Histochemical classification based upon reaction types and its application to carbohydrate histochemistry

Summary A method of classification is presented, which divides histochemical visualization reactions into categories based on general reaction types. This scheme is dependent upon the reaction between two elements, the substrate and the probe. The substrate represents a tissue component(s) with one or more reactive groups that can combine directly with the probe. Alternatively, the substrate reactive groups are chemically modified (activation) with a suitable reagent before reaction with the probe. Probes are of three types: those that yield a coloured product, those that result in a colourless product, and those that produce a coloured product only after a further reaction.Methods used in carbohydrate histochemistry are divided into one, two and three probe reactions. Two probe reactions are further subdivided into sequences involving one or two coloured products (one and two dye sequences); three probe reactions into sequences involving one, two or three coloured products (one, two and three dye sequences). This classification permits the rationalization and organization of methods, and provides a framework for the examination of existing methods and the development of new ones.     

Multiple Phenotypic Changes Associated with Large-Scale Horizontal Gene Transfer

Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e., changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmids and phage, little is known about the magnitude or number of such costs after the transfer of larger regions. Here we describe numerous phenotypic changes that occur after a large-scale horizontal transfer event (∼1 Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.     

The polymerase chain reaction: a new epidemiological tool for investigating cervical human papillomavirus infection.

The polymerase chain reaction is an in vitro method for primer directed enzymatic amplification of specific target DNA sequences. The technique was used to detect human papillomavirus types 11 and 16 simultaneously in cellular DNA recovered from cervical smears in 38 women referred for colposcopy to evaluate cytological abnormality and 10 women with no history of cytological abnormality. The polymerase chain reaction was shown to be both specific and sensitive in detecting human papillomavirus DNA such that a single human papillomavirus molecule was detected in 10(5) cells. Of the 38 women with cytological abnormality, all were positive for human papillomavirus on testing with the polymerase chain reaction; 36 were infected with human papillomavirus type 16 and 22 dually infected with human papillomavirus types 11 and 16. Seven of the 10 women with no cytological abnormality were also infected with human papillomavirus type 11 or 16. The use of the polymerase chain reaction will facilitate epidemiological investigation of the aetiological role of human papillomavirus in cervical neoplasia. This preliminary analysis suggests that the prevalence of human papillomavirus infection is greater than previously reported.     

The importance of Loch Lomond National Nature Reserve for Fish

Loch Lomond NNR with 19 fish species is ranked top in fish conservation value of 235 NNRs in Great Britain due to species diversity, presence of rare species and unusual forms and combinations.     

A new species of Polystoma (Monogenea: Polystomatidae) parasitic in Hyperolius marmoratus (Anura: Hyperoliidae) in South Africa

Polystoma marmorati n. sp. is described as a new polystomatid species parasitic in the urinary bladder of the painted reed frog Hyperolius marmoratus marmoratus collected in southern Natal, South Africa. Parasite prevalence varied from 14.5 to 47.4% and the mean intensity from 1.0 to 1.1. The hamuli of the new species have a characteristic, partly fragmented appearance, a feature also seen in Polystoma batchvarivi, the only other polystome described from a species of the genus Hyperolius. The similarity between the two species, in spite of their geographical separation, is commented upon.     

Carapace movements associated with ventilation and irrigation of the branchial chambers in the semaphore crab,Heloecius cordiformis (Decapoda: Brachyura: Ocypodidae)

