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PubMed2005

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This article reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies, and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing, and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high quality, appropriately anatomically tagged scientific results. In optimized protocols is a source of inefficiency in current life science research. Improvement in this area will significantly increase life science quality and productivity. The article is divided into introduction, materials, protocols, and notes sections. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this article, readers are advised to read through the entire article first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.

Biomarkers↗

PubMed2005

Systems cell biology knowledge created from high content screening.

High content screening (HCS), the large-scale automated analysis of the temporal and spatial changes in cells and cell constituents in arrays of cells, has the potential to create enormous systems cell biology knowledge bases. HCS is being employed along with the continuum of the early drug discovery process, including lead optimization where new knowledge is being used to facilitate the decision-making process. We demonstrate methodology to build new systems cell biology knowledge using a multiplexed HCS assay, designed with the aid of knowledge-mining tools, to measure the phenotypic response of a panel of human tumor cell types to a panel of natural product-derived microtubule-targeted anticancer agents and their synthetic analogs. We show how this new systems cell biology knowledge can be used to design a lead compound optimization strategy for at least two members of the panel, (-)-laulimalide and (+)-discodermolide, that exploits cell killing activity while minimally perturbing the regulation of the cell cycle and the stability of microtubules. Furthermore, this methodology can also be applied to basic biomedical research on cells.

Antineoplastic Agents↗

PubMed2003

A bicistronic expression system for bacterial production of authentic human interleukin-18.

Interleukin-18 (IL-18) is activated and released from immune effector cells to stimulate acquired and innate immune responses involving T and natural killer (NK) cells. The release of IL-18 from mammalian cells is linked to its proteolytic activation by caspases including interleukin 1 converting enzyme (ICE). The absence of a signal peptide sequence and the requirement for coupled activation and cellular release have presented challenges for the large-scale recombinant production of IL-18. In this study, we have explored methods for the direct production of authentic human IL-18 toward the development of a large-scale production system. Expression of mature IL-18 directly in Escherichia coli with a methionine initiating codon leads to the production of MetIL-18 that is dramatically less potent in bioassays than IL-18 produced as a pro-peptide and activated in vitro. To produce an authentic IL-18, we have devised a bicistronic expression system for the coupled transcription and translation of ProIL-18 with caspase-1 (ICE) or caspase-4 (ICE-rel II, TX, ICH-2). Mature IL-18 with an authentic N-terminus was produced and has a biological activity and potency comparable to that of in vitro processed mature IL-18. Optimization of this system for the maximal production yields can be accomplished by modulating the temperature, to affect the rate of caspase activation and to favor the accumulation of ProIL-18, prior to its proteolytic processing by activated caspase. The effect of temperature is particularly profound for the caspase-4 co-expression process, enabling optimized production levels of over 150 mg/L in shake flasks at 25 degrees C. An alternative bicistronic expression design utilizing a precise ubiquitin IL-18 fusion, processed by co-expressed ubiquitinase, was also successfully used to generate fully active IL-18, thereby demonstrating that the pro-sequence of IL-18 is not required for recombinant IL-18 production.

Amino Acid Sequence↗

PubMed2004

The system design of UV-assisted catalytic oxidation process--degradation of 2,4-D.

Unlike the conventional first- or second-order model, a novel approach to design for the removal of 2,4-dichlorophenoxy (2,4-D) by the UV-catalytic oxidation process (UVCOP) was investigated. Two distinctive parameters, initial decay rate and maximum oxidative capacity, were characterized. By using these parameters, the performance of the degradation of 2,4-D by UVCOP regarding to the reagent dosages could be successfully predicted. Low concentrations of ferrous ion was found to be a rate-limiting factor for the process while the dosage of hydrogen peroxide was concluded as a dominant species in determining the maximum oxidation capacities. This information can be used to optimize the treatment process and achieve the expected performance target; an "optimal-dose model" was developed accordingly. The model is an intelligent and useful tool to evaluate the optimal doses of hydrogen peroxide with the minimum dose of ferrous ion, which leads to a better design of the treatment process.

