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PubMed2002

Heterogeneous nucleation of supercooled water, and the effect of an added catalyst.

The statistics of liquid-to-crystal nucleation are measured rigorously by using a recently developed automated lag-time apparatus (ALTA). A single sample, in this case a sample of pure water both with and without an (insoluble) AgI crystal, is repeatedly cooled, nucleated, and thawed. Analysis of the data, coupled with a second kind of experiment, shows that the statistics of nucleation are consistent with a first-order kinetic mechanism over a wide range of supercooling temperatures. The limitations of classical nucleation theory are exhibited. Our analysis unifies many related experiments in biology, physics, chemistry, and chemical engineering.

Catalysis↗
PubMed1991

Use of site-directed mutagenesis to enhance the epitope-shielding effect of covalent modification of proteins with polyethylene glycol.

Modification by covalent attachment of polyethylene glycol (PEG) can reduce the immunogenicity and prolong the circulating life of proteins, but the utility of this approach for any protein is restricted by the number and distribution of PEG attachment sites (e.g., epsilon-amino groups of lysine residues). We have developed a strategy for introducing additional sites for PEG attachment by using site-directed mutagenesis to selectively replace arginine with lysine codons and tested it with purine nucleoside phosphorylase (PNP) from Escherichia coli, an extremely stable but immunogenic enzyme, that could potentially be used to treat an inherited deficiency of PNP. A triple mutant, RK3, possessing three Arg----Lys substitutions was constructed that increased the number of lysines per PNP subunit from 14 to 17, providing an additional 18 potential PEG attachment sites per hexameric enzyme molecule. The wild-type and RK3 enzymes had similar catalytic activity, antigenicity, and immunogenicity. After PEG modification, both enzymes retained catalytic activity, the plasma half-life of both enzymes in mice increased from approximately 4 hr to 4 days, and the binding of both enzymes by antisera raised against each unmodified enzyme was markedly diminished. However, antibody raised against wild-type PEG-PNP did not bind the PEG-RK3 enzyme. PEG-RK3 PNP was also substantially less immunogenic than wild-type PEG-PNP. Accelerated antibody-mediated clearance of PEG-PNP occurred in 2 of 12 mice treated with PEG-RK3 PNP, compared with 10 of 16 mice treated with the modified wild-type enzyme. This combined use of directed mutagenesis and PEG modification is aimed at permitting the widest choice of proteins, including products of genetic and chemical "engineering," to be used for therapy of inherited and acquired disorders.

Amino Acid Sequence↗
PubMed2007

Neuronal apoptotic signaling pathways probed and intervened by synthetically and modularly modified (SMM) chemokines.

As the main coreceptors for human immunodeficiency virus type 1 (HIV-1) entry, CXCR4 and CCR5 play important roles in HIV-associated dementia (HAD). HIV-1 glycoprotein gp120 contributes to HAD by causing neuronal damage and death, either directly by triggering apoptotic pathways or indirectly by stimulating glial cells to release neurotoxins. Here, to understand the mechanism of CXCR4 or CCR5 signaling in neuronal apoptosis associated with HAD, we have applied synthetically and modularly modified (SMM)-chemokine analogs derived from natural stromal cell-derived factor-1alpha or viral macrophage inflammatory protein-II as chemical probes of the mechanism(s) whereby these SMM-chemokines prevent or promote neuronal apoptosis. We show that inherently neurotoxic natural ligands of CXCR4, such as stromal cell-derived factor-1alpha or viral macrophage inflammatory protein-II, can be modified to protect neurons from apoptosis induced by CXCR4-preferring gp120(IIIB), and that the inhibition of CCR5 by antagonist SMM-chemokines, unlike neuroprotective CCR5 natural ligands, leads to neurotoxicity by activating a p38 mitogen-activated protein kinase (MAPK)-dependent pathway. Furthermore, we discover distinct signaling pathways activated by different chemokine ligands that are either natural agonists or synthetic antagonists, thus demonstrating a chemical biology strategy of using chemically engineered inhibitors of chemokine receptors to study the signaling mechanism of neuronal apoptosis and survival.

AIDS Dementia Complex↗
PubMed2004

Simultaneous carbon and nitrogen removal in anoxic-aerobic circulating fluidized bed biological reactor (CFBBR).

