Comment on "Combination of cupric ion with hydroxylamine and hydrogen peroxide for the control of bacterial biofilms on RO membranes by Hye-Jin Lee, Hyung-Eun Kim, Changha Lee [Water Research 110, 2017, 83-90]".

Science.gov (United States)

Chen, Long; Peng, Ying; Tang, Min; Wu, Feng

2017-07-01

The methodology employed by Lee et al. to terminate their bactericidal assays was found to be flawed via our demonstrations. Briefly, EDTA or sulfite combining with cupric ion did not fully terminate, and instead even boosted the P. aeruginosa death. We therefore suggested them to seek for other means of reaction termination, such as the combination of buffering agent PBS and Cu(II)-complexing agent EDTA. Copyright © 2017 Elsevier Ltd. All rights reserved.

A facile approach for cupric ion detection in aqueous media using polyethyleneimine/PMMA core-shell fluorescent nanoparticles

International Nuclear Information System (INIS)

Chen Jian; Zeng Fang; Wu Shuizhu; Su Junhua; Zhao Jianqing; Tong Zhen

2009-01-01

A facile approach was developed to produce a dye-doped core-shell nanoparticle chemosensor for detecting Cu 2+ in aqueous media. The core-shell nanoparticle sensor was prepared by a one-step emulsifier-free polymerization, followed by the doping of the fluorescent dye Nile red (9-diethylamino- 5H-benzo[alpha] phenoxazine-5-one, NR) into the particles. For the nanoparticles, the hydrophilic polyethyleneimine (PEI) chain segments serve as the shell and the hydrophobic polymethyl methacrylate (PMMA) constitutes the core of the nanoparticles. The non-toxic and biocompatible PEI chain segments on the nanoparticle surface exhibit a high affinity for Cu 2+ ions in aqueous media, and the quenching of the NR fluorescence is observed upon binding of Cu 2+ ions. This makes the core-shell nanoparticle system a water-dispersible chemosensor for Cu 2+ ion detection. The quenching of fluorescence arises through intraparticle energy transfer (FRET) from the dye in the hydrophobic PMMA core to the Cu 2+ /PEI complexes on the nanoparticle surface. The energy transfer efficiency for PEI/PMMA particles with different diameters was determined, and it is found that the smaller nanoparticle sample exhibits higher quenching efficiency, and the limit for Cu 2+ detection is 1 μM for a nanoparticle sample with a diameter of ∼30 nm. The response of the fluorescent nanoparticle towards different metal ions was investigated and the nanoparticle chemosensor displays high selectivity and antidisturbance for the Cu 2+ ion among the metal ions examined (Na + , K + , Mg 2+ , Ca 2+ , Zn 2+ , Hg 2+ , Mn 2+ , Fe 2+ , Ni 2+ , Co 2+ and Pb 2+ ). This emulsifier-free, biocompatible and sensitive fluorescent nanoparticle sensor may find applications in cupric ion detection in the biological and environmental areas.

A facile approach for cupric ion detection in aqueous media using polyethyleneimine/PMMA core-shell fluorescent nanoparticles.

Science.gov (United States)

Chen, Jian; Zeng, Fang; Wu, Shuizhu; Su, Junhua; Zhao, Jianqing; Tong, Zhen

2009-09-09

A facile approach was developed to produce a dye-doped core-shell nanoparticle chemosensor for detecting Cu(2+) in aqueous media. The core-shell nanoparticle sensor was prepared by a one-step emulsifier-free polymerization, followed by the doping of the fluorescent dye Nile red (9-diethylamino- 5H-benzo[alpha] phenoxazine-5-one, NR) into the particles. For the nanoparticles, the hydrophilic polyethyleneimine (PEI) chain segments serve as the shell and the hydrophobic polymethyl methacrylate (PMMA) constitutes the core of the nanoparticles. The non-toxic and biocompatible PEI chain segments on the nanoparticle surface exhibit a high affinity for Cu(2+) ions in aqueous media, and the quenching of the NR fluorescence is observed upon binding of Cu(2+) ions. This makes the core-shell nanoparticle system a water-dispersible chemosensor for Cu(2+) ion detection. The quenching of fluorescence arises through intraparticle energy transfer (FRET) from the dye in the hydrophobic PMMA core to the Cu(2+)/PEI complexes on the nanoparticle surface. The energy transfer efficiency for PEI/PMMA particles with different diameters was determined, and it is found that the smaller nanoparticle sample exhibits higher quenching efficiency, and the limit for Cu(2+) detection is 1 microM for a nanoparticle sample with a diameter of approximately 30 nm. The response of the fluorescent nanoparticle towards different metal ions was investigated and the nanoparticle chemosensor displays high selectivity and antidisturbance for the Cu(2+) ion among the metal ions examined (Na(+), K(+), Mg(2+), Ca(2+), Zn(2+), Hg(2+), Mn(2+), Fe(2+), Ni(2+), Co(2+) and Pb(2+)). This emulsifier-free, biocompatible and sensitive fluorescent nanoparticle sensor may find applications in cupric ion detection in the biological and environmental areas.

A facile approach for cupric ion detection in aqueous media using polyethyleneimine/PMMA core-shell fluorescent nanoparticles

Science.gov (United States)

Chen, Jian; Zeng, Fang; Wu, Shuizhu; Su, Junhua; Zhao, Jianqing; Tong, Zhen

2009-09-01

A facile approach was developed to produce a dye-doped core-shell nanoparticle chemosensor for detecting Cu2+ in aqueous media. The core-shell nanoparticle sensor was prepared by a one-step emulsifier-free polymerization, followed by the doping of the fluorescent dye Nile red (9-diethylamino- 5H-benzo[alpha] phenoxazine-5-one, NR) into the particles. For the nanoparticles, the hydrophilic polyethyleneimine (PEI) chain segments serve as the shell and the hydrophobic polymethyl methacrylate (PMMA) constitutes the core of the nanoparticles. The non-toxic and biocompatible PEI chain segments on the nanoparticle surface exhibit a high affinity for Cu2+ ions in aqueous media, and the quenching of the NR fluorescence is observed upon binding of Cu2+ ions. This makes the core-shell nanoparticle system a water-dispersible chemosensor for Cu2+ ion detection. The quenching of fluorescence arises through intraparticle energy transfer (FRET) from the dye in the hydrophobic PMMA core to the Cu2+/PEI complexes on the nanoparticle surface. The energy transfer efficiency for PEI/PMMA particles with different diameters was determined, and it is found that the smaller nanoparticle sample exhibits higher quenching efficiency, and the limit for Cu2+ detection is 1 µM for a nanoparticle sample with a diameter of ~30 nm. The response of the fluorescent nanoparticle towards different metal ions was investigated and the nanoparticle chemosensor displays high selectivity and antidisturbance for the Cu2+ ion among the metal ions examined (Na+, K+, Mg2+, Ca2+, Zn2+, Hg2+, Mn2+, Fe2+, Ni2+, Co2+ and Pb2+). This emulsifier-free, biocompatible and sensitive fluorescent nanoparticle sensor may find applications in cupric ion detection in the biological and environmental areas.

Leaching behavior and chemical stability of copper butyl xanthate complex under acidic conditions.

Science.gov (United States)

Chang, Yi Kuo; Chang, Juu En; Chiang, Li Choung

2003-08-01

Although xanthate addition can be used for treating copper-containing wastewater, a better understanding of the leaching toxicity and the stability characteristics of the copper xanthate complexes formed is essential. This work was undertaken to evaluate the leaching behavior of copper xanthate complex precipitates by means of toxicity characteristics leaching procedure (TCLP) and semi-dynamic leaching test (SDLT) using 1 N acetic acid solution as the leachant. Also, the chemical stability of the copper xanthate complex during extraction has been examined with the studying of variation of chemical structure using UV-vis, Fourier transform infrared and X-ray photoelectron spectroscopies (XPS). Both TCLP and SDLT results showed that a negligible amount of copper ion was leached out from the copper xanthate complex precipitate, indicating that the complex exhibited a high degree of copper leaching stability under acidic conditions. Nevertheless, chemical structure of the copper xanthate complex precipitate varied during the leaching tests. XPS data suggested that the copper xanthate complex initially contained both cupric and cuprous xanthate, but the unstable cupric xanthate change to the cuprous form after acid extraction, indicating the cuprous xanthate to be the final stabilizing structure. Despite that, the changes of chemical structure did not induce the rapid leaching of copper from the copper xanthate complex.

The effect of preparation conditions and the ionizing radiation on the kinetics of cupric oxide reduction by hydrogen

International Nuclear Information System (INIS)

Pospisil, M.; Taras, P.

1977-01-01

Cupric oxide reduction in the temperature interval 170 to 350 degC was studied by thermogravimetry. The reduction kinetics can be quantitatively described by the modified Prout-Tompkinson equation, with the apparent activation energy varying within the limits (4.94 to 5.82)x10 4 J/mol. Irregularities observed during the reduction of the oxide of the oxalate origin are due to the high content of the metallic phase. The p-semiconducting nature of these oxides was proved for all samples. The effect of the pre-irradiation of samples with γ-rays (with an absorbed dose of (1.4 to 4.75)x10 6 J/kg) on the reduction kinetics depends on the origin of the cupric oxide. In contrast to NiO no correlation between the content of super-stoichiometric oxygen and the reduction kinetics was found. After irradiation with γ-rays or with fast neutrons at a dose of 79.8 J/kg the reduction rate increases and the activation energy decreases regardless of the oxide origin. At the same time the concentration of the ionic form of super-stoichiometric oxygen increases. (author)

Emergence of biological complexity: Criticality, renewal and memory

International Nuclear Information System (INIS)

Grigolini, Paolo

2015-01-01

The key purpose of this article is to establish a connection between two emerging fields of research in theoretical biology. The former focuses on the concept of criticality borrowed from physics that is expected to be extensible to biology through a robust theoretical approach that although not yet available shall eventually shed light into the origin of cognition. The latter, largely based on the tracking of single molecules diffusing in biological cells, is bringing to the general attention the need to go beyond the ergodic assumption currently done in the traditional statistical physics. We show that replacing critical slowing down with temporal complexity explains why biological systems at criticality are resilient and why long-range correlations are compatible with the free-will condition necessary for the emergence of cognition. Temporal complexity generates ergodicity breakdown and requires new forms of response of complex systems to external stimuli. We concisely illustrate these new forms of information transport and we also address the challenging issue of combining temporal complexity with coherence and renewal with infinite memory.

Complexity, Analysis and Control of Singular Biological Systems

CERN Document Server

Zhang, Qingling; Zhang, Xue

2012-01-01

Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

Finding optimal interaction interface alignments between biological complexes

KAUST Repository

Cui, Xuefeng; Naveed, Hammad; Gao, Xin

2015-01-01

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which

Predictive modelling of complex agronomic and biological systems.

Science.gov (United States)

Keurentjes, Joost J B; Molenaar, Jaap; Zwaan, Bas J

2013-09-01

Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead. © 2013 John Wiley & Sons Ltd.

Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

DEFF Research Database (Denmark)

Green, Sara; Serban, Maria; Scholl, Raphael

2018-01-01

of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

Complex biological and bio-inspired systems

Energy Technology Data Exchange (ETDEWEB)

Ecke, Robert E [Los Alamos National Laboratory

2009-01-01

The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

Methods of Separation of Total Rare Earths in Low-Alloy Constructional Steels

Science.gov (United States)

1954-11-10

investigation of the effects of added anions upon the absorption spectra of the rare earths elements has been continued. The effects of tartrate in...complexes, the equilibrium among the di-hydrogen cupric EDTA complex, uncomplexed cupric ions, the monohydrogen rare earth- EDTA complex and rare...solutions used are described. A polaro- graphic method for determining cupric ion concentration in support- ing KNOj solutions, and thereby supporting

Mössbauer study of some biological iron complexes

Indian Academy of Sciences (India)

Abstract. Some biological complexes containing iron are investigated experimentally at room temperature using the Mössbauer resonance. The complexes show quadrupole doublet and Kramer's degeneracy is found to exist. The electric field gradient, difference in s-electron densities and quadrupole coupling constant ...

Finding optimal interaction interface alignments between biological complexes

KAUST Repository

Cui, Xuefeng

2015-06-13

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

Cupric citrate as growth promoter for broiler chickens in different rearing stages Citrato cúprico como promotor de crescimento de frangos de corte diferentes em fases de criação

Directory of Open Access Journals (Sweden)

Mônica Maria de Almeida Brainer

2003-01-01

Full Text Available Feeding cupric citrate as alternative to cupric sulfate to broilers has been suggested in the literature. Day-old male broiler chicks (1,200 were used in an experiment to evaluate the efficacy of cupric citrate supplementation (75 mg Cu kg-1 during the 1-21, 22-42 or 1-42 d periods in comparison to an unsupplemented diet and a diet supplemented with cupric sulfate (200 mg Cu kg-1, 1-42 d. A randomized block design was used, with five treatments, six replicates and 40 birds per pen. The diets, based on corn and soybean meal, and water were offered ad libitum during the 42-day experimental period. Over the entire period, there was no effect of copper supplementation (P > 0.05 on bird live weight, weight gain, feed intake, feed conversion and mortality. Cupric citrate supplementation on the 22-42 d period resulted in worse feed conversion as compared to broilers receiving cupric sulfate (2.014 vs. 1.967, P Citrato cúprico foi apontado como alternativa ao sulfato cúprico como promotor de crescimento na dieta de frangos. Este trabalho avaliou a eficácia do citrato cúprico em diferentes fases da criação de frangos de corte. Foram utilizados 1200 pintos machos, em um experimento em blocos casualizados, com cinco tratamentos, seis repetições e 40 aves por parcela. Os tratamentos consistiram de uma dieta não suplementada ou suplementada com citrato cúprico anidro (75 mg Cu kg-1 de 1 a 21 dias, de 22 a 42 dias ou de 1 a 42 dias, ou com sulfato cúprico pentahidratado (200 mg Cu kg-1 de 1 a 42 dias. Foram avaliados o desempenho das aves e o resíduo de cobre na cama. Dietas, à base de milho e farelo de soja, e água foram fornecidas à vontade durante todo o período experimental. Não houve efeito da suplementação de cobre (P > 0,05 sobre o peso vivo, ganho de peso, consumo de ração, conversão alimentar e mortalidade mais refugagem. Os frangos que receberam citrato cúprico na ração a partir dos 22 dias tiveram, no período 22-42 dias

Complex fluids in biological systems experiment, theory, and computation

CERN Document Server

2015-01-01

This book serves as an introduction to the continuum mechanics and mathematical modeling of complex fluids in living systems. The form and function of living systems are intimately tied to the nature of surrounding fluid environments, which commonly exhibit nonlinear and history dependent responses to forces and displacements. With ever-increasing capabilities in the visualization and manipulation of biological systems, research on the fundamental phenomena, models, measurements, and analysis of complex fluids has taken a number of exciting directions. In this book, many of the world’s foremost experts explore key topics such as: Macro- and micro-rheological techniques for measuring the material properties of complex biofluids and the subtleties of data interpretation Experimental observations and rheology of complex biological materials, including mucus, cell membranes, the cytoskeleton, and blood The motility of microorganisms in complex fluids and the dynamics of active suspensions Challenges and solut...

Bioinspired tannic acid-copper complexes as selective coating for nanofiltration membranes

KAUST Repository

Chakrabarty, Tina

2017-04-27

Bio-polyphenols that are present in tea, date fruits, chockolate and many other plants have been recognized as scaffold material for the manufacture of composite filtration membranes. These phenolic biomolecules possess abundant gallol (1,2,3-trihydroxyphenyl) and catechol (1,2-dihydroxyphenyl) functional groups, which allow the spontaneous formation of a thin polymerized layer at the right pH conditions. Here, we report a facile and cost-effective method to coat porous membranes via the complexation of tannic acid (TA) and cupric acetate (mono hydrate) through co-deposition. The modified membranes were investigated by XPS, ATR/FTIR, water contact angle, SEM and water permeance for a structural and morphological analysis. The obtained results reveal that the modified membranes with TA and cupric acetate (CuII) developed a thin skin layer, which showed excellent hydrophilicity with good water permeance. These membranes were tested with different molecular weight polyethylene glycols (PEG) in aqueous solution; the MWCO was around 600 Daltons.

Microstructural and electrical properties of PVA/PVP polymer blend films doped with cupric sulphate

Energy Technology Data Exchange (ETDEWEB)

Hemalatha, K.; Gowtham, G. K.; Somashekarappa, H., E-mail: drhssappa@gmail.com [Department of Physics, Yuvaraja’s College, University of Mysore, Mysore 570 005, Karnataka (India); Mahadevaiah,; Urs, G. Thejas; Somashekar, R. [Department of Studies in Material Sciences, University of Mysore, Mysore 570 006, Karnataka (India)

2016-05-23

A series of polyvinyl alcohol (PVA)/polyvinyl pyrrolidone (PVP) polymer blends added with different concentrations of cupric sulphate (CuSO{sub 4}) were prepared by solution casting method and were subjected to X-ray diffraction (XRD) and Ac conductance measurements. An attempt has been made to study the changes in crystal imperfection parameters in PVA/PVP blend films with the increase in concentration of CuSO{sub 4}. Results show that decrease in micro crystalline parameter values is accompanied with increase in the amorphous content in the film which is the reason for film to have more flexibility, biodegradability and good ionic conductivity. AC conductance measurements in these films show that the conductivity increases as the concentration of CuSO{sub 4} increases. These films were suitable for electro chemical applications.

NTP technical report on the toxicity studies of Cupric Sulfate (CAS No. 7758-99-8) Administered in Drinking Water and Feed to F344/N Rats and B6C3F1 Mice.

Science.gov (United States)

Hebert, Charles

1993-07-01

Cupric sulfate is an inorganic salt which is widely used in industry, agriculture, and veterinary medicine. Its applications include use as an algicide in potable waters and as a feed additive and therapeutic agent in swine, sheep, and cattle. Because copper salts are found in human water supplies, toxicity studies of cupric sulfate pentahydrate were conducted in male and female F344/N rats and B6C3F1 mice by the drinking water (2-week studies only) and dosed feed routes (2-week and 13-week studies). Animals were evaluated for hematology, clinical chemistry, urinalysis, reproductive toxicity, tissue metal accumulation, and histopathology. In the 2-week drinking water studies, groups of five rats and five mice per sex received cupric sulfate at concentrations of 300 to 30,000 ppm for 15 days. One female rat, one male mouse, and three female mice in the 3000 ppm groups and all rats and mice in the 10,000 and 30,000 ppm groups died before the end of the studies. The remaining mice and rats in the 3000 ppm groups gained little or lost weight. Water consumption in the three highest dose groups of both species was reduced by more than 65%. Clinical signs observed in these groups were typical of those seen in moribund animals and were attributed to dehydration. The only gross or microscopic change specifically related to cupric sulfate toxicity was an increase in the size and number of cytoplasmic protein droplets in the epithelium of the renal proximal convoluted tubule in male rats from the 300 and 1000-ppm groups. In the 2-week feed studies, groups of five rats and five mice per sex were fed diets containing 1000 to 16,000 ppm cupric sulfate. No chemical-related deaths occurred in any dose group. Compared to the controls, rats and mice in the two highest dose groups had reduced body weight gains which were attributed to decreased feed consumption. Hyperplasia with hyperkeratosis of the squamous epithelium on the limiting ridge of the forestomach was seen in rats and

Comparative toxicity and biodistribution of copper nanoparticles and cupric ions in rats

Directory of Open Access Journals (Sweden)

Lee IC

2016-06-01

Full Text Available In-Chul Lee,1 Je-Won Ko,1 Sung-Hyeuk Park,1 Je-Oh Lim,1 In-Sik Shin,1 Changjong Moon,1 Sung-Hwan Kim,2 Jeong-Doo Heo,3 Jong-Choon Kim1 1College of Veterinary Medicine BK21 Plus Project Team, Chonnam National University, Gwangju, 2Jeonbuk Department of Inhalation Research, Korea Institute of Toxicology, Jeongeup, 3Gyeongnam Department of Environment and Toxicology, Korea Institute of Toxicology, Gyeongnam, Republic of Korea Abstract: Despite widespread use and prospective biomedical applications of copper nanoparticles (Cu NPs, their biosafety issues and kinetics remain unclear. Thus, the aim of this study was to compare the detailed in vivo toxicity of Cu NPs and cupric ions (CuCl2; Cu ions after a single oral dose. We determined the physicochemical characteristics of Cu NPs, including morphology, hydrodynamic size, zeta potential, and dissolution in gastric (pH 1.5, vehicle (pH 6.5, and intestinal (pH 7.8 conditions. We also evaluated the kinetics of Cu following a single equivalent dose (500 mg/kg of Cu NPs and Cu ions. Cu NPs had highest dissolution (84.5% only in gastric conditions when compared with complete dissolution of Cu ions under various physiological milieus. Kinetic analysis revealed that highest Cu levels in blood and tested organs of Cu NP-treated rats were 15%–25% lower than that of Cu ions. Similar to the case of Cu ions, Cu levels in the tested organs (especially liver, kidney, and spleen of Cu NP-treated rats increased significantly when compared with the vehicle control. However, delay in reaching the highest level and biopersistence of Cu were observed in the blood and tested organs of Cu NP-treated rats compared with Cu ions. Extremely high levels of Cu in feces indicated that unabsorbed Cu NPs or absorbed Cu ions were predominantly eliminated through liver/feces. Cu NPs exerted apparent toxicological effects at higher dose levels compared with Cu ions and showed sex-dependent differences in mortality, biochemistry, and

Circulating immune complexes – reviewing the biological roles in ...

African Journals Online (AJOL)

Circulating immune complexes – reviewing the biological roles in human immune function and exercise. ... studies that have investigated CIC's following exercise and proposes that a comprehensive understanding and interpretation of immune system responses to exercise should take these complexes into consideration.

Carbon Nanoparticles decorated with cupric oxide Nanoparticles prepared by laser ablation in liquid as an antibacterial therapeutic agent

Science.gov (United States)

Khashan, Khawla S.; Jabir, Majid S.; Abdulameer, Farah A.

2018-03-01

Carbon nanoparticles (CNPs) decorated with cupric oxide nanoparticles (CuO NPs) were prepared by laser ablation in water, and their antibacterial activity was examined. X-ray diffraction measurements demonstrated the presence of carbon phases and different CuO phases, and results were confirmed by Fourier transform infrared analysis. Energy- Dispersive spectra showed the presence of C, O, and Cu in the final product. Transmission electron micrographs revealed that the CNPs were 10-80 nm in size and spherical; after being decorated with CuO NPs, particles became 5-50 nm in size and uniform in shape. The absorption spectrum of decorated Nanoparticles indicated the appearance of a new peak at 254-264 nm in addition to the fundamental peak at 228 nm. We then examined the antibacterial activity of the decorated CNPs for both gram-negative and -positive bacteria using the agar-well-diffusion method. The mode of action was determined using acridine orange-ethidium bromide staining to detect reactive oxygen species, and bacterial morphological change was studied by scanning electron microscopy. Results showed that CNPs decorated with 43% CuO NPs had the highest antibacterial activity for gram-positive bacteria. The CNPs acted on the cytoplasmic membrane and nucleic acid of bacteria, which led to a loss of cell-wall integrity, increased cell-wall permeability, and nucleic acid damage. The results offer a novel way to synthesis Carbon nanoparticles decorated with cupric oxide nanoparticles and could use them as novel antibacterial agent in future for pharmaceutical and biomedical applications.

Synthesis, Physical Characterization and Biological Activity of Some Schiff Base Complexes

Directory of Open Access Journals (Sweden)

R. Rajavel

2008-01-01

Full Text Available Structural modification of organic molecule has considerable biological relevance. Further, coordination of a biomolecules to the metal ions significantly alters the effectiveness of the biomolecules. In view of the antimicrobial activity ligand [bis-(2-aminobenzaldehyde] malonoyl dihydrazone], metal complexes with Cu(II, Ni(II, Zn(II and oxovanadium(IV have been synthesized and found to be potential antimicrobial agents. An attempt is also made to correlate the biological activities with geometry of the complexes. The complexes have been characterized by elemental analysis, molar conductance, spectra and cyclicvoltammetric measurements. The structural assessment of the complexes has been carried out based on electronic, infrared and molar conductivity values.

EPR spectroscopy of complex biological iron-sulfur systems.

Science.gov (United States)

Hagen, Wilfred R

2018-02-21

From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.

How do precision medicine and system biology response to human body's complex adaptability?

Science.gov (United States)

Yuan, Bing

2016-12-01

In the field of life sciences, although system biology and "precision medicine" introduce some complex scientifific methods and techniques, it is still based on the "analysis-reconstruction" of reductionist theory as a whole. Adaptability of complex system increase system behaviour uncertainty as well as the difficulties of precise identifification and control. It also put systems biology research into trouble. To grasp the behaviour and characteristics of organism fundamentally, systems biology has to abandon the "analysis-reconstruction" concept. In accordance with the guidelines of complexity science, systems biology should build organism model from holistic level, just like the Chinese medicine did in dealing with human body and disease. When we study the living body from the holistic level, we will fifind the adaptability of complex system is not the obstacle that increases the diffificulty of problem solving. It is the "exceptional", "right-hand man" that helping us to deal with the complexity of life more effectively.

Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective

NARCIS (Netherlands)

Bosse, T.; Jonker, C.M.; Treur, J.

2005-01-01

This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics

Exploitation of complex network topology for link prediction in biological interactomes

KAUST Repository

Alanis Lobato, Gregorio

2014-06-01

The network representation of the interactions between proteins and genes allows for a holistic perspective of the complex machinery underlying the living cell. However, the large number of interacting entities within the cell makes network construction a daunting and arduous task, prone to errors and missing information. Fortunately, the structure of biological networks is not different from that of other complex systems, such as social networks, the world-wide web or power grids, for which growth models have been proposed to better understand their structure and function. This means that we can design tools based on these models in order to exploit the topology of biological interactomes with the aim to construct more complete and reliable maps of the cell. In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable and biologically meaningful information that enriches the datasets to which we have access today.

Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

Science.gov (United States)

Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

2017-07-05

Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

From globally coupled maps to complex-systems biology

Energy Technology Data Exchange (ETDEWEB)

Kaneko, Kunihiko, E-mail: kaneko@complex.c.u-tokyo.ac.jp [Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, The University of Tokyo 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

2015-09-15

Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

Linking structural features of protein complexes and biological function.

Science.gov (United States)

Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

2015-09-01

Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

Screening the efficient biological prospects of triazole allied mixed ligand metal complexes

Science.gov (United States)

Utthra, Ponnukalai Ponya; Kumaravel, Ganesan; Raman, Natarajan

2017-12-01

Triazole appended mixed ligand complexes (1-8) of the general formula [ML (bpy/phen)2]Cl2, where M = Cu(II), Co(II), Ni(II) and Zn(II), L = triazole appended Schiff base (E)sbnd N-(4-nitrobenzylidene)-1H-1,2,4-triazol-3-amine and bpy/phen = 2,2‧-bipyridine/1,10-phenanthroline, have been synthesized. The design and synthesis of this elaborate ligand has been performed with the aim of increasing stability and conjugation of 1,2,4 triazole, whose Schiff base derivatives are known as biologically active compounds thereby exploring their DNA binding affinity and other biological applications. The compounds have been comprehensively characterized by elemental analysis, spectroscopic methods (IR, UV-Vis, EPR, 1H and 13C NMR spectroscopy), ESI mass spectrometry and magnetic susceptibility measurements. The complexes were found to exhibit octahedral geometry. The complexes 1-8 were subjected to DNA binding techniques evaluated using UV-Vis absorption, CV, CD, Fluorescence spectroscopy and hydrodynamic measurements. Complex 5 showed a Kb value of 3.9 × 105 M-1. The DNA damaging efficacy for the complexes was observed to be high compared to the ligand. The antimicrobial screening of the compounds against bacterial and fungal strains indicates that the complexes possess excellent antimicrobial activity than the ligand. The overall biological activity of the complexes with phen as a co-ligand possessed superior potential than the ligand.

Chiral recognition of proteins having L-histidine residues on the surface with lanthanide ion complex incorporated-molecularly imprinted fluorescent nanoparticles

International Nuclear Information System (INIS)

Uzun, Lokman; Uzek, Recep; Şenel, Serap; Say, Ridvan; Denizli, Adil

2013-01-01

In this study, lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles were synthesized. A combination of three novel approaches was applied for the purpose. First, lanthanide ions [Terbium(III)] were complexed with N-methacryloyl-L-histidine (MAH), polymerizable derivative of L-histidine amino acid, in order to incorporate the complex directly into the polymeric backbone. At the second stage, L-histidine molecules imprinted nanoparticles were utilized instead of whole protein imprinting in order to avoid whole drawbacks such as fragility, complexity, denaturation tendency, and conformation dependency. At the third stage following the first two steps mentioned above, imprinted L-histidine was coordinated with cupric ions [Cu(II)] to conduct the study under mild conditions. Then, molecularly imprinted fluorescent nanoparticles synthesized were used for L-histidine adsorption from aqueous solution to optimize conditions for adsorption and fluorimetric detection. Finally, usability of nanoparticles was investigated for chiral biorecognition using stereoisomer, D-histidine, racemic mixture, D,L-histidine, proteins with surface L-histidine residue, lysozyme, cytochrome C, or without ribonuclease A. The results revealed that the proposed polymerization strategy could make significant contribution to the solution of chronic problems of fluorescent component introduction into polymers. Additionally, the fluorescent nanoparticles reported here could be used for selective separation and fluorescent monitoring purposes. Highlights: • Lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles • Direct incorporation of the fluorescent complex into polymeric backbone. • Imprinting by assistance of cupric ion coordination into nanoparticles • Evaluation of the chiral biorecognition ability of nanoparticles • Simultaneous selective separation and fluorescent monitoring

Chiral recognition of proteins having L-histidine residues on the surface with lanthanide ion complex incorporated-molecularly imprinted fluorescent nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Uzun, Lokman, E-mail: lokman@hacettepe.edu.tr [Hacettepe University, Department of Chemistry, 06381, Ankara (Turkey); Uzek, Recep; Şenel, Serap [Hacettepe University, Department of Chemistry, 06381, Ankara (Turkey); Say, Ridvan [Anadolu University, Department of Chemistry, 26470, Eskisehir (Turkey); Denizli, Adil [Hacettepe University, Department of Chemistry, 06381, Ankara (Turkey)

2013-08-01

In this study, lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles were synthesized. A combination of three novel approaches was applied for the purpose. First, lanthanide ions [Terbium(III)] were complexed with N-methacryloyl-L-histidine (MAH), polymerizable derivative of L-histidine amino acid, in order to incorporate the complex directly into the polymeric backbone. At the second stage, L-histidine molecules imprinted nanoparticles were utilized instead of whole protein imprinting in order to avoid whole drawbacks such as fragility, complexity, denaturation tendency, and conformation dependency. At the third stage following the first two steps mentioned above, imprinted L-histidine was coordinated with cupric ions [Cu(II)] to conduct the study under mild conditions. Then, molecularly imprinted fluorescent nanoparticles synthesized were used for L-histidine adsorption from aqueous solution to optimize conditions for adsorption and fluorimetric detection. Finally, usability of nanoparticles was investigated for chiral biorecognition using stereoisomer, D-histidine, racemic mixture, D,L-histidine, proteins with surface L-histidine residue, lysozyme, cytochrome C, or without ribonuclease A. The results revealed that the proposed polymerization strategy could make significant contribution to the solution of chronic problems of fluorescent component introduction into polymers. Additionally, the fluorescent nanoparticles reported here could be used for selective separation and fluorescent monitoring purposes. Highlights: • Lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles • Direct incorporation of the fluorescent complex into polymeric backbone. • Imprinting by assistance of cupric ion coordination into nanoparticles • Evaluation of the chiral biorecognition ability of nanoparticles • Simultaneous selective separation and fluorescent monitoring.

A microfluidic dialysis device for complex biological mixture SERS analysis

KAUST Repository

Perozziello, Gerardo; Candeloro, Patrizio; Gentile, Francesco T.; Coluccio, Maria Laura; Tallerico, Marco; De Grazia, Antonio; Nicastri, Annalisa; Perri, Angela Mena; Parrotta, Elvira; Pardeo, Francesca; Catalano, Rossella; Cuda, Giovanni; Di Fabrizio, Enzo M.

2015-01-01

In this paper, we present a microfluidic device fabricated with a simple and inexpensive process allowing rapid filtering of peptides from a complex mixture. The polymer microfluidic device can be used for sample preparation in biological

Degeneracy: a link between evolvability, robustness and complexity in biological systems

Directory of Open Access Journals (Sweden)

Whitacre James M

2010-02-01

Full Text Available Abstract A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability.

Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

Science.gov (United States)

Jalili, Mahdi

2018-03-01

I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology.

Science.gov (United States)

Sudhir, Putty-Reddy; Chen, Chung-Hsuan

2016-03-22

A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.

Reflecting on complexity of biological systems: Kant and beyond?

Science.gov (United States)

Van de Vijver, Gertrudis; Van Speybroeck, Linda; Vandevyvere, Windy

2003-01-01

Living organisms are currently most often seen as complex dynamical systems that develop and evolve in relation to complex environments. Reflections on the meaning of the complex dynamical nature of living systems show an overwhelming multiplicity in approaches, descriptions, definitions and methodologies. Instead of sustaining an epistemic pluralism, which often functions as a philosophical armistice in which tolerance and so-called neutrality discharge proponents of the burden to clarify the sources and conditions of agreement and disagreement, this paper aims at analysing: (i) what has been Kant's original conceptualisation of living organisms as natural purposes; (ii) how the current perspectives are to be related to Kant's viewpoint; (iii) what are the main trends in current complexity thinking. One of the basic ideas is that the attention for structure and its epistemological consequences witness to a great extent of Kant's viewpoint, and that the idea of organisational stratification today constitutes a different breeding ground within which complexity issues are raised. The various approaches of complexity in biological systems are captured in terms of two different styles, universalism and (weak and strong) constructivism, between which hybrid forms exist.

Life: An Introduction to Complex Systems Biology

CERN Document Server

Kaneko, Kunihiko

2006-01-01

What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there? This book examines life not from the reductionist point of view, but rather asks the question: what are the universal properties of living systems and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.

Exploitation of complex network topology for link prediction in biological interactomes

KAUST Repository

Alanis Lobato, Gregorio

2014-01-01

In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable

Complexity: the organizing principle at the interface of biological (dis ...

Indian Academy of Sciences (India)

RAMRAY BHAT

2017-07-05

Jul 5, 2017 ... opment of complexity theory in the context of biological systems. ... (DST), a mathematical enterprise that deals with the behaviour of ... and application of programming to trace the dynamical .... with the resultant organization being regulated by the ... more regular the pattern, the smaller the program needed.

The complexity of DNA damage: relevance to biological consequences

International Nuclear Information System (INIS)

Ward, J.F.

1994-01-01

Ionizing radiation causes both singly and multiply damaged sites in DNA when the range of radical migration is limited by the presence of hydroxyl radical scavengers (e.g. within cells). Multiply damaged sites are considered to be more biologically relevant because of the challenges they present to cellular repair mechanisms. These sites occur in the form of DNA double-strand breaks (dsb) but also as other multiple damages that can be converted to dsb during attempted repair. The presence of a dsb can lead to loss of base sequence information and/or can permit the two ends of a break to separate and rejoin with the wrong partner. (Multiply damaged sites may also be the biologically relevant type of damage caused by other agents, such as UVA, B and/or C light, and some antitumour antibiotics). The quantitative data available from radiation studies of DNA are shown to support the proposed mechanisms for the production of complex damage in cellular DNA, i.e. via scavengable and non-scavengable mechanisms. The yields of complex damages can in turn be used to support the conclusion that cellular mutations are a consequence of the presence of these damages within a gene. (Author)

Activation of persulfate/copper by hydroxylamine via accelerating the cupric/cuprous redox couple.

Science.gov (United States)

Zhou, Peng; Zhang, Jing; Liang, Juan; Zhang, Yongli; Liu, Ya; Liu, Bei

2016-01-01

Cuprous copper [Cu(I)] reacts with sodium persulfate (PDS) to generate sulfate radical SO4(-)•, but it has been seldom investigated owing to its instability and difficulty in dissolving it. This study proposes a new method to regenerate Cu(I) from cupric copper [Cu(II)] by addition of hydroxylamine (HA) to induce the continuous production of radicals through active PDS, and investigates the resulting enhanced methyl orange (MO) degradation efficiency and mechanism in the new system. HA accelerated the degradation of MO markedly in the pH range from 6.0 to 8.0 in the HA/Cu(II)/PDS process. Both SO4(-)• and hydroxyl radicals (•OH) were considered as the primary reactive radicals in the process. The MO degradation in the HA/Cu(II)/PDS process can be divided into three stages: the fast stage, the transitory stage, and the low stage. MO degradation was enhanced with increased dosage of PDS. Although high dosage of HA could accelerate the transformation of the Cu(II)/Cu(I) cycle to produce more reactive radicals, excess HA can quench the reactive radicals. This study indicates that through a copper-redox cycling mechanism by HA, the production of SO4(-)• and •OH can be strongly enhanced, and the effective pH range can be expanded to neutral conditions.

A comparison of the application of a biological and phenetic species concept in the Hebeloma crustuliniforme complex within a phylogenetic framework

DEFF Research Database (Denmark)

Aanen, Duur Kornelis; Kuyper, T.W.

2004-01-01

a major factor. Intercompatibility tests and DNA based phylogenies indicate that most biological species are very closely related and hence provide support for the claim that correspondence between a biological species concept and a phenetic species concept in the H. crustuliniforme complex is not likely...... biological species in that complex. Based on two nuclear sequences, we present a best estimate of the phylogeny of biological species within the complex. Using this phylogeny, on the basis of strict monophyly only two species can be morphologically recognised among 22 biological species. Relaxing......A method is presented to derive an operational phenetic species concept for the Hebeloma crustuliniforme complex in northwestern Europe. The complex was found to consist of at least 22 biological species (intercompatibility groups; ICGs). Almost none of these biological species could be recognised...

Kirigami artificial muscles with complex biologically inspired morphologies

International Nuclear Information System (INIS)

Sareh, Sina; Rossiter, Jonathan

2013-01-01

In this paper we present bio-inspired smart structures which exploit the actuation of flexible ionic polymer composites and the kirigami design principle. Kirigami design is used to convert planar actuators into active 3D structures capable of large out-of-plane displacement and that replicate biological mechanisms. Here we present the burstbot, a fluid control and propulsion mechanism based on the atrioventricular cuspid valve, and the vortibot, a spiral actuator based on Vorticella campanula, a ciliate protozoa. Models derived from biological counterparts are used as a platform for design optimization and actuator performance measurement. The symmetric and asymmetric fluid interactions of the burstbot are investigated and the effectiveness in fluid transport applications is demonstrated. The vortibot actuator is geometrically optimized as a camera positioner capable of 360° scanning. Experimental results for a one-turn spiral actuator show complex actuation derived from a single degree of freedom control signal. (paper)

Large, dynamic, multi-protein complexes: a challenge for structural biology

Czech Academy of Sciences Publication Activity Database

Rozycki, B.; Bouřa, Evžen

2014-01-01

Roč. 26, č. 46 (2014), 463103/1-463103/11 ISSN 0953-8984 R&D Projects: GA MŠk LO1302 EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : protein structure * multi-protein complexes * hybrid methods of structural biology Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.346, year: 2014

Chemometric and Statistical Analyses of ToF-SIMS Spectra of Increasingly Complex Biological Samples

Energy Technology Data Exchange (ETDEWEB)

Berman, E S; Wu, L; Fortson, S L; Nelson, D O; Kulp, K S; Wu, K J

2007-10-24

Characterizing and classifying molecular variation within biological samples is critical for determining fundamental mechanisms of biological processes that will lead to new insights including improved disease understanding. Towards these ends, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to examine increasingly complex samples of biological relevance, including monosaccharide isomers, pure proteins, complex protein mixtures, and mouse embryo tissues. The complex mass spectral data sets produced were analyzed using five common statistical and chemometric multivariate analysis techniques: principal component analysis (PCA), linear discriminant analysis (LDA), partial least squares discriminant analysis (PLSDA), soft independent modeling of class analogy (SIMCA), and decision tree analysis by recursive partitioning. PCA was found to be a valuable first step in multivariate analysis, providing insight both into the relative groupings of samples and into the molecular basis for those groupings. For the monosaccharides, pure proteins and protein mixture samples, all of LDA, PLSDA, and SIMCA were found to produce excellent classification given a sufficient number of compound variables calculated. For the mouse embryo tissues, however, SIMCA did not produce as accurate a classification. The decision tree analysis was found to be the least successful for all the data sets, providing neither as accurate a classification nor chemical insight for any of the tested samples. Based on these results we conclude that as the complexity of the sample increases, so must the sophistication of the multivariate technique used to classify the samples. PCA is a preferred first step for understanding ToF-SIMS data that can be followed by either LDA or PLSDA for effective classification analysis. This study demonstrates the strength of ToF-SIMS combined with multivariate statistical and chemometric techniques to classify increasingly complex biological samples

Using Simple Manipulatives to Improve Student Comprehension of a Complex Biological Process: Protein Synthesis

Science.gov (United States)

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article…

Biological Recovery of Platinum Complexes from Diluted Aqueous Streams by Axenic Cultures.

Directory of Open Access Journals (Sweden)

Synthia Maes

Full Text Available The widespread use of platinum in high-tech and catalytic applications has led to the production of diverse Pt loaded wastewaters. Effective recovery strategies are needed for the treatment of low concentrated waste streams to prevent pollution and to stimulate recovery of this precious resource. The biological recovery of five common environmental Pt-complexes was studied under acidic conditions; the chloro-complexes PtCl42- and PtCl62-, the amine-complex Pt(NH34Cl2 and the pharmaceutical complexes cisplatin and carboplatin. Five bacterial species were screened on their platinum recovery potential; the Gram-negative species Shewanella oneidensis MR-1, Cupriavidus metallidurans CH34, Geobacter metallireducens, and Pseudomonas stutzeri, and the Gram-positive species Bacillus toyonensis. Overall, PtCl42- and PtCl62- were completely recovered by all bacterial species while only S. oneidensis and C. metallidurans were able to recover cisplatin quantitatively (99%, all in the presence of H2 as electron donor at pH 2. Carboplatin was only partly recovered (max. 25% at pH 7, whereas no recovery was observed in the case of the Pt-tetraamine complex. Transmission electron microscopy (TEM revealed the presence of both intra- and extracellular platinum particles. Flow cytometry based microbial viability assessment demonstrated the decrease in number of intact bacterial cells during platinum reduction and indicated C. metallidurans to be the most resistant species. This study showed the effective and complete biological recovery of three common Pt-complexes, and estimated the fate and transport of the Pt-complexes in wastewater treatment plants and the natural environment.

A study of ruthenium complexes of some biologically relevant a-N ...

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences; Volume 112; Issue 3. A study of ruthenium complexes of some biologically relevant ∙ -N-heterocyclic ... Author Affiliations. P Sengupta1 S Ghosh1. Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, India ...

[Physico-chemical features of dinitrosyl iron complexes with natural thiol-containing ligands underlying biological activities of these complexes].

Science.gov (United States)

Vanin, A F; Borodulin, R R; Kubrina, L N; Mikoian, V D; Burbaev, D Sh

2013-01-01

Current notions and new experimental data of the authors on physico-chemical features of dinitrosyl iron complexes with natural thiol-containing ligands (glutathione or cysteine), underlying the ability of the complexes to act as NO molecule and nitrosonium ion donors, are considered. This ability determines various biological activities of dinitrosyl iron complexes--inducing long-lasting vasodilation and thereby long-lasting hypotension in human and animals, inhibiting pellet aggregation, increasing red blood cell elasticity, thereby stimulating microcirculation, and reducing necrotic zone in animals with myocardial infarction. Moreover, dinitrosyl iron complexes are capable of accelerating skin wound healing, improving the function of penile cavernous tissue, blocking apoptosis development in cell cultures. When decomposed dinitrosyl iron complexes can exert cytotoxic effect that can be used for curing infectious and carcinogenic pathologies.

Transition metal complexes of some biologically active ligands; synthesis characterization and bioactivities

International Nuclear Information System (INIS)

Rehman, S.; Ali, N.; Nisar, M.

2009-01-01

Transition/representative transition metals complexes of biologically active chelating agent 1,2-dipyrolodinoethane were synthesized and characterized through spectral and analytical data. The complexes are of the formula (M(L)X/sub 2/). Where (M = Co (II), Ni (II), Cu (II), Zn (II), Hg (II) and Cd (II) and X = CI, Br, NO/sub 3/). Tetrahedral geometry has been proposed to these-metal complexes with the help of magnetic measurements, elemental analysis, chemical stoichiometry and spectroscopic data Antibacterial activity of the ligand and its metal complexes were screened against Eschereschi coli, Klebsiello pneumonia, Proteus mirabilis, Proteus vulhari, Streptococcus pneumonia, Salmonella Iyphi, Bacilh,s anthrax, Streptococcus fecalis and Staphylococcus aureus. Complexes were found to be active against Eschereschi coli, Klebsiella pneumonia, Proteus mirabilis and Proteus vulharis. (author)

Evaluating the biological activity of oil-polluted soils using a complex index

Science.gov (United States)

Kabirov, R. R.; Kireeva, N. A.; Kabirov, T. R.; Dubovik, I. Ye.; Yakupova, A. B.; Safiullina, L. M.