2,4-Dichlorophenoxyacetic Acid↗

PubMedDate not supplied

Design of a sequencing batch reactor sequence with an input load partition in a simulation-based experimental environment.

A study is presented that considers optimization of a sequencing batch reactor (SBR) operational sequence. Optimization is performed with the aid of a laboratory pilot plant and a process model. The model was included in the study to facilitate a search for optimal operating conditions because performing experiments solely on the pilot plant would be rather extensive, expensive, and time-consuming. The model used in the study is the well-known Activated Sludge Model No.1 with minor modifications. The optimization addresses a split-feed operating mode with input load partitioned into two parts and with two successions of aerobic-anoxic phases. In the study, the duration of batch phases and the time of the second input addition are optimized so that the desired effluent nitrogen concentration is achieved and the need for external carbon addition in the anoxic phase is reduced or eliminated. When an optimal SBR sequence computed by the model was verified on the pilot plant, better performance of the actual process was also achieved, although some phenomena were observed that were not predicted by the model. Results of the study indicate that the available wastewater treatment plant models, although a simplification of reality, can be usefully applied for process optimization.

Equipment Design↗

PubMed1996

Studies on epoxy compound fixation.

Bioprostheses derived from collagenous tissues have to be fixed and subsequently sterilized before they can be implanted in humans. Clinically, the most commonly used fixative is glutaraldehyde. However, the tendency for glutaraldehyde to markedly alter tissue stiffness and promote tissue calcification are well-recognized drawbacks of this fixative. To address the deficiencies with the glutaraldehyde-fixed tissue, a new fixative, epoxy compound, was used to fix biological prostheses. The study was undertaken to investigate the fixation rates and crosslinking densities of biological tissues fixed with various epoxy compounds. These epoxy compounds are different in their chemical structures. Glutaraldehyde was used as a control. The fixation rates and crosslinking densities of the fixed tissues were determined by measuring their fixation indices and denaturation temperatures, respectively. Generally, the epoxy-fixed tissues were more pliable than the glutaraldehyde-fixed one. Furthermore, the tissues fixed with monofunctional epoxy compound were more pliable than those fixed with multifunctional epoxy compounds. With increasing pH or temperature, the fixation rate of epoxy compound increased. However, the number of epoxide functional groups did not seem to affect the fixation rate of the epoxy compound. The fixation rate of glutaraldehyde was faster than that of epoxy compounds. Additionally, the crosslinking density of the glutaraldehyde-fixed tissue was greater than that of the epoxy-fixed counterparts. Moreover, it was noted that the denaturation temperatures of the tissues fixed with glutaraldehyde or multifunctional epoxy compounds were significantly higher than the fresh ones (p < 0.05), while that fixed with monofunctional epoxy compound stayed roughly the same throughout the entire fixation process (p > 0.05). The results obtained in this study may be used to optimize the fixation process for developing bioprostheses fixed with epoxy compounds.

Animals↗

PubMed2003

Movable contactless-conductivity detector for microchip capillary electrophoresis.

A new movable contactless-conductivity detection system for microchip capillary electrophoresis is introduced. Such a versatile system relies on positioning the detector at different points along the separation channel via "sliding" the electrode holder. The new movable microchip detection system offers distinct improvements compared to common fixed-location conductivity detectors. For example, placing the detector at different locations along the microchannel offers useful insights into the separation process. Three-dimensional plots of resolution/channel length/separation voltage can be used for optimizing the separation process and selecting the analysis time. The system enables rapid switching between "total" (unresolved) and "individual" (resolved/fingerprint) signals on the basis of placing the detector at the beginning and end of the separation channel, respectively. By moving the detector to a shorter effective separation length, after eluting fast-migrating ions, shorter analysis times can be achieved (through faster detection of late-eluting analytes). These and other improvements in the analytical performance and insights into the separation process are illustrated in connection with the detection of low-energy ionic explosives and nerve agent degradation products.