Biological nutrient removal (BNR) in municipal wastewater treatment to remove carbonaceous substrates and nutrients, has recently become increasingly popular worldwide due to increasingly stringent regulations. Biological fluidized bed (BFB) technology, which could be potentially used for BNR, can provide some advantages such as high efficiency and a compact structure. This work shows the results of simultaneous elimination of organic carbon and nitrogen using a circulating fluidized bed biological reactor (CFBBR, which has been developed recently for chemical engineering processes. The CFBBR has two fluidized beds, running as anoxic and aerobic processes to accomplish simultaneous nitrification and denitrification, with continuous liquid recirculation through the anoxic bed and the aerobic bed. Soluble COD concentrations in the effluent ranging from 4 to 20 mg l(-1) were obtained at varying COD loading rates; ammonia nitrogen removal efficiencies averaged in excess of 99% at a minimum total hydraulic retention time (HRT) of 2.0 hours over a temperature range of 25 degrees C to 28 degrees C. Effluent nitrate nitrogen concentration of less than 5 mg l(-1) was achieved by increasing effluent recycle rate. No nitrite accumulation was observed either in the anoxic bed or in the aerobic bed. The system was able to treat grit chamber effluent wastewater at a HRT of 2.0 hours while achieving average effluent BOD, COD, NH3-N, TKN, nitrates, total phosphate, TSS and VSS concentrations of 10 mg l(-1), 18 mg l(-1), 1.3 mg l(-1), 1.5 mg l(-1), 7 mg l(-1), 2.0 mg l(-1), 10 mg l(-1) and 8 mg l(-1) respectively. The CFBBR appears to be not only an excellent alternative for conventional activated sludge type BNR technologies but also capable of processing much higher loadings that are suitable for industrial applications.

Bacteria, Aerobic↗
PubMed2004

Interpretation of environmental tracers in groundwater systems with stagnant water zones.

Lumped-parameter models are commonly applied for determining the age of water from time records of transient environmental tracers. The simplest models (e.g. piston flow or exponential) are also applicable for dating based on the decay or accumulation of tracers in groundwater systems. The models are based on the assumption that the transit time distribution function (exit age distribution function) of the tracer particles in the investigated system adequately represents the distribution of flow lines and is described by a simple function. A chosen or fitted function (called the response function) describes the transit time distribution of a tracer which would be observed at the output (discharge area, spring, stream, or pumping wells) in the case of an instantaneous injection at the entrance (recharge area). Due to large space and time scales, response functions are not measurable in groundwater systems, therefore, functions known from other fields of science, mainly from chemical engineering, are usually used. The type of response function and the values of its parameters define the lumped-parameter model of a system. The main parameter is the mean transit time of tracer through the system, which under favourable conditions may represent the mean age of mobile water. The parameters of the model are found by fitting calculated concentrations to the experimental records of concentrations measured at the outlet. The mean transit time of tracer (often called the tracer age), whether equal to the mean age of water or not, serves in adequate combinations with other data for determining other useful parameters, e.g. the recharge rate or the content of water in the system. The transit time distribution and its mean value serve for confirmation or determination of the conceptual model of the system and/or estimation of its potential vulnerability to anthropogenic pollution. In the interpretation of environmental tracer data with the aid of the lumped-parameter models, the influence of diffusion exchange between mobile water and stagnant or quasi-stagnant water is seldom considered, though it leads to large differences between tracer and water ages. Therefore, the article is focused on the transit time distribution functions of the most common lumped-parameter models, particularly those applicable for the interpretation of environmental tracer data in double-porosity aquifers, or aquifers in which aquitard diffusion may play an important role. A case study is recalled for a confined aquifer in which the diffusion exchange with aquitard most probably strongly influenced the transport of environmental tracers. Another case study presented is related to the interpretation of environmental tracer data obtained from lysimeters installed in the unsaturated zone with a fraction of stagnant water.

Chlorine↗
PubMed2003

Mechanisms and prevention of plant tissue collapse during dehydration: a critical review.

The appearance and functional properties are primordial in the quality assessment of semifinished fruit and vegetable products. These properties are often associated with shrunken, shriveled, darkened materials of poor rehydration ability after been subjected to air-drying--the most used drying method in the food industry. Fruits and vegetables are cellular tissues containing gas-filled pores that tend to collapse when subjected to dehydration. Collapse is an overall term that has different meanings and scale-settings in the literature depending on whether the author is a plant physiologist, a food technologist, a chemical engineer, or a material scientist. Some clarifications are given in this particular but wide field. The purpose of this work was to make a state-of-the-art contribution to the structural and textural effects of different types of dehydration on edible plant products and give a basis for preventing this phenomenon. The plant tissue is described, and the primordial role of the cell wall in keeping the structural integrity is emphasized. Water and its functionality at macro and micro levels of the cellular tissue are reviewed as well as its transport during dehydration. The effects of both dehydration and rehydration are described in detail, and the term "textural collapse" is proposed as an alternative to structural collapse.

