Enhancing tree belt productivity through capture of short‐slope runoff water

A selection of multi‐stemmed, drought‐tolerant mallee eucalypts, planted in belt form and integrated with crops in dryland agricultural areas of Australia, may be able to produce biomass as a commercially attractive feedstock for biofuel production. This study aimed to determine if small (40–50 cm high) bunds along mallee belts could trap otherwise underutilized surface water runoff within paddocks, thereby increasing water available to the mallee trees and their growth rates. An experiment was established in 5 year‐old Eucalyptus polybractea (RT Baker) mallee belts near the town of Narrogin in the central wheatbelt area of Western Australia. Bunds led to significant (12%) increases in biomass accumulation after about 2 years and 35% increases at around 3 years. Bunds also led to significant increases in predawn leaf water potential and significant decreases in soil water deficit within 12 months, which persisted for the remainder of the 39 month trial. We suggest that the increase in biomass accumulation was largely due to increased water availability, but that increased nutrient supply from run‐on and trapping of organic residues may have also had some effect on bunded plots, despite our attempts to mitigate this effect by experimentally adding nutrients to all treatments. Results show that installing bunds along mallee belts would be a cost‐effective investment at sites where within‐paddock runoff is likely (i.e. gently sloping and with a loamy sand or heavier soil texture). Installation costs should be offset by improved biomass production within a few years and ongoing improvements in growth over the long term.     

Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology

Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction‐site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare‐cutting restriction enzymes and strict size selection of the library allowing sequencing of a relatively small number of genomic fragments with high sequencing depth. We applied this approach to a common freshwater fish species, the Eurasian perch (Perca fluviatilis L.), and generated over 2.2 MB of novel sequence data consisting of ~17 000 contigs, identified 1259 single nucleotide polymorphisms (SNPs). We also estimated genetic differentiation between the DNA pools from freshwater (Lake Peipus) and brackish water (the Baltic Sea) populations and identified SNPs with the strongest signal of differentiation that could be used for robust individual assignment in the future. This work represents an important step towards developing genomic resources and genetic tools for the Eurasian perch. We expect that our ddRAD sequencing protocol for semiconductor sequencing technology will be useful alternative for currently available RAD protocols.     

Generation of potent mouse monoclonal antibodies to self-proteins using T-cell epitope “tags”

Immunization of mice or rats with a "non-self" protein is a commonly used method to obtain monoclonal antibodies, and relies on the immune system''s ability to recognize the immunogen as foreign. Immunization of an antigen with 100% identity to the endogenous protein, however, will not elicit a robust immune response. To develop antibodies to mouse proteins, we focused on the potential for breaking such immune tolerance by genetically fusing two independent T-cell epitope-containing sequences (from tetanus toxin (TT) and diphtheria toxin fragment A (DTA)) to a mouse protein, mouse ST2 (mST2). Wild-type CD1 mice were immunized with three mST2 tagged proteins (Fc, TT and DTA) and the specific serum response was determined. Only in mice immunized with the T-cell epitope-containing antigens were specific mST2 serum responses detected; hybridomas generated from these mice secreted highly sequence-diverse IgGs that were capable of binding mST2 and inhibiting the interaction of mST2 with its ligand, mouse interleukin (IL)-33 (mIL-33). Of the hundreds of antibodies profiled, we identified five potent antibodies that were able to inhibit IL-33 induced IL-6 release in a mast cell assay; notably one such antibody was sufficiently potent to suppress IL-5 release and eosinophilia infiltration in an Alternaria alternata challenge mouse model of asthma. This study demonstrated, for the first time, that T-cell epitope-containing tags have the ability to break tolerance in wild-type mice to 100% conserved proteins, and it provides a compelling argument for the broader use of this approach to generate antibodies against any mouse protein or conserved ortholog.     