2012-02-01

A complex index characterizing the biological activity of soils (BAS) is suggested. It is based on an estimate of the level of activity of catalase; the number of heterotrophic and hydrocarbon oxidizing microorganisms, microscopic fungi, algae, and cyanobacteria; and the degree of development of higher plants and insects in the studied soil. The data on using the BAS coefficient for evaluating the efficiency of rehabilitation measures for oil-polluted soils are given. Such measures included introducing the following biological preparations: Lenoil based on a natural consortium of microorganisms Bacillus brevis and Arthrobacter sp.; the Azolen biofertilizer with complex action based on Azotobacter vinelandii; the Belvitamil biopreparation, which is the active silt of pulp and paper production; and a ready-mixed industrial association of aerobic and anaerobic microorganisms that contains hydrocarbon oxidizing microorganisms of the Arthrobacter, Bacillus, Candida, Desulfovibrio, and Pseudomonas genera.

Determination of permeability of ultra-fine cupric oxide aerosol through military filters and protective filters

Science.gov (United States)

Kellnerová, E.; Večeřa, Z.; Kellner, J.; Zeman, T.; Navrátil, J.

2018-03-01

The paper evaluates the filtration and sorption efficiency of selected types of military combined filters and protective filters. The testing was carried out with the use of ultra-fine aerosol containing cupric oxide nanoparticles ranging in size from 7.6 nm to 299.6 nm. The measurements of nanoparticles were carried out using a scanning mobility particle sizer before and after the passage through the filter and a developed sampling device at the level of particle number concentration approximately 750000 particles·cm-3. The basic parameters of permeability of ultra-fine aerosol passing through the tested material were evaluated, in particular particle size, efficiency of nanoparticle capture by filter, permeability coefficient and overall filtration efficiency. Results indicate that the military filter and particle filters exhibited the highest aerosol permeability especially in the nanoparticle size range between 100–200 nm, while the MOF filters had the highest permeability in the range of 200 to 300 nm. The Filter Nuclear and the Health and Safety filter had 100% nanoparticle capture efficiency and were therefore the most effective. The obtained measurement results have shown that the filtration efficiency over the entire measured range of nanoparticles was sufficient; however, it was different for particular particle sizes.

Biosynthesis of nano cupric oxide on cotton using Seidlitzia rosmarinus ashes utilizing bio, photo, acid sensing and leaching properties.

Science.gov (United States)

Bashiri Rezaie, Ali; Montazer, Majid; Rad, Mahnaz Mahmoudi

2017-12-01

In this research, a facile, rapid and eco-friendly method is introduced for synthesis and loading of cupric oxide on cellulosic chains of cotton fabric with functional properties. Seidlitzia rosmarinus ashes and copper acetate were employed as a natural source of alkaline and metal salt without further chemical materials. The treated samples indicated very good antibacterial activities toward both pathogen Staphylococcus aureus as Gram-positive and Escherichia coli as Gram-negative bacteria. Significant self-cleaning properties against degradation of methylene blue stain under UV irradiation were found. The sensing properties of high concentrated inorganic and organic acids such as sulfuric and formic acids based on colorimetric alterations of the treated fabrics were also confirmed showing acid leaching effects of the treated fabrics. Further, the treated samples showed coloring effects with an enhancement on the physio-mechanical properties including tensile strength, crease recovery angle and hydrophobocity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Novel synthesis on poly (vinyl alcohol): characterization, complexation a biological activity

International Nuclear Information System (INIS)

El-Sawy, N.M.; Elassar, A.Z.; Al-Fulaij, O.

2002-01-01

Poly(vinyl alcohol), PVA, readily condensed with phenyl hydrazine and malononitrile in basic medium to give the hydrazone and pyran derivatives, respectively. PVA reacted with chloroacetonitrile, biuet and thiophene carbonyl chloride to give modified polymeric materials. While addition of PVA to acrylonitrile and phenyl isothiocyanate gives the ether and thiocarbamate ester derivatives, respectively. Hydroxylamine hydrochloride reacted with the modified, carbonitrile containing, polymer to give the amidoxime derivative. The amidoximated products of PVA and carbamate ester of polymeric material were complexed with CUCL2 solution. The complex materials were confirmed by using UV and ESDS measurements. The morphology of PVA and complex with CUII was observed by SEM. Biological activity of some of the prepared compounds was investigated toward bacteria and fungi

Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

Directory of Open Access Journals (Sweden)

Schwieger Michael

2005-01-01

Full Text Available Abstract Background Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships. Results Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications. Conclusions The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends.

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

Science.gov (United States)

Urrios, Arturo; de Nadal, Eulàlia; Solé, Ricard; Posas, Francesc

2016-01-01

Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined. PMID:26829588

Measurement of the Cupric Ion Concentration in the Simulation of the Focusing effect

Energy Technology Data Exchange (ETDEWEB)

Moon, Je-Young; Hong, Seung-Hyun; Chung, Bum-Jin [Kyung Hee University, Seoul (Korea, Republic of)

2015-10-15

The Rayleigh number and aspect ratio (H/R) ranged from 8.49x10{sup 7} to 5.43x10{sup 9} and 0.135 to 0.541 respectively. In order to simulate the different temperature conditions of top and side wall, an electrical resistance was attached to the top wall so that it is mimics hotter wall condition. The heat transfer experiments were replaced by mass transfer experiments based on the heat and mass transfer analogy concept. A sulfuric acid-copper sulfate (H{sub 2}SO{sub 4} - CuSO{sub 4}) electroplating system was adopted as the mass transfer system. The experimental study was performed to investigate the focusing effect according to the different temperature conditions and the height in metallic layer. This work devised a method to simulate the different cooling conditions of the top and side walls and adopted an electrical resistance to the top plate. The electrical resistance was varied for the height of side wall. The experimental results agreed well with the Rayleigh-Benard convection correlations of Dropkin and Somerscales and Globe and Dropkin. The heat transfer was enhanced by increasing the electrical resistance and decreasing the height of side wall. The focusing effect at the side wall was improved by the hotter top wall condition. In order to overcome the limitations of mass transfer, this work tried to measure the cupric ion concentration. The methods of concentration measurement are RGB, Brightness, ICP and PIV. The key of RGB, Brightness and PIV method is the clear images of the thermal boundary layer.

Synthesis, characterization and biological activities of semicarbazones and their copper complexes.

Science.gov (United States)

Venkatachalam, Taracad K; Bernhardt, Paul V; Noble, Chris J; Fletcher, Nicholas; Pierens, Gregory K; Thurecht, Kris J; Reutens, David C

2016-09-01

Substituted semicarbazones/thiosemicarbazones and their copper complexes have been prepared and several single crystal structures examined. The copper complexes of these semicarbazone/thiosemicarbazones were prepared and several crystal structures examined. The single crystal X-ray structure of the pyridyl-substituted semicarbazone showed two types of copper complexes, a monomer and a dimer. We also found that the p-nitrophenyl semicarbazone formed a conventional 'magic lantern' acetate-bridged dimer. Electron Paramagnetic Resonance (EPR) of several of the copper complexes was consistent with the results of single crystal X-ray crystallography. The EPR spectra of the p-nitrophenyl semicarbazone copper complex in dimethylsulfoxide (DMSO) showed the presence of two species, confirming the structural information. Since thiosemicarbazones and semicarbazones have been reported to exhibit anticancer activity, we examined the anticancer activity of several of the derivatives reported in the present study and interestingly only the thiosemicarbazone showed activity while the semicarbazones were not active indicating that introduction of sulphur atom alters the biological profile of these thiosemicarbazones. Copyright © 2016 Elsevier Inc. All rights reserved.

Biological significance of complex N-glycans in plants and their impact on plant physiology.

Science.gov (United States)

Strasser, Richard

2014-01-01

Asparagine (N)-linked protein glycosylation is a ubiquitous co- and post-translational modification which can alter the biological function of proteins and consequently affects the development, growth, and physiology of organisms. Despite an increasing knowledge of N-glycan biosynthesis and processing, we still understand very little about the biological function of individual N-glycan structures in plants. In particular, the N-glycan-processing steps mediated by Golgi-resident enzymes create a structurally diverse set of protein-linked carbohydrate structures. Some of these complex N-glycan modifications like the presence of β1,2-xylose, core α1,3-fucose or the Lewis a-epitope are characteristic for plants and are evolutionary highly conserved. In mammals, complex N-glycans are involved in different cellular processes including molecular recognition and signaling events. In contrast, the complex N-glycan function is still largely unknown in plants. Here, in this short review, I focus on important recent developments and discuss their implications for future research in plant glycobiology and plant biotechnology.

Entropy as a method to investigate complex biological systems. An alternative view on the biological transition from healthy aging to frailty

Directory of Open Access Journals (Sweden)

Roberto Siciliano

2017-07-01

Full Text Available Everyone is subject to a process of progressive deterioration of control mechanisms, which supervise the complex network of human physiological functions, reducing the individual ability to adapt to emerging situations of stress or change. In the light of results obtained during the last years, it appears that some of the tools of nonlinear dynamics, first developed for the physical sciences are well suited for studies of biological systems. We believe that, considering the level of order or complexity of the anatomical apparatus by measuring a physical quantity, which is the entropy, we can evaluate the health status or vice versa fragility of a biological system. In particular, a reduction in the entropy value, indicates modification of the structural order with a progressive reduction of functional reserve of the individual, which is associated with a failure to adapt to stress conditions, difficult to be analyzed and documented with a unique traditional biochemical or biomolecular vision. Therefore, in this paper, we present a method that, conceptually combines complexity, disease and aging, alloys Poisson statistics, predictive of the personal level of health, to the entropy value indicating the status of bio-dynamic and functional body, seen as a complex and open thermodynamic system.

When physics is not "just physics": complexity science invites new measurement frames for exploring the physics of cognitive and biological development.

Science.gov (United States)

Kelty-Stephen, Damian; Dixon, James A

2012-01-01

The neurobiological sciences have struggled to resolve the physical foundations for biological and cognitive phenomena with a suspicion that biological and cognitive systems, capable of exhibiting and contributing to structure within themselves and through their contexts, are fundamentally distinct or autonomous from purely physical systems. Complexity science offers new physics-based approaches to explaining biological and cognitive phenomena. In response to controversy over whether complexity science might seek to "explain away" biology and cognition as "just physics," we propose that complexity science serves as an application of recent advances in physics to phenomena in biology and cognition without reducing or undermining the integrity of the phenomena to be explained. We highlight that physics is, like the neurobiological sciences, an evolving field and that the threat of reduction is overstated. We propose that distinctions between biological and cognitive systems from physical systems are pretheoretical and thus optional. We review our own work applying insights from post-classical physics regarding turbulence and fractal fluctuations to the problems of developing cognitive structure. Far from hoping to reduce biology and cognition to "nothing but" physics, we present our view that complexity science offers new explanatory frameworks for considering physical foundations of biological and cognitive phenomena.

Using multi-criteria analysis of simulation models to understand complex biological systems

Science.gov (United States)

Maureen C. Kennedy; E. David. Ford

2011-01-01

Scientists frequently use computer-simulation models to help solve complex biological problems. Typically, such models are highly integrated, they produce multiple outputs, and standard methods of model analysis are ill suited for evaluating them. We show how multi-criteria optimization with Pareto optimality allows for model outputs to be compared to multiple system...

Metal-containing Complexes of Lactams, Imidazoles, and Benzimidazoles and Their Biological Activity

Science.gov (United States)

Kukalenko, S. S.; Bovykin, B. A.; Shestakova, S. I.; Omel'chenko, A. M.

1985-07-01

The results of the latest investigations of the problem of the synthesis of metal-containing complexes of lactams, imidazoles, and benzimidazoles, their structure, and their stability in solutions are surveyed. Some data on their biological activity (pesticide and pharmacological) and the mechanism of their physiological action are presented. The bibliography includes 190 references.

Synthesis, spectroscopic and biological studies of transition metal complexes of novel schiff bases derived from amoxicillin and sugars

International Nuclear Information System (INIS)

Naz, N.

2009-01-01

Fe (II), Co (II) and Ni (II) metal complexes of new Schiff bases derived from amoxicillin with sugars (D-Glucose, D-Galactose and D-Mannose) have been synthesized and characterized by elemental analysis, FTIR, electronic absorption, and atomic absorption spectroscopy, magnetic moment measurements and thermal analysis. It has been found that Schiff bases behave as bi-dentate ligands forming complexes with 1:2 (metal:ligand) stoichiometry. The complexes were neutral as confirmed by their low conductance values. The biological applications of complexes have been studied on two gram negative (Escherichia coli and Pseudomonas aeruginosa) and two gram positive (Bacillus subtilis and Staphylococcus aureus) microorganisms by Agar diffusion disc method. It has been found that all the complexes have higher biological activities than the pure amoxicillin. (author)

Biologic activity of porphyromonas endodontalis complex lipids.

Science.gov (United States)

Mirucki, Christopher S; Abedi, Mehran; Jiang, Jin; Zhu, Qiang; Wang, Yu-Hsiung; Safavi, Kamran E; Clark, Robert B; Nichols, Frank C

2014-09-01

Periapical infections secondary to pulpal necrosis are associated with bacterial contamination of the pulp. Porphyromonas endodontalis, a gram-negative organism, is considered to be a pulpal pathogen. P. gingivalis is phylogenetically related to P. endodontalis and synthesizes several classes of novel complex lipids that possess biological activity, including the capacity to promote osteoclastogenesis and osteoclast activation. The purpose of this study was to extract and characterize constituent lipids of P. endodontalis and evaluate their capacity to promote proinflammatory secretory responses in the macrophage cell line, RAW 264.7, as well as their capacity to promote osteoclastogenesis and inhibit osteoblast activity. Constituent lipids of both organisms were fractionated by high-performance liquid chromatography and were structurally characterized using electrospray mass spectrometry or electrospray-mass spectrometry/mass spectrometry. The virulence potential of P. endodontalis lipids was then compared with known biologically active lipids isolated from P. gingivalis. P. endodontalis total lipids were shown to promote tumor necrosis factor alpha secretion from RAW 264.7 cells, and the serine lipid fraction appeared to account for the majority of this effect. P. endodontalis lipid preparations also increased osteoclast formation from RAW 264.7 cells, but osteoblast differentiation in culture was inhibited and appeared to be dependent on Toll-like receptor 2 expression. These effects underscore the importance of P. endodontalis lipids in promoting inflammatory and bone cell activation processes that could lead to periapical pathology. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Analysis of undergraduate students' conceptual models of a complex biological system across a diverse body of learners

Science.gov (United States)

Dirnbeck, Matthew R.

Biological systems pose a challenge both for learners and teachers because they are complex systems mediated by feedback loops; networks of cause-effect relationships; and non-linear, hierarchical, and emergent properties. Teachers and scientists routinely use models to communicate ideas about complex systems. Model-based pedagogies engage students in model construction as a means of practicing higher-order reasoning skills. One such modeling paradigm describes systems in terms of their structures, behaviors, and functions (SBF). The SBF framework is a simple modeling language that has been used to teach about complex biological systems. Here, we used student-generated SBF models to assess students' causal reasoning in the context of a novel biological problem on an exam. We compared students' performance on the modeling problem, their performance on a set of knowledge/comprehension questions, and their performance on a set of scientific reasoning questions. We found that students who performed well on knowledge and understanding questions also constructed more networked, higher quality models. Previous studies have shown that learners' mental maps increase in complexity with increased expertise. We wanted to investigate if biology students with varying levels of training in biology showed a similar pattern when constructing system models. In a pilot study, we administered the same modeling problem to two additional groups of students: 1) an animal physiology course for students pursuing a major in biology (n=37) and 2) an exercise physiology course for non-majors (n=27). We found that there was no significant difference in model organization across the three student populations, but there was a significant difference in the ability to represent function between the three populations. Between the three groups the non-majors had the lowest function scores, the introductory majors had the middle function scores, and the upper division majors had the highest function

Modelling and Simulating Complex Systems in Biology: introducing NetBioDyn : A Pedagogical and Intuitive Agent-Based Software

OpenAIRE

Ballet, Pascal; Rivière, Jérémy; Pothet, Alain; Théron, Michaël; Pichavant, Karine; Abautret, Frank; Fronville, Alexandra; Rodin, Vincent

2017-01-01

International audience; Modelling and teaching complex biological systems is a difficult process. Multi-Agent Based Simulations (MABS) have proved to be an appropriate approach both in research and education when dealing with such systems including emergent, self-organizing phenomena. This chapter presents NetBioDyn, an original software aimed at biologists (students, teachers, researchers) to easily build and simulate complex biological mechanisms observed in multicellular and molecular syst...

Novel Spectroscopic and Electrochemical Sensors and Nanoprobes for the Characterization of Food and Biological Antioxidants.

Science.gov (United States)

Apak, Reşat; Demirci Çekiç, Sema; Üzer, Ayşem; Çelik, Saliha Esin; Bener, Mustafa; Bekdeşer, Burcu; Can, Ziya; Sağlam, Şener; Önem, Ayşe Nur; Erçağ, Erol

2018-01-11

Since an unbalanced excess of reactive oxygen/nitrogen species (ROS/RNS) causes various diseases, determination of antioxidants that can counter oxidative stress is important in food and biological analyses. Optical/electrochemical nanosensors have attracted attention in antioxidant activity (AOA) assessment because of their increased sensitivity and selectivity. Optical sensors offer advantages such as low cost, flexibility, remote control, speed, miniaturization and on-site/in situ analysis. Electrochemical sensors using noble metal nanoparticles on modified electrodes better catalyze bioelectrochemical reactions. We summarize the design principles of colorimetric sensors and nanoprobes for food antioxidants (including electron-transfer based and ROS/RNS scavenging assays) and important milestones contributed by our laboratory. We present novel sensors and nanoprobes together with their mechanisms and analytical performances. Our colorimetric sensors for AOA measurement made use of cupric-neocuproine and ferric-phenanthroline complexes immobilized on a Nafion membrane. We recently designed an optical oxidant/antioxidant sensor using N , N -dimethyl- p -phenylene diamine (DMPD) as probe, from which ROS produced colored DMPD-quinone cationic radicals electrostatically retained on a Nafion membrane. The attenuation of initial color by antioxidants enabled indirect AOA estimation. The surface plasmon resonance absorption of silver nanoparticles as a result of enlargement of citrate-reduced seed particles by antioxidant addition enabled a linear response of AOA. We determined biothiols with Ellman reagent-derivatized gold nanoparticles.

Measurement of the Cupric Ion Concentration Variation near Electrodes in the Copper Electroplating System

Energy Technology Data Exchange (ETDEWEB)

Moon, Je Young; Chung, Bum Jin [KAERI, Daejeon (Korea, Republic of)

2016-05-15

The heat fluxes to the side wall imposed at the upper metallic layer, are known to increase with the reduction of layer height. This 'Focusing effect' is varied by cooling condition of upper boundary and height of the metallic layer. The heat transfer experiments were replaced by mass transfer experiments based on the heat and mass transfer analogy concept. When the electroplating system is adopted as the mass transfer system, in order to simulate the different temperature conditions of top and side walls, an electrical resistance was attached to the top wall so that it is mimics hotter wall condition. Because the quantitative temperature conditions according to the electrical resistance were unknown, the methodology development is necessary. The electrical resistance was adopted to the top plate. But the quantitative temperature conditions depending on the electrical resistance were unknown. In order to overcome the limitations of mass transfer, this work tried to measure the cupric ion concentration. The methods of concentration measurement are RGB, Brightness, ICP, PIV, and Interferometry. The key of RGB, Brightness and PIV method is the clear images of the concentration boundary layer corresponding the thermal boundary layer of heat transfer. The results for ICP method can be got by taking the trace sample of a solution, accurately. The formation of patterns in the interferometry is very important. The characteristics of the interference pattern depend on the nature of the light source, the precise orientation of the mirrors, etc. The methodology of concentration measurement is still under development stage.

Measurement of the Cupric Ion Concentration Variation near Electrodes in the Copper Electroplating System

International Nuclear Information System (INIS)

Moon, Je Young; Chung, Bum Jin

2016-01-01

The heat fluxes to the side wall imposed at the upper metallic layer, are known to increase with the reduction of layer height. This 'Focusing effect' is varied by cooling condition of upper boundary and height of the metallic layer. The heat transfer experiments were replaced by mass transfer experiments based on the heat and mass transfer analogy concept. When the electroplating system is adopted as the mass transfer system, in order to simulate the different temperature conditions of top and side walls, an electrical resistance was attached to the top wall so that it is mimics hotter wall condition. Because the quantitative temperature conditions according to the electrical resistance were unknown, the methodology development is necessary. The electrical resistance was adopted to the top plate. But the quantitative temperature conditions depending on the electrical resistance were unknown. In order to overcome the limitations of mass transfer, this work tried to measure the cupric ion concentration. The methods of concentration measurement are RGB, Brightness, ICP, PIV, and Interferometry. The key of RGB, Brightness and PIV method is the clear images of the concentration boundary layer corresponding the thermal boundary layer of heat transfer. The results for ICP method can be got by taking the trace sample of a solution, accurately. The formation of patterns in the interferometry is very important. The characteristics of the interference pattern depend on the nature of the light source, the precise orientation of the mirrors, etc. The methodology of concentration measurement is still under development stage.

Potential Trace Metal–Organic Complexation in the Atmosphere

Directory of Open Access Journals (Sweden)

Hiroshi Okochi

2002-01-01

Full Text Available It is possible that metal–organic complexation enhances the uptake of gaseous organic compounds and the solubility of metals in aerosols and atmospheric water. We investigated potential atmospheric organic ligands and the enhanced uptake of hydroxy-, oxo-, and dicarboxylic acids as well as dicarbonyls into atmospheric aqueous aerosol. We examined complexation with transition metals (iron, manganese, nickel, copper, zinc and lead on the basis of available references and our experimental data. Humic-like substances are most likely ligands in the atmosphere, although this is a poorly characterized material. A number of polycarboxylic acids and hydroxy forms (e.g., citric and tartronic acids effectively complex metals such as copper in atmospheric aerosols. The simple equilibrium model calculations show that the effect of the complexation on the gas–aqueous phase partition of gaseous atmospheric ligands is quite small for the ligands with the high physical Henry’s law constants, e.g., dicarboxylic acids represented by oxalic acid, even if they have high affinity with metal ions. The lower Henry’s law constants of the α-dicarbonyls, such as glyoxal and methylglyoxal, mean that the complexation could lead to profound increases in their partition into the aqueous phase. Despite quantum mechanical arguments for copper–glyoxal complexes, experiments showed no evidence of complexation between either hydrated or unhydrated α-dicarbonyls and the cupric ion. By contrast the β-dicarbonyl, malondialdehyde, has properties that would allow it to partition into atmospheric water via the complexation with metal ions under some conditions.

Assessing the Possibility of Biological Complexity on Other Worlds, with an Estimate of the Occurrence of Complex Life in the Milky Way Galaxy

Directory of Open Access Journals (Sweden)

Louis N. Irwin

2014-05-01

Full Text Available Rational speculation about biological evolution on other worlds is one of the outstanding challenges in astrobiology. With the growing confirmation that multiplanetary systems abound in the universe, the prospect that life occurs redundantly throughout the cosmos is gaining widespread support. Given the enormous number of possible abodes for life likely to be discovered on an ongoing basis, the prospect that life could have evolved into complex, macro-organismic communities in at least some cases merits consideration. Toward that end, we here propose a Biological Complexity Index (BCI, designed to provide a quantitative estimate of the relative probability that complex, macro-organismic life forms could have emerged on other worlds. The BCI ranks planets and moons by basic, first-order characteristics detectable with available technology. By our calculation only 11 (~1.7% of the extrasolar planets known to date have a BCI above that of Europa; but by extrapolation, the total of such planets could exceed 100 million in our galaxy alone. This is the first quantitative assessment of the plausibility of complex life throughout the universe based on empirical data. It supports the view that the evolution of complex life on other worlds is rare in frequency but large in absolute number.

Enhancement of heat dissipation of LED module with cupric-oxide composite coating on aluminum-alloy heat sink

International Nuclear Information System (INIS)

Kim, Donghyun; Lee, Junghoon; Kim, Junho; Choi, Chang-Hwan; Chung, Wonsub

2015-01-01

Highlights: • We fabricate the CuO/resin composite coating layer on aluminum alloy heat sink. • CuO/resin coating considerably improved the surface emissivity. • The LED junction temperature was reduced by CuO/resin coated heat sink. • The thermal resistance of heat sink was decreased by CuO/resin composite coating at 200 μm thickness. - Abstract: A composite coating composed of cupric oxide (CuO) and silicon-based resin was applied to an aluminum-alloy heat sink for a light emitting diode (LED) module. The purpose of the composite coating is to improve the heat dissipation performance of heat sink by enhancing thermal radiation emission. The heat dissipation performance was investigated in terms of LED junction temperature and thermal resistance using a thermal transient method. The CuO and silicon-based resin composite coating showed higher emissivity, and the lower junction temperature and thermal resistance of the heat sink was achieved. In addition, a continuous operation test of the LED chip with the heat sink revealed that the surface treated with the CuO composite coating stably dissipated heat without degradation. In conclusion, the composite coating proposed here showed a significant improvement of the heat dissipation performance of the aluminum-alloy heat sink due to the enhanced thermal radiation property.

PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

Science.gov (United States)

Domijan, Mirela; Brown, Paul E; Shulgin, Boris V; Rand, David A

2016-03-10

Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and

Systems Biology and Health Systems Complexity in;

NARCIS (Netherlands)

Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

2016-01-01

Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

Development trend of radiation biology research-systems radiation biology

International Nuclear Information System (INIS)

Min Rui

2010-01-01

Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

Three-dimensional sponge-like architectured cupric oxides as high-power and long-life anode material for lithium rechargeable batteries

International Nuclear Information System (INIS)

Choi, Chung Seok; Park, Young-Uk; Kim, Hyungsub; Kim, Na Rae; Kang, Kisuk; Lee, Hyuck Mo

2012-01-01

Cupric oxide (CuO) nanoparticles (NPs) with three-dimensional (3D) sponge structure are obtained through the sintering of Cu NPs at 360 °C. Their morphology is analyzed by transmission electron microscopy (TEM) and scanning electron microscopy (SEM), and their crystal structure is checked by X-ray diffraction. CuO NPs have a 3D porous structure. The NPs are assembled to form larger secondary particles with many empty spaces among them, and they have a CuO phase after the heat treatment. CuO NPs with this novel architecture exhibit good electrochemical performance as anode material. The anode material with a sponge-like structure is prepared at 360 °C, as the Li-ion battery exhibits a high electrochemical capacity of 674 mAh g −1 . When the sample is sintered at 360 °C, the charge/discharge capacities increase gradually and cycle up to 50 cycles at a C/10 rate, exhibiting excellent rate capability compared with earlier reported CuO/CuO-composite anodes. Electrochemical impedance spectroscopy (EIS) measurements suggest that the superior electrical conductivity of the sample sintered at 360 °C is the main factor responsible for the improved power capability.

Spectroscopic, thermal, catalytic and biological studies of Cu(II) azo dye complexes

Science.gov (United States)

El-Sonbati, A. Z.; Diab, M. A.; El-Bindary, A. A.; Shoair, A. F.; Hussein, M. A.; El-Boz, R. A.

2017-08-01

New complexes of copper(II) with azo compounds of 5-amino-2-(aryl diazenyl)phenol (HLn) are prepared and investigated by elemental analyses, molar conductance, IR, 1H NMR, UV-Visible, mass, ESR spectra, magnetic susceptibility measurements and thermal analyses. The complexes have a square planar structure and general formula [Cu(Ln)(OAc)]H2O. Study the catalytic activities of Cu(II) complexes toward oxidation of benzyl alcohol derivatives to carbonyl compounds were tested using H2O2 as the oxidant. The intrinsic binding constants (Kb) of the ligands (HLn) and Cu(II) complexes (1-4) with CT-DNA are determined. The formed compounds have been tested for biological activity of antioxidants, antibacterial against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria and yeast Candida albicans. Antibiotic (Ampicillin) and antifungal against (Colitrimazole) and cytotoxic compounds HL1, HL2, HL3 and complex (1) showed moderate to good activity against S. aureus, E. coli and Candida albicans, and also to be moderate on antioxidants and toxic substances. Molecular docking is used to predict the binding between the ligands with the receptor of breast cancer (2a91).

Treatment of complex biological mixtures with pulsed electric fields An energy transfer characterization

International Nuclear Information System (INIS)

Schrive, Luc

2004-01-01

Sewage sludge from waste water treatment plants is a complex biological mixture and a problematic by-product because of valorisation restrictions. In order to limit its production, pulsed electric fields (PEF) were studied because of their biological effects and their potentially physico-chemical action. This work demonstrated a paradoxical phenomenon: cell lysis triggered a respirometric activation followed by a delayed lethality. This phenomenon was related to the leakage of internal compounds which were immediately bio-assimilated. At high energy expense, the plasmic membrane permeabilization led to cell death. Practically, with the technical configuration of the equipment, no hydrolysis was detected. This limitation decreases the interest for excess sludge reduction, but for the same reason, PEF cold sterilization technique can be assessed as a promising process. The representation of the electric energy transfer from electrodes to cell was exchanged by the study of mass transfer from the biological cell to the surrounding media under an electromotive force. Thus, the survival rate was modelled by a Sherwood number taking account of electrical, biological and hydraulic parameters. (author) [fr

Development of a new catalase activity assay for biological samples using optical CUPRAC sensor.

Science.gov (United States)

Bekdeşer, Burcu; Özyürek, Mustafa; Güçlü, Kubilay; Alkan, Fulya Üstün; Apak, Reşat

2014-11-11

A novel catalase activity assay was developed for biological samples (liver and kidney tissue homogenates) using a rapid and low-cost optical sensor-based 'cupric reducing antioxidant capacity' (CUPRAC) method. The reagent, copper(II)-neocuproine (Cu(II)-Nc) complex, was immobilized onto a cation-exchanger film of Nafion, and the absorbance changes associated with the formation of the highly-colored Cu(I)-Nc chelate as a result of reaction with hydrogen peroxide (H2O2) was measured at 450 nm. When catalase was absent, H2O2 produced the CUPRAC chromophore, whereas catalase, being an effective H2O2 scavenger, completely annihilated the CUPRAC signal due to H2O2. Thus, the CUPRAC absorbance due to H2O2 oxidation concomitant with Cu(I)-Nc formation decreased proportionally with catalase. The developed sensor gave a linear response over a wide concentration range of H2O2 (0.68-78.6 μM). This optical sensor-based method applicable to tissue homogenates proved to be efficient for low hydrogen peroxide concentrations (physiological and nontoxic levels) to which the widely used UV method is not accurately responsive. Thus, conventional problems of the UV method arising from relatively low sensitivity and selectivity, and absorbance disturbance due to gaseous oxygen evolution were overcome. The catalase findings of the proposed method for tissue homogenates were statistically alike with those of HPLC. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis, characterization, and biological activity of a new palladium(II) complex with deoxyalliin

Energy Technology Data Exchange (ETDEWEB)

Corbi, P.P.; Massabni, A.C. [Inst. de Quimica - UNESP, Dept., Dept. de Quimica Geral e Inoganica, Araraquara (Brazil)]. E-mail: pedrocorbi@yahoo.com; Moreira, A.G. [Inst. de Quimica - UNESP, Dept. de Quimica Geral e Inoganica, Araraquara (Brazil); Faculdade de Medicina de Ribeirao Preto - USP, Dept. de Bioquimica e Imunologia, Ribeirao Preto (Brazil); Medrano, F.J. [Laboratorio Nacional de Luz Sincrotron - LNLS, Campinas (Brazil); Jasiulionis, M.G. [Escola Paulista de Medicina - UNIFESP, Dept. de Micro-Imuno-Parasitologia, Sao Paulo (Brazil); Costa-Neto, C.M. [Faculdade de Medicina de Ribeirao Preto - USP, Dept. de Bioquimica e Imunologia, Ribeirao Preto (Brazil)

2005-02-15

Synthesis, characterization, and biological activity of a new water-soluble Pd(II)-deoxyalliin (S-allyl-L-cysteine) complex are described in this article. Elemental and thermal analysis for the complex are consistent with the formula [Pd(C{sub 6}H{sub 10}NO{sub 2}S){sub 2}]. {sup 13}C NMR, {sup 1}H NMR, and IR spectroscopy show coordination of the ligand to Pd(II) through S and N atoms in a square planar geometry. Final residue of the thermal treatment was identified as a mixture of PdO and metallic Pd. Antiproliferative assays using aqueous solutions of the complex against HeLa and TM5 tumor cells showed a pronounced activity of the complex even at low concentrations. After incubation for 24 h, the complex induced cytotoxic effect over HeLa cells when used at concentrations higher than 0.40 mmol/L. At lower concentrations, the complex was nontoxic, indicating its action is probably due to cell cycle arrest, rather than cell death. In agreement with these results, the flow cytometric analysis indicated that after incubation for 24 h at low concentrations of the complex cells are arrested in G0/G1. (author)

Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions.

Science.gov (United States)

Vernon, Ian; Liu, Junli; Goldstein, Michael; Rowe, James; Topping, Jen; Lindsey, Keith

2018-01-02

Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the needs of the analysis, and need to be compared to observed data of various forms. The correct analysis of such models usually requires a global parameter search, over a high dimensional parameter space, that incorporates and respects the most important sources of uncertainty. This can be an extremely difficult task, but it is essential for any meaningful inference or prediction to be made about any biological system. It hence represents a fundamental challenge for the whole of systems biology. Bayesian statistical methodology for the uncertainty analysis of complex models is introduced, which is designed to address the high dimensional global parameter search problem. Bayesian emulators that mimic the systems biology model but which are extremely fast to evaluate are embeded within an iterative history match: an efficient method to search high dimensional spaces within a more formal statistical setting, while incorporating major sources of uncertainty. The approach is demonstrated via application to a model of hormonal crosstalk in Arabidopsis root development, which has 32 rate parameters, for which we identify the sets of rate parameter values that lead to acceptable matches between model output and observed trend data. The multiple insights into the model's structure that this analysis provides are discussed. The methodology is applied to a second related model, and the biological consequences of the resulting comparison, including the evaluation of gene functions, are described. Bayesian uncertainty analysis for complex models using both emulators and history matching is shown to be a powerful technique that can greatly aid the study of a large class of systems biology models. It both provides insight into model behaviour

Complex formation of blueberry (Vaccinium angustifolium) anthocyanins during freeze-drying and its influence on their biological activity.

Science.gov (United States)

Correa-Betanzo, Julieta; Padmanabhan, Priya; Corredig, Milena; Subramanian, Jayasankar; Paliyath, Gopinadhan

2015-03-25

Biological activity of polyphenols is influenced by their uptake and is highly influenced by their interactions with the food matrix. This study evaluated the complex formation of blueberry polyphenols with fruit matrixes such as pectin and cellulose and their effect on the biological and antiproliferative properties of human colon cell lines HT-29 and CRL 1790. Free or complexed polyphenols were isolated by dialyzing aqueous or methanolic blueberry homogenates. Seven phenolic compounds and thirteen anthocyanins were identified in blueberry extracts. Blueberry extracts showed varying degrees of antioxidant and antiproliferative activities, as well as α-glucosidase activity. Fruit matrix containing cellulose and pectin, or purified polygalacturonic acid and cellulose, did not retain polyphenols and showed very low antioxidant or antiproliferative activities. These findings suggest that interactions between polyphenols and the food matrix may be more complex than a simple association and may play an important role in the bioefficacy of blueberry polyphenols.

Application of Biologically Based Lumping To Investigate the Toxicokinetic Interactions of a Complex Gasoline Mixture.

Science.gov (United States)

Jasper, Micah N; Martin, Sheppard A; Oshiro, Wendy M; Ford, Jermaine; Bushnell, Philip J; El-Masri, Hisham

2016-03-15

People are often exposed to complex mixtures of environmental chemicals such as gasoline, tobacco smoke, water contaminants, or food additives. We developed an approach that applies chemical lumping methods to complex mixtures, in this case gasoline, based on biologically relevant parameters used in physiologically based pharmacokinetic (PBPK) modeling. Inhalation exposures were performed with rats to evaluate the performance of our PBPK model and chemical lumping method. There were 109 chemicals identified and quantified in the vapor in the chamber. The time-course toxicokinetic profiles of 10 target chemicals were also determined from blood samples collected during and following the in vivo experiments. A general PBPK model was used to compare the experimental data to the simulated values of blood concentration for 10 target chemicals with various numbers of lumps, iteratively increasing from 0 to 99. Large reductions in simulation error were gained by incorporating enzymatic chemical interactions, in comparison to simulating the individual chemicals separately. The error was further reduced by lumping the 99 nontarget chemicals. The same biologically based lumping approach can be used to simplify any complex mixture with tens, hundreds, or thousands of constituents.

Biological properties of novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles

KAUST Repository

Novak, Maria S.; Bü chel, Gabriel E.; Keppler, Bernhard K.; Jakupec, Michael A.

2016-01-01

Since the discovery that nitric oxide (NO) is a physiologically relevant molecule, there has been great interest in the use of metal nitrosyl compounds as antitumor pharmaceuticals. Particularly interesting are those complexes which can deliver NO to biological targets. Ruthenium- and osmium-based compounds offer lower toxicity compared to other metals and show different mechanisms of action as well as different spectra of activity compared to platinum-based drugs. Novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles were studied to elucidate their cytotoxicity and possible interactions with DNA. Apoptosis induction, changes of mitochondrial transmembrane potential and possible formation of reactive oxygen species were investigated as indicators of NO-mediated damage by flow cytometry. Results suggest that ruthenium- and osmium-nitrosyl complexes with the general formula (indazolium)[cis/trans-MCl4(NO)(1H-indazole)] have pronounced cytotoxic potency in cancer cell lines. Especially the more potent ruthenium complexes strongly induce apoptosis associated with depolarization of mitochondrial membranes, and elevated reactive oxygen species levels. Furthermore, a slight yet not unequivocal trend to accumulation of intracellular cyclic guanosine monophosphate attributable to NO-mediated effects was observed.

Biological properties of novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles

KAUST Repository

Novak, Maria S.

2016-03-09

Since the discovery that nitric oxide (NO) is a physiologically relevant molecule, there has been great interest in the use of metal nitrosyl compounds as antitumor pharmaceuticals. Particularly interesting are those complexes which can deliver NO to biological targets. Ruthenium- and osmium-based compounds offer lower toxicity compared to other metals and show different mechanisms of action as well as different spectra of activity compared to platinum-based drugs. Novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles were studied to elucidate their cytotoxicity and possible interactions with DNA. Apoptosis induction, changes of mitochondrial transmembrane potential and possible formation of reactive oxygen species were investigated as indicators of NO-mediated damage by flow cytometry. Results suggest that ruthenium- and osmium-nitrosyl complexes with the general formula (indazolium)[cis/trans-MCl4(NO)(1H-indazole)] have pronounced cytotoxic potency in cancer cell lines. Especially the more potent ruthenium complexes strongly induce apoptosis associated with depolarization of mitochondrial membranes, and elevated reactive oxygen species levels. Furthermore, a slight yet not unequivocal trend to accumulation of intracellular cyclic guanosine monophosphate attributable to NO-mediated effects was observed.

Oxidative leaching process with cupric ion in hydrochloric acid media for recovery of Pd and Rh from spent catalytic converters.

Science.gov (United States)

Nogueira, C A; Paiva, A P; Oliveira, P C; Costa, M C; da Costa, A M Rosa

2014-08-15

The recycling of platinum-group metals from wastes such as autocatalytic converters is getting growing attention due to the scarcity of these precious metals and the market pressure originated by increase of demand in current and emerging applications. Hydrometallurgical treatment of such wastes is an alternative way to the most usual pyrometallurgical processes based on smelter operations. This paper focuses on the development of a leaching process using cupric chloride as oxidising agent, in HCl media, for recovery of palladium and rhodium from a spent catalyst. The chloride media allows the adequate conditions for oxidising and solubilising the metals, as demonstrated by equilibrium calculations based on thermodynamic data. The experimental study of the leaching process revealed that Pd solubilisation is clearly easier than that of Rh. The factors temperature, time, and HCl and Cu(2+) concentrations were significant regarding Pd and Rh leaching, the latter requiring higher factor values to achieve the same results. Leaching yields of 95% Pd and 86% Rh were achieved under optimised conditions (T = 80 °C, t = 4h, [HCl] = 6M, [Cu(2+)] = 0.3M). Copyright © 2014 Elsevier B.V. All rights reserved.

Simulation of biological flow and transport in complex geometries using embedded boundary/volume-of-fluid methods

International Nuclear Information System (INIS)

Trebotich, David

2007-01-01

We have developed a simulation capability to model multiscale flow and transport in complex biological systems based on algorithms and software infrastructure developed under the SciDAC APDEC CET. The foundation of this work is a new hybrid fluid-particle method for modeling polymer fluids in irregular microscale geometries that enables long-time simulation of validation experiments. Both continuum viscoelastic and discrete particle representations have been used to model the constitutive behavior of polymer fluids. Complex flow environment geometries are represented on Cartesian grids using an implicit function. Direct simulation of flow in the irregular geometry is then possible using embedded boundary/volume-of-fluid methods without loss of geometric detail. This capability has been used to simulate biological flows in a variety of application geometries including biomedical microdevices, anatomical structures and porous media

Dermal tumorigen PAH and complex mixtures for biological research

International Nuclear Information System (INIS)

Griest, W.H.; Guerin, M.R.; Ho, C.

1985-01-01

Thirteen commercially available, commonly reported four-five ring dermal tumorigen PAHs, were determined in a set of complex mixtures consisting of crude and upgraded coal liquids, and petroleum crude oils and their distillate fractions. Semi-preparative scale, normal phase high performance liquid chromatographic fractionation followed by capillary column gas chromatography or gas chromatography-mass spectroscopy were used for the measurements. Deuterated or carbon-14 labeled PAH served as internal standards or allowed recovery corrections. Approaches for the preparation and measurement of radiolabeled PAH were examined to provide chemical probes for biological study. Synthetic routes for production of 14 C labeled dihydrobenzo[a]pyrene and 14 C- or 3 H 10-azabenzo[a]pyrene are being studied to provide tracers for fundamental studies in tracheal transplant and skin penetration systems. (DT)

Beyond disease susceptibility-Leveraging genome-wide association studies for new insights into complex disease biology.

Science.gov (United States)

Lee, J C

2017-12-01

Genetic studies in complex diseases have been highly successful, but have also been largely one-dimensional: predominantly focusing on the genetic contribution to disease susceptibility. While this is undoubtedly important-indeed it is a pre-requisite for understanding the mechanisms underlying disease development-there are many other important aspects of disease biology that have received comparatively little attention. In this review, I will discuss how existing genetic data can be leveraged to provide new insights into other aspects of disease biology, why such insights could change the way we think about complex disease, and how this could provide opportunities for better therapies and/or facilitate personalised medicine. To do this, I will use the example of Crohn's disease-a chronic form of inflammatory bowel disease that has been one of the main success stories in complex disease genetics. Indeed, thanks to genetic studies, we now have a much more detailed understanding of the processes involved in Crohn's disease development, but still know relatively little about what determines the subsequent disease course (prognosis) and why this differs so considerably between individuals. I will discuss how we came to realise that genetic variation plays an important role in determining disease prognosis and how this has changed the way we think about Crohn's disease genetics. This will illustrate how phenotypic data can be used to leverage new insights from genetic data and will provide a broadly applicable framework that could yield new insights into the biology of multiple diseases. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Systematic metabolite annotation and identification in complex biological extracts : combining robust mass spectrometry fragmentation and nuclear magnetic resonance spectroscopy

NARCIS (Netherlands)

Hooft, van der J.J.J.

2012-01-01

Detailed knowledge of the chemical content of organisms, organs, tissues, and cells is needed to fully characterize complex biological systems. The high chemical variety of compounds present in biological systems is illustrated by the presence of a large variety of compounds, ranging from apolar

Mechanism and kinetics of thermal decomposition of ammoniacal complex of copper oxalate

International Nuclear Information System (INIS)

Prasad, R.

2003-01-01

A complex precursor has been synthesized by dissolving copper oxalate in liquor ammonia followed by drying. The thermal decomposition of the precursor has been studied in different atmospheres, air/nitrogen. The mechanism of decomposition of the precursor in air is not as simple one as in nitrogen. In nitrogen, it involves endothermic deammoniation followed by decomposition to finely divided elemental particles of copper. Whereas in air, decomposition and simultaneous oxidation of the residual products (oxidative decomposition), make the process complex and relatively bigger particle of cupric oxide are obtained as final product. The products of decomposition in different atmospheres have been characterized by X-ray diffraction and particle size analysis. The stoichiometric formula, Cu(NH 3 ) 2 C 2 O 4 of the precursor is established from elemental analysis and TG measurements, and it is designated as copper amino oxalate (CAO). In nitrogen atmosphere, the deammoniation and decomposition have been found to be zero and first order, respectively. The values of activation energy have been found to be 102.52 and 95.38 kJ/mol for deammoniation and decomposition, respectively

Complex systems of biological interest stability under ionising radiations

International Nuclear Information System (INIS)

Maclot, Sylvain

2014-01-01

This PhD work presents the study of stability of molecular systems of biological interest in the gas phase after interaction with ionising radiations. The use of ionising radiation can probe the physical chemistry of complex systems at the molecular scale and thus consider their intrinsic properties. Beyond the fundamental aspect, this work is part of the overall understanding of radiation effects on living organisms and in particular the use of ionizing radiation in radiotherapy. Specifically, this study focused on the use of low-energy multiply charged ions (tens of keV) provided by the GANIL (Caen), which includes most of the experiments presented. In addition, experiments using VUV photons were also conducted at synchrotron ELETTRA (Trieste, Italy). The bio-molecular systems studied are amino acids and nucleic acid constituents. Using an experimental crossed beams device allows interaction between biomolecules and ionising radiation leads mainly to the ionization and fragmentation of the system. The study of its relaxation dynamics is by time-of-flight mass spectrometry coupled to a coincidences measurements method. It is shown that an approach combining experiment and theory allows a detailed study of the fragmentation dynamics of complex systems. The results indicate that fragmentation is generally governed by the Coulomb repulsion but the intramolecular rearrangements involve specific relaxation mechanisms. (author) [fr

Comprehension of complex biological processes by analytical methods: how far can we go using mass spectrometry?