Journal Article↗

PubMed2001

ThermoEnergy Ammonia Recovery Process for municipal and agricultural wastes.

The Ammonia Recovery Process (ARP) is an award-winning, low-cost, environmentally responsible method of recovering nitrogen, in the form of ammonia, from various dilute waste streams and converting it into concentrated ammonium sulfate. The ThermoEnergy Biogas System utilizes the new chemisorption-based ARP to recover ammonia from anaerobically digested wastes. The process provides for optimal biogas production and significantly reduced nitrogen levels in the treated water discharge. Process flows for the ammonia recovery and ThermoEnergy biogas processes are presented and discussed. A comparison with other techniques such as biological nitrogen removal is made. The ARP technology uses reversible chemisorption and double salt crystal precipitation to recover and concentrate the ammonia. The ARP technology was successfully proven in a recent large-scale field demonstration at New York City's Oakwood Beach Wastewater Treatment Plant, located on Staten Island. This project was a joint effort with Foster Wheeler Environmental Corporation, the Civil Engineering Research Foundation, and New York City Department of Environmental Protection. Independent validated plant data show that ARP consistently recovers up to 99.9% of the ammonia from the city's centrate waste stream (derived from dewatering of sewage sludge), as ammonium sulfate. ARP technology can reduce the nitrogen (ammonia) discharged daily into local bodies of water by municipalities, concentrated animal farming operations, and industry. Recent advances to ARP enhance its performance and economic competitiveness in comparison to stripping or ammonia destruction technologies.

Agriculture↗

PubMed1997

LEMMA: a language for easy medical models analysis.

The quality of health care systems and processes is becoming a prominent problem and more and more efforts are devoted to define methodologies and tools to measure and assure quality of care. New methods are required to optimize health care processes to guarantee high quality standards within (limited) available resources. Resource optimizations able to preserve the quality of treatments require good models of medical processes. This paper presents LEMMA, a new notation to model medical processes. LEMMA provides physicians with intuitive graphical elements to design their models. At the same time a high level timed Petri net corresponding to the designed model is built automatically. In this way, LEMMA models are ascribed formal semantics and can be executed and analyzed automatically. The dual language approach followed in this paper allows physicians to gain all the benefits of formal methods without being proficient in them. Medical users manage simple graphical elements, while Petri nets ensure formality and validation capabilities. In this way LEMMA mixes formal and informal notations, overcoming the problems of both the approaches. The definition of the notation has been supported by the development of an environment to design LEMMA models. The environment, besides letting us experiment with the notation, has been employed to define and analyze real case studies.

Computer Communication Networks↗

PubMed2005

MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm.

The prediction of ligand binding sites is an essential part of the drug discovery process. Knowing the location of binding sites greatly facilitates the search for hits, the lead optimization process, the design of site-directed mutagenesis experiments and the hunt for structural features that influence the selectivity of binding in order to minimize the drug's adverse effects. However, docking is still the rate-limiting step for such predictions; consequently, much more efficient algorithms are required. In this article, the design of the MEDock web server is described. The goal of this sever is to provide an efficient utility for predicting ligand binding sites. The MEDock web server incorporates a global search strategy that exploits the maximum entropy property of the Gaussian probability distribution in the context of information theory. As a result of the global search strategy, the optimization algorithm incorporated in MEDock is significantly superior when dealing with very rugged energy landscapes, which usually have insurmountable barriers. This article describes four different benchmark cases that span a diverse set of different types of ligand binding interactions. These benchmarks were compared with the use of the Lamarckian genetic algorithm (LGA), which is the major workhorse of the well-known AutoDock program. These results demonstrate that MEDock consistently converged to the correct binding modes with significantly smaller numbers of energy evaluations than the LGA required. When judged by a threshold of the number of energy evaluations consumed in the docking simulation, MEDock also greatly elevates the rate of accurate predictions for all benchmark cases. MEDock is available at http://medock.csie.ntu.edu.tw/ and http://bioinfo.mc.ntu.edu.tw/medock/.

