Detecting early-warning signals for influenza A pandemic based on protein dynamical network biomarkers

The outbreak of influenza A comes from a relatively stable state is a critical phenomenon on epidemic. In this paper, influenza A varying from different states is studied in the method of dynamical network biomarkers (DNB). Through studying DNB of influenza A virus protein, we can detect the warning signals of outbreak for influenza A and obtain a composite index. The composite index varies along with the state of pandemic influenza, which gives a clue showing the turn point of outbreak. The low value (<1) steady state of the composite index means influenza A is normally in the relatively steady stage. Meanwhile, if the composite index of a certain year increases by more than 0.8 relative to the previous year and it is less than 1 and it increases sharply and reaches a peak being larger than 1 in next year, it means the year is normal in the critical state before outbreak and the next year is normally in the outbreak state. Therefore, we can predict the outbreak of influenza A and identify the critical state before influenza A outbreak or outbreak state by observing the variation of index value.     

Robustness of early warning signals for catastrophic and non‐catastrophic transitions

Early warning signals (EWS) are statistical indicators that a rapid regime shift may be forthcoming. Their development has given ecologists hope of predicting rapid regime shifts before they occur. Accurate predictions, however, rely on the signals being appropriate to the system in question. Most of the EWS commonly applied in ecology have been studied in the context of one specific type of regime shift (the type brought on by a saddle‐node bifurcation, at which one stable equilibrium point collides with an unstable equilibrium and disappears) under one particular perturbation scheme (temporally uncorrelated noise that perturbs the net population growth rate in a density independent way). Whether and when these EWS can be applied to other ecological situations remains relatively unknown, and certainly underappreciated. We study a range of models with different types of dynamical transitions (including rapid regime shifts) and several perturbation schemes (density‐dependent uncorrelated or temporally‐correlated noise) and test the ability of EWS to warn of an approaching transition. We also test the sensitivity of our results to the amount of available pre‐transition data and various decisions that must be made in the analysis (i.e. the rolling window size and smoothing bandwidth used to compute the EWS). We find that EWS generally work well to signal an impending saddle‐node bifurcation, regardless of the autocorrelation or intensity of the noise. However, EWS do not reliably appear as expected for other types of transition. EWS were often very sensitive to the length of the pre‐transition time series analyzed, and usually less sensitive to other decisions. We conclude that the EWS perform well for saddle‐node bifurcation in a range of noise environments, but different methods should be used to predict other types of regime shifts. As a consequence, knowledge of the mechanism behind a possible regime shift is needed before EWS can be used to predict it.     

Identification of functional lncRNAs in atrial fibrillation by integrative analysis of the lncRNA-mRNA network based on competing endogenous RNAs hypothesis

A mounting body of evidence has suggested that long noncoding RNAs (lncRNAs) play critical roles in human diseases by acting as competing endogenous RNAs (ceRNAs). However, the functions and ceRNA mechanisms of lncRNAs in atrial fibrillation (AF) remain to date unclear. In this study, we constructed an AF-related lncRNA-mRNA network (AFLMN) based on ceRNA theory, by integrating probe reannotation pipeline and microRNA (miRNA)-target regulatory interactions. Two lncRNAs with central topological properties in the AFLMN were first obtained. By using bidirectional hierarchical clustering, we identified two modules containing four lncRNAs, which were significantly enriched in many known pathways of AF. To elucidate the ceRNA interactions in certain disease or normal condition, the dysregulated lncRNA-mRNA crosstalks in AF were further analyzed, and six hub lncRNAs were obtained from the network. Furthermore, random walk analysis of the AFLMN suggested that lncRNA RP11-296O14.3 may function importantly in the pathological process of AF. All these eight lncRNAs that were identified from previous steps (RP11-363E7.4, GAS5, RP11-410L14.2, HAGLR, RP11-421L21.3, RP11-111K18.2, HOTAIRM1, and RP11-296O14.3) exhibited a strong diagnostic power for AF. The results of our study provide new insights into the functional roles and regulatory mechanisms of lncRNAs in AF, and facilitate the discovery of novel diagnostic biomarkers or therapeutic targets.     

