroneous advice on them in both older and modern statistics texts and their utility in certain narrow areas of applied research. Of those articles with data sets susceptible to one‐tailed tests, at least 24% in Animal Behaviour and at least 13% in Oecologia used one‐tailed tests at least once. They were used 35% more frequently with nonparametric methods than with parametric ones and about twice as often in 1989 as in 2005. Debate in the psychological literature of the 1950s established the logical criterion that one‐tailed tests should be restricted to situations where there is interest only in results in one direction. ‘Interest’ should be defined; however, in terms of collective or societal interest and not by the individual investigator. By this ‘collective interest’ criterion, all uses of one‐tailed tests in the journals surveyed seem invalid. In his book Nonparametric Statistics, S. Siegel unrelentingly suggested the use of one‐tailed tests whenever the investigator predicts the direction of a result. That work has been a major proximate source of confusion on this issue, but so are most recent statistics textbooks. The utility of one‐tailed tests in research aimed at obtaining regulatory approval of new drugs and new pesticides is briefly described, to exemplify the narrow range of research situations where such tests can be appropriate. These situations are characterized by null hypotheses stating that the difference or effect size does not exceed, or is at least as great as, some ‘amount of practical interest’. One‐tailed tests rarely should be used for basic or applied research in ecology, animal behaviour or any other science.     

Floral ontogenetic evidence of repeated speciation via paedomorphosis in subtribe Orchidinae (Orchidaceae)

Thoroughly sampled molecular phylogenies of the dominantly European orchid subtribe Orchidinae were used to identify a pair and a triplet of recently diverged species in which: (1) divergence involved substantial changes in floral morphology, particularly in the labellar lobes and spur; and (2) the polarity of those changes could be inferred phylogenetically. Floral ontogeny in the selected species was documented in detail through macromorphological, light microscopic, and scanning electron microscopic study of a wide range of ontogenetic stages. All study species showed differentiation of perianth segments earlier than the gynostemium. Unsurprisingly, component parts of the basic floral organs (gymnostemial auricles and rostellum, labellar lateral lobes, and spur) were initiated relatively late, the spur and ovary continuing to expand beyond anthesis. The predominant evolutionary pattern identified in the two case studies was paedomorphosis via progenesis (earlier offset of growth); this credibly explained the reduction in spur size and lateral lobing of the labellum in Gymnadenia odoratissima and, especially, G. austriaca relative to G. conopsea. Loss of resupination in G. austriaca was best viewed as the deletion of a formerly terminal ontogenetic stage. Radical reduction of the spur of Dactylorhiza viridis relative to D. fuchsii was also attributed to progenesis, although the long, narrow outline and relatively short central lobe of its labellum were attributed to increased growth of the lateral lobes (i.e. hypermorphosis resulting in peramorphosis). Microscopic study of epidermal cell types on the labellum and spur suggested a degree of decoupling of micromorphological from macromorphological transitions, although both were subject to heterochronic shifts. Each of the two case studies was consistent with, but not proof of, saltational macroevolution operating via functional changes in one or more key developmental genes. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157 , 429–454.     

A Test for Genetic Exchange in Mixed Infections of Leishmania major in the Sand Fly Phlebotomus papatasi

We tested if genetic exchange was observable between two strains of Leishmania major (Trypanosomatidae) during mixed infection of the sand fly Phlebotomus papatasi. Previous studies suggested that genetic exchange may occur in natural populations of Leishmania at a low frequency, but experimental crosses examining small numbers of progeny (<60) did not reveal hybrid parasites. Accordingly, a strategy was devised to increase the number of progeny that could be screened by 100-fold. Clonal derivatives from two strains that were infective to flies and contained numerous restriction fragment length polymorphisms were characterized and selected for resistance to methotrexate or tunicamycin by gene amplification. A successfully mixed infection of P. papatasi was obtained, and a method was developed for directly plating promastigotes from the gut contents of infected flies onto selective media. Twenty-five hundred independent progeny were scored for the presence of both drug resistance markers. No hybrid parasites were observed, indicating that the frequency of genetic exchange in this cross must be less than 4 times 10^-4. The lines and methods established in this work may prove useful in future studies of the mechanism and frequency of gene exchange in Leishmania.     

A New Method for Strain Identification of Rhizobium trifolii in Nodules

An indirect haemagglutination test has been developed for the detection of strains of Rhizobium trifolii in nodules of subterranean clover plants. Preserved sheep red blood cells, coated with isolated specific rhizobial lipopolysaccharide, were used as the indicator of agglutination; these cells were agglutinated by specific antilipopolysaccharide antibody. Detection of lipopolysaccharide antigen in a suspension of nodular tissue was carried out by reacting the suspension with antilipopolysaccharide antibody prior to the addition of coated red blood cells. The presence of antigen in the suspension was indicated by an inhibition of agglutination. The test was more sensitive than agglutination and immunodiffusion in the detection of rhizobial lipopolysaccharide antigens, and could be used for the rapid screening of large numbers of nodules.     

Glucose Utilization by Euglena gracilis var. bacillaris at Higher pH*

SYNOPSIS. Euglena gracilis var. bacillaris is able to grow luxuriantly on glucose in a mineral salts medium at pH 6.8–7.1 following an adaptation period of about 200 hr. If adapted cells are used as an inoculum or if 0.1% glycine is included in the medium, the lag is shortened to 70–100 hr. Inclusion of 0.1% acetate in the medium produces a diphasic growth pattern, with acetate being metabolized first, followed by the later (about 400 hr) utilization of the glucose. Glucose utilization was found to be sensitive to pH as compared to growth on ethyl alcohol. However, glycine partially overcame this sensitivity. Glycine is maximally stimulatory with regard to growth on glucose at pH 7.0 at a concentration of 0.03%, thus suggesting that it functions as a sparking substance. Glycine markedly stimulates the assimilation of ¹⁴C-glucose. A number of Krebs cycle acids and amino acids were also found to stimulate ¹⁴C-glucose assimilation at neutral pH. Adaptation to glucose utilization at neutral pH was due to the appearance of mutants able to grow more rapidly under these conditions. The nature of this mutation was not determined.     

The Effect of Acetate on Euglena gracilis var. bacillaris as a Function of Environmental Conditions

SYNOPSIS. Acetate, a widely used substrate for the growth of Euglena gracilis var. bacillaris , becomes lethal to these organisms at pH's below 5.0. The kinetics, as well as the extent of acetate-induced death, depend upon both the hydrogen ion and acetate concentrations. Formic, propionic, butyric, and fluoroacetic acids also kill E. gracilis at low pH's, whereas fumaric, malic, succinic and pyruvic acids do not under these conditions.
It is suggested that death is caused by a lowering of the intra-cellular pH, due to the release of hydrogen ion brought into the cell by freely penetrating undissociated acetate molecules.