Algorithms↗

PubMed2003

Synthesis of functionalized 1,4-cyclohexadienes through intramolecular anionic dearomatization of N-alkyl-N-benzyldiphenylphosphinamides. Insight into the reaction mechanism.

A generalization of the intramolecular nucleophilic dearomatization-electrophilic alkylation reactions of N-alkyl-N-benzyldiphenylphosphinamide anions is presented. The process has been optimized by analyzing the effects of metalation and quench times, additives, the nature of the electrophiles used (MeI, CF(3)SO(3)Me, Me(3)O(+)BF(4)(-), AllylBr, PhCH(2)Br, BrCH(2)CO(2)Me, and RCH=O, where R = Ph, 4-Cl-C(6)H(4), 4-MeO-C(6)H(4), and (i)()Pr), and the alkyl substituent linked to the nitrogen of the phosphinamide. Both HMPA and DMPU act as catalysts. The latter proved to be much more efficient for obtaining high yields of substituted tetrahydrobenzo[c][1,2]-1lambda(5)-phospholes containing a 1,4-cyclohexadiene system with very high regio- and diastereoselectivity. Steric effects in the neighborhood of the benzylic anion tend to decrease the stereoselectivity of the anionic cyclization. The optimization study also served to shed light on the reaction mechanism of the dearomatization process by identifying several intermediate species and showing the reversibility of the anionic cyclization step as well as of the reaction with aldehydes.

Journal Article↗

PubMed1997

Processing of mammalian and plant S-adenosylmethionine decarboxylase proenzymes.

S-Adenosylmethionine decarboxylase (AdoMetDC) is a pyruvoyl enzyme, and the pyruvate is formed in an intramolecular reaction that cleaves a proenzyme precursor and converts a serine residue into pyruvate. The wild type potato AdoMetDC proenzyme processed much faster than the human proenzyme and did not require putrescine for an optimal rate of processing despite the presence of three acidic residues (equivalent to Glu11, Glu178, and Glu256) that were demonstrated in previous studies to be required for the putrescine activation of human AdoMetDC proenzyme processing (Stanley, B. A., Shantz, L. M., and Pegg, A. E. (1994) J. Biol. Chem. 269, 7901-7907). A fourth residue that is also needed for the putrescine stimulation of human AdoMetDC proenzyme processing was identified in the present studies, and this residue (Asp174) is not present in the potato sequence. The site of potato AdoMetDC proenzyme processing was found to be Ser73 in the conserved sequence, YVLSESS, which is the equivalent of Ser68 in the human sequence. Replacement of the serine precursor with threonine or cysteine by site-directed mutagenesis in either the potato or the human AdoMetDC proenzyme did not prevent processing but caused a significant reduction in the rate. Although the COOH-terminal regions of the known eukaryotic AdoMetDCs are not conserved, only relatively small truncations of 8 residues from the human protein and 25 residues from the potato proenzyme were compatible with processing. The maximally truncated proteins show no similarity in COOH-terminal amino acid sequence but each contained 46 amino acid residues after the last conserved sequence, suggesting that the length of this section of the protein is essential for maintaining the proenzyme conformation needed for autocatalytic processing.

Adenosylmethionine Decarboxylase↗

PubMedDate not supplied

Dynamical control of the dialysis process. Part I: Structural considerations and first mathematical approach.