P‐glycoprotein (ABCB1) inhibited network of mitochondrion transport along microtubule and BMP signal‐induced cell shape in chimpanzee left cerebrum by systems‐theoretical analysis

We constructed the significant low‐expression P‐glycoprotein (ABCB1) inhibited transport and signal network in chimpanzee compared with high‐expression (fold change ≥2) the human left cerebrum in GEO data set, by using integration of gene regulatory activated and inhibited network inference method with gene ontology (GO) analysis. Our result showed that ABCB1 transport and signal upstream network RAB2A inhibited ABCB1, and downstream ABCB1‐inhibited SMAD1_2, NCK2, SLC25A46, GDF10, RASGRP1, EGFR, LRPPRC, RASSF2, RASA4, CA2, CBLB, UBR5, SLC25A16, ITGB3BP, DDIT4, PDPN, RAB2A in chimpanzee left cerebrum. We obtained that the different biological processes of ABCB1 inhibited transport and signal network repressed carbon dioxide transport, ER to Golgi vesicle‐mediated transport, folic acid transport, mitochondrion transport along microtubule, water transport, BMP signaling pathway, Ras protein signal transduction, transforming growth factor beta receptor signaling pathway in chimpanzee compared with the inhibited network of the human left cerebrum, as a result of inducing inhibition of mitochondrion transport along microtubule and BMP signal‐induced cell shape in chimpanzee left cerebrum. Our hypothesis was verified by the same and different biological processes of ABCB1 inhibited transport and signal network of chimpanzee compared with the corresponding activated network of chimpanzee and the human left cerebrum, respectively. Copyright © 2012 John Wiley & Sons, Ltd.     

Cybernetic models based on lumped elementary modes accurately predict strain‐specific metabolic function

In a recent article, Song and Ramkrishna (Song and Ramkrishna [2010]. Biotechnol Bioeng 106(2):271–284) proposed a lumped hybrid cybernetic model (L‐HCM) towards extracting maximum information about metabolic function from a minimum of data. This approach views the total uptake flux as distributed among lumped elementary modes (L‐EMs) so as to maximize a prescribed metabolic objective such as growth or uptake rate. L‐EM is computed as a weighted average of EMs where the weights are related to the yields of vital products (i.e., biomass and ATP). In this article, we further enhance the predictive power of L‐HCMs through modifications in lumping weights with additional parameters that can be tuned with data viewed to be critical. The resulting model is able to make predictions of diverse metabolic behaviors varying greatly with strain types as evidenced from case studies of anaerobic growth of various Escherichia coli strains. Incorporation of the new lumping formula into L‐HCM remarkably improves model predictions with a few critical data, thus presenting L‐HCM as a dynamic tool as being not only qualitatively correct but also quantitatively accurate. Biotechnol. Bioeng. 2011; 108:127–140. © 2010 Wiley Periodicals, Inc.     

Impact of cultivation conditions on N‐glycosylation of influenza virus a hemagglutinin produced in MDCK cell culture

Manufacturers worldwide produce influenza vaccines in different host systems. So far, either fertilized chicken eggs or mammalian cell lines are used. In all these vaccines, hemagglutinin (HA) and neuraminidase are the major components. Both are highly abundant glycoproteins in the viral envelope, and particularly HA is able to induce a strong and protective immune response. The quality characteristics of glycoproteins, such as specific activity, antigenicity, immunogenicity, binding avidity, and receptor‐binding specificity can strongly depend on changes or differences in their glycosylation pattern (potential N‐glycosylation occupancy as well as glycan composition). In this study, capillary gel electrophoresis with laser‐induced fluorescence detection (CGE‐LIF) based glycoanalysis (N‐glycan fingerprinting) was used to determine the impact of cultivation conditions on the HA N‐glycosylation pattern of Madin–Darby canine kidney (MDCK) cell‐derived influenza virus A PR/8/34 (H1N1). We found that adaptation of adherent cells to serum‐free growth has only a minor impact on the HA N‐glycosylation pattern. Only relative abundances of N‐glycan structures are affected. In contrast, host cell adaptation to serum‐free suspension growth resulted in significant changes in the HA N‐glycosylation pattern regarding the presence of specific N‐glycans as well as their abundance. Further controls such as different suppliers for influenza virus A PR/8/34 (H1N1) seed strains, different cultivation scales and vessels in standard or high cell density mode, different virus production media varying in either composition or trypsin activity, different temperatures during virus replication and finally, the impact of β‐propiolactone inactivation resulted—at best—only in minor changes in the relative N‐glycan structure abundances of the HA N‐glycosylation pattern. Surprisingly, these results demonstrate a rather stable HA N‐glycosylation pattern despite various (significant) changes in upstream processing. Only the adaptation of the production host cell line to serum‐free suspension growth significantly influenced HA N‐glycosylation regarding both, the type of attached glycan structures as well as their abundances. Biotechnol. Bioeng. 2013; 110: 1691–1703. © 2013 Wiley Periodicals, Inc.     