Desiccation↗
PubMed1986

Application of response-surface methodology to detect interactions of genotoxic agents in cultured mammalian cells.

Response-surface methodology (RSM) techniques provide a useful statistical approach for the design and analysis of experiments involving multiple variables. Although it has been used for some time in the areas of chemical engineering and agriculture, RSM has only recently been applied to the solution of biological problems. Here we have utilized RSM to investigate the interaction of two direct-acting, monofunctional alkylating agents [ethyl methanesulfonate (EMS) and ethylnitrosourea (ENU)] in Chinese hamster V79 cells with respect to the in vitro induction of sister chromatid exchanges (SCEs). A factorial design was employed in which the cells were exposed to the agents singly and in simultaneous combinations for 4 h. The cells were collected for SCE determination 30 h after treatment. The analysis revealed concentration-dependent increases in SCEs for both of the agents, with ENU being the more effective on an equimolar basis. In addition, single- and multiple-agent interactions were detected. The most important finding was that over the treatment range studied, a significant negative interaction occurs between EMS and ENU with regard to SCE induction. It is suggested that RSM not only may be useful in determining the statistical relevance of experimental variables but also may generate hypotheses the evaluation of which could provide additional insights into the underlying mechanisms involved.

Animals↗
PubMed2001

Project, design, and use of a pilot plant for nanocapsule production.

The aim of this study was to find the scale-up parameters necessary for the preparation of nanocapsules (NCs) for pharmaceutical purposes. Starting from the laboratory scale (0.06 L), we designed and assembled a pilot plant (2 L) to produce NCs with the so-called emulsification-diffusion technique. We wanted to check if classical tools adequate for the pharmaceutical industry and for industrial scale-up purposes according to well-known chemical engineering technique could be used to perform the NC preparation. Experiments were carried out by varying some operative parameters, such as the impeller speed, the agitation duration for the emulsion preparation, and the reagent concentrations. As expected, good accordance between the NC produced at the laboratory scale and at the pilot plant scale was obtained. We conclude that the pilot plant can be used to perform a scale-up study of the industrial production of NC.

Capsules↗
PubMed2006

What do -omics mean for the science and policy of the nutritional sciences?

The development of systems biology is revolutionizing the way we are studying and learning about human health. It is a way of thinking and a systematic attempt to integrate information from several fields of study (physical, biological, chemical, engineering, etc) to develop a more kinetic and real-time understanding of complex biological processes. It uses mathematical modeling tools to chart dynamic interactions between the components of a biological system, eg, genes, transcripts, proteins, metabolites, and cells, to simulate and analyze networks and pathways and the spatial and temporal relations that exist in biological systems. The term -omics represents the rigorous study of various collections of molecules, biological processes, or physiologic functions and structures as systems, represented most prominently by genomics. In the field of nutrition, had a systems approach been applied to evaluating the effect of vitamin A status on mortality rates in young children in developing countries, it might not have taken 20 y to go from the initial epidemiologic observations to global vitamin A supplementation programs. Better understanding of the functional biology of retinoids on different tissues that mediate host resistance to infection, and their synergistic interactions in biological, metabolic, and functional terms, could have provided a plausible mechanism for the observed effect on mortality. There are 3 policy take-home messages: 1) When controversies exist, invest in the science needed to sort them out. 2) Increase the amounts of money available for health research and interventions relevant to developing countries. 3) Ensure that policymakers understand the issues and why they are important and understand the science and its relevance.

Animals↗
PubMed2026

Prediction of bacterial protein-compound interactions with only positive samples.

MOTIVATION: Prediction of Compound-Protein Interactions (CPI) in bacteria is crucial to advance various pharmaceutical and chemical engineering fields, including biocatalysis, drug discovery, and industrial processing. However, current CPI models cannot be applied for bacterial CPI prediction due to the lack of curated negative interaction samples. RESULTS: We propose a novel Positive-Unlabeled (PU) learning framework, named BIN-PU, to address this limitation. BIN-PU generates pseudo positive and negative labels from known positive interaction data, enabling effective training of deep learning models for CPI prediction. We also propose a weighted positive loss function that weights to truly positive samples. We have validated BIN-PU coupled with multiple CPI backbone models, comparing the performance with the existing PU models using bacterial cytochrome P450 (CYP) data. Extensive experiments demonstrate the superiority of BIN-PU over the benchmark models in predicting CPIs with only truly positive samples. Furthermore, we have validated BIN-PU on additional bacterial proteins obtained from literature review, human CYP datasets, and uncurated data for its reproducibility. We have also validated the CPI prediction for the uncurated CYP data with biological and biophysical experiments. BIN-PU represents a significant advancement in CPI prediction for bacterial proteins, opening new possibilities for improving predictive models in related biological interaction tasks. AVAILABILITY AND IMPLEMENTATION: The source code and data are available at https://github.com/datax-lab/CYP.