International Nuclear Information System (INIS)

Gerner, C.

2013-01-01

Comprehensive understanding of complex biological processes is the basis for many biomedical issues of great relevance for modern society including risk assessment, drug development, quality control of industrial products and many more. Screening methods provide means for investigating biological samples without research hypothesis. However, the first boom of analytical screening efforts has passed and we again need to ask whether and how to apply screening methods. Mass spectrometry is a modern tool with unrivalled analytical capacities. This applies to all relevant characteristics of analytical methods such as specificity, sensitivity, accuracy, multiplicity and diversity of applications. Indeed, mass spectrometry qualifies to deal with complexity. Chronic inflammation is a common feature of almost all relevant diseases challenging our modern society; these diseases are apparently highly diverse and include arteriosclerosis, cancer, back pain, neurodegenerative diseases, depression and other. The complexity of mechanisms regulating chronic inflammation is the reason for the practical challenge to deal with it. The presentation shall give an overview of capabilities and limitations of the application of this analytical tool to solve critical questions with great relevance for our society. (author)

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

Science.gov (United States)

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

7th Annual Systems Biology Symposium: Systems Biology and Engineering

Energy Technology Data Exchange (ETDEWEB)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

Cupric ion reducing antioxidant capacity assay for antioxidants in human serum and for hydroxyl radical scavengers.

Science.gov (United States)

Apak, Reşat; Güçlü, Kubilay; Ozyürek, Mustafa; Bektaşoğlu, Burcu; Bener, Mustafa

2010-01-01

Tests measuring the combined antioxidant effect of the nonenzymatic defenses in biological fluids may be useful in providing an index of the organism's capability to counteract reactive species known as pro-oxidants, resist oxidative damage, and combat oxidative stress-related diseases. The selected chromogenic redox reagent for the assay of human serum should be easily accessible, stable, selective, and respond to all types of biologically important antioxidants such as ascorbic acid, alpha-tocopherol, beta-carotene, reduced glutathione (GSH), uric acid, and bilirubin, regardless of chemical type or hydrophilicity. Our recently developed cupric reducing antioxidant capacity (CUPRAC) spectrophotometric method for a number of polyphenols and flavonoids using the copper(II)-neocuproine reagent in ammonium acetate buffer is now applied to a complete series of plasma antioxidants for the assay of total antioxidant capacity of serum, and the resulting absorbance at 450 nm is recorded either directly (e.g., for ascorbic acid, alpha-tocopherol, and glutathione) or after incubation at 50 degrees C for 20 min (e.g., for uric acid, bilirubin, and albumin), quantitation being made by means of a calibration curve. The lipophilic antioxidants, alpha-tocopherol and beta-carotene, are assayed in dichloromethane. Lipophilic antioxidants of serum are extracted with n-hexane from an ethanolic solution of serum subjected to centrifugation. Hydrophilic antioxidants of serum are assayed in the centrifugate after perchloric acid precipitation of proteins. The CUPRAC molar absorptivities, linear ranges, and TEAC (trolox equivalent antioxidant capacity) coefficients of the serum antioxidants are established, and the results are evaluated in comparison with the findings of the ABTS/TEAC reference method. The intra- and inter-assay coefficients of variation (CVs) are 0.7 and 1.5%, respectively, for serum. The CUPRAC assay proved to be efficient for glutathione and thiol-type antioxidants

Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity.

Science.gov (United States)

Speijer, Dave

2011-05-01

Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes. Copyright © 2011 WILEY Periodicals, Inc.

Cu(II AND Zn(II COMPLEX COMPOUNDS WITH BIGUANIDES AROMATIC DERIVATIVES. SYNTHESIS, CHARACTERIZATION, BIOLOGICAL ACTIVITY

Directory of Open Access Journals (Sweden)

Ticuţa Negreanu-Pîrjol

2011-05-01

Full Text Available In this paper we report the synthesis, physical-chemical characterization and antimicrobial activity of some new complex compounds of hetero-aromatic biguanides ligands, chlorhexidine base (CHX and chlorhexidine diacetate (CHXac2 with metallic ions Cu(II and Zn(II, in different molar ratio. The synthesized complexes were characterized by elemental chemical analysis and differential thermal analysis. The stereochemistry of the metallic ions was determined by infrared spectra, UV-Vis, EPR spectroscopy and magnetic susceptibility in the aim to establish the complexes structures. The biological activity of the new complex compounds was identified in solid technique by measuring minimum inhibition diameter of bacterial and fungal culture, against three standard pathogen strains, Escherichia coli ATCC 25922, Staphilococcus aureus ATCC 25923 and Candida albicans ATCC 10231. The results show an increased specific antimicrobial activity for the complexes chlorhexidine:Cu(II 1:1 and 1:2 compared with the one of the Zn(II complexes.

Dose prescription complexity versus tumor control probability in biologically conformal radiotherapy

International Nuclear Information System (INIS)

South, C. P.; Evans, P. M.; Partridge, M.

2009-01-01

The technical feasibility and potential benefits of voxel-based nonuniform dose prescriptions for biologically heterogeneous tumors have been widely demonstrated. In some cases, an ''ideal'' dose prescription has been generated by individualizing the dose to every voxel within the target, but often this voxel-based prescription has been discretized into a small number of compartments. The number of dose levels utilized and the methods used for prescribing doses and assigning tumor voxels to different dose compartments have varied significantly. The authors present an investigation into the relationship between the complexity of the dose prescription and the tumor control probability (TCP) for a number of these methods. The linear quadratic model of cell killing was used in conjunction with a number of modeled tumors heterogeneous in clonogen density, oxygenation, or proliferation. Models based on simple mathematical functions, published biological data, and biological image data were investigated. Target voxels were assigned to dose compartments using (i) simple rules based on the initial biological distribution, (ii) iterative methods designed to maximize the achievable TCP, or (iii) methods based on an ideal dose prescription. The relative performance of the simple rules was found to depend on the form of heterogeneity of the tumor, while the iterative and ideal dose methods performed comparably for all models investigated. In all cases the maximum achievable TCP was approached within the first few (typically two to five) compartments. Results suggest that irrespective of the pattern of heterogeneity, the optimal dose prescription can be well approximated using only a few dose levels but only if both the compartment boundaries and prescribed dose levels are well chosen.

Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Son N.; Liyu, Andrey V.; Chu, Rosalie K.; Anderton, Christopher R.; Laskin, Julia

2017-01-17

A new approach for constant distance mode mass spectrometry imaging of biological samples using nanospray desorption electrospray ionization (nano-DESI MSI) was developed by integrating a shear-force probe with nano-DESI probe. The technical concept and basic instrumental setup as well as general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enables constant-distance imaging mode via a computer controlled closed feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus Subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites including non-ribosomal peptides (surfactin, plipastatin and iturin) and iron-bound heme on the surface of living bacterial colonies ranging in diameter from 10 mm to 13 mm with height variations of up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Constant-mode nano-DESI MSI is ideally suited for imaging biological samples of complex topography in their native state.

Complex network problems in physics, computer science and biology

Science.gov (United States)

Cojocaru, Radu Ionut

There is a close relation between physics and mathematics and the exchange of ideas between these two sciences are well established. However until few years ago there was no such a close relation between physics and computer science. Even more, only recently biologists started to use methods and tools from statistical physics in order to study the behavior of complex system. In this thesis we concentrate on applying and analyzing several methods borrowed from computer science to biology and also we use methods from statistical physics in solving hard problems from computer science. In recent years physicists have been interested in studying the behavior of complex networks. Physics is an experimental science in which theoretical predictions are compared to experiments. In this definition, the term prediction plays a very important role: although the system is complex, it is still possible to get predictions for its behavior, but these predictions are of a probabilistic nature. Spin glasses, lattice gases or the Potts model are a few examples of complex systems in physics. Spin glasses and many frustrated antiferromagnets map exactly to computer science problems in the NP-hard class defined in Chapter 1. In Chapter 1 we discuss a common result from artificial intelligence (AI) which shows that there are some problems which are NP-complete, with the implication that these problems are difficult to solve. We introduce a few well known hard problems from computer science (Satisfiability, Coloring, Vertex Cover together with Maximum Independent Set and Number Partitioning) and then discuss their mapping to problems from physics. In Chapter 2 we provide a short review of combinatorial optimization algorithms and their applications to ground state problems in disordered systems. We discuss the cavity method initially developed for studying the Sherrington-Kirkpatrick model of spin glasses. We extend this model to the study of a specific case of spin glass on the Bethe

Mixing and Processing of Complex Biological Fluids

National Research Council Canada - National Science Library

Liepmann, Dorian

2003-01-01

... of microfluidic control on the makeup and molecular structure of biological fluids. For this project, we focused on two critical fluids that are biologically significant and that are of critical importance to DoD...

Y-12 National Security Complex Biological Monitoring and Abatement Program 2007 Calendar Yeare Report

Energy Technology Data Exchange (ETDEWEB)

Peterson, M.J.; Greeley, M. S. Jr.; Morris, G. W.; Roy, W. K.; Ryan, M. G.; Smith, J. G.; Southworth, G. R.

2008-07-01

The National Pollutant Discharge Elimination System (NPDES) permit issued for the Oak Ridge Y-12 National Security Complex (Y-12 Complex) which became effective May 1, 2006, continued a requirement for a Biological Monitoring and Abatement Program (BMAP). The BMAP was originally developed in 1985 to demonstrate that the effluent limitations established for the Y-12 Complex protected the classified uses of the receiving stream (East Fork Poplar Creek: EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). The objectives of the current BMAP are similar, specifically to assess stream ecological conditions relative to regulatory limits and criteria, to assess ecological impacts as well as recovery in response to Y-12 operations, and to investigate the causes of continuing impacts. The BMAP consists of three tasks that reflect complementary approaches to evaluating the effects of the Y-12 Complex discharges on the biotic integrity of EFPC. These tasks include: (1) bioaccumulation monitoring, (2) benthic macroinvertebrate community monitoring, and (3) fish community monitoring. As required by the NPDES permit, the BMAP benthic macroinvertebrate community monitoring task includes studies to annually evaluate the receiving stream's biological integrity in comparison to TN Water Quality Criteria. BMAP monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) appropriate habitat distribution, and (5) access. The primary sampling sites include upper EFPC at kilometers (EFKs) 24.4 and 23.4 [upstream and downstream of Lake Reality (LR) respectively]; EFK 18.7 (also EFK 18.2 and 19), located

Biological activities of Umbilicaria crustulosa (Ach.) frey acetone extract

OpenAIRE

Zlatanović Ivana; Stanković Miroslava; Stankov-Jovanović Vesna; Mitić Violeta; Zrnzević Ivana; Đorđević Aleksandra; Stojanović Gordana

2017-01-01

This paper reports for the first time the effect of an acetone extract of Umbilicaria crustulosa on the micronucleus distribution of human lymphocytes, and on the cholinesterase activity and antioxidant activity by the cupric ion reducing antioxidant capacity (CUPRAC) method. Additionally, the total phenolic compounds (TPC) and the antioxidant properties were estimated via DPPH, ABTS and TRP assays. Moreover, the antibacterial activity against two Gram-positive and three Gram-negative bacteri...

Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.

Science.gov (United States)

Transtrum, Mark K; Qiu, Peng

2016-05-01

The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior.

Combined HPLC-CUPRAC (cupric ion reducing antioxidant capacity) assay of parsley, celery leaves, and nettle.

Science.gov (United States)

Yildiz, Leyla; Başkan, Kevser Sözgen; Tütem, Esma; Apak, Reşat

2008-10-19

This study aims to identify the essential antioxidant compounds present in parsley (Petroselinum sativum) and celery (Apium graveolens) leaves belonging to the Umbelliferae (Apiaceae) family, and in stinging nettle (Urtica dioica) belonging to Urticaceae family, to measure the total antioxidant capacity (TAC) of these compounds with CUPRAC (cupric ion reducing antioxidant capacity) and ABTS spectrophotometric methods, and to correlate the TAC with high performance liquid chromatography (HPLC) findings. The CUPRAC spectrophotometric method of TAC assay using copper(II)-neocuproine (2,9-dimethyl-1,10-phenanthroline) as the chromogenic oxidant was developed in our laboratories. The individual antioxidant constituents of plant extracts were identified and quantified by HPLC on a C18 column using a modified mobile phase of gradient elution comprised of MeOH-0.2% o-phosphoric acid and UV detection for polyphenols at 280 nm. The TAC values of HPLC-quantified antioxidant constituents were found, and compared for the first time with those found by CUPRAC. The TAC of HPLC-quantified compounds accounted for a relatively high percentage of the observed CUPRAC capacities of plant extracts, namely 81% of nettle, 60-77% of parsley (in different hydrolyzates of extract and solid sample), and 41-57% of celery leaves (in different hydrolyzates). The CUPRAC total capacities of the 70% MeOH extracts of studied plants (in the units of mmol trolox g(-1)plant) were in the order: celery leaves>nettle>parsley. The TAC calculated with the aid of HPLC-spectrophotometry did not compensate for 100% of the CUPRAC total capacities, because all flavonoid glycosides subjected to hydrolysis were either not detectable with HPLC, or not converted to the corresponding aglycons (i.e., easily detectable and quantifiable with HPLC) during the hydrolysis step.

From Molecules to Life: Quantifying the Complexity of Chemical and Biological Systems in the Universe.

Science.gov (United States)

Böttcher, Thomas

2018-01-01

Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms. Entities with a certain level of information complexity directly require a functionally complex mechanism for their production or replication and are hence indicative for life-like systems. In order to describe entities combining molecular and information complexity, the term biogenic unit was introduced. Exemplified biogenic unit complexities were calculated for ribozymes, protein enzymes, multimeric protein complexes, and even an entire virus particle. Complexities of prokaryotic and eukaryotic cells, as well as multicellular organisms, were estimated. Thereby distinct evolutionary stages in complexity space were identified. The here developed approach to compare the complexity of biogenic units allows for the first time to address the gradual characteristics of prebiotic and life-like systems without the need for a definition of life. This operational concept may guide our search for life in the Universe, and it may direct the investigations of prebiotic trajectories that lead towards the evolution of complexity at the origins of life.

A chemical-biological evaluation of rhodium(I) N-heterocyclic carbene complexes as prospective anticancer drugs.

Science.gov (United States)

Oehninger, Luciano; Küster, Laura Nadine; Schmidt, Claudia; Muñoz-Castro, Alvaro; Prokop, Aram; Ott, Ingo

2013-12-23

Rhodium(I) complexes bearing N-heterocyclic carbene (NHC) ligands have been widely used in catalytic chemistry, but there are very few reports of biological properties of these organometallics. A series of Rh(I)-NHC derivatives with 1,5-cyclooctadiene and CO as secondary ligands were synthesized, characterized, and biologically investigated as prospective antitumor drug candidates. Pronounced antiproliferative effects were noted for all complexes, along with moderate inhibitory activity of thioredoxin reductase (TrxR) and efficient binding to biomolecules (DNA, albumin). Biodistribution studies showed that the presence of albumin lowered the cellular uptake and confirmed the transport of rhodium into the nuclei. Changes in the mitochondrial membrane potential (MMP) were observed as well as DNA fragmentation in wild-type and daunorubicin- or vincristine-resistant Nalm-6 leukemia cells. Overall, these studies indicated that Rh(I)-NHC fragments could be used as partial structures of new antitumor agents, in particular in those drugs designed to address resistant malignant tissues. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, spectroscopic characterization and in vitro cytotoxicities of new organometallic palladium complexes with biologically active β-diketones; Biological evaluation probing of the interaction mechanism with DNA/Protein and molecular docking

Science.gov (United States)

Karami, Kazem; Rafiee, Mina; Lighvan, Zohreh Mehri; Zakariazadeh, Mostafa; Faal, Ali Yeganeh; Esmaeili, Seyed-Alireza; Momtazi-Borojeni, Amir Abbas

2018-02-01

[Pd{(C,N)sbnd C6H4CH (CH3)NH}(CUR)] (3) and [Pd2{(C,N)sbnd C6H4CH(CH3)NH2}2(μ-N3CS2)] (4) [cur = 1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dion] novel organometallic complexes with biologically active ligands have been prepared and characterized via elemental analysis, multinuclear spectroscopic techniques (1H, and 13C NMR and IR) and their biological activities, including antitumoral activity and DNA-protein interactions have been investigated. Fluorescence spectroscopy used to study the interaction of the complexes with BSA have shown the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary structure of BSA in the presence of the complexes. In the meantime, spectroscopy and competitive titration have been applied to investigate the interaction of complexes with Warfarin and Ibuprofen site markers for sites I and II, respectively, with BSA. The results have suggested that the locations of complexes 3 and 4 are sites II and I, respectively. UV-Vis spectroscopy, emission titration and helix melting methods have been used to study the interaction of these complexes with CT-DNA, indicating that complexes are bound to CT-DNA by intercalation binding mode. In addition, good cytotoxic activity against MCF-7 (human breast cancer) and JURKAT (human leukemia) cell line has been shown by both complexes whereas low cytotoxicity was exerted on normal peripheral blood mononuclear cells.

Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network

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Pooja Sharma

2018-06-01

Full Text Available Protein complexes are known to play a major role in controlling cellular activity in a living being. Identifying complexes from raw protein protein interactions (PPIs is an important area of research. Earlier work has been limited mostly to yeast. Such protein complex identification methods, when applied to large human PPIs often give poor performance. We introduce a novel method called CSC to detect protein complexes. The method is evaluated in terms of positive predictive value, sensitivity and accuracy using the datasets of the model organism, yeast and humans. CSC outperforms several other competing algorithms for both organisms. Further, we present a framework to establish the usefulness of CSC in analyzing the influence of a given disease gene in a complex topologically as well as biologically considering eight major association factors. Keywords: Protein complex, Connectivity, Semantic similarity, Contribution

Absence of hydrocortisone from cytoplasmic hormone-protein complexes formed in vivo after administration of biologically active doses of [3H] hydrocortisone

International Nuclear Information System (INIS)

Voigt, J.; Grote, H.; Sekeris, C.E.

1981-01-01

After administration of [ 3 H] hydrocortisone to adrenalectomized rats, hormone-protein complexes were isolated from liver cytosol by DEAE-cellulose chromatography. After application of biologically active and inactive doses of hydrocortisone five binding components were detected eluting at the same salt concentrations as the hormone-protein complexes observed after incubation of cytosol with [ 3 H] hydrocortisone in vitro. The isolated hormone-protein fractions were acidified and extracted with ethylacetate and the steroids were analyzed by thin-layer chromatography. No significant amount of hydrocortisone could be detected in any of the complexes formed in vivo 5-60 min after administration of biologically active doses of hydrocortisone. 3xi,11β,17α,20xi, 21-Pentahydroxypregnane, steroidal carboxy acids, glucuronides and a very polar conjugate of hydrocortisone were found in the different fractions. After an in vivo dose of hydrocortisone of about 1/5000th of the minimal dose required for enzyme induction, hydrocortisone could be found in all the cytoplasmic hormone-protein complexes formed. In contrast to the cytoplasmic hormone-protein complexes, hydrocortisone could be readily demonstrated in nuclei isolated after the administration of biologically active doses of hormone, although acid metabolites were found to represent the main part of the radioactive compounds present in the nuclei. These acid metabolites were located in the nuclear envelope. (orig.)

Physics and biology

International Nuclear Information System (INIS)

Frauenfelder, H.

1988-01-01

The author points out that the coupling between physics and biology is becoming closer as time goes on. He tries to show that physical studies on biological systems not only yield insight into biology but also provide results of interest to physics. Biological systems are extremly complex system. Ideally one would like to understand the behavior of such systems in terms of the behavior of its constituent atoms. Since in small organisms this may be 10 20 atoms, it is clear these are not simple many-body systems. He reviews the basic elements of cells and then considers the broader questions of structure, complexity, and function, which must be looked at on levels from the cell to the organism. Despite the vast amount of observational material already in existence, biophysics and biological physics are only at a beginning. We can expect that physics will continue to interact strongly with biology. Actually, the connection also includes chemistry and mathematics. New tools that become available in physics will continue to be applied to biological problems. We can expect that the flow of information will not be one way; biological systems will provide new information on many old and new parts of physics, from reaction theory and transport phenomena to complexity, cooperativity, and nonlinear processes

PREFACE: Complex Networks: from Biology to Information Technology

Science.gov (United States)

Barrat, A.; Boccaletti, S.; Caldarelli, G.; Chessa, A.; Latora, V.; Motter, A. E.

2008-06-01

The field of complex networks is one of the most active areas in contemporary statistical physics. Ten years after seminal work initiated the modern study of networks, interest in the field is in fact still growing, as indicated by the ever increasing number of publications in network science. The reason for such a resounding success is most likely the simplicity and broad significance of the approach that, through graph theory, allows researchers to address a variety of different complex systems within a common framework. This special issue comprises a selection of contributions presented at the workshop 'Complex Networks: from Biology to Information Technology' held in July 2007 in Pula (Cagliari), Italy as a satellite of the general conference STATPHYS23. The contributions cover a wide range of problems that are currently among the most important questions in the area of complex networks and that are likely to stimulate future research. The issue is organised into four sections. The first two sections describe 'methods' to study the structure and the dynamics of complex networks, respectively. After this methodological part, the issue proceeds with a section on applications to biological systems. The issue closes with a section concentrating on applications to the study of social and technological networks. The first section, entitled Methods: The Structure, consists of six contributions focused on the characterisation and analysis of structural properties of complex networks: The paper Motif-based communities in complex networks by Arenas et al is a study of the occurrence of characteristic small subgraphs in complex networks. These subgraphs, known as motifs, are used to define general classes of nodes and their communities by extending the mathematical expression of the Newman-Girvan modularity. The same line of research, aimed at characterising network structure through the analysis of particular subgraphs, is explored by Bianconi and Gulbahce in Algorithm

Synthesis, Spectroscopic Characterization and Biological Activities of Transition Metal Complexes Derived from a Tridentate Schiff Base

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J. Senthil Kumaran

2013-01-01

Full Text Available A new series of Cu (II, Ni (II, Co (II and Zn (II complexes have been synthesized from the Schiff base derived from 4-hydroxy-3-methoxybenzylidine-4-aminoantipyrine and 2-aminophenol. The structural features have been determined from their elemental analysis, magnetic susceptibility, molar conductance, Mass, IR, UV-Vis, 1H-NMR, 13C-NMR and ESR spectral studies. The redox behavior of the copper complex has been studied by cyclic voltammetry. The data confirm that the complexes have composition of ML2 type. The electronic absorption spectral data of the complexes propose an octahedral geometry around the central metal ion. All the metal complexes with DNA structure were guided by the presence of inter-molecular C–H⋯O and C–H⋯N hydrogen bonds. The biological activity of the synthesized compounds were tested against the bacterial species such as Bacillus subtilis, Staphylococcus aureus, Proteus vulgaris and fungal species such as Candida albicans by the well-diffusion method.

Removal of Trace Elements by Cupric Oxide Nanoparticles from Uranium In Situ Recovery Bleed Water and Its Effect on Cell Viability

Science.gov (United States)

Schilz, Jodi R.; Reddy, K. J.; Nair, Sreejayan; Johnson, Thomas E.; Tjalkens, Ronald B.; Krueger, Kem P.; Clark, Suzanne

2015-01-01

In situ recovery (ISR) is the predominant method of uranium extraction in the United States. During ISR, uranium is leached from an ore body and extracted through ion exchange. The resultant production bleed water (PBW) contains contaminants such as arsenic and other heavy metals. Samples of PBW from an active ISR uranium facility were treated with cupric oxide nanoparticles (CuO-NPs). CuO-NP treatment of PBW reduced priority contaminants, including arsenic, selenium, uranium, and vanadium. Untreated and CuO-NP treated PBW was used as the liquid component of the cell growth media and changes in viability were determined by the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay in human embryonic kidney (HEK 293) and human hepatocellular carcinoma (Hep G2) cells. CuO-NP treatment was associated with improved HEK and HEP cell viability. Limitations of this method include dilution of the PBW by growth media components and during osmolality adjustment as well as necessary pH adjustment. This method is limited in its wider context due to dilution effects and changes in the pH of the PBW which is traditionally slightly acidic however; this method could have a broader use assessing CuO-NP treatment in more neutral waters. PMID:26132311

Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

Energy Technology Data Exchange (ETDEWEB)

Manno, D; Filippo, E; Fiore, R; Serra, A [Dipartimento di Scienza dei Materiali, Universita del Salento, Lecce (Italy); Urso, E; Rizzello, A; Maffia, M [Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita del Salento, Lecce (Italy)

2010-04-23

Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP{sup C}. In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP{sup C} at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

International Nuclear Information System (INIS)

Manno, D; Filippo, E; Fiore, R; Serra, A; Urso, E; Rizzello, A; Maffia, M

2010-01-01

Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP C . In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP C at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

Three-dimensional models of cancer for pharmacology and cancer cell biology: capturing tumor complexity in vitro/ex vivo.

Science.gov (United States)

Hickman, John A; Graeser, Ralph; de Hoogt, Ronald; Vidic, Suzana; Brito, Catarina; Gutekunst, Matthias; van der Kuip, Heiko

2014-09-01

Cancers are complex and heterogeneous pathological "organs" in a dynamic interplay with their host. Models of human cancer in vitro, used in cancer biology and drug discovery, are generally highly reductionist. These cancer models do not incorporate complexity or heterogeneity. This raises the question as to whether the cancer models' biochemical circuitry (not their genome) represents, with sufficient fidelity, a tumor in situ. Around 95% of new anticancer drugs eventually fail in clinical trial, despite robust indications of activity in existing in vitro pre-clinical models. Innovative models are required that better capture tumor biology. An important feature of all tissues, and tumors, is that cells grow in three dimensions. Advances in generating and characterizing simple and complex (with added stromal components) three-dimensional in vitro models (3D models) are reviewed in this article. The application of stirred bioreactors to permit both scale-up/scale-down of these cancer models and, importantly, methods to permit controlled changes in environment (pH, nutrients, and oxygen) are also described. The challenges of generating thin tumor slices, their utility, and potential advantages and disadvantages are discussed. These in vitro/ex vivo models represent a distinct move to capture the realities of tumor biology in situ, but significant characterization work still remains to be done in order to show that their biochemical circuitry accurately reflects that of a tumor. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Informing biological design by integration of systems and synthetic biology.

Science.gov (United States)

Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

Synthesis, spectroscopic and biological studies of transition metal complexes of novel schiff bases derived from cephradine and sugars

International Nuclear Information System (INIS)

Naz, N.; Iqbal, M.Z.

2011-01-01

Fe(II), Co(II) and Ni(II) metal complexes of novel schiff bases derived from Cephradine and sugars (D-Glucose, L. Arabinose and D-Galactose) were synthesized and characterized by elemental analysis, magnetic susceptibility, thermal analysis, electronic absorption and FT-IR spectral studies. It has been found that schiff bases behave as bi-dentate-ligands forming complexes with 1:2 (metal:ligand) stoichiometry. the neutral nature of the complexes was confirmed by their low conductance values. The biological activities of complexes have been evaluated against two gram negative (Escherichia coli and Pseudomonas aeruginosa) and two gram positive (Bacillus subtilis and staphylococcus aureus) bacteria by Agar diffusion disc method. It has been found that the complexes have higher activity as compared to the pure Cephradine against the same bacteria. (author)

Quantification of biopharmaceuticals and biomarkers in complex biological matrices: a comparison of liquid chromatography coupled to tandem mass spectrometry and ligand binding assays

NARCIS (Netherlands)

Bults, Peter; van de Merbel, Nico C; Bischoff, Rainer

2015-01-01

The quantification of proteins (biopharmaceuticals or biomarkers) in complex biological samples such as blood plasma requires exquisite sensitivity and selectivity, as all biological matrices contain myriads of proteins that are all made of the same 20 proteinogenic amino acids, notwithstanding

Towards physical principles of biological evolution

Science.gov (United States)

Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

2018-03-01

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice

Geometric triangular chiral hexagon crystal-like complexes organization in pathological tissues biological collision order.

Directory of Open Access Journals (Sweden)

Jairo A Díaz

Full Text Available The present study describes and documents self-assembly of geometric triangular chiral hexagon crystal like complex organizations (GTCHC in human pathological tissues. The authors have found this architectural geometric expression at macroscopic and microscopic levels mainly in cancer processes. This study is based essentially on macroscopic and histopathologic analyses of 3000 surgical specimens: 2600 inflammatory lesions and 400 malignant tumours. Geometric complexes identified photographically at macroscopic level were located in the gross surgical specimen, and these areas were carefully dissected. Samples were taken to carry out histologic analysis. Based on the hypothesis of a collision genesis mechanism and because it is difficult to carry out an appropriate methodological observation in biological systems, the authors designed a model base on other dynamic systems to obtain indirect information in which a strong white flash wave light discharge, generated by an electronic device, hits over the lines of electrical conductance structured in helicoidal pattern. In their experimental model, the authors were able to reproduce and to predict polarity, chirality, helicoid geometry, triangular and hexagonal clusters through electromagnetic sequential collisions. They determined that similar events among constituents of extracelular matrix which drive and produce piezoelectric activity are responsible for the genesis of GTCHC complexes in pathological tissues. This research suggests that molecular crystals represented by triangular chiral hexagons derived from a collision-attraction event against collagen type I fibrils emerge at microscopic and macroscopic scales presenting a lateral assembly of each side of hypertrophy helicoid fibers, that represent energy flow in cooperative hierarchically chiral electromagnetic interaction in pathological tissues and arises as a geometry of the equilibrium in perturbed biological systems. Further

Geometric triangular chiral hexagon crystal-like complexes organization in pathological tissues biological collision order.

Science.gov (United States)

Díaz, Jairo A; Jaramillo, Natalia A; Murillo, Mauricio F

2007-12-12

The present study describes and documents self-assembly of geometric triangular chiral hexagon crystal like complex organizations (GTCHC) in human pathological tissues. The authors have found this architectural geometric expression at macroscopic and microscopic levels mainly in cancer processes. This study is based essentially on macroscopic and histopathologic analyses of 3000 surgical specimens: 2600 inflammatory lesions and 400 malignant tumours. Geometric complexes identified photographically at macroscopic level were located in the gross surgical specimen, and these areas were carefully dissected. Samples were taken to carry out histologic analysis. Based on the hypothesis of a collision genesis mechanism and because it is difficult to carry out an appropriate methodological observation in biological systems, the authors designed a model base on other dynamic systems to obtain indirect information in which a strong white flash wave light discharge, generated by an electronic device, hits over the lines of electrical conductance structured in helicoidal pattern. In their experimental model, the authors were able to reproduce and to predict polarity, chirality, helicoid geometry, triangular and hexagonal clusters through electromagnetic sequential collisions. They determined that similar events among constituents of extracelular matrix which drive and produce piezoelectric activity are responsible for the genesis of GTCHC complexes in pathological tissues. This research suggests that molecular crystals represented by triangular chiral hexagons derived from a collision-attraction event against collagen type I fibrils emerge at microscopic and macroscopic scales presenting a lateral assembly of each side of hypertrophy helicoid fibers, that represent energy flow in cooperative hierarchically chiral electromagnetic interaction in pathological tissues and arises as a geometry of the equilibrium in perturbed biological systems. Further interdisciplinary studies must

40 CFR Appendix A to Part 414 - Non-Complexed Metal-Bearing Waste Streams and Cyanide-Bearing Waste Streams

Science.gov (United States)

2010-07-01

... Mercaptan/Ethanol + Hydrogen sulfide Methanol/H.P. Synthesis from natural gas via synthetic gas Oxo Alcohols... + Ammonia n-Propyl alcohol/Hydrogenation of propionaldehyde, Oxo process SAN resin/Suspension polymerization... methanol Acetaldehyde/Oxidation of ethylene with cupric chloride catalyst Acetic acid/Catalytic oxidation...

Drosophila melanogaster--the model organism of choice for the complex biology of multi-cellular organisms

Science.gov (United States)

Beckingham, Kathleen M.; Armstrong, J. Douglas; Texada, Michael J.; Munjaal, Ravi; Baker, Dean A.

2005-01-01

Drosophila melanogaster has been intensely studied for almost 100 years. The sophisticated array of genetic and molecular tools that have evolved for analysis of gene function in this organism are unique. Further, Drosophila is a complex multi-cellular organism in which many aspects of development and behavior parallel those in human beings. These combined advantages have permitted research in Drosophila to make seminal contributions to the understanding of fundamental biological processes and ensure that Drosophila will continue to provide unique insights in the genomic era. An overview of the genetic methodologies available in Drosophila is given here, together with examples of outstanding recent contributions of Drosophila to our understanding of cell and organismal biology. The growing contribution of Drosophila to our knowledge of gravity-related responses is addressed.

The complex jujube genome provides insights into fruit tree biology.

Science.gov (United States)

Liu, Meng-Jun; Zhao, Jin; Cai, Qing-Le; Liu, Guo-Cheng; Wang, Jiu-Rui; Zhao, Zhi-Hui; Liu, Ping; Dai, Li; Yan, Guijun; Wang, Wen-Jiang; Li, Xian-Song; Chen, Yan; Sun, Yu-Dong; Liu, Zhi-Guo; Lin, Min-Juan; Xiao, Jing; Chen, Ying-Ying; Li, Xiao-Feng; Wu, Bin; Ma, Yong; Jian, Jian-Bo; Yang, Wei; Yuan, Zan; Sun, Xue-Chao; Wei, Yan-Li; Yu, Li-Li; Zhang, Chi; Liao, Sheng-Guang; He, Rong-Jun; Guang, Xuan-Min; Wang, Zhuo; Zhang, Yue-Yang; Luo, Long-Hai

2014-10-28

The jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The final assembly spans 437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone frequent inter-chromosome fusions and segmental duplications, but no recent whole-genome duplication. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees.

Radiosynthesis and biological evaluation of the 99mTc-tricarbonyl moxifloxacin dithiocarbamate complex as a potential Staphylococcus aureus infection radiotracer

International Nuclear Information System (INIS)

Shah, Syed Qaiser; Khan, Muhammad Rafiullah

2011-01-01

In the present investigation, radiosynthesis of the 99m Tc-tricarbonyl moxifloxacin dithiocarbamate complex ( 99m Tc(CO) 3 -MXND) and its biological evaluation in male Wister rats (MWR) artificially infected with Staphylococcus aureus (S. aureus) was assessed. The 99m Tc(CO) 3 -MXND complex was radiochemically examined in terms of stability in saline and in serum and biologically its in-vitro binding with S. aureus and percent absorption in MWR models. Radiochemically the 99m Tc(CO) 3 -MXND complex showed more than 90% stability in saline up to 240 min and in serum 14.95% undesirable species was appeared within 16 h. In-vitro the 99m Tc(CO) 3 -MXND complex showed saturated binding with S. aureus. In MWR artificially infected with live S. aureus the complex showed about six fold higher uptakes in the infected muscle as compared to the normal muscle. However, insignificant change in the uptake of 99m Tc(CO) 3 -MXND complex in the infected and inflamed or normal muscle was observed in the MWR infected with heat killed S. aureus. The 99m Tc(CO) 3 -MXND complex disappeared from the circulatory system and appeared in the urinary system within 60-90 min followed by excretion through normal route of urinary system. Based on the elevated and stable radiochemical succumb in saline, serum, saturated in-vitro binding with S. aureus and higher accumulation in the target organ of the MWR, we recommend the 99m Tc(CO) 3 -MXND complex for radio-localization of the infection induced by S. aureus in human.

Industrial systems biology and its impact on synthetic biology of yeast cell factories

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

Ferric and cobaltous hydroacid complexes for forward osmosis (FO) processes

KAUST Repository

Ge, Qingchun; Fu, Fengjiang; Chung, Neal Tai-Shung

2014-01-01

Cupric and ferric hydroacid complexes have proven their advantages as draw solutes in forward osmosis in terms of high water fluxes, negligible reverse solute fluxes and easy recovery (Ge and Chung, 2013. Hydroacid complexes: A new class of draw solutes to promote forward osmosis (FO) processes. Chemical Communications 49, 8471-8473.). In this study, cobaltous hydroacid complexes were explored as draw solutes and compared with the ferric hydroacid complex to study the factors influencing their FO performance. The solutions of the cobaltous complexes produce high osmotic pressures due to the presence of abundant hydrophilic groups. These solutes are able to dissociate and form a multi-charged anion and Na+ cations in water. In addition, these complexes have expanded structures which lead to negligible reverse solute fluxes and provide relatively easy approaches in regeneration. These characteristics make the newly synthesized cobaltous complexes appropriate as draw solutes. The FO performance of the cobaltous and ferric-citric acid (Fe-CA) complexes were evaluated respectively through cellulose acetate membranes, thin-film composite membranes fabricated on polyethersulfone supports (referred as TFC-PES), and polybenzimidazole and PES dual-layer (referred as PBI/PES) hollow fiber membranes. Under the conditions of DI water as the feed and facing the support layer of TFC-PES FO membranes (PRO mode), draw solutions at 2.0M produced relatively high water fluxes of 39-48 LMH (Lm-2hr-1) with negligible reverse solute fluxes. A water flux of 17.4 LMH was achieved when model seawater of 3.5wt.% NaCl replaced DI water as the feed and 2.0M Fe-CA as the draw solution under the same conditions. The performance of these hydroacid complexes surpasses those of the synthetic draw solutes developed in recent years. This observation, along with the relatively easy regeneration, makes these complexes very promising as a novel class of draw solutes. © 2014 Elsevier Ltd.

Ferric and cobaltous hydroacid complexes for forward osmosis (FO) processes

KAUST Repository

Ge, Qingchun

2014-07-01

Cupric and ferric hydroacid complexes have proven their advantages as draw solutes in forward osmosis in terms of high water fluxes, negligible reverse solute fluxes and easy recovery (Ge and Chung, 2013. Hydroacid complexes: A new class of draw solutes to promote forward osmosis (FO) processes. Chemical Communications 49, 8471-8473.). In this study, cobaltous hydroacid complexes were explored as draw solutes and compared with the ferric hydroacid complex to study the factors influencing their FO performance. The solutions of the cobaltous complexes produce high osmotic pressures due to the presence of abundant hydrophilic groups. These solutes are able to dissociate and form a multi-charged anion and Na+ cations in water. In addition, these complexes have expanded structures which lead to negligible reverse solute fluxes and provide relatively easy approaches in regeneration. These characteristics make the newly synthesized cobaltous complexes appropriate as draw solutes. The FO performance of the cobaltous and ferric-citric acid (Fe-CA) complexes were evaluated respectively through cellulose acetate membranes, thin-film composite membranes fabricated on polyethersulfone supports (referred as TFC-PES), and polybenzimidazole and PES dual-layer (referred as PBI/PES) hollow fiber membranes. Under the conditions of DI water as the feed and facing the support layer of TFC-PES FO membranes (PRO mode), draw solutions at 2.0M produced relatively high water fluxes of 39-48 LMH (Lm-2hr-1) with negligible reverse solute fluxes. A water flux of 17.4 LMH was achieved when model seawater of 3.5wt.% NaCl replaced DI water as the feed and 2.0M Fe-CA as the draw solution under the same conditions. The performance of these hydroacid complexes surpasses those of the synthetic draw solutes developed in recent years. This observation, along with the relatively easy regeneration, makes these complexes very promising as a novel class of draw solutes. © 2014 Elsevier Ltd.

Synthesis, Characterization and Biological Evaluation of Transition Metal Complexes Derived from N, S Bidentate Ligands

Directory of Open Access Journals (Sweden)

Enis Nadia Md Yusof

2015-05-01

Full Text Available Two bidentate NS ligands were synthesized by the condensation reaction of S-2-methylbenzyldithiocarbazate (S2MBDTC with 2-methoxybenzaldehyde (2MB and 3-methoxybenzaldehyde (3MB. The ligands were reacted separately with acetates of Cu(II, Ni(II and Zn(II yielding 1:2 (metal:ligand complexes. The metal complexes formed were expected to have a general formula of [M(NS2] where M = Cu2+, Ni2+, and Zn2+. These compounds were characterized by elemental analysis, molar conductivity, magnetic susceptibility and various spectroscopic techniques. The magnetic susceptibility measurements and spectral results supported the predicted coordination geometry in which the Schiff bases behaved as bidentate NS donor ligands coordinating via the azomethine nitrogen and thiolate sulfur. The molecular structures of the isomeric S2M2MBH (1 and S2M3MBH (2 were established by X-ray crystallography to have very similar l-shaped structures. The Schiff bases and their metal complexes were evaluated for their biological activities against estrogen receptor-positive (MCF-7 and estrogen receptor-negative (MDA-MB-231 breast cancer cell lines. Only the Cu(II complexes showed marked cytotoxicity against the cancer cell lines. Both Schiff bases and other metal complexes were found to be inactive. In concordance with the cytotoxicity studies, the DNA binding studies indicated that Cu(II complexes have a strong DNA binding affinity.

Patrick Air Force Base Storm Water Pollution Prevention Plan.

Science.gov (United States)

1994-09-01

7758987 Cupric sulfate 77-47-4 Hexachlorocyclopentadliene 10380297 Cupric sulfate, ammoniated 67-72-1 H-exachloroethane 815827 Cupric tartrate 76-47-01...28300745 Antimony potassium 75-00-3 Chloroethane (Ethyl chlo- tartrate ride) 7789619 Antimony tribromide 67-66-3 Chloroform 10025919 Antimony...5 p-Cresol 7787475 Beryllium chloride 1319-77-3 Cresol (mixed isomers) 7787497 Beryllium fluoride 142712 Cupric acetate 7787555 Beryllium nitrate

Influence of the nucleobase on the physicochemical characteristics and biological activities of Sb{sup V}-ribonucleoside complexes

Energy Technology Data Exchange (ETDEWEB)

Ferreira, Claudio S.; Demicheli, Cynthia, E-mail: demichel@netuno.lcc.ufmg.b [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Rocha, Iara C.M. da; Melo, Maria N. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Parasitologia; Monte Neto, Rubens L.; Frezard, Frederic [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Fisiologia e Biofisica

2010-07-01

The influence of the nucleobase (uracyl, U; cytosine, C; adenine, A; guanine, G) on the physicochemical characteristics and in vitro biological activities of Sb{sup V}-ribonucleoside complexes has been investigated. The 1:1 Sb-U and Sb-C complexes were characterized by NMR and ESI-MS spectroscopies and elemental analysis. The stability constant and the apparent association and dissociation rate constants of 1:1 Sb{sup V}-U, Sb{sup V}-C and Sb{sup V}-A complexes were determined. Although Sb{sup V} most probably binds via oxygen atoms to the same 2' and 3' positions in the different nucleosides, the ribose conformational changes and the physicochemical characteristics of the complex depend on the nucleobase. The nucleobase had a strong influence on the cytotoxicity against macrophages and the antileishmanial activity of the Sb{sup V}-ribonucleoside complexes. The Sb{sup V}-purine complexes were more cytotoxic and more effective against Leishmania chagasi than the Sb{sup V}-pyrimidine complexes, supporting the model that the interaction of Sb{sup V} with purine nucleosides may mediate the antileishmanial activity of pentavalent antimonial drugs. (author)

Synthesis, characterization and biological assay of Salicylaldehyde Schiff base Cu(II) complexes and their precursors

Science.gov (United States)

Iftikhar, Bushra; Javed, Kanwal; Khan, Muhammad Saif Ullah; Akhter, Zareen; Mirza, Bushra; Mckee, Vickie

2018-03-01

Three new Schiff base ligands were synthesized by the reaction of Salicylaldehyde with semi-aromatic diamines, prepared by the reduction of corresponding dinitro-compounds, and were further used for the formation of complexes with Cu(II) metal ion. The structural features of the synthesized compounds were confirmed by their physical properties and infrared, electronic and NMR spectroscopic techniques. The studies revealed that the synthesized Schiff bases existed as tetradentate ligands and bonded to the metal ion through the phenolic oxygen and azomethine nitrogen. One of the dinitro precursors was also analyzed by single crystal X-ray crystallography, which showed that it crystallizes in monoclinic system with space group P2/n. The thermal behavior of the Cu(II) complexes was determined by thermogravimetric analysis (TGA) and kinetic parameters were evaluated from the data. Schiff base ligands, their precursors and metal complexes were also screened for antibacterial, antifungal, antitumor, Brine shrimp lethality, DPPH free radical scavenging and DNA damage assays. The results of these analyses indicated the substantial potential of the synthesized Schiff bases, their precursors and Cu(II) complexes in biological field as future drugs.

SWIM: a computational tool to unveiling crucial nodes in complex biological networks.

Science.gov (United States)

Paci, Paola; Colombo, Teresa; Fiscon, Giulia; Gurtner, Aymone; Pavesi, Giulio; Farina, Lorenzo

2017-03-20

SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called "fight-club hubs", characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called "switch genes", appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance. Here, we applied SWIM to a large panel of cancer datasets from The Cancer Genome Atlas, in order to highlight switch genes that could be critically associated with the drastic changes in the physiological state of cells or tissues induced by the cancer development. We discovered that switch genes are found in all cancers we studied and they encompass protein coding genes and non-coding RNAs, recovering many known key cancer players but also many new potential biomarkers not yet characterized in cancer context. Furthermore, SWIM is amenable to detect switch genes in different organisms and cell conditions, with the potential to uncover important players in biologically relevant scenarios, including but not limited to human cancer.

Y-12 National Security Complex Biological Monitoring And Abatement Program 2008 Calendar Year Report

Energy Technology Data Exchange (ETDEWEB)

Peterson, M. J.; Greeley Jr., M. S.; Mathews, T. J.; Morris, G. W.; Roy, W. K.; Ryon, M. G.; Smith, J. G.; Southworth, G. R.