Identifying Stakeholders’ Views on the Eco‐efficiency Assessment of a Municipal Solid Waste Management System

Life cycle assessment (LCA) is one of the most popular methods of technical‐environmental assessment for informing environmental policies, as, for instance, in municipal solid waste (MSW) management. Because MSW management involves many stakeholders with possibly conflicting interests, the implementation of an LCA‐based policy can, however, be blocked or delayed. A stakeholder assessment of future scenarios helps identify conflicting interests and anticipate barriers of sustainable MSW management systems. This article presents such an approach for Swiss waste glass‐packaging disposal, currently undergoing a policy review. In an online survey, stakeholders (N = 85) were asked to assess disposal scenarios showing different LCA‐based eco‐efficiencies with respect to their desirability and probability of occurrence. Scenarios with higher eco‐efficiency than the current system are more desirable and considered more probable than those with lower eco‐efficiency. A combination of inland recycling and downcycling to foam glass (insulation material) in Switzerland is desired by all stakeholders and is more eco‐efficient than the current system. In contrast, institutions of MSW management, such as national and regional environmental protection agencies, judge a scenario in which nearly all cullet would be recycled in the only Swiss glass‐packaging factory as more desirable than supply and demand stakeholders of waste glass‐packaging. Such a scenario involves a monopsony rejected by many municipalities and scrap traders. Such an assessment procedure can provide vital information guiding the formulation of environmental policies.     

Direct competitive chemiluminescence immunoassays based on gold‐coated magnetic particles for detection of chloramphenicol

Direct competitive chemiluminescence immunoassays (CLIA) based on gold‐coated magnetic nanospheres (Au‐MNPs) were developed for rapid analysis of chloramphenicol (CAP). The Au‐MNPs were modified with carboxyl groups and amino groups by 11‐mercaptoundecanoic acid (MUA) and cysteamine respectively, and then were respectively conjugated with CAP base and CAP succinate via an activating reaction using 1‐ethyl‐3‐(3‐dimethylaminopropyl)carbodiimide hydrochloride (EDC) and N‐hydroxysuccinimide (NHS). NSP‐DMAE‐NHS, a new and effective luminescence reagent, was employed to label anti‐CAP antibody (mAb) as a tracer in direct CLIA for CAP detection using a ‘homemade’ luminescent measurement system that was set up with a photomultiplier tube (PMT) and a photon counting unit linked to a computer. The sensitivities and limits of detection (LODs) of the two methods were obtained and compared according to the inhibition curves. The 50% inhibition concentration (IC₅₀) values of the two methods were about 0.044 ng/mL and 0.072 ng/mL respectively and LODs were approximately 0.001 ng/mL and 0.006 ng/mL respectively. To our knowledge, they were much more sensitive than any traditional enzyme‐linked immunosorbent assay (ELISA) ever reported. Moreover, the new luminescence reagent NSP‐DMAE‐NHS is much more sensitive and stable than luminol and its derivatives, contributing to the sensitivity enhancement. Copyright © 2015 John Wiley & Sons, Ltd.     