Bacterial Proteins↗
PubMed1993

Solution conformation of a synthetic bis-headed inhibitor of trypsin and carboxypeptidase A: new structural alignment between the squash inhibitors and the potato carboxypeptidase inhibitor.

The trypsin carboxypeptidase peptide inhibitor (TCPI) which inhibits both trypsin and carboxypeptidase A has been chemically engineered by modification of the Ecballium elaterium trypsin inhibitor II (EETI-II). The solution conformation of TCPI, studied by two-dimensional nuclear magnetic resonance, was shown to be very close to those of squash inhibitors. Only limited deviations of the trypsin binding loop compared to its location in the EETI-II/trypsin complex were detected. It was also shown that the position of the C-terminal tail did not significantly change from the position observed in the complex between carboxypeptidase A and the potato carboxypeptidase inhibitor (PCI). The conformation of TCPI was carefully compared with the PCI one and a new structural alignment between the two microproteins is proposed. This alignment points out the very good conservation in the two inhibitors of a subdomain comprising segments 7-15, 19-22 and 25-28. Most importantly, the 2-19 disulfide bridge of TCPI was not structurally conserved in PCI and appeared to be rather unimportant for the early folding process of these molecules. This result agrees with the recent observation that the 2-19 bridge is the last to be formed in the folding of the squash inhibitor EETI-II and suggests that this is also the case during the folding of the potato carboxypeptidase inhibitor.

Amino Acid Sequence↗
PubMed2002

Neutrality condition and response law for nonlinear reaction-diffusion equations, with application to population genetics.

We study a general class of nonlinear macroscopic evolution equations with "transport" and "reaction" terms which describe the dynamics of a species of moving individuals (atoms, molecules, quasiparticles, organisms, etc.). We consider that two types of individuals exist, "not marked" and "marked," respectively. We assume that the concentrations of both types of individuals are measurable and that they obey a neutrality condition, that is, the kinetic and transport properties of the "not marked" and "marked" individuals are identical. We suggest a response experiment, which consists in varying the fraction of "marked" individuals with the preservation of total fluxes, and show that the response of the system can be represented by a linear superposition law even though the underlying dynamics of the system is in general highly nonlinear. The linear response law is valid even for large perturbations and is not the result of a linearization procedure but rather a necessary consequence of the neutrality condition. First, we apply the response theorem to chemical kinetics, where the "marked species" is a molecule labeled with a radioactive isotope and there is no kinetic isotope effect. The susceptibility function of the response law can be related to the reaction mechanism of the process. Secondly we study the geographical distribution of the nonrecurrent, nonreversible neutral mutations of the nonrecombining portion of the Y chromosome from human populations and show that the fraction of mutants at a given point in space and time obeys a linear response law of the type introduced in this paper. The theory may be used for evaluating the geographic position and the moment in time where and when a mutation originated.

Biochemical Phenomena↗
PubMed2005

Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors.

Nonlinear control techniques by means of a software sensor that are commonly used in chemical engineering could be also applied to genetic regulation processes. We provide here a realistic formulation of this procedure by introducing an additive white Gaussian noise, which is usually found in experimental data. Besides, we include model errors, meaning that we assume we do not know the nonlinear regulation function of the process. In order to illustrate this procedure, we employ the Goodwin dynamics of the concentrations [B. C. Goodwin, (Academic, New York, 1963)] in the simple form recently applied to single gene systems and some operon cases [H. De Jong, J. Comput. Biol. 9, 67 (2002)], which involves the dynamics of the mRNA, given protein and metabolite concentrations. Further, we present results for a three gene case in coregulated sets of transcription units as they occur in prokaryotes. However, instead of considering their full dynamics, we use only the data of the metabolites and a designed software sensor. We also show, more generally, that it is possible to rebuild the complete set of nonmeasured concentrations despite the uncertainties in the regulation function or, even more, in the case of not knowing the mRNA dynamics. In addition, the rebuilding of concentrations is not affected by the perturbation due to the additive white Gaussian noise and also we managed to filter the noisy output of the biological system.

