Disease and the abundance and distribution of bird populations: a summary

Over the past few years, I have written several reviews about the effects of infectious diseases upon the distribution and abundance of their host populations. One general review and synthesis is in the fmd chapter of a book whose earlier chapters focus mainly on human diseases (Anderson & May 1991). A bird-specific discussion, with particular reference to conservation issues, is given by Dobson and May (1991). Broadly related questions about the invasion, persistence and spread of infectious diseases within animal communities are explored by Anderson and May (1986) and with emphasis on bird populations by Dobson and May (1986). Also relevant are a set of papers from the Society for Conservation Biology's first-ever symposium on Conservation and Disease (for an overview, see May 1988, Scott 1988).
Rather than burdening the literature with a recapitulation of these existing reviews, this paper gives a sign-posted guide for those who are not familiar with this particular literature. I first sketch reasons for believing that infectious diseases play an important part in the life history of birds. Next I point towards an analytic framework for understanding the dynamics of host-pathogen associations. Finally I list some of the implications for the conservation biology of bird populations.     

Identification of senescent cells in multipotent mesenchymal stromal cell cultures: Current methods and future directions

Regardless of their tissue of origin, multipotent mesenchymal stromal cells (MSCs) are commonly expanded in vitro for several population doublings to achieve a sufficient number of cells for therapy. Prolonged MSC expansion has been shown to result in phenotypical, morphological and gene expression changes in MSCs, which ultimately lead to the state of senescence. The presence of senescent cells in therapeutic MSC batches is undesirable because it reduces their viability, differentiation potential and trophic capabilities. Additionally, senescent cells acquire senescence-activated secretory phenotype, which may not only induce apoptosis in the neighboring host cells following MSC transplantation, but also trigger local inflammatory reactions. This review outlines the current and promising new methodologies for the identification of senescent cells in MSC cultures, with a particular emphasis on non-destructive and label-free methodologies. Technologies allowing identification of individual senescent cells, based on new surface markers, offer potential advantage for targeted senescent cell removal using new-generation senolytic agents, and subsequent production of therapeutic MSC batches fully devoid of senescent cells. Methods or a combination of methods that are non-destructive and label-free, for example, involving cell size and spectroscopic measurements, could be the best way forward because they do not modify the cells of interest, thus maximizing the final output of therapeutic-grade MSC cultures. The further incorporation of machine learning methods has also recently shown promise in facilitating, automating and enhancing the analysis of these measured data.     

Do trails affect relative abundance estimates of rainforest frogs and lizards?

The selection of a sampling protocol is critical to study amphibian and reptile communities and in many instances researchers have combined the use of visual encounter surveys (VES) conducted on trails and off trails. The effect of human‐made trails on relative abundance estimates of amphibians and reptiles has been assessed in a few temperate locations, but data are lacking for tropical sites. Our study was designed to address this issue by comparing abundance estimates of frogs and lizards on and off trails in a lowland rainforest in south‐eastern Perú. We used nocturnal VES to sample frogs and lizards along transects established on trails and off trails in two different forest types. We found that the observed relative abundance estimates of frogs and lizards were affected by the location of transects (on trail vs. off trail) and the type of forest (floodplain forest vs. terra firme forest). We also found an interaction between the two main effects, indicating that the effect of transect location with respect to trails varies as a function of habitat. Observed frog abundances were higher on trails than off trails, indicating that studies that include VES on trails will bias relative abundance estimates in contrast to studies that include only VES off trails. We suggest that transects should be established only off trails, especially for monitoring studies because trail use by humans can have a strong influence on observed animal abundance.     

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Next‐generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan ‘BIN’ ontology, which is tailored for functional annotation of plant ‘omics’ data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan‐to‐GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator .     

Riccia fruticulosa O.F.Müll., 1782 and blue Metzgeria (Marchantiophyta) in Europe

Riccia fruticulosa O.F.Müll., 1782 from Norway is a valid name, referring to Riccardia palmata (Hedw.) Carruth. In 1785 Dickson misidentified British plants of a blue Metzgeria as R. fruticulosa . The European blue species of Metzgeria is conspecific with M. violacea (Ach.) Dumort., which replaces M. fruticulosa auct. The true origin of the type of Jungermannia violacea Ach., 1805 is probably Tierra del Fuego (rather than Dusky Bay, New Zealand), where the species is widespread. Reports from Australasia, Asia and Africa are all erroneous. The blue colour of Jungermanniales is found only in living plants and is derived from the oil-bodies. In contrast, that of Metzgeria appears only after death; its biological function is unknown.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 142 , 229−235.