2009-07-01

The National Pollutant Discharge Elimination System (NPDES) permit issued for the Oak Ridge Y-12 National Security Complex (Y-12 Complex) which became effective May 1, 2006, continued a requirement for a Biological Monitoring and Abatement Program (BMAP). The BMAP was originally developed in 1985 to demonstrate that the effluent limitations established for the Y-12 Complex protected the classified uses of the receiving stream (East Fork Poplar Creek: EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). The objectives of the current BMAP are similar, specifically to assess stream ecological conditions relative to regulatory limits and criteria, to assess ecological impacts as well as recovery in response to Y-12 operations, and to investigate the causes of continuing impacts. The BMAP consists of three tasks that reflect complementary approaches to evaluating the effects of the Y-12 Complex discharges on the biotic integrity of EFPC. These tasks include: (1) bioaccumulation monitoring, (2) benthic macroinvertebrate community monitoring, and (3) fish community monitoring. As required by the NPDES permit, the BMAP benthic macroinvertebrate community monitoring task includes studies to annually evaluate the receiving stream's biological integrity in comparison to TN Water Quality Criteria. BMAP monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) appropriate habitat distribution, and (5) access. The primary sampling sites include upper EFPC at kilometers (EFKs) 24.4 and 23.4 [upstream and downstream of Lake Reality (LR) respectively]; EFK 18.7 (also EFK 18.2 and 19), located off

From structure of the complex to understanding of the biology

Energy Technology Data Exchange (ETDEWEB)

Rossmann, Michael G., E-mail: mr@purdue.edu [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Arisaka, Fumio [Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Kanamaru, Shuji [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Kostyuchenko, Victor A. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Mesyanzhinov, Vadim V.; Shneider, Mikhail M. [Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, 117997 (Russian Federation); Morais, Marc C.; Leiman, Petr G. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Palermo, Laura M.; Parrish, Colin R. [James A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (United States); Xiao, Chuan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States)

2007-01-01

The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.

From structure of the complex to understanding of the biology

International Nuclear Information System (INIS)

Rossmann, Michael G.; Arisaka, Fumio; Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan; Kanamaru, Shuji; Kostyuchenko, Victor A.; Mesyanzhinov, Vadim V.; Shneider, Mikhail M.; Morais, Marc C.; Leiman, Petr G.; Palermo, Laura M.; Parrish, Colin R.; Xiao, Chuan

2007-01-01

The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle

Synthesis, Characterization and Spectral Studies of Noble Heterobinuclear Complexes of Transition Metal Ions and their Biological Activity

Directory of Open Access Journals (Sweden)

Netra Pal Singh

2011-01-01

Full Text Available Some noble heterobinuclear complexes of transition metal ions with bis(salicylaldehydemalonyl-dihydrazone in the presence of 5-nitroindazole Cu(II / Ni(II- chloride of the type [ML1M‘L2Cl2] or [ML1FeL2Cl2]Cl, where M = Ni(II, Cu(II and M' = Mn(II, Co(II, have been prepared. All the complexes have been characterized by IR, UV vis and EPR spectroscopy, elemental analysis, magnetic moment and molar conductance measurement. Spectral studies and magnetic moment measurement in DMF suggest the covalent nature of the complexes, except the [ML1FeL2Cl2]Cl complex which is 1:1 electrolyte. An octahedral geometry is proposed for M‘ and square planer for M for the heterobinuclear complexes. The low value of magnetic moment and overlapping EPR signals are due to spin crossover since both of the metals have unpaired electrons with same molecular symmetry. The lowering of the magnetic moment has been discussed. The biological activity (antifungal and antibacterial of the represented compounds has been studied.

Co(II) and Cd(II) Complexes Derived from Heterocyclic Schiff-Bases: Synthesis, Structural Characterisation, and Biological Activity

Science.gov (United States)

Ahmed, Riyadh M.; Yousif, Enaam I.; Al-Jeboori, Mohamad J.

2013-01-01

New monomeric cobalt and cadmium complexes with Schiff-bases, namely, N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]furan-2-carbohydrazide (L1) and N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]thiophene-2-carbohydrazide (L2) are reported. Schiff-base ligands L1 and L2 were derived from condensation of 3-hydroxy-4-methoxybenzaldehyde (iso-vanillin) with furan-2-carboxylic acid hydrazide and thiophene-2-carboxylic acid hydrazide, respectively. Complexes of the general formula [M(L)2]Cl2 (where M = Co(II) or Cd(II), L = L1 or L2) have been obtained from the reaction of the corresponding metal chloride with the ligands. The ligands and their metal complexes were characterised by spectroscopic methods (FTIR, UV-Vis, 1H, and 13C NMR spectra), elemental analysis, metal content, magnetic measurement, and conductance. These studies revealed the formation of four-coordinate complexes in which the geometry about metal ion is tetrahedral. Biological activity of the ligands and their metal complexes against gram positive bacterial strain Bacillus (G+) and gram negative bacteria Pseudomonas (G−) revealed that the metal complexes become less resistive to the microbial activities as compared to the free ligands. PMID:24027449

A Tryptoline Ring-Distortion Strategy Leads to Complex and Diverse Biologically Active Molecules from the Indole Alkaloid Yohimbine.

Science.gov (United States)

Paciaroni, Nicholas G; Ratnayake, Ranjala; Matthews, James H; Norwood, Verrill M; Arnold, Austin C; Dang, Long H; Luesch, Hendrik; Huigens, Robert W

2017-03-28

High-throughput screening (HTS) is the primary driver to current drug-discovery efforts. New therapeutic agents that enter the market are a direct reflection of the structurally simple compounds that make up screening libraries. Unlike medically relevant natural products (e.g., morphine), small molecules currently being screened have a low fraction of sp 3 character and few, if any, stereogenic centers. Although simple compounds have been useful in drugging certain biological targets (e.g., protein kinases), more sophisticated targets (e.g., transcription factors) have largely evaded the discovery of new clinical agents from screening collections. Herein, a tryptoline ring-distortion strategy is described that enables the rapid synthesis of 70 complex and diverse compounds from yohimbine (1); an indole alkaloid. The compounds that were synthesized had architecturally complex and unique scaffolds, unlike 1 and other scaffolds. These compounds were subjected to phenotypic screens and reporter gene assays, leading to the identification of new compounds that possessed various biological activities, including antiproliferative activities against cancer cells with functional hypoxia-inducible factors, nitric oxide inhibition, and inhibition and activation of the antioxidant response element. This tryptoline ring-distortion strategy can begin to address diversity problems in screening libraries, while occupying biologically relevant chemical space in areas critical to human health. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Repair Responses of Dental Pulp to Tooth Injury and Biological Properties of Dentin-pulp Complex

OpenAIRE

大島, 勇人; Ohshima, Hayato

2004-01-01

Regeneration-the creation of a new tissue after the original one has been lost-is the fundamental biological capability in an organism. Numerous organs are considered to contain stem cells referred to as adult stem cells, even in the adult. Adult stem cells can give rise to a limited set of adult tissue types. In the field of clinical dentistry, it is well-known that the dentin-pulp complex is capable of repair after tooth injuries such as tooth replantation/transplantation or restorative pro...

Temperature-dependent phase transitions in zeptoliter volumes of a complex biological membrane

International Nuclear Information System (INIS)

Nikiforov, Maxim P; Jesse, Stephen; Kalinin, Sergei V; Hohlbauch, Sophia; Proksch, Roger; King, William P; Voitchovsky, Kislon; Contera, Sonia Antoranz

2011-01-01

Phase transitions in purple membrane have been a topic of debate for the past two decades. In this work we present studies of a reversible transition of purple membrane in the 50-60 deg. C range in zeptoliter volumes under different heating regimes (global heating and local heating). The temperature of the reversible phase transition is 52 ± 5 deg. C for both local and global heating, supporting the hypothesis that this transition is mainly due to a structural rearrangement of bR molecules and trimers. To achieve high resolution measurements of temperature-dependent phase transitions, a new scanning probe microscopy-based method was developed. We believe that our new technique can be extended to other biological systems and can contribute to the understanding of inhomogeneous phase transitions in complex systems.

Bions: a family of biomimetic mineralo-organic complexes derived from biological fluids.

Directory of Open Access Journals (Sweden)

Cheng-Yeu Wu

Full Text Available Mineralo-organic nanoparticles form spontaneously in human body fluids when the concentrations of calcium and phosphate ions exceed saturation. We have shown previously that these mineralo-organic nanoparticles possess biomimetic properties and can reproduce the whole phenomenology of the so-called nanobacteria-mineralized entities initially described as the smallest microorganisms on earth. Here, we examine the possibility that various charged elements and ions may form mineral nanoparticles with similar properties in biological fluids. Remarkably, all the elements tested, including sodium, magnesium, aluminum, calcium, manganese, iron, cobalt, nickel, copper, zinc, strontium, and barium form mineralo-organic particles with bacteria-like morphologies and other complex shapes following precipitation with phosphate in body fluids. Upon formation, these mineralo-organic particles, which we term bions, invariably accumulate carbonate apatite during incubation in biological fluids; yet, the particles also incorporate additional elements and thus reflect the ionic milieu in which they form. Bions initially harbor an amorphous mineral phase that gradually converts to crystals in culture. Our results show that serum produces a dual inhibition-seeding effect on bion formation. Using a comprehensive proteomic analysis, we identify a wide range of proteins that bind to these mineral particles during incubation in medium containing serum. The two main binding proteins identified, albumin and fetuin-A, act as both inhibitors and seeders of bions in culture. Notably, bions possess several biomimetic properties, including the possibility to increase in size and number and to be sub-cultured in fresh culture medium. Based on these results, we propose that bions represent biological, mineralo-organic particles that may form in the body under both physiological and pathological homeostasis conditions. These mineralo-organic particles may be part of a

Industrial systems biology and its impact on synthetic biology of yeast cell factories.

Science.gov (United States)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-06-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Biological activities of some Fluoroquinolones-metal complexes

African Journals Online (AJOL)

McRoy

DNA cleavage studies of some synthesized metal complexes of fluoroquinolone ... Although the FQs are generally characterized by a broad antimicrobial spectrum ..... six Coordinate 3rd metal complexes with N- (5 –Phenyl-3,4- thiadiazol-2-yl).

The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

Science.gov (United States)

Pollard, Thomas D

2014-12-02

This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Biological design in science classrooms

Science.gov (United States)

Scott, Eugenie C.; Matzke, Nicholas J.

2007-01-01

Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront “intelligent design” (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older “creation science” movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education. PMID:17494747

Biological Screening of Newly Synthesized BIAN N-Heterocyclic Gold Carbene Complexes in Zebrafish Embryos

Science.gov (United States)

Farooq, Muhammad; Abu Taha, Nael; Butorac, Rachel R.; Evans, Daniel Anthony; Elzatahry, Ahmed A.; Elsayed, Elsayed Ahmed; Wadaan, Mohammad A. M.; Al-Deyab, Salem S.; Cowley, Alan H.

2015-01-01

N-Heterocyclic carbene (NHC) metal complexes possess diverse biological activities but have yet to be extensively explored as potential chemotherapeutic agents. We have previously reported the synthesis of a new class of NHC metal complexes N-heterocyclic with acetate [IPr(BIAN)AuOAc] and chloride [IPr(BIAN)AuCl] ligands. In the experiments reported herein, the zebrafish embryos were exposed to serial dilutions of each of these complexes for 10–12 h. One hundred percent mortality was observed at concentrations ≥50 µM. At sub-lethal concentrations (10–30 µM), both compounds influenced zebrafish embryonic development. However, quite diverse categories of abnormalities were found in exposed embryos with each compound. Severe brain deformation and notochord degeneration were evident in the case of [IPr(BIAN)AuOAc]. The zebrafish embryos treated with [IPr(BIAN)AuCl] exhibited stunted growth and consequently had smaller body sizes. A depletion of 30%–40% glutathione was detected in the treated embryos, which could account for one of the possible mechanism of neurotoxicity. The fact that these compounds are capable of both affecting the growth and also compromising antioxidant systems by elevating intracellular ROS production implies that they could play an important role as a new breed of therapeutic molecules. PMID:26501273

Improving off-line accelerated tryptic digestion. Towards fast-lane proteolysis of complex biological samples.

Science.gov (United States)

Vukovic, Jadranka; Loftheim, Håvard; Winther, Bjørn; Reubsaet, J Léon E

2008-06-27

Off-line digestion of proteins using immobilized trypsin beads is studied with respect to the format of the digestion reactor, the digestion conditions, the comparison with in-solution digestion and its use in complex biological samples. The use of the filter vial as the most appropriate digestion reactor enables simple, efficient and easy-to-handle off-line digestion of the proteins on trypsin beads. It was shown that complex proteins like bovine serum albumin (BSA) need much longer time (89 min) and elevated temperature (37 degrees C) to be digested to an acceptable level compared to smaller proteins like cytochrome c (5 min, room temperature). Comparing the BSA digestion using immobilized trypsin beads with conventional in-solution digestion (overnight at 37 degrees C), it was shown that comparable results were obtained with respect to sequence coverage (>90%) and amount of missed cleavages (in both cases around 20 peptides with 1 or 2 missed cleavages were detected). However, the digestion using immobilized trypsin beads was considerable less time consuming. Good reproducibility and signal intensities were obtained for the digestion products of BSA in a complex urine sample. In addition to this, peptide products of proteins typically present in urine were identified.

Oxidative leaching process with cupric ion in hydrochloric acid media for recovery of Pd and Rh from spent catalytic converters

Energy Technology Data Exchange (ETDEWEB)

Nogueira, C.A., E-mail: carlos.nogueira@lneg.pt [Laboratório Nacional de Energia e Geologia, I.P., Campus do Lumiar, 1649-038 Lisboa (Portugal); Paiva, A.P., E-mail: appaiva@fc.ul.pt [Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa (Portugal); Oliveira, P.C. [Laboratório Nacional de Energia e Geologia, I.P., Campus do Lumiar, 1649-038 Lisboa (Portugal); Costa, M.C., E-mail: mcorada@ualg.pt [Centro de Ciências do Mar, Departamento de Química e Farmácia, Faculdade de Ciências e de Tecnologia, Campus de Gambelas, 8005-139 Faro (Portugal); Costa, A.M. Rosa da, E-mail: amcosta@ualg.pt [Centro de Investigação em Química do Algarve, Departamento de Química e Farmácia, Faculdade de Ciências e de Tecnologia, Campus de Gambelas, 8005-139 Faro (Portugal)

2014-08-15

Highlights: • A new leaching process based on Cu{sup 2+}/HCl media for recovering Pd and Rh from spent autocatalytic converters is presented. • Palladium and rhodium were efficiently leached, with attained maximum yields of 95% and 86%, respectively. • Temperature, time, and HCl and Cu{sup 2+} concentrations were found to be significant factors in the leaching of Pd and Rh. - Abstract: The recycling of platinum-group metals from wastes such as autocatalytic converters is getting growing attention due to the scarcity of these precious metals and the market pressure originated by increase of demand in current and emerging applications. Hydrometallurgical treatment of such wastes is an alternative way to the most usual pyrometallurgical processes based on smelter operations. This paper focuses on the development of a leaching process using cupric chloride as oxidising agent, in HCl media, for recovery of palladium and rhodium from a spent catalyst. The chloride media allows the adequate conditions for oxidising and solubilising the metals, as demonstrated by equilibrium calculations based on thermodynamic data. The experimental study of the leaching process revealed that Pd solubilisation is clearly easier than that of Rh. The factors temperature, time, and HCl and Cu{sup 2+} concentrations were significant regarding Pd and Rh leaching, the latter requiring higher factor values to achieve the same results. Leaching yields of 95% Pd and 86% Rh were achieved under optimised conditions (T = 80 °C, t = 4 h, [HCl] = 6 M, [Cu{sup 2+}] = 0.3 M)

Complex chemistry

International Nuclear Information System (INIS)

Kim, Bong Gon; Kim, Jae Sang; Kim, Jin Eun; Lee, Boo Yeon

2006-06-01

This book introduces complex chemistry with ten chapters, which include development of complex chemistry on history coordination theory and Warner's coordination theory and new development of complex chemistry, nomenclature on complex with conception and define, chemical formula on coordination compound, symbol of stereochemistry, stereo structure and isomerism, electron structure and bond theory on complex, structure of complex like NMR and XAFS, balance and reaction on solution, an organo-metallic chemistry, biology inorganic chemistry, material chemistry of complex, design of complex and calculation chemistry.

Alkali Metal Ion Complexes with Phosphates, Nucleotides, Amino Acids, and Related Ligands of Biological Relevance. Their Properties in Solution.

Science.gov (United States)

Crea, Francesco; De Stefano, Concetta; Foti, Claudia; Lando, Gabriele; Milea, Demetrio; Sammartano, Silvio

2016-01-01

Alkali metal ions play very important roles in all biological systems, some of them are essential for life. Their concentration depends on several physiological factors and is very variable. For example, sodium concentrations in human fluids vary from quite low (e.g., 8.2 mmol dm(-3) in mature maternal milk) to high values (0.14 mol dm(-3) in blood plasma). While many data on the concentration of Na(+) and K(+) in various fluids are available, the information on other alkali metal cations is scarce. Since many vital functions depend on the network of interactions occurring in various biofluids, this chapter reviews their complex formation with phosphates, nucleotides, amino acids, and related ligands of biological relevance. Literature data on this topic are quite rare if compared to other cations. Generally, the stability of alkali metal ion complexes of organic and inorganic ligands is rather low (usually log K  Na(+) > K(+) > Rb(+) > Cs(+). For example, for citrate it is: log K ML = 0.88, 0.80, 0.48, 0.38, and 0.13 at 25 °C and infinite dilution. Some considerations are made on the main aspects related to the difficulties in the determination of weak complexes. The importance of the alkali metal ion complexes was also studied in the light of modelling natural fluids and in the use of these cations as probes for different processes. Some empirical relationships are proposed for the dependence of the stability constants of Na(+) complexes on the ligand charge, as well as for correlations among log K values of NaL, KL or LiL species (L = generic ligand).

Radiocharacterization of the 99mTc-rufloxacin complex and biological evaluation in Staphylococcus aureus infected rat model

International Nuclear Information System (INIS)

Syed Qaiser Shah; Muhammad Rafiullah Khan

2011-01-01

99m Tc-rufloxacin ( 99m Tc-RUN) complex was prepared by reaction of different amounts of reduced sodium pertechnetate with different amount of Rufloxacin (RUN) antibiotic for the in vivo scintigraphic localization of the Staphylococcus aureus (S. aureus) infectious foci in Male Wister Rats (MWR) model. The 99m Tc-RUN complex was radiochemically and biologically characterized in terms of radiochemical stability in saline, serum, in vitro binding with S. aureus and biodistribution in artificially infected with S. aureus MWR. The 99m Tc-RUN complex showed stability more than 90% up to 240 min in normal saline with a maximum stability value of 98.10 ± 0.18% at 30 min after reconstitution. At 37 deg C the complex showed in vitro permanence in serum up to 16 h with 13.90% side products during incubation. The 99m Tc-RUN complex showed saturated in vitro binding with S. aureus at different intervals with a maximum uptake value of 71.50%. Infected to normal muscle, infected to inflamed and inflamed to normal muscles ratios were approximately 6.04, 4.31 and 1.40. Based on the stability of the complex in saline, serum, in vitro binding with S. aureus and biodistribution results, the 99m Tc-RUN complex is recommended for in vivo scintigraphic localization of the S. aureus in vivo infectious foci in human. (author)

Syntheses, structural elucidation, thermal properties, theoretical quantum chemical studies (DFT and biological studies of barbituric–hydrazone complexes

Directory of Open Access Journals (Sweden)

Amina A. Soayed

2015-03-01

Full Text Available Condensation of barbituric acid with hydrazine hydrate yielded barbiturichydrazone (L which was characterized using IR, 1H NMR and mass spectra. The Co(II, Ni(II and Cu(II complexes derived from this ligand have been synthesized and structurally characterized by elemental analyses, spectroscopic methods (IR, UV–Vis and ESR and thermal analyses (TGA, DTG and DTA and the structures were further elucidated using quantum chemical density functional theory. Complexes of L were found to have the ML.nH2O stoichiometry with either tetrahedral or octahedral geometry. The ESR data showed the Cu(II complex to be in a tetragonal geometry. Theoretical investigation of the electronic structure of metal complexes at the TD-DFT/B3LYP level of theory has been carried out and discussed. The fundamental vibrational wavenumbers were calculated and a good agreement between observed and scaled calculated wavenumbers was achieved. Thermal studies were performed to deduce the stabilities of the ligand and complexes. Thermodynamic parameters, such as the order of reactions (n, activation energy ΔE∗, enthalpy of reaction ΔH∗ and entropy ΔS∗ were calculated from DTA curves using Horowitz–Metzger method. The ligand L and its complexes have been screened for their antifungal and antibacterial activities and were found to possess better biological activities compared to those of unsubstituted barbituric acid complexes.

A Study on Carbon Fiber (Long Fiber) Reinforced Copper Matrix Composite

Science.gov (United States)

1990-03-30

complex may be coke phosphate, 7 EDTA, NTA, tartrate , citrate, etc. added by proper amount of op series activating agent. It has the following property...significantly improved. Discharge with large current is proper in order to reduce the time of electrodeposition, so acidity cupric sulphate solution is

Environmental Review Guide for Operations (ERGO) - A Compliance Assessment Manual for Use at All USACE Civil-Funded Projects and Facilities

Science.gov (United States)

1994-03-01

23-8 Cupric oxalate 100 5893-66-3 Cupric sulfate 10 7758-98-7 Cupric sulfate ammoniated 100 10380-2% Cupric tartrate 100 81582 W Cyanides (soluble...sulfamate 5000 7773-06-0) Ammonium sulfate x 7783-20-2 (solution) Ammonium sulfide 100 12135-76-1 Ammonium sulfite 5000 10196-04-0 Ammonium tartrate 5000...14307-43-8 Ammonium tartrate 5000 3164-29-2 Ammonium thiocyanate 5000 1762-95-4 Ammonium vanadate 1000 P119 7803-55-6 Amphetamine 1000 300-62-9 Amyl

Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds.

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Fang, Lingzhao; Sahana, Goutam; Ma, Peipei; Su, Guosheng; Yu, Ying; Zhang, Shengli; Lund, Mogens Sandø; Sørensen, Peter

2017-08-10

A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic regions defined by genes grouped on the basis of "Gene Ontology" (GO), and that incorporating this independent biological information into genomic prediction models might improve their predictive ability. Four complex traits (i.e., milk, fat and protein yields, and mastitis) together with imputed sequence variants in Holstein (HOL) and Jersey (JER) cattle were analysed. We first carried out a post-GWAS analysis in a HOL training population to assess the degree of enrichment of the association signals in the gene regions defined by each GO term. We then extended the genomic best linear unbiased prediction model (GBLUP) to a genomic feature BLUP (GFBLUP) model, including an additional genomic effect quantifying the joint effect of a group of variants located in a genomic feature. The GBLUP model using a single random effect assumes that all genomic variants contribute to the genomic relationship equally, whereas GFBLUP attributes different weights to the individual genomic relationships in the prediction equation based on the estimated genomic parameters. Our results demonstrate that the immune-relevant GO terms were more associated with mastitis than milk production, and several biologically meaningful GO terms improved the prediction accuracy with GFBLUP for the four traits, as compared with GBLUP. The improvement of the genomic prediction between breeds (the average increase across the four traits was 0.161) was more apparent than that it was within the HOL (the average increase across the four traits was 0.020). Our genomic feature modelling approaches provide a framework to simultaneously explore the genetic architecture and genomic prediction of complex traits by taking advantage of

Chiral recognition of proteins having L-histidine residues on the surface with lanthanide ion complex incorporated-molecularly imprinted fluorescent nanoparticles.

Science.gov (United States)

Uzun, Lokman; Uzek, Recep; Senel, Serap; Say, Ridvan; Denizli, Adil

2013-08-01

In this study, lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles were synthesized. A combination of three novel approaches was applied for the purpose. First, lanthanide ions [Terbium(III)] were complexed with N-methacryloyl-L-histidine (MAH), polymerizable derivative of L-histidine amino acid, in order to incorporate the complex directly into the polymeric backbone. At the second stage, L-histidine molecules imprinted nanoparticles were utilized instead of whole protein imprinting in order to avoid whole drawbacks such as fragility, complexity, denaturation tendency, and conformation dependency. At the third stage following the first two steps mentioned above, imprinted L-histidine was coordinated with cupric ions [Cu(II)] to conduct the study under mild conditions. Then, molecularly imprinted fluorescent nanoparticles synthesized were used for L-histidine adsorption from aqueous solution to optimize conditions for adsorption and fluorimetric detection. Finally, usability of nanoparticles was investigated for chiral biorecognition using stereoisomer, D-histidine, racemic mixture, D,L-histidine, proteins with surface L-histidine residue, lysozyme, cytochrome C, or without ribonuclease A. The results revealed that the proposed polymerization strategy could make significant contribution to the solution of chronic problems of fluorescent component introduction into polymers. Additionally, the fluorescent nanoparticles reported here could be used for selective separation and fluorescent monitoring purposes. Copyright © 2013 Elsevier B.V. All rights reserved.

Phylogenetics and genetic diversity of the Cotesia flavipes complex of parasitoid wasps (Hymenoptera: Braconidae), biological control agents of lepidopteran stemborers.

Science.gov (United States)

Muirhead, Kate A; Murphy, Nicholas P; Sallam, Nader; Donnellan, Stephen C; Austin, Andrew D

2012-06-01

The Cotesia flavipes complex of parasitoid wasps (Hymenoptera: Braconidae) are economically important for the biological control of lepidopteran stemboring pests associated with gramineous crops. Some members of the complex successfully parasitize numerous stemborer pest species, however certain geographic populations have demonstrated variation in the range of hosts that they parasitize. In addition, the morphology of the complex is highly conserved and considerable confusion surrounds the identity of species and host-associated biotypes. We generated nucleotide sequence data for two mtDNA genes (COI, 16S) and three anonymous nuclear loci (CfBN, CfCN, CfEN) for the C. flavipes complex. To analyze genetic variation and relationships among populations we used (1) concatenated mtDNA and nDNA data, (2) a nDNA multilocus network approach, and (3) two species tree inference methods, i.e. Bayesian estimation of species trees (BEST) and Bayesian inference of species trees from multilocus data with (*)BEAST. All phylogenetic analyses provide strong support for monophyly of the complex and the presence of at least four species, C. chilonis (from China and Japan), C. sesamiae (from Africa), C. flavipes (originating from the Indo-Asia region but introduced into Africa and the New World), and C. nonagriae (from Australia and Papua New Guinea). Haplotype diversity of geographic populations relates to historical biogeographic barriers and biological control introductions, and reflects previous reports of ecological variation in these species. Strong discordance was found between the mitochondrial and nuclear markers in the Papua New Guinea haplotypes, which may be an outcome of hybridization and introgression of C. flavipes and C. nonagriae. The position of Cotesia flavipes from Japan was not well supported in any analysis and was the sister taxon to C. nonagriae (mtDNA, (*)BEAST), C. flavipes (nDNA) or C. flavipes+C. nonagriae (BEST) and, may represent a cryptic species. The

Modeling complex biological flows in multi-scale systems using the APDEC framework

Science.gov (United States)

Trebotich, David

2006-09-01

We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

High stability and biological activity of the copper(II) complexes of alloferon 1 analogues containing tryptophan.

Science.gov (United States)

Kadej, Agnieszka; Kuczer, Mariola; Czarniewska, Elżbieta; Urbański, Arkadiusz; Rosiński, Grzegorz; Kowalik-Jankowska, Teresa

2016-10-01

Copper(II) complex formation processes between the alloferon 1 (Allo1) (HGVSGHGQHGVHG) analogues where the tryptophan residue is introducing in the place His residue H1W, H6W, H9W and H12W have been studied by potentiometric, UV-visible, CD and EPR spectroscopic, and MS methods. For all analogues of alloferon 1 complex speciation have been obtained for a 1:1 metal-to-ligand molar ratio and 2:1 of H1W because of precipitation at higher (2:1, 3:1 and 4:1) ratios. At physiological pH7.4 and a 1:1 metal-to-ligand molar ratio the tryptophan analogues of alloferon 1 form the CuH -1 L and/or CuH -2 L complexes with the 4N binding mode. The introduction of tryptophan in place of histidine residues changes the distribution diagram of the complexes formed with the change of pH and their stability constants compared to the respective substituted alanine analogues of alloferon 1. The CuH -1 L, CuH -2 L and CuH -3 L complexes of the tryptophan analogues are more stable from 1 to 5 log units in comparison to those of the alanine analogues. This stabilization of the complexes may result from cation(Cu(II))-π and indole/imidazole ring interactions. The induction of apoptosis in vivo, in Tenebrio molitor cells by the ligands and their copper(II) complexes at pH7.4 was studied. The biological results show that copper(II) ions in vivo did not cause any apparent apoptotic features. The most active were the H12W peptide and Cu(II)-H12W complex formed at pH7.4. Copyright © 2016 Elsevier Inc. All rights reserved.

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

Biological activities of Umbilicaria crustulosa (Ach. frey acetone extract

Directory of Open Access Journals (Sweden)

Zlatanović Ivana

2017-01-01

Full Text Available This paper reports for the first time the effect of an acetone extract of Umbilicaria crustulosa on the micronucleus distribution of human lymphocytes, and on the cholinesterase activity and antioxidant activity by the cupric ion reducing antioxidant capacity (CUPRAC method. Additionally, the total phenolic compounds (TPC and the antioxidant properties were estimated via DPPH, ABTS and TRP assays. Moreover, the antibacterial activity against two Gram-positive and three Gram-negative bacteria were determined. Acetone extract of U. crustulosa at concentration of 1 and 2 μg mL-1 decreased a frequency of micronuclei (MN by 10.8 and 16.8 %, respectively, acting more or slightly less than the synthetic protector amifostine (AMF, WR-2721, 11.4 %, at concentration of 1 μg mL-1. The tested extract did not inhibit cholinesterase activity nor did it exhibit activity toward the examined bacteria. The extract reduced the concentration of DPPH and ABTS radicals by 88.7 and 96.2 %, respectively. Values for total reducing power (TRP and cupric reducing capacity (CUPRAC were 0.6197±0.0166 μg ascorbic acid equivalents (AAE per mg of dry extract, and 19.7641±1.6546 μg trolox equivalents (TE per mg of dry extract, respectively. The total phenol content was 350.4188 ±14.587 μg gallic acid equivalents (GAE per mg of dry extract. The results of the present study showed that U. crustulosa acetone extract is a promising candidate for in vivo experiments considering its antioxidant activity and protective effect on human lymphocytes. [Projekat Ministarstva nauke Republike Srbije, br. 172047

Top-down models in biology: explanation and control of complex living systems above the molecular level.

Science.gov (United States)

Pezzulo, Giovanni; Levin, Michael

2016-11-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

EPR Characterization of Dinitrosyl Iron Complexes with Thiol-Containing Ligands as an Approach to Their Identification in Biological Objects: An Overview.

Science.gov (United States)

Vanin, Anatoly F

2018-06-01

The overview demonstrates how the use of only one physico-chemical approach, viz., the electron paramagnetic resonance method, allowed detection and identification of dinitrosyl iron complexes with thiol-containing ligands in various animal and bacterial cells. These complexes are formed in biological objects in the paramagnetic (electron paramagnetic resonance-active) mononuclear and diamagnetic (electron paramagnetic resonance-silent) binuclear forms and control the activity of nitrogen monoxide, one of the most universal regulators of metabolic processes in the organism. The analysis of electronic and spatial structures of dinitrosyl iron complex sheds additional light on the mechanism whereby dinitrosyl iron complex with thiol-containing ligands function in human and animal cells as donors of nitrogen monoxide and its ionized form, viz., nitrosonium ions (NO + ).

Octamer-binding protein 4 affects the cell biology and phenotypic transition of lung cancer cells involving β-catenin/E-cadherin complex degradation.

Science.gov (United States)

Chen, Zhong-Shu; Ling, Dong-Jin; Zhang, Yang-De; Feng, Jian-Xiong; Zhang, Xue-Yu; Shi, Tian-Sheng

2015-03-01

Clinical studies have reported evidence for the involvement of octamer‑binding protein 4 (Oct4) in the tumorigenicity and progression of lung cancer; however, the role of Oct4 in lung cancer cell biology in vitro and its mechanism of action remain to be elucidated. Mortality among lung cancer patients is more frequently due to metastasis rather than their primary tumors. Epithelial‑mesenchymal transition (EMT) is a prominent biological event for the induction of epithelial cancer metastasis. The aim of the present study was to investigate whether Oct4 had the capacity to induce lung cancer cell metastasis via the promoting the EMT in vitro. Moreover, the effect of Oct4 on the β‑catenin/E‑cadherin complex, associated with EMT, was examined using immunofluorescence and immunoprecipitation assays as well as western blot analysis. The results demonstrated that Oct4 enhanced cell invasion and adhesion accompanied by the downregulation of epithelial marker cytokeratin, and upregulation of the mesenchymal markers vimentin and N‑cadherin. Furthermore, Oct4 induced EMT of lung cancer cells by promoting β‑catenin/E‑cadherin complex degradation and regulating nuclear localization of β‑catenin. In conclusion, the present study indicated that Oct4 affected the cell biology of lung cancer cells in vitro through promoting lung cancer cell metastasis via EMT; in addition, the results suggested that the association and degradation of the β‑catenin/E‑cadherin complex was regulated by Oct4 during the process of EMT.

Biological activities of some Fluoroquinolones-metal complexes

African Journals Online (AJOL)

McRoy

Background: Metal ions play a vital role in the design of more biologically active drugs. Aim: The paper reviewed the .... 2H2O by direct reaction of copper(II) sulphate pentahydrate with ciprofloxacin in distilled water. ... membered ring and the chloride ion completes the seven coordination around the Ca2+ion.[37-39].

Omics/systems biology and cancer cachexia.

Science.gov (United States)

Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

2016-06-01

Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

The biology of personalized cancer medicine: facing individual complexities underlying hallmark capabilities.

Science.gov (United States)

De Palma, Michele; Hanahan, Douglas

2012-04-01

It is a time of great promise and expectation for the applications of knowledge about mechanisms of cancer toward more effective and enduring therapies for human disease. Conceptualizations such as the hallmarks of cancer are providing an organizing principle with which to distill and rationalize the abject complexities of cancer phenotypes and genotypes across the spectrum of the human disease. A countervailing reality, however, involves the variable and often transitory responses to most mechanism-based targeted therapies, returning full circle to the complexity, arguing that the unique biology and genetics of a patient's tumor will in the future necessarily need to be incorporated into the decisions about optimal treatment strategies, the frontier of personalized cancer medicine. This perspective highlights considerations, metrics, and methods that may prove instrumental in charting the landscape of evaluating individual tumors so to better inform diagnosis, prognosis, and therapy. Integral to the consideration is remarkable heterogeneity and variability, evidently embedded in cancer cells, but likely also in the cell types composing the supportive and interactive stroma of the tumor microenvironment (e.g., leukocytes and fibroblasts), whose diversity in form, regulation, function, and abundance may prove to rival that of the cancer cells themselves. By comprehensively interrogating both parenchyma and stroma of patients' cancers with a suite of parametric tools, the promise of mechanism-based therapy may truly be realized. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Efficient sample preparation from complex biological samples using a sliding lid for immobilized droplet extractions.

Science.gov (United States)

Casavant, Benjamin P; Guckenberger, David J; Beebe, David J; Berry, Scott M

2014-07-01

Sample preparation is a major bottleneck in many biological processes. Paramagnetic particles (PMPs) are a ubiquitous method for isolating analytes of interest from biological samples and are used for their ability to thoroughly sample a solution and be easily collected with a magnet. There are three main methods by which PMPs are used for sample preparation: (1) removal of fluid from the analyte-bound PMPs, (2) removal of analyte-bound PMPs from the solution, and (3) removal of the substrate (with immobilized analyte-bound PMPs). In this paper, we explore the third and least studied method for PMP-based sample preparation using a platform termed Sliding Lid for Immobilized Droplet Extractions (SLIDE). SLIDE leverages principles of surface tension and patterned hydrophobicity to create a simple-to-operate platform for sample isolation (cells, DNA, RNA, protein) and preparation (cell staining) without the need for time-intensive wash steps, use of immiscible fluids, or precise pinning geometries. Compared to other standard isolation protocols using PMPs, SLIDE is able to perform rapid sample preparation with low (0.6%) carryover of contaminants from the original sample. The natural recirculation occurring within the pinned droplets of SLIDE make possible the performance of multistep cell staining protocols within the SLIDE by simply resting the lid over the various sample droplets. SLIDE demonstrates a simple easy to use platform for sample preparation on a range of complex biological samples.

Synthetic biology: engineering molecular computers

CERN Multimedia

CERN. Geneva

2018-01-01

Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...

A Method for Selective Depletion of Zn(II) Ions from Complex Biological Media and Evaluation of Cellular Consequences of Zn(II) Deficiency

Science.gov (United States)

Richardson, Christopher E. R.; Cunden, Lisa S.; Butty, Vincent L.; Nolan, Elizabeth M.; Lippard, Stephen J.; Shoulders, Matthew D.

2018-01-01

We describe the preparation, evaluation, and application of an S100A12 protein-conjugated solid support, hereafter the “A12-resin,” that can remove 99% of Zn(II) from complex biological solutions without significantly perturbing the concentrations of other metal ions. The A12-resin can be applied to selectively deplete Zn(II) from diverse tissue culture media and from other biological fluids, including human serum. To further demonstrate the utility of this approach, we investigated metabolic, transcriptomic, and metallomic responses of HEK293 cells cultured in medium depleted of Zn(II) using S100A12. The resulting data provide insight into how cells respond to acute Zn(II) deficiency. We expect that the A12-resin will facilitate interrogation of disrupted Zn(II) homeostasis in biological settings, uncovering novel roles for Zn(II) in biology. PMID:29334734

Rhodium complexes as therapeutic agents.

Science.gov (United States)

Ma, Dik-Lung; Wang, Modi; Mao, Zhifeng; Yang, Chao; Ng, Chan-Tat; Leung, Chung-Hang

2016-02-21

The landscape of inorganic medicinal chemistry has been dominated by the investigation of platinum, and to a lesser extent ruthenium, complexes over the past few decades. Recently, complexes based on other metal centers such as rhodium have attracted attention due to their tunable chemical and biological properties as well as distinct mechanisms of action. This perspective highlights recent examples of rhodium complexes that show diverse biological activities against various targets, including enzymes and protein-protein interactions.

On the Edge of Mathematics and Biology Integration: Improving Quantitative Skills in Undergraduate Biology Education

Science.gov (United States)

Feser, Jason; Vasaly, Helen; Herrera, Jose

2013-01-01

In this paper, the authors describe how two institutions are helping their undergraduate biology students build quantitative competencies. Incorporation of quantitative skills and reasoning in biology are framed through a discussion of two cases that both concern introductory biology courses, but differ in the complexity of the mathematics and the…

Synthesis, characterization and antifungal efficacy of C-coordinated O-carboxymethyl chitosan Cu(II) complexes.

Science.gov (United States)

Liu, Weixiang; Qin, Yukun; Liu, Song; Xing, Ronge; Yu, Huahua; Chen, Xiaolin; Li, Kecheng; Li, Pengcheng

2017-03-15

A novel type of O-carboxymethyl chitosan Schiff bases (O-CSPX) was synthesized via a condensation reaction. After the coordination reaction of cupric ions, Cu(II) complexes (O-CSPX-Cu) were achieved. The theoretical structure of O-CSPX-Cu calculated by Gaussian 09 reveals that the copper ions underwent dsp 2 hybridization, coordinated by the carbon atom in the p-π conjugate group and the oxygen atoms in the acetate ion. Then, the structures were confirmed by FT-IR, 1 H NMR, CP-MAS 13 C NMR, elemental analysis, DSC and XRD. The antifungal properties of O-CSPX-Cu against Phytophthora capsici (P. capsici), Gibberella zeae (G. zeae) and Glomerella cingulata (G. cingulata) were evaluated at concentrations ranging from 0.05mg/mL to 0.20mg/mL. The experiments indicated that the derivatives have significantly enhanced antifungal activity after copper ion complexation compared with the original chitosan. Moreover, it was shown that 0.20mg/mL of O-CSP3-Cu and O-CSP4-Cu can 100% inhibit the growth of P. capsici. The experimental results reveal that the antifungal efficiency is related to the space steric hindrance on the benzene ring, which may provide a novel direction for the development of copper fungicides. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reduction theories elucidate the origins of complex biological rhythms generated by interacting delay-induced oscillations.

Directory of Open Access Journals (Sweden)

Ikuhiro Yamaguchi

Full Text Available Time delay is known to induce sustained oscillations in many biological systems such as electroencephalogram (EEG activities and gene regulations. Furthermore, interactions among delay-induced oscillations can generate complex collective rhythms, which play important functional roles. However, due to their intrinsic infinite dimensionality, theoretical analysis of interacting delay-induced oscillations has been limited. Here, we show that the two primary methods for finite-dimensional limit cycles, namely, the center manifold reduction in the vicinity of the Hopf bifurcation and the phase reduction for weak interactions, can successfully be applied to interacting infinite-dimensional delay-induced oscillations. We systematically derive the complex Ginzburg-Landau equation and the phase equation without delay for general interaction networks. Based on the reduced low-dimensional equations, we demonstrate that diffusive (linearly attractive coupling between a pair of delay-induced oscillations can exhibit nontrivial amplitude death and multimodal phase locking. Our analysis provides unique insights into experimentally observed EEG activities such as sudden transitions among different phase-locked states and occurrence of epileptic seizures.

New Insights Into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems

Science.gov (United States)

Aliashkevich, Alena; Alvarez, Laura; Cava, Felipe

2018-01-01

In the environment bacteria share their habitat with a great diversity of organisms, from microbes to humans, animals and plants. In these complex communities, the production of extracellular effectors is a common strategy to control the biodiversity by interfering with the growth and/or viability of nearby microbes. One of such effectors relies on the production and release of extracellular D-amino acids which regulate diverse cellular processes such as cell wall biogenesis, biofilm integrity, and spore germination. Non-canonical D-amino acids are mainly produced by broad spectrum racemases (Bsr). Bsr’s promiscuity allows it to generate high concentrations of D-amino acids in environments with variable compositions of L-amino acids. However, it was not clear until recent whether these molecules exhibit divergent functions. Here we review the distinctive biological roles of D-amino acids, their mechanisms of action and their modulatory properties of the biodiversity of complex eco-systems. PMID:29681896

Biological evaluation of transdichloridoplatinum(II) complexes with 3- and 4-acetylpyridine in comparison to cisplatin

International Nuclear Information System (INIS)

Filipovic, Lana; Arandelovic, Sandra; Gligorijevic, Nevenka; Krivokuca, Ana; Jankovic, Radmila; Srdic-Rajic, Tatjana; Rakic, Gordana; Tesic, Zivoslav; Radulovic, Sinisa

2013-01-01

In our previous study we reported the synthesis and cytotoxicity of two trans-platinum(II) complexes: trans-[PtCl 2 (3-acetylpyridine) 2 ] (1) and trans-[PtCl 2 (4-acetylpyridine) 2 ] (2), revealing significant cytotoxic potential of 2. In order to evaluate the mechanism underlying biological activity of both trans-Pt(II) isomers, comparative studies versus cisplatin were performed in HeLa, MRC-5 and MS1 cells. The cytotoxic activity of the investigated complexes was determined using SRB assay. The colagenolytic activity was determined using gelatin zymography, while the effect of platinum complexes on matrix metalloproteinases 2 and 9 mRNA expression was evaluated by quantitative real-time PCR. Apoptotic potential and cell cycle alterations were determined by FACS analyses. Western blot analysis was used to evaluate the effect on expression of DNA-repair enzyme ERCC1, and quantitative real-time PCR was used for the ERCC1 mRNA expression analysis. In vitro antiangiogenic potential was determined by tube formation assay. Platinum content in intracellular DNA and proteins was determined by inductively coupled plasma-optical emission spectrometry. Compound 2 displayed an apparent cytoselective profile, and flow cytometry analysis in HeLa cells indicated that 2 exerted antiproliferative effect through apoptosis induction, while 1 induced both apoptosis and necrosis. Action of 1 and 2, as analyzed by quantitative real-time PCR and Western blot, was associated with down-regulation of ERCC1. Both trans-complexes inhibited MMP-9 mRNA expression in HeLa, while 2 significantly abrogated in vitro tubulogenesis in MS1 cells. The ability of 2 to induce multiple and selective in vitro cytotoxic effects encourages further investigations of trans-platinum(II) complexes with substituted pyridines

Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

Science.gov (United States)

De Domenico, Manlio

2018-03-01

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

Characterization and biological activity of Solidago canadensis complex.

