Land-use intensification reduces functional redundancy and response diversity in plant communities

Ecosystem resilience depends on functional redundancy (the number of species contributing similarly to an ecosystem function) and response diversity (how functionally similar species respond differently to disturbance). Here, we explore how land-use change impacts these attributes in plant communities, using data from 18 land-use intensity gradients that represent five biomes and > 2800 species. We identify functional groups using multivariate analysis of plant traits which influence ecosystem processes. Functional redundancy is calculated as the species richness within each group, and response diversity as the multivariate within-group dispersion in response trait space, using traits that influence responses to disturbances. Meta-analysis across all datasets showed that land-use intensification significantly reduced both functional redundancy and response diversity, although specific relationships varied considerably among the different land-use gradients. These results indicate that intensified management of ecosystems for resource extraction can increase their vulnerability to future disturbances.
Ecology Letters (2010) 13: 76–86     

Combining regulated and constitutive protein expression significantly boosts protein expression by increasing productivity without affecting CHO cell growth

Chinese hamster ovary (CHO) cells are commonly used for the expression of therapeutic proteins. To increase the titer output of CHO production cultures either specific productivity (Qp), growth, or both need to be increased. Generally, Qp and growth are inversely correlated and cell lines with high Qp have slower growth and vice versa. During the cell line development (CLD) process, the faster-growing cells tend to take over the culture and represent the majority of the isolated clones post single cell cloning. In this study, combinations of regulated and constitutive expression systems were used to supertransfect targeted integration (TI) cell lines expressing the same antibody either constitutively or under-regulated expression. Clone screening with a hybrid expression system (inducible + constitutive) allowed identification and selection of higher titer clones under uninduced conditions, without a negative impact on cell growth during clone selection and expansion. Induction of the regulated promoter(s) during the production phase increased the Qp without negatively affecting growth, resulting in approximately twofold higher titers (from 3.5 to 6–7 g/L). This was also confirmed using a 2-site TI host where the gene of interest was expressed inducibly from Site 1 and constitutively from Site 2. Our findings suggest that such a hybrid expression CLD system can be used to increase production titers, providing a novel approach for expression of therapeutic proteins with high titer market demands.     

Production of acidocin B, a bacteriocin of Lactobacillus acidophilus M46 is a plasmid-encoded trait: Plasmid curing, genetic marking by in vivo plasmid integration, and gene transfer

Abstract Plasmid-curing studies suggest that acidocin B production is encoded by the 14-kb plasmid pCV461 in Lactobacillus acidophilus M46. Loss of pCV461 from the original producer strain M46 did not coincide with loss of immunity to acidocin B. Bacteriocin activity determination after SDS-PAGE showed that a substance of 2.4 kDa, absent in the culture supernatant of the mutant strain M46A2, lacking pCV461, represented acidocin B activity. In order to introduce a positive selection criterion, pCV461 was marked in vivo by the erythromycin resistance marker of pE194, present on pUC19 containing a 1.4-kb Hin dIII fragment of pCV461, after plasmid integration. Introduction of this recombinant plasmid into the mutant strain M46A2 or Lactobacillus plantarum resulted in erythromycin-resistant, acidocin B-producing transformants, showing unambiguously that acidocin B is encoded by pCV461.     

Experimental Assessment of the Effects of Environmental Factors and Longitudinal Position on Alpha and Beta Diversities of Aquatic Insects in a Neotropical Stream

We evaluated the effect of environmental factors on the abundance and genera richness of aquatic insects colonizing artificial substrates. We also assessed the relative effects of environmental factors on assemblage variation (beta diversity), and contrasted its magnitude with the variation associated with the spatial position of reaches in a Neotropical stream. Homogeneous and heterogeneous bricks were installed in seven stream reaches and removed after 60d. Substrate type and organic matter showed significant effects on abundance. For observed richness, substrate type was the only important variable. For rarefied richness, no explanatory variable was important. A NMDS ordination of bricks revealed the effect of spatial position and substrate type. A partial Redundancy Analysis (pRDA) indicated that the environmental matrix explained 12.44% of the total variation, while reach position explained 7.41%. We conclude that at local scale (reaches 430–920 m apart), environmental factors, especially substrate heterogeneity, were important in determining the alpha and beta diversities of the insect assemblage in the stream (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Morphological integration and modularity in Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae) hind wings

The morphological integration of the hind wings of the western corn rootworm Diabrotica virgifera virgifera LeConte was investigated to get a better insight of the undergone by this invasive species. Geometric morphometric methods were used to test two modularity hypotheses associated with the wing development and function (hypothesis H1: anterior/posterior or H2: distal/proximal wing parts). Both hypotheses were rejected and the results showed the integrated behavior of the hind wings of D. v. virgifera. The hypothesized modules do not represent separate units of variation, so in a similar fashion as exhibited by the model species Drosophila melanogaster, the hind wings of D. v. virgifera act as a single functional unit. The moderate covariation strength found between anterior and posterior and distal and proximal parts of the hind wing of D. v. virgifera confirms its integrated behavior. We conclude that the wing shape shows internal integration, which could enable flexibility and thus enhance flight maneuverability. This study contributes to the understanding of morphological integration and modularity on a non-model organism. Additionally, these findings lay the groundwork for future flight performance and biogeographical studies on how wing shape and size vary across the endemic and expanded/invaded range in the USA and Europe infested with D. v. virgifera.     

New Applications for Phage Integrases

Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ?C31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line.     

The Evolution of Modularity in the Mammalian Skull II: Evolutionary Consequences

Changes in patterns and magnitudes of integration may influence the ability of a species to respond to selection. Consequently, modularity has often been linked to the concept of evolvability, but their relationship has rarely been tested empirically. One possible explanation is the lack of analytical tools to compare patterns and magnitudes of integration among diverse groups that explicitly relate these aspects to the quantitative genetics framework. We apply such framework here using the multivariate response to selection equation to simulate the evolutionary behavior of several mammalian orders in terms of their flexibility, evolvability and constraints in the skull. We interpreted these simulation results in light of the integration patterns and magnitudes of the same mammalian groups, described in a companion paper. We found that larger magnitudes of integration were associated with a blur of the modules in the skull and to larger portions of the total variation explained by size variation, which in turn can exert a strong evolutionary constraint, thus decreasing the evolutionary flexibility. Conversely, lower overall magnitudes of integration were associated with distinct modules in the skull, to smaller fraction of the total variation associated with size and, consequently, to weaker constraints and more evolutionary flexibility. Flexibility and constraints are, therefore, two sides of the same coin and we found them to be quite variable among mammals. Neither the overall magnitude of morphological integration, the modularity itself, nor its consequences in terms of constraints and flexibility, were associated with absolute size of the organisms, but were strongly associated with the proportion of the total variation in skull morphology captured by size. Therefore, the history of the mammalian skull is marked by a trade-off between modularity and evolvability. Our data provide evidence that, despite the stasis in integration patterns, the plasticity in the magnitude of integration in the skull had important consequences in terms of evolutionary flexibility of the mammalian lineages.     

Genome-scale models of bacterial metabolism: reconstruction and applications

Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities.