Fuzzy k-means classification of topo-climatic data as an aid to forest mapping in the Greater Yellowstone Area, USA

Previous attempts to quantify topographic controls on vegetation have often been frustrated by issues concerning the number of variables of interest and the tendency of classification methods to create discrete classes though species have overlapping property sets (niches). Methods of fuzzy k-means classification have been used to address class overlap in ecological and geographical data but previously their usefulness has been limited when data sets are large or include artefacts that may occur through the derivation of topo-climatic attributes from gridded digital elevation models. This paper presents ways to overcome these limitations using GIS, spatial sampling methods, fuzzy k-means classification, and statistical modelling of the derived stream topology. Using data from a ca. 3600 km² forested site in the Greater Yellowstone Area, we demonstrate the creation of meaningful, spatially coherent topo-climatic classes through a fuzzy k-means classification of topo-climatic data derived from 100 m gridded digital elevation models (DEMs); these classes were successfully extrapolated to adjacent areas covering a total of ca. 10000 km². Independently derived land cover data and middle infrared corrected Landsat TM derived estimates of Normalised Difference Vegetation Index (M_NDVI) at 575 independently sampled sites were used to evaluate the topo-climatic classes and test their extrapolation to the larger area. Relations between topo-climatic classes and land cover were tested by ² analysis which demonstrated strong associations between topo-climatic class and 11 of the 15 cover classes. Relations between M_NDVI and topo-climatic classes proved to be stronger than relations between M_NDVI and the independent cover classes. We conclude that the fuzzy k-means procedure yields sensible and stable topo-climatic classes that can be used for the rapid mapping of large areas. The value of these methods for quantifying topographic controls on biodiversity and the strength of their relations with computed NDVI values warrant further investigation.     

The effect of whole body lipid on early sexual maturation of 1+ age male chinook salmon (Oncorhynchus tshawytscha)

Early sexual maturation of male chinook salmon (maturation 1 to 4 years prior to females in the same age class) results in reduced effectiveness of stock enhancement programs and a financial loss to the salmon farming industry. Previous studies in Atlantic salmon have shown that the age of maturity in males is affected by growth and/or body energy stores, but the relative roles of these two factors are not well understood. Therefore, an experiment was designed to determine when spermatogenesis was initiated, to characterize the endocrine changes during the onset of puberty in male salmon, and to determine if the level of whole-body lipid affects the incidence of early male maturation in a wild stock (Yakima River) of 1+ spring chinook salmon. Fry were fed a commercial diet from February until August and were then divided into groups of 320 fish (mean weight, 5.6 g) and fed one of five experimental diets (two replicate groups/diet) containing 4%, 9%, 14%, 18% or 22% lipid and 82%, 77%, 73%, 69%, or 65% protein for 13 months. Fish were reared on natural photoperiod and ambient temperature (6°C to 16°C), and pair-fed to a level based on the tank with the lowest feed consumption. Fish were weighed monthly and sampled to determine body composition, pituitary follicle-stimulating hormone (FSH) and luteinizing hormone (LH) levels, plasma insulin-like growth factor I (IGF-I) levels, and stage of gonadal development.

Throughout the experimental period the mean fish weight was similar among treatment groups. However, from December through the end of the experiment in the following September, maturing males were significantly larger than nonmaturing fish. Initial lipid levels in 0-age experimental fish were near 6%, which is similar to wild fish of the same stock and age captured in the Yakima River during August. Fish fed diets containing more than 4% lipid increased in whole-body lipid content during the first 2 months of feeding and then maintained at relatively constant levels during the course of the experiment. Whole-body lipid levels for the dietary treatment groups averaged 5.6%, 7.1%, 8.2%, 9.4%, and 9.6% from October through the following September.

Based on histological examination of the testes of experimental fish, type B spermatogonia and primary spermatocytes were first observed in some of the yearling males during November. These were designated maturing males. Pituitary FSH levels were significantly higher in maturing than nonmaturing males at this time and for the remainder of the study. Pituitary FSH levels increased as spermatogenesis proceeded in maturing fish, whereas pituitary LH levels increased in maturing 1+ males only during July and August, when testes were in late stages of spermatogenesis and in September during spermiation. Plasma IGF-I levels were significantly higher in maturing males than nonmaturing fish from December through the end of experiment. Since maturing males were significantly larger than nonmaturing fish of both sexes from December through September, the difference in IGF-I levels could be due to differences in growth or due to maturation.

