Building a PGC-LC-MS <Emphasis Type="Italic">N</Emphasis>-glycan retention library and elution mapping resource

Porous graphitised carbon-liquid chromatography (PGC-LC) has been proven to be a powerful technique for the analysis and characterisation of complex mixtures of isomeric and isobaric glycan structures. Here we evaluate the elution behaviour of N-glycans on PGC-LC and thereby provide the potential of using chromatographic separation properties, together with mass spectrometry (MS) fragmentation, to determine glycan structure assignments more easily. We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. Over 100 glycan structures were determined by MS/MS, and together with targeted exoglycosidase digestions, created a N-glycan PGC retention library covering a full spectrum of biologically significant N-glycans from pauci mannose to sialylated tetra-antennary classes. The resultant PGC retention library (http://www.glycostore.org/showPgc) incorporates retention times and supporting fragmentation spectra including exoglycosidase digestion products, and provides detailed knowledge on the elution properties of N-glycans by PGC-LC. Consequently, this platform should serve as a valuable resource for facilitating the detailed analysis of the glycosylation of both purified recombinant, and complex mixtures of, glycoproteins using established workflows.     

Fertile plant regeneration from cell suspension and protoplast cultures of barley (t Hordeum vulgare cv. Schooner)

Fertile plants were regenerated from both cell suspension and protoplast-derived cultures of the two-row barley, Hordeum vulgare L. cv. Schooner. Embryogenic calluses, derived from immature embryos, were used to establish suspension cultures. More than 100 plants, with variable seed set, have been regenerated from six embryogenic cell suspension cultures. Protoplasts isolated from three suspension cultures divided and when the resultant embryogenic proto-calluses were transferred to regeneration medium both green and albino shoots were produced. The green shoots were transferred to growth regulator-free medium and plantlets that developed strong root systems were potted in soil and grown to maturity in the glasshouse. Root tip analysis of plants regenerated from cell suspension cultures revealed the expected 2N = 14 complement of chromosomes. However, chromosomal analysis of protoplast-derived plants showed numerical variation among a proportion of the regenerants. This revised version was published online in June 2006 with corrections to the Cover Date.     

Molecular Biology Meets the Learning Sciences: Visualizations in Education and Outreach

Scientific visualizations (illustrations, three-dimensional models, animations, simulations, etc.) play an essential role in biology education, particularly when it comes to communicating phenomena occurring at the submicroscopic levels, beyond the level of unaided observation and without comparable counterparts at the macroscopic level. Students struggle with understanding the sizes of cells, molecules, and atoms in relation to one another as well as differentiating between the various time scales within which each of these levels is functioning. Visualizations can be powerful tools of intuition, playing a critical role in transforming the way students think about the scientific realm. However, a greater understanding of how the design features and affordances of different visualization modalities support learning is required if we are to provide pedagogically impactful experiences.     

Targeting the SASP to combat ageing: Mitochondria as possible intracellular allies?

Anti‐senescence therapies, such as drugs that specifically kill senescent cells, to stave off ageing are currently under investigation. While these interventions show promise, their potential pitfalls are discussed herein. We have shown that the mitochondria are essential for development of senescence and many of the associated phenotypes, including the often detrimental senescence‐associated secretory phenotype (SASP). Here, we disentangle many ways in which the mitochondria may influence senescence and development of the SASP and focus on possible pathways that could be exploited for future generation of anti‐senescence therapies with a clear aim; to specifically eliminate the problematic features of senescent cells, while maintaining their beneficial characteristics.     