Science.gov (United States)

Šutovská, M; Capek, P; Kocmálová, M; Fraňová, S; Pawlaczyk, I; Gancarz, R

2013-01-01

Polyphenolic-polysaccharide-protein complex has been isolated from flowers of Solidago canadensis L. by hot alkaline extraction procedure. Compositional analyses of S canadensis complex revealed the presence of carbohydrates (43 wt%), protein (27 wt%), phenolics (12 wt%), uronic acids (10 wt%) and inorganic material (8 wt%). The carbohydrate part was rich in neutral sugars (81 wt%) while uronids were determined in lower amount (19 wt%). Monosaccharide analysis of carbohydrate part revealed the presence of five main sugar components, i.e. rhamnose (~23 wt%), arabinose (~20 wt%), uronic acids (~19 wt%), galactose (~17 wt%) and glucose (~14 wt%), and indicated thus the presence of rhamnogalacturonan and arabinogalactan in S. canadensis complex. HPLC analysis of complex showed one single peak of molecule mass at 11.2 kDa. Antitussive activity tests, performed in three doses of Solidago complex, showed the reduction of the number of cough efforts in the dose-dependent manner. Higher doses (50 and 75 mg/kg b.w.) were shown to be by 15 and 20% more effective than that of lower one (25mg/kg b.w.). However, the antitussive effect of the highest dose (75 mg/kg b.w.) was by 10% lower in comparison with that of codeine, the strongest antitussive agent. Besides, the highest dose of the complex (75 mg/kg b.w.) significantly decreased values of specific airways resistance and their effect remained longer as that of salbutamol, a representative of classic antiasthmatic drugs. Copyright © 2012 Elsevier B.V. All rights reserved.

Photocytotoxic lanthanide complexes

Indian Academy of Sciences (India)

Among many applications of lanthanides, gadolinium complexes are used as magnetic resonance imaging (MRI) contrast agents in clinical radiology and luminescent lanthanides for bioanalysis, imaging and sensing. The chemistry of photoactive lanthanide complexes showing biological applications is of recent origin.

Synthetic biology: programming cells for biomedical applications.

Science.gov (United States)

Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

2012-01-01

The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.

Effect of Deposition Time on the Photoelectrochemical Properties of Cupric Oxide Thin Films Synthesized via Electrodeposition Method

Directory of Open Access Journals (Sweden)

Yaw Chong Siang

2016-01-01

Full Text Available The main aim of this study was to investigate the effect of deposition time on the physicochemical and photoelectrochemical properties of cupric oxide (CuO thin films synthesized via electrodeposition method. Firstly, the electrodeposition of amorphous CuO films on fluorine-doped tin oxide (FTO working electrodes with varying deposition time between 5 and 30 min was carried out, followed by annealing treatment at 500 °C. Resultant nanocrystalline CuO thin films were characterised using field emission-scanning electron microscopy (FE-SEM, photocurrent density, and photoluminescence measurements. Through FE-SEM analysis, it was observed that the surface of thin films was composed of irregular-sized CuO nanocrystals. A smaller CuO nanocrystals size will lead to a higher photoactivity due to the increase in overall catalytic surface area. In addition, the smaller CuO nanocrystals size will prolongs the electron-hole recombination rate due to the increase in copious amount of surface defects. From this study, it was revealed that the relationship between deposition time and CuO film thickness was non-linear. This could be due to the detachment of CuO thin films from the FTO surface at an increasing amount of CuO mass being deposited. It was observed that the amount of light absorbed by CuO thin films increased with film thickness until a certain extent whereby, any further increase in the film thickness will result in a reduction of light photon penetration. Therefore, the CuO nanocrystals size and film thickness have to be compromised in order to yield a higher catalytic surface area and a lower rate of surface charge recombination. Finally, it was found that the deposition time of 15 min resulted in an average CuO nanocrystals size of 73.7 nm, optimum film thickness of 0.73 μm, and corresponding photocurrent density of 0.23 mA/cm2 at the potential bias of - 0.3 V (versus Ag/AgCl. The PL spectra for the deposition time of 15 min has the lowest

Dissolved trace metal (Cu, Cd, Co, Ni, and Ag) distribution and Cu speciation in the southern Yellow Sea and Bohai Sea, China

Science.gov (United States)

Li, Li; Xiaojing, Wang; Jihua, Liu; Xuefa, Shi

2017-02-01

Trace metals play an important role in biogeochemical cycling in ocean systems. However, because the use of trace metal clean sampling and analytical techniques has been limited in coastal China, there are few accurate trace metal data for that region. This work studied spatial distribution of selected dissolved trace metals (Ag, Cu, Co, Cd, and Ni) and Cu speciation in the southern Yellow Sea (SYS) and Bohai Sea (BS). In general, the average metal (Cu, Co, Cd, and Ni) concentrations found in the SYS were lower by a factor of two than those in BS, and they are comparable to dissolved trace metal concentrations in coastal seawater of the United States and Europe. Possible sources and sinks and physical and biological processes that influenced the distribution of these trace metals in the study region were further examined. Close relationships were found between the trace metal spatial distribution with local freshwater discharge and processes such as sediment resuspension and biological uptake. Ag, owing to its extremely low concentrations, exhibited a unique distribution pattern that magnified the influences from the physical and biological processes. Cu speciation in the water column showed that, in the study region, Cu was strongly complexed with organic ligands and concentrations of free cupric ion were in the range of 10-12.6-10-13.2 mol L-1. The distribution of Cu-complexing ligand, indicated by values of the side reaction coefficient α', was similar to the Chl a distribution, suggesting that in situ biota production may be one main source of Cu-complexing organic ligand.

Mathematical models in biology bringing mathematics to life

CERN Document Server

Ferraro, Maria; Guarracino, Mario

2015-01-01

This book presents an exciting collection of contributions based on the workshop “Bringing Maths to Life” held October 27-29, 2014 in Naples, Italy.  The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content...

Ferric reductase genes involved in high-affinity iron uptake are differentially regulated in yeast and hyphae of Candida albicans.

Science.gov (United States)

Jeeves, Rose E; Mason, Robert P; Woodacre, Alexandra; Cashmore, Annette M

2011-09-01

The pathogenic yeast Candida albicans possesses a reductive iron uptake system which is active in iron-restricted conditions. The sequestration of iron by this mechanism initially requires the reduction of free iron to the soluble ferrous form, which is catalysed by ferric reductase proteins. Reduced iron is then taken up into the cell by a complex of a multicopper oxidase protein and an iron transport protein. Multicopper oxidase proteins require copper to function and so reductive iron and copper uptake are inextricably linked. It has previously been established that Fre10 is the major cell surface ferric reductase in C. albicans and that transcription of FRE10 is regulated in response to iron levels. We demonstrate here that Fre10 is also a cupric reductase and that Fre7 also makes a significant contribution to cell surface ferric and cupric reductase activity. It is also shown, for the first time, that transcription of FRE10 and FRE7 is lower in hyphae compared to yeast and that this leads to a corresponding decrease in cell surface ferric, but not cupric, reductase activity. This demonstrates that the regulation of two virulence determinants, the reductive iron uptake system and the morphological form of C. albicans, are linked. Copyright © 2011 John Wiley & Sons, Ltd.

Data warehousing in molecular biology.

Science.gov (United States)

Schönbach, C; Kowalski-Saunders, P; Brusic, V

2000-05-01

In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data represent a major challenge in data warehousing for molecular biology. By combining experiences in other domains with our findings from building a model database, we have defined the requirements for data warehousing in molecular biology.

Quantum Biology

Directory of Open Access Journals (Sweden)

Alessandro Sergi

2009-06-01

Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

Synthesis of the arginine labelled by {sup 15}N on the amidine group; Synthese de l'arginine marquee par {sup 15}N dans le groupe amidine

Energy Technology Data Exchange (ETDEWEB)

Pichat, L; Clement, J [Commissariat a l' Energie Atomique, Saclay(France). Centre d' Etudes Nucleaires

1955-07-01

For some biologic studies, it was necessarily to have (+) arginine marked by nitrogen 15 in the amidine group. This report describes the synthesis of the labelled arginine. The first step is the synthesis of the methyl-isourated hydro-chlorate, the intermediate reactive, from the ClNH{sub 4} isotope. The arginine is obtained from the ornithine which we previously blocked the amino group as cupric complex. The mean yield in arginine reaches 30%, based on the ammonium chloride uses. (M.B.) [French] Pour certaines etudes biologiques, il etait indispensable de disposer de (+) arginine marquee par l'azote 15 dans le groupement amidine. Ce rapport decrit la synthese de l'ariginine marquee. La premiere etape est la synthese du chlorhydrate de methylisouree, intermediaire reactif, a partir du ClNH{sub 4} isotopique. L'obtention de l'arginine est obtenue a partir de l'ornithine dont on a prealablement bloque le groupe amino sous forme de complexe cuivrique. Le rendement global moyen en arginine atteint 30 %, base sur le chlorure d'ammonium utilise. (M.B.)

Physical Complexity and Cognitive Evolution

Science.gov (United States)

Jedlicka, Peter

Our intuition tells us that there is a general trend in the evolution of nature, a trend towards greater complexity. However, there are several definitions of complexity and hence it is difficult to argue for or against the validity of this intuition. Christoph Adami has recently introduced a novel measure called physical complexity that assigns low complexity to both ordered and random systems and high complexity to those in between. Physical complexity measures the amount of information that an organism stores in its genome about the environment in which it evolves. The theory of physical complexity predicts that evolution increases the amount of `knowledge' an organism accumulates about its niche. It might be fruitful to generalize Adami's concept of complexity to the entire evolution (including the evolution of man). Physical complexity fits nicely into the philosophical framework of cognitive biology which considers biological evolution as a progressing process of accumulation of knowledge (as a gradual increase of epistemic complexity). According to this paradigm, evolution is a cognitive `ratchet' that pushes the organisms unidirectionally towards higher complexity. Dynamic environment continually creates problems to be solved. To survive in the environment means to solve the problem, and the solution is an embodied knowledge. Cognitive biology (as well as the theory of physical complexity) uses the concepts of information and entropy and views the evolution from both the information-theoretical and thermodynamical perspective. Concerning humans as conscious beings, it seems necessary to postulate an emergence of a new kind of knowledge - a self-aware and self-referential knowledge. Appearence of selfreflection in evolution indicates that the human brain reached a new qualitative level in the epistemic complexity.

40 CFR 117.3 - Determination of reportable quantities.

Science.gov (United States)

2010-07-01

... A 10 (4.54) Lead fluoride A 10 (4.54) Lead iodide A 10 (4.54) Lead nitrate A 10 (4.54) Lead stearate... fluoride X 1 (0.454) Beryllium nitrate X 1 (0.454) Butyl acetate D 5,000 (2,270) Butylamine C 1,000 (454) n... B 100 (45.4) Cupric acetoarsenite X 1 (0.454) Cupric chloride A 10 (4.54) Cupric nitrate B 100 (45.4...

Genomewide effects of peroxisome proliferator-activated receptor gamma in macrophages and dendritic cells--revealing complexity through systems biology.

Science.gov (United States)

Cuaranta-Monroy, Ixchelt; Kiss, Mate; Simandi, Zoltan; Nagy, Laszlo

2015-09-01

Systems biology approaches have become indispensable tools in biomedical and basic research. These data integrating bioinformatic methods gained prominence after high-throughput technologies became available to investigate complex cellular processes, such as transcriptional regulation and protein-protein interactions, on a scale that had not been studied before. Immunology is one of the medical fields that systems biology impacted profoundly due to the plasticity of cell types involved and the accessibility of a wide range of experimental models. In this review, we summarize the most important recent genomewide studies exploring the function of peroxisome proliferator-activated receptor γ in macrophages and dendritic cells. PPARγ ChIP-seq experiments were performed in adipocytes derived from embryonic stem cells to complement the existing data sets and to provide comparators to macrophage data. Finally, lists of regulated genes generated from such experiments were analysed with bioinformatics and system biology approaches. We show that genomewide studies utilizing high-throughput data acquisition methods made it possible to gain deeper insights into the role of PPARγ in these immune cell types. We also demonstrate that analysis and visualization of data using network-based approaches can be used to identify novel genes and functions regulated by the receptor. The example of PPARγ in macrophages and dendritic cells highlights the crucial importance of systems biology approaches in establishing novel cellular functions for long-known signaling pathways. © 2015 Stichting European Society for Clinical Investigation Journal Foundation.

Systems Biology — the Broader Perspective

Directory of Open Access Journals (Sweden)

Jonathan Bard

2013-06-01

Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

Frontiers in mathematical biology

CERN Document Server

1994-01-01

Volume 100, which is the final volume of the LNBM series serves to commemorate the acievements in two decades of this influential collection of books in mathematical biology. The contributions, by the leading mathematical biologists, survey the state of the art in the subject, and offer speculative, philosophical and critical analyses of the key issues confronting the field. The papers address fundamental issues in cell and molecular biology, organismal biology, evolutionary biology, population ecology, community and ecosystem ecology, and applied biology, plus the explicit and implicit mathematical challenges. Cross-cuttting issues involve the problem of variation among units in nonlinear systems, and the related problems of the interactions among phenomena across scales of space, time and organizational complexity.

Can a Multimedia Tool Help Students' Learning Performance in Complex Biology Subjects?

Science.gov (United States)

Koseoglu, Pinar; Efendioglu, Akin

2015-01-01

The aim of the present study was to determine the effects of multimedia-based biology teaching (Mbio) and teacher-centered biology (TCbio) instruction approaches on learners' biology achievements, as well as their views towards learning approaches. During the research process, an experimental design with two groups, TCbio (n = 22) and Mbio (n =…

Network biology concepts in complex disease comorbidities

DEFF Research Database (Denmark)

Hu, Jessica Xin; Thomas, Cecilia Engel; Brunak, Søren

2016-01-01

collected electronically, disease co-occurrences are starting to be quantitatively characterized. Linking network dynamics to the real-life, non-ideal patient in whom diseases co-occur and interact provides a valuable basis for generating hypotheses on molecular disease mechanisms, and provides knowledge......The co-occurrence of diseases can inform the underlying network biology of shared and multifunctional genes and pathways. In addition, comorbidities help to elucidate the effects of external exposures, such as diet, lifestyle and patient care. With worldwide health transaction data now often being...

Heuristic Strategies in Systems Biology

Directory of Open Access Journals (Sweden)

Fridolin Gross

2016-06-01

Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

A microfluidic dialysis device for complex biological mixture SERS analysis

KAUST Repository

Perozziello, Gerardo

2015-08-01

In this paper, we present a microfluidic device fabricated with a simple and inexpensive process allowing rapid filtering of peptides from a complex mixture. The polymer microfluidic device can be used for sample preparation in biological applications. The device is fabricated by micromilling and solvent assisted bonding, in which a microdialysis membrane (cut-off of 12-14 kDa) is sandwiched in between an upper and a bottom microfluidic chamber. An external frame connects the microfluidic device to external tubes, microvalves and syringe pumps. Bonding strength and interface sealing are pneumatically tested. Microfluidic protocols are also described by using the presented device to filter a sample composed of specific peptides (MW 1553.73 Da, at a concentration of 1.0 ng/μl) derived from the BRCA1 protein, a tumor-suppressor molecule which plays a pivotal role in the development of breast cancer, and albumin (MW 66.5 kDa, at a concentration of 35 μg/μl), the most represented protein in human plasma. The filtered samples coming out from the microfluidic device were subsequently deposited on a SERS (surface enhanced Raman scattering) substrate for further analysis by Raman spectroscopy. By using this approach, we were able to sort the small peptides from the bigger and highly concentrated protein albumin and to detect them by using a label-free technique at a resolution down to 1.0 ng/μl.

On the holistic approach in cellular and cancer biology: nonlinearity, complexity, and quasi-determinism of the dynamic cellular network.

Science.gov (United States)

Waliszewski, P; Molski, M; Konarski, J

1998-06-01

A keystone of the molecular reductionist approach to cellular biology is a specific deductive strategy relating genotype to phenotype-two distinct categories. This relationship is based on the assumption that the intermediary cellular network of actively transcribed genes and their regulatory elements is deterministic (i.e., a link between expression of a gene and a phenotypic trait can always be identified, and evolution of the network in time is predetermined). However, experimental data suggest that the relationship between genotype and phenotype is nonbijective (i.e., a gene can contribute to the emergence of more than just one phenotypic trait or a phenotypic trait can be determined by expression of several genes). This implies nonlinearity (i.e., lack of the proportional relationship between input and the outcome), complexity (i.e. emergence of the hierarchical network of multiple cross-interacting elements that is sensitive to initial conditions, possesses multiple equilibria, organizes spontaneously into different morphological patterns, and is controlled in dispersed rather than centralized manner), and quasi-determinism (i.e., coexistence of deterministic and nondeterministic events) of the network. Nonlinearity within the space of the cellular molecular events underlies the existence of a fractal structure within a number of metabolic processes, and patterns of tissue growth, which is measured experimentally as a fractal dimension. Because of its complexity, the same phenotype can be associated with a number of alternative sequences of cellular events. Moreover, the primary cause initiating phenotypic evolution of cells such as malignant transformation can be favored probabilistically, but not identified unequivocally. Thermodynamic fluctuations of energy rather than gene mutations, the material traits of the fluctuations alter both the molecular and informational structure of the network. Then, the interplay between deterministic chaos, complexity, self

Using synthetic biology to make cells tomorrow's test tubes.

Science.gov (United States)

Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

2016-04-18

The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

Stability Constants of Some Biologically Important Pyrazoles and Their Ni2+ Complexes in Different Dielectric Constant of Medium

Directory of Open Access Journals (Sweden)

S. D. Deosarkar

2012-01-01

Full Text Available The proton-ligand stability constants of some biologically important new pyrazoles and formation constants of their complexes with Ni(II were determined at 0.1 mol dm-3 ionic strength and at 303.15 K in different dielectric constant of dioxane-water mixture by potentiometric method. The Calvin-Bjerrum's pH-titration technique as used by Irving and Rossotti was used for determination of stability constants. The results enabled to study the electrostatic forces of attraction between metal ion and ligand with changes in dielectric constant of the medium.

Complex-forming capacity of some biologically active imidazoles

Energy Technology Data Exchange (ETDEWEB)

Lenarcik, B; Wisniewski, M

1983-01-01

By using the potentiometric and spectrophotometric methods, formation of Co(2), Cu(2), Zn(2), Ni(2) and Cd(2) complexes of (3S-cis)-3-ethyl-dihydro-4-((1-methyl-1H-imidazol-5-yl)-methyl)-2(3H)-furanone (pilocarpine, PLC), 4,5-dihydro-2-(phenylmethyl)-1H-imidazole (tolazoline, TLZ), 2-methyl-5-nitro-1H-imidazole-1-ethanol (metronidazole, MET) and 1H-imidazole-4-ethanamine (histamine, HIST) was investigated. The stability constants, ..beta../sub n/, of these complexes were determined. It was shown that the electron-donor strength of the ligands was controlled by the heterocyclic nitrogen atom, and that the formation of the Zn(2)-PLC complex was accompanied by the change in the structure of the coordination sphere of the metal. With Cu(2), the PLC and TLZ ligands were shown to enhance the Jahn-Teller deformation.

Biological timekeeping

DEFF Research Database (Denmark)

Lloyd, David

2016-01-01

, the networks that connect differenttime domains and the oscillations, rhythms and biological clocks that coordinate andsynchronise the complexity of the living state.“It is the pattern maintained by this homeostasis, which is the touchstone ofour personal identity. Our tissues change as we live: the food we...

A modified Wright-Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity.

Science.gov (United States)

Zhao, Lei; Gossmann, Toni I; Waxman, David

2016-03-21

The Wright-Fisher model is an important model in evolutionary biology and population genetics. It has been applied in numerous analyses of finite populations with discrete generations. It is recognised that real populations can behave, in some key aspects, as though their size that is not the census size, N, but rather a smaller size, namely the effective population size, Ne. However, in the Wright-Fisher model, there is no distinction between the effective and census population sizes. Equivalently, we can say that in this model, Ne coincides with N. The Wright-Fisher model therefore lacks an important aspect of biological realism. Here, we present a method that allows Ne to be directly incorporated into the Wright-Fisher model. The modified model involves matrices whose size is determined by Ne. Thus apart from increased biological realism, the modified model also has reduced computational complexity, particularly so when Ne⪡N. For complex problems, it may be hard or impossible to numerically analyse the most commonly-used approximation of the Wright-Fisher model that incorporates Ne, namely the diffusion approximation. An alternative approach is simulation. However, the simulations need to be sufficiently detailed that they yield an effective size that is different to the census size. Simulations may also be time consuming and have attendant statistical errors. The method presented in this work may then be the only alternative to simulations, when Ne differs from N. We illustrate the straightforward application of the method to some problems involving allele fixation and the determination of the equilibrium site frequency spectrum. We then apply the method to the problem of fixation when three alleles are segregating in a population. This latter problem is significantly more complex than a two allele problem and since the diffusion equation cannot be numerically solved, the only other way Ne can be incorporated into the analysis is by simulation. We have

Structural biological composites: An overview

Science.gov (United States)

Meyers, Marc A.; Lin, Albert Y. M.; Seki, Yasuaki; Chen, Po-Yu; Kad, Bimal K.; Bodde, Sara

2006-07-01

Biological materials are complex composites that are hierarchically structured and multifunctional. Their mechanical properties are often outstanding, considering the weak constituents from which they are assembled. They are for the most part composed of brittle (often, mineral) and ductile (organic) components. These complex structures, which have risen from millions of years of evolution, are inspiring materials scientists in the design of novel materials. This paper discusses the overall design principles in biological structural composites and illustrates them for five examples; sea spicules, the abalone shell, the conch shell, the toucan and hornbill beaks, and the sheep crab exoskeleton.

Integrating biological redesign: where synthetic biology came from and where it needs to go.

Science.gov (United States)

Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

2014-03-27

Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

Thermal Stabilization of Biologics with Photoresponsive Hydrogels.

Science.gov (United States)

Sridhar, Balaji V; Janczy, John R; Hatlevik, Øyvind; Wolfson, Gabriel; Anseth, Kristi S; Tibbitt, Mark W

2018-03-12

Modern medicine, biological research, and clinical diagnostics depend on the reliable supply and storage of complex biomolecules. However, biomolecules are inherently susceptible to thermal stress and the global distribution of value-added biologics, including vaccines, biotherapeutics, and Research Use Only (RUO) proteins, requires an integrated cold chain from point of manufacture to point of use. To mitigate reliance on the cold chain, formulations have been engineered to protect biologics from thermal stress, including materials-based strategies that impart thermal stability via direct encapsulation of the molecule. While direct encapsulation has demonstrated pronounced stabilization of proteins and complex biological fluids, no solution offers thermal stability while enabling facile and on-demand release from the encapsulating material, a critical feature for broad use. Here we show that direct encapsulation within synthetic, photoresponsive hydrogels protected biologics from thermal stress and afforded user-defined release at the point of use. The poly(ethylene glycol) (PEG)-based hydrogel was formed via a bioorthogonal, click reaction in the presence of biologics without impact on biologic activity. Cleavage of the installed photolabile moiety enabled subsequent dissolution of the network with light and release of the encapsulated biologic. Hydrogel encapsulation improved stability for encapsulated enzymes commonly used in molecular biology (β-galactosidase, alkaline phosphatase, and T4 DNA ligase) following thermal stress. β-galactosidase and alkaline phosphatase were stabilized for 4 weeks at temperatures up to 60 °C, and for 60 min at 85 °C for alkaline phosphatase. T4 DNA ligase, which loses activity rapidly at moderately elevated temperatures, was protected during thermal stress of 40 °C for 24 h and 60 °C for 30 min. These data demonstrate a general method to employ reversible polymer networks as robust excipients for thermal stability of complex

Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

Science.gov (United States)

De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

2010-03-01

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

Photoactive platinum(II) complexes of nonsteroidal anti-inflammatory drug naproxen: Interaction with biological targets, antioxidant activity and cytotoxicity.

Science.gov (United States)

Srivastava, Payal; Singh, Khushbu; Verma, Madhu; Sivakumar, Sri; Patra, Ashis K

2018-01-20

The effect on the therapeutic efficacy of Pt(II) complexes on combining non-steroidal anti-inflammatory drugs (NSAIDs) is an attractive strategy to circumvent chronic inflammation mediated by cancer and metastasis. Two square-planar platinum(II) complexes: [Pt(dach)(nap)Cl] (1) and [Pt(dach)(nap) 2 ] (2), where dach = (1R,2R)-dichloro(cyclohexane-1,2-diamine) and NSAID drug naproxen (nap), have been designed for studying their biological activity. The naproxen bound to the Pt(II) centre get released upon photoirradiation with low-power UV-A light as confirmed by the significant enhancement in emission intensities of the complexes. The compounds were evaluated for their photophysical properties, photostability, reactivity with 5'-guanosine monophophosphate (5'-GMP), interactions with CT-DNA and BSA, antioxidant activity and reactive oxygen species mediated photo-induced DNA damage properties. ESI-MS studies demonstrated the formation of bis-adduct with 5'-GMP and the formation of Pt II -DNA crosslinks by gel electrophoretic mobility shift assay and ITC studies. The interaction of the complexes 1 and 2 with the CT-DNA exhibits potential binding affinity (K b  ∼ 10 4  M -1 , K app ∼ 10 5  M -1 ), implying intercalation to CT-DNA through planar naphthyl ring of the complexes. Both the complexes also exhibit strong binding affinity towards BSA (K BSA ∼ 10 5  M -1 ). The complexes exhibit efficient DNA damage activity on irradiation at 365 nm via formation of singlet oxygen ( 1 O 2 ) and hydroxyl radical ( • OH) under physiological conditions. Both the complexes were cytotoxic in dark and exhibit significant enhancement of cytotoxicity upon photo-exposure against HeLa and HepG2 cancer cells giving IC 50 values ranging from 8 to 12 μM for 1 and 2. The cellular internalization data showed cytosolic and nuclear localization of the complexes in the HeLa cells. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Complexity in the biological recovery of Tatra Mountain lakes from acidification

Czech Academy of Sciences Publication Activity Database

Stuchlík, Evžen; Bitušík, P.; Hardekopf, D.W.; Hořická, Zuzana; Kahounová, M.; Tátosová, J.; Vondrák, Daniel; Dočkalová, Kateřina

2017-01-01

Roč. 228, č. 5 (2017), č. článku 184. ISSN 0049-6979 R&D Projects: GA ČR(CZ) GA14-09231S Institutional support: RVO:60077344 Keywords : phytoplankton * zooplankton * chironomids * oligotrophication * eutrophication Subject RIV: DA - Hydrology ; Limnology OBOR OECD: Marine biology, freshwater biology, limnology Impact factor: 1.702, year: 2016

Analysis of nanoparticle biomolecule complexes.

Science.gov (United States)

Gunnarsson, Stefán B; Bernfur, Katja; Mikkelsen, Anders; Cedervall, Tommy

2018-03-01

Nanoparticles exposed to biological fluids adsorb biomolecules on their surface forming a biomolecular corona. This corona determines, on a molecular level, the interactions and impact the newly formed complex has on cells and organisms. The corona formation as well as the physiological and toxicological relevance are commonly investigated. However, an acknowledged but rarely addressed problem in many fields of nanobiotechnology is aggregation and broadened size distribution of nanoparticles following their interactions with the molecules of biological fluids. In blood serum, TiO 2 nanoparticles form complexes with a size distribution from 30 nm to more than 500 nm. In this study we have separated these complexes, with good resolution, using preparative centrifugation in a sucrose gradient. Two main apparent size populations were obtained, a fast sedimenting population of complexes that formed a pellet in the preparative centrifugation tube, and a slow sedimenting complex population still suspended in the gradient after centrifugation. Concentration and surface area dependent differences are found in the biomolecular corona between the slow and fast sedimenting fractions. There are more immunoglobulins, lipid binding proteins, and lipid-rich complexes at higher serum concentrations. Sedimentation rate and the biomolecular corona are important factors for evaluating any experiment including nanoparticle exposure. Our results show that traditional description of nanoparticles in biological fluids is an oversimplification and that more thorough characterisations are needed.

A Friendly-Biological Reactor SIMulator (BioReSIM for studying biological processes in wastewater treatment processes

Directory of Open Access Journals (Sweden)

Raul Molina

2014-12-01

Full Text Available Biological processes for wastewater treatments are inherently dynamic systems because of the large variations in the influent wastewater flow rate, concentration composition and the adaptive behavior of the involved microorganisms. Moreover, the sludge retention time (SRT is a critical factor to understand the bioreactor performances when changes in the influent or in the operation conditions take place. Since SRT are usually in the range of 10-30 days, the performance of biological reactors needs a long time to be monitored in a regular laboratory demonstration, limiting the knowledge that can be obtained in the experimental lab practice. In order to overcome this lack, mathematical models and computer simulations are useful tools to describe biochemical processes and predict the overall performance of bioreactors under different working operation conditions and variations of the inlet wastewater composition. The mathematical solution of the model could be difficult as numerous biochemical processes can be considered. Additionally, biological reactors description (mass balance, etc. needs models represented by partial or/and ordinary differential equations associated to algebraic expressions, that require complex computational codes to obtain the numerical solutions. Different kind of software for mathematical modeling can be used, from large degree of freedom simulators capable of free models definition (as AQUASIM, to closed predefined model structure programs (as BIOWIN. The first ones usually require long learning curves, whereas the second ones could be excessively rigid for specific wastewater treatment systems. As alternative, we present Biological Reactor SIMulator (BioReSIM, a MATLAB code for the simulation of sequencing batch reactors (SBR and rotating biological contactors (RBC as biological systems of suspended and attached biomass for wastewater treatment, respectively. This BioReSIM allows the evaluation of simple and complex

Studies on the changes of biologically active complexes of sunflower oil, tard, and butter under gamma irradiation

International Nuclear Information System (INIS)

Ivanov, A.; Stamatov, D.

1976-01-01

Investigations of changes in the biologically active complex of sunflower oil, lard and butter under the influence of gamma rays: The points examined are the effect of small, medium and large doses (10 4 , 10 6 and 10 7 ) of gamma rays (Co 60 ) and the after-effect on the carotenes, tocopherols, sterols and linoleic acid in sunflower oil, lard and butter. Under these conditions, only the carotenes and tocopherols are subjected to changes to the point of destruction. What was found is a good correlative connection between the changes in the tocopherols and the degree of oxidation of the corresponding fats. (orig.) [de

Learning Cell Biology as a Team: A Project-Based Approach to Upper-Division Cell Biology

Science.gov (United States)

Wright, Robin; Boggs, James

2002-01-01

To help students develop successful strategies for learning how to learn and communicate complex information in cell biology, we developed a quarter-long cell biology class based on team projects. Each team researches a particular human disease and presents information about the cellular structure or process affected by the disease, the cellular…

Ion-Exchange Sample Displacement Chromatography as a Method for Fast and Simple Isolation of Low- and High-Abundance Proteins from Complex Biological Mixtures

Directory of Open Access Journals (Sweden)

Martina Srajer Gajdosik

2014-01-01

Full Text Available Sample displacement chromatography (SDC in reversed phase and ion-exchange modes was introduced at the end of 1980s. This chromatographic method was first used for preparative purification of synthetic peptides, and subsequently adapted for protein fractionation, mainly in anion-exchange mode. In the past few years, SDC has been successfully used for enrichment of low- and medium-abundance proteins from complex biological fluids on both monolithic and bulk chromatographic supports. If aqueous mobile phase is used with the application of mild chromatographic conditions, isolated proteins are not denatured and can also keep their biological activity. In this paper, the use of SDC in anion-exchange mode on a high-capacity chromatographic resin for separation of proteins from complex biological mixtures such as human plasma is demonstrated. By use of three and more columns coupled in series during sample application, and subsequent parallel elution of detached columns, additional separation of bound proteins was achieved. Highly enriched human serum albumin fraction and a number of physiologically active medium- and low-abundance proteins could be fractionated and detected by electrospray ionization tandem mass spectrometry (ESI-MS/MS and matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS. The use of the aforementioned columns that can be sanitized with 1 M sodium hydroxide for further application of SDC in biotechnology and food technology was discussed.

Can a multimedia tool help students' learning performance in complex biology subjects?

Directory of Open Access Journals (Sweden)

Pinar Koseoglu

2015-11-01

Full Text Available The aim of the present study was to determine the effects of multimedia-based biology teaching (Mbio and teacher-centered biology (TCbio instruction approaches on learners' biology achievements, as well as their views towards learning approaches. During the research process, an experimental design with two groups, TCbio (n = 22 and Mbio (n = 26, were used. The results of the study proved that the Mbio approach was more effective than the TCbio approach with regard to supporting meaningful learning, academic achievement, enjoyment and motivation. Moreover, the TCbio approach is ineffective in terms of time management, engaging attention, and the need for repetition of subjects. Additionally, the results were discussed in terms of teaching, learning, multimedia design as well as biology teaching/learning.

Biologically active new Fe(II, Co(II, Ni(II, Cu(II, Zn(II and Cd(II complexes of N-(2-thienylmethylenemethanamine

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C. SPÎNU

2008-04-01

Full Text Available Iron(II, cobalt(II, nickel (II, copper (II, zinc(II and cadmium(II complexes of the type ML2Cl2, where M is a metal and L is the Schiff base N-(2-thienylmethylenemethanamine (TNAM formed by the condensation of 2-thiophenecarboxaldehyde and methylamine, were prepared and characterized by elemental analysis as well as magnetic and spectroscopic measurements. The elemental analyses suggest the stoichiometry to be 1:2 (metal:ligand. Magnetic susceptibility data coupled with electronic, ESR and Mössbauer spectra suggest a distorted octahedral structure for the Fe(II, Co(II and Ni(II complexes, a square-planar geometry for the Cu(II compound and a tetrahedral geometry for the Zn(II and Cd(II complexes. The infrared and NMR spectra of the complexes agree with co-ordination to the central metal atom through nitrogen and sulphur atoms. Conductance measurements suggest the non-electrolytic nature of the complexes, except for the Cu(II, Zn(II and Cd(II complexes, which are 1:2 electrolytes. The Schiff base and its metal chelates were screened for their biological activity against Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa and the metal chelates were found to possess better antibacterial activity than that of the uncomplexed Schiff base.

Encyclopedia of Complexity and Systems Science

CERN Document Server

Meyers, Robert A

2009-01-01

Encyclopedia of Complexity and Systems Science provides an authoritative single source for understanding and applying the concepts of complexity theory together with the tools and measures for analyzing complex systems in all fields of science and engineering. The science and tools of complexity and systems science include theories of self-organization, complex systems, synergetics, dynamical systems, turbulence, catastrophes, instabilities, nonlinearity, stochastic processes, chaos, neural networks, cellular automata, adaptive systems, and genetic algorithms. Examples of near-term problems and major unknowns that can be approached through complexity and systems science include: The structure, history and future of the universe; the biological basis of consciousness; the integration of genomics, proteomics and bioinformatics as systems biology; human longevity limits; the limits of computing; sustainability of life on earth; predictability, dynamics and extent of earthquakes, hurricanes, tsunamis, and other n...

Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks.

Science.gov (United States)

Kastrup, Christian J; Runyon, Matthew K; Lucchetta, Elena M; Price, Jessica M; Ismagilov, Rustem F

2008-04-01

Understanding the spatial dynamics of biochemical networks is both fundamentally important for understanding life at the systems level and also has practical implications for medicine, engineering, biology, and chemistry. Studies at the level of individual reactions provide essential information about the function, interactions, and localization of individual molecular species and reactions in a network. However, analyzing the spatial dynamics of complex biochemical networks at this level is difficult. Biochemical networks are nonequilibrium systems containing dozens to hundreds of reactions with nonlinear and time-dependent interactions, and these interactions are influenced by diffusion, flow, and the relative values of state-dependent kinetic parameters. To achieve an overall understanding of the spatial dynamics of a network and the global mechanisms that drive its function, networks must be analyzed as a whole, where all of the components and influential parameters of a network are simultaneously considered. Here, we describe chemical concepts and microfluidic tools developed for network-level investigations of the spatial dynamics of these networks. Modular approaches can be used to simplify these networks by separating them into modules, and simple experimental or computational models can be created by replacing each module with a single reaction. Microfluidics can be used to implement these models as well as to analyze and perturb the complex network itself with spatial control on the micrometer scale. We also describe the application of these network-level approaches to elucidate the mechanisms governing the spatial dynamics of two networkshemostasis (blood clotting) and early patterning of the Drosophila embryo. To investigate the dynamics of the complex network of hemostasis, we simplified the network by using a modular mechanism and created a chemical model based on this mechanism by using microfluidics. Then, we used the mechanism and the model to

Structural, luminescence and biological studies of trivalent lanthanide complexes with N,N Prime -bis(2-hydroxynaphthylmethylidene)-1,3-propanediamine Schiff base ligand

Energy Technology Data Exchange (ETDEWEB)

Taha, Ziyad A., E-mail: tahaz33@just.edu.jo [Department of Applied Chemistry, Faculty of Arts and Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110 (Jordan); Ajlouni, Abdulaziz M. [Department of Applied Chemistry, Faculty of Arts and Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110 (Jordan); Al Momani, Waleed [Department of Allied Medical Sciences, Al Balqa Applied University (Jordan)

2012-11-15

New eight lanthanide metal complexes were prepared. These complexes were characterized by elemental analysis, molar conductivity measurements, spectral analysis ({sup 1}H NMR, FT-IR, UV-vis), luminescence and thermal gravimetric analysis. All Ln(III) complexes were 1:1 electrolytes as established by their molar conductivities. The microanalysis and spectroscopic analysis revealed eight-coordinated environments around lanthanide ions with two nitrate ligands behaving in a bidentate manner. The other four positions were found to be occupied with tetradentate L{sub III} ligand. Tb-L{sub III} and Sm-L{sub III} complexes exhibited characteristic luminescence emissions of the central metal ions and this was attributed to efficient energy transfer from the ligand to the metal center. The L{sub III} and Ln-L{sub III} complexes showed antibacterial activity against a number of pathogenic bacteria. - Highlights: Black-Right-Pointing-Pointer Ln(III) ion adopts an eight-coordinate geometry. Black-Right-Pointing-Pointer Luminescence spectra of Sm-L{sub III} and Tb-L{sub III} complexes display the metal centered line emission. Black-Right-Pointing-Pointer Energy transfer process from L{sub III} to Sm in Sm-L{sub III} complex is more efficient than to Tb in Tb-L{sub III} complex. Black-Right-Pointing-Pointer Ln(III) complexes may serve as models for biologically important species.

Modular analysis of biological networks.

Science.gov (United States)

Kaltenbach, Hans-Michael; Stelling, Jörg

2012-01-01

The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.

Synchronization in complex networks

Energy Technology Data Exchange (ETDEWEB)

Arenas, A.; Diaz-Guilera, A.; Moreno, Y.; Zhou, C.; Kurths, J.

2007-12-12

Synchronization processes in populations of locally interacting elements are in the focus of intense research in physical, biological, chemical, technological and social systems. The many efforts devoted to understand synchronization phenomena in natural systems take now advantage of the recent theory of complex networks. In this review, we report the advances in the comprehension of synchronization phenomena when oscillating elements are constrained to interact in a complex network topology. We also overview the new emergent features coming out from the interplay between the structure and the function of the underlying pattern of connections. Extensive numerical work as well as analytical approaches to the problem are presented. Finally, we review several applications of synchronization in complex networks to different disciplines: biological systems and neuroscience, engineering and computer science, and economy and social sciences.

Synthesis characterization and biological evaluation of a novel mixed ligand 99mTc complex as potential brain imaging agent

International Nuclear Information System (INIS)

Rey, A.; Manta, E.; Leon, A.; Papadopoulos, M.; Pirmettis, Y.; Raptopoulou, C.; Chiotellis, E.; Leon, E.; Mallo, L.

1998-01-01

One approach in the design of neutral oxotechnetium complexes is based on the simultaneous substitution of a tridentate dianionic ligand and a monodentate monoanionic coligand on a [Tc(V)O] +3 precursor. Following this ''mixed ligand'' concept, a novel 99m Tc complex with N,N-bis(2-mercaptoethyl)-N'N'-diethylethylenediamine as ligand and 1-octanethiol as coligand is prepared and evaluated as potential brain radiopharmaceutical. Preparation of the complex at tracer level was accomplished by using 99m Tc-glucoheptonate as precursor. The substitution was optimized and a coligand/ligand ratio of 5 was selected. Under this conditions the labeling yield was over 80% and a major product (with radiochemical purity > 80%) was isolated by HPLC methods and used for biological evaluation. Chemical characterization at carrier level was developed using the corresponding rhenium complex as structural model. The Re complex was also prepared by substitution method and isolated as a crystalline product. The crystals were characterized by UV-vis and IR spectra and elemental analysis. Results were consistent with the expected ReOLC structure. X ray crystallographic study demonstrated that the complex adopts a distorted trigonal bipyramidal geometry. The basal plane is defined by the SS atoms of the ligand and the oxo group, while the N of the ligand and the S of the colligand occupy the two apical positions. All sulphur atoms underwent ionization leading to the formation of a neutral compound. 99 Tc complex was also prepared. Although it was not isolated due to the small amount of reagents employed, the HPLC profile was identical to the one observed for the rhenium complex suggesting the same chemical structure. Biodistribution in mice demonstrated early brain uptake, fast blood clearance, excretion through hepatobiliary system and a brain/blood ratio that increased significantly with time. (author)

Systems Biology of Metabolism: Annual Review of Biochemistry

DEFF Research Database (Denmark)

Nielsen, Jens

2017-01-01

Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

Practising Conservation Biology in a Virtual Rainforest World

Science.gov (United States)

Schedlbauer, Jessica L.; Nadolny, Larysa; Woolfrey, Joan

2016-01-01

The interdisciplinary science of conservation biology provides undergraduate biology students with the opportunity to connect the biological sciences with disciplines including economics, social science and philosophy to address challenging conservation issues. Because of its complexity, students do not often have the opportunity to practise…

Developments in the Tools and Methodologies of Synthetic Biology

Science.gov (United States)

Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.; Freemont, Paul

2014-01-01

Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community. PMID:25505788

Developments in the tools and methodologies of synthetic biology

Directory of Open Access Journals (Sweden)

Richard eKelwick

2014-11-01

Full Text Available Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices or systems. However, biological systems are generally complex and unpredictable and are therefore intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a ‘body of knowledge’ from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled and its functionality tested. At each stage of the design cycle an expanding repertoire of tools is being developed. In this review we highlight several of these tools in terms of their applications and benefits to the synthetic biology community.

Potentiometric studies on ternary complexes involving some divalent transition metal ions, gallic acid and biologically abundant aliphatic dicarboxylic acids in aqueous solutions

Directory of Open Access Journals (Sweden)

Abdelatty Mohamed Radalla

2015-06-01

Full Text Available Formation of binary and ternary complexes of the divalent transition metal ions, Cu2+, Ni2+, Co2+ and Zn2+ with gallic acid and the biologically important aliphatic dicarboxylic acids (adipic, succinic, malic, malonic, maleic, tartaric and oxalic acids were investigated by means of the potentiometric technique at 25 °C and I = 0.10 mol dm−3 NaNO3. The acid-base properties of the ligands were investigated and discussed. The acidity constants of gallic acid and aliphatic dicarboxylic acids were determined and used for determining the stability constants of the binary and ternary complexes formed in the aqueous medium under the above experimental conditions. The formation of the different 1:1 and 1:2 binary complexes and 1:1:1 ternary complexes are inferred from the corresponding potentiometric pH-metric titration curves. The ternary complex formation was found to occur in a stepwise manner. The stability constants of these binary and ternary systems were calculated. The values of Δ log K, percentage of relative stabilization (%R.S. and log X were evaluated and discussed. The concentration distribution of the various complex species formed in solution was evaluated and discussed. The mode of chelation of ternary complexes formed was ascertained by conductivity measurements.

Bloch Surface Waves Biosensors for High Sensitivity Detection of Soluble ERBB2 in a Complex Biological Environment.

Science.gov (United States)

Sinibaldi, Alberto; Sampaoli, Camilla; Danz, Norbert; Munzert, Peter; Sonntag, Frank; Centola, Fabio; Occhicone, Agostino; Tremante, Elisa; Giacomini, Patrizio; Michelotti, Francesco

2017-08-17

We report on the use of one-dimensional photonic crystals to detect clinically relevant concentrations of the cancer biomarker ERBB2 in cell lysates. Overexpression of the ERBB2 protein is associated with aggressive breast cancer subtypes. To detect soluble ERBB2, we developed an optical set-up which operates in both label-free and fluorescence modes. The detection approach makes use of a sandwich assay, in which the one-dimensional photonic crystals sustaining Bloch surface waves are modified with monoclonal antibodies, in order to guarantee high specificity during the biological recognition. We present the results of exemplary protein G based label-free assays in complex biological matrices, reaching an estimated limit of detection of 0.5 ng/mL. On-chip and chip-to-chip variability of the results is addressed too, providing repeatability rates. Moreover, results on fluorescence operation demonstrate the capability to perform high sensitive cancer biomarker assays reaching a resolution of 0.6 ng/mL, without protein G assistance. The resolution obtained in both modes meets international guidelines and recommendations (15 ng/mL) for ERBB2 quantification assays, providing an alternative tool to phenotype and diagnose molecular cancer subtypes.

Biologic surveys for the Sandia National Laboratories, Coyote Canyon Test Complex, Kirtland Air Force Base, Albuquerque, New Mexico

Energy Technology Data Exchange (ETDEWEB)

Sullivan, R.M. [4115 Allen Dr., Kingsville, TX (United States); Knight, P.J. [Marron and Associates, Inc., Corrales, NM (United States)

1994-05-25

This report provides results of a comprehensive biologic survey performed in Coyote Canyon Test Complex (CCTC), Sandia National Laboratories (SNL), Bernalillo County, New Mexico, which was conducted during the spring and summer of 1992 and 1993. CCTC is sited on land owned by the Department of Energy (DOE) and Kirtland Air Force Base and managed by SNL. The survey covered 3,760 acres of land, most of which is rarely disturbed by CCTC operations. Absence of grazing by livestock and possibly native ungulates, and relative to the general condition of private range lands throughout New Mexico, and relative to other grazing lands in central New Mexico. Widely dispersed, low intensity use by SNL as well as prohibition of grazing has probably contributed to abundance of special status species such as grama grass cactus within the CCTC area. This report evaluates threatened and endangered species found in the area, as well as comprehensive assessment of biologic habitats. Included are analyses of potential impacts and mitigative measures designed to reduce or eliminate potential impacts. Included is a summary of CCTC program and testing activities.

