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Background The late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins, originally found in plants but now being found in non-plant species. Their precise function is unknown, though considerable evidence suggests that LEA proteins are involved in desiccation resistance. Using a number of statistically-based bioinformatics tools the classification of a large set of LEA proteins, covering all Groups, is reexamined together with some previous findings. Searches based on peptide composition return proteins with similar composition to different LEA Groups; keyword clustering is then applied to reveal keywords and phrases suggestive of the Groups' properties.

Two alternative hypotheses may account for the low fruit:flower ratios regularly observed in many species of plants. First, a low fruit:flower ratio may be a passive “nonadaptive” consequence of external stressors that destroy flowers or limit their pollination. Alternatively, a low fruit:flower ratio may be a result of adaptations that enhance plant fitness, perhaps by allowing the plants to compensate for the very stressors that limit fruit set. We tested these nonadaptive and adaptive hypotheses using Solanum carolinense (horsenettle), an herbaceous plant that generally exhibits a low fruit:flower ratio. Horsenettle often suffers substantial flower loss to herbivores and fruit set can be pollen limited. We present experimental evidence that neither floral destruction by herbivores nor pollen limitation directly affected fruit:flower ratio. Instead, the low fruit:flower ratio was an adaptive consequence of the production of “surplus” flowers. These flowers served as reserve ovaries that enabled...

Background Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human upper respiratory tract is common and lack of clearance by the immune system is likely due to the emergence of seroresistant genetic lineages. No active bacteriophages or prophages have been described in this species. This study was undertaken to identify and categorise prophages in M. catarrhalis, their genetic diversity and the relationship of such diversity with the host-species phylogeny. Results This study presents a comparative analysis of 32 putative prophages identified in 95 phylogenetically variable, newly sequenced M. catarrhalis genomes. The prophages were genotypically classified into four diverse clades. The genetic synteny of each clade is similar to the group 1 phage family Siphoviridae, however, they form genotypic clusters that are distinct from other members of this family. No core genetic sequences exist across the 32 prophages despite clades 2, 3, and 4 sharing the most sequence identity. The analysis of non-structural prophage genes (coding the integrase, and terminase), and portal gene showed that the respective genes were identical for clades 2, 3, and 4, but unique for clade 1. Empirical analysis calculated that these genes are unexpectedly hyperconserved, under purifying selection, suggesting a tightly regulated functional role. As such, it is improbable that the prophages are decaying remnants but stable components of a fluctuating, flexible and unpredictable system ultimately maintained by functional constraints on non-structural and packaging genes. Additionally, the plate encoding genes were well conserved across all four prophage clades, and the tail fibre genes, commonly responsible for receptor recognition, were clustered into three major groups distributed across the prophage clades. A pan-genome of 283,622 bp was identified, and the prophages were mapped onto the diverse M. catarrhalis multi-locus sequence type (MLST) backbone. Conclusion This study has provided the first evidence of putatively mobile prophages in M. catarrhalis, identifying a diverse and fluctuating system dependent on the hyperconservation of a few key, non-structural genes. Some prophages harbour virulence-related genes, and potentially influence the physiology and virulence of M. catarrhalis. Importantly our data will provide supporting information on the identification of novel prophages in other species by adding greater weight to the identification of non-structural genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2104-1) contains supplementary material, which is available to authorized users.

Terminal-restriction fragment length polymorphism (T-RFLP) and length heterogeneity-polymerase chain reaction (LH-PCR) are DNA fingerprinting technologies which use PCR amplification of a gene of interest e.g. small subunit rRNA gene, to study microbial community structure and dynamics. Either one or both of the forward and reverse strand primers used to amplify the gene are fluorescently labelled. The products of restriction endonuclease digestion are electrophoresed with an automated sequencer that detects only the terminal (labelled) restriction fragments (T-RFs). In LH-PCR, products are electrophoresed without digestion, with different fragment lengths being due to inherent variation in the amplified sequence. A novel software system, TRUFFLER, has been developed to mimic this process in silico allowing comparison of experimental data against databases of theoretically determined T-RFs. As a given combination of forward and reverse primers and restriction endonuclease can yield identical T-RFs across a number of species, combinations of different endonucleases (and/or primers) are typically used In addition to fragment length data, data on fluorescence levels is also available. Computationally, this can be viewed as a constraint satisfaction problem which can be solved to allow identification of the dominant members of the microbial community, often down to individual species or at least genus level, and their relative proportions.

The POPPs is a suite of inter-related software tools which allow the user to discover what is statistically ‘unusual’ in the composition of an unknown protein, or to automatically cluster proteins into families based on peptide composition. Finally, the user can search for related proteins based on peptide composition. Statistically based peptide composition provides a view of proteins that is, to some extent, orthogonal to that provided by sequence. In a test study, the POPP suite is able to regroup into their families sets of approximately 100 randomised Pfam protein domains. The POPPs suite is used to explore the diverse set of late embryogenesis abundant (LEA) proteins. Availability: Contact the author. Contact: mw263@cam.ac.uk Keywords: protein clustering; clustering algorithms; protein search; peptide composition; Pfam; late embryogenesis abundant proteins.

Using the example of the pioneer British university teacher and economic geographer G. G. Chisholm, the author discusses qualities desirable in a university teacher of geography, considers some of the problems of teaching geography in British universities and polytechnics at the present time and indicates some directions in which further improvements may be sought. OUR Institute was founded by university teachersl yet, with a few exceptions,2 little attention has been given in Presidential Addresses or generally in the Transactions to the teaching task that occupies most of us for much of our time. It is also surprising that, in a period of expansion of universities and polytechnics, the Institute, certainly until recently, has done relatively little to stimulate discussion on the problems and the achievements of teaching geography at university level. Personally, I find it helpful to look back sometimes at the work of our predecessors, partly to absorb their experience and partly to find points of reference from which to test progress and current standards. And so I begin with an example from the past, from the first modern phase in the growth of our subject as a university discipline in Britain. George Goudie Chisholm was among the university teachers of that period. Chisholm had been born in Edinburgh in i850.3 He took degrees in the University of Edinburgh, first in philosophy in I870 and then in natural sciences in I883. By the time of his second graduation he had already commenced his career as an author, having published Switzerland: its scenery and people in i88i and The Two Hemispheres in 1882. He became a Fellow of the Royal Geographical Society in I884 and his name appears as an author in early issues of the Scottish Geographical Magazine. Chisholm's early work was in a Glasgow publisher's office and his career as a teacher seems to date from 1895 when, at the age of 45, he moved to London and became involved in what we would now call extra-mural or extension lecturing. The Council minutes of Birkbeck College, London, for 29 June I896, include the resolution that 'a Course of Lectures on Commercial Geography in connection with the London Society for the Extension of University Teaching be arranged for the Autumn and Winter Terms at a cost of ?25 per term', and Mr Chisholm was engaged for this task.4 In I898 Birkbeck College agreed to continue the lectures on the understanding that a grant of ?50 be promised by the Technical Education Board. His work at Birkbeck continued until I908 when, after one year of lectures from L. W. Lyde, J. F. Unstead took up an appointment in geography in I909 at a salary of ?65 per annum. Chisholm, meanwhile, had played an active part in lecturing in geography in other places: he became secretary of the London University Board of Studies in Geography in I903 and played an influential part in the Board's work in developing geographical studies in the University. He was in close contact with Mackinder at this time and one can imagine his regular journeys by suburban train from his homes in Camberwell, Balham and later in Upper Tooting to the University head