Individual optimization of the dialysis process requires the (open-loop or closed-loop) control of many different variables, e.g. plasma ion concentrations, acid base state, volemic state and hemodynamic quantities. For this purpose a general concept for multiple-input-multiple-output (MIMO) control of the dialysis process is presented. The controlled variables have been differentiated into variables which can be modeled mechanistically (primary controlled variables, PCVs) and (hemodynamic) variables for which no mechanistic model has been developed up to now (secondary controlled variables, SCVs). Accordingly the controller is decomposed into two stages. Stage 1 contains an expert system which links the PCVs to the SCVs and provides the generation of optimal profiles for the PCVs with respect to maximum hemodynamic stability of the patient. Stage 2 is a tracking controller for the PCVs. An algorithm for the multidimensional tracking problem at stage 2 has been developed. It can be used for open-loop and future closed-loop control. The algorithm has been tested for 4 controlled (plasma Na+, plasma K+, plasma volume and ratio between intra- and extracellular volume) and 3 control variables (dialysate Na+, dialysate K+, ultrafiltration rate) up to now. It renders possible the exact tracking of the prescribed trajectories as long as all points are reachable under consideration of all physical and physiological boundary conditions. If they are not, appropriate weighting of the conflicting optimization goals must be applied. An extension towards more than 4 controlled variables is possible on principle. Main advantages of the method are its mathematical simplicity and the applicability of standard optimization subroutines.

Algorithms↗

PubMed1979

Elongation of DNA complementary to the 5' end of the avian sarcoma virus genome by the virion-associated RNA-dependent DNA polymerase.

RNA-dependent DNA synthesis in a virion-associated reaction has been described as being dependent upon the detergent concentration used for disruption of the virion. In this study, the Triton X-100 concentration was found to affect the elongation of the initially synthesized DNA complementary to the last approximately 100 nucleotides at the 5' end of the RNA (cDNA100). Whereas elongation of cDNA100 increased with time of incubation at the optimal detergent concentration, this process was retarded at higher detergent concentrations. At the optimal detergent concentration, elongated DNA was of low chemical complexity, indicating that extension of cDNA100 occurred at a unique site on the RNA. Higher than optimal detergent concentrations resulted in nonspecific elongation and in DNA of high chemical complexity. This was shown by oligopyrimidine tract analysis. Furthermore, actinomycin D was observed to inhibit the elongation of cDNA100 at the optimal detergent concentration. The nature of the elongation process was elucidated by analysis of DNA synthesized in a virion-associated reaction in the presence of bacteriophage Qbeta RNA. At the optimal detergent concentration DNA complementary only to avian sarcoma virus RNA was synthesized, whereas at higher concentrations DNA was copied from both avian sarcoma virus and Qbeta RNA. We conclude that the elongation mechanism of cDNA100 is affected by the detergent concentration and elongation is unspecific at higher than optimal detergent concentrations. The mechanism by which the nonionic detergent stimulates DNA synthesis has not yet been resolve. We assume that other factors in addition to DNA polymerase are involved in elongation of cDNA100.

Alpharetrovirus↗

PubMed2002

A complementary-metal-oxide-semiconductor-field-effect-transistor-compatible atomic force microscopy tip fabrication process and integrated atomic force microscopy cantilevers fabricated with this process.

A complementary-metal-oxide-semiconductor-field-effect-transistor-compatible process for the fabrication of atomic force microscopy cantilevers with integrated tips has been developed. For the first time, the tips are fabricated after the completion of the regular complementary metal-oxide-semiconductor-field-effect-transistor fabrication process sequence. On-chip circuit components, such as piezoresistive deflection sensors, deflection actuators, and amplifiers, are fabricated on the mirror-polished surface of the wafer, ensuring optimal performance. The tip fabrication process is based on anisotropic silicon etching at low temperature using a tetramethylammonium hydroxide solution. The anisotropic etching process has been optimized to ensure process controllability. Using the described process, complementary-metal-oxide-semiconductor-field-effect-transistor-based cantilevers with piezoresistive deflection sensors and integrated tips have been successfully fabricated. Force-distance curves and scanning images in constant-force mode have been recorded.

Journal Article↗

PubMed2003

Sustainable chemistry: starting points and prospects.

