Integrated framework of nonlinear prediction and process monitoring for complex biological processes

Bioprocesses and biosystems have nonlinear and multiple operation patterns depending on the influent loads, temperatures, the activity of microorganisms, and other factors. In this paper, an integrated framework of nonlinear modeling and process monitoring methods is developed for a complex biological process. The proposed method is based on modeling by fuzzy partial least squares (FPLS) and on process monitoring by a statistical decomposition, which is suitable for predicting and supervising a nonlinear biological process. Case studies in the bio-simulated process and industrial biological plant show that the proposed method can give superior prediction and monitoring performance in complex biological plants compared to other linear and nonlinear methods, since it can effectively capture the nonlinear causal relationship within the biosystem. This gives us the integrated framework that is able to both model and monitor the nonlinear bioprocess simultaneously.     

水生态一、二级分区技术框架

水生态功能分区是流域水环境分类、分级、分区、分期管理的基础。回顾总结国内外水生态功能分区工作的基础上,针对我国流域水生态功能一、二级分区工作,提出了一个可供参考的分区指标体系,探讨了流域尺度水生态分区技术框架的构建以及可能存在的问题。该技术框架主要由3部分内容组成:环境要素对水生态因子的驱动机制、分区指标体系和分区技术。作为技术框架的理论依据,驱动机制分析首先以水-陆生态水文耦合模型为框架对环境要素如何影响水生态系统功能进行阐述。指标体系是技术框架的基础部分,主要包括水生态因子和环境要素两大类,其中一级分区指标包括气候、水文和地貌等要素,二级分区指标包括水质、水生动植物、藻类、土壤、植被、土地利用和社会经济要素。针对一、二级水生态功能区采用"自上而下"和"自下而上"的分区方法,为技术框架付诸现实提供了保障。为正在进行的各大流域水生态功能分区工作提供一定的参考依据,同时也希望在这些具体分区工作的基础上能进一步完善本分区技术框架。     

Syntheses, structures and magnetic properties of Mn(II), Co(II) and Ni(II) metal-organic frameworks constructed from 1,3,5-benzenetricarboxylate and formate ligands

Three compounds, [(CH₃)₂NH₂][M₃(BTC)(HCOO)₄(H₂O)]·H₂O (M = Mn (1), Co (2), Ni (3), H₃BTC = 1,3,5-benzenetricarboxylic acid), were synthesized under hydrothermal conditions and were characterized by single crystal and powder X-ray diffraction, IR spectra, elemental analysis, coupled TG-MS and magnetic measurements. Compounds 1-3 are isostructural analogues and crystallize in monoclinic space group P2₁/c. Each metal ion in these compounds connects to six oxygen atoms to form a MO₆ octahedron. Six MO₆ octahedra link to each other to form a corner-shared hexameric M₆ cluster, which is linked by BTC ligands to form two-dimensional layers. The two-dimensional layers are further connected by formic ions to form a three-dimensional network with channels, where (CH₃)₂NH₂⁺ ions and water molecular are located. Magnetic measurements indicate that anti-ferromagnetic ordering occurs at low temperature for these compounds.     

Hydrothermal synthesis and characterization of a novel 3D open framework structure of mixed valence ethylenediamine-vanadium phosphate: [C2H10N2][(HVO3)(HVO2) (PO4)]

A new three-dimensional open framework structure of mixed valence ethylenediamine-vanadium phosphate [C₂H₁₀N₂][(HV^IVO₃)(HV^VO₂)(PO₄)] (1), has been synthesized under mild hydrothermal conditions and characterized by elemental analyses, IR, fluorescent spectrum, TG-DTA and single crystal X-ray diffraction. Compound 1 exhibits a novel three-dimensional (3D) vanadium phosphate anion framework composed of vanadium, phosphate, and oxygen atoms through covalent bonds, with the diprotonated ethylenediamine [NH₃CH₂CH₂NH₃]²⁺ cations residing in the channels along c-axis. The organic diprotonated ethylenediamine cations interact with the O atoms in the inorganic network through hydrogen bonds. The electrochemical behavior of 1 has also been studied in detail by cyclic voltammograms, which is very important for practical applications in electrode modification. Furthermore, the strong photoluminescence property of compound 1 is also measured at room temperature.     