Algorithms↗
PubMed2006

Mathematical basis for a general theory of Laplacian transport towards irregular interfaces.

The theory of Laplacian transport towards and across irregular surfaces is reformulated in terms of the Dirichlet-to-Neumann operator and its spectral characteristics. This permits us to obtain an exact equivalent circuit for the impedance of a working interface of arbitrary shape. The important result is that only very few eigenmodes of this operator do govern the entire response of a macroscopic system. This property drastically simplifies the understanding of irregular or prefractal interfaces. The results can be applied in electrochemistry, physiology and chemical engineering, fields where exchange processes across surfaces with complex geometry are ubiquitous.

Journal Article↗
PubMed2003

Probing the surface area of a cement-based material by nuclear magnetic relaxation dispersion.

We show how nuclear magnetic spin-lattice relaxation dispersion of 1H water can provide a direct reliable value of the specific surface area of a cement-based material. The remarkable features of the relaxation dispersion support an interpretation in terms of coupled solid-liquid relaxation at pore interfaces, surface diffusion, and nuclear paramagnetic relaxation. The measurement is sufficiently fast to be applied continuously during the progressive hydration and setting of the material. This method is relevant to other chemically reactive porous media in chemical engineering and oil recovery.

Journal Article↗
PubMed2005

What makes a boundary less accessible.

For the growth and transport processes driven by Laplacian fields, the accessibility of an interface for Brownian motion is characterized by the harmonic measure. Its multifractal properties help one to understand how the irregular geometry of biological membranes, metallic electrodes, porous catalysts, or growing aggregates is "seen" by diffusing particles. To clarify this point, we performed an extensive numerical study of the harmonic measure on two families of self-similar triangular Koch curves of variable Hausdorff dimension which may represent branched pore networks or fjordlike rough interfaces. Although these structures are apparently different, the multifractal properties of the harmonic measure in two cases are found to be very close for curves of small Hausdorff dimensions and to differ for higher irregularity. This provides new insight into optimization problems in chemical engineering.

Journal Article↗
PubMed1997

Enzymatic semisynthesis of dicarba analogs of calcitonin.

The semisynthesis of eel[L-alpha-aminosuberic acid]calcitonin (elcatonin) was accomplished by alpha-chymotrypsin-catalyzed coupling of two peptide segments in a single reaction without the protection of any functional group. The eel calcitonin-(10-32)-peptide was prepared by a gene manipulation. The esters of cyclic desamino nonapeptide (segment 1-9) were synthesized by the conventional solution method including a thermolysin-mediated resolution of DL-alpha-aminosuberic acid via one-step tripeptide synthesis leading to the 7-9 sequence. The main aim of this work was to determine the conditions for protease-catalyzed segment condensation while avoiding a concurrent cleavage of other proteolytically labile peptide bonds in the hormone. The alpha-chymotrypsin condensation strategy under usual conditions led to a complicated mixture of split products with an insignificant amount of the required peptide. When the coupling reaction was carried out at 0 degrees C, the reaction resulted in a satisfactory yield of elcatonin with the complete conversion of the acyl donor (1-9 segment) accompanied by negligible concurrent peptide bond digestion. The same strategy was employed for the preparation of analogous dicarba salmon calcitonin using a synthetic elcatonin-(10-32)-peptide. Both calcitonin analogs exhibited hypocalcemic activity corresponding to the international standard of elcatonin. We demonstrate in this work a peptide synthesis based on the combination of genetic engineering, chemical synthesis and proteinase-catalyzed segment condensation. This approach enables effective incorporation of an unnatural amino acid into calcitonins without the side-chain protection.

Amino Acid Sequence↗
PubMed1992

Artificial cells: 35 years.

The first artificial cells were prepared 35 years ago. They contain biologically active materials. They are now being used in medicine and biotechnology. Artificial cells containing adsorbents are already a routine form of treatment in hemoperfusion. This includes treatment for acute poisoning, high blood aluminum and iron, kidney failure, some types of acute liver failure, and other conditions. Artificial cells are being tested for use as red blood cell substitutes. Artificial cells containing cell culture are being tested in animals for the treatment of diabetes, liver failure, and others. Artificial cells containing enzymes are being tested for treatment in hereditary enzyme deficiency diseases and other diseases. Artificial cells containing complex enzyme system can convert wastes like urea and ammonia into useful amino acids. In biotechnology, artificial cells are being used for the production of monoclonal antibodies, interferons, and other biotechnological products. They are also being investigated for use in other applications in biotechnology, chemical engineering, and medicine.

Animals↗