Impact of supramolecular interactions of dextran‐β‐cyclodextrin polymers on invertase activity in freeze‐dried systems

β‐Cyclodextrin (β‐CD)‐grafted dextrans with spacer arms of different length were employed to evaluate the impact of supramolecular interactions on invertase activity. The modified dextrans were used as single additives or combined with trehalose in freeze‐dried formulations containing invertase. Enzyme activity conservation was analyzed after freeze‐drying and thermal treatment. The change of glass transition temperature (T_g) was also evaluated and related to effective interactions. Outstanding differences on enzyme stability were mainly related to the effect of the spacer arm length on polymer–enzyme interactions, since both the degree of substitution and the molecular weight were similar for the two polymers. This change of effective interactions was also manifested in the pronounced reduction of T_g values, and were related to the chemical modification of the backbone during oxidation, and to the attachment of the β‐CD units with spacer arms of different length on dextran. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:791–798, 2015     

‘Turn‐off’ fluorescence strategy for determination of hexavalent chromium ions based on copper nanoclusters

Cu nanoclusters (CuNCs) capped by tannic acid (TA) (CuNCs@TA) can be used as a highly sensitive fluorescent probe for Cr(VI) detection. Therefore, a fluorescence detection method for Cr(VI) can be established according to the fluorescence quenching of CuNCs@TA that is caused immediately after the addition of Cr(VI). The fluorescence quenching efficiency of CuNCs@TA was linearly correlated with Cr(VI) concentration within the range 0.03–60 μM, and the detection limit for Cr(VI) was 5 nM. This method was demonstrated to be suitable for detecting Cr(VI) in actual water samples. We found that sodium thiosulfate (ST) can redox with Cr(VI) and therefore restore the fluorescence of CuNCs@TA. The mechanism of CuNCs@TA fluorescence quenching and enhancement by Cr(VI) and ST was investigated in detail. The ‘turn‐on’ fluorescent sensor is of practical significance and has broad application prospects.     

Detection of membrane protein–protein interaction in planta based on dual‐intein‐coupled tripartite split‐GFP association

Despite the great interest in identifying protein–protein interactions (PPIs) in biological systems, only a few attempts have been made at large‐scale PPI screening in planta. Unlike biochemical assays, bimolecular fluorescence complementation allows visualization of transient and weak PPIs in vivo at subcellular resolution. However, when the non‐fluorescent fragments are highly expressed, spontaneous and irreversible self‐assembly of the split halves can easily generate false positives. The recently developed tripartite split‐GFP system was shown to be a reliable PPI reporter in mammalian and yeast cells. In this study, we adapted this methodology, in combination with the β‐estradiol‐inducible expression cassette, for the detection of membrane PPIs in planta. Using a transient expression assay by agroinfiltration of Nicotiana benthamiana leaves, we demonstrate the utility of the tripartite split‐GFP association in plant cells and affirm that the tripartite split‐GFP system yields no spurious background signal even with abundant fusion proteins readily accessible to the compartments of interaction. By validating a few of the Arabidopsis PPIs, including the membrane PPIs implicated in phosphate homeostasis, we proved the fidelity of this assay for detection of PPIs in various cellular compartments in planta. Moreover, the technique combining the tripartite split‐GFP association and dual‐intein‐mediated cleavage of polyprotein precursor is feasible in stably transformed Arabidopsis plants. Our results provide a proof‐of‐concept implementation of the tripartite split‐GFP system as a potential tool for membrane PPI screens in planta.     

A mechanistic theory of personality‐dependent movement behaviour based on dynamic energy budgets

Consistent between‐individual differences in movement are widely recognised across taxa. In addition, foraging plasticity at the within‐individual level suggests a behavioural dependency on the internal energy demand. Because behaviour co‐varies with fast‐slow life history (LH) strategies in an adaptive context, as theoretically predicted by the pace‐of‐life syndrome hypothesis, mass/energy fluxes should link behaviour and its plasticity with physiology at both between‐ and within‐individual levels. However, a mechanistic framework driving these links in a fluctuating ecological context is lacking. Focusing on home range behaviour, we propose a novel behavioural‐bioenergetics theoretical model to address such complexities at the individual level based on energy balance. We propose explicit mechanistic links between behaviour, physiology/metabolism and LH by merging two well‐founded theories, the movement ecology paradigm and the dynamic energetic budget theory. Overall, our behavioural‐bioenergetics model integrates the mechanisms explaining how (1) behavioural between‐ and within‐individual variabilities connect with internal state variable dynamics, (2) physiology and behaviour are explicitly interconnected by mass/energy fluxes, and (3) different LHs may arise from both behavioural and physiological variabilities in a given ecological context. Our novel theoretical model reveals encouraging opportunities for empiricists and theoreticians to delve into the eco‐evolutionary processes that favour or hinder the development of between‐individual differences in behaviour and the evolution of personality‐dependent movement syndromes.     

