Construction of a large phage-displayed human antibody domain library with a scaffold based on a newly identified highly soluble, stable heavy chain variable domain

Currently, almost all U.S. Food and Drug Administration-approved therapeutic antibodies and the vast majority of those in clinical trials are full-size antibodies mostly in an immunoglobulin G1 format of about 150 kDa in size. Two fundamental problems for such large molecules are their poor penetration into tissues (e.g., solid tumors) and poor or absent binding to regions on the surface of some molecules [e.g., on the human immunodeficiency virus envelope glycoprotein (Env)] that are accessible by molecules of smaller size. We have identified a phage-displayed heavy chain-only antibody by panning of a large (size, ∼ 1.5 × 10¹⁰) human naive Fab (antigen-binding fragment) library against an Env and found that the heavy chain variable domain (V_H) of this antibody, designated as m0, was independently folded, stable, highly soluble, monomeric, and expressed at high levels in bacteria. m0 was used as a scaffold to construct a large (size, ∼ 2.5 × 10¹⁰), highly diversified phage-displayed human V_H library by grafting naturally occurring complementarity-determining regions (CDRs) 2 and 3 of heavy chains from five human antibody Fab libraries and by randomly mutating four putative solvent-accessible residues in CDR1 to A, D, S, or Y. The sequence diversity of all CDRs was determined from 143 randomly selected clones. Most of these V_Hs were with different CDR2 origins (six of seven groups of V_H germlines) or CDR3 lengths (ranging from 7 to 24 residues) and could be purified directly from the soluble fraction of the Escherichia coli periplasm. The quality of the library was also validated by successful selection of high-affinity V_Hs against viral and cancer-related antigens; all selected V_Hs were monomeric, easily expressed, and purified with high solubility and yield. This library could be a valuable source of antibodies targeting size-restricted epitopes and antigens in obstructed locations where efficient penetration could be critical for successful treatment.     

Applying life-history strategies for freshwater macroinvertebrates to lentic waters

• 1 Effective environmental management requires a sound understanding of the causal mechanisms underlying the relationship of species with their environment. Mechanistic explanations linking species and environment are ultimately based on species traits. Many tools for ecological assessment and biomonitoring lack such explanations. Elsewhere, we have defined life‐history strategies, based on the interrelations between species traits and their functional implications.
• 2 This study tests the hypothesis that life‐history strategies represent different solutions to particular ecological problems, thus connecting species and their environment through species traits. Data on aquatic macroinvertebrates in a variety of waterbodies were analysed in terms of life‐history strategies. These waterbodies differed in environmental conditions and macroinvertebrate assemblages. Solutions to the ecological problems present in each type of water body were expected to be reflected in the abundance of (species exhibiting) different life‐history strategies.
• 3 Results show clear differences in strategy composition between the different water types, which could be related to the prevailing environmental conditions through mechanistic explanations. For example, species with a long period of juvenile development and a synchronized emergence of short‐lived adults were most dominant in large mesotrophic waterbodies with stable and predictable environmental conditions. In contrast, species that have a rapid development and spread successive reproduction attempts over a longer time period were most abundant in waterbodies with fluctuating and less predictable environmental conditions.
• 4 Differences in strategy composition provide insight into the prevailing environmental conditions related to temporal predictability, and habitat favourability, from the perspective of the species themselves. By reducing diverse species assemblages to a small number of strategies, representing easily interpretable relationships, this approach may be useful in environmental quality assessment programmes, including those required by the European Water Framework Directive. Based on mechanistic explanations, life‐history strategies may generate testable predictions and guide future research. Further research may focus on expanding life‐history strategies to include other species groups and ecosystems.

     

Olive oil history,production and by-product management

In this review paper, the history of the olive tree and the development of the main olive oil extraction systems employed in the past are presented. Furthermore, the management techniques employed from antiquity until today for the treatment of olive mill wastewater (OMW), which constitutes the most important by-product of olive oil production, are addressed and compared. Reference is also made to global olive oil production, the environmental impacts of the uncontrolled disposal of OMW, and to the legal framework concerning its management in the main olive oil producing countries. Other by-products of olive processing are also discussed.     