Ramet Demography of a Clonal Invader, <Emphasis Type="Italic">Arundo donax</Emphasis> (Poaceae), in Southern California

Arundo donax L. is a rhizomatous perennial, asexually reproducing species that has invaded riparian habitats throughout Mediterranean climate zones. This research evaluated ramet demography of A. donax in two California riparian communities that differed in nitrogen availability. Quadrats were established along 100 m transects at each site and oriented across the advancing fronts of established populations. Morphology and phenology were assessed monthly over 1 year for calculation of demographic parameters and rhizomes were excavated and mapped at the end of the experiment. A. donax exhibited seasonal patterns of recruitment but no dormancy at the high nitrogen site, while at the low nitrogen site no recruitment occurred in the winter and maximum recruitment was delayed by a month relative to the high nitrogen site. Spread of A. donax was delayed until spring and lower overall in the low nitrogen site compared to the high nitrogen site, where lower initial density, greater production of shoots, and higher linear and areal addition indicated that this population was spreading more rapidly. Temperature and precipitation influenced seasonality and amount of recruitment of A. donax in this study. Several recently established, immature clumps were found in gaps at the low nitrogen site, likely due to flood-mediated dispersal of propagules. Recruitment in these clumps occurred from shoot buds, in contrast to the mature populations that reproduced from rhizome buds. Ecologically based management strategies for A. donax and other exotic species should account for differences such as those described here and be tailored to local conditions where the species occurs.     

Assortative mating by multiple ornaments in northern cardinals (Cardinalis cardinalis)

In positive assortative mating, individuals of similar phenotypemate together more frequently than expected by chance. Assortativemating by a variety of qualities, including ornamentation, iswell documented in birds. Studies of assortative mating by ornamentshave focused on single, highly conspicuous ornaments, but manyspecies of birds possess multiple ornaments in both sexes. Wecompared ornament expressions between mates of northern cardinals(Cardinalis cardinalis) to determine if assortative mating occurredby one or more of the four ornaments displayed by both sexes.All cardinals possess tall head crests and red-orange bills.In addition, males have black face masks and entirely red bodyplumage, whereas females have blackish face masks and red underwingcoverts. We predicted that cardinals mate assortatively by plumagecolor because red plumage expression has been shown to indicatequality in both sexes. We found that cardinals mate assortativelyby plumage and bill color, the two ornaments colored by carotenoidpigments, but not by mask expression or crest length. Whetherthis mating pattern arises by mutual mate choice or intrasexualselection is not known.     

Adapt,move or die – how will tropical coral reef fishes cope with ocean warming?

Previous studies hailed thermal tolerance and the capacity for organisms to acclimate and adapt as the primary pathways for species survival under climate change. Here we challenge this theory. Over the past decade, more than 365 tropical stenothermal fish species have been documented moving poleward, away from ocean warming hotspots where temperatures 2–3 °C above long‐term annual means can compromise critical physiological processes. We examined the capacity of a model species – a thermally sensitive coral reef fish, Chromis viridis (Pomacentridae) – to use preference behaviour to regulate its body temperature. Movement could potentially circumvent the physiological stress response associated with elevated temperatures and may be a strategy relied upon before genetic adaptation can be effectuated. Individuals were maintained at one of six temperatures (23, 25, 27, 29, 31 and 33 °C) for at least 6 weeks. We compared the relative importance of acclimation temperature to changes in upper critical thermal limits, aerobic metabolic scope and thermal preference. While acclimation temperature positively affected the upper critical thermal limit, neither aerobic metabolic scope nor thermal preference exhibited such plasticity. Importantly, when given the choice to stay in a habitat reflecting their acclimation temperatures or relocate, fish acclimated to end‐of‐century predicted temperatures (i.e. 31 or 33 °C) preferentially sought out cooler temperatures, those equivalent to long‐term summer averages in their natural habitats (~29 °C). This was also the temperature providing the greatest aerobic metabolic scope and body condition across all treatments. Consequently, acclimation can confer plasticity in some performance traits, but may be an unreliable indicator of the ultimate survival and distribution of mobile stenothermal species under global warming. Conversely, thermal preference can arise long before, and remain long after, the harmful effects of elevated ocean temperatures take hold and may be the primary driver of the escalating poleward migration of species.