The effect of network biology on drug toxicology

DEFF Research Database (Denmark)

Gautier, Laurent; Taboureau, Olivier; Audouze, Karine Marie Laure

2013-01-01

Introduction: The high failure rate of drug candidates due to toxicity, during clinical trials, is a critical issue in drug discovery. Network biology has become a promising approach, in this regard, using the increasingly large amount of biological and chemical data available and combining...... it with bioinformatics. With this approach, the assessment of chemical safety can be done across multiple scales of complexity from molecular to cellular and system levels in human health. Network biology can be used at several levels of complexity. Areas covered: This review describes the strengths and limitations...... of network biology. The authors specifically assess this approach across different biological scales when it is applied to toxicity. Expert opinion: There has been much progress made with the amount of data that is generated by various omics technologies. With this large amount of useful data, network...

Analysis of complex networks from biology to linguistics

CERN Document Server

Dehmer, Matthias

2009-01-01

Mathematical problems such as graph theory problems are of increasing importance for the analysis of modelling data in biomedical research such as in systems biology, neuronal network modelling etc. This book follows a new approach of including graph theory from a mathematical perspective with specific applications of graph theory in biomedical and computational sciences. The book is written by renowned experts in the field and offers valuable background information for a wide audience.

Structural, thermal, morphological and biological studies of proton-transfer complexes formed from 4-aminoantipyrine with quinol and picric acid

Science.gov (United States)

Adam, Abdel Majid A.

2013-03-01

4-Aminoantipyrine (4AAP) is widely used in the pharmaceutical industry, biochemical experiments and environmental monitoring. However, residual amounts of 4AAP in the environment may pose a threat to human health. To provide basic data that can be used to extract or eliminate 4AAP from the environment, the proton-transfer complexes of 4AAP with quinol (QL) and picric acid (PA) were synthesized and spectroscopically investigated. The interactions afforded two new proton-transfer salts named 1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-aminium-4-hydroxyphenolate and 1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-aminium-2,4,6-trinitrophenolate for QL and PA, respectively, via a 1:1 stoichiometry. Elemental analysis (CHN), electronic absorption, spectrophotometric titration, IR, Raman, 1H NMR and X-ray diffraction were used to characterize the new products. The thermal stability of the synthesized CT complexes was investigated using thermogravimetric (TG) analyses, and the morphology and particle size of these complexes were obtained from scanning electron microscopy (SEM). It was found that PA and 4AAP immediately formed a yellow precipitate with a remarkable sponge-like morphology and good thermal stability up to 180 °C. Finally, the biological activities of the newly synthesized CT complexes were tested for their antibacterial and antifungal activities. The results indicated that the [(4AAP)(QL)] complex exhibited strong antimicrobial activities against various bacterial and fungal strains compared with standard drugs.

[Application of microelectronics CAD tools to synthetic biology].

Science.gov (United States)

Madec, Morgan; Haiech, Jacques; Rosati, Élise; Rezgui, Abir; Gendrault, Yves; Lallement, Christophe

2017-02-01

Synthetic biology is an emerging science that aims to create new biological functions that do not exist in nature, based on the knowledge acquired in life science over the last century. Since the beginning of this century, several projects in synthetic biology have emerged. The complexity of the developed artificial bio-functions is relatively low so that empirical design methods could be used for the design process. Nevertheless, with the increasing complexity of biological circuits, this is no longer the case and a large number of computer aided design softwares have been developed in the past few years. These tools include languages for the behavioral description and the mathematical modelling of biological systems, simulators at different levels of abstraction, libraries of biological devices and circuit design automation algorithms. All of these tools already exist in other fields of engineering sciences, particularly in microelectronics. This is the approach that is put forward in this paper. © 2017 médecine/sciences – Inserm.

Use of Graph Database for the Integration of Heterogeneous Biological Data.

Science.gov (United States)

Yoon, Byoung-Ha; Kim, Seon-Kyu; Kim, Seon-Young

2017-03-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

On the interplay between mathematics and biology: hallmarks toward a new systems biology.

Science.gov (United States)

Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

2015-03-01

This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

Identification of important nodes in directed biological networks: a network motif approach.

Directory of Open Access Journals (Sweden)

Pei Wang

Full Text Available Identification of important nodes in complex networks has attracted an increasing attention over the last decade. Various measures have been proposed to characterize the importance of nodes in complex networks, such as the degree, betweenness and PageRank. Different measures consider different aspects of complex networks. Although there are numerous results reported on undirected complex networks, few results have been reported on directed biological networks. Based on network motifs and principal component analysis (PCA, this paper aims at introducing a new measure to characterize node importance in directed biological networks. Investigations on five real-world biological networks indicate that the proposed method can robustly identify actually important nodes in different networks, such as finding command interneurons, global regulators and non-hub but evolutionary conserved actually important nodes in biological networks. Receiver Operating Characteristic (ROC curves for the five networks indicate remarkable prediction accuracy of the proposed measure. The proposed index provides an alternative complex network metric. Potential implications of the related investigations include identifying network control and regulation targets, biological networks modeling and analysis, as well as networked medicine.

Regulation of microtubule nucleation mediated by gamma-tubulin complexes

Czech Academy of Sciences Publication Activity Database

Sulimenko, Vadym; Hájková, Zuzana; Klebanovych, Anastasiya; Dráber, Pavel

2017-01-01

Roč. 254, č. 3 (2017), s. 1187-1199 ISSN 0033-183X R&D Projects: GA MŠk(CZ) LD13015 Institutional support: RVO:68378050 Keywords : mitotic spindle formation * ring complex * fission yeast * organizing centers * protein complex * golgi-complex * cell-cycle * pole body * augmin * centrosome * Centrosomes * Microtubule nucleation * Microtubule-organizing centers * Non-centrosomal nucleation sites * Spindle pole bodies * gamma-Tubulin complexes Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Cell biology Impact factor: 2.870, year: 2016

Pharmacologically significant tetraaza macrocyclic metal complexes ...

Indian Academy of Sciences (India)

MOHAMMAD SHAKIR

2017-11-22

Nov 22, 2017 ... structural biological models.6 Hence, biological prop- erties of ... poor water solubility, exhibits intrinsic resistance and ..... pdb). The metal complex files were drawn using. ChemDraw (MM2) and their energies were minimized.

The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

Science.gov (United States)

Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

2012-01-01

Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

Third International Conference on Complex Systems

CERN Document Server

Minai, Ali A; Unifying Themes in Complex Systems

2006-01-01

In recent years, scientists have applied the principles of complex systems science to increasingly diverse fields. The results have been nothing short of remarkable: their novel approaches have provided answers to long-standing questions in biology, ecology, physics, engineering, computer science, economics, psychology and sociology. The Third International Conference on Complex Systems attracted over 400 researchers from around the world. The conference aimed to encourage cross-fertilization between the many disciplines represented and to deepen our understanding of the properties common to all complex systems. This volume contains over 35 papers selected from those presented at the conference on topics including: self-organization in biology, ecological systems, language, economic modeling, ecological systems, artificial life, robotics, and complexity and art. ALI MINAI is an Affiliate of the New England Complex Systems Institute and an Associate Professor in the Department of Electrical and Computer Engine...

Biology, ecology and control of the Penthaleus species complex (Acari: Penthaleidae).

Science.gov (United States)

Umina, Paul A; Hoffmann, Ary A; Weeks, Andrew R

2004-01-01

Blue oat mites, Penthaleus spp. (Acari: Penthaleidae), are major agricultural pests in southern Australia and other parts of the world, attacking various pasture, vegetable and crop plants. Management of these mites has been complicated by the recent discovery of three cryptic pest species of Penthaleus, whereas prior research had assumed a single species. The taxonomy, population genetics, ecology, biology and control of the Penthaleus spp. complex are reviewed. Adult Penthaleus have a dark blue-black body approximately 1 mm in length, and eight red-orange legs. Within Australia, they are winter pests completing two or three generations a season, depending on conditions. The summer is passed as diapausing eggs, when long-distance dispersal is thought to occur. The Penthaleus spp. reproduce by thelytokous parthenogenesis, with populations comprising clones that differ ecologically. The three pest Penthaleus spp. differ markedly in their distributions, plant hosts, timing of diapause egg production and response to pesticides, highlighting the need to develop control strategies that consider each species separately. Chemicals are the main weapons used in current control programs, however research continues into alternative more sustainable management options. Host plant resistance, crop rotations, conservation of natural enemies, and improved timing of pesticide application would improve the management of these pests. The most cost-effective and environmentally acceptable means of control will result from the integration of these practices combined with the development of a simple field-based kit to distinguish the different mite species.

Methylene Diphosphonate Chemical and Biological control of MDP complex

International Nuclear Information System (INIS)

Aungurarat, Angkanan; Ngamprayad, Tippanan

2000-01-01

Technetium-9 9m MDP easy prepared from MDP kits which different sources such as OAP (In house), SIGMA. The resulting Tc 9 9m -MDP preparations were controlled in chemical and biological tests to compare the different results in these cases: radiochemical purity, the quantity of starting material and biodistribution result

Complexity and Chaos - State-of-the-Art; Formulations and Measures of Complexity

Science.gov (United States)

2007-09-01

196] GREEN , DG. Syntactic modelling and simulation. Simulation, 1990, 54, 281-286. [197] GREEN , DG. Emergent Behaviour in Biological...Systems. In GREEN , DG; BOSSOMAIER, TJ (Eds). Complex Systems - From Biology to Computation. Amsterdam: OS Press, 1993, 24-35. [198] GREENBERG, WJ. A...Transactions on Systems, Man and Cybernetics, 1989, 19, 1073-1077. [369] RAMSEY, FP. The foundations of mathematics. London: Routledge & Kegan Paul, 1950

Mammalian Synthetic Biology: Engineering Biological Systems.

Science.gov (United States)

Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

2017-06-21

The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

Synthesis, characterization and biological evaluation of a novel "3 + 1" mixed ligand 99mTc complex having an aliphatic thiol as coligand.

Science.gov (United States)

Rey, A; Papadopoulos, M; Leon, E; Mallo, L; Pirmettis, Y; Manta, E; Raptopoulou, C; Chiotellis, E; Leon, A

2001-03-01

A novel "3 + 1" mixed ligand 99mTc complex with N,N-bis(2-mercaptoethyl)-N'N'-diethyl-ethilenediamine as ligand and 1-octanethiol as coligand was prepared and evaluated as potential brain radiopharmaceutical. Preparation at tracer level was accomplished by substitution, using 99mTc-glucoheptonate as precursor and a coligand/ligand ratio of 5. Under these conditions the labeling yield was over 80% and a major product with radiochemical purity >80% was isolated by HPLC methods and used for biological evaluation. Chemical characterization at carrier level was developed using the corresponding rhenium and 99gTc complexes. Results were consistent with the expected "3 + 1" structure and X-ray diffraction study demonstrated that the complex adopted a distorted trigonal bipyramidal geometry. All sulphur atoms underwent ionization leading to the formation of a neutral compound. Biodistribution in mice demonstrated early brain uptake, fast blood clearance and excretion through hepatobiliary system. Although brain/blood ratio increased significantly with time, this novel 99mTc complex did not exhibit ideal properties as brain perfusion radiopharmaceutical since brain uptake was too low.

Synthesis, characterization and biological evaluation of a novel ''3+1'' mixed ligand 99mTc complex having an aliphatic thiol as coligand

International Nuclear Information System (INIS)

Rey, A.; Papadopoulos, M.; Leon, E.; Mallo, L.; Pirmettis, Y.; Manta, E.; Raptopoulou, C.; Chiotellis, E.; Leon, A.

2001-01-01

A novel ''3+1'' mixed ligand 99m Tc complex with N,N-bis(2-mercaptoethyl)-N'N'-diethyl-ethilenediamine as ligand and 1-octanethiol as coligand was prepared and evaluated as potential brain radiopharmaceutical. Preparation at tracer level was accomplished by substitution, using 99m Tc-glucoheptonate as precursor and a coligand/ligand ratio of 5. Under these conditions the labeling yield was over 80% and a major product with radiochemical purity >80% was isolated by HPLC methods and used for biological evaluation. Chemical characterization at carrier level was developed using the corresponding rhenium and 99g Tc complexes. Results were consistent with the expected ''3+1'' structure and X-ray diffraction study demonstrated that the complex adopted a distorted trigonal bipyramidal geometry. All sulphur atoms underwent ionization leading to the formation of a neutral compound. Biodistribution in mice demonstrated early brain uptake, fast blood clearance and excretion through hepatobiliary system. Although brain/blood ratio increased significantly with time, this novel 99m Tc complex did not exhibit ideal properties as brain perfusion radiopharmaceutical since brain uptake was too low

Functional alteration of breast muscle fatty acid profile by ...

African Journals Online (AJOL)

ajl yemi

2011-03-28

Mar 28, 2011 ... copper (Pesti and Bakalli, 1996), α-tocopherol acetate. (Ashgar et al., 1989) and n-3 fatty acid ..... Pesti GM, Bakalli RI (1996). Studies on the feeding of cupric sulfate pentahydrate and cupric citrate to broiler chickens. Poult.

Inhibitory effects of ascorbic acid, vitamin E, and vitamin B-complex on the biological activities induced by Bothrops venom.

Science.gov (United States)

Oliveira, Carlos Henrique de Moura; Assaid Simão, Anderson; Marcussi, Silvana

2016-01-01

Natural compounds have been widely studied with the aim of complementing antiophidic serum therapy. The present study evaluated the inhibitory potential of ascorbic acid and a vitamin complex, composed of ascorbic acid, vitamin E, and all the B-complex vitamins, on the biological activities induced by snake venoms. The effect of vitamins was evaluated on the phospholipase, proteolytic, coagulant, and fibrinogenolytic activities induced by Bothrops moojeni (Viperidae), B. jararacussu, and B. alternatus snake venoms, and the hemagglutinating activity induced by B. jararacussu venom. The vitamin complex (1:5 and 1:10 ratios) totally inhibited the fibrinogenolytic activity and partially the phospholipase activity and proteolytic activity on azocasein induced by the evaluated venoms. Significant inhibition was observed in the coagulation of human plasma induced by venoms from B. alternatus (1:2.5 and 1:5, to vitamin complex and ascorbic acid) and B. moojeni (1:2.5 and 1:5, to vitamin complex and ascorbic acid). Ascorbic acid inhibited 100% of the proteolytic activities of B. moojeni and B. alternatus on azocasein, at 1:10 ratio, the effects of all the venoms on fibrinogen, the hemagglutinating activity of B. jararacussu venom, and also extended the plasma coagulation time induced by all venoms analyzed. The vitamins analyzed showed relevant in vitro inhibitory potential over the activities induced by Bothrops venoms, suggesting their interaction with toxins belonging to the phospholipase A2, protease, and lectin classes. The results can aid further research in clarifying the possible mechanisms of interaction between vitamins and snake enzymes.

The impact of technetium-99m-radiopharmaceuticals' design on their biological behavior

International Nuclear Information System (INIS)

Jankovic, D.Lj.; Djokic, D.Dj. . E-mail address of corresponding author: drinaj@vin.bg.ac.yu; Jankovic, D.)

2005-01-01

The coordination has a great and not always predictable impact on the in-vivo behaviour of the small molecule into which the technetium-bearing chelate units is integrated. The different valence state of technetium in the complexes with some ligands changes the properties of these complexes, such as physico-chemical parameters and biological behaviour. The change of their biological behaviour has a great impact on quality of imaging study and on radiation dose to the patient. The results of the labelling of DPD and EHIDA with 99mTc(I) and their biological behaviour, in comparison with the same one for 99mTc(III)-DPD and 99mTc(III)-EHIDA complexes, confirmed that different oxidation state of 99mTc make possible forming variety of complexes with quite a different and unexpected biological behaviour. (author)

Ligand-independent interaction of the type I interferon receptor complex is necessary to observe its biological activity.

Science.gov (United States)

Krause, Christopher D; Digioia, Gina; Izotova, Lara S; Xie, Junxia; Kim, Youngsun; Schwartz, Barbara J; Mirochnitchenko, Olga V; Pestka, Sidney

2013-10-01

Ectopic coexpression of the two chains of the Type I and Type III interferon (IFN) receptor complexes (IFN-αR1 and IFN-αR2c, or IFN-λR1 and IL-10R2) yielded sensitivity to IFN-alpha or IFN-lambda in only some cells. We found that IFN-αR1 and IFN-αR2c exhibit FRET only when expressed at equivalent and low levels. Expanded clonal cell lines expressing both IFN-αR1 and IFN-αR2c were sensitive to IFN-alpha only when IFN-αR1 and IFN-αR2c exhibited FRET in the absence of human IFN-alpha. Coexpression of RACK-1 or Jak1 enhanced the affinity of the interaction between IFN-αR1 and IFN-αR2c. Both IFN-αR1 and IFN-αR2c exhibited FRET with Jak1 and Tyk2. Together with data showing that disruption of the preassociation between the IFN-gamma receptor chains inhibited its biological activity, we propose that biologically active IFN receptors require ligand-independent juxtaposition of IFN receptor chains assisted by their associated cytosolic proteins. Copyright © 2013 Elsevier Ltd. All rights reserved.

[New materia medica project: synthetic biology based bioactive metabolites research in medicinal plant].

Science.gov (United States)

Wang, Yong

2017-03-25

In the last decade, synthetic biology research has been gradually transited from monocellular parts or devices toward more complex multicellular systems. The emerging plant synthetic biology is regarded as the "next chapter" of synthetic biology. The complex and diverse plant metabolism as the entry point, plant synthetic biology research not only helps us understand how real life is working, but also facilitates us to learn how to design and construct more complex artificial life. Bioactive compounds innovation and large-scale production are expected to be breakthrough with the redesigned plant metabolism as well. In this review, we discuss the research progress in plant synthetic biology and propose the new materia medica project to lift the level of traditional Chinese herbal medicine research.

Two Dogmas of Biology

Directory of Open Access Journals (Sweden)

Leonore Fleming

2017-01-01

Full Text Available The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of a strictly deterministic framework is unnecessarily hindering to biology. By removing the dogma of determinism, biological methods, including reductive methods, can be expanded to include stochastic models and probabilistic interpretations. Thus, the dogma of reductionism can be saved once its ties with determinism are severed. In this paper, I analyze two problems that have faced molecular biology for the last 50 years—protein folding and cancer. Both cases demonstrate the long influence of reductionism and determinism on molecular biology, as well as how abandoning determinism has opened the door to more probabilistic and unconstrained reductive methods in biology.

Complex-Shaped Microcomponents by the Reactive Conversion of Biological Templates

National Research Council Canada - National Science Library

Sandhage, Kenneth

2004-01-01

This project has been aimed at: 1) identifying gas/solid reaction conditions for converting biologically-derived micro/nanotemplates into other oxides without a loss of the starting 3-D shape and fine features, and 2...

Radiation chemistry in development and research of radiation biology

International Nuclear Information System (INIS)

Min Rui

2010-01-01

During the establishment and development of radiation biology, radiation chemistry acts like bridge which units the spatial and temporal insight coming from radiation physics with radiation biology. The theory, model, and methodology of radiation chemistry play an important role in promoting research and development of radiation biology. Following research development of radiation biology effects towards systems radiation biology the illustration and exploration both diversity of biological responses and complex process of biological effect occurring remain to need the theory, model, and methodology come from radiation chemistry. (authors)

Practical approaches to biological inorganic chemistry

CERN Document Server

Louro, Ricardo O

2012-01-01

The book reviews the use of spectroscopic and related methods to investigate the complex structures and mechanisms of biological inorganic systems that contain metals. Each chapter presents an overview of the technique including relevant theory, clearly explains what it is and how it works and then presents how the technique is actually used to evaluate biological structures. Practical examples and problems are included to illustrate each technique and to aid understanding. Designed for students and researchers who want to learn both the basics, and more advanced aspects of bioinorganic chemistry. It includes many colour illustrations enable easier visualization of molecular mechanisms and structures. It provides worked examples and problems that are included to illustrate and test the reader's understanding of each technique. It is written by a multi-author team who use and teach the most important techniques used today to analyse complex biological structures.

Graphics processing units in bioinformatics, computational biology and systems biology.

Science.gov (United States)

Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

2017-09-01

Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

Synthesis, chemical and biological studies on new Fe(3+)-glycosilated beta-diketo complexes for the treatment of iron deficiency.

Science.gov (United States)

Arezzini, Beatrice; Ferrali, Marco; Ferrari, Erika; Frassineti, Chiara; Lazzari, Sandra; Marverti, Gaetano; Spagnolo, Ferdinando; Saladini, Monica

2008-11-01

A simple synthetic pathway to obtain glycosilated beta-diketo derivatives is proposed. These compounds show a good iron(III) affinity therefore we may suggest the use of their Fe(3+)-complexes as oral iron supplements in the treatment of anaemia. The glycosilated compounds (6-GlcH, 6-GlcOH and 6-GlcOCH(3)) are characterized by means of spectroscopic (UV, (1)H and (13)C NMR) and potentiometric techniques; they have a good water solubility, are kinetically stable in physiological condition (t(1/2)>100h) and show a low cytotoxicity also in high concentrations (IC(50)>400 microM). They are able to bind Fe(3+) ion in acid condition (pH approximately 2) forming complex species thermodynamically more stable than those of other ligands commonly used in the treatment of iron deficiency. The iron complexes show also a good kinetic stability both in acidic and physiological pH and have a good lypophilicity (logP>-0.7) that suggests an efficient gastrointestinal absorption in view of their possible use in oral therapy. In addition they demonstrate a poor affinity for competitive biological metal ion such as Ca(2+), and in particular 6-GlcOCH(3) is able to inhibit lipid peroxidation.

THE ROLE OF PIPE AGEING IN COPPER CORROSION BY-PRODUCT RELEASE

Science.gov (United States)

The presence of sulphate, bicarbonate and orthophosphate can change the type of solid present in systems containing cupric ion or cupric hydroxide solids. In some cases, a short-term reduction in copper solubility is realized, but over longer periods of time formation of basic c...

Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud.

Science.gov (United States)

Burns, Malcolm; Wiseman, Gordon; Knight, Angus; Bramley, Peter; Foster, Lucy; Rollinson, Sophie; Damant, Andrew; Primrose, Sandy

2016-01-07

Following a report on a significant amount of horse DNA being detected in a beef burger product on sale to the public at a UK supermarket in early 2013, the Elliott report was published in 2014 and contained a list of recommendations for helping ensure food integrity. One of the recommendations included improving laboratory testing capacity and capability to ensure a harmonised approach for testing for food authenticity. Molecular biologists have developed exquisitely sensitive methods based on the polymerase chain reaction (PCR) or mass spectrometry for detecting the presence of particular nucleic acid or peptide/protein sequences. These methods have been shown to be specific and sensitive in terms of lower limits of applicability, but they are largely qualitative in nature. Historically, the conversion of these qualitative techniques into reliable quantitative methods has been beset with problems even when used on relatively simple sample matrices. When the methods are applied to complex sample matrices, as found in many foods, the problems are magnified resulting in a high measurement uncertainty associated with the result which may mean that the assay is not fit for purpose. However, recent advances in the technology and the understanding of molecular biology approaches have further given rise to the re-assessment of these methods for their quantitative potential. This review focuses on important issues for consideration when validating a molecular biology assay and the various factors that can impact on the measurement uncertainty of a result associated with molecular biology approaches used in detection of food fraud, with a particular focus on quantitative PCR-based and proteomics assays.

BlenX-based compositional modeling of complex reaction mechanisms

Directory of Open Access Journals (Sweden)

Judit Zámborszky

2010-02-01

Full Text Available Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.

Philosophy of Systems and Synthetic Biology

DEFF Research Database (Denmark)

Green, Sara

2017-01-01

This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

Large branched self-assembled DNA complexes

International Nuclear Information System (INIS)

Tosch, Paul; Waelti, Christoph; Middelberg, Anton P J; Davies, A Giles

2007-01-01

Many biological molecules have been demonstrated to self-assemble into complex structures and networks by using their very efficient and selective molecular recognition processes. The use of biological molecules as scaffolds for the construction of functional devices by self-assembling nanoscale complexes onto the scaffolds has recently attracted significant attention and many different applications in this field have emerged. In particular DNA, owing to its inherent sophisticated self-organization and molecular recognition properties, has served widely as a scaffold for various nanotechnological self-assembly applications, with metallic and semiconducting nanoparticles, proteins, macromolecular complexes, inter alia, being assembled onto designed DNA scaffolds. Such scaffolds may typically contain multiple branch-points and comprise a number of DNA molecules selfassembled into the desired configuration. Previously, several studies have used synthetic methods to produce the constituent DNA of the scaffolds, but this typically constrains the size of the complexes. For applications that require larger self-assembling DNA complexes, several tens of nanometers or more, other techniques need to be employed. In this article, we discuss a generic technique to generate large branched DNA macromolecular complexes

Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

OpenAIRE

Shuo Gu; Jianfeng Pei

2017-01-01

With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regula...

Spectral studies, thermal investigation and biological activity of some metal complexes derived from (E)-N‧-(1-(4-aminophenyl)ethylidene)morpholine-4-carbothiohydrazide

Science.gov (United States)

El-Samanody, El-Sayed A.; Polis, Magdy W.; Emara, Esam M.

2017-09-01

A new series of biologically active Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) complexes derived from the novel thiosemicarbazone ligand; (E)-N‧-(1-(4-aminophenyl)ethylidene)morpholine-4-carbothiohydrazide (HL) were synthesized. The mode of bonding of the ligand and the geometrical structures of its metal complexes were achieved by different analytical and spectral methods. The ligand coordinated with metal ions in a neutral bidentate fashion through the thione sulfur and azomethine nitrogen atoms. All metal complexes adopted octahedral geometry, except Cu(II) complexes (3, 6, 7) which have a square planar structure. The general thermal decomposition pathways of the ligand along with its metal complexes were explained. The thermal stability of the complexes is controlled by the number of outer and inner sphere water molecules, ionic radii and the steric hindrance. The activation thermodynamic parameters; (activation energy (E*), enthalpy of activation (ΔH*), entropy of activation (ΔS*) and Gibbs free energy (ΔG*)) along with order of reaction (n) were estimated from DTG curves. The ESR spectra of Cu(II) complexes indicated that (dx2-y2)1 is the ground state with covalence character of metal-ligand bonds. The molluscicidal and biochemical effects of the ligand and its Ni(II); Cu(II) complexes (2; 3, 5, 7) along with their combinations with metaldehyde were screened in vitro on the mucous gland of Eobania vermiculata. The tested compounds exhibited a significant toxicity against the tested animals and have almost the same toxic effect of metaldehyde which increases the mucous secretion of the snails and leads to death.

Review of Biological Network Data and Its Applications

Directory of Open Access Journals (Sweden)

Donghyeon Yu

2013-12-01

Full Text Available Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

Quantitative computational models of molecular self-assembly in systems biology.

Science.gov (United States)

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

Synthesis and Biological Evaluation of Ru(II) and Pt(II) Complexes Bearing Carboxyl Groups as Potential Anticancer Targeted Drugs.

Science.gov (United States)

Martínez, Ma Ángeles; Carranza, M Pilar; Massaguer, Anna; Santos, Lucia; Organero, Juan A; Aliende, Cristina; de Llorens, Rafael; Ng-Choi, Iteng; Feliu, Lidia; Planas, Marta; Rodríguez, Ana M; Manzano, Blanca R; Espino, Gustavo; Jalón, Félix A

2017-11-20

The synthesis and characterization of Pt(II) (1 and 2) and Ru(II) arene (3 and 4) or polypyridine (5 and 6) complexes is described. With the aim of having a functional group to form bioconjugates, one uncoordinated carboxyl group has been introduced in all complexes. Some of the complexes were selected for their potential in photodynamic therapy (PDT). The molecular structures of complexes 2 and 5, as well as that of the sodium salt of the 4'-(4-carboxyphenyl)-2,2':6',2″-terpyridine ligand (cptpy), were determined by X-ray diffraction. Different techniques were used to evaluate the binding capacity to model DNA molecules, and MTT cytotoxicity assays were performed against four cell lines. Compounds 3, 4, and 5 showed little tendency to bind to DNA and exhibited poor biological activity. Compound 2 behaves as bonded to DNA probably through a covalent interaction, although its cytotoxicity was very low. Compound 1 and possibly 6, both of which contain a cptpy ligand, were able to intercalate with DNA, but toxicity was not observed for 6. However, compound 1 was active in all cell lines tested. Clonogenic assays and apoptosis induction studies were also performed on the PC-3 line for 1. The photodynamic behavior for complexes 1, 5, and 6 indicated that their nuclease activity was enhanced after irradiation at λ = 447 nm. The cell viability was significantly reduced only in the case of 5. The different behavior in the absence or presence of light makes complex 5 a potential prodrug of interest in PDT. Molecular docking studies followed by molecular dynamics simulations for 1 and the counterpart without the carboxyl group confirmed the experimental data that pointed to an intercalation mechanism. The cytotoxicity of 1 and the potential of 5 in PDT make them good candidates for subsequent conjugation, through the carboxyl group, to "selected peptides" which could facilitate the selective vectorization of the complex toward receptors that are overexpressed in

FY 1997 report on the results of the industrial technology R and D project. Development of technology to use biological resources such as the complex biological system (Development of biological use petroleum substitution fuel production technology); 1997 nendo fukugo seibutsukei nado seibutsu shigen riyo gijutsu kaihatsu seika hokokusho. Seibutsu riyo sekiyu daitai nenryo seizo gijutsu no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-03-01

Experimental researches were conducted and the FY 1997 results were reported with the aim of establishing analytical technology for the complex biological system by which the complex biological system can be analyzed in such a state as it is using the molecular biological method. In the study of the molecular genetic analytical technology, PCR primers used for amplification of topoisomerase II genes of the whole eukaryote was designed. As to the histochemical analytical technology, a study was made on the new constitution microorganism detection method by the hybridization method and the antibody specific dyeing method, and the following were conducted: manifestation in quantity of colibacillus and the recovery, refining, and construction of peptide library by fuzzy display method. Concerning the functional analytical technology, technological researches were made such as the environmental adaptation mechanism of high thermophile and the information transfer mechanism among bacteria through cell membranes for elucidation of the special environment detection/response mechanism and the special environment adaptation/resistance mechanism. As to the separation/culture technology, various anaerobic microorganisms were separated from marine sponge for the development of a method of culturing in 3D matrices. (NEDO)

Structure-based characterization of multiprotein complexes.

Science.gov (United States)

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

2014-07-08

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Physicochemical and biological properties of new steroid metal complexes

International Nuclear Information System (INIS)

Huber, R.

1980-04-01

The aim of this investigation was to prepare stable steroid metal chelates by chemical conversion of the natural steroid hormones testerone, 5α-dihydrotestosterone (5α-DHT) and estradiol and to characterize these by means of their spectroscopic and other physico-chemical properties. In addition, various measuring techniques for the qualitative and quantitative study of complex stabilities and hydrolytic properties were employed. The distribution of some tritiated steroid metal complexes in the tissues of rats was tested using whole animal autoradiography, mainly with a view to identifying whether selective concentration occurs in certain organs. (orig.) [de

Synthesis of the 99mTc(CO)3-trovafloxacin dithiocarbamate complex and biological characterization in artificially methicillin-resistant Staphylococcus aureus infected rats model

International Nuclear Information System (INIS)

Syed Qaiser Shah; Muhammad Rafiullah Khan

2011-01-01

Synthesis of the 99m Tc(CO) 3 -trovafloxacin dithiocarbamate ( 99m Tc(CO) 3 -TVND) complex and biological characterization in artificially Staphylococcus aureus (S. aureus) infected rats model was assessed. The suitability of the complex was evaluated and compared with 99m TcN-TVND, in terms of radiochemical immovability in saline, in vitro permanence in serum, in vitro binding with S. aureus and biodistribution in Male Sprague-Dawley rats (MSDR). After 30 min of the reconstitution both the complexes showed maximum radiochemical stabilities in saline and remain more than 90% stable up to 120 min. However the 99m Tc(CO) 3 -TVND showed to some extent higher stability than 99m TcN-TVND complex. In serum 1.75% less de-tagging was observed than 99m TcN-TVND complex. Both the complexes showed saturated in vitro binding with S. aureus and no significant difference were observed between the uptakes. Six fold uptakes were noted in the infected muscle as compared to the inflamed and normal muscles of the MDSR. The uptake of the 99m Tc(CO) 3 -TVND in infected muscle of the MSDR was 2.25% high as compared to the 99m TcN-TVND complex. Based on radiochemical stabilities in saline, serum, in vitro binding with MRSA and significantly higher uptake in the infected muscle, we recommend both the complexes for in vivo investigation of the MRSA infection in human. (author)

Synthesis, spectral studies and biological evaluation of 2-aminonicotinic acid metal complexes

Science.gov (United States)

Nawaz, Muhammad; Abbasi, Muhammad Waseem; Hisaindee, Soleiman; Zaki, Muhammad Javed; Abbas, Hira Fatima; Mengting, Hu; Ahmed, M. Arif

2016-05-01

We synthesized 2-aminonicotinic acid (2-ANA) complexes with metals such as Co(II), Fe(III), Ni(II), Mn(II), Zn(II), Ag(I),Cr(III), Cd(II) and Cu(II) in aqueous media. The complexes were characterized and elucidated using FT-IR, UV-Vis, a fluorescence spectrophotometer and thermo gravimetric analysis (TGA). TGA data showed that the stoichiometry of complexes was 1:2 metal/ligand except for Ag(I) and Mn(II) where the ratio was 1:1. The metal complexes showed varied antibacterial, fungicidal and nematicidal activities. The silver and zinc complexes showed highest activity against Bacillus subtilis and Bacillus licheniformis respectively. Fusarium oxysporum was highly susceptible to nickel and copper complexes whereas Macrophomina phaseolina was completely inert to the complexes. The silver and cadmium complexes were effective against the root-knot nematode Meloidogyne javanica.

Biological Complexities in Radiation Carcinogenesis and Cancer Radiotherapy: Impact of New Biological Paradigms

Directory of Open Access Journals (Sweden)

Hossein Mozdarani

2012-01-01

Full Text Available Although radiation carcinogenesis has been shown both experimentally and epidemiologically, the use of ionizing radiation is also one of the major modalities in cancer treatment. Various known cellular and molecular events are involved in carcinogenesis. Apart from the known phenomena, there could be implications for carcinogenesis and cancer prevention due to other biological processes such as the bystander effect, the abscopal effect, intrinsic radiosensitivity and radioadaptation. Bystander effects have consequences for mutation initiated cancer paradigms of radiation carcinogenesis, which provide the mechanistic justification for low-dose risk estimates. The abscopal effect is potentially important for tumor control and is mediated through cytokines and/or the immune system (mainly cell-mediated immunity. It results from loss of growth and stimulatory and/or immunosuppressive factors from the tumor. Intrinsic radiosensitivity is a feature of some cancer prone chromosomal breakage syndromes such as ataxia telangectiasia. Radiosensitivity is manifested as higher chromosomal aberrations and DNA repair impairment is now known as a good biomarker for breast cancer screening and prediction of prognosis. However, it is not yet known whether this effect is good or bad for those receiving radiation or radiomimetic agents for treatment. Radiation hormesis is another major concern for carcinogenesis. This process which protects cells from higher doses of radiation or radio mimic chemicals, may lead to the escape of cells from mitotic death or apoptosis and put cells with a lower amount of damage into the process of cancer induction. Therefore, any of these biological phenomena could have impact on another process giving rise to genome instability of cells which are not in the field of radiation but still receiving a lower amount of radiation. For prevention of radiation induced carcinogenesis or risk assessment as well as for successful radiation

Human Development V: Biochemistry Unable to Explain the Emergence of Biological Form (Morphogenesis and Therefore a New Principle as Source of Biological Information is Needed

Directory of Open Access Journals (Sweden)

Søren Ventegodt

2006-01-01

Full Text Available Today's biomedicine builds on the conviction that biochemistry can explain the creation of the body, its anatomy and physiology. Unfortunately there are still deep mysteries strangely “fighting back” when we try to define and understand the organism and its creation in the ontogenesis as emerging from biochemistry. In analysing this from a theoretical perspective using a mathematical model focusing on the noise in complex chemical systems we argue that evolving biological structure cannot in principle be a product of chemistry. In this paper we go through the chemical gradient model and argue that this is not able to explain the ontogenesis. We discuss the used gradients as information carriers in chemical self-organizing systems and argue that by use of the “Turing structures” we are only able to modelling the mostly simple biological systems. The bio-chemical model is only able to model simple organization but not to explain the complexity of biological phenomena. We conclude that we seemingly have presented a formal proof (a NO-GO theorem that the self-organizing chemical systems that are using chemical gradients are not able to explain complex biological matters as the ontogenesis. We need a fundamentally new, information-carrying principle to understand biological information and biological order.

Synthesis, spectral studies and biological evaluation of 2-aminonicotinic acid metal complexes.

Science.gov (United States)

Nawaz, Muhammad; Abbasi, Muhammad Waseem; Hisaindee, Soleiman; Zaki, Muhammad Javed; Abbas, Hira Fatima; Mengting, Hu; Ahmed, M Arif

2016-05-15

We synthesized 2-aminonicotinic acid (2-ANA) complexes with metals such as Co(II), Fe(III), Ni(II), Mn(II), Zn(II), Ag(I),Cr(III), Cd(II) and Cu(II) in aqueous media. The complexes were characterized and elucidated using FT-IR, UV-Vis, a fluorescence spectrophotometer and thermo gravimetric analysis (TGA). TGA data showed that the stoichiometry of complexes was 1:2 metal/ligand except for Ag(I) and Mn(II) where the ratio was 1:1. The metal complexes showed varied antibacterial, fungicidal and nematicidal activities. The silver and zinc complexes showed highest activity against Bacillus subtilis and Bacillus licheniformis respectively. Fusarium oxysporum was highly susceptible to nickel and copper complexes whereas Macrophomina phaseolina was completely inert to the complexes. The silver and cadmium complexes were effective against the root-knot nematode Meloidogyne javanica. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis, spectral, thermal and biological studies of transition metal complexes of 4-hydroxy-3-[3-(4-hydroxyphenyl-acryloyl]-6-methyl-2H-pyran-2-one

Directory of Open Access Journals (Sweden)

BALASAHEB R. ARBAD

2011-09-01

Full Text Available The solid complexes of Mn(II, Fe(III, Co(II, Ni(II, and Cu(II with 4-hydroxy-3-[(2E-3-(4-hydroxyphenylprop-2-enoyl]-6-methyl-2H-pyran-2-one, derived from 3-acetyl-6-methyl-2H-pyran-2,4(3H-dione (dehydroacetic acid and 4-hydroxybenzaldehyde, were synthesized and characterized by elemental analysis, conductometry, thermal analysis, magnetic measurements, IR, 1H-NMR and UV–Vis spectroscopy and a biological study. From the analytical and spectral data, the stoichiometry of the complexes was found to be 1:2 (metal:ligand. The physico–chemical data suggest a distorted octahedral geometry for the Cu(II complexes and an octahedral geometry for all the other complexes. The thermal decomposition of all the complexes was studied by the TG–DTA method. The synthesized ligand and its metal complexes were screened for their in vitro antibacterial activity against Gram-negative (Escherichia coli and Gram-positive (Staphylococcus aureus bacterial strains and for in vitro antifungal activity against Aspergillus flavus, Curvularia lunata and Penicillium notatum. The results of these studies showed the metal complexes to be more antibacterial/antifungal against one or more species as compared with the non-complexed ligand.

Rapid classification of biological components

Energy Technology Data Exchange (ETDEWEB)

Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

2013-10-15

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

Rapid classification of biological components

Energy Technology Data Exchange (ETDEWEB)

Thompson, Vicki S. (Idaho Falls, ID); Barrett, Karen B. (Meridian, ID); Key, Diane E. (Idaho Falls, ID)

2010-03-23

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

Rapid classification of biological components

Energy Technology Data Exchange (ETDEWEB)

Thompson, Vicki S. (Idaho Falls, ID); Barrett, Karen B. (Meridian, ID); Key, Diane E. (Idaho Falls, ID)

2010-03-23

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, Cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens of the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

Rapid classification of biological components

Energy Technology Data Exchange (ETDEWEB)

Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

2006-01-24

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine, methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.

Entropy for the Complexity of Physiological Signal Dynamics.

Science.gov (United States)

Zhang, Xiaohua Douglas

2017-01-01

Recently, the rapid development of large data storage technologies, mobile network technology, and portable medical devices makes it possible to measure, record, store, and track analysis of biological dynamics. Portable noninvasive medical devices are crucial to capture individual characteristics of biological dynamics. The wearable noninvasive medical devices and the analysis/management of related digital medical data will revolutionize the management and treatment of diseases, subsequently resulting in the establishment of a new healthcare system. One of the key features that can be extracted from the data obtained by wearable noninvasive medical device is the complexity of physiological signals, which can be represented by entropy of biological dynamics contained in the physiological signals measured by these continuous monitoring medical devices. Thus, in this chapter I present the major concepts of entropy that are commonly used to measure the complexity of biological dynamics. The concepts include Shannon entropy, Kolmogorov entropy, Renyi entropy, approximate entropy, sample entropy, and multiscale entropy. I also demonstrate an example of using entropy for the complexity of glucose dynamics.

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes.

Science.gov (United States)

Hassani-Pak, Keywan; Rawlings, Christopher

2017-06-13

Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects. Here we review several bioinformatics tools and databases that play an important role in biological knowledge discovery and candidate gene prioritization. We conclude with several key challenges that need to be addressed in order to facilitate biological knowledge discovery in the future.

Epidemic processes in complex networks

OpenAIRE

Pastor Satorras, Romualdo; Castellano, Claudio; Van Mieghem, Piet; Vespignani, Alessandro

2015-01-01

In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world networks have a profound impact on the behavior of equilibrium and nonequilibrium phenomena occurring in various systems, and the study of epidemic spreading is central to our understanding of the unfolding of dynamical processes in complex networks. The t...

1-Methyl-5-Nitrotetrazole and 2-Methyl-5-Nitrotetrazole. Part 1. Synthesis, Characterisation and Detection, and Molecular Complex

Science.gov (United States)

1980-06-01

sulfate pentahydrate (0.5 g) in water (120 cm3) was added dropwise, over a period of 90 minutes, to a stirred solution of sodium nitrite (42.4 g) in...nltrotetrazole (2) via Diazotlsation of 6 A solution of 6 (2.00 g), 98% sulfuric acid (4.0 cm3) and cupric sulfat . pentahydrate (0.4 g) in water (60...from 5 was much cleaner. A further intriguing observation is that the conversion of 5 to 1 is catalysed by copper ions whereas that of 6 to 2 is not

A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions

Science.gov (United States)

Koorehdavoudi, Hana; Bogdan, Paul

2016-06-01

Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Science.gov (United States)

Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

Science.gov (United States)

Li, Min; Li, Dongyan; Tang, Yu; Wu, Fangxiang; Wang, Jianxin

2017-08-31

Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.

Molecular eyes: proteins that transform light into biological information

NARCIS (Netherlands)

Kennis, J.T.M.; Mathes, T.

2013-01-01

Most biological photoreceptors are protein/cofactor complexes that induce a physiological reaction upon absorption of a photon. Therefore, these proteins represent signal converters that translate light into biological information. Researchers use this property to stimulate and study various

Biological Soft Robotics.

Science.gov (United States)

Feinberg, Adam W

2015-01-01

In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

ChemProt: A disease chemical biology database

DEFF Research Database (Denmark)

Taboureau, Olivier; Oprea, Tudor I.

2013-01-01

The integration of chemistry, biology, and informatics to study drug actions across multiple biological targets, pathways, and biological systems is an emerging paradigm in drug discovery. Rather than reducing a complex system to simplistic models, fields such as chemogenomics and translational...... informatics are seeking to build a holistic model for a better understanding of the drug pharmacology and clinical effects. Here we will present a webserver called ChemProt that can assist, in silico, the drug actions in the context of cellular and disease networks and contribute in the field of disease...... chemical biology, drug repurposing, and off-target effects prediction....

A probabilistic framework for identifying biosignatures using Pathway Complexity

Science.gov (United States)

Marshall, Stuart M.; Murray, Alastair R. G.; Cronin, Leroy

2017-11-01

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes-whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call `Pathway Complexity', that allows us not only to threshold the abiotic-biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Effect of addition of heavy metal ion on decolouration and degradation of azo dye in aqueous solution by gamma irradiation combined with ozone

International Nuclear Information System (INIS)

Lee, M.J.; Jin, J.H.; Nho, Y.C.; Arai, H.

1998-01-01

In decomposition of azo dyes solution by simultaneous application of gamma-ray and ozone treatment, the effect of addition of heavy metal ion upon decolouration and decomposition was studied. Cupric ion was used as a heavy metal ion. For the aqueous solution with and without addition of cupric ion, the degree of decolouration of 552 nm, the changes of pH, the reduction of TOC and BOD were measured as function of dose under condition of fixed concentration of ozone. It appeared that the addition of cupric ion played a positive role in decomposition of azo dye solution, but played a negative role in decolouration

Synthesis, structural, spectroscopic and biological studies of Schiff base complexes

Science.gov (United States)

Diab, M. A.; El-Sonbati, A. Z.; Shoair, A. F.; Eldesoky, A. M.; El-Far, N. M.