Review of genes in development: re-reading the molecular paradigm

Genes in Development is a collection of 13 stimulating essays on "post genomic" approaches to the concept of the gene. At the risk of caricaturing some complex balances, the contributors tend to be skeptical about genetic determinism, the central dogma of molecular biology, reductionism, genes as programs and the concept of the gene as a DNA sequence. They tend to like emergent properties, complexity theory, the parity thesis for developmental resources, developmental systems theory, and membranes. But within this broad weltanschauung the essays in Genes in Development vary widely in their interests and emphases––from the history of twentieth century genetics to the social and ethical issues raised by contemporary genetics––which makes for an attractive and valuable collection.     

Comparison of metabolite production capability indices generated by network analysis methods

A framework of constraint-based reconstruction and analysis (COBRA) is used for modeling large-scale metabolic networks. In COBRA, extreme pathway and optimization analyses are commonly used to study the properties of networks. While the results of both methods are completely consistent, extreme pathway analysis is considered to be better because of its wider representational ability. In this study, we assessed these two methods by computational knockout experiments. We examined a simple pathway model and found that the extreme pathway method led to misguided conclusions in specific cases, while optimization analysis calculated the correct knockout effects. We also investigated the Escherichia coli metabolic pathway model, and found that these methods result in inconsistent interpretations of the network properties. IN CONCLUSION: it has been claimed that these two methods result in the same producible metabolites, but we found a difference in individual results for a biological pathway. Our results could provide helpful guidance for when to use the methods, particularly extreme pathway analysis.     

Milestones in ecological thought — A canon for plant ecology

Abstract. Scientific progress in plant ecology is at risk of being obscured by increasing ignorance of major works in the field. The driving force seems to be the twin seductions of novelty and crowd psychology. I illustrate this tendency with three examples from plant community ecology that span the past thirty years of ecological research. I offer, as one solution, the concept of a canon: a short list of essential books that we assume all students and co‐workers have read, a short list that summarizes the wisdom of the discipline. A canon can be likened to DNA, be it in music, art, or science, as it carries forward through time the key ideas that have worked in the past. Without a canon, there is no memory of past achievement, no context for appreciating current work, and no way of judging the quality of newer productions. I suggest 20 essential books (the short canon), and 22 complementary readings, for a total of 42 books needed in any young professional's library on plant ecology.     

Geomorphology and fish assemblages in a Piedmont river basin, U.S.A.

1. We investigated linkages between fishes and fluvial geomorphology in 31 wadeable streams in the Etowah River basin in northern Georgia, U.S.A. Streams were stratified into three catchment sizes of approximately 15, 50 and 100 km², and fishes and geomorphology were sampled at the reach scale (i.e. 20–40 times stream width). 2. Non‐metric multidimensional scaling (NMDS) identified 85% of the among‐site variation in fish assemblage structure and identified strong patterns in species composition across sites. Assemblages shifted from domination by centrarchids, and other pool species that spawn in fine sediments and have generalised food preferences, to darter‐cyprinid‐redhorse sucker complexes that inhabit riffles and runs, feed primarily on invertebrates, and spawn on coarser stream beds. 3. Richness and density were correlated with basin area, a measure of stream size, but species composition was best predicted (i.e. |r| between 0.60–0.82) by reach‐level geomorphic variables (stream slope, bed texture, bed mobility and tractive force) that were unrelated to stream size. Stream slope was the dominant factor controlling stream habitat. Low slope streams had smaller bed particles, more fines in riffles, lower tractive force and greater bed mobility compared with high slope streams. 4. Our results contrast with the ‘River Continuum Concept’ which argues that stream assemblages vary predictably along stream size gradients. Our findings support the ‘Process Domains Concept’, which argues that local‐scale geomorphic processes determine the stream habitat and disturbance regimes that influence stream communities.     

Selecting agri-environmental indicators for monitoring and assessment of environmental management in the example of landscape parks in Poland

The objective of this article is to assess the condition of and hazards to the natural environment in selected landscape parks in Poland with respect to the impact of agricultural management using the DPSIR method. Our proposed set of indicators, based on generally available and applicable data, shows at the local scale, in a simple way, the condition of functioning of the balance between the natural environment and agricultural management and it assesses the level of repair works in the context of the records of the environmental protection program. The highest negative impact of agricultural management in the areas studied is noticed in the soil environment as well as the contexts of biodiversity and landscape. On the other hand, the lowest influence of agricultural economy was noted in the cases of the atmosphere and hydrosphere. The results of the aggregated indicators also showed lower or higher dependencies between the coverage and the use of the area in landscape parks and the condition of particular elements of the environment and the landscape.