Trait‐divergence assembly rules have been demonstrated: Limiting similarity lives! A reply to Grime

The recent Forum contribution by Grime (2006) contrasts the MacArthur/Diamond assembly‐rule approach to studying plant communities with the study of environmental trait gradients. Both are valid and useful. In doing so, Grime declares that the assembly rules model, in which negative interactions between plants act with limiting similarity to cause local trait divergence, is “not supported by empirical study of plant communities”. This is, he says, the agony of community ecology. I show that there is now abundant evidence for assembly rules, and no agony.     

The Pressurized Porous Surface Model: An improved tool to study bacterial behavior under a wide range of environmentally relevant matric potentials

To study bacterial behavior under varying hydration conditions similar to surface soil, we have developed a system called the Pressurized Porous Surface Model (PPSM). Thin liquid films created by imposing a matric potential of − 0.4 MPa impact gene expression and colony development in Pseudomonas putida.     

Assessing water scarcity by simultaneously considering environmental flow requirements,water quantity,and water quality

Water scarcity is a widespread problem in many parts of the world. Most previous methods of water scarcity assessment only considered water quantity, and ignored water quality. In addition, the environmental flow requirement (EFR) was commonly not explicitly considered in the assessment. In this study, we developed an approach to assess water scarcity by considering both water quantity and quality, while at the same time explicitly considering EFR. We applied this quantity–quality-EFR (QQE) approach for the Huangqihai River Basin in Inner Mongolia, China. We found that to keep the river ecosystem health at a “good” level (i.e., suitable for swimming, fishing, and aquaculture), 26% of the total blue water resources should be allocated to meet the EFR. When such a “good” level is maintained, the quantity- and quality-based water scarcity indicators were 1.3 and 14.2, respectively; both were above the threshold of 1.0. The QQE water scarcity indicator thus can be expressed as 1.3(26%)|14.2, indicating that the basin was suffering from scarcity problems related to both water quantity and water quality for a given rate of EFR. The current water consumption has resulted in degradation of the basin's river ecosystems, and the EFR cannot be met in 3 months of a year. To reverse this situation, future policies should aim to reduce water use and pollution discharge, meet the EFR for maintaining healthy river ecosystems, and substantially improve pollution treatment.     

Three-dimensional perfused cell culture

Compelling evidence suggests the limitation and shortcomings of the current and well established cell culture method using multi-well plates, flasks and Petri dishes. These are particularly important when cell functions are sensitive to the local microenvironment, cell–cell and cell–extracellular matrix interactions. There is a clear need for advanced cell culture systems which mimic in vivo and more physiological conditions. This review summarises and analyses recent progress in three dimensional (3D) cell culture with perfusion as the next generation cell culture tools, while excluding engineered tissue culture where three dimensional scaffold has to be used for structural support and perfusion for overcoming mass transfer control. Apart from research activities in academic community, product development in industry is also included in this review.     

Changes in plant species richness and productivity in response to decreased nitrogen inputs in grassland in southern England

Biomass production and plant species diversity in grassland in southern England was monitored before and after a change from conventional to organic farming. Our 18-year study, part of the UK's Environmental Change Network long-term monitoring programme, showed that the cessation of artificial fertiliser use on grassland after conversion to organic farming resulted in a decrease in biomass production and an increase in plant species richness. Grassland productivity decreased immediately after fertiliser application ceased, and after two years the annual total biomass production had fallen by over 50%. In the subsequent decade, total annual grassland productivity did not change significantly, and yields reached 31–66% of the levels recorded pre-management change. Plant species richness that had remained stable during the first 5 years of our study under conventional farming, increased by 300% over the following 13 years under organic farm management. We suggest that the change in productivity is due to the altered composition of species within the plots. In the first few years after the change in farming practice, high yielding, nitrogen-loving plants were outcompeted by lower yielding grasses and forbs, and these species remained in the plots in the following years. This study shows that grassland can be converted from an environment lacking in plant species diversity to a relatively species-rich pasture within 10–15 years, simply by stopping or suspending nitrogen additions. We demonstrate that the trade-off for increasing species richness is a decrease in productivity. Grassland in the UK is often not only managed from a conservation perspective, but to also produce a profitable yield. By considering the species composition and encouraging specific beneficial species such as legumes, it may be possible to improve biomass productivity and reduce the trade-off.     

Probing binding mechanism of interleukin-6 and olokizumab: in silico design of potential lead antibodies for autoimmune and inflammatory diseases

Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated in silico to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen–antibody (Ag???Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag???Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.     

Multi-species response to rapid environmental change in a large estuary system: A biochronological approach

The sensitivity of species to environmental change is dependent on their ecological requirements (i.e. specialist v. generalist), and hence likely to be species-specific. Identifying species level variation in environmental sensitivity informs assessments of community vulnerability and assists in developing adaptive management strategies. We investigated species-specific sensitivity in fish to understand the vulnerability of differing life histories and ecological requirements to rapid environmental alteration (i.e. drought). Biochronologies of fish growth, based on increment widths in otoliths, were analysed using a mixed modelling approach. We assessed multi-decadal responses in fish growth to environmental variation in the terminal system of Australia’s largest river, for three long-lived fish species with differing life histories and ecological requirements: a freshwater specialist and two estuarine generalists. Biochronologies were between 20 and 38 years long, spanned a decade of severe drought and showed considerable inter-annual variation in growth. Precipitation influenced the growth of the obligate freshwater specialist, Macquaria ambigua ambigua. Temperature and salinity influenced the growth of the two estuarine generalists: Argyrosomus japonicus (estuarine opportunist) and Acanthopagrus butcheri (estuarine dependent), respectively. These results suggest that generalisations about how species respond to environmental change may mask species-specific responses to dependent on the constraints of their ecological requirements (i.e. specialist v. generalist). These findings also highlight the importance of considering the diversity of life history strategies that inhabit an ecosystem when developing conservation and management strategies.