The percentage of maturing males was significantly influenced by whole-body lipid, increasing from 34% in fish fed the 4% lipid diet to 45% in fish fed the 22% lipid diet. These data suggest that whole-body lipid levels influenced the incidence of maturation of male spring chinook salmon. In addition, both endocrine and histological indicators suggest that maturation was initiated in males approximately a full year prior to the time the fish will spawn.     

A survey investigating the current practice of French health professionals regarding infection risk after monkey bites

International tourism is steadily increasing, with 15% of travellers reporting health problems when they come back. Animal bites represent 2% of consulting causes, of which 20% are due to monkey bites. The Monkey B virus (Macacine alphaherpesvirus 1) is an alphaherpesvirus (Herpesviridae, genus Simplexvirus) enzootic in macaques (Genus Macaca). Zoonotic infections with the Monkey B virus following exposure to macaques are exceptionally rare, but can cause fatal encephalomyelitis in humans. An observational survey was undertaken in 2018 to assess the practice of French health professionals regarding infection risk after monkey bites. French health professionals practicing in vaccination and rabies centres were specifically targeted for this study. Standardized questionnaires were sent by email to a sample of French health professionals. They were asked to participate on a voluntary and anonymous basis. The questionnaires requested epidemiological details and included multiple‐choice questions about the infection management of monkey bites. The response rate was 33.5%. The frequency of monkey bites in 2017 was variable with a minority of centres managing more than 6 per year (12%), 46% managing 1–5 monkey bites and 42% none. Most of the monkey bites were described as occurring in South Asia at tourist sites, on naked upper limbs, shortly after the travellers arrived at their destination. Tetanus status verification, rabies post‐exposure prophylaxis and antibiotic therapy were said to be prescribed in most cases. Knowledge about the Monkey B virus was reported as scarce for 38% of the participants. The number of monkey bites managed per year per centre varied greatly but practices regarding infectious risk after monkey bites were generally homogeneous. The risk of Monkey B virus transmission did not readily come to mind in the differential diagnosis of infection risk for many French health professionals.     

Coiled-coil irregularities and instabilities in group A Streptococcus M1 are required for virulence

Antigenically variable M proteins are major virulence factors and immunogens of the human pathogen group A Streptococcus (GAS). Here, we report the approximately 3 angstrom resolution structure of a GAS M1 fragment containing the regions responsible for eliciting type-specific, protective immunity and for binding fibrinogen, which promotes M1 proinflammatory and antiphagocytic functions. The structure revealed substantial irregularities and instabilities throughout the coiled coil of the M1 fragment. Similar structural irregularities occur in myosin and tropomyosin, explaining the patterns of cross-reactivity seen in autoimmune sequelae of GAS infection. Sequence idealization of a large segment of the M1 coiled coil enhanced stability but diminished fibrinogen binding, proinflammatory effects, and antibody cross-reactivity, whereas it left protective immunogenicity undiminished. Idealized M proteins appear to have promise as vaccine immunogens.     

Impacts of fishing low-trophic level species on marine ecosystems

Low-trophic level species account for more than 30% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low-trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield (MSY) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80% of MSY.     

Intragenic vectors for gene transfer without foreign DNA

The intragenic vector system involves identifying functional equivalents of vector components from the genome of a specific crop species (or related species to which it can be hybridised) and using these DNA sequences to assemble vectors for transformation of that plant species. This system offers an attractive alternative to current genetic engineering strategies where vectors are based on DNA sequences that usually originate from bacteria. The construction of intragenic vectors enables the well-defined genetic improvement of plants with all transferred DNA originating from within the gene pool already available to plant breeders. In this manner genes can be introgressed into elite cultivars in a single step without linkage drag and without the incorporation of foreign DNA. The resulting plants are non-transgenic, although they are derived using the tools of molecular biology and plant transformation. The use of intragenic vectors for the transfer of genes from within the gene pools of crops may help to alleviate some of the major public concerns over the deployment of GM crops in agriculture, notably the ethical issue associated with the transfer of DNA across wide taxonomic boundaries. This paper reviews the progress toward the development and use of intragenic vectors and the implications of their use for the genetic improvement of crops. Dedicated to the late Hans Sandbrink for his enthusiasm in helping to develop intragenic vectors