The paradoxical effects of nutrient ratios and supply rates on an outbreaking insect herbivore, the Australian plague locust

1. The Australian plague locust, Chortoicetes terminifera, develops following rainfall in an environment dominated by two host plants, the annual Dactyloctenium radulans and the perennial Astrebla lappacea. This simple system provides an ideal opportunity to explore the relationship between plant quality, individual herbivore performance and population responses. 2. We compared the two grasses chemically and structurally, and the behavioural, physiological and developmental responses of locust nymphs to these diets. 3. The grasses appeared to be of similar nutritional quality in terms of their chemical composition, although they differed in their physical properties. Early instar nymphs performed equally well on both grasses. However, older nymphs consuming D. radulans developed faster, survived better and attained a higher body weight compared with those consuming A. lappacea. 4. The differences in performance by the older nymphs related to the rate and ratio of supply of carbohydrate and protein from the two grasses, with less carbohydrate being assimilated from A. lappacea than D. radulans per unit of protein assimilated. Experiments showed that these differences arose as a direct result of the physical barrier to nutrient extraction provided by cell walls and indirectly through the amount of water contained within each cell. Paradoxically, nitrogen did not limit performance in the traditional sense through shortage,but rather its relative excess in A. lappacea appeared to impede intake and assimilation of adequate carbohydrate. 5. As a consequence, we predict that the length of time D. radulans remains available following rainfall will influence plaguing dynamics, although not for the reasons previously thought. 6. The results highlight the need to consider nutrient balance and actual rates of supply (rather than simply measuring the chemical composition of the plant) when attempting to understand herbivore nutritional ecology.     

Comparison of Post‐mining Rehabilitation with Reference Ecosystems in Monsoonal Eucalypt Woodlands,Northern Australia

Rehabilitation of post‐mining lands frequently aims to create “self‐sustaining” systems. Where native vegetation is the designated post‐mining land use, it is generally assumed that rehabilitation that is similar to local native ecosystems is more likely to be sustainable. I compared landscape functionality, plant community composition, and vegetation structure in (1) reference sites representing pre‐mining native forest; (2) reference sites representing potential landscape analogues for the post‐mining landscape; and (3) a 23‐year chronosequence of post‐mining rehabilitation on the Weipa bauxite plateau, Cape York Peninsula, Australia. The trends across the post‐mining chronosequence indicate that vegetation growth is rapid in the first 5–8 years, and then slows with mean height approaching an asymptote after approximately 15 years. Landscape function indices showed a response that coincided with vegetation growth. Vegetation composition was significantly different from reference native forest. Most importantly, from the perspective of creating self‐sustaining ecosystems, the contribution of local framework species to vegetation in rehabilitation was significantly lower than in reference native forest. I discuss the results in relation to theoretical models of succession and conclude that without management intervention, differences between post‐mining rehabilitation and native forest are likely to be persistent.     

Molecular basis of recognition of human osteopontin by 23C3, a potential therapeutic antibody for treatment of rheumatoid arthritis

Osteopontin plays an important role in the development and perpetuation of rheumatoid arthritis (RA). Antibodies targeting osteopontin have shown promising therapeutic benefits against this disease. We have previously reported a novel anti-RA monoclonal antibody, namely, 23C3, and shown it capable of alleviating the symptoms of RA in a murine collagen-induced arthritis model, restoring the cytokine production profile in joint tissues, and reducing T-cell recall responses to collagen type II. We describe here the crystal structure of 23C3 in complex with its epitope peptide. Analyses of the complex structure reveal the molecular mechanism of osteopontin recognition by 23C3. The peptide folds into two tandem β-turns, and two key residues of the peptide are identified to be critical for the recognition by 23C3: TrpP43 is deeply embedded into a hydrophobic pocket formed by AlaL34, TyrL36, LeuL46, TyrL49, PheL91, and MetH102 and therefore has extensive hydrophobic interactions with 23C3, while AspP47 has a network of hydrophilic interactions with residues ArgH50, ArgH52, SerH53, and AsnH56 of the antibody. Besides the complementarity-determining region loops, the framework region L2 of 23C3 is also shown to interact with the epitope peptide, which is not common in the antibody-antigen interactions and thus could be exploited in the engineering of 23C3. These results not only provide valuable information for further improvement of 23C3 such as chimerization or humanization for its therapeutic application, but also reveal the features of this specific epitope of osteopontin that may be useful for the development of new antibody drugs against RA.     

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.