2017-08-01

Schiff base ligand 4-((pyridin-2- yl)methyleneamino)-1,2-dihydro-2,3-dimethyl-1-phenylpyrazol-5-one (PDMP) and its complexes were prepared and characterized on the basis of elemental analysis, IR, mass spectra and thermogravimetric analysis. All results confirm that the complexes have 1:1 (M: PMDP) stoichiometric formula [M(PMDP)Cl2H2O ] (M = Cu(II), Co(II), Ni(II) and Mn(II)), [Cd(PMDP)Cl2] and the ligand behaves as a bi/tridentate forming five-membered chelating ring towards the metal ions, bonding through azomethine nitrogen/exocyclic carbonyl oxygen, azomethine pyridine nitrogen and exocyclic carbonyl oxygen. The shift in the band positions of the groups involved in coordination has been utilized to estimate the metal-nitrogen and/or oxygen bond lengths. The complexes of Co(II), Ni(II) and Cu(II) are paramagnetic and the magnetic as well as spectral data suggest octahedral geometry, whereas the Cd(II) complex is tetrahedral. The XRD studies show that both the ligand and its metal complexes (1 and 3) show polycrystalline with crystal structure. Molecular docking was used to predict the binding between PMDP ligand and the receptors. The corrosion inhibition of mild steel in 2 M HCl solution by PDMP was explored utilizing potentiodynamic polarization, electrochemical impedance spectroscopy (EIS) and (EFM) electrochemical frequency modulation method. Potentiodynamic polarization demonstrated that PDMP compound is mixed-type inhibitor. EIS spectra exhibit one capacitive loop and confirm the protective ability. The percentage of inhibition efficiency was found to increase with increasing the inhibitor concentration.

Analytical, Characterization and Stability Studies of Chemicals, Bulk Drugs and Drug Formulations

Science.gov (United States)

1997-10-01

assay, Report No. 933. 19. WR-242511AF, BM19356, 8-[(4-amino-l-methylbutyl)amino]-5-(1-hexyloxy)-6-methoxy- 4-methylquinoline DL- tartrate , assay...colorimetric protein assay based on complexation between bicinchoninic acid and cuprous ion, which results from reduction of cupric ion by a protein, was...amino-l-methylbutyl)amino]-5-(1-hexyloxy)-6-methoxy-4- methylquinoline DL- tartrate , shelf life, 3- and 6-month samplings, Report No. 738; 9-, 12-, 18

Complexity for Artificial Substrates (

NARCIS (Netherlands)

Loke, L.H.L.; Jachowski, N.R.; Bouma, T.J.; Ladle, R.J.; Todd, P.A.

2014-01-01

Physical habitat complexity regulates the structure and function of biological communities, although the mechanisms underlying this relationship remain unclear. Urbanisation, pollution, unsustainable resource exploitation and climate change have resulted in the widespread simplification (and loss)

Molecular Cloning Designer Simulator (MCDS: All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

Directory of Open Access Journals (Sweden)

Zhenyu Shi

2016-12-01

Full Text Available Molecular Cloning Designer Simulator (MCDS is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1 it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2 it can perform a user-defined workflow of cloning steps in a single execution of the software; (3 it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4 it includes experimental information to conveniently guide wet lab work; and (5 it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. Keywords: BioCAD, Genetic engineering software, Molecular cloning software, Synthetic biology, Workflow simulation and management

[Progress in synthetic biology of "973 Funding Program" in China].

Science.gov (United States)

Chen, Guoqiang; Wang, Ying

2015-06-01

This paper reviews progresses made in China from 2011 in areas of "Synthetic Biology" supported by State Basic Research 973 Program. Till the end of 2014, 9 "synthetic biology" projects have been initiated with emphasis on "microbial manufactures" with the 973 Funding Program. Combined with the very recent launch of one project on "mammalian cell synthetic biology" and another on "plant synthetic biology", Chinese "synthetic biology" research reflects its focus on "manufactures" while not giving up efforts on "synthetic biology" of complex systems.

Complex and biofluids: From Maxwell to nowadays

Science.gov (United States)

Misbah, Chaouqi

2009-11-01

Complex fluids are the rule in biology and in many industrial applications. Typical examples are blood, cartilage, and polymer solutions. Unlike water (as well as domestic oils, soft clear drinks, and so on), the law(s) describing the behavior of complex fluids are not yet fully established. The complexity arises from strong coupling between microscopic scales (like the motion of a red blood cell in the case of blood, or a polymer molecule for a polymer solution) and the global scale of the flow (say at the scale of a blood artery, or a channel in laboratory experiments). In this issue entitled Complex and Biofluids a large panel of experimental and theoretical problems of complex fluids is exposed. The topics range from dilute polymer solutions, food products, to biology (blood flow, cell and tissue mechanics). One of the earliest model put forward as an attempt to describe a complex fluid was suggested a long time ago by James Clerk Maxwell (in 1867). Other famous scientists, like Einstein (in 1906), and Taylor (in 1932) have made important contributions to the field, but the topic of complex fluids still continues to pose a formidable challenge to science. This field has known during the past decade an unbelievable upsurge of interest in many branches of science (physics, mechanics, chemistry, biology, medical science, mathematics, and so on). Understanding complex fluids is viewed as one of the biggest challenge of the present century. This synthesis will provide a simple introduction to the topic, summarize the main contribution of this issue, and list major open questions in this field. To cite this article: C. Misbah, C. R. Physique 10 (2009).

Impact of reclamation treatment on the biological activity of soils of the solonetz complex in Western Siberia

Science.gov (United States)

Berezin, L. V.; Khamova, O. F.; Paderina, E. V.; Gindemit, A. M.

2014-11-01

The abundance and activity of the soil microflora were studied in a field experiment with the use of green manure crops to assess the impact of reclamation measures on the biological activity of soils of the solonetz complex. The number of microorganisms in the plow soil horizon increased in the background of the green fallows as compared to the black ones. Coefficients of mineralization, immobilization, and transformation of organic compounds were calculated for different variants of the soil treatment. The value of the mineralization coefficient indicates the intense decomposition of the green manure that entered the soil. In the first year, peas were actively decomposed, while oats, in the second year (aftereffect). The activity of the soil enzymes (invertase, urease, and catalase) was determined. A close relationship between the catalase activity and the intensity of the microbiological processes in the soils was revealed.

Application to biological data

Indian Academy of Sciences (India)

Reduction of dimensionality has emerged as a routine process in modelling complex biological systems. A large number of feature selection techniques have been reported in the literature to improve model performance in terms of accuracy and speed. In the present article an unsupervised feature selection technique is ...

Dominating biological networks.

Directory of Open Access Journals (Sweden)

Tijana Milenković

Full Text Available Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of "biologically central (BC" genes (i.e., their protein products, such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network.To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its "spine" that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks.

Methodology for designing and manufacturing complex biologically inspired soft robotic fluidic actuators: prosthetic hand case study.

Science.gov (United States)

Thompson-Bean, E; Das, R; McDaid, A

2016-10-31

We present a novel methodology for the design and manufacture of complex biologically inspired soft robotic fluidic actuators. The methodology is applied to the design and manufacture of a prosthetic for the hand. Real human hands are scanned to produce a 3D model of a finger, and pneumatic networks are implemented within it to produce a biomimetic bending motion. The finger is then partitioned into material sections, and a genetic algorithm based optimization, using finite element analysis, is employed to discover the optimal material for each section. This is based on two biomimetic performance criteria. Two sets of optimizations using two material sets are performed. Promising optimized material arrangements are fabricated using two techniques to validate the optimization routine, and the fabricated and simulated results are compared. We find that the optimization is successful in producing biomimetic soft robotic fingers and that fabrication of the fingers is possible. Limitations and paths for development are discussed. This methodology can be applied for other fluidic soft robotic devices.

Contemporary issues in evolutionary biology

Indian Academy of Sciences (India)

These discussions included, among others, the possible consequences of nonDNA-based inheritance—epigenetics and cultural evolution, niche construction, and developmental mechanisms on our understanding of the evolutionary process, speciation, complexity in biology, and constructing a formal evolutionary theory.

Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability

Science.gov (United States)

Pathak, Rajesh Kumar; Gupta, Sanjay Mohan; Gaur, Vikram Singh; Pandey, Dinesh

2015-01-01

Abstract In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes. PMID:26484978

ChemProt: a disease chemical biology database

DEFF Research Database (Denmark)

Taboureau, Olivier; Nielsen, Sonny Kim; Audouze, Karine Marie Laure

2011-01-01

Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network...... biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). We assembled more than 700 000 unique chemicals with biological annotation for 30...... evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram...

Prediction of Biomolecular Complexes

KAUST Repository

Vangone, Anna; Oliva, Romina; Cavallo, Luigi; Bonvin, Alexandre M. J. J.

2017-01-01

Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

Prediction of Biomolecular Complexes

KAUST Repository

Vangone, Anna

2017-04-12

Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

Hemoglobin and Myoglobin as Reducing Agents in Biological Systems. Redox Reactions of Globins with Copper and Iron Salts and Complexes.

Science.gov (United States)

Postnikova, G B; Shekhovtsova, E A

2016-12-01

In addition to reversible O2 binding, respiratory proteins of the globin family, hemoglobin (Hb) and myoglobin (Mb), participate in redox reactions with various metal complexes, including biologically significant ones, such as those of copper and iron. HbO 2 and MbO 2 are present in cells in large amounts and, as redox agents, can contribute to maintaining cell redox state and resisting oxidative stress. Divalent copper complexes with high redox potentials (E 0 , 200-600 mV) and high stability constants, such as [Cu(phen) 2 ] 2+ , [Cu(dmphen) 2 ] 2+ , and CuDTA oxidize ferrous heme proteins by the simple outer-sphere electron transfer mechanism through overlapping π-orbitals of the heme and the copper complex. Weaker oxidants, such as Cu2+, CuEDTA, CuNTA, CuCit, CuATP, and CuHis (E 0 ≤ 100-150 mV) react with HbO 2 and MbO 2 through preliminary binding to the protein with substitution of the metal ligands with protein groups and subsequent intramolecular electron transfer in the complex (the site-specific outer-sphere electron transfer mechanism). Oxidation of HbO 2 and MbO 2 by potassium ferricyanide and Fe(3) complexes with NTA, EDTA, CDTA, ATP, 2,3-DPG, citrate, and pyrophosphate PP i proceeds mainly through the simple outer-sphere electron transfer mechanism via the exposed heme edge. According to Marcus theory, the rate of this reaction correlates with the difference in redox potentials of the reagents and their self-exchange rates. For charged reagents, the reaction may be preceded by their nonspecific binding to the protein due to electrostatic interactions. The reactions of LbO 2 with carboxylate Fe complexes, unlike its reactions with ferricyanide, occur via the site-specific outer-sphere electron transfer mechanism, even though the same reagents oxidize structurally similar MbO 2 and cytochrome b 5 via the simple outer-sphere electron transfer mechanism. Of particular biological interest is HbO 2 and MbO 2 transformation into met-forms in the presence

Towards the understanding of network information processing in biology

Science.gov (United States)

Singh, Vijay

Living organisms perform incredibly well in detecting a signal present in the environment. This information processing is achieved near optimally and quite reliably, even though the sources of signals are highly variable and complex. The work in the last few decades has given us a fair understanding of how individual signal processing units like neurons and cell receptors process signals, but the principles of collective information processing on biological networks are far from clear. Information processing in biological networks, like the brain, metabolic circuits, cellular-signaling circuits, etc., involves complex interactions among a large number of units (neurons, receptors). The combinatorially large number of states such a system can exist in makes it impossible to study these systems from the first principles, starting from the interactions between the basic units. The principles of collective information processing on such complex networks can be identified using coarse graining approaches. This could provide insights into the organization and function of complex biological networks. Here I study models of biological networks using continuum dynamics, renormalization, maximum likelihood estimation and information theory. Such coarse graining approaches identify features that are essential for certain processes performed by underlying biological networks. We find that long-range connections in the brain allow for global scale feature detection in a signal. These also suppress the noise and remove any gaps present in the signal. Hierarchical organization with long-range connections leads to large-scale connectivity at low synapse numbers. Time delays can be utilized to separate a mixture of signals with temporal scales. Our observations indicate that the rules in multivariate signal processing are quite different from traditional single unit signal processing.

Cu(II complexes of an ionic liquid-based Schiff base [1-{2-(2-hydroxy benzylidene amino ethyl}-3-methyl­imidazolium]Pf6: Synthesis, characterization and biological activities

Directory of Open Access Journals (Sweden)

Saha Sanjoy

2015-01-01

Full Text Available Two Cu(II complexes of an ionic liquid based Schiff base 1-{2-(2-hydroxybenzylideneamino ethyl}-3-methylimidazolium hexaflurophosphate, were prepared and characterized by different analytical and spectroscopic methods such as elemental analysis, magnetic susceptibility, UV-Vis, IR, NMR and mass spectroscopy. The Schiff base ligand was found to act as a potential bidentate chelating ligand with N, O donor sites and formed 1:2 metal chelates with Cu(II salts. The synthesized Cu(II complexes were tested for biological activity.

Quantum chemical investigation of levofloxacin-boron complexes: A computational approach

Science.gov (United States)

Sayin, Koray; Karakaş, Duran

2018-04-01

Quantum chemical calculations are performed over some boron complexes with levofloxacin. Boron complex with fluorine atoms are optimized at three different methods (HF, B3LYP and M062X) with 6-31 + G(d) basis set. The best level is determined as M062X/6-31 + G(d) by comparison of experimental and calculated results of complex (1). The other complexes are optimized by using the best level. Structural properties, IR and NMR spectrum are examined in detail. Biological activities of mentioned complexes are investigated by some quantum chemical descriptors and molecular docking analyses. As a result, biological activities of complex (2) and (4) are close to each other and higher than those of other complexes. Additionally, NLO properties of mentioned complexes are investigated by some quantum chemical parameters. It is found that complex (3) is the best candidate for NLO applications.

Seasonal allergic rhinitis and systems biology-oriented biomarker discovery

NARCIS (Netherlands)

Baars, E.W.; Nierop, A.F.M.; Savelkoul, H.F.J.

2015-01-01

There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems

The mathematics and mechanics of biological growth

CERN Document Server

Goriely, Alain

2017-01-01

This monograph presents a general mechanical theory for biological growth. It provides both a conceptual and a technical foundation for the understanding and analysis of problems arising in biology and physiology. The theory and methods is illustrated on a wide range of examples and applications. A process of extreme complexity, growth plays a fundamental role in many biological processes and is considered to be the hallmark of life itself. Its description has been one of the fundamental problems of life sciences, but until recently, it has not attracted much attention from mathematicians, physicists, and engineers. The author herein presents the first major technical monograph on the problem of growth since D’Arcy Wentworth Thompson’s 1917 book On Growth and Form. The emphasis of the book is on the proper mathematical formulation of growth kinematics and mechanics. Accordingly, the discussion proceeds in order of complexity and the book is divided into five parts. First, a general introduction on the pro...

Evolution, Entropy, & Biological Information

Science.gov (United States)

Peterson, Jacob

2014-01-01

A logical question to be expected from students: "How could life develop, that is, change, evolve from simple, primitive organisms into the complex forms existing today, while at the same time there is a generally observed decline and disorganization--the second law of thermodynamics?" The explanations in biology textbooks relied upon by…

An efficient grid layout algorithm for biological networks utilizing various biological attributes

Directory of Open Access Journals (Sweden)

Kato Mitsuru

2007-03-01

Full Text Available Abstract Background Clearly visualized biopathways provide a great help in understanding biological systems. However, manual drawing of large-scale biopathways is time consuming. We proposed a grid layout algorithm that can handle gene-regulatory networks and signal transduction pathways by considering edge-edge crossing, node-edge crossing, distance measure between nodes, and subcellular localization information from Gene Ontology. Consequently, the layout algorithm succeeded in drastically reducing these crossings in the apoptosis model. However, for larger-scale networks, we encountered three problems: (i the initial layout is often very far from any local optimum because nodes are initially placed at random, (ii from a biological viewpoint, human layouts still exceed automatic layouts in understanding because except subcellular localization, it does not fully utilize biological information of pathways, and (iii it employs a local search strategy in which the neighborhood is obtained by moving one node at each step, and automatic layouts suggest that simultaneous movements of multiple nodes are necessary for better layouts, while such extension may face worsening the time complexity. Results We propose a new grid layout algorithm. To address problem (i, we devised a new force-directed algorithm whose output is suitable as the initial layout. For (ii, we considered that an appropriate alignment of nodes having the same biological attribute is one of the most important factors of the comprehension, and we defined a new score function that gives an advantage to such configurations. For solving problem (iii, we developed a search strategy that considers swapping nodes as well as moving a node, while keeping the order of the time complexity. Though a naïve implementation increases by one order, the time complexity, we solved this difficulty by devising a method that caches differences between scores of a layout and its possible updates

Synthesis of technetium-99m labeled clinafloxacin (99mTc-CNN) complex and biological evaluation as a potential Staphylococcus aureus infection imaging agent

International Nuclear Information System (INIS)

Syed Qaiser Shah; Muhammad Rafiullah Khan

2011-01-01

In the present study synthesis of the 99m Tc-CNN complex and its efficacy as a prospective Staphylococcus aureus (S. aureus) infection imaging agent was assessed. The 99m Tc-CNN complex was characterized in terms of stability in saline, serum, in vitro binding with S. aureus and in vivo percent absorption in male Wister rats (MWR) infected with live and heat killed S. aureus. Radiochemically the 99m Tc-CNN complex showed stable behavior in saline and serum at different intervals. At 30 min after reconstitution the complex showed maximum radiochemical purity (RCP) yield of 97.55 ± 0.22%. The RCP yield decreased to 90.50 ± 0.18% within 240 min. In serum, 18.15% unwanted side product was appeared within 16 h of the incubation. In vitro saturated binding with S. aureus was observed at different intervals with a 62.00% maximum at 90 min. Normal percent in vivo uptake was observed in MWR artificially infected with live S. aureus with a five times higher in the infected muscle as compared to the inflamed and normal muscles. No difference in the percent uptake of the complex in MWR infected with heat killed S. aureus in the infected, inflamed and normal muscles were observed. Based on the promising in vitro and in vivo radiochemical and biological characteristics, we recommend the 99m Tc-CNN complex for in vivo localization of the S. aureus infectious foci. (author)

Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

Directory of Open Access Journals (Sweden)

Shuo Gu

2017-01-01

Full Text Available With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective.

Science.gov (United States)

Gu, Shuo; Pei, Jianfeng

2017-01-01

With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

Deciphering the language between biological and synthetic materials

Directory of Open Access Journals (Sweden)

Paolo A. Netti

2014-06-01

Full Text Available Chemical signals propagating through aqueous environment are at the basis of the language utilized by living systems to exchange information. In the last years, molecular biology has partly disclosed the grammar and the syntax of this complex language revealing the fascinating world of molecular communication that is the foundation of biological development.

Application of E-infinity theory to biology

International Nuclear Information System (INIS)

He Jihuan

2006-01-01

Albert Einstein combined continuous space and time into his special relativity, El-Naschie discovered the transfinite discontinuity of space-time in his E-infinity theory where infinity of dimensions was created. We find a partner of both space-time and E-infinity in biology. In our theory, the number of cells in an organism endows an additional dimension in biology, leading to explanation of many complex phenomena

Flexible automated approach for quantitative liquid handling of complex biological samples.

Science.gov (United States)

Palandra, Joe; Weller, David; Hudson, Gary; Li, Jeff; Osgood, Sarah; Hudson, Emily; Zhong, Min; Buchholz, Lisa; Cohen, Lucinda H

2007-11-01

A fully automated protein precipitation technique for biological sample preparation has been developed for the quantitation of drugs in various biological matrixes. All liquid handling during sample preparation was automated using a Hamilton MicroLab Star Robotic workstation, which included the preparation of standards and controls from a Watson laboratory information management system generated work list, shaking of 96-well plates, and vacuum application. Processing time is less than 30 s per sample or approximately 45 min per 96-well plate, which is then immediately ready for injection onto an LC-MS/MS system. An overview of the process workflow is discussed, including the software development. Validation data are also provided, including specific liquid class data as well as comparative data of automated vs manual preparation using both quality controls and actual sample data. The efficiencies gained from this automated approach are described.

Real-Time Tracking the Synthesis and Degradation of Albumin in Complex Biological Systems with a near-Infrared Fluorescent Probe.

Science.gov (United States)

Jin, Qiang; Feng, Lei; Zhang, Shui-Jun; Wang, Dan-Dan; Wang, Fang-Jun; Zhang, Yi; Cui, Jing-Nan; Guo, Wen-Zhi; Ge, Guang-Bo; Yang, Ling

2017-09-19

In this study, a novel fluorescent detection system for biological sensing of human albumin (HA) was developed on the basis of the pseudoesterase activity and substrate preference of HA. The designed near-infrared (NIR) fluorescent probe (DDAP) could be effectively hydrolyzed by HA, accompanied by significant changes in both color and fluorescence spectrum. The sensing mechanism was fully investigated by fluorescence spectroscopy, NMR, and mass spectra. DDAP exhibited excellent selectivity and sensitivity toward HA over a variety of human plasma proteins, hydrolases, and abundant biomolecules found in human body. The probe has been successfully applied to measure native HA in diluted plasma samples and the secreted HA in the hepatocyte culture supernatant. DDAP has also been used for fluorescence imaging of HA reabsorption in living renal cells, and the results show that the probe exhibits good cell permeability, low cytotoxicity and high imaging resolution. Furthermore, DDAP has been successfully used for real-time tracking the uptaking and degradation of albumin in ex vivo mouse kidney models for the first time. All these results clearly demonstrated that DDAP-based assay held great promise for real-time sensing and tracking HA in complex biological systems, which would be very useful for basic researches and clinical diagnosis of HA-associated diseases.

Failure Analysis Techniques for the Evaluation of Electrical and Electronic Components in Aircraft Accident Investigations

Science.gov (United States)

1990-08-01

Buffering agent Cupric sulfate CuSO4 Stain (Copper Subsulfate) Cupric nitrate Cu(NO 3 ) 2 Constituent preferential (Copper Nitrate) silicon etch...hypophosphite Sodium potassium NaKC4 H4 O 6 . H Z 0 Buffer used in silicon tartrate crystal studies Sodium silicate Na 2 SiO3 9H2 0 Etchant; coater Sodium

Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing.

Science.gov (United States)

Chakravarti, Deboki; Cho, Jang Hwan; Weinberg, Benjamin H; Wong, Nicole M; Wong, Wilson W

2016-04-18

Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad and vital role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when developing systems around living cells.

Development of Composite Spectrophotometric Procedures for the Analysis of Low-Alloy Steels and of Aluminum and Its Alloys

Science.gov (United States)

1952-11-01

COPPER lb Although copper can be determined by measurement of the blue cupric ammonia complex, the reaction is not very sensitive and is subject to...alkaline solution of the sample con- taining tartrate , provided a means of separation of copper by extraction of WADO TR 52-246 1 the copper bensoinoximate...potassium tartrate ), and sodium hydroxide solution added to ad- just the pH within the range ll3 to 12-3. After adding alpha-benzoinoxime the mixture was

Protein scaffolds and higher-order complexes in synthetic biology

NARCIS (Netherlands)

den Hamer, A.; Rosier, B.J.H.M.; Brunsveld, L.; de Greef, T.F.A.; Ryadnov, M.; Brunsveld, L.; Suga, H.

2017-01-01

Interactions between proteins control molecular functions such as signalling or metabolic activity. Assembly of proteins via scaffold proteins or in higher-order complexes is a key regulatory mechanism. Understanding and functionally applying this concept requires the construction, study, and

Disordered Plamonics and Complex Metamaterials

KAUST Repository

Gongora, J. S. Totero

2017-01-01

Complex systems are ensembles of interconnected elements where mutual interaction and an optimized amount of disorder produce advanced functionalities. These systems are abundant in our daily experience: typical examples are the brain, biological

Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

Science.gov (United States)

Degrazio, Dominick

Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

A comprehensive in vitro biological investigation of metal complexes ...

African Journals Online (AJOL)

Md. Mahabob Ullah Mazumder

... Journal of Medicine journal homepage: http://www.elsevier.com/locate/ajme .... two new complexes containing Fe (III) and Mo(VI) of two tridentate ONO donor · sets ligands. Der Chem Sin. .... Pharmaceuticals (Basel). 2014;7(4):453–463. 13.

The Physics of Proteins An Introduction to Biological Physics and Molecular Biophysics

CERN Document Server

Frauenfelder, Hans; Chan, Winnie S

2010-01-01

Physics and the life sciences have established new connections within the past few decades, resulting in biological physics as an established subfield with strong groups working in many physics departments. These interactions between physics and biology form a two-way street with physics providing new tools and concepts for understanding life, while biological systems can yield new insights into the physics of complex systems. To address the challenges of this interdisciplinary area, The Physics of Proteins: An Introduction to Biological Physics and Molecular Biophysics is divided into three interconnected sections. In Parts I and II, early chapters introduce the terminology and describe the main biological systems that physicists will encounter. Similarities between biomolecules, glasses, and solids are stressed with an emphasis on the fundamental concepts of living systems. The central section (Parts III and IV) delves into the dynamics of complex systems. A main theme is the realization that biological sys...

Leveraging advances in biology to design biomaterials

Science.gov (United States)

Darnell, Max; Mooney, David J.

2017-12-01

Biomaterials have dramatically increased in functionality and complexity, allowing unprecedented control over the cells that interact with them. From these engineering advances arises the prospect of improved biomaterial-based therapies, yet practical constraints favour simplicity. Tools from the biology community are enabling high-resolution and high-throughput bioassays that, if incorporated into a biomaterial design framework, could help achieve unprecedented functionality while minimizing the complexity of designs by identifying the most important material parameters and biological outputs. However, to avoid data explosions and to effectively match the information content of an assay with the goal of the experiment, material screens and bioassays must be arranged in specific ways. By borrowing methods to design experiments and workflows from the bioprocess engineering community, we outline a framework for the incorporation of next-generation bioassays into biomaterials design to effectively optimize function while minimizing complexity. This framework can inspire biomaterials designs that maximize functionality and translatability.

Measurement Frontiers in Molecular Biology

Science.gov (United States)

Laderman, Stephen

2009-03-01

Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

Materials Manufactured from 3D Printed Synthetic Biology Arrays

Science.gov (United States)

Gentry, Diana; Micks, Ashley

2013-01-01

Many complex, biologically-derived materials have extremely useful properties (think wood or silk), but are unsuitable for space-related applications due to production, manufacturing, or processing limitations. Large-scale ecosystem-based production, such as raising and harvesting trees for wood, is impractical in a self-contained habitat such as a space station or potential Mars colony. Manufacturing requirements, such as the specialized equipment needed to harvest and process cotton, add too much upmass for current launch technology. Cells in nature are already highly specialized for making complex biological materials on a micro scale. We envision combining these strengths with the recently emergent technologies of synthetic biology and 3D printing to create 3D-structured arrays of cells that are bioengineered to secrete different materials in a specified three-dimensional pattern.

New and Old Aspects of Complexity in Modern Research

CERN Document Server

Musaev, Djamaladdin

2012-01-01

Complexity occurs in biological and synthetic systems alike.  This general phenomenon has been addressed in recent publications by investigators in disciplines ranging from chemistry and biology to psychology and philosophy.  Studies of complexity for molecular scientists have focussed on breaking symmetry, dissipative processes, and emergence.  Investigators in the social and medical sciences have focused on neurophenomenology, cognitive approaches and self-consciousness.  Complexity in both structure and function is inherent in many scientific disciplines of current significance and also in technologies of current importance that are rapidly evolving to address global societal needs.  Several of these multifaceted scientific disciplines are addressed in this book including complexity from the general and philosophical perspective, magnetic phenomena, control of self assembly and function in large multicomponent clusters, application of theory to probe structure and mechanism in highly complex molecular...

Technetium complexation by macrocyclic compounds

International Nuclear Information System (INIS)

Li Fan Yu.

1983-01-01

Research in nuclear medicine are directed towards the labelling of biological molecules, however, sup(99m)Tc does not show sufficient affinity for these molecules. The aim of this study was to evaluate the ability of macrocyclic compounds to bind strongly technetium in order to be used as complexation intermediate. The reducing agents used were a stannous complex and sodium dithionite. Cryptates and polyesters are not good complexing agents. They form two complexes: a 2:1 sandwich complex or 3:2 and a 1:1 complex. Cyclams are good complexing agents for technetium their complexations strength was determined by competition with pyrophosphate, gluconate and DTPA. Using the method of ligand exchange, the oxidation state of technetium in the Tc-cyclam complex was IV or V. They are 1:1 cationic complexes, the complex charge is +1. The biodistribution in rats of labelling solutions containing (cyclam 14 ane N 4 ) C 12 H 25 shows a good urinary excretion without intoxication risks [fr

STRUCTURES AND BIOLOGICAL ACTIVITY OF CUPROPHYLLINS

Directory of Open Access Journals (Sweden)

Martynov A.V.

2017-06-01

Full Text Available Chlorophylls (a, b are the porphyrin compounds and most common chemical in the plant’s world. In fact, these compounds are an obligatory intermediate product both in energy metabolism and in plant catabolism. At the same time, currently there are few pharmaceutical preparations on the pharmaceutical market based on chlorophylls. Dyes based on hydrolyzed chlorophyll are successfully used in the food industry. Commercial chlorophylline is a copper complex of hydrolyzed chlorophylls. As shown earlier in TLC, the chlorophyllin mixture contains a large number of different compounds. It is like water-soluble saponified derivatives in the form of sodium-magnesium complexes, and similar structures in the form of a complex with copper. The latter are more brightly colored, soluble in water and widely used as coloring agents in cooking. In this case, if the initial chlorophyll was not found to have a pronounced biological activity, the substituted derivatives in the form of copper complexes possessed a number of new unique biological properties. Non-hydrolyzed hydrophobic cuprophylline obtained from eucalyptus leaves possessed high antimicrobial activity to most strains of staphylococci, inclusion resistant to antimicrobials and multiresistant strains. This drug is called Chlorophyllipt, it is allowed to be used as a medicinal product and is one of the oldest antibacterial drugs from plants on the market. It is marketed as ethanoic and oily solutions for topical use, and as an alcohol solution for intravenous injections. Its main purpose is the fight against staphylococcal infections. Recently, found that the oral administration of chlorophyllipt activates cellular immunity and indirectly exhibits antiviral activity. Another compound of cuprophyllin is water-soluble chlorophyllin. Some authors show the variability of the structure and biological activity of cuprophyllins. Different derivatives of chlorophyll have different biological activity

Multi-level and hybrid modelling approaches for systems biology.

Science.gov (United States)

Bardini, R; Politano, G; Benso, A; Di Carlo, S

2017-01-01

During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

Reconstruction of biological networks based on life science data integration.

Science.gov (United States)

Kormeier, Benjamin; Hippe, Klaus; Arrigo, Patrizio; Töpel, Thoralf; Janowski, Sebastian; Hofestädt, Ralf

2010-10-27

For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH--an integration toolkit for building life science data warehouses, CardioVINEdb--a information system for biological data in cardiovascular-disease and VANESA--a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

Systems Biology of the Fluxome

Directory of Open Access Journals (Sweden)

Miguel A. Aon

2015-07-01

Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

Morphogenesis and pattern formation in biological systems experiments and models

CERN Document Server

Noji, Sumihare; Ueno, Naoto; Maini, Philip

2003-01-01

A central goal of current biology is to decode the mechanisms that underlie the processes of morphogenesis and pattern formation. Concerned with the analysis of those phenomena, this book covers a broad range of research fields, including developmental biology, molecular biology, plant morphogenesis, ecology, epidemiology, medicine, paleontology, evolutionary biology, mathematical biology, and computational biology. In Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, experimental and theoretical aspects of biology are integrated for the construction and investigation of models of complex processes. This collection of articles on the latest advances by leading researchers not only brings together work from a wide spectrum of disciplines, but also provides a stepping-stone to the creation of new areas of discovery.

The Mediator Complex and Lipid Metabolism

OpenAIRE

Zhang, Yi; Xiaoli,; Zhao, Xiaoping; Yang, Fajun

2013-01-01

The precise control of gene expression is essential for all biological processes. In addition to DNA-binding transcription factors, numerous transcription cofactors contribute another layer of regulation of gene transcription in eukaryotic cells. One of such transcription cofactors is the highly conserved Mediator complex, which has multiple subunits and is involved in various biological processes through directly interacting with relevant transcription factors. Although the current understan...

Frontiers of NMR in Molecular Biology

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-08-25

NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

How do biological systems escape 'chaotic' state?

Indian Academy of Sciences (India)

B J Rao

2018-02-13

Feb 13, 2018 ... Lorencova 2016), sociology, physics, computer science, economics and even biology ... dynamic complexity associated with them at multiple levels? .... Social anthropology and the science of chaos (Oxford: Berghahn Books).

Plant Systems Biology at the Single-Cell Level.

Science.gov (United States)

Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

2017-11-01

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

the organizing principle at the interface of biological (dis)order

Indian Academy of Sciences (India)

Complexity: the organizing principle at the interface of biological (dis)order ... in a quantifiable fashion, as the amount of information, an informatic template ... We propose that the complexity of living systems can be understood through two ...

VISUALIZATION OF BIOLOGICAL TISSUE IMPEDANCE PARAMETERS

Directory of Open Access Journals (Sweden)

V. I. Bankov

2016-01-01

Full Text Available Objective. Investigation the opportunity for measurement of biological tissue impedance to visualize its parameters.Materials and methods. Studies were undertook on the experimental facility, consists of registrating measuring cell, constructed from flat inductors system, formed in oscillatory circuit, herewith investigated biological tissue is the part of this oscillatory circuit. An excitation of oscillatory circuit fulfilled by means of exciter inductor which forms impulse complex modulated electromagnetic field (ICM EMF. The measurement process and visualizations provided by set of certificated instruments: a digital oscillograph AKTAKOM ADS-2221MV, a digital generator АКТАКОМ AWG-4150 (both with software and a gauge RLC E7-22. Comparative dynamic studies of fixed volume and weight pig’s blood, adipose tissue, muscular tissue impedance were conducted by contact versus contactless methods. Contactless method in contrast to contact method gives opportunity to obtain the real morphological visualization of biological tissue irrespective of their nature.Results. Comparison of contact and contactless methods of impedance measurement shows that the inductance to capacitance ratio X(L / X(C was equal: 17 – for muscular tissue, 4 – for blood, 1 – for adipose tissue. It demonstrates the technical correspondence of both impedance registration methods. If propose the base relevance of X (L and X (C parameters for biological tissue impedance so contactless measurement method for sure shows insulating properties of adipose tissue and high conductivity for blood and muscular tissue in fixed volume-weight parameters. Registration of biological tissue impedance complex parameters by contactless method with the help of induced ICM EMF in fixed volume of biological tissue uncovers the most important informative volumes to characterize morphofunctional condition of biological tissue namely X (L / X (C.Conclusion. Contactless method of biological

Optical sensors and their applications for probing biological systems

DEFF Research Database (Denmark)

Palanco, Marta Espina

There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant and mammal......There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant...... of a trapped cell. The project could provide new insights into the desired biosensor for future membrane-protein cell studies....

Agent-based modelling in synthetic biology.

Science.gov (United States)

Gorochowski, Thomas E

2016-11-30

Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. © 2016 The Author(s).

Synthesis of 99mTcV ≡ N-Pazufloxacin dithiocarbamate complex and biological evaluation in Wister rats artificially infected with Escherichia coli

International Nuclear Information System (INIS)

Syed Qaiser Shah; Muhammad Rafiullah Khan

2011-01-01

99m Tc ≡ N-Pazufloxacin dithiocarbamate ( 99m Tc ≡ N-PZN) complex was synthesized through the [ 99m Tc ≡ N] 2+ core and its aptness was radiochemically and biologically evaluated in terms of radiochemical purity (RCP) in saline, in vitro stability in serum, in vitro bacterial uptake and percent in vivo uptake in male Wister rats (MWR) artificially infected with alive and heat killed Escherichia coli (E. coli). The 99m Tc ≡ N-PZN complex showed more than 90% RCP up to 4 h after reconstitution in normal saline at room temperature with a maximum RCP value of 98.40 ± 0.28% (at 30 min). At 37 deg C in serum the complex showed stable behaviour up to 4 h with the appearance of 15.95% undesirable by products within 16 h of the incubation. The complex showed saturated in vitro binding with E. coli with a maximum uptake of 74.25 ± 0.50% (at 90 min). Normal biodistribution behaviour was noted with a sixfold higher accumulation in the muscle of the MWR, artificially infected with live E. coli as compared to the MWR infected with heat killed E. coli, inflamed and normal muscle. The high RCP in saline, elevated in vitro stability in serum, saturated in vitro binding with E. coli and the sixfold higher accumulation in the infected (live) muscle of the MWR as compared to the inflamed and normal muscle, recognized the aptness of the 99m Tc ≡ N-PZND complex as a prospective E. coli in vivo infection radiotracer. (author)

A systems biology approach to studying Tai Chi, physiological complexity and healthy aging: design and rationale of a pragmatic randomized controlled trial.

Science.gov (United States)

Wayne, Peter M; Manor, Brad; Novak, Vera; Costa, Madelena D; Hausdorff, Jeffrey M; Goldberger, Ary L; Ahn, Andrew C; Yeh, Gloria Y; Peng, C-K; Lough, Matthew; Davis, Roger B; Quilty, Mary T; Lipsitz, Lewis A

2013-01-01

Aging is typically associated with progressive multi-system impairment that leads to decreased physical and cognitive function and reduced adaptability to stress. Due to its capacity to characterize complex dynamics within and between physiological systems, the emerging field of complex systems biology and its array of quantitative tools show great promise for improving our understanding of aging, monitoring senescence, and providing biomarkers for evaluating novel interventions, including promising mind-body exercises, that treat age-related disease and promote healthy aging. An ongoing, two-arm randomized clinical trial is evaluating the potential of Tai Chi mind-body exercise to attenuate age-related loss of complexity. A total of 60 Tai Chi-naïve healthy older adults (aged 50-79) are being randomized to either six months of Tai Chi training (n=30), or to a waitlist control receiving unaltered usual medical care (n=30). Our primary outcomes are complexity-based measures of heart rate, standing postural sway and gait stride interval dynamics assessed at 3 and 6months. Multiscale entropy and detrended fluctuation analysis are used as entropy- and fractal-based measures of complexity, respectively. Secondary outcomes include measures of physical and psychological function and tests of physiological adaptability also assessed at 3 and 6months. Results of this study may lead to novel biomarkers that help us monitor and understand the physiological processes of aging and explore the potential benefits of Tai Chi and related mind-body exercises for healthy aging. Copyright © 2012 Elsevier Inc. All rights reserved.

Biology and Mechanics of Blood Flows Part I: Biology

CERN Document Server

Thiriet, Marc

2008-01-01

Biology and Mechanics of Blood Flows presents the basic knowledge and state-of-the-art techniques necessary to carry out investigations of the cardiovascular system using modeling and simulation. Part I of this two-volume sequence, Biology, addresses the nanoscopic and microscopic scales. The nanoscale corresponds to the scale of biochemical reaction cascades involved in cell adaptation to mechanical stresses among other stimuli. The microscale is the scale of stress-induced tissue remodeling associated with acute or chronic loadings. The cardiovascular system, like any physiological system, has a complicated three-dimensional structure and composition. Its time dependent behavior is regulated, and this complex system has many components. In this authoritative work, the author provides a survey of relevant cell components and processes, with detailed coverage of the electrical and mechanical behaviors of vascular cells, tissues, and organs. Because the behaviors of vascular cells and tissues are tightly coupl...

Arbitrary protein−protein docking targets biologically relevant interfaces

International Nuclear Information System (INIS)

Martin, Juliette; Lavery, Richard

2012-01-01

Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking using PEBP (Phosphatidylethanolamine binding

Arbitrary protein−protein docking targets biologically relevant interfaces

Directory of Open Access Journals (Sweden)

Martin Juliette

2012-05-01

Full Text Available Abstract Background Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. Results In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking

21 CFR 184.1261 - Copper sulfate.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Copper sulfate. 184.1261 Section 184.1261 Food and... Substances Affirmed as GRAS § 184.1261 Copper sulfate. (a) Copper sulfate (cupric sulfate, CuSO4·5H2O, CAS... the reaction of sulfuric acid with cupric oxide or with copper metal. (b) The ingredient must be of a...

Application of micro-thin-layer chromatography as a simple fractionation tool for fast screening of raw extracts derived from complex biological, pharmaceutical and environmental samples

International Nuclear Information System (INIS)

Zarzycki, Pawel K.; Slaczka, Magdalena M.; Zarzycka, Magdalena B.; Wlodarczyk, Elzbieta; Baran, Michal J.

2011-01-01

The main goal of present paper is to demonstrate the separation and detection capability of micro-TLC technique involving simple one step liquid extraction protocols of complex materials without multi-steps sample pre-purification. In the present studies target components (cyanobacteria pigments, lipids and fullerenes) were isolated from heavy loading complex matrices including spirulina dried cells, birds' feathers and fatty oils as well as soot samples derived from biomass fuel and fossils-fired home heating systems. In each case isocratic separation protocol involving less that 1 mL of one component or binary mixture mobile phases can be completed within time of 5-8 min. Sensitive detection of components of interest was performed via fluorescence or staining techniques using iodine or phosphomolybdic acid. Described methodology can be applied for fast fractionation or screening of whole range of target substances as well as chemo-taxonomic studies and fingerprinting of complex mixtures, which are present in raw biological or environmental samples.

Application of micro-thin-layer chromatography as a simple fractionation tool for fast screening of raw extracts derived from complex biological, pharmaceutical and environmental samples

Energy Technology Data Exchange (ETDEWEB)

Zarzycki, Pawel K., E-mail: pawel_k_z@hotmail.com [Section of Toxicology and Bioanalytics, Department of Civil and Environmental Engineering, Koszalin University of Technology, Sniadeckich 2, 75-453 Koszalin (Poland); Slaczka, Magdalena M.; Zarzycka, Magdalena B.; Wlodarczyk, Elzbieta; Baran, Michal J. [Section of Toxicology and Bioanalytics, Department of Civil and Environmental Engineering, Koszalin University of Technology, Sniadeckich 2, 75-453 Koszalin (Poland)

2011-03-04

The main goal of present paper is to demonstrate the separation and detection capability of micro-TLC technique involving simple one step liquid extraction protocols of complex materials without multi-steps sample pre-purification. In the present studies target components (cyanobacteria pigments, lipids and fullerenes) were isolated from heavy loading complex matrices including spirulina dried cells, birds' feathers and fatty oils as well as soot samples derived from biomass fuel and fossils-fired home heating systems. In each case isocratic separation protocol involving less that 1 mL of one component or binary mixture mobile phases can be completed within time of 5-8 min. Sensitive detection of components of interest was performed via fluorescence or staining techniques using iodine or phosphomolybdic acid. Described methodology can be applied for fast fractionation or screening of whole range of target substances as well as chemo-taxonomic studies and fingerprinting of complex mixtures, which are present in raw biological or environmental samples.

Labeling of thymidine analog with an organometallic complex of technetium-99m for diagnostic of cancer: radiochemical and biological evaluation

International Nuclear Information System (INIS)

Santos, Rodrigo Luis Silva Ribeiro

2007-01-01

Thymidine analogs have been labeled with different radioisotopes due to their potential in monitoring the uncontrollable cell proliferation. Considering that the radioisotopes technetium-99m still keep a privileged position as a marker due to its chemical and nuclear properties, this dissertation was constituted by the developed of a new technique of labeling of thymidine analog with 99m Tc, by means of the organometallic complex. The aims of this research were: synthesis of the organometallic complex technetium-99m-carbonyl, thymidine labeling with this precursor, evaluation of stability, and radiochemical e biological evaluation with healthy and tumor-bearing animals. The preparation of the organometallic precursor, using the CO gas, was easily achieved, as well as the labeling of thymidine with this precursor, resulting itself a radiochemical pureness of ≥ 97% and ≥ 94%, respectively. Chromatography systems with good levels of trustworthiness were used, ensuring the qualification and quantification of the radiochemical samples. The result of in vitro testing of lipophilicity disclosed that the radiolabeled complex is hydrophilic, with a partition coefficient (log P) of -1.48. The precursor complex and the radiolabeled have good radiochemical stability up to 6 h in room temperature. The cysteine and histidine challenge indicated losses between 8 and 1 1 % for concentrations until 300 mM. The biodistribution assay in healthy mice revealed rapid blood clearance and low uptake by general organs with renal and hepatobiliary excretion. The tumor concentration was low with values of 0.28 and 0.18 %ID/g for lung and breast cancer, respectively. The results imply more studies in other tumor models or the modification of the structure of the organic molecule that act like ligand. (author)

The Origin and Evolution of Complex Enough Systems in Biology

OpenAIRE

Brändas, Erkki

2017-01-01

Recent criticisms of Neo-Darwinism are considered and disputed within the setting of recent advances in chemical physics. A related query, viz., the ontological thesis, that everything is physical, confronts a crucial test on the validity of reductionism as a fundamental approach to science.  While traditional ‘physicalism’ interprets evolution as a sequence of physical accidents governed by the second law of thermodynamics, the concepts of biology concern processes that owe their goal-direct...

Synthesis, characterization and biological profile of metal and azo-metal complexes of embelin

Directory of Open Access Journals (Sweden)

R. Aravindhan

2014-12-01

Full Text Available The present study emphasizes synthesis and bioprofiling of embelin, embelin-metal (EM and embelin-azo-metal (EAM complexes in detail. EM complexes were prepared using pure embelin and d-block transition elements, namely Mn, Fe, Co, Ni, Cu, and Zn. Similarly, EAM complexes were synthesized using phenyl azo-embelin with the said transition metals. Embelin, EM, and EAM complexes were subjected to ultra violet visible spectroscopy, Fourier transform infrared spectroscopy, nuclear magnetic resonance, electrospray ionization mass spectrometry, thermogravimetric analysis, carbon hydrogen nitrogen sulfur analysis. With regard to bioprofiling, the test complexes were studied for the antioxidant and antimicrobial activities. Results revealed that the prepared EM and EAM complexes form octahedral complexes with embelin with the yield in the range of 45–75%. All the instrumental analyses authenticate the interaction of metals with bidentate embelin through its enolic and quinonic oxygen atoms as [M(Emb2(H2O2]H2O and [M(Emb-Azo2(H2O2]. The antioxidant profile studies suggested that upon complexation with metals, the free radical scavenging activity of embelin reduced significantly. But, with regard to antimicrobial activity, cobalt and nickel embelin complexes displayed>80% growth inhibition in comparison with embelin alone. The hemolytic activity studies suggested that both embelin and the metal complexes are non-hemolytic. The reason for the reduction in antioxidant and an increase in antimicrobial activities were discussed in detail.