AFM‐ and NSOM‐based force spectroscopy and distribution analysis of CD69 molecules on human CD4+ T cell membrane

Although CD69 is well known as an early T cell‐activation marker, the possibility that CD69 are distributed as nano‐structures on membrane for immune regulation during T cell activation has not been tested. In this study, nanoscale features of CD69 expression on activated T cells were determined using the atomic force microscopy (AFM) topographic and force‐binding nanotechnology as well as near‐field scanning optical microscopy (NSOM)‐/fluorescence quantum dot (QD)‐based nanosacle imaging. Unstimulated CD4⁺ T cells showed neglectable numbers of membrane CD69 spots binding to the CD69 Ab‐functinalized AFM tip, and no detectable QD‐bound CD69 as examined by NSOM/QD‐based imaging. In contrast, Phytohemagglutinin (PHA)‐activated CD4⁺ T cells expressed CD69, and displayed many force‐binding spots binding to the CD69 Ab‐functionalized AFM tip on about 45% of cell membrane, with mean binding‐rupture forces 276 ± 71 pN. Most CD69 molecules appeared to be expressed as 100–200 nm nanoclusters on the membrane of PHA‐activated CD4⁺ T cells. Meanwhile, NSOM/QD‐based nanoscale imaging showed that CD69 were non‐uniformly distributed as 80–200 nm nanoclusters on cell‐membrane of PHA‐activated CD4⁺ T cells. This study represents the first demonstration of the nano‐biology of CD69 expression during T cell activation. Copyright © 2009 John Wiley & Sons, Ltd.     

Dynamic imaging and quantification of subcellular motion with eigen‐decomposition optical coherence tomography‐based variance analysis

The dynamic properties of subcellular organism are important biomarkers of the health. Imaging subcellular level dynamics provides effective solutions for evaluating cell metabolism and testing the responses of cells to pathogens and drugs in pharmaceutical engineering. In this paper, we demonstrate an innovative approach to contrast the subcellular motion by using eigen decomposition (ED)‐based variance analysis of time‐dependent complex optical coherence tomography signals. This method reveals a superior advantage of contrast to noise ratio when compared with the approach that employs intensity decorrelation. Furthermore, the eigen values derived from ED processing are calculated and applied to assess the power ratios of complex signal invariance that decreases exponentially along time dimension. The validation experiments are performed on the patterned samples of yeast powder mixed with gelatin/TiO2 water solution. Additionally, the proposed method is used to image mouse cerebral cortex in normal and pathological conditions, suggesting the practicality of variance power mapping in analyzing cortical neural activities. The technique promises efficient measurement of subcellular motions with high sensitivity and high throughput for in vivo and in situ applications.     

Evaluation of Modeling Approaches to Determine End‐of‐Life Flows Associated with Buildings: A Viennese Case Study on Wood and Contaminants

Dynamic material flow analysis enables the forecasting of secondary raw material potential for waste volumes in future periods, by assessing past, present, and future stocks and flows of materials in the anthroposphere. Analyses of waste streams of buildings stocks are uncertain with respect to data and model structure. Wood construction in Viennese buildings serve as a case study to compare different modeling approaches for determining end‐of‐life (EoL) wood and corresponding contaminant flows (lead, chlorine, and polycyclic aromatic hydrocarbons). A delayed input and a leaching stock modeling approach are used to determine wood stocks and flows from 1950 until 2100. Cross‐checking with independent estimates and sensitivity analyses are used to evaluate the results’ plausibility. In the situation of the given data in the present case study, the delay approach is a better choice for historical observations of EoL wood and for analyses at a substance level. It has some major drawbacks for future predictions at the goods level, though, as the durability of a large number of historical buildings with considerably higher wood content is not reflected in the model. The wood content parameter differs strongly for the building periods and has therefore the highest influence on the results. Based on this knowledge, general recommendations can be derived for analyses on waste flows of buildings at a goods and substance level.