Summary Carapace movements in crabs are briefly reviewed. While on land and recirculating branchial water, the Australian semaphore crab Heloecius cordiformis (Decapoda: Ocypodidae), a semi-terrestrial air-breathing mangrove crab, sequentially depresses and elevates its carapace relative to its thorax (0.5–1 mm excursion) in a regular pump-like manner. In quiescent crabs each carapace-pumping cycle lasts about 4 s; carapace depression takes 3 s and elevation 1 s. Carapace movements are brought about by pressures generated within the branchial chambers by the scaphognathites, probably in combination with carapace muscles. Carapace movements are associated with bilaterally synchronised scaphognathite activity. Unilateral scaphognathite activity was not observed. During normal forward recirculation of branchial water the scaphognathites beat at about 1.5 Hz (slow-forward pumping) and the lungs (epibranchial chambers) are not ventilated. In Heloecius, the lungs are not physically separated from the gills below by an anatomical barrier. Lung ventilation is accomplished during the following sequence of events: the carapace is lowered and the scaphognathites pump in a fast-forward mode at about 2.8 Hz. This activity preferentially pumps air out of the lungs and generates suction within the branchial chambers (4–10 cm H₂O below ambient) which draws water from external body surfaces into the hypobranchial space below and around the gills. At the end of the carapace's downward travel the scaphognathites switch from fast-forward to fastreverse beating at about 4 Hz. This pumps air into the lungs and the carapace elevates. As a result, during carapace elevation the water which had previously been drawn into the branchial chambers by fast-forward pumping activity is released and flows out between the legs and into the abdominosternal cavity. When the carapace reaches its original resting or up position the scaphognathites switch from fast-reverse to slowforward beating to re-establish water recirculation through the branchial chambers. This cycle is subsequently repeated. In stationary crabs, there are 2 carapace-pumping cycles per minute, increasing to 14 per minute in active crabs (walking). When water is absent, the lungs are preferentially ventilated by slow-reverse scaphognathite pumping activity. Carapace movements do not occur in the absence of branchial water. Carapace pumping is thought to provide a mechanism which permits the scaphognathites to ventilate the lungs in the presence of recirculating branchial water, without this water interfering with lung ventilation or being lost to the environment.Abbreviations FF, FR, SF, SR fast-forward, fast-reverse, slowforward, slow-reverse scaphognathite pumping - MEA Milne Edwards aperture     

FLUXNET and modelling the global carbon cycle

Measurements of the net CO₂ flux between terrestrial ecosystems and the atmosphere using the eddy covariance technique have the potential to underpin our interpretation of regional CO₂ source–sink patterns, CO₂ flux responses to forcings, and predictions of the future terrestrial C balance. Information contained in FLUXNET eddy covariance data has multiple uses for the development and application of global carbon models, including evaluation/validation, calibration, process parameterization, and data assimilation. This paper reviews examples of these uses, compares global estimates of the dynamics of the global carbon cycle, and suggests ways of improving the utility of such data for global carbon modelling. Net ecosystem exchange of CO₂ (NEE) predicted by different terrestrial biosphere models compares favourably with FLUXNET observations at diurnal and seasonal timescales. However, complete model validation, particularly over the full annual cycle, requires information on the balance between assimilation and decomposition processes, information not readily available for most FLUXNET sites. Site history, when known, can greatly help constrain the model‐data comparison. Flux measurements made over four vegetation types were used to calibrate the land‐surface scheme of the Goddard Institute for Space Studies global climate model, significantly improving simulated climate and demonstrating the utility of diurnal FLUXNET data for climate modelling. Land‐surface temperatures in many regions cool due to higher canopy conductances and latent heat fluxes, and the spatial distribution of CO₂ uptake provides a significant additional constraint on the realism of simulated surface fluxes. FLUXNET data are used to calibrate a global production efficiency model (PEM). This model is forced by satellite‐measured absorbed radiation and suggests that global net primary production (NPP) increased 6.2% over 1982–1999. Good agreement is found between global trends in NPP estimated by the PEM and a dynamic global vegetation model (DGVM), and between the DGVM and estimates of global NEE derived from a global inversion of atmospheric CO₂ measurements. Combining the PEM, DGVM, and inversion results suggests that CO₂ fertilization is playing a major role in current increases in NPP, with lesser impacts from increasing N deposition and growing season length. Both the PEM and the inversion identify the Amazon basin as a key region for the current net terrestrial CO₂ uptake (i.e. 33% of global NEE), as well as its interannual variability. The inversion's global NEE estimate of −1.2 Pg [C] yr⁻¹ for 1982–1995 is compatible with the PEM‐ and DGVM‐predicted trends in NPP. There is, thus, a convergence in understanding derived from process‐based models, remote‐sensing‐based observations, and inversion of atmospheric data. Future advances in field measurement techniques, including eddy covariance (particularly concerning the problem of night‐time fluxes in dense canopies and of advection or flow distortion over complex terrain), will result in improved constraints on land‐atmosphere CO₂ fluxes and the rigorous attribution of mechanisms to the current terrestrial net CO₂ uptake and its spatial and temporal heterogeneity. Global ecosystem models play a fundamental role in linking information derived from FLUXNET measurements to atmospheric CO₂ variability. A number of recommendations concerning FLUXNET data are made, including a request for more comprehensive site data (particularly historical information), more measurements in undisturbed ecosystems, and the systematic provision of error estimates. The greatest value of current FLUXNET data for global carbon cycle modelling is in evaluating process representations, rather than in providing an unbiased estimate of net CO₂ exchange.