Life Is Simple—Biologic Complexity Is an Epiphenomenon

Directory of Open Access Journals (Sweden)

John S. Torday

2016-04-01

Full Text Available Life originated from unicellular organisms by circumventing the Second Law of Thermodynamics using the First Principles of Physiology, namely negentropy, chemiosmosis and homeostatic regulation of calcium and lipids. It is hypothesized that multicellular organisms are merely contrivances or tools, used by unicellular organisms as agents for the acquisition of epigenetic inheritance. The First Principles of Physiology, which initially evolved in unicellular organisms are the exapted constraints that maintain, sustain and perpetuate that process. To ensure fidelity to this mechanism, we must return to the first principles of the unicellular state as the determinants of the primary level of selection pressure during the life cycle. The power of this approach is reflected by examples of its predictive value. This perspective on life is a “game changer”, mechanistically rendering transparent many dogmas, teleologies and tautologies that constrain the current descriptive view of Biology.

Micro/nanofabricated environments for synthetic biology.

Science.gov (United States)

Collier, C Patrick; Simpson, Michael L

2011-08-01

A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.

Systems Biology and Stem Cell Pluripotency

DEFF Research Database (Denmark)

Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

2016-01-01

Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

ADAM: analysis of discrete models of biological systems using computer algebra.

Science.gov (United States)

Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

2011-07-20

Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web

Synthetic biology and its promises

Directory of Open Access Journals (Sweden)

José Manuel De Cózar Escalante

2016-12-01

Full Text Available Synthetic biology is a new science and emerging technology, or rather a technoscience, which converges with others such as nanotechnology, information technology, robotics, artificial intelligence and neuroscience. All have common features that could have highly concerning social and environmental impacts. With its ambitious goals of controlling complexity, redesigning and creating new living entities, synthetic biology perfectly exemplifies the new bioeconomic reality. This requires expanding the focus of the discussion beyond the limited comparative analysis of risks and benefits, to address uncertainties, reassign responsibilities and initiate a thorough social assessment of what is at stake.

An Introductory Review of Parallel Independent Component Analysis (p-ICA and a Guide to Applying p-ICA to Genetic Data and Imaging Phenotypes to Identify Disease-Associated Biological Pathways and Systems in Common Complex Disorders

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Godfrey D Pearlson

2015-09-01

Full Text Available Complex inherited phenotypes, including those for many common medical and psychiatric diseases, are most likely underpinned by multiple genes contributing to interlocking molecular biological processes, along with environmental factors (Owen et al., 2010. Despite this, genotyping strategies for complex, inherited, disease-related phenotypes mostly employ univariate analyses, e.g. genome wide association (GWA. Such procedures most often identify isolated risk-related SNPs or loci, not the underlying biological pathways necessary to help guide the development of novel treatment approaches. This article focuses on the multivariate analysis strategy of parallel (i.e. simultaneous combination of SNP and neuroimage information independent component analysis (p-ICA, which typically yields large clusters of functionally related SNPs statistically correlated with phenotype components, whose overall molecular biologic relevance is inferred subsequently using annotation software suites. Because this is a novel approach, whose details are relatively new to the field we summarize its underlying principles and address conceptual questions regarding interpretation of resulting data and provide practical illustrations of the method.

Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

Energy Technology Data Exchange (ETDEWEB)

Gregurick, S.; Fredrickson, J. K.; Stevens, R.

2009-03-01

Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

Synthetic biology, inspired by synthetic chemistry.

Science.gov (United States)

Malinova, V; Nallani, M; Meier, W P; Sinner, E K

2012-07-16

The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

The use of information theory in evolutionary biology.

Science.gov (United States)

Adami, Christoph

2012-05-01

Information is a key concept in evolutionary biology. Information stored in a biological organism's genome is used to generate the organism and to maintain and control it. Information is also that which evolves. When a population adapts to a local environment, information about this environment is fixed in a representative genome. However, when an environment changes, information can be lost. At the same time, information is processed by animal brains to survive in complex environments, and the capacity for information processing also evolves. Here, I review applications of information theory to the evolution of proteins and to the evolution of information processing in simulated agents that adapt to perform a complex task. © 2012 New York Academy of Sciences.

Reconstruction of biological networks based on life science data integration

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Kormeier Benjamin

2010-06-01

Full Text Available For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH - an integration toolkit for building life science data warehouses, CardioVINEdb - a information system for biological data in cardiovascular-disease and VANESA- a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

Mammalian Toxicological Evaluation of TNT Wastewaters. Volume II. Acute and Subacute Mammalian Toxicity of TNT and LAP Mixture

Science.gov (United States)

1979-06-01

with a strongly alkaline sodium potassium tartrate buffer and sulfanilic acid to yield a green complex, which can be quantitated at 600 nm against a...pot-_ssium tartrate changes the pH to highly alkaline and moves the absorbanc.e maximum to 600 nm- The aboorbauce at 600 nm is proportional to the tntal...solution of tablet and sodium hydroxide provides alkaline media, Cupric ions (++-) are reduced to cuprous oxide (Cu2 0O), giving a color change from blue

Oxovanadium(IV) complexes of non-steroidal anti-inflammatory drugs: synthesis, spectroscopy, and antimicrobial activity

International Nuclear Information System (INIS)

Muhammad, N.; Ali, S.; Shahzadi, S.; Khan, A.N.

2008-01-01

Oxovanadium(IV) complexes with four different non-steroidal anti-inflammatory drugs have been synthesized. These complexes were characterized by different analytical techniques such as CHN, IR, UV-Vis spectroscopy, and mass spectrometry. The IR data show the bidentate nature of the ligands and reveal hexacoordinate geometry in the solid state. The complexes were tested for their biological activity against six different bacterial strains and plant pathogens, and all complexes showed good biological activity with few exceptions [ru

An integrative approach to inferring biologically meaningful gene modules

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Wang Kai

2011-07-01

Full Text Available Abstract Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

Science.gov (United States)

Beal, Jacob; Lu, Ting; Weiss, Ron

2011-01-01

The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks. Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.

Stable carbon (12/13C) and nitrogen (14/15N) isotopes as a tool for identifying the sources of cyanide in wastes and contaminated soils-A method development

International Nuclear Information System (INIS)

Weihmann, Jenny; Mansfeldt, Tim; Schulte, Ulrike

2007-01-01

The occurrence of iron-cyanide complexes in the environment is of concern, since they are potentially hazardous. In order to determine the source of iron-cyanide complexes in contaminated soils and wastes, we developed a method based on the stable isotope ratios 13 C/ 12 C and 15 N/ 14 N of the complexed cyanide-ion (CN - ). The method was tested on three pure chemicals and two industrials wastes: blast-furnace sludge (BFS) and gas-purifier waste (GPW). The iron-cyanide complexes were converted into the solid cupric ferrocyanide, Cu 2 [Fe(China) 6 ].7H 2 O, followed by combustion and determination of the isotope-ratios by continuous flow isotope ratio mass spectrometry. Cupric ferrocyanide was obtained from the materials by (i) an alkaline extraction with 1 M NaOH and (ii) a distillate digestion. The [Fe(China) 6 ] 4- of the alkaline extraction was precipitated after adding Cu 2+ . The CN - of the distillate digestion was at first complexed with Fe 2+ under inert conditions and then precipitated after adding Cu 2+ . The δ 13 C-values obtained by the two methods differed slightly up to 1-3 per mille for standards and BFS. The difference was larger for alkaline-extracted GPW (4-7 per mille ), since non-cyanide C was co-extracted and co-precipitated. Therefore the distillate digestion technique is recommended when determining the C isotope ratios in samples rich in organic carbon. Since the δ 13 C-values of BFS are in the range of -30 to -24 per mille and of -17 to -5 per mille for GPW, carbon seems to be a suitable tracer for identifying the source of cyanide in both wastes. However, the δ 15 N-values overlapped for BFS and GPW, making nitrogen unsuitable as a tracer

A differential genome-wide transcriptome analysis: impact of cellular copper on complex biological processes like aging and development.

Directory of Open Access Journals (Sweden)

Jörg Servos

explain the underlying mechanisms controlling complex biological processes like aging and development.

A program code generator for multiphysics biological simulation using markup languages.

Science.gov (United States)

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

Network science of biological systems at different scales: A review

Science.gov (United States)

Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

2018-03-01

Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

Toxicological evaluation of complex industrial wastes: Implications for exposure assessment

Energy Technology Data Exchange (ETDEWEB)

DeMarini, D.M.; Gallagher, J.E.; Houk, V.S.; Simmons, J.E.

1989-01-01

A variety of short-term bioassays to construct a battery of tests that could be used for assessing the biological effects of potentially hazardous complex industrial wastes were evaluated. Ten samples were studied for hepatotoxicity: These samples and an additional five were studied for mutagenicity. Although the data are limited to these samples, the results suggest that the Salmonella assay (either TA98 or TA100) or a prophage-induction assay (both in the presence of S9) in combination with determination of relative liver weight and levels of a set of serum enzymes in rats would provide a battery of tests suitable to characterize complex industrial wastes for mutagenic and hepatotoxic potential. The biological activities exhibited by the wastes were not readily predicted by the chemical profiles of the wastes, emphasizing the importance of characterizing potentially hazardous complex industrial wastes by both chemical and biological means.

Structural, spectral, DFT and biological studies on macrocyclic mononuclear ruthenium (II) complexes

Science.gov (United States)

Muthukkumar, M.; Kamal, C.; Venkatesh, G.; Kaya, C.; Kaya, S.; Enoch, Israel V. M. V.; Vennila, P.; Rajavel, R.

2017-11-01

Macrocyclic mononuclear ruthenium (II) complexes have been synthesized by condensation method [Ru (L1, L2, L3) Cl2] L1 = (C36 H31 N9), L2= (C42H36N8), L3= (C32H32 N8)]. These ruthenium complexes have been established by elemental analyses and spectroscopic techniques (Fourier transform infrared spectroscopy (FT-IR), 1H- nuclear magnetic resonance (NMR), 13C- NMR and Electrospray ionization mass spectrometry (ESI-MS)). The coordination mode of the ligand has been confirmed and the octahedral geometry around the ruthenium ion has been revealed. Binding affinity and binding mode of ruthenium (II) complexes with Bovine serum Albumin (BSA) have been characterized by Emission spectra analysis. UV-Visible and fluorescence spectroscopic techniques have also been utilized to examine the interaction between ligand and its complexes L1, L2, & L3 with BSA. Chemical parameters and molecular structure of Ru (II) complexes L1H, L2H, & L3H have been determined by DFT coupled with B3LYP/6-311G** functional in both the gaseous and aqueous phases.

Synthesis, characterization and biological evaluation of ruthenium flavanol complexes against breast cancer

Science.gov (United States)

Singh, Ashok Kumar; Saxena, Gunjan; Sahabjada; Arshad, M.

2017-06-01

Four Ru(II) DMSO complexes (M1R-M4R) having substituted flavones viz. 3-Hydroxy-2-(4-methoxyphenyl)-4H-chromen-4-one (HL1), 3-Hydroxy-2-(4-nitrophenyl)-4H-chromen-4-one (HL2), 3-Hydroxy-2-(4-dimethylaminophenyl)-4H-chromen-4-one (HL3) and 3-Hydroxy-2-(4-chlorophenyl)-4H-chromen-4-one (HL4) were synthesized and characterized by elemental analysis, IR, UV-Vis, 1H NMR spectroscopies and ESI-MS. The molecular structures of the complexes were investigated by integrated spectroscopic and computational techniques (DFT). Both ligands as well as their complexes were screened for anticancer activities against breast cancer cell lines MCF-7. Cytotoxicity was assayed by MTT [3-(4, 5-dimethyl thiazol-2-yl)-2, 5-diphenyl tetrazolium bromide] assay. All ligands and their complexes exhibited significant cytotoxic potential of 5-40 μM concentration at incubation period of 24 h. The cell cytotoxicity increased significantly in a concentration-dependent manner. In this series of compounds, HL2 (IC50 17.2 μM) and its complex M2R (IC50 16 μM) induced the highest cytotoxicity.

Mammalian synthetic biology for studying the cell.

Science.gov (United States)

Mathur, Melina; Xiang, Joy S; Smolke, Christina D

2017-01-02

Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

The bottom-up approach to defining life : deciphering the functional organization of biological cells via multi-objective representation of biological complexity from molecules to cells

Directory of Open Access Journals (Sweden)

Sathish ePeriyasamy

2013-12-01

Full Text Available In silico representation of cellular systems needs to represent the adaptive dynamics of biological cells, recognizing a cell’s multi-objective topology formed by spatially and temporally cohesive intracellular structures. The design of these models needs to address the hierarchical and concurrent nature of cellular functions and incorporate the ability to self-organise in response to transitions between healthy and pathological phases, and adapt accordingly. The functions of biological systems are constantly evolving, due to the ever changing demands of their environment. Biological systems meet these demands by pursuing objectives, aided by their constituents, giving rise to biological functions. A biological cell is organised into an objective/task hierarchy. These objective hierarchy corresponds to the nested nature of temporally cohesive structures and representing them will facilitate in studying pleiotropy and polygeny by modeling causalities propagating across multiple interconnected intracellular processes. Although biological adaptations occur in physiological, developmental and reproductive timescales, the paper is focused on adaptations that occur within physiological timescales, where the biomolecular activities contributing to functional organisation, play a key role in cellular physiology. The paper proposes a multi-scale and multi-objective modelling approach from the bottom-up by representing temporally cohesive structures for multi-tasking of intracellular processes. Further the paper characterises the properties and constraints that are consequential to the organisational and adaptive dynamics in biological cells.

bond activation and catalysis by Ru -pac complexes

Indian Academy of Sciences (India)

and their reactivity towards oxidation of a few organic compounds. Keywords. Kinetics; catalysis; -O–O- bond activation; Ru-pac complex; oxidation. 1. Introduction. Ru-pac complexes exhibit catalytic properties,1 in homogeneous conditions in the presence of oxygen atom donors, that mimic the biological enzymatic oxi-.

Method to detect biological particles

International Nuclear Information System (INIS)

Giaever, I.

1976-01-01

A medical-diagnostic method to detect immunological as well as other specific reactions is described. According to the invention, first reactive particles (e.g. antibodies) are adsorbed on the surface of a solid, non-reactive substrate. The coated substrate is subjected to a solution which one assumes to contain the second biological particles (e.g. antigens) which are specific to the first and form complexes with these. A preferential radioactive labelling (e.g. with iodine 125) of the second biological particle is then directly or indirectly carried out. Clearage follows labelling in order to separate the second biological particles from the first ones. A specific splitting agent can selectively break the bond of both types of particle. The splitting agent solution is finally separated off and its content is investigated for the presence of labelling. (VJ) [de

Partitioning of genomic variance using biological pathways

DEFF Research Database (Denmark)

Edwards, Stefan McKinnon; Janss, Luc; Madsen, Per

and that these variants are enriched for genes that are connected in biological pathways or for likely functional effects on genes. These biological findings provide valuable insight for developing better genomic models. These are statistical models for predicting complex trait phenotypes on the basis of SNP......-data and trait phenotypes and can account for a much larger fraction of the heritable component. A disadvantage is that this “black-box” modelling approach conceals the biological mechanisms underlying the trait. We propose to open the “black-box” by building SNP-set genomic models that evaluate the collective...... action of multiple SNPs in genes, biological pathways or other external findings on the trait phenotype. As proof of concept we have tested the modelling framework on several traits in dairy cattle....

Hierarchical complexity and the size limits of life.

Science.gov (United States)

Heim, Noel A; Payne, Jonathan L; Finnegan, Seth; Knope, Matthew L; Kowalewski, Michał; Lyons, S Kathleen; McShea, Daniel W; Novack-Gottshall, Philip M; Smith, Felisa A; Wang, Steve C

2017-06-28

Over the past 3.8 billion years, the maximum size of life has increased by approximately 18 orders of magnitude. Much of this increase is associated with two major evolutionary innovations: the evolution of eukaryotes from prokaryotic cells approximately 1.9 billion years ago (Ga), and multicellular life diversifying from unicellular ancestors approximately 0.6 Ga. However, the quantitative relationship between organismal size and structural complexity remains poorly documented. We assessed this relationship using a comprehensive dataset that includes organismal size and level of biological complexity for 11 172 extant genera. We find that the distributions of sizes within complexity levels are unimodal, whereas the aggregate distribution is multimodal. Moreover, both the mean size and the range of size occupied increases with each additional level of complexity. Increases in size range are non-symmetric: the maximum organismal size increases more than the minimum. The majority of the observed increase in organismal size over the history of life on the Earth is accounted for by two discrete jumps in complexity rather than evolutionary trends within levels of complexity. Our results provide quantitative support for an evolutionary expansion away from a minimal size constraint and suggest a fundamental rescaling of the constraints on minimal and maximal size as biological complexity increases. © 2017 The Author(s).

Thinking in complexity the complex dynamics of matter, mind, and mankind

CERN Document Server

Mainzer, Klaus

1994-01-01

The theory of nonlinear complex systems has become a successful and widely used problem-solving approach in the natural sciences - from laser physics, quantum chaos and meteorology to molecular modeling in chemistry and computer simulations of cell growth in biology In recent times it has been recognized that many of the social, ecological and political problems of mankind are also of a global, complex and nonlinear nature And one of the most exciting topics of present scientific and public interest is the idea that even the human mind is governed largely by the nonlinear dynamics of complex systems In this wide-ranging but concise treatment Prof Mainzer discusses, in nontechnical language, the common framework behind these endeavours Special emphasis is given to the evolution of new structures in natural and cultural systems and it is seen clearly how the new integrative approach of complexity theory can give new insights that were not available using traditional reductionistic methods

Hypoxia targeting copper complexes

International Nuclear Information System (INIS)

Dearling, J.L.

1998-11-01

The importance and incidence of tumour hypoxia, its measurement and current treatments available, including pharmacological and radiopharmacological methods of targeting hypoxia, are discussed. A variety of in vitro and in vivo methods for imposing hypoxia have been developed and are reviewed. Copper, its chemistry, biochemistry and radiochemistry, the potential for use of copper radionuclides and its use to date in this field is considered with particular reference to the thiosemicarbazones. Their biological activity, metal chelation, in vitro and in vivo studies of their radiocopper complexes and the potential for their use as hypoxia targeting radiopharmaceuticals is described. The reduction of the copper(II) complex to copper(l), its pivotal importance in their biological behaviour, and the potential for manipulation of this to effect hypoxia selectivity are described. An in vitro method for assessing the hypoxia selectivity of radiopharmaceuticals is reported. The rapid deoxygenation and high viability of a mammalian cell culture in this system is discussed and factors which may affect the cellular uptake of a radiopharmaceutical are described. The design, synthesis and complexation with copper and radiocopper of a range of bis(thiosemicarbazones) is reported. Synthesis of these compounds is simple giving high yields of pure products. The characteristics of the radiocopper complexes ( 64 Cu) including lipophilicity and redox activity are reported (reduction potentials in the range -0.314 - -0.590 V). High cellular uptakes of the radiocopper complexes of the ligands, in hypoxic and normoxic EMT6 and CHO320 cells, were observed. Extremes of selectivity are shown ranging from the hypoxia selective 64 Cu(II)ATSM to normoxic cell selective 64 Cu(II)GTS. The selectivities observed are compared with the physico chemical characteristics of the complexes. A good correlation exists between selectivity of the complex and its Cu(II)/Cu(I) reduction potential, with hypoxia

The navigation of biological hyperspace

Science.gov (United States)

Conway Morris, Simon

2003-04-01

A recurrent argument against the reality of biological evolution is the claim that there is insufficient time for the emergence of biological complexity. Such a view is a staple of creation "scientists", but even cosmologists and biochemists have been overheard murmuring similar sentiments. Certainly the stock response, that the scientific evidence for evolution is overwhelming, must be made. However, it is also the case that whilst the efficacity of natural selection is not in dispute, it is context-free and fails to explain the specificities of life. This observation is usually greeted with a Gallic shrug: "Yes, the biosphere is very rich, but so what?" Indeed, the standard scientific response is that evolution is dogged by contingent happenstance, with the implication that a given complexity, say intelligence, is an evolutionary fluke. This, however, is inconsistent with the ubiquity of evolutionary convergence. Here I outline the argument for such convergence providing a "road-map" of possibilities that arguably has universal applications and as importantly points to a much deeper structure to life.

Systems biology approach to bioremediation

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

2012-06-01

Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

Effects of human serun albumin in some biological properties of rhodium(II complexes

Directory of Open Access Journals (Sweden)

Espósito Breno P.

2000-01-01

Full Text Available The affinities for human albumin (HSA of five rhodium(II complexes of general formula [Rh2(bridge4] (bridge = acetate, propionate, butyrate, trifluoroacetate and trifluoroacetamidate were determined by spectrophotometry. In the case of the alkylcarboxylates, an inverse correlation of affinity with their liposolubilities was observed. Diffusion of the free or protein-bound complexes into Ehrlich cells in vitro seems to be primarily governed by the hydrophobic character of the complex. The complex [Rh2(tfc4] exhibited affinity towards the protein (K = 214.1 as well as cell partition both in the absence (32.1% and presence (48.6% of HSA. The compound HSA: [Rh2(tfc4] has had its antitumoral action in tumor-bearing Balb-c mice investigated, showing that HSA can be a drug reservoir for the rhodium complex.

Neutron scattering applications in structural biology: now and the future

Energy Technology Data Exchange (ETDEWEB)

Trewhella, J [Los Alamos National Lab., NM (United States)

1996-05-01

Neutrons have an important role to play in structural biology. Neutron crystallography, small-angle neutron scattering and inelastic neutron scattering techniques all contribute unique information on biomolecular structures. In particular, solution scattering techniques give critical information on the conformations and dispositions of the components of complex assemblies under a wide variety of relevant conditions. The power of these methods is demonstrated here by studies of protein/DNA complexes, and Ca{sup 2+}-binding proteins complexed with their regulatory targets. In addition, we demonstrate the utility of a new structural approach using neutron resonance scattering. The impact of biological neutron scattering to date has been constrained principally by the available fluxes at neutron sources and the true potential of these approaches will only be realized with the development of new more powerful neutron sources. (author)

Introduction to symposium: Arthropods and wildlife conservation: synergy in complex biological systems

Science.gov (United States)

The symposium will discuss the effects of arthropods and other stressors on wildlife conservation programs. Speakers with affiliations in wildlife biology, parasitology and entomology will be included in the program. Research of national and international interest will be presented....

Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems

Science.gov (United States)

Demongeot, Jacques; Goles, Eric; Morvan, Michel; Noual, Mathilde; Sené, Sylvain

2010-01-01

One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally. PMID:20700525

Attraction basins as gauges of robustness against boundary conditions in biological complex systems.

Directory of Open Access Journals (Sweden)

Jacques Demongeot

Full Text Available One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally.

Moessbauer effect study of iron(III)-inidazolidine nitroxyl-free radical ligand complex

Energy Technology Data Exchange (ETDEWEB)

Mulaba, A. [Technikon Witwatersrand, Metallurgy Department (South Africa); Kiremire, E. [University of the Witwatersrand, Chemistry Department (South Africa); Pollak, H. [University of the Witwatersrand, Physics Department (South Africa); Boeyens, J. [University of the Witwatersrand, Chemistry Department (South Africa)

1999-09-15

A new complex, [Fe(acac)L{sub 2}], bearing inidazolidine nitroxyl-free radical ligand (L{sup -}) was recently synthesised for biological studies. It proved to be biologically active against African sleeping sickness, plasmodium falciparum (malaria), leishmaniasis and chaga disease causative agents. Three ESR well resolved peaks indicated the presence of a free (unpaired) and chemically active electron in the complex. The structural complex ferric iron was found at the centre of two electric gradient whose the biggest is suggested to be initiated by the unpaired charge. No distinction between different cis isomers could be made.

Moessbauer effect study of iron(III)-inidazolidine nitroxyl-free radical ligand complex

International Nuclear Information System (INIS)

Mulaba, A.; Kiremire, E.; Pollak, H.; Boeyens, J.

1999-01-01

A new complex, [Fe(acac)L 2 ], bearing inidazolidine nitroxyl-free radical ligand (L - ) was recently synthesised for biological studies. It proved to be biologically active against African sleeping sickness, plasmodium falciparum (malaria), leishmaniasis and chaga disease causative agents. Three ESR well resolved peaks indicated the presence of a free (unpaired) and chemically active electron in the complex. The structural complex ferric iron was found at the centre of two electric gradient whose the biggest is suggested to be initiated by the unpaired charge. No distinction between different cis isomers could be made

Diversity of the Cryptococcus neoformans-Cryptococcus gattii species complex.

NARCIS (Netherlands)

Bovers, M.; Hagen, F.; Boekhout, T.

2008-01-01

More than 110 years of study of the Cryptococcus neoformans and Cryptococcus gattii species complex has resulted in an enormous accumulation of fundamental and applied biological and clinical knowledge. Recent developments in our understanding of the diversity within the species complex are

Tris-diamine-derived transition metal complexes of flurbiprofen as ...

African Journals Online (AJOL)

admin

butyrylcholinesterase (BChE) inhibitory activities. Method: Tris-diamine-derived transition metal complexes of Co(II), Ni(II), and Mn(II) were synthesized and characterized ... Conductance measurements indicated that diamine-derived metal complexes of ..... contributes to enhanced biological activity, and provides novel ...

3D complex: a structural classification of protein complexes.

Directory of Open Access Journals (Sweden)

Emmanuel D Levy

2006-11-01

Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

Carbon-13 NMR spectroscopy of biological systems

CERN Document Server

Beckmann, Nicolau

1995-01-01

This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

A mathematical framework for agent based models of complex biological networks.

Science.gov (United States)

Hinkelmann, Franziska; Murrugarra, David; Jarrah, Abdul Salam; Laubenbacher, Reinhard

2011-07-01

Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models, it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis. This mathematical framework can also accommodate other model types such as Boolean networks and the more general logical models, as well as Petri nets.

Electrospun poly(ε-caprolactone) matrices containing silver sulfadiazine complexed with β-cyclodextrin as a new pharmaceutical dosage form to wound healing: preliminary physicochemical and biological evaluation.

Science.gov (United States)

Souza, Sarah Oliveira Lamas; Cotrim, Monique Alvarenga Pinto; Oréfice, Rodrigo Lambert; Carvalho, Suzana Gonçalves; Dutra, Jessyca Aparecida Paes; de Paula Careta, Francisco; Resende, Juliana Alves; Villanova, Janaina Cecília Oliveira

2018-05-10

Cooperation between researchers in the areas of medical, pharmaceutical and materials science has facilitated the development of pharmaceutical dosage forms that elicit therapeutic effects and protective action with a single product. In addition to optimizing pharmacologic action, such dosage forms provide greater patient comfort and increase success and treatment compliance. In the present work, we prepared semipermeable bioactive electrospun fibers for use as wound dressings containing silver sulfadiazine complexed with β-cyclodextrin in a poly(Ɛ-caprolactone) nanofiber matrix aiming to reduce the direct contact between silver and skin and to modulate the drug release. Wound dressings were prepared by electrospinning, and were subjected to ATR-FT-IR and TG/DTG assays to evaluate drug stability. The hydrophilicity of the fibrous nanostructure in water and PBS buffer was studied by goniometry. Electrospun fibers permeability and swelling capacity were assessed, and a dissolution test was performed. In vitro biological tests were realized to investigate the biological compatibility and antimicrobial activity. We obtained flexible matrices that were each approximately 1.0 g in weight. The electrospun fibers were shown to be semipermeable, with water vapor transmission and swelling indexes compatible with the proposed objective. The hydrophilicity was moderate. Matrices containing pure drug modulated drug release adequately during 24 h but presented a high hemolytic index. Complexation promoted a decrease in the hemolytic index and in the drug release but did not negatively impact antimicrobial activity. The drug was released predominantly by diffusion. These results indicate that electrospun PCL matrices containing β-cyclodextrin/silver sulfadiazine inclusion complexes are a promising pharmaceutical dosage form for wound healing.

[Biologic therapy in idiopathic inflammatory myopathy].

Science.gov (United States)

Selva-O'Callaghan, Albert; Ramos Casals, Manel; Grau Junyent, Josep M

2014-09-15

The aim of this article is to study the evidence-based knowledge related to the use of biological therapies in patients diagnosed with idiopathic inflammatory myopathy (dermatomyositis, polymyositis and inclusion body myositis). In this review the leading published studies related to the use of biological therapy in patients with myositis are analysed; mainly those with high methodological standards, that means randomized and controlled studies. Methodological drawbacks due to the rarity and heterogeneity of these complex diseases are also addressed. Up to now is not possible to ascertain the biologics as a recommended therapy in patients with myositis, at least based in the current evidence-based knowledge, although it can not be neglected as a therapeutic option in some clinical situations, taking into account the scarce of effective treatments in those patients, especially in refractory myositis. Future studies probably will help to better define the role of biological therapies in patients with idiopathic inflammatory myopathy. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

Scattering methods in complex fluids

CERN Document Server

Chen, Sow-Hsin

2015-01-01

Summarising recent research on the physics of complex liquids, this in-depth analysis examines the topic of complex liquids from a modern perspective, addressing experimental, computational and theoretical aspects of the field. Selecting only the most interesting contemporary developments in this rich field of research, the authors present multiple examples including aggregation, gel formation and glass transition, in systems undergoing percolation, at criticality, or in supercooled states. Connecting experiments and simulation with key theoretical principles, and covering numerous systems including micelles, micro-emulsions, biological systems, and cement pastes, this unique text is an invaluable resource for graduate students and researchers looking to explore and understand the expanding field of complex fluids.

European Conference on Complex Systems 2012

CERN Document Server

Kirkilionis, Markus; Nicolis, Gregoire

2013-01-01

The European Conference on Complex Systems, held under the patronage of the Complex Systems Society, is an annual event that has become the leading European conference devoted to complexity science. ECCS'12, its ninth edition, took place in Brussels, during the first week of September 2012. It gathered about 650 scholars representing a wide range of topics relating to complex systems research, with emphasis on interdisciplinary approaches. More specifically, the following tracks were covered:  1. Foundations of Complex Systems 2. Complexity, Information and Computation 3. Prediction, Policy and Planning, Environment 4. Biological Complexity 5. Interacting Populations, Collective Behavior 6. Social Systems, Economics and Finance This book contains a selection of the contributions presented at the conference and its satellite meetings. Its contents reflect the extent, diversity and richness of research areas in the field, both fundamental and applied.  

The combined effect of complex mixes of poisons on the organism of white rats in 30-day round-the-clock inhalation and measures of biological prevention

OpenAIRE

MIRZAKARIMOVA MALOKHAT ABDUVAKHIDOVNA

2016-01-01

The direction of “biological prevention” in the field of hygiene of the environment, which is understood as the complex of measures directed to the increase in resistance of individual person and population to exposure of harmful factors of the industrial and ambient environment, are increasingly being developed over the last years. For biopreventive maintenance only the means are used harmless at long application in preventive effective dosage. In this context in the industrial towns for res...

Mass amplifying probe for sensitive fluorescence anisotropy detection of small molecules in complex biological samples.

Science.gov (United States)

Cui, Liang; Zou, Yuan; Lin, Ninghang; Zhu, Zhi; Jenkins, Gareth; Yang, Chaoyong James

2012-07-03

detection of small molecules by means of FA in complex biological samples.

Filtration device for rapid separation of biological particles from complex matrices

Science.gov (United States)

Kim, Sangil; Naraghi-Arani, Pejman; Liou, Megan

2018-01-09

Methods and systems for filtering of biological particles are disclosed. Filtering membranes separate adjacent chambers. Through osmotic or electrokinetic processes, flow of particles is carried out through the filtering membranes. Cells, viruses and cell waste can be filtered depending on the size of the pores of the membrane. A polymer brush can be applied to a surface of the membrane to enhance filtering and prevent fouling.

Mesoscale modeling: solving complex flows in biology and biotechnology.

Science.gov (United States)

Mills, Zachary Grant; Mao, Wenbin; Alexeev, Alexander

2013-07-01

Fluids are involved in practically all physiological activities of living organisms. However, biological and biorelated flows are hard to analyze due to the inherent combination of interdependent effects and processes that occur on a multitude of spatial and temporal scales. Recent advances in mesoscale simulations enable researchers to tackle problems that are central for the understanding of such flows. Furthermore, computational modeling effectively facilitates the development of novel therapeutic approaches. Among other methods, dissipative particle dynamics and the lattice Boltzmann method have become increasingly popular during recent years due to their ability to solve a large variety of problems. In this review, we discuss recent applications of these mesoscale methods to several fluid-related problems in medicine, bioengineering, and biotechnology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nonlinear Phenomena in Complex Systems: From Nano to Macro Scale

CERN Document Server

Stanley, H

2014-01-01

Topics of complex system physics and their interdisciplinary applications to different problems in seismology, biology, economy, sociology,  energy and nanotechnology are covered in this new work from renowned experts in their fields.  In  particular, contributed papers contain original results on network science, earthquake dynamics, econophysics, sociophysics, nanoscience and biological physics. Most of the papers use interdisciplinary approaches based on statistical physics, quantum physics and other topics of complex system physics.  Papers on econophysics and sociophysics are focussed on societal aspects of physics such as, opinion dynamics, public debates and financial and economic stability. This work will be of interest to statistical physicists, economists, biologists, seismologists and all scientists working in interdisciplinary topics of complexity.

On complexity and homogeneity measures in predicting biological aggressiveness of prostate cancer; Implication of the cellular automata model of tumor growth.

Science.gov (United States)

Tanase, Mihai; Waliszewski, Przemyslaw

2015-12-01

We propose a novel approach for the quantitative evaluation of aggressiveness in prostate carcinomas. The spatial distribution of cancer cell nuclei was characterized by the global spatial fractal dimensions D0, D1, and D2. Two hundred eighteen prostate carcinomas were stratified into the classes of equivalence using results of ROC analysis. A simulation of the cellular automata mix defined a theoretical frame for a specific geometric representation of the cell nuclei distribution called a local structure correlation diagram (LSCD). The LSCD and dispersion Hd were computed for each carcinoma. Data mining generated some quantitative criteria describing tumor aggressiveness. Alterations in tumor architecture along progression were associated with some changes in both shape and the quantitative characteristics of the LSCD consistent with those in the automata mix model. Low-grade prostate carcinomas with low complexity and very low biological aggressiveness are defined by the condition D0 1.764 and Hd < 38. The novel homogeneity measure Hd identifies carcinomas with very low aggressiveness within the class of complexity C1 or carcinomas with very high aggressiveness in the class C7. © 2015 Wiley Periodicals, Inc.

Synthetic biology analysed tools for discussion and evaluation

CERN Document Server

2016-01-01

Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic bi...

Metal based biologically active compounds: Design, synthesis, DNA binding and antidiabetic activity of 6-methyl-3-formyl chromone derived hydrazones and their metal (II) complexes.

Science.gov (United States)

Philip, Jessica Elizabeth; Shahid, Muhammad; Prathapachandra Kurup, M R; Velayudhan, Mohanan Puzhavoorparambil

2017-10-01

Two chromone hydrazone ligands HL 1 and HL 2 were synthesized and characterized by elemental analyses, IR, 1 H NMR & 13 C NMR, electronic absorption and mass spectra. The reactions of the chromone hydrazones with transition metals such as Ni, Cu, and Zn (II) salts of acetate afforded mononuclear metal complexes. Characterization and structure elucidation of the prepared chromone hydrazone metal (II) complexes were done by elemental, IR, electronic, EPR spectra and thermo gravimetric analyses as well as conductivity and magnetic susceptibility measurements. The spectroscopic data showed that the ligand acts as a mono basic bidentate with coordination sites are azomethine nitrogen and hydrazonic oxygen, and they exhibited distorted geometry. The biological studies involved antidiabetic activity i.e. enzyme inhibition of α-amylase and α-glucosidase, Calf Thymus - DNA (CT-DNA) interaction and molecular docking. Potential capacity of synthesized compounds to inhibit the α-amylase and α-glucosidase activity was assayed whereas DNA interaction studies were carried out with the help UV-Vis absorption titration and viscosity method. The docking studies of chromone hydrazones show that they are minor groove binders. Complexes were found to be good DNA - intercalates. Chromone hydrazones and its transition metal complexes have shown comparable antidiabetic activity with a standard drug acarbose. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural insights into transcription complexes

NARCIS (Netherlands)

Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

2011-01-01

Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

Structure-volume relationships: singular volume effects produced by cupric ion-globular protein interaction.

Science.gov (United States)

Katz, S; Shinaberry, G; Heck, E L; Squire, W

1980-08-05

The nature of the volume isotherms produced by the coordination of Cu(II) with ovalbumin and bovine serum albumin differs substantially from the adsorption isotherms produced by these systems. Whereas there was increased binding of Cu(II) associated with a pH increase from pH 5.3 to pH 7.4, the volume isotherms for these systems did not exhibit this type of pH dependence. The volume changes were determined at 30.0 +/- 0.001 degrees C with microdilatometers which could be read to 0.01 muL. The binding isotherms for ovalbumin at pH 5.3 and 7.4 and for bovine serum albumin at pH 5.3 was resolved by a Scatchard plot to yield the appropriate thermodynamic parameters. An algorithm was derived to calculate the distribution of the individual PMi complexes, i.e., PMi-1 + M in equilibrium (Ki) PMi where i equals 1, 2, 3, ..., n moles of cation, M, bound per mole of protein, P, for the above systems. The volume isotherms were then resolved in terms of the constituent delta Vi terms, i.e., the volume change produced by the formation of the individual PMi complexes. These values were verified by an independent graphical differentiation procedure. The coordination of Cu(II) to BSA at pH 7.4 produced a cooperative adsorption isotherm which was not amenable to a Scatchard analysis. The resultant anomalous volume isotherm was resolved into a component related to Cu(II)-site interaction and a negative volume effect attributable to a conformational change induced by complex formation. This structural transition which occurs at physiological pH may constitute a control mechanism for regulating the serum level of Cu(II) and possibly other divalent ions.

Nature, computation and complexity

International Nuclear Information System (INIS)

Binder, P-M; Ellis, G F R

2016-01-01

The issue of whether the unfolding of events in the world can be considered a computation is explored in this paper. We come to different conclusions for inert and for living systems (‘no’ and ‘qualified yes’, respectively). We suggest that physical computation as we know it exists only as a tool of complex biological systems: us. (paper)

Electrochemiluminescence from Tunicate, Tunichrome--Metal Complexes and Other Biological Samples (Postprint)

Science.gov (United States)

1996-05-17

terrestrial grass ( Eleusine indica ) was gathered from wooded areas around St Andrew Sound. Several blades of each plant species were crushed with...that live (green) grass (E. indica ) extracts exhibited high solution-phase ECL levels 200 ~ Ill c Cll .. .E .J 0 w c Ill Cll :;: 900 800...Figure 12. Comparison of intrinsic biological ECL from live (green) and dead (brown) terrestrial grass (E. indica ) and liv’ seagrass (T. testudinum

Morphogenetic Engineering Toward Programmable Complex Systems

CERN Document Server

Sayama, Hiroki; Michel, Olivier

2012-01-01

Generally, spontaneous pattern formation phenomena are random and repetitive, whereas elaborate devices are the deterministic product of human design. Yet, biological organisms and collective insect constructions are exceptional examples of complex systems that are both self-organized and architectural.   This book is the first initiative of its kind toward establishing a new field of research, Morphogenetic Engineering, to explore the modeling and implementation of “self-architecturing” systems. Particular emphasis is placed on the programmability and computational abilities of self-organization, properties that are often underappreciated in complex systems science—while, conversely, the benefits of self-organization are often underappreciated in engineering methodologies.   Altogether, the aim of this work is to provide a framework for and examples of a larger class of “self-architecturing” systems, while addressing fundamental questions such as   > How do biological organisms carry out morphog...

Managing bioengineering complexity with AI techniques.

Science.gov (United States)

Beal, Jacob; Adler, Aaron; Yaman, Fusun

2016-10-01

Our capabilities for systematic design and engineering of biological systems are rapidly increasing. Effectively engineering such systems, however, requires the synthesis of a rapidly expanding and changing complex body of knowledge, protocols, and methodologies. Many of the problems in managing this complexity, however, appear susceptible to being addressed by artificial intelligence (AI) techniques, i.e., methods enabling computers to represent, acquire, and employ knowledge. Such methods can be employed to automate physical and informational "routine" work and thus better allow humans to focus their attention on the deeper scientific and engineering issues. This paper examines the potential impact of AI on the engineering of biological organisms through the lens of a typical organism engineering workflow. We identify a number of key opportunities for significant impact, as well as challenges that must be overcome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Palladium polypyridyl complexes: synthesis, characterization, DNA interaction and biological activity on Leishmania (L.) mexicana

International Nuclear Information System (INIS)

Navarro, Maribel; Betancourt, Adelmo; Hernandez, Clara; Marchan, Edgar

2008-01-01

This paper describes the search for new potential chemotherapeutic agents based on transition metal complexes with planar ligands. In this study, palladium polypyridyl complexes were synthesized and characterized by elemental analysis, NMR, UV-VIS and IR spectroscopies. The interaction of the complexes with DNA was also investigated by spectroscopic methods. All metal-to-ligand charge transfer (MLCT) bands of the palladium polypyridyl complexes exhibited hypochromism and red shift in the presence of DNA. The binding constant and viscosity data suggested that the complexes [PdCl 2 (phen)] and [PdCl 2 (phendiamine)] interact with DNA by electrostatic forces. Additionally, these complexes induced an important leishmanistatic effect on L. (L.) mexicana promastigotes at the final concentration of 10 μmol L -1 in 48 h. (author)

Multiplexed Engineering in Biology.

Science.gov (United States)

Rogers, Jameson K; Church, George M

2016-03-01

Biotechnology is the manufacturing technology of the future. However, engineering biology is complex, and many possible genetic designs must be evaluated to find cells that produce high levels of a desired drug or chemical. Recent advances have enabled the design and construction of billions of genetic variants per day, but evaluation capacity remains limited to thousands of variants per day. Here we evaluate biological engineering through the lens of the design–build–test cycle framework and highlight the role that multiplexing has had in transforming the design and build steps. We describe a multiplexed solution to the ‘test’ step that is enabled by new research. Achieving a multiplexed test step will permit a fully multiplexed engineering cycle and boost the throughput of biobased product development by up to a millionfold.

Reprint of: Application of micro-thin-layer chromatography as a simple fractionation tool for fast screening of raw extracts derived from complex biological, pharmaceutical and environmental samples

International Nuclear Information System (INIS)

Zarzycki, Paweł K.; Ślączka, Magdalena M.; Zarzycka, Magdalena B.; Włodarczyk, Elżbieta; Baran, Michał J.

2012-01-01

The main goal of present paper is to demonstrate the separation and detection capability of micro-TLC technique involving simple one step liquid extraction protocols of complex materials without multi-steps sample pre-purification. In the present studies target components (cyanobacteria pigments, lipids and fullerenes) were isolated from heavy loading complex matrices including spirulina dried cells, birds’ feathers and fatty oils as well as soot samples derived from biomass fuel and fossils-fired home heating systems. In each case isocratic separation protocol involving less that 1 mL of one component or binary mixture mobile phases can be completed within time of 5–8 min. Sensitive detection of components of interest was performed via fluorescence or staining techniques using iodine or phosphomolybdic acid. Described methodology can be applied for fast fractionation or screening of whole range of target substances as well as chemo-taxonomic studies and fingerprinting of complex mixtures, which are present in raw biological or environmental samples.

Reprint of: Application of micro-thin-layer chromatography as a simple fractionation tool for fast screening of raw extracts derived from complex biological, pharmaceutical and environmental samples

Energy Technology Data Exchange (ETDEWEB)

Zarzycki, Pawel K., E-mail: pawel_k_z@hotmail.com [Section of Toxicology and Bioanalytics, Department of Civil and Environmental Engineering, Koszalin University of Technology, Sniadeckich 2, 75-453 Koszalin (Poland); Slaczka, Magdalena M.; Zarzycka, Magdalena B.; Wlodarczyk, Elzbieta; Baran, Michal J. [Section of Toxicology and Bioanalytics, Department of Civil and Environmental Engineering, Koszalin University of Technology, Sniadeckich 2, 75-453 Koszalin (Poland)

2012-02-24

The main goal of present paper is to demonstrate the separation and detection capability of micro-TLC technique involving simple one step liquid extraction protocols of complex materials without multi-steps sample pre-purification. In the present studies target components (cyanobacteria pigments, lipids and fullerenes) were isolated from heavy loading complex matrices including spirulina dried cells, birds' feathers and fatty oils as well as soot samples derived from biomass fuel and fossils-fired home heating systems. In each case isocratic separation protocol involving less that 1 mL of one component or binary mixture mobile phases can be completed within time of 5-8 min. Sensitive detection of components of interest was performed via fluorescence or staining techniques using iodine or phosphomolybdic acid. Described methodology can be applied for fast fractionation or screening of whole range of target substances as well as chemo-taxonomic studies and fingerprinting of complex mixtures, which are present in raw biological or environmental samples.

Pedagogy of complex relationality exploring complexity theory, neuro-phenomenology, and attentiveness for education