We review here the concept of sustainable chemistry (SC), which is still in its early development. One important element of SC is commonly defined as chemical research aiming at the optimization of chemical processes and products with respect to energy and material consumption, inherent safety, toxicity, environmental degradability, and so on. An increasing number of assessment systems containing quantitative indicators for these aspects are currently being developed. In addition, however, SC should also address the societal aspect of sustainability. With respect to scientific research, the societal aspect is defined here by two requirements: (1) the assumptions, objectives and implications of chemical research and its technical application should be made more transparent to various societal actors; (2) uncertainty and ignorance should be treated more explicitly in the course of scientific research. Meeting these requirements is necessary in order to lift the division between the allegedly disinterested and non-normative scientific research and the value-laden sphere of societal needs, preferences and decision-making situations. This, in turn, is understood here as a contribution to a more sustainable scientific practice. We illustrate the two elements of SC-optimization of products and processes as well as including the societal aspect-with the examples of environmental chemistry, green chemistry and the environmental assessment of chemical products. While considerable progress has been made in these fields, the societal aspect of SC remains to be recognized more fully in all branches of chemical research. One prerequisite for this is the inclusion of SC into chemical education from the very beginning.

Chemistry↗

PubMed1998

Selection, optimization, and compensation as strategies of life management: correlations with subjective indicators of successful aging.

The usefulness of self-reported processes of selection, optimization, and compensation (SOC) for predicting on a correlational level the subjective indicators of successful aging was examined. The sample of Berlin residents was a subset of the participants of the Berlin Aging Study. Three domains (marked by 6 variables) served as outcome measures of successful aging: subjective well-being, positive emotions, and absence of feelings of loneliness. Results confirm the central hypothesis of the SOC model: People who reported using SOC-related life-management behaviors (which were unrelated in content to the outcome measures) had higher scores on the 3 indicators of successful aging. The relationships obtained were robust even after controlling for other measures of successful mastery such as personal life investment, neuroticism, extraversion, openness, control beliefs, intelligence, subjective health, or age.

Adaptation, Psychological↗

PubMed2026

Microalgae-Mediated Synthesis of Gold Nanoparticles from Indonesian Chlorella vulgaris InaCC M205 with Potential Anticancer Properties for Biomedical Application.

Sustainable nanomaterial synthesis has emerged as a critical strategy to reduce the environmental burden associated with conventional chemical synthesis method. Microalgae-derived biomolecules offer a promising platform for the green production of metal nanoparticles due to their rich bioactive compounds capable of acting as natural reducing and stabilizing agents. Here, we report the eco-friendly synthesis of gold nanoparticles (AuNPs) using extract of Indonesian microalga Chlorella vulgaris extract. To optimize the synthesis process, the effects of precursor-to-extract ratio, temperature, and incubation time were evaluated. Optimal synthesis of C5-AuNPs was obtained at 37 °C for 20 h with precursor to extract ratio of 6:4, resulting in moderately stable C5-AuNPs characterized by a surface plasmon resonance (SPR) peak at 541 nm. Furthermore, Fourier-transmission infra-red (FT-IR) analysis revealed the involvement of functional groups of C. vulgaris extract in the interaction with Au+ during the production of C5-AuNPs. Transmission electron microscopy (TEM) demonstrated the formation of uniformly spherical nanoparticles with an average diameter of approximately 8.8 nm. Biological evaluation showed that the synthesized C5-AuNPs exerted pronounced dose-dependent cytotoxicity against MCF-7 breast cancer cells with an IC50 threshold of 21.17 ppm, while no toxicity appears in normal HEK293 cells. Mechanistically, the C5-AuNPs induced early apoptosis and inhibit cell-cycle progression at the stage of G0/G1. Collectively, these findings demonstrate that C. vulgaris-mediated AuNPs represent a promising preliminary in vitro findings for cancer therapy candidate.

Gold↗