High resolution imaging of collagen organisation and synthesis using a versatile collagen specific probe

Collagen is the protein primarily responsible for the load-bearing properties of tissues and collagen architecture is one of the main determinants of the mechanical properties of tissues. Visualisation of changes in collagen three-dimensional structure is essential in order to improve our understanding of collagen fibril formation and remodelling, e.g. in tissue engineering experiments. A recently developed collagen probe, based on a natural collagen binding protein (CNA35) conjugated to a fluorescent dye, showed to be much more specific to collagen than existing fluorescent techniques currently used for collagen visualisation in live tissues. In this paper, imaging with this fluorescent CNA35 probe was compared to imaging with second harmonic generation (SHG) and the imaging of two- and three-dimensional collagen organisation was further developed. A range of samples (cell culture, blood vessels and engineered tissues) was imaged to illustrate the potential of this collagen probe. This images of collagen organisation showed improved detail compared to images generated with SHG, which is currently the most effective method for viewing three-dimensional collagen organisation in tissues. In conclusion, the fluorescent CNA35 probe allows easy access to high resolution imaging of collagen, ranging from very young fibrils to more mature collagen fibres. Furthermore, this probe enabled real-time visualisation of collagen synthesis in cell culture, which provides new opportunities to study collagen synthesis and remodelling.     

Time, transients and elasticity

How does life history affects the short‐term elasticities of population growth rate? We decompose short‐term elasticity as a sum of (i) the effect of the perturbation in rates on the unperturbed population structure and (ii) the effect of the original vital rates on the difference in structure between the original and the perturbed population. We provide exact analytical formulas for these components. In a population at its stable stage distribution (SSD), short‐term elasticity is determined mainly by the SSD and reproductive value. In a non‐stable population, short‐term elasticity depends also on the projection of initial structure on the SSD, equal to population momentum. Non‐stable stage structures matter most to elasticity if stages are missing that take time to fill in. We show how the demographic damping rate of the original population determines the rate at which short‐term elasticity converges to its limiting values.     

Bud banks and their role in vegetative regeneration – A literature review and proposal for simple classification and assessment

While sexual regeneration of plants after disturbance is relatively well understood, vegetative regeneration has attracted some attention only recently. Its role along environmental gradients and across biomes is poorly known and standard methods for assessment are not yet established. We review current knowledge about the role of bud banks in vegetative regeneration and the diversity of their modes of functioning. The similarities and differences between bud banks and seed banks are illustrated, focusing on dormancy, dispersability, seasonal dynamics, longevity and storage of carbohydrates. We try to formulate some principles that unify bud bank functioning across habitats and growth forms: (1) the bud banks consist of all buds which may be used for vegetative regeneration, including those formed adventitiously only after injury; (2) vertical distribution of buds reflects avoidance of disturbance; (3) seasonal changes in the bud bank make vegetative regeneration sensitive to timing of disturbance; and (4) ability to form adventitious buds provides a potential for vegetative regeneration from roots, stumps and leaves. Based on these principles, a simple classification of bud banks is presented similar to the classification of seed banks. Bud bank traits are considered in relation to severity, timing and frequency of disturbance. These include vertical distribution and seasonal fluctuations in the number of buds. Methods for quantitative assessment of bud numbers and resprouting capacity are reviewed, and a new approach based on indirect bud counts is proposed. The suggested concept of bud banks may be widely used in studies focusing on plant functional traits in relation to disturbance regimes at the levels of plant individuals, populations and communities. Its further development may incorporate adjustments for areas with non-seasonal climate and refinements for some growth forms, such as epiphytes.     

F2L, a peptide derived from heme-binding protein, inhibits formyl peptide receptor-mediated signaling

F2L is an acetylated amino-terminal peptide derived from the cleavage of the human heme-binding protein. Very recently, F2L was identified as an endogenous chemoattractant peptide acting specifically through formyl peptide receptor-like (FPRL)2. In the present study, we report that F2L stimulates chemotactic migration in human neutrophils. However, F2L inhibits formyl peptide receptor (FPR) and FPRL1 activities, resulting in the complete inhibition of intracellular calcium increases, and superoxide generation induced by N-formyl-Met-Leu-Phe, MMK-1, or Trp-Lys-Tyr-Met-Val-d-Met (WKYMVm) in human neutrophils. In terms of the inhibitory role of F2L on FPR- and FPRL-mediated signaling, we found that F2L competitively inhibits the binding of (125)I-WKYMVm to its specific receptors, FPR and FPRL1. F2L is the first endogenous molecule that inhibits FPR- and FPRL1-mediated signaling, and is expected to be useful in the study of FPR and FPRL1 signaling and in the development of drugs to treat diseases involving the FPR family of receptors.